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Development of time-resolved spectroscopic systems with micro-flow devices and their application to the molecular mechanism of ABC transporters

Research Project

Project/Area Number 15H05476
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Physical chemistry
Research InstitutionKobe University

Principal Investigator

KIMURA TETSUNARI  神戸大学, 理学研究科, 特命講師 (70506906)

Co-Investigator(Renkei-kenkyūsha) TSUBAKI Motonari  神戸大学, 大学院理学研究科, 教授 (00145046)
SUGIMOTO Hiroshi  理化学研究所, 放射光科学研究センター, 専任研究員 (90344043)
SHIRO Yoshitsugu  兵庫県立大学, 大学院生命理学研究科, 教授 (70183051)
Research Collaborator HAYASHI Sae  
ONISHI Kizashi  
SHIMONAKA Misato  
FUJII Koichi  
TAKEDA Hanae  
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥24,830,000 (Direct Cost: ¥19,100,000、Indirect Cost: ¥5,730,000)
Fiscal Year 2017: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2016: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2015: ¥16,770,000 (Direct Cost: ¥12,900,000、Indirect Cost: ¥3,870,000)
Keywords時間分解分光法 / マイクロ流路デバイス / 顕微分光 / X線自由電子レーザー / 赤外分光法 / 時間分解計測 / ABCトランスポーター / 顕微分光測定 / ダイナミクス / ヘム / マイクロ流体デバイス / 時間分解測定 / 分光法 / 膜タンパク質 / タンパク質ダイナミクス / 赤外吸収分光法 / 可視吸収分光法 / 蛍光寿命測定 / マイクロデバイス
Outline of Final Research Achievements

The novel time-resolved measurement systems that are applicable to many proteins have been developed by combining micro-fluidic techniques and spectroscopic measurements. In addition, time-resolved serial-femtosecond x-ray crystallography was developed by using the micro-fluidic mixer, allowing us to monitor the conformational changes in protein during the expression of functions in real-time manner. These novel measurement systems were applied to the ABC transporter, clarifying its transport and structural dynamics.

Report

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

    (40 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (7 results) Journal Article (9 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 9 results,  Open Access: 6 results,  Acknowledgement Compliant: 2 results) Presentation (23 results) (of which Int'l Joint Research: 3 results,  Invited: 5 results) Remarks (1 results)

  • [Int'l Joint Research] California Institute of Technology(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] University of Grenoble Alpes/European Synchrotron Radiation Facility(France)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] University of Gothenburg/Uppsala University(Sweden)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Pohang Univ. of Sci. and Tech.(韓国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Paul Scherrer Institute/ETH Zurich(Switzerland)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Freie University Berlin/Deutsches Elektronen-Synchrotron DESY/University of Hamburg(Germany)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research]

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Ultraprecision cutting of single-crystal calcium fluoride for fabricating micro flow cells2018

    • Author(s)
      Ryo KOMIYA, Tetsunari KIMURA, Takashi NOMURA, Minoru KUBO, Jiwang YAN
    • Journal Title

      Journal of Advanced Mechanical Design, Systems, and Manufacturing

      Volume: 12 Issue: 1 Pages: JAMDSM0021-JAMDSM0021

    • DOI

      10.1299/jamdsm.2018jamdsm0021

    • NAID

      130006386864

    • ISSN
      1881-3054
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.2017

    • Author(s)
      Shimada, A.†, Kubo, M.†, Baba, S.† et al. (29人中2番目)(†equal contribution)
    • Journal Title

      Sci. Adv.

      Volume: 3 Issue: 7

    • DOI

      10.1126/sciadv.1603042

    • NAID

      120006363290

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Nanosecond pump probe device for time-resolved serial femtosecond crystallography developed at SACLA2017

    • Author(s)
      Kubo Minoru、Nango Eriko、Murata Michio、Neutze Richard、Yabashi Makina、Iwata So, その他18名
    • Journal Title

      Journal of Synchrotron Radiation

      Volume: 24 Issue: 5 Pages: 1086-1091

    • DOI

      10.1107/s160057751701030x

    • NAID

      120006363292

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate2017

    • Author(s)
      Tosha Takehiko、Kubo Minoru, et. al
    • Journal Title

      Nature Communications

      Volume: 8 Issue: 1 Pages: 1-9

    • DOI

      10.1038/s41467-017-01702-1

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.2017

    • Author(s)
      Suga, M.†, Akita, F.†, Sugahara, M.†, Kubo, M.†, Nakajima, Y.† et al. (†equal contribution)(38人中1番目)
    • Journal Title

      Nature

      Volume: 543 Issue: 7643 Pages: 131-135

    • DOI

      10.1038/nature21400

    • NAID

      120006344935

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] A three dimensional movie of structural changes in bacteriorhodopsin.2016

    • Author(s)
      Nango, E., Royant, A.†, Kubo, M.† et al. (†equal contribution)(45名中2番目)
    • Journal Title

      Science

      Volume: 354 Issue: 6319 Pages: 1552-1557

    • DOI

      10.1126/science.aah3497

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography.2016

    • Author(s)
      Nogly, P., et al. (40人中8番目)
    • Journal Title

      Nat. Commun.

      Volume: 7 Issue: 1 Pages: 12314-12314

    • DOI

      10.1038/ncomms12314

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [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 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Nearly On-axis Spectroscopic System for Simultaneously Measuring UV-visible Absorption and X-ray Diffraction in the SPring-8 Structural Genomics Beamline2016

    • Author(s)
      M. Sakaguchi, T. Kimura, T. Nishida, T. Tosha, Y. Yamaguchi, S. Yanagisawa, G. Ueno, H. Murakami, H. Ago, M. Yamamoto, T. Ogura, Y. Shiro, M. Kubo
    • Journal Title

      J. Synchro. Rad.

      Volume: 23 Issue: 1 Pages: 334-338

    • DOI

      10.1107/s1600577515018275

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 新規リアルタイム観察装置の開発によるタンパク質の分子機構解明への挑戦2018

    • Author(s)
      木村哲就
    • Organizer
      第6回K-CONNEX研究会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] ABCトランスポーターの機能・構造ダイナミクス(仮題)2017

    • Author(s)
      木村哲就
    • Organizer
      第55回日本生物物理学会年会
    • Place of Presentation
      熊本大学(熊本市)
    • Year and Date
      2017-09-19
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] ABCトランスポーターの分子機構解明を目指した時間分解測定法の開発2017

    • Author(s)
      木村哲就、林沙英、大西萌、杉本宏、城宜嗣、小堀康弘、池本夕佳
    • Organizer
      第43回生体分子科学討論会
    • Place of Presentation
      カレッジプラザ & IYATAKA(秋田市)
    • Year and Date
      2017-06-23
    • Related Report
      2016 Annual Research Report
  • [Presentation] マイクロ流路ミキサーを用いた時間分解分光測定によるABCトランスポーターの輸送機構解析2017

    • Author(s)
      木村哲就、林沙英、大西萌、杉本宏、城宜嗣、小堀康弘、池本夕佳
    • Organizer
      第17回日本蛋白質科学会年会
    • Place of Presentation
      仙台国際センター(仙台市)
    • Year and Date
      2017-06-20
    • Related Report
      2016 Annual Research Report
  • [Presentation] 時間分解可視吸収分光測定によるヘムABCトランスポーターの輸送メカニズム解析2017

    • Author(s)
      林沙英、城宜嗣、杉本宏、木村哲就
    • Organizer
      第17回日本蛋白質科学会年会
    • Place of Presentation
      仙台国際センター(仙台市)
    • Year and Date
      2017-06-20
    • Related Report
      2016 Annual Research Report
  • [Presentation] 時間分解可視吸収分光測定によるヘム ABC トランスポーターの輸送メカニズム解析2017

    • Author(s)
      林沙英, 城宜嗣, 杉本宏, 木村哲就
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] マイクロ流路ミキサーを用いた時間分解分光測定による ABC トランスポーターの分子機構解析2017

    • Author(s)
      木村哲就, 林沙英, 大西萌, 城宜嗣, 杉本宏, 池本夕佳
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] ABCトランスポーターの分子機構解明を目指した時間分解測定法の開発2017

    • Author(s)
      木村哲就, 林沙英, 大西萌, 城宜嗣, 杉本宏, 小堀康弘, 池本夕佳
    • Organizer
      第44回生体分子科学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 可視吸収分光測定によるヘムABCトランスポーター; BhuUVの輸送メカニズム解析2017

    • Author(s)
      林沙英, 城宜嗣, 杉本宏, 木村哲就
    • Organizer
      第44回体分子科学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 時間分解分光法によるABCトランスポーターの輸送とATP加水分解過程の直接観察2017

    • Author(s)
      木村哲就
    • Organizer
      日本生物物理学会第54回年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 線虫cytochrome b561ホモログ・Cecytb-2の分子機能解明2017

    • Author(s)
      藤村美香, 三浦雅央, 木村哲就, 鍔木基成
    • Organizer
      日本生物物理学会第54回年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 時間分解可視・赤外吸収分光法を用いた一酸化窒素還元酵素のNO還元反応機構の解明2017

    • Author(s)
      武田英恵, 木村哲就, 野村高志, 松林明子, 石井頌子, 當舎武彦, 城宜嗣, 久保稔
    • Organizer
      日本生物物理学会第54回年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 可視吸収分光測定によるヘムABCトランスポーター; BhuUVの輸送メカニズム解析2017

    • Author(s)
      林沙英, 城宜嗣, 杉本宏, 木村哲就
    • Organizer
      2017年度生命科学系学会合同年次大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 線虫cytochrome b561ホモログ・Cecytb-2の分子機能解明2017

    • Author(s)
      藤村美香, 三浦雅央, 木村哲就, 鍔木基成
    • Organizer
      2017年度生命科学系学会合同年次大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Intermediate structures of the catalytic site in membrane proteins revealed by time-resolved spectroscopy with micro-channel devices.2016

    • Author(s)
      T. Kimura, H. Takeda, S. Ishii, T. Tosha, Y. Shiro, M. Kubo
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Structural dynamics in the enzymatic reaction of membrane protein; nitric oxide reductase, revealed by the novel time-resolved spectroscopic measurements.2016

    • Author(s)
      T. Kimura, H. Takeda, S. Ishii, T. Tosha, Y. Shiro, M. Kubo
    • Organizer
      42nd Naito Conference "In the Vanguard of Structural Biology: Revolutionizing Life Sciences"
    • Place of Presentation
      シャトレーゼ ガトーキングダム サッポロ(北海道札幌市)
    • Year and Date
      2016-10-04
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] マイクロ流路フロー・フラッシュ時間分解赤外分光法による一酸化窒素還元酵素の反応機構解析2016

    • Author(s)
      木村哲就、武田英恵、石井頌子、當舎武彦、城宜嗣、久保稔
    • Organizer
      第43回生体分子科学討論会
    • Place of Presentation
      名古屋大学(名古屋市)
    • Year and Date
      2016-06-24
    • Related Report
      2016 Annual Research Report
  • [Presentation] NO reduction mechanism in the binuclear catalytic center of nitric oxide reductase revealed by novel micro-channel flow-flash spectrometers.2016

    • Author(s)
      T. Kimura, H. Takeda, S. Ishii, T. Tosha, Y. Shiro, M. Kubo
    • Organizer
      Gordon Research Conference "Metallocofactors"
    • Place of Presentation
      Stonehill College (Easton, MA, USA)
    • Year and Date
      2016-06-12
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Molecular mechanism of the catalytic reaction of NO reductase revealed by novel time-resolved visible/IR absorption spectrometers with microfluidic device2016

    • Author(s)
      Tetsunari Kimura, Hanae Takeda, Shoko Ishii, Takehiko Tosha, Yoshitsugu Shiro, Minoru Kubo
    • Organizer
      Biophysical Society 60th Annual Meeting
    • Place of Presentation
      Los Angeles, CA, USA
    • Year and Date
      2016-02-27
    • Related Report
      2015 Annual Research Report
  • [Presentation] Development of a time-resolved visible/IR absorption spectrometer with a novel microfluidic device and its application to catalytic reaction of NO reductase2015

    • Author(s)
      Tetsunari Kimura, Shoko Ishii, Takehiko Tosha, Yoshitsugu Shiro, Minoru Kubo
    • Organizer
      PacifiChem 2015
    • Place of Presentation
      Honolulu, HI, USA
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] マイクロ流体フロー・フラッシュ赤外分光測定系による一酸化窒素還元酵素の触媒反応の実時間観察2015

    • Author(s)
      木村哲就, 石井頌子, 當舎武彦, 城宜嗣, 久保稔
    • Organizer
      第9回分子科学討論会
    • Place of Presentation
      東京工業大学(東京都・目黒区)
    • Year and Date
      2015-09-16
    • Related Report
      2015 Annual Research Report
  • [Presentation] マイクロ流路を用いたフローフラッシュ赤外吸収分光法の開発と一酸化窒素還元酵素の反応中間体解析への応用2015

    • Author(s)
      木村哲就, 石井頌子, 當舎武彦, 城宜嗣, 久保稔
    • Organizer
      日本生物物理学会第52回年会
    • Place of Presentation
      金沢大学(石川県・金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] マイクロ流体フローを用いた一酸化窒素還元酵素の触媒反応の動的分光観察2015

    • Author(s)
      木村哲就
    • Organizer
      第15回日本蛋白質科学会年会:若手奨励賞シンポジウム
    • Place of Presentation
      あわぎんホール(徳島県・徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Remarks] タンパク質中の原子の動き、自由電子レーザーにより動画撮影に成功

    • URL

      http://www.kobe-u.ac.jp/NEWS/research/2016_12_26_01.html

    • Related Report
      2016 Annual Research Report

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Published: 2015-04-16   Modified: 2022-10-14  

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