Uncovering the structural flexibility of SARS-CoV-2 glycoprotein spike variants
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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 Sentences Resources 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 IgGsuggested: NoneExperimental Models: Cell Lines Sentences Resources 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. HEK293suggested: None… 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 Sentences Resources 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 IgGsuggested: NoneExperimental Models: Cell Lines Sentences Resources 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. HEK293suggested: NoneRecombinant DNA Sentences Resources 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. pCIneosuggested: RRID:Addgene_115360)Software and Algorithms Sentences Resources The raw data were imported to Proteome Discoverer 2.4 (Thermofisher Scientific) software to perform protein identification analysis. Proteome Discoverersuggested: (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 Laboratoriessuggested: (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 Prismsuggested: (GraphPad Prism, RRID:SCR_002798)GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Statistical Analysis: We used Minitab 17 software for statistical analysis. Minitabsuggested: (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.
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- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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