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SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome
SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression, and replication, which depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address t...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8249329/ https://www.ncbi.nlm.nih.gov/pubmed/34031561 http://dx.doi.org/10.1038/s41557-021-00707-0 |
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author | Zimmerman, Maxwell I. Porter, Justin R. Ward, Michael D. Singh, Sukrit Vithani, Neha Meller, Artur Mallimadugula, Upasana L. Kuhn, Catherine E. Borowsky, Jonathan H. Wiewiora, Rafal P. Hurley, Matthew F. D. Harbison, Aoife M Fogarty, Carl A Coffland, Joseph E. Fadda, Elisa Voelz, Vincent A. Chodera, John D. Bowman, Gregory R. |
author_facet | Zimmerman, Maxwell I. Porter, Justin R. Ward, Michael D. Singh, Sukrit Vithani, Neha Meller, Artur Mallimadugula, Upasana L. Kuhn, Catherine E. Borowsky, Jonathan H. Wiewiora, Rafal P. Hurley, Matthew F. D. Harbison, Aoife M Fogarty, Carl A Coffland, Joseph E. Fadda, Elisa Voelz, Vincent A. Chodera, John D. Bowman, Gregory R. |
author_sort | Zimmerman, Maxwell I. |
collection | PubMed |
description | SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression, and replication, which depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate an unprecedented 0.1 seconds of the viral proteome. Our simulations capture dramatic opening of the apo Spike complex, far beyond that seen experimentally, which explains and successfully predicts the existence of ‘cryptic’ epitopes. Different Spike homologues modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also observe dramatic conformational changes across the proteome, which reveal over 50 ‘cryptic’ pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas. |
format | Online Article Text |
id | pubmed-8249329 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
record_format | MEDLINE/PubMed |
spelling | pubmed-82493292021-07-02 SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome Zimmerman, Maxwell I. Porter, Justin R. Ward, Michael D. Singh, Sukrit Vithani, Neha Meller, Artur Mallimadugula, Upasana L. Kuhn, Catherine E. Borowsky, Jonathan H. Wiewiora, Rafal P. Hurley, Matthew F. D. Harbison, Aoife M Fogarty, Carl A Coffland, Joseph E. Fadda, Elisa Voelz, Vincent A. Chodera, John D. Bowman, Gregory R. Nat Chem Article SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression, and replication, which depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate an unprecedented 0.1 seconds of the viral proteome. Our simulations capture dramatic opening of the apo Spike complex, far beyond that seen experimentally, which explains and successfully predicts the existence of ‘cryptic’ epitopes. Different Spike homologues modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also observe dramatic conformational changes across the proteome, which reveal over 50 ‘cryptic’ pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas. 2021-05-24 2021-07 /pmc/articles/PMC8249329/ /pubmed/34031561 http://dx.doi.org/10.1038/s41557-021-00707-0 Text en https://creativecommons.org/licenses/by/4.0/It is made available under a CC-BY 4.0 International license (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Zimmerman, Maxwell I. Porter, Justin R. Ward, Michael D. Singh, Sukrit Vithani, Neha Meller, Artur Mallimadugula, Upasana L. Kuhn, Catherine E. Borowsky, Jonathan H. Wiewiora, Rafal P. Hurley, Matthew F. D. Harbison, Aoife M Fogarty, Carl A Coffland, Joseph E. Fadda, Elisa Voelz, Vincent A. Chodera, John D. Bowman, Gregory R. SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome |
title | SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome |
title_full | SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome |
title_fullStr | SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome |
title_full_unstemmed | SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome |
title_short | SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome |
title_sort | sars-cov-2 simulations go exascale to capture spike opening and reveal cryptic pockets across the proteome |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8249329/ https://www.ncbi.nlm.nih.gov/pubmed/34031561 http://dx.doi.org/10.1038/s41557-021-00707-0 |
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