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Theoretical study on mechanism of proton transfer in photosynthetic proteins based on protein structures

Research Project

Project/Area Number 26800224
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Biological physics/Chemical physics/Soft matter physics
Research InstitutionThe University of Tokyo

Principal Investigator

Saito Keisuke  東京大学, 先端科学技術研究センター, 講師 (20514516)

Project Period (FY) 2014-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2015: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2014: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Keywords光合成 / プロトン移動 / 水分解 / 量子化学 / 分子動力学 / 水素結合 / 酸解離定数 / 蛋白質 / 酸素発生 / 蛋白質構造 / 理論化学 / 光化学系II / NMR化学シフト / 量子化学計算 / 酸解離定数pKa / 水分解反応 / 理論計算 / 水分子
Outline of Final Research Achievements

In photosynthesis of higher plants and algae, the photosystem II (PSII) protein catalyzes a water-splitting reaction where two water molecules are split into one oxygen molecule and four protons by using light energy. We clarified the reaction mechanism of the water-splitting reaction by using quantum chemical calculations. The reaction is composed of four steps. In the first step, one proton is transferred through a water chain near the active site (the Mn4CaO5 cluster) of PSII. In the third step, other proton is transferred via the asparagine side chain (D1-Asp61) located at the vicinity of the Mn4CaO5 cluster. The remaining protons are released when turning over from the fourth step to the first step.

Report

(5 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (30 results)

All 2018 2017 2016 2015 2014 Other

All Journal Article (11 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 10 results,  Open Access: 9 results,  Acknowledgement Compliant: 4 results) Presentation (18 results) (of which Int'l Joint Research: 3 results,  Invited: 12 results) Remarks (1 results)

  • [Journal Article] O2 evolution and recovery of the water-oxidizing enzyme2018

    • Author(s)
      Kawashima Keisuke、Takaoka Tomohiro、Kimura Hiroki、Saito Keisuke、Ishikita Hiroshi
    • Journal Title

      Nature Communications

      Volume: 9 Issue: 1 Pages: 1247-1247

    • DOI

      10.1038/s41467-018-03545-w

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Absorption-energy calculations of chlorophyll a and b with an explicit solvent model2018

    • Author(s)
      Saito Keisuke、Suzuki Takumi、Ishikita Hiroshi
    • Journal Title

      Journal of Photochemistry and Photobiology A: Chemistry

      Volume: 358 Pages: 422-431

    • DOI

      10.1016/j.jphotochem.2017.10.003

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Redox potentials of ubiquinone, menaquinone, phylloquinone, and plastoquinone in aqueous solution2017

    • Author(s)
      Kishi, K. Saito, Y. Kato, H. Ishikita
    • Journal Title

      Photosynth. Res

      Volume: 134 Issue: 2 Pages: 193-200

    • DOI

      10.1007/s11120-017-0433-4

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Existence of an Isolated Hydronium Ion in the Interior of Proteins2017

    • Author(s)
      Ikeda Takuya、Saito Keisuke、Hasegawa Ryo、Ishikita Hiroshi
    • Journal Title

      Angewandte Chemie

      Volume: 129 Issue: 31 Pages: 9279-9282

    • DOI

      10.1002/ange.201705512

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Origins of water molecules in the photosystem II crystal structure2017

    • Author(s)
      Naoki Sakashita, Hiroshi C. Watanabe, Takuya Ikeda, Keisuke Saito, Hiroshi Ishikita
    • Journal Title

      Biochemistry

      Volume: 56 Issue: 24 Pages: 3049-3057

    • DOI

      10.1021/acs.biochem.7b00220

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] pKa of ubiquinone, menaquinone, phylloquinone, plastoquinone, and rhodoquinone in aqueous solution2017

    • Author(s)
      Ryo Hasegawa, Keisuke Saito, Tomohiro Takaoka, and Hiroshi Ishikita*
    • Journal Title

      Photosynth. Res.

      Volume: 印刷中 Issue: 1-3 Pages: 297-304

    • DOI

      10.1007/s11120-017-0382-y

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] 光合成水分解反応におけるプロトン移動2017

    • Author(s)
      斉藤圭亮
    • Journal Title

      生物物理

      Volume: 330 Pages: 098-100

    • NAID

      130005509477

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] pKa of a proton conducting water chain in photosystem II2016

    • Author(s)
      Tomohiro Takaoka, Naoki Sakashita, Keisuke Saito, and Hiroshi Ishikita*
    • Journal Title

      J. Phys. Chem. Lett.

      Volume: 7 Issue: 10 Pages: 1925-1932

    • DOI

      10.1021/acs.jpclett.6b00656

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Energetics of the proton transfer pathway for tyrosine D in photosystem II2016

    • Author(s)
      Keisuke Saito*, Naoki Sakashita, and Hiroshi Ishikita
    • Journal Title

      Aust. J. Chem.

      Volume: 69 Issue: 9 Pages: 991-998

    • DOI

      10.1071/ch16248

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Energetics of proton release on the first oxidation step in the water-oxidizing enzyme2015

    • Author(s)
      K. Saito, A. W. Rutherford, H. Ishikita
    • Journal Title

      Nature Communications

      Volume: 6 Issue: 1 Pages: 8488-8488

    • DOI

      10.1038/ncomms9488

    • NAID

      120006348507

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] クロロフィルのかたちは機能にどう影響を及ぼすか: Photosystem IIを例に2015

    • Author(s)
      斉藤圭亮,石北央
    • Journal Title

      植物の生長調節 Regulation of Plant Growth & Development

      Volume: 50 Pages: 133-138

    • NAID

      110010014906

    • Related Report
      2015 Research-status Report
  • [Presentation] 光化学系IIにおける酸素発生反応と水の再取り込みの機構2018

    • Author(s)
      河島圭佑,高岡友裕,木村一貴,斉藤圭亮,石北央
    • Organizer
      第59回日本植物生理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Theoretical investigation based on molecular structures reveals reaction mechanisms in photosynthetic membrane proteins2017

    • Author(s)
      K.Saito
    • Organizer
      第55回生物物理学会年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 光合成蛋白質内の水分子のシミュレーション2017

    • Author(s)
      斉藤圭亮
    • Organizer
      第5回JCAHPCセミナー
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 光合成蛋白質の理論解析で知るプロトンと水の移動経路2017

    • Author(s)
      斉藤圭亮
    • Organizer
      平成29年度ラン藻ゲノム交流会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 蛋白質の理論化学解析で光合成反応をする2016

    • Author(s)
      斉藤圭亮
    • Organizer
      化学系学協会東北大会
    • Place of Presentation
      いわき明星大学 (福島県)
    • Year and Date
      2016-09-10
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Energetics of the proton transfer from tyrosine D in photosystem II: comparison with tyrosine Z2016

    • Author(s)
      K. Saito
    • Organizer
      7th Meeting “Photosynthesis Research for Sustainability”
    • Place of Presentation
      Pushchino (ロシア)
    • Year and Date
      2016-06-19
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 光化学系の構造に基づく理論解析からわかること2016

    • Author(s)
      斉藤圭亮
    • Organizer
      第7回日本光合成学会年会
    • Place of Presentation
      東京理科大学葛飾キャンパス (東京都)
    • Year and Date
      2016-05-27
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] 光合成水分解反応の初期に起こる蛋白質内プロトン移動の経路と機構2016

    • Author(s)
      斉藤圭亮、石北央
    • Organizer
      日本物理学第71回年次大会
    • Place of Presentation
      東北学院大学
    • Year and Date
      2016-03-22
    • Related Report
      2015 Research-status Report
  • [Presentation] The first proton release on the water-oxidizing reaction in photosystem II2016

    • Author(s)
      Keisuke Saito
    • Organizer
      7th OCARINA International Symposium
    • Place of Presentation
      大阪市立大学
    • Year and Date
      2016-03-17
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Mehanicsm of Long-Distance Proton Transfer in Photosynthetic Protein2016

    • Author(s)
      Keisuke Saito
    • Organizer
      the Seventh Asia-Pacific Conference of Theoretical and Computational Chemistry (APCTCC 7)
    • Place of Presentation
      高雄,台湾
    • Year and Date
      2016-01-26
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 構造に基づく理論解析で蛋白質の分子機構を探る2016

    • Author(s)
      斉藤圭亮
    • Organizer
      第1 0 回日本化学会東海支部若手研究者フォーラム
    • Place of Presentation
      名古屋大学 (愛知県)
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] 蛋白質におけるプロトン移動:短い水素結合の役割2015

    • Author(s)
      斉藤圭亮、石北央
    • Organizer
      第15回東京大学生命科学シンポジウム
    • Place of Presentation
      東京大学
    • Year and Date
      2015-06-27
    • Related Report
      2015 Research-status Report
  • [Presentation] 光合成光化学系IIにおけるMnCaクラスターの歪んだ椅子型構造の起源2015

    • Author(s)
      斉藤圭亮、石北央
    • Organizer
      日本物理学第70回年次大会
    • Place of Presentation
      東京都新宿区
    • Year and Date
      2015-03-21
    • Related Report
      2014 Research-status Report
  • [Presentation] 光合成光化学系IIにおけるMnCaクラスターの歪んだ椅子型構造の起源2015

    • Author(s)
      斉藤圭亮、石北央
    • Organizer
      第56回日本植物生理学会年会
    • Place of Presentation
      東京都世田谷区
    • Year and Date
      2015-03-16
    • Related Report
      2014 Research-status Report
  • [Presentation] 光合成蛋白質の中のクロロフィルのかたちと機能2015

    • Author(s)
      斉藤圭亮
    • Organizer
      やわらか光受容分子の理解と利用に迫るブレインストーミング研究会
    • Place of Presentation
      岡山県瀬戸内市
    • Year and Date
      2015-01-24 – 2015-01-25
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 蛋白質におけるプロトン移動 ~短い水素結合の役割~2015

    • Author(s)
      斉藤圭亮
    • Organizer
      生体分子系量子化学計算の最前線
    • Place of Presentation
      埼玉県和光市
    • Year and Date
      2015-01-22
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 光合成光化学系IIにおけるMnCaクラスターの歪んだ椅子型構造の起源2014

    • Author(s)
      斉藤圭亮、石北央
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌市
    • Year and Date
      2014-09-25
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Proton Transfer Mechanisms in Photosystem II: Quinone Reduction and Tyrosine Radical Formation2014

    • Author(s)
      K. Saito, A. W. Rutherford, H. Ishikita
    • Organizer
      Tokyo ATPase Workshop
    • Place of Presentation
      東京都文京区
    • Year and Date
      2014-06-02
    • Related Report
      2014 Research-status Report
  • [Remarks] 光合成水分解反応初期に利用される水素イオン移動経路を解明~これまでの定説を覆す結果に~

    • URL

      http://www.rcast.u-tokyo.ac.jp/pressrelease/2015_ja.html#20151007

    • Related Report
      2015 Research-status Report

URL: 

Published: 2014-04-04   Modified: 2019-03-29  

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