id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-263970-9w6ciglv	Marquez-Miranda, Valeria	Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites	2020-10-22		.txt	text/plain	2882	166	53	SARS-CoV-2 ORF3a is believed to form ion channels, which may be involved in the modulation of virus release, and has been implicated in various cellular processes like the up-regulation of fibrinogen expression in lung epithelial cells, downregulation of type 1 interferon receptor, caspase-dependent apoptosis, and increasing IFNAR1 ubiquitination. Here we used this dimeric structure to perform full atom molecular dynamic simulations and electrostatic potential calculations to ask questions concerning the dimers' stability and whether ions could be populating specific regions of the channel. To assess the impact of the ion occupancies described above, we obtained the electrostatic potential maps for the ORF3a channel for the initial configuration, and the last frame, at the end of a trajectory of 500 ns of the molecular dynamics simulations, by employing the Poison-Boltzmann approach implemented in the APBS package [12] . This analysis shows that the entry of Cl-ions through the inter-subunit tunnel into the central polar cavity and the accumulation of K+ ions at the cytosolic domain's surface changed the channel's electrostatic profile.	./cache/cord-263970-9w6ciglv.txt	./txt/cord-263970-9w6ciglv.txt