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Chemomechanical network modeling for molecular motor dynamics of kinesin

Research Project

Project/Area Number 25610121
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Biological physics/Chemical physics/Soft matter physics
Research InstitutionOkayama University

Principal Investigator

Sumi Tomonari  岡山大学, 自然科学研究科, 准教授 (40345955)

Research Collaborator Klumpp Stefan  Max-Planck Institute (MPI) of Colloids and Interfaces
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2015: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2014: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2013: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords分子モーター / 化学-力学共役機構 / 確率的モデリング / 力学的破断過程 / 一分子観測 / キネシン / 溶媒和自由エネルギー / 密度汎関数理論 / 単一分子計測 / ダイニン
Outline of Final Research Achievements

We present a chemomechanical network model of molecular motor kinesin that is systematically developed on the basis of experimental observations, and demonstrate that it can qualitatively reproduce available all the experimental results of motor dynamics. The analysis of the local excess fluxes shows that an ATP-concentration dependence of the dominant forward stepping cycle and (2) supports a gated rear head mechanism where the forward step is controlled by ATP hydrolysis and the resulting ADP-bound state of the rear head at saturating ATP levels. The network picture suggests that for saturating ATP concentration, the energy from ATP hydrolysis is used to concentrate the chemical transition flux on the network to a force-generating state that can produce the power stroke. At low ATP levels, the energy is used to avoid states that are fragile against backward load because the leading head is weakly bound to microtubule.

Report

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

    (35 results)

All 2016 2015 2014 2013

All Journal Article (10 results) (of which Peer Reviewed: 10 results,  Acknowledgement Compliant: 4 results,  Open Access: 1 results) Presentation (25 results) (of which Int'l Joint Research: 1 results,  Invited: 4 results)

  • [Journal Article] Driving forces for the pressure-induced aggregation of poly(N-isopropylacrylamide) in water2016

    • Author(s)
      K. Mochizuki, T. Sumi, K. Koga
    • Journal Title

      Phys. Chem. Chem. Phys.

      Volume: 18 Issue: 6 Pages: 4697-4703

    • DOI

      10.1039/c5cp07674a

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Mean-Field Approximation to the Hydrophobic Hydration in the Liquid-Vapor Interface of Water2016

    • Author(s)
      K. Abe, T. Sumi, and K. Koga
    • Journal Title

      J. Phys. Chem. B

      Volume: 120 Issue: 8 Pages: 2012-2019

    • DOI

      10.1021/acs.jpcb.5b10169

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] A Solvation-Free-Energy Functional: A Reference-Modified Density Functional Formulation2015

    • Author(s)
      T. Sumi, A. Mitsutake, and Y. Maruyama
    • Journal Title

      Journal of Computational Chemistry

      Volume: 36 Issue: 18 Pages: 1359-1369

    • DOI

      10.1002/jcc.23942

    • NAID

      120006733912

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Erratum: “A solvation-Free-Energy Functional:
A Reference-Modified Density Functional Formulation” [J. Comput. Chem. 2015, 36, 1359–1369]2015

    • Author(s)
      T. Sumi, A. Mitsutake, and Y. Maruyama
    • Journal Title

      Journal of Computational Chemistry

      Volume: 36 Pages: 2009-2011

    • DOI

      10.1002/jcc.24035

    • NAID

      120006733907

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Time series data analysis using DFA2014

    • Author(s)
      A. Okumoto , T. Akiyama , H. Sekino , and T. Sumi
    • Journal Title

      AIP Conference Proceedings

      Volume: 1585 Pages: 175-180

    • DOI

      10.1063/1.4866638

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Temperature dependence of local solubility of hydrophobic molecules in the liquid-vapor interface of water2014

    • Author(s)
      Kiharu Abe , Tomonari Sumi , and Kenichiro Koga
    • Journal Title

      The Journal of Chemical Physics

      Volume: 141 Issue: 18

    • DOI

      10.1063/1.4896236

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Model-potential-free analysis of small angle scattering of proteins in solution: insights into solvent effects on protein–protein interaction2014

    • Author(s)
      Tomonari Sumi, Hiroshi Imamura, Takeshi Morita, Yasuhiro Isogai, and Keiko Nishikawa
    • Journal Title

      Phys. Chem. Chem. Phys.

      Volume: 16 Issue: 46 Pages: 25492-25497

    • DOI

      10.1039/c4cp03606a

    • NAID

      120006733910

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] A model-free method for extracting interaction potential between protein molecules using small-angle X-ray scattering2014

    • Author(s)
      Tomonari Sumi, Hiroshi Imamur, TakeshiMorita, Keiko Nishikawa
    • Journal Title

      Journal of Molecular Liquids

      Volume: 200 Pages: 42-46

    • DOI

      10.1016/j.molliq.2014.03.014

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Effects of hydrophobic hydration on polymer chains immersed in supercooled water2013

    • Author(s)
      Tomonari Sumi and Hideo Sekino
    • Journal Title

      RSC Advances

      Volume: 3 Issue: 31 Pages: 12743-12750

    • DOI

      10.1039/c3ra41320a

    • NAID

      120006733906

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Modulation of the intermolecular interaction of myoglobin by removal of the heme2013

    • Author(s)
      H. Imamura, T. Morita, T. Sumi, Y. Isogai, M. Kato and K. Nishikawa
    • Journal Title

      J. Synchrotron Radiation

      Volume: 20 Issue: 6 Pages: 919-922

    • DOI

      10.1107/s0909049513022772

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] キネシンの化学-力学状態遷移ネットワーク: ATP濃度および外部負荷依存性2016

    • Author(s)
      T. Sumi and S. Klumpp
    • Organizer
      日本物理学会第71回年次大会
    • Place of Presentation
      東北学院大学
    • Year and Date
      2016-03-19
    • Related Report
      2015 Annual Research Report
  • [Presentation] 剛体球参照系を用いた密度汎関数理論に基づく新しい溶媒和自由エネルギー表式2015

    • Author(s)
      丸山豊,光武亜代理,墨智成
    • Organizer
      計算統計物理学研究会 第6回研究会
    • Place of Presentation
      名古屋大学
    • Year and Date
      2015-11-21
    • Related Report
      2015 Annual Research Report
  • [Presentation] AGGREGATION AND DISPERSION PROCESS OF POLYMER-CONJUGATED GOLD NANOPARTICLES USING MODEL-PTENTIAL-FREE METHOD2015

    • Author(s)
      T. Morita, N. Uehara and T. Sumi
    • Organizer
      SAS 2015
    • Place of Presentation
      Berlin, Germany
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 剛体球参照系を用いた密度汎関数理論に基づく新しい溶媒和自由エネルギー表式2015

    • Author(s)
      丸山豊,光武 亜代理,墨智成
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] 界面における疎水効果2015

    • Author(s)
      甲賀研一郎,阿部紀遥,墨智成
    • Organizer
      第66回コロイドおよび界面化学討論会
    • Place of Presentation
      鹿児島大学
    • Year and Date
      2015-09-10
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 剛体球参照系を用いた密度汎関数理論に基づく新しい溶媒和自由エネルギー表式2014

    • Author(s)
      丸山豊,墨智成,光武亜代理
    • Organizer
      第28回分子シミュレーション討論会
    • Place of Presentation
      仙台
    • Year and Date
      2014-11-12 – 2014-11-14
    • Related Report
      2014 Research-status Report
  • [Presentation] 剛体球参照系を用いた新たな密度汎関数理論の定式化:単純液体への適用2014

    • Author(s)
      墨智成,丸山豊
    • Organizer
      第28回分子シミュレーション討論会
    • Place of Presentation
      仙台
    • Year and Date
      2014-11-12 – 2014-11-14
    • Related Report
      2014 Research-status Report
  • [Presentation] Chemomechanical network modeling of kinesin2014

    • Author(s)
      T. Sumi and S. Klumpp
    • Organizer
      The 52st Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Sapporo, Japan
    • Year and Date
      2014-10-25 – 2014-10-27
    • Related Report
      2014 Research-status Report
  • [Presentation] 小角X線散乱による金ナノ粒子の凝集・分散過程の粒子間構造因子2014

    • Author(s)
      森田 剛, 墨 智成
    • Organizer
      第8回分子科学会2014
    • Place of Presentation
      東広島
    • Year and Date
      2014-09-21 – 2014-09-24
    • Related Report
      2014 Research-status Report
  • [Presentation] Solute-induced fluctuations in binary solvent mixture2014

    • Author(s)
      T. Sumi and T. Morita
    • Organizer
      International Meeting on Applications of Statistical Mechanics of Molecular Liquid on Soft Matter
    • Place of Presentation
      Bangkok, Thailand
    • Year and Date
      2014-09-14 – 2014-09-17
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Solute-induced fluctuations in binary solvent mixture2014

    • Author(s)
      T. Sumi and T. Morita
    • Organizer
      EMLG - JMLG annual meeting 2014
    • Place of Presentation
      Roma, Italy
    • Year and Date
      2014-09-07 – 2014-09-12
    • Related Report
      2014 Research-status Report
  • [Presentation] Model-free method for extracting protein-protein interactions in solutions using small-angle X-ray scattering data2014

    • Author(s)
      T. Sumi, H. Imamura, T. Morita, Y. Isogai, and K. Nishikawa
    • Organizer
      9th Liquid Matter Conference
    • Place of Presentation
      Lisbon, Portugal
    • Year and Date
      2014-07-21 – 2014-07-25
    • Related Report
      2014 Research-status Report
  • [Presentation] A reference-modified density-functional theory for improving solvation free energy2014

    • Author(s)
      T. Sumi, Y. Maruyama, and K. Koga
    • Organizer
      The 8th Mini-Symposium on Liquids (MSL2014)
    • Place of Presentation
      Okayama, Japan
    • Year and Date
      2014-07-05
    • Related Report
      2014 Research-status Report
  • [Presentation] Effects of hydrophobic hydration on polymer chains immersed in supercooled water2014

    • Author(s)
      T. Sumi and H. Sekino
    • Organizer
      International Conference on Water Science
    • Place of Presentation
      Peking, China
    • Year and Date
      2014-04-14 – 2014-04-17
    • Related Report
      2014 Research-status Report
  • [Presentation] A model-potential-free analysis of protein-protein interactions using small-angle X-ray scattering2013

    • Author(s)
      T. Sumi, H. Imamura, T. Morita, Y. Isogai, and K. Nishikawa
    • Organizer
      3rd International Conference on Molecular Simulation (ICMS2013)
    • Place of Presentation
      神戸国際会議場
    • Related Report
      2013 Research-status Report
  • [Presentation] 蛋白質間相互作用と溶媒効果2013

    • Author(s)
      墨智成, 今村比呂志, 森田剛, 磯貝泰弘, 西川恵子
    • Organizer
      2013年日本化学会中国四国支部:若手セッション企画「機能性ソフトマテリアルと分子統計化学」
    • Place of Presentation
      広島大学
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] An integral equation approach for protein interactions using small-angle X-ray scattering data2013

    • Author(s)
      T. Sumi, H. Imamura, T. Morita, Y. Isogai, and K. Nishikawa
    • Organizer
      The 51st Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      京都国際会議場
    • Related Report
      2013 Research-status Report
  • [Presentation] The 51st Annual Meeting of the Biophysical Society of Japan2013

    • Author(s)
      H. Imamura, T. Morita, T. Sumi, Y. Isogai, Minoru Kato, and K. Nishikawa
    • Organizer
      Protein’s arrangement in aqueous solution before the self-assemblies: A small angle X-ray scattering study
    • Place of Presentation
      京都国際会議場
    • Related Report
      2013 Research-status Report
  • [Presentation] 第7回分子科学会20132013

    • Author(s)
      今村 比呂志,森田 剛,墨 智成,磯貝 泰弘,加藤 稔,西川 恵子
    • Organizer
      小角X線散乱法による球状タンパク質の分子間相互作用の評価
    • Place of Presentation
      京都
    • Related Report
      2013 Research-status Report
  • [Presentation] Multiscale Motility of Molecular Motors2013

    • Author(s)
      T. Sumi and S. Klumpp
    • Organizer
      Revisit of chemomechanical network theory of kinesin
    • Place of Presentation
      Potsdam, Germany
    • Related Report
      2013 Research-status Report
  • [Presentation] 密度汎関数理論を用いた水溶液中での高分子シミュレーション2013

    • Author(s)
      墨智成, 関野秀男
    • Organizer
      第62回高分子討論会:特定テーマ「材料研究を加速する計算科学」
    • Place of Presentation
      金沢大学
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] An integral equation study of protein interactions using small-angle X-ray scattering data2013

    • Author(s)
      T. Sumi, H. Imamura, and K. Nishikawa
    • Organizer
      7th Mini-symposium on liquids(MSL7, 2013)
    • Place of Presentation
      Fukuoka, Japan
    • Related Report
      2013 Research-status Report
  • [Presentation] Small angle x-ray scattering and integral equation approach for intermolecular interaction potential of globular proteins2013

    • Author(s)
      H. Imamura, T. Morita, T. Sumi, Y. Isogai, M. Kato, and K. Nishikawa
    • Organizer
      The 33rd international conference on solution chemistry
    • Place of Presentation
      Kyoto, Japan
    • Related Report
      2013 Research-status Report
  • [Presentation] 小角X線散乱および積分方程式理論による球状タンパク質(ミオグロビンとリゾチーム)の分子間相互作用の解析2013

    • Author(s)
      今村比呂志,墨智成,森田剛,磯貝泰弘,加藤稔,西川恵子
    • Organizer
      蛋白質科学会2013
    • Place of Presentation
      鳥取
    • Related Report
      2013 Research-status Report
  • [Presentation] Modulation of intermolecular interaction by the haem binding in myoglobin2013

    • Author(s)
      H. Imamura, T. Morita, T. Sumi, Y. Isogai, M. Kato, K. Nishikawa
    • Organizer
      4th International Symposium on Diffraction Structural Biology
    • Place of Presentation
      Nagoya, Japan
    • Related Report
      2013 Research-status Report

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Published: 2014-07-25   Modified: 2019-07-29  

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