SARS-CoV-2 beta variant substitutions alter spike glycoprotein receptor binding domain structure and stability

  1. Daniel L. Moss
  2. Jay Rappaport

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Abstract

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  1. Version published to 10.1016/j.jbc.2021.101371
  2. Version published to 10.1101/2021.05.11.443443v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.05.11.443443: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Recombinant DNA
    SentencesResources
    The RBD variant containing three substitutions (K417N/E484K/N5101Y) was synthesized and cloned by Genscript into the pcDNA3.1 vector and subcloned into pCAGGS.
    pcDNA3.1
    suggested: RRID:Addgene_79663)
    pCAGGS
    suggested: RRID:Addgene_18926)
    Software and Algorithms
    SentencesResources
    Molecular Dynamic Simulations: Molecular dynamic simulations were performed with the GROMACS 2020.5 package17,33 with the CHARMM36 all-atom force field18 and the TIP3P water model34.
    GROMACS
    suggested: (GROMACS, RRID:SCR_014565)
    Analysis was performed with GROMACS, VMD 1.9.336, PyMOL and GraphPad Prism.
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Gels were imaged with a Chemidoc MP imaging system (Bio-Rad, CA) and analyzed with ImageJ software.
    ImageJ
    suggested: (ImageJ, RRID:SCR_003070)

    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: We detected the following sentences addressing limitations in the study:
    However, the caveat here is that the RBD does not exist in isolation but rather as part of the much larger spike glycoprotein and therefore the effects of these substitutions on structure and stability will likely not translate to the larger molecule but may still be relevant for understanding the evolution of SARS-CoV-2. The presence of K417N alone and N501Y alone significantly stabilized the RBD relative to wild-type and it is unclear from the simulation data how this was achieved for the N501Y substitution found in the B.1.1.7 variant. Surprisingly the E484K substitution alone significantly destabilized the RBD relative to wild-type. Our simulation data suggest that E484K alone reduces overall hydrogen bond content in the RBD. Reduced hydrogen bond content may explain the observed decrease in stability and suggests that the elimination of specific interactions between residue 484 and other RBD residues alone cannot explain the observed reduction in RBD stability. Finally, we tested the stability of RBD variants by limited proteolysis with cathepsin S. Protein susceptibility to limited proteolysis is a robust measure of protein stability and has also been linked to protein immunogenicity19,20,23,24. We observed that the K417N substitution increased proteolytic resistance at all time points while the E484K and all three substitutions together (K417N/E484K/N501Y) decreased resistance after 15 and 30 minutes of incubation. The N501Y variant exhibited increased proteolytic resi...

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2021.05.11.443443v1 on bioRxiv