Predicted pH-dependent stability of SARS-CoV-2 spike protein trimer from interfacial acidic groups

  1. Vanessa R. Lobo
  2. Jim Warwicker

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Abstract

Transition between receptor binding domain (RBD) up and down forms of the SARS-CoV-2 spike protein trimer is coupled to receptor binding and is one route by which variants can alter viral properties. It is becoming apparent that key roles in the transition are played by pH and a more compact closed form, termed locked. Calculations of pH-dependence are made for a large set of spike trimers, including locked form trimer structures that have recently become available. Several acidic sidechains become sufficiently buried in the locked form to give a predicted pH-dependence in the mild acidic range, with stabilisation of the locked form as pH reduces from 7.5 to 5, consistent with emerging characterisation by cryo-electron microscopy. The calculated pH effects in pre-fusion spike trimers are modulated mainly by aspartic acid residues, rather than the more familiar histidine role at mild acidic pH. These acidic sidechains are generally surface located and weakly interacting when not in a locked conformation. In this model, their replacement (perhaps with asparagine) would remove the pH-dependent destabilisation of locked spike trimer conformations, and increase their recovery at neutral pH. This would provide an alternative or supplement to the insertion of disulphide linkages for stabilising spike protein trimers, with potential relevance for vaccine design.

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    SciScore for 10.1101/2021.06.06.447235: (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
    SentencesResources
    To maintain balance, 8 trimers were used for each sub-group, again with binding partners (ACE2, antibody fragments) removed.
    ACE2
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    Molecular viewers used to analyse spike proteins were NGL [34], Swiss PDB Viewer [35], and PyMOL.
    Swiss PDB Viewer
    suggested: None
    Software and Algorithms
    SentencesResources
    2.1 Structural data: A set of 129 SARS-CoV-2 spike trimer structures was retrieved from the RCSB/PDB [26] in January 2021, from a list of list generated by probing the SARS-CoV-2 spike sequence, UniProt [27] id P0DTC2, with the Basic Local Alignment Search Tool (BLAST) [28] into the RCSB/PDB at the National Center for Biotechnology Information, and subsequent checking for SARS-CoV-2 amongst the coronavirus spike proteins returned.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    2.2 Sequence data: Sequences of spike proteins from the seven coronaviruses currently known to infect humans were aligned with the Clustal Omega [30] implementation at the European Bioinformatics Institute [31], and amino acid conservation relative to SARS-CoV-2 spike protein noted at particular sites.
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    The seven S protein sequences included (with UniProt identifiers) were SARS-CoV-2 (P0DTC2), SARS (P59594), MERS (K9N5Q8), HCoV-HKU1 (Q5MQD0), HCoV-OC43 (P36334), HCoV-NL63 (Q6Q1S2), and HCoV-229E (P15423).
    UniProt
    suggested: (UniProtKB, RRID:SCR_004426)
    Molecular viewers used to analyse spike proteins were NGL [34], Swiss PDB Viewer [35], and PyMOL.
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    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).

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    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.
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    • No protocol registration statement was detected.

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

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  2. Version published to 10.1101/2021.06.06.447235v1 on bioRxiv
  3. Version published to 10.1016/j.csbj.2021.08.049