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Analysis of the SARS-CoV-2 spike protein glycan shield: implications for immune recognition

View ORCID ProfileOliver C. Grant, View ORCID ProfileDavid Montgomery, Keigo Ito, View ORCID ProfileRobert J. Woods
doi: https://doi.org/10.1101/2020.04.07.030445
Oliver C. Grant
Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
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David Montgomery
Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
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Keigo Ito
Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
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Robert J. Woods
Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
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  • For correspondence: rwoods@ccrc.uga.edu
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Abstract

Here we have generated 3D structures of glycoforms of the spike (S) glycoprotein from SARS-CoV-2, based on reported 3D structures and glycomics data for the protein produced in HEK293 cells. We also analyze structures for glycoforms representing those present in the nascent glycoproteins (prior to enzymatic modifications in the Golgi), as well as those that are commonly observed on antigens present in other viruses.

These models were subjected to molecular dynamics (MD) simulation to determine the extent to which glycan microheterogeneity impacts the antigenicity of the S glycoprotein. Lastly, we have identified peptides in the S glycoprotein that are likely to be presented in human leukocyte antigen (HLA) complexes, and discuss the role of S protein glycosylation in potentially modulating the adaptive immune response to the SARS-CoV-2 virus or to a related vaccine.

The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the exception of the ACE2 receptor binding domain, and also that the degree of shielding is largely insensitive to the specific glycoform. Despite the relatively modest contribution of the glycans to the total molecular weight (17% for the HEK293 glycoform) the level of surface shielding is disproportionately high at 42%.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • http://glycam.org/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 01, 2020.
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Analysis of the SARS-CoV-2 spike protein glycan shield: implications for immune recognition
Oliver C. Grant, David Montgomery, Keigo Ito, Robert J. Woods
bioRxiv 2020.04.07.030445; doi: https://doi.org/10.1101/2020.04.07.030445
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Analysis of the SARS-CoV-2 spike protein glycan shield: implications for immune recognition
Oliver C. Grant, David Montgomery, Keigo Ito, Robert J. Woods
bioRxiv 2020.04.07.030445; doi: https://doi.org/10.1101/2020.04.07.030445

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