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Theoretical study on molecular mechanisms of protein functions

Research Project

Project/Area Number 25291034
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Biophysics
Research InstitutionKyoto University

Principal Investigator

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

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥17,940,000 (Direct Cost: ¥13,800,000、Indirect Cost: ¥4,140,000)
Fiscal Year 2015: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2014: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2013: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Keywords分子シミュレーション / ハイブリッド法 / タンパク質 / 酵素反応 / シグナル伝達タンパク質 / 光受容体 / 分子モーター / ハイブリッド QM/MM 法 / 分子動力学シミュレーション / 酵素 / モータータンパク質 / アロステリック効果 / G タンパク質 / 光受容タンパク質 / 光受容体タンパク質 / 多極子相互作用
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 enzymatic catalysis of Ras-GAP GTPase and its mutants, photoactivation process of rhodopsin visual receptor, and chemo-mechanical coupling of F1-ATPase molecular motor.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (33 results)

All 2015 2014 2013

All Journal Article (12 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 11 results,  Open Access: 3 results,  Acknowledgement Compliant: 3 results) Presentation (21 results) (of which Int'l Joint Research: 4 results,  Invited: 21 results)

  • [Journal Article] Atomistic design of microbial opsin-based blue-shifted optogenetics tools2015

    • Author(s)
      Kato HE, Kamiya M, Sugo S, Ito J, Taniguchi R, Orito A, Hirata K, Inutsuka A,Yamanaka A, Maturana AD, Ishitani R, Sudo Y, Hayashi S, Nureki O
    • Journal Title

      Nat Commun

      Volume: 6 Issue: 1 Pages: 7177-7177

    • DOI

      10.1038/ncomms8177

    • NAID

      120005745621

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Linear response path following: a molecular dynamics method to simulate global conformational changes of protein upon ligand binding2015

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

      Journal of Chemical Theory and Computation

      Volume: 11 Issue: 7 Pages: 2900-2917

    • DOI

      10.1021/acs.jctc.5b00120

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Molecular dynamics of channelrhodopsin at the early stages of channel opening2015

    • Author(s)
      Mizuki Takemoto, Hideaki E. Kato, Michio Koyama, Jumpei Ito, Motoshi Kamiya, Shigehiko Hayashi, Andres D. Maturana, Karl Deisseroth, Ryuichiro Ishitani, and Osamu Nureki
    • Journal Title

      PLoS ONE

      Volume: 10 Issue: 6 Pages: 0131094-0131094

    • DOI

      10.1371/journal.pone.0131094

    • NAID

      120005947158

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Molecular mechanism of wide photoabsorption spectral shifts of color variants of human cellular retinol binding protein II2015

    • Author(s)
      Cheng Cheng, Motoshi Kamiya, Yoshihiro Uchida, and Shigehiko Hayashi
    • Journal Title

      Journal of the American Chemical Society

      Volume: 137 Issue: 41 Pages: 13362-13370

    • DOI

      10.1021/jacs.5b08316

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Role of bulk water environment in regulation of functional hydrogen-bond network in photoactive yellow protein2015

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

      Journal of Physical Chemistry B

      Volume: 119 Issue: 51 Pages: 15537-15549

    • DOI

      10.1021/acs.jpcb.5b07555

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Converting a light-driven proton pump into a light-gated proton channel2015

    • Author(s)
      K. Inoue, T. Tsukamoto, K. Shimono, Y. Suzuki, S. Miyauchi, S. Hayashi, H. Kandori, Y. Sudo*
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 137 Issue: 9 Pages: 3291-3299

    • DOI

      10.1021/ja511788f

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Silencing neurons with light2014

    • Author(s)
      Shigehiko Hayashi
    • Journal Title

      Science

      Volume: 344 Issue: 6182 Pages: 369-370

    • DOI

      10.1126/science.1253616

    • Related Report
      2014 Annual Research Report
  • [Journal Article] Theoretical study on excited states of bacteriochlorophyll a in solutions with density functional assessment2014

    • Author(s)
      Masahiro Higashi, Takahiro Kosugi, Shigehiko Hayashi, and Shinji Saito
    • Journal Title

      Journal of Physical Chemistry B

      Volume: 118 Issue: 37 Pages: 10906-10918

    • DOI

      10.1021/jp507259g

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Key Chemical Factors of Arginine Finger Catalysis of F1-ATPase Clarified by an Unnatural Amino Acid Mutation2014

    • Author(s)
      Yukawa A, Iino R, Watanabe R, Hayashi S and Noji H
    • Journal Title

      Biochemistry

      Volume: 54 Issue: 2 Pages: 472-480

    • DOI

      10.1021/bi501138b

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] ATP hydrolysis mechanism in kinesin studied by combined quantum-mechanical molecular-mechanical metadynamics2013

    • Author(s)
      M. J. McGrath、I-F. W. Kuo, S.Hayashi, S. Takada
    • Journal Title

      J. Amer. Chem. Soc.

      Volume: (in press) Issue: 24 Pages: 8908-891

    • DOI

      10.1021/ja401540g

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A blue-shifted light-driven proton pump for neural silencing2013

    • Author(s)
      Sudo, Y., Okazaki, A., Ono, H., Yagasaki, J., Sugo, S., Kamiya, M., Reissig, L., Inoue, K., Ihara, K., Kandori, H., Takagi, S., Hayashi, S.
    • Journal Title

      J. Biol. Chem.

      Volume: 288 Issue: 28 Pages: 20624-20632

    • DOI

      10.1074/jbc.m113.475533

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Facile Catch and Release of Fullerenes Using a Photoresponsive Molecular Tube2013

    • Author(s)
      N. Kishi, M. Akita, M. Kamiya, S. Hayashi, H. -F. Hsu, M. Yoshizawa
    • Journal Title

      Journal of the Arnerican Chemical Society

      Volume: 135 Issue: 35 Pages: 12976-12979

    • DOI

      10.1021/ja406893y

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Presentation] Understanding and designing color variants of retinal biding proteins by molecular simulations2015

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Pacifichem2015 Symposium “Chemistry and Applications of Retinal Proteins: From Microbes to Humans”
    • Place of Presentation
      Honolulu, USA
    • Year and Date
      2015-12-18
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Crucial Role of Protein Flexibility in Enzymatic Catalysis2015

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Pacifichem2015 Symposium “Interplay between Chemistry and Dynamics in Biomolecular Machines”
    • Place of Presentation
      Honolulu, USA
    • Year and Date
      2015-12-16
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Role of Bound Water Molecules Inside Proteins in Their Functional Processes2015

    • Author(s)
      林 重彦
    • Organizer
      日本生物物理学会・シンポジウム “ポンプ、酵素、モーター、機能の鍵:pKa”
    • Place of Presentation
      金沢・石川
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Crucial Role of Protein Flexibility in Enzymatic Catalysis2015

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      IUPAC-2015 45th World Chemistry Congress
    • Place of Presentation
      釜山・韓国
    • Year and Date
      2015-08-09
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 柔らかいタンパク質の分子機能の理解と設計2015

    • Author(s)
      林 重彦
    • Organizer
      第 12 回 AMO 討論会
    • Place of Presentation
      東京
    • Year and Date
      2015-06-19
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Atomistic Understanding and Design of Microbial Opsin-based Optogenetics Tools2015

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Albany 2015: Conversation 19
    • Place of Presentation
      Albany, USA
    • Year and Date
      2015-06-09
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] タンパク質の pKa 制御とプロトン能動輸送の分子機構2015

    • Author(s)
      林 重彦
    • Organizer
      分子研研究会「膜タンパク質内部のプロトン透過を考える」
    • Place of Presentation
      岡崎・愛知
    • Year and Date
      2015-04-20
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Crucial Role of Protein Flexibility in Enzymatic Catalysis2015

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      4th Indo-German Meeting on Modeling of Chemical and Biological Reactivity (MCBR4)
    • Place of Presentation
      Heidelberg, Germany
    • Year and Date
      2015-02-23 – 2015-02-25
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 柔らかいタンパク質の分子機能の理解と設計2015

    • Author(s)
      林 重彦
    • Organizer
      理研シンポジウム「生体分子系量子化学計算の最前線」
    • Place of Presentation
      和光・埼玉
    • Year and Date
      2015-01-22 – 2015-01-23
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 柔らかいタンパク質の分子機能の理解と設計2014

    • Author(s)
      林 重彦
    • Organizer
      CBI 学会 2014 年大会 プレナリーレクチャー
    • Place of Presentation
      東京
    • Year and Date
      2014-10-28 – 2014-10-30
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Understanding and Designing Color Variants of Retinal Biding Proteins by Molecular Simulations2014

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      16th International Conference on Retinal Proteins
    • Place of Presentation
      長浜・滋賀
    • Year and Date
      2014-10-05 – 2014-10-10
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 柔らかいタンパク質の分子機能の理解と設計2014

    • Author(s)
      林 重彦
    • Organizer
      第 14 回蛋白質科学会年会 公募型シンポジウム
    • Place of Presentation
      横浜・神奈川
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Catalytic mechanism of NTPases2014

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Tokyo ATPase Workshop
    • Place of Presentation
      東京
    • Year and Date
      2014-06-02 – 2014-06-03
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Crucial Role of Protein Flexibility in Enzymatic Catalysis2014

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Les Houches-TSRC Workshop on Protein Dynamics
    • Place of Presentation
      Les Houches, France
    • Year and Date
      2014-05-18 – 2014-05-23
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Crucial Role of Protein Flexibility in Enzymatic Catalysis2014

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      CRC-EC Joint Symposium on Chemical Theory on Complex System
    • Place of Presentation
      Atlanta, USA
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 柔らかいタンパク質の分子機能の理解と設計2014

    • Author(s)
      林 重彦
    • Organizer
      自然科学研究機構計算科学研究センタースーパーコンピュータワークショップ 2014「計算化学の最新の成果と展開」
    • Place of Presentation
      岡崎・愛知
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 酵素機能における分子の柔らかさの役割2014

    • Author(s)
      林 重彦
    • Organizer
      日本化学会第 94 春季年会中長期テーマシンポジウム「複雑系のための分子科学-理論研究によるアプローチ」
    • Place of Presentation
      名古屋・愛知
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 光受容タンパク質の光吸収・蛍光スペクトルの理論的理解と合理的制御2013

    • Author(s)
      林 重彦
    • Organizer
      蛋白研セミナー「光の、光による、光のための蛋白質科学」
    • Place of Presentation
      吹田・大阪
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] ハイブリッド分子シミュレーションでみる酵素の活性と柔らかさ2013

    • Author(s)
      林 重彦
    • Organizer
      第 13 回蛋白質科学会ワークショップ「計算科学と計測科学の協働により明らかになる蛋白質構造ダイナミクスの現状と将来
    • Place of Presentation
      鳥取
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Crucial Role of Protein Flexibility in Enzymatic Catalysis2013

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Telluride Science Research Center Workshop on “Protein Dynamics”
    • Place of Presentation
      Telluride, USA
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Crucial Role of Protein Flexibility in Enzymatic Catalysis2013

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      3rd International Conference on Molecular Simulations
    • Place of Presentation
      神戸・兵庫
    • Related Report
      2013 Annual Research Report
    • Invited

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Published: 2013-05-21   Modified: 2019-07-29  

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