Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity
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Abstract
The spike (S) glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the binding to the permissive cells. The receptor-binding domain (RBD) of SARS-CoV-2 S protein directly interacts with the human angiotensin-converting enzyme 2 (ACE2) on the host cell membrane. In this study, we used computational saturation mutagenesis approaches, including structure-based energy calculations and sequence-based pathogenicity predictions, to quantify the systemic effects of missense mutations on SARS-CoV-2 S protein structure and function. A total of 18 354 mutations in S protein were analyzed, and we discovered that most of these mutations could destabilize the entire S protein and its RBD. Specifically, residues G431 and S514 in SARS-CoV-2 RBD are important for S protein stability. We analyzed 384 experimentally verified S missense variations and revealed that the dominant pandemic form, D614G, can stabilize the entire S protein. Moreover, many mutations in N-linked glycosylation sites can increase the stability of the S protein. In addition, we investigated 3705 mutations in SARS-CoV-2 RBD and 11 324 mutations in human ACE2 and found that SARS-CoV-2 neighbor residues G496 and F497 and ACE2 residues D355 and Y41 are critical for the RBD–ACE2 interaction. The findings comprehensively provide potential target sites in the development of drugs and vaccines against COVID-19.
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SciScore for 10.1101/2020.05.21.109835: (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 To study the protein stability of wide type SARS-CoV-2 S, we separated the A chain of 6VYB and introduced P986K and P987V mutations using FoldX (23). FoldXsuggested: (FoldX, RRID:SCR_008522)The PyMOL (http://www.pymol.org/) was used to generate protein structural images and perform structure alignments. PyMOLsuggested: (PyMOL, RRID:SCR_000305)Sequence Analysis and Mutation Pathogenicity: The amino acid sequences of S protein of SARS-CoV-2 (Entry: P0DTC2), SARS-CoV (Entry: P59594) and MERS-CoV (Entry: K9N5Q8) and human ACE2 (Entry: Q9BYF1) were downloaded from UniProt (24). Mutation …SciScore for 10.1101/2020.05.21.109835: (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 To study the protein stability of wide type SARS-CoV-2 S, we separated the A chain of 6VYB and introduced P986K and P987V mutations using FoldX (23). FoldXsuggested: (FoldX, RRID:SCR_008522)The PyMOL (http://www.pymol.org/) was used to generate protein structural images and perform structure alignments. PyMOLsuggested: (PyMOL, RRID:SCR_000305)Sequence Analysis and Mutation Pathogenicity: The amino acid sequences of S protein of SARS-CoV-2 (Entry: P0DTC2), SARS-CoV (Entry: P59594) and MERS-CoV (Entry: K9N5Q8) and human ACE2 (Entry: Q9BYF1) were downloaded from UniProt (24). Mutation Pathogenicitysuggested: NoneThe pairwise sequence alignment was carried out using EMBOSS Water multiple sequence alignment was performed using Clustal Omega and (25). EMBOSSsuggested: (EMBOSS, RRID:SCR_008493)Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)R package (https://www.r-project.org/) was used to generate graphs and perform ANOVA test and t test in statistical comparisons of ΔΔG and ΔΔΔG values and SNAP scores. https://www.r-project.org/suggested: (R Project for Statistical Computing, RRID:SCR_001905)SNAPsuggested: (SNAP, RRID:SCR_007936)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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 34, 36 and 30. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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