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A hybrid extended ensemble simulation study on the folding process of proteins

Research Project

Project/Area Number 24570189
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biophysics
Research InstitutionKinki University

Principal Investigator

YONEZAWA Yasushige  近畿大学, 先端技術総合研究所, 教授 (40248753)

Co-Investigator(Kenkyū-buntansha) KIKUGAWA Gouta  東北大学, 講師 (90435644)
FUJISAWA Masao  近畿大学, 生物理工学部, 教授 (20258065)
YOSHIDA Hisashi  近畿大学, 生物理工学部, 教授 (50278735)
Co-Investigator(Renkei-kenkyūsha) TACHIBANA Hideki  近畿大学, 生物理工学部, 教授 (70126118)
AKASAKA Kazuyuki  近畿大学, 先端技術総合研究所, 客員教授 (50025368)
Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2013: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2012: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Keywords蛋白質 / 分子シミュレーション / 拡張アンサンブル法 / 蛋白質構造 / 反応座標 / 構造空間探索 / 蛋白質フォールディング / フォールディング / 分子動力学シミュレーション
Outline of Final Research Achievements

We have applied our extended ensemble simulation, MCMD-METAD hybrid method to the several typical issues of protein simulations. Our method has a remarkable advantages against old similar methods, providing clear convergence property. We implemented the method to our molecular dynamics simulation program. Moreover, we then developed a novel long-range potential which significantly accelerates simulations. We implemented it to our simulation program, evaluating properties of several bio-systems. As a results, we found that the search ability of taboo like method, such as METAD, is strongly depend on the pre-determined reaction coordinate. This suggests the good reaction coordinate determination is of paramount importance for protein simulation studies.

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • 2012 Research-status Report
  • Research Products

    (11 results)

All 2014 2013

All Journal Article (2 results) (of which Peer Reviewed: 2 results) Presentation (9 results) (of which Invited: 2 results)

  • [Journal Article] Molecular Dynamics Study of the Phosphorylation Effect on the Conformational States of the C-terminal Domain of RNA Polymerase II2014

    • Author(s)
      Y.Yonezawa
    • Journal Title

      J. Phys. Chem. B

      Volume: 118 Issue: 17 Pages: 4471-4478

    • DOI

      10.1021/jp4101976

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Electrostatic properties of water models evaluated by a long-range potential based solely on the Wolf charge-neutral condition2013

    • Author(s)
      Yasushige Yonezawa
    • Journal Title

      Chemical Physics Letter

      Volume: 556 Pages: 308-314

    • DOI

      10.1016/j.cplett.2012.12.028

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Presentation] マルチカノニカル分子動力学法によるRNAポリメラーゼII-C末端領域の構造空間探索2014

    • Author(s)
      米澤康滋
    • Organizer
      分子シミュレーション討論会
    • Place of Presentation
      仙台市民会館(宮城県仙台市)
    • Year and Date
      2014-11-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] HPC と 蛋白質分子計算科学シミュレーション2014

    • Author(s)
      米澤康滋
    • Organizer
      筑波大学計算科学センターセミナー
    • Place of Presentation
      筑波大学計算科学センター(茨城県つくば市)
    • Year and Date
      2014-11-07
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] RNAポリメラーゼC末端領域構造の分子シミュレーション研究2014

    • Author(s)
      米澤康滋
    • Organizer
      第8回分子科学討論会
    • Place of Presentation
      広島大学(広島県東広島市)
    • Year and Date
      2014-09-22
    • Related Report
      2014 Annual Research Report
  • [Presentation] 分子動力学シミュレーションによる真核生物RNAポリメラーゼIIのC末端領域の構造特性の研究2014

    • Author(s)
      米澤康滋
    • Organizer
      第41回生体分子科学討論会
    • Place of Presentation
      九州大学西新プラザ(福岡県福岡市)
    • Year and Date
      2014-06-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] RNA ポリメラーゼ II の C 末端領域の分子シミュレーションによる構造空間解析2014

    • Author(s)
      米澤康滋
    • Organizer
      第17回理論化学討論会
    • Place of Presentation
      名古屋大学(愛知県名古屋市)
    • Year and Date
      2014-05-22 – 2014-05-24
    • Related Report
      2014 Annual Research Report
  • [Presentation] COMPUTATIONAL STUDY ON THE DYNAMIC CONFORMATIONAL CHANGE OF C-TERMINAL DOMAIN OF RNA POLRIMERASE II2014

    • Author(s)
      米澤康滋
    • Organizer
      「動的秩序と機能」第2回公開国際シンポジウム
    • Place of Presentation
      キャンパスプラザ京都(京都府京都市)
    • Related Report
      2013 Research-status Report
  • [Presentation] 構造と機能に関わる蛋白質の自由エネルギー地形探索2013

    • Author(s)
      米澤康滋
    • Organizer
      化学反応経路探索のニューフロンティア2013
    • Place of Presentation
      福井謙一記念研究センター(京都府京都市)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] マルチカノニカル法によるRNAポリメラーゼC末端領域の研究2013

    • Author(s)
      米澤康滋
    • Organizer
      第7回分子科学討論会
    • Place of Presentation
      京都テルサ(京都府京都市)
    • Related Report
      2013 Research-status Report
  • [Presentation] Study on the C-terminal domain of eukaryotic RNA polymerase II by2013

    • Author(s)
      米澤康滋
    • Organizer
      第3回分子シミュレーション国際学会(ICMS2013)
    • Place of Presentation
      神戸国際会議場(兵庫県神戸市)
    • Related Report
      2013 Research-status Report

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Published: 2013-05-31   Modified: 2019-07-29  

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