Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 541 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 13013 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 46 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 529 protein 118 SARS 112 cell 84 RNA 62 virus 59 dna 54 Fig 39 figure 25 structure 22 sequence 21 Golgi 20 vaccine 20 study 20 peptide 20 membrane 20 gene 20 expression 17 human 17 University 17 CoV-2 17 ACE2 16 viral 16 result 16 plant 16 acid 16 COVID-19 15 PCR 14 interaction 14 activity 14 HIV-1 12 drug 12 Protein 12 MHC 11 high 11 epitope 10 antibody 10 NMR 10 Institute 10 IFN 10 ATP 9 receptor 9 increase 9 HCV 8 patient 8 method 8 lipid 8 host 8 effect 8 PEDV 8 IBV Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 80337 protein 45488 cell 23222 virus 12741 study 12152 membrane 12087 structure 11437 gene 11200 peptide 11174 expression 10713 interaction 10548 sequence 10280 % 10154 activity 10068 acid 9557 analysis 8890 receptor 8511 effect 8460 domain 8404 result 8241 method 8154 infection 8112 system 8105 disease 7891 level 7822 function 7815 role 7436 response 7342 type 6888 site 6855 antibody 6822 host 6655 factor 6521 model 6309 mechanism 6250 mouse 6218 residue 6130 group 6087 drug 5914 process 5913 patient 5867 pathway 5540 dna 5537 complex 5467 molecule 5382 target 5347 surface 5324 enzyme 5275 datum 5260 region 5110 time Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 16082 al 13320 et 13072 . 8728 SARS 7913 RNA 3938 C 3796 CoV-2 3664 Fig 2866 S 2709 M 2665 CoV 2597 T 2585 N 2475 MS 2183 ER 2145 Golgi 2057 II 1923 B 1896 University 1873 A 1789 Protein 1650 HIV-1 1453 IFN 1440 mRNA 1432 PCR 1428 E. 1402 ACE2 1373 K 1370 S. 1362 DNA 1337 pH 1276 NMR 1190 Table 1131 HIV 1098 mg 1064 D 1047 COVID-19 1039 MHC 1039 L 1029 F 1008 ELISA 986 C. 967 M. 926 HCV 862 ATP 858 Coronavirus 847 S1 843 CD4 839 G 830 Institute Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 19976 we 13980 it 4748 they 3535 i 1738 them 709 us 475 itself 316 one 263 he 209 themselves 100 you 43 she 40 mrnas 33 me 22 nsp10 11 ourselves 11 nsp15 10 ifitm3 9 him 8 ashcs 7 s 7 p~ 7 imagej 7 her 6 e3s 6 c328 4 u 4 mg 4 iga+ 4 grasp55 3 yourself 3 wtgfp 3 svlps 3 rab8 3 orf16 3 oneself 3 isg15-/-bmdm 3 interleukin-15 3 igg4 3 iga1 3 esat-6 3 cdc37 3 bl21-codonplus(de3)-ripl 3 a1-antitrypsin 2 tecpr2 2 tbx5 2 t98hr 2 stnfα 2 rss1gfp 2 rsba Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 198518 be 33075 have 25221 use 13716 show 11996 bind 8184 base 7553 induce 6747 find 6672 contain 6655 identify 6337 include 6224 increase 5676 suggest 5537 associate 5405 involve 5300 express 4650 do 4549 compare 4450 require 4377 provide 4363 determine 4322 mediate 4148 indicate 4141 know 4064 follow 3962 develop 3952 reveal 3924 observe 3920 lead 3793 produce 3791 form 3773 regulate 3741 result 3711 perform 3693 obtain 3631 demonstrate 3585 reduce 3516 target 3495 inhibit 3470 cause 3407 investigate 3365 study 3309 detect 3241 report 3203 derive 3182 predict 3107 describe 3107 allow 3036 interact 2957 encode Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 14230 not 12905 - 12732 also 11038 viral 10601 high 10312 human 8867 different 8767 other 8179 such 7698 specific 6519 well 6387 more 6089 molecular 5909 however 5558 only 5344 structural 5098 most 5075 cellular 4787 low 4651 new 4580 important 4526 several 4309 as 4262 small 4228 immune 4131 non 4087 first 4023 further 3991 large 3987 functional 3938 thus 3668 many 3426 dependent 3414 single 3303 novel 3223 similar 3220 like 3198 anti 3109 potential 3105 then 3067 therefore 3051 present 3024 recombinant 2981 highly 2898 various 2803 significant 2759 biological 2700 major 2694 respectively 2660 early Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 1541 most 778 least 625 good 624 high 419 Most 224 large 165 low 99 great 88 late 85 strong 81 short 80 small 73 close 61 simple 46 near 45 early 38 long 26 big 20 bad 19 fast 18 vRNA 18 steep 12 new 9 weak 8 HbA1 7 pdqu 7 easy 7 Panx1 6 safe 6 old 5 slow 5 common 5 broad 5 NS1(ED 5 -which 5 -peptides 4 fit 4 deep 4 deadly 4 clear 4 cheap 4 bright 4 Trpv6 4 Least 3 poor 3 fine 3 ausgela 3 -I 2 ® 2 tight Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 3557 most 529 least 198 well 11 highest 6 smallest 4 worst 4 lowest 4 erv1 3 long 3 fast 3 -tag 2 vrna 2 panx1 2 early 1 shortest 1 pi3p 1 lumo)-highest 1 deepest 1 clustalw 1 cfdna 1 biggest 1 -spectroscopic 1 -i Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 41 doi.org 23 www 16 www.ncbi.nlm.nih.gov 16 www.ebi.ac.uk 15 github.com 13 tools.iedb.org 11 www.rcsb.org 11 www.cbs.dtu.dk 8 sites.google.com 8 pubs.acs.org 8 creativecommons.org 7 web.expasy.org 7 dx.doi.org 7 blast.ncbi.nlm.nih.gov 6 www.ddg-pharmfac.net 6 string-db.org 6 crossbar.kansil.org 6 crdd.osdd.net 5 zhanglab.ccmb.med.umich.edu 5 www.uniprot.org 5 www.matrixscience.com 5 www.gisaid.org 5 www.expasy.org 5 swissmodel.expasy.org 5 orcid.org 4 www.frontiersin.org 4 clinicaltrials.gov 3 www.wwpdb.org 3 www.who.int 3 www.nature.com 3 www.mdpi.com 3 www.jcat.de 3 www.imtech.res.in 3 www.drugbank.ca 3 www.ddgpharmfac.net 3 tools.immuneepitope.org 3 tisigner.com 3 servicesn.mbi.ucla.edu 3 pymol.org 3 proteininformatics.org 3 prodata.swmed.edu 3 ilir.uk 3 glycam.org 3 galaxy.seoklab.org 3 dev.glycam.org 3 creativecommons 3 bioinformatics.hitsz.edu.cn 3 150.146.2.1 2 zinc15.docking.org 2 zinc.docking.org Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 23 http://www 6 http://www.rcsb.org/ 5 http://www.uniprot.org/ 5 http://www.gisaid.org/ 5 http://web.expasy.org/protparam/ 5 http://sites.google.com/site/supplementcovid19work/files 5 http://pubs.acs.org/journal/acsodf 5 http://doi.org/10.1101/2020.08.22.20176669 4 http://tools.iedb.org/bcell/ 4 http://string-db.org/ 4 http://doi.org/10.1038/s41467-020-17652-0 4 http://creativecommons.org/licenses/by/4.0/ 3 http://zhanglab.ccmb.med.umich.edu/I-TASSER/ 3 http://www.ncbi.nlm.nih.gov/genbank/ 3 http://www.ncbi.nlm.nih.gov/ 3 http://www.matrixscience.com/ 3 http://www.jcat.de/ 3 http://tools.iedb.org/mhcii/ 3 http://tisigner.com/sodope 3 http://pymol.org/2/ 3 http://doi.org/10 3 http://crossbar.kansil.org/covid_main.php 3 http://creativecommons.org/ 3 http://creativecommons 3 http://crdd.osdd.net/raghava/ifnepitope/ 3 http://blast.ncbi.nlm.nih.gov/Blast.cgi 2 http://zinc.docking.org/substances/subsets/fda/ 2 http://zhanglab.ccmb.med.umich.edu/ModRefiner/ 2 http://www.wwpdb.org/documentation/carbohydrate-remediation 2 http://www.virologyj.com/content/2/1/70 2 http://www.viprbrc.org 2 http://www.snapgene.com/ 2 http://www.openrasmol.org/ 2 http://www.nig.cineca.it/ 2 http://www.ncbi 2 http://www.matrixscience.com 2 http://www.jci-bioinfo.cn/iNR-Drug/ 2 http://www.isiknowledge.com/ 2 http://www.glycanstructure.org/ 2 http://www.frontiersin.org/articles/10.3389/fmicb 2 http://www.frontiersin.org/articles/10.3389/fimmu 2 http://www.ebi.ac.uk/intact 2 http://www.ddgpharmfac.net/vaxijen/VaxiJen/VaxiJen.html 2 http://www.ddg-pharmfac.net/vaxijen/ 2 http://www.compbio.dundee.ac 2 http://www.cgl.ucsf.edu/chimera/ 2 http://www.cbs.dtu.dk/services/TMHMM/ 2 http://www.cbs.dtu.dk/services/ 2 http://www.cbs.dtu.dk/ 2 http://tools.iedb.org/ellipro/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 3 ubakir@metu.edu.tr 2 pcalik@metu.edu.tr 2 ozdamar@eng.ankara.edu.tr 2 mnq@biocentrum.dtu.dk 2 esipov@ibch.ru 2 dpetrides@intelligen.com 2 dkilic@yildiz.edu.tr 2 calik@eng.ankara.edu.tr 2 brivas@uvigo.es 2 barslan@eng.ankara.edu.tr 2 achaudhury@umassd.edu 1 zomorodi@nrcgeb.ac.ir 1 zoltan.kapui@sanofi-aventis.com 1 zhaoxx@gsau.edu.cn 1 yurst@inr.liu.se 1 yoshiyuki-tamada@senju.co.jp 1 ymkoo@inha.ac.kr 1 yhathout@binghamton.edu 1 yangyongxin66@yahoo.com.cn 1 xavier.lories@arlenda.com 1 wonhur@kangwon.ac.kr 1 willem.devos@wur.nl 1 v.medvedev@univercells.com 1 ut@biocentrum.dtu.dk 1 tvede@bmb.sdu.dk 1 tompa@enzim.hu 1 tmatsui@comb.u-ryukyu.ac.jp 1 tmandelclausen@health.ucsd.edu 1 tig@biocentrum.dtu.dk 1 thalmann@ics-cnrs.unistra.fr 1 tcherno@emory.edu 1 tavernarakis@imbb.forth.gr 1 takasumi@suou.waseda.jp 1 svharten@gmail.com 1 sunjhe@sjtu.edu.cn 1 stamou@nano.ku.dk 1 spela.peternel@ki.si 1 sissel.lokra@lnb.hihm.no 1 silas.villas-boas@agresearch.co.nz 1 shindo@arif.pref.akita.jp 1 sh@fsc.chalmers.se 1 schang@tier.org.tw 1 saleh38@hotmail.com 1 s.sharkh@hzdr.de 1 s.buus@immi.ku.dk 1 roumestand@cbs.cnrs.fr 1 rkj@imtech.res.in 1 riar5400@rediffmail.com 1 rebecca.lew@med.monash.edu.au 1 rbuxeda@uprm.edu Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 77 receptor binding domain 57 cells were then 53 protein is not 52 levels were significantly 48 proteins are also 40 proteins are not 35 protein was not 32 protein is also 32 proteins do not 31 protein does not 29 proteins were also 28 protein was also 27 cells are not 26 cells did not 24 activity is not 23 protein is important 23 results are consistent 22 proteins did not 22 proteins were not 22 rna binding proteins 19 levels were higher 19 levels were not 19 protein is essential 19 protein is highly 19 protein is responsible 19 rna binding protein 18 protein is able 18 proteins have also 18 proteins is not 17 protein binding sites 17 proteins are present 17 proteins were then 16 effect was not 16 expression is not 16 protein is present 16 proteins are often 16 results were also 15 activity was not 15 protein did not 15 proteins are highly 15 proteins is also 15 studies have also 14 cells are able 14 cells do not 14 cells is not 14 protein has also 14 proteins have not 14 sequence is not 13 activity is also 13 cells were not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 5 sequences have no mutation 4 function is not clear 4 protein is not essential 4 proteins are not only 3 cells are not only 3 expression has no effect 3 genes are not essential 3 protein is not always 3 protein is not necessarily 3 protein is not only 3 proteins have not yet 2 activity has not yet 2 analysis showed no significant 2 cells are not able 2 cells are not yet 2 cells is not well 2 cells is not yet 2 domain is not yet 2 effects were not due 2 infection is not well 2 interactions are not sufficient 2 levels were not different 2 levels were not statistically 2 protein does not necessarily 2 protein is not clearly 2 protein is not normally 2 proteins are not essential 2 proteins are not strictly 2 proteins does not necessarily 2 proteins is not sufficient 2 receptor are not disordered 2 results are not different 2 structure is not yet 1 % had no detectable 1 % had no significant 1 % showed no antibody 1 . indicated not significant 1 acid is not normally 1 acid is not very 1 acid was not necessarily 1 acids are not equally 1 acids are not natural 1 acids are not trans 1 acids are not visible 1 acids do not generally 1 acids has no influence 1 acids was no longer 1 activities are not commonly 1 activities are not well 1 activity are not well A rudimentary bibliography -------------------------- id = cord-302514-rstvf3mc author = Abbas, Wasim title = The eEF1A Proteins: At the Crossroads of Oncogenesis, Apoptosis, and Viral Infections date = 2015-04-07 keywords = Akt; cell; eEF1A2; protein summary = Eukaryotic translation elongation factors 1 alpha, eEF1A1 and eEF1A2, are not only translation factors but also pleiotropic proteins that are highly expressed in human tumors, including breast cancer, ovarian cancer, and lung cancer. Overexpression of eEF1A2 protein up-regulates overall PI4K activity and cellular phosphatidylinositol 4-phosphate (PI4P) generation in human cells. In addition, high-resolution analysis of genomic aberration by metaphase and comparative genomic hybridization array identify the involvement of the 20q region, suggesting the potential role of eEF1A2 as a candidate tumor gene in lung cancer cell lines (41) . eEF1A2 interacts directly with Prx-1 and protects the cells from stress-induced apoptosis by the down-regulation of caspase-3 and caspase-8 activation parallel to increased expression of the pro-survival factor Akt (76, 77) . Elongation factor 1 alpha interacts with phospho-Akt in breast cancer cells and regulates their proliferation, survival and motility Expression profile of eukaryotic translation factors in human cancer tissues and cell lines doi = 10.3389/fonc.2015.00075 id = cord-274056-9t3kneoo author = Abd Elwahaab, Marwa A. title = A Statistical Similarity/Dissimilarity Analysis of Protein Sequences Based on a Novel Group Representative Vector date = 2019-05-08 keywords = protein; sequence summary = title: A Statistical Similarity/Dissimilarity Analysis of Protein Sequences Based on a Novel Group Representative Vector For beta globin protein sequences, seven species are selected in our sample set: human, chimpanzee, gorilla, mouse, rat, gallus, and opossum, as illustrated in Table 1 . The similarity/dissimilarity vectors that are corresponding to beta globin, ND5, and spike protein sequences are illustrated in Tables 9, 10, and 11, respectively, based on the two methods discussed before. The results in Table 10 show that both the magnitude ( 5 ) and the angle ( 5 ) can measure similarity/dissimilarity degree well among ND5 protein sequences as shown in Figure 2 . The similarity/dissimilarity analysis among the seven beta globin sequences measured according to ( 5 ) is illustrated in Table 12 and shown in Figure 4 . The similarity/dissimilarity analysis among the beta globin sequences measured according to (GR spike ) is illustrated in Table 14 and shown in Figure 6 . doi = 10.1155/2019/8702968 id = cord-347714-vxxhglx7 author = Abitogun, Folagbade title = COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date = 2020-10-14 keywords = HLA; SARS; epitope; protein summary = (10, 11) The structure of the spike glycoprotein of the virus is also an extended similarity with SARS-CoV, (4) which together with COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding other proteins of the virus are candidates for vaccine development and are being explored in different settings due to the active roles of the proteins in the infectivity of the virus. (18) However studies have shown that full length spike protein vaccines for SARS-CoV may lead to antibody mediated disease enhancement causing inflammatory and liver damage in animal models (19, 20) which is why in this manuscript, we applied immuno-informatics "in silico" approaches to identify potential CD8+ cytotoxic T Cell epitopes from proteins of SARS-CoV-2, SARS-CoV and MERS-CoV. Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach doi = 10.1101/2020.10.14.339689 id = cord-327934-hjimlb6i author = Acar, Delphine D. title = Identification of peptide domains involved in the subcellular localization of the feline coronavirus 3b protein date = 2019-10-01 keywords = EGFP; Fig; Tom20; protein summary = Transfection of different cell types with FCoV 3b fused to enhanced green fluorescent protein (EGFP) or 3×FLAG confirmed localization of FCoV 3b in the mitochondria and nucleoli. Transport of larger proteins to the nucleus, however, is an ATP-dependent active process driven by nuclear localization signals (NLSs), which are typically characterized by clusters of basic amino acids (reviewed in [38] [39] [40] [41] [42] ). The nucleocapsid proteins of several members of the order Nidovirales, such as porcine reproductive and respiratory syndrome virus (PRRSV, family Arteriviridae) [70, [77] [78] [79] [80] , transmissible gastroenteritis virus (TGEV) [81] , mouse hepatitis virus (MHV) [81, 82] and infectious bronchitis virus (IBV) [82] [83] [84] [85] (family Coronaviridae), also target the nucleolus and have been shown to incorporate one or more potential NLSs. Similarly, the SARS-CoV 3b protein was predicted to have two overlapping NLSs, a pat4 and bipartite motif, that were shown to be associated with nuclear (nucleolar) localization [27] . doi = 10.1099/jgv.0.001321 id = cord-341701-zropd3mo author = Adhikari, Subash title = A high-stringency blueprint of the human proteome date = 2020-10-16 keywords = Chr; Fig; SARS; hpp; human; pe1; protein; proteome summary = During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. • Be a focal point for life sciences researchers, pathologists, clinicians and industry communities seeking to translate and leverage proteomic and proteogenomic data to improve human health through: (i) greater understanding of the molecular mechanisms of common and rare diseases, (ii) identification of pathophysiological changes to generate disease and wellness diagnostic biomarkers, and (iii) development of new effective and safe personalized therapeutics. The HPP Ab Resource Pillar, ostensibly led by the Human Protein Atlas (HPA; www.proteinatlas.org), was initiated in 2003 and uses Ab-based strategies to analyse spatio-temporal aspects of the proteome 39 . Community encouragement to identify biological data that complement high-stringency MS strategies to accelerate discovery and understanding of human proteome PE2,3,4 missing proteins. doi = 10.1038/s41467-020-19045-9 id = cord-325230-3kg4oe4g author = Agol, Vadim I. title = Viral security proteins: counteracting host defences date = 2010-11-09 keywords = RNA; protein; viral; virus summary = These proteins include: capsid proteins; an RNA-dependent RNA polymerase (3D pol ); a protein (VPg, or 3B) that serves as a primer for the initiation of RNA synthesis; an ATPase with a conserved superfamily 3 helicase motif (2C ATPase ) and an essential but poorly defined role in viral RNA replication; a chymotrypsin-like protease (3C pro ), which, as the mature protein or as a precursor, is a major factor in polyprotein processing; two hydrophobic membrane-binding proteins (2B and 3A) that participate in the generation of a virus-friendly environment; and, flanking the precursor of the capsid proteins, one or two highly variable proteins (L and 2A), the structure and functions of which are the subject of this Review. doi = 10.1038/nrmicro2452 id = cord-333089-ufyzqgqk author = Aguilar-Pineda, Jorge Alberto title = Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry date = 2020-07-29 keywords = ACE2; RBD; SARS; figure; protein summary = Based on the structural complementarity and steric impediments between the S protein and human ACE2 (hACE2) protein membranes, we mapped the glycosylation sites of both models [21] [22] [23] [24] and performed molecular dynamics simulations (MDS) by 250 ns to stabilize the glycosylated SARS-CoV2 spike (S) and hACE2 complex (suppl. Given the possibility that occupancy at glycosylated residues or S-RBD binding sites by estrogens could modify the affinity of the SARS-CoV2 virus and alter entry into the cell thereby reducing infectivity, we sought to further examine these interactions using a range of complementary experimental approaches (see Table S1 ). In an effort to explore the potential protective effects of female sex hormones against SARS-CoV-2 infection, we examined the impact of estradiol (17β-diol) and a dietary-derived phytoestrogen (S-equol) on hACE2 structure and protein expression by a combination of in silico modeling, in vitro, and in vivo analysis. doi = 10.1101/2020.07.29.227249 id = cord-258624-041cf99j author = Ahmad, Sajjad title = Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics date = 2020-05-23 keywords = COVID-19; MEPVC; SARS; epitope; protein; vaccine summary = doi = 10.1016/j.ejps.2020.105387 id = cord-103528-3tib5o1m author = Ahmed, Asad title = DEELIG: A Deep Learning-based approach to predict protein-ligand binding affinity date = 2020-09-28 keywords = affinity; ligand; protein summary = title: DEELIG: A Deep Learning-based approach to predict protein-ligand binding affinity Here, we have incorporated Convolutional Neural Networks that find spatial relationships among data to help us predict affinity of binding of proteins in whole superfamilies towards a diverse set of ligands. Initial raw data database created contained protein structures in PDB format, protein sequences in FASTA format, ligand in SDF format and binding affinity values of corresponding protein-ligand pairs for 5464 complexes. We propose a deep-learning based approach to predict ligand (eg., drug)-target binding affinity using only structures of target protein (PDB format) and ligand (SDF format) as inputs. We have trained two models to predict the binding affinity between protein and ligand in a given complex. We have constructed a novel dataset that represents a diverse set of ligands and using a novel deep learning based approach we have achieved significant improvement in prediction of binding affinity of protein-ligand complexes. doi = 10.1101/2020.09.28.316224 id = cord-290445-vb53bih9 author = Ahmed, Shiek SSJ title = Interplay of host regulatory network on SARS-CoV-2 binding and replication machinery date = 2020-04-23 keywords = Fig; SARS; protein summary = Secondly, the viral replication machinery network from SET-B with 332 seed proteins extended to 1486 neighboring proteins with 11438 interacting edges which representing the mechanism attributed to evasion of the SARS-CoV2 genome into the host. Similarly, the viral replication machinery network was acquired with 1522 proteins with 9747 interacting edges showing the complex SARS-CoV-2 mechanism in the human lungs. These common molecules represent the inter-connecting mechanism involved in the transcription machinery, immune response, cell growth and/or maintenance, transport, metabolism, protein metabolism, cell communication and signal transduction that activated upon virus binding and has been subsequently utilized for viral replication process (S5 Table) Also mapping with other viral infection dataset, 50 hub proteins of the replication machinery network have noticed in influenza virus infection (S4 Table) , which suggests SARS-CoV2 and influenza may have a similar mode of host infection machinery [17] . The molecular pathways of interconnecting protein hubs could be the intermediate phase that connects the receptor activation mechanism and viral replication process (Fig 10) . doi = 10.1101/2020.04.20.050138 id = cord-016442-3su3x6ed author = Aiking, Harry title = Transition Feasibility and Implications for Stakeholders date = 2006 keywords = NPF; PROFETAS; meat; protein; transition summary = doi = 10.1007/1-4020-4842-4_7 id = cord-338485-4zqeq1se author = Aiking, Harry title = The next protein transition() date = 2018-07-27 keywords = Aiking; Boer; FAO; food; protein; western summary = With respect to sustainability, this is none too early, for there is a growing consensus that animal protein has disproportionate environmental impacts, particularly when produced in intensive production systems employing massive use of feed crops (Aiking, 2014; McMichael, Powles, Butler, & Uauy, 2007; Smil, 2001; Steinfeld et al., 2006; Westhoek et al., 2011) . Animal protein products such as meat and dairy are important to them from an economic perspective, but when employing intensive production systems these are wasteful of plant protein from an environmental point of view and inherently, therefore, wasteful of the resources required to grow feed crops, such as land, water, phosphate and fuel. Increase awareness of the impacts of animal-based protein on the environment, the urgency of this issue and the availability of solutions, but take into account that science-based health and sustainability arguments in favour of a diet change do not sufficiently reach consumers or are too difficult for them to comprehend (de Boer & Aiking, 2017) . doi = 10.1016/j.tifs.2018.07.008 id = cord-319563-9lwr6k8p author = Aitekenov, Sultan title = Review: Detection and quantification of proteins in human urine date = 2020-10-14 keywords = Raman; albumin; detection; mass; protein; urinary; urine summary = This review focuses on the instrumental quantification (electrophoresis, chromatography, immunoassays, mass spectrometry, fluorescence spectroscopy, the infrared spectroscopy, and Raman spectroscopy) of proteins (the most of all albumin) in human urine matrix. Among the reasons that make urine challenging for researchers to analyze are: urine matrix is complex, it consists of various inorganic and organic compounds, from low-molar mass molecules to polymers; urine could contain cells, such as blood cells, or bacteria, which changes the composition of urine in time rapidly; an analytical method for diagnosis of proteinuria should cover protein presence in urine in a wide range from 0.01 mg/ml to 10 mg/ml. focuses on urinary proteins as potential biomarkers for mainly urine diseases, and capillary electrophoresis coupled mass spectroscopy as an instrumental method [33] . In this review, we focused on instrumental determination of abundant proteins in urine by electrophoresis, chromatography, mass spectrometry, immunoassay, fluorescence, IR, and Raman spectroscopy. doi = 10.1016/j.talanta.2020.121718 id = cord-034191-qqb2knmo author = Alayi, Tchilabalo D. title = Tandem Mass Tag-Based Serum Proteome Profiling for Biomarker Discovery in Young Duchenne Muscular Dystrophy Boys date = 2020-10-06 keywords = DMD; Duchenne; TMT; USA; figure; protein; serum summary = In this study, we sought to optimize and standardize a serum processing workflow in combination with tandem mass tag (TMT) multiplexing strategy to systematically survey the serum proteome of young untreated DMD boys and agematched healthy controls and identify biomarkers associated in the early stages of the disease. Serum samples from 4 year-old glucocorticoid naive DMD patients (n = 9) and age-matched healthy controls (n = 9) were processed for proteome profiling using our standardized multiplexing TMT-based mass spectrometry method described above. As expected, a large number of identified biomarkers (50%) that were found to be elevated in sera of these young DMD boys relative to the healthy controls were of muscle origin based on Gene Ontology molecular function annotations ( Figure S2 ) and information collected using Mass Spectrometry Data Analysis tools. doi = 10.1021/acsomega.0c03206 id = cord-294125-v2dr4hm0 author = Albert, Manuel title = ISG15, a Small Molecule with Huge Implications: Regulation of Mitochondrial Homeostasis date = 2018-11-13 keywords = IFN; cell; isg15; mitochondrial; protein; virus summary = doi = 10.3390/v10110629 id = cord-319780-rfj9t99r author = Alexander, S.P.H. title = A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29 date = 2020-05-01 keywords = ACE2; COVID-19; MERS; RNA; SARS; TMPRSS2; cell; link; protein summary = Analysis of the co-crystal structure suggested that the SARS spike protein binds to the active site of angiotensin converting enzyme 2 (ACE2, Li et al., 2005) . A truncated version of human recombinant ACE2, lacking the transmembrane domain, mitigated against SARS-CoV infection of cells (Li et al., 2003) and has been used in animal models to reduce symptoms of severe acute lung failure , diabetic nephropathy (Oudit et al., 2010) and cardiac hypertrophy and fibrosis . A recent cryo-EM structure suggested that ACE2 and B 0 AT1/SLC6A19 form a heterodimer which pairs up through interfaces between the two ACE2 partners (Figure 1) , with the RBD of SARS-CoV-2 spike protein binding to the peptidase active site of ACE2 suggesting that B 0 AT1/SLC6A19 may facilitate entry of the novel coronavirus. Tumor necrosis factor- convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) doi = 10.1111/bph.15094 id = cord-355924-8sk9al0n author = Allam, Loubna title = Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules date = 2020-10-21 keywords = GRP78; SARS; Spike; protein summary = Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein. For this purpose, a targeted analysis of the expression of candidate genes involved in SARS-CoV-2 infection confirmed the presence of the GRP78 protein in vitro in epithelial cells of the human respiratory tract and lung tissue. In this direction, our study focused on the repositioning of approved drugs as well as the investigation of other bioactive compounds that may prevent the penetration of SARS-CoV-2 into host cells by targeting the region of GRP78 that is required for the interaction with the Spike protein of the virus. Inhibition of the interaction between the spike protein SARS-CoV-2 and the receptor by blocking the GRP78 is a strategy interesting to identify drugs that decrease the rate of viral infection. doi = 10.1177/1177932220965505 id = cord-281552-zfjy3m3i author = Alsaadi, Entedar A. J. title = Identification of a Membrane Binding Peptide in the Envelope Protein of MHV Coronavirus date = 2020-09-22 keywords = MHV; SARS; protein summary = Here, we test E-derived peptides for membrane binding activity in vitro and confirm those identified as positive in the context of the full length protein expressed in two different cell types. Relative densitometry of the HSP and LSP bands revealed significant differences among the mutants with regard to their localisation to the different membrane fractions of E expressing insect cells ( Figure 5B ) and confirmed a role for the amphipathic MHV CoV E 50-64 peptide in membrane interaction. An amphipathic helix, EPTM, detected in the post-TM region of E, was suggested by bioinformatics analysis and assessed for direct membrane interaction in vitro by binding to GUVs. For comparison, the predicted E protein TM domain, ETM, and an established membrane active peptide from the influenza M2 protein were also included. Following expression of the complete E protein with mutations in the same identified peptide, altered membrane binding in two distinct cell types, mammalian and insect, was apparent. doi = 10.3390/v12091054 id = cord-004672-0lf5j8lo author = Anderson, Kevin title = Structural and physiological properties of mengovirus: Avirulent, hemagglutination-defective mutants express altered alpha (1 D) proteins and are adsorption-defective date = 1987 keywords = mutant; protein; virus summary = doi = 10.1007/bf01313891 id = cord-312489-ywep0c08 author = Andoh, Kiyohiko title = Decreased neutralizing antigenicity in IBV S1 protein expressed from mammalian cells date = 2015-10-02 keywords = IBV; protein; recombinant summary = We evaluated the antigenicity of recombinant infectious bronchitis virus (IBV) S1 protein expressed in mammalian cells. Native S1 ELISA detected similar titers in the sera of animals immunized with recombinant S1 protein compared to those in sera of chickens immunized with inactivated virus (Fig. 6b ) (Control experiments (data not shown) demonstrated that mock and unvaccinated control groups did not differ from each other in VN and ELISA tests of anti-S1 activity.) These results indicated that while recombinant S1 protein retained antigenicity (the ability to induce antibodies against S1 protein), the resulting antibodies was decreased its neutralizing activity, in contrast to those induced by inactivated virus. The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus doi = 10.1016/j.virusres.2015.06.019 id = cord-010260-8lnpujip author = Anthonsen, Henrik W. title = The blind watchmaker and rational protein engineering date = 1994-08-31 keywords = Fig; NMR; electrostatic; method; protein; sequence; structure summary = doi = 10.1016/0168-1656(94)90152-x id = cord-291210-ghjseynl author = Arbely, Eyal title = A Highly Unusual Palindromic Transmembrane Helical Hairpin Formed by SARS Coronavirus E Protein date = 2004-08-13 keywords = SCoV; figure; protein summary = doi = 10.1016/j.jmb.2004.06.044 id = cord-272467-8heg5iql author = Armstrong, John title = Expression of coronavirus E1 and rotavirus VP10 membrane proteins from synthetic RNA date = 2004-02-19 keywords = Golgi; protein summary = doi = 10.1002/jcb.240350206 id = cord-341378-pw60qx7c author = Armstrong, John title = Sequence and topology of a model intracellular membrane protein, E1 glycoprotein, from a coronavirus date = 1984 keywords = membrane; protein summary = In combination with a previous study of its assembly into the endoplasmic reticulum membrane(9), the sequence reveals several unusual features of the protein which may be related to its intracellular localization. In the eukaryotic cell, both secreted and plasma membrane proteins are synthesized at the endoplasmic reticulum, then transported, via the Golgi complex, to the ceU surface 1 -4. Here we present the primary structure of the protein, determined by analysis of eDNA clones prepared from viral mRNA. In combination with a previous stu''!} of its assembly into the endoplasmic reticulum membrane , the sequence reveals several unusual features of the protein which may be related to its intracellular localization. Thus, the El glycoprotein is potentially a convenient model for studying those features of a membrane protein that determine its arrest at a particular destination on the membrane transport pathway. doi = 10.1038/308751a0 id = cord-336364-2ust3qoq author = Artigas, Laura title = In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm date = 2020-10-02 keywords = ARD; SARS; protein; set summary = title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm This has provided 3 sets of proteins related with the infection process: 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lungcells infection set, and 3) acute respiratory distress (ARD) set. According to the findings by GUILDify, we confirm the effect of the combination of pirfenidone and melatonin in the entry points of the SARS-CoV-2 infection, specifically the neighbours of furin and GRP-78, and some proteins associated with ARD. 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lung-cells infection set, and 3) acute respiratory distress (ARD) set that is composed of 6 subsets (Alveolar macrophages, Monocytes, Neutrophils, Intermediate phase ARD, Late phase ARD and ARD cytokine storm). doi = 10.1371/journal.pone.0240149 id = cord-009959-erh8ggh3 author = BENTLEY, WILLIAM E. title = Development of an Efficient Bioprocess for Poultry Vaccines Using High‐density Insect Cell Culture date = 2006-12-17 keywords = IBDV; baculovirus; cell; culture; protein summary = Several general articles, manuals, and review articles have been published that describe both the expression system''" and novel process engineering aspects.%" In this work, we subdivide the entire bioprocess into three key areas: (1) metabolism of infected cells and specific heterologous protein yield; (2) bioreactor configuration and high cell density continuous culture; and (3) integration of expression and product separation. Caron el al." restored recombinant protein production at higher cell density by renewing the medium at the time of infection. High-level recombinant protein production in bioreactors using the baculovirus insect cell expression system Quantification of cell culture factors affecting recombinant protein yields in baculovirus-infected insect cells Effects of oxygen/glucose/glutamine feeding on insect cell baculovirus protein expression: A study on epoxide hydroxylase production Ecdysteroids increase the yield of recombinant protein produced in baculovirus insect cell expression system A continuous flow bioreactor system for the production of recombinant proteins using the insect cell-baculovirus expression system doi = 10.1111/j.1749-6632.1994.tb44387.x id = cord-000257-ampip7od author = Bagowski, Christoph P title = The Nature of Protein Domain Evolution: Shaping the Interaction Network date = 2010-08-17 keywords = domain; evolution; protein; sequence summary = doi = 10.2174/138920210791616725 id = cord-303494-tofch4j7 author = Bai, Juan title = Identification of VP1 peptides diagnostic of encephalomyocarditis virus from swine date = 2014-12-30 keywords = EMCV; VP1; figure; protein summary = In order to map the minimal sequences of the epitopes recognized by McAbs, the series of truncated recombinant proteins were used in Western blot was to identify the reactivity of each of 10 anti-VP1 McAbs. The results showed that McAbs (6E11, 7A7 and 7C9) could reacted with fragments (F11, F9 and F3) containing the six amino acids V(2)ENAEK(7), but not reacted with the fragments with the deletion of any one of the six amino acids (F10, F7 and F8). Meanwhile, those purified truncated fragment proteins were used as the antigens in ELISA to detect the levels of those McAbs. The results showed that the OD 450 values of McAbs (6E11, 7A7 and 7C9) in F1, F3, F9 and F11 groups were significantly higher than those in F6, F7, F8 and F10 (p < 0.01) ( Figure 4A ). doi = 10.1186/s12985-014-0226-8 id = cord-256340-w4z5avld author = Bailer, SM title = Connecting viral with cellular interactomes date = 2009-07-24 keywords = interaction; protein; y2h summary = Genome-scale screens for intraviral and virus–host protein interactions and the analysis of literature-curated datasets are able to provide a novel, comprehensive perspective of viruses, and virus-infected cells. Until now, large-scale interaction screens were predominantly performed with the yeast-two-hybrid (Y2H) system; however, alternative high-throughput technologies detecting binary protein interactions or protein complexes have been developed. The Y2H system as the standard assay for the evaluation of interactomes Essentially all high-throughput approaches to identify binary protein interactions on a genome-scale currently rely on the Gal4-based yeast-two-hybrid (Y2H) system ( Figure 1 ) developed in 1989 [1] . Despite certain limitations the Y2H system is used by the majority of groups because of its enormous efficacy and the data discussed in this review are all based on Y2H screens as all currently published large-scale studies on intraviral or virus-host protein interactions are based on them. More recent approaches on intraviral interactomes include several members of the herpesvirus family [15 ,16 ,19 Scheme of HSV-1 virus particle with protein interactions detected in a genome-wide Y2H screen. doi = 10.1016/j.mib.2009.06.004 id = cord-319754-5isw53wl author = Balgoma, David title = Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date = 2020-08-31 keywords = HCV; SARS; cell; fusion; lipid; membrane; protein; virus summary = Some viruses may use different entry mechanisms, this feature being likely dependent upon the membrane lipid composition of the host cell they infect as well as the particular cell surface factor attachment used. The question regarding whether the lipid-raft domains may serve as platforms to concentrate the proteins required for viral entry and, even though some evidence exists, to activate signaling pathways inside the host cell still remains unsolved. More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . doi = 10.3390/metabo10090356 id = cord-342189-ya05m58o author = Banerjee, Abhik K. title = SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date = 2020-10-08 keywords = GFP; IFN; NSP1; RNA; SARS; SRP; figure; protein summary = Here, we comprehensively define the interactions between each SARS-CoV-2 protein and human RNAs. We show that 10 viral proteins form highly specific interactions with mRNAs or ncRNAs, including those involved in progressive steps of host cell protein production. We show J o u r n a l P r e -p r o o f 5 that NSP16 binds to the mRNA recognition domains of the U1 and U2 RNA components of the spliceosome and acts to suppress global mRNA splicing in SARS-CoV-2-infected human cells. We identified several pathogenic functions of SARS-CoV-2 in human cells -including global inhibition of host mRNA splicing, protein translation, and membrane protein trafficking -and described the molecular mechanisms by which the virus acts to disrupt these essential cell processes. doi = 10.1016/j.cell.2020.10.004 id = cord-356064-q56jnhss author = Bartel, Sebastian title = Proteome analysis of vaccinia virus IHD-W-infected HEK 293 cells with 2-dimensional gel electrophoresis and MALDI-PSD-TOF MS of on solid phase support N-terminally sulfonated peptides date = 2011-08-01 keywords = IHD; PSD; SPITC; VACV; protein summary = title: Proteome analysis of vaccinia virus IHD-W-infected HEK 293 cells with 2-dimensional gel electrophoresis and MALDI-PSD-TOF MS of on solid phase support N-terminally sulfonated peptides In this report the proteome of HEK293 cells infected with Vaccinia Virus strain IHD-W was analyzed by 2-dimensional gel electrophoresis and MALDI-PSD-TOF MS in a bottom-up approach. Derivatization of peptides with 4-sulfophenyl isothiocyanate (SPITC) carried out on ZipTipμ-C18 columns enabled protein identification via the peptides'' primary sequence, providing improved s/n ratios as well as signal intensities of the PSD spectra. The E3L gene product has been identified in HEK 293 cells infected with active VACV IHD-W, which is in correlation to proteome analysis of VACV virions that indicate that the putative double-stranded RNA binding protein (D-1) is not present in the virion but is expressed in the early replication phase. Proteome analysis of vaccinia virus IHD-W-infected HEK 293 cells with 2-dimensional gel electrophoresis and MALDI-PSD-TOF MS of on solid phase support N-terminally sulfonated peptides doi = 10.1186/1743-422x-8-380 id = cord-262043-66qle52a author = Basit, Abdul title = Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent date = 2020-05-20 keywords = ACE2; RBD; SARS; protein summary = Spike (S) glycoprotein is the structural protein of SARS-CoV-2 located on the envelope surface, involve in interaction with angiotensin converting enzyme 2 (ACE2), a cell surface receptor, followed by entry into the host cell. The protein-protein docking and molecular dynamic simulation showed that tACE2 has higher binding affinity for RBD and form more stabilized complex with RBD than the intact ACE2. We designed a truncated version (tACE2) of ACE2 receptor covering the binding residues and performed protein-protein docking and molecular dynamic simulations to analyze its binding affinity for RBD and complex stability. Based on the HADDOCK score and the docking RMSD value, the docked complexes of ACE2 and tACE2 with RBD were analyzed for binding affinity DG (kcal mol À1 ) and stability using protein binding energy prediction (PRODIGY) server (Xue et al., 2016) . doi = 10.1080/07391102.2020.1768150 id = cord-330337-d41imvo7 author = Basu, Souradip title = Impact of clade specific mutations on structural fidelity of SARS-CoV-2 proteins date = 2020-10-20 keywords = SARS; mutation; protein summary = Our observations and analysis direct us to identify that all the major mutations have a negative impact in context of stability of the viral proteins under study and the mutant proteins suffer both structural and functional alterations as a result of the mutations. The secondary structure of the wild type and the mutant proteins along with their degree of disordered residues and accessible surface area was predicted using the primary sequence of the protein. Each of the seven proteins were assigned a score of either ''-1'' or ''0'', for each of the four computational tools used for epitope prediction, where ''-1'' corresponds to any change in number or binding efficacy of antigenic determinants, that may have surfaced because of mutation and ''0'' corresponds to no changes between wild type and mutant forms. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure doi = 10.1101/2020.10.20.347021 id = cord-018265-twp33bb6 author = Becker, Pablo D. title = Community-acquired pneumonia: paving the way towards new vaccination concepts date = 2007 keywords = RSV; SARS; dna; protein; response; vaccine; virus summary = A live vaccine based on a master virus strain developed at the Institute of Applied Microbiology (Austria) by growing wild influenza virus in Vero cells at 25°C was also demonstrated to be safe, well-tolerated and immunogenic after intranasal immunization in young adults [18]. Candidate vaccines should be able to replicate and induce a protective immune response in young infants, even in the presence of maternally acquired antibodies. This demonstrates that antibodies play a major role in protection against this disease, whereas T-cell immunity targeted to internal viral proteins appears to contribute to clearance. The second generation of PS-based conjugate vaccines stimulates stronger antibody responses, even in infants, young children and immune deficient individuals, as well as immunological memory. The resulting proteins are then used to perform immunological and/or functional studies to select the most promising candidates (e.g., able to induce the production of microbicidal or neutralizing antibodies, capacity to confer protective immunity). doi = 10.1007/978-3-7643-7563-8_10 id = cord-300418-s4wt5gim author = Bedford, Lynn title = Ubiquitin-like protein conjugation and the ubiquitin–proteasome system as drug targets date = 2010-12-10 keywords = UBL; UPS; protein; ring; ubiquitin summary = In this Review, we first provide an overview of the enzyme classes in the UPS and UBL pathways that represent potential therapeutic targets, highlighting considerations that are important for drug discovery and recent progress in the development of small-molecule inhibitors. Studies using NF-κB-dependent human cancer models have demonstrated increased levels of the CRL1β TRCP substrate pIκBα and inhibition of NF-κB activity and apoptosis 116, 117 , suggesting the feasibility of NAE inhibition for the treatment of disease that is associated with constitutively active NF-κB signalling 112 The recent discovery of the importance of linear ubiquitin chains in NF-κB activation extends the complexity of the regulation of the system. As expected, ubiquitin-dependent processes, including the degradation of ubiquitylated proteins by the 26S proteasome, by autophagy and in the endosome-lysosome pathway, have central roles in neuronal development, homeostasis and disease. doi = 10.1038/nrd3321 id = cord-319614-4qi59pbz author = Benej, Martin title = Quantitative Proteomics Reveal Peroxiredoxin Perturbation Upon Persistent Lymphocytic Choriomeningitis Virus Infection in Human Cells date = 2019-10-25 keywords = Akt; LCMV; ROS; cell; protein summary = Experimental data indicate that during persistent infection, lymphocytic choriomeningitis virus (LCMV) may both directly or indirectly modulate regulatory cellular processes and alter cellular functions that are not critical for survival, but are essential for cell homeostasis. Increased levels of ROS were accompanied by changes in the pattern of telomere restriction fragments (TRFs) in infected cells and mediated activation of hypoxia-inducible transcription factor-1 (HIF-1) and phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathways. These data suggest that LCMV maintains its replication in persistently infected cells by regulating redox signaling through modulation of local levels of H 2 O 2 and subsequent activation of cellular processes that it uses for its own benefit. Notably, the treatment with antioxidants also resulted in reduced levels of viral NP in HeLa, as well as in A549 LCMV-infected cells, suggesting a link between ROS-dependent signaling and virus replication (Figures 7B,D and Supplementary Figure S2B ). doi = 10.3389/fmicb.2019.02438 id = cord-274366-t138l6px author = Benetti, Elisa title = ACE2 gene variants may underlie interindividual variability and susceptibility to COVID-19 in the Italian population date = 2020-07-17 keywords = ACE2; SARS; italian; protein; variant summary = Taking advantage of the Network of Italian Genomes (NIG), a consortium established to generate a public database (NIG-db) containing aggregate variant frequencies data for the Italian population (http://www.nig.cineca.it/), here we describe the genetic variation of ACE2 in the Italian population, one of the newly affected countries by the SARS-CoV-2 outbreak causing COVID-19. In order to shed light on the role of ACE2 variants on interindividual variability and susceptibility to COVID-19 in Italian population we performed WES analysis on a cohort of 131 patients and 258 controls who agreed in participating to the study (see "Materials and methods"). These variants which surround residual essentials for the SARS-CoV-2 spike protein binding were predicted to likely affect the cleavage-dependent virion intake, such as the polymorphic c.2158A>G p.(Asn720Asp) (allele frequency 0.011) which lies four amino acids from the cleavage sequence of TMPRSS2 or to have a substantial impact on protein structure and spike protein interaction by MD simulation (Fig. 3a) . doi = 10.1038/s41431-020-0691-z id = cord-314746-1o0rf0ii author = Bergasa-Caceres, Fernando title = Interdiction of Protein Folding for Therapeutic Drug Development in SARS CoV-2 date = 2020-08-10 keywords = Protein; SARS; SCM; contact summary = [Image: see text] In this article, we predict the folding initiation events of the ribose phosphatase domain of protein Nsp3 and the receptor binding domain of the spike protein from the severe acute respiratory syndrome (SARS) coronavirus-2. The identification of the primary contacts along the folding pathway of viral proteins constitutes an important result for at least two reasons: (a) the sequences of the specific segments involved in the primary contacts provide a template to specify candidate peptide drugs of inhibitory effect with the maximum possible contact affinity to compete with the natural folding mechanism; and (b) it provides insight for further investigation into the subsequent folding steps leading to a fully functional viral protein, potentially providing for additional FITRs. The fact that the primary contact is defined by the interaction between two well defined amino acid sequences suggests that a strategy to develop FITR-based therapeutic drugs could be one utilizing trial peptide drugs as suggested above. doi = 10.1021/acs.jpcb.0c03716 id = cord-103320-2rpr7aph author = Bhandari, Bikash K. title = Solubility-Weighted Index: fast and accurate prediction of protein solubility date = 2020-03-26 keywords = Fig; Protein; SWI; Solubility; biology summary = Results We have discovered that global structural flexibility, which can be modeled by normalised B-factors, accurately predicts the solubility of 12,216 recombinant proteins expressed in Escherichia coli. Protein solubility, at least in part, depends upon extrinsic factors such as ionic strength, temperature and pH, as well as intrinsic factors-the physicochemical properties of the protein sequence and structure, including molecular weight, amino acid composition, hydrophobicity, aromaticity, isoelectric point, structural propensities and the polarity of surface residues (Wilkinson and Harrison 1991; Chiti et al. 2003 ) Among these sets of B-factors, sequence composition scoring using the most recently published set of normalised B-factors produced the highest AUC score ( To improve the prediction accuracy of solubility, we iteratively refined the weights of amino acid residues using the Nelder-Mead optimisation algorithm (Nelder and Mead 1965) . To understand the properties of soluble and insoluble proteins, we determined the enrichment of amino acid residues in the PSI:Biology targets relative to the eSOL sequences (see Methods). doi = 10.1101/2020.02.15.951012 id = cord-323358-05bk91lm author = Bhaskar, Sathyamoorthy title = Engineering protein nanocages as carriers for biomedical applications date = 2017-04-07 keywords = cell; nanocage; protein; virus summary = We review natural and synthetic protein nanocages that have been modified using chemical and genetic engineering techniques to impart non-natural functions that are responsive to the complex cellular microenvironment of malignant cells while delivering molecular cargos with improved efficiencies and minimal toxicity. 1, 3 Examples of naturederived nanocarriers include protein nanocages such as viruses, ferritin and many others that are formed by the self-assembly of protein subunits, resulting in a cage-like structure. 8 In this review, we focus on natural and synthetic protein scaffolds engineered with specific functional groups to impart non-native functions, including aiding the delivery of active molecules through targeting of malignant cells and overcoming cellular barriers. 3 In addition to cell targeting ability and gene delivery efficiency, these protein-based multifaceted systems have highly ordered spatial configurations, and the stability and functionality of these materials have already been established through intensive research with advances in understanding virus infection, replication and assembly pathways. doi = 10.1038/am.2016.128 id = cord-252536-gfx4cq03 author = Bieniossek, Christoph title = MultiBac: expanding the research toolbox for multiprotein complexes date = 2011-12-07 keywords = MultiBac; complex; dna; gene; protein summary = It consists of an array of small synthetic DNA plasmids, an engineered baculovirus genome derived from the Autographa californica nuclear polyhedrosis virus (AcNPV; see Glossary) that is used to infect cells of the caterpillar Spodoptera frugiperda, and a set of protocols detailing every step from gene insertion into the plasmids to production of protein complexes in cultured insect cells [19, 20] . Donors and acceptors contain a resistance marker, a short imperfect inverted repeat (LoxP), an expression cassette consisting of a baculoviral promoter (p10 or polh), a DNA segment for inserting heterologous genes, and an efficient signal for eukaryotic polyadenylation (Figure 1a ). Two outstanding examples of the utility of MultiBac are the elegant production of the entire anaphase promoting complex, APC/Ca large (1.1 MDa) 13-subunit multiprotein assembly that regulates defined cell cycle transitions [34] and the recent crystal structure elucidation of the Mediator head modulea transcription factor complex that is essential for the expression of class II genes in eukaryotes [35] . doi = 10.1016/j.tibs.2011.10.005 id = cord-000012-p56v8wi1 author = Bigot, Yves title = Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis date = 2008-09-18 keywords = dna; gene; genome; protein; virus summary = doi = 10.1186/1471-2148-8-253 id = cord-318551-c1qr27lg author = Boguszewska‐Chachulska, Anna M. title = Rna Viruses Redirect Host Factors to Better Amplify Their Genome date = 2005-12-29 keywords = RNA; protein; replication; virus summary = (Adapted with permission from Pasternak et al., 2001.) Transcription of segmented (À) strand RNA viruses such as the Orthomyxoviridae, Arenaviridae, Bunyaviridae, and Tenuiviruses requires a primer to initiate synthesis of the mRNAs. This is achieved by cap-snatching in which the replicase complex, or a protein thereof, binds to the 5 0 region of cell mRNAs, cleaves off the cap together with generally 7-15 nucleotides from the 5 0 end of the cell mRNA, and uses this fragment as a primer to initiate synthesis of the viral mRNAs (Bouloy et al., 1978; Nguyen and Haenni, 2003) . (1996) PV, poliovirus; MHV, mouse hepatitis virus; WNV, West Nile virus; BVDV, bovine viral diarrhea virus; HPIV-3, human parainfluenza virus-3; IG (À), intergenic region in (À) RNA; UTR, untranslated region; Leader RNA (À), 3'' end of (À) RNA; Leader RNA (þ), 5'' end of (þ) RNA; HF, host factor; PCBP, poly(C)-binding protein; PABP, poly(A)-binding protein; hnRNP A1, heterogeneous nuclear ribonucleoprotein A1; PTB, polypyrimidine tract-binding protein; TIA-1, T-cell-activated intracellular antigen; TIAR, TIA-1-related; RHA, RNA helicase A; GAPDH, glyceraldehyde-3-phosphate dehydrogenase. doi = 10.1016/s0065-3527(05)65002-6 id = cord-268326-sbz3uk5h author = Bonam, Srinivasa Reddy title = Lysosomes as a therapeutic target date = 2019-09-02 keywords = CMA; Gaucher; TFEB; autophagy; cathepsin; cell; disease; lysosomal; lysosome; patient; protein summary = With a focus on lysosomal dysfunction in autoimmune disorders and neurodegenerative diseases — including lupus, rheumatoid arthritis, multiple sclerosis, Alzheimer disease and Parkinson disease — this Review critically analyses progress and opportunities for therapeutically targeting lysosomal proteins and processes, particularly with small molecules and peptide drugs. Alterations in lysosomal functions, either in the fusion processes involved in the general pathways mentioned above or related to the function of lyso somal enzymes and non enzymatic proteins, can result in broad detrimental effects, including failure to clear potentially toxic cellular waste, inflammation, apopto sis and dysregulation of cellular signalling 8 . doi = 10.1038/s41573-019-0036-1 id = cord-001567-3bw7jbzq author = Borlak, Jürgen title = Proteome mapping of epidermal growth factor induced hepatocellular carcinomas identifies novel cell metabolism targets and mitogen activated protein kinase signalling events date = 2015-02-25 keywords = EGF; EGFR; HCC; additional; expression; figure; liver; protein; table; tumour summary = doi = 10.1186/s12864-015-1312-z id = cord-325943-3hvy7b7c author = Bouwman, Kim M. title = Guinea Fowl Coronavirus Diversity Has Phenotypic Consequences for Glycan and Tissue Binding date = 2019-05-01 keywords = Fig; glycan; protein summary = Glycan array analysis revealed that, in addition to the previously elucidated biantennary di-N-acetyllactosamine (diLacNAc) receptor, viral attachment S1 proteins from GfCoV/2014 and GfCoV/2011 can bind to glycans capped with alpha-2,6-linked sialic acids. Our data indicate that diversity in GfCoV viral attachment proteins results in differences in degrees of affinity for glycan receptors, as well as altered avidity for intestinal tract tissues, which might have consequences for GfCoV tissue tropism and pathogenesis in guinea fowls. Glycan and tissue binding analyses of GfCoV/2011 and GfCoV/2014 recombinant spike S1 proteins revealed that while both proteins had the same specificities, GfCoV/2014 S1 had a much higher affinity toward glycan receptors and tissues of the lower gastrointestinal tract, in agreement with the observed replication of the virus in these tissues from field cases. doi = 10.1128/jvi.00067-19 id = cord-017866-h5ttoo0z author = Bowman, Grant R. title = Biogenesis of Dense-Core Secretory Granules date = 2010-05-27 keywords = DCG; Golgi; ISG; TGN; cell; granule; protein; secretory summary = For such regulated exocytosis, the vesicles that carry newly-synthesized protein from the TGN accumulate in the cytoplasm until specific extracellular events trigger their fusion with the plasma membrane, resulting in the release of vesicle contents.f The vesicles involved are called dense-core granules (DCGs), the name reflecting the fact that the contents are so highly condensed that they form a large electron-dense plug in the vesicle lumen. In support of this hypothesis, recent studies have suggested that prohormone convertases 1 and 2, which are responsible for proteolytic cleavageof lumenal proteins during granule maturation, are sorted to ISGs by virtue of C-terminal membrane raft-associated tails, which are by themselves necessary and sufficient for targeting to DCGs,uo 120 Additionally, cytoplasmic signals on some transmembrane proteins appear to play important roles in sorting, but the mechanisms are unknown. doi = 10.1007/978-0-387-93877-6_10 id = cord-003817-k3m72uxw author = Braun, Elisabeth title = Furin‐mediated protein processing in infectious diseases and cancer date = 2019-08-05 keywords = Env; cell; cleavage; furin; protein; virus summary = For example, avirulent Newcastle disease virus (NDV) strains harbour a monobasic cleavage site in their Fusion (F) protein and result only in local infections (mainly in the respiratory tract) since expression of the respective host proteases is limited to a few cell types. Notably, proteolytic processing of Env depends on correct N-linked glycosylation as aberrant carbohydrate side chains may result in subcellular mistrafficking or sequestration of Env. 49 Most likely, HIV-1 takes advantage of the redundancy of several proprotein convertases recognising the polybasic cleavage motif in Env. Furin, PCSK5, PCSK6 and PCSK7 have all been shown to cleave gp160 in cells, albeit with different efficiencies. 59, 60 Notably, a subset of H9N2 lowly pathogenic avian influenza A virus strains also harbour R-S-K-R↓ or R-S-R-R↓ sites that are not only cleaved by trypsin-like proteases, such as TMPRSS2 or HAT, but also by PCSKs. 61 However, their cleavage is only efficient in the presence of very high amounts of furin or upon mutation of a glycosylation site in HA. doi = 10.1002/cti2.1073 id = cord-136540-2h2braww author = Buehler, Markus J. title = Liquified protein vibrations, classification and cross-paradigm de novo image generation using deep neural networks date = 2020-04-16 keywords = image; neural; protein summary = Here we present a method to transform these molecular vibrations into materialized vibrations of thin water films using acoustic actuators, leading to complex patterns of surface waves, and using the resulting macroscopic images in further processing using deep convolutional neural networks. Specifically, the patterns of water surface waves for each protein structure is used to build training sets for neural networks, aimed to classify and further process the patterns. Once trained, the neural network model is capable of discerning different proteins solely by analyzing the macroscopic surface wave patterns in the water film. This article focuses on a different perspective and reports a distinct, complementary and translational approach, in which we transform these molecular vibrations into vibrations of thin water films using acoustic actuators, leading to visual images of complex materialized patterns of surface waves. We use DeepDream [39] to generate novel images by activating select layers in the deep neural network, based on the model trained against the water surface images. doi = nan id = cord-171099-d0qr84xg author = Buehler, Markus J. title = Nanomechanical sonification of the 2019-nCoV coronavirus spike protein through a materiomusical approach date = 2020-03-30 keywords = protein; sound; structure; virus summary = Presenting musical encoding in two versions one in the amino-acid scale and one based on equal temperament tuning the method allows for expressing protein structures in audible space, offering novel avenues to represent, analyze and design architectural features across lengthand time-scales. We further report a hierarchical frequency spectrum analysis of five distinct protein structures, which offer insights into how genetic mutations, and the binding of the virus spike protein to the human ACE2 cell receptor directly influence the audio. What you hear is a multi-layered algorithmic composition featuring both the vibrational spectrum of the entire protein (expressed in sound and rhythmic elements), the sequence and folding of amino acids that compose the virus spike structure, as well as interwoven melodiesforming counterpoint music -reflecting the complex hierarchical intersecting geometry of the protein. doi = nan id = cord-266147-s8rxzm0t author = Burnouf, Thierry title = Modern Plasma Fractionation date = 2007-03-28 keywords = FVIII; plasma; product; protein; treatment; viral summary = doi = 10.1016/j.tmrv.2006.11.001 id = cord-355913-fhvt1ht1 author = Burrell, Christopher J. title = Virus Replication date = 2016-11-11 keywords = RNA; cell; dna; protein; viral; virus summary = Little is known about what determines whether a given picornavirus positive-sense RNA molecule will be directed (1) to a replication complex (a structure bound to smooth endoplasmic reticulum), where it serves as template for transcription by RNA-dependent RNA polymerase into negative-sense RNA, or (2) to a ribosome, where it serves as mRNA for translation into protein, or (3) to a procapsid, with which it associates to form a virion. In the case of positive-sense single-stranded RNA viruses, the incoming RNA genome can bind directly to ribosomes and be translated in full or in part without the need for any prior transcription; all other forms of incoming viral RNA must first be transcribed to produce mRNA, in order to begin the process of expression of the infecting viral genome. doi = 10.1016/b978-0-12-375156-0.00004-7 id = cord-018647-bveks6t1 author = Butnariu, Monica title = Plant Nanobionics: Application of Nanobiosensors in Plant Biology date = 2019-10-01 keywords = NBS; NBSs; electrode; enzyme; gene; plant; protein; reaction summary = Chemical or biological NBS functions on the principle of signal emission (voltage or electrical, photonic) in response to a chemical reaction involve a chemical or biological receptor, R (macrocyclic ligand, antibody enzyme), that binds to a specific target molecule of a sample to be studied, the analyte, A. Analysis of signals in plant nanobionics aims at processing signals recorded by measurements in order to extract the maximum of useful information for diagnostics and These devices are mostly used in genetic engineering in agriculture, where it is necessary to know the mechanisms of reaction and the affinity of enzymes and microorganisms for different substrates of interest and signaling molecules. The reaction is monitored by an integrated detector (transducer) that measures the stationary or transition states or the final reaction product via the immobilized biocidal product in NBSs. Types of commonly used biocatalysts are enzymes (simple or enzymatic complexes)-most commonly used as recognition systems, cells, microorganisms (bacteria, fungi, eukaryotic cells, or yeasts), cellular organs, or component (cell walls, mitochondria) sections of plant or animal tissues. doi = 10.1007/978-3-030-16379-2_12 id = cord-333309-21czobqy author = Byun, Hyewon title = ERAD and how viruses exploit it date = 2014-07-03 keywords = CD4; ERAD; MHC; Rem; protein summary = Interaction of lectin-type and other chaperones with ERAD substrates allows association with members of the protein disulfide isomerase (PDI) family, which generally are characterized by one or more thioredoxin-like motifs (CXXC; Brodsky and Skach, 2011) . In contrast to the rhomboid proteases, the Derlins lack proteolytic activity, suggesting that these proteins bind to ERAD substrates and target them to E3 ligases for ubiquitination and to p97 for membrane extraction (Brodsky, 2012) . These ubiquitin ligases are members of the cytosolic SCF (S-phase kinase-associated protein 1 (Skp1)-Cullin 1 (Cul1)-F-box) family, where the F-box components of the SCF complex recognize the N-glycans of the retrotranslocated substrate, e.g., Fbs1 and Fbs2 (Yoshida, 2007) . A proteasomal ATPase contributes to dislocation of endoplasmic reticulum-associated degradation (ERAD) substrates The viral E3 ubiquitin ligase mK3 uses the Derlin/p97 endoplasmic reticulum-associated degradation pathway to mediate down-regulation of major histocompatibility complex class I proteins doi = 10.3389/fmicb.2014.00330 id = cord-297960-4x1j0iqg author = Bösl, Korbinian title = Common Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis date = 2019-10-04 keywords = figure; host; protein; viral; virus summary = doi = 10.3389/fimmu.2019.02186 id = cord-339333-7tpnbr8q author = CHEN, YUXIAN title = Comparative serum proteome expression of the steroid-induced femoral head osteonecrosis in adults date = 2014-11-12 keywords = SONFH; a2mg; patient; protein summary = The differentially-expressed protein spots were subjected to in-gel trypsin digestion followed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The purpose of the present study is to find potential biomarkers of the SONFH by using proteomic technology to analyze serum protein profiles in patients with SONFH and the healthy control group. To ensure the reproducibility, accuracy and objectivity of the experiments, the following steps were Differentially-expressed protein spots were identified from the two-dimensional difference gel electrophoresis profiling of human plasma, with a lower abundance in the steroid-induced femoral head osteonecrosis group compared to the control group. In the present study, four proteins (C3, C4, ITIH4 and A2MG) showed lower expression in the serum of patients with SONFH than that of the normal subjects. The present study shows that the expression of C3, C4, ITIH4 and A2MG were significantly altered in patients with SONFH. doi = 10.3892/etm.2014.2069 id = cord-286219-qcx5ehnh author = Calistri, Arianna title = The Ubiquitin-Conjugating System: Multiple Roles in Viral Replication and Infection date = 2014-05-06 keywords = HIV-1; Vpr; Vpu; protein; viral; virus summary = In this review we will present several examples of the complex interplay that links viruses and the ubiquitin conjugation machinery, with a special focus on the mechanisms evolved by the human immunodeficiency virus to escape from cellular restriction factors and to exit from infected cells. Furthermore, small DNA viruses with known oncogenic activity, such as the human papillomavirus (HPV), adenoviruses and polyomaviruses, take control of the cell cycle by usurping specific cellular Ub ligase complexes to target crucial cell cycle regulators such as p53 and the protein of the retinoblastoma (pRB) for degradation [58] . In addition to this important function, which is likely required for proper trafficking and maturation of the viral envelope glycoproteins, Vpu has been more recently characterized for yet another crucial role, connected with the ability of the virus to evade a specific IFN-1 induced antiviral factor: the B cell stromal factor 2 (BST-2) or tetherin. doi = 10.3390/cells3020386 id = cord-314642-oobbdgzh author = Campbell, Allan title = The future of bacteriophage biology date = 2003 keywords = Cro; dna; gene; phage; protein summary = Several molecules of λ-integrase form an assemblage (the INTASOME) that binds to a specific segment of phage DNA, recruits the bacterial insertion sites into the complex, then makes concerted single-strand cuts in the two DNAs. The strand cutting proceeds through the covalent joining of a 3′ phosphate to a tyrosine of the integrase protein. Further efforts in this direction are desirable, not just for their intrinsic interest but also as models for viruses that infect eukaryotic hosts; for example, it is well documented that members of the coronavirus group, which has attracted attention recently through the emergence of a deadly new human pathogen that causes severe acute respiratory syndrome (SARS), undergo frequent recombination in nature 10, 11 . doi = 10.1038/nrg1089 id = cord-272986-ebgusf3o author = Cao, Yipeng title = Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel date = 2020-05-17 keywords = SARS; ion; protein summary = doi = 10.1101/2020.05.17.099143 id = cord-325559-di8lljoi author = Cappello, Francesco title = Does SARS-CoV-2 Trigger Stress-Induced Autoimmunity by Molecular Mimicry? A Hypothesis date = 2020-06-29 keywords = COVID-19; SARS; cell; clinical; protein summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induced disease (COVID-19) is a planetary emergency that is urging many research groups to redirect their efforts and to channel their experience towards understanding its pathogenesis. These human epitopes, in turn, can be recognized by circulating antibodies made against crossreactive microbial antigens; these antibodies behave like autoantibodies, causing the destruction of the stressed cells, representing a typical example of pathology caused by molecular mimicry and manifested as autoimmunity [30] . We hypothesize that, at the basis of the generalized activation of the immune system, there are molecular mimicry phenomena: the antibodies produced against the virus could turn into autoantibodies against crossreactive proteins expressed on human cells, causing autoimmunity with cell destruction. We hypothesize that, at the basis of the generalized activation of the immune system, there are molecular mimicry phenomena: the antibodies produced against the virus could turn into autoantibodies against crossreactive proteins expressed on human cells, causing autoimmunity with cell destruction. doi = 10.3390/jcm9072038 id = cord-000372-wzwpyvll author = Castelló, Alfredo title = The Multifaceted Poliovirus 2A Protease: Regulation of Gene Expression by Picornavirus Proteases date = 2011-04-14 keywords = Nup98; RNA; pro; protein summary = These findings are in agreement with the fact that host mRNA transcription takes place in 2A pro -expressing cells when both translation and RNA nuclear export are inhibited, upon cleavage of eIF4G and Nups [17] . In this regard, PV 2A pro has been very useful for examining the requirements for eIF4G to translate different cellular or viral mRNAs. In addition to this, in this paper, we have highlighted the role of PV 2A pro not only in the processing of the poliovirus polyprotein but also in the interaction with the host-cell. In particular, PV 2A pro cleaves cell proteins involved in transcription, pre-mRNA splicing, nucleus/cytoplasm transport and translation, in order to hijack those host functions and to concentrate the cellular resources on the production of the viral progeny. doi = 10.1155/2011/369648 id = cord-302490-em1tiz7s author = Cañadas, Olga title = Lipid–Protein and Protein–Protein Interactions in the Pulmonary Surfactant System and Their Role in Lung Homeostasis date = 2020-05-25 keywords = AE2C; LPS; Surfactant; protein summary = To fulfill this crucial role, alveolar epithelial type II cells (AE2C) secrete pulmonary surfactant, a lipid-protein complex that forms a surface active film at the respiratory interface, allowing its stability and avoiding alveolar collapse during expiration [3, 4] . On the other hand, the structure of surfactant aggregates does not influence its uptake by AMs [169] , and although SP-D is able to bind to the surface of these cells to modulate inflammation, the homeostasis/immune roles of the protein seem to be independently regulated [94] . Surfactant proteins and lipids have been shown to provide immune protection against respiratory pathogens, both directly by limiting inflammation and promoting pathogen clearance, and indirectly by activating molecular and cellular mechanisms that contribute to restore lung homeostasis [15, [181] [182] [183] . Anionic pulmonary surfactant phospholipids inhibit inflammatory responses from alveolar macrophages and U937 cells by binding the lipopolysaccharide-interacting proteins CD14 and MD-2 doi = 10.3390/ijms21103708 id = cord-275023-0z219rcy author = Cerofolini, Linda title = Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes date = 2020-07-29 keywords = SARS; orientation; protein; surface summary = title: Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes In this manuscript, we apply a simple computational model, based on united-residue modelling, to the prediction of the orientation of the receptor binding domain of the SARS-CoV-2 spike protein on surfaces commonly used in lateral-flow devices. In this manuscript we apply a very simple method based on a unitedresidue modelling of protein-surface interactions, to specifically address the problem of determining the orientation of the SARS-CoV-2 Spike protein Receptor Binding Domain (RBD) on a few prototypical surfaces for biomedical use. In this work, we describe the use of united-residue modelling for the prediction of the orientation of the receptor binding domain of the spike protein of the novel coronavirus SARS-CoV-2, a protein of high immunological relevance at the most commonly used surfaces for the preparation of lateral-flow immunochemical devices. doi = 10.1016/j.bpc.2020.106441 id = cord-324325-rmlrhyf2 author = Chan, Wai S title = Coronaviral hypothetical and structural proteins were found in the intestinal surface enterocytes and pneumocytes of severe acute respiratory syndrome (SARS) date = 2005-05-13 keywords = SARS; protein summary = Immunohistochemical studies on different human tissues, including a cohort of nine autopsies, two liver biopsies and intestinal biopsies of SARS patients, further confirmed the existence of coronaviral hypothetical and structural proteins in the cytoplasm of pneumocytes and small intestinal surface enterocytes in SARS patients. In those tissue sections showing positive signals for immunohistochemical staining, we further performed immunohistochemical studies using all other antibodies tested positive in SARS-CoV-infected Vero E6 cells. The cellular distribution of SARS-CoV protein and viral genome in immunohistochemical-positive lung and small intestine sections was further evaluated by immunofluorescence-fluorescence in situ hybridization analysis (Figure 4) . 3 In Vero E6 cells, positive cytoplasmic immunohistochemical signals were detected by Figure 3 Immunohistochemical studies of antipeptide antibody SARS-AbS13a against the nucleocapsid protein on small intestine sections. In addition, in the study of tissue sections, only those cells with viral genome detected by fluorescence in situ hybridization were positive for immunohistochemical stainings for the antipeptide antibodies. doi = 10.1038/modpathol.3800439 id = cord-000264-o80duxhs author = Chandramouli, Kondethimmanahalli title = Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity date = 2009-12-08 keywords = ICAT; analysis; mass; peptide; protein; proteomic summary = doi = 10.4061/2009/239204 id = cord-279598-xzionafe author = Chang, Chia-Yu title = Identification of Neutralizing Monoclonal Antibodies Targeting Novel Conformational Epitopes of the Porcine Epidemic Diarrhoea Virus Spike Protein date = 2019-02-21 keywords = PEDV; protein summary = title: Identification of Neutralizing Monoclonal Antibodies Targeting Novel Conformational Epitopes of the Porcine Epidemic Diarrhoea Virus Spike Protein However, E10E-1-10, which targets a novel neutralizing epitope as shown with ICC staining, was also capable of binding to the full-length PEDV spike protein as well as truncated PEDV proteins, S 1-639 , S 1-575 , S 1-509 , S 1-501 , and S 1-485 with appropriate dilution effects. Similar to the results obtained by ICC staining, E10E-1-10 showed no binding ability www.nature.com/scientificreports www.nature.com/scientificreports/ toward PEDV S 1-435 by ELISA and therefore, an NmAb targeting a novel epitope of the new variant of PEDV specifically at a.a. 435-485 in the S1 region was confirmed. To further determine whether the binding of neutralizing epitopes require conformational integrity, immunodot blotting was performed by denaturing the various truncated PEDV spike proteins. Cell Attachment Domains of the Porcine Epidemic Diarrhea Virus Spike Protein Are Key Targets of Neutralizing Antibodies doi = 10.1038/s41598-019-39844-5 id = cord-342639-vf9n2vf9 author = Chang, Chung-ke title = Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging date = 2013-05-23 keywords = CTD; SARS; protein summary = For disulfide trapping experiments, we chose mutation sites that would form disulfide linkages based on the crystal packing structures of the SARS-CoV N protein CTD ( Figure 1 ) [9] . Within the crystal asymmetric unit, the SARS-CoV N protein CTD packs as an octamer which stacks to form a helical arrangement with a continuous positively charged surface that could potentially allow the RNA to bind to it through electrostatic interactions ( Fig. 1 ) [9] . By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that SARS-CoV N protein is capable of transient oligomerization in solution through the CTD in the absence of nucleic acids. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA doi = 10.1371/journal.pone.0065045 id = cord-337825-ujq9mxk7 author = Chen, Bin title = Overview of lethal human coronaviruses date = 2020-06-10 keywords = ACE2; CoV; CoV-2; East; MERS; Middle; SARS; coronavirus; protein summary = Coronaviruses are the largest +ssRNA viruses and contain at least 14 ORFs, 16 protein combines with viral RNA to form a nucleocapsid, which is involved in the replication of SARS-CoV and is the most abundant protein in virus-infected cells. MERS-CoV can infect T-cells from human lymphoid organs and causes the peripheral blood inducing apoptosis by intrinsic and extrinsic pathways, thus avoiding host immune response detection method, Nanopore Targeted Sequencing, also has the potential for efficiently detecting viruses in a reasonable time. The structural and accessory proteins M, ORF 4a, ORF 4b, and ORF 5 of Middle East respiratory syndrome coronavirus (MERS-CoV) are potent interferon antagonists Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein Identification of a receptor-binding domain in the S protein of the novel human coronavirus Middle East respiratory syndrome coronavirus as an essential target for vaccine development Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine doi = 10.1038/s41392-020-0190-2 id = cord-330668-7aw17jf8 author = Chen, Cheng-Chang title = ORF8a of SARS-CoV forms an ion channel: Experiments and molecular dynamics simulations date = 2011-02-28 keywords = Fig; model; protein summary = The protein is synthesized using solid phase peptide synthesis and reconstituted into artificial lipid bilayers that forms cation-selective ion channels with a main conductance level of 8.9±0.8pS at elevated temperature (38.5°C). Computational modeling studies including multi nanosecond molecular dynamics simulations in a hydrated POPC lipid bilayer are done with a 22 amino acid transmembrane helix to predict a putative homooligomeric helical bundle model. Before embedding low energy models into lipid bilayers two amino acids residues of the protein were added at the N and C termini of each of the helices in each bundle model to account for the consequences of their interaction with the lipid bilayer during the simulation. The idealized monomeric TM helix based on the consensus sequence Leu-3 to Val-20 (Fig. 1A) shows clustering of hydrophilic residues (Thr-8, Ser-11, Ser-14 and Thr-18) on one side suggesting that the four hydrophilic amino acids form the lumen of the pore in a homooligomeric helical bundle channel model. doi = 10.1016/j.bbamem.2010.08.004 id = cord-335310-61wibso4 author = Chen, Hui-Wen title = Synthetic virus-like particles prepared via protein corona formation enable effective vaccination in an avian model of coronavirus infection date = 2016-08-15 keywords = Fig; IBV; PBS; nanoparticle; protein summary = Herein, a facile approach to formulate synthetic virus-like particles (sVLPs) is demonstrated by exploiting the phenomenon of protein corona formation induced by the high-energy surfaces of synthetic nanoparticles. As compared to inoculation with free proteins, vaccination with the sVLPs showed enhanced lymphatic antigen delivery, stronger antibody titers, increased splenic T-cell response, and reduced infection-associated symptoms in an avian model of coronavirus infection. Comparison to a commercial whole inactivated virus vaccine also showed evidence of superior antiviral protection by the sVLPs. The study demonstrates a simple yet robust method in bridging viral antigens with synthetic nanoparticles for improved vaccine application; it has practical implications in the management of human viral infections as well as in animal agriculture. In the present study, vaccination with the sVLPs resulted in enhanced humoral and cellular immune responses, improving protection against an avian model of coronavirus infection as compared to free protein antigens and a commercial WIV vaccine. doi = 10.1016/j.biomaterials.2016.08.018 id = cord-011602-hzqayt3n author = Chen, Jianlin title = Targeting Intrinsically Disordered Proteins through Dynamic Interactions date = 2020-05-11 keywords = IDP; NMR; disordered; ensemble; protein summary = doi = 10.3390/biom10050743 id = cord-313932-f0a1qh7p author = Chen, Peng title = Establishment and validation of a drug-target microarray for SARS-CoV-2 date = 2020-07-21 keywords = protein; target summary = Here, we constructed a COVID-19 protein microarray of potential therapy targets, which contains the main drug targets to the SARS-COV-2 virus and the anti-virus, anti-inflammatory cellar targets of the host. For protein target research of traditional Chinese medicine, it is usually carried out through network pharmacology and bioinformatics, for example, by obtaining the main active ingredients of LianhuaQingwen capsule, molecular docking method was used to predict the possible targets [11, 12] . The latest research showed EIF4E2 as an important host interaction protein with virus, potential to be a drug target for COVID-19 [24] . NFkB1-P50 protein is an important target of andrographolide, a traditional Chinese medicine product with immunoregulation function, and their binding site has been widely verified [26] (Figure 3A ). Here, we use the method of network pharmacology molecular docking to predict the binding ability of these two natural products to the protein targets. doi = 10.1016/j.bbrc.2020.05.217 id = cord-314321-klb8oe9q author = Chen, Serena H. title = Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets date = 2020-04-18 keywords = SARS; protein; structure summary = Recent experimental structures of the SARS-CoV-2 S protein receptor binding domain (RBD) in complex with ACE2 provide detailed interface information [4] , [6] ; targeting this interface represents an active area of research for therapeutic development [11] . By first comparing the S protein protomer structure of SARS-CoV-2 to those from previous human coronaviruses, we identified distinct clusters for each virus in the 3-D latent space, where representative structures from these clusters highlight their differences in domain flexibility. To further understand the molecular structures of different human coronavirus S proteins and the oligomeric state of SARS-CoV-2 S protein, we deployed a custom-built deep learning architecture, a convolutional variational autoencoder (CVAE), to encode the high dimensional protein structures from the MD simulations into lower dimensional latent spaces. The size of each resulting matrix was also 191 ⇥ 191, and we merged a total of 10,000 distance matrices of the protomer and trimer of SARS-CoV-2 S protein. doi = 10.1101/2020.04.17.047548 id = cord-320015-lbr2q4qh author = Chinchar, V. Gregory title = The Molecular Biology of Frog Virus 3 and other Iridoviruses Infecting Cold-Blooded Vertebrates date = 2011-10-20 keywords = FV3; dna; protein; viral; virus summary = Additional IE and DE proteins include proteins that may play roles in blocking host immune responses such as a virus-encoded, CARD (caspase activation and recruitment domain) motif-containing protein (vCARD), β-hydroxysteroid dehydrogenase (βHSD), and a RNAse III-like protein, catalytic proteins involved in nucleic acid synthesis (Proliferating Cell Nuclear Antigen [PCNA], DNA methyltransferase [DMTase], the large and small subunits of the viral homolog of cellular RNA polymerase II [vPOL-IIα and -IIβ], transcription factor IIS), catalytic proteins that may act to increase dTTP pool sizes and influence host range (deoxyuridine triphosphatase [dUTPase], deoxynucleotide kinase, the large and small subunits of ribonucleotide reductase), and proteins non-essential for replication in vitro, but needed for growth in vivo (the 18K protein) [22] . Lastly, Sample and co-workers observed that KD of the 18K IE protein had no observable effect on viral gene expression or replication in vitro suggesting that, at least in fathead minnow cells, 18K was not required for the production of infectious virions. doi = 10.3390/v3101959 id = cord-014852-6friw2ek author = Chumakov, S. P. title = Organization and regulation of nucleocytoplasmic transport date = 2010-04-24 keywords = NES; NPC; Nup; nuclear; protein summary = Nuclear RanGTP is capable of releasing the target protein from an imported complex upon binding with karyo pherins. The main properties that allow karyopherins to ensure efficient nuclear transport are their capabilities of binding with a target protein (directly or through an adaptor) and interacting with Nup or RanGTP [12] . Structural studies of karyopherin β1 in complex with the phenylalanine-glycine (FG) repeat contain ing fragment of yeast Nup showed that the interactions between the two proteins are mostly hydrophobic and involve the phenylalanine residues of Nup. The karyo pherin molecule forms two hydrophobic pockets: between HEAT repeats 5 and 6 and between repeats 6 and 7. NTF2 interacts with RanGDP, which is the main cytoplasmic form of Ran. The NTF2-RanGDP complex is transferred into the nucleus, which is due to the ability of NTF2 to interact with low affinity with FG containing Nup proteins, as karyopherins do. One of the key steps of nuclear transport is the interaction of importins and exportins with the NLS or NES of a target protein. doi = 10.1134/s0026893310020020 id = cord-256156-mywhe6w9 author = Clausen, Thomas Mandel title = SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2 date = 2020-09-14 keywords = ACE2; Fig; RBD; SARS; cell; protein summary = doi = 10.1016/j.cell.2020.09.033 id = cord-222664-4qyrtzhu author = Coban, Mathew title = Attacking COVID-19 Progression using Multi-Drug Therapy for Synergetic Target Engagement date = 2020-07-06 keywords = Ace2; COVID-19; Caulfield; Fig; SARS; Tmprss2; protein summary = We have therefore initiated a computational dynamics drug pipeline using molecular modeling, structure simulation, docking and machine learning models to predict the inhibitory activity of several million compounds against two essential SARS-CoV-2 viral proteins and their host protein interactors; S/Ace2, Tmprss2, Cathepsins L and K, and Mpro to prevent binding, membrane fusion and replication of the virus, respectively. Using a computational pipeline that aimed to expeditiously identify lead compounds against COVID-19, we combined compound library preparation, molecular modeling, and structure simulations to generate an ensemble of conformations and increase high quality docking outcomes against two essential SARS-CoV-2 viral proteins and their host protein interactions; S/Ace2, Tmprss2, Cathepsin L and K, and M pro that are known to control both viral binding, entry and virus replication (Fig. 1A) . doi = nan id = cord-276456-oa6hh7ky author = Collins, R.N. title = 5.14 The Biophysics of Membrane Fusion date = 2012-05-03 keywords = fusion; lipid; membrane; protein; snare summary = It will be challenging to distinguish between the lipid simply being a scaffold for a multitude of proteins involved with trafficking at the plasma membrane, and having a direct function in the bilayer rearrangements of fusion and fission. 38 The requirements for specific amino acids at certain positions and for a defined length in the fusion peptide have been further supported by the NMR-solved structure of fusion peptide in detergent micelles and in model lipid membranes 43,52 stabilized by a charge-dipole interaction between the N-terminal Gly and the dipole moment of helix 2 54 (Figure 6 ). The energetics and topology of SNARE complex formation may influence local bending of the a-helix at the interfacial region, which in turn could generate local membrane destabilization to aid fusion ( Figure 8) . How conformational changes amongst SNARE proteins and their accessory factors control the thermodynamics and kinetics of docking, lipid mixing and content mixing after membrane fusion remain open questions. doi = 10.1016/b978-0-12-374920-8.00523-3 id = cord-103430-x6zzuu7v author = Contu, Lara title = Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay date = 2020-10-12 keywords = NMD; RNA; figure; protein; sfv summary = Among the many identified cellular interactors of SFV proteins, the enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD) was striking, reflecting the virus'' hijacking of the translation machinery and indicating viral countermeasures for escaping NMD by inhibiting NMD at later time points during the infectious cycle. Gene ontology (GO) enrichment analyses of protein complexes that could 10 form between the identified host interactors revealed highly significant GO terms related to 11 translation and Nonsense-mediated mRNA Decay (NMD). In addition to ribosomal proteins, many other RNA binding proteins were also 37 identified as having a potential role in SFV replication (Figure 3a (nsP1, nsP2, nsP3-Z, nsP4, capsid and Env) as well as for the merged list (All baits) was also applied. doi = 10.1101/2020.10.12.335497 id = cord-316273-vo6j8zb0 author = Cosset, François-Loic title = Cell Entry of Enveloped Viruses date = 2011-02-08 keywords = Ebola; HIV; HIV-1; cell; fusion; protein; receptor; virus summary = On the one hand, they acquired a domain to bind to a specific cellular protein, named "receptor." On the other hand, they developed in a different manner, according to the genus of the virus, a function of fusion that allows the destabilization of the membrane and the opening of a pore through which the genetic material will enter the cell. Thus, we need to distinguish cell surface molecules such as heparan sulfate proteoglycans, DC-SIGN, or integrins that can enhance infections by concentrating retroviruses onto cells (Bounou et al., 2002; Geijtenbeek et al., 2000; Jinno-Oue et al., 2001; Mondor et al., 1998; Pohlmann et al., 2001; Saphire et al., 2001) from authentic receptors that induce conformational changes in EnvGP that are a prerequisite for fusion of the viral and cellular membranes. doi = 10.1016/b978-0-12-380860-8.00004-5 id = cord-277424-9aimvogs author = Criscitiello, Michael F. title = Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)—Novel insights into camelid immunity date = 2019-11-13 keywords = Magnadóttir; deiminate; deimination; llama; pad; protein; serum; western summary = In serum, 103 deiminated proteins were overall identified, including key immune and metabolic mediators including complement components, immunoglobulin-based nanobodies, adiponectin and heat shock proteins. Further deiminated proteins identified in llama serum and serumderived EVs by F95 enrichment and LCeMS/MS analysis included key proteins of camelid innate and adaptive immunity, nuclear proteins, as well as proteins involved in metabolic function. Deimination protein candidates identified here in llama serum and EVs, which are involved in immune, nuclear and metabolic functions, are further discussed below, including where appropriate in a comparative context with relevant human diseases. As a structurally analogous immunoglobulin in shark, new antigen receptor (NAR) (Greenberg et al., 1995; Barelle et al., 2009; Flajnik and Dooley, 2009; De Silva et al., 2019) was recently also found to be deiminated (Criscitiello et al., 2019) , our current finding may provide novel insights into function of these immune proteins and be useful for refinement in therapeutic nanobody development. doi = 10.1016/j.molimm.2019.10.017 id = cord-000003-ejv2xln0 author = Crouch, Erika C title = Surfactant protein-D and pulmonary host defense date = 2000-08-25 keywords = Surfactant; protein summary = SP-D, a collagenous calcium-dependent lectin (or collectin), binds to surface glycoconjugates expressed by a wide variety of microorganisms, and to oligosaccharides associated with the surface of various complex organic antigens. The phenotype of macrophages isolated from the lungs of SP-D-deficient mice is altered, and there is circumstantial evidence that abnormal oxidant metabolism and/or increased metalloproteinase expression contributes to the development of emphysema. The potential consequences of this interaction include the following: varying degrees of lectin-dependent aggregation (namely, microbial agglutination), enhanced binding of microorganisms or microbial aggregates to their ''receptors'' on host cells, phagocyte activation, and opsonic enhancement of phagocytosis and killing, potentially involving one or more cellular receptors for SP-D. Although the protein has been immunolocalized to alveolar macrophage membranes and distributes together with SP-D in many different human tissues [10 • ,77], it has not yet been shown to mediate the binding of SP-D to these cells or to participate in signal transduction events. doi = 10.1186/rr19 id = cord-016126-i7z0tdrk author = Dangi, Mehak title = Advanced In Silico Tools for Designing of Antigenic Epitope as Potential Vaccine Candidates Against Coronavirus date = 2018-10-14 keywords = protein; vaccine summary = doi = 10.1007/978-981-13-1562-6_15 id = cord-103255-4k13re9y author = Daniell, Henry title = Medical molecular farming: production of antibodies, biopharmaceuticals and edible vaccines in plants date = 2001-05-01 keywords = antibody; plant; protein; transgenic summary = The production of recombinant proteins in plants has many potential advantages for generating biopharmaceuticals relevant to clinical medicine. In the decade since the expression and assembly of immunoglobulin (Ig) heavy and light chains into functional antibodies was first shown in transgenic tobacco, plants have proven to be versatile production systems for many forms of antibodies. Other advantages of tobacco include its relative ease of genetic manipulation, production of large numbers of seeds (up to a million per plant) and an impending need to explore alternate uses for this hazardous crop. However, the most attractive species for expressing subunit vaccine components should have high levels of soluble protein that is stable during storage; seed crops such as cereals are particularly suitable. Induction of a protective antibody response to foot and mouth disease in mice following oral or parenteral immunization with alfalfa transgenic plants expressing the viral structural protein VP1 doi = 10.1016/s1360-1385(01)01922-7 id = cord-354950-kmpbdvof author = Demurtas, Olivia C. title = Antigen Production in Plant to Tackle Infectious Diseases Flare Up: The Case of SARS date = 2016-02-05 keywords = SARS; figure; plant; protein summary = Here we demonstrate the transient expression in Nicotiana benthamiana of two important antigenic determinants of the SARS-CoV, the nucleocapsid protein (N) and the membrane protein (M) using a virus-derived vector or agro-infiltration, respectively. Here we demonstrate the transient expression in Nicotiana benthamiana of two important antigenic determinants of the SARS-CoV, the nucleocapsid protein (N) and the membrane protein (M) using a virus-derived vector or agro-infiltration, respectively. In addition, the WHO guidelines for SARS diagnosis, developed during the outbreak in 2003, suggested the use of N-based ELISA for specific IgG detection as confirmatory test of SARS-CoV infection (World Health Organization [WHO] , 2003 SARS: Laboratory diagnostic tests) due to the ability of the host to mount an early antibody response against the N protein (Che et al., 2004) . As the plant-derived recombinant M protein, the M RLV was also specifically recognized by the mouse anti-M pAb ( Figure 6C ) that had previously validated by Immunofluorescence Antibody Assay (IFA) in SARS CoV infected Vero cells (Carattoli et al., 2005) . doi = 10.3389/fpls.2016.00054 id = cord-303555-mwu72q7w author = Dent, Paul title = Cell Signaling and Translational Developmental Therapeutics date = 2020-10-06 keywords = Activation; Insulin; Kinase; Protein; RAS; Receptor; cell; drug summary = Thus, by the mid-to late-1980s a large body of literature existed which argued that signal transduction pathways consisted of a receptor linked to a large GTP-binding protein which in turn regulated an enzyme that generated "second messengers;" the second messengers would then diffuse throughout the cytosol activating cellular processes, predominantly for metabolism. For the EGFR and other subsequently discovered membrane associated tyrosine kinases, e.g. the non-receptor SCR family and the fibroblast growth factor receptor (FGFR) family, understanding how these enzymes signaled into the cell again initially rested on studies using traditional biochemical methods. [71] [72] [73] [74] [75] [76] Contemporaneously with these studies, researchers were determining how receptor tyrosine kinases regulated RAS family small GTP binding proteins, and other groups determining how RAS proteins signaled downstream off the plasma membrane and into the cytosol. doi = 10.1016/b978-0-12-820472-6.00002-5 id = cord-287410-boxxlopy author = Devi, Arpita title = In silico designing of multi-epitope vaccine construct against human coronavirus infections date = 2020-08-10 keywords = SARS; construct; protein; vaccine summary = Band T-cell epitopes of the spike proteins have been predicted and designed into a multi-epitope vaccine construct. To predict the probable immune response of the designed multi-epitope vaccine construct in human immune system, in silico immune simulations were conducted using the C-ImmSim server (http://150.146.2.1/C-IMMSIM/index.php) (Rapin et al., 2010) . C-ImmSim is a novel in silico approach for the study of the mammalian immune system The tool is a combination of a mesoscopic scale simulator of the immune system with machine learning techniques for molecular-level predictions of major histocompatibility complex (MHC)-peptide-binding interactions, linear B-cell epitope discovery, and protein-protein potential estimation. The antigenicity of the vaccine construct including the adjuvant sequence and His-tag was predicted by the VaxiJen 2.0 server to be 0.6452 with a bacteria model at a threshold of 0.4. doi = 10.1080/07391102.2020.1804460 id = cord-298301-p1zj6jg9 author = Dey, Lopamudra title = Machine Learning Techniques for Sequence-based Prediction of Viral-Host Interactions between SARS-CoV-2 and Human Proteins date = 2020-09-03 keywords = COVID-19; PPI; SARS; human; protein summary = doi = 10.1016/j.bj.2020.08.003 id = cord-281528-xy8j5jiv author = Di Paola, Luisa title = The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach date = 2020-06-17 keywords = ACE2; AMR; SARS; figure; protein summary = All of the adopted analyses converged toward a specific region (allosteric modulation region [AMR]), present in both complexes and predicted to act as an allosteric site modulating the binding of the spike protein with ACE2. Preliminary results on hepcidin (a molecule with strong structural and sequence with AMR) indicated an inhibitory effect on the binding affinity of the spike protein toward the ACE2 protein. We also provided biophysical evidence based on the elastic network modeling (ENM) approach, combined with perturbation-response scanning (PRS) 36 that AMRs in both viruses acted as a mediator of intermolecular allostery between the S protein and ACE2. The map of the participation coefficient projected onto the ribbon structure of the SARS-CoV/ACE2 complex ( Figure 1C ) shows an active region (P > 0) in the junction between the fusion peptide and the trimeric bulk phase of the spike protein. doi = 10.1021/acs.jproteome.0c00273 id = cord-312332-rwmuucsp author = Dicker, Kate title = The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date = 2020-09-10 keywords = ESCRT; HIV-1; RNA; protein; viral; virus summary = title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity Different proteomic studies have identified hundreds of cellular factors within the particles of several RNA viruses [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] , many of which are RBPs. Here, we discuss the ''knowns'' and ''unknowns'' of the roles that virion-incorporated cellular RBPs could play in the assembly of viral particles and the early steps of infection in the new host cell. Many ivRBPs such as annexins, heat shock family proteins (HSP), peptidylprolyl isomerase A (PPIA -also cyclophilin A), eukaryotic translation elongation factors (EEF), heterogeneous nuclear ribonucleoproteins (HNRNP) or poly(rC) binding protein 1 (PCBP1), have been linked to infection in multiple ways (Fig. S2) , and here we show that they are incorporated in the particles of several viruses (Table S1B) . doi = 10.1016/j.semcdb.2020.08.002 id = cord-279432-aik5bo6o author = Digard, Paul title = Complex formation between influenza virus polymerase proteins expressed in Xenopus oocytes date = 1989-07-31 keywords = PB2; protein summary = As seen in virus-infected cells, all three P proteins associated into an immunoprecipitable complex, suggesting that the system has considerable promise for the reconstruction of an active influenza RNA polymerase. In view of the fact that the P proteins must interact with RNA, it seemed possible that the high sedimentation values obtained for individually expressed PBl and PB2 (Fig. 4) and for complexes containing PBl and PB2 could have arisen from the polypeptides binding to RNA present in the lysate. Furthermore, RNase treatment of lysates containing individually expressed PB2 also failed to affect its sedimentation pattern (not shown), suggesting that the heterogeneous size distribution of the P protein complexes is not the result of association with RNA. Here, we have demonstrated the feasibility of producing all three influenza virus polymerase proteins for functional studies by the translation of in vitro transcribed mRNA analogs in Xenopus oocytes. The three influenza virus polymerase (P) proteins not associated with viral nucleocapsids in the infected cell are in the form of a complex doi = 10.1016/0042-6822(89)90523-0 id = cord-260440-e63pgcir author = Dinjaski, Nina title = Smart polyhydroxyalkanoate nanobeads by protein based functionalization date = 2015-02-24 keywords = PHA; Pseudomonas; gram; granule; production; protein summary = In vivo PHA modification based on peptide functionalization of PHA nano-beads using GAPs for recombinant protein anchoring to the PHA granule or nonspecific binding and in vivo chemical modification through incorporation of functional group in the side chain of the polymer applying metabolic engineering and systems biology approach. 30 The main advantages of this in vitro cell-free system are: i) the possibility of tight control of nanoparticle disassembly and reassembly process; ii) absence of competition among the recombinant GAP-fusion and wild type proteins; iii) tight control over particle size and immobilized protein/active agent concentration; iv) possibility of endotoxin removal, crucial for the design of every biomedical setup. 18 In completely different context to in vivo tag binding, in vitro synthesized PHA nanoparticles and in vitro hydrophobic binding of PhaP fusion proteins with protein ligands (e.g., mannosylated human α1-acid glycoprotein (hAGP) and human epidermal growth factor (hEGF)) have been reported as another outstanding application of phasins for receptor-mediated drug delivery. doi = 10.1016/j.nano.2015.01.018 id = cord-252147-bvtchcbt author = Domingo-Espín, Joan title = Engineered Biological Entities for Drug Delivery and Gene Therapy: Protein Nanoparticles date = 2011-11-15 keywords = VLP; cell; delivery; dna; drug; gene; like; particle; peptide; protein; virus summary = Modular protein engineering, virus-like particles (VLPs), and other self-assembling entities are envisioned as modulatable novel protein nanoparticles able to include many desirable properties in the correct delivery of drugs and nucleic acids. 120 Modular fusion proteins that combine distinct functions required for cell type-specific uptake and intracellular delivery of DNA or drugs present an attractive approach for the development of self-assembling vectors for targeted gene or drug delivery. 215, 216 Although VLP-based vaccines have been primarily developed for their use against the corresponding virus, in the last decades genetic engineering or chemical modifications have been applied in order to generate chimeric VLPs. Thus, on the one hand, commonly short heterologous peptide epitopes or full proteins that are unable to form VLPs or that are unsafe for vaccination have been presented on surface-exposed loops or fused to N-or C-exposed termini of structural viral capsid proteins on VLPs. 154, 161, 210 Different HPV, 217-219 HBV, 220,221 parvovirus, 222, 223 and chimeric polyoma VLPs have been engineered 170, 175 and tested for different applications including vaccination against viral or bacterial diseases, against virus-induced tumors, and more recently, for immunotherapy of nonviral cancer. doi = 10.1016/b978-0-12-416020-0.00006-1 id = cord-266444-rw94yls8 author = Dominguez Andres, Ana title = SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells date = 2020-08-19 keywords = CoV-2; Fig; ORF9c; SARS; protein summary = The interactome and proteome studies identified cellular processes affected by SARS-CoV-2 infection or specific viral proteins, notably innate immune signaling (19, 20, 23, (28) (29) (30) , ubiquitin ligase activities (19, 20, 23, (28) (29) (30) , p38 mitogenactivated protein kinase (MAPK) signaling (19, 20, 23, (28) (29) (30) . To assess if there were notable differences in the intensity of the changes in protein abundance in response to proteasome inhibition, we calculated relative changes in protein abundance between control and ORF9c-expressing cells from both the DMSO and MG132 conditions for proteins associated with IFN signaling or the ubiquitin proteasome (UBP) system and antigen presentation (Fig. 2D ). In contrast to the proteomic results that revealed predominant downregulation of proteins following ORF9c expression, RNA-seq analysis showed a similar number of transcripts were increased or decreased in the presence or absence of MG132 (Fig. 3A, table S2 ). doi = 10.1101/2020.08.18.256776 id = cord-306111-wn1gxhk9 author = Dommett, R. M. title = Mannose‐binding lectin in innate immunity: past, present and future date = 2006-09-01 keywords = HIV; MBL; infection; lectin; mannose; protein summary = Third MBL mutation in codon 52 (variant D) described (52) 1995 Polymorphisms found in promoter region of MBL gene (55) 1997 Second MASP found to activate complement (20) MBL mutations are an important risk factor for infections in children (132) 1998 Reconstitution of opsonizing activity by infusion of purified MBL into MBL-deficient humans (112) 1999 Truncated form of MASP-2 -MAp19 (21) 2000 Complement-activating complex of ficolins and MASP (133) MBL shown to bind to clinically relevant organisms (15) Structural aspects of MBL doi = 10.1111/j.1399-0039.2006.00649.x id = cord-298251-u36lb44w author = Donaldson, Julie G. title = Arf Family G Proteins and their regulators: roles in membrane transport, development and disease date = 2011-05-18 keywords = ARF1; ARF6; GEF; Golgi; arf; protein summary = Members of the ADP-ribosylation factor (ARF) family of guanine-nucleotide-binding (G) proteins, including the ARF-like (ARL) proteins and SAR1, regulate membrane traffic and organelle structure by recruiting cargo-sorting coat proteins, modulating membrane lipid composition, and interacting with regulators of other G proteins. ARF proteins at the trans-Golgi network (TGN) also recruit heterotetrameric clathrin adaptor protein 1 (AP1), AP3 and AP4, as well as the three monomeric Golgi-localized, γ-ear-containing, ADP-ribosylation factor-binding Figure 1 | The domain structure and regulation of ARF and ARLs. a | A schematic of representative ADP-ribosylation factor (ARF), SAR1 and ARF-like (ARL) proteins, indicating the conserved amino-terminal amphipathic helix and the protein-specific lipid modifications at the N terminus. ARF6 at the plasma membrane can regulate the membrane lipid composition, alterations in cortical actin to drive protrusions (for example, during cell migration), and endocytosis of ligand-activated guanine-nucleotide-binding (G) protein-coupled receptors (GPCR) via clathrin-dependent endocytosis. doi = 10.1038/nrm3117 id = cord-010681-tmpxs9og author = Dondapati, Srujan Kumar title = Cell-Free Protein Synthesis: A Promising Option for Future Drug Development date = 2020-03-20 keywords = CFPS; CHO; cell; protein; system summary = aatRNA aminoacyl-tRNA, AAS aminoacyl-tRNA synthetase, ATP adenosine triphosphate, EF elongation factor, GSH glutathione, GSSG glutathione-disulfide, GTP guanosine-5''-triphosphate, IF initiation factor, IRES internal ribosome entry site, MP membrane protein, nCAA non-canonical amino acid, PDI protein disulfide isomerase, PEG polyethylene glycol, PTM post-translational modification, R ribosomes, t-RNA transfer RNA, TF transcription factor, UTR untranslated region, VLP virus like particle Chinese hamster ovary (CHO) Mimic the CHO cell-based production PTMs (N-glycosylation, disulfide bridging, and lipidation) Suitable for a wide range of eukaryotic and complex proteins Presence of translational active endogenous microsomes [45] High yields in CECF mode Endotoxin free Lysates used for point-of-care testing [30] Low yields especially in the batch mode [58] Cost ineffective and difficult to establish unlike E. doi = 10.1007/s40259-020-00417-y id = cord-318749-k91oku7h author = Dong, Hui-Jun title = Selective regulation in ribosome biogenesis and protein production for efficient viral translation date = 2020-10-29 keywords = IRES; RNA; protein; viral summary = Recently reported studies have demonstrated that ribosome biogenesis factors (RBFs) and ribosomal proteins (RPs) act as multifaceted regulators in selective translation of viral transcripts. Similarly, ribosomes are required for the protein synthesis of host cells and viruses, but the biogenesis factor RBFs can also impact the proliferation of virus and cell-intrinsic immune responses. The multifunctional nucleolar phosphoprotein nucleophosmin (NPM) plays a lead role in ribosome biogenesis to stimulate RNA Pol I-dependent transcription (Li and Hann 2013) and regulates SARS-CoV, IBV, HIV-1, HCV Recruited by viral proteins to facilitate viral replication Chen et al. RPS25 deletion in yeast or mammalian cells has minimal effects on cellular protein synthesis, which implies that this ribosomal protein may be selectively required for viral IRES-mediated translation (Jack et al. Conservation of multifunctional ribosomal protein metallopanstimulin-1 (RPS27) through complex evolution demonstrates its key role in growth regulation in Archaea, eukaryotic cells, DNA repair, translation and viral replication doi = 10.1007/s00203-020-02094-5 id = cord-354030-8tfg881h author = Dong, Rong title = Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches date = 2020-07-28 keywords = MHC; SARS; epitope; figure; protein; vaccine summary = The realm of immunoinformatics tools considers the mechanism of the host immune response to yield additional methodologies in the design of vaccine against diseases are cost-effective and convenient, as in silico predictions can reduce the number of experiments needed (13, 14) . In this present, we employed immunoinformatics to predict multiple immunogenic proteins from the SARS-CoV-2 proteome and thereby design a multi-epitope vaccine. developed a multi-epitope vaccine that was designed using immunoinformatics tools that potentially trigger both CD4+ and CD8+ T-cell immune responses (16) . developed a multi-epitope vaccine that was designed using immunoinformatics tools that potentially trigger both CD4+ and CD8+ T-cell immune responses (16) . A vaccine based on the spike protein could induce antibodies to block SARS-COV-2 binding and fusion or neutralize virus infection (18) , as well as induce harmful immune responses that cause liver damage (19) . To design an effective vaccine, we selected the SARS-CoV-2 protein through the above-mentioned methods for epitope prediction. Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): Immunoinformatics approach doi = 10.3389/fimmu.2020.01784 id = cord-350935-p6euuop3 author = Doğan, Tunca title = CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations date = 2020-09-15 keywords = COVID-19; SARS; protein summary = We aimed to address this issue by constructing a new biological and biomedical data resource, CROssBAR, a comprehensive system that integrates large-scale biomedical data from various resources and store them in a new NoSQL database, enrich these data with deep-learning-based prediction of relations between numerous biomedical entities, rigorously analyse the enriched data to obtain biologically meaningful modules and display them to users via easy-to-interpret, interactive and heterogenous knowledge graph (KG) representations within an open access, user-friendly and online web-service at https://crossbar.kansil.org. In this project, we aimed to address the current shortcomings by developing a comprehensive open access biomedical system entitled CROssBAR via integrating various biological databases to each other, inferring the missing relations between existing data points, and constructing informative knowledge graphs based on specific biomedical components/terms such as a disease/phenotype, biological process, gene/protein and drug/compound, or specific combinations of them. doi = 10.1101/2020.09.14.296889 id = cord-319809-33i6lzjd author = Drew, Elliot D. title = Identification of a druggable binding pocket in the spike protein reveals a key site for existing drugs potentially capable of combating Covid-19 infectivity date = 2020-07-01 keywords = Fig; pocket; protein summary = title: Identification of a druggable binding pocket in the spike protein reveals a key site for existing drugs potentially capable of combating Covid-19 infectivity RESULTS: Our analyses of this structure have revealed a key potentially druggable pocket where it might be viable to bind pharmaceutical agents to inhibit its ability to infect human cells. The results from the three methods, Autodock vina [12] , Smina [13] and Ledock [14] , were used to generate a list of 4358 poses of commercially-available drugs capable of binding into this Covid-19 spike protein pocket. This study provides a suggested list of pharmaceutical agents, identifying some of them as being from related structure families, that are available on the market and have been sanctioned for use in humans that have been shown to be capable of binding into a druggable pocket in the spike protein of Covid-19. doi = 10.1186/s12860-020-00294-x id = cord-328003-yovp8squ author = Duan, Liangwei title = The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens date = 2020-10-07 keywords = ACE2; CoV-2; RBD; SARS; protein summary = Here, we provide a comprehensive overview of the wealth of research related to the SARS-CoV-2 S glycoprotein biosynthesis, structure, function, and antigenicity, aiming to provide useful insights into the design and development of the S protein-based vaccines as well as therapeutics to prevent or treat the ongoing global spread of SARS-CoV-2/COVID-19. Prefusion structures of human coronavirus HKU1 (HCoV-HKU1) and mouse hepatitis virus S protein ectodomains without two consecutive proline mutations reveal only fully closed conformation (37, 42) , similar to that observed for a full-length, wild-type prefusion form of the SARS-CoV-2 S glycoprotein (41) . Therefore, SARS-CoV-2 evades immune surveillance also through conformational masking, which is well-documented for HIV-1 (43, 44) ; while at the same time, the S protein could transiently sample the functional state to engage ACE2, consistent with the notion that the fusion glycoprotein of highly pathogenic viruses have evolved to perform its functions while evading host neutralizing antibody responses. doi = 10.3389/fimmu.2020.576622 id = cord-286603-4p3t0vre author = Duan, Zhiqiang title = TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein date = 2020-06-27 keywords = NDV; RNA; TIFA; figure; protein summary = title: TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein Therefore, the reduced viral RNA synthesis and transcription caused by M/NLS mutation might be one of the reasons responsible for the attenuated replication of rSS1GFP-M/NLSm. Virus-host protein interactions based on quantitative proteomics analysis have become important methods in understanding cellular proteins involved in virus replication and pathogenesis [22, 23, 41, 42] . Therefore, together with the above results, we speculated that the relatively decreased expression of DEPs involved in ribosome structure, protein posttranslational modification and trafficking due to the disrupted nuclear accumulation of M protein affected viral protein synthesis and budding, which might be the third reason responsible for the attenuated replication of rSS1GFP-M/NLSm. Inflammatory responses are important aspects of the innate immune system during virus infection. doi = 10.1080/21505594.2020.1770482 id = cord-014661-mrh2pbi6 author = Dumitrascu, Georgiana R. title = Critical physiological and pathological functions of Forkhead Box O tumor suppressors date = 2013-12-31 keywords = ROS; cell; dna; factor; foxo; protein summary = FOXO proteins are considered unique cellular targets, regulating a wide variety of critical cellular processes, such as: apoptosis, oxidative stress, DNA damage repair, cell cycle, stem cell proliferation and maintenance, metabolism, angiogenesis, vascular tone, cardiovascular development, fertility, immune response and neuronal survival 4, 20 . Hence, the FOXO transcription factors control the expression of a wide spectrum of genes that regulate essential physiological cellular processes, such as cell death/cell survival, cell cycle, cell proliferation, cell differentiation/development, angiogenesis, cell metabolism, stress response and stem cell maintenance 33,34,35,36,37,38 (Figure 2) . Moreover, the consensus FOXO recognition element (FRE) -(G/C)(T/A)AA(C/T)AA -which differs from that of other forkhead proteins, seems to have a very important role in both apoptotic pathways, since matching functional FRE sites have been identified in the promoters of FOXO target genes encoding Fas ligand (FasL), insulin like growth factorbinding protein 1 (IGFBP1), the apoptotic regulator Bcl-2 interacting mediator of cell death (Bim) and others 30 . doi = 10.15190/d.2013.5 id = cord-009614-lbjesv8y author = Durmuş Tekir, Saliha D. title = Systems biology of pathogen‐host interaction: Networks of protein‐protein interaction within pathogens and pathogen‐human interactions in the post‐genomic era date = 2012-11-29 keywords = PPI; human; phi; protein summary = doi = 10.1002/biot.201200110 id = cord-033010-o5kiadfm author = Durojaye, Olanrewaju Ayodeji title = Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study date = 2020-10-02 keywords = Fig; SARS; model; protein; sequence; structure summary = RESULTS: This study describes the detailed computational process by which the 2019-nCoV main proteinase coding sequence was mapped out from the viral full genome, translated and the resultant amino acid sequence used in modeling the protein 3D structure. Our current study took advantage of the availability of the SARS CoV main proteinase amino acid sequence to map out the nucleotide coding region for the same protein in the 2019-nCoV. The predicted secondary structure composition shows a high degree of alpha helix and beta sheets, respectively, occupying 45 and 47% of the total residues with the percentage loop occupancy at 8% regarded as comparative modeling, constructs atomic models based on known structures or structures that have been determined experimentally and likewise share more than 40% sequence homology. doi = 10.1186/s43042-020-00081-5 id = cord-342118-fsmuqktd author = Dyakov, Ilya N. title = FN3 protein fragment containing two type III fibronectin domains from B. longum GT15 binds to human tumor necrosis factor alpha in vitro date = 2020-08-06 keywords = FN3; protein summary = Previously, based on the analysis of the genomes of 34 species of bifidobacteria, we 233 identified and characterized a species-specific cluster of PFNA genes, which consists of To develop a sandwich ELISA assay that would allow us to check the ability of the 298 recombinant FN3 protein to bind human cytokines, we raised polyclonal antibodies 299 specific to the recombinant FN3 protein. The resulting affinity 302 purified and concentrated preparation contained 1 mg of FN3-specific rabbit polyclonal 303 antibodies per 1 mL and was highly active -specific interaction with the FN3 protein 304 was detected even after 1:820000 dilution. To exclude the possibility of blockage of the cytokine-binding motif of the FN3 335 protein and its nonspecific adsorption onto the solid surface, we employed ELISA 336 scheme 3 described in the materials and methods section: The FN3-specific rabbit 337 polyclonal antibodies were first adsorbed onto the solid surface after which the FN3 338 protein was added as a "second layer". doi = 10.1016/j.anaerobe.2020.102247 id = cord-320092-0qnvydux author = Ehsani, Sepehr title = COVID-19 and iron dysregulation: distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein date = 2020-10-16 keywords = COVID-19; SARS; hepcidin; iron; protein; spike summary = An implication of this preliminary observation is to suggest a potential route of investigation in the coronavirus research field making use of an already-established literature on the interplay of local and systemic iron regulation, cytokine-mediated inflammatory processes, respiratory infections and the hepcidin protein. c The position of the disulfide bonds in the sequence of the mature human hepcidin is illustrated along with the potential palmitoylation residues (ten cysteines) of the cytoplasmic tail of the SARS-CoV-2 spike protein. If the sequence similarity reported here is actually playing a significant role at the cellular level, could it be that, although the cellular localizations appear to be different based on current knowledge, the SARS-CoV-2 spike protein cytoplasmic tail can partly mimic the structure of hepcidin and interact with ferroportin? In addition, a notyet-fully-established link of relevance here is the observations of a Kawasaki-disease-like systemic vasculitis syndrome in children infected with the novel Fig. 3 Summary of salient facets of coronavirus spike protein and human hepcidin biology. doi = 10.1186/s13062-020-00275-2 id = cord-334511-lx9608vy author = Emwas, Abdul-Hamid title = NMR as a “Gold Standard” Method in Drug Design and Discovery date = 2020-10-09 keywords = Based; Discovery; Drug; HSQC; NMR; NOE; Protein; STD; Spectroscopy; ligand; screening summary = The nearly ubiquitous use of virtual screening is due to its efficiency in searching massive chemical databases in order to generate lead molecules [313] that inhibit protein-protein interactions [314] , and its ability to help identity ligand (drug) binding sites on the target of interest [310] to lend insight to the mechanisms of action for lead compounds [315, 316] . The nearly ubiquitous use of virtual screening is due to its efficiency in searching massive chemical databases in order to generate lead molecules [313] that inhibit protein-protein interactions [314] , and its ability to help identity ligand (drug) binding sites on the target of interest [310] to lend insight to the mechanisms of action for lead compounds [315, 316] . Clearly, combining virtual screening with NMR-based methods is advantageous in studying how ligands (drugs) bind and interact with targets (proteins) of interest. The interactions between targets (proteins) and ligands (small molecules) can be analyzed independently of the biological systems by using ''cell-based'' NMR drug design approaches. doi = 10.3390/molecules25204597 id = cord-348360-20eq5meh author = Esposito, Dominic title = Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays date = 2020-06-04 keywords = SARS; protein; spike summary = To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. Thus, the work presented here is intended to provide a robust method for those wishing to reliably produce SARS CoV-2 spike protein in quantities sufficient for serology assays, structural biology, or simply to better understand some of the production variables affecting the yield. Nevertheless, the approaches outlined here allowed us to improve the production yield of spike protein significantly by modifying cell culture temperature and harvest time, as well as improving the purification process. To produce SARS-CoV-2 antigens for the development of serology assays, we initially followed standard procedures for secreted protein production: transfection using the manufacturer''s protocols, expression at 37°C, harvest at three days post-transfection, tangential flow filtration of the culture supernatant, immobilized metal ion chromatography with linear gradient elution, and size exclusion chromatography. doi = 10.1016/j.pep.2020.105686 id = cord-285647-9tegcrc3 author = Estrada, Ernesto title = Fractional diffusion on the human proteome as an alternative to the multi-organ damage of SARS-CoV-2 date = 2020-08-17 keywords = PPI; SARS; network; process; protein summary = By following the main subdiffusive routes across the PPI network, we identify proteins mainly expressed in the heart, cerebral cortex, thymus, testis, lymph node, kidney, among others of the organs reported to be affected by COVID-19. 25, 26 Therefore, we assume here that perturbations produced by SARS-CoV-2 proteins on the human PPI network are propagated by means of diffusive processes. Here, we propose the use of a time-fractional diffusion model on the PPI network of proteins targeted by SARS-CoV-2. We now consider how a perturbation produced by SARS-CoV-2 on a protein mainly expressed in the lungs can be propagated to proteins mainly located in other tissues (see Table S4 in the supplementary material) by a subdiffusive process. Here, we have studied the particular case in which the time-fractional diffusion equation produces a subdiffusive regime, with the use of α = 3/4 in the network of human proteins targeted by SARS-CoV-2. doi = 10.1063/5.0015626 id = cord-004673-c8qcjve9 author = Faaberg, K. S. title = Membrane association of the C-terminal half of the open reading frame 1a protein of lactate dehydrogenase-elevating virus date = 1996 keywords = Fig; ORF; protein summary = cDNAs encoding ORF 1a protein segments encompassing transmembrane segments 5 to 11 and its amphipathic C-terminal end as well as the N-terminal 80 amino acids of the downstream ORF 1b protein were transcribed and the transcripts in vitro translated in the absence and presence of microsomal membranes. Eisenberg hydrophobic moment analysis of the protein predicted the presence of eleven transmembrane segments in the C-terminal half of the molecule (amino acids 980-1852) that flank the serine protease domain, cDNAs encoding ORF la protein segments encompassing transmembrane segments 5 to 11 and its amphipathic C-terminal end as well as the N-terminal 80 amino acids of the downstream ORF lb protein were transcribed and the transcripts in vitro translated in the absence and presence of microsomal membranes. In the present study we provide strong evidence that the segment of LDV ORF la protein with transmembrane segments 5-11 (see Fig. 1 ) becomes intimately associated with endoplasmic reticulum (ER) membranes during synthesis and that none of its potential N-glycosylation sites becomes glycosylated. doi = 10.1007/bf01718835 id = cord-257584-v38tjof3 author = Fahmi, Muhamad title = Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV date = 2020-03-03 keywords = SARS; protein summary = Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. This was done using a combination of the phylogenetic tree constructed from the genome sequences and the cluster tree developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The phylogenetic analysis using complete genome sequences showed that 2019-nCoV was the most closely related to BatCoV RaTG13 and belonged to the Sarbecovirus subgenus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45) with the full support of reliability (Fig. 1) . Two (NS7b and NS8) of five nonstructural proteins were specific for 2019-nCoV and its closely related species, BatCoV RaTG13 and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45). doi = 10.1016/j.meegid.2020.104272 id = cord-355327-d3gcfepx author = Fan, Samuel W title = Conformational changes in redox pairs of protein structures date = 2009-08-01 keywords = Cys; Redox; change; disulfide; protein; structure summary = Several classes of structural changes were observed, proteins that exhibit: disulfide oxidation following expulsion of metals such as zinc; major reorganisation of the polypeptide backbone in association with disulfide redox-activity; order/disorder transitions; and changes in quaternary structure. These groups were: proteins that oxidize disulfides following expulsion of metals such as Zn; proteins that exhibited major reorganization or ''''morphing'''' of portions of the polypeptide backbone in association with disulfide redox-activity; proteins that exhibited order/disorder transitions; and proteins that exhibited changes in quaternary structure. Twenty-nine Redox Pair protein clusters with intermolecular disulfide bonds exhibit changes in quaternary structure upon oxidation/reduction. We were previously aware of two instances where subdomain morphing of proteins has been associated with reversible disulfide reduction: a redox-controlled structural reorganization of the ion channel CLIC1 proposed to regulate its insertion into membranes, 18 and sequential oxidation of the transcription factor OxyR in response to oxidative stress which modulates its quaternary structure and DNA-binding properties. doi = 10.1002/pro.175 id = cord-001244-qdld7hdc author = Fan, Yue-Nong title = iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking date = 2014-03-19 keywords = Chou; amino; drug; protein summary = In the predictor, the drug compound concerned was formulated by a 256-D (dimensional) vector derived from its molecular fingerprint, and the NR by a 500-D vector formed by incorporating its sequential evolution information and physicochemical features into the general form of pseudo amino acid composition, and the prediction engine was operated by the SVM (support vector machine) algorithm. [59] did not provide a publicly accessible web-server for their method, and hence its practical application value is quite limited, particularly for the broad experimental scientists; (b) The prediction quality can be further enhanced by incorporating some key features into the formulation of NR-drug (nuclear receptor and drug) samples via the general form of pseudo amino acid composition [60] . Prediction of G-protein-coupled receptor classes based on the concept of Chou''s pseudo amino acid composition: An approach from discrete wavelet transform doi = 10.3390/ijms15034915 id = cord-003020-q69f57el author = Farhadi, Tayebeh title = Computer-aided design of amino acid-based therapeutics: a review date = 2018-05-14 keywords = acid; amino; design; peptide; protein; structure summary = doi = 10.2147/dddt.s159767 id = cord-314567-purplsjn author = Fernández-Ponce, Cecilia title = Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date = 2018-01-04 keywords = HCV; RNA; core; protein summary = HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4 + T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4 + T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. As studies using the whole virus do not allow for the elucidation of the specific molecular mechanisms in which each protein is implicated, in this work, we focused on a single viral protein, showing that in CD4 + T cells, HCV core protein mostly localizes in the nucleus and specifically in the nucleolus where it is greatly enriched. doi = 10.3389/fmicb.2017.02595 id = cord-313988-3xjnpkqp author = Ferraz, Rosa María title = Insertional protein engineering for analytical molecular sensing date = 2006-04-03 keywords = biosensor; enzyme; protein summary = In this context, insertional protein engineering offers the possibility to develop new devices, efficiently responding to ligand interaction by dramatic conformational changes, in which the specificity and magnitude of the sensing response can be adjusted up to a convenient level for specific analyte species. Among enzyme inhibitors and other few ligand species that activate allosteric biosensors, antibodies have been noted to be specially efficient allosteric effectors [36] and the use of antigenic peptides as receptors in only-protein biosensors would offer appealing tools for the fast molecular diagnosis of infectious diseases [39, 43] . For such a sensor being efficiently responsive, appropriated permissive sites need to be selected permitting proper receptor display and signal transduction, and the whole protein might require further engineering to gain specificity and response range. Among the diversity of sensing strategies based on insertional mutagenesis two protein platforms emerge as the most explored, namely cleavable sensors responding to proteases or their inhibitors, and allosteric, among whose most efficient effectors are antibodies. doi = 10.1186/1475-2859-5-15 id = cord-257465-9yrf7ofy author = Finlay, William J. J. title = Phage Display: A Powerful Technology for the Generation of High-Specificity Affinity Reagents from Alternative Immune Sources date = 2016-05-23 keywords = antibody; phage; protein summary = doi = 10.1007/978-1-4939-6412-3_6 id = cord-330852-n7j0c4ne author = Fischer, Wolfgang B. title = Mechanism of Function of Viral Channel Proteins and Implications for Drug Development date = 2012-02-23 keywords = HIV-1; NMR; TMD; Vpu; channel; protein; virus summary = By adding data from functional studies like Cys scanning and electrophysiological measurements as mentioned as well as computational modeling data (Sansom and Kerr, 1993; Sansom et al., 1997; Zhong et al., 1998) , an approximate structural model of the tetrameric assembly of the TMDs of M2 with the histidines and tryptophans as important pore lining residues has been generated. Amiloride derivatives block ion channel activity and enhancement of virus-like particle budding caused by HIV-1 protein Vpu Backbone structure of the amantadine-blocked trans-membrane domain M2 protein channel from influenza A virus Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the Human Immunodeficiency Virus HIV-1 Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes Three-dimensional structure of the channel-forming trans-membrane domain of virus protein "u" (Vpu) from HIV-1 doi = 10.1016/b978-0-12-394305-7.00006-9 id = cord-339091-3xk2w0d2 author = Flower, Darren R title = Computer aided selection of candidate vaccine antigens date = 2010-11-03 keywords = MHC; antigen; epitope; prediction; protein; vaccine summary = The effective development of antigen prediction methods would significantly reduce the laboratory resource required to identify pathogenic proteins as candidate subunit vaccines. Initially, the pathogenic genome is scanned for "open reading frames" or ORFs. Once all ORFs have been identified, proteins are selected on the basis that they will be accessible to immune system surveillance, usually using some form of informatic-based prediction methodology or, more likely, set of methdologies. We shall below examine three key approaches: subcellular location prediction, sequence similarity, and empirical statistical approaches, typified by VaxiJen. For a protein to be accessible to surveillance by the immune system, it is often assumed to be physically external to the microbial organism or at least present on its surface rather than being sequestered away far from the roving eye of the immune system. doi = 10.1186/1745-7580-6-s2-s1 id = cord-016594-lj0us1dq author = Flower, Darren R. title = Identification of Candidate Vaccine Antigens In Silico date = 2012-09-28 keywords = MHC; antigen; prediction; protein; sequence; vaccine summary = In the wider context of the experimental discovery of vaccine antigens, with particular reference to reverse vaccinology, this chapter adumbrates the principal computational approaches currently deployed in the hunt for novel antigens: genome-level prediction of antigens, antigen identification through the use of protein sequence alignment-based approaches, antigen detection through the use of subcellular location prediction, and the use of alignment-independent approaches to antigen discovery. When looking at a reverse vaccinology process, the discovery of candidate subunit vaccines begins with a microbial genome, perhaps newly sequence, progresses through an extensive computational stage, ultimately to deliver a shortlist of antigens which can be validated through subsequent laboratory examination. Conventional empirical, experimental, laboratory-based microbiological ways to identify putative candidate antigens require cultivation of target pathogenic micro-organisms, followed by teasing out their component proteins, analysis in a series of in-vitro and in-vivo assays, animal models and with the ultimate objective of isolating one or two proteins displaying protective immunity. doi = 10.1007/978-1-4614-5070-2_3 id = cord-320790-ley91488 author = Fogg, M. J. title = Application of the use of high‐throughput technologies to the determination of protein structures of bacterial and viral pathogens date = 2006-10-04 keywords = MTB; Oxford; protein summary = Here the impact of several technologies on the structural determination of proteins from human pathogens is illustrated with selected examples, including the parallel expression of multiple constructs, the use of standardized refolding protocols and optimized crystallization screens. Here the impact of several technologies on the structural determination of proteins from human pathogens is illustrated with selected examples, including the parallel expression of multiple constructs, the use of standardized refolding protocols and optimized crystallization screens. Further development and uptake of these methodologies (see Aricescu, Assenberg et al., 2006; Aricescu, Lu et al., 2006) is likely to have a major impact on the study of difficult viral targets, as indicated by preliminary results for EBV proteins, where insect-cell expression yielded soluble protein for 50% of the proteins tested (Tarbouriech et al., 2006) Here we illustrate the impact of a number of particular SPINE-based technologies on the structure determination of pathogen targets, namely (i) multiple-construct design for a single target, (ii) optimization of protein solubility, (iii) eukaryotic expression systems, (iv) standardized refolding protocols, (v) surface engineering and (vi) other biophysical characterization. doi = 10.1107/s0907444906030915 id = cord-277293-eo3bei9x author = Fondong, Vincent N. title = Geminivirus protein structure and function date = 2013-04-25 keywords = Rep; Tomato; dna; protein summary = The replication-associated protein (Rep) encoded by the AC1 ORF (also called AL1) in bipartite geminiviruses and by C1 (also called L1) in monopartite geminiviruses (except mastreviruses) is conserved in sequence, position and function (Hanley-Bowdoin et al., 2004) and is expressed under the control of a bidirectional core promoter in the IR (Hanley-Bowdoin et al., 1999) . SINAC1 levels were shown to be higher in ToLCV-infected cells, suggesting that NAC1 is involved in viral DNA replication (Selth et al., 2005) , possibly through an interaction with REn. Recently, the Tomato leaf curl Kerala virus REn was shown to interact with Rep and enhance the Repmediated ATPase activity (Pasumarthy et al., 2010) , thus confirming a role for REn in viral DNA replication. doi = 10.1111/mpp.12032 id = cord-259237-aty0vrat author = Frabutt, Dylan A. title = Arms Race between Enveloped Viruses and the Host ERAD Machinery date = 2016-09-19 keywords = ERAD; HIV-1; UPR; protein summary = doi = 10.3390/v8090255 id = cord-252304-lwiulri7 author = Fragnoud, Romain title = Differential proteomic analysis of virus-enriched fractions obtained from plasma pools of patients with dengue fever or severe dengue date = 2015-11-14 keywords = pf4; protein summary = ELISAs were used to validate differential expression of a selection of identified host proteins in individual plasma samples of patients with dengue fever compared to patients with severe dengue. CONCLUSION: A novel technique of virion-enrichment from plasma has allowed to identify two host proteins that have prognostic value for classifying patients with acute dengue who are more likely to develop a severe dengue. Fig. 2 Ingenuity Pathway Analysis for host proteins identified in the viral-enriched plasma fraction of patients with dengue. To validate the mass spectrometry data, the levels of selected host proteins were assessed by quantitative ELISA both in the virus-enriched fraction and in individual plasma samples from DF or SD patients. In this regard, further studies are required to assess the prognostic value of host proteins associated with inflammation, complement cascade and coagulation for disease severity by analysis of additional biological samples from patients infected with DV. doi = 10.1186/s12879-015-1271-7 id = cord-016448-7imgztwe author = Frishman, D. title = Protein-protein interactions: analysis and prediction date = 2009-10-01 keywords = Cytoscape; Fig; PSI; datum; domain; interaction; network; protein summary = In general, investigating the topology of protein interaction, metabolic, signaling, and transcriptional networks allows researchers to reveal the fundamental principles of molecular organization of the cell and to interpret genome data in the context of large-scale experiments. The basic principle is fairly simple and rests implicitly on a multigraph representation: several interaction networks to be integrated, each resulting from a specific experimental or predictive method, are defined over the same set of proteins. This software provides functionalities for (i) generating biological networks, either manually or by importing interaction data from various sources, (ii) filtering interactions, (iii) displaying networks using graph layout algorithms, (iv) integrating and displaying additional information like gene expression data, and (v) performing analyses on networks, for instance, by calculating topological network properties or by identifying functional modules. The evidence can be derived from literature mining, functional associations based on Gene Ontology annotations, co-occurrence of transcriptional motifs, correlation of expression data, sequence similarity, common protein domains, shared metabolic pathway membership, and protein-protein interactions. doi = 10.1007/978-3-211-75123-7_17 id = cord-326015-ky4y2xjt author = Füllekrug, Joachim title = Protein sorting in the Golgi complex date = 1998-08-14 keywords = Golgi; protein summary = In this review, we will discuss sorting of resident proteins in the Golgi complex mainly in the context of cisternal maturation [1, 2] . An essential feature of this maturation model is the prediction that Golgi resident proteins are more concentrated in retrograde vesicles than they are in the cisternae of the Golgi apparatus. This shows that Golgi resident enzymes do form gradients across the pathway and that these are unique to the particular protein. The surprising ¢nding that the membrane spanning domain (MSD) of Golgi residents su¤ced to localise reporter molecules to the appropriate part of the pathway suggested that this domain harboured important sorting information (for review, see [22] ). As this form of coatomer is found on Golgi associated transport vesicles [50] , COP I vesicles constitute RTCs. The presence of K(X)KXX or related signals on membrane proteins other than ER residents allows for the possibility that this motif also acts later in the pathway. doi = 10.1016/s0167-4889(98)00048-2 id = cord-271091-ffn59sgf author = Galao, Rui P title = Saccharomyces cerevisiae: a versatile eukaryotic system in virology date = 2007-10-10 keywords = HCV; RNA; protein; virus; yeast summary = These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production. Although the expression of viral proteins in yeast not always necessarily reflects their role in higher eukaryotes, here we selected some examples in which the analysis in yeast of their effect on highly conserved cellular processes such as cell cycle control, apoptosis or mRNA degradation have contributed to the current understanding of the pathogenesis of important viral pathogens such as HIV-1 and HCV. The identification of the host factors involved in viral RNA replication is a priority area of research in virology because it can provide new targets for antiviral drug development. doi = 10.1186/1475-2859-6-32 id = cord-260949-w2xuf15h author = Galluzzi, Lorenzo title = Viral Control of Mitochondrial Apoptosis date = 2008-05-30 keywords = Bak; Bax; Bcl-2; MMP; PTPC; apoptosis; cell; protein summary = doi = 10.1371/journal.ppat.1000018 id = cord-302009-oqc21fah author = Geng, Xindu title = Protein folding liquid chromatography and its recent developments() date = 2007-04-15 keywords = PFLC; SEC; protein summary = Protein folding liquid chromatography (PFLC) is a new method developed in recent years, and it is widely used in molecular biology and biotechnology. When it is used in protein folding, the bioactivity recovery increases, the folded protein can be easily separated from misfolded forms, protein concentration after refolding is relatively high, and it is easy to scale up and automate, therefore it is regarded as an efficient, and close to ideal refolding method [1, 2] . In addition, by continuously changing the components of the mobile phase, different proteins can be separated with suitable folding conditions to refold and simultaneously purify in only one chromatographic run. Chaperone solvent plug SEC proposed by Liu and Chang [16] could obviously reduce precipitates formed before denatured protein entered the top of the column, and relatively high mass recovery was obtained. [57] recently proposed a relatively versatile refolding method using IEC with a silica-based weak cation exchanger, very high mass and bioactivity recoveries were obtained for denatured lysozyme. doi = 10.1016/j.jchromb.2006.10.068 id = cord-298736-9bvyp21d author = Gerold, Gisa title = Decoding protein networks during virus entry by quantitative proteomics date = 2016-06-15 keywords = HCV; SILAC; cell; protein; virus summary = doi = 10.1016/j.virusres.2015.09.006 id = cord-280360-rh37d5wc author = Gibson, David S. title = Comparative analysis of synovial fluid and plasma proteomes in juvenile arthritis – Proteomic patterns of joint inflammation in early stage disease date = 2009-05-02 keywords = JIA; fluid; patient; protein; synovial summary = title: Comparative analysis of synovial fluid and plasma proteomes in juvenile arthritis – Proteomic patterns of joint inflammation in early stage disease Comparative analysis of synovial fluid and plasma proteomes in juvenile arthritis -Proteomic patterns of joint inflammation in early stage disease 1 We initially performed a study of the proteins expressed within synovial fluid and plasma in early JIA in order to discover novel biomarkers which distinguish between local and systemic components of joint inflammation in arthritis. The simultaneous analysis of individual paired plasma and synovial fluids from ten patients ( Table 1 , study group A) was used to initially isolate joint-specific protein expression profiles, without introducing bias from inter-individual differences. A number of proteins with consistent synovial and plasma ''specific'' expression patterns are highlighted and quantified to demonstrate the ability to reliably differentiate molecular fingerprints of local and systemic disease across patient groups by this gel based approach. doi = 10.1016/j.jprot.2009.01.022 id = cord-018969-0zrnfaad author = Giese, Matthias title = Types of Recombinant Vaccines date = 2015-09-24 keywords = Fig; LPS; Shigella; antigen; cell; dna; gas; protein; tick; vaccine summary = New vaccines and vaccination strategies are being developed including the use of attenuated live mycobacteria, recombinant microorganisms, and subunits, prime-boost strategies based on the successive administration of a certain mycobacterial antigen under two different vaccine vectors, and DNA vaccines [ 1 ] . However, several animal models have been developed to study the pathogenesis of Shigella , the resulting immune response against Shigella antigens, and the protection efficacy of candidate vaccines against shigellosis: [ 31 ] . The GAS M protein is the major protective antigen and an ideal target for vaccine development; however it contains heart tissue cross-reactive epitopes particularly in the conserved region [ 98 ] . Immunization of mice with a C-region peptide GAS vaccine candidate called J8 conjugated to the carrier protein diphtheria toxoid (dT) and co-delivery with an appropriate adjuvant led to protection against systemic and mucosal GAS infection [ 104 ] (Fig. 9.29 ). doi = 10.1007/978-3-319-25832-4_9 id = cord-260345-ugd8kkor author = Giles, Ian G. title = A compendium of reviews in biochemistry and molecular biology published in the first half of 1992 date = 1992-12-31 keywords = RNA; acid; cell; dna; factor; gene; protein summary = doi = 10.1016/0020-711x(92)90283-7 id = cord-346916-jj4l9ydl author = Girardi, Erika title = Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date = 2020-08-23 keywords = Fig; PKR; RNA; protein; rig; translation; viral; virus summary = Moreover, despite the molecular mimicry set by RNA viruses to resemble cellular mRNAs and escape host recognition, the viral nucleic acid still needs to embark on a long journey through a hostile cell environment and must overcome the obstacles put in place by the host antiviral system in order to be translated and replicated. Another example, is the zinc-finger antiviral protein (ZAP), which binds vRNAs containing a ZAP response element (ZRE) and induces RNA degradation via interaction of its N-terminal domain with host decay machinery mediated [75] (Fig. 1 ). In fact, IRES elements present in the genome of different families of RNA viruses lack overall conserved features [146, 147] .The classification of viral IRESs in four types stems from their structural organization, their respective dependence on sets of translation initiation factors, and whether they use scanning or instead directly recruit ribosomes to the start codon [148] (Fig. 2) . doi = 10.1016/j.semcdb.2020.08.006 id = cord-350286-n7ylgqfu author = Giri, Rajanish title = When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date = 2020-04-03 keywords = Bat; Human; RNA; SARS; Supplementary; Table; figure; protein summary = The results of this analysis are summarized in Table 2 , which clearly shows that most of the SARS-CoV-2 proteins contain at least one MoRF, indicating that disorder does play an important role in the functionality of these viral proteins. As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Global analysis of intrinsic disorder in the replicase polyprotein 1ab Table 3 represents the PPID mean scores of 15 non-structural proteins (Nsps) derived from the Replicase polyprotein 1ab in SARS-CoV-2, Human SARS CoV, and Bat CoV. Similar to many other non-structural proteins of coronaviruses, Nsp15s from SARS-CoV-2, Human SARS, and Bat CoV are predicted to possess multiple flexible regions but contain virtually no IDPRs (see Figures 32A, 32B, and 32C) . doi = 10.1101/2020.03.13.990598 id = cord-005034-wyipzwo4 author = Gleeson, Paul A. title = Targeting of proteins to the Golgi apparatus date = 1994 keywords = Golgi; TGN; domain; protein summary = doi = 10.1007/bf00731273 id = cord-273019-hbpfz8rt author = Glingston, R. Sahaya title = Organelle dynamics and viral infections: at cross roads date = 2018-06-25 keywords = RNA; cell; infection; protein; viral; virus summary = Studies on the herpes simplex virus-1 (HSV-1) infection on Vero, BHK-21 and PtK 2 cells reported transportation of viral tegument-capsid by dynein to the cytoplasmic side of NPC [22, 23] . In order to construct these compartments, viruses alter host''s fatty acid metabolism, induce rearrangement of the membrane constituents and also recruit cellular machinery to produce proteins essential for its replication [59, 60] . Upregulation of mitophagy and degradation of the mitochondrial antiviral signalling protein (MAVS) in order to attenuate the antiviral immune response in non-small cell lung cancer (NSCLC) cells was reported upon measles virus infection [83] . The expression of matrix protein (M) of human parainfluenza virus type 3 (HPIV3) in HEK293T and HeLa cells was reported to induce mitophagy resulting in the suppression of type1 interferon response [84] . Many viruses or viral proteins are reported to localize to peroxisomes and/or exploit their functions to facilitate their replication in the host cells [108] . doi = 10.1016/j.micinf.2018.06.002 id = cord-256316-1odgm6hm author = Godet, Murielle title = TGEV corona virus ORF4 encodes a membrane protein that is incorporated into virions date = 1992-06-30 keywords = ORF4; TGEV; protein summary = Several lines of evidence lend support to the view that a gene encoding an SM-like protein is a common feature of the coronavirus genomes: (i) an ORF predicting a polypeptide with striking similarities to TGEV ORF4 was identified in the genome sequence of each of the 5 coronaviruses examined (Fig. 9 ) and the fact that TGEV SM was recognized by anti-FIPV antibodies argues for the presence of a related gene also in feline infectious peritonitis virus genome; (ii) the product expressed from the relevant MHV, BCV, and IBV ORFs was reported to have properties of a transmembrane polypeptide (Leibowitz et a/., 1988; Smith et al., 1990; Abraham et a/., 1990) ; and (iii) although expressed through a mono-, di-, or tricistronic mRNA (Abraham et a/., 1990; Budzilowicz and Weiss, 1987; Liu et al., 1991 ) the assumed SM-encoding genes are all located upstream and adjacent to the M protein gene. doi = 10.1016/0042-6822(92)90521-p id = cord-315570-khm1veuv author = González-Mora, Alejandro title = Bacteriophage-Based Vaccines: A Potent Approach for Antigen Delivery date = 2020-09-04 keywords = M13; display; dna; phage; protein; vaccine summary = This system relies on bacteriophages displaying proteins or peptides with high affinity to antigen-presenting cells or the antigen itself and at the same time they carry on their genome an eukaryotic expression cassette encoding a specific antigen with the final aim of increasing the immune response by combining both effects (Figure 1 ) [6] . developed a double-hybrid filamentous bacteriophage fd co-displaying peptides recognized by the Major Histocompatibility Complex (MHC) class I and MHC class II cell surface receptors and epitopes from the antigen MAGE aiming to enhance the anti-tumor immune activity based on CTL responses [62] . Thus, the adjuvant-like effect exhibited by phages in various vaccination studies along with their capacity to effectively present peptides or proteins to the immune system leading to the activation of cellular and humoral immune responses [40] demonstrates that engineered phage particles are a proper strategy to enhance the efficacy and safety of viral particle-based vaccines. doi = 10.3390/vaccines8030504 id = cord-325043-vqjhiv7p author = Gorbalenya, Alexander E. title = An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication date = 1989 keywords = NTP; RNA; protein; sequence summary = title: An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication These observations, taken together with the results of comparative analysis of the positions occupied by respective proteins (domains) in viral multidomain proteins, suggest that all the NTP-motif-containing proteins of positive-strand RNA viruses are homologous, constituting a highly diverged monophyletic group. Preliminary comparative analysis of the amino acid sequences of the NTP-motif-eontaining proteins of positive-strand RNA viruses by use of the programs DIAGON and OPTAL (see Methods) revealed three distinct families and some additional proteins in whose close relatives the motif was not conserved. In the present study we demonstrate that in a highly diverged group including similar proteins of positive-strand RNA viruses, the consensus sequences of the NTP-motif constitute the most strictly conserved stretches, encompassing four of the five invariant amino acid residues. doi = 10.1007/bf02102483 id = cord-013348-lsksys56 author = Goto, Keiko title = Development of Monoclonal Antibodies and Antigen-Capture ELISA for Human Parechovirus Type 3 date = 2020-09-19 keywords = ELISA; VP0; figure; protein summary = doi = 10.3390/microorganisms8091437 id = cord-020788-a33vcapl author = Gottardi, Cara J. title = Signals and Mechanisms of Sorting in Epithelial Polarity date = 2008-05-22 keywords = Golgi; MDCK; cell; membrane; protein; signal summary = At the electron-microscopic level, one of the most apparent and fundamental features of this cell type is its polarized organization of intracellular organelles and its structurally and compositionally distinct lumenal (apical) and serosal (basolateral) plasma-membrane domains. As noted above, in hepatocytes all apical proteins studied to date make use of this indirect pathway for apical delivery (Bartles et al., 1987) , while cell lines derived from intestine and kidney can employ both routes for surface delivery (Matter et al., 1990; Casanovaet al., 1991; Low et al., 1991) While the details of the routes have been determined for a number of sorting pathways, the molecular signals and recognition components which control each of them are not well understood. The observation that the influenza and vesicular stomatitis viruses bud from opposite surface domains of polarized MDCK cells (Madin Darby Canine Kidney) (Rodriguez-Boulan and Sabatini, 1978) spawned an extensive search in which chimeric and deletion analyses were applied to the problem of identifying the underlying apical and basolateral sorting signals (reviewed in Caplan and Matlin, 1989) . doi = 10.1016/s1569-2558(08)60020-x id = cord-287729-pl88otue author = Gray, Stewart M. title = Plant virus proteins involved in natural vector transmission date = 1996-07-31 keywords = protein summary = Viral proteins mediate the binding of plant viruses to vector mouthparts and the transport of virus across vector-cell membranes. They further suggest that the am&-terminal region of the coat-protein monomers assembled into virus particles is not normally available for interaction with the aphids, but that HC mediates a conformational change in the amino termiof thecoat protein that allows binding of the virus ;o the aphid (Fig. 4C) .mission is regulated mainly by the codt protein''". Site-specific mutagenesis of cucumber mosaic virus (CuMV) has identified two regions of the coat protein thar are involved in efficient transmission, and has pinpointed the amino acids needed<''. These observations biggest that one or a few amino acid changes in the coat protein could alter the vectortransmission phenotype by pre\ enring direct interaction between the virus and the vector. the environment wtthln the food canal or binding of the virus tc) the vector, all resulting in the exposure >f cleavage sites on the coat proteins. doi = 10.1016/0966-842x(96)10040-8 id = cord-325825-0lyt8gfq author = Griffiths, Samantha J. title = A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication date = 2013-08-08 keywords = IFN; Med23; Mediator; cell; figure; hsv-1; protein; virus summary = Host factors (HFs) which positively or negatively regulate HSV-1 replication were identified by screening a druggable genome siRNA library (4 siRNAs per gene) targeting 7,237 human genes against a HSV-1 reporter virus expressing the enhanced green fluorescent protein (eGFP; HSV-1 strain C12) in the epithelial Hela cell line, due to their ease of transfection and susceptibility to HSV-1 infection [34] . Combined bioinformatic analyses of protein interaction and siRNA depletion screens found a significant functional enrichment for proteins involved in transcription, and identified multi-protein complexes enriched for pro-viral HFs which strongly inhibited HSV-1 upon depletion, including the RNA-polymerase II, eIF3 and Mediator complexes ( Figure 3a) . Furthermore, qPCR analysis found depletion of Med23 inhibited the induction of IFN-l expression following HSV-1 infection of A549 cells in comparison to cells transfected with the RSCF siRNA control ( Figure 4e ). doi = 10.1371/journal.ppat.1003514 id = cord-022262-ck2lhojz author = Gromeier, Matthias title = Genetics, Pathogenesis and Evolution of Picornaviruses date = 2007-09-02 keywords = IRES; RNA; Wimmer; figure; genome; poliovirus; protein; virus summary = The following viruses have been recognized as picornaviruses on the basis of their genome sequences and physico-chemical properties as well as the result of comparative sequence analyses (see the section on Evolution): equine rhinovirus types I and 2, Aichi virus, porcine enterovirus, avian encephalomyelitis virus, infectious flacherie virus of silkworm Clusters of enteroviruses refer to groups of enteroviruses arranged predominantly according to genotypic kinship (Hyypia et al., 1997) . Briefly, when expression vectors ( Figure 12 .6E) consisting of a gag gene (encoding p17-p24; 1161 nt) of human immunodeficiency virus that was fused to the N-terminus of the poliovirus polyprotein (Andino et al., 1994; Mueller and Wimmer, 1998) were analysed after transfection into HeLa cells, the genomes were not only found to be severely impaired in viral replication but they were also genetically unstable (Mueller and Wimmer, 1997) . doi = 10.1016/b978-012220360-2/50013-1 id = cord-268416-8hw80qx8 author = Grunewald, Matthew E. title = The coronavirus nucleocapsid protein is ADP-ribosylated date = 2018-04-01 keywords = ADP; MHV; protein summary = While screening for ADP-ribosylated proteins during coronavirus (CoV) infection, we detected a ~55 kDa ADP-ribosylated protein in mouse hepatitis virus (MHV)-infected cells and in virions, which we identified as the viral nucleocapsid (N) protein. To identify potential targets of the CoV macrodomain, we analyzed infected cells for changes in ADP-ribosylation patterns utilizing antibodies specific for ADPr. We focused on cells infected with a murine CoV, mouse hepatitis virus (MHV). If the macrodomain was indeed removing the ADPr from the N protein, we would expect to see increased N protein ADP-ribosylation in cells infected with mutant virus compared to wild-type infected cells. To determine if N protein expressed in the absence of CoV infection could be ADP-ribosylated in cell culture, we transduced Vero cells with VEEV replicon particles (VRPs) encoding the MERS-CoV N protein or control GFP at different MOIs . doi = 10.1016/j.virol.2017.11.020 id = cord-034823-ogwjzfgf author = Guo, Hao-Bo title = A Suggestion of Converting Protein Intrinsic Disorder to Structural Entropy Using Shannon’s Information Theory date = 2019-06-14 keywords = protein summary = We propose a framework to convert the protein intrinsic disorder content to structural entropy (H) using Shannon''s information theory (IT). Hence, it is useful to know the relationships between the intrinsic structural entropies and the information that can be derived (Equation (3)) from the residual disorder contents, which, in turn, can be predicted based on the protein amino acid sequences. In the CR-space, Ci sets the upper limit and Ri gives the intrinsic ratio between the two quantities of the total Hi and Ii of the i-th protein Pi. Based on the Gaussian distribution in both log2C and log2R, the protein distributions in the CR-space are represented in Figure 2 , for proteins expressed in representative prokaryotes (bacteria and archaea, Figure 2A ), eukaryotes ( Figure 2B ), viruses ( Figure 2C ), and datasets collected from the DisProt database [25] and protein data bank (PDB) [26] ( Figure 2D ). doi = 10.3390/e21060591 id = cord-337032-s4g4g80w author = Gupta, Manoj Kumar title = In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel date = 2020-04-15 keywords = SARS; Vadde; protein summary = Considering this, in the present study, authors employed computational approaches for studying the structure as well as function of the human ''SARS-CoV2 E'' protein as well as its interaction with various phytochemicals. Result obtained revealed that α-helix and loops present in this protein experience random movement under optimal condition, which in turn modulate ion channel activity; thereby aiding the pathogenesis caused via SARS-CoV2 in human and other vertebrates. By considering the above information, in the present study, authors employed computational approach for identifying the best possible structure of the ''SARS-CoV2 E'' protein present in the PDB database to understand its structure and function as well as its behaviour towards various phytochemicals. Subsequently, molecular docking of the ''SARS-CoV2 E'' protein with ligands having 250 conformations using the AutoDock tool revealed that the best ten phytochemicals with minimal binding energy are TIP006452 (Belachinal), TIP005365 (Macaflavanone E), TIP003272 (Vibsanol B), TIP003258 (14 R Ã ,15-Epoxyvibsanin C), TIP005363 (Macaflavanone C), TIP000749 (Luzonoid D), TIP008605 (Grossamide K), TIP009461 ((-)-Blestriarene C), TIP005366 (Macaflavanone F) and TIP005783 (Dolichosterone). doi = 10.1080/07391102.2020.1751300 id = cord-016419-v1f6dx3e author = Gupta, Varsha title = Production of Recombinant Pharmaceutical Proteins date = 2016-10-23 keywords = RNA; cell; growth; production; protein; recombinant summary = Usage of recombinant DNA technology for large-scale production of proteins requires ample amount of time, labor, and resources, but it also offers many opportunities for economic growth. The recombinant proteins approved by FDA are obtained either from Escherichia coli or other prokaryotes; from Saccharomyces cerevisiae or other fungal species; from insect cells , mammalian cells , or human cells ; or from transgenic plants or animals. Their advantages are low cost, high mass production, scale-up, lack of human pathogens , and addition of eukaryotic PTMs. The fi rst recombinant protein obtained in 1986 from tobacco plants was human growth hormone . The vector can be modifi ed to express genes for insulin (tomato) or Hep-B surface antigen (HBsAg) for recombinant therapeutics providing a human glycosylation pattern have increased attention, and the efforts are being made for the development of novel glycoengineered cell lines for production of fully glycosylated protein therapeutic. doi = 10.1007/978-981-10-0875-7_4 id = cord-348972-r94fhpe0 author = Gussow, Ayal B. title = Machine-learning approach expands the repertoire of anti-CRISPR protein families date = 2020-07-29 keywords = Acrs; CRISPR; Cas; Supplementary; protein summary = The most striking and obvious common feature of the Acrs is their small size (weighted mean Acr length: 104 aa, Table 1 ), and the tendency to form sets of small proteins that are encoded by co-directional and closely spaced genes in (pro)virus genomes (hereafter directons; Fig. 1 , Table 1 ). As genes encoding Acrs tend to form small directons, we sought to estimate a heuristic maximum threshold for the mean directon size in a candidate family that would enrich our protein set for true Acrs. The initial set consisted of 232,616 clusters and was first filtered for clusters that included at least one member with an HTH-domain-containing protein encoded downstream, and at least one member from a self-targeting genome, two hallmark Acr characteristics 20 . doi = 10.1038/s41467-020-17652-0 id = cord-319658-u0wjgw50 author = Guven-Maiorov, Emine title = Structural host-microbiota interaction networks date = 2017-10-12 keywords = host; interaction; network; protein summary = To date, challenges in experimental techniques limit large-scale characterization of HMIs. Here we highlight an area in its infancy which we believe will increasingly engage the computational community: predicting interactions across kingdoms, and mapping these on the host cellular networks to figure out how commensal and pathogenic microbiota modulate the host signaling and broadly cross-species consequences. Systems biology approaches that integrate the HMIs with host endogenous protein interaction networks reveal the systematic trends in virulence strategies of pathogens. The availability of genome-wide high throughput omics data makes it possible to associate microbiota with certain host phenotypes at multiple levels and construct host-pathogen interaction networks at the transcriptome [21], proteome Combinatorial effects of microbial effectors and the active host pathways determine the cell response. Mimicry of interactions of critical regulatory nodes in core network modules in the immune system, may be a major way through which pathogens adversely subvert-and commensal microbiota may beneficially modulate-the host cell. doi = 10.1371/journal.pcbi.1005579 id = cord-293798-qc22cps9 author = Gómez-Mascaraque, Laura G. title = Nanostructuring Biopolymers for Improved Food Quality and Safety date = 2018-04-06 keywords = Fabra; encapsulation; food; material; oil; protein; technique summary = doi = 10.1016/b978-0-12-811449-0.00002-5 id = cord-022354-aqtceqqo author = HUNTER, ERIC title = Membrane Insertion and Transport of Viral Glycoproteins: A Mutational Analysis date = 2012-12-02 keywords = Golgi; RSV; membrane; protein; virus summary = second apolar region in gp 37 consists of a 27 amino acid long stretch of hydrophobic residues near the carboxy terminus that functions during translation to stop the movement of the protein into the lumen of the rough endoplasmic reticulum (RER) and to anchor the complex in the membrane. In order to examine the role of the signal peptide in RSV glycoprotein biosynthesis we constructed a series of deletion mutations within the 5'' coding region of the env gene using the double-stranded exonuclease BaBl. Oligonucleotide linkers of the sequence CATCGATG were ligated to the ends of the truncated molecules to introduce a unique restriction endonuclease cleavage site and to replace the deleted in-frame AUG. We found that replacement of the nonconserved region of the cytoplasmic domain with a longer unrelated sequence of amino acids from SV40 vector sequences (mutant Cl) did not alter the rate of transport to the Golgi apparatus nor the appearance of the glycoprotein on the cell surface. doi = 10.1016/b978-0-12-203460-2.50007-x id = cord-022200-hqc8r31t author = HYATT, ALEX D. title = Protein A–Gold: Nonspecific Binding and Cross-Contamination date = 2012-12-02 keywords = gold; protein summary = Some potential problems associated with protein Α -g o l d labeling are also associated with other immunocytochemical techniques, namely nonspecific staining (for example, nonspecific antibodies and electrostatic at tachment; Taylor, 1978; Behnke et al., 1986; Gosselin et al., 1986; Birrell et al., 1987) . In double-labeling experiments cross-contamination is now recognized as a problem which arises from the affinity which protein A possesses for different regions of IgG antibodies, namely the Fc and Fab regions (Roth, 1982; Endresen, 1979; Zikan, 1980) . If the larger of the gold probes is used for the visualization of the first antigen, many potential Fc binding sites (unoccupied protein A) are available for the second immunoglobulin and significant cross-contamination may therefore result. If protein Α-gold is the label, and nonspecific binding and cross-contamination are persistent problems in spite of the addition of excess free protein A, high-affinity stabilizers, adsorption of contaminat ing antibodies, and colloidal gold, then alternative labeling techniques should be pursued and evaluated. doi = 10.1016/b978-0-12-333928-7.50007-1 id = cord-279691-v5kpmk0b author = Hagemeijer, Marne C. title = Biogenesis and Dynamics of the Coronavirus Replicative Structures date = 2012-11-21 keywords = Coronavirus; Protein; RNA; Replication; SARS; Virus summary = Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. A distinctive common feature of +RNA viruses is the replication of their genomes in the cytoplasm of the host cell in association with rearranged cellular membranes that are remodeled into organelle-like membranous structures to which the viral replication-transcription complexes (RTCs) localize. The first detectable membrane rearrangements in CoV-infected cells are 200 to 350 nm organelle-like structures that have been described for both MHV [47, 62] and the SARS-CoV [5, 63] and consist of spherical vesicles containing double lipid bilayers, termed DMVs ( Figure 2 ). doi = 10.3390/v4113245 id = cord-343791-0vykwml5 author = Hainline, Kelly M. title = Progress towards the clinical translation of bio-inspired peptide and protein assemblies date = 2017-11-08 keywords = HPV; VLP; material; peptide; protein summary = These include spherical assemblies such as virus-like particles, designed protein nanoparticles, and peptide amphiphiles (Figure 1) ; and elongated structures such as β-sheet nanofibers, fiber-forming peptide amphiphiles, and filamentous phage (Figure 2) . [17, 18] Owing to their lack of a viral genome, VLP-based vaccines circumvent some risks associated Supramolecular materials composed of proteins and peptides have been receiving considerable attention toward a range of diseases and conditions from vaccines to drug delivery. [19] As alternatives to these previous platforms, VLPs were developed to display an array of epitopes that mimic the surface of native viruses more effectively than subunit or peptide vaccines, thus improving their immunogenic properties. Whereas synthetic peptides are usually not sufficiently immunogenic and require adjuvants, the Burkhard group has developed a self-assembling protein nanoparticle platform that displays both B and T cell epitopes to produce a vaccine with self-adjuvanting qualities. doi = 10.1002/adhm.201700930 id = cord-275993-isff6lp2 author = Han, Dong P title = Development of a safe neutralization assay for SARS-CoV and characterization of S-glycoprotein date = 2004-08-15 keywords = SARS; protein summary = Similar to other coronaviruses, spike (S)-glycoprotein of the virus interacts with a cellular receptor and mediates membrane fusion to allow viral entry into susceptible target cells. S-protein of coronaviruses, which is thought to function as a trimer (Delmas and Laude, 1990) , is responsible for both binding to cellular receptors and inducing membrane fusion for virus entry into target cells (Collins et al., 1982; Godet et al., 1994; Kubo et al., 1994) . Despite difficulties in detecting S-protein directly by immunoassays, proteins expressed from both pcDNA-S and pHCMV-S constructs were able to pseudotype MuLV particles to produce SARS pseudoviruses that could readily infect Vero E6 cells (Fig. 3A) . To assess whether SARS pseudoviruses we generated could be used to quantify virus-neutralizing antibodies, we examined their susceptibility to convalescent sera from SARS-CoV-infected patients. Pseudotyping of murine leukemia virus with the envelope glycoproteins of HIV generates a retroviral vector with specificity of infection for CD4-expressing cells doi = 10.1016/j.virol.2004.05.017 id = cord-272260-88l9bq4i author = Han, L.Y. title = Prediction of functional class of novel viral proteins by a statistical learning method irrespective of sequence similarity date = 2005-01-05 keywords = protein summary = The web-based software SVMProt (http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi) to some extent assigns protein functional family irrespective of sequence similarity and has been found to be useful for studying distantly related proteins [Cai, C.Z., Han, L.Y., Ji, Z.L., Chen, X., Chen, Y.Z., 2003. This suggests that SVMProt to some extent is capable of functional class assignment irrespective of sequence similarity and it is potentially useful for facilitating functional study of novel viral proteins. These include evolutionary analysis (Benner et al., 2000; Eisen, 1998) , hidden Markov models (Fujiwara and Asogawa, 2002) , structural consideration (Di Gennaro et al., 2001; Teichmann et al., 2001) , protein/gene fusion (Enright et al., 1999; Marcotte et al., 1999) , proteinprotein interactions (Bock and Gough, 2001) , motifs (Hodges and Tsai, 2002) , family classification by sequence clustering (Enright et al., 2002) , and functional family prediction by statistical learning methods (Cai et al., 2003 Han et al., 2004; Jensen et al., 2002; Karchin et al., 2002) . doi = 10.1016/j.virol.2004.10.020 id = cord-323072-4rsgeag7 author = Han, Xueqing title = The expression of SARS–CoV M gene in P. Pastoris and the diagnostic utility of the expression product date = 2004-12-01 keywords = SARS; protein summary = Since the outbreak of SARS in 2003, several laboratory diagnostic methods have been established, including real-time RT-PCR assay, whole-virus-based immunofluorescence assay (IFA), recombinant protein-based enzyme-linked immunosorbent assay (ELISA) and immunochromatographic tests, antigencapturing enzyme-linked immunosorbent assay, and Western blot (WB) assay. To test whether the recombinant M protein is effective as an ELISA antigen for detecting SARS-CoV patient serum, the sera from four healthy people and four SARS patients were used. Detection results of eight human sera by ELISA using purified recombinant M protein as antigen.# 1-4: sera from four healthy people, respectively, # 5-8: sera from four SARS patients, respectively. The results were in complete accordance with those of other assays, thus indicating that the recombinant M protein may be useful as an ELISA antigen for detecting specific antibodies to SARS-CoV in human sera. Recombinant protein-based enzyme-linked imunosorbent assay and immunochromatographic tests for detection of immunoglobulin G antibodies to severe acute respiratory syndrome (SARS) coronavirus in SARS patients doi = 10.1016/j.jviromet.2004.08.015 id = cord-307811-6e3j0pn7 author = Hao, Wei title = Binding of the SARS-CoV-2 Spike Protein to Glycans date = 2020-07-02 keywords = MERS; SARS; protein summary = Infection normally starts with the attachment of the virus to cell-surface glycans like heparan sulfate (HS) and sialic acid-containing oligosaccharides. Previous studies of many other viruses suggested that SARS-CoV-2 S protein may use other molecules on host cell surface as attachment factors to facilitate binding to the high-affinity receptor ACE2. 36 A recent study suggested that HS may bind to the receptor binding domain (RBD, the C-terminal region of the S1 subunit, Fig. 2 ) of the SARS-CoV-2 spike protein and change its conformation. 38 In this study, we systematically examined and compared the binding of the SARS-CoV-2 S protein subunits, full-length molecule and its trimer to different HS using microarray experiments (Fig. 2) . In addition to binding protein-based receptors, many viruses can interact with cell surface glycans, including GAGs and sialic acid-containing oligosaccharides. doi = 10.1101/2020.05.17.100537 id = cord-147565-mtdhdkc1 author = Harmalkar, Ameya title = Advances to tackle backbone flexibility in protein docking date = 2020-10-15 keywords = CAPRI; Protein; docking summary = doi = nan id = cord-329840-f3dsu36p author = Hati, Sanchita title = Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor date = 2020-05-11 keywords = ACE2; SARS; protein summary = In this study, the role of thiol-disulfide balance on the interactions between SARS-CoV/CoV-2 spike proteins and ACE2 was investigated using molecular dynamic simulations. The study revealed that the binding affinity was significantly impaired when all the disulfide bonds of both ACE2 and SARS-CoV/CoV-2 spike proteins were reduced to thiol groups. In the backdrop of significant mortality rate for SARS-CoV-2 (hereinafter referred to as CoV-2) infection, it is important to know if the thiol-disulfide balance plays any role on the binding of the spike glycoprotein on to the host cell receptor protein ACE2. Using these reported structures, molecular dynamics simulations and electrostatic field calculations were performed to explore the impact of thioldisulfide balance on CoV/CoV-2 and ACE2 binding affinities. The structural and dynamical changes due to the change in the redox states of cysteines in the interacting proteins were analyzed and their effects on binding free energies were studied. doi = 10.1101/2020.05.07.083147 id = cord-270594-62xotol3 author = He, Lei title = Identification and characterization of vp7 gene in Bombyx mori cytoplasmic polyhedrosis virus date = 2017-09-05 keywords = RNA; cell; protein; vp7 summary = In this study, the viral structural protein 7 (VP7) polyclonal antibody was prepared with immunized mouse to explore the presence of small VP7 gene-encoded proteins in Bombyx mori cytoplasmic polyhedrosis virus. The replication of BmCPV genome in the cultured cells and midgut of silkworm was decreased by reducing the expression level of vp7 gene using RNA interference. In immunoprecipitation experiments, using a polyclonal antiserum directed against the VP7, one additional shorter band in BmCPV infected midguts was detected, and then the band was analyzed with mass spectrum (MS), the MS results showed thatone candidate interacted protein (VP7 voltage-dependent anion-selective channel-like isoform, VDAC) was identified from silkworm. A novel protein was detected from the overexpression of vp7 gene in the BmCPV infected cultured cells, with VP7 antibody. Total proteins from the BmCPV infected silkworm midguts (from the first day to the twelfth day) were also extracted, and detected with VP7 antibody. doi = 10.1016/j.gene.2017.06.048 id = cord-002100-dt5zvebj author = He, Yonghua title = Transgenic Soybean Production of Bioactive Human Epidermal Growth Factor (EGF) date = 2016-06-17 keywords = EGF; EGFR; NEC; protein; seed; soybean summary = Phosphorylation and immunohistochemical assays on the EGF receptor in HeLa cells indicate the EGF protein produced in soybean seed is bioactive and comparable to commercially available human EGF. Epidermal growth factor protein from humans was produced in soybean seeds by constructing a plant gene expression cassette that involved a synthetic codon optimized EGF nucleotide sequence (protein sequence from Genbank accession CCQ43157). To assess the bioactivity of soybean-produced hEGF, samples were prepared from both ShEGF transgenic soybean lines and nontransgenic controls that were used to stimulate HeLa cells to induce EGFR internalization, degradation and phosphorylation. In contrast, samples prepared from control nontransgenic soybeans exhibited no apparent bioactivity showing the degradation and phosphorylation of EGFR is the result of EGF binding of either commercial rhEGF added to the media or from the hEGF produced by the transgenic soybeans. doi = 10.1371/journal.pone.0157034 id = cord-000182-ni6iyzdn author = He, Zhisong title = Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features date = 2010-03-11 keywords = Chou; drug; feature; protein summary = title: Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features Many researchers have made lots of efforts to develop useful algorithms and softwares to investigate various drug-related biological problems, such as HIV protease cleavage site prediction [18, 19] , identification of GPCR (G protein-coupled receptors) type [20, 21] , protein signal peptide prediction [22] , protein subcellular location prediction [23, 24, 25] , analysis of specificity of GalNAc-transferase protein [26] , identification of protease type [27, 28] , membrane protein type prediction [29, 30, 31, 32] , and a series of relevant webserver predictors as summarized in a recent review [33] . The drug-target benchmark datasets thus obtained for enzymes, ion-channels, GPCRs, and nuclear receptors are given in Online Supporting Information S1, S2, S3, and S4, respectively. Prediction of G-protein-coupled receptor classes based on the concept of Chou''s pseudo amino acid composition: an approach from discrete wavelet transform doi = 10.1371/journal.pone.0009603 id = cord-325282-20l9xcmg author = Helal, Mohamed A. title = Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia date = 2020-09-16 keywords = CD147; SARS; protein summary = title: Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia SARS-CoV-2 infects host cells via the interaction of its spike protein with the human angiotensin-converting enzyme 2 (hACE2) receptor. To understand the molecular basis of the potential interaction of SARS-CoV-2 to CD147, we have investigated the binding of the viral spike protein to this receptor in-silico. The entry of the virus into host cells is facilitated by binding of its transmembrane spike (S) protein with angiotensin-converting enzyme 2 (ACE-2) receptor (Hoffmann et al., 2020) . To understand the mechanism of interaction of the SARS-CoV-2 spike protein with the CD147 receptor, we have performed a four-stage in-silico study. The recently reported crystal structure of SARS-Cov-2 spike protein complex with ACE2 (PDB ID: 6LZG) reveals that the virus utilizes the external subdomain of the spike Receptor Binding Domain (RBD) to recognize the human ACE2 receptor . doi = 10.1080/07391102.2020.1822208 id = cord-316258-7hucqcaj author = Henriques, Elsa S title = Modeling of the Toll-like receptor 3 and a putative Toll-like receptor 3 antagonist encoded by the African swine fever virus date = 2011-01-28 keywords = ASFV; TLR3; protein summary = A recently identified novel ASFV viral protein (pI329L) was found to inhibit the Toll-like receptor 3 (TLR3) signaling pathway, TLR3 being a crucial "danger detector." pI329L has been predicted to be a transmembrane protein containing extracellular putative leucine-rich repeats similar to TLR3, suggesting that pI329L might act as a TLR3 decoy. As this later domain shares only remote sequence relationships with the available TLR3 templates, a more complex modeling strategy was employed that combines the iterative implementation of (multi)threading/assembly/refinement (I-TASSER) structural prediction with expertise-guided posterior refinement. On dimerization subsequent to recognition of dsRNA, TLR3 recruits the adaptor protein Toll-interleukin-1 receptor (TIR)-domain-containing adapter-inducing interferon-b (TRIF) to its cytoplasmic domain, thereby initiating a signaling cascade that results in the secretion of type I interferons and other inflammatory cytokines. doi = 10.1002/pro.554 id = cord-001726-d7iwkatn author = Henry, Kevin A. title = Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold date = 2015-08-04 keywords = M13; antibody; display; filamentous; peptide; phage; protein summary = Particular emphases are placed on: (i) the advantages of the phage as a vaccine carrier, including its high immunogenicity, relative antigenic simplicity and ability to activate a range of immune responses, (ii) the phage''s potential as a prophylactic and therapeutic agent for infectious and chronic diseases, (iii) the regularity of the virion major coat protein lattice, which enables a variety of bioconjugation and surface chemistry applications, particularly in nanomaterials, and (iv) the phage''s large population sizes and fast generation times, which make it an excellent model system for directed protein evolution. While in some cases the results of these studies have been promising, antibody epitope-based peptide vaccines are no longer an area of active research for several reasons: (i) in many cases, peptides incompletely or inadequately mimic epitopes on folded proteins (Irving et al., 2010 ; see below); (ii) antibodies against a single epitope may be of limited utility, especially for highly variable pathogens (Van Regenmortel, 2012); and (iii) for pathogens for which protective immune responses are generated efficiently during natural infection, peptide vaccines offer few advantages over recombinant subunit and live vector vaccines, which have become easier to produce over time. doi = 10.3389/fmicb.2015.00755 id = cord-254107-02bik024 author = Hillisch, Alexander title = Utility of homology models in the drug discovery process date = 2004-08-31 keywords = homology; model; protein; structure summary = The quality of these homology models, and thus their applicability to, for example, drug discovery, predominantly depends on the sequence similarity between the protein of known structure (template) and the protein to be modeled (target). In conjunction with homology models, Cengent Therapeutics (http://www.cengent.com) offers dynamic structural information generated from molecular dynamics simulations for 5500 human drug target proteins. If sequence identity is greater than ~50%, the resulting models are frequently of sufficient quality to be used in the prediction of detailed protein-ligand interactions, such as structure-based drug design and prediction of the preferred sites of metabolism of small molecules ( Figure 2 ). It has recently been shown that it is possible to design small molecules based on homology models and then to use these compounds as tools to study the physiological role of the respective target protein of that particular drug [31] . doi = 10.1016/s1359-6446(04)03196-4 id = cord-296928-wu14k7u9 author = Hofmann, Tim title = Greatest Hits—Innovative Technologies for High Throughput Identification of Bispecific Antibodies date = 2020-09-08 keywords = antibody; bispecific; cell; protein; screening summary = doi = 10.3390/ijms21186551 id = cord-000979-cav9n18w author = Hoppe, Sebastian title = Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni date = 2013-05-29 keywords = Campylobacter; PCR; RNA; protein summary = doi = 10.1371/journal.pone.0065837 id = cord-001435-ebl8yc92 author = Hoppe, Sebastian title = Identification of Antigenic Proteins of the Nosocomial Pathogen Klebsiella pneumoniae date = 2014-10-21 keywords = A.U.; KPN_00363; PCR; antibody; protein summary = Hence, a cDNA-based expression library was constructed and screened via microarrays to detect novel antigens of Klebsiella pneumoniae, a prominent agent of nosocomial infections well-known for its extensive antibiotics resistance, especially by extended-spectrum beta-lactamases (ESBL). After specificity analysis, homology survey and 3d structural modelling, one epitope sequence GAVVALSTTFA of KPN_00363, an ion channel protein, was identified harboring specificity for K. By identifying several novel antigens and their linear epitope sites, we have paved the way for crucial future research and applications including the design of point-of-care devices, vaccine development and serological screenings for a highly relevant nosocomial pathogen. Incubation with antibodies reactive to either of those two bacterial species resulted in signal intensities in the neighbourhood of the negative control independent of sequence alterations, see Figure 11 . In contrast, the other two proteins displaying linear epitopes, KPN_00363 and KPN_00459, indicated some specificity with the antibodies tested and two linear consensus sequences could be derived, GAVVALSTTFA and GIAFGAVELFD, respectively. doi = 10.1371/journal.pone.0110703 id = cord-261375-6fu3dzi9 author = Hoppe, Sebastian title = Microarray-based method for screening of immunogenic proteins from bacteria date = 2012-03-21 keywords = Campylobacter; KRX; Promega; immunogenic; protein summary = Screening of expression libraries to expose novel antigens from bacteria often lead to an abundance of false positive signals owing to the high cross reactivity of polyclonal antibodies towards the proteins of the expression host. In this paper, we describe a method to covalently attach different HaloTag ® fusion proteins on HaloLink™ slides (see Figure 1 ) and consequently perform an immunoscreening using polyclonal antibodies in a microarray format, which is a suitable method for high-throughput applications such as screening of entire expression libraries (see Figure 2 ). Using our new method, we were able to express, immobilize and screen all of nine different proteins from Campylobacter jejuni using HaloTag ® and KRX cells. We were able to clone several genes from Campylobacter jejuni into KRX cells, to express the respective proteins as fusion constructs with a HaloTag ® attached to their N-Terminus and to immobilize these proteins on microarray surfaces. doi = 10.1186/1477-3155-10-12 id = cord-010776-ura14oci author = Hosseini, Elahe Seyed title = Optimization and One-Step Purification of Recombinant V Antigen Production from Yersinia pestis date = 2020-01-02 keywords = CBD; protein summary = doi = 10.1007/s12033-019-00234-x id = cord-314039-qkrmxvaj author = Houdebine, Louis-Marie title = Production of pharmaceutical proteins by transgenic animals date = 2008-02-19 keywords = protein; recombinant; transgenic summary = Interestingly, genetically modified yeast expressing foreign genes coding for enzymes responsible for glycosylation proved able to secrete substantial amounts of recombinant proteins having carbohydrates almost similar to those found in human proteins [1] . Transgenic animals offer particularly attractive possibilities to prepare recombinant pharmaceutical proteins. Ruminants are potentially the most appropriate species to produce large amount of proteins but they need cloning or lentiviral vectors to integrate foreign genes, their reproduction is relatively slow, they do not glycosylate proteins as well as rabbits and pigs and they are sensitive to prion diseases (Tables 3 and 4) . The recombinant protein ATryn (human antithrombinIII) produced in goat milk contains less sialic acid than its native counterpart is a case in point [29] . The two major animal systems to produce pharmaceutical proteins in milk and egg white have recently been technically improved and their use as an essential source of new medicaments has become very likely. doi = 10.1016/j.cimid.2007.11.005 id = cord-264996-og3sg0qw author = Howell, Gareth J. title = Cell Biology of Membrane Trafficking in Human Disease date = 2006-09-17 keywords = COPII; Golgi; TGN; cell; disease; gene; membrane; protein; snare; transport; vesicle summary = Many of these transport intermediates or vesicles, whether derived from the ER, other internal organelles, or the plasma membrane, are ''''coated'''' with unique protein complexes, tethering factors, and regulatory factors that ensure correct targeting to an acceptor compartment. Breast cancer Caveolin-1 Deletion or dominant negative mutation of caveolin-1 promotes tumor progression Breast cancer (Bouras et al., 2004; Williams and Lisanti, 2005) (Hayasaka et al., 1993; Matsuyama et al., 2002) Chediak-Higashi syndrome (CHS) CHS1/Lyst Lyst involved in regulation of protein secretion from lysosomes -enlarged lysosomes Partial albinism, recurrent bacterial infections, impaired chemotaxis and abnormal natural killer cell function (Shiflett et al., 2002; Ward et al., 2003) 214500 Choroideremia (CHM) Rab Escort Protein 1 (REP1) RAB27a remains cytosolic due to defective geranylgeranyl modification in CHM lymphoblasts X-linked form of retinal degeneration 303100 Various mechanisms control the traYcking of proteins from the TGN by the formation and delivery of membrane-derived transport vesicles to the plasma membrane, endosomes, or lysosomal structures (Ponnambalam and Baldwin, 2003) . doi = 10.1016/s0074-7696(06)52005-4 id = cord-262585-5vjqrnwh author = Hraber, Peter title = Resources to Discover and Use Short Linear Motifs in Viral Proteins date = 2019-08-16 keywords = ELM; host; motif; protein; viral summary = doi = 10.1016/j.tibtech.2019.07.004 id = cord-001898-ntqyjqqk author = Huang, Chih-Wei title = Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly date = 2016-01-05 keywords = Fig; K315A; protein summary = The changes in tryptophan fluorescence were Dilution of monomeric K315A mutant protein denatured in 5 M GdmCl resulted in refolding to a similar conformation as the original monomeric state (Fig 5A and 5B) . Since refolding of partly unfolded monomeric mutant δ-crystallin resulted in a conformation with high exposure of hydrophobic regions, the occurrence of protein aggregation in the process was determined using light scattering measurement. An increase in fluorescence intensity resulting from binding of ThT with the aggregates over time was observed following dilution of 0.84 and 3 M GdmCl denatured monomeric mutant δ-crystallin into buffer (Fig 6B) . The unique stable conformation from unfolding of K315A mutant protein in the presence of urea suggests that the interactions provided by this residue at the interfaces may play a critical role in stabilization of the quaternary structure of δ-crystallin. doi = 10.1371/journal.pone.0145957 id = cord-319291-6l688krc author = Hung, Chun-Min title = Alignment using genetic programming with causal trees for identification of protein functions date = 2006-09-01 keywords = function; model; node; protein summary = Particularly, the model has three characteristics: (i) it is a hybrid evolutionary model with multiple fitness functions that uses genetic programming to predict protein functions on a distantly related protein family, (ii) it incorporates modified robust point matching to accurately compare all feature points using the moment invariant and thin-plate spline theorems, and (iii) the hierarchical homologies holding up a novel protein sequence in the form of a causal tree can effectively demonstrate the relationship between proteins. The hybrid model, namely Alignment using Genetic programming with Causal Tree (AGCT), is a heuristic evolutionary method that contains three basic components: (i) genetic programming with innerexchanged individual strategy, (ii) causal trees [4, 28, 31] with probabilistic reasoning, and (iii) construction of hierarchical homologies with local block-to-block alignment using the methods of moment invariant and robust points matching (RPM) [24] . doi = 10.1016/j.na.2005.09.048 id = cord-013178-li1x1m25 author = Hung, Ling-Chu title = The Monoclonal Antibody Recognized the Open Reading Frame Protein in Porcine Circovirus Type 2-Infected Peripheral Blood Mononuclear Cells date = 2020-08-29 keywords = ORF3; PCV2; USA; figure; protein summary = doi = 10.3390/v12090961 id = cord-308043-h0knm8y4 author = Hussey, Séamus title = Autophagy as an emerging dimension to adaptive and innate immunity date = 2009-08-31 keywords = Beclin-1; MHC; autophagy; cell; protein summary = These lines of evidence suggest a more elaborate TLR control of autophagy whereby TLR-adapter molecules interact with proteins from the autophagic pathway rather than by simply activating the classic hierarchical signaling cascades described heretofore. The authors demonstrated that the Atg5-Atg12 conjugate negatively regulates the antiviral immune response by interacting with the RIG-I-like receptor (s protein retinoic acid-inducible gene I (RIG-I) and IFN-␤ promoter stimulator 1 (IPS-1) thus, implying autophagy contributes to viral replication. In another study, the same group demonstrated that the fusion of influenza matrix protein 1 (MP1) with Atg8/LC3 drives this molecule to autophagosomes in different cell types and enhances recognition by antigen specific CD4+ T cells [117] . Accordingly, Atg6 silencing dampened this process, while rapamycin treatment enhanced priming of 85B-specific CD4 + T cells, strongly suggesting a role for autophagy in MHC class II presentation of antigens of bacterial origin. doi = 10.1016/j.smim.2009.05.004 id = cord-322231-jltk42dt author = Huy, Nguyen-Xuan title = Immunogenicity of an S1D epitope from porcine epidemic diarrhea virus and cholera toxin B subunit fusion protein transiently expressed in infiltrated Nicotiana benthamiana leaves date = 2016-08-23 keywords = CTB; Fig; protein; s1d summary = title: Immunogenicity of an S1D epitope from porcine epidemic diarrhea virus and cholera toxin B subunit fusion protein transiently expressed in infiltrated Nicotiana benthamiana leaves After oral administration of transiently expressed CTB–S1D fusion protein, or with bacterial cholera toxin or rice callus expressing mutant cholera toxin 61F, mice exhibited significantly greater serum IgG and sIgA levels against bacterial CTB and S1D antigen, peaking at week 6. For feeding immunization, the mice were fasted 8 h before gavage with 2.0 mL of PBS buffer pH 7.0 containing lyophilized leaf powder, which harbored 100 µg of CTB-S1D fusion protein, or with bacterial cholera toxin-bCT (Sigma) or rice callus-expressed mutant cholera toxin 61 F (Arg to Phe)-rCTX and wild-type (WT) N. Oral immunization with transient expression CTB-S1D fusion protein induced significantly higher anti-CTB, anti-S1D IgG and sIgA levels compared with the control group (Fig. 7 ). doi = 10.1007/s11240-016-1059-5 id = cord-259260-qcfgigga author = Ibrahim, Ibrahim M. title = GRP78: A cell''s response to stress date = 2019-06-01 keywords = GRP78; cancer; cell; protein; virus summary = GRP78 expression is increased in cases of ER stressors like when the cell is abridged from sugar, treated with reagents that inhibit the process of protein glycosylation or disturb the intercellular calcium storage [5] . In the standard conditions of balance in the cell (homeostasis) GRP78 is bounded in an inactive form to Activating transcription factor 6 (ATF6), protein kinase RNA-like endoplasmic reticulum kinase (PERK), and Inositol-requiring enzyme 1 (IRE1) which are UPR transmembrane stress sensors. According to the ligand or the peptide that bind to CS-GRP78, it will be activated in a defined signaling pathway that affects Besides, if the cell is cancerous, CS GRP78 will induce resistance to chemotherapy. Glucose regulated protein 78 (GRP78) inhibits apoptosis and attentinutes chemosensitivity of gemcitabine in breast cancer cell via AKT/mitochondrial apoptotic pathway De-regulation of GRP stress protein expression in human breast cancer cell lines Kringle 5 of human plasminogen induces apoptosis of endothelial and tumor cells through surface-expressed glucose-regulated protein 78 doi = 10.1016/j.lfs.2019.04.022 id = cord-312996-qzu8pkyt author = Iles, R. K. title = A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work. date = 2020-08-22 keywords = MALDI; PCR; SARS; protein summary = Testing limitations, including reagent shortages, remain a bottleneck in the battle to curtail COVID-19 spread in even the wealthiest countries [1, 2] The development of new matrix assisted laser desorption time of flight mass spectrometry (MALDI-ToF MS) diagnostics for SARS-CoV-2 detection is driven by the need for greater diagnostic capacity and alternative applications to complement standard PCR and antibody based diagnostics. Consequently studies where swab samples have been split for simultaneous analysis by RT PCR detection systems of SARS-CoV-2 RNA and by MALDI-ToF mass spectrometry for viral proteins, are compromised [4] . virus grown in vitro and mass spectra of gargle/saliva spiked with culture media from cells infected with SARS-CoV-2: S proteolytic fragments S1 and S2 were seen in all preparations and S2b only in serum free samples. These confirmed PCR-negative gargle samples were analysed by MALDI-ToF mass spectrometry 40 times; the measured peak intensities of which acted as comparative controls to the viral spiked saliva/gargle. doi = 10.1101/2020.08.22.20176669 id = cord-268239-neb6xxlf author = Illiano, Anna title = Protein Glycosylation Investigated by Mass Spectrometry: An Overview date = 2020-08-28 keywords = MRM; cell; figure; glycan; glycosylation; protein summary = For example, the alanine-proline-rich antigen (Apa) glycoprotein, expressed on the cell surface of different Mycobacteria species, induced glycan-specific T-cell response, whereas the non-glycosylated form of the same protein in Escherichia coli showed reduced stimulation of the CD4 + T-cell system compared to the native antigen, giving evidence of the crucial involvement of glycosylation in T-cell activation by Apa during infection [42] . Technological breakthroughs in mass spectrometric analysis for specific glycan epitopes provide a more molecular approach to examine potential changes in glycosylation or to display a sufficient degree of alteration in glycosylation, as mixtures of commonly occurring glycosylation patterns associated with normal cells or tumor-associated signals [82, 84] . doi = 10.3390/cells9091986 id = cord-315984-5gbhobw8 author = Isaacson, Marisa K. title = Ubiquitination, Ubiquitin-like Modifiers, and Deubiquitination in Viral Infection date = 2009-06-18 keywords = ICP0; protein; ubiquitin summary = HPV infection also leads to degradation of the retinoblastoma protein pRb through the ubiquitin-proteasome pathway (reviewed in Mammas et al., 2008) , mediated via the HPV E7-protein-induced generation of an E3 ligase complex consisting of the Cullin2 Processed ubiquitin (Ub) or ubiquitin-like modifier (Ubl) is activated with ATP by an E1 ubiquitin-activating enzyme (1) and then transferred to an E2 ubiquitin-conjugating enzyme (2). Herpes simplex virus 1 (HSV-1) infected cell protein 0 (ICP0) is a E3 ubiquitin ligase that induces polyubiquitination and degradation of a variety of proteins, including the promyelocytic leukemia (PML) protein, Sp100 (another component of PML nuclear bodies) (Chelbi-Alix and de Boutell et al., 2002) , cyclin D3 (Van Sant et al., 2001; Hagglund et al., 2002) , p53, and the cellular deubiquitinating enzyme USP7. doi = 10.1016/j.chom.2009.05.012 id = cord-304616-k92fa15l author = Izes, Aaron M. title = Assay validation and determination of in vitro binding of mefloquine to plasma proteins from clinically normal and FIP-affected cats date = 2020-08-05 keywords = fip; mefloquine; plasma; protein summary = title: Assay validation and determination of in vitro binding of mefloquine to plasma proteins from clinically normal and FIP-affected cats As cats with feline infectious peritonitis (FIP) demonstrate altered concentrations of plasma proteins, the proportion of mefloquine binding to plasma proteins in both clinically normal cats and FIP-affected cats was also investigated. Consequently, the aim of this study was two-fold: first, to develop and validate a high pressure liquid chromatography (HPLC) method to detect mefloquine in feline plasma, and second, to determine the in vitro plasma protein binding of mefloquine in both clinically normal and FIP-affected cats. Here, although a significant difference was found between the plasma protein binding of mefloquine in clinically normal and FIP-affected cats, due to the unknown biological variability of the assay, it is likely that this difference is equivocal. This study has validated an accurate and reliable assay to detect mefloquine in feline plasma and demonstrated that mefloquine is highly plasma protein bound in both clinically normal and FIP-affected cats. doi = 10.1371/journal.pone.0236754 id = cord-002711-b7mlt19n author = Jacomin, Anne-Claire title = iLIR@viral: A web resource for LIR motif-containing proteins in viruses date = 2017-08-14 keywords = LIR; autophagy; motif; protein summary = doi = 10.1080/15548627.2017.1356978 id = cord-256047-mabrmzd9 author = Jacomin, Anne-Claire title = Deubiquitinating Enzymes Related to Autophagy: New Therapeutic Opportunities? date = 2018-08-19 keywords = Beclin1; USP30; USP8; autophagy; protein; ubiquitin summary = doi = 10.3390/cells7080112 id = cord-328483-sj8i9ss2 author = Jaegle, Mike title = Protein‐Templated Fragment Ligations—From Molecular Recognition to Drug Discovery date = 2017-05-31 keywords = figure; fragment; ligation; protein; reaction; templated summary = Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") utilizing aproteinss urface as areaction vessel to catalyzethe formation of aprotein ligand with increased binding affinity.T he approache xploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations.Inthis way, chemical synthesis and bioassayare integrated in one single step.T his Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products.T he chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed. doi = 10.1002/anie.201610372 id = cord-350423-yaeduwvb author = James, Claire D. title = Viral Interactions with PDZ Domain-Containing Proteins—An Oncogenic Trait? date = 2016-01-18 keywords = DLG1; PBM; PDZ; cell; protein summary = Many of the human viruses with oncogenic capabilities, either in their natural host or in experimental systems (hepatitis B and C, human T cell leukaemia virus type 1, Kaposi sarcoma herpesvirus, human immunodeficiency virus, high-risk human papillomaviruses and adenovirus type 9), encode in their limited genome the ability to target cellular proteins containing PSD95/ DLG/ZO-1 (PDZ) interaction modules. Survival of rabies infected neuronal cells is associated with the ability of the viral envelope G protein to interact with the PDZ domain-containing serine threonine kinase MAST2, leading to the disruption of the MAST2-PTEN complex that is intimately involved in the inhibition of neuronal survival [11] . Therefore, in HPV infections the tumour suppressor forms of DLG that are involved in the negative regulation of cell proliferation might be the initial target of the E6 PBM, but during disease progression DLG1, either through mislocalization and/or the stabilization of specific pools, acquires oncogenic functions mediated by interaction with E6 [3, 127] . doi = 10.3390/pathogens5010008 id = cord-308641-vqiipbo8 author = Jankauskaitė, Justina title = SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation date = 2019-02-01 keywords = SKEMPI; protein summary = Once the checks are passed, the data is collected, including the PDB file, the chains of the interacting subunits, the mutation, the wild-type and mutant affinities (K D , M), the reference, the names of the proteins, the temperature at which the experiment is performed (T, K), the experimental method used (an extension of the category scheme of Geng et al., 2016) , notes on the entry and, when available, the association rate (k on ; M À1 s À1 ), dissociation rate (k off ; s À1 ), enthalpy (DH; kcal:mol À1 ) and entropy (DS; cal:mol À1 :K À1 ). doi = 10.1093/bioinformatics/bty635 id = cord-346314-o9fjpqaj author = Jarboui, Mohamed Ali title = Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus date = 2012-11-15 keywords = HIV-1; Jurkat; RNA; Tat; cell; figure; nucleolar; protein summary = Pathway analysis and network reconstruction revealed that Tat expression specifically resulted in the nucleolar enrichment of proteins collectively participating in ribosomal biogenesis, protein homeostasis, metabolic pathways including glycolytic, pentose phosphate, nucleotides and amino acids biosynthetic pathways, stress response, T-cell signaling pathways and genome integrity. Following the detailed annotation of the quantitative abundance changes in the nucleolar protein composition upon Tat expression, we focussed on the Tat-affected cellular complexes and signalling pathways associated with ribosome biogenesis, spliceosome, molecular chaperones, DNA replication and repair and metabolism and discuss their potential involvement in HIV-1 pathogenesis. In this study, we investigated the quantitative changes in the nucleolar proteome of Jurkat T cells constitutively expressing HIV-1 Tat (86aa) versus their Tat-negative counterpart, using stable isotope labelling with amino acids in cell culture (SILAC) technology, followed by ESI tandem mass spectrometry and implemented the experimental approach described in Figure 1A . doi = 10.1371/journal.pone.0048702 id = cord-021500-sy6lnt7b author = Jean Harry, G. title = Myelination, Dysmyelination, and Demyelination date = 2007-05-09 keywords = CNS; MBP; PLP; PNS; Schwann; cell; myelin; protein summary = The size of the fibers and the thickness of the sheaths are very different in the PNS and the CNS, but the overall surface area of myelin generated by an oligodendrocyte around multiple axons may be no larger than that formed by a Schwann cell around a single internode. Myelinating Schwann cells progress through a proliferative "premyelinating" stage, characterized by transient expression of suppressed cAMP-inducible Pou-domain transcription factor (SCIP), followed by a "promyelinating" GalC-positive stage, becoming associated with a single axon in the process. Members of the NDF growth factor family, including glial growth factor (GGF), heregulin, acetylcholine-inducing activity (ARIA), and neuregulin, are alternatively spliced products of a single gene, and these molecules are emerging as important regulators of Schwann cell lineage development (Dong et aL, 1995; Zorick and Lemke, 1996) . doi = 10.1016/b978-012648860-9.50007-8 id = cord-283096-qm7h4qui author = Jeon, Young Joo title = ISG15 and immune diseases date = 2010-02-12 keywords = IFN; ISG15; UBP43; protein; rig; ube1l summary = Some of them are type I IFN-induced proteins, such as PKR and RIG-I, and some are the key regulators that are involved in IFN signaling, such as JAK1 and STAT1, implicating the role of ISG15 and its conjugates in type I IFN-mediated innate immune responses. Viral infection also strongly induces ISG15 [18, 19] because one of its major host responses is the production of type I IFNs. A number of proteins that are involved in antiviral signaling pathways, including RIG-I, MDA-5, Mx1, PKR, STAT1, and JAK1, have been identified as target proteins for ISGylation. Swiss 3T3 cells expressing constitutively active MKK7-JNK1β fusion protein show increased resistance to apoptosis induced by vesicular stomatitis virus (VSV) infection, suggesting the involvement of JNK signaling pathway in antiviral response. acid seems to elevate the levels of ISG15 and its conjugates by stimulating cells to secrete IFNs. UBE1L is a 112-kDa protein that shows a 45% identity in amino acid sequence to the human ubiquitin-activating E1 enzyme (UBE1) [73] . doi = 10.1016/j.bbadis.2010.02.006 id = cord-332344-upsn0zb4 author = Jeswin, Joseph title = Proteomic analysis by iTRAQ in red claw crayfish, Cherax quadricarinatus, hematopoietic tissue cells post white spot syndrome virus infection date = 2016-02-01 keywords = Hpt; WSSV; hpi; infection; protein summary = To elucidate proteomic changes of Hpt cells from red claw crayfish, Cherax quadricarinatus, we have carried out isobaric tags for relative and absolute quantitation (iTRAQ) of cellular proteins at both early (1 hpi) and late stage (12 hpi) post white spot syndrome virus (WSSV) infection. Generally, these differentially expressed proteins include: 1) the metabolic process related proteins in glycolysis and glucogenesis, DNA replication, nucleotide/amino acid/fatty acid metabolism and protein biosynthesis; 2) the signal transduction related proteins like small GTPases, G-protein-alpha stimulatory subunit, proteins bearing PDZor 14-3-3-domains that help holding together and organize signaling complexes, casein kinase I and proteins of the MAP-kinase signal transduction pathway; 3) the immune defense related proteins such as α-2 macroglobulin, transglutaminase and trans-activation response RNA-binding protein 1. To further identify proteins or pathways altered during viral infection, here we report proteomic responses of crayfish Hpt cells by iTRAQ at both early (1 hpi) and late (12 hpi) stages post WSSV infection accordingly. doi = 10.1016/j.fsi.2016.01.035 id = cord-286217-3uklf2u2 author = Jiang, He-wei title = SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses date = 2020-07-14 keywords = Fig; SARS; Supplementary; protein summary = Here we construct a SARS-CoV-2 proteome microarray containing 18 out of the 28 predicted proteins and apply it to the characterization of the IgG and IgM antibodies responses in the sera from 29 convalescent patients. We detected the SARS-CoV-2-specific IgG and IgM proteins bound to the array using fluorescent-labeled anti-human antibodies, thereby generating a global assessment of each patient''s humoral antibody response. All of the samples and the controls were probed on the proteome microarray, and after data filtering and normalization, we constructed the IgG and IgM profile for each serum and performed clustering analysis to generate heatmaps (Figs. To statistically analyze the IgG responses against SARS-CoV-2 proteins, we calculated the p-values followed by multiple testing correction (or q-values), and applied significant analysis of microarray (SAM) to identify significant positive proteins (Supplementary Fig. 7 and Data 2). doi = 10.1038/s41467-020-17488-8 id = cord-298759-j965t808 author = Jiang, Nan title = Development of a robust Escherichia coli-based cell-free protein synthesis application platform date = 2020-10-17 keywords = CFPS; cell; protein summary = The Escherichia coli-based system was chosen in this study, and the model protein deGFP was expressed to explore a more efficient cell-free system. To overcome these problems, cell-free protein synthesis (CFPS) has received new attention as an emerging synthetic biology technology, because it is an open system, not limited by cell growth or cell membrane, and it allows the use of various reaction formats. The selection of extracts, the size of the plasmid, the molecular crowding effect and the metal ion J o u r n a l P r e -p r o o f effect, which are important component parameters, were explored to improve the protein expression efficiency. Based on the optimized CFPS systems, the cell-free fundamental scientific research platform, primary screening platform, and portable biomolecular synthesis platform were established. Therefore, researchers need to optimize the metal ions and the corresponding concentration for the best cell-free protein synthesis. doi = 10.1016/j.bej.2020.107830 id = cord-001093-5l0fthw3 author = Jin, Fan title = Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins date = 2013-10-03 keywords = 10074-a4; Myc; figure; protein summary = doi = 10.1371/journal.pcbi.1003249 id = cord-279586-likfvwwj author = Jin, Jian title = Effects of Sonication on the In vitro Digestibility and Structural Properties of Buckwheat Protein Isolates date = 2020-09-17 keywords = SA6T10; effect; protein; sonication summary = The present work investigated the effects of sonication at different amplitudes and durations on the in vitro digestibility of buckwheat protein isolates (BPIs). The tertiary structure analysis showed that sonication exposed the hydrophobic core buried inside the protein molecules and broke the intramolecular crosslinks, based on the increase in the surface hydrophobicity and intrinsic fluorescence and the decrease in the disulphide content. Therefore, this study was aimed at investigating the effects of sonication duration and acoustic amplitude on the in vitro digestibility of buckwheat protein isolates (BPIs). In addition, the effects of sonication on the tertiary structures (surface hydrophobicity, intrinsic fluorescence, sulfhydryl and disulfide bond contents), secondary structure, particle size, zeta-potential and microstructure of BPIs were studied to elucidate the structural mechanism underlying the effect of ultrasound on the digestibility of the proteins. doi = 10.1016/j.ultsonch.2020.105348 id = cord-301128-woe6knpv author = Joyeux, Marc title = Requirements for DNA-bridging proteins to act as topological barriers of the bacterial genome date = 2020-08-12 keywords = Fig; dna; protein summary = The results presented in this article reveal that the formation of DNA loops is by no means sufficient to create topologically independent domains and that DNA-bridging proteins must exert rather strong constraints on their binding sites in order to act as topological barriers: They must block the diffusion of the excess of twist through both binding sites and must additionally block the rotation of one DNA segment relative to the other one. We report below on our efforts to determine the minimal set of mandatory properties that allow molecular bridges to act as topological barriers and block the diffusion of torsional stress in out-of-equilibrium supercoiled chains. Since DNAbridging proteins form DNA loops by dynamically cross-linking widely separated DNA sites, the question amounts here to determine the constraints that must be imposed to beads α and β J o u r n a l P r e -p r o o f to divide the circular DNA chain into two topologically independent loops. doi = 10.1016/j.bpj.2020.08.004 id = cord-295381-0dqu3p3y author = Kamal, Adeela title = Therapeutic and diagnostic implications of Hsp90 activation date = 2004-06-01 keywords = ATP; Hsp90; cell; protein summary = Recent work has identified the role of Hsp90 in multiple signal transduction pathways and revealed that the molecular mechanism of tumor selectivity by Hsp90 inhibitors is the result of an activated, high-affinity conformation of Hsp90 in tumors. A recent study reported that the Hsp90 in tumor cells is maintained in an activated conformation by the formation of multi-chaperone complexes that have increased ATPase activity and 100-fold greater binding affinity for 17-AAG compared with the uncomplexed, latent form of Hsp90 that is present in normal cells [28] . A model for Hsp90-dependent malignant progression has been proposed in which, as tumor cells gradually accumulate mutant and overexpressed signaling proteins, Hsp90 becomes engaged in the active chaperoning and stabilization of oncoproteins and adopts a high-affinity form that is induced by bound co-chaperone proteins ( Figure 3 ) [28] . FLT3 expressing leukemias are selectively sensitive to inhibitors of the molecular chaperone heat shock protein 90 through destabilization of signal transduction-associated kinases doi = 10.1016/j.molmed.2004.04.006 id = cord-338468-c0jv3i1t author = Kanduc, Darja title = From Anti-SARS-CoV-2 Immune Responses to COVID-19 via Molecular Mimicry date = 2020-07-16 keywords = CoV-2; SARS; hexapeptide; human; protein summary = Results: Immunoreactive epitopes present in SARS-CoV-2 were mostly composed of peptide sequences present in human proteins that—when altered, mutated, deficient or, however, improperly functioning—may associate with a wide range of disorders, from respiratory distress to multiple organ failure. In the wake of such results, in order to validate (or, as well, invalidate) the cross-reactivity hypothesis, investigation was expanded here by analyzing the peptide sharing between the human host and immunoreactive epitopes that are also present in SARS-CoV-2. Table 2 documents that numerous immunoreactive SARS-CoV-2 epitopes are composed mostly or, in many instances, uniquely of peptide sequences shared with human proteins. This study shows that hexapeptides from immunoreactive epitopes present in SARS-CoV-2 are widespread among a high number of human proteins. Table S2 : Hexapeptide sharing between 233 epitopes present in SARS-CoV-2 and human proteins. Table S3 : List and short description of 460 human proteins that share hexapeptides with the 233 SARS-CoV-2 epitopes. doi = 10.3390/antib9030033 id = cord-322955-7dw32xby author = Kathwate, Gunderao H title = In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins date = 2020-06-12 keywords = SARS; cell; epitope; protein; vaccine summary = title: In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins Designed vaccine was rich in effective BCR and TCR epitopes screened from the sequence of S-protein of SARS-CoV2. Those properties are calculated by different methods at IEDB server (http://tools.iedb.org/bcell/ )like Kolaskar-Tongaonkar antigenicity scale provide physiology of the amino acid residues(45), Emini Surface accessible score for accessible surface of the epitope(46), Secondary structure of epitopes also has role in antigenicity. High scored and common peptides predicted by various tools were selected for deriving sequence of potential vaccine candidate. We designed a multi-epitopes vaccine construct from S-protein of SARS-CoV2. From various epitopes predicted by the online server based on common sequence and high score three TCR and two BCR epitopes were selected as part of COVID19 vaccine. This vaccine codes epitopes form S protein of SARS-CoV2 virus for T and B cell receptors. doi = 10.1101/2020.06.03.131755 id = cord-272268-8vrcwwll author = Kedersha, Nancy title = Chapter 4 Regulation of Translation by Stress Granules and Processing Bodies date = 2009-10-27 keywords = RNA; TIA-1; protein; stress summary = Cytoplasmic stress granules (SGs) and processing bodies (PBs) are dynamic structures that form in response to stress-induced translational arrest. Critical components of the ''''cell biology'''' of protein translation are mRNP granules known as processing bodies (PBs) and stress granules (SGs). These transient cytoplasmic ''''structures'''' are actively assembled from untranslated mRNA by a host of RNA-binding proteins, which determine whether specific transcripts will be reinitiated, degraded, or stored. In 1999, it was noted that stress-induced translational arrest causes untranslated mRNPs to assemble into large cytoplasmic ''''SGs,'''' whose formation is triggered by, and dependent upon, the phosphorylation of eIF2a. Virus infection also induces the assembly of SGs and PBs suggesting that RNA granules play a role in reprogramming mRNA translation/decay during viral infection. RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2a to the assembly of mammalian stress granules doi = 10.1016/s1877-1173(09)90004-7 id = cord-291727-4wfhuvww author = Ketteler, Robin title = On programmed ribosomal frameshifting: the alternative proteomes date = 2012-11-19 keywords = RNA; frame; protein summary = doi = 10.3389/fgene.2012.00242 id = cord-346819-11fkgzaa author = Khan, Mohd Imran title = Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight date = 2020-09-03 keywords = CoV-2; Mpro; SARS; protein summary = title: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight A novel severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) causing COVID-19 pandemic in humans, recently emerged and has exported in more than 200 countries as a result of rapid spread. Main protease (Mpro), the therapeutic target protein of SARS with maximum reported inhibitors, was thoroughly investigated and the effect of mutation on the binding affinity and structural dynamics of Mpro was studied. The genome analysis of the SARS-CoV-2 strains from 13 different countries showed a large number of mutations within the major structural proteins. This study provides a deeper insight into the emergence of these mutations within the major structural as well as nsp encoded by the SARS-CoV-2 genome from different countries. Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations backbone RMSD was also noticed (Fig 4A) . doi = 10.1371/journal.pone.0238344 id = cord-304343-m7tbdfri author = Khandia, Rekha title = A Comprehensive Review of Autophagy and Its Various Roles in Infectious, Non-Infectious, and Lifestyle Diseases: Current Knowledge and Prospects for Disease Prevention, Novel Drug Design, and Therapy date = 2019-07-03 keywords = Autophagy; Beclin; LAMP-2A; cancer; cell; disease; inhibit; lc3-ii; pathway; protein; role; virus summary = Similarly, inhibiting the mTOR signaling pathway can prevent apoptosis and even enhance necroptosis, whereas starvation, which induces autophagy, protects cells from zVAD-mediated necroptotic death [194] . For instance, autophagy has been demonstrated to be actively involved in the replication of influenza A virus (IAV), which induces autophagosome formation during the early phase of infection and later inhibits autophagosomal maturation by preventing autophagosomal-lysosomal fusion and promoting autophagosomes to accumulate in virus-infected cells [253] . (5) A novel anti-cancer molecule, HA15, which targets HSPA5/BIP was shown to induce endoplasmic reticulum stress and increase the unfolded protein response, resulting in cancer cell death through autophagy and apoptosis. (5) A novel anti-cancer molecule, HA15, which targets HSPA5/BIP was shown to induce endoplasmic reticulum stress and increase the unfolded protein response, resulting in cancer cell death through autophagy and apoptosis. In addition, the novel anti-cancer molecule HA15, which targets HSPA5/BIP, was shown to induce ER stress and increase the unfolded protein response, resulting in cancer cell death via autophagy and apoptosis [304] . doi = 10.3390/cells8070674 id = cord-341129-eo0vjcmk author = Kielian, Margaret title = Virus membrane-fusion proteins: more than one way to make a hairpin date = 2006 keywords = fusion; membrane; protein summary = Virus membrane-fusion proteins drive the fusion reaction by undergoing a major conformational change that is triggered by interactions with the target cell. The class I membrane-fusion reaction is mediated by the refolding of the fusion protein to a highly stable rod-like structure with a central trimeric α-helical coiled coil. In vitro studies using the ectodomains of both the alphavirus and flavivirus proteins showed that trimerization requires insertion of the fusion peptide into target membranes 64, 65 . However, H230A virus undergoes apparently normal conformational changes upon exposure to low pH, including heterodimer dissociation and fusion-loop exposure, cholesterol-dependent target-membrane insertion, and formation of the E1 homotrimer. Recent work indicates that exogenous domain III blocks class II membrane fusion and infection by binding to the fusion protein during the low-pH-induced conformational change 92 . doi = 10.1038/nrmicro1326 id = cord-254957-jqp1gto6 author = Klann, Kevin title = Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication date = 2020-08-11 keywords = GFR; SARS; cell; figure; protein summary = doi = 10.1016/j.molcel.2020.08.006 id = cord-266543-ng9zr299 author = Klebe, Gerhard title = Virtual ligand screening: strategies, perspectives and limitations date = 2006-06-20 keywords = HTS; docking; ligand; protein; structure summary = In consequence, either the three-dimensional (3D) structure of the macromolecular target -as given by crystal structure analyses, NMR or sophisticated homology modelling -or, at the very least, a rigid reference ligand with a known bioactive conformation mapping out the putative receptor binding site must be available [5] . If one excludes purely retrospective studies, in which the potential of a method is demonstrated by its ability to enrich putatively active molecules from a sample of anticipated nonactive ones, 50 targets have been studied to date, and reports on the discovery of mostly micromolar binding ligands in a truly predictive fashion are available (Table 1) . With respect to VS, a unique and precise assignment of the protonation states of the ligand and protein functional groups in a pK a range between 3 and 11 is essential because, for example, for docking it is important whether such a group is considered as donor or acceptor of a hydrogen bond (Krämer and Klebe, unpublished). doi = 10.1016/j.drudis.2006.05.012 id = cord-007755-o2r8ktie author = Kokoszka, Malgorzata E. title = Mapping Protein–Protein Interactions with Phage-Displayed Combinatorial Peptide Libraries and Alanine Scanning date = 2014-10-20 keywords = dna; peptide; protein summary = doi = 10.1007/978-1-4939-2020-4_12 id = cord-258363-gmgbus9i author = Kolla, Venkatadri title = Synthesis of a bacteriophage MB78 late protein by novel ribosomal frameshifting() date = 2000-08-22 keywords = MB78; dna; protein summary = doi = 10.1016/s0378-1119(00)00264-x id = cord-309384-vlk8cebh author = Kolter, Thomas title = Ganglioside Biochemistry date = 2012-12-19 keywords = GM1; GM2; GM3; Golgi; Tay; acid; cell; figure; ganglioside; membrane; protein summary = A principal difference between ganglioside biosynthesis in the Golgi apparatus and degradation in the endolysosomal compartment is that during GSL formation, membranebound glycosyltransferases interact with their membranebound glycolipid substrates by diffusion within the twodimensional plane of the lipid bilayer. As glycosidase substrates, GSLs with four carbohydrate residues or less require the additional presence of small lipid binding glycoproteins, either the GM2 activator protein or one of the four saposins A-D. In vitro, in addition to enzymes and activator proteins, also an appropriate membrane-lipid composition of the ganglioside-containing membrane is required for degradation [222] . Due to the deficiency of two enzyme activities, β-hexosaminidases A and B, storage of negatively charged glycolipids characteristic for Tay-Sachs disease and, in addition, of uncharged substrates such as GA2 in the brain and globoside in visceral organs (Figure 16 ) is observed. doi = 10.5402/2012/506160 id = cord-259505-7hiss0j3 author = Kong, Qingming title = Proteomic analysis of purified coronavirus infectious bronchitis virus particles date = 2010-06-09 keywords = HSP90; IBV; host; protein; virus summary = It is an important prerequisite for the functional studies to know the protein composition of the purified viral particles, as it allows the analysis of specific proteins and their roles during the virus life cycle, resulting in better understanding of the infection process and the pathogenesis of viruses. To date, there have been no reports about TENP associated with virus, but it''s an enriched and abundant protein identified in purified infectious bronchitis particles which suggests to us that it may be a requisite host protein in IBV life cycles. The present study 1) provides the first proteomic analysis of infectious bronchitis particles, 2) establishes the most comprehensive proteomic index of IBV and 3) shows that most of the virion incorporated host proteins have central roles in virus life cycle. doi = 10.1186/1477-5956-8-29 id = cord-017400-jxbhdch8 author = Koroleva, Olga title = Proteomic Analysis of the Plant Nucleolus date = 2007 keywords = Arabidopsis; protein summary = doi = 10.1007/978-3-540-72617-3_16 id = cord-008556-oetrdm8g author = Kozak, Marilyn title = Regulation of Protein Synthesis in Virus-Infected Animal Cells date = 2008-03-01 keywords = AUG; Kozak; RNA; VSV; cell; protein; translation; virus summary = One consequence of the scanning mechanism is that deleting the "ribosome binding site" (i.e., the normal initiator codon and flanking sequences) will not abolish translation; ribosomes will simply use the next AUG codon downstream, which, in some cases, has been shown to direct the synthesis of a biologically active, truncated protein (Downey et al., 1984; Halpern and Smiley, 1984; Katinka and Yaniv, 1982) . The best evidence for this is the ability of both EMC and SFV 26 S mRNA to be translated in EMC virus-infected cells, in which host translation is drastically inhibited by a mechanism that has not been difined, but that clearly does not involve cap binding protein (Mosenkis et al., 1985) . In wild-type adenovirus-infected cells, in which host protein synthesis is drastically reduced, both adenovirus and influenza virus mRNAs are translated efficiently. doi = 10.1016/s0065-3527(08)60265-1 id = cord-267475-6f4h3cck author = Kozak, Marilyn title = Pushing the limits of the scanning mechanism for initiation of translation date = 2002-10-16 keywords = AUG; Fig; Kozak; RNA; codon; gene; initiation; protein; scanning; translation summary = This depends on careful structural arrangements, however, which are rarely present in cellular mRNAs. Understanding the rules for initiation of translation enables understanding of human diseases in which the expression of a critical gene is reduced by mutations that add upstream AUG codons or change the context around the AUG(START) codon. (Whether the second AUG codon resides in a strong or weak context is not relevant; the ribosome reads the mRNA linearly and thus the decision to stop or to bypass the first AUG is not influenced by whether there is a better initiation site downstream.) The large number of genes that employ leaky scanning precludes discussion of the biological significance of the proteins thereby produced, but it merits noting that, for many of the viruses in Table 3 , replication requires production of both listed proteins. doi = 10.1016/s0378-1119(02)01056-9 id = cord-272241-2fwz8z8n author = Kumar, Amit title = Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach date = 2020-09-09 keywords = SARS; TLR-3; protein; vaccine summary = title: Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach Hence, in this study, we have used immunoinformatic approaches to predict highly antigenic epitopes from SARS-CoV-2 structural proteins that would evoke a strong immune response in humans. For this purpose, we have used the structural proteins: Spike, Envelope, and nucleocapsid to predict B-cell, cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) epitopes for construction of vaccine. We have also performed the docking and molecular dynamic simulations (MDS) between the vaccine and human Toll-like Receptor-3 (TLR-3) to study their binding stability. The VaxiJen 2.0 server predicts the antigenicity of the multi-epitope vaccine peptide based on the physicochemical properties of the input protein. Whereas, ANTIGENpro server predicts the antigenicity of the multi-epitopic vaccine based on the protein microarray data analysis of the target organism. Three structural proteins (spike glycoprotein, nucleocapsid, and envelope) were selected to construct a multi-epitope vaccine, which is capable of eliciting the humoral and cell-mediated immune response. doi = 10.1080/14760584.2020.1813576 id = cord-269531-7gy4epzo author = Kumar, Pankaj title = Proteomic analysis of purified turkey adenovirus 3 virions date = 2015-07-09 keywords = TAdV-3; protein summary = doi = 10.1186/s13567-015-0214-z id = cord-352371-t54zftal author = Kumar, Ravindra title = Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine date = 2017-09-04 keywords = Kumar; SVM; protein summary = RESULTS: In this study, we have reported a novel support vector machine based method for predicting endoplasmic reticulum resident proteins, named as ERPred. But these have some shortcomings like (i) among the above mentioned predictors, none were designed specifically to predict ERRPs; (ii) datasets used for training for prediction model were very old; (iii) subcellular locations were determined for a particular organism or groups (plant/animal/viral); (iv) many of them do not provide webserver/standalone software for scientific purpose and if some of them does so, they are not in working condition. Using standalone version of ScanProsite (Gattiker, Gasteiger & Bairoch, 2002) , out of 124 proteins of training dataset, we were able to find ER retention signal ([KRHQSA]-[DENQ]-E-L) in only 66 proteins, which shows that signal sequence is not present in all ERRPs. This shows that signal based approach may not be appropriate for complete ERRP repertoire prediction of any proteome. doi = 10.7717/peerj.3561 id = cord-329448-kxxy60x9 author = Kumari, Sudha title = Endocytosis unplugged: multiple ways to enter the cell date = 2010-02-02 keywords = Cdc42; GEEC; cell; endocytic; endocytosis; membrane; pathway; protein summary = These factors include one or more underlying principle in cargo enrichment, necessitating specific coat and coat-associated protein assembly, a scission mechanism, and a means to integrate these steps; several molecules and membrane parameters can influence and diversify an endocytic process. CtBP1/BARS (C-terminal-binding protein-1/brefeldin A ribosylation substrate) proteins were originally demonstrated to regulate dynamin-independent fluid uptake in a variety of cell lines, and were later reported to localize to the site of and affect macropinosome membrane closure in a phosphorylation-dependent manner [36] . Overexpression of dominant negative, GTP-binding mutants of dynamin also blocked receptor-mediated endocytosis in various cells, suggesting a role for the GTPase activity of dynamin in the clathrin-dependent endocytic process outside the nervous system. The identification of an endocytic pathway as distinct has been primarily based on associated cargo proteins or lipids, and molecular regulators; the contribution of kinetics and detailed physical mechanism to such categorization is not generally available except in some wellcharacterized situations, namely clathrin-pit endocytosis or endocytosis by actin-dependent forces in yeast. doi = 10.1038/cr.2010.19 id = cord-323768-r7jbm1et author = Lagarda-Diaz, Irlanda title = Legume Lectins: Proteins with Diverse Applications date = 2017-06-12 keywords = Phaseolus; cell; lectin; legume; plant; protein summary = Because lectins recognize and bind to specific glycoconjugates present on the surface of cells and intracellular structures; they can serve as potential target molecules for developing practical applications in the fields of food; agriculture; health and pharmaceutical research. This review presents the current knowledge of the main structural characteristics of legume lectins and the relationship of structure to the exhibited specificities; provides an overview of their particular antimicrobial; insecticidal and antitumor biological activities and describes possible applications based on the pattern of recognized glyco-targets. The isolation and purification of lectins from seeds of native plants such as Parkinsonia aculeata, Olneya tesota, Acacia constricta, Prosopis juliflora, Cercidium praecox, Caesalpinia caladenia and Phaseolus acutifolius has been described. Purification and characterization of complex carbohydrate specific isolectins from wild legume seeds: Acacia constricta is (vinorama) highly homologous to Phaseolus Vulgaris lectins doi = 10.3390/ijms18061242 id = cord-264392-he1vekrt author = Lambeth, L. S. title = Complete genome sequence of Nariva virus, a rodent paramyxovirus date = 2008-12-23 keywords = NarPV; PCR; Paramyxovirinae; protein summary = This study confirmed the classification of NarPV as a member of the subfamily Paramyxovirinae and established the close genome organization and sequence relationship between the two rodent paramyxoviruses isolated almost a decade apart and from two locations separated by more than 15,000 km. This was then followed by PCR to fill in the ''''gaps'''' using specific primers designed from NarPV Nariva virus genome 201 sequences obtained from the cDNA subtraction or degenerate primers designed using highly conserved consensus sequences of known paramyxoviruses in the subfamily Paramyxovirinae. Overall comparison of deduced sizes and amino acid sequences of all proteins indicated that NarPV is most closely related to MosPV (Table 1) genome is significantly larger (16,650 nt) than that of NarPV due to the longer untranslated regions (UTRs) located at the 3 0 end of most genes ( Fig. 1b and Table 1 ). doi = 10.1007/s00705-008-0287-3 id = cord-017817-ztp7w9yh author = Land, Walter Gottlieb title = Cell-Autonomous (Cell-Intrinsic) Stress Responses date = 2018-03-28 keywords = Nrf2; ROS; UPR; cell; dna; protein; response; stress summary = Autophagy is an evolutionarily highly conserved self-digestive process in response to environmental stress to eukaryotic cells, by which cytoplasmic components such as defective/damaged or redundant organelles or protein aggregates are delivered to the lysosome for recycling and degradation. More recent studies then revealed that these transcription factors, notably Nrf2, are activated by Keap1 as the primary negative regulator of Nrf2, that is, a molecule that simultaneously operates as a sensor protein able to perceive dyshomeostatic Subclass IIC-4 DAMPs, for example, in terms of redox changes reflecting electrophilic stress. Strikingly, a complex relationship reportedly exists between autophagy and DAMPs in cellular adaption to stress and injury and cell death characterized by a crosstalk between autophagy induction and secretion or release of DAMPs. In fact, growing evidence indicates that autophagic mechanisms are involved in regulating release and degradation of DAMPs including CALR, HMGB1, ATP, and DNA in several cell types [37, 148, 175] . doi = 10.1007/978-3-319-78655-1_18 id = cord-260708-l9w5jhsw author = Lasecka, Lidia title = The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date = 2013-12-11 keywords = CCHFV; Congo; Crimean; RNA; protein; virus summary = doi = 10.1007/s00705-013-1940-z id = cord-332811-kjgah8ts author = Lee, Do Hyun title = Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets date = 2015-06-23 keywords = Korea; PEDV; protein summary = title: Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets A codon-optimized PEDV S1 gene consisting of amino acid residues 25–749 was synthesized and used to establish a stable porcine cell line constitutively expressing a recombinant PEDV S1 protein containing the chicken immunoglobulin Fc fragment at its C-terminus. Moreover, oral passive immunization using chicken IgY raised against the PEDV S1 protein was found to control and prevent PED post-challenge in suckling piglets. All neonatal piglets except for animals in the control group were inoculated orally with 1 ml of the small-intestine homogenate containing 10 4 TCID 50 /ml PEDV field virus determined using real-time RT-PCR as described previously [10] . Immunoprophylactic effect of chicken egg yolk immunoglobulin (IgY) against porcine epidemic diarrhea virus (PEDV) in piglets doi = 10.1007/s00705-015-2494-z id = cord-285180-32bxx94u author = Lee, Sunhee title = Functional characterization and proteomic analysis of the nucleocapsid protein of porcine deltacoronavirus date = 2015-10-02 keywords = Invitrogen; cell; protein summary = Time-course Western blot analysis revealed that the PK-PDCoV-N cells stably express and accumulate robust levels of a ∼45 kDa recombinant N protein, larger than its predicted molecular weight of approximately 38 kDa possibly due to post-translational modifications and the presence of C-terminal myc and histidine tags (Fig. 1C ). To identify the differentially expressed cellular protein spots in PK-PDCoV-N cells at different time points, 10 protein spots with a statistically significant alteration, including 8 up-regulated and 2 down-regulated protein spots (Fig. 4B) , were selected and manually excised from the stained gels. These proteins showing altered expression were associated with various cellular functions including intracellular transport, metabolic processes, gene regulation, the stress response, protein synthesis, cytoskeleton networks, and cell division. Coronavirus infection of cultured cells is known to cause ER stress and to induce the UPR, which then crosstalks with various cellular signaling pathways, including mitogen-activated protein kinase cascades, autophagy, apoptosis, and innate immune responses, indicating the involvement of UPR activation in virus-host interactions and viral pathogenesis . doi = 10.1016/j.virusres.2015.06.013 id = cord-320083-0k15w624 author = Leitão, Jorge H. title = Microbial Virulence Factors date = 2020-07-27 keywords = host; protein; virulence summary = Microbial virulence factors encompass a wide range of molecules produced by pathogenic microorganisms, enhancing their ability to evade their host defenses and cause disease [...]. The paper focused on the discovery, properties and substrate specificity of the two proteases, their high specificity towards actin, and discussed their contribution to the invasiveness of Serratia, although further knowledge of the bacterium virulence factors and the cellular response mechanisms is required to fully understand the mechanism of Serratia invasion of the host cell [14] . The roles played by virulence factors produced by bacteria when crossing the central nervous system is also addressed, followed by the review of the specific traits of bacterial species more commonly associated with meningitis [15] . The authors also present a thorough review of the main virulence factors used by the organism, including pyolysin, fimbriae, extracellular matrix-binding proteins, neuraminidases, and ability to form biofilms [17] . From Gene to Protein-How Bacterial Virulence Factors Manipulate Host Gene Expression during Infection doi = 10.3390/ijms21155320 id = cord-299270-fwbz3t25 author = Lemieux, M. Joanne title = Structure and function of proteins in membranes and nanodiscs date = 2020-08-22 keywords = GPCR; lipid; membrane; protein summary = doi = 10.1016/j.bbamem.2020.183445 id = cord-260869-rym2ik0o author = Lemmermeyer, Tanja title = Characterization of monoclonal antibodies against feline coronavirus accessory protein 7b date = 2016-02-29 keywords = Fig; ORF; protein; western summary = The 7b protein has a molecular mass of $26 kDa, it is secreted from the cell and contains (i) a Cterminal KDEL-like endoplasmic reticulum (ER) retention signal, (ii) an N-terminal signal sequence of 17 amino acids and (iii) a potential N-glycosylation site at aa position 68 (Vennema et al., 1992a) . The identity of the purified protein was confirmed by SDS-PAGE and Western blotting using anti-His mAb. The protein had an apparent molecular mass of 24 kDa as judged by SDS-PAGE analysis, which is predicted for this protein, and was recognized by the His-tag-specific antibody (Fig. 1a) . Two additional minor bands in the SDS-PAGE were specifically recognized by Western blotting using the His-tag-specific mAb. These bands are consistent with a dimer and a 37-kDa degradation product, respectively, of the GST-7bDSS-His protein (Fig. 1b) . The results outlined above show that the anti-7b mAbs recognize exclusively the nonglycosylated form of the viral protein in FCoV-infected cells. doi = 10.1016/j.vetmic.2015.12.009 id = cord-290638-7ro72sv3 author = Lenstra, Johannes A. title = Antigenicity of the peplomer protein of infectious bronchitis virus date = 1989-01-31 keywords = IBV; protein summary = Abstract To study the antigenic structure of the peplomer protein of the avian coronavirus infectious bronchitis virus, fragments from the peplomer gene were generated by restriction-enzyme cleavage or by limited DNase digestion and inserted in the Escherichia coli expression plasrnid pEX (Stanley and Luzio, 1984). Recombinants expressing the IBV gene fragments were selected by immunoscreening with a rabbit antiserum or, when the expression product was not recognized antigenically, by hybridization followed by gel electrophoresis of the protein expression products. Figure 2 (C) shows a Western blot of hybrid proteins screened with this MAb. The strong binding to fragments p2, s4, psl and ps2 localizes the epitope of MAb 26.1 between residues 390 and 612, the same region that is recognized by all polyclonal sera. The localization of epitopes within stretches of 10-20 residues in several coronaviruses (Fig. 4 , unpublished results) demonstrates that the binding of antibody does not depend on particular flanking sequences, and that any nativelike folding of the epitope in the hybrid protein is confined to the same small region. doi = 10.1016/0161-5890(89)90014-x id = cord-334592-54dofkxh author = Levine, Beth title = Autophagy in immunity and inflammation date = 2011-01-20 keywords = Crohn; MHC; autophagy; cell; function; protein summary = Moreover, p62 is required for starvation and IFN-γ-induced targeting of Fau (and perhaps other ubiquitylated protein complexes) to mycobacteria-containing phagosomes, resulting in the generation of antimycobacterial Fau-derived peptides 42 .The role of p62 in innate immunity is probably evolutionarily ancient, as the Drosophila p62 orthologue REF(2)P was originally identified in a screen for modifiers of sigma virus replication 43 . The mechanisms by which autophagy genes mediate in vivo resistance to infection are not fully understood, but are likely to involve a combination of xenophagy, other autophagy-protein-dependent effects on microbial replication or survival, activation of innate and adaptive immune responses, and/or alterations in pathogen-induced cell death (Fig. 3 ). doi = 10.1038/nature09782 id = cord-021772-5v4gor2v author = Levine, Gwendolyn J. title = Cerebrospinal Fluid and Central Nervous System Cytology date = 2019-05-31 keywords = CNS; CSF; PCR; cell; cerebrospinal; dog; pleocytosis; protein summary = 45, 46 In a recent study of 106 canine CSF samples without pleocytosis (TNCC <5/μL) but containing at least 500 RBCs/μL, the mean percentage of neutrophils (45.2% versus 5.7%), percentage of samples with eosinophils present (36.8% versus 6.8%), and mean protein concentration (40 mg/dL versus 26 mg/dL) were found to be significantly increased in the samples with blood contamination when compared with controls. 4 A study of cats with CNS cryptococcosis showed organisms in 9 of 11 of the CSF samples, and a majority of cases (9 of 10) had neutrophilic pleocytosis and increased protein concentration (8 of 10). A case series of five cats showed CSF ranging from normal to marked neutrophilic pleocytosis with moderately elevated protein concentration and variable correlation to clinical outcome. 85 A study of eight dogs with natural infection (confirmed by CNS tissue-PCR and histopathology) showed lymphocytic pleocytosis in all samples and normal protein concentrations. doi = 10.1016/b978-0-323-53314-0.00014-6 id = cord-017968-17d37a2z author = Lewinski, Martin title = Systems Approaches to Map In Vivo RNA–Protein Interactions in Arabidopsis thaliana date = 2018-08-30 keywords = Arabidopsis; RNA; protein summary = doi = 10.1007/978-3-319-92967-5_5 id = cord-321386-u1imic5l author = Li, Chun title = Protein Sequence Comparison and DNA-binding Protein Identification with Generalized PseAAC and Graphical Representation date = 2018-02-17 keywords = Prot; dna; protein; sequence summary = METHODS: Based on two physicochemical properties of amino acids, a protein primary sequence was converted into a three-letter sequence, and then a graph without loops and multiple edges and its geometric line adjacency matrix were obtained. A generalized PseAAC (pseudo amino acid composition) model was thus constructed to characterize a protein sequence numerically. In addition, a generalized PseAAC based SVM (support vector machine) model was developed to identify DNA-binding proteins. Also, we develop a SVM (support vector machine) model using the generalized PseAAC to identify DNA-binding and non-binding proteins on three datasets. By combining these elements with the conventional amino acid composition (AAC), a dimensional feature vector can be constructed to numerically characterize a protein sequence: , By combining these elements with the frequencies of occurrence of 20 standard amino acids and their three representative letters, a generalized PseAAC model of a protein sequence was constructed. Numerical characterization of protein sequences based on the generalized Chou''s pseudo amino acid composition doi = 10.2174/1386207321666180130100838 id = cord-323331-80d01l6f author = Li, Jie title = Golgi Structure and Function in Health, Stress, and Diseases date = 2019-01-01 keywords = GM130; GRASP65; Golgi; TGN; Wang; protein summary = Mechanistically, GRASP proteins form homodimers via the N-terminal PDZ domains, and dimers from adjacent Golgi cisternae further oligomerize in trans and function as the "glue" that tethers the cisternae into a stack (Wang et al. Other than the well-studied GRASP65-GM130 and GM130-p115-giantin complexes, the GRIP domain containing golgins are another group of proteins associated with the Golgi structure. Depletion of αSNAP in p53 null or Bax null cells still results in apoptosis, indicating that the anti-apoptotic function is independent of p53 and Bax. Interestingly, αSNAP depletion induces apoptosis independent of the cleavage of Golgi proteins such as GRASP65, golgin-160, and p115 but rather by dysregulation of ER-Golgi vesicle cycling and possibly through ER stress (Naydenov et al. The coiled-coil membrane protein golgin-84 is a novel rab effector required for Golgi ribbon formation Caspase-mediated cleavage of the stacking protein GRASP65 is required for Golgi fragmentation during apoptosis doi = 10.1007/978-3-030-23173-6_19 id = cord-294575-kky8j9oy author = Li, Jieqiong title = Characterization of plasma proteins in children of different Mycobacterium tuberculosis infection status using label-free quantitative proteomics date = 2017-09-23 keywords = ATB; LTBI; MTB; protein summary = doi = 10.18632/oncotarget.21179 id = cord-288101-pij16jaa author = Li, Jun-Yu title = Proteomic analysis of the response of porcine adrenal gland to heat stress date = 2019-02-28 keywords = heat; pig; protein; stress summary = doi = 10.1016/j.rvsc.2018.11.004 id = cord-310680-klywz85w author = Li, Qihan title = The interaction of the SARS coronavirus non-structural protein 10 with the cellular oxido-reductase system causes an extensive cytopathic effect date = 2005-04-06 keywords = SARS; cell; protein summary = The gene for the SARS-CoV non-structural protein 10, which is located in the open reading frame of pp1a/pp1ab gene, was synthesized and used to screen for the specific cellular gene coding for the protein interacting with this nsp10 protein in a human embryo lung cDNA library using a yeast trap method. The pathological analysis of the lung tissue from the deceased patients revealed severe Abbreviations: SARS-CoV, severe acute respiratory syndrome coronavirus; BTF3, basic transcription factor-3; ATF5, activation transcription factor-5; NADH, nicotinamide adenine dinucleotide dehydrogenase; FBS, fetal bovine serum; DMEM, double minimal essential media; QDO, quartdrop-out; NC, nitrocellulose; HE, hematoxyline and eosin method; GFP, green fluorescence protein; GST, glutathione S-transferase * Corresponding author. To further investigate the contribution of this interaction to the cytopathic effect of SARS-CoV, a detection series of mitochondrial function and the activity of the oxido-reductase system in the human embryo lung fibroblast transfected with the nsp10 gene was performed. doi = 10.1016/j.jcv.2004.12.019 id = cord-024989-0o6agnrc author = Li, Qihao title = Prediction and analysis of key protein structures of 2019-nCoV date = 2020-05-12 keywords = ACE2; SARS; protein summary = Aim: The purpose of this study was to predict and analyze the structure and function of 2019-novel Coronavirus (nCoV) key proteins. Differential key protein structure analysis of 2019-nCoV Although some amino acids were inserted in two positions of nsp3 in orf1ab [23] , the insertion sites were in the nsp3b and nsp3c regions, which are mainly related to the binding reaction of nucleic acids. Back-mutating mutant amino acids to study the functional change of RBD of S protein In order to study the effect of interactional amino acid changes in 2019-nCoV-ACE2 binding region RBD, we mutated the changed three amino acid residues (Glu 470 , Gln 484 and Asn 487 ) within the RBD structure back to the original amino acids. • We elaborated the sequence and structure differences in each key protein of 2019-nCoV and other bat SARS coronaviruses (CoVs). doi = 10.2217/fvl-2020-0020 id = cord-327000-oyg3oyx1 author = Li, Shasha title = Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date = 2020-05-11 keywords = IFN; PEDV; RNA; SARS; protein; rig; virus summary = This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. Porcine epidemic diarrhea virus (PEDV) is the etiological agent of porcine epidemic diarrhea (PED) that causes an acute and highly contagious enteric disease of swine characterized by vomiting, diarrhea, dehydration, and anorexia in pigs of all ages, especially resulting in severe diarrhea and high mortality rate in piglets. Nsp3 is the largest nsp protein, containing two papain-like protease (PLP1 and PLP2) domains, of which PEDV PLP2 acts as a viral deubiquitinase (DUB), to negatively regulate type I IFN signaling [80] . The evasive strategies utilized by PEDV are classified into four major types: (1) inhibition of RLRs-mediated IFN production pathways, (2) inhibition of the activation of transcription factors responsible for IFN induction, (3) disruption of the signal cascades induced by IFN, and (4) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. doi = 10.3390/pathogens9050367 id = cord-007208-wnkjdg6y author = Li, Sheng-Hsiang title = Demonstration of a Glycoprotein Derived From the Ceacam10 Gene in Mouse Seminal Vesicle Secretions(1) date = 2005-09-01 keywords = CEACAM10; Fig; RNA; SVS; protein summary = doi = 10.1095/biolreprod.105.039651 id = cord-018276-elb93kp6 author = Li, Shitao title = Proteomics Defines Protein Interaction Network of Signaling Pathways date = 2012-12-27 keywords = YTH; interaction; protein summary = doi = 10.1007/978-94-007-5811-7_2 id = cord-003761-ikni2acz author = Li, Zengbin title = Biological Function and Application of Picornaviral 2B Protein: A New Target for Antiviral Drug Development date = 2019-06-04 keywords = FMDV; Golgi; protein summary = In this review, we mainly summarize recent research data on the viroporin or viroporin-like activity of 2B proteins, which affects the biological function of the membrane, regulates cell death, and affects the host immune response. In particular, the 2B protein may change the Ca 2+ concentration to regulate autophagy and apoptosiswhich are distinct cell death mechanisms controlled by the virus to effectively evade the host immunity, thereby promoting viral replication and release [48] [49] [50] [51] [52] . Thus, the main points of focus for research on the structure and function of the 2B protein toward ultimate drug development are: (1) mechanism of increasing membrane permeability to disturb the ion balance, (2) regulation of autophagy and apoptosis, (3) inhibition of the host immune response, and (4) promotion of viral replication and release. doi = 10.3390/v11060510 id = cord-340746-icuzy3vp author = Liang, Yunfei title = Comprehensive Antibody Epitope Mapping of the Nucleocapsid Protein of Severe Acute Respiratory Syndrome (SARS) Coronavirus: Insight into the Humoral Immunity of SARS date = 2005-08-01 keywords = Fig; SARS; epitope; protein summary = We identified the immunodominant antigenic sites responsible for the antibodies in sera from SARS patients and antisera from small animals and differentiated the linear from the conformational antibody-combining sites comprising the natural epitopes by use of yeast surface display. The full-length SARS-CoV N protein (amino acids 1-422) was expressed on the yeast cell surface, as indicated by reactivity of the Xpress epitope tag with the anti-Xpress antibody (Fig. 2) . We used heat denaturation of the fusion proteins tethered to the EBY100 yeast cell surface to categorize the specific linear and conformational SARS-CoV N protein mAb epitopes (35, 36 ) . Our subsequent determination of the antigenic structures of the N protein responsible for antibodies in polyclonal antisera from immunized mice and sera from convalescent SARS patients demonstrated the immunogenic specificity of 3 conformational (amino acids 1-69, 68 -213, and 337-422) and 3 linear (amino acids 1-69, 121-213, and 337-422) epitopes (Fig. 1C) . doi = 10.1373/clinchem.2005.051045 id = cord-258489-pyfc7jde author = Lico, Chiara title = Viral vectors for production of recombinant proteins in plants date = 2008-03-10 keywords = TMV; expression; plant; protein; virus summary = In this review, we will focus on transient production strategies using plant viral expression systems, with a particular focus on the variety of proteins produced, and their applications. The unique properties of viruses such as ease of manipulation, high level amplification, site specific recombination, strong infectivity, enhanced translation and compact and repetitive morphological structure have enabled their broad application, from basic research to product development, including the generation of robust expression systems. From the discovery of viruses in 1898 (tobacco mosaic virus, TMV) (Bos, 1999) , to the first demonstration of RNAs role in virus replication by turnip yellow mosaic virus (TYMV) (Matthews, 1989) , to the very recent discovery of gene silencing and its implication in host response to infection, gene regulation and transgene expression (Baulcombe, 1999; Lu et al., 2003; Waterhouse and Helliwell, 2003) , plant virology has played a crucial role in the understanding of the most fundamental concepts of modern biology. Thanks to the recent improvements of viral-based vectors, mAbs have been produced with transient expression systems to quickly achieve much higher production levels along with other complex proteins. doi = 10.1002/jcp.21423 id = cord-294945-hcf7gsv8 author = Lin, K.H. title = Comparative proteomic analysis of cauliflower under high temperature and flooding stresses date = 2015-02-12 keywords = H41; H69; H71; plant; protein; stress summary = The objectives of this study were to identify the proteins that were differentially regulated and the physiological changes that occurred during different time periods in ''H41'', ''H69'', and ''H71'' when responding to treatments of flooding, 40 °C, and both stresses combined. By the comparative proteomic analysis, 85 protein peaks that were differentially expressed in response to combination treatments at 0, 6, and 24 h, 69 (33 in ''H41'', 29 in ''H69'', and 9 in ''H71'') were identified, of which were cultivar specific. Compared to NFC treatment at 0 h, NFH treatment for 6 h showed that the abundances of peaks 271 (phosphoserine aminotransferase), 272 (imidazole glycerol phosphate synthase subunit hisF), Table 6 Identification of differentially expressed proteins found in cauliflower ''H71'' plants by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in comparison to combination treatments for 0 and 6 h. doi = 10.1016/j.scienta.2014.12.013 id = cord-312741-0au4nctt author = Lin, Panpan title = Coronavirus in human diseases: Mechanisms and advances in clinical treatment date = 2020-10-01 keywords = East; MERS; Middle; RNA; SARS; coronavirus; protein; respiratory; syndrome summary = 160, 161 Once the PAMPs from invaded viruses are detected, RIG-I and MDA5 interact with the mitochondrial antiviral signaling protein (MAVs) that is a mitochondrial membrane-bound F I G U R E 2 Escape mechanisms of innate immune response of SARS-CoV and MERS-CoV adaptor molecule, followed by the activation of several kinase complexes and multiple subsequent transcription factors (IRF3, IRF7, and NF-κB). Antiviral peptides analogous derived from these regions exhibited inhibition to the spike protein-mediated cell-cell fusion and viral entry in viruses such as SARS-CoV, MERS-CoV, as well as HCoV-229E. Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein doi = 10.1002/mco2.26 id = cord-279463-bli8hwda author = Lipp, Joachim title = The membrane-spanning segment of invariant chain (Iγ) contains a potentially cleavable signal sequence date = 1986-09-26 keywords = figure; membrane; protein; signal summary = As type II membrane proteins contain only a single stretch of hydrophobic amino acid residues, this might function as a signal for membrane insertion as well as a membrane anchor (Markoff et al., 1984; Spiess and Lodish, 1986) . plycat is an in-frame fusion between the 5'' region of ly encoding the cytoplas, mic, membrane-spanning segment plus 12 amino acids of the exoplasmic portion of ly and the gene encoding the cytoplasmic protein chloramphenicol acetyltransferase (CAT). After protease digestion in the presence of microsomal membranes, lyCAT* is reduced in molecular weight by about 2 kd, suggesting that it exposes 20-30 amino acid residues on the cytoplasmic side ( Figure 3 , lanes 2 and 3). This signal sequence is located in the amino-terminal half of the membrane-spanning segment, and it is cleaved when the preceding cytoplasmic domain is removed. doi = 10.1016/0092-8674(86)90710-5 id = cord-000708-iuo2cw23 author = Lippé, Roger title = Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date = 2012-05-28 keywords = cell; protein; virus summary = These studies include the alphaherpesvirinae herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV; Loret et al., 2008; Kramer et al., 2011) , the betaherpesvirinae human and murine cytomegaloviruses (HCMV and MCMV, respectively; Kattenhorn et al., 2004; Varnum et al., 2004) and the gammaherpesvirinae Kaposi sarcoma herpesvirus (KSHV), gamma herpesvirus 68 (γHV68), Epstein-Barr virus (EBV), and Alcelaphine (Bortz et al., 2003; Johannsen et al., 2004; Bechtel et al., 2005; Zhu et al., 2005; Dry et al., 2008) . Cellular stress rather than stage of the cell cycle enhances the replication and plating efficiencies of herpes simplex virus type 1 ICP0-viruses Perturbation of cell cycle progression and cellular gene expression as a function of herpes simplex virus ICP0 Herpes simplex virus 1 alpha regulatory protein ICP0 interacts with and stabilizes the cell cycle regulator cyclin D3 Identification and functional evaluation of cellular and viral factors involved in the alteration of nuclear architecture during herpes simplex virus 1 infection doi = 10.3389/fmicb.2012.00181 id = cord-013046-r6dtiu97 author = Liu, Bin title = Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection date = 2014-02-15 keywords = Chou; SVM; protein summary = title: Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection For instance, the kernel combination methodology (VBKC) (Damoulas and Girolami, 2008 ) used a single multiclass kernel machine to combine various kernels based on different feature spaces; SVM-physicochemical distance transformation (PDT) (Liu et al., 2012) combined the amino acid physicochemical properties and the profile features via PDT to incorporate the local sequence-order information of the entire protein sequences. The results obtained by these four methods on the SCOP benchmark are listed in Supplementary Table S1 of Supplementary Material S4, from which we can see that the current method outperforms SVM-Top-n-gram-combine-LSA (Liu et al., 2008) , SVM-PDT-Profile (Liu et al., 2012) and BioSVM-2L (Muda et al., 2011) and is highly comparable with Profile (Kuang et al., 2005) and HHSearch (So¨ding, 2005) , indicating that the profile-based protein representation is a promising approach to extract the evolutionary information from frequency profiles for protein remote homology detection. Protein remote homology detection by combining Chou''s pseudo amino acid composition and profile-based protein representation doi = 10.1093/bioinformatics/btt709 id = cord-350309-j4oh1z8m author = Liu, D. X. title = Coronavirus envelope protein: A small membrane protein with multiple functions date = 2007-05-29 keywords = SARS; protein summary = The E proteins from infectious bronchitis virus (IBV) and mouse hepatitis virus (MHV) are translated from the third and second ORFs of mRNA 3 and 5 of the respective viruses by a cap-independent, internal ribosomal entry mechanism [6] [7] [8] [9] [10] [11] [12] . This modification is unique to SARS-CoV E protein, and it is still unknown whether the modification can also be detected in virus-infected cells and in virions. However, the membrane topologies of SARS-CoV E protein in virions and in virusinfected cells are still unknown. Similar to other viroporins [46] , expression of SARS-CoV and MHV E protein enhanced the membrane permeability of bacterial and mammalian cells [47, 48] . These results indicate that the ion channel activity of coronavirus E protein is important for virus replication, especially in the case of some coronaviruses, such as MHV. Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells doi = 10.1007/s00018-007-7103-1 id = cord-316745-n10ia3j3 author = Liu, HongDe title = A new approach to the prediction of transmembrane structures date = 2008-05-23 keywords = MSCWT; protein summary = In this paper, a new approach, maximum spectrum of continuous wavelet transform (MSCWT), is proposed to predict TMHs. The predictions for eight SARS-CoV membrane proteins indicate that MSCWT has the same capacity with software TMpred. In this paper, MSCWT was proposed to predict TMHs of membrane proteins. MSCWT of a signal could be obtained from the following steps: firstly, choose an appreciated mother wavelet and an appreciated scale range to perform CWT; then, detect and record the CWT maximum at every translation; finally, plot the recorded maximum value to its position (translation). Figure 1 shows the TMHs predicted by MSCWT and TMpred for SARS-CoV protein Orf9 and Orf14. MSCWT has the highest accuracy rate of membrane protein sequence (84.6%), while TMpred and DAS are 75.4% and 80.0%, respectively. In this paper, the proposed new method MSCWT shows a good efficiency in predicting the positions and amounts of TMHs of membrane protein. doi = 10.1007/s11434-008-0055-5 id = cord-346965-0oq2n0af author = Liu, Zhi-Ping title = Bridging protein local structures and protein functions date = 2008-04-18 keywords = dna; function; local; method; protein; site; structure summary = The characteristics between interface and noninterface portions of a protein surface, such as sequence conservation, proportions of amino acids, secondary structure, solvent accessibility and side-chain conformational entropy, are often used to distinguish the specificity of local structures relating to protein binding function. The method relies on a simplified representation of the chemical groups found in amino acid side-chains to identify functional sites from a single protein structure and a number of its sequence homologs. (2006) improved previous approaches by combining two known measures of ''functionality'' in proteins, i.e. cleft volume and residue conservation, to develop a method for identifying the location of ligand-binding pockets in proteins. (2006) applied an SVM method to predict DNA-binding sites using the features including amino acid sequence, profile of evolutionary conservation of sequence positions, and low-resolution structural information. (2006) developed a method to predict both protein-protein binding site location and interface type (obligate or non-obligate) using a Bayesian network in combination with surface patch analysis. doi = 10.1007/s00726-008-0088-8 id = cord-305602-yzc4bosn author = Llano, Manuel title = Chapter Seven Defining Pharmacological Targets by Analysis of Virus–Host Protein Interactions date = 2018-12-31 keywords = HIV-1; interaction; protein summary = This higher than expected connectivity suggests that the direct interactions of viral proteins with host factors allow the access of the virus to cellular complexes. For example, in a TAP-MS experiment were mapped 3787 complex associations between 54 viral proteins from different viruses and 1079 host proteins (Rozenblatt-Rosen et al., 2012) , highlighting the high degree of connectivity of the interacting proteins. As discussed above, some of the host factors predicted, by the combined transcriptional profiling and in silico analyses, to interact with host proteins implicated in direct binary contacts with influenza proteins (Y2H interactors) were demonstrated to influence viral replication in functional screenings (Shapira et al., 2009 ). Most of the small molecules interfering with PPIs bind directly to the implicated surfaces of interactions (orthosteric modulators) by targeting hot spot residues or by molecular mimicry of elements of secondary structures (Arkin et al., 2014; Basse et al., 2016; Fry, 2006; Wells & McClendon, 2007; Yin & Hamilton, 2005) . doi = 10.1016/bs.apcsb.2017.11.001 id = cord-017775-qohf9pxp author = Loa, Chien Chang title = Recombinant Turkey Coronavirus Nucleocapsid Protein Expressed in Escherichia coli date = 2015-09-10 keywords = protein summary = doi = 10.1007/978-1-4939-3414-0_4 id = cord-290088-g9559ux3 author = Loh, Hwei-San title = Using transgenic plants and modified plant viruses for the development of treatments for human diseases date = 2017-08-08 keywords = plant; production; protein summary = doi = 10.1016/j.coviro.2017.07.019 id = cord-262904-0b0ljjq1 author = Lon, Jerome Rumdon title = Prediction and evolution of B cell epitopes of surface protein in SARS-CoV-2 date = 2020-10-29 keywords = SARS; epitope; protein summary = It is worth mentioning that all 6 identified epitopes were conserved in nearly 3500 SARS-CoV-2 genomes, showing that it is helpful to obtain stable and long-acting epitopes under the condition of high frequency of amino acid mutation, which deserved further study at the experiment level. On this basis, we predicted the linear and conformational B cell epitopes, analyzed the conservation of the epitopes, the adaptability and other evolutionary characteristics of the surface protein, which provided a theoretical basis for the vaccine development and prevention of SARS-CoV-2. With the amino acid sequences of the surface protein of SARS-CoV-2 of NC_045512.2 as templates, we predicted the 3D structure of E and M protein through the online server SWISS-MODEL [10] based on homology modeling method, selected the optimal structure based on the template identity and GMQE value [10] , and the rationality of the structure was evaluated by Ramachandran plot [11] with PDBsum server. doi = 10.1186/s12985-020-01437-4 id = cord-296347-fanlvxqs author = Loureiro, Joana title = Antigen Presentation and the Ubiquitin‐Proteasome System in Host–Pathogen Interactions date = 2006-12-02 keywords = CD4; HCMV; MHC; Nef; SPP; US11; US2; protein summary = We discuss the many human cytomegalovirus (HCMV)-encoded immunomodulatory genes that interfere with antigen presentation (immunoevasins) and focus on the HCMV immunoevasins US2 and US11, which induce the degradation of class I MHC heavy chains by the proteasome by catalyzing their export from the endoplasmic reticulum (ER)-membrane into the cytosol, a process termed ER dislocation. One theme that arises from the characterization of this process over the 10 years that have passed since its discovery is that HC dislocation is unique in many respects: HC molecules do not meet the requirement of being either misfolded or misassembled, yet their dislocation takes place by virtue of the presence of US2 or US11; the speed of HC degradation is unrivaled by that of any other ER-associated degradation substrates: HC half-life is reduced from hours to a mere 2-5 min in cells infected by HCMV or in ce lls expressin g either US2 or US11 ( Wiertz et al ., 1996a ,b) ; both US2 and US11 have stringent requirements in terms of which HLA alleles (Barel et al., 2003 (Barel et al., , 2006 Machold et al., 1997) or assembly, folding and ubiquitination status of the class I MHC complex (Blom et al., 2004; Furman et al., 2003; Gewurz et al., 2001) either viral protein is able to target for dislocation and proteasomal destruction. doi = 10.1016/s0065-2776(06)92006-9 id = cord-196265-mvnkkcow author = M''esz''aros, B''alint title = Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications date = 2020-04-21 keywords = ACE2; RGD; SARS; Spike; integrin; motif; protein summary = We examined the sequences of ACE2 and integrins with the Eukaryotic Linear Motif resource, ELM, and were presented with candidate short linear motifs (SLiMs) in their short, unstructured, cytosolic tails with potential roles in endocytosis, membrane dynamics, autophagy, cytoskeleton and cell signalling. Proximity-based mass spectrometry on the MHV replication complex further revealed that the RTC environment repurposes components from the host autophagy, vesicular trafficking and translation machineries (V''kovski et al., 2019) In the present work, we identify a set of conserved SLiM candidates in the ACE2 and integrin proteins, which are likely to act in the cell entry system of SARS-CoV-2. The C-terminal tail of both subunits share a high degree of sequence similarity, and similarly to ACE2, contain several known and candidate SLiMs (see Table 1 and Figure 6 ) that propagate signals in the cytoplasm and regulate integrin activity not just through intracellular pathways, but also changing the structural state of the ectodomains determining ligand binding capacity (Anthis and Campbell, 2011) . doi = nan id = cord-004400-li1sc47z author = Ma, Jingjiao title = Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus date = 2020-02-24 keywords = IFN; WSN; ns1; protein summary = doi = 10.1186/s13567-020-00747-3 id = cord-337067-j8ebslif author = Mades, Andreas title = Role of Human Sec63 in Modulating the Steady-State Levels of Multi-Spanning Membrane Proteins date = 2012-11-15 keywords = Fig; HBV.S; Sec63; cell; protein summary = The overexpression of Sec63 reduces the steady-state levels of viral and cellular multi-spanning membrane proteins in a cotranslational mode, while soluble and single-spanning ER reporters are not affected. The specific action of Sec63 is further sustained by our observations that the up-regulation of either Sec62 or two other ER proteins with lumenal J domains, like ERdj1 and ERdj4, does not compromise the steady-state level of a multi-spanning membrane reporter. Similar results were obtained with cell lysates prepared with the denaturing detergent SDS (Fig. 1B) , indicating that the observed down-regulation of HBV.S by excess Sec63 was not merely due to changes in the solubility profile. To analyze whether an up-regulation of these ERdj proteins might also affect the level of a multi-spanning membrane protein, FLAG-tagged versions of ERdj1 and ERdj4 were cotransfected with HBV.S. FLAG-specific Western blotting confirmed the ectopic expression of ERdj1 and ERdj4 in 63 and 25 kDa forms, respectively, consistent with their theoretical molecular masses (Fig. 9) . doi = 10.1371/journal.pone.0049243 id = cord-356019-k7gs1ohp author = Makhzoum, Abdullah title = Recent advances on host plants and expression cassettes'' structure and function in plant molecular pharming date = 2013-08-20 keywords = expression; plant; production; protein; recombinant summary = As molecular pharming platforms, plants are excellent biofactories for the production of drugs, antibodies, and vaccines in various host systems such as whole transgenic plants, cell suspension culture, hairy roots, and hydroponic culture [1] [2] [3] . Here, we review these aspects and report recent advances in the improvements of plant molecular pharming to increase protein yield and accumulation based on upstream and downstream processing studies and empirical essays. In addition to the importance of promoter architecture for gene expression in molecular pharming, other strategies based on using specific peptides at N-and C-termini have been employed to enhance the transcript level of recombinant proteins. For example, the production and accumulation of the recombinant human granulocyte colony-stimulating factor was significantly increased in transgenic rice suspension culture by an RNAi approach designed to suppress the cysteine proteinase gene expression or by the inhibition of proteinase [104, 105] . doi = 10.1007/s40259-013-0062-1 id = cord-022499-7d58f1k3 author = Mall, Sanjay title = Transmembrane α helices date = 2004-01-07 keywords = Golgi; bilayer; lipid; peptide; protein summary = For example, if effects were averaged over three shells of lipids, changes in fatty acyl chain lengths by 4 and 10 carbons from that giving optimal interaction would decrease lipid-protein binding constants by factors of 1.6 and 21, respectively. These results suggest that the effects of charge on the interactions between phospholipids and transmembrane ot helices will often be rather small and will be strongly dependent on the detailed structure of the peptide and its orientation in the membrane. However, there is evidence for the presence of a small number of "special" anionic phospholipids binding to some membrane proteins, acting as "cofactors." An example is provided by cytochrome c oxidase, whose crystal structure shows the presence of a lipid molecule bound between the transmembrane a helices (Iwata et al., 1995) . It could therefore be that matching of the thickness of the lipid bilayer and the transmembrane length of the protein is important in retention in ER, as was suggested for the Golgi complex. doi = 10.1016/s1063-5823(02)52014-7 id = cord-286970-4pl95r0o author = Mamipour, Mina title = An overview on molecular chaperones enhancing solubility of expressed recombinant proteins with correct folding date = 2017-04-12 keywords = ATP; Hsp70; chaperone; protein summary = In this article, we attempted to review cytoplasmic chaperones such as Hsp families and periplasmic chaperones including; generic chaperones, specialized chaperones, PPIases, and proteins involved in disulfide bond formation. Numerous studies demonstrate positive effects of molecular chaperons on correct folding formation of recombinant protein and prevention of IBs formation in the cytoplasm and periplasm [17, 18] . In this review we focused on cytoplasmic and periplasmic chaperones category and their applications in recombinant protein expression with correct folding. The Hsp90 family are highly conserved and proteins, which exist in all organisms from bacteria to humans and their expressions rises in response to the stress conditions in prokaryotic and eukaryotic LolA (B,C,D,E) periplasm space, Inner membrane and Outer membrane rapid transfer of associated lipoproteins ATP (+) [108] PapD and its family periplasm space and Outer membrane biogenesis of pilus (−) [163] FimC periplasm space interacts with each pilus subunit (−) [164] cells. doi = 10.1016/j.ijbiomac.2017.04.025 id = cord-001866-s5otdtwq author = Mandal, Nakul title = Proteomic Analysis of the Vitreous following Experimental Retinal Detachment in Rabbits date = 2015-11-18 keywords = detachment; protein; retinal; vitreous summary = doi = 10.1155/2015/583040 id = cord-259112-tkj5de7b author = Mandal, Santi M title = Inhaler with electrostatic sterilizer and use of cationic amphiphilic peptides may accelerate recovery from COVID-19 date = 2020-06-17 keywords = cap; protein summary = doi = 10.2144/btn-2020-0042 id = cord-280679-jj3wzojy author = Marblestone, Jeffrey G. title = Comparison of SUMO fusion technology with traditional gene fusion systems: Enhanced expression and solubility with SUMO date = 2006-01-01 keywords = NUS; SUMO; fusion; protein summary = For this study, three model proteins, enhanced green florescent protein (eGFP), matrix metalloprotease-13 (MMP13), and myostatin (growth differentiating factor-8, GDF8), were fused to the C termini of maltose-binding protein (MBP), glutathione S-transferase (GST), thioredoxin (TRX), NUS A, ubiquitin (Ub), and SUMO tags. Taken together, these results demonstrate that SUMO is superior to commonly used fusion tags in enhancing expression and solubility with the distinction of generating recombinant protein with native sequences. Three candidate proteins, enhanced green fluorescent protein (eGFP), and two previously described difficult-to-express proteins, matrix metalloprotease-13 (MMP13) and myostatin (growth differentiating factor-8, GDF8), were expressed as fusions with maltose-binding protein (MBP), glutathione S-transferase (GST), thioredoxin (TRX), NUS A, ubiquitin (Ub), and SUMO. The ability of commonly used fusion tags to enhance protein expression and solubility was investigated using three candidate proteins (eGFP, MMP13, and GDF8) and six fusion tags (SUMO, Ub, MBP, GST, TRX, and NUS A). doi = 10.1110/ps.051812706 id = cord-258468-52gej3co author = Marcekova, Zuzana title = Heterologous expression of full-length capsid protein of porcine circovirus 2 in Escherichia coli and its potential use for detection of antibodies date = 2009-08-05 keywords = Cap; PCV; USA; protein summary = title: Heterologous expression of full-length capsid protein of porcine circovirus 2 in Escherichia coli and its potential use for detection of antibodies coli-expressed Cap protein to self-assemble into virus-like particles (VLPs), the immunization of mice with recombinant Cap yielded antibodies with the same specificity as those raised against native PCV 2 virions. In addition, the antigenic properties of the purified Cap protein were employed in a subunit-based indirect ELISA to monitor the levels of PCV 2 specific antibodies in piglets originating from a herd which was experiencing PCV 2 infection. In order to eliminate the cluster of rare codons from the 5 end of the cap gene, the expression vector encoding a truncated variant of Cap protein ( Cap-His), which was lacking the first 16 amino acid residues, was constructed (Fig. 1B) . In summary, a bacterial expression system has been developed for the production of the full-length recombinant capsid protein of porcine circovirus type 2. doi = 10.1016/j.jviromet.2009.07.028 id = cord-005145-1l87fdmi author = Marquet-Blouin, E. title = Neutralizing immunogenicity of transgenic carrot (Daucus carota L.)-derived measles virus hemagglutinin date = 2003 keywords = plant; protein summary = Despite differences in post-translational processing viral and bacterial antigens preserved their immunogenic properties when produced in plants and induced cross-reactive and sometimes neutralizing and protective antibodies. The aim of this study was (1) to explore the potential of carrots as an expression system for antigens that is suitable for human consumption, and (2) to test whether the measles virus hemagglutinin glycoprotein would preserve its neutralizing immunogenicity in this system. Although some work has been done with transgenic carrot callus cells (Brodzik et al., 2000) , this is one of the first reports of the expression of a transgenic antigen in mature carrots, showing that high levels of virus-neutralizing antibodies can be induced with a glycoprotein produced in this plant. The flow cytometry data showed that all mice vaccinated with transgenic leaf or root extracts produced high levels of antibodies cross-reacting with the native protein independently whether virus-infected or H-protein transfected cells were used. Plant-derived measles virus hemagglutinin protein induces neutralizing antibodies in mice doi = 10.1023/a:1022354322226 id = cord-307227-x6xketcn author = Martin, William R. title = Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2 date = 2020-09-10 keywords = COVID-19; SARS; protein; toremifene summary = Here, we combine homology modeling, molecular docking, molecular dynamics simulation, and binding affinity calculations to determine potential targets for toremifene, a selective estrogen receptor modulator which we have previously identified as a SARS-CoV-2 inhibitor. These results suggest potential structural mechanisms for toremifene by blocking the spike protein and NSP14 of SARS-CoV-2, offering a drug candidate for COVID-19. 2, 3 In our initial network-based drug repurposing study, 4 we identified toremifene, another selective estrogen receptor modulator (SERM), as a strong candidate for the potential treatment of COVID-19. A drug repurposing study for SARS-CoV-1 5 indicated a low 50% effective concentration (EC 50 ) for toremifene, and noted that estrogen signaling may not be involved in the inhibitory pathway, similar to that of inhibition of Ebola. Future work will be needed to confirm these results; optimally, the determination of a cocrystal structure with Journal of Proteome Research pubs.acs.org/jpr Article NSP14 and/or the spike glycoprotein from SARS-CoV-2 with toremifene would be solved. doi = 10.1021/acs.jproteome.0c00397 id = cord-329149-1giy1fow author = Martinez-Martin, Nadia title = Technologies for Proteome-Wide Discovery of Extracellular Host-Pathogen Interactions date = 2017-02-22 keywords = cell; host; human; interaction; pathogen; protein; receptor summary = Despite SPR and related methods offering higher sensitivity for detection of transient Biochemical and MS PDGFR identified as a high affinity cell surface receptor for the CMV gHgLgO protein complex [21] Herpes simplex viruses (HSVs) Biophysical Secreted and plasma membrane-expressed glycoprotein G targets a specific set of human chemokines with high affinity [22] Human immunodeficiency virus type 1 (HIV) Despite the undoubted importance of the biochemical and biophysical approaches to the study of host-pathogen interactions, the aforementioned limitations have motivated the development of alternative technologies for large-scale analysis of ePPIs. From the initial utilization of microarrays for detection of PPI over a decade ago, human proteome chips containing thousands of recombinant proteins have been generated, some of which are now commercially available. doi = 10.1155/2017/2197615 id = cord-263315-g7os15m1 author = Martins-da-Silva, Andrea title = Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date = 2018-01-18 keywords = RNA; Virus; cell; ll5; protein; response summary = doi = 10.3390/v10010043 id = cord-316983-h4mtpcyc author = Mathé-Hubert, Hugo title = Comparative venomics of Psyttalia lounsburyi and P. concolor, two olive fruit fly parasitoids: a hypothetical role for a GH1 β-glucosidase date = 2016-10-25 keywords = Fig; Psyttalia; protein; table; venom summary = We have identified here the main venom proteins of two braconid wasps, Psyttalia lounsburyi (two strains from South Africa and Kenya) and P. To assess whether this variation between two figitid species that differ in their host range similarly exists in other parasitoid taxa, we compared here the venom composition of two braconid wasps, Psyttalia lounsburyi and P. This resulted in a total of 32 and 30 putative venom proteins for Pl and Pc respectively (Tables 1 and 2), whose relative abundance was compared using (i) the RPKM normalized number of Illumina reads from Pl and Pc venom apparatus, mapped to the assembled transcriptomes and (ii) the number of peptides matches in Mascot searches. Interestingly, most of the proteins identified in the proteomics of the reservoir (detection of the most abundant putative venom proteins only, data not shown), such as actin or paramyosin, had a predicted muscular function, as expected from microscopy observations (see above; Fig. 1 ). doi = 10.1038/srep35873 id = cord-034406-i1hbx3pz author = Matthews, Abigail A. title = Developing inhaled protein therapeutics for lung diseases date = 2020-10-30 keywords = delivery; drug; formulation; lung; protein; pulmonary summary = Biologic therapeutics such as protein/polypeptide drugs are conventionally administered systemically via intravenous injection for the treatment of diseases including lung diseases, although this approach leads to low target site accumulation and the potential risk for systemic side effects. In comparison, topical delivery of protein drugs to the lung via inhalation is deemed to be a more effective approach for lung diseases, as proteins would directly reach the target in the lung while exhibiting poor diffusion into the systemic circulation, leading to higher lung drug retention and efficacy while minimising toxicity to other organs. This means that high concentrations of the protein drug can be attained in the lung via pulmonary delivery, suggesting that lower doses of inhaled protein can have an equivalent or even superior therapeutic effect for lung diseases when compared to the higher doses that would be needed from systemic administration [9] . doi = 10.1186/s43556-020-00014-z id = cord-016652-x8t3lf1x author = Matthews, David title = Viruses and the Nucleolus date = 2011-05-23 keywords = RNA; protein; virus summary = doi = 10.1007/978-1-4614-0514-6_14 id = cord-259412-l8uta7du author = Mattossovich, Rosanna title = O(6)-alkylguanine-DNA Alkyltransferases in Microbes Living on the Edge: From Stability to Applicability date = 2020-04-20 keywords = AGT; dna; figure; protein summary = doi = 10.3390/ijms21082878 id = cord-321013-8pkrg0mx author = McBride, Ruth title = The Coronavirus Nucleocapsid Is a Multifunctional Protein date = 2014-08-07 keywords = CTD; RNA; SARS; protein summary = The coronavirus nucleocapsid (N) is a structural protein that forms complexes with genomic RNA, interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. The M protein is the main core shell component and a 16 amino acid domain (aa 237-252) on the CTD of M protein binds directly to N protein via an ionic interaction, leading to specific genome encapsidation in the budding viral particle [81] [82] [83] .The N protein therefore plays an essential structural role in the CoV virion through a network of interactions with (i) the genomic RNA; (ii) M protein and (iii) other N proteins. Amino acid residues critical for RNA-binding in the N-terminal domain of the nucleocapsid protein are essential determinants for the infectivity of coronavirus in cultured cells Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA doi = 10.3390/v6082991 id = cord-315531-2gc2dc46 author = McGarvey, Peter B. title = Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets date = 2009-09-25 keywords = Bacillus; MPD; Proteomics; datum; protein summary = (1) The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells) infected by different bacterial (Bacillus anthracis and Salmonella typhimurium) and viral (orthopox) pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. The centers have generated a heterogeneous set of experimental data using various technologies loosely defined as proteomic, but encompassing genomic, structural, immunology and protein interaction technologies, as well as more standard cell and molecular biology techniques used to validate potential targets identified via high-throughput methods. Here we describe in detail a protein-centric approach for systems integration of such a large and heterogeneous set of data from the NIAID Biodefense Proteomics program, and present scientific case studies to illustrate its application to facilitate the basic understanding of pathogen-host interactions and for the identification of potential candidates for therapeutic or diagnostic targets. doi = 10.1371/journal.pone.0007162 id = cord-021393-9loesliv author = Meade, H.M. title = EXPRESSION OF RECOMBINANT PROTEINS IN THE MILK OF TRANSGENIC ANIMALS date = 2007-09-02 keywords = expression; milk; protein; transgenic summary = To date (1997) , probably more than 50 proteins have been expressed in the milk of transgenic mice, rats, rabbits, goats, sheep, pigs, and dairy cows. Transgenes containing sequences of several milk protein genes, reviewed by Maga and Murray (1995) and Echelard (1996) , have been used to direct the expression of exogenous proteins to the lactating mammary gland. Regulatory sequences from several milk-specific genes have been isolated and tested in transgenic animals: ovine ~-lactoglobulin; murine, rat, and rabbit whey acidic protein (WAP); bovine ~-sl casein; rat, rabbit, and goat f~-casein; and guinea pig, ovine, caprine, and bovine ~-lactalbumin. A 17.2 kbp region located upstream of the rabbit WAP gene directs high level expression of a functional human protein variant in transgenic mouse milk High level production of human growth hormone in the milk of transgenic mice: The upstream region of the whey acidic protein (WAP) gene targets transgene expression to the mammary gland doi = 10.1016/b978-012253840-7/50015-8 id = cord-280429-4fota9rl author = Medvedev, Kirill E. title = Functional and evolutionary analysis of viral proteins containing a Rossmann‐like fold date = 2018-06-13 keywords = ECOD; Fig; Rossmann; dna; protein; virus summary = 10 However, structural analyses of virion architecture and coat protein topology have revealed unexpected similarities, not visible in sequence comparisons, suggesting a common origin for viruses that infect hosts residing in different domains of life. In this current work, we provide functional and evolutionary analysis of viral proteins containing a Rossmann-like fold that can be found in the Evolutionary Classification of protein Domains (ECOD) database developed in our lab. The structures represented gene products from 21 viral taxonomical families with host ranges from all kingdoms of life (http://prodata.swmed.edu/rossmann_fold/viruses/). Our analysis detected 14 different bacterial virus structure topology types defined by ECOD T-groups that contain a Rossmann-like fold (Fig. 2, 12 topology groups shown). Like the bacterial and eukaryotic branches in the tree of life, the Archea are host to a multitude of Functional and Evolutionary Analysis of Viral Proteins viruses. 61 Among viral protein structures containing the minimal Rossmann fold, 14 protein families are known helicases (http://prodata.swmed.edu/ross-mann_fold/viruses/). doi = 10.1002/pro.3438 id = cord-277811-j58qvyum author = Mehrani, Hossein title = Plasma proteomic profile of sulfur mustard exposed lung diseases patients using 2-dimensional gel electrophoresis date = 2011-01-07 keywords = patient; plasma; protein summary = title: Plasma proteomic profile of sulfur mustard exposed lung diseases patients using 2-dimensional gel electrophoresis Haptoglobin α1 chain isoforms (spots 21, 22 and 23) were only detected in the plasma of the severe lung diseases patients but were not detectable in healthy controls ( Figure 2B and 2C). In this study we present plasma proteome analysis of SM exposed patients compared to the healthy controls. In our recent study of BAL fluid proteomics patterns in SM exposed patients we also found that haptoglobin isoforms were significantly elevated in moderate and severe lung disease patients compared to mild and healthy controls [13] . In conclusion, this study complements our previous BAL fluid proteome analysis of patients exposed to SM gas which resulted in identification of number of differentially expressed proteins. Plasma proteomic profile of sulfur mustard exposed lung diseases patients using 2-dimensional gel electrophoresis doi = 10.1186/1559-0275-8-2 id = cord-335915-2apj4qy9 author = Melillo, Alessandro title = Applications of Serum Protein Electrophoresis in Exotic Pet Medicine date = 2013-01-22 keywords = albumin; globulin; protein; specie summary = The main difference between the 2 products is the absence in the serum of fribrinogen, the protein involved in the processes of coagulation; the concentration of total solids of the plasma is thus slightly higher than that of serum (about 5%) and the electrophoretic pattern from it will result in a higher incidence of b-globulin fraction where the fibrinogen normally migrates. In rabbits, the normal Serum Protein Electrophoresis (SPE) pattern lacks a clear distinction between b1-globulins and b2-globulins, as present in dogs and cats, but when gammopathies in the b region occur, usually an extension of the electrophoretic band is seen, with consequent demarcation of the 2 peaks. The first studies of serum proteins in birds were performed on domestic chickens, showing many similarities with the layout of mammals (eg, the production of APPs 18, 19 ), but also several differences: the widespread presence of prealbumin, for example, the lowest concentration of g-globulin, and conversely the more marked response to inflammatory stimuli in the b-globulin field. doi = 10.1016/j.cvex.2012.11.002 id = cord-334220-sqvfr31q author = Messina, Francesco title = Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome date = 2020-11-03 keywords = COVID-19; CoV-2; SARS; protein summary = The functional analysis for all proteins, linked to many aspects of COVID-19 pathogenesis, allows to identify the subcellular districts, where SARS-CoV-2 proteins seem to be distributed, while in each interactome built around one single viral protein, a different response was described, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. We identified possible host responses induced by specific proteins of SARS-CoV-2, underlining the important role of specific viral accessory proteins in pathogenic phenotypes of severe COVID-19 patients. In SFigure For KEGG database the gene enrichment analysis on interactomes of NS7b, ORF1a, ORF3a and ORF8 showed pathway clusters highly significant and consistent with possible pathogenic mechanisms, such as the activation of the complement and of the coagulative cascade, (29) and the TGF-β-dominated immune response (30) . We identified different host response induced by specific proteins of SARS-CoV-2, underlining the important role of ORF3a and ORF8 in phenotypes of severe COVID-19 patients. doi = 10.1101/2020.11.03.366666 id = cord-332784-xkc89uaz author = Mishra, Shashank Shekhar title = Computational investigation of potential inhibitors of novel coronavirus 2019 through structure-based virtual screening, molecular dynamics and density functional theory studies date = 2020-07-15 keywords = covid-19; hit; molecule; protein summary = The novel hit molecules identified from docking study were selected based on the docking score, binding energy calculations, and their other interactions with amino acid residues. To analyze the structural stability of the COVID-19 main protease protein-ligand complexes, molecular dynamics simulations were carried out by using Desmond in the presence of the POPC bilayer membrane (Shekhar et al., 2019) . The selected five potential hit molecules in the binding site of protease protein, interacting with amino acid residues Phe140, Gly143, Thr26, Thr190, Glu166, Pro168, Met165 and Leu141 with a docking score of À7.524 and À6.711 kcal/mol. It is found that the hydrogen bonds with Glu166 and hydrophobic interactions with Pro168, Leu167, Met 49, His41are major contributing factor for stabilizing hit molecule ZINC13144609 at the binding site which is in accordance with our docking result. doi = 10.1080/07391102.2020.1791957 id = cord-018437-yjvwa1ot author = Mitchell, Michael title = Taxonomy date = 2013-08-26 keywords = RNA; dna; genome; human; protein; virus summary = Classifi cation is based on the genomic nucleic acid used by the virus (DNA or RNA), strandedness (single or double stranded), and method of replication. The nucleocapsids of some viruses are surrounded by envelopes composed of lipid bilayers and host-or viral-encoded proteins. The sequence of negative-sense ssRNA is complementary to the coding sequence for translation, so mRNA must be synthesized by RNA polymerase, typically carried within the virion, before translation into viral proteins. Among the families of viruses able to infect humans and other vertebrate hosts, there are many species that target and cause disease in the lung. The nucleocapsid is surrounded by an envelope derived from host-cell membrane and viral envelope proteins, including hepatitis B surface antigen. The genome of human parainfl uenza viruses is ~15 kb in length with an organization and six reading frames (N, P, M, F, HN, L) typical of the Paramyxoviridae (Karron and Collins 2007 ) . doi = 10.1007/978-3-642-40605-8_3 id = cord-007648-tm0hn0hz author = Mockett, A.P.Adrian title = Envelope proteins of avian infectious bronchitis virus: Purification and biological properties date = 2002-12-20 keywords = IBV; protein summary = doi = 10.1016/0166-0934(85)90138-7 id = cord-304953-ntg8w5k4 author = Modis, Yorgo title = Relating structure to evolution in class II viral membrane fusion proteins date = 2014-02-11 keywords = class; protein summary = The striking structural similarity between the flavivirus E proteins and RVFV G -which extends to the mode of dimerization even though E and Gc dimers form different types of icosahedral lattices -is strongly suggestive of a common evolutionary origin for certain envelope proteins within the Bunyaviridae and Flaviviridae families. The conservation of an a-helical coiled coil architecture in class I viral proteins and in the SNARE family of intracellular vesicle fusion proteins provides a compelling precedent for the evolutionary transfer of a structural membrane fusion fold between host and virus during evolution. . This study showed that the Gc envelope protein from Rift Valley fever virus (from the Bunyaviridae family) has a class II fold with striking resemblances to that of E from dengue and other flaviviruses, including a propensity to form head-to-tail dimers with a hydrophobic membrane anchor, or fusion loop buried at the dimer interface. doi = 10.1016/j.coviro.2014.01.009 id = cord-333757-h12aozg2 author = Modis, Yorgo title = Class II Fusion Proteins date = 2013-07-10 keywords = fusion; membrane; protein summary = Furthermore, all available crystal structures of class II fusion proteins lack the ''stem'' region, 43 a 30-55 amino acid linker between Domain III and the C-terminal transmembrane anchor (Figs. The three-dimensional structures of four class II fusion proteins in their postfusion states 29,55,56,94 reveal striking differences from the prefusion forms (Fig. 3) , and suggest a 13 and B) two SFV E1 12 molecules in the prefusion conformation as found on the viral surface, viewed perpendicular to the viral membrane. 29, 55 A deep channel extends from the C-terminus of the crystallized fragment along the intersubunit contact between domains II to the fusion loops, in both the dengue and Semliki Forest virus postfusion trimer structures. The recently determined crystal structures of class II fusion proteins in pre 10,12-14 and postfusion 29, 55, 56 conformations offer the first direct views of fusion anchors-in this case, the fusion loops-as they insert into a target membrane (Fig. 4) . doi = 10.1007/978-1-4614-7651-1_8 id = cord-327199-ggomuomb author = Moerdyk-Schauwecker, Megan title = Cellular Proteins Associated with the Interior and Exterior of Vesicular Stomatitis Virus Virions date = 2014-08-08 keywords = RNP; VSV; protein; virion; virus summary = In another example, the presence of host complement control proteins such as CD46, CD55 and CD59 in the viral envelope has been shown to protect against antibody dependent complement mediated virus lysis in several viruses including human T cell leukemia/ lymphoma virus type I [16] , human cytomegalovirus [16] , hepatitis C virus [17] , HIV-1 [18, 19] , extracellular enveloped vaccinia virus [20] , simian virus 5 [21] and mumps virus [21] . As discussed in the previous section, proteins not associated with the interior of the virion, including proteins embedded in the host derived viral envelope, can be identified by their absence in ProK treated samples or by a size shift upon ProK treatment. While many of the proteins identified in VSV virions appear to be associated with viral assembly, budding or the host-derived viral envelope, they may also have additional functions that affect virus replication. doi = 10.1371/journal.pone.0104688 id = cord-295351-0zr2e8lh author = Mohd Ropidi, Muhammad Izzuddin title = Endoplasmic reticulum: a focal point of Zika virus infection date = 2020-01-20 keywords = RNA; UPR; ZIKV; Zika; protein summary = Following ZIKV infection, the accumulation of misfolded virus polyproteins in the ER lumen overwhelms the ER protein-folding capacity leading to ER stress and triggers the activation of the UPR (Fig. 2) [47] . Following the dissociation of GRP78 that unmasks the GLS, ATF6 translocate to the Golgi apparatus and undergoes sequential proteolytic processing by Fig. 2 ZIKV-induced ER stress initiates host cell unfolded protein response (UPR). ZIKV infection induces ER stress due to the increased amount of unfolded/misfolded viral (red strand) and host cell (grey strand) protein aggregates in the ER lumen. To summarize, ZIKV virus bypasses the UPR by inhibiting stress granules assembly and reticulophagy to ensure continuous viral protein translation and virion production while simultaneously protecting the virus from host cell defense mechanisms. doi = 10.1186/s12929-020-0618-6 id = cord-289124-6w2zvvj1 author = Mok, Lawrence title = Proteomic analysis of Pteropus alecto kidney cells in response to the viral mimic, Poly I:C date = 2015-11-02 keywords = Poly; cell; protein summary = Here, we investigated the differential protein expression of immortalised Pteropus alecto kidney cells (PaKiT03) following transfection with the viral mimic, Poly I:C. Two complementary proteomic approaches, difference gel electrophoresis (DIGE) and isobaric tagging for relative and absolute quantitation (iTRAQ) were used to quantify changes in protein expression following Poly I:C stimulation at 4, 8 and 20 hr post treatment (hpt). Through iTRAQ analysis we show that Poly I:C up-regulates key glycolytic enzymes at 4 hpt within PaKiT03 cells. The analysis with DIGE of Poly I:C transfected PaKiT03 cells showed over 215 individual spots differentially regulated, however only 25 spots could be unambiguously identified by LC-MS/MS. We further assessed the response of three glycolytic enzymes, α-enolase (Eno1), phosphoglycerate mutase 1 (Pgam1) and triosephosphate isomerase 1 (Tpi1) to Poly I:C across two human (HEK293T and HeLa) and two bat cell lines (PaKiT03, PaLuT02) using immunodetection. doi = 10.1186/s12953-015-0081-6 id = cord-000642-mkwpuav6 author = Moreira, Rebeca title = Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing date = 2012-04-19 keywords = Ruditapes; immune; philippinarum; protein; sequence summary = title: Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing The 35 most frequently found contigs included a large number of immune-related genes, and a more detailed analysis showed the presence of putative members of several immune pathways and processes like the apoptosis, the toll like signaling pathway and the complement cascade. The discovery of new immune sequences was very productive and resulted in a large variety of contigs that may play a role in the defense mechanisms of Ruditapes philippinarum. Moreover, a few transcripts encoded by genes putatively involved in the clam immune response against Perkinsus olseni have been reported by cDNA library sequencing [18] . philippinarum transcriptome and another four bivalve species sequences were analyzed by comparative genomics (Crassostrea gigas of the family Ostreidae, Bathymodiolus azoricus and Mytilus galloprovincialis of the family Mytilidae and Laternula elliptica of the family Laternulidae). doi = 10.1371/journal.pone.0035009 id = cord-265887-g5zhoyo9 author = Mukherjee, Shruti title = Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain date = 2020-08-11 keywords = Golgi; SARS; membrane; protein summary = (56) Apart from these highly conserved sequences throughout the genus, there are distinct potent glycosylation sites along the stretch that can serve as chaperone interacting motifs to help in the protein folding and/or aid in J o u r n a l P r e -p r o o f Journal Pre-proof trafficking along with the cellular machinery.(57) Glycosylation of particular asparagine residues (Asn 45, Asn 48, Asn 64, and Asn 68) in the SARS-CoV has been shown to be crucial in maintaining the proteinoligomerization events associated with the host membranes. (41) The formation of a disulfide bond may also play a crucial role in the oligomerization of the E protein, forming stable dimers, trimers, and pentamers depending on its functional requirement.(105) Thus even though the TMD spans the lipid bilayer, the CxxC motif could serve as an essential key to defining the membrane-associated oligomerization events-providing newer targets for preemptive therapeutic intervention. doi = 10.1016/j.bpc.2020.106452 id = cord-271642-i71g2tmd author = Mullen, Lisa M. title = Phage display in the study of infectious diseases date = 2006-02-07 keywords = display; phage; protein summary = doi = 10.1016/j.tim.2006.01.006 id = cord-324640-2zhaknbi author = Munday, Diane C. title = Quantitative Proteomic Analysis of A549 Cells Infected with Human Respiratory Syncytial Virus date = 2010-07-20 keywords = Fig; HRSV; PML; RNA; cell; protein summary = Although RNA synthesis and virus assembly occur in the cytoplasm, HRSV is known to induce nuclear responses in the host cell as replication alters global gene expression. More recently, 2DE was used to compare the potential effect of several different negative strand RNA viruses, including HRSV, parainfluenza virus, human metap-neumovirus, measles virus, and influenza virus, on the host cell proteome with common changes in proteins involved with apoptosis and endoplasmic reticulum stress being highlighted (27) . Together, the indirect immunofluorescence confocal microscopy images supported the observations from the quantitative proteomic analysis that the abundance of mitochondrial proteins (particularly pore proteins) was altered in HRSV-infected cells. Potential Disruption of Proteins Involved in Nucleocytoplasmic Trafficking-Network pathway analysis indicated that the abundance of nuclear pore complex components and proteins involved in the nucleocytoplasmic trafficking of proteins and RNA differed between HRSV-infected and mock-infected cells (Fig. 4) . doi = 10.1074/mcp.m110.001859 id = cord-265087-g4k6pc82 author = Munteanu, Cristian Robert title = Natural/random protein classification models based on star network topological indices date = 2008-10-21 keywords = Chou; protein summary = In conclusion, this study extends for the first time the classical TIs to protein star network TIs by proposing a model that can predict if a protein/fragment of protein is natural or random using only the amino acid sequence data. Using graphic approaches to study biological systems can provide useful insights, as indicated by many previous studies on a series of important biological topics, such as enzyme-catalyzed reactions (Andraos, 2008; Chou, 1989; Forsen, 1980, 1981; Chou and Liu, 1981; Chou et al., 1979; King and Altman, 1956; Kuzmic et al., 1992; Myers and Palmer, 1985; Zhou and Deng, 1984) , protein folding kinetics (Chou, 1990) , inhibition kinetics of processive nucleic acid polymerases and nucleases (Althaus et al., 1993a (Althaus et al., , b, c, 1994a (Althaus et al., , b, 1996 Chou et al., 1994) , analysis of codon usage (Chou and Zhang, 1992; Chou, 1993, 1994) , base frequencies in the anti-sense strands , and analysis of DNA sequence (Qi et al., 2007) . doi = 10.1016/j.jtbi.2008.07.018 id = cord-327744-5k8np850 author = Munteanu, Cristian Robert title = Multi-target QPDR classification model for human breast and colon cancer-related proteins using star graph topological indices date = 2009-03-21 keywords = HBC; HCC; cancer; protein summary = In conclusion, we shown that, using simple input data such is the primary protein sequence and the simples linear analysis, it is possible to obtain accurate classification models that can predict if a new protein related with two types of cancer. The primary protein sequence is transformed in connectivity star graph''s TIs that are used by a statistical linear method in order to construct an input-coded multi-target classification model. The best classification model predicted the probability of presence in HBC/HCC cancer for any of these mutated proteins and the results were analysed with two-way joining clustering analysis method (tw-JCA) from STATISTICA (StatSoft.Inc., 2002). This study is proposing two cancer/non-cancer input-coded multi-target classification models for HBC and HCC using the star network TIs of the protein amino acid sequences. doi = 10.1016/j.jtbi.2008.11.017 id = cord-004719-3stcx0dd author = Mushegian, A. R. title = Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems date = 1993 keywords = RNA; movement; protein; virus summary = In several groups of positive-strand RNA viruses, the movement function is provided by the proteins encoded by the so-called triple gene block including two putative small membrane-associated proteins and a putative RNA helicase. It is concluded that classification of movement proteins based on comparison of their amino acid sequences does not correlate with the type of genome nucleic acid or with grouping of viruses based on phylogenetic analysis of replicative proteins or with the virus host range. Limited sequence similarities were observed between i) movement proteins of dianthoviruses and the MIP family of cellular integral membrane proteins, and ii) between movement proteins of bromoviruses and cucumoviruses and M1 protein of influenza viruses which is involved in nuclear export of viral ribonucleoproteins. With representative sequences of plant virus genomes from many groups available, efforts were made to identify regions of similarity between known movement proteins and to predict movement functions for uncharacterized ORFs. Early observations made by this approach have been reviewed previously (e.g. doi = 10.1007/bf01313766 id = cord-321762-7kiahjyy author = Nandy, Ashesh title = Chapter 5 The GRANCH Techniques for Analysis of DNA, RNA and Protein Sequences date = 2015-12-31 keywords = dna; graphical; protein; representation; sequence summary = We presented our scheme at the First Indo-US Workshop on Mathematical Chemistry in Shantiniketan, West Bengal, India in 1998 [10] where we reported, as stated in the abstract, that "Geometrisation of macromolecular sequences in the form of a graphical representation provides one … technique where the nucleotides in a gene sequence can be viewed as objects in a 4-dimensional space; the method can be extended, in principle, to include, say proteins, in a 20-dimensional space. This review is a brief introduction to the readers of this new and exciting field of research on graphical representation and numerical characterization (GRANCH) of bio-molecular sequences, based on the talk I presented at the Second Mathematical Chemistry Workshop of the Americas in Bogota, Colombia, in July 2010 [13] . doi = 10.1016/b978-1-68108-053-6.50005-3 id = cord-266481-9afb0yvt author = Naskalska, Antonina title = Membrane Protein of Human Coronavirus NL63 Is Responsible for Interaction with the Adhesion Receptor date = 2019-07-17 keywords = NL63; cell; protein summary = We have previously shown that the virus uses heparan sulfate proteoglycans (HSPGs) as the initial attachment factors, facilitating viral entry into the cell. However, we recently reported that heparan sulfate (HS) proteoglycans (HSPGs) are required for effective adhesion of the virus to the cell surface and that such an interaction enhances the infection process (12) . To further validate this result, we blocked the virus-ACE2 interaction with anti-ACE2 antibody, which resulted in inhibition of MENS VLP internalization but not adhesion to the cell surface (Fig. 3) . Using flow cytometry, we next investigated whether the adhesion of MEN and MENS VLPs to the cell surface involves interaction with HSPGs, as has been shown for HCoV-NL63. Mapping of the receptor-binding domain and amino acids critical for attachment in the spike protein of avian coronavirus infectious bronchitis virus doi = 10.1128/jvi.00355-19 id = cord-319884-d8n0aokl author = Natesan, Mohan title = Protein Microarrays and Biomarkers of Infectious Disease date = 2010-12-16 keywords = USA; antibody; dna; microarray; protein summary = Fluorescencebased detection of protein interactions is similar to gene array methods, and data analysis often employs approaches previously developed for genome and transcription studies. A standard assay for measuring antibody interactions with proteins of the vaccinia proteome microarray was first developed with a pool of therapeutic human sera collected from vaccinia-immune individuals (VIg) and this data was compared to results obtained from individuals vaccinated against smallpox using Dryvax. Results from this study suggested that antibodies from vaccination recognized a small number of proteins shared with pathogenic viral strains, while recovery from infection also involved humoral immunity to antigens uniquely recognized within the monkeypox virus proteome (unpublished data). For example, a protein array produced from the outer membrane proteins of Pseudomonas aeruginosa was constructed [38] to study the immune response in patients, and several antibody-binding antigens were identified by this group as potential diagnostic markers. doi = 10.3390/ijms11125165 id = cord-279629-t1xjy12y author = Nazneen Akhand, Mst Rubaiat title = Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine date = 2020-04-15 keywords = COVID-19; SARS; protein; vaccine summary = The present in silico study aimed to predict a novel chimeric vaccines by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Hence, the study was designed to develop a chimeric recombinant vaccine against COVID-19 by targeting four major structural proteins of the pathogen, while revealing the evolutionary history of different species of coronavirus based on whole genome and protein domain-based phylogeny. Apart from the human coronaviruses, we introduced other coronaviruses which choose different species of bats, whale, turkey, rat, mink, ferret, swine, camel, rabbit, cow and others as host (Supplementary TableDomain analysis of spike protein of coronaviruses reveals that they contain mainly one signature domains namely, coronavirus S2 glycoprotein (IPR002552), which is present in all the candidates. Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach. doi = 10.1101/2020.04.15.036285 id = cord-253466-7gpije5d author = Netherton, Christopher title = A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication date = 2007-08-31 keywords = ASFV; Fig; Golgi; Poliovirus; RNA; african; dna; protein; replication; virus summary = Significantly, Poliovirus infection causes enrichment of GEFs in membranes containing replicase proteins, and this would provide a mechanism for increasing levels of Arf1-GTP at sites of virus replication. There is evidence that Tobacco mosaic virus also uses the ER as a site of replication because the replicase enzyme and viral RNA are located on the ER of infected cells, and infection causes major changes in ER morphology (Reichel and Beachy, 1998) , including ER aggregation and formation of lamella structures. Even though these viruses infect a diverse range of hosts from different phyla, including vertebrates [poxviruses, African swine fever virus (ASFV)], arthropods (entomopox, ASFV, chloriridoviruses), amphibians and fish (Ranavirus, Megalocytivirus, and Lymphocystivirus genera of the Iridoviridae family), marine algae (phycodnaviruses), and protozoa (mimivirus), they all generate cytoplasmic factories as major sites of virus assembly and replication (illustrated in Fig. 4 ). Formation of DNA replication structures in herpes virus-infected cells requires a viral DNA binding protein doi = 10.1016/s0065-3527(07)70004-0 id = cord-276988-bvsz5q6d author = Neu, Carolin T. title = Post-Transcriptional Expression Control in Platelet Biogenesis and Function date = 2020-10-15 keywords = RBM15; RNA; cell; expression; megakaryocyte; platelet; protein summary = Additionally, we will focus on the currently known concepts of post-transcriptional control mechanisms important for RNA fate within platelets with a special emphasis on RBPs. Blood platelets-the major players in hemostasis-are small anucleate cell fragments with a characteristic discoid shape and a diameter of 1 to 3 µm that originate from megakaryocytes (MKs). The m 7 G cap and poly(A) tail promote mRNA translation and stability, while the UTRs expose sequences for RNA-binding proteins (RBPs) and regulatory sites for microRNA (miRNA)-mediated translational and degradation control [45, [52] [53] [54] . Moreover, RNA-Seq analysis of platelet miRNAs in patients with myocardial infarction revealed nine differentially expressed platelet miRNAs compared to healthy controls, which were released upon platelet aggregation and taken up by endothelial cells via a vesicle-dependent mechanism [80] . Megakaryopoiesis, megakaryocyte maturation, as well as platelet formation, were shown to be highly complex processes that are regulated on multiple levels including epigenetic, transcriptional as well as post-transcriptional gene expression control mechanisms. doi = 10.3390/ijms21207614 id = cord-279418-3r1ijafm author = Nevers, Quentin title = Negri bodies and other virus membrane-less replication compartments() date = 2020-08-21 keywords = PML; Protein; RNA; Virus summary = We particularly examine the interplay between viral factories and the cellular innate immune response, of which several components also form membrane-less condensates in infected cells. With the rapid identification of cellular membraneless compartments and proteins that undergo LLPS in vitro, a major challenge in the field is to demonstrate unambiguously that a specific structure is indeed a phase-separated liquid body in the cellular context. Until now, only a few specific cellular factors, which directly interact with viral proteins such as the nucleoproteins and phosphoproteins of MNV, have been shown to concentrate in these structures. Upon Infection, Cellular WD Repeat-Containing Protein 5 (WDR5) Localizes to Cytoplasmic Inclusion Bodies and Enhances Measles Virus Replication The Ebola Virus Nucleoprotein Recruits the Nuclear RNA Export Factor NXF1 into Inclusion Bodies to Facilitate Viral Protein Expression The Cellular Protein CAD is Recruited into Ebola Virus Inclusion Bodies by the Nucleoprotein NP to Facilitate Genome Replication and Transcription doi = 10.1016/j.bbamcr.2020.118831 id = cord-319722-udqu5jub author = Ng, Eddy W. Y. title = Advances in MALDI Mass Spectrometry in Clinical Diagnostic Applications date = 2013-04-07 keywords = MALDI; SELDI; TOF; mass; protein; serum summary = One commonly used approach for identification of disease-specific biomarkers is to compare the quantitative biomolecule profiles of plasma/serum specimens from the patients with the target disease and control subjects without the disease. For example, after immunoprecipitation of amyloid-beta peptides from the cerebral spinal fluid, different amyloid-beta isoforms as well as their corresponding stable-isotope labeled internal standards appear as individual peaks of expected m/z values in a MALDI-TOF mass spectrum, and their quantities can be measured with high accuracy with intra-assay CVs <10% [33] . Surface-enhanced laser desorption/ionization TOF mass spectrometry (SELDI-TOF MS) is a variant of MALDI-TOF MS, and is mainly designed for quantitative analysis of proteins in biological samples. It may be because SELDI-TOF MS was the first high-throughput technology that allowed quantitative profiling and comparison of the serum/plasma proteins in a large number of patient samples within a very short period of time. doi = 10.1007/128_2012_413 id = cord-255371-o9oxchq6 author = Nguyen, Thanh Thi title = Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) date = 2020-07-10 keywords = SARS; mutation; protein; sequence summary = doi = 10.1101/2020.07.10.171769 id = cord-282604-xp71rkxc author = Nikolaev, EN title = Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein date = 2020-05-25 keywords = SARS; protein summary = title: Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group [4]. We have performed a pilot study on nasopharynx epithelial swabs already collected from patients with CODIV-19 for RT-qPCR and showed confident identification of the N protein of the SARS CoV-2 virus by mass-spectrometry with the use of a very basic sample preparation procedure. Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients doi = 10.1101/2020.05.24.113043 id = cord-336119-8g37xsys author = Nimgampalle, Mallikarjuna title = Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets date = 2020-06-24 keywords = Chloroquine; Hydroxychloroquine; SARS; protein; table summary = Our current study also shows that some of the chemically synthesized Chloroquine derivatives can also potentially inhibit various SARS-CoV-2 viral proteins by binding to them and concomitantly effectively disrupting the active site of these proteins. By using in-silico molecular docking studies, the binding potential of Chloroquine and its derivatives with different SARS-CoV-2 proteins involved in viral replication was evaluated. Based on the recent reports, some of the essential regulatory proteins and enzymes associated with the pathogenesis of SARS-CoV-2 were selected as drug targets such as the Spike glycoprotein that enables virus internalization, RNA dependent RNA polymerase that supports replication of viral genetic material, Chimeric RBD (Receptor binding domain) that interacts with the ACE 2, Main protease responsible for cleaving the viral polypeptide, Non-structural Protein3, Nonstructural Protein 10, Non-structural Protein 9 (Replicase Table 3 . doi = 10.1080/07391102.2020.1782265 id = cord-324667-wmhdw1qs author = Nishtala, Krishnatej title = Tear biomarkers for keratoconus date = 2016-08-04 keywords = disease; keratoconus; protein; tear summary = Advances in technologies such as mass spectrometry and NMR have helped in studying and understanding molecular changes in the tear proteome, lipidome and metabolome relating to an ocular disease condition. Enzyme linked immunosorbent assay (ELISA) analysis of capillary collected tears in 28 [61] , 30 [62] and 94 [63] patients with keratoconus in three different studies showed elevated levels of inflammatory markers IL-6, TNFα and MMP9. Protein levels of gross cystic disease fluid protein-15/ prolactin-inducible protein (PIP) and zinc-alpha-2glycoprotein have been found to be elevated in tears of 36 patients by proteomic analysis, suggesting their application as prognostic markers for keratoconus [72] ( Table 2 ). A multi-omics approach integrating data from proteomics, lipidomics and metabolomics is the need of the hour for studying tear fluid as an important source of biomarkers in keratoconus to lead to effective prognosis and treatment of the disease. doi = 10.1186/s40662-016-0051-9 id = cord-314751-i9rxesrg author = Oh, Jongsuk title = Immunogenicity and protective efficacy of recombinant S1 domain of the porcine epidemic diarrhea virus spike protein date = 2014-07-10 keywords = PEDV; protein summary = In this study, a codon-optimized PEDV S1 gene containing amino acid residues 25–738 was synthesized based on a multiple alignment of the S amino acid sequences of PEDV field isolates and used to establish a stable porcine cell line constitutively expressing the PEDV S1 protein. In the present study, therefore, we first synthesized a full-length, codon-optimized PEDV S1 gene and then generated a stable porcine-origin cell line constitutively expressing the recombinant S1 protein. These results were coincident with the rabbit study described above, since the rabbit antisera generated by immunization with the recombinant S1 protein also contained low levels of neutralizing antibodies to the heterologous PEDV vaccine strain. In the present study, the first aim was to stably express the full-length, codon-optimized S1 gene of PEDV in porcine-origin cells and to evaluate the immunogenicity and efficacy of the recombinant S1 protein. doi = 10.1007/s00705-014-2163-7 id = cord-023740-g84fa45m author = Oldstone, Michael B.A. title = Mimicry by Virus of Host Molecules: Implications for Autoimmune Disease date = 2014-06-27 keywords = protein; virus summary = Monoclonal antibodies against 11 different viruses including DNA and RNA viruses known to cause human infection from the herpes virus group, vaccinia virus, myxoviruses, paramyxoviruses, arenaviruses, flaviviruses, alphaviruses, rhabdovirus, and coronaviruses cross-react with host cell determinants expressed on uninfected tissues. other examples (reviewed in Oldstone and Notkins, 1986 ) suggest a mechanism whereby immune reactants directed against a viral or microbial component may cross-react with a host component and generate autoimmune disease. Since, on the basis of antibody cross-reactivity, many viruses share antigenic sites with normal host cell components, the next step was to look for crossreactive capability in eliciting autoimmunity and related disease. The most likely mechanism by which molecular mimicry would cause disease is by eliciting an immune response against a determinant shared between the host and the virus to bring forth a tissue-specific immune response, presumably capable of destroying cells and eventually the tissue. doi = 10.1016/b978-0-12-174685-8.50079-2 id = cord-004435-l66ost6q author = Oli, Angus Nnamdi title = Immunoinformatics and Vaccine Development: An Overview date = 2020-02-26 keywords = HLA; antigenic; immune; protein; vaccine summary = doi = 10.2147/itt.s241064 id = cord-332948-h297ukuu author = Olotu, Fisayo A. title = Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. date = 2020-10-16 keywords = CoV-2; RBD; SARS; protein; site summary = authors: Olotu, Fisayo A.; Omolabi, Kehinde F.; Soliman, Mahmoud E.S. title: Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. 30 Identification of other functional (allosteric) sites on the prefusion S protein could present another dynamic and effective approach of preventing SARS-CoV-2 infectivity relative to its interaction with the host cell ACE2 and proteases. 53 Relatively, this study was implemented to (i) identify potential druggable sites across the S1 and S2 domains of the SARS-CoV-2 S protein other than the RBD-hACE2 interface (ii) perform high-throughput (virtual) screening of ~1500 FDA approved drugs against the most druggable site(s) (iii) investigate the binding dynamics and interaction mechanisms of the compounds and their consequential effects on the S-protein RBD-ACE2 complex. We believe this systematic study will be able to provide structural and molecular insights into possible allosteric sites on SARS-CoV-2 S protein suitable for selective targeting and structureComputational methodologies doi = 10.1016/j.imu.2020.100451 id = cord-262119-s6hc7fxs author = Ostaszewski, Marek title = COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms date = 2020-10-27 keywords = ACE2; COVID-19; CoV-2; Coronavirus; Disease; Map; SARS; SBML; cell; pathway; protein summary = title: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms The molecular pathophysiology that links SARS-CoV-2 infection to the clinical manifestations and course of COVID-19 is complex and spans multiple biological pathways, cell types and organs [2, 3] . With this goal in mind, we initiated a collaborative effort involving over 230 biocurators, domain experts, modelers and data analysts from 120 institutions in 30 countries to develop the COVID-19 Disease Map, an open-access collection of curated computational diagrams and models of molecular mechanisms implicated in the disease [4] . The COVID-19 Disease Map diagrams, available in layout-aware systems biology formats and integrated with external repositories, are available in several formats allowing a range of computational analyses, including network analysis and Boolean, kinetic or multiscale simulations. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms doi = 10.1101/2020.10.26.356014 id = cord-017887-pj6pal35 author = OuYang, Bo title = Structural and Functional Properties of Viral Membrane Proteins date = 2018-06-29 keywords = HIV-1; NMR; TMD; channel; protein summary = Functional mutagenesis studies have suggested that, at least in the cases of HIV-1 and influenza A viruses, the TM domains (TMDs) of fusion proteins are not merely membrane anchors, but play important roles in membrane fusion and viral infectivity. Apart from the channels and fusion proteins, some viruses have developed enzymatic domains anchored to the membrane, e.g., the polymerases of the hepatitis C virus and the neurominidase of the influenza viruses. Unlike many other broad-spectrum antivirals, Arbidol has an established mechanism of action against the HAs in influenza A and B viruses that involves the inhibition of virus-mediated membrane fusion and thus viral entry [50] . The NMR structure of the HIV-1 Env TMD may provide some clues for how other viral fusion proteins oligomerize in the membrane. Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes doi = 10.1007/978-981-13-0532-0_6 id = cord-345712-gmzue6lj author = Palazzo, Luca title = ADP‐ribosylation: new facets of an ancient modification date = 2017-04-26 keywords = ADP; Fig; Streptomyces; dna; protein; ribosylation summary = Altogether, ADPribosylation is a widespread modification that controls a vast number of cellular processes, including DNA damage repair, transcription, cell-cycle progression, cell division, unfolded protein response, aging, nitrogen fixation, microbial pathogenicity, cell death and many others [7, 14, [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] . As a consequence, macrodomain-containing proteins are involved in a diverse set of cellular functions, such as chromatin remodelling and DNA-damage repair, oxidative stress response, metabolic processes and pathogenic mechanisms [3,5,10-13,30,37, 53, 54, [59] [60] [61] . Studies looking either at the genomic context of ADPribosylating systems or their evolution in bacteria suggest that ADP-ribosylation might be involved in the regulation of many crucial cellular processes including bacterial persistence, oxidative stress response and adaptation to the host environment in general [5, 9, 49, 154] . doi = 10.1111/febs.14078 id = cord-310947-aqau2n7q author = Pan, Ji''An title = Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date = 2008-10-01 keywords = Fig; RNA; SARS; interaction; protein summary = In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV) and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12) provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. However, the viral protein interaction maps have been generated until now only for a limited number of viruses, including T7 bacteriophage [1] , vaccinia virus [2] , potato virus A [3] , pea seed-borne mosaic virus [3] , wheat steak mosaic virus [4] , hepatitis C virus [5, 6] , porcine teschovirus [7] , Kaposi sarcoma-associated herpesvirus [8] , and very recently severe acute respiratory syndrome coronavirus (SARS-CoV) [9, 10] . doi = 10.1371/journal.pone.0003299 id = cord-260057-2m6jdvtc author = Pandey, Preeti title = Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis date = 2020-09-23 keywords = Fig; NSP6; RMSD; SARS; complex; protein summary = doi = 10.1007/s00109-020-01980-1 id = cord-002842-4evbeijx author = Pandey, Rajan Kumar title = Novel Immunoinformatics Approaches to Design Multi-epitope Subunit Vaccine for Malaria by Investigating Anopheles Salivary Protein date = 2018-01-18 keywords = Anopheles; CTL; epitope; protein; vaccine summary = doi = 10.1038/s41598-018-19456-1 id = cord-009792-e2vvi8qo author = Pandit, SB title = Structural and Functional Characterization of Gene Products Encoded in the Human Genome by Homology Detection date = 2008-01-03 keywords = Pfam; human; protein summary = doi = 10.1080/15216540400006105 id = cord-304607-td0776wj author = Paszkiewicz, Konrad H. title = Omics, Bioinformatics, and Infectious Disease Research date = 2010-12-24 keywords = gene; genome; protein; sequence summary = This chapter discusses the current state of play of bioinformatics related to genomics and transcriptomics, briefs metagenomics that finds use in infectious disease research as well as the random sequencing of genomes from a variety of organisms. Bioinformatics plays a key role at several steps in genomics, comparative genomics, and functional genomics: sequence alignment, assembly, identification of single nucleotide polymorphisms (SNP), gene prediction, quantitative analysis of transcription data, etc. The term "metagenomics" was originally used to describe the sequencing of genomes of uncultured microorganisms in order to explore their abilities to produce natural products (Handelsman et al., 1998 , Rondon et al., 2000 and subsequently resulted in novel insights into the ecology and evolution of microorganisms on a scale not imagined possible before (see Cardenas and Tiedje, 2008; Hugenholtz and Tyson, 2008 for an overview). However, metagenomics now finds use in infectious disease research as well as the random sequencing of genomes from a variety of organisms from, for example, patient material that could lead to the identification of the cause of disease. doi = 10.1016/b978-0-12-384890-1.00018-2 id = cord-011184-ohdukhqt author = Patil, Shital P. title = Plant-Derived Bioactive Peptides: A Treatment to Cure Diabetes date = 2019-07-22 keywords = glucose; peptide; protein summary = doi = 10.1007/s10989-019-09899-z id = cord-010938-12igesqw author = Patra, Prasanta title = Epitope-Based Vaccine Designing of Nocardia asteroides Targeting the Virulence Factor Mce-Family Protein by Immunoinformatics Approach date = 2019-08-21 keywords = Mce; protein summary = title: Epitope-Based Vaccine Designing of Nocardia asteroides Targeting the Virulence Factor Mce-Family Protein by Immunoinformatics Approach Appropriate structural identity of the virulence factor Mce-family protein generated through Phyre2 server and subsequently validated by ProSA and PROCHECK program suite. Consequently the targeted protein sequence has been crucially analyzed through several authentic web prediction portals focus to extract the functional epitopes leading to narrative vaccine generation against Nocardiosis disease. The server utilizes recurrent neural network technique to locate the specific B-cell epitopes present in targeted protein sequence. Amino acid sequence of virulence factor Mce-family protein has been submitted to the server and a zip file containing predictions is comes out as systematic result component. ABCpred server predicts 20 linear epitopes (Table 1) within the virulence factor Mce-family protein of 20 amino The structural profile of virulence factor Mce family protein also been mapped out via Phyre2 server that will be fundamental for therapeutics to design the vaccine. doi = 10.1007/s10989-019-09921-4 id = cord-266617-z8uecyl6 author = Pavesi, Angelo title = Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation date = 2019-04-03 keywords = gene; overlap; protein summary = Analysis of nucleotide and amino acid sequences revealed that half of overlaps undergo asymmetric evolution, as the protein from one frame shows a number of substitutions significantly higher than that of the protein from the other frame. I classified a pair of homologous overlaps as a case of symmetric evolution, if the number of amino acid substitutions in the Up1-Up2 alignment did not significantly differ from that in the Down1-Down2 alignment (chi-square < 3.84). In alternative, I classified a pair of homologous overlaps as a case of asymmetric evolution, if the number of amino acid substitutions in the Up1-Up2 alignment was significantly different from that in the Down1-Down2 alignment (chi-square > 3.84). The analysis of the pattern of nucleotide substitutions in the 75 pairs of homologous overlaps revealed 39 and 36 cases of symmetric and asymmetric evolution, respectively (Supplementary Table S2 ). doi = 10.1016/j.virol.2019.03.017 id = cord-294712-kvvxmvqo author = Pelosse, Martin title = MultiBac: from protein complex structures to synthetic viral nanosystems date = 2017-10-30 keywords = MultiBac; cell; complex; dna; protein summary = The MultiBac baculovirus/insect cell expression vector system was conceived as a user-friendly, modular tool-kit for producing multiprotein complexes for structural biology applications. We then turned our attention to eukaryotic methods, specifically an expression vector system relying on a recombinant baculovirus, to infect insect cell cultures for producing the complexes in which we had interest. This particular feature, and the-at least conceptually-relative ease of manipulating baculovirus in the laboratory by non-expert users, was exciting and led us on to the development of MultiBac: a baculovirus/insect cell system specifically engineered for expressing functional multiprotein complexes in the quality and quantity required for high-resolution structural and mechanistic studies [7] [8] [9] [10] [11] . The introduced genome alterations resulted in a virus that exhibited delayed lysis of the insect cells, allowing the production of recombinant protein complexes at very high levels while the cells seemingly remained intact [11] . The MultiBac baculovirus/insect cell expression vector system for producing complex protein biologics doi = 10.1186/s12915-017-0447-6 id = cord-002967-yy3bennu author = Penna, Fabio title = Modulating Metabolism to Improve Cancer-Induced Muscle Wasting date = 2018-01-29 keywords = cachexia; cancer; muscle; protein summary = doi = 10.1155/2018/7153610 id = cord-014901-d9szap94 author = Permyakova, N. V. title = State of research in the field of the creation of plant vaccines for veterinary use date = 2015-01-04 keywords = cell; expression; plant; protein; vaccine summary = Transgenic plants as an alternative of costly systems of recombinant immunogenic protein expression are the source for the production of cheap and highly efficient biotherapeuticals of new generation, including plant vaccines. Of principal importance of this work development was the creation of the "edible vaccine" concept, the essence of which is the use of genetically modified plants containing protein anti gens of infectious agents for oral delivery of relevant antigens to the mucosa of the gastrointestinal tract of warm blooded animals. Preparation of medicinal substances for the pro duction of veterinary products is based on various approaches, including biotechnology using genetically modified (transgenic) organisms for these purposes; such expression systems as bacteria, yeast, cells of insects and mammals are used. This review is devoted to the analysis of possibilities of producing recombinant immunogenic proteins for veterinary use on the basis of plant expression systems, and the history of the concept of "edible vaccines" for animal immunization. doi = 10.1134/s1021443715010100 id = cord-150183-zzzyewjb author = Phillips, J. C. title = Synchronized Attachment and the Darwinian Evolution of Coronaviruses CoV-1 and CoV-2 date = 2020-08-27 keywords = CoV-2; protein summary = These are (CoV-1 site numbering from Uniprot P59594): 546Gln to Leu; 556 and 561Ser to Ala; and 568Ser to Leu. The differences associated with each of these mutations are hydropathically large (~50-100 in the MZ scale [4] ; all 20 amino acids span a range from most hydrophilic to most hydrophobic of 170). The central hydrophilic level set, absent from CoV-1 and present in CoV-2, is our main result ( There is an excellent review of the principles of self-organized criticality in living matter [3] . Some readers may be interested in the connections between hydropathic scaling theory of proteins and the more general synchronization of complex networks. Now that we are in the genomic age, with a very large sequence data base available for many proteins and many species, the discovery of these 20 fractals [5, 13] opens a new biophysics field of accurate thermodynamic analysis of small but medically important evolutionary differences. doi = nan id = cord-193133-puqcbf8t author = Piplani, Sakshi title = In silico comparison of spike protein-ACE2 binding affinities across species; significance for the possible origin of the SARS-CoV-2 virus date = 2020-05-13 keywords = ACE2; CoV-2; SARS; protein summary = The devastating impact of the COVID19 pandemic caused by SARS coronavirus 2 (SARSCoV2) has raised important questions on the origins of this virus, the mechanisms of any zoonotic transfer from exotic animals to humans, whether companion animals or those used for commercial purposes can act as reservoirs for infection, and the reasons for the large variations in susceptibilities across animal species. Here we show how computational chemistry methods from structure-based drug design can be used to determine the relative binding affinities of the SARS-CoV-2 spike protein for its receptor, angiotensin converting enzyme (ACE)-2, a critical initiating event for SARS-CoV-2 infection, across multiple common and exotic animal species. 31, 32 Molecular docking was performed on the homology modelled SARS-CoV-2 spike protein with human and animal ACE2 proteins. The molecular dynamics simulation of complexes of SARS-CoV-2 spike protein and ACE2 receptors of various species were performed for 100ns. doi = nan id = cord-352481-iq3wor3w author = Postic, Guillaume title = An information gain-based approach for evaluating protein structure models date = 2020-08-18 keywords = OBS; PMF; TIG; protein summary = Although these statistical potentials are not to be confused with their physics-based counterparts of the same name—i.e. PMFs obtained by molecular dynamics simulations—their particular success in assessing the native-like character of protein structure predictions has lead authors to consider the computed scores as approximations of the free energy. In this article, we present a conceptually new method for ranking protein structure models by quality, which is (i) independent of any physics-based explanation and (ii) relevant to statistics and to a general definition of information gain. As a proof of concept, we have built two scoring functions, respectively based on the new and the PMF equations, and compared their performance at ranking predicted structures of proteins by their quality. Using the reference dataset 3DRobot (n=60,200 structures) [35] , we show that the scoring function built with our new formalism is more accurate than statistical PMFs, based on three types of performance evaluation. doi = 10.1016/j.csbj.2020.08.013 id = cord-029957-q7v5gli8 author = Prabhu, D. title = In silico Functional Annotation and Characterization of Hypothetical Proteins from Serratia marcescens FGI94 date = 2020-07-31 keywords = dna; functional; protein summary = Two proteins AGB81206.1 and AGB83112.1 were predicted as a member of the exonuclease-endonuclease-phosphate domain super family which plays a crucial role in the intracellular signaling activities in bacteria (Dlakic, 2000) . The observed function of the HPs helps to understand the crucial role of new proteins in bacterial growth and can be targeted as a potential targets for drug discovery. The protein AGB80728.1 was predicted as Translocation and Assembly Module (TAM), which plays a major role in outer membrane biogenesis and virulence mechanisms in bacterial kingdom (Josts et al., 2017) . This kind of proteins are found in wide variety of prokaryotic and eukaryotic organisms and plays an vital role in cell processes and associated with virulence mechanisms of bacterial pathogens (Cerveny et al., 2013) . Various types of enzymes, transporters, cell division, binding proteins were characterized which play an essential role in the growth, survival virulence and pathogenesis of S. doi = 10.1134/s1062359020300019 id = cord-294677-l1b4mw9d author = Prashantha, C.N. title = Molecular screening of antimalarial, antiviral, anti-inflammatory and HIV protease inhibitors against spike glycoprotein of Coronavirus date = 2020-10-13 keywords = Coronavirus; SARS; protein summary = doi = 10.1016/j.jmgm.2020.107769 id = cord-022235-6ircruag author = Pugsley, Anthony P. title = Later stages in the eukaryotic secretory pathway date = 2012-12-02 keywords = Golgi; TGN; cell; protein; secretory; section summary = Microinjected antibodies recognizing the C-terminal, cytoplasmic tails of plasma membrane proteins can prevent their trans port to the cell surface (25, 590) , but this is probably due to antibodyinduced changes in protein conformation which make the protein incom petent for transport along the secretory pathway, rather than to inhibition of receptor-secretory protein interactions. (545) found that pro-a-factor processing was blocked by sec mutations, which prevented protein movement through the Golgi, and that mature α factor was normally present in secretory vesicles en route to the cell surface. The TGN is the most acidic Golgi compartment, although the pH is almost certainly not as low as in secretory granules (823) or in lysosomal sorting vesicles, in which low pH causes the dissociation of lysosomal proteins from the mannose-6-phosphate receptor (577) (see Section V.G.5). (1022) also observed the transient accumulation of one of these enzymes in coated vesicles, which, they proposed, are specifically involved in the sorting of lysosomal proteins from the secretory pathway. doi = 10.1016/b978-0-12-566770-8.50009-4 id = cord-274424-juj71nc5 author = Pulford, David J. title = Intracellular processing of the porcine coronavirus transmissible gastroenteritis virus spike protein expressed by recombinant vaccinia virus date = 1991-06-30 keywords = Fig; TGEV; protein summary = Abstract The Spike (S) protein from a virulent British field isolate of porcine transmissible gastroenteritis virus (TGEV) FS772/70 was constructed from cDNA and inserted into the vaccinia virus (VV) thymidine kinase gene locus under the control of the VV early/late gene P7.5K promoter. In this paper we report the construction of a FS772/ 70 cDNA S gene and its expression by a recombinant vaccina virus (rVV) to study the antigenicity and cellular localization of the S protein. Expression of the recombinant spike antigens TGEV gene products synthesized by vTS-1 and vTSA-1 were analyzed by pulse labeling rVV-infected HTK-cells with L-[35S]methionine in the presence or absence of 10 pg ml-'' tunicamycin for 6 hr. The lack of detectable ~160 or ~130 in the culture medium of vTS-l-and vTSA-l-infected cells, respectively (Fig. 4 lanes 4 and 7) , could result from the levels being too low to be detected by the antibodies due to reduction in synthesis or the lack of glycosylation of the S protein in the presence of tunicamycin. doi = 10.1016/0042-6822(91)90617-k id = cord-004181-exbs3tz7 author = Pumchan, Ansaya title = Novel Chimeric Multiepitope Vaccine for Streptococcosis Disease in Nile Tilapia (Oreochromis niloticus Linn.) date = 2020-01-17 keywords = Nile; dna; protein; vaccine summary = doi = 10.1038/s41598-019-57283-0 id = cord-341564-fvuwick5 author = Qi, Zhao-Hui title = Novel Method of 3-Dimensional Graphical Representation for Proteins and Its Application date = 2018-06-12 keywords = protein; sequence summary = From these, we can see that physicochemical properties are widely applied with graphical representation of protein sequences by these researchers and their results seem well. In this article, we propose a 3-dimensional (3D) graphic representation of protein sequences based on 10 physicochemical properties [17] [18] [19] [20] [21] of amino acids and the BLOSUM62 matrix. In this article, we propose a 3-dimensional (3D) graphic representation of protein sequences based on 10 physicochemical properties [17] [18] [19] [20] [21] of amino acids and the BLOSUM62 matrix. Therefore, to mine essential information from a protein sequence, we propose an effective graphical method combining physicochemical properties of amino acids and the BLOSUM62 matrix. An efficient numerical method for protein sequences similarity analysis based on a new two-dimensional graphical representation F-Curve, a graphical representation of protein sequences for similarity analysis based on physicochemical properties of amino acids doi = 10.1177/1176934318777755 id = cord-310909-nc82a70n author = Qiu, Maofeng title = Antibody responses to individual proteins of SARS coronavirus and their neutralization activities date = 2005-04-13 keywords = SARS; protein summary = In this study, 13 recombinant proteins associated with four structural proteins (S, E, M and N) and five putative uncharacterized proteins (3a, 3b, 6, 7a and 9b) of the SARS-CoV were prepared and used for screening and monitoring their specific IgG antibodies in SARS patient sera by protein microarray. In the present study, to understand the profile of antibodies to individual proteins of the SARS-CoV, 13 recombinant proteins associated with four structural proteins (S, E, M and N) and five putative uncharacterized proteins (3a, 3b, 6, 7a and 9b) of this virus were prepared and used to screen and monitor their specific IgG antibodies in SARS patient sera using protein microarray, and the rabbit antisera to recombi-nant proteins S3 (aa 241-591), N (full length), 3a (aa 125-274) and 9b (full length) were prepared and used to investigate their neutralizing activity to the SARS-CoV infection in Vero E6 cells. doi = 10.1016/j.micinf.2005.02.006 id = cord-003144-nqkw5v3w author = Qu, Zehui title = Label‐Free Quantitative Proteomic Analysis of Differentially Expressed Membrane Proteins of Pulmonary Alveolar Macrophages Infected with Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus and Its Attenuated Strain date = 2017-11-24 keywords = PRRSV; protein summary = title: Label‐Free Quantitative Proteomic Analysis of Differentially Expressed Membrane Proteins of Pulmonary Alveolar Macrophages Infected with Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus and Its Attenuated Strain Significant differences exist between the highly pathogenic (HP) porcine reproductive and respiratory syndrome virus (PRRSV) and its attenuated pathogenic (AP) strain in the ability to infect host cells. This is the first attempt to explore the differential characteristics between HP‐PRRSV and its attenuated PRRSV infected PAMs focusing on membrane proteins which will be of great help to further understand the different infective mechanisms of HP‐PRRSV and AP‐PRRSV. Differentially expressed proteins between control and HP-PRRSV-infected cells (Con/HP) and the www.advancedsciencenews.com www.proteomics-journal.com p <0.01 and ratio >2 or <0.5 indicated quantitative difference between two groups. By analyzing detected proteins in HP-infected, AP-PRRSV-infected, and control group, proteins related to the immune response or virus replication were identified that may elucidate unique pathways used by different virulent PRRSVs for cell entry, virus replication, and immune escape mechanisms. doi = 10.1002/pmic.201700101 id = cord-338980-pygykil7 author = Rahaman, Jordon title = Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses date = 2016-11-09 keywords = MERS; SARS; protein; site summary = Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the >10,000 starting sites across all coronaviruses in this study. For the DISOPRED2 predictions that were inferred using the nr database, the continuous disorder propensities for every site in a protein were mapped onto their corresponding position in the multiple sequence alignment as raw disorder propensities and as binary states, order or disorder, using a cutoff of 5. For regions with five or more consecutive sites that were 100% conserved in sequence across 1) all CoV or 2) across the MERS and SARS clades, the information of structural disorder prediction from IUPred and DISOPRED2 was used to identify all ungapped sites that were consistently predicted to have 100% conserved order. doi = 10.1093/gbe/evw246 id = cord-190540-zf5ksac2 author = Rakshit, Kausik title = An effective approach to reduce the penetration potential of Sars-Cov-2 and other viruses by spike protein: Through surface particle electrostatic charge negotiation date = 2020-06-18 keywords = SARS; charge; protein summary = title: An effective approach to reduce the penetration potential of Sars-Cov-2 and other viruses by spike protein: Through surface particle electrostatic charge negotiation Reviewing the works of different authors, regarding charges, surface charge densities ({sigma}), charge mobility ({mu}) and electrostatic potentials of different aerosols under varied experimental conditions, a similar intensive study has also been carried out to investigate the electron donating and accepting (hole donating) properties of the spike proteins (S-proteins) of different RNA and DNA viruses, including SARS-COV-2. The electrostatic charges accumulated in the layers between the Gr IV Ge is sufficient enough to either fuse or repel the charges of the spike proteins of the RNA, DNA viruses including SARS-Cov-2 (RNA virus) or the aerosols. doi = nan id = cord-339558-li65qvq9 author = Rana, Rashmi title = A comprehensive overview of proteomics approach for COVID 19: new perspectives in target therapy strategies date = 2020-11-02 keywords = SARS; protein summary = Structural proteome analysis of earlier SARS epidemic in 2003 revealed a large array of proteins that could be targeted for this pandemic too. They used affinity purification followed by mass spectrometry analysis and statistical modeling of the MS1level quantitative data which allowed the identification of 1484 interactions between 1086 cellular proteins and 24 SARS-CoV bait proteins. 2013 ) A recently published study involves the development of an Opto-microfluidic sensing platform to rapidly detect antibodies against SARS-CoV2 spike protein in diluted human plasma with high sensitivity. It is the first study to detect the SARS-CoV-2 antigens in the blood plasma of COVID-19-positive patients. Mass spectrometric identification of SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry doi = 10.1007/s42485-020-00052-9 id = cord-018493-q24f86e9 author = Ranjan, Prabhat title = Importance of Natural Proteins in Infectious Diseases date = 2015-08-08 keywords = cell; disease; like; protein summary = Other extracellular proteins like invasive enzymes, e.g., coagulase, contributes to the formation of fibrin walls around staphylococcal lesions [10] ; exotoxins (proteins released extracellularly), like neurotoxin (Tetanus toxin, by Clostridium tetani, Botulinum toxin by Clostridium botulinum) [11] and cytotoxins (Diphtheria toxin produced by Corynebacterium dipthereae) [12, 13] , also known as A-B toxins (consisting of 2 subunits: one binds to cell surface receptor and the other is transferred into the cell to damage the cell) [14] , cytolytic toxins (attacking cell constituents causing lysis) like hemolysins produced by Bordetella pertussis, inducing apoptosis of host cells, super antigen toxins (e.g., superantigen, sized 22KDa produced by 5-25 % of Staphylococcus aureus isolates, causing toxic shock syndrome (TSS) by stimulating the release of large amounts of interleukin-1, interleukin-2 and tumor necrosis factor, etc.) [15] . Nucleotide-binding and oligomerization domain (NOD)-like receptors (NLRs) are a group of evolutionarily conserved intracellular proteinaceous PRRs that play a vital role in innate immunity and host physiology, in both plants and animals [30, 31] . Heat shock proteins can be expressed on the surface of infected cells, and this is likely to provide a target for the innate immune response. doi = 10.1007/978-81-322-2491-4_8 id = cord-011012-5mev3otu author = Rathore, Abhishek Singh title = Production and immunogenicity of Fubc subunit protein redesigned from DENV envelope protein date = 2020-03-30 keywords = DENV; Fubc; protein summary = doi = 10.1007/s00253-020-10541-y id = cord-298802-a5h91axf author = Ravindran, Madhu Sudhan title = Molecular chaperones: from proteostasis to pathogenesis date = 2018-06-22 keywords = Hsp70; protein summary = doi = 10.1111/febs.14576 id = cord-199630-2lmwnfda author = Ray, Sumanta title = Predicting potential drug targets and repurposable drugs for COVID-19 via a deep generative model for graphs date = 2020-07-05 keywords = SARS; drug; host; node; protein summary = Therefore, host-(1) We link existing high-quality, long-term curated and refined, large scale drug/protein -protein interaction data with (2) molecular interaction data on SARS-CoV-2 itself, raised only a handful of weeks ago, (3) exploit the resulting overarching network using most advanced, AI boosted techniques (4) for repurposing drugs in the fight against SARS-CoV-2 (5) in the frame of HDT based strategies. As for (3)-(5), we will highlight interactions between SARS-Cov-2-host protein and human proteins important for the virus to persist using most advanced deep learning techniques that cater to exploiting network data. As per our simulation study, a large fraction, if not the vast majority of the predictions establish true, hence actionable interactions between drugs on the one hand and SARS-CoV-2 associated human proteins (hence of use in HDT) on the other hand. doi = nan id = cord-000674-36jzzy77 author = Reggiori, Fulvio title = Autophagy: More Than a Nonselective Pathway date = 2012-05-15 keywords = Atg; Cvt; autophagy; figure; lc3; protein summary = doi = 10.1155/2012/219625 id = cord-261159-9pkg7mbh author = Regnier, Fred E. title = Chromatography of complex protein mixtures date = 1987-07-17 keywords = IEC; RPC; SEC; column; exchange; protein summary = Although large amounts of organic solvent are occasionally used in the mobile phase to solubilize proteins, as in the case of chloroplast proteins [ 181, most IEC separations are carried out with either non-ionic detergents or the 3-[ ( 3-chloroamidopropyl) dimethylammonio] -l-trifluoroacetic acid ( CHAPS) zwitterion [ 24,251. Using a series of polyethylene glycol alkyl ether (C,E,) detergents as a mobile phase additive it was possible to show that both alkyl chain length and the number of glycol residues influenced resolution of Escherichiu coZi K-12 membrane proteins in anion-exchange separations [ 191 (C&E, was optimal) . Elution of proteins and peptide fragments from RPC columns was achieved with mobile phases containing 5% formic acid. In the case of red blood cell membrane proteins, the resolution of 1000 A pore diameter organic resin-based sorbents was superior to 300 A pore diameter silica-based materials when the columns were eluted with a TFA-acetonitrile mobile phase [ 261. doi = 10.1016/0378-4347(87)80007-5 id = cord-018479-mvnm98hv author = Rehm, Fabian B. H. title = Applications of Microbial Biopolymers in Display Technology date = 2017-11-16 keywords = PHA; Rehm; protein summary = Such beads have been demonstrated in diverse applications, including fluorescence-activated cell sorting, enzyme-linked immunosorbent assays, microarrays, diagnostic skin test for tuberculosis, vaccines, protein purification, and affinity bioseparation. Most recently, PHA inclusions with GFP and MOG fused to PhaP or PhaC, such that each granule is simultaneously displaying two protein-based functionalities, were examined in the context of FACS, providing proof-of-concept for the biotechnological application of bifunctional PHA beads which may extend beyond FACS ). This study demonstrated that V HH domains from camelid antibodies, designed ankyrin repeat proteins (DARPins) and OB-folds (OBodies), could be densely displayed on PHA beads resulting in high affinity binding resins for purification of various target proteins. Overall, PhaC engineering such as N-or C-terminal fusions and/or insertions enabled efficient display of binding domains for interaction with target compounds resulting in purification performance suitable for application as bioseparation resin. doi = 10.1007/978-3-319-50436-0_377 id = cord-010604-3d37o05y author = Rein, Theo title = Post-translational modifications and stress adaptation: the paradigm of FKBP51 date = 2020-04-29 keywords = FKBP51; PTM; SKP2; protein summary = doi = 10.1042/bst20190332 id = cord-321275-7haq0e38 author = Renzi, Fabiana title = Large-scale purification and crystallization of the endoribonuclease XendoU: troubleshooting with His-tagged proteins date = 2006-02-28 keywords = protein summary = The tendency of the recombinant enzyme to aggregate could be reversed upon the addition of chelating agents (EDTA, imidazole): aggregation is a potential drawback when purifying and crystallizing His-tagged proteins, which are widely used, especially in high-throughput structural studies. Subsequent screening resulted in the growth of crystals (300 Â 300 Â 300 mm) in 40% (NH 4 ) 2 SO 4 , 0.2 M sodium citrate pH 6 at 293 K which belonged to space group P3 1 21 but diffracted poorly; the resolution was improved by cocrystallization with 50 mM uridine 5 0 -monophosphate (5 0 -UMP), which may bind to the active site, possibly inducing the stabilization of flexible regions (Fig. 2a) . Large-scale expression of His-tagged XendoU resulted in soluble protein that was heterogeneously aggregated, a condition that affects crystallization (Wilson, 2003) . doi = 10.1107/s1744309106006373 id = cord-320713-b37c8aye author = Roberts, Lisa O. title = Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date = 2009-10-27 keywords = IRES; PABP; PKR; RNA; protein; translation; viral; virus summary = 6 The rate of translation initiation in mammalian cells is also controlled by sequence elements within the 5 0 -and 3 0 -UTRs of mRNAs which regulate this process by providing sites for interaction of regulatory proteins and RNAs. These include upstream open reading frames (uORFs), microRNA (miRNA) target sites, and polyadenylation elements. 5 It was suggested that alternative eIF4F complexes lacking PABP could selectively promote the synthesis of viral, but not host, proteins, so that KSHV-encoded mRNAs would compete more effectively for host translation machinery in infected cells. Picornavirus translation is directed by internal ribosome entry sites (IRESs) within the 5 0 -UTRs of the viral RNAs. The central one-third of eIF4G, containing the eIF3 and one eIF4A-binding domain, is sufficient to support translation initiation from these IRESs. 43 This allows picornavirus RNAs to compete effectively for the host translation machinery following infection, although the situation appears to be more complicated than this (see Section III). doi = 10.1016/s1877-1173(09)90009-6 id = cord-329844-w969lczb author = Robson, B. title = Bioinformatics studies on a function of the SARS-CoV-2 spike glycoprotein as the binding of host sialic acid glycans date = 2020-06-08 keywords = SARS; acid; bind; glycan; protein; residue; sialic; sugar summary = The location of any sialic acid glycan binding region of SARS-CoV-2 is, a priori unclear, although intuitively (a) it would likely be associated with the cap or knob at the outer end of the spike protein, or (b) at least not involve exactly the same domain as is required for other important functions. An algorithm for predicting the domains and proteins involved in sialic acid glycan binding is developed in the course of the project described in Results Section 4, but this is primarily of a highly empirical nature. This, plus a sequence rather than three dimensional structure perspective, and a specific focus on binding sialic acid glycans rather than sugars in general, resulted in a substantial difference in scores from another major method of predicting sugar binding regions of proteins also discussed later below. doi = 10.1016/j.compbiomed.2020.103849 id = cord-333262-xvfl7ycj author = Robson, B. title = COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date = 2020-04-11 keywords = ACE2; COVID-19; KRSFIEDLLFNKV; SARS; Wuhan; bind; peptide; protein; spike; virus summary = The Wuhan and related isolates revealed a coronavirus that resides in the subgenus Sarbecovirus of the genus Betacoronavirus [2] , and although genetically distinct from its predecessor SARS-CoV it appeared to have similar external binding proteins, meaning here the spike glycoprotein discussed extensively in the present paper. In brief summary, the justifications for the ensemble pharmacophore in the coronavirus case, i.e. the contributions to "fuzziness", include parsimony, that proteins and parts of proteins sometimes have more than one function [12] encouraged by limited numbers of accessible sites (due to e.g. glycosylation) and exemplified by parallel alternative mechanisms of cell entry, multiple methods of drug action, escape from scientific defense measures by virus mutation, polymorphism of human proteins involved, different expression levels of human proteins involved, and the potential problem of the "specter of vaccine development" (concerns about missing the appropriate region of the virus that allows common cold viruses to escape the appropriate immune response). doi = 10.1016/j.compbiomed.2020.103749 id = cord-276966-wmelyonk author = Roe, Kevin title = A proposed treatment for pathogenic enveloped viruses having high rates of mutation or replication date = 2020-07-08 keywords = cell; pathogen; protein summary = In targeting specific viral pathogens, dual-protein ligand masks (for brevity, henceforth called dualprotein ligands) should be able to create a quick and powerful immune memory response with existing memory immune cells against some viral pathogens or virus infected cells, without some of the practical limitations of vaccines. Dual-protein ligands could induce an immune response by mimicking the key parts of antigens that activate existing immune memory cells or innate immune cells to attack tagged viral pathogens. All rights reserved One treatment option injects dual-protein ligands into the blood stream or localized regions to mask pathogenic surface proteins used by viruses to infect mammalian cells. Targeted dual-protein ligands could mask viral surface proteins to quickly treat some untreatable virus infections by using already existing immune cells. doi = 10.1111/sji.12928 id = cord-341324-f9g9gitn author = Rojas, José M. title = Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway date = 2020-10-21 keywords = IFN; IRF3; PRR; RNA; protein; rig; virus summary = This includes for instance cooperating in PRR recognition of viral PAMPs, stabilizing signaling complexes to improve their resistance to degradation, stopping virus entry, blocking viral capsid formation, impairing trafficking and budding of virions from the infected cells, but also modulating the IFN response to avoid the toxicity of these potent immune mediators. The phosphorylated STAT1/STAT2 heterodimer associates with interferon regulatory factor 9 (IRF9) to form the transcriptional factor complex ISGF3, which translocate to the nucleus and binds the IFN-response elements (ISRE) in ISG promoters leading to the expression of ISG products [36] (Fig. 2 The oligoadenylate synthetase (OAS)-latent RNase (RNase L) pathway is another IFN-inducible pathway that provides the cell with an effector mechanism upon recognition of viral dsRNA (reviewed in [44] ). doi = 10.1007/s00018-020-03671-z id = cord-306733-df36w6l7 author = Rosales-Mendoza, Sergio title = What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date = 2020-04-14 keywords = COVID-19; SARS; plant; protein; vaccine; virus summary = Transient nuclear genome transformation Rapid production; high productivity; implemented at the industrial level Seed bank cannot be generated; requires purification of the antigen to eliminate toxic compounds from the host and ag-robacteria residues S protein; multiepitope vaccines A chimeric protein of GFP and amino acids 1-658 of the SARS-CoV-1 S protein (S1:GFP) was transiently expressed in tobacco leaves and stably transformed in tobacco and lettuce. No immunization assays were performed The SARS-CoV-1 N protein was transiently expressed in Nicotiana benthamiana, which induced in mice high levels of IgG1 and IgG2a and up regulation of IFN-γ and IL-10 in splenocytes. The precedents of SARS-CoV-1 and MERS antigens expressed in recombinant systems leading to the formation of VLPs constitute important guides for the topic of COVID-19 vaccine development. Thus, VLPs based on the main SARS-CoV-2 structural proteins is an attractive approach for vaccine development against coronavirus infections. doi = 10.3390/vaccines8020183 id = cord-282859-uxltqopq author = Rosati, A title = BAG3: a multifaceted protein that regulates major cell pathways date = 2011-04-07 keywords = BAG3; bag; cell; protein summary = These multifaceted interactions underlie BAG3 ability to modulate major biological processes, that is, apoptosis, development, cytoskeleton organization and autophagy, thereby mediating cell adaptive responses to stressful stimuli. By modulating these pathways, BAG3 appears to mediate cell adaptive responses to stressful stimuli, and its alterations result in altered homeostasis and reduced cytoprotection, explaining why its expression is often found deregulated in a vast series of tumors. 12, 19 In humans, bag3 gene expression is constitutive in myocytes, a few other normal cell types and several primary tumors or tumor cell lines (lymphoid or myeloid leukemias, lymphomas, myeloma, neuroblastoma, pancreas, thyroid, breast and prostate carcinomas, melanoma, osteosarcoma, kidney, colon and ovary cancers, glioblastoma). 67 Similarly to what we described above for apoptosis, the ability of BAG3 to regulate cell adhesion appears to rely on multiple interactions of this protein through different structural domains. doi = 10.1038/cddis.2011.24 id = cord-270273-a4iu9qg6 author = Ruiz, Federico M. title = Chicken GRIFIN: Structural characterization in crystals and in solution date = 2017-12-15 keywords = Fig; GRIFIN; galectin; lactose; protein summary = The case study on galectins (b-galactoside-binding proteins with b-sandwich fold and a sequence signature responsible for ligand contact [5] ) is describing such a network with overlapping and distinct expression profiles [6e8]. In this study, the availability of crystals of the same protein obtained at different conditions documents the very low degree of influence of the pH value on the galectin fold, with some variability in unit cell Looking closely at the interface region between the two subunits of C-GRIFIN''s homodimer, it is established by the F1/S1 strands from the N-and C-termini of each subunit in the homodimer (residues 4e14/127-136) (Fig. 4B) . Taking analysis of C-GRIFIN and lactose binding again to the level of a solution in this report, measuring extent and profile of HDX in the absence and presence of ligand can identify the contact site. doi = 10.1016/j.biochi.2017.12.003 id = cord-274080-884x48on author = Rumlová, Michaela title = In vitro methods for testing antiviral drugs date = 2018-06-30 keywords = HBV; HCV; HIV-1; RNA; cell; dna; protein; viral; virus summary = For the majority of animal viruses, the activation of these fusion or penetration mechanisms occurs through conformational changes and structural rearrangements in viral surface proteins and/or the whole virion shell that may destabilize the capsid core. D: Three mechanisms (I.-III.) of DNA viruses replication are shown: (I): Following entry and uncoating, the DNA genome is transported to the nucleus; products of early genes (regulatory proteins, transcription factors) regulate the synthesis of viral enzymes (e.g. DNA polymerase) required for genome replication; expression of late genes encoding structural capsid proteins in the cytosol, they are then transported into nucleus where packaging and pre-assembly take place; preassembled procapsids exit the nucleus and leave the cell (e.g. Herpesviruses). Here, we provide an overview of in vitro methods, including cell-based assays, that may be suitable for screening of antivirotics that interfere with the key steps of viral life cycles and target either virus or cell-encoded proteins required for the infectivity. doi = 10.1016/j.biotechadv.2017.12.016 id = cord-018018-2yyv8vuy author = Rybicki, Ed title = History and Promise of Plant-Made Vaccines for Animals date = 2018-07-04 keywords = expression; plant; protein; vaccine summary = 1995) was also used to demonstrate the efficacy of two very different plant-made papillomavirus vaccines, a few years after the demonstration that Human papillomavirus L1 major capsid protein virus-like particles could be produced in transgenic tobacco or potato (Biemelt et al. The early historical account of molecular farming for veterinary vaccines given above gives an idea of the array of technologies available and used up to the mid-2000s: transgenic and transplastomic expression of subunit proteins; recombinant plant viruses either used to express whole vaccine candidate genes, or to display chosen peptides fused to their capsid proteins; fusion of vaccine protein genes to carrier proteins to improve immunogenicity, including by inherent adjuvant properties; candidate parenteral and oral vaccines to both viruses and bacteria; therapeutics for animals made in plants; use of plant cell cultures to make antigens. doi = 10.1007/978-3-319-90137-4_1 id = cord-292985-w62xaa4f author = Römer, Rudolf A. title = Flexibility and mobility of SARS-CoV-2-related protein structures date = 2020-07-12 keywords = SARS; protein; structure summary = We are using a recent protein flexibility modelling approach, combining protein structural rigidity with possible motion consistent with chemical bonds and sterics. 34 We have performed our analysis through multiple conformational steps starting from the crystal structures of SARS-CoV-2-related proteins as currently deposited in the PDB. In Fig. 1 (a) we see that for the crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain (PDB:6m3m), the largest rigid cluster in the pristine structure, i.e. at E cut = 0, largely remains rigid through the dilution process of consecutively lowering E cut values. Last, a protein with 2nd-order rigidity should have the most complex behaviour in terms of flexibility since new possible mobility can be expected throughout the range of E cut values. Moving along directions proposed by an elastic normal model analysis of the crystal structure, we can therefore construct possible motion trajectories that are fully consistent with the bond network and steric constraints. doi = 10.1101/2020.07.12.199364 id = cord-355477-7xd93aqv author = SATIJA, NAMITA title = The Molecular Biology of SARS Coronavirus date = 2007-04-23 keywords = RNA; SARS; protein summary = abstract: Severe acute respiratory syndrome (SARS) is the first emerging infectious disease of the 21st century that has been highly transmissible and fatal and was caused by a previously unknown coronavirus (SARS‐CoV). Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Recombinant severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein forms a dimer through its C-terminal domain Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells doi = 10.1196/annals.1408.002 id = cord-023726-2fduzqyb author = STRAUSS, JAMES H. title = The Structure of Viruses date = 2012-07-27 keywords = Fig; RNA; protein; structure; virus summary = Also shown for each family is the presence or absence of an envelope in the virion, the triangulation number (defined later) if the virus is icosahedral, the morphology of the nucleocapsid or core, and figure numbers where the structures of members of a family are illustrated. Structural studies of viruses have shown that the capsid proteins that form the virions of many plant and animal icosahedral viruses have a common fold. The largest particle is the nucleocapsid of herpes simplex virus, which is 1250 Å in diameter and has T=16 symmetry (the virion is enveloped but only the nucleocapsid is regular FIGURE 2.5 Gallery of three-dimensional reconstructions of icosahedral viruses from cryoelectron micrographs. For most RNA viruses, nucleocapsids can be recognized as distinct structures within the infected cell and can be isolated from virions by treatment with detergents that dissolve the envelope. doi = 10.1016/b978-0-12-373741-0.50005-2 id = cord-288673-ku3tmjd3 author = Sabotič, Jerica title = Microbial and fungal protease inhibitors—current and potential applications date = 2012-01-05 keywords = Barrett; Rawlings; Staphylococcus; cysteine; family; inhibitor; plant; protease; protein; target summary = Because proteases play essential roles in life and death processes in all living organisms and because peptide bond hydrolysis is irreversible, anomalies in proteolytic activities lead to numerous pathological conditions, including cancer, neurodegenerative disorders and inflammatory and cardiovascular diseases, as well as bacterial, viral and parasitic diseases (Lopez-Otin and Bond 2008; Turk 2006) . Another important oral cavity pathogen involved in periodontal disease, Porphyromonas gingivalis, in addition to a few cysteine proteases (discussed further in the following), produces a serine protease, a prolyl tripeptidyl peptidase PtpA (family S9), which is involved in degrading host connective tissue, providing nutrients for bacterial growth (Banbula et al. Several proteases of the serine catalytic type have also been targeted for the design of specific protease inhibitors for use in cancer treatment, including the urokinase plasminogen activator and matriptase (Abbenante and Fairlie 2005; Bialas and Kafarski 2009; Ulisse et al. doi = 10.1007/s00253-011-3834-x id = cord-286301-7sjw5ci7 author = Sadasivan, Jibin title = Cytoplasmic tail of coronavirus spike protein has intracellular targeting signals date = 2017-04-18 keywords = OC43; SARS; protein summary = SARS-S-Y was absent from surface in most of the cells and localized at the intracellular compartments (figure 5a), and OC43-S protein was mainly localized in distinct puncta that could represent endocytic structures following internalization from the plasma membrane (figure 5b). Our studies clearly demonstrated that the KXHXX motif is the major intracellular localization signal of the full-length SARS-S protein and the C-terminal proximity is not essential. Our alanine mutation studies on the KXHXX motif confirm the importance of the lysine and histidine in the full-length wild-type HCoV-SARS S protein; the mutant protein showed localization in plasma membrane instead of the usual ER and ERGIC. In contrast, Lysosomal acid phosphatase, also a type I membrane protein with a cytosolic tail GYXXØ motif located 7 residues from both transmembrane domain and the carboxy termini (Tm-RMQAQPPGYRHVADGEDHA) delivered mainly via the cell surface (Braun et al. doi = 10.1007/s12038-017-9676-7 id = cord-020757-q4ivezyq author = Saikumar, Pothana title = Apoptosis and Cell Death: Relevance to Lung date = 2010-05-21 keywords = Fas; TNF; apoptosis; cell; death; protein summary = The extrinsic pathway involves binding of death ligands such as tumor necrosis factor-α (TNF-α), CD95 ligand (Fas ligand), and TNF-related apoptosis-inducing ligand (TRAIL) to their cognate cell surface receptors TNFR1, CD95/Fas, TRAIL-R1, TRAIL-R2, and the DR series of receptors, 29 resulting in the activation of initiator caspase-8 (also known as FADD-homologous ICE/CED-3-like protease or FLICE) and subsequent activation of effector caspase-3 ( Figure 4 .2). In cytotoxic T lymphocyte-induced death, granzyme B, which enters the cell through membrane channels formed by the protein perforin, activates caspases by cleaving them directly or indirectly. Intracellular Pathways: Lack of survival stimuli (withdrawal of growth factor, hypoxia, genotoxic substances, etc.) is thought to generate apoptotic signals through ill-defi ned mechanisms, which lead to translocation of proapoptotic proteins such as Bax to the outer mitochondrial membrane. For example, agents that damage DNA, such as ionizing radiation and certain xenobiotics, lead to activation of p53-mediated mechanisms that commit cells to apoptosis, at least in part through transcriptional upregulation of proapoptotic proteins. doi = 10.1007/978-0-387-72430-0_4 id = cord-048471-7jszm1nd author = Salim, Omar title = Functional Analysis of the 5′ Genomic Sequence of a Bovine Norovirus date = 2008-05-14 keywords = RNA; protein summary = Although slightly larger than predicted the N-term protein was detected in a processed form in vivo, thus not only demonstrating initial translation of the ORF1 polyprotein but also activity of the viral protease. Previous studies of norovirus polyprotein processing have yielded three major products following in vitro transcription and translation, representing the uncleaved 3ABCD, N-term and 2C proteins. In addition, this important observation also confirms for the first time that the JV 3C protease was active in cells transfected with capped RNA as the size of the V5/N-term indicated successful cleavage of the protein from the ORF1 polyprotein. Unlike similarly studied human noroviruses JV initially did not appear to express the N-terminal protein, presenting the possibility that the encoding RNA sequence had a regulatory function itself, most likely involved in translation initiation in an IRES-like manner. doi = 10.1371/journal.pone.0002169 id = cord-319517-denczc6t author = Salipalli, Sandeep title = Recent advances in live cell imaging of hepatoma cells date = 2014-07-08 keywords = GFP; cell; fluorescent; fret; gene; lipid; protein summary = This review aims to provide an overview of the recent developments in the field of marker proteins (bioluminescence and fluorescent) and methodologies (fluorescent resonance energy transfer, fluorescent recovery after photobleaching and proximity ligation assay) employed as to achieve an improved imaging of biological processes in hepatoma cells. The success of live cell imaging relies on various factors including the specific imaging system, climate controlling devices for cultured cells under investigation, construction of recombinant plasmid DNA, transfer and expression of candidate genes and/or fluorescent proteins in mammalian cells. T4SS (Bartonella sp.) 60-70% 50% >70% >60% 50-60% [76] [77] [78] lipofection (1 μg) methods were used for transfection of plasmid encoding fluorescent protein (pEGFP and pEYFP) tagged to human and mouse ADRP genes in Huh-7 cells as to study the pathways of lipid droplet metabolism. doi = 10.1186/1471-2121-15-26 id = cord-318853-mxyxwkhx author = Sallie, Richard title = Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date = 2005-08-22 keywords = HBV; HCV; RNA; cell; protein; receptor; viral; virus summary = Perhaps more importantly, ineluctable generation of broad phenotypic diversity after viral RNA is translated to protein quasispecies suggests a mechanism of disease that specifically targets, and functionally disrupts, the host cell surface molecules – including hormone, lipid, cell signalling or neurotransmitter receptors – that viruses co-opt for cell entry. Hence, as relative concentrations of wild-type and variant viral proteins vary, alteration of both processivity and fidelity of RNA pol results, permitting viruses to adaptively respond to environmental changes, including immune recognition and reaction to evolving cell receptors. As clear evidence exists for viral disruption of leptin function [106] and virus-associated weight gain in humans [107] and monkeys [108] , is it possible the global epidemics of type II diabetes mellitus, insulin resistance, hyperlipidaemia and obesity now prevalent [109] [110] [111] [112] [113] [114] [115] [116] , are just that; epidemics fundamentally caused by viruses that co-opt insulin or leptin or other associated receptors for cell access and generate protein quasispecies that disrupt receptor function? doi = 10.1186/1743-422x-2-70 id = cord-033333-880jx1bt author = Salman, Saad title = In silico analysis of protein/peptide-based inhalers against SARS-CoV-2 date = 2020-10-08 keywords = SARS; protein summary = The molecular docking was performed for these inhalers including human neutralizing S230 light chain-antibody (monoclonal antibodies [mAbs]), alpha-1-antitrypsin (AAT), short-palate-lung and nasal-epithelial clone-1-derived peptides (SPLUNC1) and dornase-alfa (DA) against spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to assess their inhibitory activity. Protein-protein interaction (PPI) of COVID-19 spike glycoprotein with alpha-1-antitrypsin (1atu), dornase-alfa (4AWN), angiotensin-converting enzyme-2 (ACE-2) (PDB ID:1R4L), human palate, lung and nasal epithelium clone protein (SPLUNC1) (4n4x) and human neutralizing the S230 light chain antibody was evaluated through HawkDock. We attempted to address this issue by analyzing a variety of protein/peptide-based inhalers/antimucolytic agents and previously utilized mAb (used in asthma) to observe their possible interaction with the SARS-CoV-2 spike protein. • Molecular docking analysis of protein/peptide-based inhalers revealed that the S230 light chain antibody and dornase-alfa demonstrated a strong affinity for SARS-CoV-2 spike protein. doi = 10.2217/fvl-2020-0119 id = cord-304040-64obh7i3 author = Sande, Charles J. title = Untargeted analysis of the airway proteomes of children with respiratory infections using mass spectrometry based proteomics date = 2018-09-14 keywords = Cii; airway; protein; protocol summary = Our proteomic experiments tested the optimal approach to characterize airway proteome on swab samples eluted in UTM based on the number of proteins identified without BSA depletion (Total proteome: Protocol A) and with its depletion using a commercial kit; Allprep, Qiagen (cellular proteome: Protocol B, Ci, and Cii). Compared to previous mass-spectrometry-based proteomics studies of the upper airway, the number of proteins identified in protocol Cii, vastly exceeded the number of proteins reported in previously published reports 14, 20, 22, 23, 25, 26, 28, 29 . Further characterisation the proteomes identified in protocol Cii, was done by evaluating the expression levels of marker proteins of resident naso-oro-pharyngeal epithelial cells. In addition to these definitive upper-airway proteins, we found a consistently high level of expression of mucins (MUC1 & 5) -the main component of respiratory tract mucus -and mucosal-associated keratins, KRT4 and KRT13. Our search of T-cell associated marker and effector proteins, did not identify any such proteins in the upper-airway proteomes of any of the children in this study. doi = 10.1038/s41598-018-32072-3 id = cord-270587-k56fze59 author = Scherbinina, Sofya I. title = Three-Dimensional Structures of Carbohydrates and Where to Find Them date = 2020-10-18 keywords = Bank; Carbohydrate; Data; NMR; PDB; Protein; figure; structure summary = • Database can be freely accessed through web user interface; • Database must contain experimentally confirmed and/or predicted 3D structures (preprocessed and/or generated on-the-fly from a primary structure input) of glycans, glycoproteins, or protein-carbohydrate complexes; • Stored 3D structures must be deposited as atomic coordinates in PDB, MOL, or other format, and the structures must contain a saccharide moiety; • • Database can be freely accessed through web user interface; • Database must contain experimentally confirmed and/or predicted 3D structures (preprocessed and/or generated on-the-fly from a primary structure input) of glycans, glycoproteins, or protein-carbohydrate complexes; • Stored 3D structures must be deposited as atomic coordinates in PDB, MOL, or other format, and the structures must contain a saccharide moiety; • Currently, CHARMM36 parameterization features include monosaccharides in furanose [171] and pyranose [172] forms, glycosidic linkages between monosaccharides [171, 173] , complex carbohydrates and glycoproteins Detailed comparisons of all-chemical and dedicated force fields in a context of glycan modeling have been published [114, 139, 151, 167] . doi = 10.3390/ijms21207702 id = cord-003435-ke0az7nf author = Schlake, Thomas title = mRNA as novel technology for passive immunotherapy date = 2018-10-17 keywords = RNA; TCR; antibody; car; cell; expression; mrna; protein summary = Recombinant technologies further expanded the available therapies based on mAbs. In vitro antibody selection technologies like phage or ribosome display were developed to enable the generation of highly specific human mAbs out of libraries that may even be naïve for the specific antigens [31] [32] [33] [34] [35] [36] 1 Schematic illustration comparing active immunization and passive antibody immunotherapies. While T cell engineering for adoptive transfer inevitably requires the use of nucleic acids encoding a target-specific receptor, antibody immunotherapy can deploy recombinant proteins. However, the effects of mRNA modifications on translation, immunostimulation and resulting protein expression appear to be variable, for instance dependent on the type of target cells. In comparison to a single transfer of cells with retroviral CAR expression, an mRNA-encoded receptor required three consecutive lymphocyte infusions to obtain a comparable antitumor effect [262] . doi = 10.1007/s00018-018-2935-4 id = cord-020664-m47ejlsn author = Schlüter, Klaus-Dieter title = Intrakrine, parakrine und autokrine Funktionen des PTH/PTHrP-Systems date = 2006 keywords = PTH; PTHrP; der; die; expression; hormone; parathyroid; protein; und summary = Ein groûer Unterschied zwischen dem namensgebenden Peptid der Familie, PTH, und den beiden strukturverwandten Proteinen PTHrP und TIP39 ist, dass PTHrP und TIP39 hauptsåchlich auto-, para-oder intrakrin wirken, wohingegen die PTH-Effekte vorwiegend endokriner Natur sind. Demgegençber gibt es aber auch Untersuchungen, die zeigen, dass in der N-terminalen Region von PTH und PTHrP ebenfalls Sequenzen vorhanden sind, die den PLC/PKC-Signal-Weg aktivieren kaennen (Takasu et al. Aufgrund des Vorkommens von biologisch aktiven mittregionalen PTHrP-Fragmenten kann vermutet werden, dass fçr diese Teilpeptide auch entsprechende Rezeptoren existieren, da diese Peptide nicht in der Lage sind, mit dem klassischen PTH1R zu interagieren. Transgene Måuse, die entweder PTHrP oder aber PTH1R in den Glattmuskelzellen der Gefåûe çberexprimieren, sind hypotensiv und weisen eine gestaerte Reaktion bei Applikation von Vasodilatoren auf Qian et al. 1028±1035 a 1.6 Intrakrine, parakrine und autokrine Funktionen des PTH/PTHrP-Systems Nickols GA, Nana AD, Nickols MA, DiPette DJ, Asimakis GK (1989) Hypotension and cardiac stimulation due to the parathyroid hormone-related protein, humoral hypercalcemia of malignancy factor doi = 10.1007/3-540-28782-5_6 id = cord-017326-1caeui30 author = Seay, Montrell title = Digesting Oneself and Digesting Microbes: Autophagy as a Host Response to Viral Infection date = 2005 keywords = Beclin; PKR; autophagy; cell; protein; virus summary = Genetic studies in yeast and mammalian cells have also shown that the eIF2 kinase signaling pathway is required for starvation and herpes simplex virus-induced autophagy 18 . The role of some of the Atg proteins, including ones that act in the lipid kinase signaling complex and in the ubiquitin-like conjugation pathways, has been studied in plant and mammalian viral infections (see Table 1 ). Together, the studies of Sindbis virus infection in neurons overexpressing beclin 1 or in cultured cells lacking beclin 1 or atg5 demonstrate a role for mammalian autophagy genes in both restricting viral replication and in protection against virus-induced cell death. The interferon-inducible, antiviral PKR signaling pathway positively regulates autophagy, and both mammalian and plant autophagy genes restrict viral replication and protect against virus-induced cell death. The interferon-inducible, antiviral PKR signaling pathway positively regulates autophagy, and both mammalian and plant autophagy genes restrict viral replication and protect against virus-induced cell death. doi = 10.1007/1-4020-3242-0_11 id = cord-266977-5swwc6kr author = Secker, Thomas.J. title = Journal of Hospital Infection A cold water, ultrasonic activated stream efficiently removes proteins and prion-associated amyloid from surgical stainless steel date = 2020-09-19 keywords = UAS; prion; protein; surgical summary = authors: Secker, Thomas.J.; Leighton, Timothy.G.; Offin, Douglas.G.; Birkin, Peter.R.; Hervé, Rodolphe.C.; Keevil, Charles.W. title: Journal of Hospital Infection A cold water, ultrasonic activated stream efficiently removes proteins and prion-associated amyloid from surgical stainless steel Aim: To test the efficacy of an ultrasonically activated stream for the removal of tissue 27 proteins, including prion-associated amyloid, from surgical stainless steel (SS) surfaces. This study has tested the efficacy of UAS technology for the removal of 239 total protein and prion-amyloid from stainless steel, which is considered the most difficult 240 contaminant to decontaminate in the surgical field. 335 J o u r n a l P r e -p r o o f Tissue protein (Dark grey bars) and prion-associated amyloid (light grey bars) attachment 545 from different prion-infected brain homogenates (22L, ME7 and 263K) to surgical stainless 546 steel pre and post treatment with an ultrasonically activated stream (UAS) (Graph A). doi = 10.1016/j.jhin.2020.09.021 id = cord-007211-prygoc0q author = Segawa, Hiroaki title = The Roles of Individual Cysteine Residues of Sendai Virus Fusion Protein in Intracellular Transport(1) date = 1998-06-17 keywords = cysteine; protein summary = doi = 10.1093/oxfordjournals.jbchem.a022044 id = cord-002973-bkr4ndl2 author = Seifi, Morteza title = Accurate prediction of functional, structural, and stability changes in PITX2 mutations using in silico bioinformatics algorithms date = 2018-04-17 keywords = PITX2; Rieger; protein; variant summary = Our results showed that for PITX2, and likely other members of this homeodomain transcription factor family, MutPred, Provean, PMUT, molecular modeling, and CUPSAT can reliably be used to predict PITX2 missense variants pathogenicity. The protein sequence and/or protein structure with mutational position and amino acid residue of 18 previously functionally characterized pathogenic PITX2 missense variants, plus 16 SNPs with a population frequency of higher than 0.05% (thus considered benign polymorphisms), were used to test the predictive value of eleven common bioinformatics prediction programs; SIFT, PolyPhen-2, PANTHER-PSEP, MutPred, MutationTaster, Provean, PMUT, FATHMM, nsSNPAnalyzer, Align GV-GD, and REVEL (Table 4 and Table 5 ). To assess the performance of eight different stability predictor programs (DUET, SDM, mCSM, I-Mutant3.0, MUpro, iPTREE-STAB, CUPSAT, and iStable) in predicting the effect of missense mutations on PITX2 protein stability, the change in protein stability (ΔΔG) were computed for all 24 PITX2 homeodomain variants (15 functionally characterised and 9 functionally uncharacterised mutations) (Table 7) . doi = 10.1371/journal.pone.0195971 id = cord-292958-k5d5fo3i author = Sekhon, Simranjeet Singh title = Porcine epidemic diarrhea (PED) infection, diagnosis and vaccination: A mini review date = 2017-01-04 keywords = PCR; PEDV; ped; porcine; protein summary = Porcine epidemic diarrhea virus (PEDV) is a main etiology causing severe enteric disease in piglets with clinical signs of anorexia, vomiting, diarrhea and dehydration resulting in loss of condition and death within a few days. Many techniques are available for the detection of PEDV from fecal materials, small infected intestines sample, including reverse transcript polymerase chain reaction (RT-PCR), direct immunofluorescence tests (IF), indirect fluorescence antibody tests (IFA), immunohistochemistry techniques (IHC), in situ hydridization, electron microscopy and enzyme-linked immunosorbent assays (ELISA) 2 . (2012) used the Vero cell cultures to isolate CHGD-01 PEDV strain as well as employed direct immunofluorescence assay and EM technique to investigate its specific cytopathic effects in the outbreak of diarrhea in Guangdong (South China) swine 18 . The RT-PCR system in this study could effectively detect PEDV RNA from viral mixtures or small intestinal/ fecal samples in very low number of virus within short time. doi = 10.1007/s13530-016-0287-8 id = cord-342634-4ouhdjsr author = Semrad, Katharina title = Proteins with RNA Chaperone Activity: A World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding date = 2010-12-26 keywords = RNA; activity; chaperone; protein summary = In brief, the group of proteins with RNA chaperone activity includes proteins that, first, open up misfolded structures without requirement of ATP and that, second, are dispensable once the RNA has been folded. coli showed that 1/3 of the tested proteins possesses strong RNA chaperone activity in vitro in the trans-splicing assay [21] . E. coli contains nine members of the csp family and CspA, the major cold-shock protein and CspE were identified to interact non-specifically with RNA molecules and to possess nucleic acid melting activities [44] [45] [46] . Later, a detailed study on possible functions of Ro RNPs, which are Ro ribonucleoprotein complexes, composed of a small noncoding cytoplasmic RNA, termed Y RNA and its protein partners was conducted: besides the permanently associated proteins Ro60 and La, subpopulations of Ro-RNPs also contain hnRNP I and hnRNP K, both of which exhibited strong RNA chaperone activity in vitro in the transsplicing and the cis-splicing assay [22] . doi = 10.1155/2011/532908 id = cord-342756-rgm9ffpk author = Senger, Mario Roberto title = COVID-19: molecular targets, drug repurposing and new avenues for drug discovery date = 2020-10-02 keywords = ACE2; COVID-19; CoV-2; Fig; MERS; RNA; SARS; clinical; drug; protein summary = Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. In the following topic, we will review SARS-CoV-2 structure and mechanism of infection in order to discuss molecular targets from the virus or its human host that are being considered for drug repurposing and perhaps future development of new drugs. (128) Its role as a functional receptor of SARS-CoV-2 S protein in host cells makes this protein a potential drug target to treat COVID-19. (138) TMPRSS2 has a major role in SARS-CoV-2 cell entry and replication, and thus represents an interesting therapeutic target since its inhibitors could potentially block virus infection in its initial stages. (199) A robust preclinical drug discovery pipeline comprising in vitro, and in vivo models of SARS-CoV-2 infection is particularly important to identify new antivirals for human COVID-19 treatment. doi = 10.1590/0074-02760200254 id = cord-350558-qfdp4ov9 author = Shaban, Mohammed Samer title = Inhibiting coronavirus replication in cultured cells by chemical ER stress date = 2020-08-26 keywords = Fig; cell; protein summary = We found that the ER stress inducer thapsigargin efficiently inhibits coronavirus (HCoV-229E, MERS-CoV, SARS-CoV-2) replication in different cell types, (partially) restores the virus-induced translational shut-down, and counteracts the CoV-mediated downregulation of IRE1α and the ER chaperone BiP. A detailed proteomics analysis reveals multiple thapsigargin-78 regulated pathways and a network of proteins that are suppressed by CoV but (re)activated by 79 chemically stressed infected cells. we determined the expression levels of 166 components of the ER stress pathway KEGG 04141 85 "protein processing in endoplasmic reticulum" in human HuH7 liver cells, a commonly used cellular 86 model for CoV replication, in response to infections with HCoV-229E and MERS-CoV, respectively. The highly inducible HERPUD1 protein has an essential scaffolding function for the organization of searching our proteomics data for further ERAD factors we were able to retrieve a total of 34 (for 284 MERS-CoV) and 20 (for SARS-CoV-2) proteins of the canonical ERQC and ERAD pathways for 285 which a differential expression was observed in virus-infected cells treated with thapsigargin (Fig. 286 5H) . doi = 10.1101/2020.08.26.266304 id = cord-322926-xlwsj3v2 author = Shanmugaraj, Balamurugan title = Plant Molecular Farming: A Viable Platform for Recombinant Biopharmaceutical Production date = 2020-07-04 keywords = expression; plant; production; protein summary = Given the speed advantages, and proven viability of the plant production platform, the transient expression system in particular could be employed to produce recombinant proteins at high levels to meet the sudden demand for production of viral antigens or antiviral proteins that could be used as research reagents, emergency vaccines (SARS-CoV-2 subunit and virus-like particle vaccines), or other biopharmaceuticals to fight against COVID-19 [25, 124] . Given the speed advantages, and proven viability of the plant production platform, the transient expression system in particular could be employed to produce recombinant proteins at high levels to meet the sudden demand for production of viral antigens or antiviral proteins that could be used as research reagents, emergency vaccines (SARS-CoV-2 subunit and virus-like particle vaccines), or other biopharmaceuticals to fight against COVID-19 [25, 124] . doi = 10.3390/plants9070842 id = cord-290472-w77cmljm author = Sharon, Donald title = Systems Biology Approaches to Disease Marker Discovery date = 2010-06-09 keywords = RNA; SARS; cancer; disease; marker; protein summary = doi = 10.3233/dma-2010-0707 id = cord-008293-5cwb5g3h author = Shaw, Shyh-Yu title = Analogous amino acid sequences in myelin proteolipid and viral proteins date = 1986-10-27 keywords = MBP; protein summary = doi = 10.1016/0014-5793(86)81502-2 id = cord-000884-zq8kqf6h author = Shen, Hsin-Hui title = Reconstitution of Membrane Proteins into Model Membranes: Seeking Better Ways to Retain Protein Activities date = 2013-01-14 keywords = activity; bilayer; lipid; membrane; protein summary = doi = 10.3390/ijms14011589 id = cord-345088-krb1eidw author = Shen, S title = A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature date = 2004-09-01 keywords = IBV; cell; protein summary = title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature Here, we report the emergence and isolation of two temperature sensitive (ts) mutants and a revertant in the process of cold-adaptation of coronavirus infectious bronchitis virus (IBV) to a monkey kidney cell line. Evidence presented demonstrated that the Q(294)-to-L(294) mutation, located at a highly conserved domain of the S1 subunit, might hamper processing of the S protein to a matured 180-kDa, endo-glycosidase H-resistant glycoprotein and the translocation of the protein to the cell surface. In virus-infected cells, the Endo-H sensitive, 155-kDa form of ts291602 was abundant at the nonpermissive temperature, clearly indicating that the mutant S protein was trimmed in the ER and cis-Golgi but was not transported to the trans-Golgi. doi = 10.1016/j.virol.2004.06.016 id = cord-003070-6oca1mrm author = Shen, Wen-Jun title = RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence date = 2018-02-28 keywords = Pred; RNA; RPI; protein summary = doi = 10.3390/molecules23030540 id = cord-330475-mameyzih author = Shi, Da title = Molecular Characterizations of Subcellular Localization Signals in the Nucleocapsid Protein of Porcine Epidemic Diarrhea Virus date = 2014-03-13 keywords = NES; PEDV; protein summary = Furthermore, by utilizing fusion proteins with green fluorescent protein (GFP), deletion mutations or site-directed mutagenesis of PEDV N protein, coupled with live cell imaging and confocal microscopy, it was revealed that, a region spanning amino acids (aa), 71–90 in region 1 of the N protein was sufficient for nucleolar localization and R87 and R89 were critical for its function. The B23.1-DsRed fusion protein was used to tag the nucleolus, so we could analyze nucleolar localization properties and colocalization in cotransfected cells by live cell imaging (direct fluorescence) or confocal microscopy. These expression plasmids were transfected into Vero E6 cells, the nuclear was stained with DAPI at 24 h post-transfection indicated that amino acids 148-220 directed AcGFP to the cytoplasm and nucleus and had a subcellular localization similar to AcGFP. doi = 10.3390/v6031253 id = cord-354050-kcn67stj author = Shi, Guoli title = More than meets the I: the diverse antiviral and cellular functions of interferon-induced transmembrane proteins date = 2017-11-21 keywords = Env; HIV-1; IFITM; cell; protein summary = Most of what we know about the antiviral activities of IFITM proteins results from work using IAV and vesicular stomatitis virus (VSV), which perform pH-dependent fusion reactions in endosomes to gain access to the cell interior [22] . As the primary determinant for virus-cell attachment and the subsequent fusion reaction, the viral envelope glycoprotein (Env) was suspected to play an important role in whether or not HIV-1 and related lentiviruses are subject to inhibition by IFITM proteins. In addition to restricting virus entry, recent findings indicate that IFITM proteins perform antiviral functions impacting late stages of the HIV-1 life cycle. This antiviral activity is enhanced upon expression of an IFITM3 mutant that is defective for endocytosis, indicating that restriction of HIV-1 virion infectivity is performed at the plasma membrane [5] . Nonetheless, the recent identification of Env variants that are resistant to the IFITM3-mediated restriction of virion infectivity confirms this viral protein as an important determinant. doi = 10.1186/s12977-017-0377-y id = cord-281101-gv1sgbk1 author = Shin, Gu-Choul title = Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein date = 2006-08-30 keywords = ELISA; SARS; protein summary = Severe acute respiratory syndrome-coronavirus nucleocapsid (SARS-CoV N) protein has been found to be important to the processes related to viral pathogenesis, such as virus replication, interference of the cell process and modulation of host immune response; detection of the antigen has been used for the early diagnosis of infection. Reactivity of SARS-N mAbs with SARS-CoV infected cells was determined by immunofluorescence assay, performed according to the instructions of the manufacturer (Euroimmun, Germany). To further assess the specificity of the mAbs, antigen-capture ELISA was performed with human coronavirus-infected cell lysates and BrSARS-N protein as positive control (Fig. 6B) . (B) Cross-reactivity of SARS-N mAbs was examined by antigen-capture ELISA using human coronavirus OC43 lysates (256 HA unit), BrSARS-N protein (500 ng/well) and PBST buffer with 1% BSA as control. These mAbs were available for use in detecting SARS-CoV N protein by various diagnostic methods, such as immunoblot assay, immunofluorescence assay and antigen-capture ELISA (Table 3) . doi = 10.1016/j.virusres.2006.07.004 id = cord-009636-5kddituy author = Shirbaghaee, Zeinab title = Different applications of virus‐like particles in biology and medicine: Vaccination and delivery systems date = 2015-12-22 keywords = HBV; HPV; VLP; cell; protein summary = doi = 10.1002/bip.22759 id = cord-287477-aios0h8s author = Sicari, Daria title = Role of the early secretory pathway in SARS-CoV-2 infection date = 2020-07-28 keywords = Golgi; SARS; protein summary = CoV-2 infection starts when its spike (S) protein binds to angiotensin I-converting enzyme 2 (ACE2) receptors on the host cell membrane (Lake, 2020; Letko et al., 2020) . Thus, virion spread critically depends on recruiting the most efficient secretory machineries of host cells (Su et al., 2016; Proteins of the early secretory pathway bound by SARS-CoV-2 As the entire world asks for ways to stop CoV-2, many laboratories are investigating the virus''s Achilles heel(s). The role of glycosylation and protein quality control in SARS-CoV-2 infections Most CoVs bud at the ERGIC level ( Fig. 1) and are then transported along the exocytic pathway (Klumperman et al., 1994; Stertz et al., 2007) . We observed enrichment for five host-derived virus-interacting proteins (GOLGB1, PDE4DIP, TOR1A, HMOX1, and HYOU1) involved in different processes and related to quality control and ER-Golgi homeostasis maintenance. doi = 10.1083/jcb.202006005 id = cord-290290-wyx9ib7s author = Sinegubova, Maria V. title = High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector date = 2020-11-05 keywords = CHO; CoV-2; RBD; SARS; cell; protein summary = title: High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector Based on the previously developed p1.1 vector, containing the regulatory sequences of the Eukaryotic translation elongation factor 1 alpha gene (EEF1A1) from Chinese hamster, we created two expression constructs encoding SARS-CoV-2 RBD with C-terminal c-myc and polyhistidine tags. Previously we have developed the plasmid vector p1.1, containing large fragments of non-coding DNA from the EEF1A1 gene of the Chinese hamster and fragment of the Epstein-Barr virus long terminal repeat concatemer [21] and employed it for unusually high-level expression of various proteins in CHO cells, including blood clotting factors VIII [22] , IX [23] , and heterodimeric follicle-stimulating hormone [24] . We have proposed that SARS-CoV-2 RBD, suitable for in vitro diagnostics use, may be expressed in large quantities by stably transfected CHO cells, bearing the EEF1A1-based plasmid. doi = 10.1101/2020.11.04.368092 id = cord-281005-6gi18vka author = Singh, Praveen Kumar title = Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development date = 2020-09-01 keywords = RBD; SARS; protein summary = title: Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development Therefore, we aimed to predict the mutations in the spike protein (S) of the SARS-CoV-2 genomes available worldwide and analyze its impact on the antigenicity. A total of 1,604 spike proteins were extracted from 1,325 complete genome and 279 partial spike coding sequences of SARS-CoV-2 available in NCBI till May 1, 2020 and subjected to multiple sequence alignment to find the mutations corresponding to the reported single nucleotide polymorphisms (SNPs) in the genomic study. In this study, we aimed to predict the mutations in the spike protein (S) of SARS-CoV-2 genomes available in the database (whole genome sequences as well as partial coding sequences of spike protein) and analyze the effect of each mutation on the antigenicity of the predicted epitopes. doi = 10.1055/s-0040-1715790 id = cord-260225-bc1hr0fr author = Sirpilla, Olivia title = SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date = 2020-07-20 keywords = Coronavirus; NMD; Protein; RNA; Respiratory; SARS; Syndrome; acute summary = doi = 10.1021/acs.jproteome.0c00421 id = cord-298369-66ifwtlp author = Smith, Sherri A. title = Pharmacokinetic and Pharmacodynamic Considerations for Drugs Binding to Alpha-1-Acid Glycoprotein date = 2018-12-28 keywords = AAG; drug; glycoprotein; human; protein summary = The importance of plasma protein binding primarily resides in its impact on pharmacokinetic properties such as clearance (CL) and volume of distribution (V ss ), with serum albumin, lipoproteins and alpha-1 acid glycoprotein (AAG) being the major proteins involved in sequestering drugs in plasma (1) . While AAG represents a relatively small portion (~1-3%) of the total plasma proteins, compared to~60% composition of albumin, it can play a significant role in drug binding and pharmacokinetics (PK) (43) . Since AAG levels increase in most disease states (46) , drugs with a high affinity may demonstrate higher binding (lower fraction unbound, f u ) and altered PK properties (e.g. lower total CL), lower V ss . Effect of the plasticizer DEHP in blood collection bags on human plasma fraction unbound determination for Alpha-1-Acid Glycoprotein (AAG) binding drugs doi = 10.1007/s11095-018-2551-x id = cord-259603-bh198xgl author = Snijder, E.J. title = The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing date = 2016-09-14 keywords = CoV; Fig; MHV; RNA; SARS; ZBD; protein summary = Reverse-genetics studies targeting specific residues in SARS-CoV nsp7 confirmed the protein''s importance for virus replication (Subissi et al., 2014b) , although the impact of single point mutations was smaller than anticipated on the basis of the biochemical characterization of the RNA-binding properties of nsp7-containing protein complexes in vitro (see later). The large number of viral subunits in these complexes (Subissi et al., 2014a) , the likely requirement for host factors (van Hemert et al., 2008) , and the concept of RNA synthesis occurring in a dedicated microenvironment in the infected cell (Knoops et al., 2008; V''Kovski et al., 2015) complicate the straightforward characterization of the CoV RdRp. To reconstitute the enzyme''s activities in vitro, purified recombinant nsp12 is a key reagent but, for many years, such studies were hampered by poor nsp12 expression in Escherichia coli. doi = 10.1016/bs.aivir.2016.08.008 id = cord-300429-b0zev8zb author = Sobocińska, Justyna title = Protein Palmitoylation and Its Role in Bacterial and Viral Infections date = 2018-01-19 keywords = acid; cell; fatty; membrane; palmitoylation; protein summary = We highlight recent data on protein S-palmitoylation in pathogens and their hosts obtained owing to the development of methods based on click chemistry and acyl-biotin exchange allowing proteomic analysis of protein lipidation. Given the large variety of chemical reporters preferentially mimicking distinct fatty acids, recent years have witnessed a plethora of chemistry-based proteomic studies not only on palmitoylated but also myristoylated proteins and proteins bearing the GPI anchor, including those of pathogens and immune cells (10, 14, 85, 86, 114) The aBe Method Reveals Protein The envelope is rich in transmembrane, often S-palmitoylated, glycoproteins called spikes, which can bind to cognate receptors on the host cell plasma membrane triggering endocytosis of the virion, mediate subsequent fusion of the viral and cellular membranes allowing entry of the viral genome to the cytoplasm, and are also involved in the budding of newly formed virus particles from the cell. doi = 10.3389/fimmu.2017.02003 id = cord-296794-ml2luc1t author = Sollner, Johannes title = Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins date = 2008-01-07 keywords = AROC; acid; epitope; protein summary = This work assesses in how far correlation between antigenicity, variability, post-translational modifications and protectivity/functional relevance can be put to use in a predictive model without the availability of 3D data. Classification into presumably protective or non-protective epitopes is conducted using three independently determined parameters: predicted B-cell antigenicity, sequence variability and conservation of post-translational modification motifs. These results are relativated later in this work when using only potentially relevant domains of a protein antigen, indicating systematic problems of the way B-cell epitope prediction validation is usually conducted. Briefly, proteins were completely scored for antigenicity/protectivity but amino-acid scores in regions outside domains assumed to be surface exposed were set to 0 thus leading to a generic classification as non-protective. On this compilation protectivity prediction using PCA19 in combination with variability and modification likelihood performed significantly better after domain-accessibility filtering as measured by AROC values, while without filtering performance was comparable (although again slightly better) to antigenicity validation results on the Blythe et.al validation-set. doi = 10.1186/1745-7580-4-1 id = cord-287266-sd5izamc author = Song, Zhenhui title = EIF4A2 interacts with the membrane protein of transmissible gastroenteritis coronavirus and plays a role in virus replication date = 2019-04-30 keywords = EIF4A2; TGEV; protein summary = title: EIF4A2 interacts with the membrane protein of transmissible gastroenteritis coronavirus and plays a role in virus replication Using the GST pull-down approach and a CO-IP assay, the M protein was found to interact with porcine intestinal cells via eukaryotic translation initiation factor 4-alpha (EIF4A2), an essential component of the cellular translational machinery. The present study provides mechanistic insight into the interaction between the TGEV M protein and intestinal cells which contributes to the understanding of coronavirus replication and may be useful for the development of novel therapeutic strategies for TGEV infection. In the present study, using yeast two-hybrid screening, seven cellular proteins, including eukaryotic translation initiation factor 4-alpha (EIF4A2), were identified to be M-ligands. Moreover, previous reports have shown that EIF4A2 interacts with VP1 of infectious bursal disease virus (IBD) and inhibits the RNA polymerase activity of IBDV to reduce its replication in host cells (Tacken et al., 2004; Gao et al., 2017) . doi = 10.1016/j.rvsc.2018.12.005 id = cord-281124-4nhy35xn author = Soowannayan, Chumporn title = RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp date = 2011-08-03 keywords = GAV; RNA; protein summary = To examine this domain in more detail, the 18 aa peptide (M(11)PVRRPLPPQPPRNARLI(29)) encompassing this sequence was synthesized and found to bind nucleic acids similarly to the full-length N protein in EMSAs. The data indicate a fundamental role for the GAV N protein proline/arginine-rich domain in nucleating genomic ssRNA to form nucleocapsids. In a preliminary attempt to identify an RNA packaging signal in the GAV genome, EMSAs were performed using ssRNAs synthesized to various genome regions including (i) an ORF1b gene 39-region spanning the relative position to the genome packaging signal identified in MHV [28] , (ii) a 39-terminal genome region corresponding in position to the region in the infectious bronchitis virus (IBV) genome reported to contain an RNA binding domain [29] and (iii) the 59-genomic RNA terminus which, in coronaviruses, has also been reported to interact specifically with N protein [30] . doi = 10.1371/journal.pone.0022156 id = cord-006331-s2qf98lj author = Spiridonova, V. A. title = Molecular recognition elements: DNA/RNA-aptamers to proteins date = 2010-05-23 keywords = HIV; RNA; SELEX; aptamer; dna; protein summary = After 16 rounds of selection from the 2'' amino modified RNA library the isolated aptamers formed a complex with FVIIa characterized by the K d value of 11.3 ± 1.3 nM. performed RNA selection to FIXa; after eight rounds of selection they found an aptamer, which bound to FIXa with the K d value of 0.65 ± 0.2 nM and exhibited 5000 fold higher affinity to FIXa compared with FVIIa, FXa, FXIa and activated protein C [20] . These aptamers formed a complex with ΔNS3 with the K d value of 10 nM, caused 90% inhibition of protease activity of the ΔNS3 peptide and full sized NS3 bound to a maltose binding protein (MBP NS3). Four teen rounds of selection yielded the RNA aptamer, exhibiting high affinity binding to p50 and inhibition of NF kB binding to DNA by preventing protein dimerization [91] . doi = 10.1134/s1990750810020046 id = cord-300625-fvirvpyl author = Srinivasan, Suhas title = Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins date = 2020-03-25 keywords = SARS; interaction; protein; structural summary = doi = 10.3390/v12040360 id = cord-254909-8zgvovu4 author = Srivastava, Rajneesh title = Serum profiling of leptospirosis patients to investigate proteomic alterations() date = 2012-12-05 keywords = DIGE; leptospirosis; protein summary = In this study, we have performed a proteomic analysis of serum samples from leptospirosis patients (n = 6), febrile controls (falciparum malaria) (n = 8) and healthy subjects (n = 18) to obtain an insight about disease pathogenesis and host immune responses in leptospiral infections. During the database search following parameters were specified: human taxonomy, trypsin digestion with one missed cleavage, carbamidomethyl (C) as fixed modification, oxidation (M) as variable modification, peptide mass tolerance set at 75 ppm and MS/MS tolerance of 0.4 Da. Western blot analysis was performed with serum samples from controls (healthy and febrile) and leptospirosis patients (n = 6) to validate the differential expression of some of the target proteins identified in 2DE and 2D-DIGE experiments. Aiming at analysis of host serum proteome alteration due to leptospirosis, we have identified several differentially expressed proteins and modulation of multiple physiological processes and pathways, including inflammation mediated acute phase responses, complement pathways, heterotrimeric G-protein signaling pathway, coagulation cascade and hemostasis in patients suffering from leptospiral infection. doi = 10.1016/j.jprot.2012.04.007 id = cord-261961-u4d0vvmq author = St-Germain, Jonathan R. title = A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date = 2020-08-28 keywords = SARS; protein; virus summary = doi = 10.1101/2020.08.28.269175 id = cord-329493-ueqlhgn0 author = Stadler, Konrad title = SARS — beginning to understand a new virus date = 2003 keywords = CoV; RNA; SARS; protein; virus summary = A new infectious disease, known as severe acute respiratory syndrome (SARS), appeared in the Guangdong province of southern China in 2002. When Thiel and colleagues 20 isolated one genomic and eight subgenomic RNAs from the FRA strain and sequenced their 5′ ends, they identified a conserved sequence (5′ACGAAC3′) that was located in coronaviruses: S, spike protein; E, envelope protein; M, membrane glycoprotein; and N, nucleocapsid protein. Alternatively, these antigens could be delivered by DNA immunization by Figure 6 | The S1 domain of SARS-CoV spike is structurally related to group 2 coronaviruses. Schematic representation of cysteine positions in the S1 domains of group 1, 2 and 3 coronaviruses, compared with the SARS-CoV spike protein. The complete genome sequence of a SARS-CoV isolate (FRA) and experimental data on its key RNA elements and protein functions are described. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection doi = 10.1038/nrmicro775 id = cord-256325-q70rky3r author = Stewart, Cameron R. title = A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease date = 2017-07-04 keywords = IFN; RNA; protein; virus summary = title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease Here we largely focus on findings from two recent RNAi screens to identify protein-coding genes and host-encoded microRNAs impacting the henipavirus infection cycle in human cells. X-ray data have suggested that the methylation of rRNA requires the formation of this complex with involvement of four fibrillarin molecules interacting with different regions of the target rRNAs. The yeast equivalent of fibrillarin, NOP1, has been more extensively studied than the human counterpart but fibrillarin is a well-conserved protein in most organisms, reinforcing the notion that all post-transcriptional processes involving fibrillarin such as chemical modification (methylation) of rRNA, pre-rRNA cleavage and ribosome assembly are essential for proper cellular functioning (Rodriguez-Corona et al. Deffrasnes and colleagues showed that siRNA-mediated knockdown of fibrillarin expression dramatically reduced HeV protein production and viral genome replication but did not impact viral fusion, and that fibrillarin catalytic activity was essential to henipavirus infection. doi = 10.1007/82_2017_28 id = cord-352172-g0jiaenw author = Stoevesandt, Oda title = Protein microarrays: high-throughput tools for proteomics date = 2014-01-09 keywords = antibody; array; dna; microarray; protein summary = While conventionally made by the spotting of purified proteins, recent advances in technology have made it possible to produce protein microarrays through in situ cell-free synthesis directly from corresponding DNA arrays. Protein microarray technology has rapidly developed into one of the most active areas in biotechnology today, and is being increasingly applied for the high-throughput discovery of molecular interactions, profiling of protein expression and monitoring of protein modifications. While genome sequencing and annotations provide comprehensive information on protein-encoding genes, and DNA arrays analyze gene expression at the mRNA level, these technologies need to be complemented by functional proteomic studies in order to better understand protein activities, expression levels and interactions at the system level. A reverse-phase micro array approach has been successfully applied to discover distinct pathway-activation differences among breast cancer cell lines, demonstrating the use of array-based ana lysis for multiple pharmacodynamic biomarkers responding to targeted kinase inhibitors [108] . doi = 10.1586/epr.09.2 id = cord-000479-u87eaaj8 author = Stolf, Beatriz S. title = Protein Disulfide Isomerase and Host-Pathogen Interaction date = 2011-10-11 keywords = Leishmania; MHC; PDI; protein summary = These especially affect (i) pathogen entry through protein redox switches and redox modification (i.e., intraand interdisulfide and cysteine oxidation) and (ii) phagocytic ROS production via Nox family NADPH oxidase enzyme and the control of phagolysosome function with key implications for antigen processing. Among the many redox sensitive proteins that are altered during the course of different infections, protein disulfide isomerase (PDI-) mediated redox switches have been associated with pathogen attachment-internalization, antigen processing in the ER/phagosome, and the regulation of ROS production by Nox family enzymes. PDI is thought to attach to lipids, glycans, and integral membrane proteins via electrostatic interactions at the cell plasma membrane [14, 15] , where its reductive activity mediates the infection of different pathogens ( Figure 2 , discussed later). Protein disulfide isomerase (PDI) associates with NADPH oxidase and is required for phagocytosis of Leishmania chagasi promastigotes by macrophages doi = 10.1100/2011/289182 id = cord-298922-k568hlf4 author = Sun, Dongbo title = Analysis of protein expression changes of the Vero E6 cells infected with classic PEDV strain CV777 by using quantitative proteomic technique date = 2015-06-15 keywords = PEDV; Vero; protein summary = Among the disease-related functions, certain anti-viral pathways and proteins, such as the RIG-I-like receptor, Rap1, autophagy, mitogen-activated protein kinase, PI3K-Akt and Jak-STAT signaling pathways, and integrin β2/β3 and cystatin-C proteins, represented potential factors in PEDV infection. In our current study, we used a quantitative proteomics approach based on an iTRAQ tandem mass spectrometry (MS/MS) technique to identify proteins differentially expressed between PEDV-infected and mock-infected Vero E6 cells. To verify the differential expression of the selected DEPs, equivalent volumes of the cell lysate replicates from the PEDV-infected (V1-V3) and mock-infected (C1-C3) Vero E6 cells were pooled into the V and C samples, respectively, and western blotting was performed as described above, with the following exceptions: a 1:1000 dilution of the polyclonal antibodies anti-␤ tubulin, anti-integrin-␤3, anti-cystatin-C, anti-protein S100-A2, anti-apolipoprotein E4, and anti-centrin from rabbit (Beijing Biosynthesis Biotechnology, Beijing, China) was used as the primary antibody, and a 1:5000 dilution of the HRP-conjugated goat anti-rabbit IgG (Sigma-Aldrich, St. Louis, USA) was used as the secondary antibody. doi = 10.1016/j.jviromet.2015.03.002 id = cord-289026-v09m2fzw author = Sun, Yan-gang title = Characterization of the interaction between recombinant porcine aminopeptidase N and spike glycoprotein of porcine epidemic diarrhea virus date = 2018-10-01 keywords = Fig; PEDV; protein summary = Infection by its causative agent PED virus (PEDV), an Alpha-coronavirus, was previously proven to be mediated by its spike (S) glycoprotein and a cellular receptor porcine aminopeptidase N (pAPN). We then assayed the purified target proteins through immunogenicity tests, PEDV binding interference assays, circular dichroism (CD) measurements, pAPN activity assay and structural determination, demonstrating that they were biologically functional. Based on the results above, recombinant pAPN ectodomain was obtained as dimers, and PEDV S1 or S1t protein existed as monomers, which showed similar natures of mammalian APN [43] and other coronavirus S proteins [48] [49] [50] as previously reported. In the current study, three canonical assays were carried out to characterize the interaction between pAPN ectodomain and PEDV S1 or S1t protein since these functional target proteins were successfully prepared. Identification and comparison of receptor binding characteristics of the spike protein of two porcine epidemic diarrhea virus strains doi = 10.1016/j.ijbiomac.2018.05.167 id = cord-330715-olypwdoq author = Sun, Zeyu title = Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications date = 2020-08-30 keywords = HCoV-19; SARS; protein summary = title: Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications In this study, we report a comprehensive N-glycosylation profile-as well as other PTMs-of the HCoV-19 S protein and hACE2, elucidated by high-resolution mass spectrometry (MS) analyses. To resolve glycan camouflage on the surface of the HCoV-19 S protein and hACE2, intact glycopeptides derived from protease digestion and fractionated by HILIC were directly subjected to LC-MSMS analysis specifically designed to detect peptides with extra molecular weight due to N-glycan attachment. Fig. 2 (c) provides a summary of the most dominant N-glycan composition and predicted structure for each site of the HCoV-19 spike protein and hACE2. When the spike proteins from HCoV-19 and SARS-CoV were compared, it was noticeable that the majority of differences in the glycosylation sites occurred in the distal S1 subunit, resulting in a significant difference in the glycan profile in the outermost canopy of the virus formed by spike trimer clusters. doi = 10.1016/j.eng.2020.07.014 id = cord-023865-6rafp3x3 author = Surjit, Milan title = The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential date = 2009-07-22 keywords = RNA; SARS; protein summary = Towards the end of the article, we will also discuss some recent reports regarding the possible clinically relevant use of the nucleocapsid protein, as a candidate diagnostic tool and vaccine against SARS-CoV infection. Interestingly, biochemically mediated inhibition of GSK3 activity in SARS-CoV infected cells also leads to around 80% reduction in viral titer and subsequent induction of a virus-induced cytopathic effect. Further, S-phase specific gene products like cyclin E and CDK2 were found to be downregulated in SARS-CoV infected cell lysate, which suggested that the observed phenomenon may be relevant in vivo. Based on this observation, Palese''s laboratory has studied the IFN inhibitory property of different SARS-CoV proteins, which revealed that ORF3, ORF6 as well as the N-protein have the ability to independently inhibit IFN production through different mechanisms. Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells doi = 10.1007/978-3-642-03683-5_9 id = cord-279106-3ffa9djf author = Syatila Ab Ghani, Nur title = Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: the case for COVID-19 date = 2020-10-21 keywords = COVID-19; PDBID; SARS; drug; protein summary = In this work, the three-dimensional arrangements of amino acid side chains in known drug binding sites (substructures) were used to search for similarly arranged sites in SARS-CoV-2 protein structures in the Protein Data Bank for the potential repositioning of approved compounds. The investigations of binding properties in disease-related proteins derived from the comparison of amino acid substructure arrangements allows for effective mechanism driven decision making to rank and select only the compounds with the highest potential for success and safety to be prioritized for clinical trials or treatments. In the case of the COVID-19 pandemic caused by the SARS-CoV-2 virus, we demonstrate that the pipeline can identify candidate compounds quickly and sustainably in combination with associated risk factors derived from the analysis of potential off-target site binding by the compounds to be repurposed. 33 In this work, amino acid side chain similarity searching was utilized to propose alternative target sites in 34 SARS-CoV-2 protein structures for drug repositioning. doi = 10.1016/j.csbj.2020.10.013 id = cord-265642-7mu530yp author = Syomin, B. V. title = Virus-Like Particles as an Instrument of Vaccine Production date = 2019-06-17 keywords = VLP; antigen; particle; protein; vaccine; virus summary = doi = 10.1134/s0026893319030154 id = cord-026012-r0w0jbpg author = TENNANT, BUD C. title = Gastrointestinal Function date = 2014-06-27 keywords = absorption; acid; amino; bile; cell; enzyme; intestinal; protein; secretion; transport summary = In the dog, gastric juice is produced in the resting state at a rate of approximately 5 ml/hour (Gray and Bûcher, 1941) , and the composition is similar to that of the basal component, containing practi cally no peptic activity or hydrochloric acid. When the flow of gastric juice is stimulated maximally, the dog may produce 80 ml or more per hour (Gray and Bûcher, 1941) , and this secretion contains large amounts of peptic activity and hydrochloric acid. The endopeptidases and exopep(Table II) , producing free amino acids, which are absorbed directly, or small peptides, which are further hydrolyzed by the aminopeptidases of the intestinal mucosa (see Section III,C). Despite the long interest in and controversy regarding the subject of this section, the relative amounts of the various types of protein digestion products, i.e., peptides and amino acids, which are actually absorbed by intestinal mucosal cells during normal digestion are still not known. doi = 10.1016/b978-0-12-396350-5.50013-9 id = cord-253987-83h861lp author = Tada, Takuya title = A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture date = 2020-09-17 keywords = ACE2; SARS; figure; protein summary = The disulfide-bonded ACE2 microbody protein inhibited entry of lentiviral SARS-CoV-2 spike protein pseudotyped virus and live SARS-CoV-2 with a potency 10-fold higher than unmodified soluble ACE2 and was active after initial virus binding to the cell. In SARS-CoV-2 entry, the virus attaches to the target cell through the interaction of the spike glycoprotein (S) with its receptor, the angiotensin-converting enzyme 2 (ACE2) (Li, 2015; Li et al., 2005; Li et al., 2003) , a plasma membrane protein carboxypeptidase that degrades angiotensin II to angiotensin-(1-7) [Ang-(1-7)] a vasodilator that promotes sodium transport in the regulation of cardiac function and blood pressure (Kuba et al., 2010; Riordan, 2003; Tikellis and Thomas, 2012) . To determine the relative antiviral activity of soluble ACE2 and the ACE2 microbody proteins, we tested their ability to block the infection SARS-CoV-2 Δ19 S protein pseudotyped GFP/luciferase reporter virus. doi = 10.1101/2020.09.16.300319 id = cord-333966-st6gyozv author = Taherkhani, Reza title = Design and production of a multiepitope construct derived from hepatitis E virus capsid protein date = 2015-03-17 keywords = HEV; HLA; ORF2; protein summary = The aim of this study was to design a high density multiepitope protein, which can be a promising multiepitope vaccine candidate against Hepatitis E virus (HEV). Therefore, the present study was undertaken to design a high density multiepitope protein compromising four HTL epitopes with high-affinity binding to the HLA molecules using the in silico analysis, and to evaluate the immunological properties of this protein in vitro. In brief, approximately 1 Â 10 5 cells/well of PBMCs of each sample in RPMI 1640 and 10% FCS were added to four wells of round-bottom 96-well plates in total volume of 180 ml/well, stimulated with 20 ml/well of truncated ORF2 protein (10 mg/ml), high density multiepitope (10 mg/ml) and Phytohemagglutinin (PHA) (5 mg/ml) (Sigma-Aldrich) separately, and incubated at 37˚C for 4 days. IFN-g ELISPOT responses to high density multiepitope protein and truncated ORF2 protein were found significantly higher in HEV-recovered individuals than control group (P < 0.001). doi = 10.1002/jmv.24171 id = cord-302414-g5onwhg1 author = Tahir ul Qamar, Muhammad title = Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2 date = 2020-09-16 keywords = MESV; SARS; epitope; protein; table summary = Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast Band Tcell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV. The purpose of this study was to pinpoint the potential T-cell and B-cell epitopes from SARS-CoV-2 structural proteins which can be further joined through adjuvant and linkers to design a multiepitope-based subunit vaccine (MESV). Here, we explored the development of epitope-based vaccines targeting the structural proteins (S, M, and E) of the SARS-CoV-2. Taken together, we characterized SARS-CoV-2 structural proteins (S, E, and M) for antigenic epitopes and proposed a potential MESV utilizing various immunoinformatics and computational approaches. doi = 10.1186/s40249-020-00752-w id = cord-254100-u6x5zd4i author = Taliansky, M.E. title = Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems date = 2010-10-15 keywords = Hiscox; ORF3; RNA; nucleolus; protein; virus summary = An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. As their name suggests, MPs are involved in virus spread in infected plants, and the potential role of fibrillarin in this process will be discussed in Section IV.B. The multifunctional PVA (potato virus A)-encoded viral genomelinked protein (VPg) is also able to interact with fibrillarin (Rajamäki and Bonfiglioli et al. doi = 10.1016/b978-0-12-385034-8.00005-3 id = cord-336542-6asieplk author = Tanco, Sebastián title = Structure–Function Analysis of the Short Splicing Variant Carboxypeptidase Encoded by Drosophila melanogaster silver date = 2010-08-20 keywords = CPD; Drosophila; Fig; protein summary = Overall, DmCPD1Bs conforms to the structure of N/E-type funnelins/M14B metallopeptidases, but it has two unique structural elements potentially involved in regulation of its activity: (i) two contiguous surface cysteines that may become palmitoylated and target the enzyme to membranes, thus providing control through localization, and (ii) a surface hot spot targetable by peptidases that would provide a regulatory mechanism through proteolytic inactivation. Given that the fruit fly possesses orthologs of only two out of the five proteolytically competent N/E-type funnelins found in higher vertebrates, DmCPD1Bs may represent a functional analog of at least one of the missing mammalian CPs. The silver (svr) gene was discovered in Drosophila melanogaster by Bridges in the early 1920s and it maps near the distal end of chromosome X. [3] [4] [5] [6] The long variants possess the overall modular structure and sequence features of carboxypeptidase D (CPD), a glycosylated 180-kDa enzyme studied since the middle 1990s in fruit fly, mouse, rat, duck, bovine, chicken, and humans. doi = 10.1016/j.jmb.2010.06.035 id = cord-329403-jzrlywfe author = Teo, Su Hui Catherine title = A NS1-binding monoclonal antibody interacts with two residues that are highly conserved in seasonal as well as newly emerged influenza A virus date = 2019-03-06 keywords = GST; ns1; ns1(ed; protein summary = In this study, we have generated a novel monoclonal antibody (mAb) 19H9 and epitope mapping revealed that two residues, P85 and Y89, of NS1 are essential for interacting with this mAb. Furthermore, residues P85 and Y89 are found to be highly conserved across different IAV subtypes, namely seasonal H1N1 and H3N2, as well as the highly pathogenic H5N1 and H5N6 avian strains. The membrane was then washed and full-length NS1 transfected cell lysates were subjected to IP with mAb 19H9 and protein A agarose beads followed by detection of immunoprecipitated proteins using rabbit anti-Myc antibody in Western blot. To delineate the epitope of NS1 recognized by mAb 19H9, a series of NS1 truncation mutants consisting of residues 1-84, 1-100, 91-230 and 85-230 were generated and their expression levels in transiently transfected 293T cells were verified using an anti-Myc antibody ( Fig. 2A, upper panel) . doi = 10.1093/femspd/ftz012 id = cord-283035-tpqf458q author = Thanthrige-Don, Niroshan title = Analyses of the spleen proteome of chickens infected with Marek''s disease virus date = 2009-08-01 keywords = MDV; MHC; Marek; protein; spot summary = In total, 61 protein spots representing 48 host proteins were detected as either quantitatively (false discovery rate (FDR) ≤ 0.05 and fold change ≥ 2) or qualitatively differentially expressed at least once during different sampling points. A representative gel image showing 2D gel electrophoresis map of the relative locations of spots that displayed significant quantitative differential expression (FDR ≤ 0.05 and fold change ≥ 2) at least once during different sampling times. Comparison of total numbers of significantly differentially expressed protein spots in MDV-infected spleens at various sampling time points. Venn diagram summarizing the spots that were significantly differentially expressed in the spleen tissues of MDV-infected chickens according to their corresponding time of sampling. In the present study, we have profiled the global protein expression changes in the chicken spleen in response to MDV infection at various time points representing the different phases of MDV life cycle. Proteomics analysis of differential expression of cellular proteins in response to avian H9N2 virus infection in human cells doi = 10.1016/j.virol.2009.05.020 id = cord-007092-ukqvhzws author = Themsakul, Sirintra title = Secretion of M2e:HBc fusion protein by Lactobacillus casei using Cwh signal peptide date = 2016-09-08 keywords = protein summary = doi = 10.1093/femsle/fnw209 id = cord-337158-0iw2kcaf author = Tiernan, Hannah title = ATR-FTIR spectroscopy and spectroscopic imaging for the analysis of biopharmaceuticals date = 2020-06-22 keywords = ATR; Amide; FTIR; Infrared; Protein; biopharmaceutical; spectroscopy summary = Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) spectroscopy is a label-free, non-destructive technique that can be applied to a vast range of biological applications, from imaging cancer tissues and live cells, to determining protein content and secondary structure composition. This characterisation commonly involves the use of techniques such as liquid chromatography tandem mass spectrometry (LC-MS-MS) to monitor changes in mass, 16 high pressure liquid chromatography (HPLC) to determine impurity profiles of samples, 17 and infrared spectroscopy (IR) to identify impurities and compare biosimilars to the original, ''reference drugs''. 75 ATR-FTIR spectroscopy has also been used extensively to study proteins, in particular biopharmaceuticals, and exciting research has shown the potential applications of it to investigate and monitor changes effectively in PTMs and secondary structures. For example, Grosshans et al used in-line FTIR spectroscopy, along with partial least squares (PLS) analysis, as an effective process analytical tool (PAT) for preparative protein chromatography, they found it to be useful to distinguish and selectively identify proteins based on their secondary structure. doi = 10.1016/j.saa.2020.118636 id = cord-013315-plptulfb author = Tilocca, Bruno title = Immunoinformatic-Based Prediction of Candidate Epitopes for the Diagnosis and Control of Paratuberculosis (Johne’s Disease) date = 2020-08-27 keywords = MAP; MHC; Mycobacterium; epitope; protein summary = doi = 10.3390/pathogens9090705 id = cord-280878-1kt51viz author = To, Janet title = Targeting the Channel Activity of Viroporins date = 2016-01-07 keywords = Amt; HCV; Vpu; channel; protein; virus summary = For other viroporins, these studies are still mostly in their infancy, although a highresolution structure of the hepatitis C virus (HCV) p7 protein has been recently described (Ouyang et al., 2013) that may be useful for the rational design of p7 channel inhibitors in the future. Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain The small hydrophobic protein of the human respiratory syncytial virus forms pentameric ion channels NMR structure and ion channel activity of the p7 protein from hepatitis C virus Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus doi = 10.1016/bs.apcsb.2015.12.003 id = cord-002835-qaogpxy9 author = Too, Issac Horng Khit title = Prohibitin plays a critical role in Enterovirus 71 neuropathogenesis date = 2018-01-11 keywords = EV71; Fig; NSC-34; PHB; Roc; cell; protein summary = doi = 10.1371/journal.ppat.1006778 id = cord-292688-w4zvfkyl author = Tooze, Sharon A title = Biogenesis of secretory granules in the trans-Golgi network of neuroendocrine and endocrine cells date = 1998-08-14 keywords = Golgi; TGN; protein; secretory summary = An alternative hypothesis is that there is very little constitutive secretion originating from the TGN of regulated cells, and that most molecules in the biosynthetic pathway exit into ISGs. In the ISG, the non-secretory granule proteins would presumably be sorted from the regulated secretory proteins via interaction with a receptor and removed from the ISG in constitutive-like vesicles. Depending on the cargo, distinct mechanisms could be used for selection to increase the e¤ciency of removal of nonsecretory granule proteins from the maturing ISGs. While the mechanisms involved in the formation of both constitutive and regulated secretory vesicles from the TGN is largely unknown there have been recent reports which suggest that both these budding reactions maybe unique in that they function independently of known coat proteins. In the PC12 cell assay, the same e¡ect was observed with [AlF 4 ] À and several other lines of evidence demonstrated that heterotrimeric GTP-binding proteins are involved in the regulation of post-Golgi vesicle formation (see [71] for review). doi = 10.1016/s0167-4889(98)00059-7 id = cord-017999-saxwqc2j author = Travers, Andrew A. title = Gene Regulation by HMGA and HMGB Chromosomal Proteins and Related Architectural DNA-Binding Proteins date = 2005 keywords = HMG; HMGA; HMGB; dna; protein summary = The eukaryotic abundant high mobility group HMGA and HMGB proteins can act as architectural transcription factors by promoting the assembly of higher-order protein-DNA complexes which can either activate or repress gene expression. Similarly rat SSRPl has been shown to facilitate the DNA binding of serum response factor and human SSRPl is associated with the y isoform of p63 in vivo at the endogenous MDM22inAp2nfl''"^^ promoters.^^ In most of these cases, the interaction of the HMG protein with the transcription factor has been detected in vitro and could, in principle, serve as the mechanism for recruitment of HMGB 1 or 2 to particular DNA sites. doi = 10.1007/0-387-29148-2_11 id = cord-012878-j9vndxgg author = Tremblay, Reynald title = High-yield expression of recombinant soybean agglutinin in plants using transient and stable systems date = 2010-06-18 keywords = Fig; Nicotiana; SBA; protein summary = doi = 10.1007/s11248-010-9419-0 id = cord-351559-az4pgi9k author = Turjya, Rafeed Rahman title = Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date = 2020-06-29 keywords = RNA; SARS; protein summary = Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. Conclusions Our investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option. doi = 10.1101/2020.06.29.177204 id = cord-257802-vgizgq2y author = Uttamchandani, Mahesh title = Applications of microarrays in pathogen detection and biodefence date = 2008-11-12 keywords = SARS; dna; microarray; pathogen; protein summary = Advances in miniaturizing this initial PCR step, for instance the development of Review Glossary Biodefence: defensive measures against biological threats, including natural/ emerging pathogens and bioterror agents, that have significant potential to endanger public health Detection: identifying the presence of target pathogen(s) from clinical or environmental samples. (b) Antibody microarrays can be used to detect pathogen proteins or antigens that might be present in environmental samples as an indication of contamination or for diagnostic purposes to determine pathogen infection in human tissues. fabricated a customized Affymetrix microarray containing 53 660 probes to detect DNA amplified from 18 different pathogenic microorganisms simultaneously, including pathogens from the US CDC''s list of bioterrorism agents, such as Bacillus anthracis (which causes anthrax), Clostridium botulinum (which generates the botulinum toxin), Yersinia pestis (which causes bubonic plague) and the Ebola virus [17] . doi = 10.1016/j.tibtech.2008.09.004 id = cord-301827-a7hnuxy5 author = Uversky, Vladimir N title = A decade and a half of protein intrinsic disorder: Biology still waits for physics date = 2013-04-29 keywords = IDPs; bind; disorder; function; interaction; intrinsic; protein; region; sequence; structure summary = 94 Therefore, the abundance and peculiarities of the charged residues distribution within the protein sequences might determine physical and biological properties of extended IDPs and IDPRs. Also, simple polymer physics-based reasoning can give reasonably well-justified explanation of the conformational behavior of extended IDPs. In general, the conformational behavior of IDPs is characterized by the low cooperativity (or the complete lack thereof) of the denaturant-induced unfolding, lack of the measurable excess heat absorption peak(s) characteristic for the melting of ordered proteins, "turned out" response to heat and changes in pH, and the ability to gain structure in the presence of various binding partners. 183 This analysis revealed that proteins involved in regulation and execution of PCD possess substantial amount of intrinsic disorder and IDPRs were implemented in a number of crucial functions, such as protein-protein interactions, interactions with other partners including nucleic acids and other ligands, were shown to be enriched in post-translational modification sites, and were characterized by specific evolutionary patterns. doi = 10.1002/pro.2261 id = cord-306904-8iteddug author = Uversky, Vladimir N title = Unreported intrinsic disorder in proteins: Building connections to the literature on IDPs date = 2014-12-12 keywords = LGN; Xis; disordered; dna; figure; human; protein; residue summary = 86 Figure 8C represents the results of the computational disorder analysis in human APC (UniProt ID: P04070) and shows that mentioned loops enriched in basic residues are predicted to be disordered or very flexible, thereby providing an interesting mechanistic plane for the molecular basis of APC recognition and binding of FVIII. 96 Figure 8E shows that although human PECAM-1 (UniProt ID: P16284) is predicted to be mostly ordered, the residues, phosphorylation of which is crucial for its function (Y 663 and Y 686 ), are located within the highly disordered C-terminal tail. 210 Figure 14C represents the results of the disorder analysis of human AMSH (UniProt ID: O95630) and shows that this protein contains a long IDPR (residues 90-250) thereby illustrating that the N-terminal part of the analyzed catalytic domain is predicted to be disordered. [222] [223] [224] Figure 14D shows that human Purb protein (UniProt ID: O35295) is predicted to possess significant amount of functionally important intrinsic disorder. doi = 10.4161/21690693.2014.970499 id = cord-310847-63gh2tg4 author = Uversky, Vladimir N title = The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins date = 2013-04-01 keywords = Glu; PGA; acid; domain; glutamic; protein; region; residue; rich; structure summary = 5, 10, 46 In fact, in comparison with ordered proteins, IDPs/IDPRs are characterized by noticeable biases in their amino acid compositions, 5, 8, 10, [46] [47] [48] containing less of so-called "order-promoting" residues (cysteine, tryptophan, isoleucine, tyrosine, phenylalanine, leucine, histidine, valine, asparagines and methionine, which are mostly hydrophobic residues which are commonly found within the hydrophobic cores of foldable proteins) and more of "disorder-promoting" residues (lysine, glutamine, serine, glutamic acid and proline, which are mostly polar and charged residues, which are typically located at the surface of foldable proteins) (Fig. 1A) . Glutamic acid is an important functional residue of ordered proteins, where it can be involved in the formation of specific electrostatic valves inside the pores of ion channels, or can play unique catalytic roles in the active sites doi = 10.4161/idp.24684 id = cord-319609-y0gdjn64 author = Van Duyne, Rachel title = The identification of unique serum proteins of HIV-1 latently infected long-term non-progressor patients date = 2010-07-06 keywords = HAART; HIV-1; INK4A; LTNP; cell; protein summary = In particular, the analysis of HIV-1 infected serum is an attractive medium with which to identify altered protein expression due to the ease and non-invasive methods of collecting samples as well as the corresponding insight into the in vivo interaction of the virus with infected cells/tissue. We have analyzed and compared serum samples from HIV-1 infected subjects who are being treated using highly active antiretroviral therapy (HAART) to those who are latently infected but have not progressed to AIDS despite the absence of treatment, i.e. long term non-progressors (LTNPs). In order to gain insight into the reason why p16 INK4A may be present preferentially in the serum of LTNP patients, we treated latently infected HIV-1 cell lines (J1.1 and U1) with exogenous purified GST-p16 INK4A Figure 4A depicts an RT assay which measures the viral reverse transcriptase activity of infected cells and is an indicator of functional particle production. doi = 10.1186/1742-6405-7-21 id = cord-243806-26n22jbx author = Vandelli, Andrea title = Structural analysis of SARS-CoV-2 and prediction of the human interactome date = 2020-03-30 keywords = Fig; RNA; SARS; protein summary = Here, we performed sequence and structural alignments among 62 SARS-CoV-2 strains and identified the conservation of specific elements in the spike S region, which provides clues on the evolution of domains involved in the binding to ACE2 and sialic acid. As highly structured regions of RNA molecules have strong propensity to form stable contacts with proteins 14 and promote assembly of specific complexes 15, 16 , SARS-CoV-2 domains enriched in double-stranded content are expected to establish interactions within host cells that are important to replicate the virus 17 . Analysis of functional annotations carried out with GeneMania 46 revealed that proteins interacting with the 5'' of SARS-CoV-2 RNA are associated with regulatory pathways involving NOTCH2, MYC and MAX that have been previously connected to viral infection processes ( Fig. 4E) 47, 48 . doi = nan id = cord-284648-yznlgzir author = Varanko, Anastasia title = Recent trends in protein and peptide-based biomaterials for advanced drug delivery date = 2020-08-29 keywords = Collagen; DOX; ELP; HSA; RLP; SELP; XTEN; albumin; delivery; drug; figure; nanoparticle; protein; release; self summary = Albumin is the most abundant protein in human plasma and has a set of properties that make it a unique molecular carrier for drugs: (i) it is a natural physiological carrier of native ligands and nutrients; (ii) it bypasses systemic clearance and degradation by the body''s own innate mechanisms, so that it has an exceptionally long half-life of 19 days in humans, and similarly long half-lives in most animal species [123] [124] [125] [126] ; (iii) it preferentially accumulates at sites of vascular leakiness; (iv) it is highly internalized and metabolized by rapidly growing, nutrient-starved cancer cells; and (v) it is biodegradable and has no known systemic toxicity. Other notable examples of albumin-based delivery systems involve the genetic fusion of ABD to various therapeutic proteins including affibodies [165, 166] , human soluble complement receptor type 1 [167] , single chain antibody-drug conjugates [168] , insulin-like growth factor II [169] , immunotoxins [170] , and respiratory syncytial virus subgroup A (RSV-A) G protein (G2Na) [171] . doi = 10.1016/j.addr.2020.08.008 id = cord-031937-qhlatg84 author = Verma, Anukriti title = Elucidating potential molecular signatures through host-microbe interactions for reactive arthritis and inflammatory bowel disease using combinatorial approach date = 2020-09-15 keywords = HLA; IBD; KYNU; host; microbe; protein summary = In-silico analysis involving text mining, metabolic network reconstruction, simulation, filtering, host-microbe interaction, docking and molecular mimicry studies results in robust drug target/s and biomarker/s for co-evolved IBD and ReA. The contributions of the microorganisms in the co-evolved IBD and ReA as part of the disease network was created through the interactive maps of the essential host interaction proteins (verified using literature survey) and the information processed through gene expression data analysis 64 . The pathways of the above host interacting proteins were found out using KEGG database that provides ontologies for proteins related to biological processes 67 www.nature.com/scientificreports/ Subsequently, the role of drugs or inhibitors used to suppress the effect of IBD and ReA such as indomethacin, prednisone, ciprofloxacin, sulfasalazine, azathioprine, methotrexate and hydroxychloroquine was scored in the disease network through their docking studies against the potential targets (both host as well microbial targets) as per published methodologies 68, 69 . doi = 10.1038/s41598-020-71674-8 id = cord-029747-8f463wz0 author = Viedma-Poyatos, Álvaro title = Type III intermediate filaments as targets and effectors of electrophiles and oxidants date = 2020-07-17 keywords = GFAP; cell; cysteine; filament; modification; protein; residue; vimentin summary = The type III IFs, vimentin, desmin, peripherin and glial fibrillary acidic protein (GFAP), are targets for diverse modifications by oxidants and electrophiles, for which their conserved cysteine residue emerges as a hot spot. Appearance of carbonyl groups on proteins can occur by several mechanisms, including oxidation of amino acid lateral chains, oxidative deamination or formation of certain adducts with compounds that retain a free carbonyl group, as in some types of lipoxidation, like Michael addition of cyPG or of HNE, or after glycation or glycoxidation. Early studies using cytoskeleton preparations from several cell types subjected to oxidative in vitro crosslinking with Cu 2+ -phenanthroline showed the formation of homo-and heterodimers of either vimentin and desmin or vimentin and GFAP, which led to propose that both proteins were present in hybrid filaments [85, 86] . doi = 10.1016/j.redox.2020.101582 id = cord-016095-jop2rx61 author = Vignais, Pierre V. title = Challenges for Experimentation on Living Beings at the Dawn of the 21(st) Century date = 2010-06-08 keywords = ATP; France; Man; RNA; University; able; cell; century; chapter; dna; experimental; figure; gene; genetic; human; live; protein; research summary = Instead of setting out to discover unknown mechanisms by analyzing effects that are dependent on specific causes, with some uncertainty as to the possible success of the enterprise being undertaken, which is the foundation stone of the Bernardian paradigm of the experimental method, many current research projects give themselves achievable and programmable objectives that depend upon the means available to them: sequencing of genomes with a view to comparing them, recognition of sequence similarities in proteins coded for by genes belonging to different species, with the aim of putting together phylogenetic trees, synthesis of interesting proteins in transgenic animals and plants, analysis of the three-dimensional structure of proteins, in order to find sites that are likely to fix medicinal substances, and synthesis of molecular species able to recognize pathogenic targets. doi = 10.1007/978-90-481-3767-1_5 id = cord-002179-v8lpw4r7 author = Viktorovskaya, Olga V. title = Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements date = 2016-08-24 keywords = DENV; Fig; RNA; UPRT; protein summary = doi = 10.1371/journal.pntd.0004921 id = cord-048360-n9sih438 author = Villard, Viviane title = Rapid Identification of Malaria Vaccine Candidates Based on α-Helical Coiled Coil Protein Motif date = 2007-07-25 keywords = antibody; figure; peptide; protein; table summary = To identify malaria antigens for vaccine development, we selected α-helical coiled coil domains of proteins predicted to be present in the parasite erythrocytic stage. Here, we focus on the Pf parasite erythrocytic stage, a target of protective antibodies and describe a straightforward, rapid procedure based on bioinformatic analysis of a-helical coiled-coil motifs and peptide synthesis. With regard to the structural features and cellular location prediction of the proteins corresponding to the peptides selected for ADCI assays ( Table 1) , 15 of the proteins contain a pentapeptide conforming to the PEXEL consensus [19, 20; 21, 22] , but that none of these have a position within the amino acid sequence that conforms to the location of known active PEXEL motifs (see Materials and Methods and membrane segments, and none of them has a GPI anchor. In conclusion, an approach combining a genome-wide search by bioinformatics of a-helical coiled coil protein motifs and chemical synthesis can lead to the rapid identification and development of new malaria vaccine candidates. doi = 10.1371/journal.pone.0000645 id = cord-304306-rxjahqwh author = Vlachakis, Dimitrios title = Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic date = 2020-10-08 keywords = COVID-19; CoV-2; RNA; SARS; protein summary = The currently available antiviral option for hospitalized patients is remdesivir, which may inhibit the replication process by targeting the RdRp. Previously proposed treatments for hospitalized patients included hydroxychloroquine, which thought to disrupt virus endocytosis, and lopinavir/ritonavir, which thought to inhibit SARs-CoV-2 main protease (Astuti and Ysrafil, 2020; Magro, 2020) . Silibilin is predicted to have a dual activity against SARS-CoV-2 infection; silibilin can potentially reduce viral replication activity by targeting NSP12 as a remdesivir-like inhibitor, and modulate inflammatory responses by direct inhibition of STAT3 (BoschBarrera et al., 2020) . A recombinant form of the human ACE2 protein was synthesized as a therapeutic treatment for COVID-19, functioning as a decoy for SARS-CoV-2 and essentially preventing the virus from binding to the cell surface ACE2 (Schuster et al., 2010) . Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response doi = 10.1016/j.fct.2020.111805 id = cord-307731-a2fqmaly author = Vázquez, Javier title = Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches date = 2020-10-15 keywords = ligand; protein summary = In particular, the compounds obtained in the final rank order lead to meaningful increases in both performance and robustness over the single-modality approaches, but the results also demonstrate the sensitivity of the performance to the target structural details (i.e., the nature of the template ligand in measurements of molecular similarity and the reference protein pocket in docking studies) [67, 68] . In particular, the compounds obtained in the final rank order lead to meaningful increases in both performance and robustness over the single-modality approaches, but the results also demonstrate the sensitivity of the performance to the target structural details (i.e., the nature of the template ligand in measurements of molecular similarity and the reference protein pocket in docking studies) [67, 68] . doi = 10.3390/molecules25204723 id = cord-291086-goidlh08 author = Walker, Peter J. title = Rhabdovirus accessory genes date = 2011-09-14 keywords = ORF; protein summary = doi = 10.1016/j.virusres.2011.09.004 id = cord-021626-ck2kybtp author = Walker-Smith, John title = Dietary protein intolerance date = 2013-10-21 keywords = Smith; Walker; cow; intolerance; milk; protein summary = Abnormalities of the small intestinal mucosa have been reported in children suffering temporary intolerances to cows'' milk protein, soy protein, gluten, eggs, chicken, ground rice and fish. The involvement of IgE in the immunological response of the lamina propria to milk challenge in children with cows'' milk protein intolerance has been described by Shiner and her colleagues (1975) , also by Kilby, Walker-Smith and Wood (1976) , who showed an increase in IgE cell numbers in the small intestinal mucosa after a milk challenge in a child with cows'' milk sensitive enteropathy. One remarkable exception is the case report of Watt, Pincott and Harries in 1983 of a child with coeliac disease whose small intestinal mucosa was responsive to cows'' milk until at least the age of 7 years. In addition to the above challenge procedure, related to small intestinal biopsy, various laboratory tests have been studied to help to diagnose cows'' milk protein intolerance. doi = 10.1016/b978-0-407-01320-9.50011-x id = cord-347710-ff64y6ef author = Wan, Qianya title = Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date = 2020-07-13 keywords = A71; ATP; HBV; HCV; HIV-1; Heat; Hsc70; Hsp27; Hsp90; RNA; cell; dna; protein; virus summary = hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. 6, 13 It is well known that Hsp90 not only interacts and contributes to RNA polymerase assembly and nuclear import of some (−) ssRNA viruses (e.g., PB2 of influenza virus), but plays crucial roles in the folding process of viral capsid proteins and virion assemblies as well. 17, 18 As a critical component of cellular protein surveillance, the ATP-dependent molecular chaperone protects cells from damage caused by stress and takes part in a number of folding processes, including folding of newly synthesized polypeptides, recognition and refolding of misfolded or aggregated proteins, solubilization or degradation of proteins, transporting proteins, assembly or disassembly of oligomeric protein complexes, and the regulation of certain natively folded proteins. doi = 10.1038/s41392-020-00233-4 id = cord-299413-3o6mdx3e author = Wang, Hui title = Advantages of mRNA display selections over other selection techniques for investigation of protein–protein interactions date = 2014-01-09 keywords = display; library; mrna; protein; selection summary = doi = 10.1586/epr.11.15 id = cord-354547-eomm1sl5 author = Wang, Jibin title = Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding date = 2009-03-16 keywords = Fig; IBV; protein summary = title: Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding In this study, we report that interaction between coronavirus membrane protein (M) and actin with functional implication in facilitating virion assembly and budding. Similarly, analysis of cells expressing the M protein either on its own or together with the Myc-tagged actin by Western blot with anti-M polyclonal antibodies showed the detection of the full-length glycosylated (two upper bands) and unglycosylated (25 kDa) forms of the M protein (Fig. 2, lanes 5 and 6) . In cells transfected with both wild type and MD5 constructs with or without IBV infection, detection of similar amounts of M protein was observed (Fig. 5b, top two panels, lanes 1 and 2) , suggesting that both constructs were expressed at similar efficiencies. doi = 10.1371/journal.pone.0004908 id = cord-262268-gm99cadh author = Wang, Jingqiang title = Assessment of Immunoreactive Synthetic Peptides from the Structural Proteins of Severe Acute Respiratory Syndrome Coronavirus date = 2003-12-01 keywords = ELISA; SARS; protein summary = Consequently, we thoroughly investigated the immunoreactivities with patient sera of a series of synthesized peptides from SARS-coronavirus structural proteins. Results: Four epitopic sites, S599, M137, N66, and N371-404, located in the SARS-coronavirus S, M, and N proteins, respectively, were detected by screening synthesized peptides. The peptides representing the COOH terminus of the N protein, in particular N371 and N385, had high absorbance/cutoff value ratios with the highest positive detection rate and the lowest hydrophobicity score among all of the synthesized peptides (Fig. 1C, and Fig. 3 in the online Data Supplement). The other 17 peptides reacted only slightly with the sera from SARS patients and gave low detection rates, suggesting that the regions of the S protein covered by these peptides have no epitopic site. The patient sera preincubated with 4 mg/L S599 or N385 gave a 25-30% lower response in the ELISA (data not shown), suggesting that the two peptides could compete with SARS coronavirus for binding to the antibodies in SARS serum. doi = 10.1373/clinchem.2003.023184 id = cord-003297-fewy8y4a author = Wang, Ming-Yang title = A Comprehensive In Silico Method to Study the QSTR of the Aconitine Alkaloids for Designing Novel Drugs date = 2018-09-18 keywords = PPI; QSTR; aconitine; figure; network; protein summary = A combined in silico method was developed to predict potential protein targets that are involved in cardiotoxicity induced by aconitine alkaloids and to study the quantitative structure–toxicity relationship (QSTR) of these compounds. To obtain a deeper insight on the relationship between the toxicity and the structure of aconitine alkaloids, the present study utilized QSAR models built in Sybyl software that possess internal robustness and external high predictions. The contour maps around aconitine alkaloids generated by comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) were combined with the interactions between ligand substituents and amino acids obtained from docking results to gain insight on the relationship between the structure of aconitine alkaloids and their toxicity. Finally, we combined the ligand-based 3D-QSTR analysis with the structure-based molecular docking study to identify the necessary moiety related to the cardiotoxicity mechanism of the aconitine alkaloids (in Figure 10 ). doi = 10.3390/molecules23092385 id = cord-193489-u6ewlh16 author = Wang, Rui title = Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine date = 2020-04-29 keywords = CoV-2; SARS; SNP; protein summary = Based on the genotyping of 6156 genome samples collected up to April 24, 2020, we report that SARS-CoV-2 has had 4459 alarmingly mutations which can be clustered into five subtypes. Genetic identification and characterization of the geographic distribution, intercontinental evolution, and global trends of SARS-CoV-2 is the most efficient approach for studying COVID-19 genomic epidemiology and offer the molecular foundation for region-specific SARS-CoV-2 vaccine design, drug discovery, and diagnostic development [10] . We use K-means methods to cluster SARS-CoV-2 mutations, which provides the updated molecular information for the region-specific design of vaccines, drugs, and diagnoses. Table 5 presents the statistics of single mutations on various SARS-CoV-2 proteins that occurred in the recorded genomes between January 5, 2020, and April 24, 2020. Specifically, nucleocapsid protein has both the highest number of mutations per residues of 0.56 and the highest h-index of 27, suggesting that it is the most non-conservative protein in SARS-CoV-2 genomes. doi = nan id = cord-258784-9bdd9krr author = Wei, Chiming title = New technology and clinical applications of nanomedicine: Highlights of the second annual meeting of the American Academy of Nanomedicine (Part I) date = 2006-12-31 keywords = AANM; Dr.; Nanomedicine; University; cell; protein summary = During the Presidential Lecture, Chiming Wei, MD, PhD, of Johns Hopkins University, summarized new published and unpublished findings and results in each nanomedicine research area, and also reviewed the new nanotechnologies and clinical applications in nanomedicine development. The significance of these investigations lies in the development of platform technologies including nanoscale molecular imaging, drug delivery, gene delivery, and diagnostic approaches. Dendrimer-based nanomedicine was developed for protein mimicry research, nanopharmaceuticals, diagnostic imaging with contrast agents, and targeted drug delivery in cancer cells. In Canada some of the important nanomedicine research areas include intelligent drug delivery systems; vaccine and gene delivery nanosystems; polymeric systems and devices; biochips; lab-on-achip; artificial cells; anti-cancer, immune-, neural-and musculoskeletal systems; nanoscale targeting; tissue and cellular engineering; novel biomaterials; and molecular imaging. For the junior YIA scientists, Jean-Christophe Rochet of Purdue University received first place for his work to develop nanoimaging-based approaches for detection and analysis of protein misfolding states. doi = 10.1016/j.nano.2006.11.001 id = cord-287450-hydy874v author = Wendt, K Ulrich title = Structures and diseases date = 2008 keywords = Institute; University; protein; structure summary = In early September 2007, about 180 structural biologists and biochemists met in the picturesque town of Murnau, located near Staffelsee Lake in the Bavarian alpine upland, to reflect on these questions and discuss recent biostructural data on the molecular determinants of human diseases, including microbial and viral infections, protein misfolding diseases, cancer and metabolic disorders. Starting the session on viral diseases, Rolf Hilgenfeld (University of Lübeck) reviewed the work from his laboratory on proteases of RNA viruses, such as severe acute respiratory syndrome (SARS) coronavirus and coxsackievirus B3, and also highlighted recent structural data on falcipain-2 from Plasmodium falciparum, discussing implications for the design of active-site directed and allosteric inhibitors for these cysteine proteases 14 . Günter Fritz (University of Konstanz) presented the unpublished structure of the ligand binding domain of RAGE, a multiligand receptor for advanced glycation end products, S100 proteins, HMGB1 and amyloid-β, whose activation is key to numerous chronic diseases such as diabetes, inflammation, arteriosclerosis and neurodegeneration, making it a potential therapeutic target 32, 33 . doi = 10.1038/nsmb0208-117 id = cord-313694-p2sgaypq author = West, Christopher M. title = Current ideas on the significance of protein glycosylation date = 1986 keywords = Golgi; carbohydrate; cell; glycoprotein; protein; structure summary = The alternate view is that carbohydrate structures participate in numerous specific interactions with discrete protein receptors, and that these interactions lead to predictable modifications in the localization or activity of the glycoprotein. The notion of a ''non-specific'' role for carbohydrate has received perhaps its strongest support from studies on cells whose glycosylation processes have been globally altered by mutation or drugs. Consideration of the possible role of carbohydrate in other molecular associations with the plasma membrane will be considered below in sections on hormone-receptor interactions and cellsubstratum (e.g., extracellular matrix) and cell-cell adhesion. Considerable evidence has been adduced that various parasites such as viruses, bacteria, protozoa, etc., possess carbohydrate binding proteins which can interact with sugar structures on the surfaces of cells with which the parasites associate (167, 168, (116) (117) (118) (119) . In any case, antibodies and lectins may model potential receptors in cells which might specifically recognize carbohydrate-associated structures. doi = 10.1007/bf00230632 id = cord-264031-0y7xbgun author = Wierbowski, Shayne D. title = A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions date = 2020-10-13 keywords = CoV-2; SARS; human; interface; protein summary = title: A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions This resource includes docked structures for all interactions with protein structures, enrichment analysis of variation along interfaces, predicted ΔΔG between SARS-CoV and SARS-CoV-2 variants for each interaction, predicted impact of natural human population variation on binding affinity, and a further prioritized set of drug repurposing candidates predicted to overlap with protein interfaces†. Further, we explore the utility of our interactome modeling approach in identifying key 99 interactions undergoing evolution along viral protein interfaces, highlighting population variants on 100 human interfaces that could modulate the strength of viral-host interactions to confer protection from or 101 susceptibility to COVID-19, and prioritizing drug candidates predicted to bind competitively at viral-102 human interaction interfaces. doi = 10.1101/2020.10.13.308676 id = cord-306624-1mjmttec author = Wodrich, Harald title = A Capsid-Encoded PPxY-Motif Facilitates Adenovirus Entry date = 2010-03-19 keywords = MTOC; Nedd4.2; figure; protein summary = We show that the PPxY motif in protein VI is involved in its efficient microtubule-mediated transport and mutating it in the virus alters the intracellular targeting of Ads towards the MTOC region concomitant with a post-entry block in viral infectivity. To identify possible trafficking determinants, we analyzed the sequences of protein VI from several Ad serotypes and identified a highly conserved ubiquitin-ligase interacting motif present in PPxY-type viral late domains (PPxY, Figure S2 ). To determine whether the M1 mutation influences Ad cell entry, we performed a fluorescent focus forming assay and stained cells at 8, 12 and 24 h post-infection for expression of the E2A protein, which marks the appearance of viral replication centers ( Figure 2D and data not shown). In addition to the increase of protein VI capsid association, Ad5-VI-M1 appeared to be more evenly distributed throughout the cell and did not efficiently accumulate at the MTOC region ( Figure 3B , images to the left). doi = 10.1371/journal.ppat.1000808 id = cord-103509-hynnba03 author = Wong, Ten-Tsao title = A self-assembled protein nanoparticle serving as a one-shot vaccine carrier date = 2020-09-18 keywords = AH3-GFP; Fig; protein summary = From these two clues, it was hypothesized that AH3-GFP fusion protein form stable protein complex through hydrophobic interaction mediated by N-terminal AH3 peptide. Using the same protocol, AH3-GFP was found to co-sedimented with the bacterial membrane (Fig. S3A) as well as the AH3-sfGFP-hM2e fusion protein but not a free GFP protein (Fig S3B) These results are consistent with our protein structure modeling that Arg11 serves as a main contact point for dimer stacking also it mediates the electrostatic interaction with mutated Glu13 (Fig. 3E ). These results suggest that the two point mutations of AH3 in I8L and K13E enable the formation of a stable, high antigenic protein complex that stimulates long lasting immune responses in a single immunization. The result suggests that although carrier protein AH3-sfGFP also has high antigenicity, it did not interfere with the immune response against the heterologous protein, hM2e (Fig. 5B, 5C) doi = 10.1101/2020.09.16.299149 id = cord-252576-1ec545o2 author = Wu, Xiangli title = An antifungal defensin from Phaseolus vulgaris cv. ‘Cloud Bean’ date = 2011-01-15 keywords = antifungal; protein summary = An antifungal peptide with a defensin-like sequence and exhibiting a molecular mass of 7.3 kDa was purified from dried seeds of Phaseolus vulgaris ''Cloud Bean''. After elution of unadsorbed proteins (fraction S1), adsorbed proteins were desorbed with a linear concentration (0-1 M) gradient of NaCl. The fraction with antifungal activity (S2) was then further fractionated by fast protein liquid chromatography on a Superdex 75 HR 10/30 column (GE Healthcare) in 0.2 M NH 4 HCO 3 buffer (pH 8.5). Antiproliferative activity toward tumor cells is also an attribute of defensins (Wong and Ng 2003) , defensin-like peptides and also other antifungal proteins including ribosome inactivating proteins (Lam et al. Some antifungal proteins including defensin-like peptides (Wong and Ng 2003) , protease inhibitors (Ye et al. The present findings on cloud bean defensin is reminiscent of the observation that mungin, an antifungal protein from mung beans, is without HIV-1 reverse transcriptase inhibitory activity (Ye and Ng 2000) . Concurrent purification of two defense proteins from French bean seeds: a defensin-like antifungal peptide and a hemagglutinin doi = 10.1016/j.phymed.2010.06.010 id = cord-340387-ohkjheat author = Wynne, James W. title = Purification and Characterisation of Immunoglobulins from the Australian Black Flying Fox (Pteropus alecto) Using Anti-Fab Affinity Chromatography Reveals the Low Abundance of IgA date = 2013-01-07 keywords = Fig; Protein; SDS summary = title: Purification and Characterisation of Immunoglobulins from the Australian Black Flying Fox (Pteropus alecto) Using Anti-Fab Affinity Chromatography Reveals the Low Abundance of IgA To further understand the antibody response of bats, the present study purified and characterised the major immunoglobulin classes from healthy black flying foxes, Pteropus alecto. Considering that in other mammalian species, immunoglobulins IgG, IgM and IgA are present in relatively high abundance in serum and tissues, we anticipated that bats would possess a similar immunoglobulin profile. IgG-depleted samples were fractionated by affinity chromatography on immobilised anti-Fab-specific antibodies adopting the same procedure as that described for immobilised Protein A and G except that the binding and washing buffer consisted of 0.3 M NaCl in 50 mM phosphate buffer, pH 7.4. Two major bands were detected by reducing SDS-PAGE in the eluate from both serum and plasma samples; a 66-70 kDa band representative of IgM H , and a 25 kDa band representative of immunoglobulin light chain ( Fig. 3A and 3B ). doi = 10.1371/journal.pone.0052930 id = cord-274393-1geyuxtk author = Xie, Wenyan title = Mutations in the Leucine Zipper-Like Motif of the Human Parainfluenza Virus 3 Fusion Protein Impair Fusion Activity date = 2015-12-23 keywords = cell; protein summary = doi = 10.1159/000441978 id = cord-000575-g1ob16b9 author = Xie, Xiao-li title = Protein sequence analysis based on hydropathy profile of amino acids date = 2012-01-27 keywords = dna; protein summary = A new method to analyze the similarity/dissimilarity of protein sequence was proposed based on the conditional probability of the protein sequence. Based on the graphical representation, it is possible to numerically characterize DNA sequence and further quantitatively measure similarity of different DNA sequences. This is mainly because extension of DNA graphical representation to protein sequences would enormously increase the number of possible alternative assignments for the 20 amino acids. The graphical representation of protein sequence cannot only describe amino acid sequence, but also measure similarity/ dissimilarity of different protein sequences. In this paper, we converted a protein sequence into three-letter sequence based on hydropathy profile of amino acid and defined the three curves to represent different hydropathy features. The method is based on the graphical representation and conditional probability taken as the numerical characterization of the protein sequence. Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation doi = 10.1631/jzus.b1100052 id = cord-328046-5us4se5o author = Xu, H. Y. title = Further Identification and Characterization of Novel Intermediate and Mature Cleavage Products Released from the ORF 1b Region of the Avian Coronavirus Infectious Bronchitis Virus 1a/1b Polyprotein date = 2001-09-30 keywords = Fig; IBV; protein summary = In cells infected with avian coronavirus infectious bronchitis virus (IBV), three proteins of 100, 39, and 35 kDa, respectively, were previously identified as mature cleavage products released from the 1b region of the 1a/1b polyprotein by the 3C-like proteinase. Immunofluorescent staining of IBV-infected cells and cells expressing individual cleavage products showed that the 100-, 68-, and 58-kDa proteins were associated with the membranes of the endoplasmic reticulum, and the 39and 35-kDa proteins displayed diffuse distribution patterns. Taken together with the Q 3928 -S 2929 dipeptide bond (encoded by nucleotides 12310-12315) identified as the N-terminal cleavage site of the 100-kDa protein, cleavage at these positions would result in the release of five mature products with molecular masses of approximately 100, 68, 58, 39, and 35 kDa. Among them, the 100-, 39-, and 35-kDa proteins were specifically identified in IBV-infected cells (Liu et al., 1994 . doi = 10.1006/viro.2001.1098 id = cord-018963-2lia97db author = Xu, Ying title = Protein Structure Prediction by Protein Threading date = 2010-04-29 keywords = fold; protein; sequence; structure; threading summary = Their follow-up work (Elofsson et aI., 1996; Fischer and Eisenberg, 1996; Fischer et aI., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et aI., 1992) on protein fold recognition led to the development of a new brand ofpowerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many ofthe proteins encoded in the hundreds of genomes that have been sequenced up to now. doi = 10.1007/978-0-387-68825-1_1 id = cord-262748-v4xue7ha author = Xu, Yongtao title = Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine date = 2015-12-04 keywords = SVM; peptide; protein; virus summary = doi = 10.1371/journal.pone.0144171 id = cord-286635-7aflpgxd author = YANG, Yong-xin title = Comparative Proteomic Analysis of Plasma from Clinical Healthy Cows and Mastitic Cows date = 2009-10-31 keywords = cow; protein summary = After staining with silver nitrate and Coomassie Blue, differential expression proteins were detected by PDQuest 7.4 software, and then subjected to ion trap mass spectrometer equipped with a Surveyor HPLC System, differential spots of protein were identified. This investigation was to detect the expressed proteins in plasma from clinical mastitic and healthy dairy cows by 2-DE providing a platform for parallel analysis, and then, to identify differential proteins by ion trap mass spectrometer equipped with HPLC System, in order to probe the pathogenesis of mastitis and find new biomarkers of mastitis-associated proteins for diagnosis and treatment. To probe protein expression pattern changes in plasma from healthy dairy cows and clinical mastitic cows, this subject analyzed and identified differential protein spots using 2-DE and ion trap mass spectrometer equipped with HPLC System. doi = 10.1016/s1671-2927(08)60337-5 id = cord-274293-kzmch37j author = Yang, Li title = Tandem mass tag-based quantitative proteomic analysis of lycorine treatment in highly pathogenic avian influenza H5N1 virus infection date = 2019-10-02 keywords = Nup93; protein summary = Therefore, we performed a comparative proteomic analysis to identify changes in protein expression in AIV-infected Madin-Darby Canine Kidney cells treated with lycorine. Therefore, we performed a comparative proteomic analysis to determine the effects of lycorine at the protein level in GD178-infected MDCK cells to understand its mode of action. The functional classification of DEPs was conducted by KEGG enrichment analysis, and each protein was assigned to at least one of the following pathways: human T-lymphotropic virus-1 infection pathway (path: ko05166), cell adhesion molecules (CAMs) (path: ko04514), epidermal growth factor receptor tyrosine kinase inhibitor resistance (path: ko01521), Janus kinase-STAT signaling pathway (path: ko04630), and pancreatic cancer (path: ko05212) (Fig. 3C) . As a result, AIV infection may induce Nup93 to complete the viral cycle, and the process of protein targeting into Nup93 after lycorine treatment may partly be explained by the blockage of vRNPs in the host cellular nucleus. Functional proteomic studies of lycorine-treated MDCK cells on highly pathogenic avian influenza H5N1 virus infection doi = 10.7717/peerj.7697 id = cord-321441-t1v0pu0w author = Yang, Yiming title = Polycistronic Genome Segment Evolution and Gain and Loss of FAST Protein Function during Fusogenic Orthoreovirus Speciation date = 2020-06-29 keywords = ARV; ORF; cell; fast; figure; protein summary = New phylogenetic analyses that included the atypical waterfowl subgroup of avian reoviruses and recently identified new orthoreovirus species indicate a more complex relationship between reovirus speciation and fusogenic capacity, with numerous predicted internal indels and 5''-terminal extensions driving the evolution of the orthoreovirus'' polycistronic genome segments and their encoded FAST and fiber proteins. We further show that two distinct post-speciation genetic events led to the loss of fusion in the waterfowl isolates of avian reovirus, a recombination event that replaced the p10 FAST protein with a heterologous, non-fusogenic protein and point substitutions in a conserved motif that destroyed the p10 assembly into multimeric fusion platforms. MdRVs are divided into two subgroups, the "classical" and "novel" MdRVs. Classical Muscovy duck reoviruses (MdRVc) possess a bicistronic S4 genome segment encoding a truncated fiber protein of 269 residues and a p11 protein that lacks sequence similarity to the p10 FAST proteins of ARV, ARVN, and NBV ( Figure 1B ) [50] . doi = 10.3390/v12070702 id = cord-275124-7l53bvp1 author = Yao, Minghui title = A potential treatment for COVID-19 based on modal characteristics and dynamic responses analysis of 2019-nCoV date = 2020-10-21 keywords = protein; spike summary = The finite element analysis (FEA) is used to study the modal characteristics of the tuned 2019-nCoV model and mistuned 2019-nCoV model in blood, respectively. Because of the relatively heavy mass of the sphere body compared to spike proteins, its modes are rigid body motion, which the sphere of COVID-19 model is fixed in modal analysis. Based on the first-order bending vibration form, the lumped mechanical model is established as illustrated in Fig. 5 . The harmonic response is conducted after the modal analysis of the mistuned 2019-nCoV model, and acceleration excitation is set as 1 mm/s 2 , as shown in Fig. 6 . (1) The frequencies of the tuned 2019-nCoV model are very close to each other, and they are all first-order bending vibrations. The frequencies of the realistic mistuned 2019-nCoV model are a range of frequencies close to each other, and every frequency corresponds to the first-order bending vibration of one spike protein. doi = 10.1007/s11071-020-06019-1 id = cord-261472-qcu73sdu author = Yao, Yong Xiu title = Cleavage and Serum Reactivity of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein date = 2004-07-01 keywords = SARS; protein summary = Severe acute respiratory syndrome (SARS) coronavirus (SCoV) spike (S) protein is the major surface antigen of the virus and is responsible for receptor binding and the generation of neutralizing antibody. To investigate SCoV S protein, full-length and individual domains of S protein were expressed on the surface of insect cells and were characterized for cleavability and reactivity with serum samples obtained from patients during the convalescent phase of SARS. The possible use of insect cell-displayed S protein for diagnostic application was assessed by examining fragment reactivity with serum samples from patients infected with human CoV 229E and also with serum from a patient with suspected but clinically unconfirmed SARS (serum sample 3118). Of the 2 assay formats we used, nondenatured S protein present on the cell surface provided the most sensitive detection of antibodies, with clear shifts in fluorescence for serum samples from patients with suspected but clinically unconfirmed SARS. doi = 10.1086/421280 id = cord-253844-y6xdcf20 author = Yesudhas, Dhanusha title = COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics date = 2020-09-04 keywords = ACE2; CoV-2; SARS; human; protein; receptor summary = In SARS-CoV-2 infection, intrinsically disordered regions are observed at the interface of the spike protein and ACE2 receptor, providing a shape complementarity to the complex. SUMMARY: The overall history and mechanism of entry of SARS-CoV-2 along with structural study of spike-ACE2 complex provide insights to understand disease pathogenesis and development of vaccines and drugs. The sequence similarity between SARS-CoV-2 and SARS-CoV spike proteins explains the possibility of binding to the same receptor angiotensin converting enzyme 2 (ACE2) in the host cell [14] . In this review, we discuss the history of coronaviruses in both humans and animals, their transmissions, mechanism of host cell entry and the structural studies, explaining active and inactive receptor binding of spike protein and the key residues playing an important role in the receptor binding. During viral infection, spike protein (~ 1300 amino acid residues) is cleaved by host proteases into receptor binding subunit S1 and membrane fusion subunit S2. doi = 10.1007/s15010-020-01516-2 id = cord-329625-hx2rsi91 author = You, Jae-Hwan title = A model for the dynamic nuclear/nucleolar/cytoplasmic trafficking of the porcine reproductive and respiratory syndrome virus (PRRSV) nucleocapsid protein based on live cell imaging date = 2008-08-15 keywords = EGFP; PRRSV; protein summary = title: A model for the dynamic nuclear/nucleolar/cytoplasmic trafficking of the porcine reproductive and respiratory syndrome virus (PRRSV) nucleocapsid protein based on live cell imaging Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus, in common with many other positive strand RNA viruses, encodes a nucleocapsid (N) protein which can localise not only to the cytoplasm but also to the nucleolus in virus-infected cells and cells over-expressing N protein. To investigate whether the trafficking of N protein between the cytoplasm and the nucleus/nucleolus was associated with microtubules or energy dependent, the mobility of EGFP-PRRSV-N protein was compared in 3D4/31 cells incubated at 37°C in the presence and absence of nocodazole (60ng/ml nocodazole (Sigma) for 16h), a microtubule inhibitor, or incubated at 10°C. In approximately 10% of cells expressing EGFP-PRRSV-N protein fluorescence was observed in the cytoplasm, but only if imaging was adjusted so that the fluorescent signal in the nucleus/nucleolus was above the linear range (for example Fig. 8C, lower panels) . doi = 10.1016/j.virol.2008.04.037 id = cord-298242-iuskpoug author = Yu, Alvin title = A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion date = 2020-10-02 keywords = SARS; protein summary = doi = 10.1101/2020.10.02.323915 id = cord-002739-7t1o19kn author = Yu, Xiaobo title = Multiplexed Nucleic Acid Programmable Protein Arrays date = 2017-09-20 keywords = NAPPA; array; figure; protein summary = Methods: In this work, we developed the Multiplexed Nucleic Acid Programmable Protein Array (M-NAPPA), which significantly increases the number of displayed proteins by multiplexing as many as five different gene plasmids within a printed spot. Protein-protein interactions and serological antibody assays using human viral proteome microarrays demonstrated that comparable hits were detected by M-NAPPA and non-multiplexed NAPPA arrays. We developed the Multiplexed Nucleic Acid Programmable Protein Array (M-NAPPA) method by combining as many as five different DNA plasmids within one spot, which increases the number of displayed proteins per microarray by five-fold. To decrease the cost of high throughput screening experiments, we hypothesized that the plasmid cDNA encoding for different proteins could be multiplexed (by combining M different plasmids) within each feature to create a high-density array, M-NAPPA ( Figure 1A) . Since the multiplex concept to increase feature density was successful in detecting protein-protein interactions and serological antibody responses on planar microarrays, we wanted to determine whether M-NAPPA could also be applied to a nano-well microarray platform. doi = 10.7150/thno.20151 id = cord-012682-7goljir4 author = Yuan, Meng title = N-myristoylation: from cell biology to translational medicine date = 2020-03-18 keywords = NMT1; NMT2; myristoylation; nmt; protein summary = N-myristoylation refers to the attachment of 14-carbon fatty acid myristates to the N-terminal glycine of proteins by N-myristoyltransferases (NMT) and affects their physiology such as plasma targeting, subcellular tracking and localization, thereby influencing the function of proteins. For example, it was reported that both N-myristoylation and palmitoylation appear to have opposing roles and different membrane lipid microdomain preferences for the G protein-membrane interactions I (Gαi1) monomer, which are likely due to the conformational differences in the presence of different fatty acids [31] . Potential targets of cancer treatments Given that altered NMT expression is observed in many types of cancer tissues and because many N-myristoylated proteins are involved in signaling processes that regulate cell proliferation, growth and death, it has been proposed that N-myristoylation or NMTs can be considered as therapeutic targets for cancer. doi = 10.1038/s41401-020-0388-4 id = cord-297324-me5ff1pb author = Zeng, Rong title = Characterization of the 3a Protein of SARS-associated Coronavirus in Infected Vero E6 Cells and SARS Patients() date = 2004-07-30 keywords = SARS; figure; protein summary = doi = 10.1016/j.jmb.2004.06.016 id = cord-347661-q9lgliph author = Zevenhoven-Dobbe, Jessika C. title = Production of Monospecific Rabbit Antisera Recognizing Nidovirus Proteins date = 2007-11-28 keywords = PBS; SDS; cell; peptide; protein summary = The use as antigens of either synthetic peptides (coupled to a carrier protein) or proteins expressed in Escherichia coli is described, and detailed protocols for immunization and preparation of test bleeds are provided. Furthermore, in the context of specific research questions, polyclonal antisera may sometimes even be preferred over monoclonal antibodies since they contain a mixture of immunoglobulin molecules, derived from different B-cell lines in the immunized animal, often recognizing multiple epitopes of the target protein. The antiserum used here was raised against a domain in the C-terminal region of pp1a of the arterivirus EAV (8) and recognizes a large set of processing intermediates and end products, which are indicated by arrowheads: (A) Western blot analysis: EAV-and mock-infected cell lysates were prepared at 8 h postinfection, run on an SDS-polyacrylamide gel, blotted to PVDF membrane, and incubated with the postimmune serum at a 1:1000 dilution. doi = 10.1007/978-1-59745-181-9_16 id = cord-284990-klsl1nzn author = Zhang, Dapeng title = A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems date = 2011-02-08 keywords = CDI; SUKH; domain; figure; protein; toxin summary = doi = 10.1093/nar/gkr036 id = cord-103709-86hv27vh author = Zhang, Dong Yan title = Prefusion spike protein stabilization through computational mutagenesis date = 2020-06-19 keywords = SARS; SASA; protein summary = doi = 10.1101/2020.06.17.157081 id = cord-349774-898tmq14 author = Zhang, Haiyang title = Proteasome activator PA28γ-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein date = 2020-06-16 keywords = SARS; protein summary = title: Proteasome activator PA28γ-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein Here, we report for the first time that the 11S proteasomal activator PA28γ regulates the intracellular abundance of the SARS-CoV-2 N protein (nCoV N). These results suggest that PA28γ binding is important in regulating 20S proteasome activity, which in turn regulates levels of the critical nCoV N nucleocapsid protein of SARS-CoV-2, furthering our understanding of the pathogenesis of COVID-19. The SARS-CoV-2 nucleocapsid protein (hereafter, referred to as nCoV N) accounts for the largest proportion of viral structure proteins and is the most abundant protein in virus-infected cells. PA28γ could be critical for degrading the SARS-CoV-19 nCoV N protein in the nucleus as part of the 20S proteasome, which acts to degrade proteins in a ubiquitin-independent manner, such as seen in the hepatitis C virus (HCV) core protein [11] . Interactions of SARS Coronavirus Nucleocapsid Protein with the host cell proteasome subunit p42 doi = 10.1016/j.bbrc.2020.06.058 id = cord-024193-khdvj6t5 author = Zhang, Hong title = Peptide Arrays date = 2012-01-17 keywords = array; kinase; microarray; peptide; protein summary = Despite the concern over the potential loss of structural information as a result of the use of peptides as opposed to proteins as molecular probes, peptide arrays have been implemented in a broad range of applications including antibody screening and epitope mapping, characterization of molecular interactions, and enzymatic activity profiling, and they have become a valuable tool for proteomics research. Similarly to DNA/oligonucleotide microarrays, arrays for proteomics studies feature a wide range of molecules including recombinant proteins, complex protein samples, antibodies, peptides, or small molecules that are assembled in an addressable fashion on planar surfaces to allow parallel interrogations for activity and interactions associated with biomolecules at the protein level. doi = 10.1007/978-3-642-28203-4_7 id = cord-300884-rqfxe0x1 author = Zhang, Jianqiang title = Genomic characterization of equine coronavirus date = 2007-12-05 keywords = OC43; RNA; protein summary = Analysis of the sequence identified 11 open reading frames which encode two replicase polyproteins, five structural proteins (hemagglutinin esterase, spike, envelope, membrane, and nucleocapsid) and four accessory proteins (NS2, p4.7, p12.7, and I). In contrast to the replicase proteins which are directly translated from the genomic RNA, coronavirus structural and accessory proteins are expressed from a nested set of 3′ coterminal subgenomic (sg) mRNAs that also possess a common 5′ leader sequence derived from the 5′ end of the genome (Pasternak et al., 2006; Sawicki et al., 2007) . Following multiple alignments with the S proteins of other group 2a coronaviruses, a potential cleavage recognition sequence (RRQRR) was identified at residues 764-768 which would predict a cleavage between amino acids 768 and 769, separating the ECoV S protein into S1 and S2 subunits (Fig. 1) . doi = 10.1016/j.virol.2007.06.035 id = cord-332317-wrztpeb8 author = Zhang, Xin title = Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus date = 2015-03-16 keywords = TGEV; protein summary = Nucleocapsid (N) protein of transmissible gastroenteritis virus (TGEV) packages viral RNA genome to form a ribonucleoprotein complex. The present study thus provides protein-related information about interaction of TGEV N protein with host cell that should be useful for understanding host cell response to coronavirus pathogenesis infection and the underlying mechanism of coronavirus replication. Recently, some reports showed that N protein of TGEV play an important role in host cell for virus replication. Three cellular proteins, hnRNP U, ACTN4, and vimentin, were identified both by GST-N pull down and Co-IP in TGEV-infected cells, which should have more biological importance in the context of infection. The interaction between the cellular vimentin and N protein of TGEV was confirmed in TGEV-infected ST cells. Host cell proteins interacting with the 3 end of TGEV coronavirus genome influence virus replication EF1A interacting with nucleocapsid protein of transmissible gastroenteritis coronavirus and plays a role in virus replication doi = 10.1016/j.virusres.2014.12.013 id = cord-257392-u6jy6w1m author = Zhao, Yanfeng title = Proteomic analysis of primary duck hepatocytes infected with duck hepatitis B virus date = 2010-06-07 keywords = DHBV; infection; protein summary = In this report, we explored global changes in cellular protein expression in DHBV infected PDHs by two-dimension gel electrophoresis (2-DE) combined with MALDI-TOF/TOF tandem mass spectrometry (MS/MS). The down-regulated expression of beta-actin and annexin A2 was confirmed by Western blot analysis, and potential roles of some differentially expressed proteins in the virus-infected cells have been discussed. CONCLUSIONS: Differentially expressed proteins of DHBV infected PDHs revealed by 2-DE, are involved in carbohydrate metabolism, amino acid metabolism, stress responses and cytoskeleton processes etc, providing the insight to understanding of interactions between hepadnavirus and hepatocytes and molecular mechanisms of hepadnavirus pathogenesis. Expression levels of annexin A2, beta-actin, Hsp70, destrin, and lamin A were validated by Western blot analysis to confirm the dynamic alterations of protein expression during DHBV infection. In summary, the present study explored global changes in cellular protein expression of hepadnavirus infection by 2-DE analysis, using a natural DHBV-PDHs infection system. doi = 10.1186/1477-5956-8-28 id = cord-271693-7tg21up3 author = Zheng, Fan title = Identifying persistent structures in multiscale ‘omics data date = 2020-10-03 keywords = Fig; Supplementary; community; protein summary = Many different approaches have been devised or applied to detect structures in biological data, including standard clustering, network community detection, and low-dimensional data projection [5] [6] [7] , some of which can be tuned for sensitivity to objects of a certain size or scale (so-called ''resolution parameters'') [8, 9] . We first explored the idea of measuring community persistence via analysis of synthetic datasets [15] in which communities were simulated and embedded in the similarity network at two different scales (Supplementary Fig. 1a; Methods) . Application to protein-protein interaction networks from budding yeast and human found that HiDeF captured knowledge in GO more significantly than previous pipelines proposed for this task, including the NeXO approach to hierarchical community detection [23] and standard hierarchical clustering of pairwise protein distances calculated by three recent network embedding approaches [24] [25] [26] (Fig. 3a, Fig. 7) . doi = 10.1101/2020.06.16.151555 id = cord-290904-ngvhk0qy author = Zheng, Zhiqiang title = Monoclonal antibodies for the S2 subunit of spike of SARS-CoV-1 cross-react with the newly-emerged SARS-CoV-2 date = 2020-07-16 keywords = CoV-2; SARS; protein summary = In this study, we aim to verify if the sequence of the immunogen used to generate mAb 1A9, as well as three other mAbs, is conserved in different coronaviruses and if these mAbs bind to the S protein of SARS-CoV-2 expressed in mammalian cell lines. IF analysis performed on transiently transfected COS-7 cells showed binding of the four mAbs to this S protein fragment of SARS-CoV-2 ( Figure 2B ). Utility of monoclonal antibody 1A9 for detection of S protein in a sandwich ELISA format and in SARS-CoV-2 infected cells Based on indirect ELISA data, mAb 1A9 has the strongest binding to S protein when compared with the other three mAbs. Hence, a sandwich ELISA was performed to determine if it can be paired with the human mAb CR3022 which is known to bind to the S1 subunit of SARS-CoV-2. doi = 10.2807/1560-7917.es.2020.25.28.2000291 id = cord-271470-j58mr9xk author = Zhu, Feifei title = Glycoproteome in silkworm Bombyx mori and alteration by BmCPV infection date = 2020-04-29 keywords = protein; silkworm summary = doi = 10.1016/j.jprot.2020.103802 id = cord-048344-ps3mnpzq author = Zhu, Xiaowei title = ProCAT: a data analysis approach for protein microarrays date = 2006-11-16 keywords = protein; signal; spot summary = Here we report a new approach, ProCAT, which corrects for background bias and spatial artifacts, identifies significant signals, filters nonspecific spots, and normalizes the resulting signal to protein abundance. In addition, spatial variations can be reduced efficiently through a novel two-parameter signal normalization approach and calling positive spots locally. A scaling method that reduces signal variations among spots of the same proteins at different array locations decreases spatial artifacts. The average values are then used to correct the signal of the central spot to To test the performance of this two-parameter scaling approach for signal normalization within one slide, we designed a test microarray containing multiple positive controls printed at different positions on the slide. Processed data including analysis parameters, a list of positive spots with protein annotations, and normalized signal intensities will be available for the users to download from the server. doi = 10.1186/gb-2006-7-11-r110 id = cord-305143-mqd4ioj4 author = Zmasek, Christian M. title = Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO) date = 2019-01-06 keywords = Herpesviridae; Pfam; dna; domain; protein summary = Coupled with their genome complexity and the availability of numerous complete genome sequences, this deep evolutionary history makes herpesviruses a tractable and informative model to study virus genome evolution at the levels of gene duplication and protein domain rearrangement. In addition, the gene tree for human herpesvirus uracil DNA glycosylases ( Fig. 1B ) precisely recapitulates the herpesvirus species tree (Fig. 1A) ; therefore, this protein family can be inferred to have evolved from a single common ancestor and without any gene duplications or domain rearrangements (see Table 2 for virus-specific gene names). Phylogenetic analysis of human herpesvirus DNA polymerase proteins, plus related proteins from selected mammalian herpesviruses, shows that, similar to the glycoprotein B family, DNA polymerases of the Herpesviride evolved without gene duplication. doi = 10.1016/j.virol.2019.01.005 id = cord-284208-8fsqgkw5 author = Zolla, Lello title = Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins date = 2008-11-07 keywords = drug; plasma; protein; proteomic summary = In the near future, pharmacoproteomics, the use of proteomic technologies in the field of drug discovery and development, and interactomics, the branch of proteomics which is concerned with identifying interactions between proteins, will allow researchers to (i) know the specific protein changes that occur in biological compartments in response to drug administration; (ii) design small novel therapeutic molecules that can have extended half-lives if carried by plasma protein in the blood stream. In the near future, pharmacoproteomics, the use of proteomic technologies in the field of drug discovery and development, and interactomics, the branch of proteomics which is concerned with identifying interactions between proteins, will allow researchers to (i) know the specific protein changes that occur in biological compartments in response to drug administration; (ii) design small novel therapeutic molecules that can have extended half-lives if carried by plasma protein in the blood stream. doi = 10.1016/j.drudis.2008.09.013 id = cord-269011-230p8rsf author = de Haan, Cornelis A.M. title = Molecular Interactions in the Assembly of Coronaviruses date = 2005-08-31 keywords = Golgi; MHV; RNA; protein summary = Biochemical and theoretical studies led to a topological model for the MHV M protein Rottier et al., 1984 Rottier et al., , 1986 , in which the polypeptide spans the lipid bilayer three times, leaving a small amino-terminal domain (15-35 residues) in the lumen of intracellular organelles (or outside the virus), whereas the carboxyterminal half of the protein is located on the cytoplasmic side of the membrane (or inside the virion). Using a mutational approach including deletions, insertions, and substitutions, both the transmembrane domain and the cysteine-rich region immediately downstream thereof, but not the carboxy-terminal part of the cytoplasmic tail, were shown to be important for MHV S protein-induced cell-cell fusion (Bos et al., 1995; Chang and Gombold, 2001; Chang et al., 2000) The cleavage requirements of the S proteins for the biological activities of the coronavirus spike remain enigmatic. doi = 10.1016/s0065-3527(05)64006-7 id = cord-317675-s1ac5vcx author = de Marco, Ario title = Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli date = 2009-05-14 keywords = Escherichia; bond; coli; disulfide; expression; protein summary = The cytoplasmic accumulation of thioredoxin as a consequence of its recombinant overexpression in wild type bacteria was proposed for increasing the yields of coexpressed eukaryotic proteins without disulfide bonds in their native structure [191] . Fusions between recombinant scFvs and thioredoxin 1 expressed in trxB -, gorbacteria resulted in increased cytoplasmic yields [196] , correct folding of a scFv against the c-Met receptor [188] , and of the first domain of the multiple Kazal-type inhibitor LEKTI, a polypeptide that contains two disulfide bridges in its native structure [197] . In the case of a serpin domain, AD494 cells did not improve the total amount of soluble recombinant protein accumulated in the cytoplasm with respect to wild type bacteria, but it was correctly folded and active, whilst the protein expressed in the control cells did not form the essential disulfide bonds [210] . doi = 10.1186/1475-2859-8-26 id = cord-031957-df4luh5v author = dos Santos-Silva, Carlos André title = Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era date = 2020-09-02 keywords = amp; antimicrobial; figure; model; peptide; pin; plant; protein; sequence; structure summary = 19 Plant AMPs are the central focus of the present review, comprising information on their structural features (at genomic, gene, and protein levels), resources, and bioinformatic tools available, besides the proposition of an annotation routine. 26 Plant AMPs are also classified into families considering protein sequence similarity, cysteine motifs, and distinctive patterns of disulfide bonds, which determine the folding of the tertiary structure. 27, 31 These AMP categories will be detailed in the next sections, together with other groups here considered (Impatienlike, Macadamia [β-barrelins], Puroindoline (PIN), and Thaumatin-like protein [TLP]) and the recently described αhairpinin AMPs. The description includes comments on their structure, pattern for regular expression (REGEX) analysis (when available), functions, tissue-specificity, and scientific data availability. 179 As to the TLP structure, this protein presents characteristic thaumatin signature (PS00316): 180, 181 Most of the TLPs have molecular mass ranging from 21 to 26 kDa, 163 possessing 16 conserved cysteine residues (Supplementary Figure S8) involved in the formation of 8 disulfide bonds, 182 which help in the stability of the molecule, allowing a correct folding even under extreme conditions of temperature and pH. doi = 10.1177/1177932220952739 id = cord-001835-0s7ok4uw author = nan title = Abstracts of the 29th Annual Symposium of The Protein Society date = 2015-10-01 keywords = ATP; Biology; Ca21; Chemistry; Department; Institute; NADPH; NMR; PDB; RNA; Science; Tau; University; activity; base; bind; binding; cell; change; complex; design; dna; domain; enzyme; form; function; high; interaction; membrane; method; molecular; peptide; process; protein; residue; result; role; sequence; site; structure; study summary = Altogether, these results indicate that, although PHDs might be more selective for HIF as a substrate as it was initially thought, the enzymatic activity of the prolyl hydroxylases is possibly influenced by a number of other proteins that can directly bind to PHDs. Non-natural aminoacids via the MIO-enzyme toolkit Alina Filip 1 , Judith H Bartha-V ari 1 , Gergely B an oczy 2 , L aszl o Poppe 2 , Csaba Paizs 1 , Florin-Dan Irimie 1 1 Biocatalysis and Biotransformation Research Group, Department of Chemistry, UBB, 2 Department of Organic Chemistry and Technology An attractive enzymatic route to enantiomerically pure to the highly valuable a-or b-aromatic amino acids involves the use of aromatic ammonia lyases (ALs) and aminomutases (AMs). Continuing our studies of the effect of like-charged residues on protein-folding mechanisms, in this work, we investigated, by means of NMR spectroscopy and molecular-dynamics simulations, two short fragments of the human Pin1 WW domain [hPin1(14-24); hPin1(15-23)] and one single point mutation system derived from hPin1(14-24) in which the original charged residues were replaced with non-polar alanine residues. doi = 10.1002/pro.2823 id = cord-004534-jqm1hxps author = nan title = Abstract date = 2009-06-09 keywords = AFM; ATP; Biology; Biophysics; Chemistry; Department; FCS; France; GFP; Genova; Germany; Hyp; Institute; Italy; Molecular; Physics; RNA; Sciences; University; cell; dna; fluorescence; fret; interaction; lipid; membrane; protein; result; structure; study summary = HIV-1 to efficiently complete a replication cycle has to integrate its genome into the host cellular DNA.After HIV-1 enters target cells,neosynthesized viral DNA forms along with other proteins the pre-integration complex (PIC).PICs are then transported into the nucleus where integration,catalyzed by the viral integrase,takes place.HIV-1 viral particles engineered to incorporate integrase fused to EGFP have proven effective to study PICs within nuclei of infected cells.In this study we report the live imaging analysis of nuclear PIC dynamics obtained by time-lapse microscopy.Intranuclear trajectories of IN-EGFP-labeled PIC were collected in three dimensions and examined by both mean squared displacement (MSD) and cage diameter (CD) analysis.In CD the maximum distances measured between two positions occupied by a PIC in a time window of 2 minutes were calculated while in our MSD analysis 5-minute long trajectory segments were considered.Remarkably,MSD revealed the presence of an underlying active transport mechanism.To test the possible role of actin filaments,PIC nuclear trafficking was analyzed in cells treated with latrunculin B (actin polymerization inhibitor).Preliminary results suggest that the disruption of actin function impairs the active nuclear movement of PICs. Second harmonic generation microscopy reveals sarcomere contractile dynamics of cardiomyocytes N. doi = 10.1007/s00249-009-0478-1 id = cord-004584-bcw90f5b author = nan title = Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary date = 2011-08-06 keywords = AFM; ATP; Biophysics; Department; FCS; Germany; Institute; RNA; University; cell; change; channel; complex; different; dna; dynamic; effect; fluorescence; fret; high; interaction; lipid; mechanism; membrane; model; molecular; molecule; process; protein; result; structure; study; surface; system summary = Our goals are two-fold: (1) to monitor conformational changes in each domain upon its binding to specific ligands and then to correlate the observed changes with structural differences between the CRDs and (2) to investigate the interaction between the CRDs and lipid model membranes. Cholesterol-assisted lipid and protein interactions such as the integration into lipid nanodomains are considered to play a functional part in a whole range of membrane-associated processes, but their direct and non-invasive observation in living cells is impeded by the resolution limit of [200nm of a conventional far-field optical microscope. Therefore, to investigate the dynamic and complex membrane lateral organization in living cells, we have developed an original approach based on molecule diffusion measurements performed by fluorescence correlation spectroscopy at different spatial scales (spot variable FCS, svFCS) (1). doi = 10.1007/s00249-011-0734-z id = cord-004879-pgyzluwp author = nan title = Programmed cell death date = 1994 keywords = ATP; Basel; Bern; Drosophila; Institut; Lausanne; NMDA; PCR; PKC; RNA; Switzerland; TNF; University; acid; activity; cell; dna; expression; gene; high; human; increase; level; mouse; protein; receptor; result; sequence; study; type summary = Furthermore kinetic experiments after complementation of HIV=RT p66 with KIV-RT pSl indicated that HIV-RT pSl can restore rate and extent of strand displacement activity by HIV-RT p66 compared to the HIV-RT heterodimer D66/D51, suggesting a function of the 51 kDa polypeptide, The mouse mammary tumor virus proviral DNA contains an open reading frame in the 3'' long terminal repeat which can code for a 36 kDa polypeptide with a putative transmembrane sequence and five N-linked glycosylation sites. To this end we used constructs encoding the c-fos (and c-jun) genes fused to the hormone-binding domain of the human estrogen receptor, designated c-FosER (and c-JunER), We could show that short-term activation (30 mins.) of c-FosER by estradiole (E2) led to the disruption of epithelial cell polarity within 24 hours, as characterized by the expression of apical and basolateral marker proteins. doi = 10.1007/bf02033112 id = cord-004948-ad3i9wgj author = nan title = 7th International Congress on Amino Acids and Proteins : Vienna, Austria, August 6–10, 2001 date = 2001 keywords = Department; GABA; HPLC; Institute; Japan; NMDA; Research; Sciences; Tau; University; acid; activity; amino; cell; dna; effect; increase; level; protein; rat; result; study; taurine summary = doi = 10.1007/s007260170030 id = cord-006229-7yoilsho author = nan title = Abstracts of the 82(nd) Annual Meeting of the German Society for Experimental and Clinical Pharmacology and Toxicology (DGPT) and the 18(th) Annual Meeting of the Network Clinical Pharmacology Germany (VKliPha) in cooperation with the Arbeitsgemeinschaft für Angewandte Humanpharmakologie e.V. (AGAH) date = 2016-02-06 keywords = 3-mcpd; GRK2; Germany; IL-6; LPS; OCT1; PKA; PLN; STW; THP-1; VPA; activation; assay; cell; concentration; different; dna; drug; effect; expression; fret; high; human; increase; level; method; model; mouse; potential; protein; receptor; result; s1p; study; test; treatment; trpc5; western summary = It directly activates Protein Kinase A (PKA) or the Exchange protein directly activated by cAMP (Epac) which is a guanine exchange factor (GEF) for the small monomeric GTPase Rap. As Human umbilical vein endothelial cells (HUVEC) express both cAMP effectors (Epac1 and PKA), we investigated the role of cAMP-signaling using a spheroid based sprouting assay as an in vitro model for angiogenesis. After activation, S1P receptors regulate important processes in the progression of renal diseases, such as mesangial cell migration Methods and Results: Here we demonstrate that dexamethasone treatment lowered S1P 1 mRNA and protein expression levels in rat mesangial cells measured by TaqMan® and Western blot analyses. The aim of this study was to investigate the relevance of IGFBP5 in cardiogenesis and cardiac remodeling and its role as a potential target for ameliorating stress-induced cardiac remodeling Methods and Results: We investigated the expression of Igfbp5 in murine cardiac tissue at different developmental stages by qPCR normalized to Tpt1 (Tumor Protein, Translationally-Controlled 1). doi = 10.1007/s00210-016-1213-y id = cord-006230-xta38e7j author = nan title = Deutsche Gesellschaft für Experimentelle und Klinische Pharmakologie und Toxikologie e.V. date = 2012-02-22 keywords = ATP; ERK; Germany; IL-6; Institut; LPS; NDPK; PCR; PKA; Pharmakologie; RKIP; ROS; Rac1; TNF; TRPC6; TRPM3; TTC; Toxikologie; Universität; V79; activity; cell; concentration; dna; effect; expression; gene; human; increase; level; mouse; protein; receptor; result; study; western summary = Here, we will present our analysis of Ca 2+ signaling following stimulation of the FcεRI receptor and application of secretagogues that are supposed to affect Ca 2+ -dependent mast cell activation such as adenosine, endothelin-1, substance P and compound 48/80 in BMMCs and PMCs derived from mouse lines with inactivation of TRPC1, TRPC3, TRPC4, TRPC5 or TRPC6 since specific antagonists are still lacking for these TRP channels. These data indicate that increased PP2A activity is associated with modified gene expression in TG hearts possibly affecting stress response and regulation of cell signalling. As demonstrated by qPCR and Western blot experiments, mesangial cells showed a marked time-and dose-dependent upregulation of CSE mRNA and protein levels after treatment with platelet-derived growth factor (PDGF-BB). The transcription factor cAMP response element (CRE)-binding protein (CREB) plays a critical role in regulating gene expression in response to activation of the cAMPdependent signaling pathway, which is implicated in the pathophysiology of heart failure. doi = 10.1007/s00210-012-0736-0 id = cord-006860-a3b8hyyr author = nan title = 40th Annual Meeting of the GTH (Gesellschaft für Thrombose- und Hämostaseforschung) date = 1996 keywords = ADP; APC; APTT; DVT; ELISA; FXII; Germany; HUVEC; INR; LMWH; Leiden; PAI; PCR; STA; TEG; VIII; activity; blood; cell; dna; factor; hat; heparin; high; increase; level; patient; plasma; platelet; protein; result; study; time summary = Dept of Pediatrics, University Hospitals Kiel and Mtinster, Germany Resistance to activated protein C (APCR), in the majority of cases associated with the Arg 506 Gin point mutation in the factor V gene is present in more than 50 % of patients < 60 years of age with unexplained thrombophilia. The regular APC resistance test is not applicable to plasma from Orally anticoagulated (OAC) or heparinized patients due to decreased levels of vitamin K-dependent clotting factors and to thrombin inhibition by antithrombin, respectively. On admission an extensive coagulation screen yielded the following results (n/normal, t/elevated, I/reduced, +/positive, -/negative): PT t, aPTT t, Tr n, factor II, V, VIII n, factor VII, IX, XI, XII /,, fibrinogan t, ATIII n, protein C, S *, activated protein C sensitivity ratio 1.92 ($), FV-Leidenmutation PCR -, fibrinolytic system n, TAT t, Ft÷2 t, lupus anticoagulant +, heparin induced platelet antibodies +; no diagnosis of a specific autoimmuna disorder could be made. doi = 10.1007/bf00641048 id = cord-008777-i2reanan author = nan title = ECB12: 12th European Congess on Biotechnology date = 2005-07-19 keywords = Ankara; Biology; Biotechnology; Chemical; Denmark; Department; Engineering; Escherichia; Faculty; Germany; HPLC; Institute; PCR; Research; Science; Technical; Technology; Turkey; University; acid; activity; analysis; bacillus; cell; concentration; condition; culture; different; dna; effect; enzyme; expression; fermentation; gene; growth; high; increase; medium; method; process; produce; production; protein; result; strain; study; system summary = Mollerup Department of Chemical Engineering, Building 229, DTU, 2800 Lyngby, Denmark A variety of factors that govern the properties of proteins are utilized in the development of chromatographic processes for the recovery of biological products including the binding and release of protons, the non-covalent association with non-polar groups (often hydrophobic interactions), the association of small ions (ion exchange) and the highly specific antigen-antibody interaction (affinity interactions). Such fermenters will be needed in order to meet the increasing pressure on costs for low price commodity type products such as single cell protein or food and technical grade enzymes, and to meet the demands of the new wave of white biotech, in which bio-produced chemicals must be made at prices competitive with those of the traditional chemical industry. The presentation will focus on use of the sensitive sandwich hybridization technology for the quantitative analysis of process relevant marker genes in different kind of microbial cell cultures with a focus on the production of recombinant proteins. doi = 10.1016/j.jbiotec.2005.06.005 id = cord-014368-4nasrbs6 author = nan title = Gene Chip for Viral Discovery date = 2003-11-17 keywords = Hirschman; cell; dna; gene; protein; signal summary = As they report in this paper, Miguel Nicolelis and colleagues have helped clarify some of the fundamental issues surrounding the programming and use of BMIs. Presenting results from a series of long-term studies in monkeys, they demonstrate that the same set of brain cells can control two distinct movements, the reaching and grasping of a robotic arm. RAG genes regulate the genetic recombination and ultimate cell surface expression of TCRs. Using chemical inhibitors and mutant human T cell lines deficient in critical signaling components involved in antigen receptor-dependent pathways, the researchers found that the loss of specific functions or specific proteins affected an unexpected set of target genes. But these studies also establish a model for investigating other signaling systems, to determine whether biologically functional basal signaling is a rare phenomenon or whether it is a fundamental cell process needed to control the profile of gene expression in the quiescent state. doi = 10.1371/journal.pbio.0000003 id = cord-014462-11ggaqf1 author = nan title = Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date = 2011-04-21 keywords = BTV; CMV; CTV; ELISA; India; PCR; Pradesh; RNA; RTBV; disease; dna; gene; isolate; plant; protein; sequence; study; vaccine; virus summary = Molecular diagnosis based on reverse transcription (RT)-PCR s.a. one step or nested PCR, nucleic acid sequence based amplification (NASBA), or real time RT-PCR, has gradually replaced the virus isolation method as the new standard for the detection of dengue virus in acute phase serum samples. Non-genetic methods of management of these diseases include quarantine measures, eradication of infected plants and weed hosts, crop rotation, use of certified virus-free seed or planting stock and use of pesticides to control insect vector populations implicated in transmission of viruses. The results of this study indicate that NS1 antigen based ELISA test can be an useful tool to detect the dengue virus infection in patients during the early acute phase of disease since appearance of IgM antibodies usually occur after fifth day of the infection. The studies showed high level of expression in case of constructed vector as compared to infected virus for the specific protein. doi = 10.1007/s13337-011-0027-2 id = cord-014597-66vd2mdu author = nan title = Abstracts from the 25th European Society for Animal Cell Technology Meeting: Cell Technologies for Innovative Therapies: Lausanne, Switzerland. 14-17 May 2017 date = 2018-03-15 keywords = CHO; Fig; HEK293; MVA; PEI; batch; cell; chinese; culture; dna; expression; gene; high; increase; line; medium; process; production; protein; table summary = Irrespective of the cell culture-based system and production scale, PEIpro® and PEIpro®-HQ have led to efficient viral vector yields superior to 10 7 IG/mL and 10 9 VG/mL, respectively for lentiviruses and AAVs Background Continuous perfusion process is making a comeback as a competing upstream manufacturing technology for the production of Biopharmaceuticals compared to the standard fed batch processes. To evaluate the impact of feed-spiking compared with cultivation in basal medium only, the cell line was grown in bioreactors under controlled conditions to determine cellspecific metabolic rates, nutrient consumption, and byproduct accumulation over the process time. Through the interchangeability of signal peptides between products and even species, a large variety can be used to enhance protein expression in already existing production systems Materials and methods At first the influence of four different natural SPs (SP (7), (8), (9) and (10)) was compared on the secreted amount of an IgG4 model antibody (product A) in fed batches using a CHO DG44 host cell line. doi = 10.1186/s12919-018-0097-x id = cord-014685-ihh30q6f author = nan title = Posters P788 - P999 date = 2005-09-21 keywords = Department; France; Institute; Japan; RNA; University; cell; dna; membrane; protein; structure; study summary = This study has attempted to analyse the structural properties of membrane peptides and proteins through the use of model systems that have been designed to mimic their natural counterparts: Podlubnaya 2 1 Institute of Theoretical and Experimental Biophysics RAS, 2 Pushchino State University Amyloid brils are formed by proteins or their peptides in the result of a conformational transition from alpha helix into beta-sheet structure. Analysis of the results of such studies indicate that folding of SNase fragments is dominated by developing the local and non-local nucleation sites from native-like secondary structures and by intensifying the longrange interactions of residues at nucleation sites with residues further removed in sequence. The results show that at different pH values the aggregation processes of both proteins follow different pathways determined by the variations in the native structure and by the details of the involved conformational changes. doi = 10.1007/s00249-005-0504-x id = cord-014864-0d682m0n author = nan title = Biomedical vignette date = 2008-10-26 keywords = CTGF; RVLM; cell; protein summary = doi = 10.1007/s11373-008-9279-2 id = cord-020097-eh5deunk author = nan title = Cumulative Author Index for 2006 (Volumes 115–122) date = 2006-10-27 keywords = cell; protein; virus summary = Modulation of PKR activity in cells infected by bovine viral diarrhea virus Complete genome analysis of RFLP 184 isolates of porcine reproductive and respiratory syndrome virus Phylogenetic analysis of the gag region encoding the matrix protein of small ruminant lentiviruses: Comparative analysis and molecular epidemiological applications TATAbinding protein and TBP-associated factors during herpes simplex virus type 1 infection: Localization at viral DNA replication sites Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein Efficient inhibition of hepatitis B virus replication by small interfering RNAs targeted to the viral X gene in mice Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein A deletion and point mutation study of the human papillomavirus type 16 major capsid gene Sequencing and comparative analysis of a pig bovine viral diarrhea virus genome Antigenic structure analysis of glycosylated protein 3 of porcine reproductive and respiratory syndrome virus doi = 10.1016/s0168-1702(06)00318-2 id = cord-020101-5rib7pe8 author = nan title = Cumulative Author Index for 2008 date = 2008-11-17 keywords = HIV-1; gene; protein; virus summary = Cauliflower mosaic virus gene VI product N-terminus contains regions involved in resistance-breakage, self-association and interactions with movement protein Intrahost evolution of envelope glycoprotein and OrfA sequences after experimental infection of cats with a molecular clone and a biological isolate of feline immunodeficiency virus DC-SIGN enhances infection of cells with glycosylated West Nile virus in vitro and virus replication in human dendritic cells induces production of Increase in proto-oncogene mRNA transcript levels in bovine lymphoid cells infected with a cytopathic type 2 bovine viral diarrhea virus Complete genome sequence analysis of dengue virus type 2 isolated in Modulation of hepatitis B virus replication by expression of polymerasesurface fusion protein through splicing: Implications for viral persistence Induction of apoptosis in Vero cells by Newcastle disease virus requires viral replication, de-novo protein synthesis and caspase activation Mechanisms of inhibition of HIV replication by non-nucleoside reverse transcriptase inhibitors doi = 10.1016/s0168-1702(08)00367-5 id = cord-020235-stcrozdw author = nan title = Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date = 2012-03-15 keywords = HSV; Inst; RNA; Univ; cell; dna; protein; viral; virus summary = Hepatitis A virus (HAV) was isolated directly from human stool in diploid human fibroplasrs, Viral antigen was expressed only after 210 days of incubation of the infected cultures. Univ., 0-8700 Wiirzburg Effect of Measles (SSPE) Antiserum on Viral Surface Proteins and Hormone Receptor Activity in C6/SSPE Persistently Infected Cells BARRETT, P. Inst, of Genetics, Univ., 0-5000 Co logne Virus-Cell DNA Recombinants in Human Cells Lytically Infected by Ad2 NEUMANN, R., WEYER, U., and DOERFLER, W. In vitro, however, the gag-specific peptide sequences are cleaved off upon addition of the purified viral piS protease; in the case of the replication-defective, transforming avian sarcoma virus PRC II the cleaved nongag part has a ryrosine-phosphorylaring kinase activity similar to that described for the RSV src-gene product pp60 src . f. Virologie, Univ., D·6300 Giefen, 3 A protein of a molecular weight of about 38.000 d has been found to be phosphorylated 1 h after the onset of cell transformation by Rous sarcoma virus (RSV). doi = 10.1016/s0174-3031(82)80128-5 id = cord-022779-himray6q author = nan title = Abstracts of oral presentations date = 2005-06-10 keywords = activity; peptide; protein summary = Here we present a novel strategy to synthesize proteins through a chemical ligation using unprotected peptide segments. Using short portions (7-11 amino acid) rich in positively charged residues from either human lactoferricin or the MARCKS protein as templates, a panel of 70 peptides each possessing a specific chemical structure was synthesized. Subsequent functionalization of such azide groups via Staudinger or "Click" chemistry should provide a convenient method for linking proteins with a diverse array of probes, biomolecules, surfaces and other materials under mild conditions. Moreover, the advantages of peptide and protein chemical synthesis over recombinant-DNA methods are increasingly being used to provide rapid structure-activity information of complex bioactive peptides, small proteins and functional receptor domains. Thus, these new peptides bear all of the requirements which are necessary for formation of cooperatively interacting helical structures and, furthermore, contain domains for cooperative sheet aggregation as well. doi = 10.1002/bip.20321 id = cord-022888-dnsdg04n author = nan title = Poster Sessions date = 2009-08-19 keywords = APC; BCR; CD14; CD4; CD8; CMV; CTL; EBV; ELISA; Germany; HCV; HIV; HLA; IBD; IFN; IL-10; IL-2; IL-4; IL-6; Immunology; Institute; LPS; MHC; NKT; PCR; RNA; SLE; TCR; TGF; TLR; TLR4; TNF; University; antigen; cell; dna; expression; immune; mouse; patient; protein; response; result; study; th1; th2 summary = Methods: Phospho-specific Western blot analyses were performed to verify the functionality of the different IFN-g pathway components, intra-and extracellular flow cytometry experiments were employed to determine the expression of antigen processing components and HLA class I cell surface antigens, quantitative real time-PCR experiments to confirm the absence of JAK2 and presence of pathway relevant molecules as well as, genomic PCR and chromosome typing technique to prove the deletion of JAK2. In order to accomplish these objectives we induced priming or tolerance of ovalbumin (OVA 323-339 peptide)-specific T cells from DO11.10 TCR transgenic mice in vitro or, following adoptive transfer of near physiologically relevant numbers of such cells into recipients, in vivo and correlated functional outcome (via proliferation and cytokine readout assays or antibody production) with E3 ubiquitin-protein ligases expression and the ubiquitination status of the TCR signalling machinery. doi = 10.1002/eji.200990224 id = cord-022940-atbjwpo5 author = nan title = Poster Sessions date = 2016-09-07 keywords = Akt; Ankara; Biology; Department; ELISA; Faculty; GSH; HCC; IL-6; IMA; Institute; Istanbul; MCF-7; MDA; MTT; P-02.08.5; P-09.04.4; PCR; PON1; RNA; ROS; Research; Russian; SOD; Sciences; TAS; TNF; TOS; Turkey; University; activity; analysis; cancer; cell; conclusion; control; dna; effect; expression; gene; group; high; increase; introduction; level; method; patient; protein; result; study; tissue; treatment; turkish; western summary = We have studied the effect of inhibition of IRE1 (inositol requiring enzyme 1), which is a central mediator of endoplasmic reticulum stress and controls cell proliferation and tumor growth, on hypoxic regulation of the expression of different proliferation related genes in U87 glioma cells. Transient inhibition of Akt and mTOR protein kinase activation in tumor cells followed by reactivation of signaling pathway did not result in a time-dependent difference on EGFR, HER2 and HER3 expression levels. In our study we aimed to determine cytotoxic effect of RES in K562 human CML cell line and to evaluate the expressions of miRNAs that are associated with genetics of leukemia after treatment with RES; to investigate target genes of miRNAs which show significant expression alterations and molecular mechanisms of RES treatment. doi = 10.1111/febs.13808 id = cord-022955-vy0qgtll author = nan title = Proteases date = 2005-06-20 keywords = APC; GCPII; Met; University; activity; cell; enzyme; human; inhibitor; nedd4; peptide; protease; protein; result; serine; site; study; substrate summary = In order to understand the molecular basis of the enzyme-substrate binding mechanism, we employ the synthetic peptide and mass spectrometry-based approaches to investigate the significance of selected amino acid residues that are flanking both sides of the SARS-CoV 3CL pro cleavage site. To contribute to the assignment of a physiological role to genomic-derived peptidases and to make them more accessible for the drug discovery process, we have undertaken a program consisting of mRNA expression profiling, full-length recombinant expression in insect cells, purification and determination of the catalytic activity for the human proteolytic enzymes. This comprehensive analysis of the local backbone properties of SGTI in the free and in the complex form made possible to identify conformational similarities and differences responsible for its efficient binding to the enzyme, and provides a good basis for further studying the structural aspects of protease inhibitor specificity. doi = 10.1111/j.1742-4658.2005.4739_4.x id = cord-023026-2r84ndzv author = nan title = Posters date = 2013-06-14 keywords = ATP; Alzheimer; BBB; BDNF; CNS; EAE; GABA; GFAP; GFP; GLT-1; IL-6; LPS; MBP; NMDA; OPC; PCR; SCI; SOD1; SVZ; Schwann; University; astrocyte; brain; cell; expression; increase; microglia; mouse; ng2; protein; result; role; study summary = Thus, this work provides the basis to identify molecular pathways regulated by distinct niche/environmental signals and involved in the heterogeneity of adult OPCs. Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative demyelinating disease of the central nervous system (CNS) characterized by inflammation, which leads to formation of demyelinating areas due to loss of oligodendrocytes, astrogliosis and, finally, axonal degeneration. Taken together, these results demonstrate the important role of miR-200b in modulating the MAPK pathway via c-Jun which in turn affects different aspects of the inflammatory process accompanying microglia activation including cytokine response, NO production, phagocytosis and neuronal cell death. For this purpose, coronal cryostat free-floating sections from the brain of both adult transgenic mice and their corresponding wild-type (Wt) littermates, were processed for the study of astrocytes using GFAP immunohistochemistry and microglia using antibodies against Iba1 and several markers commonly related to the activated phenotype of these microglial cells, such as CD16/32 (Fc receptor), F4/80, CD11b, CD206, CD150 and MHC-II. doi = 10.1002/glia.22530 id = cord-023143-fcno330z author = nan title = Molecular aspects of viral immunity date = 2004-02-19 keywords = CD4; CD8; CNS; CTL; HIV; HIV-1; HLA; IFN; LCMV; MHC; cell; infection; mouse; protein; response; viral; virus summary = Based on a variety of experimental evidence, it is clear that demyelination induced in SJUJ mice by infection with the BeAn strain of TMEV is a Thl-mediated event: (a) disease induction is suppressed in T cell-deprived mice and by in vivo treatment with anti-I-A and anti-CD4 antibodies; (b) disease susceptibility correlates temporally with the development of TMEV-specific, MHC-class Il-restricted DTH responses and with a predominance of anti-viral lgG2a antibody; (c) activated (Le., lL-2RC) T cells infiltrating the CNS are exclusively of the CD4+ phenotype, and (d) proinflammatory cytokines (IFNq and TNF-p) are predominantly produced in the CNS. These results have important implications for a possible viral trigger in MS as they indicate that chronic demyelination in TMEV-infected mice is initiated in the absence of demonstrable neuroantigen-specific autoimmune responses and are consistent with a model wherein early myelin damage is mediated via primarily by mononuclear phagocytes recruited to the CNS and activated by pro-inflammatory cytokines produced by TMEV-specific Thl cells. doi = 10.1002/jcb.240591009 id = cord-023208-w99gc5nx author = nan title = Poster Presentation Abstracts date = 2006-09-01 keywords = Fmoc; Gly; HPLC; Lys; NH2; NMR; Pro; RGD; RNA; Tyr; acid; activity; amino; bind; cell; dna; high; interaction; method; peptide; protein; receptor; result; sequence; structure; study summary = In order to develop a synthetic protocol by an automated instrumentation, increasing yield, purity of the crude, and reaction time, a microwave-assisted solid phase peptide synthesis was validated comparing the use of the new generation of Triazine-Based Coupling Reagents (TBCRs) with a series of commonly used ones. Ubiquitinium is a well known mechanism in protein degredation of Eukaryotic cells ,in which many obsolte and corrupted three dimentional structure protein ,become marked by covalent attachment of ubuquitin through a multi-step enzymatic pathway.Ubiquitin is a small ,8.5 kDa peptide of 76 amino acid residues that targets such substrtes for proteolysis in proteasome .Recnt studies showed that an extra cellular ubiquitination process also taking place in the epididymes of humans and other animals marks protein on the surface of the defective sperm .it appears that structurally and functionally defective sperm become surface ubiquitinated by epididymal epithelial cells. This head-to-tailcyclized 14-amino-acid peptide contains one disulfide bridge and a lysine residue (Lys5) present in the P1 position, which is responsible for inhibitor specificity.As was reported by us and other groups, SFTI-1 analogues with one cycle only retain trypsin inhibitory activity. doi = 10.1002/psc.797 id = cord-023209-un2ysc2v author = nan title = Poster Presentations date = 2008-10-07 keywords = Ala; Arg; Asp; Fmoc; Glu; Gly; HPLC; Leu; Lys; NMR; Phe; Thr; Trp; Tyr; University; VEGF; Val; acid; activity; amino; bind; cell; dna; high; peptide; pro; protein; receptor; residue; result; sequence; structure; study; synthesis summary = Site-specifi c PEGylation of human IgG1-Fab using a rationally designed trypsin variant In the present contribution we report on a novel, highly selective biocatalytic method enabling C-terminal modifi cations of proteins with artifi cial functionalities under native state conditions. Recently, our group report a novel approach to a totally synthetic vaccine which consists of FMDV (Foot and Mouth Disease Virus) VP1 peptides, prepared by covalent conjugation of peptide biomolecules with membrane active carbochain polyelectrolytes In the present study, peptide epitops of VP1 protein both 135-161(P1) amino acid residues (Ser-Lys-Tyr-Ser-Thr-Thr-Gly-Glu-Arg-Thr-Arg-Thr-Arg-Gly-Asp-Leu-Gly-Ala-Leu-Ala-Ala-Arg-Val-Ala-Thr-Gln-Leu-Pro-Ala) and triptophan (Trp) containing on the N terminus 135-161 amino acid residues (Trp-135-161) (P2) were synthesized by using the microwave assisted solid-phase methods. Using as a template a peptide, already identifi ed, with agonist activity against PTPRJ(H-[Cys-His-His-Asn-Leu-Thr-His-Ala-Cys]-OH), here we report a structure-activity study carried out through endocyclic modifi cations (Ala-scan, D-substitutions, single residue deletions, substitutions of the disulfi de bridge) and the preliminary biological results of this set of compounds. doi = 10.1002/psc.1090 id = cord-023225-5quigar4 author = nan title = Posters date = 2012-08-21 keywords = Aib; Ang; Cys; Fmoc; Gly; HPLC; Ile; Leu; Lys; NMR; PNA; Phe; SPPS; University; acid; activity; amino; cell; dna; group; peptide; protein; residue; structure; study; synthesis summary = To further explore the structure-function relationship, a viable synthesis strategy for pseudodesmin A analogues was developed, based on side-chain attachment of the first amino acid to the solid support, followed by stepwise Fmoc solid-phase synthesis of the linear peptide precursor and on-resin head-to-tail cyclization. The cases when the amino acid sequence of a fragment coincided with part of the primary structure of a natural oligopeptide were recorded in the Total protein chemical synthesis requires a case by case design and optimization which is governed by factors such as the solubility of the individual peptide segments, their primary sequence and in particular the presence of "difficult" amino acid residues at ligation junctions such as proline or the location of cysteines. In this study we present synthesis of two series of peptide libraries, which were designed by substitution of Leu in the P5, P6 position of our control peptide (Ac-LLLLRVKR-AMBA) with each of nineteen amino acid residues in order to verifying its influence on activity and selectivity of the resulting analogues. doi = 10.1002/psc.2449 id = cord-023647-dlqs8ay9 author = nan title = Sequences and topology date = 2003-03-21 keywords = Evolution; Family; Gene; Human; Protein; acid; sequence summary = Nucleotide Sequence Analysis of the L G~ne of Vesicular Stomafltia Virus (New Jersey Serotype) --Identification of Conserved Domai~L~ in L Proteins of Nonsegmented Negative-Strand RNA Viruses DERSE I~ Equine Infectious Anemia Virus tat--Insights into the Structure, Function, and Evolution of Lentivtrus tran.~Activator Proteins Ho~tu~ ~ s71 is a Ehylngcueticellly Distinct Human Endogenous Reteovtgal 1Rlement with Structural mad Sequence Homology to Simian Sarcoma Virus (SSV). Distinct Fercedoxins from Rhodobacter-Capsulstus -Complete Amino Acid Sequences and Molecular Evolution Complete Amino Acid Sequence and Homologies of Human Erythrocyte Membrane Protein Band 4.2. Identification of Two Highly Conserved Amino Acid Sequences Amon~ the ~x-subunits and Molecular ~ The Predicted Amino Acid Sequence of ct-lnternexin is that of a novel Neuronal lntegmedla~ ~ent Protein Inttaspecific Evolution of a Gene Family Coding for Urinary Proteins Attalysi~ of CDNA for Human ~ AJudgyrin I~dicltes a Repeated Structure with Homology to Tissue-Differentiation a~td Cell-Cycle Control Protein doi = 10.1016/0959-440x(91)90051-t id = cord-023770-ymxapsv6 author = nan title = Closteroviridae date = 2011-11-23 keywords = CTV; RNA; protein summary = In general, capsid proteins and their homologs (CPm) show a significant degree of sequence conservation and the duplicate copies probably retain the general spatial folding and some crucial properties of the CPs. Notable exception are a group of ampeloviruses with the smallest genomes in the family [e.g. grapevine leafrollassociated virus 4 (GLRaV-4), GLRaV-5, GLRaV-6, GLRaV-9, pineapple mealybug wilt-associated virus 1(PMWaV-1) and PMWaV-3] which do not appear to possess CPm. The genome expression strategy is based on: (i) proteolytic processing of the polyprotein encoded by ORF1a; (ii) 1 Pos. ssRNA ribosomal frameshift for the expression of the RdRp domain encoded by ORF1b, a mechanism not found in other ()RNA plant viruses; (iii) expression of the downstream ORFs via the formation of a nested set of 3 co-terminal sub-genomic RNAs (sgRNAs). doi = 10.1016/b978-0-12-384684-6.00085-9 id = cord-031907-ilhr3iu5 author = nan title = ISEV2020 Abstract Book date = 2020-07-15 keywords = CD63; CD81; CD9; CDC; CRC; CSF; ELISA; Exo; Extracellular; GBM; HER2; HIV; Health; Institute; L1CAM; MDA; MSC; NIH; NTA; Nanoparticle; National; PCR; RNA; Research; SEC; TEM; Tau; USA; University; analysis; cancer; cell; conclusion; dna; exosome; expression; high; human; introduction; isolate; marker; method; patient; plasma; protein; result; sample; size; study; summary; vesicle; western summary = L.M., and the National Institutes of Health (R35GM119623) to T.R.G. The addition of a size exclusion chromatography step to various urinary extracellular vesicle concentrating methods reveals differences in the small RNA profile Introduction: Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases, however non-vesicular RNA (e.g. associated with proteins) is also present within urine. We then evaluated efficiency of heart targeting for eAAV9 or eAAV6 and standard AAV9 or AAV6 encoding for EGFP, mCherry or firefly luciferase in different human cell lines in vitro, in black mouse and in passive immunity nude mouse model in vivo using flow cytometry, confocal microscopy, Langendorff perfusion system and Methods: HLHS patients (n = 3) after Glenn procedure and swine (n = 3) after PAB were given RV injections of allogeneic/xenogeneic MSCs. Donor-specific, HLA-I+, exosomes were isolated from plasma. doi = 10.1080/20013078.2020.1784511 id = cord-104279-choywmwd author = nan title = Membrane protein sorting in the yeast secretory pathway: evidence that the vacuole may be the default compartment date = 1992-10-01 keywords = DPAP; Fig; Golgi; membrane; protein summary = First, to determine if the lumenal domain was sorted to the vacuole when expressed in the secretory pathway as a soluble protein, a gene fusion was used to create the protein ctFss-B, consisting of the NH2-terminal ER-targeting signal sequence of prepro-t~ factor fused to the lumenal domain of DPAP B at residue 49 ( Fig. 1 B) . To ad-dress the possibility that the mutant constructs analyzed in this study were mislocalized to the plasma membrane followed by rapid endocytic uptake to the vacuole, indirect immunofluorescence experiments were performed on BB-Inv, B-A-B, A20-BB, and/x22-AA-B expressed in a secl strain at 34~ As a positive control for accumulation in secretory vesicles, the localization of the fusion protein Fusl-LacZp was analyzed (Trueheart et al., 1987) . doi = nan id = cord-104282-90t1m430 author = nan title = Microsomal aldehyde dehydrogenase is localized to the endoplasmic reticulum via its carboxyl-terminal 35 amino acids date = 1994-09-02 keywords = CAT; COS-1; Fig; protein summary = Abbreviations used in this paper: CAT, chloramphenicol acetyltransferase; FP2, NADPH-cytochrome P-450 reductase; msALDH, microsomal aldehyde dehydrogenase; PBS(+), PBS containing 1 mM CaCI2 and 0.5 mM MgCI2; PDI, protein disulfide isomerase; PTP, protein tyrosine phosphatase; STE, sucrose solution containing 10 mM Tris-HCl, pH 7.4, 1 mM EDTA, 10 t~g/ml leupepdn A, 0.5 mM PMSF, and 10 U/ml Trasyol; SRP, signal recognition particle. The nucleotide sequence predicts a polypeptide of 484 amino acids, and the most characteristic feature of this membrane-bound ALDH is carboxyl-terminal 35 amino acids, consisting of a stem region (amino acids 450-463) and a hydrophobic domain (amino acids 464-480) followed by a short hydrophilic tail region (amino acids 481-484) as shown in Fig. 1 . These data, together with those from subcellular fractionation, suggested that the carboxyl-terminal portion of msALDH including the hydrophobic sequence (amino acid 464-480) was necessary for both its ER localization and the tight association with the ER membrane. doi = nan id = cord-289710-ucguzgdm author = nan title = Yeast Kex1p is a Golgi-associated membrane protein: deletions in a cytoplasmic targeting domain result in mislocalization to the vacuolar membrane date = 1992-12-02 keywords = Bussey; Golgi; Hpa; Kexlp; protein summary = In addition to soluble proteins, the cell surface appears to be the default destination for mammalian ER, Golgi, and lysosomal membrane proteins as removal of their respective retention/targeting signals results in their delivery to the plasma membrane (Machamer and Rose, 1987; Jackson et al., 1990; Williams and Fukuda, 1990) . Kexlp is predicted to be a type I transmembrane protein with a large amino-terminal protease domain in the lumen of the secretory pathway, a single membrane-spanning domain, and a smaller carboxy-terminai domain positioned cytoplasmicaUy. The observation that KEX/cells intracellularly retain Kexlp activity prompted an analysis to determine in which secretory compartment Kexlp resided, and how it achieved such retention. The above results indicated that Kexlp-Hpa was membrane associated, had received glycosyl modifications in the Golgi apparatus, gave wild-type levels of total activity, and was retained intracellularly; yet processed the K1 killer toxin precursor to a lesser extent than Kexlp. doi = nan id = cord-300796-rmjv56ia author = nan title = The signal sequence of the p62 protein of Semliki Forest virus is involved in initiation but not in completing chain translocation date = 1990-09-01 keywords = Fig; p62; protein; sequence summary = In this work we show that the p62 protein of Semliki Forest virus contains an uncleaved signal sequence at its NH2-terminus and that this becomes glycosylated early during synthesis and translocation of the p62 polypeptide. As the glycosylation of the signal sequence most likely occurs after its release from the ER membrane our results suggest that this region has no role in completing the transfer process. Furthermore, the p62-reporter hybrid should be translocated across microsomal membranes and possibly glycosylated at Asn~3 of the p62 sequence if the 40 residues long NH2-terminal p62 peptide carries a signal sequence. This must involve Asn~3 of the p62 peptide as it is part of the only potential glycosylation site on the hybrid polypeptides (Garoff et al., 1980 ; references on dhfr sequence in legend to Fig. 1) , Finally, we can also conclude that the p62 signal sequence does not provide a stable membrane anchor to the translocated chain. doi = nan id = cord-327883-s9nbr5y8 author = nan title = Section Virology date = 1990-03-31 keywords = EBV; HCMV; HSV; antibody; cell; dna; protein; virus summary = By improving the enzyme-linked immunosorbent assay (ELISA) for HSV-2-antibodies and additional testing of sera by Western blot, we were able to specifically identify HSV-l-and HSV-2-antibodies in serum samples. To get some insight into the molecular basis of processes controlling the viral expression we studied the sequence-specific DNA-protein interactions within the genomic regulatory regions. for Med. Microbiology, Univ., D-5300 Bonn Semiquantitative detection of Hepatitis B Virus (HBV) DNA in sera of infected individuals has become an important means of modern serological hepatitis diagnostics. THOMSSEN 1 In the course of acute Epstein-Barr virus (EBV) infection IgM antibodies always occur against two cellular antigens that were characterized as proteins with a molecular weight of 26 kD (p26) and 29 kD (p29), respectively. The frequency and specificity of antibodies to P-gene encoded proteins of human hepatitis B virus was tested in sera of acute and chronically infected patients with and without hepatocellular carcinoma (HCC). doi = 10.1016/s0934-8840(11)80039-3 id = cord-306261-yc2y2xak author = van Tricht, Ewoud title = Fast, selective and quantitative protein profiling of adenovirus-vector based vaccines by ultra-performance liquid chromatography date = 2018-12-28 keywords = TFA; UPLC; protein summary = The new RP-UPLC method was successfully validated for protein profiling and relative quantification of proteins in vaccine products based on adenovirus vector types 26 and 35. By calculating the relative peak areas of all peaks in the chromatogram and identifying new peaks in the chromatogram, the method also allows the detections of degradation products in the sample Additional requirements for the method development were: a chromatographic run time of less than 30 min, baseline separation of all relevant adenovirus proteins allowing for their quantification, and an increased method robustness. The linear gradient with three slopes was replaced by a single-slope linear gradient to improve elution reproducibility and the flow rate was increased The critical method parameters of the RP-UPLC method were studied in a screening design of experiments to assess their impact on the method''s run time and the resolution between the adenovirus proteins.: The following conditions were evaluated: gradient start composition (0-20% solvent B), gradient end composition (45-65% solvent B), gradient run time (17-25 min), TFA concentration (0.04-0.12%), and column temperature (40-70 • C). doi = 10.1016/j.chroma.2018.10.045 id = cord-355377-b0rcg3rt author = van der Vlag, R. title = Analytical Methods in Protein-Templated Dynamic Combinatorial Chemistry date = 2017-06-29 keywords = DCC; dcl; nmr; protein; scheme summary = Protein-templated dynamic combinatorial chemistry (DCC) has emerged as a powerful method to identify new inhibitors given that it enables the protein to select its own best binder(s) from a library of interconverting compounds. Both DCLs showed a very clear amplification of acylhydrazones: t-butylphenyl and thiophenyl acylhydrazones 4-5c and 4-5g were amplified in presence of hGST P1-1 and SjGST, Scheme 3 Generation of acylhydrazone-based dynamic combinatorial libraries of (A) aldehydes 4 or 6 and hydrazides 5a-j. The protein concentration can be very low, but 1 H-waterLOGSY 21 can be limited by the exchange kinetics of the reversibly formed protein-ligand complexes and might still suffer from overlapping signals, especially for large DCLs. In 2013, the same group introduced a competition-based 1 H-NMR method to screen binders for human 2-oxoglutarate (2OG)dependent oxygenases. doi = 10.1016/b978-0-12-409547-2.12559-4 id = cord-270514-36k9xo7f author = van der Woude, Roosmarijn title = Drivers of recombinant soluble influenza A virus hemagglutinin and neuraminidase expression in mammalian cells date = 2020-08-14 keywords = protein summary = Recombinant soluble trimeric influenza A virus hemagglutinins (HA) and tetrameric neuraminidases (NAs) have proven to be excellent tools to decipher biological properties. The two surface envelope proteins of IAV have opposing functions; the trimeric hemagglutinin (HA) binds to sialic acid containing glycans to enable the virus to enter cells, 1,2 the tetrameric neuraminidase (NA) cleaves sialic acids to release new viral particles from the membrane. However, we observed a significant increase in expression yields and determined that it reduced the use of expensive antibodies and provided an excellent handle, as well as an internal read out, of a glycan binding protein. The N-terminal sfGFP increases yields, maintains biological activity, structure and antigenicity, and aids protein quantitation during expression and purification. To determine that sfGFP-NA fusions are enzymatically, antigenically and structurally similar to their non-fused counterparts, we analyzed the GCN4, TB, and sfGFP-TB-N2 proteins with MUNANA and NA specific antibodies (Figure 3 ). doi = 10.1002/pro.3918 id = cord-309043-dlmx12vt author = von Brunn, Albrecht title = Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date = 2007-05-23 keywords = RNA; SARS; interaction; protein; y2h summary = The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. There are reports that a number of MHV and SARS-CoV replicase proteins colocalize and eventually interact in cytoplasmic membrane bound complexes, in which viral RNA synthesis occurs [18, 19] . We therefore cloned the SARS-CoV ORFeome by recombinatorial cloning (GATEWAY technology) and performed a genome-wide analysis for viral protein interactions by yeast-two-hybrid (Y2H) matrix screen. To systematically study the subcellular localization of viral proteins within eukaryotic HeLa cells the SARS-CoV ORFs were transfected in eukaryotic vectors with either N-or C-terminal Flag tags and detected with an anti-Flag antibody. In this study we report the cloning of the complete ORFeome of SARS-CoV and the results of a matrix-based yeast two-hybrid screen of pairwise viral protein-protein interactions. doi = 10.1371/journal.pone.0000459 id = cord-006636-xgikbdns author = Ühlein, E. title = Übersicht Über neue ernährungswissenschaftliche Publikationen date = 1964-02-01 keywords = Ern; Nutrition; Studies; Zur; acid; der; die; effect; feed; food; growth; influence; metabolism; milk; protein; study; und; vitamin; yon summary = L. : Effect of a low dietary level of three types of fat on reproductive performance and tissue lipid content of the vitamin B6-deficicnt female rat. H.: Effect of dietary protein and fat on growth, protein utilization, and carcass composition of pigs fed purified diets. Effect of food fats on concentration of ketone bodies and citric acid level in blood and tissues Effect of a low dietary level of three types of fat on reproductive performance and tissue lipid content of the vitamin B6-defieient female rat The effect on the serum cholesterol levels of the consumption of a special dietary fat with a high content of unsaturated fatty acids in elderly people Effect of protein intake and cold exposure on selected liver enzymes associated with amino acid metabolism Effect of protein intake and cold exposure on selected liver enzymes associated with amino acid metabolism doi = 10.1007/bf02021334