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Structural analyses of green fluorescent protein with ultra-high accuracy

Research Project

Project/Area Number 17H03643
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Structural biochemistry
Research InstitutionKyoto University

Principal Investigator

Takeda Kazuki  京都大学, 理学研究科, 准教授 (30332290)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥17,030,000 (Direct Cost: ¥13,100,000、Indirect Cost: ¥3,930,000)
Fiscal Year 2019: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2018: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
Fiscal Year 2017: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Keywordsタンパク質 / X線 / 蛍光 / エックス線 / 結晶 / 電荷密度解析 / 中性子線解析
Outline of Final Research Achievements

The charge-density analysis can provide the information about the density distribution of outer shell electrons, the atomic charge and the position of hydrogen atoms, which is essential for understanding the physical and chemical properties. However, few reports are available on the analysis in protein molecules. In this research, we performed the charge density analysis of green fluorescent protein (GFP) at resolution of 0.78 A. The precise electronic structure gives information about the valence electron distribution, the atomic charge and the weak interaction. Meanwhile, neutron crystallography using perdeuteration protein is effective method for determining the positions of hydrogen atoms. We evaluated the influence of physical properties and structure by perdeuteration and performed the neutron diffraction experiment. A series of studies quantified the weak interactions between the chromophore and the protein environment and enable us to explain the properties of GFP.

Academic Significance and Societal Importance of the Research Achievements

電荷密度解析は電子構造を実験的に決定する手法であり、分子の物性を直接議論することが可能である。本研究では、結合次数や結合エネルギー、非共有結合性の相互作用などを定量的に決定することができた。得られた結果は量子化学計算との比較が可能な精度であるため、理論と実験の相補的な発展を促すものである。一方、タンパク質の構造情報は薬剤開発においても広く利用されている。タンパク質や薬剤候補分子の電荷や価電子の分布は作用機序に深く関与しているが、通常の構造解析からは決定できない。電荷密度解析の汎用化は相互作用予測や評価精度の向上と効率化にもつながるため、将来的には創薬にも応用できると考えられる。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (6 results)

All 2020 2019 2018 2017

All Journal Article (3 results) (of which Peer Reviewed: 3 results,  Open Access: 3 results) Presentation (3 results)

  • [Journal Article] 生命科学の飛躍のために一層深まるタンパク質結晶学の役割-タンパク質の超高分解能電荷密度解析2020

    • Author(s)
      高場圭章、長谷川和也、竹田一旗
    • Journal Title

      日本結晶学会誌

      Volume: 62

    • NAID

      130007849708

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-angstrom resolutions2019

    • Author(s)
      Tai Yang、Takaba Kiyofumi、Hanazono Yuya、Dao Hoang-Anh、Miki Kunio、Takeda Kazuki
    • Journal Title

      Acta Crystallographica Section D Structural Biology

      Volume: 75 Issue: 12 Pages: 1096-1106

    • DOI

      10.1107/s2059798319014608

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Subatomic resolution X-ray structures of green fluorescent protein2019

    • Author(s)
      Takaba Kiyofumi、Tai Yang、Eki Haruhiko、Dao Hoang-Anh、Hanazono Yuya、Hasegawa Kazuya、Miki Kunio、Takeda Kazuki
    • Journal Title

      IUCrJ

      Volume: 6 Issue: 3 Pages: 387-400

    • DOI

      10.1107/s205225251900246x

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Sensitivity to the radiation dose of buried waters in Green Fluorescent Protein2018

    • Author(s)
      Dao Hoang Anh, Takaba Kiyofumi, Tai Yang, Hasegawa Nagayuki, Takeda Kazuki
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] TOF-Laue法中性子線回折データのスケーリング方法の開発2017

    • Author(s)
      花園祐矢、竹田一旗、平野 優、玉田太郎、日下勝弘、三木邦夫
    • Organizer
      日本中性子学会第17回年会(福岡)
    • Related Report
      2017 Annual Research Report
  • [Presentation] 完全重水素化GFPのX線結晶構造解析及び中性子線データ測定2017

    • Author(s)
      タイ ヨウ、花園祐矢、高場圭章、三木邦夫、竹田一旗
    • Organizer
      日本中性子学会第17回年会(福岡)
    • Related Report
      2017 Annual Research Report

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Published: 2017-04-28   Modified: 2021-02-19  

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