Nature Communications (May 2024)
SARS-CoV-2 Mpro responds to oxidation by forming disulfide and NOS/SONOS bonds
- Patrick Y. A. Reinke,
- Robin Schubert,
- Dominik Oberthür,
- Marina Galchenkova,
- Aida Rahmani Mashhour,
- Sebastian Günther,
- Anaïs Chretien,
- Adam Round,
- Brandon Charles Seychell,
- Brenna Norton-Baker,
- Chan Kim,
- Christina Schmidt,
- Faisal H. M. Koua,
- Alexandra Tolstikova,
- Wiebke Ewert,
- Gisel Esperanza Peña Murillo,
- Grant Mills,
- Henry Kirkwood,
- Hévila Brognaro,
- Huijong Han,
- Jayanath Koliyadu,
- Joachim Schulz,
- Johan Bielecki,
- Julia Lieske,
- Julia Maracke,
- Juraj Knoska,
- Kristina Lorenzen,
- Lea Brings,
- Marcin Sikorski,
- Marco Kloos,
- Mohammad Vakili,
- Patrik Vagovic,
- Philipp Middendorf,
- Raphael de Wijn,
- Richard Bean,
- Romain Letrun,
- Seonghyun Han,
- Sven Falke,
- Tian Geng,
- Tokushi Sato,
- Vasundara Srinivasan,
- Yoonhee Kim,
- Oleksandr M. Yefanov,
- Luca Gelisio,
- Tobias Beck,
- Andrew S. Doré,
- Adrian P. Mancuso,
- Christian Betzel,
- Saša Bajt,
- Lars Redecke,
- Henry N. Chapman,
- Alke Meents,
- Dušan Turk,
- Winfried Hinrichs,
- Thomas J. Lane
Affiliations
- Patrick Y. A. Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Robin Schubert
- European XFEL GmbH
- Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Aida Rahmani Mashhour
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Anaïs Chretien
- European XFEL GmbH
- Adam Round
- European XFEL GmbH
- Brandon Charles Seychell
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg
- Brenna Norton-Baker
- Max Plank Institute for the Structure and Dynamics of Matter
- Chan Kim
- European XFEL GmbH
- Christina Schmidt
- European XFEL GmbH
- Faisal H. M. Koua
- European XFEL GmbH
- Alexandra Tolstikova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Wiebke Ewert
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Gisel Esperanza Peña Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Grant Mills
- European XFEL GmbH
- Henry Kirkwood
- European XFEL GmbH
- Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg
- Huijong Han
- European XFEL GmbH
- Jayanath Koliyadu
- European XFEL GmbH
- Joachim Schulz
- European XFEL GmbH
- Johan Bielecki
- European XFEL GmbH
- Julia Lieske
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Julia Maracke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Juraj Knoska
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Kristina Lorenzen
- European XFEL GmbH
- Lea Brings
- European XFEL GmbH
- Marcin Sikorski
- European XFEL GmbH
- Marco Kloos
- European XFEL GmbH
- Mohammad Vakili
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Patrik Vagovic
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Philipp Middendorf
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Raphael de Wijn
- European XFEL GmbH
- Richard Bean
- European XFEL GmbH
- Romain Letrun
- European XFEL GmbH
- Seonghyun Han
- European XFEL GmbH
- Sven Falke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Tian Geng
- Sosei Heptares
- Tokushi Sato
- European XFEL GmbH
- Vasundara Srinivasan
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg
- Yoonhee Kim
- European XFEL GmbH
- Oleksandr M. Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Luca Gelisio
- European XFEL GmbH
- Tobias Beck
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg
- Andrew S. Doré
- Sosei Heptares
- Adrian P. Mancuso
- European XFEL GmbH
- Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg
- Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Lars Redecke
- Institute of Biochemistry, Universität zu Lübeck
- Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- Dušan Turk
- Jožef Stefan Institute, Jamova cesta 39
- Winfried Hinrichs
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4
- Thomas J. Lane
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY
- DOI
- https://doi.org/10.1038/s41467-024-48109-3
- Journal volume & issue
-
Vol. 15,
no. 1
pp. 1 – 10
Abstract
Abstract The main protease (Mpro) of SARS-CoV-2 is critical for viral function and a key drug target. Mpro is only active when reduced; turnover ceases upon oxidation but is restored by re-reduction. This suggests the system has evolved to survive periods in an oxidative environment, but the mechanism of this protection has not been confirmed. Here, we report a crystal structure of oxidized Mpro showing a disulfide bond between the active site cysteine, C145, and a distal cysteine, C117. Previous work proposed this disulfide provides the mechanism of protection from irreversible oxidation. Mpro forms an obligate homodimer, and the C117-C145 structure shows disruption of interactions bridging the dimer interface, implying a correlation between oxidation and dimerization. We confirm dimer stability is weakened in solution upon oxidation. Finally, we observe the protein’s crystallization behavior is linked to its redox state. Oxidized Mpro spontaneously forms a distinct, more loosely packed lattice. Seeding with crystals of this lattice yields a structure with an oxidation pattern incorporating one cysteine-lysine-cysteine (SONOS) and two lysine-cysteine (NOS) bridges. These structures further our understanding of the oxidative regulation of Mpro and the crystallization conditions necessary to study this structurally.
