Study on rotation mechanisms of F1 molecular motor using molecular simulations

2012 Fiscal Year Final Research Report

• Project/Area Number: 22300102
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: Yokohama City University
• Principal Investigator: IKEGUCHI Mitsunori 横浜市立大学, 大学院・生命ナノシステム科学研究科, 准教授 (60261955)
• Project Period (FY): 2010 – 2012
• Keywords: 分子モーター / F1-ATPase / 分子動力学 / 分子シミュレーション / 立体構造変化

Research Abstract

In this study, the rotation mechanism of the F1 molecular motor was investigated using molecular simulations. Conformational changes in the B subunit, an engine of the F1 molecular motor, were analyzed using equilibrium and free-energy MD simulations. Further, based on the results of MD simulations and statistical thermodynamics theory applied for the XBR complex, the packing exchange model, in which the exchange of inter-subunit packing induces the rotational motion of the molecular motor, was proposed.

Research Products

• [Journal Article] Molecular dynamics simulations of yeast F1-ATPase before and after 16-degree rotation of the γ Subunit (2012)
  • Author(s): Y. Ito, T. Yoshidome, N. Matubayasi, M. Kinoshita, M. Ikeguchi
  • Journal Title: J. Phys. Chem. B Volume: 117 Pages: 3298-3307
  • DOI: DOI:10.1021/jp312499u
  • Peer Reviewed
• [Journal Article] Molecular mechanism of ATP hydrolysis in F1-ATPase revealed by molecular simulations and single molecule observations (2012)
  • Author(s): S. Hayashi, H. Ueno, A.R. Shaikh, M. Umemura, M. Kamiya, Y. Ito, M. Ikeguchi, Y. Komoriya, R. Iino, H. Noji
  • Journal Title: J. Am. Chem. Soc Volume: 134 Pages: 8447-8454
  • DOI: DOI:10.1021/ja211027m
  • Peer Reviewed
• [Journal Article] Structural characteristics of yeast F1-ATPase before and after 16-degree rotation of the γ subunit: Theoretical analysis focused on the water-entropy effect (2012)
  • Author(s): T. Yoshidome, Y. Ito, N. Matubayasi, M. Ikeguchi, M. Kinoshita
  • Journal Title: J. Chem. Phys Pages: 8
  • DOI: DOI:10.1063/1.4734298
  • Peer Reviewed
• [Journal Article] Role of the DELSEED loop in torque transmission of F1-ATPase (2012)
  • Author(s): M. Tanigawara, K.V. Tabata, Y. Ito, J. Ito, R. Watanabe, H. Ueno, M. Ikeguchi, H. Noji
  • Journal Title: Biophys. J. Volume: 103 Pages: 970-978
  • DOI: DOI:10.1016/j.bpj.2012.06.054
  • Peer Reviewed
• [Journal Article] Mechanism of the conformational change of the F1-ATPase β subunit revealed by free-energy simulations (2011)
  • Author(s): Y. Ito, T. Oroguchi, M. Ikeguchi
  • Journal Title: J. Am. Chem. Soc. Volume: 133 Pages: 3372-3380
  • DOI: DOI:10.1021/ja1070152
  • Peer Reviewed
• [Journal Article] Rotation mechanism of F1-ATPase: crucial importance of water-entropy effect (2011)
  • Author(s): T. Yoshidome, Y. Ito, M. Ikeguchi, M. Kinoshita
  • Journal Title: J. Am. Chem. Soc Volume: 133 Pages: 4030-4039
  • DOI: DOI:10.1021/ja109594y
  • Peer Reviewed
• [Journal Article] Structural and functional analysis of the intrinsic inhibitor subunit εof F1-ATPase from photosynthetic organisms (2010)
  • Author(s): H. Yagi, H. Konno, T. Murakami-Fuse, A. Isu, T. Oroguchi, H. Akutsu, M. Ikeguchi, T. Hisabori
  • Journal Title: Biochem. J Volume: 425 Pages: 85-94
  • DOI: DOI:10.1042/BJ20091247
  • Peer Reviewed
• [Journal Article] Structural fluctuation and concerted motions in F1-ATPase: a molecular dynamics study (2010)
  • Author(s): Y. Ito, M. Ikeguchi
  • Journal Title: J. Comput. Chem Volume: 31 Pages: 2175-2185
  • DOI: DOI:10.1002/jcc.21508
  • Peer Reviewed
• [Journal Article] Molecular dynamics simulations of the isolated β subunit of F1-ATPase (2010)
  • Author(s): Y. Ito, M. Ikeguchi
  • Journal Title: Chem. Phys. Lett Volume: 490 Pages: 80-83
  • DOI: DOI:10.1016/j.cplett.2010.03.015
  • Peer Reviewed
• [Presentation] Molecular dynamics simulation on structural characteristics of yeast F1-ATPase before and after 16-degree rotation of gamma subunit (2013)
  • Author(s): Y. Ito, T. Yoshidome, N. Matubayasi, M.Kinoshita, M. Ikeguchi
  • Organizer: The 57th Annual Meeting of Biophysical Society
  • Place of Presentation: Philadelphia, USA
  • Year and Date: 2013-02-06
• [Presentation] Theoretical study on rotation mechanism of molecular motor F1-ATPase (2012)
  • Author(s): M. Ikeguchi
  • Organizer: The 12th KIAS Conference on Protein Structure and Function
  • Place of Presentation: Seoul, Korea.招待講演
  • Year and Date: 2012-10-13
• [Presentation] F1 分子モーターの分子シミュレーション (2012)
  • Author(s): 池口満徳
  • Organizer: F1 分子モーターの分子シミュレーション
  • Place of Presentation: 岡崎
  • Year and Date: 2012-10-10
• [Presentation] Molecular dynamics simulation on structural characteristics of yeast F1-ATPase before and after 16-degree rotation of gamma subunit (2012)
  • Author(s): Y. Ito, T. Yoshidome, N. Matsubayashi, M.Kinoshita, M. Ikeguchi
  • Organizer: 日本生物物理学会第50回年会
  • Place of Presentation: 名古屋
  • Year and Date: 2012-09-24
• [Presentation] Mechanism of the conformational change of the F1-ATPase β subunit revealed by free-energy simulations (2012)
  • Author(s): Y. Ito, T. Oroguchi, M. Ikeguchi
  • Organizer: 56th Annual Meeting of Biophysical Society
  • Place of Presentation: San Diego, USA
  • Year and Date: 2012-02-29
• [Presentation] A novel rotation mechanism of F1-ATPase based on the water-entropy effect (2012)
  • Author(s): T. Yoshidome, Y. Ito, N. Matubayasi, M.Ikeguchi, M. Kinoshita
  • Organizer: 56th Annual Meeting of Biophysical Society
  • Place of Presentation: San Diego, USA
  • Year and Date: 2012-02-29
• [Presentation] M. Tanigawara, J. Ito, Y. Ito, R. Watanabe, K. Koyasu, M. Ikeguchi, K. V. Tabata, H.Noji (2011)
  • Author(s): M. Tanigawara, J. Ito, Y. Ito, R. Watanabe, K. Koyasu, M. Ikeguchi, K. V. Tabata, H.Noji
  • Organizer: 日本生物物理学会第49回年会
  • Place of Presentation: 姫路
  • Year and Date: 2011-09-18
• [Presentation] A theoretical analysis on water-entropy change in yeast F1-ATPase during 16 degrees rotation of gamma subunit (2011)
  • Author(s): T.Yoshidome, M. Ikeguchi, M. Kinoshita
  • Organizer: 日本生物物理学会第49回年会
  • Place of Presentation: 姫路
  • Year and Date: 2011-09-18
• [Presentation] Theoretical study on rotational mechanism of F1 molecular motor and asymmetric structures (2011)
  • Author(s): M.Ikeguchi
  • Organizer: 日本生物物理学会第49回年会
  • Place of Presentation: 姫路
  • Year and Date: 2011-09-18
• [Presentation] Theoretical study on rotation mechanism of molecular motor F1-ATPase (2010)
  • Author(s): M.Ikeguchi
  • Organizer: International Chemical Congress of Pacific Basin Societies
  • Place of Presentation: Honolulu, USA
  • Year and Date: 2010-12-20
• [Presentation] F1-ATPase の回転のメカニズムにおける水のエントロピーの重要性 (2010)
  • Author(s): 吉留崇,伊藤祐子,池口満徳,木下正弘
  • Organizer: 日本物理学会秋季大会
  • Place of Presentation: 大阪
  • Year and Date: 2010-09-26
• [Presentation] Crucial importance of translational entropy of water in rotation mechanism of F1-ATPase (2010)
  • Author(s): T. Yoshidome, Y. Ito, M. Ikeguchi, M. Kinoshita
  • Organizer: 日本生物物理学会第48回年会
  • Place of Presentation: 仙台
  • Year and Date: 2010-09-22
• [Presentation] Investigation of the conformational change of the F1-ATPase (βsubunit) via molecular dynamics simulation (2010)
  • Author(s): Y. Ito, T. Oroguchi, M. Ikeguchi
  • Organizer: 日本生物物理学会第48回年会
  • Place of Presentation: 仙台
  • Year and Date: 2010-09-22