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

Hyeonuk Woo, Sang-Jun Park, View ORCID ProfileYeol Kyo Choi, Taeyong Park, Maham Tanveer, Yiwei Cao, Nathan R. Kern, View ORCID ProfileJumin Lee, View ORCID ProfileMin Sun Yeom, View ORCID ProfileTristan Croll, View ORCID ProfileChaok Seok, View ORCID ProfileWonpil Im
doi: https://doi.org/10.1101/2020.05.20.103325
Hyeonuk Woo
1Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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Sang-Jun Park
2Departments of Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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Yeol Kyo Choi
3Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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Taeyong Park
1Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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Maham Tanveer
3Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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Yiwei Cao
3Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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Nathan R. Kern
2Departments of Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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Jumin Lee
3Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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Min Sun Yeom
4Korean Institute of Science and Technology Information, Daejeon 34141, Republic of Korea
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  • ORCID record for Min Sun Yeom
Tristan Croll
5Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
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  • For correspondence: tic20@cam.ac.uk chaok@snu.ac.kr wonpil@lehigh.edu
Chaok Seok
1Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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  • For correspondence: tic20@cam.ac.uk chaok@snu.ac.kr wonpil@lehigh.edu
Wonpil Im
2Departments of Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
3Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
6School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
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  • For correspondence: tic20@cam.ac.uk chaok@snu.ac.kr wonpil@lehigh.edu
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ABSTRACT

This technical study describes all-atom modeling and simulation of a fully-glycosylated fulllength 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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • http://www.charmm-gui.org/docs/archive/covid19

  • http://www.charmm-gui.org/demo/cov_2_s/1

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted May 21, 2020.
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Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane
Hyeonuk Woo, Sang-Jun Park, Yeol Kyo Choi, Taeyong Park, Maham Tanveer, Yiwei Cao, Nathan R. Kern, Jumin Lee, Min Sun Yeom, Tristan Croll, Chaok Seok, Wonpil Im
bioRxiv 2020.05.20.103325; doi: https://doi.org/10.1101/2020.05.20.103325
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Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane
Hyeonuk Woo, Sang-Jun Park, Yeol Kyo Choi, Taeyong Park, Maham Tanveer, Yiwei Cao, Nathan R. Kern, Jumin Lee, Min Sun Yeom, Tristan Croll, Chaok Seok, Wonpil Im
bioRxiv 2020.05.20.103325; doi: https://doi.org/10.1101/2020.05.20.103325

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