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Molecular Dynamics Simulations of F1-ATPase

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Protein Conformational Dynamics

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 805))

Abstract

F1-ATPase is a rotary motor enzyme. Despite many theoretical and experimental studies, the molecular mechanism of the motor rotation is still not fully understood. However, plenty of available data provide a clue as to how this molecular motor rotates: with nucleotide perturbations, the catalytically active β subunit propagates its structural changes to the entire α3β3 complex via both sides of the subunits, resulting that asymmetry is created in the α3β3 hexamer ring. In the sequential reaction step, the structure of the asymmetrical α3β3 complex changes from one state to the other due to the nucleotide perturbations, and the γ subunit axis follows the sequentially changing α3β3 structure. Therefore, there are mainly two essential elements for motor rotation: the conformational change of the β subunit and the asymmetrical structure of the α3β3 subunit complex. Therefore, this chapter reports a series of studies focused on these two elements via combinational approaches of molecular dynamics (MD) simulations and experimental or other theoretical studies. In addition to the motor rotation factors, the combined study also revealed other important elements of F1-ATPase, such as torque transmission and the chemical reaction pathway, which is described in the later part of this chapter. All of these results provide insight into the rotational mechanism and deepen the understanding of this molecular motor.

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Acknowledgments

The authors are grateful to all of our collaborators for their cooperation and helpful discussions. This work was supported by the following: a Grant-in-Aid for the Japan Society for the Promotion of Science (JSPS) fellows; Grants-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT); Grants-in-Aid for Scientific Research (B); the Grand Challenges in Next-Generation Integrated Simulation of Living Matter, a part of the Development and Use of the Next-Generation Supercomputer Project of MEXT; the Platform for Drug Design, Informatics and Structural Life Sciences (MEXT); and the X-ray Free Electron Laser Priority Strategy Program (MEXT).

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  1. Department of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan

    Yuko Ito & Mitsunori Ikeguchi

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  1. Yuko Ito
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  2. Mitsunori Ikeguchi
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Correspondence to Yuko Ito or Mitsunori Ikeguchi .

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  1. Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, People's Republic of China

    Ke-li Han

  2. The Scripps Research Institute, La Jolla, California, USA

    Xin Zhang

  3. Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, People's Republic of China

    Ming-jun Yang

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Ito, Y., Ikeguchi, M. (2014). Molecular Dynamics Simulations of F1-ATPase. In: Han, Kl., Zhang, X., Yang, Mj. (eds) Protein Conformational Dynamics. Advances in Experimental Medicine and Biology, vol 805. Springer, Cham. https://doi.org/10.1007/978-3-319-02970-2_17

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