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Structural analysis of the complex between Fd and Fd-dependent proteins considering their redox states strictly

Research Project

Project/Area Number 21H02417
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43020:Structural biochemistry-related
Research InstitutionOsaka University

Principal Investigator

Kurisu Genji  大阪大学, 蛋白質研究所, 教授 (90294131)

Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000)
Fiscal Year 2023: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2022: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2021: ¥7,020,000 (Direct Cost: ¥5,400,000、Indirect Cost: ¥1,620,000)
Keywords構造生物学 / 光合成 / 電子伝達 / 金属蛋白質 / レドックス代謝 / 金属タンパク質 / 生物物理学 / 電子伝達複合体
Outline of Research at the Start

葉緑体内のレドックス代謝反応の多くは,電子伝達タンパク質フェレドキシン(Fd)に依存して駆動される。しかし,Fdとレドックス代謝酵素の複合体形成は過渡的で,酵素反応が進行すると複合体は解離してしまう。そのため構造解析には困難と妥協が伴った。研究代表者は,自身のこれまでの研究の蓄積からFdの酸化還元状態は比較的小さな構造変化であっても,過渡的複合体形成を考える上では非常に重大であると考えるに至った。そこで,高度化してきた再構成金属タンパク質の活用をベースに,原理的に不可能と考えられてきた「酸化型」と「還元型」とで形成する活性型複合体の精密構造解析を行う。

Outline of Final Research Achievements

In this study, I have investigated the electron-transfer complexes formed transiently in three pairs: 1) the structure of photosystem I complex (PS1: LHC1) with Ga-substituted Fd from Green Alga was analyzed in three states, and new findings were made on the structural changes and dissociation of the new subunits from the PSI upon binding of Ga-substituted Fd. 2) For the structural analysis of cyanobacterial photosystem I (PS1) complexed with Ga-substituted Fd, we succeeded in obtaining a very high resolution of 1.97 A, as initially expected. 3) For the structural analysis of the complex of Native Fd in the reduced state and reconstituted permanently oxidized HydA1 (odt type) was not completed due to technical difficulties in obtaining the suitable crystals for X-ray analysis.

Academic Significance and Societal Importance of the Research Achievements

高度化してきた再構成金属タンパク質の活用をベースに,原理的に不可能と考えられてきた「酸化型」と「還元型」とで形成する活性型複合体の精密構造解析を行った。具体的には,2種類の光化学系IとFdとの構造解析を高分解能で行い,構造決定が待たれている緑藻型のFd依存性[FeFe]ヒドロゲナーゼの構造解析にも同様の方法を展開した。前者については,想定通りの結果を得て論文発表を行ったが,緑藻型[FeFe]ヒドロゲナーゼについては結晶化することができなかった。結晶化不要のCryo-EMに切り替えて活性型構造解析を展開している。本研究により,Redox状態を厳密にコントロールすることの重要性を示すことができた。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • Research Products

    (36 results)

All 2023 2022 2021 Other

All Int'l Joint Research (8 results) Journal Article (11 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 10 results,  Open Access: 7 results) Presentation (15 results) (of which Int'l Joint Research: 2 results) Remarks (2 results)

  • [Int'l Joint Research] Ruhr University Bochum(ドイツ)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Department of Biological Sciences/Purdue University(米国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Department of Biotechnology and Biology/Ruhr University Bochum(ドイツ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Department of Plant Biology/University of Muenster(ドイツ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Department of Biological Sciences/Purdue University(米国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] Department of Biotechnology and Biology/Ruhr University Bochum(ドイツ)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] Department of Plant Biology/University of Muenster(ドイツ)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] Korean Basic Science Institute(韓国)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Crystal structure of the stalk region of axonemal inner‐arm dynein‐d reveals unique features in the coiled‐coil and microtubule‐binding domain2023

    • Author(s)
      Ko Seolmin、Toda Akiyuki、Tanaka Hideaki、Yu Jian、Kurisu Genji
    • Journal Title

      FEBS Letters

      Volume: 597 Issue: 17 Pages: 2149-2160

    • DOI

      10.1002/1873-3468.14690

    • Related Report
      2023 Annual Research Report
  • [Journal Article] Three structures of PSI-LHCI from Chlamydomonas reinhardtii suggest a resting state re-activated by ferredoxin2023

    • Author(s)
      Gerle Christoph、Misumi Yuko、Kawamoto Akihiro、Tanaka Hideaki、Kubota-Kawai Hisako、Tokutsu Ryutaro、Kim Eunchul、Chorev Dror、Abe Kazuhiro、Robinson Carol V.、Mitsuoka Kaoru、Minagawa Jun、Kurisu Genji
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - Bioenergetics

      Volume: 1864 Issue: 4 Pages: 148986-148986

    • DOI

      10.1016/j.bbabio.2023.148986

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Regulation of motor activity of ciliary outer-arm dynein by the light chain 1; Implications from the structure of the light chain bound to the microtubule-binding domain of the heavy chain2023

    • Author(s)
      Yagi Toshiki、Toda Akiyuki、Ichikawa Muneyoshi、Kurisu Genji
    • Journal Title

      Biophysics and Physicobiology

      Volume: 20 Issue: 1 Pages: n/a

    • DOI

      10.2142/biophysico.bppb-v20.0008

    • ISSN
      2189-4779
    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Soluble domains of cytochrome c-556 and Rieske iron?sulfur protein from Chlorobaculum tepidum: Crystal structures and interaction analysis2023

    • Author(s)
      Kishimoto Hiraku、Azai Chihiro、Yamamoto Tomoya、Mutoh Risa、Nakaniwa Tetsuko、Tanaka Hideaki、Miyanoiri Yohei、Kurisu Genji、Oh-oka Hirozo
    • Journal Title

      Current Research in Structural Biology

      Volume: 5 Pages: 100101-100101

    • DOI

      10.1016/j.crstbi.2023.100101

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Isothermal titration calorimetry of membrane protein interactions: FNR and the cytochrome b6f complex2022

    • Author(s)
      Zakharov Stanislav D.、Savikhin Sergei、Misumi Yuko、Kurisu Genji、Cramer William A.
    • Journal Title

      Biophysical Journal

      Volume: 121 Issue: 2 Pages: 300-308

    • DOI

      10.1016/j.bpj.2021.12.014

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Energy transfer fluctuation observed by single-molecule spectroscopy of red-shifted bacteriochlorophyll in the homodimeric photosynthetic reaction center2022

    • Author(s)
      Kondo Toru、Mutoh Risa、Arai Shun、Kurisu Genji、Oh-oka Hirozo、Fujiyoshi Satoru、Matsushita Michio
    • Journal Title

      The Journal of Chemical Physics

      Volume: 156 Issue: 10 Pages: 105102-105102

    • DOI

      10.1063/5.0077290

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structures of multisubunit membrane complexes with the CRYO ARM 2002022

    • Author(s)
      Gerle Christoph、Kishikawa Jun-ichi、Yamaguchi Tomoko、Nakanishi Atsuko、?oruh Orkun、Makino Fumiaki、Miyata Tomoko、Kawamoto Akihiro、Yokoyama Ken、Namba Keiichi、Kurisu Genji、Kato Takayuki
    • Journal Title

      Microscopy

      Volume: 71 Issue: 5 Pages: 249-261

    • DOI

      10.1093/jmicro/dfac037

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structure of cyanobacterial photosystem I complexed with ferredoxin at 1.97?? resolution2022

    • Author(s)
      Li Jiannan、Hamaoka Noriyuki、Makino Fumiaki、Kawamoto Akihiro、Lin Yuxi、R?gner Matthias、Nowaczyk Marc M.、Lee Young-Ho、Namba Keiichi、Gerle Christoph、Kurisu Genji
    • Journal Title

      Communications Biology

      Volume: 5 Issue: 1 Pages: 951-951

    • DOI

      10.1038/s42003-022-03926-4

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Crystal structure and reaction mechanism of a bacterial Mg‐dechelatase homolog from the Chloroflexi <i>Anaerolineae</i>2022

    • Author(s)
      Dey Debayan、Nishijima Masayoshi、Tanaka Ryouichi、Kurisu Genji、Tanaka Hideaki、Ito Hisashi
    • Journal Title

      Protein Science

      Volume: 31 Issue: 10

    • DOI

      10.1002/pro.4430

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations2022

    • Author(s)
      Nakayoshi Tomoki、Ohnishi Yusuke、Tanaka Hideaki、Kurisu Genji、Kondo Hiroko X.、Takano Yu
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 23 Issue: 24 Pages: 15913-15913

    • DOI

      10.3390/ijms232415913

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural insights into blue-green light utilization by marine green algal light harvesting complex II at 2.78 Å2022

    • Author(s)
      Seki Soichiro、Nakaniwa Tetsuko、Castro-Hartmann Pablo、Sader Kasim、Kawamoto Akihiro、Tanaka Hideaki、Qian Pu、Kurisu Genji、Fujii Ritsuko
    • Journal Title

      BBA Advances

      Volume: 2 Pages: 100064

    • DOI

      10.1016/j.bbadva.2022.100064

    • URL

      https://ocu-omu.repo.nii.ac.jp/records/2019661

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Structural and functional analysis of the carbonic anhydrase from marine diatom Phaeodactylum tricornutum2023

    • Author(s)
      Negoro H, Tanaka H, Shimakawa G, Kawamoto A, Matsuda Y, Kurisu G.
    • Organizer
      26th Congress of the International Union of Crystallography
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Neutron crystallographic study of ferredoxin-NADP+ reductase2023

    • Author(s)
      Uenaka M, Ohnishi Y, Tanaka H, Kurisu G
    • Organizer
      26th Congress of the International Union of Crystallography
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Structure of cyanobacterial photosystem I complexed with ferredoxin and cyrtochrome c6 at 1.97 A resolution2023

    • Author(s)
      Jiannan Li, Noriyuki Hamaoka, Fumiaki Makino, Akihiro Kawamoto, Keiichi Namba, Christoph Gerle, Genji Kurisu
    • Organizer
      第61回日本生物物理学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Structural study on the bacteriosin pectocin M1 from Pectobacterium catorovorum2023

    • Author(s)
      Nawee Jantarit, Hideaki Tanaka, Genji Kurisu
    • Organizer
      第61回日本生物物理学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Structural and functional analysis of the carbonic anhydrase from marine diatom Phaeodactylum tricornutum2023

    • Author(s)
      Hiroto Negoro, Hideaki Tanaka, Ginga Shimakawa, Hiroyasu Koteishi, Akihiro Kawamoto, Yusuke Matsuda, Genji Kurisu
    • Organizer
      第61回日本生物物理学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Computational analysis of the structure and motion of the plant-type ferredoxin using long-time molecular dynamics simulations2023

    • Author(s)
      Tomoki Nakayoshi, Yusuke Ohnishi, Hideaki Tanaka, Genji Kurisu, Yu Takano
    • Organizer
      第61回日本生物物理学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] フェレドキシンNADP+還元酵素の中性子結晶構造解析2023

    • Author(s)
      上中みどり,大西裕介,田中秀明,栗栖源嗣
    • Organizer
      令和5年度日本結晶学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Structure of cyanobacterial photosystem I complexed with Cytochrome c6 and Ferredoxin2022

    • Author(s)
      Jiannan Li、浜岡紀之、牧野文信、川本晃大、難波啓一、Christoph Gerle、栗栖源嗣
    • Organizer
      日本蛋白質科学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Neutron crystallographic analysis of ferredoxin-NADP+ reductase2022

    • Author(s)
      Midori UENKA, Yusuke OHNISI, Hideaki TANAKA, Genji KURISU
    • Organizer
      日本生物物理学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Cryo-EM structure of cytochrome b6f complex from Chlamydomonas reinhardtii reveals the functional domain movement of Rieske ISP2022

    • Author(s)
      Hatsuki Tanabe, Shinichiro Ozawa,Akihiro Kawamoto, Hideaki Tanaka, Yuichiro Takahashi Genji Kurisu
    • Organizer
      日本生物物理学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Structural study of RubisCO from diatom Thalassiosira pseudonana and its interaction with novel pyrenoid proteins2022

    • Author(s)
      Taiki Fukuzawa, Rei Toda, Hermanus Nawely, Natumi Morishima, Ryosuke Okubo, Yoshinori Tsuji, Kawamoto Akihiro, Hideaki Tanaka, Christoph Gerle, Yusuke Matuda, Genji Kurisu
    • Organizer
      日本生物物理学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] フェレドキシン NADP+ 還元酵素の中性子結晶構造解析2021

    • Author(s)
      上中みどり、大西裕介、田中秀明、栗栖源嗣
    • Organizer
      日本結晶学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 珪藻Thalassiosira pseudonana由来ルビスコのX線結晶構造解析2021

    • Author(s)
      福澤大喜、東田怜、Hermanus Nawaly、森嶋菜摘、大久保亮佑、田中秀明、川本晃大、Christoph Gerle、松田祐介、栗栖源嗣
    • Organizer
      日本結晶学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 光合成型複合体Iの高分解能構造解析を目指した高純度精製2021

    • Author(s)
      浜岡 紀之、三角 裕子、川本 晃大、田中 秀明、小沼 剛、池上 貴久、栗栖 源嗣
    • Organizer
      日本結晶学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 緑藻クラミドモナス由来シトクロムb6f複合体のpH依存的活性調節機構の構造基盤2021

    • Author(s)
      田辺 初希、小澤 真一郎、川本 晃大、田中 秀明、高橋 裕一郎、栗栖 源嗣
    • Organizer
      日本結晶学会
    • Related Report
      2021 Annual Research Report
  • [Remarks] 蛋白質結晶学研究室

    • URL

      http://www.protein.osaka-u.ac.jp/crystallography/

    • Related Report
      2023 Annual Research Report
  • [Remarks] 大阪大学蛋白質研究所蛋白質結晶学研究室

    • URL

      http://www.protein.osaka-u.ac.jp/crystallography/

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report

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Published: 2021-04-28   Modified: 2025-01-30  

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