Site-specific steric control of SARS-CoV-2 spike glycosylation

  1. Joel D. Allen
  2. Himanshi Chawla
  3. Firdaus Samsudin
  4. Lorena Zuzic
  5. Aishwary Tukaram Shivgan
  6. Yasunori Watanabe
  7. Wan-ting He
  8. Sean Callaghan
  9. Ge Song
  10. Peter Yong
  11. Philip J. M. Brouwer
  12. Yutong Song
  13. Yongfei Cai
  14. Helen M. E. Duyvesteyn
  15. Tomas Malinauskas
  16. Joeri Kint
  17. Paco Pino
  18. Maria J. Wurm
  19. Martin Frank
  20. Bing Chen
  21. David I. Stuart
  22. Rogier W. Sanders
  23. Raiees Andrabi
  24. Dennis R. Burton
  25. Sai Li
  26. Peter J. Bond
  27. Max Crispin

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Abstract

A central tenet in the design of vaccines is the display of native-like antigens in the elicitation of protective immunity. The abundance of N-linked glycans across the SARS-CoV-2 spike protein is a potential source of heterogeneity between the many different vaccine candidates under investigation. Here, we investigate the glycosylation of recombinant SARS-CoV-2 spike proteins from five different laboratories and compare them against infectious virus S protein. We find patterns which are conserved across all samples and this can be associated with site-specific stalling of glycan maturation which act as a highly sensitive reporter of protein structure. Molecular dynamics (MD) simulations of a fully glycosylated spike support s a model of steric restrictions that shape enzymatic processing of the glycans. These results suggest that recombinant spike-based SARS-CoV-2 immunogen glycosylation reproducibly recapitulates signatures of viral glycosylation.

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  1. ScreenIT

    SciScore for 10.1101/2021.03.08.433764: (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

    Experimental Models: Cell Lines
    SentencesResources
    Spike ectodomain was expressed by transient transfection HEK293T (ATCC, CRL-3216) cells for 6 days at 30 °C.
    HEK293T
    suggested: None
    S protein was expressed in HEK 293F cells.
    HEK 293F
    suggested: RRID:CVCL_6642)
    Software and Algorithms
    SentencesResources
    The S protein concentration was determined by the Nanodrop method using the proteins peptidic molecular weight and extinction coefficient as determined by the online ExPASy software (ProtParam).
    ExPASy
    suggested: None
    Integrative modelling and molecular dynamics simulation: The model of S protein was built using Modeller 9.2175 with three structural templates: i) the cryo-EM structure of SARS-CoV-2 S ECD in the open state (PDB: 6VSB)29, ii) the NMR structure of SAR-CoV S HR2 domain (PDB: 2FXP) 61, and iii) the NMR structure of HIV-1 gp-41 TM domain (PDB: 5JYN)62.
    Modeller
    suggested: (MODELLER, RRID:SCR_008395)

    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.

    About SciScore

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  2. Version published to 10.1101/2021.03.08.433764v1 on bioRxiv