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bioRxiv · 10.1101/2021.05.03.437411

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro)

Ebrahim, A.·Riley, B. T.·Kumaran, D.·Andi, B.·Fuchs, M. R.·McSweeney, S.·Keedy, D. A.
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Abstract

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or Mpro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of Mpro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded Mpro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for Mpro, including mobile solvent interleaved between the catalytic dyad, mercurial conformational heterogeneity in a key substrate-binding loop, and a far-reaching intramolecular network bridging the active site and dimer interface. Our results may inspire new strategies for antiviral drug development to counter-punch COVID-19 and combat future coronavirus pandemics. SynopsisX-ray crystallography at variable temperature for SARS-CoV-2 Mpro reveals a complex conformational landscape, including mobile solvent at the catalytic dyad, mercurial conformational heterogeneity in a key substrate-binding loop, and an intramolecular network bridging the active site and dimer interface.

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Ebrahim, A., Riley, B. T., Kumaran, D., Andi, B., Fuchs, M. R., McSweeney, S., Keedy, D. A.. 2021-05-03. The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro). https://doi.org/10.1101/2021.05.03.437411

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