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Biochemical analysis of low thermal isomerization mechanism of rod visual pigment.

Research Project

Project/Area Number 26650119
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Animal physiology/Animal behavior
Research InstitutionKyoto University

Principal Investigator

Shichida Yoshinori  京都大学, 理学(系)研究科(研究院), 教授 (60127090)

Project Period (FY) 2014-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2014: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords視物質 / 視細胞 / 暗ノイズ / 生化学的方法 / 分子進化 / 生化学的手法
Outline of Final Research Achievements

Low dark noise is a prerequisite for rod cells, which mediate our dim-light vision. The low dark noise is achieved by the extremely stable character of the rod visual pigment, rhodopsin, which evolved from less stable cone visual pigments. We have developed a biochemical method to quickly evaluate the thermal isomerization rate of the chromophore in visual pigments. Using an isomerization locked chromophore, we confirmed that thermal isomerization rate of the chromophore in rhodopsin is about 1/1000 of that of cone visual pigment and identified two critical residues (E122 and I189) in the chromophore binding pocket which account for the extremely low thermal activation rate of rhodopsin. Furthermore, we found that anura blue-sensitive cone visual pigment expressed in green rods acquired the low thermal isomerization rate of the chromophore by the specific mutation during the molecular evolution, which led to optimization for scotopic vision.

Report

(3 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • Research Products

    (15 results)

All 2016 2015 2014 Other

All Journal Article (6 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 6 results,  Open Access: 3 results,  Acknowledgement Compliant: 3 results) Presentation (6 results) (of which Int'l Joint Research: 2 results,  Invited: 2 results) Book (2 results) Remarks (1 results)

  • [Journal Article] Origin of the low thermal isomerization rate of rhodopsin chromophore2015

    • Author(s)
      Yanagawa, M.; Kojima, K.; Yamashita, T.; Iwamoto, Y.; Matsuyama, T.; Nakanishi, K.; Yamano, Y.; Wada, A.; Sako, Y.; Shichida, Y.
    • Journal Title

      Sci. Rep.

      Volume: 5 Issue: 1 Pages: 11081-11081

    • DOI

      10.1038/srep11081

    • NAID

      120005690204

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Helical rearrangement of photoactivated rhodopsin in monomeric and dimeric forms probed by high-angle X-ray scattering.2015

    • Author(s)
      Imamoto Y, Kojima K, Oka T, Maeda R, Shichida Y
    • Journal Title

      Photochem. Photobiol. Sci.

      Volume: 14(11) Issue: 11 Pages: 1965-1973

    • DOI

      10.1039/c5pp00175g

    • NAID

      120005741088

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Diversification of non-visual photopigment parapinopsin in spectral sensitivity for diverse pineal functions2015

    • Author(s)
      M. Koyanagi, S. Wada, E. Kawano-Yamashita, Y. Hara, S. Kuraku, S. Kosaka, K. Kawakami, S. Tamotsu, H. Tsukamoto, Y. Shichida, A. Terakita
    • Journal Title

      BMC Biology

      Volume: 13 Issue: 1 Pages: 73-73

    • DOI

      10.1186/s12915-015-0174-9

    • NAID

      120005758203

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Diversity of active states in TMT opsins2015

    • Author(s)
      K. Sakai
    • Journal Title

      PLoS One

      Volume: 10 Issue: 10 Pages: 1-12

    • DOI

      10.1371/journal.pone.0141238

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Intramolecular interactions that induce helical rearrangement upon rhodopsin activation: Light-induced structural changes in metarhodopsin IIa probed by cysteine S-H stretching vibrations2014

    • Author(s)
      Y. Yamazaki, T. Nagata, A. Terakita, H. Kandori, Y. Shichida, Y. Imamoto*
    • Journal Title

      J. Biol. Chem

      Volume: 289 Issue: 20 Pages: 13792-13800

    • DOI

      10.1074/jbc.m113.527606

    • NAID

      120005741087

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Contribution of glutamic acid in the conserved E/DRY triad to the functional properties of rhodopsin.2014

    • Author(s)
      Sato, K., Yamashita, T., and Shichida, Y.
    • Journal Title

      Biochemistry

      Volume: 53 Issue: 27 Pages: 4420-4425

    • DOI

      10.1021/bi5003772

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Thermal isomerization of chromophore in rod and cone visual pigments2015

    • Author(s)
      Y. Shichida
    • Organizer
      Pacifichem 2015
    • Place of Presentation
      Honolulu, USA
    • Year and Date
      2015-12-19
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Molecular evolution of the low thermal isomerization rate of rhodopsin chromophore2015

    • Author(s)
      Y. Shichida
    • Organizer
      7th AOCP
    • Place of Presentation
      Taipei, Taiwan
    • Year and Date
      2015-11-18
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 両生類の緑桿体に含まれる青色錐体視物質の熱活性化頻度2015

    • Author(s)
      松谷優樹、小島慧一、柳川正隆、山下高廣、今元泰、山野由美子、和田昭盛、七田芳則
    • Organizer
      日本動物学会大86回大会
    • Place of Presentation
      新潟
    • Year and Date
      2015-09-17
    • Related Report
      2015 Annual Research Report
  • [Presentation] 視物質の低い熱活性化頻度をもたらす分子メカニズム2015

    • Author(s)
      小島慧一、柳川正隆、山下高廣、松谷優樹、今元泰、松山オジョス武、中西香爾、山野由美子、和田昭盛、佐甲靖志、七田芳則
    • Organizer
      日本生物物理学会第53回年会
    • Place of Presentation
      金沢
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] ロドプシンの低い熱活性化頻度の分子メカニズム2014

    • Author(s)
      小島慧一、柳川正隆、山下高廣、今元泰、松山武、中西香爾、山野由美子、和田昭盛、佐甲靖志、七田芳則
    • Organizer
      日本生物物理学会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Research-status Report
  • [Presentation] ロドプシン発色団の低い熱異性化速度の生化学的測定2014

    • Author(s)
      柳川正隆、小島慧一、山下高廣、今元泰、松山武、中西香爾、山野由美子、和田昭盛、佐甲靖志、七田芳則
    • Organizer
      日本動物学会
    • Place of Presentation
      東北大学
    • Year and Date
      2014-09-11 – 2014-09-13
    • Related Report
      2014 Research-status Report
  • [Book] 光と生命の辞典2016

    • Author(s)
      七田芳則
    • Total Pages
      422
    • Publisher
      朝倉書店
    • Related Report
      2015 Annual Research Report
  • [Book] Vertebrate Photoreceptors2014

    • Author(s)
      Sato, K. and Shichida, Y.
    • Total Pages
      349
    • Publisher
      Springer
    • Related Report
      2014 Research-status Report
  • [Remarks] 七田研ホームページ

    • URL

      http://photo1.biophys.kyoto-u.ac.jp/shichida/home_jp.html

    • Related Report
      2015 Annual Research Report 2014 Research-status Report

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Published: 2014-04-04   Modified: 2017-05-10  

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