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AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

https://doi.org/10.1177/10943420211006452

Casalino, Lorenzo; Dommer, Abigail C; Gaieb, Zied; Barros, Emilia P; Sztain, Terra; Ahn, Surl-Hee; Trifan, Anda; Brace, Alexander; Bogetti, Anthony T; Clyde, Austin; et al (September 2021, The International Journal of High Performance Computing Applications)

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike’s full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.
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The flexibility of ACE2 in the context of SARS-CoV-2 infection

https://doi.org/10.1016/j.bpj.2020.10.036

Barros, Emilia P.; Casalino, Lorenzo; Gaieb, Zied; Dommer, Abigail C.; Wang, Yuzhang; Fallon, Lucy; Raguette, Lauren; Belfon, Kellon; Simmerling, Carlos; Amaro, Rommie E. (March 2021, Biophysical Journal)
null (Ed.)
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A multiscale coarse-grained model of the SARS-CoV-2 virion

https://doi.org/10.1016/j.bpj.2020.10.048

Yu, Alvin; Pak, Alexander J.; He, Peng; Monje-Galvan, Viviana; Casalino, Lorenzo; Gaieb, Zied; Dommer, Abigail C.; Amaro, Rommie E.; Voth, Gregory A. (March 2021, Biophysical Journal)
null (Ed.)
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Biomolecular Simulations in the Time of COVID-19, and After

https://doi.org/10.1109/MCSE.2020.3024155

Amaro, Rommie E.; Mulholland, Adrian J. (November 2020, Computing in Science & Engineering)
null (Ed.)
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Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein

https://doi.org/10.1021/acscentsci.0c01056

Casalino, Lorenzo; Gaieb, Zied; Goldsmith, Jory A.; Hjorth, Christy K.; Dommer, Abigail C.; Harbison, Aoife M.; Fogarty, Carl A.; Barros, Emilia P.; Taylor, Bryn C.; McLellan, Jason S.; et al (October 2020, ACS Central Science)
null (Ed.)
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A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19

https://doi.org/10.1021/acs.jcim.0c00319

Amaro, Rommie E.; Mulholland, Adrian J. (June 2020, Journal of Chemical Information and Modeling)
null (Ed.)
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