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Molecular mechanisms of the ion channel gating

Research Project

Project/Area Number 15H05594
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Biophysics
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

MORI Takaharu  国立研究開発法人理化学研究所, 杉田理論分子科学研究室, 研究員 (90402445)

Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥22,750,000 (Direct Cost: ¥17,500,000、Indirect Cost: ¥5,250,000)
Fiscal Year 2017: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
Fiscal Year 2016: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2015: ¥7,930,000 (Direct Cost: ¥6,100,000、Indirect Cost: ¥1,830,000)
Keywords分子動力学 / 膜タンパク質 / イオンチャネル / 分子動力学計算 / 生物物理 / 蛋白質 / 生体膜 / 分子動力学シミュレーション / 分子シミュレーション
Outline of Final Research Achievements

Since membrane proteins are large bimolecular systems, it is difficult to simulate their large conformational changes like gating of ion channel proteins by using conventional methods. To solve such problems, we developed new methods such as the multi-dimensional replica-exchange method, implicit solvent model, and parallel computing algorithm for cryo-EM flexible fitting. By using these methods, we simulated the P2X4 receptor, and elucidated the molecular mechanisms of the channel gating.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (13 results)

All 2017 2016 2015

All Journal Article (1 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 1 results,  Open Access: 1 results) Presentation (12 results) (of which Int'l Joint Research: 2 results)

  • [Journal Article] Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms2016

    • Author(s)
      Takaharu Mori, Naoyuki Miyashita, Wonpil Im, Michael Feig, Yuji Sugita
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - Biomembranes

      Volume: in Press Issue: 7 Pages: 1635-1651

    • DOI

      10.1016/j.bbamem.2015.12.032

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 拡張アンサンブルシミュレーションによる膜輸送体の動作原理の解明2017

    • Author(s)
      森貴治
    • Organizer
      第4回HPCI成果報告会
    • Related Report
      2017 Annual Research Report
  • [Presentation] プロトン透過が関与する膜タンパク質の動作原理の解明2017

    • Author(s)
      森貴治
    • Organizer
      第4回HPCI成果報告会
    • Related Report
      2017 Annual Research Report
  • [Presentation] クライオ電子顕微鏡像フィッティングシミュレーションの新規並列計算法の開発2017

    • Author(s)
      森貴治、Marta Kulik、宮下治、Florence Tama、杉田有治
    • Organizer
      第31回分子シミュレーション討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Efficient parallel computation for flexible fitting of cryo-EM density map2017

    • Author(s)
      Takaharu Mori, Osamu Miyashita, Yuji Sugita
    • Organizer
      Biophysical Society Thematic Meeting “Conformational Ensembles from Experimental Data and Computer Simulations”
    • Related Report
      2017 Annual Research Report
  • [Presentation] 新規連続体近似モデルを用いた膜タンパク質のシミュレーション2017

    • Author(s)
      森貴治、杉田有治
    • Organizer
      日本物理学会 2017年秋季大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 膜模倣環境の膜タンパク質構造への影響を評価する新規シミュレーション法の開発2017

    • Author(s)
      森貴治、杉田有治
    • Organizer
      第17回 日本蛋白質科学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Molecular mechanisms of proton transfer in the protein secretion motor SecDF2017

    • Author(s)
      Takaharu Mori, Tomoya Tsukazaki, Yuji Sugita
    • Organizer
      IUPAB & EBSA 2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] 新規Implicit membraneモデルの開発と膜タンパク質系への応用2017

    • Author(s)
      森貴治、杉田有治
    • Organizer
      日本物理学会第72回年次大会
    • Place of Presentation
      大阪
    • Related Report
      2016 Annual Research Report
  • [Presentation] 拡張アンサンブル法の混合脂質二重膜系への応用2015

    • Author(s)
      森貴治、杉田有治
    • Organizer
      第29回分子シミュレーション討論会
    • Place of Presentation
      朱鷺メッセ(新潟県・新潟市)
    • Year and Date
      2015-11-30
    • Related Report
      2015 Annual Research Report
  • [Presentation] Multidimensional surface-tension replica-exchange molecular-dynamics simulations of biological membranes2015

    • Author(s)
      Takaharu Mori, Yuji Sugita
    • Organizer
      Supercomputational Life Science 2015
    • Place of Presentation
      東京大学(東京都・文京区)
    • Year and Date
      2015-10-20
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Replica-exchange molecular-dynamics simulations of mixed lipid bilayer systems2015

    • Author(s)
      Takaharu Mori, Yuji Sugita
    • Organizer
      Biophysical Society Thematic Meeting “Biophysics of Proteins at Surfaces: Assembly, Activation, Signaling”
    • Place of Presentation
      コンプルテンセ大学(スペイン・マドリッド)
    • Year and Date
      2015-10-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 膜タンパク質-脂質相互作用の定量的解析法の開発と応用2015

    • Author(s)
      森貴治、杉田有治
    • Organizer
      第53回生物物理学会年会
    • Place of Presentation
      金沢大学(石川県・金沢市)
    • Year and Date
      2015-09-15
    • Related Report
      2015 Annual Research Report

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Published: 2015-04-16   Modified: 2019-03-29  

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