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Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane

Accepted version
Peer-reviewed

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Authors

Woo, Hyeonuk 
Park, Sang-Jun 
Choi, Yeol Kyo 
Park, Taeyong 
Tanveer, Maham 

Abstract

This technical studydescribes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) proteinin a viral membrane. First, starting from PDB:6VSBand 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXYmodeling suite. Then, using the recently-determined most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. These fully-glycosylated full-length S protein model structures were assessed and further refined against the low-resolution data in their respective experimental maps using ISOLDE. We then used CHARMM-GUI Membrane Builder to place the S proteins in a viral membrane and performed all-atom molecular dynamics simulations. All structures are available in CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19), so researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of COVID-19.

Description

Keywords

Betacoronavirus, Crystallography, X-Ray, Glycosylation, Humans, Models, Molecular, Molecular Dynamics Simulation, Polysaccharides, Protein Structure, Secondary, SARS-CoV-2, Spike Glycoprotein, Coronavirus

Journal Title

The Journal of Physical Chemistry B

Conference Name

Journal ISSN

1520-6106
1520-5207

Volume Title

Publisher

American Chemical Society (ACS)

Rights

All rights reserved
Sponsorship
Wellcome Trust (082961/Z/07/A)
Wellcome Trust (209407/Z/17/Z)