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Development of computational method of solvation dynaics and the application to ATP hydrolysys

Planned Research

Project AreaWater plays a key role in ATP hydrolysis and ATP-driven functions of proteins
Project/Area Number 20118003
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionRitsumeikan University

Principal Investigator

TAKAHASHI Takuya  立命館大学, 生命科学部, 教授 (70262102)

Project Period (FY) 2008 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥41,340,000 (Direct Cost: ¥31,800,000、Indirect Cost: ¥9,540,000)
Fiscal Year 2012: ¥7,670,000 (Direct Cost: ¥5,900,000、Indirect Cost: ¥1,770,000)
Fiscal Year 2011: ¥7,670,000 (Direct Cost: ¥5,900,000、Indirect Cost: ¥1,770,000)
Fiscal Year 2010: ¥12,090,000 (Direct Cost: ¥9,300,000、Indirect Cost: ¥2,790,000)
Fiscal Year 2009: ¥7,670,000 (Direct Cost: ¥5,900,000、Indirect Cost: ¥1,770,000)
Fiscal Year 2008: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Keywords水和 / MD / QM / ハイパーモバイル水 / ダイナミクス / 水モデル / ATP 加水分解 / イオン / ATP加水分解
Research Abstract

Various functions that describe the dynamics change of the system in each step of the ATP hydrolysis (rotational relaxation time and self-diffusion coefficient) were calculated and in some case faster movement of water than bulk water was found. Around monoatomic ions, we confirmed that the combination of conventional ion and water model parameters could not reproduce faster movement of water than bulk. Therefore, we developed a new water model based on the TIP5P water model, and reproduced the faster movement of water around monoatomic ions. We also performed xhaustive calculations for polyphosphate molecules including the study of electronic states for the force field improvements. We developed computational techniques for high-speed calculation of solvent effects on macromolecules such as proteins, and quantitative evaluation of the molecular interactions was achieved.

Report

(7 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report   Self-evaluation Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (49 results)

All 2013 2012 2011 2010 2009 2008 Other

All Journal Article (7 results) (of which Peer Reviewed: 7 results) Presentation (36 results) Book (2 results) Remarks (4 results)

  • [Journal Article] Assessment of dynamic properties of water around a monov alent ion: A classical molecular dy namics simulation study2011

    • Author(s)
      Ikuo Kurisaki, Takuya Takahashi
    • Journal Title

      Computational and Theoretical Chemistry

      Volume: 巻:966 Pages: 26-30

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Synthesis of Uniform and Dispersive Calcium Carbonate Nanoparticles in a Protein Cage through Control of Electrostatic Potential2011

    • Author(s)
      Hiroko Fukano, Takuya Takahashi, Mamoru Aizawa, and Hideyuki Yoshimura、
    • Journal Title

      Inorganic Chemistry

      Volume: 巻:50 Pages: 6526-6532

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Assessment of dynamic properties of water around a monovalent ion : A classical molecular dynamics simulation study2011

    • Author(s)
      Ikuo Kurisaki, Takuya Takahashi
    • Journal Title

      Computational and Theoretical Chemistry

      Volume: 966 Issue: 1-3 Pages: 26-30

    • DOI

      10.1016/j.comptc.2011.02.004

    • Related Report
      2011 Annual Research Report 2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Synthesis of Uniform and Dispersive Calcium Carbonate Nanoparticles in a Protein Cage through Control of Electrostatic Potential2011

    • Author(s)
      Hiroko Fukano, Takuya Takahashi, Mamoru Aizawa, Hideyuki Yoshimura
    • Journal Title

      Inorganic Chemistry

      Volume: 50 Issue: 14 Pages: 6526-6532

    • DOI

      10.1021/ic200117x

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Assessment of dynamic properties of water around a monovalent ion : A classical molecular dynamics simulation study2011

    • Author(s)
      Ikuo Kurisaki, Takuya Takahashi
    • Journal Title

      Computational and Theoretical Chemistry 966

      Pages: 26-30

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Crystal Habits of Cubic Insulin and Evaluation of Intermolecular Interactions by Macrobond and EET Analyses2009

    • Author(s)
      Masanori Ootaki, Shigeru Endo, Yoko Sugawara and Takuya Takahashi
    • Journal Title

      Journal of Crystal Growth

      Volume: 巻:311 Pages: 4226-4234

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal Habits of Cubic Insulin and Evaluation of Intermolecular Interactions by Macrobond and EET Analyses2009

    • Author(s)
      Masanori Ootaki、Shigeru Endo、Yoko Sugawara, Takuya Takahashi
    • Journal Title

      Journal of Crystal Growth 311

      Pages: 4226-4234

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Presentation] Surface polarity and energy analyses of protein-protein interactions in crystals2013

    • Author(s)
      S. Yamamura, M. Ootaki, S. Endo, T. Takahashi and Y. Sugawara
    • Organizer
      4th International Symposium on Diffraction Structural Biology
    • Place of Presentation
      名古屋市中小企業振興会館(愛知県)
    • Year and Date
      2013-05-27
    • Related Report
      2012 Final Research Report
  • [Presentation] Calculation of dynamics and charges of water around small solute molecules: MD and QM calculations2012

    • Author(s)
      Takuya Takahashi
    • Organizer
      第50 回日本生物物理学会年会
    • Place of Presentation
      名古屋大学(愛知県)
    • Year and Date
      2012-09-22
    • Related Report
      2012 Final Research Report
  • [Presentation] Investigation of force field parameter effect on solvation dynamics2012

    • Author(s)
      Yoshito Kondo, Takuya Takahashi
    • Organizer
      第50 回日本生物物理学会年会
    • Place of Presentation
      名古屋大学(愛知県)
    • Year and Date
      2012-09-22
    • Related Report
      2012 Final Research Report
  • [Presentation] Calculation of dynamics and charges of water around small solute molecules: MD and QM calculations2012

    • Author(s)
      Takuya Takahashi
    • Organizer
      第50回 日本生物物理学会 年会
    • Place of Presentation
      名古屋大学 愛知県
    • Year and Date
      2012-09-22
    • Related Report
      2012 Annual Research Report
  • [Presentation] Investigation of force field parameter effect on solvation dynamics2012

    • Author(s)
      Yoshito Kondo, Takuya Takahashi
    • Organizer
      第50回 日本生物物理学会 年会
    • Place of Presentation
      名古屋大学 愛知県
    • Year and Date
      2012-09-22
    • Related Report
      2012 Annual Research Report
  • [Presentation] Assessment of dynamic properties of water around ions and biomolecules: MD and QM calculations2011

    • Author(s)
      高橋卓也 栗崎以久男
    • Organizer
      日本生物物理学会第49 回年会
    • Place of Presentation
      兵庫県立大学姫路・書写キャンパス(兵庫県)
    • Year and Date
      2011-09-17
    • Related Report
      2012 Final Research Report
  • [Presentation] Assessment of dynamic properties of water around ions and biomolecules : MD and QM calculations2011

    • Author(s)
      高橋卓也, 栗崎以久男
    • Organizer
      日本生物物理学会第49回年会
    • Place of Presentation
      兵庫県立大学姫路・書写キャンパス(兵庫県)
    • Year and Date
      2011-09-17
    • Related Report
      2011 Annual Research Report
  • [Presentation] MD simulations and QM calculations to elucidate solvation dynamics around several solute molecules2011

    • Author(s)
      Takuya Takahashi
    • Organizer
      The 2nd international symposium on "Multi-scale Simulations of Biological and Soft Materials"
    • Place of Presentation
      Shiran Kaikan, Kyoto University, Kyoto
    • Year and Date
      2011-09-10
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
  • [Presentation] リボヌクレーゼA の結晶形の安定性に及ぼす溶媒効果の連続誘電体モデルによる計算2011

    • Author(s)
      高橋 卓也、猿渡 茂、田草川 英昇、村松 憲吾、菅原 洋子
    • Organizer
      第11 回日本蛋白質科学会年会
    • Place of Presentation
      ホテル阪急エキスポパーク(大阪府)
    • Year and Date
      2011-06-09
    • Related Report
      2012 Final Research Report
  • [Presentation] リボヌクレーゼAの結晶形の安定性に及ぼす溶媒効果の連続誘電体モデルによる計算2011

    • Author(s)
      高橋卓也、猿渡茂、田草川英昇、村松憲吾、菅原洋子
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      ホテル阪急エキスポパーク(大阪府)
    • Year and Date
      2011-06-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] MD and QM calculations to reproduce water dynamics around several solute molecules2011

    • Author(s)
      高橋卓也 栗崎以久男
    • Organizer
      物性研・CMSI・次世代ナノ情報合同研究会
    • Place of Presentation
      東京大学・柏キャンパス(千葉県)
    • Year and Date
      2011-01-05
    • Related Report
      2012 Final Research Report 2010 Self-evaluation Report
  • [Presentation] MD and QM calculations to reproduce water dynamics around several solute molecules2011

    • Author(s)
      高橋卓也
    • Organizer
      物性研・CMSI・次世代ナノ情報合同研究会
    • Place of Presentation
      東京大学・柏キャンパス(千葉)
    • Year and Date
      2011-01-05
    • Related Report
      2010 Annual Research Report
  • [Presentation] MD simulations and QM calculations of water around small solute2010

    • Author(s)
      Takuya TAKAHASHI, Ikuo KURISAKI
    • Organizer
      4th symposium on "Fluctuations and Functions"
    • Place of Presentation
      ピアザ淡海(滋賀県)
    • Year and Date
      2010-11-30
    • Related Report
      2012 Final Research Report
  • [Presentation] Challenge to reproduction of hyper-mobile water around monovalent ions: classical molecular dynamics study2010

    • Author(s)
      Ikuo KURISAKI 、Takuya TAKAHASHI
    • Organizer
      4th symposium on " Fluctuations and Functions"
    • Place of Presentation
      ピアザ淡海(滋賀県)
    • Year and Date
      2010-11-30
    • Related Report
      2012 Final Research Report
  • [Presentation] Calculations of dynamics of water around biomolecules and ions2010

    • Author(s)
      高橋卓也 栗崎以久男
    • Organizer
      日本生物物理学会第48 回年会
    • Place of Presentation
      東北大学(宮城県)
    • Year and Date
      2010-09-21
    • Related Report
      2012 Final Research Report
  • [Presentation] Reproduction of dynamics of water around an ion by refining water model2010

    • Author(s)
      栗崎以久男 高橋卓也
    • Organizer
      日本生物物理学会第48 回年会
    • Place of Presentation
      東北大学(宮城県)
    • Year and Date
      2010-09-21
    • Related Report
      2012 Final Research Report
  • [Presentation] Calculations of dynamics of water around biomolecules and ions2010

    • Author(s)
      高橋卓也, 栗崎以久男
    • Organizer
      日本生物物理学会第48回年会
    • Place of Presentation
      東北大学(宮城県)
    • Year and Date
      2010-09-21
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] Reproduction of dynamics of water around an ionby refining water model2010

    • Author(s)
      栗崎以久男, 高橋卓也
    • Organizer
      日本生物物理学会第48回年会
    • Place of Presentation
      東北大学(宮城県)
    • Year and Date
      2010-09-21
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] Reproduction of dynamics of water around an ion by refining water model2010

    • Author(s)
      栗崎以久男, 高橋卓也
    • Organizer
      日本生物物理学会第48回年会
    • Place of Presentation
      東北大学(宮城)
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] Calculations of dynamics of water around biomolecules and ions2010

    • Author(s)
      高橋卓也, 栗崎以久男
    • Organizer
      日本生物物理学会第48回年会
    • Place of Presentation
      東北大学(宮城)
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] 生体分子と、その周囲の水のダイナミクスと分極電荷の計算2010

    • Author(s)
      高橋卓也
    • Organizer
      第10 回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道)
    • Year and Date
      2010-06-17
    • Related Report
      2012 Final Research Report
  • [Presentation] 生体分子とその周囲の水のダイナミクスと分極電荷の計算2010

    • Author(s)
      高橋卓也
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道)
    • Year and Date
      2010-06-17
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] 生体分子と、その周囲の水のダイナミクスと分極電荷の計算2010

    • Author(s)
      高橋卓也
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道)
    • Year and Date
      2010-06-17
    • Related Report
      2010 Annual Research Report
  • [Presentation] 立方晶ブタインスリンの晶相変化と分子間相互作用2010

    • Author(s)
      大滝正訓、猿渡茂、菅原洋子、高橋卓也
    • Organizer
      第65回物理学会年会
    • Place of Presentation
      岡山大学、岡山県
    • Related Report
      2009 Annual Research Report
  • [Presentation] 溶質周囲の水のダイナミクスと分極電荷の計算2009

    • Author(s)
      塩見友樹、石尾広武、高橋卓也
    • Organizer
      第23回分子シミュレーション討論会
    • Place of Presentation
      名古屋市吹上ホール(愛知県)
    • Year and Date
      2009-12-03
    • Related Report
      2012 Final Research Report
  • [Presentation] 溶質周囲の水のダイナミクスと分極電荷の計算2009

    • Author(s)
      塩見友樹、石尾広武、高橋卓也
    • Organizer
      第23回分子シミュレーション討論会
    • Place of Presentation
      吹上ホール、愛知県
    • Year and Date
      2009-12-03
    • Related Report
      2009 Annual Research Report
  • [Presentation] Calculations of dynamics and polarized charges of water molecules in ATP hydrolysis2009

    • Author(s)
      高橋卓也、石尾広武 、塩見友樹、鈴木誠
    • Organizer
      日本生物物理学会第47 回年会
    • Place of Presentation
      徳島文理大学(徳島県)
    • Year and Date
      2009-10-31
    • Related Report
      2012 Final Research Report
  • [Presentation] 溶質周囲の水のダイナミクスと分極電荷計算2009

    • Author(s)
      塩見友樹、石尾広武、高橋卓也
    • Organizer
      第3 回分子科学討論会
    • Place of Presentation
      名古屋大学(愛知県)
    • Year and Date
      2009-09-24
    • Related Report
      2012 Final Research Report
  • [Presentation] 生体分子およびイオン周囲の水のMD シミュレーションと量子化学計算2009

    • Author(s)
      高橋 卓也、猿渡 茂、田草川 英昇、村松 憲吾、菅原 洋子
    • Organizer
      第9 回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ(熊本県)
    • Year and Date
      2009-05-22
    • Related Report
      2012 Final Research Report
  • [Presentation] 生体分子およびイオン周囲の水のMDシミュレーションと量子化学計算2009

    • Author(s)
      高橋卓也
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ、熊本県
    • Related Report
      2009 Annual Research Report
  • [Presentation] Calculations of dynamics and polarized charges of water molecules in ATP hydrolysis2009

    • Author(s)
      Takuya Takahashi, Hiromu Ishio, Tomoki Shiomi, Makoto Suzuki
    • Organizer
      日本生物物理学会第47回年会
    • Place of Presentation
      徳島文理大学、徳島県
    • Related Report
      2009 Annual Research Report
  • [Presentation] 溶質分子周囲の水のダイナミックス計算2008

    • Author(s)
      高橋卓也
    • Organizer
      分子の電荷と形の効果、学会名等:バイオスーパーコンピューティングシンポジウム(BSCS)2008
    • Place of Presentation
      MY PLAZAホール(東京都)
    • Year and Date
      2008-12-26
    • Related Report
      2012 Final Research Report
  • [Presentation] Investigation of hydrating water dynamics through MD and QM2008

    • Author(s)
      高橋卓也
    • Organizer
      日本生物物理学会第46 回年会
    • Place of Presentation
      福岡国際会議場(福岡県)
    • Year and Date
      2008-12-04
    • Related Report
      2012 Final Research Report
  • [Presentation] 分子動力学と量子化学計算による水和現象の予測2008

    • Author(s)
      塩見友樹、高橋卓也
    • Organizer
      日本生物物理学会第46 回年会
    • Place of Presentation
      福岡国際会議場(福岡県)
    • Year and Date
      2008-12-03
    • Related Report
      2012 Final Research Report
  • [Presentation] 分子動力学と量子化学計算による水和現象の予測Investigation of hydrating water dynamics through MD and QM2008

    • Author(s)
      高橋卓也
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡国際会議場(福岡県)
    • Year and Date
      2008-12-03
    • Related Report
      2008 Annual Research Report
  • [Presentation] Three-dimensional imaging of interface atoms using crystal-truncation rod scattering2008

    • Author(s)
      Masanori Ootaki, Shigeru Endo, Yoko Sugawara, Takuya Takahashi, and Masayosi Nakasako
    • Organizer
      XXI Congress and General Assembly of the International Union of Crystallography
    • Place of Presentation
      大阪国際会議場(大阪府)
    • Related Report
      2012 Final Research Report
  • [Book] Molecular Dynamics - Studies of Synthetic and Biological Macromolecules, Practical Estimation of TCR-pMHC Binding Free-Energy Based on the Dielectric Model and the Coarse-Grained Model2012

    • Author(s)
      Tsurui Hiromichi, Takuya Takahashi
    • Total Pages
      432
    • Publisher
      InTech - Open Access Company
    • Related Report
      2012 Final Research Report
  • [Book] Molecular Dynamics-Studies of Synthetic and Biological Macrom olecules, ISBN:978-953-51-0444-5 Practical Estimation of TCR-pMHC Binding Free-Energy Based on the Dielectric Model and the Coarse-Grained Model2012

    • Author(s)
      Tsurui Hiromichi, Takuya Takahashi
    • Total Pages
      432
    • Publisher
      InTech-Open Access Company
    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://www.ritsumei.ac.jp/~tkhs/kaken.pdf

    • Related Report
      2012 Final Research Report
  • [Remarks] http://www.ritsumei.ac.jp/~tkhs/kaken.pdf

    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://www.ritsumei.ac.jp/~tkhs/kaken.pdf

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://www.ritsumei.ac.jp/~tkhs/kaken21.pdf

    • Related Report
      2009 Annual Research Report

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Published: 2008-04-01   Modified: 2018-03-28  

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