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Molecular mechanism of chemical-mechanical energy conversion of F1 molecular motor studied by molecular simulations

Planned Research

Project AreaInnovative nanoscience of supermolecular motor proteins working in biomembranes
Project/Area Number 18074004
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionKyoto University

Principal Investigator

HAYASHI Shigehiko  Kyoto University, 大学院・理学研究科, 准教授 (70402758)

Co-Investigator(Kenkyū-buntansha) IKEGUCHI Mitsunori  横浜市立大学, 大学院・生命ナノシステム科学研究所, 准教授 (60261955)
Project Period (FY) 2006 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥119,400,000 (Direct Cost: ¥119,400,000)
Fiscal Year 2010: ¥19,800,000 (Direct Cost: ¥19,800,000)
Fiscal Year 2009: ¥28,300,000 (Direct Cost: ¥28,300,000)
Fiscal Year 2008: ¥28,300,000 (Direct Cost: ¥28,300,000)
Fiscal Year 2007: ¥23,200,000 (Direct Cost: ¥23,200,000)
Fiscal Year 2006: ¥19,800,000 (Direct Cost: ¥19,800,000)
Keywords分子モーター / 酵素反応 / 分子シミュレーション / QM / MM法 / 分子動力学法 / F_1-ATPase / QM/MM法 / 自由エネルギー計算 / 酵素設計 / 分子軌道法 / ハイブリッドQM / F1-ATP合成酵素 / ATP加水分解 / ローダミン蛍光分子
Research Abstract

Molecular mechanism of chemical-mechanical conversion of a reversible rotary motor protein, F1-ATPase, was revealed in electronic and atomic details through molecular simulations. Molecular mechanisms of catalysis of ATP hydrolysis and its regulation were elucidated by means of a hybrid quantum mechanical/molecular mechanical method. Based on the reaction profile revealed, a mutant enzyme with increased catalytic activity was designed theoretically. Molecular dynamics simulations unveiled in an atomic detail protein structural changes responsible for the motor motion.

Report

(7 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report   Self-evaluation Report ( PDF )
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • Research Products

    (106 results)

All 2011 2010 2009 2008 2007 2006 Other

All Journal Article (41 results) (of which Peer Reviewed: 34 results) Presentation (60 results) Book (5 results)

  • [Journal Article] On the rotation mechanism of F1-ATPase: crucial importance of water-entropy effect2011

    • Author(s)
      T.Yoshidome, Y.Ito, M.Ikeguchi, M.Kinoshita
    • Journal Title

      Journal of the American Chemical Society vol.133

      Pages: 4030-4039

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mechanism of the conformational change of the F1-ATPase β subunit revealed by free-energy simulations2011

    • Author(s)
      Y.Ito, T.Oroguchi, M.Ikeguchi
    • Journal Title

      Journal of the American Chemical Society vol.133

      Pages: 3372-3380

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Local entropy difference upon a substrate binding of a psychrophilic α-amylase and a mesophilic homologue2011

    • Author(s)
      T.Kosugi, S.Hayashi
    • Journal Title

      Chemical Physics Letters vol.501

      Pages: 517-522

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Local entropy difference upon a substrate binding of a psychrophilic α-amylase and a mesophilic homologue2011

    • Author(s)
      Takahiro Kosugi, Shigehiko Hayashi
    • Journal Title

      Chemical Physics Letters

      Volume: 501 Pages: 517-522

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mechanism of the conformational change of the F1-ATPase β subunit revealed by free-energy simulations2011

    • Author(s)
      Y.Ito, T.Oroguchi, M.Ikeguchi
    • Journal Title

      Journal of the American Chemical Society

      Volume: 133 Pages: 3372-3380

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] On the rotation mechanism of F_1-ATPase : crucial importance of water-entropy effect2011

    • Author(s)
      T.Yoshidome, Y.Ito, M.Ikeguchi, M.Kinoshita
    • Journal Title

      Journal of the American Chemical Society

      Volume: 133 Pages: 4030-4039

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein collective motions coupled to ligand migration in myoglobin2010

    • Author(s)
      Y.Nishihara, S.Kato, S.Hayashi
    • Journal Title

      Biophysical Journal vol.98

      Pages: 1649-1657

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural and functional analysis of the intrinsic inhibitor subunit ε of F1-ATPase from photosynthetic organisms2010

    • Author(s)
      H.Yagi, H.Konno, T.Murakami-Fuse, A.Isu, T.Oroguchi, H.Akutsu, M.Ikeguchi, T.Hisabori
    • Journal Title

      Biophysical Journal vol.425

      Pages: 85-94

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural fluctuation and concerted motions in F1-ATPase: a molecular dynamics study2010

    • Author(s)
      Y.Ito, M.Ikeguchi
    • Journal Title

      Journal of Computational Chemistry vol.31

      Pages: 2175-2185

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics simulations of the isolated β subunit of F1-ATPase2010

    • Author(s)
      Y.Ito, M.Ikeguchi
    • Journal Title

      Chemical Physics Letters vol.490

      Pages: 80-83

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Protein collective motions coupled to ligand migration in myoglobin2010

    • Author(s)
      Yasutaka Nishihara, Shigeki Kato, Shigehiko Hayashi
    • Journal Title

      Biophysical Journal

      Volume: 98 Pages: 1649-1657

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics simulations of the isolated β subunit of Fl-ATPase2010

    • Author(s)
      Y.Ito, M.Ikeguchi
    • Journal Title

      Chemical Physics Letters 490

      Pages: 80-83

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural fluctuation and concerted motions in F1-ATPase : a molecular dynamics study2010

    • Author(s)
      Y.Ito, M.Ikeguchi
    • Journal Title

      Journal of Computational Chemistry (印刷中)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural and functional analysis of the intrinsic inhibitor subunit e of F1-ATPase from photosynthetic organisms2010

    • Author(s)
      H.Yagi, H.Konno, T.Murakami-Fuse, A.Isu, T.Oroguchi, H.Akutsu, M.Ikeguchi, T.Hisabori
    • Journal Title

      Biophysical Journal 425

      Pages: 85-94

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Proton transfer reactions in reaction center of photosynthetic bacteria,Rhodobacter sphaeroides2009

    • Author(s)
      Y.Kaneko, S.Hayashi, I.Ohmine
    • Journal Title

      Journal of Physical Chemistry B vol.113

      Pages: 8993-9003

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Electronic coulombic coupling of excitation-energy transfer in xanthorhodopsin2009

    • Author(s)
      Kazuhiro Fujimoto, Shigehiko Hayashi
    • Journal Title

      Journal of the American Chemical Society 131

      Pages: 14152-14153

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Proton transfer reactions in reaction center of photosynthetic bacteria, Rhodobacter sphaeroides2009

    • Author(s)
      Yu Kaneko, Shigehiko Hayashi, Iwao Ohmine
    • Journal Title

      Journal of Physical Chemistry B 113

      Pages: 8993-9003

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics simulations and x-ray scattering data analysis2009

    • Author(s)
      T. Oroguchi, H. Hashimoto, T. Shimizu, M. Sato, M. Ikeguchi
    • Journal Title

      Biophys. J. 96

      Pages: 2808-2822

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation2009

    • Author(s)
      Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten
    • Journal Title

      Biophysical Journal 96

      Pages: 403-416

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Intrinsic dynamics of restriction endonuclease Eco0109I studied by molecular dynamics simulations and x-ray scattering data analysis2009

    • Author(s)
      T. Oroguchi, H. Hashimoto, T. Shimizu, M. Sato, M. Ikeguchi
    • Journal Title

      Biophys. J. 96

      Pages: 2808-2822

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Linear response theory in dihedral angle space for protein structural change upon ligand binding2009

    • Author(s)
      S. Omori, S. Fuchigami, M. Ikeguchi, A. Kidera
    • Journal Title

      J. Comput. Chem.

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Water transport in aquaporins : molecular dynamics simulations2009

    • Author(s)
      M. Ikeguchi
    • Journal Title

      Frontiers in Bioscience 14

      Pages: 1283-1291

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A search for ligand diffusion pathway in mioglobin using a metadynamics simulation2008

    • Author(s)
      Yasutaka Nishihara, Shigehiko Hayashi, and Shigeki Kato
    • Journal Title

      Chemical Physics Letters 464

      Pages: 220-225

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mechanism of efficient firefly bioluminescence via adiabatic transition state and seam of sloped conical intersection2008

    • Author(s)
      Lung Wa Chung, Shigehiko Hayashi, Marcus Lundberg, Toru Nakatsu, Hiroaki Kato, and Keiji Morokuma
    • Journal Title

      Journal of the American Chemical Society 130

      Pages: 12880-12881

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of the SUMO-interacting motif of MCAF1 bound to SUMO-32008

    • Author(s)
      N. Sekiyama, T. Ikegami, T. Yamane, H. Ikeguchi, Y. Uchimura, D. Baba, M. Ariyoshi, H. Tochio, H. Saitoh, M. Shirakama
    • Journal Title

      J. Biol. Chem. 283

      Pages: 35966-35975

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] アクアポリンの水透過過程の比較分子シミュレーション2008

    • Author(s)
      木寺詔紀, 池口満徳
    • Journal Title

      生化学 80

      Pages: 940-947

    • NAID

      10022594695

    • Related Report
      2008 Annual Research Report
  • [Journal Article] Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in expplicit water environment.2008

    • Author(s)
      T. Yamane, H. Okamura, M. Ikeguchi, Y. Nishimura, A. Kidera
    • Journal Title

      Proteins: Structure, Function, and Bioinformatics 71

      Pages: 1970-1983

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transition state determination of enzyme reaction on free energy surface: Application to chorismate mutase2007

    • Author(s)
      M.Higashi, S.Hayashi, S.Kato
    • Journal Title

      Chemical Physics Letters vol.437

      Pages: 293-297

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] 分子シミュレーションによるF1-ATPaseの構造機能解析2007

    • Author(s)
      林重彦
    • Journal Title

      蛋白質核酸酵素 vol.52

      Pages: 329-334

    • Related Report
      2010 Final Research Report
  • [Journal Article] 生物系の分子動力学シミュレーション2007

    • Author(s)
      池口満徳
    • Journal Title

      日本物理学会誌 vol.62

      Pages: 777-784

    • NAID

      110006436909

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Transition state determination of enzyme reaction on free energy surface: Application to chorismate mutase.2007

    • Author(s)
      Higashi, M., Hayashi, S., Kato, S.
    • Journal Title

      Chem. Phys. Lett. 437

      Pages: 293-297

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Geometry optimization based on linear response free energy with quantum mechanical/molecular mechanical method: Applications to Menshutkin-type and Claisen rearrangement reactions in aqueous solution.2007

    • Author(s)
      Masahiro Higashi, Shigehiko Hayashi, and Shigeki Kato
    • Journal Title

      Journal of Chemical Physics 126

      Pages: 144503-144503

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transition state determination of enzyme reaction on free energy surface: Application to chorismate mutase2007

    • Author(s)
      Masahiro Higashi, Shigehiko Hayashi, and Shigeki Kato
    • Journal Title

      Chemical Physics Letters 437

      Pages: 293-297

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 分子シミュレーションによるF1-ATPaseの構造機能解析2007

    • Author(s)
      林 重彦
    • Journal Title

      蛋白質核酸酵素 52

      Pages: 329-334

    • Related Report
      2007 Annual Research Report
  • [Journal Article] Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations2007

    • Author(s)
      M. Hashido, A. Kidera, M. Ikeguchi
    • Journal Title

      Biophys. J. 93

      Pages: 373-385

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Unfolding pathways of goat α-lactalbumin as revealed in multiple alignment of molecular dynamics trajectories2007

    • Author(s)
      T. Oroguchi, M. Ikeguchi, M. Ota, K. Kuwajima, A. Kidera
    • Journal Title

      J. Mol. Biol. 371

      Pages: 1354-1364

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 生物系の分子動力学シミュレーション.2007

    • Author(s)
      地口満徳
    • Journal Title

      日本物理学会誌 62

      Pages: 777-784

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transition state determination of enzyme reaction on free energy surface : Application to chorismate mutase2007

    • Author(s)
      M.Higashi, S.Hayashi, S.Kato
    • Journal Title

      Chem.Phys.Lett. 437

      Pages: 293-297

    • Related Report
      2006 Annual Research Report
  • [Journal Article] 分子シミュレーションによるF1-ATPaseの構造機能解析2007

    • Author(s)
      林 重彦
    • Journal Title

      蛋白質核酸酵素 52・4

      Pages: 329-334

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Physical basis for characterizing native structures of proteins2007

    • Author(s)
      Y.Harano, R.Roth, Y.Sugita, M.Ikeguchi, M.Kinoshita
    • Journal Title

      Chem.Phys.Lett. 437

      Pages: 112-116

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Water Transport in Aquaporins : Osmotic Permeability Matrix Analysis of Molecular Dynamics Simulations

    • Author(s)
      M.Hashido, A.Kidera, M.Ikeguchi
    • Journal Title

      Biophys.J. (in press)

    • Related Report
      2006 Annual Research Report
  • [Presentation] Chemical reactions and molecular dynamics in functional processes of motor and photoreceptor proteins2010

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Pacifichem 2010 Symposium "Computational Quantum Chemistry : Theory and Interactions with Experiment"
    • Place of Presentation
      Honolulu(米国)(招待講演)
    • Year and Date
      2010-12-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] 分子シミュレーションによるタンパク質機能の分子機構の解明2010

    • Author(s)
      林重彦
    • Organizer
      新学術領域研究「高次π 空間の創発と機能開発」第三回公開シンポジウム
    • Place of Presentation
      分子科学研究所
    • Year and Date
      2010-03-15
    • Related Report
      2010 Final Research Report
  • [Presentation] 分子シミュレーションによるタンパク質機能の分子機構の解明2010

    • Author(s)
      林重彦
    • Organizer
      新学術領域研究「高次π空間の創発と機能開発」第三回公開シンポジウム
    • Place of Presentation
      分子科学研究所
    • Year and Date
      2010-03-15
    • Related Report
      2009 Annual Research Report
  • [Presentation] Photochemical Reaction Dynamics of Retinal Proteins2010

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      69th Okazaki Conference on "New Frontier in Quantum Chemical Dynamics"
    • Place of Presentation
      分子科学研究所
    • Year and Date
      2010-02-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] Chemical reactions and molecular dynamics in functional processes of motor and photoreceptor proteins2010

    • Author(s)
      S.Hayashi
    • Organizer
      Pacifichem 2010 Symposium "Computational Quantum Chemistry: Theory and Interactions with Experiment"
    • Place of Presentation
      Honolulu(米国)
    • Related Report
      2010 Final Research Report
  • [Presentation] Theoretical study on rotation mechanism of molecular motor F1-ATPase2010

    • Author(s)
      M.Ikeguchi
    • Organizer
      Pacifichem 2010 Symposium "Computational Quantum Chemistry: Theory and Interactions with Experiment"
    • Place of Presentation
      Honolulu(米国)
    • Related Report
      2010 Final Research Report
  • [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
    • Related Report
      2010 Annual Research Report 2010 Final Research Report
  • [Presentation] Investigation of the conformational change of the F1-ATPase (β subunit) via molecular dynamics simulation2010

    • 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
    • Related Report
      2010 Final Research Report
  • [Presentation] Crucial importance of translational entropy of water in rotation mechanism of F1-ATPase2010

    • 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
    • Related Report
      2010 Final Research Report
  • [Presentation] Investigation of the conformational change of the F_1-ATPase (βsubunit) via molecular dynamics simulation2010

    • 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
    • Related Report
      2010 Annual Research Report
  • [Presentation] Crucial importance of translational entropy of water in rotation mechanism of F_1-ATPase2010

    • 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
    • Related Report
      2010 Annual Research Report
  • [Presentation] Theoretical study on rotation mechanism of molecular motor F_1-ATPase2010

    • Author(s)
      M.Ikeguchi
    • Organizer
      Pacifichem 2010
    • Place of Presentation
      Honolulu(米国)(招待講演)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Chemical Reactions and Molecular Dynamics in Functional Processes of Motor and Photoreceptor Proteins2009

    • Author(s)
      S.Hayashi
    • Organizer
      2nd Japan-Korea Seminar on Biomolecular Sciences-Experiments and Simulations
    • Place of Presentation
      名古屋大学
    • Year and Date
      2009-12-23
    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Presentation] タンパク質中の化学反応経路2009

    • Author(s)
      林重彦
    • Organizer
      シンポジウム「化学反応経路探索のニューフロンティア」
    • Place of Presentation
      豊田理化学研究所
    • Year and Date
      2009-09-25
    • Related Report
      2009 Annual Research Report
  • [Presentation] タンパク質内化学反応の分子機構に関する理論的研究2009

    • Author(s)
      林重彦
    • Organizer
      日本化学会東北支部・物理化学コロキウム
    • Place of Presentation
      日本大学
    • Year and Date
      2009-09-20
    • Related Report
      2009 Annual Research Report
  • [Presentation] Molecular Simulations on Enzymatic Reactions and Structural Dynamics of F1-ATPase2009

    • Author(s)
      S.Hayashi, M.Umemura, Y.Ito, M.Ikeguchi
    • Organizer
      International Symposium on "Innovative Nanoscience of Supermolecular Motor Proteins Working in Biomembrane"
    • Place of Presentation
      京都大学
    • Year and Date
      2009-09-09
    • Related Report
      2010 Final Research Report
  • [Presentation] Molecular Simulations on Enzymatic Reactions and Structural Dynamics of Fl-ATPase2009

    • Author(s)
      Shigehiko Hayashi, Myco Umemura, Yuko Ito, Mitsunori Ikeguchi
    • Organizer
      International Symposium on "Innovative Nanoscience of Supermolecular Motor Proteins Working in Biomembrane"
    • Place of Presentation
      京都大学
    • Year and Date
      2009-09-09
    • Related Report
      2009 Annual Research Report
  • [Presentation] 生体機能の分子理論2009

    • Author(s)
      林重彦
    • Organizer
      実在系の分子理論・研究交流会
    • Place of Presentation
      金沢文化ホール
    • Year and Date
      2009-09-04
    • Related Report
      2009 Annual Research Report
  • [Presentation] Molecular Mechanisms of Enzymatic Activities in Motor and Photoreceptor Proteins2009

    • Author(s)
      S.Hayashi
    • Organizer
      CREST International Symposium on Theory and Simulations of Complex Molecular Systems
    • Place of Presentation
      福井謙一記念研究センター
    • Year and Date
      2009-07-21
    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Presentation] Molecular Dynamics in Functional Processes of Photosensitive Proteins2009

    • Author(s)
      S.Hayashi
    • Organizer
      Japan-Korea Symposium on Molecular Science 2009 "Chemical Dynamics in Materials and Biological
    • Place of Presentation
      淡路夢舞台国際会議場
    • Year and Date
      2009-07-13
    • Related Report
      2010 Final Research Report
  • [Presentation] Molecular Dynamics in Functional Processes of Photosensitive Proteins2009

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Japan-Korea Symposium on Molecular Science 2009 "Chemical Dynamics in Materials and Biological Molecular Sciences"
    • Place of Presentation
      淡路夢舞台国際会議場
    • Year and Date
      2009-07-13
    • Related Report
      2009 Annual Research Report
  • [Presentation] Molecular Dynamics in Functional Processes of Photoreceptor Proteins2009

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      International Symposium on "Reaction Dynamics of Many-Body Chemical Systems"
    • Place of Presentation
      京都大学
    • Year and Date
      2009-06-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] ロドプシンのエネルギー変換と情報変換:理論的解析の現状と展望2009

    • Author(s)
      林重彦
    • Organizer
      第三回分子科学会シンポジウム「ロドプシンのエネルギー変換と情報変換」
    • Place of Presentation
      東京工業大学
    • Year and Date
      2009-06-12
    • Related Report
      2009 Annual Research Report
  • [Presentation] Structural fluctuation and cooperativity in F1-ATPase: a molecular dynamics study2009

    • Author(s)
      Y.Ito, M.Ikeguchi
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      徳島文理大学
    • Related Report
      2010 Final Research Report
  • [Presentation] 分子動力学を用いたF1-ATPaseの構造と機能解析2009

    • Author(s)
      伊藤祐子, 池口満徳
    • Organizer
      日本蛋白質科学会第9回年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ
    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Presentation] Structure analysis of F1-ATPase via molecular dynamics2009

    • Author(s)
      Y.Ito, M.Ikeguchi
    • Organizer
      53rd Annual Meeting of Biophysical Society
    • Place of Presentation
      Boston.
    • Related Report
      2010 Final Research Report
  • [Presentation] Conformational change of F_1-ATPase ε subunit upon ATP binding studied by molecular dynamics simulations and X-ray scattering2009

    • Author(s)
      T.Oroguchi, T.Kato-Yamada, H.Hashimoto, S.Unzai, M.Sato, M.Ikeguchi
    • Organizer
      53rd Annual Meeting of Biophysical Society
    • Place of Presentation
      Boston.
    • Related Report
      2010 Final Research Report
  • [Presentation] Structural fluctuation and cooperativity in F1-ATPase : a molecular dynamics study2009

    • Author(s)
      Y.Ito, M.Ikeguchi
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      徳島文理大学
    • Related Report
      2009 Annual Research Report
  • [Presentation] Structure analysis of F1-ATPase via molecular dynamics2009

    • Author(s)
      Y. Ito and M. Ikeguchi
    • Organizer
      53rd Annual Meeting of Biophysical Society
    • Place of Presentation
      Boston
    • Related Report
      2008 Annual Research Report
  • [Presentation] Conformational change of F1-ATPase ε subunit upon ATP binding studied by molecular dynamics simulations and X-ray scattering2009

    • Author(s)
      T. Oroguchi, T. Kato-Yamada, H. Hashimoto, S. Unzai, M. Sato, M. Ikeguchi
    • Organizer
      53rd Annual Meeting of Biophysical Society
    • Place of Presentation
      Boston
    • Related Report
      2008 Annual Research Report
  • [Presentation] ハイブリッド分子シミュレーションで探るF1-ATPase分子モーターの化学-力学エネルギー変換機構2008

    • Author(s)
      林重彦
    • Organizer
      生物物理学会シンポジウム「F1-ATPase 分子モーターの分子機構」
    • Place of Presentation
      神奈川・横浜
    • Year and Date
      2008-12-22
    • Related Report
      2010 Final Research Report
  • [Presentation] ハイブリッド分子シミュレーションで探るF1-ATPase分子モーターの化学-力学エネルギー変換機構2008

    • Author(s)
      林 重彦
    • Organizer
      生物物理学会シンポジウム「F1-ATPase分子モーターの分子機構」
    • Place of Presentation
      神奈川・横浜
    • Year and Date
      2008-12-22
    • Related Report
      2007 Annual Research Report
  • [Presentation] Molecular Mechanism of ATP hydrolysis reaction in F1-ATPase molecular motor2008

    • Author(s)
      A.R.Shaikh, Y.Ito, M.Ikeguchi, H.Ueno, H.Noji, S.Hayashi
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2010 Final Research Report 2008 Annual Research Report
  • [Presentation] Structure and function analysis of F1-ATPase bymolecular dynamics2008

    • Author(s)
      Y.Ito, M.Ikeguchi
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2010 Final Research Report
  • [Presentation] Conformational change of F1-ATPase epsilon subunit upon ATP binding studied by molecular dynamics simulations and X-ray scattering2008

    • Author(s)
      T.Oroguchi, T.Kato-Yamada, H.Hashimoto, S.Unzai, M.Ikeguchi
    • Organizer
      日本生物物理学会第46回年会
    • Related Report
      2010 Final Research Report
  • [Presentation] Chemical Reactions in Photoreceptor and Motor Proteins Studied by hybrid QM/MM Simulations2008

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Telluride Science Research Center Workshop on "Protein Dynamics"
    • Place of Presentation
      Telluride , Colorado (USA)
    • Related Report
      2008 Self-evaluation Report
  • [Presentation] Structure and function analysis of F1-ATPase by molecular dynamics2008

    • Author(s)
      Y. Ito and M. Ikeguchi
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2008 Annual Research Report
  • [Presentation] Conformational change of F1-ATPase epsilon subunit upon ATP binding studied by molecular dynamics simulations and X-ray scattering2008

    • Author(s)
      T. Oroguchi, T. Kato-Yamada, H. Hashithoto, S. Unzai, M. Ikeguchi
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2008 Annual Research Report
  • [Presentation] Water-mediated interactions between DNA and the PhoB DNA binding/transactivation domain2008

    • Author(s)
      T. Yaname, H. Okamura, M. Ikeguchi, Y. Nishimura, A. Kidera
    • Organizer
      52st Annual Meeting of Biophysical Society
    • Place of Presentation
      Long Beach, California
    • Related Report
      2007 Annual Research Report
  • [Presentation] Dynamics of Eco0109I studied by small-angle x-ray scattering experiments and molecular dynamics simulations2008

    • Author(s)
      T. Oroguchi, M. Sato, M. Ikeguchi
    • Organizer
      52st Annual Meeting of Biophysical Society
    • Place of Presentation
      Long Beach, California
    • Related Report
      2007 Annual Research Report
  • [Presentation] 分子シミュレーションで探るタンパク質の光受容と機能2007

    • Author(s)
      林 重彦
    • Organizer
      特定領域「実在系の分子理論」A02・A03班合同研究会「実験と理論のインタープレイ」
    • Place of Presentation
      東京・早稲田
    • Year and Date
      2007-11-16
    • Related Report
      2007 Annual Research Report
  • [Presentation] Chemical Reactions in Photoreceptor and Motor Proteins Studied by hybrid QM/MM Simulations2007

    • Author(s)
      S.Hayashi
    • Organizer
      Telluride Science Research Center Workshop on "Protein Dynamics"
    • Place of Presentation
      Telluride, Colorado.
    • Year and Date
      2007-08-01
    • Related Report
      2010 Final Research Report
  • [Presentation] Chemical Reactions in Photoreceptor and Motor Proteins Studied by hybrid QM/MM Simulations2007

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Telluride Science Research Center Workshop on "Protein Dynamics"
    • Place of Presentation
      Telluride, Colorado
    • Year and Date
      2007-08-01
    • Related Report
      2007 Annual Research Report
  • [Presentation] Chemical Reactions in Photoreceptor and Motor Proteins Studied by hybrid QM/MM Simulations2007

    • Author(s)
      S.Hayashi
    • Organizer
      I2CAM Exploratory Workshop "Quantum Dynamics and Biomolecular Function"
    • Place of Presentation
      Yeppoon, Australia.
    • Year and Date
      2007-04-12
    • Related Report
      2010 Final Research Report
  • [Presentation] Chemical Reactions in Photoreceptor and Motor Proteins Studied by hybrid QM/MM Simulations2007

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      I2CAM Exploratory Workshop "Quantum Dynamics and Biomolecular Function"
    • Place of Presentation
      Yeppoon, Australia
    • Year and Date
      2007-04-12
    • Related Report
      2007 Annual Research Report
  • [Presentation] 分子動力学シミュレーションによるF1-ATPaseの構造変化の研究2007

    • Author(s)
      池口満徳
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Related Report
      2010 Final Research Report
  • [Presentation] Detecting domain motions of proteins in molecular dynamics simulations and normal mode analyses2007

    • Author(s)
      M.Ikeguchi, S.Fuchigami, A.Kidera
    • Organizer
      50th Annual Meeting of Biophysical Society
    • Place of Presentation
      Baltimore, Maryland.
    • Related Report
      2010 Final Research Report
  • [Presentation] タンパク質立体構造変化における経路の多様性とメカニズム:アデニル酸キナーゼの場合2007

    • Author(s)
      渕上壮太郎, 地口満徳, 木寺詔紀
    • Organizer
      日本蛋白質科学会第7回年会
    • Place of Presentation
      仙台
    • Related Report
      2007 Annual Research Report
  • [Presentation] PhoBのDNA結合ドメインのダイナミクスの解析2007

    • Author(s)
      山根努, 岡村英保, 港口満徳, 木寺詔紀, 西村善文
    • Organizer
      日本蛋白質料学会第7回年会
    • Place of Presentation
      仙台
    • Related Report
      2007 Annual Research Report
  • [Presentation] 低分子リガンド結合に伴う構造変化のデータベース解析2007

    • Author(s)
      雨宮崇之, 小池亮太郎, 渕上壮太郎, 港口満徳, 木寺詔紀
    • Organizer
      日本蛋白質料学会第7回年会
    • Place of Presentation
      仙台
    • Related Report
      2007 Annual Research Report
  • [Presentation] 線形応答理論による蛋白質構造変化の記述:内部座標系2007

    • Author(s)
      大森聡, 渕上壮太郎, 池口満徳, 木寺詔紀
    • Organizer
      日本蛋白質科学会第7回年会
    • Place of Presentation
      仙台
    • Related Report
      2007 Annual Research Report
  • [Presentation] 分子動力学シミュレーションによるFl-ATPaseの構造変化の研究2007

    • Author(s)
      池口満徳
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] IP3レセプター・リガンド結合コアのIP3非結合時分子動力学シミュレーション2007

    • Author(s)
      井田洋一, 渕上壮太郎, 池口満徳, 木寺詔紀
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] リガンド結合による蛋白質の構造変化の動的過程:時間依存の摂動による線形応答理論2007

    • Author(s)
      成富佑輔, 渕上壮太郎, 池口満徳, 木寺詔紀
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] X線小角散乱及び分子動力学計算を用いたII型制限酵素Eco0109Iの溶液中ダイナミックスと水和2007

    • Author(s)
      笠口友隆, 佐藤衛, 池口満徳
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] F型ATP合成酵素cリングの空孔に存在するリン脂質は何分子か?:分子動力学シミュレーションによる推定2007

    • Author(s)
      渕上壮太郎, 中島恭子, 池口満徳, 木寺詔紀
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] センソリーロドプシンIIトランスデューサーHAMPドメインの分子動力学研究2007

    • Author(s)
      西方公郎, 渕上壮太郎, 池口満徳, 木寺詔紀
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Related Report
      2007 Annual Research Report
  • [Presentation] Chemical Reactions in Photoreceptor and Motor Proteins Studied by hybrid QM/MM Simulations2006

    • Author(s)
      S.Hayashi
    • Organizer
      Discussion on "Theory and Simulation of biomolecular nano-machines"
    • Place of Presentation
      兵庫・舞子
    • Related Report
      2010 Final Research Report
  • [Presentation] 膜超分子の分子シミュレーション2006

    • Author(s)
      池口満徳、林重彦
    • Organizer
      日本分子生物学会2006フォーラム「分子生物学の未来」シンポジウム「生命科学の革新的ナノバイオロジー」
    • Place of Presentation
      愛知・名古屋
    • Related Report
      2010 Final Research Report
  • [Presentation] Molecular Dynamics Simulations of Protein Folding/Unfolding2006

    • Author(s)
      Ikeguchi, M.
    • Organizer
      The 3rd Open Workshop: Chemistry of Biological Process Created by Water and Biomolecules
    • Place of Presentation
      National Institutes of Natural Sciences, Okazaki (Japan).
    • Related Report
      2008 Self-evaluation Report
  • [Book] Springer Verlag2009

    • Author(s)
      K.Kuwajima, T.Oroguchi, T.Nakamura, M.Ikeguchi, A.Kidera
    • Total Pages
      24
    • Publisher
      Experimental and simulation studies of the folding/unfolding of goat α-lactoalbumin, in Water and Biomolecules: Physical Chemistry of Life Phenomena
    • Related Report
      2010 Final Research Report
  • [Book] Experimental and simulation studies of the folding/unfolding of goat α-lactoalbumin, in Water and Biomolecules : Physical Chemistry of Life Phenomena2009

    • Author(s)
      K. Kuwajima, T. Oroguchi, T. Nakamura, M. Ikeguchi, A. Kidera
    • Total Pages
      24
    • Publisher
      Springer Verlag
    • Related Report
      2008 Annual Research Report
  • [Book] 化学同人2008

    • Author(s)
      池口満徳
    • Total Pages
      6
    • Publisher
      最新分子マシンナノで働く"高度な機械"を目指を目指して水を輸送する分子マシンアクアポリンの分子シミュレーション
    • Related Report
      2010 Final Research Report
  • [Book] 最新分子マシン ナノで働く"高度な機械"を目指して-水を輸送する分子マシン アクアポリンの分子シミュレーション2008

    • Author(s)
      池口満徳
    • Total Pages
      6
    • Publisher
      化学同人
    • Related Report
      2008 Self-evaluation Report
  • [Book] 最新分子マシンナノで働く″高度な機械″を目指して水を輸送する分子マシン アクアポリンの分子シミュレーション2008

    • Author(s)
      池口満徳
    • Total Pages
      6
    • Publisher
      化学同人
    • Related Report
      2007 Annual Research Report

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Published: 2006-04-01   Modified: 2018-03-28  

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