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Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography

View ORCID ProfileAlexander M. Wolff, Eriko Nango, Iris D. Young, Aaron S. Brewster, Minoru Kubo, Takashi Nomura, Michihiro Sugahara, Shigeki Owada, Benjamin A. Barad, Kazutaka Ito, Asmit Bhowmick, Sergio Carbajo, Tomoya Hino, James M. Holton, Dohyun Im, Lee J. O’Riordan, Tomoyuki Tanaka, Rie Tanaka, Raymond G. Sierra, Fumiaki Yumoto, Kensuke Tono, So Iwata, Nicholas K. Sauter, View ORCID ProfileJames S. Fraser, View ORCID ProfileMichael C. Thompson
doi: https://doi.org/10.1101/2022.06.10.495662
Alexander M. Wolff
1Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
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Eriko Nango
2RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
3Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
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  • For correspondence: eriko.nango.c4@tohoku.ac.jp mthompson30@ucmerced.edu
Iris D. Young
4Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
5Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Aaron S. Brewster
5Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Minoru Kubo
2RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
6Department of Life Science, Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
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Takashi Nomura
2RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
6Department of Life Science, Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
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Michihiro Sugahara
2RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
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Shigeki Owada
2RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
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Benjamin A. Barad
4Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
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Kazutaka Ito
7Laboratory for Drug Discovery, Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni-shi, Shizuoka 410-2321, Japan
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Asmit Bhowmick
5Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Sergio Carbajo
8Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
9Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA, USA
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Tomoya Hino
10Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101, Koyama-cho Minami, Tottori 680-8552, Japan
11Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
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James M. Holton
5Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
12Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
13SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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Dohyun Im
14Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Lee J. O’Riordan
5Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Tomoyuki Tanaka
2RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
14Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Rie Tanaka
2RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
14Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Raymond G. Sierra
8Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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Fumiaki Yumoto
16Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan
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Kensuke Tono
2RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
15Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
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So Iwata
2RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
14Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Nicholas K. Sauter
5Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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James S. Fraser
4Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
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Michael C. Thompson
1Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
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  • ORCID record for Michael C. Thompson
  • For correspondence: eriko.nango.c4@tohoku.ac.jp mthompson30@ucmerced.edu
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Abstract

Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to trigger conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the sub-millisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature-jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

Competing Interest Statement

The authors have declared no competing interest.

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 June 12, 2022.
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Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography
Alexander M. Wolff, Eriko Nango, Iris D. Young, Aaron S. Brewster, Minoru Kubo, Takashi Nomura, Michihiro Sugahara, Shigeki Owada, Benjamin A. Barad, Kazutaka Ito, Asmit Bhowmick, Sergio Carbajo, Tomoya Hino, James M. Holton, Dohyun Im, Lee J. O’Riordan, Tomoyuki Tanaka, Rie Tanaka, Raymond G. Sierra, Fumiaki Yumoto, Kensuke Tono, So Iwata, Nicholas K. Sauter, James S. Fraser, Michael C. Thompson
bioRxiv 2022.06.10.495662; doi: https://doi.org/10.1101/2022.06.10.495662
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Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography
Alexander M. Wolff, Eriko Nango, Iris D. Young, Aaron S. Brewster, Minoru Kubo, Takashi Nomura, Michihiro Sugahara, Shigeki Owada, Benjamin A. Barad, Kazutaka Ito, Asmit Bhowmick, Sergio Carbajo, Tomoya Hino, James M. Holton, Dohyun Im, Lee J. O’Riordan, Tomoyuki Tanaka, Rie Tanaka, Raymond G. Sierra, Fumiaki Yumoto, Kensuke Tono, So Iwata, Nicholas K. Sauter, James S. Fraser, Michael C. Thompson
bioRxiv 2022.06.10.495662; doi: https://doi.org/10.1101/2022.06.10.495662

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