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The study on the proton pump coupling mechanism of cytochrome c oxidase by new time-resolved vibrational spectroscopy

Research Project

Project/Area Number 15K05393
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionNara Institute of Science and Technology (2018)
University of Hyogo (2015-2017)

Principal Investigator

Nakashima Satoru  奈良先端科学技術大学院大学, 研究推進機構, URA(チーフ) (80263234)

Project Period (FY) 2015-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2017: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywordsチトクローム酸化酵素 / プロトンポンプ共役機構 / 時間分解赤外分光法 / 時間分解共鳴ラマン分光法 / 反応中間体 / 酸素還元反応 / プロトン放出サイト / ダイナミクス / 時間分解ラマン分光法 / プロトンポンプ / Water pool / カルボキシル基 / 共鳴ラマン分光法 / フェムト秒レーザ / フローシステム / 共役機構 / 振動分光法 / 時間分解 / 逐次的反応
Outline of Final Research Achievements

Cytochrome c oxidase (CcO) carries proton pumping in the membrane coupled with the reduction reaction of oxygen. In order to clarify the details of this coupling mechanism, I traced the oxygen reduction reaction dynamics with time-resolved IR (TRIR) absorption spectroscopy. For the first time, we have developed a flow cell system that allows us to observe the reaction and perform TRIR measurements to observe protonated residues. As a result of detailed analysis, in the course of the reaction, 1. The proton supply site first undergoes structural change, 2. Sequential desorption of protons at the proton release site, 3. Structural change at the proton storage site occurs synchronously with the reaction. This is the world's first example of real-time, direct observation of proton pump related residues in CcO in a buffer solution under physiological conditions.

Academic Significance and Societal Importance of the Research Achievements

ミトコンドリアが生体エネルギー工場と呼ばれるのは、その中でチトクロムc酸化酵素(CcO)が呼吸した酸素で燃焼させて生命活動のエネルギー源を得ているためで、地球上のほとんどの生命体にとり必須の酵素である。しかしこの酵素反応の不具合は活性酸素種を発生させ、様々な疾病(癌、心筋梗塞、脳卒中、アルツハイマー等)の根本原因となる。その不具合は、酵素の内部のほんのわずかな水素結合の違いで起こると言われていて、原子レベルでの機構解明が必須である。本研究はその酵素反応を実際に起こっている状態で直接観測することに成功したもので、こうした原因解明や、燃料電池といった環境負荷の少ないデバイスへの展開も期待できる。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (23 results)

All 2019 2018 2017 2016 2015 Other

All Journal Article (3 results) (of which Peer Reviewed: 3 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (19 results) (of which Int'l Joint Research: 6 results,  Invited: 5 results) Remarks (1 results)

  • [Journal Article] New Assay Method Based on Raman Spectroscopy for Enzymes Reacting with Gaseous Substrates2019

    • Author(s)
      Y. Kawahara‐Nakagawa, K. Nishikawa, S. Nakashima, S. Inoue, T. Ohta, T. Ogura, Y. Shigeta, K. Fukutani, T. Yagi, and Y. Higuchi
    • Journal Title

      Protein Science

      Volume: 28 Issue: 3 Pages: 663-670

    • DOI

      10.1002/pro.3569

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Performance of a time-resolved IR facility for assessment of protonation T states and polarity changes in carboxyl groups in a large membrane protein, mammalian cytochrome c oxidase, under turnover conditions in a sub-millisecond time resolution2018

    • Author(s)
      Chen Li, Tatsuhito Nishiguchi, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Takashi Ogura, Satoru Nakashima
    • Journal Title

      Biochimica et Biophysica Acta

      Volume: 1859 Issue: 10 Pages: 1045-1050

    • DOI

      10.1016/j.bbabio.2018.05.015

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Infrared and Raman spectroscopic studies on the reaction mechanism of cytochrome c oxidase2015

    • Author(s)
      Satoru Nakashima, Takashi Ogura and Teizo Kitagawa
    • Journal Title

      Biochim. Biophy. Acta

      Volume: 1847 Pages: 86-97

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Proton Pumping Dynamics during Catalytic Cycle in Cytochrome c Oxidase Revealed by Time-Resolved IR Spectroscopy2018

    • Author(s)
      Satoru Nakashima, Chen Li, Tatsuhito Nishiguchi, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Takashi Ogura
    • Organizer
      10th International Conference on Porphyrins and Phthalocyanines
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Proton pumping mechanism of cytochrome c oxidase by time-resolved vibrational spectroscopy2018

    • Author(s)
      Satoru Nakashima
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Protein Dynamics Relevant to Proton Pump by Cytochrome c Oxidase: Resonance Raman Spectroscopy2017

    • Author(s)
      Satoru Nakashima,Takashi Ogura, Yoshiyuki Nakagawa, Kyoko Shinzawa-Itoh、 Shinya Yoshikawa
    • Organizer
      CanBIC-6
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Elucidating the proton pumping mechanisms of cytochrome c oxidase by time resolved IR spectroscopy2017

    • Author(s)
      Chen Li, Tatsuhito Nishiguchi, Shun Yamauchi, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Satoru Nakashima, Takashi Ogura
    • Organizer
      第44回生体分子科学討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] 中川 由佳,西川 幸志,垣本 敦子,中島聡,樋口 芳樹,小倉 尚志2017

    • Author(s)
      ラマン分光によるヒトロゲナーセ活性測定法の開発
    • Organizer
      第44回生体分子科学討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] Reaction Chase of a Very Small Amount of Enzyme Protein by the Droplet Collision Method2017

    • Author(s)
      Satoru Nakashima, Akari Watanabe, Yoshiaki Nishihata, Saori Hodokami, Takashi Ogura
    • Organizer
      The 5th International Symposium on“Studying the Function of Soft Molecular Systems”
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] The coupling mechanism between proton pumping and oxygen reduction reaction of cytochrome c oxidase revealed by time-resolved vibrational spectroscopy2017

    • Author(s)
      S.Nakashima,Y.Nakagawa,LiChen, K.Shinzawa-Itoh,S.Yoshikawa,T.Ogura
    • Organizer
      The 5th International Symposium on“Studying the Function of Soft Molecular Systems”
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Elucidating the mechanisms of proton pumping in cytochrome c oxidase by time resolved IR spectroscopy2016

    • Author(s)
      Chen Li, Tatsuhito Nishiguchi, Shun Yamauchi, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Satoru Nakashima, Takashi Ogura
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場 茨城県つくば市
    • Year and Date
      2016-11-24
    • Related Report
      2016 Research-status Report
  • [Presentation] Coupling mechanism of cytochrome c oxidase studied by time-resolved resonance Raman spectroscopy2016

    • Author(s)
      中島聡・中川善之・伊藤-新澤恭子・吉川信也・小倉尚志
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場 茨城県つくば市
    • Year and Date
      2016-11-24
    • Related Report
      2016 Research-status Report
  • [Presentation] The effect of the hydrogen bond network on the oxygen reduction reaction of cytochrome c oxidase2016

    • Author(s)
      中島聡・中川善之・伊藤-新澤恭子・吉川信也・小倉尚志
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場 茨城県つくば市
    • Year and Date
      2016-11-24
    • Related Report
      2016 Research-status Report
  • [Presentation] The Coupling Mechanism Between Proton Pumping and Oxygen Reduction Reaction in Cytochrome c Oxidase2016

    • Author(s)
      Satoru Nakashim, Chen Li, Tatsuhito Nishiguchi, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Takashi Ogura
    • Organizer
      International Conference on Porphyrins and Phthalocynanines - 9
    • Place of Presentation
      中華人民共和国・南京市
    • Year and Date
      2016-07-04
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 時間分解振動分光法によるチトクロームc酸化酵素のプロトンポンプ共役機構の研究2016

    • Author(s)
      中島聡、中川善之、Li Chen、新澤-伊藤 恭子、吉川 信也、小倉 尚志
    • Organizer
      第43回生体分子科学討論会2016
    • Place of Presentation
      名古屋大学 愛知県名古屋市
    • Year and Date
      2016-06-24
    • Related Report
      2016 Research-status Report
  • [Presentation] Dynamics at the reaction site of cytochrome c oxidase studied by time-resolved resonance Raman spectroscopy2016

    • Author(s)
      中島聡・中川善之・伊藤-新澤恭子・吉川信也・小倉尚志
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場 福岡県福岡市
    • Year and Date
      2016-06-07
    • Related Report
      2016 Research-status Report
  • [Presentation] 時間分解振動分光法によるチトクローム酸化酵素の酸素還元反応とプロトンポンプ機構の相関2016

    • Author(s)
      中島聡
    • Organizer
      「柔らかな分子系」第 5 回全体合宿会議
    • Place of Presentation
      ホテルベルナティオ 新潟県十日町市
    • Year and Date
      2016-05-30
    • Related Report
      2016 Research-status Report
  • [Presentation] 時間分解共鳴ラマン分光法によるチトクロムc酸化酵素のCO光解離に伴う構造ダイナミクスの研究2016

    • Author(s)
      中川 善之・新澤-伊藤 恭子・吉川 信也・中島 聡・小倉 尚志
    • Organizer
      日本化学会第96春季年会
    • Place of Presentation
      京都府京田辺市
    • Year and Date
      2016-03-27
    • Related Report
      2015 Research-status Report
  • [Presentation] Time-resolved IR spectroscopic studies for proton pumping mechanisms of cytochrome c oxidase2016

    • Author(s)
      Chen Li, Tatsuhito Nishiguchi, Shun Yamauchi , Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Satoru Nakashima, Takashi Ogura
    • Organizer
      日本化学会第96春季年会
    • Place of Presentation
      京都府京田辺市
    • Year and Date
      2016-03-27
    • Related Report
      2015 Research-status Report
  • [Presentation] Coupling mechanism in the reaction of cytochrome c oxidase revealed by newly developed time-resolved IR measurements2015

    • Author(s)
      Satoru Nakashima
    • Organizer
      SciX2015
    • Place of Presentation
      Providence, USA
    • Year and Date
      2015-10-27
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] チトクロームc酸化酵素における酸素還元反応とプロトンポンプ共役機構2015

    • Author(s)
      中島 聡・西口達人・Li Chen・新澤-伊藤 恭子・吉川 信也・小倉 尚志
    • Organizer
      第53回生物物理学会年会
    • Place of Presentation
      石川県金沢市
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Presentation] チトクロームc酸化酵素の酸素還元反応とプロトンポンプの共役機構2015

    • Author(s)
      中島 聡、西口 善人、Chen Li、中川 善之、青柳 裕大、新澤-伊藤 恭子、吉川 信也、小倉 尚志
    • Organizer
      第42回生体分子科学討論会
    • Place of Presentation
      群馬県高崎市
    • Year and Date
      2015-06-12
    • Related Report
      2015 Research-status Report
  • [Remarks] Molecular Biophysics II

    • URL

      http://proxy.sci.u-hyogo.ac.jp/life/biophys2/biophys2_2013/main_japanese.htm

    • Related Report
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2020-03-30  

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