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2022 Fiscal Year Annual Research Report

Elucidation of the mechanisms for light-induced water-splitting and light energy utilization in photosynthesis

Research Project

Project/Area Number 22H04916
Research InstitutionOkayama University

Principal Investigator

沈 建仁  岡山大学, 異分野基礎科学研究所, 教授 (60261161)

Co-Investigator(Kenkyū-buntansha) 庄司 光男  筑波大学, 計算科学研究センター, 助教 (00593550)
秋田 総理  岡山大学, 異分野基礎科学研究所, 准教授 (50751418)
菅 倫寛  岡山大学, 異分野基礎科学研究所, 教授 (60634920)
山口 兆  大阪大学, 産業科学研究所, 招へい教授 (80029537)
Project Period (FY) 2022-04-01 – 2027-03-31
Keywords光合成 / 光化学系II / 水分解 / 酸素発生 / エネルギー移動 / 高精度量子力学計算 / Coupled-Cluster (CC)計算 / 人工光合成
Outline of Annual Research Achievements

本研究の目的は、光合成における光誘導水分解反応の機構と光エネルギーの高効率利用機構の解明である。光誘導水分解反応の機構解析では、時分割ポンプ-プローブシリアルフェムト秒X線結晶構造解析法(SFX法)を用いて、光化学系II(PSII)のマイクロ結晶に1または2閃光照射で得られたS2, S3中間状態の形成について、nsec-msecの時間範囲でデータを収集し、解析した。その結果、S3状態で新たな酸素原子(O6)が挿入される前にMn4CaO5クラスター及びその周辺で様々な構造変化が起き、特にD1-Glu189近傍で新たな酸素原子(O6*)が出現し、それがO6の前駆体であることを発見した。これらの発見は、PSIIによる水分解・酸素発生反応の機構解明に重要な意味を持っている。それらの実験結果を検証するため、高精度量子化学計算を実施するための専用計算機システムを筑波大学計算科学研究センターに設置し、MnクラスターでのCoupled Cluster(CC)計算が実行できることを確認し、まずはS1状態の計算、大規模モデル、スピン状態の検討を行った。さらに基質である水の挿入経路、産物であるプロトンの排出経路に寄与する水素結合ネットワークを理論的に検討した。プロトンの排出経路を特定するため、D1タンパク質のアミノ酸置換体を作成し、それらが水分解反応の活性に対する影響を解析した。
光エネルギーの高効率利用機構の解明においては、クライオ電子顕微鏡を用いて灰色藻Cyanophora paradoxa由来光化学系I(PSI)四量体、始原的シアノバクテリアであるGloeobacter violaceusのPSI三量体構造及び珪藻由来PSII-FCPIIの高分解能構造等を解析した。また、光捕集アンテナでの励起エネルギー移動効率について、理論モデルを構築し、そのダイナミックス研究を進めた。

Current Status of Research Progress
Current Status of Research Progress

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

Reason

当初計画していた、水分解反応の機構解明に関しては、計画通りポンプ-プローブシリアルフェムト秒結晶構造解析法を用いてデータを収集し、解析して、それらを取りまとめて出版する準備ができた。理論計算では、専用計算機システムを設置し、Coupled Cluster法を用いた計算のための準備を進めた。また、アミノ酸置換体の作製・解析も計画通りに進めた。さらに光エネルギー高効率利用機構の解明では、異なる生物から異なるPSI複合体やPSII-FCPII複合体の構造を解析し、それらに関する理論計算の準備を進めた。

Strategy for Future Research Activity

今後は計画通りに研究を進める予定です。まずPSIIの水分解反応機構の解析では、S1→S2、およびS2→S3遷移に伴う時間分割シリアルフェムト秒のデータの構造解析を終了させ、研究結果を発表する。また、ナノ秒以下の短い時間帯で、光照射により誘導される色素やタンパク質の構造変化を解析するため、時間分割ポンプ-プローブシリアルフェムト秒実験を行い、データを収集する。そして前年度に着手した、励起された状態のみを強調して可視化するための電子密度マップを計算する手法の開発を継続する。また、これまで解析したS1, S2, S3状態の構造について、専用計算機システムを利用してCoupled Cluster(CC)計算を系統的に実施し、それぞれの状態でのプロトン化状態、Mnのスピン状態について大規模モデルで定量的に評価する。さらに上記のCC計算結果を出来るだけ再現出来るようにDFT汎関数を改良し、PSIIの大きい(350原子以上)クラスターモデルのQM、QM/MM計算に適用する。また、クライオ電子顕微鏡を用いて収集したPSII二量体の高分解能データについては、電子線によるダメージの無い外挿マップの計算を終了させ、水素原子の有無を特定し、論文にまとめる。
光エネルギーの高効率利用機構解析については、様々な藻類の野生株および変異株から光化学系-集光性色素タンパク質超複合体を精製し、生化学および分光学的特性を明らかにすると同時に、得られた試料を用いて、クライオ電子顕微鏡単粒子構造解析により立体構造を明らかにする。得られた分子構造に基づき、それぞれの複合体における光捕集アンテナ色素から光化学系反応中心への光エネルギーの移動経路や強光条件に適応するための光エネルギー逸散機構、及び光合成生物の光捕集機構の進化を明らかにする。

  • Research Products

    (37 results)

All 2023 2022 Other

All Int'l Joint Research (3 results) Journal Article (21 results) (of which Int'l Joint Research: 8 results,  Peer Reviewed: 21 results,  Open Access: 8 results) Presentation (11 results) (of which Int'l Joint Research: 10 results,  Invited: 11 results) Book (1 results) Remarks (1 results)

  • [Int'l Joint Research] Biological Research Centre, Szeged(ハンガリー)

    • Country Name
      HUNGARY
    • Counterpart Institution
      Biological Research Centre, Szeged
  • [Int'l Joint Research] 中国科学院植物学研究所(中国)

    • Country Name
      CHINA
    • Counterpart Institution
      中国科学院植物学研究所
  • [Int'l Joint Research] University of Strasbourg(フランス)

    • Country Name
      FRANCE
    • Counterpart Institution
      University of Strasbourg
  • [Journal Article] Photoinduced chlorophyll charge transfer state identified in the light-harvesting complex II from a marine green alga Bryopsis corticulans2023

    • Author(s)
      Li Dan-Hong、Wang Wenda、Zhou Cuicui、Zhang Yan、Zhao Songhao、Zhou Yi-Ming、Gao Rong-Yao、Yao Hai-Dan、Fu Li-Min、Wang Peng、Shen Jian-Ren、Kuang Tingyun、Zhang Jian-Ping
    • Journal Title

      iScience

      Volume: 26 Pages: 105761~105761

    • DOI

      10.1016/j.isci.2022.105761

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Enantiomeric Excesses of Aminonitrile Precursors Determine the Homochirality of Amino Acids2023

    • Author(s)
      Shoji Mitsuo、Kitazawa Yuya、Sato Akimasa、Watanabe Natsuki、Boero Mauro、Shigeta Yasuteru、Umemura Masayuki
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 14 Pages: 3243~3248

    • DOI

      10.1021/acs.jpclett.2c03862

    • Peer Reviewed
  • [Journal Article] Structure of a tetrameric photosystem I from a glaucophyte alga Cyanophora paradoxa2022

    • Author(s)
      Kato Koji、Nagao Ryo、Ueno Yoshifumi、Yokono Makio、Suzuki Takehiro、Jiang Tian-Yi、Dohmae Naoshi、Akita Fusamichi、Akimoto Seiji、Miyazaki Naoyuki、Shen Jian-Ren
    • Journal Title

      Nature Communications

      Volume: 13 Pages: 1679

    • DOI

      10.1038/s41467-022-29303-7

    • Peer Reviewed / Open Access
  • [Journal Article] Structural basis for the absence of low-energy chlorophylls in a photosystem I trimer from Gloeobacter violaceus2022

    • Author(s)
      Kato Koji、Hamaguchi Tasuku、Nagao Ryo、Kawakami Keisuke、Ueno Yoshifumi、Suzuki Takehiro、Uchida Hiroko、Murakami Akio、Nakajima Yoshiki、Yokono Makio、Akimoto Seiji、Dohmae Naoshi、Yonekura Koji、Shen Jian-Ren
    • Journal Title

      eLife

      Volume: 11 Pages: 73990

    • DOI

      10.7554/eLife.73990

    • Peer Reviewed / Open Access
  • [Journal Article] Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex2022

    • Author(s)
      Nagao Ryo、Kato Koji、Kumazawa Minoru、Ifuku Kentaro、Yokono Makio、Suzuki Takehiro、Dohmae Naoshi、Akita Fusamichi、Akimoto Seiji、Miyazaki Naoyuki、Shen Jian-Ren
    • Journal Title

      Nature Communications

      Volume: 13 Pages: 1764

    • DOI

      10.1038/s41467-022-29294-5

    • Peer Reviewed / Open Access
  • [Journal Article] Ultrafast excitation quenching by the oxidized photosystem II reaction center2022

    • Author(s)
      Akhtar Parveen、Sipka Gabor、Han Wenhui、Li Xingyue、Han Guangye、Shen Jian-Ren、Garab Gyozo、Tan Howe-Siang、Lambrev Petar H.
    • Journal Title

      The Journal of Chemical Physics

      Volume: 156 Pages: 145101~145101

    • DOI

      10.1063/5.0086046

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Excited-state intermediates in a designer protein encoding a phototrigger caught by an X-ray free-electron laser2022

    • Author(s)
      Liu X.、Liu P.、Li H.、Xu Z.、Jia L.、Xia Y.、Yu M.、Tang W.、Zhu X.、Chen C.、Zhang Y.、Nango E.、Tanaka R.、Luo F.、Kato K.、Nakajima Y.、Kishi S.、Yu H.、Matsubara N.、Owada S.、Tono K.、Iwata S.、Yu L.-J.、Shen J.-R.、Wang J.
    • Journal Title

      Nature Chemistry

      Volume: 14 Pages: 1054~1060

    • DOI

      10.1038/s41557-022-00992-3

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Effects of mutations of D1-R323, D1-N322, D1-D319, D1-H304 on the functioning of photosystem II in Thermosynechococcus vulcanus2022

    • Author(s)
      Zhu Qingjun、Yang Yanyan、Xiao Yanan、Han Wenhui、Li Xingyue、Wang Wenda、Kuang Tingyun、Shen Jian-Ren、Han Guangye
    • Journal Title

      Photosynthesis Research

      Volume: 152 Pages: 193~206

    • DOI

      10.1007/s11120-022-00920-z

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Geometric, electronic and spin structures of the CaMn4O5 catalyst for water oxidation in oxygen-evolving photosystem II. Interplay between experiments and theoretical computations2022

    • Author(s)
      Yamaguchi Kizashi、Shoji Mitsuo、Isobe Hiroshi、Kawakami Takashi、Miyagawa Koichi、Suga Michihiro、Akita Fusamichi、Shen Jian-Ren
    • Journal Title

      Coordination Chemistry Reviews

      Volume: 471 Pages: 214742~214742

    • DOI

      10.1016/j.ccr.2022.214742

    • Peer Reviewed
  • [Journal Article] Excitation relaxation dynamics of carotenoids constituting the diadinoxanthin cycle2022

    • Author(s)
      Kagatani Kohei、Nagao Ryo、Shen Jian-Ren、Yamano Yumiko、Takaichi Shinichi、Akimoto Seiji
    • Journal Title

      Photosynthesis Research

      Volume: 154 Pages: 13~19

    • DOI

      10.1007/s11120-022-00944-5

    • Peer Reviewed
  • [Journal Article] Exciton quenching by oxidized chlorophyll Z across the two adjacent monomers in a photosystem II core dimer2022

    • Author(s)
      Mohamed Ahmed、Nishi Shunsuke、Kawakami Keisuke、Shen Jian-Ren、Itoh Shigeru、Fukumura Hiroshi、Shibata Yutaka
    • Journal Title

      Photosynthesis Research

      Volume: 154 Pages: 277~289

    • DOI

      10.1007/s11120-022-00948-1

    • Peer Reviewed
  • [Journal Article] Simulating the low-temperature, metastable electrochromism of Photosystem I: Applications to <i>Thermosynechococcus vulcanus</i> and <i>Chroococcidiopsis thermalis</i>2022

    • Author(s)
      Langley J.、Purchase R.、Viola S.、Fantuzzi A.、Davis G. A.、Shen Jian-Ren、Rutherford A. W.、Krausz E.、Cox N.
    • Journal Title

      The Journal of Chemical Physics

      Volume: 157 Pages: 125103~125103

    • DOI

      10.1063/5.0100431

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Roles of the Flexible Primary Coordination Sphere of the Mn<sub>4</sub>CaO<sub><i>x</i></sub>Cluster: What Are the Immediate Decay Products of the<b>S<sub>3</sub></b>State?2022

    • Author(s)
      Isobe Hiroshi、Shoji Mitsuo、Suzuki Takayoshi、Shen Jian-Ren、Yamaguchi Kizashi
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 126 Pages: 7212~7228

    • DOI

      10.1021/acs.jpcb.2c02596

    • Peer Reviewed
  • [Journal Article] Crystal structures of photosystem II from a cyanobacterium expressing psbA in comparison to psbA reveal differences in the D1 subunit2022

    • Author(s)
      Nakajima Yoshiki、Ugai-Amo Natsumi、Tone Naoki、Nakagawa Akiko、Iwai Masako、Ikeuchi Masahiko、Sugiura Miwa、Suga Michihiro、Shen Jian-Ren
    • Journal Title

      Journal of Biological Chemistry

      Volume: 298 Pages: 102668~102668

    • DOI

      10.1016/j.jbc.2022.102668

    • Peer Reviewed / Open Access
  • [Journal Article] A Possible Mechanism for Aggregation-Induced Chlorophyll Fluorescence Quenching in Light-Harvesting Complex II from the Marine Green Alga <i>Bryopsis corticulans</i>2022

    • Author(s)
      Yao Hai-Dan、Li Dan-Hong、Gao Rong-Yao、Zhou Cuicui、Wang Wenda、Wang Peng、Shen Jian-Ren、Kuang Tingyun、Zhang Jian-Ping
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 126 Pages: 9580~9590

    • DOI

      10.1021/acs.jpcb.2c05823

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Characterization of the Rate-Limiting Steps in the Dark-To-Light Transitions of Closed Photosystem II: Temperature Dependence and Invariance of Waiting Times during Multiple Light Reactions2022

    • Author(s)
      Magyar Melinda、Sipka Gabor、Han Wenhui、Li Xingyue、Han Guangye、Shen Jian-Ren、Lambrev Petar H.、Garab Gyozo
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 24 Pages: 94~94

    • DOI

      10.3390/ijms24010094

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Light-induced reversible reorganizations in closed Type II reaction centre complexes: physiological roles and physical mechanisms2022

    • Author(s)
      Sipka G.、Nagy L.、Magyar M.、Akhtar P.、Shen J.-R.、Holzwarth A. R.、Lambrev P. H.、Garab G.
    • Journal Title

      Open Biology

      Volume: 12 Pages: 220297

    • DOI

      10.1098/rsob.220297

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase2022

    • Author(s)
      Shoji Mitsuo、Murakawa Takeshi、Nakanishi Shota、Boero Mauro、Shigeta Yasuteru、Hayashi Hideyuki、Okajima Toshihide
    • Journal Title

      Chemical Science

      Volume: 13 Pages: 10923~10938

    • DOI

      10.1039/D2SC01356H

    • Peer Reviewed / Open Access
  • [Journal Article] Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic Syntheses2022

    • Author(s)
      Shoji Mitsuo、Watanabe Natsuki、Hori Yuta、Furuya Kenji、Umemura Masayuki、Boero Mauro、Shigeta Yasuteru
    • Journal Title

      Astrobiology

      Volume: 22 Pages: 1129~1142

    • DOI

      10.1089/ast.2022.0011

    • Peer Reviewed
  • [Journal Article] Elucidation of a multiple S3 intermediates model for water oxidation in the oxygen evolving complex of photosystem II. Calcium-assisted concerted O O bond formation2022

    • Author(s)
      Yamaguchi Kizashi、Miyagawa Koichi、Shoji Mitsuo、Isobe Hiroshi、Kawakami Takashi
    • Journal Title

      Chemical Physics Letters

      Volume: 806 Pages: 140042

    • DOI

      10.1016/j.cplett.2022.140042

    • Peer Reviewed
  • [Journal Article] Relative energies among S3 intermediates in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Possible pathways of water insertion in the S2 to S3 transition2022

    • Author(s)
      Miyagawa Koichi、Shoji Mitsuo、Isobe Hiroshi、Kawakami Takashi、Nakajima Takahito、Yamaguchi Kizashi
    • Journal Title

      Chemical Physics Letters

      Volume: 793 Pages: 139439

    • DOI

      10.1016/j.cplett.2022.139439

    • Peer Reviewed
  • [Presentation] Structure of Photosystem and the Mechanism of Photosynthetic Water Oxidation2022

    • Author(s)
      Jian-Ren Shen
    • Organizer
      Annual Research Frontier Symposium, Alabama State University (Online), USA
    • Int'l Joint Research / Invited
  • [Presentation] Structure of photosystem II and the mechanism of water oxidation2022

    • Author(s)
      Jian-Ren Shen
    • Organizer
      Nobel Symposium #168 “Visions of bio-inorganic chemistry: Metals and the molecules of life”, Stockholm, Sweden
    • Int'l Joint Research / Invited
  • [Presentation] Crystal structure of photosystem II and the mechanism of water oxidation2022

    • Author(s)
      Jian-Ren Shen
    • Organizer
      Seminar in Stockholm University, Stockholm, Sweden
    • Int'l Joint Research / Invited
  • [Presentation] The engine of life driven by light -- Structure of photosystem II and the mechanism of photosynthetic water-splitting2022

    • Author(s)
      Jian-Ren Shen
    • Organizer
      GREGORI AMINOFF PRIZE SYMOPSIUM 2022, The Royal Swedish Academy of Sciences, Stockholm, Sweden
    • Int'l Joint Research / Invited
  • [Presentation] Structural studies of photosystem II water oxidation and other photosystem-light harvesting protein supercomplexes from different organisms2022

    • Author(s)
      Jian-Ren Shen
    • Organizer
      18th International Congress on Photosynthesis Research (ISPR2022), New Zealand
    • Int'l Joint Research / Invited
  • [Presentation] X-ray free electron lasers reveal the molecular mechanism for water oxidation in photosystem II2022

    • Author(s)
      Michihiro Suga
    • Organizer
      18th International Congress on Photosynthesis Research (ISPR2022), New Zealand
    • Int'l Joint Research / Invited
  • [Presentation] New structural insights on water-oxidation catalyst and the diversity of photosystem II2022

    • Author(s)
      Jian-Ren Shen
    • Organizer
      Satellite Meeting on Mechanisms of Water Oxidation, in conjunction with ISPR18 (ISPR2022), New Zealand
    • Int'l Joint Research / Invited
  • [Presentation] Structural dynamics and substrate binding to the oxygen-evolving complex studied by time-resolved X-ray crystallography of PSII2022

    • Author(s)
      Michi Suga, Hongjie Li, Yoshiki Nakajima, Daichi Yamada, Kana Hashimoto, So Iwata, Minoru Kubo, and Jian-Ren Shen
    • Organizer
      Satellite Meeting on Mechanisms of Water Oxidation, in conjunction with ISPR18 (ISPR2022), New Zealand
    • Int'l Joint Research / Invited
  • [Presentation] Studies on the molecular mechanism for water oxidation in photosystem II2022

    • Author(s)
      菅 倫寛
    • Organizer
      The 22nd Annual Meeting of the Photobiology Association of Japan
    • Invited
  • [Presentation] Structure of photosystem II and the mechanism of water oxidation2022

    • Author(s)
      Jian-Ren Shen
    • Organizer
      10th Asian Biological Inorganic Chemistry Conference (AsBIC10), Kobe
    • Int'l Joint Research / Invited
  • [Presentation] Natural selection of the Mn cluster in the photosynthetic water oxidation2022

    • Author(s)
      Mitsuo Shoji
    • Organizer
      Satellite Meeting to 18th International Congress on Photosynthesis Research (WOX-ICPR2022), University of Otago, Dunedin, New Zealand
    • Int'l Joint Research / Invited
  • [Book] Subcell. Biochem. 992022

    • Author(s)
      Jian-Ren Shen
    • Total Pages
      27
    • Publisher
      Springer
    • ISBN
      9783031007927
  • [Remarks] 研究室ホームページ

    • URL

      http://www.riis.okayama-u.ac.jp/department/core2/

URL: 

Published: 2023-12-25  

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