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Elucidation of membrane protein proton transfer dynamics by time-resolved vibrational spectroscopy

Research Project

Project/Area Number 23550022
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionUniversity of Hyogo

Principal Investigator

NAKASHIMA Satoru  兵庫県立大学, 生命理学研究科, 准教授 (80263234)

Project Period (FY) 2011-04-28 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2013: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2012: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2011: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywordsチトクローム酸化酵素 / 時間分解赤外分光法 / 共鳴ラマン分光法 / プロトンポンプ / 蛋白質ダイナミクス / 膜蛋白質 / 共役機構 / 蛋白質 / 新規赤外分光法 / 溶液内タンパク質 / 酸素還元反応 / 赤外分光
Outline of Final Research Achievements

To investigate the coupling mechanism of the oxygen reduction reaction to water molecule and proton pumping in cytochrome c oxidase, new flow system that enable the time-resolved spectroscopy has been developed. By using this system, in the initial reaction process, heme a3 and His protein-reaction site interaction changed immediately changes to adjust the oxygen affinity. And it was also confirmed that it synchronizes with the open-close of the gate through water channel. This is the first example that observed the coupling mechanisms of the oxygen reduction reaction and the proton pumping in real time by the experimental observation. Furthermore, it was clarified that oxygen binds to CuB before ligate to heme a3, and it controlled the timing of the start of the oxygen reduction reaction. These observations exhibit that oxygen reduction reaction itself controlled the proton pumping mechanisms.

Report

(5 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (38 results)

All 2015 2014 2013 2012 2011 Other

All Journal Article (7 results) (of which Peer Reviewed: 7 results,  Acknowledgement Compliant: 1 results) Presentation (29 results) (of which Invited: 3 results) Remarks (2 results)

  • [Journal Article] Infrared and Raman spectroscopic investigation of the reaction mechanism of cytochrome c oxidase2015

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

      Biochimica et Biophysica Acta

      Volume: 1847 Issue: 1 Pages: 86-97

    • DOI

      10.1016/j.bbabio.2014.08.002

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Effective Pumping Proton Collection Facilitated by a Copper Site (CuB) of Bovine Heart Cytochrome c Oxidase, Revealed by a Newly Developed Time-resolved Infrared System2013

    • Author(s)
      Minoru Kubo, Satoru Nakashima, Satoru Yamaguchi, Takashi Ogura, Masao Mochizuki, Jiyoung Kang, Masaru Tateno, Kyoko Shinzawa-Itoh, Koji Kato and Shinya Yoshikawa
    • Journal Title

      J. Biol. Chem.

      Volume: 288 Issue: 42 Pages: 30259-30269

    • DOI

      10.1074/jbc.m113.473983

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] An intermediate conformational state during ligand binding to cytochrome c oxidase detected by time-resolved resonance Raman analyses of heme peripheral groups2012

    • Author(s)
      Izumi Ishigami, Takeshi Nishigaki, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Satoru Nakashima and Takashi Ogura
    • Journal Title

      Chem. Lett.

      Volume: 2 Issue: 2 Pages: 178-180

    • DOI

      10.1246/cl.2012.178

    • NAID

      130004426495

    • Related Report
      2012 Research-status Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Site-specific protein dynamics in communication pathway from sensor to signaling domain of oxygen sensor protein, HemAT-Bs : time-resolved ultraviolet resonance Raman study2012

    • Author(s)
      S. El-Mashtoly, M. Kubo, Y. Gu, H. Sawai, S. Nakashima, T. Ogura, S. Aono, T. Kitagawa
    • Journal Title

      J. Biol. Chem

      Volume: 287 Issue: 24 Pages: 19973-19984

    • DOI

      10.1074/jbc.m112.357855

    • Related Report
      2012 Research-status Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Development of Highly Sensitive Nanosecond Time-Resolved IR Apparatus Applicable to Protein System in H2O2012

    • Author(s)
      Satoru Nakashima*, Minoru Kubo, Satoru Yamaguchi, Takashi Ogura, Masao Mochizuki, Kyoko Shinzawa-Itoh, Shinya Yoshikawa
    • Journal Title

      Biophys. Biochim. Acta

      Volume: 1817 Pages: 150-150

    • DOI

      10.1016/j.bbabio.2012.06.395

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Synthesis, Characterization, and Reactivity of Hypochlorito-Iron(III) Porphyrin Complexe2012

    • Author(s)
      Zhiqi Cong, Sachiko Yanagisawa, Takuya Kurahashi, Takashi Ogura, Satoru Nakashima, and Hiroshi Fujii
    • Journal Title

      J. Am. Chem. Soc

      Volume: 134 Issue: 51 Pages: 20617-20620

    • DOI

      10.1021/ja3108774

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structural Dynamics of<i>Ec</i>DOS Heme Domain Revealed by Time-Resolved Ultraviolet Resonance Raman Spectroscopy2011

    • Author(s)
      El-Mashtoly, Samir; Kubo, Minoru; Nakashima, Satoru; Shimizu, Toru; Kitagawa, Teizo
    • Journal Title

      J. Phys. Chem. Lett.

      Volume: 2 Issue: 17 Pages: 2212-2217

    • DOI

      10.1021/jz201017y

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Presentation] Newly developed systems of time-resolved IR spectroscopy for elucidating the oxygen reduction reaction of cytochrome c oxidase2015

    • Author(s)
      Chen Li、西口達人、新澤-伊藤恭子、吉川信也、中島聡、小倉尚志
    • Organizer
      第15回蛋白質学会年会
    • Place of Presentation
      あわぎんホール(徳島県徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2014 Annual Research Report
  • [Presentation] チトクロムc酸化酵素の反応初期過程の研究2015

    • Author(s)
      西口達人、Chen Li、新澤-伊藤恭子、吉川信也、中島聡、小倉尚志
    • Organizer
      日本化学会第95回春季年会
    • Place of Presentation
      日本大学(千葉県船橋市)
    • Year and Date
      2015-03-28
    • Related Report
      2014 Annual Research Report
  • [Presentation] The time-resolved resonance Raman study(TR3) on the dynamics of cytochrome c oxidase2015

    • 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95回春季年会
    • Place of Presentation
      日本大学(千葉県船橋市)
    • Year and Date
      2015-03-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Vibrational spectroscopic studies of the coupling mechanism in the initial stage of the reaction of cytochrome c oxidase2014

    • Author(s)
      Satoru Nakashima, Minoru Kubo, Izumi Ishigami, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Takashi Ogura
    • Organizer
      2nd Institute of Picobiology International Symposium
    • Place of Presentation
      KAST(兵庫県赤穂郡上郡町)
    • Year and Date
      2014-10-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] チトクローム酸化酵素の反応初期過程における共役機構の解明2014

    • Author(s)
      中島 聡・久保 稔・石上 泉・新澤-伊藤 恭子・吉川 信也・小倉 尚志
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道札幌市)
    • Year and Date
      2014-09-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] チトクロムc酸化酵素の酸素還元反応の時間分解赤外吸収測定を目的とした酸素肺フローシステムの開発2014

    • Author(s)
      西口達人、新澤-伊藤恭子、吉川信也、中島聡、小倉尚志
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道札幌市)
    • Year and Date
      2014-09-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] 振動分光法による蛋白質機能の研究2014

    • Author(s)
      中島聡
    • Organizer
      生物無機化学夏期セミナー
    • Place of Presentation
      圓教寺会館(兵庫県姫路市)
    • Year and Date
      2014-08-29
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 時間分解振動分光法でみたチトクローム酸化酵素の反応初期過程での共役機構2014

    • Author(s)
      中島 聡、久保 稔、石上 泉、新澤-伊藤 恭子、吉川 信也、小倉 尚志
    • Organizer
      第41回生体分子科学討論会
    • Place of Presentation
      九州大学西新プラザ(福岡県福岡市)
    • Year and Date
      2014-06-06
    • Related Report
      2014 Annual Research Report
  • [Presentation] チトクローム酸化酵素の反応初期過程での共役機構2014

    • Author(s)
      中島 聡、久保 稔、石上 泉、新澤-伊藤 恭子、吉川 信也、小倉 尚志
    • Organizer
      第6回日本生物物理学会中四国支部大会
    • Place of Presentation
      とりぎん文化会館(鳥取県鳥取市)
    • Year and Date
      2014-05-17
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] チトクロム c 酸化酵素の酸素還元反応の時間分解赤外吸収測定を目的とした酸素肺フローシステムの開発2013

    • Author(s)
      中島聡・西口達人・久保稔・望月正雄・新澤恭子・吉川信 也・小倉尚志
    • Organizer
      化学会第93回春期年会
    • Place of Presentation
      立命館大学くさつキャンパス(滋賀県)
    • Related Report
      2012 Research-status Report
  • [Presentation] Proton Pump Mechanism of Cytochrome c Oxidase Elucidated by Highly Sensitive Time-Resolved IR Spectroscopy2012

    • Author(s)
      Satoru Nakashima, Minoru Kubo, Satoru Yamaguchi, Takashi Ogura, Masao Mochizukia, Kyoko Shinzawa-Itoh, Shinya Yoshikawa
    • Organizer
      Internatinal Conference on Porphyrin and Phtalocyanin 7
    • Place of Presentation
      韓国済州島
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] Development of Highly Sensitive Nanosecond Time-Resolved IR Apparatus Applicable to Protein System in H2O2012

    • Author(s)
      Satoru Nakashima, Minoru Kubo, Satoru Yamaguchi, Takashi Ogura, Masao Mochizuki, Kyoko Shinzawa-Itoh, Shinya Yoshikawa
    • Organizer
      Europian Bioenergetic Conference 2012
    • Place of Presentation
      ドイツ、フライブルグ
    • Related Report
      2012 Research-status Report
  • [Presentation] Nanosecond time-resolved infrared basis for a bulge of the transmembrane helix between hemes a and a3 to facilitate highly efficient proton pumping by bovine heart cytochrome c oxidase2012

    • Author(s)
      Satoru Nakashima, Shinya Yoshikawa, Minoru Kubo, Satoru Yamaguchi, Takashi Ogura, Masao Mochizuki, JiYoung Kang, Masaru Tateno, Kazumasa Muramoto, Kyoko Shinzawa-Itoh
    • Organizer
      Europian Bioenergetic Conference 2012
    • Place of Presentation
      ドイツ、フライブルグ
    • Related Report
      2012 Research-status Report
  • [Presentation] An Intermediate Conformation of Cytochrome Oxidase in the Ligand-Free State Identified by Time-Resolved Resonance Raman Spectroscopy2012

    • Author(s)
      Izumi Ishigami, Takeshi Nishigaki, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Satoru Nakashima, Takashi Ogura
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学東山キャンパス(愛知県)
    • Related Report
      2012 Research-status Report
  • [Presentation] ポンプ・プローブレーザーと同期したパルスフローシステムの開発 とそれを用いたタンパク質の時間分解赤外分光解析2012

    • Author(s)
      Minoru Kubo , Satoru Nakashima , Masao Mochizuki , Kyoko Shinzawa-Itoh , Shinya Yoshikawa, Takashi Ogura
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学東山キャンパス(愛知県)
    • Related Report
      2012 Research-status Report
  • [Presentation] チトクロム酸化酵素のリガンド解離構造ダイナミクス:新規高精度時間分解赤外分光装置を用いた追跡2011

    • Author(s)
      中島聡, 久保稔, 山口悟, 望月正雄, 伊藤-新澤恭子, 吉川信也, 小倉尚志
    • Organizer
      生体分子科学討論会
    • Place of Presentation
      つくば大学(茨城県)
    • Related Report
      2011 Research-status Report
  • [Presentation] Dynamic Regulation of Water Channel Gate in Cytochrome c Oxidase Probed by a Newly Developed Time-Resolved IR Spectrometer2011

    • Author(s)
      Satoru Nakashima, Minoru Kubo, Satoru Yamaguchi, Masao Mochizuki, Kyoko Shinzawa, Shinya Yoshikawa, Takashi Ogura
    • Organizer
      International Symposium
    • Place of Presentation
      札幌市(北海道)
    • Related Report
      2011 Research-status Report
  • [Presentation] 水溶液中のタンパク質の高感度時間分解赤外分光測定2011

    • Author(s)
      久保稔, 山口悟, 望月正雄, 伊藤-新澤 恭子, 吉川信也, 小倉尚志, 中島聡
    • Organizer
      分子科学討論会
    • Place of Presentation
      札幌コンベンションセンター(北海道)
    • Related Report
      2011 Research-status Report
  • [Presentation] チトクロムc酸化酵素のタンパク質構造ダイナミクスと反応機構:共鳴ラマン分光法2011

    • Author(s)
      Izumi Ishigami, Takeshi Nishigaki, Satoru Nakashima, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Takashi Ogura
    • Organizer
      生物物理学会年会
    • Place of Presentation
      兵庫県立大(兵庫県)
    • Related Report
      2011 Research-status Report
  • [Presentation] ウシ心筋チトクロムc酸化酵素における水チャネルの動的ゲーティング機構:新規時間分解赤外分光光度計を用いた解析2011

    • Author(s)
      久保稔, 山口悟, 望月正雄, 伊藤-新澤 恭子, 吉川信也, 小倉尚志, 中島聡
    • Organizer
      生物物理学会年会
    • Place of Presentation
      兵庫県立大(兵庫県)
    • Related Report
      2011 Research-status Report
  • [Presentation] チトクロムc酸化酵素のCN光解離反応機構:共鳴ラマン分光法2011

    • Author(s)
      Takeshi Nishigaki, Izumi Ishigami, Satoru Nakashima, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Takashi Ogura
    • Organizer
      生物物理学会年会
    • Place of Presentation
      兵庫県立大(兵庫県)
    • Related Report
      2011 Research-status Report
  • [Presentation] フェムト秒レーザを用いた高感度時間分解赤外分光装置の開発と蛋白質への応用2011

    • Author(s)
      久保稔, 山口悟, 望月正雄, 伊藤-新澤 恭子, 吉川信也, 小倉尚志, 中島聡
    • Organizer
      日本分光学会
    • Place of Presentation
      理研横浜研究所(神奈川県)
    • Related Report
      2011 Research-status Report
  • [Presentation] チトクロム酸化酵素におけるプロトンポンプのゲート機構 -高精度時間分解赤外分光法によるダイナミクスの解明-2011

    • Author(s)
      中島 聡
    • Organizer
      特定領域「高次系」合同班会議(招待講演)
    • Place of Presentation
      沖縄残波岬ロイヤルホテル(沖縄県)
    • Related Report
      2011 Research-status Report
  • [Presentation] チトクロムc酸化酵素の酸素還元反応の時間分解赤外吸収測定を目的とした酸素肺フローシステムの開発と評価

    • Author(s)
      西 口達人・引田理英・新澤-伊藤恭子・吉川信也・中島 聡・小倉尚志
    • Organizer
      日本化学会第94春季年会
    • Place of Presentation
      名古屋大学(愛知県)
    • Related Report
      2013 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反応初期過 程

    • Author(s)
      中島 聡・久保 稔・石上 泉・新澤-伊藤恭子・吉川信也・小倉尚志
    • Organizer
      日本化学会第94春季年会
    • Place of Presentation
      名古屋大学(愛知県)
    • Related Report
      2013 Research-status Report
  • [Presentation] Proton pumping mechanism by dynamic hydrogen bond ordering in cytochrome c oxidase

    • Author(s)
      Satoru Nakashima, Minoru Kubo, Shinya Yoshikawa, Takashi Ogura
    • Organizer
      The 2nd International Symposium on Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
    • Place of Presentation
      キャンパスプラザ京都(京都府)
    • Related Report
      2013 Research-status Report
  • [Presentation] Development of the flow system with an artificial oxygen lung aimed at measuring time-resolved IR spectra of the oxygen reduction reaction of cytochrome c oxidase

    • Author(s)
      Tatsuhito Nishiguchi, Masahide Hikita, Kyoko Sinzawa-Itoh, Shinya Yoshikawa, Satoru Nakashima, and Takashi Ogura
    • Organizer
      第1回ピコバイオロジー研究所国際シンポジウム
    • Place of Presentation
      理研播磨地区(兵庫県)
    • Related Report
      2013 Research-status Report
  • [Presentation] Initial reaction dynamics of bovine heart cytochrome c oxidase revealed by time-resolved vibrational spectroscopy

    • Author(s)
      Satoru Nakashima, Minoru Kubo, Izumi Ishigami, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Takashi Ogura
    • Organizer
      第1回ピコバイオロジー研究所国際シンポジウム
    • Place of Presentation
      理研播磨地区(兵庫県)
    • Related Report
      2013 Research-status Report
  • [Presentation] Development of the flow system with an oxygen lung aiming at IR measurement on the oxygen reduction reaction of cytochrome c oxidase

    • Author(s)
      Tatsuhito Nishiguchi, Masahide Hikita, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Satoru Nakashima, Takashi Ogura
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      国立京都国際会館(京都府)
    • Related Report
      2013 Research-status Report
  • [Remarks] ピコバイオロジー専攻・生体物質構造学Ⅱ分野

    • URL

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

    • Related Report
      2014 Annual Research Report
  • [Remarks] ピコバイオロジー専攻・生体物質構造学II分野

    • URL

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

    • Related Report
      2012 Research-status Report

URL: 

Published: 2011-08-05   Modified: 2019-07-29  

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