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prediction of proton transfer in proteins based on hydrogen-bond network structures

Research Project

Project/Area Number 18H01186
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 13040:Biophysics, chemical physics and soft matter physics-related
Research InstitutionThe University of Tokyo

Principal Investigator

斉藤 圭亮  東京大学, 先端科学技術研究センター, 准教授 (20514516)

Project Period (FY) 2018-04-01 – 2022-03-31
Project Status Granted (Fiscal Year 2021)
Budget Amount *help
¥17,030,000 (Direct Cost: ¥13,100,000、Indirect Cost: ¥3,930,000)
Fiscal Year 2021: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2020: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2019: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2018: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Keywords水素結合 / ネットワーク / プロトン移動 / QM/MM法 / 分子動力学法 / 光合成 / アクアポリン / 光化学系II
Outline of Annual Research Achievements

プロトン移動の実例を集めるため,植物や藻類の光合成において水を分解し酸素を発生する反応を触媒する蛋白質である光化学系IIに着目し,次のことを明らかにした.これらの成果はすべて国際誌に論文として発表済みである.
■1)酸素発生反応に伴って最初に放出されるプロトン放出機構を水輸送膜蛋白質アクアポリンと比較した.光化学系IIでは,蛋白質内部に結合している少数の水分子のゆらぎが他の水分子に比べて特異的に小さく,それらの水分子により高効率なプロトン輸送を可能にする経路が形成されていることがわかった.■2)酸素発生反応に伴って2,3番目に放出される2つのプロトン放出経路に関わる重要なアミノ残基の変異体について解析することで,プロトン放出機構を特定した.■3)光化学系IIで起こるプロトン共役電子移動過程について調べた.プロトン移動を促進すると指摘されている「低障壁水素結合」が,電子移動をも促進していることをはじめて示し,その機構も明らかにした.■4)触媒部位の錯体を構成するCa原子が①周辺の水素結合ネットワークの形状を保つ役割,②反応中のプロトン移動を促進する役割,③正常に電子移動するための電位を調整する役割,の3つを担っていることを明らかにした.■5)触媒部位の錯体を構成するMn原子に配位している水分子(W1, W2)とCaに配位している水分子(W3, W4)の酸解離定数(pKa)を算出した.蛋白質中では近くの酸性アミノ酸側鎖(D1-Asp61)により,W1が特異的に脱プロトン化,すなわちプロトン移動を起こしやすいことを明らかにした.

Current Status of Research Progress
Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

具体的な蛋白質についてプロトン移動可能な経路とプロトン移動不可能な経路の特徴を明らかにすることができたため.

Strategy for Future Research Activity

主に光合成に関係する具体的な蛋白質について,様々なプロトン移動可能な経路とプロトン移動不可能な経路の特徴が明らかになった.プロトン移動を行う蛋白質は他にもあるので,今後は光合成以外の蛋白質についても,実例を調べ,得られた特徴を一般化できるかどうかを検討する予定である.

Report

(3 results)
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report

Research Products

(26 results)

All 2021 2020 2019 2018

All Journal Article (17 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 17 results,  Open Access: 16 results) Presentation (9 results) (of which Int'l Joint Research: 1 results,  Invited: 4 results)

  • [Journal Article] Proton transfer pathway from the oxygen-evolving complex in photosystem II substantiated by extensive mutagenesis2021

    • Author(s)
      Kuroda Hiroshi、Kawashima Keisuke、Ueda Kazuyo、Ikeda Takuya、Saito Keisuke、Ninomiya Ryo、Hida Chisato、Takahashi Yuichiro、Ishikita Hiroshi
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - Bioenergetics

      Volume: 1862 Pages: 148329-148329

    • DOI

      10.1016/j.bbabio.2020.148329

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mechanism of absorption wavelength shifts in anion channelrhodopsin-1 mutants2021

    • Author(s)
      Tsujimura Masaki、Noji Tomoyasu、Saito Keisuke、Kojima Keiichi、Sudo Yuki、Ishikita Hiroshi
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - Bioenergetics

      Volume: 1862 Pages: 148349-148349

    • DOI

      10.1016/j.bbabio.2020.148349

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Nature of Asymmetric Electron Transfer in the Symmetric Pathways of Photosystem I2021

    • Author(s)
      Mitsuhashi Koji、Tamura Hiroyuki、Saito Keisuke、Ishikita Hiroshi
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 125 Pages: 2879-2885

    • DOI

      10.1021/acs.jpcb.0c10885

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Two Distinct Oxygen-Radical Conformations in the X-ray Free Electron Laser Structures of Photosystem II2021

    • Author(s)
      Mandal Manoj、Saito Keisuke、Ishikita Hiroshi
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 12 Pages: 4032-4037

    • DOI

      10.1021/acs.jpclett.1c00814

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Redox potentials along the redox-active low-barrier H-bonds in electron transfer pathways2020

    • Author(s)
      Saito Keisuke、Mandal Manoj、Ishikita Hiroshi
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 22 Pages: 25467-25473

    • DOI

      10.1039/d0cp04265j

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Energetics of Ionized Water Molecules in the H-Bond Network near the Ca2+ and Cl? Binding Sites in Photosystem II2020

    • Author(s)
      Saito Keisuke、Mandal Manoj、Ishikita Hiroshi
    • Journal Title

      Biochemistry

      Volume: 59 Pages: 3216-3224

    • DOI

      10.1021/acs.biochem.0c00177

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] pKa of the ligand water molecules in the oxygen-evolving Mn4CaO5 cluster in photosystem II2020

    • Author(s)
      Saito Keisuke、Nakagawa Minesato、Ishikita Hiroshi
    • Journal Title

      Communications Chemistry

      Volume: 3 Pages: 89-89

    • DOI

      10.1038/s42004-020-00336-7

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Acquirement of water-splitting ability and alteration of the charge-separation mechanism in photosynthetic reaction centers2020

    • Author(s)
      Tamura Hiroyuki、Saito Keisuke、Ishikita Hiroshi
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 117 Pages: 16373-16382

    • DOI

      10.1073/pnas.2000895117

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Rigidly hydrogen-bonded water molecules facilitate proton transfer in photosystem II2020

    • Author(s)
      Sakashita Naoki、Ishikita Hiroshi、Saito Keisuke
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 22 Pages: 15831-15841

    • DOI

      10.1039/d0cp00295j

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Nature of the Short Oxygen?Oxygen Distance in the Mn4CaO6 Complex of Photosystem II Crystals2020

    • Author(s)
      Mandal Manoj、Saito Keisuke、Ishikita Hiroshi
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 11 Pages: 10262-10268

    • DOI

      10.1021/acs.jpclett.0c02868

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dependence of the chlorophyll wavelength on the orientation of a charged group: Why does the accessory chlorophyll have a low site energy in photosystem II?2020

    • Author(s)
      Saito Keisuke、Mitsuhashi Koji、Ishikita Hiroshi
    • Journal Title

      Journal of Photochemistry and Photobiology A: Chemistry

      Volume: 402 Pages: 112799-112799

    • DOI

      10.1016/j.jphotochem.2020.112799

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Vectorial Proton Transport Mechanism of RxR, a Phylogenetically Distinct and Thermally Stable Microbial Rhodopsin2020

    • Author(s)
      Kojima Keiichi、Ueta Tetsuya、Noji Tomoyasu、Saito Keisuke、Kanehara Kanae、Yoshizawa Susumu、Ishikita Hiroshi、Sudo Yuki
    • Journal Title

      Sci. Rep.

      Volume: 10 Pages: 1-11

    • DOI

      10.1038/s41598-019-57122-2

    • NAID

      120006884916

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Redox Potential of the Oxygen-Evolving Complex in the Electron Transfer Cascade of Photosystem II2019

    • Author(s)
      Mandal Manoj、Kawashima Keisuke、Saito Keisuke、Ishikita Hiroshi
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 11 Pages: 249-255

    • DOI

      10.1021/acs.jpclett.9b02831

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mechanism of protonation of the over-reduced Mn4CaO5 cluster in photosystem II2019

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

      Biochimica et Biophysica Acta (BBA) - Bioenergetics

      Volume: 1860 Pages: 148059-148059

    • DOI

      10.1016/j.bbabio.2019.148059

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mechanism of Radical Formation in the H-Bond Network of D1-Asn298 in Photosystem II2018

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

      Biochemistry

      Volume: 57 Pages: 4997-5004

    • DOI

      10.1021/acs.biochem.8b00574

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Selective Removal of B800 Bacteriochlorophyll a from Light-Harvesting Complex 2 of the Purple Photosynthetic Bacterium Phaeospirillum molischianum2018

    • Author(s)
      Saga Yoshitaka、Hirota Keiya、Matsui Sayaka、Asakawa Hitoshi、Ishikita Hiroshi、Saito Keisuke
    • Journal Title

      Biochemistry

      Volume: 57 Pages: 3075-3083

    • DOI

      10.1021/acs.biochem.8b00259

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [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 Pages: 1247-1247

    • DOI

      10.1038/s41467-018-03545-w

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Effect of chlorophyll epimerization on the electron transfer in photosystem I reaction center2020

    • Author(s)
      三橋 孝司, 斉藤 圭亮, 石北 央
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Origin of exchange couplings of the Mn4CaO5 cluster in photosystem II2020

    • Author(s)
      西尾 俊哉, 斉藤 圭亮, 石北 央
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Mechanism of absorption wavelength shifts in anion channelrhodopsin mutants2020

    • Author(s)
      辻村 真樹, 野地 智康, 小島 慧一, 須藤 雄気, 石北 央
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 光化学系IIにおける過還元Mn4CaO5錯体のプロトン化機構2019

    • Author(s)
      斉藤圭亮、石北 央
    • Organizer
      第 27 回 「光合成セミナー2019:反応中心と色素系の多様性」
    • Related Report
      2019 Annual Research Report
  • [Presentation] 蛋白質構造に基づく理論化学で光合成のしくみを理解する2019

    • Author(s)
      斉藤圭亮
    • Organizer
      令和元年第一回高圧力蛋白質研究センターセミナー
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Mechanism of proton, electron and energy transfers in photosynthetic proteins2019

    • Author(s)
      Keisuke Saito
    • Organizer
      光合成日米二国間セミナー
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 光化学系II における水分解酸素発生反応の分子機構2018

    • Author(s)
      斉藤 圭亮
    • Organizer
      生物物理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 光合成蛋白質におけるエネルギー変換と情報伝達の分子機構2018

    • Author(s)
      斉藤 圭亮
    • Organizer
      蛋白研セミナー:生体分子内情報伝達機構の 新展開
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 光合成蛋白質における分子内電子・プロトン・エネルギー移動2018

    • Author(s)
      斉藤 圭亮
    • Organizer
      蛋白質科学会
    • Related Report
      2018 Annual Research Report
    • Invited

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Published: 2018-04-23   Modified: 2022-12-28  

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