ORCID Profile
0000-0001-5642-6041
Current Organisation
Lehigh University
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Publisher: American Chemical Society (ACS)
Date: 10-03-2021
Publisher: Cold Spring Harbor Laboratory
Date: 21-05-2020
DOI: 10.1101/2020.05.20.103325
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 ( ocs/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.
Publisher: Cold Spring Harbor Laboratory
Date: 18-10-2020
DOI: 10.1101/2020.10.18.343715
Abstract: The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates host cell entry by binding to angiotensin-converting enzyme 2 (ACE2), and is considered the major target for drug and vaccine development. We previously built fully-glycosylated full-length SARS-CoV-2 S protein models in a viral membrane including both open and closed conformations of receptor binding domain (RBD) and different templates for the stalk region. In this work, multiple μs-long all-atom molecular dynamics simulations were performed to provide deeper insight into the structure and dynamics of S protein, and glycan functions. Our simulations reveal that the highly flexible stalk is composed of two independent joints and most probable S protein orientations are competent for ACE2 binding. We identify multiple glycans stabilizing the open and/or closed states of RBD, and demonstrate that the exposure of antibody epitopes can be captured by detailed antibody-glycan clash analysis instead of a commonly-used accessible surface area analysis that tends to overestimate the impact of glycan shielding and neglect possible detailed interactions between glycan and antibody. Overall, our observations offer structural and dynamic insight into SARS-CoV-2 S protein and potentialize for guiding the design of effective antiviral therapeutics.
Publisher: American Chemical Society (ACS)
Date: 08-10-2020
Publisher: Springer Science and Business Media LLC
Date: 28-04-2022
Publisher: American Chemical Society (ACS)
Date: 19-06-2020
No related grants have been discovered for Wonpil Im.