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Molecular mechanisms in a visual transduction system of invertebrate rhodopsin

Research Project

Project/Area Number 24370043
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Structural biochemistry
Research InstitutionNagoya University

Principal Investigator

Murakami Midori  名古屋大学, 理学(系)研究科(研究院), 助教 (20324387)

Co-Investigator(Kenkyū-buntansha) Kouyama Tsutomu  名古屋大学, 大学院理学研究科, 教授 (30170210)
Project Period (FY) 2012-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥15,860,000 (Direct Cost: ¥12,200,000、Indirect Cost: ¥3,660,000)
Fiscal Year 2014: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2013: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2012: ¥9,100,000 (Direct Cost: ¥7,000,000、Indirect Cost: ¥2,100,000)
Keywordsロドプシン / 光情報変換 / 結晶構造解析 / 光受容 / X線結晶構造解析 / 情報伝達
Outline of Final Research Achievements

Blue light illumination at 100 K induced a red-shift of the absorption maximum, indicating that an equilibrium state of three isomeric states, Rhodopsin, Batho and 9-cis isorhodopsin was established. When this crystal was warmed to 240K, the absorption maximum was blue-shifted. Accurate estimation of isomer composition under this condition suggested that Batho was converted to LM with no change in the contents of the other states. We collected diffraction data set and calculate the difference electron density maps. It indicates that the conformational changes are located at the vicinity of the active site upon formation the LM intermediate. The larger movements of helices that characterize meta formation are not initiated at the early stage of photocycle in squid rhodopsin, but occur during the transition from LM to Meta. We try to crystallize the Acid Meta state of squid rhodopsin and succeed to obtain some new crystals which can diffract up to high resolution.

Report

(5 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (51 results)

All 2015 2014 2013 2012

All Journal Article (9 results) (of which Peer Reviewed: 9 results,  Open Access: 4 results) Presentation (41 results) (of which Int'l Joint Research: 2 results,  Invited: 2 results) Book (1 results)

  • [Journal Article] Structural comparison between the open and closed forms of citrate synthase from <i>Thermus thermophilus</i> HB82015

    • Author(s)
      E Kanamori E, Kawaguchi S, Kuramitsu S, Kouyama T, Murakami M
    • Journal Title

      Biophysics and Physicobiology

      Volume: 12 Issue: 0 Pages: 47-56

    • DOI

      10.2142/biophysico.12.0_47

    • NAID

      130005103943

    • ISSN
      2189-4779
    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin2015

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

      PloS one

      Volume: 10 Issue: 5 Pages: e0126970-e0126970

    • DOI

      10.1371/journal.pone.0126970

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Crystal structures of the L1, L2, N, and O states of pharaonis halorhodopsin2015

    • Author(s)
      Kouyama T, Kawaguchi H, Nakanishi T, Kubo H, Murakami M
    • Journal Title

      Biophys. J.

      Volume: 108 Issue: 11 Pages: 2680-2690

    • DOI

      10.1016/j.bpj.2015.04.027

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 膜タンパク質の立体構造解析の現状2015

    • Author(s)
      神山勉
    • Journal Title

      パリティ

      Volume: 30 Pages: 6-64

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of cruxrhodopsin-3 from Haloarcula vallismortis2014

    • Author(s)
      Chan SK, Kitajima-Ihara T, Fujii R, Gotoh T, Murakami M, Ihara K, Kouyama T
    • Journal Title

      PLoS One

      Volume: 9 Issue: 9 Pages: 1-10

    • DOI

      10.1371/journal.pone.0108362

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure of archaerhodopsin-2 at 1.8 A resolution2014

    • Author(s)
      Kouyama T, Fujii R, Kanada S, Nakanishi T, Chan SK, Murakami M
    • Journal Title

      Acta Crystallogr.

      Volume: D70 Issue: 10 Pages: 2692-2701

    • DOI

      10.1107/s1399004714017313

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of deltarhodopsin-3 from Haloterrigena thermotolerans.2013

    • Author(s)
      Zhang J., Mizuno K., Murata Y., Koide H., Murakami M., Ihara K., Kouyama T.
    • Journal Title

      Proteins

      Volume: 81 Issue: 9 Pages: 1585-1592

    • DOI

      10.1002/prot.24316

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide.2013

    • Author(s)
      Nakanishi T., Kanada S., Murakami M., Ihara K.,
    • Journal Title

      Biophys. J.

      Volume: 104 Issue: 2 Pages: 377-385

    • DOI

      10.1016/j.bpj.2012.12.018

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Proteins2012

    • Author(s)
      Zhang J.
    • Journal Title

      Crystal structure of the O intermediate of the Leu93→Ala mutant of bacteriorhodopsin

      Volume: 80 Issue: 10 Pages: 2384-2396

    • DOI

      10.1002/prot.24124

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] Structural changes of squid rhodopsin during the thermal relaxation process in the P62 crystal2015

    • Author(s)
      Murakami M, Kouyama T
    • Organizer
      Pacifichem 2015
    • Place of Presentation
      Honolulu
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Crystallographic study of the LM intermediate of squid rhodopsin2015

    • Author(s)
      村上緑,神山勉
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] プロトン輸送性ロドプシンにおける低障壁水素結合の役割2015

    • Author(s)
      神山勉
    • Organizer
      日本物理学会第70回年次大会
    • Place of Presentation
      東京
    • Year and Date
      2015-03-21 – 2015-03-24
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] イカロドプシンの光異性化-熱的緩和反応の結晶構造解析2015

    • Author(s)
      村上緑,神山勉
    • Organizer
      日本物理学会第70回年次大会
    • Place of Presentation
      東京
    • Year and Date
      2015-03-21 – 2015-03-24
    • Related Report
      2014 Annual Research Report
  • [Presentation] Higher order structure of cruxrhodopsin from Haloarcula vallismortis and its photostability2015

    • Author(s)
      S. K. Chan, T. Kitajima, M. Murakami, K. Ihara, T. Kouyama
    • Organizer
      生物物理学会中部支部講演会
    • Place of Presentation
      岡崎
    • Year and Date
      2015-03-10
    • Related Report
      2014 Annual Research Report
  • [Presentation] イカロドプシンのp62結晶における光異性化から熱緩和までの構造変化2015

    • Author(s)
      村上緑,神山勉
    • Organizer
      生物物理学会中部支部講演会
    • Place of Presentation
      岡崎
    • Year and Date
      2015-03-10
    • Related Report
      2014 Annual Research Report
  • [Presentation] Conformational changes in helices C and F of pharaonis halorhodopsin during the ion pumping cycle2014

    • Author(s)
      T. Kouyama
    • Organizer
      16th International Conference on Retinal Proteins
    • Place of Presentation
      長浜
    • Year and Date
      2014-10-05 – 2014-10-09
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] A chimeric proton-pumping rhodopsin designed for crystallographic analysis of light-induced structural changes2014

    • Author(s)
      S. Uyama, T. Kitajima-Ihara, M. Murakami, K. Ihara, T. Kouyama
    • Organizer
      16th International Conference on Retinal Proteins
    • Place of Presentation
      長浜
    • Year and Date
      2014-10-05 – 2014-10-09
    • Related Report
      2014 Annual Research Report
  • [Presentation] Crystallographic study on the N state of pharaonis halorhodopsin2014

    • Author(s)
      H. Kawaguchi, T. Nakanishi, M. Murakami, T. Kouyama
    • Organizer
      16th International Conference on Retinal Proteins
    • Place of Presentation
      長浜
    • Year and Date
      2014-10-05 – 2014-10-09
    • Related Report
      2014 Annual Research Report
  • [Presentation] Crystal structure of cruxrhodopsin-3 from Haloarcula vallismortis2014

    • Author(s)
      S. K. Chan, T. Kitajima-Ihara, M. Murakami, K. Ihara, T. Kouyama
    • Organizer
      16th International Conference on Retinal Proteins
    • Place of Presentation
      長浜
    • Year and Date
      2014-10-05 – 2014-10-09
    • Related Report
      2014 Annual Research Report
  • [Presentation] New crystal forms of squid rhodopsin2014

    • Author(s)
      M. Murakami, T. Kouyama
    • Organizer
      日本生物物理学会第52回年会
    • Place of Presentation
      札幌
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] バクテリオロドプシン-ハロロドプシン-キメラ蛋白質の光反応サイクル2014

    • Author(s)
      S. Uyama, T. Kitajima, M. Murakami, T. Kouyama
    • Organizer
      日本生物物理学会第52回年会
    • Place of Presentation
      札幌
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] 凍結割断低温原子間力顕微鏡の製作2014

    • Author(s)
      N. Kuga, T. Gotoh, T. Kouyama
    • Organizer
      日本生物物理学会第52回年会
    • Place of Presentation
      札幌
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] クラックスロドプシンの3量体構造と光安定性2014

    • Author(s)
      S. K. Chan, T. Kitajima, M. Murakami, K. Ihara, T. Kouyama
    • Organizer
      日本生物物理学会第52回年会
    • Place of Presentation
      札幌
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] ファラオニス・ハロロドプシンのN中間体の結晶構造解析2014

    • Author(s)
      川口春樹,中西太市,久保宏樹,井原邦夫村上緑,神山勉
    • Organizer
      日本生物物理学会第52回年会
    • Place of Presentation
      札幌
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] 発色団を導入したイカロドプシン結晶の吸光特性2014

    • Author(s)
      村上緑,神山勉
    • Organizer
      日本物理学会第69回年次大会
    • Place of Presentation
      平塚
    • Related Report
      2013 Annual Research Report
  • [Presentation] X-ray structural analysis of the N photoreaction intermediate of halorhodopsin in complex with bromide ions2014

    • Author(s)
      H Kawaguchi, T Nakanishi, H Kubo, K Ihara, M Murakami, T Kouyama
    • Organizer
      The IGER International Symposium on Science of Molecular Assembly and Biomolecular Systems 2014
    • Place of Presentation
      名古屋
    • Related Report
      2013 Annual Research Report
  • [Presentation] Investigation of a pre-crystallization solution of octopus rhodopsin by cryo-electron microscopy2014

    • Author(s)
      Shinji UYAMA, Katsuhide MIZUNO, Youko NAKAMURA, Toshiaki GOTO, Midori MURAKAMI, Tsutomu KOUYAMA
    • Organizer
      The IGER International Symposium on Science of Molecular Assembly and Biomolecular Systems 2014
    • Place of Presentation
      名古屋
    • Related Report
      2013 Annual Research Report
  • [Presentation] Observation of bacteriorhodopsin crystal structure by freeze fracture atomic force microscopy2014

    • Author(s)
      Naoto KUGA,Toshiaki GOTO, Tsutomu KOUYAMA
    • Organizer
      The IGER International Symposium on Science of Molecular Assembly and Biomolecular Systems 2014
    • Place of Presentation
      名古屋
    • Related Report
      2013 Annual Research Report
  • [Presentation] クライオ原子間力顕微鏡によるバクテリオロドプシンの結晶化過程の観察2013

    • Author(s)
      林駿甫汐, 我直登, 五藤俊明, 神山勉
    • Organizer
      平成24年度生物物理学会中部支部講演会
    • Place of Presentation
      名古屋
    • Year and Date
      2013-02-19
    • Related Report
      2012 Annual Research Report
  • [Presentation] ハロロドプシンのハライドイオン輸送サイクルにおける構造変化2013

    • Author(s)
      川口春樹, 中西太市, 久保宏樹, 井原邦夫, 村上緑, 神山勉
    • Organizer
      平成24年度生物物理学会中部支部講演会
    • Place of Presentation
      名古屋
    • Year and Date
      2013-02-19
    • Related Report
      2012 Annual Research Report
  • [Presentation] Crystallographic study of cruxrhodopsin-3 from Haloarcula vallismortis2013

    • Author(s)
      S.K.Chan, T.Kitajima, M.Murakami, K.Ihara.T.Kouyama
    • Organizer
      平成24年度生物物理学会中部支部講演会
    • Place of Presentation
      名古屋
    • Year and Date
      2013-02-19
    • Related Report
      2012 Annual Research Report
  • [Presentation] X-ray cryatallography study of crusrhodopsin from Haloarcula vallismortis2013

    • Author(s)
      S. K. Chan
    • Organizer
      IGER Annual meeting 2012
    • Place of Presentation
      名古屋
    • Year and Date
      2013-01-10
    • Related Report
      2012 Annual Research Report
  • [Presentation] ハロロドプシン-臭素イオン複合体のN光反応中間体のX線結晶構造解析2013

    • Author(s)
      川口春樹,中西太市,久保宏樹,井原邦夫村上緑,神山勉
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Trapping the photoactive form of squid rhodopsin in the P62 crytal2013

    • Author(s)
      村上緑,神山勉
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] フリーズフラクチャー原子間力顕微鏡によるバクテリオロドプシンの3次元結晶の観察2013

    • Author(s)
      久我直登,五藤俊明,神山勉
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Crystal structure of cruxrhodopsin-3 from Haloarcula vallismortis2013

    • Author(s)
      S. K. Chan, T. Kitajima, M. Murakami, K. Ihara, T. Kouyama
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] ロドプシン群蛋白質の光誘起構造変化に関するX線結晶解析2013

    • Author(s)
      神山勉
    • Organizer
      日本生物物理学会第51回年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] クライオ原子間力顕微鏡によるバクテリオロドプシンの結晶化過程の観察2013

    • Author(s)
      林駿甫, 久我直登, 五藤俊明, 神山勉
    • Organizer
      日本物理学会第68回年次大会
    • Place of Presentation
      広島
    • Related Report
      2012 Annual Research Report
  • [Presentation] ハロロドプシンのハライドイオン輸送体の反応状態の構造解析2013

    • Author(s)
      川口春樹, 中西太市, 井原邦夫, 神山勉
    • Organizer
      日本物理学会第68回年次大会
    • Place of Presentation
      広島
    • Related Report
      2012 Annual Research Report
  • [Presentation] X線結晶構造から観るイカロドプシンの光反応初期過程2013

    • Author(s)
      村上緑, 神山勉
    • Organizer
      日本物理学会第68回年次大会
    • Place of Presentation
      広島
    • Related Report
      2012 Annual Research Report
  • [Presentation] X-ray crystallography study of cruxrhodopsin from Haloarcula vallismortis2013

    • Author(s)
      S. K. Chan, T.Kitajima, M.Murakami, K.Ihara, T.Kouyama
    • Organizer
      日本物理学会第68回年次大会
    • Place of Presentation
      広島
    • Related Report
      2012 Annual Research Report
  • [Presentation] ロドプシンのX線結晶構造解析-結晶学と分光学で探るわたしたちがモノを見るしくみ-2012

    • Author(s)
      村上緑
    • Organizer
      名古屋大学女性研究者サイエンスフォーラム
    • Place of Presentation
      名古屋
    • Year and Date
      2012-08-09
    • Related Report
      2012 Annual Research Report
  • [Presentation] Crystal structure of the lumi intermediate of squid rhodopsin2012

    • Author(s)
      M.Murakami, T.Kouyama
    • Organizer
      15th International Conference on Retinal Proteins
    • Place of Presentation
      Ascona(招待講演)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Crystal structure of an M state of the azide complex of pharaonis Halorhodopsin2012

    • Author(s)
      T.Kouyama
    • Organizer
      15th International Conference on Retinal Proteins
    • Place of Presentation
      Ascona(招待講演)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Photo-activation mechanism of squid rhodopsin2012

    • Author(s)
      村上緑, 神山勉
    • Organizer
      日本生物物理学会第50回年会
    • Place of Presentation
      名古屋(招待講演)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Large deformation of helix F upon formation of the M intermediate of the azide-bound purple form of pharaonis halorhodopsin2012

    • Author(s)
      中西太市, 金田創運, 村上緑, 井原邦夫, 神山勉
    • Organizer
      日本生物物理学会第50回年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] Crystal Structure of deltarhodospin from Haloterrigena Thermotolerans2012

    • Author(s)
      張進, 水野克秀, 神山勉
    • Organizer
      日本生物物理学会第50回年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] X-ray crystallography of retinal proteins2012

    • Author(s)
      T. Kouyama
    • Organizer
      IGER International Symposium on Science of Molecular Assembly and Biomolecular Systems 2012
    • Place of Presentation
      Nagoya
    • Related Report
      2012 Annual Research Report
  • [Presentation] Structural analysis of biological molecules by cryogenic atomic force microscopy2012

    • Author(s)
      S. Hayashi, T. Kouyama,
    • Organizer
      IGER International Symposium on Science of Molecular Assembly and Biomolecular Systems 2012
    • Place of Presentation
      Nagoya
    • Related Report
      2012 Annual Research Report
  • [Presentation] Large deformation of helix F upon formation of tlie in intermediate of the azide-bound purple form of pharaonis halorhodopsin2012

    • Author(s)
      T. Nakanishi, S. Kanada, M. Murakami, K. Ihara, T. Kouyama
    • Organizer
      IGER International Symposium on Science of Molecular Assembly and Biomolecular Systems 2012
    • Place of Presentation
      Nagoya
    • Related Report
      2012 Annual Research Report
  • [Book] 日本の結晶学(II) その輝かしい発展2014

    • Author(s)
      村上緑
    • Total Pages
      485
    • Publisher
      日本結晶学会「日本の結晶学(II)」出版編集委員会
    • Related Report
      2014 Annual Research Report

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Published: 2012-04-24   Modified: 2019-07-29  

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