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Development of observation of protein dynamics in nanometer region around an active center using molecular near-field vibrational spectroscopy

Research Project

Project/Area Number 16K13933
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Physical chemistry
Research InstitutionOsaka University

Principal Investigator

Mizuno Misao  大阪大学, 理学研究科, 助教 (10464257)

Research Collaborator Kawarabata Momoko  
Lou Lanqingqing  
Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2017: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2016: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords分子近接場振動分光法 / 共鳴ハイパーラマン散乱 / 分子の対称性 / ヘム / ヘムタンパク質 / 対称中心 / 対称性 / 局所構造観測 / ナノメートル構造 / ダイナミクス観測
Outline of Final Research Achievements

We tried to develop a new probe to selectively observe protein dynamics using molecular near-field vibrational spectroscopy. In resonance hyper-Raman processes for centrosymmetric molecules, it was reported that hyper-Raman scattering of their surrounding molecules can be observed due to intermolecular vibronic coupling. Etioheme is a centrosymmetric molecule and can be reconstituted into hemeproteins instead of heme as an intrinsic active site. In etioheme solutions, we were able to observe hyper-Raman scattering of the surroundings, such as solvent molecules and ligated imidazole molecules. These results indicates possibilities of new methodology for measurements of local protein dynamics around the active center in proteins.

Academic Significance and Societal Importance of the Research Achievements

振動分光法をもちいると、サブナノメートルの空間分解能で化学結合の微小変化を検出できます。従来の時間分解共鳴ラマン分光法によるヘムタンパク質の構造ダイナミクス観測では、プローブ部位が、ヘムとその軸配位子であるアミノ酸残基、および芳香族アミノ酸残基に限定されていました。本研究では、第三のダイナミクス観測プローブ部位としてこれまで観測ができなかったヘム周辺のアミノ酸残基の局所構造変化の時間分解計測法を開拓しました。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (22 results)

All 2019 2018 2017 2016 Other

All Journal Article (12 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 12 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (7 results) (of which Int'l Joint Research: 3 results,  Invited: 3 results) Remarks (3 results)

  • [Journal Article] Distortion and a Strong Hydrogen Bond in the Retinal Chromophore Enable Sodium Ion Transport by the Sodium Ion Pump KR22019

    • Author(s)
      Nao Nishimura, Misao Mizuno, Hideki Kandori, and Yasuhisa Mizutani
    • Journal Title

      J. Phys. Chem. B

      Volume: 印刷中 Issue: 16 Pages: 3430-3440

    • DOI

      10.1021/acs.jpcb.9b00928

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins2018

    • Author(s)
      Yamashita Satoshi、Mizuno Misao、Tran Duy Phuoc、Dokainish Hisham、Kitao Akio、Mizutani Yasuhisa
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 122 Issue: 22 Pages: 5877-5884

    • DOI

      10.1021/acs.jpcb.8b03518

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Production of a Light-Gated Proton Channel by Replacing the Retinal Chromophore with Its Synthetic Vinylene Derivative.2018

    • Author(s)
      R. Takayama, A. Kaneko , T. Okitsu, S. P. Tsunoda, K. Shimono , M. Mizuno, K. Kojima, T. Tsukamoto, H. Kandori, Y. Mizutani, A. Wada, Y. Sudo
    • Journal Title

      J Phys Chem Lett

      Volume: 9 Issue: 11 Pages: 2857-2862

    • DOI

      10.1021/acs.jpclett.8b00879

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High thermal stability of oligomeric assemblies of Thermophilic rhodopsin in a lipid environment.2018

    • Author(s)
      Tomomi Shionoya, Misao Mizuno, Takashi Tsukamoto, Kento Ikeda, Hayato Seki, Keiichi Kojima, Mikihiro Shibata, Izuru Kawamura, Yuki Sudo, and Yasuhisa Mizutani
    • Journal Title

      J. Phys. Chem. B

      Volume: 122 Issue: 27 Pages: 6945-6953

    • DOI

      10.1021/acs.jpcb.8b04894

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Resonance Raman Investigation of the Chromophore Structure of Heliorhodopsins2018

    • Author(s)
      Otomo Akihiro、Mizuno Misao、Singh Manish、Shihoya Wataru、Inoue Keiichi、Nureki Osamu、B?j? Oded、Kandori Hideki、Mizutani Yasuhisa
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 9 Issue: 22 Pages: 6431-6436

    • DOI

      10.1021/acs.jpclett.8b02741

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Tertiary Dynamics of Human Adult Hemoglobin Fixed in R and T Quaternary Structures2018

    • Author(s)
      Shanyan Chang, Misao Mizuno, Haruto Ishikawa and Yasuhisa Mizutani
    • Journal Title

      Phys. Chem. Chem. Phys.

      Volume: 20 Issue: 5 Pages: 3363-3372

    • DOI

      10.1039/c7cp06287g

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structural Evolution of a Retinal Chromophore in the Photocycle of Halorhodopsin from Natronobacterium pharaonis2018

    • Author(s)
      Misao Mizuno, Ayumi Nakajima, Hideki Kandori, and Yasuhisa Mizutani
    • Journal Title

      J. Phys. Chem. A

      Volume: 122 Issue: 9 Pages: 2411-2423

    • DOI

      10.1021/acs.jpca.7b12332

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Opn5L1 is a retinal receptor that behaves as a reverse and self-regenerating photoreceptor2018

    • Author(s)
      Sato Keita、Yamashita Takahiro、Ohuchi Hideyo、Takeuchi Atsuko、Gotoh Hitoshi、Ono Katsuhiko、Mizuno Misao、Mizutani Yasuhisa、Tomonari Sayuri、Sakai Kazumi、Imamoto Yasushi、Wada Akimori、Shichida Yoshinori
    • Journal Title

      Nature Communications

      Volume: 9 Issue: 1 Pages: 1255

    • DOI

      10.1038/s41467-018-03603-3

    • NAID

      120006535079

    • URL

      https://tokushima-u.repo.nii.ac.jp/records/2005614

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Demonstration of a light-driven SO42- transporter and its spectroscopic characteristics2017

    • Author(s)
      Niho A, Yoshizawa S, Tsukamoto T, Kurihara M, Tahara S, Nakajima Y, Mizuno M, Kuramochi H, Tahara T, Mizutani Y, *Sudo Y.
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 139 Issue: 12 Pages: 4376-4389

    • DOI

      10.1021/jacs.6b12139

    • NAID

      120006425837

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Importance of Atomic Contacts in Vibrational Energy Flow in Proteins2016

    • Author(s)
      Masato Kondoh, Misao Mizuno, and Yasuhisa Mizutani
    • Journal Title

      J. Phys. Chem. Lett.

      Volume: 7 Issue: 11 Pages: 1950-1954

    • DOI

      10.1021/acs.jpclett.6b00785

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Regulatory Implications of Structural Changes in Tyr201 of the Oxygen Sensor Protein FixL2016

    • Author(s)
      Takeo Yamawaki, Haruto Ishikawa, Misao Mizuno, Hiro Nakamura, Yoshitsugu Shiro, and Yasuhisa Mizutani
    • Journal Title

      Biochemistry

      Volume: 55 Issue: 29 Pages: 4027-4035

    • DOI

      10.1021/acs.biochem.6b00405

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] A Study of the Dynamics of the Heme Pocket and C-helix in CooA Upon CO Dissociation Using Time-resolved Visible and UV Resonance Raman Spectroscopy2016

    • Author(s)
      Akihiro Otomo, Haruto Ishikawa, Misao Mizuno, Tetsunari Kimura, Minoru Kubo, Yoshitsugu Shiro, Shigetoshi Aono, and Yasuhisa Mizutani
    • Journal Title

      J. Phys. Chem. B

      Volume: 120 Issue: 32 Pages: 7836-7843

    • DOI

      10.1021/acs.jpcb.6b05634

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Presentation] Light-driven cation pump mechanism of a sodium ion pump derived by its chromophore structure of photointermediates2018

    • Author(s)
      Misao Mizuno
    • Organizer
      The XXVI International Conference on Raman Spectroscopy (ICORS2018)
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 脊椎動物がもつ新規光センサーOpn5L1の不活性状態の発色団構造2018

    • Author(s)
      水野 操、水谷 泰久、佐藤 恵太、大内 淑代、山下 高廣、酒井 佳寿美、今元 泰、七田 芳則、山野 由美子、和田 昭盛
    • Organizer
      第12回分子科学討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Spectral features of heme with higher symmetry in myoglobin2017

    • Author(s)
      Momoko Kawarabata, Misao Mizuno, and Yasuhisa Mizutani
    • Organizer
      日本化学会第96春季年会
    • Place of Presentation
      慶応義塾大学日吉キャンパス
    • Year and Date
      2017-03-16
    • Related Report
      2016 Research-status Report
  • [Presentation] Determining factors for ion pumping mechanism in microbial rhodopsins2017

    • Author(s)
      Misao Mizuno
    • Organizer
      18th International Conference on Time-resolved Vibrational Spectroscopy (TRVS2017)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] ナトリウムイオンポンプの発色団構造と光駆動カチオン輸送機構2017

    • Author(s)
      西村 尚, 水野 操, 神取 秀樹, 水谷 泰久
    • Organizer
      第11回分子科学討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] ハロロドプシン光反応中間体のレチナール発色団に対する水分子の役割2016

    • Author(s)
      水野 操、神取 秀樹、水谷 泰久
    • Organizer
      第10回分子科学討論会
    • Place of Presentation
      神戸ファッションマート
    • Year and Date
      2016-09-13
    • Related Report
      2016 Research-status Report
  • [Presentation] Structural evolution of the retinal chromophore in the photocycle of microbial rhodopsins2016

    • Author(s)
      Misao Mizuno
    • Organizer
      4th Awaji International Workshop on “Electron Spin Science & Technology: Biological and Materials Science Oriented Applications”
    • Place of Presentation
      淡路夢舞台国際会議場
    • Year and Date
      2016-06-19
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Remarks] 大阪大学大学院理学研究科 化学専攻 生物物理化学研究室

    • URL

      http://www.chem.sci.osaka-u.ac.jp/lab/mizutani/index-jp.html

    • Related Report
      2018 Annual Research Report
  • [Remarks] 大阪大学 大学院理学研究科 化学専攻 生物物理化学研究室

    • URL

      http://www.chem.sci.osaka-u.ac.jp/lab/mizutani/index-jp.html

    • Related Report
      2017 Research-status Report
  • [Remarks] 大阪大学 大学院理学研究科 化学専攻 生物物理化学研究室

    • URL

      http://www.chem.sci.osaka-u.ac.jp/lab/mizutani/index-jp.html

    • Related Report
      2016 Research-status Report

URL: 

Published: 2016-04-21   Modified: 2020-03-30  

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