key: cord-272986-ebgusf3o
authors: Cao, Yipeng; Yang, Rui; Wang, Wei; Lee, Imshik; Zhang, Ruiping; Zhang, Wenwen; Sun, Jiana; Xu, Bo; Meng, Xiangfei
title: Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel
date: 2020-05-17
journal: bioRxiv
DOI: 10.1101/2020.05.17.099143
sha: 
doc_id: 272986
cord_uid: ebgusf3o

Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus (SARS-CoV-2) and represents the causative agent of a potentially fatal disease that is of public health emergency of international concern. Coronaviruses, including SARS-CoV-2, encode an envelope (E) protein, which is a small, hydrophobic membrane protein; the E protein of SARS-CoV-2 has high homology with that of severe acute respiratory syndrome coronavirus. (SARS-CoV) In this study, we provide insights into the function of the SARS-CoV-2 E protein channel and the ion and water permeation mechanisms on the basis of combined in silico methods. Our results suggest that the pentameric E protein promotes the penetration of monovalent ions through the channel. Analysis of the potential mean force (PMF), pore radius and diffusion coefficient reveals that Leu10 and Phe19 are the hydrophobic gates of the channel. In addition, the pore demonstrated a clear wetting/dewetting transition with monovalent cation selectivity under transmembrane voltage, which indicates that it is a hydrophobic voltage-dependent channel. Overall, these results provide structural-basis insights and molecular-dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SARS-CoV-2 E protein channel.

COVID-19 is a severe and highly contagious respiratory illness that was first reported in China in early December 2019. Subsequently, the virus has spread worldwide. As of May 6, 2020, millions of cases have been confirmed, and hundreds of thousands have died. The World Health Organization (WHO) announced a global pandemic for COVID-19 in March 2020. In addition to the hazards of the disease itself, it has also led to a severe turbulence in international financial markets and may cause serious consequences such as a financial crisis. COVID-19 is a disease caused by a new coronavirus named SARS-CoV-2. It is speculated that it originated from bats and was transmitted to humans through an intermediate host (some kind of wildlife). Its symptoms include fever, general malaise, dry cough, shortness of breath, and respiratory distress. Comparing similar diseases, including severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), which are also caused by coronaviruses, the mortality rates for SARS and MERS were 10% and 36%, respectively 1 . Currently, COVID-19 has a mortality rate of 1 to 10% in different countries but appears to be more contagious than SARS and MERS 2 3 4 5 .

Similar to other coronaviruses, SARS-CoV-2 is a long positive-sense, long single-stranded (30 kb) RNA virus. The structure of different human coronaviruses (HCoVs) is similar. The viral genome is packed by nucleocapsid (N) proteins, forming a helicoidal nucleocapsid protected by a lipid envelope 6 . Several viral proteins, including the spike (S), envelope (E), and membrane (M) proteins, are embedded within a lipid envelope 7 8 . Studies have shown that S, M, and N proteins play important roles in receptor binding and virion budding. For example, the M protein participates in virus germination and interacts with the N and S proteins. The S protein has immune recognition sites and can be used to design vaccines 9 .

Currently, the importance of the E protein has not been fully revealed. Evidence suggests that the E protein maintains its morphology after virus assembly by interacting with the M protein 10 11 12 . When an E protein gene mutation occurs, it promotes apoptosis. Recent studies have shown that coronaviruses have a viroporin that can self-assemble into a pentameric structure and have ion selectivity. When there is a transmembrane voltage, the ion channel characteristics of viroporins are more significant. In addition, the Asn25Ala and Val18Phe mutations could destroy ion channel activity 13 . This indicates that the E protein may play an important role in regulating the ion equilibrium inside and outside the viral envelope.

The ion channel activity of the E protein can lead to increased levels of the inflammatory cytokines IL-1β, TNF and IL-6 in the lungs, leading to the occurrence of an "inflammatory storm" 14 . This plays a key role in the progression of the disease and may cause the patient's condition to suddenly deteriorate and lead to death. In addition, its evolutionary conservatism may be an important cause of viral cross-host infection 15 16 17 .

Although previous studies have suggested that the E protein of coronaviruses such as SARS and MERS oligomerizes and has ion permeability, the specific mechanism of ion permeability and channel properties remain to be explored due to the lack of a crystal structure for the E protein. In 2014, Li et al 17 identified the SARS-CoV E protein monomer structure. In 2018, Surya et al. extracted the pentamer structure of the SARS E protein by nuclear magnetic resonance (NMR) 18 , which provided strong support for the study of the SARS-CoV-2 E protein pentamer ion permeability mechanism.

In this study, we obtained the amino acid sequence of the SARS-CoV-2 E protein from the National Center for Biotechnology Information (NCBI) database 19 . The E protein pentamer model of SARS-CoV-2 was built by using the homology modeling method, and the reasonableness of the model was evaluated. Subsequently, µs-level molecular dynamics (MD) simulations were performed to evaluate the pentamer's stability in the membrane environment. We tried to use potential mean force (PMF) to reveal the permeability of different physiological ions and water molecules in the pores of the E protein pentamer. The characteristics of the pentameric channel were analyzed by combining the channel diffusion coefficient and geometric properties. In addition, computational electrophysiology was applied for different transmembrane voltages of the system to reveal the effect of the voltage on the ion permeability of the pentameric E protein.

Overall, exploring the mechanisms of the pentameric SARS-CoV-2 E protein not only provides valuable insights into the conduction of the channel but also has important implications for our understanding of the difference between SARS-CoV-2 and other coronaviruses. Sequence alignment and homology modeling Figure 1A shows the sequence alignment between the E proteins of two human coronaviruses (SARS-CoV and SARS-CoV-2 sequence) made by Clustal X software.

The blue dotted rectangle in Figure 1B 

The Rampage online program 20 was used to evaluate the accuracy of the SARS-CoV-2 pentameric E protein model. More than 98.9% of the amino acids are within the acceptable range, suggesting that the SARS-CoV-2 E protein is similar to the SARS E protein NMR model. Subsequently, a 1000 ns (1 µs) MD simulation was performed to evaluate the stability of pentameric E protein embedded in the membrane environment. The root-mean-square deviation (RMSD) of the model is shown in Figure 2 , and the red and blue curves represent the whole protein and TM region, respectively. In the first 200 ns, the RMSD continued to rise, indicating that the model needed longer optimization (compared with other ion channels) to reach the pentameric structure equilibrium. During the last 800 ns, the curves plateaued. The RMSD of the whole protein and the TM region converged at ~0.4 and ~0.3 nm, respectively. There is a 0.1 nm difference between the whole protein and TM region.

These findings are consistent with other ion channel data that show that the TM region has a higher stability than the other parts of the membrane protein 21 . 

The permeability of the SARS-CoV-2 pentameric E protein channel is very important for understanding the replication ability of viruses in cells and how they are secreted into the extracellular medium 22 . It is possible to examine a profile of the free energy of a single ion or water as a function of its position along the pore axis by calculation of PMF. In this simulation, the ions or water molecules are restrained to a continuous position along the z-axis and move freely in the pore's xy plane. Moreover, other parts of the system (proteins, ions, water molecules, and lipids) can move freely and reach equilibrium.

The PMF of important physiological ions (Mg2 + ; Ca 2+ ; Cl-; K + and Na + ) and the water molecules as a function of their position along the pore (z)-axis were calculated separately. Figure 3A shows the PMF of ions and water molecules permeating through the SARS-CoV-2 E protein pentamer pore. Z M is defined as the axial direction along the pore, which is from -3 ~ 3 nm (the length of umbrella sampling is 6 nm in total). From the PMF curve, we found that the energy barriers of monovalent and divalent ions have a significant difference. The maximum energy barriers of the two divalent ions Ca 2+ and Mg 2+ are 60 kJ/mol and 70 kJ/mol, respectively. In contrast, the PMFs of the monovalent ions Na + and K + are ~ 12 kJ/mol and ~20 kJ/mol, respectively, while the Cl-energy barrier is ~ 30 kJ/mol, which is significantly smaller than that of Ca 2+ and Mg 2+ . From an energy perspective, the SARS-CoV-2 pentameric E protein is almost impermeable to divalent ions. This confirms the previous hypothesis that the SARS-CoV and MERS-CoV E protein channel is a monovalent cation channel 23 24 .

The maximum energy barrier in descending order is as follows: Na + <K + <Cl-<Mg 2+ <Ca 2+ . Additionally, the barrier of water molecules is only ~ 5 k/mol, which is similar to the energy threshold of free diffusion in liquid. Interestingly, there is no obvious peak in the PMF curve for Na + ions and water molecules. This result indicates that the E protein pentamer pores are not permeable to divalent ions. The difference in the energy barrier between the monovalent cations is large, suggesting that the channel has selective permeability for specific ions.

To explore the permeability of the channel, we calculated the diffusion coefficient (D C ) using a single K + ion as a probe. By fitting the K + mean square displacement (MSD) with the Einstein equation (MSD = 2D(c)t), we obtained the diffusion coefficient. As shown in Figure 3B , the average diffusion coefficient of K + outside the pore is ~ 2.0×10 -5 ±0.4 cm 2 /s, which is consistent with the experimental data of K + in the liquid environment 25 . However, the D C decreases by approximately 70% when the K + probe is in the channel pore. The D C curve of the internal channel pore has a flat bottom and is similar to the PMF. The mid-value of D C = 0.35×10 -5 ±0.2 cm 2 /s indicates that there is a large obstacle for probe diffusion in the inner pore, showing a similar value to other narrow hydrophobic pores 26 27 .

Next, we used the solubility-diffusion equation (Eq 1) 28 29 to evaluate the permeability coefficient (P) between two different ions.

Eq 1

In Eq 1, PMF(z) and D(z) are functions of PMF and DC along the z-axis, z1 denotes a position on one side of the pore and z2 denotes a position on the other side. Kb is the Boltzmann constant, and T is the simulation temperature. The part of the PMF in the TM region is approximate to the graph of the quadratic function, so the PMF(Z) uses quadratic function fitting. The linear fitting of the corresponding D C gives the function D(z). The ratios of the P for Na + , K + and Cl-in the maximum energy barrier region were simply evaluated. P Na+ /P K+ = 22.42, P K+ /P Cl-= 5.82, and P H2O /P Na+ = 402.57. 

COVID-19 is an unprecedented threat to humanity. To understand the infection, the replication mechanism of the virus in the human body is particularly important.

Currently, research on the pathogenic mechanism and infection route of COVID-19 mainly focuses on the S protein 38 The SARS-CoV-2 E protein pentamer has been considered an unknown nature ion channel. There is significant similarity in the TM region sequences (reaching 91.8%) and high gene homology between the SARS-CoV and SARS-CoV-2 E proteins; five different residues are all located at the region of interaction between the protein and membrane, while the sequences of the TM region are completely identical. The highly conserved TM region also suggests similar E protein functions in different coronavirus subtypes. As the RMSD of the E protein pentamer during the 1 µs MD simulation, the structure has a certain flexibility, showing that its geometric deformation can make the channel permeable to ions and water molecules. Figure 2 shows that the TM region of the SARS-CoV-2 E protein remains relatively stable during the simulation, indicating the stability of the pentamer in the membrane environment, which is consistent with previous studies of SARS-CoV and MERS-CoV.

The free energy calculation of the ions permeating through the SARS-CoV-2 pentameric E protein channel strongly suggests that the pore has selection permeability for monovalent ions. The maximum energy barriers of Na + , K + , and Clare 15 kJ/mol, 20 kJ/mol, and 30 kJ/mol, respectively. The comparison of the P values for Na + , K + and Clshows that the P of Na + is 22 times greater than that of K + , while the P of K + is 6 times greater than that of Cl -. Although the computational permeability coefficient is two times higher or lower than that observed experimentally for SARS-CoV, it still shows a very large gap in the permeation between ions and water molecules. Additionally, there is no obvious peak in the PMF when Na + and water molecules permeate through the channel, further supporting that Na + and water molecules have less penetration resistance at the inner pore. This further confirmed the selectively for Na + . The ion selectivity of SARS-CoV-2 is different from that of SARS-CoV 23 . Because the maximum energy barrier of Mg 2+

and Ca 2+ is 2 ~ 3 times higher than that of the monovalent ions, divalent ions cannot overcome such a very large energy barrier under the simulation environment. The conformational analysis indicates that it is mainly caused by the geometric size of the pore (Fig 6) .

The importance of transmembrane voltage on viroporin has been found in many viruses, including HIV1 Vpu oligomers and the hepatitis C virus (HCV) p7 protein, etc. 42 43 44 . Although it has been observed in many experiments, this mechanism has not been revealed. Because water molecules play an important role in hydrophobic The channel wetting/dewetting transitions appeared under different transmembrane voltages, and the radius of the pore increased. Meanwhile, the capacity to contain water molecules also increased. Further analysis of the trajectories revealed that the monovalent cations (Na + and K + ) will permeate through the pore with water molecules when the transmembrane voltage is > 0.3 V.

Computational electrophysiology also explained that the transmembrane voltage led to an easier wetting transition for the channel. The range for keeping the channel open should be between 0.15 V and2 0.45 V. Na + and K + could be cotransported during water permeation, which is very similar to that in many hydrophobic channels 45 46 47 48 . Intriguingly, we did not observe Clconduction, which may be because chloride ions could not overcome the energy barrier under the maximum transmembrane voltage. In addition, the change in the pore radius at different voltages highlights two important sites, where the geometric radius changes the most, corresponding to Leu10 and Phe19. Phe19 contains a benzene ring group at the hydrophobic surface of the inner pore as a hydrophobic gate. The isopropyl group of Leu10 at the bottom of the pore prevents the reverse penetration (Fig 6A) . Previous studies indicated that Asn15Val and Val25Phe mutations will make the channel dysfunctional. This may be due to the additional side chain groups in the pores caused by these mutations (especially the benzene ring in Val25Phe), making 1) the radius of the pores decrease and 2) the hydrophobicity of the pores increase. In short, these mutations may increase the energy barrier, negatively affecting the wetting transition and causing the channel to be functionally closed.

Therefore, the SARS-CoV-2 E protein pentamer is a voltage-dependent hydrophobic channel. We propose that the E protein may play an essential role in the virus infection and replication processes through the following mechanisms: 1) The monovalent selective permeation of the E protein pentamer ion channel may change the intracellular pH, providing a suitable microenvironment for virus replication. 2)

Selective permeation can form a transmembrane voltage, creating feedback regulation and maintaining an intracellular microenvironment that is suitable for viral growth.

3)

The disintegration of the ion equilibrium of the intracellular area affect the charges coming from the cell through ion channels in the cell membrane, changing the pH and making it easier for the virus to fuse with the cell membrane. This is the infection mechanism of the avian coronavirus as well as some types of influenza viruses 49 50 . 4) It has a certain signal transduction function.

Although the pentameric SARS-CoV-2 E protein crystal structure is not yet available, 

Preparation of the SARS-CoV-2 pentameric E protein-membrane simulation system

The amino acids sequence of the human coronaviruses E proteins were downloaded from the National Center for Biotechnology Information (NCBI 

To obtain the equilibrated pentameric SARS-CoV-2 E protein model, Charmm36

all-atom force field 53 was chosen for MD simulation. The MD time step was set at 2 fs. Electrostatic interactions were described using the Particle Mesh Ewald (PME) algorithm 54 with a cut-off of 1.2 nm. The LINCS algorithm 55 was used to constrain the bond lengths. The pressure was maintained semi-isotropically at 1 bar at both x and y directions using the Perinello-Rahman barostat algorithm 56 and the system temperature was maintained at 310 K by the Nose-Hoover thermostat 57 . Then, a 1000 ns (1 µs) MD simulations were performed for the E protein pentameric.

Umbrella sampling

The initial system for umbrella sampling simulations was derived from the equilibrated pentameric SARS-CoV-2 E protein mentioned above. A single ion that maintain physiological activity (Na + , K + , Ca 2+ , Mg 2+ , Cl -) or water molecule was placed at successive positions along the central pore axis by using GROMACS pull code. Energy minimization was performed before simulation for optimizing the water and ions position. The reaction coordinate defined from z +3 to -3 nm with the mass center at z = 0 nm, with a spacing of 0.1 nm between successive windows, resulting in 60 umbrella sampling simulation systems. The probe ion or water molecules were harmonically restrained by a force constant of 2000 kJ mol/nm 2 same with the pore direction. Each window was performed a 5 ns total umbrella sampling simulation. The initial 2 ns for system equilibration, then a subsequent 3 ns was applied for analysis.

The PMFs were computed by the weighted histogram analysis method (WHAM) 58 , and the profile was generated by Gromacs protocol 'g_wham' 59 . Bootstrap analysis (N = 50) was used to estimate statistical error and the '-cycl' parameter was used to make the value equal.

The Diffusion-coefficient was calculated using the method described by Shirvanyants et al. 60 . We restrained the E-protein pentamer helix backbones and made the side chains, membrane, water and ions free to move. Due to the ion selectivity is related to the side chain of inner pore 61 , the backbone restraint maintained the E-protein pentamer tertiary structure but the side-chain flexibility in the inner pore was not influenced. A K + as the probe ion, the calculation system was used in the same manner as for umbrella sampling. The ion mean-square displacement (MSD) was calculated along the pore's Z-axis. A total of 25 simulation systems were obtained, each widows interval distance of the K + being set as 0.24 nm. The umbrella restraint was used to maintain the K + ion's position on the x-y plane of the pore. The Einstein equation MSD=2D(z)t was used to calculate the diffusion coefficient by the protocol g_msd. The umbrella restraint can be disregarded for these analyses because of the restraint force was negligible compared to thermally induced RMS fluctuations.

Computational electrophysiology (CE) is a good tool for simulating the ion conduction ability of a channel under transmembrane voltage. We established a sandwich structure including three parts (membrane-protein-water) as described by

Kutzner et al. 62 as shown in Fig 4A, each water layer contained a different number of ions. Due to the imbalance of the ion distribution of the water layer, the ions gradient will produce transmembrane voltage. Specific transmembrane voltage can be applied to the simulation system by adjusting the number of ions between the water layers. In this study, we built the SARS-CoV-2 E protein sandwich system. The initial single layer system was equilibrium for 50 ns to make the structures stable. Then the single-layer system was duplicated along the z direction. The resulting system had a size of around 11×11×22 nm 3 

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This study was supported by the National Natural Science Foundation of China 

All other authors declare no competing interests.