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Theoretical determination of protonation states of the manganese cluster in photosystem II

Publicly Offered Research

Project AreaCreation of novel light energy conversion system through elucidation of the molecular mechanism of photosynthesis and its artificial design in terms of time and space
Project/Area Number 18H05161
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Research InstitutionKyoto University

Principal Investigator

林 重彦  京都大学, 理学研究科, 教授 (70402758)

Project Period (FY) 2018-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2019: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
Fiscal Year 2018: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
Keywords光合成タンパク質 / 酸化還元金属錯体 / 分子シミュレーション / 量子化学計算 / 分子動力学シミュレーション / QM/MM 法 / 分子動力学計算 / 酸化還元電位計算
Outline of Annual Research Achievements

酸化・還元が関わるタンパク質や金属錯体の機能活性化機構に関する分子シミュレーション手法を開発し、光合成系II(PSII)及びそのアナログ金属錯体の酸化状態生成に関する理論的研究を行った。我々が開発したQM/MM 自由エネルギー構造最適化法である QM/MM RWFE-SCF 法を用いて、酸化・還元による反応活性部位の複雑な電子状態・構造遷移を非経験的量子化学(QM)法に基づきパラメータフリーで精度良く記述し、更にそれに相関するタンパク質の大域的な構造変化を長時間の分子動力学(MD)法により記述することにより、分子機能活性化に関する電子状態と分子ダイナミクスの統一的な理論的解析を行った。以下に、研究成果の詳細を述べる。

1. PSII のプロトン化状態の同定 PSIIが糖脂質膜環境に埋め込まれたシミュレーション系を用いて、マンガンクラスターを中心とする反応活性部位を非経験的 QM 領域とした QM/MM 自由エネルギー構造最適化計算を行い、S1 及び S2 状態の 8 個の酸化/プロトン化状態モデルに対して酸化エネルギー及びプロトン化エネルギーをパラメータフリーで直接計算することにより、プロトン化状態の同定に成功した。反応活性部位とタンパク質環境の相互作用の解析により、タンパク質の酸性・塩基性側鎖がつくる電荷の影響と媒質の再配向エネルギーの両者の適切な記述が必要であることを見出した。
2. 人工マンガンクラスタ錯体の酸化過程の解析 PSII の反応活性部位に類似の人口マンガンクラスター錯体の酸化過程に関して、QM/MM RWFE-SCF 法を用いて解析した。アセトニトリル溶媒中の S1 及び S2 状態の自由エネルギー最適化構造を決定すると共に、酸素発生反応の基質分子である水分子の配位をアセトニトリル・水混合溶媒の拡張アンサンブル MD シミュレーションにより解析した。

Research Progress Status

令和元年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和元年度が最終年度であるため、記入しない。

Report

(2 results)
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (22 results)

All 2019 2018

All Journal Article (1 results) (of which Peer Reviewed: 1 results,  Open Access: 1 results) Presentation (21 results) (of which Int'l Joint Research: 10 results,  Invited: 11 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
  • [Presentation] Atomistically deciphering functional processes of photoreceptor membrane proteins with molecular simulations2019

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      第19回日本蛋白質科学会年会・第71回日本細胞生物学会大会 合同年次大会 共催シンポジウム「最先端の実験科学と計算科学が明らかにする膜タンパク質の精緻な反応機構」
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Atomistically deciphering functional processes of transporter and redox proteins with molecular simulations2019

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Telluride Science Research Center Workshop on “Protein Dynamics”
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Atomistically deciphering functional processes of photoreceptor proteins with molecular simulations2019

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Frontiers in Multiscale Modelling of Photoreceptor Proteins
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Determination of protonated states for native and mutant structures of HIV-1 protease with indinavir by free energy calculations2019

    • Author(s)
      Masahiko Taguchi, Ryo Oyama, Masahiro Kaneso, Shigehiko Hayashi
    • Organizer
      第57回生物物理学会年会シンポジウム「ポスト「京」始動を見据えた計算創薬の新展開」
    • Related Report
      2019 Annual Research Report
  • [Presentation] Theoretical study on an enzymatic reaction of the hammerhead ribozyme2019

    • Author(s)
      Ayaka Matsuyama, Masahiko Taguchi, Shigehiko Hayashi
    • Organizer
      第57回生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Theoretical study on molecular mechanics of natural anion channelrhodopsin GtACR12019

    • Author(s)
      Takafumi Shikakura, Cheng Cheng, Shigehiko Hayashi
    • Organizer
      第57回生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] An ab initio method of evaluating redox potential for metalloprotein2019

    • Author(s)
      Cheng Cheng, Shigehiko Hayashi
    • Organizer
      第57回生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Theoretical study on molecular mechanism of a light-driven ion transport of Halorhodopsin from Natronomonas pharaonis2019

    • Author(s)
      Ryo Oyama, Taisuke Hasegawa, Shigehiko Hayashi
    • Organizer
      第57回日本生物物理学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Atomistically deciphering functional processes of photoreceptor and redox proteins with molecular simulations2019

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Ninth Conference of the Asia-Pacific Association of the Theoretical and Computational Chemists (APATCC2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Atomistically deciphering functional processes of photoreceptor and redox proteins with hybrid molecular simulations2019

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      Indo-Japan Workshop Frontiers in Molecular Spectroscopy: From Fundamentals to Applications in Chemistry and Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Atomistically deciphering functional processes of transporter and redox proteins with molecular simulations2019

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      5th International Conference on Molecular Simulation (ICMS 2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Atomistically Deciphering Redox Processes of Metalloproteins with Hybrid Molecular Simulations2019

    • Author(s)
      Shigehiko Hayashi
    • Organizer
      3rd International Solar Fuels Conference (ISF-3) International Conference on Artificial Photosynthesis-2019 (ICARP2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [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

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Published: 2018-04-23   Modified: 2021-01-27  

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