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Molecular simulation study on the rotation mechanism of V-ATPase

Research Project

Project/Area Number 25291036
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Biophysics
Research InstitutionYokohama City University

Principal Investigator

IKEGUCHI Mitsunori  横浜市立大学, 生命医科学研究科, 教授 (60261955)

Co-Investigator(Renkei-kenkyūsha) MURATA Takeshi  千葉大学, 理学研究科, 教授 (80415322)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000)
Fiscal Year 2015: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2014: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2013: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
KeywordsV型ATPase / 分子動力学 / マルチスケールシミュレーション / 分子モーター / 分子シミュレーション / V1-ATPase / 回転機構
Outline of Final Research Achievements

The rotation mechanism of molecular motor V-ATPase, which transports ions utilizing ATP-hydrolysis energies, was studied using molecular dynamics (MD) simulations. Multiscale MD simulations employing both an all-atom model involving hydrogen atoms and a coarse-grained model approximating amino acids as particles successfully reproduced the rotation of a central stalk in V-ATPase. From analyses of the trajectories, the rotation mechanism of V-ATPase was elucidated structurally.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (20 results)

All 2015 2014 2013

All Journal Article (4 results) (of which Peer Reviewed: 4 results,  Acknowledgement Compliant: 3 results) Presentation (14 results) (of which Invited: 5 results) Book (2 results)

  • [Journal Article] An accurate and efficient computation method of the hydration free energy of a large, complex molecule2015

    • Author(s)
      T. Yoshidome, T. Ekimoto, N. Matubayasi, Y. Harano, M. Kinoshita, and M. Ikeguchi
    • Journal Title

      J. Chem. Phys.

      Volume: 142 Issue: 17 Pages: 175101-11

    • DOI

      10.1063/1.4919636

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] The Mechanism of the ab (alpha beta) Conformational Change in F1-ATPase After the ATP Hydrolysis: Free-energy Simulation2015

    • Author(s)
      Yuko Ito, Mitsunori Ikeguchi
    • Journal Title

      Biophysical Journal

      Volume: 108 Issue: 1 Pages: 85-97

    • DOI

      10.1016/j.bpj.2014.11.1853

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Finite-Size Effect on the Charging Free Energy of Protein in Explicit Solvent2015

    • Author(s)
      Toru Ekimoto, Nobuyuki Matubayasi, Mitsunori Ikeguchi
    • Journal Title

      J. Chem. Theory Comput.

      Volume: 11 Issue: 1 Pages: 215-223

    • DOI

      10.1021/ct5008394

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Functional rotation induced by alternating protonation states in the multidrug transporter AcrB: All-atom molecular dynamics simulations.2013

    • Author(s)
      T. Yamane, S. Murakami, M. Ikeguchi
    • Journal Title

      Biochemistry

      Volume: 52 Issue: 43 Pages: 7648-7658

    • DOI

      10.1021/bi400119v

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Presentation] Rotation mechanism of V1-ATPase studied by multi-scale MD simulation2015

    • Author(s)
      Yuta Isaka, Yuichi Kokabu, Toru Ekimoto, Takeshi Murat, Mitsunori Ikeguchi
    • Organizer
      日本生物物理学会第53回年会
    • Place of Presentation
      金沢大学
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Conformational Dynamics of Multidrug Efflux Transporter AcrB2015

    • Author(s)
      Mitsunori Ikeguchi
    • Organizer
      日本生物物理学会第53回年会
    • Place of Presentation
      金沢大学
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] マルチスケール分子動力学シミュレーションによる V1-ATPase の回転機構の解明2015

    • Author(s)
      井阪 悠太、小甲 裕一、浴本 亨、 村田 武士、池口 満徳
    • Organizer
      日本蛋白質科学会第15回年会
    • Place of Presentation
      徳島あわぎんホール
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] Course-grained molecular dynamics simulation of V1-ATPase2014

    • Author(s)
      Hiroki Kashimura, Yuta Isaka, Yuichi Kokabu, Mitsunori Ikeguchi
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Rotation mechanism of V1-ATPase studied by MD simulation2014

    • Author(s)
      Yuta Isaka, Takeshi Murata, Mitsunori Ikeguchi
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Molecular dynamics simulations of the β subunit in F1-ATPase: Relation between the large-scale structural change and common motifs2014

    • Author(s)
      Yuko Ito, Mitsunori Ikeguchi
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] MD シミュレーションによる V1-ATPase の回転機構の解明2014

    • Author(s)
      井阪 悠太、池口 満徳
    • Organizer
      日本蛋白質科学会第14回年会
    • Place of Presentation
      横浜ワークピア
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] 分子動力学計算を使って明らかにした F1-ATPase の回転機構2014

    • Author(s)
      伊藤 祐子、池口 満徳
    • Organizer
      日本蛋白質科学会第14回年会
    • Place of Presentation
      横浜ワークピア
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Free energy simulations for the conformational change of the αβ subunits in F1-ATPase after the ATP hydrolysis2014

    • Author(s)
      Yuko Ito, Mitsunori Ikeguchi
    • Organizer
      58th Annual Meeting of Biophysical Society
    • Place of Presentation
      San Francisco, California, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] Rotation mechanism of V1-ATPase studied by steered MD simulations2013

    • Author(s)
      Yuta Isaka, Ichiro Yamato, Takeshi Murata, Mitsunori Ikeguchi
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] All-atom hydration analysis of the β subunit in F1-ATPase2013

    • Author(s)
      Toru Ekimoto, Mitsunori Ikeguchi, Nobuyuki Matubayasi
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Protein structural fluctuations investigated by small-angle X-ray solution scattering and molecular dynamics simulations2013

    • Author(s)
      Tomotaka Oroguchi, Mitsunori Ikeguchi
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Molecular dynamics simulations of biomolecular motor F1-ATPase2013

    • Author(s)
      Mitsunori Ikeguchi
    • Organizer
      CMSI International Satellite Meeting in NAGOYA
    • Place of Presentation
      名古屋
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Comparison of ssDNA- and dsDNA-binding affinity of RecA recombinase using the PBSA method2013

    • Author(s)
      Yuichi Kokabu, Mitsunori Ikeguchi
    • Organizer
      The 3rd International Conference on New frontier of the research in RecA-family recombinase and its accessory proteins
    • Place of Presentation
      Nantes, France
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Book] 全原子分子動力学計算が解き明かす回転分子モーターの作用機構.1分子ナノバイオ計測2014

    • Author(s)
      伊藤祐子、池口満徳
    • Publisher
      化学同人
    • Related Report
      2014 Annual Research Report
  • [Book] Molecular dynamics simulations of F1-ATPase, in Protein Conformational Dynamics2014

    • Author(s)
      Y. Ito and M. Ikeguchi
    • Publisher
      Springer
    • Related Report
      2013 Annual Research Report

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Published: 2013-05-21   Modified: 2019-07-29  

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