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Development of novel time-resolved diffusion method and application to detection of protein conformation and intermolecular interaction

Research Project

Project/Area Number 17H03008
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical chemistry
Research InstitutionKyoto University

Principal Investigator

Terazima Masahide  京都大学, 理学研究科, 教授 (00188674)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000)
Fiscal Year 2019: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2018: ¥8,060,000 (Direct Cost: ¥6,200,000、Indirect Cost: ¥1,860,000)
Fiscal Year 2017: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Keywordsタンパク質反応 / 分子間相互作用 / 光反応 / 拡散 / 熱力学 / 拡散係数 / タンパク質 / 反応 / 時間分解
Outline of Final Research Achievements

A method of time-resolved rotational diffusion coefficient measurement was developed to investigate conformation change dynamics of proteins during reactions. For this purpose, luminescence from a metal complex that has a long lifetime was used. Some mutants of Lysozume were prepared and the probe molecule was bound to some sites of that protein. It was confirmed that the secondary structure does not change by the probe molecule. From the decay rate of the polarization of the luminescence, the rotational diffusion coefficient was determined as a function of the concentration of a denaturant. It is interesting to find that the rotational diffusion rate depends on the position of the probe molecule. This result indicates that the unfolding process should not be described by the two-state model, which has been reported by many researchers so far. A new stopped flow system was also developed to be used for the time-resolved rotational diffusion coefficient method.

Academic Significance and Societal Importance of the Research Achievements

タンパク質の機能発現を分子レベルで解明することは、生命科学や医学や薬学においても非常に重要なテーマである。このために、X線結晶解析を主とする構造解析が国家レベルの巨大予算で行われているが、そうした静的構造だけでなく動的特性の解明が反応機構を明らかにするために不可欠である。このために、種々の分光法が開発されてきたが、そうした分光法でも検出できない暗い過程が多く存在する。この難点を克服するために、ここでは時間分解並進拡散係数法とともに時間分解回転拡散係数法を提案し、そのシステム開発を行った。この研究は、多くの学術分野で役に立つ方法というだけでなく、医療や薬開発などの社会的に重要な分野に応用できる。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (62 results)

All 2020 2019 2018 2017 Other

All Journal Article (17 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 17 results) Presentation (43 results) (of which Int'l Joint Research: 12 results,  Invited: 6 results) Remarks (2 results)

  • [Journal Article] Spiropyran labeling for sensitive probing of protein diffusion by the transient grating method2020

    • Author(s)
      S. Takaramoto, Y. Nakasone, K. Sadakane, S. Maruta, M. Terazima
    • Journal Title

      Chem. Phys. Lett.

      Volume: 739 Pages: 136919-136919

    • DOI

      10.1016/j.cplett.2019.136919

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 過渡回折格子法が拓くバイオサイエンス2020

    • Author(s)
      高門輝,寺嶋正秀
    • Journal Title

      応用物理

      Volume: 89 Pages: 30-34

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Time-Resolved Study of Interprotein Signaling Process of a Blue Light Sensor PapB-PapA Complex2019

    • Author(s)
      Nakasone, Y., Kikukawa, K., Masuda, S. and Terazima, M.
    • Journal Title

      J. Phys. Chem. B

      Volume: in press Issue: 15 Pages: 3210-3218

    • DOI

      10.1021/acs.jpcb.9b00196

    • Related Report
      2019 Annual Research Report 2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics of conformation changes in full-length Phytochrome from cyanobacterium Synechocystis sp. PCC6803 (Cph1) monitored by time-resolved translational diffusion detection2019

    • Author(s)
      K.Takeda, M. Terazima
    • Journal Title

      Biochemistry

      Volume: 58 Issue: 24 Pages: 2720-2729

    • DOI

      10.1021/acs.biochem.9b00081

    • NAID

      120006653008

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Time-Resolved Diffusion Detection with Microstopped Flow System2019

    • Author(s)
      Nakasone Yusuke、Takaramoto Shunki、Terazima Masahide
    • Journal Title

      Analytical Chemistry

      Volume: 91 Issue: 18 Pages: 11987-11993

    • DOI

      10.1021/acs.analchem.9b02897

    • NAID

      120006731124

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enhanced conformational fluctuations during protein reactions2019

    • Author(s)
      M.Terazima
    • Journal Title

      Chem.Lett.

      Volume: 48 Issue: 8 Pages: 802-810

    • DOI

      10.1246/cl.190195

    • NAID

      130007687666

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The Photoreaction Dynamics and Its Diversity of Phototropin Studied by the Transient Grating Method2019

    • Author(s)
      中曽根祐介, 寺嶋正秀
    • Journal Title

      Seibutsu Butsuri

      Volume: 59 Issue: 3 Pages: 144-146

    • DOI

      10.2142/biophys.59.144

    • NAID

      130007653149

    • ISSN
      0582-4052, 1347-4219
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics of conformation changes in full-length Phytochrome from cyanobacterium Synechocystis sp. PCC6803 (Cph1) monitored by time-resolved translational diffusion detection2019

    • Author(s)
      K. Takeda, M. Terazima
    • Journal Title

      Biochemistry

      Volume: -

    • NAID

      120006653008

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Photoreaction Dynamics of LOV1 and LOV2 of Phototropin from Chlamydomonas reinhardtii2018

    • Author(s)
      Nakasone Yusuke、Ohshima Masumi、Okajima Koji、Tokutomi Satoru、Terazima Masahide
    • Journal Title

      J.Phys.Chem.B

      Volume: 122 Issue: 6 Pages: 1801-1815

    • DOI

      10.1021/acs.jpcb.7b10266

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sequential DNA Binding and Dimerization Processes of the Photosensory Protein EL2222018

    • Author(s)
      Takakado Akira、Nakasone Yusuke、Terazima Masahide
    • Journal Title

      Biochemistry

      Volume: 57 Issue: 10 Pages: 1603-1610

    • DOI

      10.1021/acs.biochem.7b01206

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Photoreaction of BlrP1: the role of a nonlinear photo-intensity sensor2018

    • Author(s)
      Shibata Kosei、Nakasone Yusuke、Terazima Masahide
    • Journal Title

      Phys.Chem.Chem.Phys.

      Volume: 20 Issue: 12 Pages: 8133-8142

    • DOI

      10.1039/c7cp08436f

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Photoinduced orientation change of the dimer structure of the Pr-I state of Cph1Δ22018

    • Author(s)
      K. Takeda, M. Terazima
    • Journal Title

      Biochemistry

      Volume: 57 Issue: 33 Pages: 5058-5071

    • DOI

      10.1021/acs.biochem.8b00605

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Novel physical chemistry approaches in biophysical researches with advanced application of lasers: Detection and manipulation2018

    • Author(s)
      Iwata Koichi、Terazima Masahide、Masuhara Hiroshi
    • Journal Title

      BBA

      Volume: 1862 Issue: 2 Pages: 335-357

    • DOI

      10.1016/j.bbagen.2017.11.003

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] 光熱変換現象の時間分解検出と化学反応解析への応用2018

    • Author(s)
      寺嶋正秀
    • Journal Title

      分光研究

      Volume: 67 Pages: 22-34

    • NAID

      40021548275

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Light-Induced Conformational Changes of LOV2-Kinase and the Linker Region in Arabidopsis Phototropin22017

    • Author(s)
      Takakado Akira、Nakasone Yusuke、Okajima Koji、Tokutomi Satoru、Terazima Masahide
    • Journal Title

      J.Phys.Chem.B

      Volume: 121 Issue: 17 Pages: 4414-4421

    • DOI

      10.1021/acs.jpcb.7b01552

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comparative study of thylakoid membranes in terminal heterocysts and vegetative cells from two cyanobacteria, Rivularia M-261 and Anabaena variabilis, by fluorescence and absorption spectral microscopy2017

    • Author(s)
      Nozue S, Katayama M, Terazima M, *Kumazaki S
    • Journal Title

      Biochim Biophys Acta

      Volume: 1858 Issue: 9 Pages: 742-749

    • DOI

      10.1016/j.bbabio.2017.05.007

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Photoinduced dimerization of a photosensory DNA-binding protein EL222 and its LOV domain2017

    • Author(s)
      Takakado Akira、Nakasone Yusuke、Terazima Masahide
    • Journal Title

      Phys.Chem.Chem.Phys.

      Volume: 19 Issue: 36 Pages: 24855-24865

    • DOI

      10.1039/c7cp03686h

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Presentation] アゾベンゼン誘導体の光誘起核形成に関する時間分解測定2019

    • Author(s)
      中岡育也,中曽根祐介,杉安和憲,寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] ストップトフローシステムと高速拡散観測手法の融合によるタンパク質反応の検出2019

    • Author(s)
      宝本俊輝,中曽根祐介,寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] バクテリオフィトクロムDrBphPの光反応ダイナミクス2019

    • Author(s)
      立川景也,武田公利,中曽根祐介,寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 青色光センサータンパク質EB1のBLUFドメインの光励起によるダイマー化反応2019

    • Author(s)
      柴田耕生,中曽根祐介,寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 分子夾雑系における光センサー蛋白質の動的挙動―揺らぎと反応ダイナミクス―2019

    • Author(s)
      中曽根 祐介, 村上 大斗, 寺嶋 正秀
    • Organizer
      日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 光センサータンパク質PYPと下流分子PBPによる励起波長依存的な会合・解離反応ダイナミクス2019

    • Author(s)
      金 穂香, 中曽根 祐介, 高門 輝, 山崎 洋一, 上久保 裕生, 寺嶋 正秀
    • Organizer
      日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] LOVドメイン型光活性化アデニル酸シクラーゼmPACの光反応ダイナミクス2019

    • Author(s)
      生駒 美里, 中曽根 祐介, 寺嶋 正秀
    • Organizer
      日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 光センサーLOV2ドメインの光反応中間体の構造揺らぎ検出2019

    • Author(s)
      床次 俊郎, 中曽根 祐介, 寺嶋 正秀
    • Organizer
      日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] TG法を用いたOCPとFRPの時間分解相互作用ダイナミクスの検出2019

    • Author(s)
      大畑 貴聖, 中曽根 祐介, 寺嶋 正秀
    • Organizer
      日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 時間分解拡散法から観る光で触媒活性を制御するタンパク質BlrP1反応2019

    • Author(s)
      柴田耕生, 中曽根 祐介, 寺嶋 正秀
    • Organizer
      第42回溶液化学シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] Nonlinear light intensity dependence of photocatalytic reaction of a blue light sensor protein BlrP12019

    • Author(s)
      Masahide Terazima
    • Organizer
      International Conference on Photocatalysis and Photoenergy 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Time-resolved compressibility change of short lived intermediate species during a protein reaction2019

    • Author(s)
      Masahide Terazima, Kunisato Kuroi, Yusuke Nakasone
    • Organizer
      The 12th International Workshop on Subsecond Thermophysics
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Time-resolved detection of photoinduced heating and volume changes during protein reactions2019

    • Author(s)
      Masahide Terazima
    • Organizer
      International Conference on Photoacoustic and Photothermal Phenomena
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 光センサー蛋白質PYPの光反応および下流分子PBPとの相互作用に対するpH依存性2019

    • Author(s)
      金穂香, 中曽根祐介, 高門輝, 山崎洋一, 上久保裕生, 寺嶋正秀
    • Organizer
      日本化学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] バクテリアの走光性制御タンパク質PixDの10量体構造とその安定性2019

    • Author(s)
      床次俊郎, 中曽根祐介, 寺嶋正秀
    • Organizer
      日本化学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 光活性化アデニル酸シクラーゼの光反応ダイナミクス2019

    • Author(s)
      中曽根祐介, 寺嶋正秀
    • Organizer
      日本化学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] フォトクロミック分子を利用した蛋白質の高時間分解拡散観測手法2019

    • Author(s)
      宝本俊輝, 中曽根祐介, 寺嶋正秀
    • Organizer
      日本化学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] バクテリオフィトクロムDrBphPの光反応ダイナミクス2019

    • Author(s)
      立川景也, 武田公利, 中曽根祐介, 寺嶋正秀
    • Organizer
      日本化学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Time-resolved diffusion sensor reveals DNA recognition dynamics of proteins2019

    • Author(s)
      M. Terazima
    • Organizer
      Pittcon 2019
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Thermodynamical properties of short lived intermediates to reveal driving force of reactions of a blue light photosensor protein2018

    • Author(s)
      M. Terazima
    • Organizer
      30th ESAT - European Seminar on Applied Thermodynamics
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Time-resolve diffusion technique to probe conformation changes during protein reactions in aqueous solution2018

    • Author(s)
      M. Terazima
    • Organizer
      The 12th Mini-Symposium on Liquids
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 青色光受容タンパク質PYPと下流分子PBPによる複合体形成ダイナミクスの検出2018

    • Author(s)
      金穂香,中曽根祐介,高門輝,山崎洋一,上久保裕生,寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 青色光センサータンパク質PixDの分子機能におけるC末端領域の重要性2018

    • Author(s)
      床次俊郎,中曽根祐介,寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] バクテリオフィトクロムDrBphP光受容ドメインの光反応ダイナミクス2018

    • Author(s)
      立川景也,武田公利,中曽根祐介,寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Protein diffusion probed by the transient grating method with a photochromic molecule2018

    • Author(s)
      S. Takaramoto, Y. Nakasone, M. Terazima
    • Organizer
      日本生物物理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Diversity of photochemical reactions of Flavin-based photoreceptors2018

    • Author(s)
      Y. Nakasone, M. Terazima
    • Organizer
      日本生物物理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Dynamics of protein-water interaction and conformation changes during reactions2018

    • Author(s)
      M. Terazima
    • Organizer
      EMLG/JMLG 2018 & 41st SSCJ
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Reaction Dynamics of Photo-induced Protein-DNA Interaction2018

    • Author(s)
      M. Terazima
    • Organizer
      Trombay Symposium on Radiation & Photochemistry
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] いかにして刺激受容後にタンパク質分子全体の構造変化過程や標的分子との分子間反応過程を時間分解で捉えるか2017

    • Author(s)
      寺嶋正秀
    • Organizer
      分子研研究会「触媒反応であるタンパク質反応を分子科学的観点から捉える」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Light induced heating and volume changes to reveal protein reactions2017

    • Author(s)
      M. Terazima
    • Organizer
      9th International Conference on Photoacoustic and Photothermal Phenomena
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Multiphoton excitation controls inter-protein interaction of light sensory proteins2017

    • Author(s)
      M. Terazima
    • Organizer
      Gordon Research Conference on photochemistry
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Time-resolved compressibility measurement reveals driving force of protein reactions2017

    • Author(s)
      T. Nakajima, Y. Nakasone, S. Tokutomi, K. Okajima, M. Terazima
    • Organizer
      21st European conference on thermophysical properties
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Application of the stopped-flow TG method to the denaturation of a photosensory protein2017

    • Author(s)
      S. Takaramoto, Y. Nakasone, M. Terazima
    • Organizer
      生物物理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Time-resolved study of protein reactions using the transient grating method combined with a stopped-flow apparatus2017

    • Author(s)
      Y. Nakasone, S. Takaramoto, M. Terazima
    • Organizer
      生物物理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Study on the diversity of photoreactions among various homologous PixD proteins2017

    • Author(s)
      S. Tokonami, Y. Nakasone, M. Terazima
    • Organizer
      生物物理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Transient grating method revealed a DNA binding process of a light sensor protein EL2222017

    • Author(s)
      A. Takakado, Y. Nakasone, M. Terazima
    • Organizer
      生物物理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 赤色光センサータンパク質Cph1の光受容ドメインからキナーゼへの構造変化過程2017

    • Author(s)
      武田公利,寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 青色光受容タンパク質BlrP1の光強度依存性と光反応ダイナミクス2017

    • Author(s)
      柴田耕生, 中曽根祐介, 寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] アゾベンゼンで制御する光応答性DNAの反応ダイナミクス2017

    • Author(s)
      端村航,中曽根祐介,大威英晃,神谷由紀子,浅沼浩之,寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 光センサーBLUFドメインの光反応:遅い吸収変化の由来2017

    • Author(s)
      小野瀬森彦,中曽根祐介,柴田耕生,寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] ストップトフローと過渡回折格子法を組み合わせた蛋白質反応検出法2017

    • Author(s)
      中曽根祐介,宝本俊輝,寺嶋正秀
    • Organizer
      分子科学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 時間分解拡散法から観るタンパク質とDNAの結合ダイナミクス2017

    • Author(s)
      高門輝, 中曽根祐介, 寺嶋正秀
    • Organizer
      溶液化学シンポジウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] Time-resolved diffusion technique can detect conformation dynamics of photosensor proteins2017

    • Author(s)
      M. Terazima
    • Organizer
      Asia Oceania Conference on Photobiology
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Remarks] 京都大学大学院理学研究科化学専攻光物理化学研究室

    • URL

      http://kuchem.kyoto-u.ac.jp/hikari/

    • Related Report
      2019 Annual Research Report 2018 Annual Research Report
  • [Remarks] 京都大学大学院理学研究科化学専攻 光物理化学研究室

    • URL

      http://kuchem.kyoto-u.ac.jp/hikari/

    • Related Report
      2017 Annual Research Report

URL: 

Published: 2017-04-28   Modified: 2021-02-19  

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