Effect on the conformations of the spike protein of SARS‐CoV‐2 due to mutation
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Abstract
The spike protein of SARS‐CoV‐2 mediates receptor binding and cell entry and is the key immunogenic target for virus neutralization and the present attention of many vaccine layouts. It exhibits significant conformational flexibility. We study the structural fluctuations of spike protein among the most common mutations that appeared in the variant of concerns (VOC). We report the thermodynamics of conformational changes in mutant spike protein with respect to the wild‐type from the distributions of the dihedral angles obtained from the equilibrium configurations generated via all‐atom molecular dynamics simulations. We find that the mutation causes the increase in distance between the N‐terminal domain and receptor binding domain, leading to an obtuse angle cosine θ distribution in the trimeric structure in spike protein. Thus, an increase in open state is conferred to the more infectious variants of SARS‐CoV‐2. The thermodynamically destabilized and disordered residues of receptor binding motif among the mutant variants of spike protein are proposed to serve as better binding sites for the host factor. We identify a short stretch of region connecting the N‐terminal domain and receptor binding domain forming a linker loop where many residues undergo stabilization in the open state compared to the closed one.
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SciScore for 10.1101/2022.05.11.491583: (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 We use periodic boundary conditions, spc216 water model and GROMOS9353a632 force field for simulations in GROMACS 2018.6 package. 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.
Result…
SciScore for 10.1101/2022.05.11.491583: (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 We use periodic boundary conditions, spc216 water model and GROMOS9353a632 force field for simulations in GROMACS 2018.6 package. 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.
Results from scite Reference Check: We found no unreliable references.
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