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

This technical study describes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB:6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure predict...

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Bibliographic Details
Published in:bioRxiv 2020-06
Main Authors: Woo, Hyeonuk, Sang-Jun, Park, Choi, Yeol Kyo, Park, Taeyong, Maham Tanveer, Cao, Yiwei, Kern, Nathan R, Lee, Jumin, Min Sun Yeom, Croll, Tristan I, Chaok Seok, Im, Wonpil
Format: Article
Language:English
Subjects:
Archives & records
Biophysics
Coronaviruses
COVID-19
Membrane proteins
N-glycans
Polysaccharides
Protein structure
Proteins
Severe acute respiratory syndrome coronavirus 2
Spike protein
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Summary:This technical study describes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB:6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY modeling 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. Competing Interest Statement The authors have declared no competing interest. Footnotes * http://www.charmm-gui.org/docs/archive/covid19 * http://www.charmm-gui.org/demo/cov_2_s/1
ISSN:2692-8205
DOI:10.1101/2020.05.20.103325