Authors
Hyeonuk Woo, Sang-Jun 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 date
2020/6/19
Journal
The journal of physical chemistry B
Volume
124
Issue
33
Pages
7128-7137
Publisher
American Chemical Society
Description
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 …
Total citations
202020212022202320242082853514
Scholar articles
H Woo, SJ Park, YK Choi, T Park, M Tanveer, Y Cao… - The journal of physical chemistry B, 2020