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Single-molecule analysis of DNA binding proteins using DNA array(Fostering Joint International Research)

Research Project

Project/Area Number 16KK0157
Research Category

Fund for the Promotion of Joint International Research (Fostering Joint International Research)

Allocation TypeMulti-year Fund
Research Field Biophysics
Research InstitutionTohoku University

Principal Investigator

Kamagata Kiyoto  東北大学, 多元物質科学研究所, 准教授 (90432492)

Project Period (FY) 2017 – 2019
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥15,210,000 (Direct Cost: ¥11,700,000、Indirect Cost: ¥3,510,000)
KeywordsDNA / DNA結合タンパク質 / 単分子蛍光顕微鏡 / スライディング / 拡散 / 障害物 / 単分子計測 / 1分子計測(SMD) / 蛋白質 / 遺伝子 / 分子認識 / 生体分子
Outline of Final Research Achievements

We analyzed the function of DNA-binding proteins using developed DNA aligned array and single-molecule fluorescence microscopy. We found that architectural DNA-binding proteins slide along DNA with continuous contacts to DNA. We identified the key residues to affect the sliding dynamics using mutation analysis. Although we expected that DNA-binding proteins bound to DNA block the movement by proteins along DNA, we found that an architectural DNA-binding protein can bypass other DNA-binding proteins along DNA.

Academic Significance and Societal Importance of the Research Achievements

DNA結合タンパク質は、DNAの標的配列に結合し細胞の機能を制御することが知られている。本研究では、単分子顕微鏡を用いて、実際にDNA結合タンパク質がDNA上の動きを可視化することで、分子レベルでのメカニズムを解明した。また、DNA結合タンパク質の標的DNA配列への結合が阻害されると、様々な疾患になることも知られている。将来的に、本研究で明らかとなったDNA結合タンパク質の機能メカニズムを用いて、DNA結合タンパク質の関わる創薬研究が期待される。

Report

(2 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • Research Products

    (23 results)

All 2020 2019 2017 Other

All Int'l Joint Research (2 results) Journal Article (5 results) (of which Peer Reviewed: 5 results,  Open Access: 3 results) Presentation (14 results) (of which Int'l Joint Research: 4 results,  Invited: 10 results) Remarks (2 results)

  • [Int'l Joint Research] カリフォルニア大学ロサンゼルス校(米国)2020

    • Year and Date
      2020-02-19
    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] カリフォルニア大学ロサンゼルス校(米国)2017

    • Year and Date
      2017-08-06
    • Related Report
      2019 Annual Research Report
  • [Journal Article] Liquid-like droplet formation by tumor suppressor p53 induced by multivalent electrostatic interactions between two disordered domains2020

    • Author(s)
      Kamagata Kiyoto、Kanbayashi Saori、Honda Masaya、Itoh Yuji、Takahashi Hiroto、Kameda Tomoshi、Nagatsugi Fumi、Takahashi Satoshi
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 580-580

    • DOI

      10.1038/s41598-020-57521-w

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] How p53 molecules solve the target DNA search problem2020

    • Author(s)
      Kamagata, K., Itoh, Y., Subekti, D.R.G.
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 21 Issue: 3 Pages: 1-13

    • DOI

      10.3390/ijms21031031

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] How Does Tumor Suppressor Protein p53 Solve the Target DNA Search Problem?2019

    • Author(s)
      鎌形 清人、伊藤 優志, Dwiky Rendra Graha Subekti
    • Journal Title

      Butsuri

      Volume: 74 Issue: 7 Pages: 472-475

    • DOI

      10.11316/butsuri.74.7_472

    • NAID

      130007761032

    • ISSN
      0029-0181, 2423-8872
    • Year and Date
      2019-07-05
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The mechanosensitive channel YbdG from Escherichia coli has a role in adaptation to osmotic up-shock.2019

    • Author(s)
      Shun Amemiya, Hayato Toyoda, Mami Kimura, Hiromi Saito, Hiroshi Kobayashi, Kunio Ihara 3 , Kiyoto Kamagata 4 , Ryuji Kawabata 5 , Setsu Kato, Yutaka Nakashimada, Tadaomi Furuta, Shin Hamamoto, Nobuyuki Uozumi
    • Journal Title

      Journal of Biological Chemistry

      Volume: 294 (33) Issue: 33 Pages: 12281-12292

    • DOI

      10.1074/jbc.ra118.007340

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rational design using sequence information only produces a peptide that binds to the intrinsically disordered region of p532019

    • Author(s)
      Kamagata Kiyoto、Mano Eriko、Itoh Yuji、Wakamoto Takuro、Kitahara Ryo、Kanbayashi Saori、Takahashi Hiroto、Murata Agato、Kameda Tomoshi
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 8584-8584

    • DOI

      10.1038/s41598-019-44688-0

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] DNA・タンパク質の複合系の単分子計測2020

    • Author(s)
      鎌形清人
    • Organizer
      核酸科学懇談会2020
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] がん抑制タンパク質はどのように標的 DNA 探索問題を解くのか? ー単分子計測的アプローチー2020

    • Author(s)
      鎌形清人
    • Organizer
      DNA損傷・修復と高強度レーザー化学の交差点
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] RATIONAL DESIGN OF PEPTIDE TARGETING INTRINSICALLY DISORDERED PROTEIN p53 -REGULATION OF FUNCTION AND PHASE SEPARATION.2020

    • Author(s)
      Kiyoto Kamagata, Ryo Kitahara, Tomoshi Kameda
    • Organizer
      64th Annual Meeting of the Biological Society
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] TRANSIENT BINDING AND NON-ROTATIONAL COUPLED MOTION OF P53 REVEALED BY SUB-MILLISECOND RESOLVED SINGLE-MOLECULE FLUORESCENCE TRACKING.2020

    • Author(s)
      Dwiky R.G. Subekti, Satoshi Takahashi, Kiyoto Kamagata
    • Organizer
      64th Annual Meeting of the Biological Society
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 天然変性タンパク質p53は液-液相分離するのか?2019

    • Author(s)
      鎌形清人
    • Organizer
      第2回LLPS研究会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 天然変性タンパク質p53を標的としたペプチドの人工設計-液液相分離の制御-2019

    • Author(s)
      鎌形清人, 間野絵梨子, 伊藤優志, 上林さおり, 本多優也, 北原亮, 亀田倫史
    • Organizer
      第19回蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] がん抑制タンパク質p53の液液相分離と人工設計ペプチドによる制御2019

    • Author(s)
      鎌形清人
    • Organizer
      大阪大学蛋白研セミナー・第3回LLPS研究会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Rational design of peptide targeting intrinsically disordered protein p53 -regulation of function and phase-phase separation-2019

    • Author(s)
      鎌形清人
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] How does tumor suppressor p53 search for target DNA sequence? -single molecule approach-2019

    • Author(s)
      鎌形清人
    • Organizer
      第43回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Current trend of phase separation2019

    • Author(s)
      Kameda T, Kurumida Y, Nakamichi N, Ikeda K, Kitahara R, Kamagata K
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] DNAオリガミ技術を用いたDNA結合タンパク質の機能解析法の開発2019

    • Author(s)
      鎌形清人、鈴木勇輝、Reid C. Johnson 、呉以寧
    • Organizer
      アンサンブルリコレクションシンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] Observation of tumor suppressor p53 ssearch dynamics using sub-millisecond resolverd Ssingle-molecule fluorescence microscopy2019

    • Author(s)
      Dwiky R.G. Subekti, Agato Murata, Yuji Itoh, Satoshi Takahashi, Kiyoto Kamagata
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Engeneering of gemone editing protein Cas9 that slides along DNA faster and might eneble efficient target search2019

    • Author(s)
      Dwiky R.G. Subekti, Satoshi Takahashi, Kiyoto Kamagata
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Observation of Tumor Suppressor p53 Search Dynamics using Sub-millisecond Resolved Single-molecule Fluorescence Microscopy2019

    • Author(s)
      Dwiky R.G. Subekti, Agato Murata, Yuji Itoh, Satoshi Takahashi, Kiyoto Kamagata
    • Organizer
      第19回東北大学多元物質科学研究所研究発表会
    • Related Report
      2019 Annual Research Report
  • [Remarks] がん抑制タンパク質p53の天然変性領域を標的としたペプチドの人工設計(プレスリリース)

    • URL

      https://www.tohoku.ac.jp/japanese/2019/07/press20190628-01-pepuchido.html

    • Related Report
      2019 Annual Research Report
  • [Remarks] がん抑制タンパク質p53の液滴形成現象の発見 ― がん抑制機構の解明に期待 ―(プレスリリース)

    • URL

      https://www.tohoku.ac.jp/japanese/2020/01/press20200120-01-p53.html

    • Related Report
      2019 Annual Research Report

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Published: 2017-03-15   Modified: 2021-02-19  

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