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Crystallographic study of water-spilitting reaction in photosystem II

Research Project

Project/Area Number 16KT0058
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Transition State Control
Research InstitutionOkayama University

Principal Investigator

Umena Yasufumi  岡山大学, 異分野基礎科学研究所, 特別契約職員(准教授) (10468267)

Project Period (FY) 2016-07-19 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥18,200,000 (Direct Cost: ¥14,000,000、Indirect Cost: ¥4,200,000)
Fiscal Year 2018: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2017: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2016: ¥8,190,000 (Direct Cost: ¥6,300,000、Indirect Cost: ¥1,890,000)
Keywords光合成 / 結晶構造解析 / マンガン金属錯体 / 放射光X線 / 異常分散効果 / 反応中間体 / 時間分割構造解析 / 遷移金属の酸化還元状態 / 蛋白質結晶 / 反応中間状態 / 光合成蛋白質 / 光化学系II蛋白質 / 異常分散項差電子密度マップ / 光励起 / 微小結晶 / X線結晶構造解析 / 膜蛋白質 / タンパク質の微小結晶 / 異常分散項差フーリエマップ / タンパク質結晶のFT-IR / 構造生物学 / 構造・機能予測 / 光生物
Outline of Final Research Achievements

Oxygen-evolving Photosystem II (PSII) protein in photosynthetic organisms has a Mn4CaO5 cluster as the reaction center of catalyzing a water-splitting reaction. In this study, the oxidation state in each of four Mn atoms in the cluster was investigated as well as the crystal structure of PSII in the four intermediate states of the reaction. To understand the detailed process of the water-splitting reaction in PSII, we developed a novel crystallographic analysis method using the wavelength of the absorption inflection point of a target metal atom. We prepared a lot of tinny PSII crystal, excited by pulse-laser, and then cryo-fixed. Both redox properties of each Mn atom in the cluster and crystal structure of PSII were simultaneously analyzed. As a result, we observed the redox changes in each Mn atom in the process of water-splitting reaction. Simultaneously with this redox analysis, we also captured the movements of water and proteins in PSII in the process of PSII.

Academic Significance and Societal Importance of the Research Achievements

本研究は、光合成の光と水によるエネルギー変換の仕組みを理解するため、光化学系II蛋白質(photosystem II; PSII)の触媒中心の4つMn金属原子と蛋白質構造の構造化学的な研究を行った。まず、Mnの電子状態と蛋白質の動きを同時に分析する結晶学的手法を開発した。この手法により、PSIIが水を分解する反応過程におけるMnとPSIIの原子レベルの変化を捉えることができた。もし光合成反応を化学的に理解できれば、太陽電池のような電力ではなく、水からエネルギー源を作り出す人工光合成の手がかりが期待される。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (24 results)

All 2019 2018 2017 2016

All Journal Article (9 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 9 results,  Open Access: 5 results,  Acknowledgement Compliant: 3 results) Presentation (15 results) (of which Int'l Joint Research: 6 results,  Invited: 7 results)

  • [Journal Article] β-Carotene Probes the Energy Transfer Pathway in the Photosystem II Core Complex2019

    • Author(s)
      Yoneda Yusuke、Nagasawa Yutaka、Umena Yasufumi、Miyasaka Hiroshi
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 10 Issue: 13 Pages: 3710-3714

    • DOI

      10.1021/acs.jpclett.9b01072

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An alternative plant-like cyanobacterial ferredoxin with unprecedented structural and functional properties2019

    • Author(s)
      Motomura Taiki、Zuccarello Lidia、S?tif Pierre、Boussac Alain、Umena Yasufumi、Lemaire David、Tripathy Jatindra N.、Sugiura Miwa、Hienerwadel Rainer、Shen Jian-Ren、Berthomieu Catherine
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - Bioenergetics

      Volume: 1860 Issue: 11 Pages: 148084-148084

    • DOI

      10.1016/j.bbabio.2019.148084

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A versatile experimental system for tracking ultrafast chemical reactions with X-ray free-electron lasers2019

    • Author(s)
      Katayama Tetsuo、Nozawa Shunsuke、Umena Yasufumi、Lee SungHee、Togashi Tadashi、Owada Shigeki、Yabashi Makina
    • Journal Title

      Structural Dynamics

      Volume: 6 Issue: 5 Pages: 054302-054302

    • DOI

      10.1063/1.5111795

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser2019

    • Author(s)
      Suga M、Akita F、Yamashita K、Nakajima Y、Ueno G、Li H、Yamane T、Hirata K、Umena Y、Yonekura S、Yu L-J、Murakami H、Nomura T、Kimura T、Kubo M、Baba S、Kumasaka T、Tono K、Yabashi M、Isobe H、Yamaguchi K、Yamamoto M、Ago H、Shen J-R
    • Journal Title

      Science

      Volume: 366 Issue: 6463 Pages: 334-338

    • DOI

      10.1126/science.aax6998

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Fourier Transform Infrared Analysis of the S-State Cycle of Water Oxidation in the Microcrystals of Photosystem II2018

    • Author(s)
      Kato Yuki、Akita Fusamichi、Nakajima Yoshiki、Suga Michihiro、Umena Yasufumi、Shen Jian-Ren、Noguchi Takumi
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 9 Issue: 9 Pages: 2121-2126

    • DOI

      10.1021/acs.jpclett.8b00638

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Understanding Two Different Structures in the Dark Stable State of the Oxygen-Evolving Complex of Photosystem?II: Applicability of the Jahn-Teller Deformation Formula2017

    • Author(s)
      Shoji Mitsuo、Isobe Hiroshi、Tanaka Ayako、Fukushima Yoshimasa、Kawakami Keisuke、Umena Yasufumi、Kamiya Nobuo、Nakajima Takahito、Yamaguchi Kizashi
    • Journal Title

      ChemPhotoChem

      Volume: 2 Issue: 3 Pages: 257-270

    • DOI

      10.1002/cptc.201700162

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mutual relationships between structural and functional changes in a PsbM-deletion mutant of photosystem II2017

    • Author(s)
      S. Uto, K. Kawakami, Y. Umena, M. Iwai, M. Ikeuchi, J.-R. Shenf and N. Kamiya
    • Journal Title

      Faraday Discussions

      Volume: 印刷中 Pages: 107-120

    • DOI

      10.1039/c6fd00213g

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.2017

    • Author(s)
      Suga, M.†, Akita, F.†, Sugahara, M.†, Kubo, M.†, Nakajima, Y.† et al. (†equal contribution)(38人中1番目)
    • Journal Title

      Nature

      Volume: 543 Issue: 7643 Pages: 131-135

    • DOI

      10.1038/nature21400

    • NAID

      120006344935

    • Related Report
      2017 Research-status Report 2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Dynamics of Excitation Energy Transfer Between the Subunits of Photosystem II Dimer.2016

    • Author(s)
      Yusuke Yoneda, Tetsuro Katayama, Yutaka Nagasawa, Hiroshi Miyasaka and Yasufumi Umena
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 138 Issue: 36 Pages: 11599-11605

    • DOI

      10.1021/jacs.6b04316

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] 光合成で働く光化学系II複合体の結晶構造解析に基づく機能解明2019

    • Author(s)
      梅名泰史
    • Organizer
      2019年度日本生化学会九州支部例会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Crystallographic study on estimation of the valence of each of the four Mn atoms in Photosystem II using anomalous diffraction techniques2019

    • Author(s)
      Yasufumi Umena, Keisuke Kawakami, Nobuo Kamiya, Yoshiaki Kawano, Keitaro Yamashita, Hideo Ago, Masaki Yamamoto, Jian-Ren Shen
    • Organizer
      69th American Crystallography Association Annual meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Study of functional structures in photosystem II revealed by pH dependent structural changes2019

    • Author(s)
      Yasufumi Umena, Mayuho Adachi, Jian-Ren Shen
    • Organizer
      第19回日本蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Crystallographic study on estimation of the valence of each of the four Mn atoms in Photosystem II using anomalous diffraction techniques2019

    • Author(s)
      Yasufumi Umena, Keisuke Kawakami, Nobuo Kamiya, Yoshiaki Kawano, Keitaro Yamashita, Hideo Ago, Masaki Yamamoto, Jian-Ren Shen
    • Organizer
      2019 the American Crystallographic Association’s Annual Meeting
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Analysis of the individual valences of four Mn atoms in photosystem II crystals using anomalous diffraction technique2018

    • Author(s)
      Yasufumi Umena Keisuke Kawakami, Nobuo Kamiya and Jian-Ren Shen
    • Organizer
      第56回 日本生物物理学会年会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Proton transfer inhibition by molecular anion substitutions in Photosystem II2017

    • Author(s)
      Yasufumi Umena, Shouya Tamaru, Jian-Ren Shen
    • Organizer
      24th Congress and General Assembly of the International Union of Crystallography (IUCr2017)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 塩素イオンを分子陰イオンへ置換した PSIIの結晶構造解析による阻害機構の解明2017

    • Author(s)
      梅名泰史,田丸翔也,沈建仁
    • Organizer
      第8回日本光合成学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Mn-oxidation states in PSII2017

    • Author(s)
      Yasufumi Umena
    • Organizer
      Japan-France Joint Workshop on the Structure and Function of Photosystem II
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 光化学系IIと阻害剤アジ化物イオンとの共結晶化とX線結晶構造解析2016

    • Author(s)
      田丸 翔也, 梅名 泰史, 沈 建仁
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば、茨城(ポスター)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] 活性阻害剤アジ化物イオンが結合した光化学系 II 蛋白質の X 線結晶構造解析2016

    • Author(s)
      梅名泰史・田丸翔也・沈建仁
    • Organizer
      日本結晶学会平成28年度年会
    • Place of Presentation
      水戸、茨城(ポスター)
    • Year and Date
      2016-11-17
    • Related Report
      2016 Research-status Report
  • [Presentation] 光化学系IIタンパク質における混合原子価Mn4CaO5クラスターの結晶構造解析2016

    • Author(s)
      梅名泰史, 川上恵典, 神谷信夫, 沈建仁
    • Organizer
      第55回電子スピンサイエンス学会年会
    • Place of Presentation
      大阪市立大学、大阪
    • Year and Date
      2016-11-10
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Crystallographic studies of the valence of four Mn atoms in photosystem II using anomalous diffraction technique2016

    • Author(s)
      Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen
    • Organizer
      The 42nd Naito Conference
    • Place of Presentation
      札幌、北海道(ポスター)
    • Year and Date
      2016-10-04
    • Related Report
      2016 Research-status Report
  • [Presentation] Estimation of valences and radiation damage of four Mn atoms in photosystem II crystals using anomalous diffraction analysis2016

    • Author(s)
      Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen
    • Organizer
      The 12th International Conference on Biology and Synchrotron Radiation (BSR 2016)
    • Place of Presentation
      Menlo Park, CA, USA (ポスター)
    • Year and Date
      2016-08-21
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Valences and radiation damage of four Mn atoms in photosystem II crystals revealed by anomalous diffraction analysis2016

    • Author(s)
      Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen,
    • Organizer
      The 17th International Congress on Photosynthesis Research
    • Place of Presentation
      Maastricht, Netherlands(ポスター)
    • Year and Date
      2016-08-07
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Crystal structure analysis of photosystem II complex from an SQDG-deficient mutant of Thermosynechococcus elongatus2016

    • Author(s)
      Y. Nakajma, Y. Umena, K. Endo, H. Wada, J.-R. Shen
    • Organizer
      The 17th International Congress on Photosynthesis Research
    • Place of Presentation
      Maastricht, Netherlands(ポスター)
    • Year and Date
      2016-08-07
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research

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Published: 2016-07-20   Modified: 2023-03-08  

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