Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane | Zendy

Hyeonuk Woo | Zendy; SangJun Park | Zendy; Yeol Kyo Choi | Zendy; Taeyong Park | Zendy; Maham Tanveer | Zendy; Yiwei Cao | Zendy; Nathan R. Kern | Zendy; Jumin Lee | Zendy; Min Sun Yeom | Zendy; Tristan I. Croll | Zendy; Chaok Seok | Zendy; Wonpil Im | Zendy

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Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

Author(s) -

Hyeonuk Woo,

SangJun Park,

Yeol Kyo Choi,

Taeyong Park,

Maham Tanveer,

Yiwei Cao,

Nathan R. Kern,

Jumin Lee,

Min Sun Yeom,

Tristan I. Croll,

Chaok Seok,

Wonpil Im

Publication year - 2020

Publication title -

the journal of physical chemistry b

Language(s) - Uncategorized

Resource type - Journals

SCImago Journal Rank - 0.864

H-Index - 392

eISSN - 1520-6106

pISSN - 1520-5207

DOI - 10.1021/acs.jpcb.0c04553

Subject(s) - glycan , protein data bank (rcsb pdb) , protein structure prediction , viral membrane , loop modeling , computer science , molecular dynamics , computational biology , protein structure , membrane protein , viral protein , suite , bioinformatics , chemistry , glycoprotein , membrane , biology , virology , biochemistry , virus , computational chemistry , history , archaeology , viral envelope

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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