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Improvement of sequence specificity of DNA-binding protein using computational and experimental approaches

Research Project

Project/Area Number 26330339
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionNational Institutes for Quantum and Radiological Science and Technology (2016)
Japan Atomic Energy Agency (2014-2015)

Principal Investigator

KONO HIDETOSHI  国立研究開発法人量子科学技術研究開発機構, 関西光科学研究所 量子生命科学研究部, グループリーダー(定常) (40291918)

Co-Investigator(Renkei-kenkyūsha) SUNAMI Tomoko  国立研究開発法人量子科学技術研究開発機構, 関西光科学研究所 量子生命科学研究部, 主幹研究員 (50554648)
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2014: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
KeywordsDNA結合蛋白質 / 分子シミュレーション / 生体生命情報学 / バイオインフォマティクス / 蛋白質設計 / B1H / タンパク質設計 / DNA結合 / 配列特異性 / モデリング / DNA結合タンパク質 / デザイン / 分子設計
Outline of Final Research Achievements

We successfully created a designed-protein which can bind to a target DNA sequence with high specificity. In the design, we connected two DNA-binding proteins after engineered one mutation which reduces the affinity of the monomer. Then, we combined these domains to create a dimer protein and confirmed that it binds to the target sequence by B1H assay. In addition, to understand the DNA sequence dependent, physico-chemical property, we carried out molecular dynamics simuations on many DNA sequences. We extracted some feature parameters from the sampled conformations using a machine learning technique. We found that the values of the feature parameters at transcription binding sites as well as within 200bp up and down streams from the binding sites are different from those of non-binding sites.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report

Research Products

(8 results)

All 2017 2016 2015 2014

All Journal Article (1 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 1 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (7 results) (of which Invited: 2 results)

  • [Journal Article] Genome-wide transcription factor activities are explained by intrinsic conformational dynamics of binding-sites and distal flanking-regions2017

    • Author(s)
      Andrabi, M.; Hutchins, A. P.; Miranda-Saavedra, D.; Kono, H.; Nussinov, R.; Mizuguchi, K.; Ahamd, S.
    • Journal Title

      Scientific Reports

      Volume: 印刷中

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] Revisiting DNA conformations in crystal structures2016

    • Author(s)
      Sunami, T.; Chatake, T.; Kono, H.
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      茨城・つくば・つくば国際会議場 (国内)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] エングレイルドホメオドメインを用いた新規転写因子設計2016

    • Author(s)
      角南智子; 河野秀俊
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡・福岡・福岡国際会議場 (国内)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] 転写因子のアクティビィティは結合サイト及びその周辺領域のDNA特性の関係できまる2016

    • Author(s)
      河野秀俊
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡・福岡・福岡国際会議場 (国内)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 構造多形をもつ生体高分子の全原子モデルの構築2016

    • Author(s)
      河野秀俊
    • Organizer
      JSBi関西地域部会 第21回バイオメディカル研究会
    • Place of Presentation
      大阪・大阪・グランフロント大阪 (国内)
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Designing a new artificial transcription factor based on engrailed homeodomain2015

    • Author(s)
      角南智子、河野秀俊
    • Organizer
      第38 回日本分子生物学会
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Research-status Report
  • [Presentation] Designing a new artificial transcription factor based on engrailed homeodomain2015

    • Author(s)
      角南智子、河野秀俊
    • Organizer
      第15回日本蛋白質科学会年会
    • 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 Research-status Report
  • [Presentation] Designing a new artificial transcription factor based on engrailed homeodomain2014

    • Author(s)
      角南智子、河野秀俊
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター(札幌)
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Research-status Report

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Published: 2014-04-04   Modified: 2018-03-22  

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