SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

• Published in: bioRxiv 2020-10
• Main Authors: 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
• Format: Article
• Language: English
• Subjects: Antiviral agents; Biophysics; Coronaviruses; COVID-19; Immune response; Pandemics; Proteomes; Severe acute respiratory syndrome coronavirus 2
• ISSN: 2692-8205; 2692-8205
• DOI: 10.1101/2020.06.27.175430

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.