PT  - JOURNAL ARTICLE
AU  - Mateusz Sikora
AU  - Sören von Bülow
AU  - Florian E. C. Blanc
AU  - Michael Gecht
AU  - Roberto Covino
AU  - Gerhard Hummer
TI  - Map of SARS-CoV-2 spike epitopes not shielded by glycans
AID  - 10.1101/2020.07.03.186825
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.07.03.186825
4099  - http://biorxiv.org/content/early/2020/07/03/2020.07.03.186825.short
4100  - http://biorxiv.org/content/early/2020/07/03/2020.07.03.186825.full
AB  - 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.