Uncovering the structural flexibility of SARS-CoV-2 glycoprotein spike variants

  1. Hiam R. S. Arruda
  2. Tulio M. Lima
  3. Renata G. F. Alvim
  4. Fernanda B. A. Victorio
  5. Daniel P. B. Abreu
  6. Federico F. Marsili
  7. Karen D. Cruz
  8. Patricia Sosa-Acosta
  9. Mauricio Quinones-Vega
  10. Jéssica de S. Guedes
  11. Fábio C. S. Nogueira
  12. Jerson L. Silva
  13. Leda R. Castilho
  14. Guilherme A. P. de Oliveira

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Abstract

The severe acute respiratory syndrome CoV-2 rapidly spread worldwide, causing a pandemic. After a period of evolutionary stasis, a set of SARS-CoV-2 mutations has arisen in the spike, the leading glycoprotein at the viral envelope and the primary antigenic candidate for vaccines against the 2019 CoV disease (COVID-19). Here, we present comparative biochemical data of the glycosylated full-length ancestral and D614G spike together with three other highly transmissible strains classified by the World Health Organization as variants of concern (VOC): beta, gamma, and delta. By showing that only D614G early variant has less hydrophobic surface exposure and trimer persistence at mid-temperatures, we place D614G with features that support a model of temporary fitness advantage for virus spillover worldwide. Further, during the SARS-CoV-2 adaptation, the spike accumulates alterations leading to less structural rigidity. The decreased trimer stability observed for the ancestral and the gamma strain and the presence of D614G uncoupled conformations mean higher ACE-2 affinities when compared to the beta and delta strains. Mapping the energetic landscape and flexibility of spike variants is necessary to improve vaccine development.

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    SciScore for 10.1101/2022.04.20.488873: (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
    After that, anti-human IgG (Fc specific)-peroxidase antibody (Sigma-Aldrich, Cat# SAB3701282-2MG, Lot# RI34900) was added at 1:10,000 dilution, and the plate was incubated at room temperature for 1 h.
    anti-human IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    The variants contained the respective mutations as follows Production and purification of spike variants: Stable, recombinant HEK293 cell lines were generated to produce each spike protein by transfecting the suspension-adapted HEK293-3F6 (NRC, Canada) parental cell line with each plasmid described above.
    HEK293
    suggested: None
    Recombinant DNA
    SentencesResources
    The genes coding for the D614G, beta, gamma, and delta variants were synthesized at Genscript (Piscataway, USA) and cloned into the pCIneo vector (Promega, USA) to facilitate stable expression in mammalian cells.
    pCIneo
    suggested: RRID:Addgene_115360)
    Software and Algorithms
    SentencesResources
    The raw data were imported to Proteome Discoverer 2.4 (Thermofisher Scientific) software to perform protein identification analysis.
    Proteome Discoverer
    suggested: (Proteome Discoverer, RRID:SCR_014477)
    The absorbance was read at 450 nm with 655 nm background compensation in iMark Microplate Absorbance Reader (BIO-RAD Laboratories).
    BIO-RAD Laboratories
    suggested: (Bio-Rad Laboratories, RRID:SCR_008426)
    The half-maximal effective response (EC50) was carried out by fitting the curve to a four-parameter logistic regression by GraphPad Prism version 8 (GraphPad Software, San Diego, California, USA)
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Statistical Analysis: We used Minitab 17 software for statistical analysis.
    Minitab
    suggested: (Minitab, RRID:SCR_014483)

    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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  2. Version published to 10.1101/2022.04.20.488873v1 on bioRxiv