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Computation of the free-energy landscape of a protein involving α and β secondary-structure elements

Research Project

Project/Area Number 19570156
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionOsaka University

Principal Investigator

HIGO Junichi  Osaka University, 臨床医工学融合研究教育センター, 特任研究員 (80265719)

Project Period (FY) 2007 – 2008
Project Status Completed (Fiscal Year 2008)
Budget Amount *help
¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2008: ¥260,000 (Direct Cost: ¥200,000、Indirect Cost: ¥60,000)
Fiscal Year 2007: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Keywordsフォールディング / 自由エネルギー地形 / マルチカノニカル / WWドメイン / ヒューマニン
Research Abstract

α/βの両方の二次構造を含む50残基のタンパク質Pina WW domain の自由エネルギー地形を求めるために、水をあらわに取り込んだ全原子タンパク質モデルでマルチカノニカル分子動力学計算を行った。天然構造から変性構造までを含む多様な立体構造集団を得て、自由エネルギー地形を求めた。シミュレーションは安価な小規模クラスターマシンを使用した。また、多数本のマルチカノニカルランを統合し、構造探索の効率を高める手法を開発した

Report

(3 results)
  • 2008 Annual Research Report   Final Research Report ( PDF )
  • 2007 Annual Research Report
  • Research Products

    (35 results)

All 2009 2008 2007

All Journal Article (7 results) (of which Peer Reviewed: 7 results) Presentation (26 results) Book (2 results)

  • [Journal Article] Verifying trivial parallelization of multicanonical molecular dynamics for conformational sampling of a polypeptide in explicit water2009

    • Author(s)
      J. Higo, N. Kamiya, T. Sugihara, Y.Yonezawa, H. Nakamur
    • Journal Title

      Chem. Phys. Lett 473

      Pages: 326-329

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Parallelization of Markov chain generation and its application to the multicanonical method2009

    • Author(s)
      T. Sugihara, J. Higo, H. Nakamura
    • Journal Title

      J. Phys. Soc. Jpn. (in press)

    • NAID

      10025962130

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] arXiv2009

    • Author(s)
      Takanori Sugihara, Junichi Higo, Haruki Nakamura
    • Journal Title

      0812

      Pages: 2964-2964

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure dependency of a 24-residue peptide humanin on solvent and preferential solvation by trifluoroethanol studied by multicanonical sampling2008

    • Author(s)
      R. Yagisawa, N. Kamiya, J. Ikebe, K.Umezawa, J. Higo
    • Journal Title

      Chem. Phys. Lett. 455

      Pages: 293-296

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure dependency of a 24-residue peptide humanin on solvent and preferential solvation by trifluoroethanol studied by multicanonical sampling2008

    • Author(s)
      Ryosuke Yagisawa
    • Journal Title

      Chemical Physics Letters 455

      Pages: 293-296

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces2008

    • Author(s)
      Kazuyosi Ikeda
    • Journal Title

      BMC Structural Biology 8

      Pages: 37-37

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure dependency of a 24-residue peptide humanin on solvent and preferential solvation by trifluoroethanol studied by multicanonical sampling2008

    • Author(s)
      Ryosuke Yagisawa
    • Journal Title

      Chemical Physics Letters (in press)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] アルツハイマーβアミロイドペプチド構造の分子シミュレーション2009

    • Author(s)
      肥後順一
    • Organizer
      物理学会年会(春)
    • Place of Presentation
      東京
    • Year and Date
      2009-03-29
    • Related Report
      2008 Final Research Report
  • [Presentation] Fair current, vortex, and drying/wetting water flow around lysozyme investigated by molecular dynamics simulation2008

    • Author(s)
      K. Umezawa, R. Morikawa, H. Nakamura, J.Higo
    • Organizer
      生物物理学会年会
    • Place of Presentation
      福岡
    • Year and Date
      2008-12-05
    • Related Report
      2008 Final Research Report
  • [Presentation] Identification of essential variables for medium-size protein-segment and application to structural class assignment2008

    • Author(s)
      K. Ikeda, J. Higo, K. Tomii
    • Organizer
      生物物理学会年会
    • Place of Presentation
      福岡
    • Year and Date
      2008-12-04
    • Related Report
      2008 Final Research Report
  • [Presentation] Two types universality of a fold universe of 50-residue segment2008

    • Author(s)
      J. Ito, Y. Sonobe, K. Ikeda, K. Tomii, A.Yamagishi, J. Higo
    • Organizer
      生物物理学会年会
    • Place of Presentation
      福岡
    • Year and Date
      2008-12-04
    • Related Report
      2008 Final Research Report
  • [Presentation] Structure variation of a 24-residue peptide on solvent, and preferential solvation by trifluroethanol by multicanonical sampling2008

    • Author(s)
      R. Yagisawa, N. Kamiya, A. Yamagishi, J.Higo
    • Organizer
      生物物理学会年会
    • Place of Presentation
      福岡
    • Year and Date
      2008-12-03
    • Related Report
      2008 Final Research Report
  • [Presentation] Multicanonical molecular dynamics simulation of a protein with 57 residues in explicit water2008

    • Author(s)
      J, Ikebe, J. Higo, H. Nakamura
    • Organizer
      生物物理学会年会
    • Place of Presentation
      福岡
    • Year and Date
      2008-12-03
    • Related Report
      2008 Final Research Report
  • [Presentation] Brownian dynamics simulation of hERG potassium ion channel and development of an accurate molecular docking method for protein and ligand2008

    • Author(s)
      N. Kamiya, J. Higo
    • Organizer
      The 3rd MEI International Symposium
    • Place of Presentation
      San Francisco, USA.
    • Year and Date
      2008-11-30
    • Related Report
      2008 Final Research Report
  • [Presentation] アルファ/べータ両方の二次構造要素を含む40残基蛋白質のフォールディングシミュレーション2008

    • Author(s)
      肥後順一、池部仁善、神谷成敏、中村春木
    • Organizer
      物理学会年会(秋)
    • Place of Presentation
      山形
    • Year and Date
      2008-09-22
    • Related Report
      2008 Final Research Report
  • [Presentation] アルファ/ベーダ両方の二次構造要素を含む40残基蛋白質のフォールディングシミュレーション2008

    • Author(s)
      肥後順一
    • Organizer
      日本物理学会2008年秋期大会
    • Place of Presentation
      岩手大学上田キャンパス
    • Year and Date
      2008-09-22
    • Related Report
      2008 Annual Research Report
  • [Presentation] マルチカノニカル分子動力学法によるアミロイドペプチドの会合シミュレーション2008

    • Author(s)
      神谷成敏,米澤康滋、中村春木、肥後順一
    • Organizer
      物理学会年会(秋)
    • Place of Presentation
      山形
    • Year and Date
      2008-09-20
    • Related Report
      2008 Final Research Report
  • [Presentation] 蛋白質周辺における水分子の協調的挙動の分子動力学シミュレーションによる解析2008

    • Author(s)
      梅澤公二、肥後順一、中村春木、田代櫻子、神藤平三郎
    • Organizer
      物理学会年会(秋)
    • Place of Presentation
      山形
    • Year and Date
      2008-09-20
    • Related Report
      2008 Final Research Report
  • [Presentation] マルチカノニカル分子動力学シミュレーションによって描かれるdisordered protein (水中アミロイドβ 12-36 残基断片)の自由エネルギー地形2008

    • Author(s)
      池部仁善、神谷成敏、伊東純一,神藤平三郎、中村春木、肥後順一
    • Organizer
      物理学会年会(秋)
    • Place of Presentation
      山形
    • Year and Date
      2008-09-20
    • Related Report
      2008 Final Research Report
  • [Presentation] An enhanced conformational sampling of a 40-residue protein consisting of alpha and beta secondary structures in explicit solvent2008

    • Author(s)
      J. Higo, N. Kamiya
    • Organizer
      The Joint 2nd Pacific Rim International Conference on Protein Science and 4th Asian-Oceania Human Proteome Organization
    • Place of Presentation
      ケアンズ、オーストラリア
    • Year and Date
      2008-06-24
    • Related Report
      2008 Final Research Report
  • [Presentation] Assembly simulation of four peptide chains in explicit water by multicanonical molecular dynamics2008

    • Author(s)
      N. Kamiya, Y. Yonezawa, H. Nakamura, J.Higo
    • Organizer
      The Joint 2nd Pacific Rim International Conference on Protein Science and 4th Asian-Oceania Human Proteome Organization
    • Place of Presentation
      ケアンズ、オーストラリア
    • Year and Date
      2008-06-24
    • Related Report
      2008 Final Research Report
  • [Presentation] アルファ/ベータ両二次構造を含む40残基蛋白質の立体構造サンプリング2008

    • Author(s)
      肥後順一、池部仁善、神谷成敏、中村春木
    • Organizer
      蛋白質科学会年会
    • Place of Presentation
      東京
    • Year and Date
      2008-06-11
    • Related Report
      2008 Final Research Report
  • [Presentation] 蛋白質周辺における水の協調的な流れの分子動力学シミュレーションによる解析2008

    • Author(s)
      梅澤公二、肥後順一、山岸明彦、中村春木、田代櫻子、神藤平三郎
    • Organizer
      蛋白質科学会年会
    • Place of Presentation
      東京
    • Year and Date
      2008-06-11
    • Related Report
      2008 Final Research Report
  • [Presentation] マルチカノニカル分子動力学法によるアミロイドペプチド4本鎖の会合シミュレーション2008

    • Author(s)
      神谷成敏、米澤康滋、中村春木、肥後順一
    • Organizer
      蛋白質科学会年会
    • Place of Presentation
      東京
    • Year and Date
      2008-06-10
    • Related Report
      2008 Final Research Report
  • [Presentation] Disordered proteinである水中アルツハイマーβアミロイドペプチドAβ(12-36)の自由エネルギー地形2008

    • Author(s)
      池部仁善、神谷成敏、伊東純一、神藤平三郎、肥後順一
    • Organizer
      蛋白質科学会年会
    • Place of Presentation
      東京
    • Year and Date
      2008-06-10
    • Related Report
      2008 Final Research Report
  • [Presentation] マルチカノニカル分子動力学法による水中および30%TFE溶液中でのhumaninの自由エネルギー地形2007

    • Author(s)
      八木沢良介
    • Organizer
      第45回生物物理学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川)
    • Year and Date
      2007-12-21
    • Related Report
      2007 Annual Research Report
  • [Presentation] Prediction of protein structure from the free-energy landscapes2007

    • Author(s)
      J. Higo, N. Kamiya
    • Organizer
      The 2nd MEI International Symposium
    • Place of Presentation
      Osaka
    • Year and Date
      2007-12-08
    • Related Report
      2008 Final Research Report
  • [Presentation] Structure universe of 50-residue protein segments constructed by residue-residue native contacts2007

    • Author(s)
      Y. Sonobe, J. Ito, A. Yamagishi, K. Tomii, J.Higo
    • Organizer
      情報計算化学生物学会2007年大会
    • Place of Presentation
      広島
    • Year and Date
      2007-10-05
    • Related Report
      2008 Final Research Report
  • [Presentation] Free-energy landscapes of humanin in water and in TFE/water using multicanonical molecular dynamics2007

    • Author(s)
      R. Yagisawa, N. Kamiya, A. Yamagishi, J.Higo
    • Organizer
      情報計算化学生物学会2007年大会
    • Place of Presentation
      広島
    • Year and Date
      2007-10-05
    • Related Report
      2008 Final Research Report
  • [Presentation] A process of protein-ligand approach mediated by solvent-dipole field2007

    • Author(s)
      N. Takano, N. Hamasaki, H. Miyagawa, A.Yamagishi, J. Higo
    • Organizer
      情報計算化学生物学会2007年大会
    • Place of Presentation
      広島
    • Year and Date
      2007-10-05
    • Related Report
      2008 Final Research Report
  • [Presentation] Conformational sampling of a 40-residue protein consisting of alpha and beta secondary-structure elements in explicit solvent2007

    • Author(s)
      J. Higo, J. Ikebe, N. Kamiya, H. Nakamura,H. Shindo
    • Organizer
      情報計算化学生物学会2007年大会
    • Place of Presentation
      広島
    • Year and Date
      2007-10-04
    • Related Report
      2008 Final Research Report
  • [Presentation] Free-energy landscape of the disordered state of an Altzheimer's beta amyloid peptide in water studied by multicanonical molecular dynamics2007

    • Author(s)
      J. Ikebe, N. Kamiya, J. Ito, H. Shindo, A.Yamagishi, J, Higo
    • Organizer
      情報計算化学生物学会2007年大会
    • Place of Presentation
      広島
    • Year and Date
      2007-10-04
    • Related Report
      2008 Final Research Report
  • [Presentation] Collective water flows around a protein : a novel insight into explicit solvent characteristics2007

    • Author(s)
      K. Umezawa, J. Higo, A. Yamagishi, S.Tashiro, H. Shindo
    • Organizer
      情報計算化学生物学会2007年大会
    • Place of Presentation
      広島
    • Year and Date
      2007-10-04
    • Related Report
      2008 Final Research Report
  • [Book] 蛋白質の水和とフォールディング2008

    • Author(s)
      肥後順一
    • Publisher
      「物性研究」(物性研究刊行会)
    • Related Report
      2008 Final Research Report
  • [Book] 物性研究2008

    • Author(s)
      肥後順一
    • Total Pages
      4
    • Publisher
      京都大学物性研究刊行会
    • Related Report
      2008 Annual Research Report

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Published: 2007-04-01   Modified: 2016-04-21  

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