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Four Dimensional Structural Analysis of Biological Ion Pumps

Research Project

Project/Area Number 17370056
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionNagoya University

Principal Investigator

KOUYAMA Tsutomu  Nagoya University, Graduate School of Science, Professor, 大学院理学研究科, 教授 (30170210)

Co-Investigator(Kenkyū-buntansha) IHARA Kunio  Nagoya University, Center for Gene Research, Assistant Prefessor, 遺伝子実験施設, 助手 (90223297)
MURAKAMI Midori  Nagoya University, Graduate school of Science, Assis tant Professor, 大学院理学研究科, 助手 (20324387)
YAMATO Takahisa  Nagoya University, Graduate school of Science, Assistant Professor, 大学院理学研究科, 助教授 (90251587)
OKUMURA Hideo  Nagoya University, Graduate school of Science, Assistant Professor, 7・1より理化学研究所の協力研究員), 産学官連携研究員 (90377903)
Project Period (FY) 2005 – 2006
Project Status Completed (Fiscal Year 2006)
Budget Amount *help
¥10,700,000 (Direct Cost: ¥10,700,000)
Fiscal Year 2006: ¥3,500,000 (Direct Cost: ¥3,500,000)
Fiscal Year 2005: ¥7,200,000 (Direct Cost: ¥7,200,000)
Keywordsbacteriorhodopsin / halorhodopsin / squid rhodopsin / proton pump / chloride pump / membrane protein / retinal protein / X-ray crystallography / レチナール蛋白質 / 生物物理 / 蛋白質 / ナノバイオ / 計算物理 / 分子機械
Research Abstract

Bacteriorhodopsin, a light-driven proton pump found in the cell membrane of halobacteria, is one of well characterized biological ion pumps. Based on the results of four-dimensional X-ray crystallographic analyses, the principal investigator and colleague have proposed a new hypothesis that bacteriorhodopsin actually functions as an antiporter of water and proton. To get supports for this hypothesis, we investigated time-resolved spectroscopy as well as X-ray crystallographic analysis of bacteriorhodopin exposed to pressurized noble gases. It was then found that when Xe or Kr atom binds specificically to a hydrophobic cavity in the cytoplasmic side of bacteriorhodopsin, the decay of the M intermediate is accelerated significantly. We also performed X-ray crystallographic analysis of archaearhodopsin-2, a light-driven proton pump found in Halorubrum, and determined its three-dimensional structure at 2.1 angstrom resolution. It was shown that the crystal of archaerhodopsin-2 is made up of stacked membranes, in each of which the trimeric complexes are arranged on a honeycomb lattice and that the second chromophore, bacterioruberin, mediates interactions between neighboring proteins within the trimer. We succeeded in getting a three-dimensional crystal of proteorhodopsin, a light-driven proton pump from a proteobacterioum. We have established to prepare a large amount of halorhodopsin, a light-driven chloride pump, after a repeated cycle of UV mutagenesis. We obtained a well-ordered three-dimensional crystal of squid rhodopsin and determined its structure at 2.8 angstrom resolution.

Report

(3 results)
  • 2006 Annual Research Report   Final Research Report Summary
  • 2005 Annual Research Report
  • Research Products

    (45 results)

All 2007 2006 2005

All Journal Article (34 results) Book (11 results)

  • [Journal Article] Crystallization and crystal properties of squid rhodopsin2007

    • Author(s)
      Murkami, M., Kitahara, R., GOtoh, T., Kouyama, T.
    • Journal Title

      Acta Crystallgr. F (In press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Annual Research Report 2006 Final Research Report Summary
  • [Journal Article] Spectral tuning of photoactive yellow protein2007

    • Author(s)
      T.Yamato, T.Ishikura, T.Kakitani, K.Kawaguchi, H.Watanabe
    • Journal Title

      Photochemistry and Photobiology 83

      Pages: 323-327

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Annual Research Report 2006 Final Research Report Summary
  • [Journal Article] Modulation of the absorption maximum of rhodopsin by amino acids in the C-terminus.2007

    • Author(s)
      S.Yokoyama, T.Tada, T.Yamato
    • Journal Title

      Photochemistry and Photobiology 83

      Pages: 236-241

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Annual Research Report 2006 Final Research Report Summary
  • [Journal Article] Crystallization and crystal properties of squid rhodopsin2007

    • Author(s)
      Murkami, M.Kitahara, R., GOtoh, T., Kouyama, T.
    • Journal Title

      Acta Crystallgr. F (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Modulation of the absorption maximum of rhodopsin by amino acids in the C-terminus2007

    • Author(s)
      S.Yokoyama, T.Tada, T.Yamato
    • Journal Title

      Photochemistry and Photobiology 83

      Pages: 236-241

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Crystal structures of archaerhodopsin-1 and -2 : Common structural motif in archaeal light-driven proton pumps2006

    • Author(s)
      Enami, N., Yoshimura, K., Murakami, M., Okumura, H., Ihara, K., Kouyama, T.
    • Journal Title

      J. Mol. Biol. 358

      Pages: 675-685

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] 光駆動プロトンポンプの4次元結晶構造解析2006

    • Author(s)
      神山 勉
    • Journal Title

      日本結晶学会誌 48

      Pages: 359-366

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Annual Research Report 2006 Final Research Report Summary
  • [Journal Article] Theoretical prediction of optical absorption peaks for photosensory receptor mutants.2006

    • Author(s)
      K.Kawaguchi, T.Yamato
    • Journal Title

      Chem. Phys. Lett. 430

      Pages: 386-390

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Annual Research Report 2006 Final Research Report Summary
  • [Journal Article] Energy transfer pathways relevant for long-range in tramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis.2006

    • Author(s)
      T.Ishikura, T.Yamato
    • Journal Title

      Chem. Phys. Lett. 432

      Pages: 533-537

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] A light-driven proton pump from Haloterrigene turkmenica : functional expression in Escherichia coli membrane and coupling with a H+ co-transporter.2006

    • Author(s)
      Kamo N., Hashiba T., Kikukawa T., Araiso T., Ihara K., Nara T.
    • Journal Title

      Biochem. Biophys. Res. Commun. 341

      Pages: 285-290

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Hydrogen-bonding interaction of the protonated Schiff base with halides in a chloride-pumping bacteriorhodopsin mutant.2006

    • Author(s)
      Shibata M., Ihara K., Kandori H.
    • Journal Title

      Biochemistry 45

      Pages: 10633-10640

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Annual Research Report 2006 Final Research Report Summary
  • [Journal Article] Crystal structures of archaerhodopsin-1 and-2 : Common structural motif in archaeal light-driven proton pumps2006

    • Author(s)
      Enami, N.Yoshimura, K., Murakami, M., Okumura, H., Ihara, K., Kouyama, T.
    • Journal Title

      J. Mol. Biol. 358

      Pages: 675-685

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Four dimensional crystallographic analyses of light-driven proton pumps2006

    • Author(s)
      Kouyama, T.
    • Journal Title

      J. Japn. Soc. Cryst. algr. 48

      Pages: 359-366

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Theoretical prediction of optical absorption peaks for photosensory receptor mutants2006

    • Author(s)
      K.Kawaguchi, T.Yamato
    • Journal Title

      Chem. Phys. Lett. 430

      Pages: 386-390

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis2006

    • Author(s)
      T.Ishikura, T.Yamato
    • Journal Title

      Chem. Phys. Lett. 432

      Pages: 533-537

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] A light-driven proton pump from Haloterrigene turkmenica : functional expression in Escherichia coli membrane and coupling with a H+ co-transporter2006

    • Author(s)
      Kamo N., Hashiba T., Kikukawa T., Araiso T., Ihara K., Nara T.
    • Journal Title

      Biochem. Biophys. Res. Commun. 341

      Pages: 285-290

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Hydrogen-bonding interaction of the protonated Schiff base with halides in a chloride-pumping bacteriorhodopsin mutant2006

    • Author(s)
      Shibata M., Ihara K., Kandori H.
    • Journal Title

      Biochemistry 45

      Pages: 10633-40

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Crystal structures of archaerhodopsin-1 and -2 : Common structural motif in archaeal light-driven proton pumps2006

    • Author(s)
      Enami, N., Yoshimura, K., Murakami, M., Okumura, H., Ihara, K., Kouyama, T.
    • Journal Title

      J. Mol. Biol.

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis.2006

    • Author(s)
      T.Ishikura, T.Yamato
    • Journal Title

      Chem. Phys. Lett. 432

      Pages: 533-537

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Temperature dependence of the inelastic tunneling, Molecular Simulation2006

    • Author(s)
      H.Nishioka, T.Yamato, T.Kakitani
    • Journal Title

      Molecular Simulation 32

      Pages: 727-734

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A light-driven proton pump from Haloterrigene turkmenica : function al expression in Escherichia coli membrane and coupling with a H+ co-transporter2006

    • Author(s)
      Kamo N., Hashiba T., Kikukawa T., Araiso T., Ihara K., Nara T.
    • Journal Title

      Biochem. Biophys. Res. Commun. 341

      Pages: 285-290

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Crystal structures of archaerhodopsin-1 and -2 : Common structural motif in archaeal light-driven proton pumps2006

    • Author(s)
      Enami, N., Yoshimura, K., Murakami, M., Okumura, H., Ihara, K., Kouyama, T.
    • Journal Title

      J.Mol.Biol. (In press)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] A light-driven proton pump from Haloterrigene turkmenica : functional expression in Escherichia coli membrane and coupling with a H+ co-transporter.2006

    • Author(s)
      Kamo N., Hashiba T., Kikukawa T., Araiso T., Ihara K., Nara T.
    • Journal Title

      Biochem.Biophys.Res.Commun. 341

      Pages: 285-290

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Crystal structures of acid blue and alkaline purple forms of bacteriorhodopsin"2005

    • Author(s)
      Okumura, H., Murkami, M., Kouyama, T.
    • Journal Title

      J. Mol. Biol. 351

      Pages: 481-495

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Crystal structure of the 13-cis isomer of bacteriorhodopsin in the dark-adapted state2005

    • Author(s)
      Nishikawa, T., Murkami, M., Kouyama, T.
    • Journal Title

      J. Mol. Biol. 352

      Pages: 319-328

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Interference, fluctuation, and alternation of electron tunneling in protein media. 2. Non-Condon theory for the energy gap dependence of electron transfer rate.2005

    • Author(s)
      H.Nishioka, A.Kimura, T.Yamato, T.Kawatsu, T.Kakitani
    • Journal Title

      J. Phys. Chem. B. 109(32)

      Pages: 15621-15635

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Interference, fluctuation, and alternation of electron tunneling in protein media. 1. Two tunneling routes in photosynthetic reaction center alternate due to thermal fluctuation of protein conformation.2005

    • Author(s)
      H.Nishioka, A.Kimura, T.Yamato, T.Kawatsu, T.Kakitani
    • Journal Title

      J. Phys. Chem. B. 109(5)

      Pages: 1978-1987

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Crystal structures of acid blue and alkaline purple forms of bacteriorhodopsin2005

    • Author(s)
      Okumura, H.Murkami, M., Kouyama, T.
    • Journal Title

      J. Mol. Biol. 351

      Pages: 481-495

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Interference, fluctuation, and alternation of electron tunneling in protein media. 2. Non-Condon theory for the energy gap dependence of electron transfer rate2005

    • Author(s)
      H.Nishioka, A.Kimura, T.Yamato, T.Kawatsu, T.Kakitani
    • Journal Title

      Phys. Chem. B. 109

      Pages: 15621-15635

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Interference, fluctuation, and alternation of electron tunneling in protein media. 1. Two tunneling routes in photosynthetic reaction center alternate due to thermal fluctuation of protein conformation2005

    • Author(s)
      H.Nishioka, A.Kimura, T.Yamato, T.Kawatsu, T.Kakitani
    • Journal Title

      J. Phys. Chem. B. 109

      Pages: 1978-1987

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Crystal structures of acid blue and, alkaline purple forms of bacteriorhodopsin2005

    • Author(s)
      Okumura, H., Murakami, M., Kouyama, T.
    • Journal Title

      J.Mol.Biol. 351

      Pages: 481-495

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Crystal structure of the 13-cis isomer of bacteriorhodopsin in the dark-adapted state2005

    • Author(s)
      Nishikawa, T., Murakami, M., Kouyama, T.
    • Journal Title

      J.Mol.Biol. 352

      Pages: 319-328

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Interference, fluctuation, and alternation of electron tunneling in protein media. 2. Non-Condon theory for the energy gap dependence of electron transfer rate.2005

    • Author(s)
      H.Nishioka, A.Kimura, T.Yamato, T.Kawatsu, T.Kakitani
    • Journal Title

      J.Phys.Chem.B. 109(32)

      Pages: 15621-15635

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Interference, fluctuation, and alternation of electron tunneling in protein media. 1. Two tunneling routes in photosynthetic reaction center alternate due to thermal fluctuation of protein conformation.2005

    • Author(s)
      H.Nishioka, A.Kimura, T.Yamato, T.Kawatsu, T.Kakitani
    • Journal Title

      J.Phys.Chem.B. 109(5)

      Pages: 1978-1987

    • Related Report
      2005 Annual Research Report
  • [Book] 生物物理学ハンドブック、(石渡信一,桂勲,桐野豊,美宅成樹 編)分担執筆2007

    • Author(s)
      神山 勉
    • Publisher
      朝倉書店(印刷中)
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Book] 生物物理学ハンドブック(石渡信一,桂勲,桐野豊,美宅成樹 編)(分担執筆)2007

    • Author(s)
      神山 勉
    • Publisher
      朝倉書店
    • Related Report
      2006 Annual Research Report
  • [Book] パリティ(大槻義彦 編)分担日本語訳「ニューラルネットワークモデルで解き明かすヘビの眼のしくみ」2007

    • Author(s)
      倭 剛久
    • Publisher
      丸善
    • Related Report
      2006 Annual Research Report
  • [Book] 生物理学ハンドブック(石渡信一・桂勲・桐野豊・美宅成樹 編)(分担執筆)2007

    • Author(s)
      倭 剛久
    • Publisher
      朝倉書店
    • Related Report
      2006 Annual Research Report
  • [Book] 光合成微生物の機能と応用、分担執筆「高度好塩菌の光エネルギー変換系」2006

    • Author(s)
      神山 勉, 吉村恵子
    • Publisher
      シーエムシー出版
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Annual Research Report 2006 Final Research Report Summary
  • [Book] 電磁場の方程式 バイオインフォマティクス事典(宮野 悟,江口 至洋,金久 實,高木 利久,中井 謙太 編)(分担執筆)2006

    • Author(s)
      倭 剛久
    • Publisher
      共立出版
    • Related Report
      2006 Annual Research Report
  • [Book] 静電場 バイオインフォマティクス事典(宮野 悟,江口 至洋,金久 實,高木 利久,中井 謙太 編)(分担執筆)2006

    • Author(s)
      倭 剛久
    • Publisher
      共立出版
    • Related Report
      2006 Annual Research Report
  • [Book] 静磁場 バイオインフォマティクス事典(宮野 悟,江口 至洋,金久 實,高木 利久,中井 謙太 編)(分担執筆)2006

    • Author(s)
      倭 剛久
    • Publisher
      共立出版
    • Related Report
      2006 Annual Research Report
  • [Book] シュレーディンガー方程式 バイオインフォマティクス事典(宮野 悟,江口 至洋,金久 實,高木 利久,中井 謙太 編)(分担執筆)2006

    • Author(s)
      倭 剛久
    • Publisher
      共立出版
    • Related Report
      2006 Annual Research Report
  • [Book] 分子起動計算 バイオインフォマティクス事典(宮野 悟,江口 至洋,金久 實,高木 利久,中井 謙太 編)(分担執筆)2006

    • Author(s)
      倭 剛久
    • Total Pages
      232
    • Publisher
      共立出版
    • Related Report
      2006 Annual Research Report
  • [Book] タンパク質による光情報処理と光エネルギー変換の分子機構 名古屋大学情報連携基盤センターニュース Vol.5(No.3)(分担執筆)2006

    • Author(s)
      倭 剛久
    • Publisher
      名古屋大学情報連携基盤センター
    • Related Report
      2006 Annual Research Report

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Published: 2005-04-01   Modified: 2019-12-17  

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