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Theoretical study of weak interactions in photoreceptor rhodopsin and DNA/RNA helical structures

Research Project

Project/Area Number 15K05408
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionQuantum Chemistry Research Institute

Principal Investigator

Miyahara Tomoo  特定非営利活動法人量子化学研究協会, 研究所, 部門長 (70397595)

Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2015: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywords弱い相互作用 / DNA・RNA / 光生命科学 / シミュレーション
Outline of Final Research Achievements

The signs at around 295 nm of the CD spectra of the DNA and RNA double-helical structures are much different between the right- and left-handed structures as well as between DNA and RNA. The SAC-CI CD spectra reproduced the features at around 295 nm of the experimental CD spectra of each DNA and RNA, and elucidated that the strong stacking interaction between the two base pairs is the origin of the negative peaks at 295 nm of the CD spectra for both DNA and RNA.
The microbial rhodopsin contains a proton pumping bacteriorhodopsin (BR), a chloride pumping halorhodopsin (HR) and a sodium-ion pumping rhodopsin (KR2). The SAC-CI studies elucidated the geometries of amino acids and water around the retinal in each intermediate, and proposed the ion-pumping mechanisms of BR, HR and KR2.

Report

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

    (15 results)

All 2018 2017 2016 2015 Other

All Journal Article (4 results) (of which Peer Reviewed: 4 results,  Acknowledgement Compliant: 1 results) Presentation (10 results) (of which Int'l Joint Research: 3 results,  Invited: 4 results) Remarks (1 results)

  • [Journal Article] Accuracy of Td-DFT in the Ultraviolet and Circular Dichroism Spectra of Deoxyguanosine and Uridine2018

    • Author(s)
      Tomoo Miyahara and Hiroshi Nakatsuji
    • Journal Title

      The Journal of Physical Chemistry A

      Volume: 122 Issue: 1 Pages: 100-118

    • DOI

      10.1021/acs.jpca.7b09733

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Circular Dichroism Spectroscopy with the SAC-CI methodology: A ChiraSac Study2018

    • Author(s)
      Tomoo Miyahara and Hiroshi Nakatsuji
    • Journal Title

      Frontiers of Quantum Chemistry

      Pages: 21-47

    • DOI

      10.1007/978-981-10-5651-2_2

    • ISBN
      9789811056505, 9789811056512
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Similarities and Differences between RNA and DNA Double-Helical Structures in Circular Dichroism Spectroscopy: A SAC-CI Study2016

    • Author(s)
      Tomoo Miyahara, Hiroshi Nakatsuji, Hiroshi Sugiyama
    • Journal Title

      The Journal of Physical Chemistry A

      Volume: 120 Issue: 45 Pages: 9008-9018

    • DOI

      10.1021/acs.jpca.6b08023

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Indicator of the Stacking Interaction in the DNA Double-Helical Structure: ChiraSac Study2015

    • Author(s)
      Tomoo Miyahara and Hiroshi Nakatsuji
    • Journal Title

      The Journal of Physical Chemistry A

      Volume: 119 Issue: 30 Pages: 8269-8278

    • DOI

      10.1021/acs.jpca.5b02848

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Presentation] NO2-の光電子スペクトルとDNA二重螺旋構造の円二色性スペクトル:SAC-CI理論研究2018

    • Author(s)
      宮原 友夫
    • Organizer
      日本分光学会遠紫外分光部会 第3回講演会「遠/深紫外光と材料物性」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Light-Driven Ion-Pumping Mechanism of Rhodopsins: SAC-CI Study2017

    • Author(s)
      Tomoo Miyahara, Hiroshi Nakatsuji
    • Organizer
      International Symposium on Bioiphysics of Rhodopsins
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 光駆動イオン輸送ロドプシンのメカニズム:SAC-CI 理論による研究2017

    • Author(s)
      宮原 友夫、中辻 博
    • Organizer
      第20回理論化学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] SAC-CI法による光受容膜蛋白質の理論的研究2017

    • Author(s)
      宮原 友夫、中辻 博
    • Organizer
      第11回分子科学討論会 仙台
    • Related Report
      2017 Annual Research Report
  • [Presentation] Photoelectron Spectrum of NO2- and Circular Dichroism Spectra of DNA Double-Helical Structures: SAC-CI study2017

    • Author(s)
      Tomoo Miyahara
    • Organizer
      The 11th Japanese-Russian workshop, Awaji Yumebutai International Conference Center
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 光駆動イオン輸送型ロドオプシンのイオン輸送メカニズムの解明2017

    • Author(s)
      宮原 友夫、中辻 博
    • Organizer
      第14回京都大学福井謙一記念研究センターシンポジウム
    • Place of Presentation
      京都大学福井謙一記念研究センター(京都)
    • Related Report
      2016 Research-status Report
  • [Presentation] 光駆動イオン輸送型ロドオプシンのイオン輸送メカニズムの解明2016

    • Author(s)
      宮原 友夫、中辻 博
    • Organizer
      第10回分子科学討論会2016神戸
    • Place of Presentation
      神戸ファッションマート(神戸)
    • Year and Date
      2016-09-13
    • Related Report
      2016 Research-status Report
  • [Presentation] DNA とRNA の二重螺旋構造と円二色性スペクトル:SAC-CI 理論による研究2016

    • Author(s)
      宮原 友夫、中辻 博
    • Organizer
      第4回CUTEシンポジウム:コンピュータ化学「京コンピュータと理論化学」
    • Place of Presentation
      三重大学(津)
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Indicator of the Stacking Interaction in the Double-Helical Structures of DNA and RNA ChiraSac Study2015

    • Author(s)
      Tomoo Miyahara and Hiroshi Nakatsuji
    • Organizer
      6th Japan-Czech-Slovakia International Symposium on Theoretical Chemistry
    • Place of Presentation
      Smolenice Castle near Bratislava, Slovakia
    • Year and Date
      2015-10-11
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 生体分子の円二色性スペクトルに関する理論研究: SAC-CI ChiraSAC study2015

    • Author(s)
      宮原 友夫、中辻 博、中嶋 浩之、黒川 悠索
    • Organizer
      第9回分子科学討論会
    • Place of Presentation
      東京工業大学
    • Year and Date
      2015-09-16
    • Related Report
      2015 Research-status Report
  • [Remarks] 量子化学研究協会研究所ホームページ

    • URL

      http://www.qcri.or.jp

    • Related Report
      2017 Annual Research Report

URL: 

Published: 2015-04-16   Modified: 2019-03-29  

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