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Theoretical Study of Molecular functions of Proteins

Research Project

Project/Area Number 16H04776
Research Category

Grant-in-Aid for Scientific Research (B)

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

Principal Investigator

Hayashi Shigehiko  京都大学, 理学研究科, 教授 (70402758)

Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2018: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2017: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2016: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Keywords分子シミュレーション / 光受容体タンパク質 / 酵素反応 / 光遺伝学 / QM/MM 法 / 分子モーター / 光受容体
Outline of Final Research Achievements

Protein functions are fulfilled by correlation among various phenomena on different spatial and temporal scales ranging from enzymatic reactions to global conformational changes of proteins. By using a novel molecular simulation approach developed recently by us, QM/MM RWFE-SCF, which is capable of describing such correlations of various phenomena on different scale, we succeeded in obtaining novel molecular mechanistic insights into photo-activation processes of LOV photo-receptor and channelrhodopsin, and enzymatic catalysis of HIV protease.

Academic Significance and Societal Importance of the Research Achievements

本研究で扱っている光受容体タンパク質や酵素では、その顕著な分子機能において、光化学反応や酵素反応などの局所的な電子状態変化と大きなタンパク質分子の構造変化のスケールの異なる現象が関わっており、従来の理論的解析が困難であった。本研究では、新規の理論的手法により、その困難を解決し、原子レベルからの分子機構の解明に成功した。これにより、神経科学分野における新規なタンパク質ツールの開発や、 HIV 感染の治療薬における薬剤耐性の問題の解決に向けての道が開かれた。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (22 results)

All 2019 2018 2017 2016

All Journal Article (7 results) (of which Peer Reviewed: 6 results,  Open Access: 5 results,  Acknowledgement Compliant: 2 results) Presentation (15 results) (of which Int'l Joint Research: 7 results,  Invited: 10 results)

  • [Journal Article] An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin2018

    • Author(s)
      Cheng Cheng, Motoshi Kamiya, Mizuki Takemoto, Ryuichiro Ishitani, Osamu Nureki, *Norio Yoshida, and *Shigehiko Hayashi
    • Journal Title

      Biophysical Journal

      Volume: 115 Issue: 7 Pages: 1281-1291

    • DOI

      10.1016/j.bpj.2018.08.024

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Atomistic modeling of alternating access of a mitochondrial ADP/ATP membrane transporter with molecular simulations2017

    • Author(s)
      Koichi Tamura and Shigehiko Hayashi*
    • Journal Title

      PLOS ONE

      Volume: 12 Issue: 7 Pages: e0181489-e0181489

    • DOI

      10.1371/journal.pone.0181489

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A polyaromatic nanocapsule as a sucrose receptor in water2017

    • Author(s)
      Masahiro Yamashina, Munetaka Akita, Taisuke Hasegawa, Shigehiko Hayashi, and Michito Yoshizawa*
    • Journal Title

      Science Advances

      Volume: 3 Issue: 8

    • DOI

      10.1126/sciadv.1701126

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] QM/MM geometry optimization on extensive free-energy surfaces for examination of enzymatic reactions and design of novel functional properties of proteins2017

    • Author(s)
      Shigehiko Hayashi*, Yoshihiro Uchida, Taisuke Hasegawa, Masahiro Higashi, Takahiro Kosugi, and Motoshi Kamiya
    • Journal Title

      Annual Review of Physical Chemistry

      Volume: 63 Issue: 1 Pages: 135-154

    • DOI

      10.1146/annurev-physchem-052516-050827

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] ハイブリッド分子シミュレーションによるロドプシン光受容体の分子機能の理解と設計2017

    • Author(s)
      林重彦
    • Journal Title

      医学のあゆみ - 第5土曜特集号「生命現象を観る-革新的な構造生命科学が観せてくれる世界」

      Volume: 262 Pages: 552-558

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Photoactivation intermediates of a G-protein coupled receptor rhodopsin investigated by a hybrid molecular simulation.2017

    • Author(s)
      Motoshi Kamiya and Shigehiko Hayashi*
    • Journal Title

      Journal of Physical Chemistry B

      Volume: 121 Issue: 15 Pages: 3842-3852

    • DOI

      10.1021/acs.jpcb.6b13050

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] X-ray crystallographic structure of thermophilic rhodopsin: implications for high thermal stability and optogenetic function2016

    • Author(s)
      Tsukamoto T, Mizutani K, Hasegawa T, Takahashi M, Honda N, Hashimoto N, Shimono K, Yamashita K, Yamamoto M, Miyauchi S, Takagi S, Hayashi S, Murata T, Sudo Y.
    • Journal Title

      J. Biol. Chem.

      Volume: in press Issue: 23 Pages: 12223-12232

    • DOI

      10.1074/jbc.m116.719815

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 分子シミュレーションによるAsLOV2光受容タンパク質の光活性化中間状態2019

    • Author(s)
      田口真彦、成セイ、東村智佳、内田芳裕、林重彦
    • Organizer
      第16回京都大学福井謙一記念研究センターシンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] Functional Molecular Dynamics of Photo-Receptor Proteins Revealed by a Hybrid Molecular Simulation Technique2018

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Indo-Japan mini-workshop “Frontiers in Molecular Spectroscopy: From Fundamentals to Applications in Chemistry and Biology”
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 柔らかな分子がもたらす分子機能の理解と設計2018

    • Author(s)
      林 重彦
    • Organizer
      近畿化学協会コンピュータ化学部会(第103回例会)公開講演会「大規模シミュレーションによる機能発現の理解~分子領域からマクロ領域まで~
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Photoactivation Intermediate of AsLOV2 Photoreceptor Protein Investigated by a Hybrid Molecular Simulation2018

    • Author(s)
      Masahiko Taguchi, Cheng Cheng, Chika Higashimura, Shigehiko Hayashi
    • Organizer
      FUKUI 2018 Satelite Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Functional molecular dynamics of rhodopsins revealed by hybrid molecular simulations2018

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      18th International Conference on Retinal Proteins
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Molecular simulation on light-activation mechanism of LOV photoreceptor protein2018

    • Author(s)
      Masahiko Taguchi, Cheng Cheng, Chika Higashimura, Shigehiko Hayashi
    • Organizer
      第56回日本生物物理学会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Functional Molecular Dynamics of Photo-Receptor Proteins Revealed by a Hybrid Molecular Simulation Technique2018

    • Author(s)
      林 重彦
    • Organizer
      第56回日本生物物理学会・シンポジウム “マルチスケール・フィジクスで見えてくる生体高分子のダイナミクスと機能機序”
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Ab initio evaluation of redox potential of metalloprotein2018

    • Author(s)
      Cheng Cheng, Shigehiko Hayashi
    • Organizer
      第56回日本生物物理学会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Theoretical study on molecular mechanism of a light-driven ion transport of Halorhodopsin2018

    • Author(s)
      Ryo Oyama,Taisuke Hasegawa,Shigehiko Hayashi
    • Organizer
      第56回日本生物物理学会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 超分子カプセルの分子内包能と動的挙動2017

    • Author(s)
      林 重彦、吉沢道人
    • Organizer
      日本化学会 第97春季年会 シンポジウム「複雑系のための分子科学―理論、計測、合成の連携で拓く柔らかな分子の新機能」
    • Place of Presentation
      日吉・神奈川
    • Year and Date
      2017-03-16
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Understanding and designing color variants of retinal binding proteins by molecular simulations2017

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      253rd American Chemical Society National Meeting (San Francisco, USA)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Understanding and designing color variants of retinal binding proteins by molecular simulations2017

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Telluride Science Research Center Workshop on “Protein Dynamics” (Telluride, USA)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Crucial Role of Protein Flexibility in Enzymatic Catalysis2016

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Japan-France-Spain Joint-Symposium on Theoretical and Computational Science of Complex Systems
    • Place of Presentation
      ソウル・韓国
    • Year and Date
      2016-09-21
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 柔らかいタンパク質の分子機能理解と設計2016

    • Author(s)
      林 重彦
    • Organizer
      第10回分子科学討論会
    • Place of Presentation
      神戸・兵庫
    • Year and Date
      2016-09-13
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Crucial Role of Protein Flexibility in Enzymatic Catalysis2016

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      IAS Focused Program on “Molecular Machines of Life: Simulations Meets Experiment
    • Place of Presentation
      香港・中国
    • Year and Date
      2016-05-23
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited

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Published: 2016-04-21   Modified: 2020-03-30  

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