Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane
| Autor: | Sang-Jun Park, Tristan I. Croll, Wonpil Im, Chaok Seok, Yeol Kyo Choi, Maham Tanveer, Hyeonuk Woo, Yiwei Cao, Min Sun Yeom, Jumin Lee, Taeyong Park, Nathan R. Kern |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Glycan
010304 chemical physics biology Computer science Protein Data Bank (RCSB PDB) Computational biology Viral membrane Protein structure prediction 010402 general chemistry 01 natural sciences Article 0104 chemical sciences Surfaces Coatings and Films Modeling and simulation Protein structure 0103 physical sciences biology.protein Materials Chemistry Spike (software development) Loop modeling Physical and Theoretical Chemistry |
| Zdroj: | The Journal of Physical Chemistry. B The Journal of Physical Chemistry B |
| ISSN: | 1520-5207 1520-6106 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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