Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane

BioRxiv : the Preprint Server for Biology
H. WooWonpil Im

Abstract

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.

Methods Mentioned

BETA
glycosylation
X-ray

Software Mentioned

PDB Reader & Manipulator
Glycan Reader & Modeler
GROMACS
Glycan Reader Modeler
CHARMM
GalaxyRefineComplex
DE Research
GUI
ISOLDE
GUI PDB Reader

Related Concepts

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Related Papers

BioRxiv : the Preprint Server for Biology
Douglas W BjellandMatthew C Keller
European Journal of Human Genetics : EJHG
Douglas W BjellandMatthew C Keller
American Journal of Human Genetics
Brian L Browning, Sharon R Browning
© 2021 Meta ULC. All rights reserved