National University Corporation Okayama University Elucidation of the high-resolution structure of the protein actin and the mechanism of ATP hydrolysis -Progress in understanding one of the most important chemical reactions of life on earth-

National University Corporation Okayama University
Elucidation of the high-resolution structure of the protein actin and the mechanism of ATP hydrolysis -Progress in understanding one of the most important chemical reactions of life on Earth-

Tokai National University Organization, Nagoya University, Hiroshima University, Okayama University, Hiroshima City University, Tokai Gakuin University, Yokohama City University, Nagaoka University of Technology, Kyushu Institute of Technology, Tokyo University of Pharmaceutical Sciences, Toyota Physical and Chemical Research Institute, Aichi Synchrotron Light Center Joint research results! October 23, 2022
National University Corporation Okayama University
https://www.okayama-u.ac.jp/
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-Points of announcement-
Elucidated the high-resolution structure of the F-type protein actin. Based on these structures, the mechanism of the ATP hydrolysis reaction was elucidated using quantum chemical calculation methods. We have greatly advanced our understanding of the common mechanism of ATP hydrolysis, one of the most important chemical reactions for sustaining life on Earth.
◆Overview
Yuichiro Maeda Specially Appointed Professor, Graduate School of Science, Nagoya University, Tokai National University Organization A research team led by Assistant Professor Yusuke Kanematsu and Specially Appointed Assistant Professor Shuichi Takeda of the Research Institute for Interdisciplinary Science, Okayama University obtained the crystal structure of the protein F-type actin at 1.15 A
resolution, and based on this, quantum chemistry. Using the QM/MM calculation method, we have clarified the mechanism of the ATP hydrolysis reaction.
ATP is the energy currency of life on Earth. The chemical energy of ATP is converted into mechanical work and information by many proteins called ATPase proteins, and is used to express various cellular functions. was not
In this study, we obtained the structure of F-type actin at a resolution of 1.15 A, both in the initial state and the final state of the reaction, at a resolution of 1.15 A, which is higher than that obtained for any other ATPase protein. solved. The elucidated ATP hydrolysis reaction mechanism is basically consistent with the reaction model proposed so far, and strongly suggests that the ATPase proteins on Earth work by a common mechanism.
Only the first half of the entire ATPase process (hydrolysis reaction process) has been elucidated this time, and the latter half (Pi dissociation process) has not been elucidated. It is expected that research on the Pi dissociation process will advance in the future. The results of this research were published on October 18, 2022 in the online version of the American scientific journal “Proceedings of the National Academy of Sciences (PNAS)”.
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Figure 1. Part of the high-resolution crystal structure (1.15 A resolution) of F-type actin. (a) AMPPNP (structural analogue of ATP), (b) ADP-Pi, (c) ADP molecules and surrounding Mg2+ (green spheres), oxygen atoms of water molecules (red spheres), both bound within actin proteins. ). The cage-shaped display is the electron density distribution, and the dotted line is the coordination bond around Mg2+. The bars and spheres are structural models based on electron density distribution.
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Figure 2. Potential energy profile along the reaction pathway of ATP hydrolysis of F-type actin. The initial state of the reaction (R: ATP bound state), the intermediate state (IM), the transition state (TS), and the final state of the reaction (P: ADP-Pi bound state). The calculation results starting from the initial state structure to the final state are shown in orange, and the calculation results starting from the final state structure to the initial state are shown in blue. The fact that the two energy profiles do not dissociate significantly, and that the structures of the initial and final states obtained by calculation closely approximate the structures obtained by
experiments, are consistent with the elucidated reaction pathway. indicates that there is The entire reaction process can be divided into four steps (marked in red).
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Figure 3. ATPase protein hydrolyzes ATP bound within the protein molecule through the ATPase process (first half process), and further releases degradation products (Pi and ADP) (second half process). Structures of Mg-ATP, Mg-ADP-Pi, Mg-ADP: carbon (pink), nitrogen (blue), phosphorus (vermillion), oxygen (red) atoms and Mg2+ (green) [Image 5

Figure 4. a. Shape of actin polymer. The flattened knot-shaped molecules are individual actin molecules. b. The shape of the actin molecule is G-type in the monomer and F-type in the polymer. [Image 6

Fig. 5. Relationship between the entire actin ATPase process and shape changes of G-type and F-type. -G and -F are G-type actins,
respectively. F-type actin is shown. Both the hydrolysis process and the Pi release process proceed only in the F form.
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Figure 6. Structure of the F1A complex. The structure obtained from the X-ray diffraction intensity of crystals of a 1:1 complex of F1 protein (fragmin domain 1) and actin. The sky blue surface is actin, and the brown ribbon is the F1 protein.
◆ Paper information
 Magazine name: Proceedings of the National Academy of Sciences of the USA (Proceedings of the National Academy of Sciences)
 Paper title: “Structures and Mechanisms of the actin ATP hydrolysis” Author: Yuichiro Maeda, Visiting Professor, Graduate School of Informatics, Nagoya University
Yusuke Kanematsu, Assistant Professor, Graduate School of Advanced Science and Engineering, Hiroshima University
Shuichi Takeda, Research Institute for Interdisciplinary Science, Okayama University, Specially Appointed Assistant Professor
Akihiro Narita Associate Professor, Department of Life Science, Graduate School of Science, Nagoya University
Toshiro Oda, Tokai Gakuin University, Faculty of Health and Welfare, Department of Comprehensive Welfare, Professor
Ryotaro Koike Assistant Professor, Department of Complex Systems Science, Graduate School of Informatics, Nagoya University
Motonori Ota, Professor, Department of Complex Systems Science, Graduate School of Informatics, Nagoya University
     Professor, Department of Medical Information Science, Graduate School of Information Science, Hiroshima City University, Yu Takano Kei Moritsugu Yokohama City University, Graduate School of Life and Medical Sciences, Specially Appointed Associate Professor
Ikuko FujiwaraNagaoka University of Technology, Institute of Technology, Department of Materials Biology, Associate Professor Kotaro Tanaka, Assistant Professor, Department of Structural Physiology, Graduate School of Cellular Physiology, Nagoya University Hideyuki Komatsu Kyushu Institute of Technology, Graduate School of Information Engineering, Department of Biochemical and Information Engineering, Associate Professor
Takayuki Nagae, Tokyo University of Pharmacy and Life Sciences, Faculty of Pharmaceutical Sciences, Department of Medical Hygiene and Pharmaceutical Sciences, Assistant Professor
The late Nobuhisa Watanabe, Professor, Synchrotron Light Research Center, Nagoya University (died March 26, 2019)
Mitsusada Iwasa Nagoya University Graduate School of Informatics Department of Complex Systems Science Collaborative Researcher  DOI: 10.1073/pnas.2122641119
URL: https://www.pnas.org/doi/10.1073/pnas.2122641119
◆ Research funds
This research was supported by the Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research (KAKENHI), Japan Agency for Medical Research and Development (AMED), Toyota Physical and Chemical Research Institute, Takeda Science Foundation, Daiko Foundation, and Actin Research Group. It’s been done.
◆ Detailed research content
Elucidation of the high-resolution structure of the protein actin and the mechanism of the ATP hydrolysis reaction-advanced understanding of one of the most important chemical reactions of life on earth-  https://www.okayama-u.ac.jp/up_load_files/press_r4/press20221020-1.pdf [Image 8

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◆ Inquiries regarding this matter
-Researcher contact information-
Yuichiro Maeda, Visiting Professor, Graduate School of Informatics, Nagoya University, Tokai National University Organization
 TEL: 090-1912-2973, 052-789-2585
 FAX: 052-747-6473
Yusuke Kanematsu, Assistant Professor, Graduate School of Advanced Science and Engineering, Hiroshima University
 TEL/FAX: 082-424-7726
Specially Appointed Assistant Professor, Research Institute for Interdisciplinary Science, Okayama University Shuichi Takeda  TEL/FAX: 086-251-7820
-Press contact-
 Tokai National University Organization Nagoya University Public Relations Office
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 Hiroshima University Public Relations Office
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-Inquiries regarding Okayama University’s industry-academia-government collaboration-
 Okayama University Organization for Research Promotion Headquarters for Industry-Academia-Government Collaboration
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