Glycans on the SARS-CoV-2 Spike Control the Receptor Binding Domain Conformation

  1. Rory Henderson
  2. Robert J Edwards
  3. Katayoun Mansouri
  4. Katarzyna Janowska
  5. Victoria Stalls
  6. Megan Kopp
  7. Barton F. Haynes
  8. Priyamvada Acharya

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Abstract

The glycan shield of the beta-coronavirus (β-CoV) Spike (S) glycoprotein provides protection from host immune responses, acting as a steric block to potentially neutralizing antibody responses. The conformationally dynamic S-protein is the primary immunogenic target of vaccine design owing to its role in host-cell fusion, displaying multiple receptor binding domain (RBD) ‘up’ and ‘down’ state configurations. Here, we investigated the potential for RBD adjacent, N-terminal domain (NTD) glycans to influence the conformational equilibrium of these RBD states. Using a combination of antigenic screens and high-resolution cryo-EM structure determination, we show that an N-glycan deletion at position 234 results in a dramatically reduced population of the ‘up’ state RBD position. Conversely, glycan deletion at position N165 results in a discernable increase in ‘up’ state RBDs. This indicates the glycan shield acts not only as a passive hinderance to antibody meditated immunity but also as a conformational control element. Together, our results demonstrate this highly dynamic conformational machine is responsive to glycan modification with implications in viral escape and vaccine design.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.26.173765: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Data were acquired using the Leginon system23 (N234A) or the EPU software (Thermo Fisher Scientific; N165A).
    Thermo Fisher Scientific
    suggested: (Thermo Fisher Scientific, RRID:SCR_008452)
    Coordinates were fit to the maps first using ISOLDE28 followed by iterative refinement using Phenix29 real space refinement and subsequent manual coordinate fitting in Coot as needed.
    Coot
    suggested: (Coot, RRID:SCR_014222)
    Structure and map analysis were performed using PyMol, Chimera26 and ChimeraX30.
    PyMol
    suggested: (PyMOL, RRID:SCR_000305)
    Sensorgram data were analyzed using the BiaEvaluation software (GE Healthcare).
    BiaEvaluation
    suggested: (BIAevaluation Software, RRID:SCR_015936)

    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 10.1101/2020.06.26.173765v2 on bioRxiv
  3. Version published to 10.1101/2020.06.26.173765v1 on bioRxiv