Structure and dynamics of the SARS‐CoV ‐2 envelope protein monomer
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Abstract
Coronaviruses, especially severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), present an ongoing threat to human wellbeing. Consequently, elucidation of molecular determinants of their function and interaction with the host is an important task. Whereas some of the coronaviral proteins are extensively characterized, others remain understudied. Here, we use molecular dynamics simulations to analyze the structure and dynamics of the SARS‐CoV‐2 envelope (E) protein (a viroporin) in the monomeric form. The protein consists of the hydrophobic α‐helical transmembrane domain (TMD) and amphiphilic α‐helices H2 and H3, connected by flexible linkers. We show that TMD has a preferable orientation in the membrane, while H2 and H3 reside at the membrane surface. Orientation of H2 is strongly influenced by palmitoylation of cysteines Cys40, Cys43, and Cys44. Glycosylation of Asn66 affects the orientation of H3. We also observe that the monomeric E protein both generates and senses the membrane curvature, preferably localizing with the C‐terminus at the convex regions of the membrane; the protein in the pentameric form displays these properties as well. Localization to curved regions may be favorable for assembly of the E protein oligomers, whereas induction of curvature may facilitate the budding of the viral particles. The presented results may be helpful for a better understanding of the function of the coronaviral E protein and viroporins in general, and for overcoming the ongoing SARS‐CoV‐2 pandemic.
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SciScore for 10.1101/2021.03.10.434722: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources The structure of the monomer with PTMs was constructed manually using PyMOL [87]. PyMOLsuggested: (PyMOL, RRID:SCR_000305)All systems were energy minimized using the steepest descent method, equilibrated and simulated using GROMACS 2019.5 (AA) and GROMACS 2020.1 (CG) [90]. GROMACSsuggested: (GROMACS, RRID:SCR_014565)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study …SciScore for 10.1101/2021.03.10.434722: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources The structure of the monomer with PTMs was constructed manually using PyMOL [87]. PyMOLsuggested: (PyMOL, RRID:SCR_000305)All systems were energy minimized using the steepest descent method, equilibrated and simulated using GROMACS 2019.5 (AA) and GROMACS 2020.1 (CG) [90]. GROMACSsuggested: (GROMACS, RRID:SCR_014565)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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