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bioRxiv · 10.1101/2020.07.03.186825

Map of SARS-CoV-2 spike epitopes not shielded by glycans.

Sikora, M.·von Bülow, S.·Blanc, F. E. C.·Gecht, M.·Covino, R.·Hummer, G.
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Abstract

The severity of the COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, calls for the urgent development of a vaccine. The primary immunological target is the SARS-CoV-2 spike (S) protein. S is exposed on the viral surface to mediate viral entry into the host cell. To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for vaccine development. We find that the extensive and inherently flexible glycan coat shields a surface area larger than expected from static structures, highlighting the importance of structural dynamics in epitope mapping.Competing Interest StatementThe authors have declared no competing interest.View Full Text

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Sikora, M., von Bülow, S., Blanc, F. E. C., Gecht, M., Covino, R., Hummer, G.. 2020-07-03. Map of SARS-CoV-2 spike epitopes not shielded by glycans.. https://doi.org/10.1101/2020.07.03.186825

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