• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Development of a method to elucidate the structural transition process by adding a time stamp to the three-dimensional structure of a protein

Research Project

Project/Area Number 19K22510
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 48:Biomedical structure and function and related fields
Research InstitutionUniversity of Fukui

Principal Investigator

Hirofumi Shimizu  福井大学, 学術研究院医学系部門, 講師 (50324158)

Co-Investigator(Kenkyū-buntansha) 安永 卓生  九州工業大学, 大学院情報工学研究院, 教授 (60251394)
Project Period (FY) 2019-06-28 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2020: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2019: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Keywords1分子計測 / 蛋白質 / X線回折 / 単粒子構造解析 / 1分子動態計測
Outline of Research at the Start

本研究では、X線1分子動態計測法と電子線単粒子解析法を組み合わせ、遷移過程における蛋白質の立体構造に時刻の情報を付加し、構造変化過程の全体像を明らかにする手法開発を目指す。動的構造変化を起こす例として、pH依存性チャネルを用いて閉状態、開閉遷移状態での単粒子構造解析を行い、観測中に中性から酸性へ変化させた際の1分子動態計測データと比較して複数遷移状態の立体構造に時刻を付与する手法開発に挑戦する。

Outline of Final Research Achievements

As a method for determining the three-dimensional structure of a protein, a single particle analysis method using a cryo-electron microscope has appeared, and it has become possible to obtain a plurality of three-dimensional structures under the same solution conditions. Since the obtained multiple three-dimensional structures lack time-series information, by fusing the single-molecule structure change of the protein with the X-ray single-molecule dynamics measurement method that can track the movement of the observation probe attached to the protein. We aim to develop a method for adding time information to a three-dimensional structure and clarifying the overall picture of the structural change process when it functions.

Academic Significance and Societal Importance of the Research Achievements

低温電子顕微鏡による単粒子解析法の登場によって、立体構造情報の飛躍的な増大が見込まれている。特に同一溶液条件でとりうる複数の立体構造を区別して解析できる点は、従来の結晶構造解析法にはなかった特徴である。本研究で、動態計測データとの融合が実現すれば、得られた立体構造に時系列情報を付与し、構造変化の全体像を解明できる。本研究では単粒子解析法によってKcsAカリウムチャネルの初期構造を得た。また、対応する条件でX線1分子動態計測を行い立体構造と比較可能な動態計測データを得た。現在、条件の精密化に取り組んでいる。

Report

(3 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • Research Products

    (11 results)

All 2020 2019 Other

All Journal Article (1 results) (of which Peer Reviewed: 1 results,  Open Access: 1 results) Presentation (9 results) (of which Int'l Joint Research: 3 results,  Invited: 1 results) Remarks (1 results)

  • [Journal Article] Diffracted X-ray tracking method for recording single-molecule protein motions2019

    • Author(s)
      Shimizu Hirofumi
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - General Subjects

      Volume: in press Issue: 2 Pages: 129361-129361

    • DOI

      10.1016/j.bbagen.2019.05.004

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] イオンチャネル構造遷移過程のX線1分子動画計測2020

    • Author(s)
      清水啓史
    • Organizer
      生理研研究会「イオンチャネルと生体膜のダイナミクス:構造生物学の先にあるもの」
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] X線1分子動態計測法の開発2020

    • Author(s)
      清水啓史
    • Organizer
      第67回中部生理学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] SINGLE-MOLECULE TWISTING MOTIONS DURING GATING OF THE HUMAN TRPV1 CHANNEL RECORDED WITH SUB-MILLISECOND TIME RESOLUTION.2020

    • Author(s)
      Hirofumi Shimizu, Takuya Kobayashi, Masayuki Iwamoto, Kentaro Kajiwara, Nagomi Kurebayashi, Haruo Ogawa, Takashi Murayama.
    • Organizer
      64th Annual Meeting of Biophysical Society
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Structural Analysis of KcsA by Cryo-EM Single Particle Analysis2019

    • Author(s)
      Hiroko Takasaki, Hirofumi Shimizu, Takuo Yasunaga
    • Organizer
      第57回日本生物物理学会
    • Related Report
      2019 Research-status Report
  • [Presentation] Structural analysis of KcsA potassium channel by Cryo-EM.2019

    • Author(s)
      Hiroko Takazaki, Hirofumi Shimizu, Takuo Yasunaga.
    • Organizer
      日本顕微鏡学会生体解析分科会 Frontiers in Cellular, Viral and Molecular Microscopy with Cryo-specimen Preparation Techniques
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] 「クライオ電子顕微鏡単粒子解析法を用いたKcsAの構造解析.」2019

    • Author(s)
      髙﨑寛子, 清水啓史, 安永卓生.
    • Organizer
      第61回日本顕微鏡学会九州支部集合・学術講演会,
    • Related Report
      2019 Research-status Report
  • [Presentation] 「X 線1 分子動態計測法に適する新たなターゲット分子の探索」2019

    • Author(s)
      清水啓史
    • Organizer
      第4回イオンチャネル研究会
    • Related Report
      2019 Research-status Report
  • [Presentation] Microfabricated Solution Chamber for High Resolution Diffracted X-ray Tracking Method to Observe Ion Channel Gating Motion2019

    • Author(s)
      Ikkei Yamauchi, Tomoki Tabuchi, Yoshikazu Hirai, Masayuki Iwamoto, Toshiyuki Tsuchiya, Hirofumi Shimizu, and Osamu Tabata
    • Organizer
      Transducers 2019
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] 「イオンチャネルの開閉機構観察のための高解像度X 線一分子動態計測用溶液チャンバの開発」2019

    • Author(s)
      山内一慶,田渕友樹,平井義和,岩本真幸,土屋智由,清水啓史,田畑修
    • Organizer
      CHEMINAS39
    • Related Report
      2019 Research-status Report
  • [Remarks] 福井大学統合生理学 研究内容

    • URL

      https://www.med.u-fukui.ac.jp/laboratory/integrative/researches/

    • Related Report
      2019 Research-status Report

URL: 

Published: 2019-07-04   Modified: 2022-01-27  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi