Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2
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Abstract
SARS-CoV-2 has considerably higher mutation rate. SARS-CoV-2 possesses a RNA dependent RNA polymerase (RdRp) which helps to replicate its genome. The mutation P323L in RdRp is associated with the loss of a particular epitope (321-327) from this protein which may influence the pathogenesis of the concern SARS-CoV-2 through the development of antibody escape variants. We consider the effect of mutations in some of the epitope regions including the naturally occurring mutation P323L on the structure of the epitope and their interface with paratope using all-atom molecular dynamics (MD) simulation studies. P323L mutations cause conformational changes in the epitope region by opening up the region associated with increase in the radius of gyration and intramolecular hydrogen bonds, making the region less accessible. Moreover, the fluctuations in the dihedral angles in the epitope:paratope (IgG) interface increase which destabilize the interface. Such mutations may help in escaping antibody mediated immunity of the host.
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SciScore for 10.1101/2021.11.18.469065: (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
Antibodies Sentences Resources Antibody i-patch Scores range from 0 to 12, with residues higher values corresponding to greater binding likelihood with antigen. antigen.suggested: NoneExperimental Models: Organisms/Strains Sentences Resources Vina1.1.2 [29] has been utilized to perform molecular docking with the drug molecule and RdRp to predict the effect of the later on drug susceptibility due to P323L mutation. Vina1.1.2suggested: NoneSoftware and Algorithms Sentences Resources 2.2 Docking studies: Antigen-antibody docking studies have been carried out using the Antibody Mode of the ClusPro server (www.cluspro.bu.edu) [28]. ClusPro serverSciScore for 10.1101/2021.11.18.469065: (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
Antibodies Sentences Resources Antibody i-patch Scores range from 0 to 12, with residues higher values corresponding to greater binding likelihood with antigen. antigen.suggested: NoneExperimental Models: Organisms/Strains Sentences Resources Vina1.1.2 [29] has been utilized to perform molecular docking with the drug molecule and RdRp to predict the effect of the later on drug susceptibility due to P323L mutation. Vina1.1.2suggested: NoneSoftware and Algorithms Sentences Resources 2.2 Docking studies: Antigen-antibody docking studies have been carried out using the Antibody Mode of the ClusPro server (www.cluspro.bu.edu) [28]. ClusPro serversuggested: (ClusPro, RRID:SCR_018248)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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