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Exploring Molecular Mechanisms for Creating Diverse Functions based on Common Structures

Research Project

Project/Area Number 20H02693
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 32010:Fundamental physical chemistry-related
Research InstitutionOsaka University

Principal Investigator

Mizutani Yasuhisa  大阪大学, 大学院理学研究科, 教授 (60270469)

Project Period (FY) 2020-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000)
Fiscal Year 2022: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2021: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2020: ¥9,230,000 (Direct Cost: ¥7,100,000、Indirect Cost: ¥2,130,000)
Keywordsアロステリー / ラマン分光法 / タンパク質ダイナミクス
Outline of Research at the Start

タンパク質は人工の分子では成し得ない高度な機能を有する。したがって、タンパク質を理解することは生命現象の理解のみならず、高度な機能性分子の創成に重要な知見を与える。タンパク質の構造-機能相関を理解するうえで重要な点は、複数のタンパク質が共通した立体構造を持ちつつ、それぞれが多様な機能を示すことである。このことは共通構造が機能の基本構造となっていることを示すとともに、その基盤の上での調節によって機能の多様性が生まれていることを強く示唆する。本研究では、タンパク質化学反応の際に起きる機能単位間の連動的構造変化を観測し、共通の立体構造から機能の多様性が生まれる機構を明らかにする。

Outline of Final Research Achievements

The difficulty in studying the physical chemistry of proteins lies in the diversity of protein structures and functions, making it difficult to find universal principles. Therefore, in this study, we focused on the common structure of proteins. Some rhodopsins selectively transport a variety of ions, including protons, sodium ions, and chloride ions, on a common three-dimensional structural basis. In addition, many oxygen-carrying proteins have a common subunit structure called globin fold but exhibit cooperativity through diverse fashions of association. These facts indicate that the common structure is the basis of the function and strongly suggest that functional diversity is caused by regulation based on the common structure. Therefore, we compared and clarified the functional mechanisms of a group of proteins that share a common structure but exhibit different functions or different association fashions.

Academic Significance and Societal Importance of the Research Achievements

化学の進展によって、化学者はある機能を持った分子を設計し、それを実際に合成することができるようになった。しかし、複数の機能単位を組み合わせ、互いに連動する、より高度な機能分子を創ることはいまだに困難である。それは合成の技術的な難しさのためではなく、連動させる原理がわからないためであり、原理がわからなければ設計のしようがないためである。「連動性を生む必要十分条件は何か?」を理解できれば、連動性をもった機能性分子を設計するための重要な知見が得られる。連動性の理解は分子機能にとって本質的な問題であり、分子の理解と制御に重要な貢献を果たす。

Report

(4 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • Research Products

    (46 results)

All 2023 2022 2021 2020 Other

All Int'l Joint Research (1 results) Journal Article (13 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 13 results,  Open Access: 1 results) Presentation (32 results) (of which Int'l Joint Research: 15 results,  Invited: 8 results)

  • [Int'l Joint Research] Weizmann Institute of Science(イスラエル)

    • Related Report
      2022 Annual Research Report
  • [Journal Article] Chromophore Structure in an Inactive State of a Novel Photosensor Protein Opn5L1: Resonance Raman Evidence for the Formation of a Deprotonated Adduct at the 11th Carbon Atom2023

    • Author(s)
      Misao Mizuno, Keita Sato, Takahiro Yamashita, Kazumi Sakai, Yasushi Imamoto, Yumiko Yamano, Akimori Wada, Hideyo Ohuchi, Yoshinori Shichida, and Yasuhisa Mizutani
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 127 Issue: 10 Pages: 2169-2176

    • DOI

      10.1021/acs.jpcb.2c08780

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein dynamics of a light-driven Na<sup>+</sup> pump rhodopsin probed using a tryptophan residue near the retinal chromophore2023

    • Author(s)
      Otomo Akihiro、Mizuno Misao、Inoue Keiichi、Kandori Hideki、Mizutani Yasuhisa
    • Journal Title

      Biophysics and Physicobiology

      Volume: 20 Issue: Supplemental Pages: n/a

    • DOI

      10.2142/biophysico.bppb-v20.s016

    • ISSN
      2189-4779
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Time-resolved spectroscopic mapping of vibrational energy flow in proteins: Understanding thermal diffusion at the nanoscale2022

    • Author(s)
      Mizutani Yasuhisa、Mizuno Misao
    • Journal Title

      The Journal of Chemical Physics

      Volume: 157 Issue: 24 Pages: 240901-240901

    • DOI

      10.1063/5.0116734

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Origin of a Double-Band Feature in the Ethylenic C=C Stretching Modes of the Retinal Chromophore in Heliorhodopsins2022

    • Author(s)
      Urui Taito、Das Ishita、Mizuno Misao、Sheves Mordechai、Mizutani Yasuhisa
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 126 Issue: 43 Pages: 8680-8688

    • DOI

      10.1021/acs.jpcb.2c04883

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Contact-Mediated Retinal-Opsin Coupling Enables Proton Pumping in Gloeobacter Rhodopsin2022

    • Author(s)
      Shionoya Tomomi、Mizuno Misao、Kandori Hideki、Mizutani Yasuhisa
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 126 Issue: 40 Pages: 7857-7869

    • DOI

      10.1021/acs.jpcb.2c04208

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cis-Trans Reisomerization Precedes Reprotonation of the Retinal Chromophore in the Photocycle of Schizorhodopsin 42022

    • Author(s)
      Hayashi Kouhei、Mizuno Misao、Kandori Hideki、Mizutani Yasuhisa
    • Journal Title

      Angewandte Chemie International Edition

      Volume: 61 Issue: 33

    • DOI

      10.1002/anie.202203149

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Regulatory Switching by Concerted Motions on the Microsecond Time Scale of the Oxygen Sensor Protein FixL2021

    • Author(s)
      Yamawaki Takeo、Mizuno Misao、Ishikawa Haruto、Takemura Kazuhiro、Kitao Akio、Shiro Yoshitsugu、Mizutani Yasuhisa
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 125 Issue: 25 Pages: 6847-6856

    • DOI

      10.1021/acs.jpcb.1c01885

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Resonance Raman Determination of Chromophore Structures of Heliorhodopsin Photointermediates2021

    • Author(s)
      Urui Taito、Mizuno Misao、Otomo Akihiro、Kandori Hideki、Mizutani Yasuhisa
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 125 Issue: 26 Pages: 7155-7162

    • DOI

      10.1021/acs.jpcb.1c04010

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Strongly hydrogen-bonded Schiff base and adjoining polyene twisting in the retinal chromophore of schizorhodopsins2021

    • Author(s)
      Tomomi Shionoya, Misao Mizuno, Manish Singh, Hideki Kandori, and Yasuhisa Mizutani
    • Journal Title

      Biochemistry

      Volume: 60 Issue: 41 Pages: 3050-3057

    • DOI

      10.1021/acs.biochem.1c00529

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Concerted Motions and Molecular Function: What Physical Chemistry We Can Learn from Light-Driven Ion-Pumping Rhodopsins2021

    • Author(s)
      Yasuhisa Mizutani
    • Journal Title

      J. Phys. Chem. B

      Volume: 125 Issue: 43 Pages: 11812-11819

    • DOI

      10.1021/acs.jpcb.1c06698

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nonbonded Atomic Contacts Drive Ultrafast Helix Motions in Myoglobin2020

    • Author(s)
      Shinya Tahara, Misao Mizuno, and Yasuhisa Mizutani
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 124 Issue: 26 Pages: 5407-5414

    • DOI

      10.1021/acs.jpcb.0c04772

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Role of atomic contacts in vibrational energy transfer in myoglobin2020

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

      Biophysical Reviews

      Volume: 12 Issue: 2 Pages: 511-518

    • DOI

      10.1007/s12551-020-00681-w

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Unique Electronic Structures of the Highly Ruffled Hemes in Heme-Degrading Enzymes ofStaphylococcus aureus, IsdG and IsdI, by Resonance Raman and Electron Paramagnetic Resonance Spectroscopies2020

    • Author(s)
      Takahashi Satoshi、Nambu Shusuke、Matsui Toshitaka、Fujii Hiroshi、Ishikawa Haruto、Mizutani Yasuhisa、Tsumoto Kouhei、Ikeda-Saito Masao
    • Journal Title

      Biochemistry

      Volume: 59 Issue: 40 Pages: 3918-3928

    • DOI

      10.1021/acs.biochem.0c00731

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Presentation] ナトリウムイオン輸送タンパク質の多量体形成に依存した分子内水素結合変化2023

    • Author(s)
      中村 大輝、水野 操、大友 章裕、神取 秀樹、水谷 泰久
    • Organizer
      日本化学会第103春季年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Contact-Mediated Retinal-Opsin Coupling Enables Proton Pumping in Gloeobacter Rhodopsin2022

    • Author(s)
      Tomomi Shionoya, Misao Mizuno, Hideki Kandori, Yasuhisa Mizutani
    • Organizer
      19th International Conference on Retinal Proteins
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Identification of Structural Changes Essential to Inward Proton Transport Common to Schizorhodopsins2022

    • Author(s)
      aito Urui, Kouhei Hayashi, Misao Mizuno, Keiichi Inoue, Hideki Kandori, Yasuhisa Mizutani
    • Organizer
      19th International Conference on Retinal Proteins
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Structural analysis on the M intermediates of inward proton-pumping xenorhodopsins2022

    • Author(s)
      Kouhei Hayashi, Taito Urui, Misao Mizuno, Hideki Kandori, Yuki Sudo, Yasuhisa Mizutani
    • Organizer
      19th International Conference on Retinal Proteins
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Resonance Raman Observation of Structural Changes in Inward Proton-Pumping Rhodopsins2022

    • Author(s)
      Yasuhisa Mizutani
    • Organizer
      19th International Conference on Retinal Proteins
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Atomic Packing and Dynamics of Proteins2022

    • Author(s)
      Yasuhisa Mizutani
    • Organizer
      20th KIAS Conference on Protein Structure and Function & The 7th Korean-Polish Conference on "Protein Folding: Theoretical and Experimental Approaches"
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] シゾロドプシンに共通する内向きプロトン輸送に重要な構造変化の同定2022

    • Author(s)
      潤井 泰斗、林 航平、水野 操、井上 圭一、神取 秀樹、水谷 泰久
    • Organizer
      第16回分子科学討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Time-resolved resonance Raman observation of the photoexcited retinal chromophore in halorhodopsin2022

    • Author(s)
      Zixuan Li, Misao Mizuno, Hideki Kandori, and Yasuhisa Mizutani
    • Organizer
      第16回分子科学討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 祖先型グロビンフォールドタンパク質の構造ダイナミクスの解明2022

    • Author(s)
      入谷 悠、石川 春人、水野 操、水谷 泰久
    • Organizer
      第16回分子科学討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Time-resolved Resonance Raman Observation of Quaternary Structural Changes of Dimeric Hemoglobin2022

    • Author(s)
      Xiang Gao, Misao Mizuno, Haruto Ishikawa, Yasuhisa Mizutani
    • Organizer
      日本化学会第102春季年会
    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
  • [Presentation] Time-resolved resonance Raman observation of the chromophore structure in primary intermediates of microbial rhodopsins2022

    • Author(s)
      Zixuan Li, Misao Mizuno, Hideki Kandori, Yasuhisa Mizutani
    • Organizer
      日本化学会第102春季年会
    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
  • [Presentation] 共鳴ラマン分光法による祖先型グロビンフォールドタンパク質のヘム-軸配位子構造の解明2022

    • Author(s)
      入谷 悠、石川 春人、水野 操、水谷 泰久
    • Organizer
      日本化学会第102春季年会
    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
  • [Presentation] 内向きプロトンポンプシゾロドプシンにみられる複数のM中間体の発色団構造解析2022

    • Author(s)
      林 航平、水野 操、神取 秀樹、水谷 泰久
    • Organizer
      日本化学会第102春季年会
    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
  • [Presentation] AlphaFold 時代にこそ重要性を増す振動分光学2022

    • Author(s)
      水谷 泰久
    • Organizer
      第22回日本蛋白質科学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Characterization of the chromophore structure in the photocycle of a new type of chloride ion-pumping rhodopsin2021

    • Author(s)
      Misao Mizuno, Naito Isimoto, Sam-Yong Park, and Yasuhisa Mizutani
    • Organizer
      Twentieth International Conference on Time-Resolved Vibrational Spectroscopy
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Interaction between retinal chromophore and opsin to enable proton transport in a light-driven proton pump GR2021

    • Author(s)
      Tomomi Shionoya, Misao Mizuno, Hideki Kandori and Yasuhisa Mizutani
    • Organizer
      Twentieth International Conference on Time-Resolved Vibrational Spectroscopy
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Resonance Raman Determination of Chromophore Structures of Heliorhodopsin Photointermediates2021

    • Author(s)
      Taito Urui, Misao Mizuno, Akihiro Otomo, Hideki Kandori, and
    • Organizer
      Twentieth International Conference on Time-Resolved Vibrational Spectroscopy
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Nonbonded Atomic Contacts Drive Functional Motions in Proteins2021

    • Author(s)
      Yasuhisa Mizutani
    • Organizer
      Twentieth International Conference on Time-Resolved Vibrational Spectroscopy
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 新規光駆動塩化物イオンポンプの光反応中間体の発色団構造解析2021

    • Author(s)
      水野操、石本 直偉士、朴 三用、水谷 泰久
    • Organizer
      第15回分子科学討論会
    • Related Report
      2021 Annual Research Report
  • [Presentation] レチナールアナログ置換によるヘリオロドプシン発色団の構造特異性の解明2021

    • Author(s)
      潤井 泰斗、水野 操、水谷 泰久
    • Organizer
      第15回分子科学討論会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Atomic Packing and Dynamics of Proteins2021

    • Author(s)
      Yasuhisa Mizutani
    • Organizer
      Telluride Science Research Center Workshop on Vibrational Dynamics
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Protonated Schiff Base of Light-Driven Ion-Pumping Rhodopsins: A Director of Ion Transport2021

    • Author(s)
      Yasuhisa Mizutani
    • Organizer
      The 11th Asian Photochemistry Conference
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Time-resolved Raman Investigations of Energy Flow at Protein-Solvent Water Interfaces2021

    • Author(s)
      Yasuhisa Mizutani
    • Organizer
      Pacifichem2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 光駆動プロトンポンプGRのプロトン輸送を誘起する発色団-オプシン相互作用2021

    • Author(s)
      塩谷 智巳、水野 操、神取 秀樹、水谷 泰久
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] ヘリオロドプシンの光サイクルにおけるレチナールシッフ塩基の水素結合強度の変遷2021

    • Author(s)
      潤井 泰斗、水野 操、神取 秀樹、水谷 泰久
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] αヘリックスの周期性を利用したタンパク質内エネルギー移動の距離依存性の解明2021

    • Author(s)
      山下 聡、水野 操、水谷 泰久
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Vibrational Energy Relaxation of Heme in Dimeric Hemoglobin2021

    • Author(s)
      Xiang Gao, Misao Mizuno, Haruto Ishikawa, Yasuhisa Mizutani
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 紫外共鳴ラマン分光法によるプロトンポンプGRのプロトン輸送過程におけるタンパク質構造変化2020

    • Author(s)
      塩谷 智巳、水野 操、神取 秀樹、水谷 泰久
    • Organizer
      分子科学会オンライン討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 新規光受容タンパク質ヘリオロドプシンが持つ光反応中間体の発色団構造2020

    • Author(s)
      潤井泰斗、水野 操、神取 秀樹、水谷 泰久
    • Organizer
      分子科学会オンライン討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Ultrafast Dynamics in Dimeric Hemoglobin Probed by Time-Resolved Resonance Raman Spectroscopy2020

    • Author(s)
      Xiang Gao, Misao Mizuno, Haruto Ishikawa, and Yasuhisa Mizutani
    • Organizer
      Asian Spectroscopy Conference 2020
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Chromophore structure in a long-lived intermediate of heliorhodopsins: switching of a hydrogen bonding partner of protonated Schiff base2020

    • Author(s)
      Taito Urui, Akihiro Otomo, Misao Mizuno, Hideki Kandori, and Yasuhisa Mizutani
    • Organizer
      Asian Spectroscopy Conference 2020
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Unique Structure of the Retinal Chromophore Enabling Sodium Ion Transport in the Sodium Ion-Pumping Protein KR22020

    • Author(s)
      Yasuhisa Mizutani
    • Organizer
      Asian Spectroscopy Conference 2020
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited

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Published: 2020-04-28   Modified: 2024-01-30  

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