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 predic...

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Published inThe journal of physical chemistry. B Vol. 124; no. 33; pp. 7128 - 7137
Main Authors Woo, Hyeonuk, Park, Sang-Jun, Choi, Yeol Kyo, Park, Taeyong, Tanveer, Maham, Cao, Yiwei, Kern, Nathan R, Lee, Jumin, Yeom, Min Sun, Croll, Tristan I, Seok, Chaok, Im, Wonpil
Format Journal Article
LanguageEnglish
Published United States American Chemical Society 20.08.2020
Subjects
B: Biophysics; Physical Chemistry of Biological Systems and Biomolecules
Betacoronavirus - chemistry
Betacoronavirus - genetics
Betacoronavirus - metabolism
Crystallography, X-Ray
Glycosylation
Humans
Models, Molecular
molecular dynamics
Molecular Dynamics Simulation
Polysaccharides - chemistry
prediction
protein structure
Protein Structure, Secondary
SARS-CoV-2
Severe acute respiratory syndrome coronavirus 2
Spike Glycoprotein, Coronavirus - chemistry
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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 that researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of COVID-19.
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ISSN:1520-6106
1520-5207
1520-5207
DOI:10.1021/acs.jpcb.0c04553