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

View ORCID ProfileAli Ebrahim, View ORCID ProfileBlake T. Riley, Desigan Kumaran, View ORCID ProfileBabak Andi, View ORCID ProfileMartin R. Fuchs, View ORCID ProfileSean McSweeney, View ORCID ProfileDaniel A. Keedy
doi: https://doi.org/10.1101/2021.05.03.437411
Ali Ebrahim
1Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
2Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
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Blake T. Riley
2Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
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Desigan Kumaran
3Biology Department, Brookhaven National Laboratory, Upton, NY 11973
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Babak Andi
4National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973
5National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, United States
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Martin R. Fuchs
4National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973
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Sean McSweeney
4National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973
5National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, United States
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Daniel A. Keedy
2Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
6Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
7Ph.D. Programs in Biochemistry, Biology, and Chemistry, The Graduate Center – City University of New York, New York, NY 10016
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  • For correspondence: dkeedy@gc.cuny.edu
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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.

Synopsis X-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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Clarification of H2Oint interpretation; supplemental files updated.

  • Glossary

    Fo-Fo
    isomorphous difference electron density map
    COVID-19
    coronavirus disease 2019
    SARS-CoV-2
    severe acute respiratory syndrome coronavirus 2
    Mpro
    SARS coronavirus main protease
  • 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 4.0 International license.
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    Posted November 07, 2021.
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    The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro)
    Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean McSweeney, Daniel A. Keedy
    bioRxiv 2021.05.03.437411; doi: https://doi.org/10.1101/2021.05.03.437411
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    The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro)
    Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean McSweeney, Daniel A. Keedy
    bioRxiv 2021.05.03.437411; doi: https://doi.org/10.1101/2021.05.03.437411

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