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Development of a novel technique for diffusion measurement and its application to the reaction of biomolecule

Research Project

Project/Area Number 15K13623
Research Category

Grant-in-Aid for Challenging Exploratory Research

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

Principal Investigator

Nakasone Yusuke  京都大学, 理学研究科, 助教 (00613019)

Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2017: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2016: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2015: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywords拡散係数 / 過渡回折格子法 / タンパク質反応 / 時間分解 / ストップトフロー / 反応ダイナミクス / タンパク質 / 拡散係数測定 / 過渡回折光子法 / 過渡吸収 / 分子間反応 / 高速混合
Outline of Final Research Achievements

The goal of this research is to establish a novel technique to study the reaction dynamics of biomolecules from a view point of diffusion coefficient change. Firstly, I have developed a stopped flow system which is optimized for the measurement of protein reaction (small amount of sample consumption, short dead time, high mixing efficiency). Combining this equipment with transient grating (TG) method, we succeeded in detection of assembly process of clock protein and denaturation dynamics of light sensor protein. I also tried to detect the diffusion process utilizing a microinjection from a slit-like pore.Monitoring the change of pattern created by the injection through the intensity change of diffracted light, the diffusion coefficient is expected to be determined. The signal, however, was not reproducible because the free diffusion is disrupted by a turbulence created by the injection. We are in the middle of development of the novel system for diffusion measurement.

Report

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

    (26 results)

All 2018 2017 2016 2015

All Journal Article (11 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 11 results,  Open Access: 6 results,  Acknowledgement Compliant: 4 results) Presentation (15 results) (of which Int'l Joint Research: 4 results,  Invited: 2 results)

  • [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
      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
      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
      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] 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
  • [Journal Article] Photochemical reactions of the LOV and the LOV-linker domains of the blue light sensor protein YtvA2016

    • Author(s)
      S. Choi,, Y. Nakasone, K. J Hellingwerf, M. Terazima
    • Journal Title

      Biochemistry

      Volume: 55 Issue: 22 Pages: 3107-3115

    • DOI

      10.1021/acs.biochem.6b00263

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Time-resolved Detection of Light-induced Dimerization of Monomeric Aureochrome-1 and Change in Affinity for DNA2016

    • Author(s)
      Y. Akiyama, Y. Nakasone, Y. Nakatani, O. Hisatomi, M. Terazima
    • Journal Title

      J. Phys. Chem. B

      Volume: 120 Issue: 30 Pages: 7360-7370

    • DOI

      10.1021/acs.jpcb.6b05760

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Dynamics of Inter-DNA Chain Interaction of Photoresponsive DNA2016

    • Author(s)
      Nakasone, Y.; Ooi, H.; Kamiya, Y.; Asanuma, H.; Terazima, M.
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 138 Issue: 29 Pages: 9001-9004

    • DOI

      10.1021/jacs.6b02525

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Anomalous pressure effects on the photoreaction of a light-sensor protein from Synechocystis, PixD (Slr1694), and the compressibility change of its intermediates2016

    • Author(s)
      T. Nakajima, K. Kuroi, Y. Nakasone, K. Okajima, M. Ikeuchi, S. Tokutomi, M. Terazima
    • Journal Title

      Phys. Chem. Chem. Phys.

      Volume: 18 Issue: 37 Pages: 25915-25925

    • DOI

      10.1039/c6cp05091c

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Time-resolved fluctuation during the photochemical reaction of a photoreceptor protein: phototropin1LOV2-linker.2016

    • Author(s)
      Kuroi K, Sato F, Nakasone Y, Zikihara K, Tokutomi S, Terazima M.
    • Journal Title

      Phys Chem Chem Phys.

      Volume: 18 Issue: 8 Pages: 6228-6238

    • DOI

      10.1039/c5cp07472j

    • NAID

      120005973369

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Reaction dynamics of the UV-B photosensor UVR8.2015

    • Author(s)
      Miyamori T, Nakasone Y, Hitomi K, Christie JM, Getzoff ED, Terazima M.
    • Journal Title

      Photochem Photobiol Sci.

      Volume: 14 Issue: 5 Pages: 995-1004

    • DOI

      10.1039/c5pp00012b

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Time-resolved study of protein reactions using the transient grating method combined with a stopped-flow apparatus2018

    • Author(s)
      中曽根祐介
    • Organizer
      新学術領域「動的秩序と機能」第6回国際シンポジウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] 光センサータンパク質phototropinの光反応と多様性2018

    • Author(s)
      中曽根祐介
    • Organizer
      日本化学会 第98春期年会
    • 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
      日本化学会第97春季年会
    • Place of Presentation
      東京
    • Year and Date
      2017-03-16
    • Related Report
      2016 Research-status Report
  • [Presentation] DIVERSITY OF PHOTOREACTIONS OF BLUE LIGHT SENSOR PHOTOTROPINS AMONG DIFFERENT ORGANISMS2017

    • Author(s)
      Yusuke Nakasone,Koji Okajima,Kenichi Hitomi, John Christie, Satoru Tokutomi,Masahide Terazima
    • Organizer
      新学術領域「動的秩序と機能」第5回国際シンポジウム
    • Place of Presentation
      東京
    • Year and Date
      2017-01-21
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 拡散・揺らぎの時間分解検出に基づくタンパク質機能の分子論的理解2017

    • Author(s)
      中曽根祐介
    • Organizer
      第40回溶液化学プレシンポジウム
    • Related Report
      2017 Annual Research Report
    • Invited
  • [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
    • Organizer
      第11回分子科学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 異なる生物種におけるフォトトロピン光反応の多様性2016

    • Author(s)
      中曽根祐介、岡島公司、人見研一、John Christie、徳富哲、寺嶋正秀
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] 青色光センサー全長フォトトロピンの光反応2016

    • Author(s)
      中曽根祐介、岡島公司、相原悠介、長谷あきら、徳富哲、寺嶋正秀
    • Organizer
      第10回分子科学討論会
    • Place of Presentation
      神戸
    • Year and Date
      2016-09-13
    • Related Report
      2016 Research-status Report
  • [Presentation] BLUFタンパク質PapBの光反応および下流分子PapAとの相互作用ダイナミクス2016

    • Author(s)
      中曽根 祐介
    • Organizer
      日本化学会第96春季年会
    • Place of Presentation
      京都
    • Year and Date
      2016-03-24
    • Related Report
      2015 Research-status Report
  • [Presentation] 過渡回折格子法で捉える生体分子の高次構造変化ダイナミクス2016

    • Author(s)
      中曽根 祐介
    • Organizer
      蛋白研セミナー「構造を基盤とする蛋白質科学における未解決問題」
    • Place of Presentation
      東京
    • Year and Date
      2016-03-01
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Transient dimerization and conformational dynamics of full-length phototropin from Chlamydomonas reinhardtii2015

    • Author(s)
      Yusuke Nakasone
    • Organizer
      Pacifichem 2015
    • Place of Presentation
      ハワイ
    • Year and Date
      2015-12-15
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Transient dimerization and conformational changes of blue light sensor protein phototropin2015

    • Author(s)
      Yusuke Nakasone
    • Organizer
      「動的秩序と機能」第4回国際シンポジウム
    • Place of Presentation
      福岡
    • Year and Date
      2015-11-22
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Photoreaction dynamics of full-length phototropin from Chlamydomonas reinhardtii and the diversity of signaling mechanism2015

    • Author(s)
      Yusuke Nakasone
    • Organizer
      The 7th Asia and Oceania Conference on Photobiology
    • Place of Presentation
      台北
    • Year and Date
      2015-11-15
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] 光応答性DNAの二重鎖形成および解離反応の時間分解検出2015

    • Author(s)
      中曽根 祐介
    • Organizer
      第9回分子科学討論会
    • Place of Presentation
      東京
    • Year and Date
      2015-09-16
    • Related Report
      2015 Research-status Report
  • [Presentation] Diversity of phototropin studied from the viewpoint of photoreaction dynamics2015

    • Author(s)
      Yusuke Nakasone
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report

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

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