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Prediction of rare events associated with biomolecules using mean force dynamics

Research Project

Project/Area Number 17K05620
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biological physics/Chemical physics/Soft matter physics
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

Morishita Tetsuya  国立研究開発法人産業技術総合研究所, 材料・化学領域, 主任研究員 (10392672)

Co-Investigator(Kenkyū-buntansha) 米澤 康滋  近畿大学, 先端技術総合研究所, 教授 (40248753)
Project Period (FY) 2017-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2020: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2019: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2018: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2017: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Keywords自由エネルギー / レア・イベント / 分子動力学 / 機械学習 / 自由エネルギー計算 / レアイベント / 生体分子 / 平均力 / 位相空間 / 化学物理 / 分子動力学シミュレーション
Outline of Final Research Achievements

We have proposed an approach that incorporates time dependence in principal component analysis to identify each of step-by-step structural changes in molecular dynamics (MD) simulations (TDPCA). The time dependence allows for re-optimization of the principal components according to the structural development, which can be exploited for enhanced sampling in MD simulations. We have also developed algorithms that allow for reconstructing free-energy profiles along collective variables (CVs) by extending the logarithmic mean-force (LogMFD) dynamics. The logarithmic parallel-dynamics (LogPD) algorithm was proposed to efficiently reconstruct free-energy profiles using multiple replicas of the system based on Crooks-Jarzynski nonequilibrium work relation. Also, isokinetic dynamics was incorporated in LogMFD/PD to enable uniform sampling along the CVs. These new approaches allow for on-the-fly free-energy estimation, which can be implemented using an open-source library, PLUMED.

Academic Significance and Societal Importance of the Research Achievements

本研究では、分子シミュレーションが抱える時間スケールに関する問題に取り組み、従来では実現不可能な長時間現象を、限られた時間内において実現できる手法開発を推進した。これにより、複雑な構造を有する生体分子やナノ物質の原子レベルの長時間挙動を予測することが可能となり、ナノ材料設計や分子材料設計、ひいては創薬におけるシミュレーションによる開発促進に繋がることが期待される。

Report

(6 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (33 results)

All 2021 2020 2019 2018 2017 Other

All Journal Article (14 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 14 results,  Open Access: 6 results) Presentation (17 results) (of which Int'l Joint Research: 1 results,  Invited: 2 results) Remarks (2 results)

  • [Journal Article] Time-dependent principal component analysis: A unified approach to high-dimensional data reduction using adiabatic dynamics2021

    • Author(s)
      Tetsuya Morishita
    • Journal Title

      The Journal of Chemical Physics

      Volume: 155 Issue: 13 Pages: 134114-134114

    • DOI

      10.1063/5.0061874

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Autoencoder-based detection of the residues involved in G protein-coupled receptor signaling2021

    • Author(s)
      Tsuchiya Yuko、Taneishi Kei、Yonezawa Yasushige
    • Journal Title

      Scientific Reports

      Volume: 11 Issue: 1 Pages: 19867-19867

    • DOI

      10.1038/s41598-021-99019-z

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mutual information analysis of the dynamic correlation between side chains in proteins2021

    • Author(s)
      Miyashita Naoyuki、Yonezawa Yasushige
    • Journal Title

      The Journal of Chemical Physics

      Volume: 155 Issue: 4 Pages: 044107-044107

    • DOI

      10.1063/5.0055662

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Path ensembles for Pin1-catalyzed cis-trans isomerization of a substrate calculated by weighted ensemble simulations2021

    • Author(s)
      Kei Moritsugu, Norifumi Yamamoto, Yasushige Yonezawa, Shin-ichi Tate, and Hiroshi Fujisaki
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 17 Issue: 4 Pages: 2522-2529

    • DOI

      10.1021/acs.jctc.0c01280

    • Related Report
      2021 Annual Research Report 2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] Rebuilding Ring-Type Assembly of Peroxiredoxin by Chemical Modification2020

    • Author(s)
      Himiyama Tomoki、Tsuchiya Yuko、Yonezawa Yasushige、Nakamura Tsutomu
    • Journal Title

      Bioconjugate Chemistry

      Volume: 32 Issue: 1 Pages: 153-160

    • DOI

      10.1021/acs.bioconjchem.0c00587

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] Atomistic detailed free‐energy landscape of intrinsically disordered protein studied by multi‐scale divide‐and‐conquer molecular dynamics simulation2020

    • Author(s)
      Shimoyama Hiromitsu、Yonezawa Yasushige
    • Journal Title

      Journal of Computational Chemistry

      Volume: 42 Issue: 1 Pages: 19-26

    • DOI

      10.1002/jcc.26429

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] Epigenetic Protection of Vertebrate Lymphoid Progenitor Cells by Dnmt12020

    • Author(s)
      Iwanami Norimasa、Takeshita Kohei、Lawir Divine-Fondzenyuy、Suetake Isao、Tajima Shoji、Sikora Katarzyna、Trancoso In?s、?Meara Connor、Siamishi Iliana、Takahama Yousuke、Furutani-Seiki Makoto、Kondoh Hisato、Yonezawa Yasushige、Schorpp Michael、Boehm Thomas
    • Journal Title

      iScience

      Volume: 23 Issue: 7 Pages: 101260-101260

    • DOI

      10.1016/j.isci.2020.101260

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Traveling without dwelling: Extending the timescale accessible to molecular dynamics simulation2019

    • Author(s)
      Morishita Tetsuya、Ito Atsushi M.
    • Journal Title

      Physical Review Research

      Volume: 1 Issue: 3 Pages: 033032-033032

    • DOI

      10.1103/physrevresearch.1.033032

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Free energy profiles of lipid translocation across pure POPC and POPC/CHOL bilayer: all-atom molecular dynamics study2019

    • Author(s)
      Saito Hiroaki、Morishita Tetsuya、Mizukami Taku、Nishiyama Ken-ichi、Kawaguchi Kazutomo、Nagao Hidemi
    • Journal Title

      Journal of Physics: Conference Series

      Volume: 1290 Issue: 1 Pages: 012020-012020

    • DOI

      10.1088/1742-6596/1290/1/012020

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Loosening of Side-Chain Packing Associated with Perturbations in Peripheral Dynamics Induced by the D76N Mutation of β2-Microglobulin Revealed by Pressure-NMR and Molecular Dynamic Simulations2019

    • Author(s)
      Sakurai Kazumasa、Tomiyama Ryosuke、Shiraki Takuma、Yonezawa Yasushige
    • Journal Title

      Biomolecules

      Volume: 9 Issue: 9 Pages: 491-491

    • DOI

      10.3390/biom9090491

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Autoencoder-Based Detection of Dynamic Allostery Triggered by Ligand Binding Based on Molecular Dynamics2019

    • Author(s)
      Yuko Tsuchiya, Kei Taneishi, Yasushige Yonezawa
    • Journal Title

      J. Chem. Inf. Model.

      Volume: 59 Issue: 9 Pages: 4043-4051

    • DOI

      10.1021/acs.jcim.9b00426

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Promoting transparency and reproducibility in enhanced molecular simulations2019

    • Author(s)
      The PLUMED consortium
    • Journal Title

      Nature Methods

      Volume: 16 Issue: 8 Pages: 670-673

    • DOI

      10.1038/s41592-019-0506-8

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction2018

    • Author(s)
      Morishita Tetsuya、Nakamura Takenobu、Shinoda Wataru、Ito Atsushi M.
    • Journal Title

      Chemical Physics Letters

      Volume: 706 Pages: 633-640

    • DOI

      10.1016/j.cplett.2018.07.011

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories2017

    • Author(s)
      Morishita Tetsuya、Yonezawa Yasushige、Ito Atsushi M.
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 13 Issue: 7 Pages: 3106-3119

    • DOI

      10.1021/acs.jctc.7b00252

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Presentation] 時間依存主成分解析による構造転移の解析とサンプリング2021

    • Author(s)
      森下徹也
    • Organizer
      第35回分子シミュレーション討論会
    • Related Report
      2021 Annual Research Report
  • [Presentation] オートエンコーダーに基づく GPCR シグナル伝達経路解析2021

    • Author(s)
      土屋裕子、種石慶、米澤康滋
    • Organizer
      蛋白質科学会ワークショップ
    • Related Report
      2021 Annual Research Report
  • [Presentation] 計算科学シミュレーションを用いたタンパク質及びタンパク質複合体の動的相関解析の困難と新たな試み2021

    • Author(s)
      米澤康滋
    • Organizer
      蛋白質科学会ワークショップ
    • Related Report
      2021 Annual Research Report
  • [Presentation] Travelling without dwelling:ポアンカレ加速ダイナミクス2019

    • Author(s)
      森下 徹也、伊藤篤史
    • Organizer
      第33回分子シミュレーション討論会
    • Related Report
      2019 Research-status Report
  • [Presentation] LogMFDによる脂質分子の膜透過自由エネルギー曲線2019

    • Author(s)
      齋藤大明、森下 徹也
    • Organizer
      第13回分子科学討論会
    • Related Report
      2019 Research-status Report
  • [Presentation] Autoencoder-based analysis of dynamic allostery on proteins by regulator binding2019

    • Author(s)
      Y. Tsutiya, T. Taneishi, Y.Yonezawa
    • Organizer
      CBI学会2019年大会
    • Related Report
      2019 Research-status Report
  • [Presentation] Conformational Changes and Interact ions of Calcium Ion Signal Transfer Protein Calmodulin and Calmodulin-binding Domain by Multi-scale and Docking Simulation2019

    • Author(s)
      Hiromitsu Shimoyama, Yasushige Yonezawa
    • Organizer
      CBI学会2019年大会
    • Related Report
      2019 Research-status Report
  • [Presentation] Conformational Changes and Interactions of Calcium Ion Signal Transfer Protein Calmodulin and Calmodulin-binding Domains by Multi-scale and Docking Simulation2019

    • Author(s)
      H.Shimoyama, Y.Yonezawa
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] Autoencoder-based analysis of dynamic allostery on proteins by regulator binding2019

    • Author(s)
      Y. Tsutiya, T. Taneishi, Y.Yonezawa
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] Influence on the structure and dynamics of Riboswich “SPANISH” and potassium ions by DFHBI2019

    • Author(s)
      L.Matsukura, N. Onishi, M.Furue, N.Miyashita, T.SHiraki, Y.Yonezawa
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] 非平衡バスアンサンブルを用いた対数平均力ダイナミクス2019

    • Author(s)
      森下徹也
    • Organizer
      スーパーコンピューターワークショップ2018
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Logarithmic mean-force dynamics and its extension: polygonal silicene formation on the Al(111) surface2019

    • Author(s)
      Tetsuya Morishita
    • Organizer
      Computational Science Workshop2019
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] タンパク質のダイナミックアロステリー2018

    • Author(s)
      米澤 康滋
    • Organizer
      第32回分子シミュレーション討論会
    • Related Report
      2018 Research-status Report
  • [Presentation] ベイズ推定によるon-the-fly平均構造-共分散行列による数理解析手法の開発2018

    • Author(s)
      米澤 康滋
    • Organizer
      第21回理論化学討論会
    • Related Report
      2018 Research-status Report
  • [Presentation] ベイズ推定によるOn-the-fly MDシミュレーション平均構造決定及び動的解析方法2018

    • Author(s)
      米澤 康滋
    • Organizer
      第18回蛋白質科学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] Pin1由来のタンパク質分解酵素の触媒部位の構造ダイナミクス2018

    • Author(s)
      伊倉 貞吉、米澤 康滋、伊藤 暢聡
    • Organizer
      第18回蛋白質科学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 非平衡パスアンサンブルに基づく対数平均力ダイナミクス2017

    • Author(s)
      森下徹也、米澤康滋、伊藤篤史
    • Organizer
      第31回分子シミュレーション討論会
    • Related Report
      2017 Research-status Report
  • [Remarks] 森下徹也のホームページ

    • URL

      https://staff.aist.go.jp/t-morishita/index_jp.html

    • Related Report
      2021 Annual Research Report
  • [Remarks] PLUMED DOCUMENT: Logarithmic mean force dynamics

    • URL

      https://www.plumed.org/doc-v2.7/user-doc/html/_l_o_g_m_f_d_m_o_d.html

    • Related Report
      2021 Annual Research Report

URL: 

Published: 2017-04-28   Modified: 2023-01-30  

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