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Neutron D/H contrast crystallography for hydrogen and hydration analysis of macromolecules

Research Project

Project/Area Number 16K05014
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Quantum beam science
Research InstitutionKyoto University

Principal Investigator

Chatake Toshiyuki  京都大学, 複合原子力科学研究所, 准教授 (30383475)

Co-Investigator(Kenkyū-buntansha) 藤原 悟  国立研究開発法人量子科学技術研究開発機構, 高崎量子応用研究所 東海量子ビーム応用研究センター, 上席研究員(定常) (10354888)
Research Collaborator TANAKA Ichiro  
Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2018: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2017: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2016: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Keywords中性子 / 水素 / 水和 / 結晶学 / 生体分子 / D/Hコントラスト / D/Hコントラスト法 / 水和構造
Outline of Final Research Achievements

Neutron protein crystallography has an advantage on detecting hydrogens in protein, hence it is a powerful tool to investigate hydrogen and hydration structures of proteins. The difference of neutron scattering lengths of deuterium and hydrogen provides the high contrast in neutron Fourier map, and this contrast (D/H contrast) is expected to imporve the accuracy of neutron protein crystallography.
In the present study, we developed programs and conducted neutron diffraction experiment using the latest neutron TOF diffractometer, in order to put our new D/H contrast algorithm to practical use. The program with graphical user interface has been completed and successfully passed in test runs. In the neutron experiment, good diffraction images have been given using large protein crystals.

Academic Significance and Societal Importance of the Research Achievements

今回作成したD/Hコントラスト法のプログラムは、中性子結晶解析の利点である水素原子と水素イオンの検出力を飛躍的に向上させることが期待される。これを利用すれば以下の利点がもたらされる。(1)生体分子内の化学反応に関係する官能基のpKaを高精度で決めることができ、生体分子の反応機構の詳細が明らかになる。(2)他の実験法では難しい水和水の詳細な立体構造が決定できる。(3)通常の解析では解析が困難な生体分子でも、コントラストによる検知力の向上により、解析が実現できる。これにより、詳細な構造情報に基づいた酵素や薬剤の分子設計が実現されれば、農学、医学、薬学など大きな波及効果が期待される。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (15 results)

All 2018 2017 2016

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 6 results,  Open Access: 2 results) Presentation (8 results)

  • [Journal Article] Cryoprotectant-free high-pressure cooling and dynamic nuclear polarization for more sensitive detection of hydrogen in neutron protein crystallography2018

    • Author(s)
      Tanaka Ichiro、Komatsuzaki Naoya、Yue Wen-Xue、Chatake Toshiyuki、Kusaka Katsuhiro、Niimura Nobuo、Miura Daisuke、Iwata Takahiro、Miyachi Yoshiyuki、Nukazuka Genki、Matsuda Hiroki
    • Journal Title

      Acta Crystallographica Section D Structural Biology

      Volume: 74 Issue: 8 Pages: 787-791

    • DOI

      10.1107/s2059798318005028

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Purification and structural characterization of water‐soluble menaquinone‐7 produced by Bacillus subtilis natto2018

    • Author(s)
      Chatake Toshiyuki、Yanagisawa Yasuhide、Inoue Rintaro、Sugiyama Masaaki、Matsuo Tatsuhito、Fujiwara Satoru、Ohsugi Tadanori、Sumi Hiroyuki
    • Journal Title

      Journal of Food Biochemistry

      Volume: 42 Issue: 6 Pages: e12630-e12630

    • DOI

      10.1111/jfbc.12630

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 生物物理学的手法を用いた納豆菌の研究 -納豆菌が生産する生理活性物質と納豆菌の放射線耐性-2018

    • Author(s)
      茶竹俊行,齊藤剛, 柳澤泰任
    • Journal Title

      放射線生物研究

      Volume: 52 Pages: 280-290

    • NAID

      40021793983

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ligation-Dependent Picosecond Dynamics in Human Hemoglobin As Revealed by Quasielastic Neutron Scattering2017

    • Author(s)
      Fujiwara Satoru、Chatake Toshiyuki、Matsuo Tatsuhito、Kono Fumiaki、Tominaga Taiki、Shibata Kaoru、Sato-Tomita Ayana、Shibayama Naoya
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 121 Issue: 34 Pages: 8069-8077

    • DOI

      10.1021/acs.jpcb.7b05182

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] DNA conformational transitions inferred from re-evaluation of m|F o| ? D|F c| electron-density maps2017

    • Author(s)
      Sunami Tomoko、Chatake Toshiyuki、Kono Hidetoshi
    • Journal Title

      Acta Crystallographica Section D Structural Biology

      Volume: 73 Issue: 7 Pages: 600-608

    • DOI

      10.1107/s2059798317007707

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] ナットウキナーゼとメナキノン-7の構造研究2017

    • Author(s)
      柳澤泰任、太田さくら、足立達美、内藤佐和、須見洋行、齊藤剛、茶竹俊行
    • Journal Title

      テンペ研究会会誌

      Volume: 印刷中

    • Related Report
      2016 Research-status Report
  • [Journal Article] Structural Insight Into Protein Binding of Boron Tracedrug UTX-97 Revealed by the Co-Crystal Structure With Lysozyme at 1.26 Angstrom Resolution.2016

    • Author(s)
      Morimoto Y, Nagasawa H, Uto Y, Chatake T, Hori H
    • Journal Title

      Journal of Pharmaceutical Scinences

      Volume: 105 Issue: 8 Pages: 2298-2301

    • DOI

      10.1016/j.xphs.2016.06.005

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Presentation] 実空間D/Hコントラスト法による中性子蛋白質結晶解析2017

    • Author(s)
      茶竹俊行、藤原悟
    • Organizer
      中性子科学会第17回年会
    • Related Report
      2017 Research-status Report
  • [Presentation] 小角散乱、中性子準弾性散乱、及び中性子結晶学による蛋白質水和水の統一的解析2017

    • Author(s)
      藤原悟、松尾 龍人、河野史明、高田慎一、杉本泰伸、菊地龍弥、中島健次、茶竹 俊行
    • Organizer
      日本生物物理学会第55回年会
    • Related Report
      2017 Research-status Report
  • [Presentation] m|Fo|-D|Fc| map 上に見いだされる DNA の構造変化の網羅的解析2017

    • Author(s)
      角南智子、茶竹俊行、河野秀俊
    • Organizer
      平成29年度日本結晶学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] 蛋白質の水和構造解明に向けたD/Hコントラスト法の利用2017

    • Author(s)
      茶竹俊行、藤原悟
    • Organizer
      京都大学原子炉実験所第51回学術講演会
    • Place of Presentation
      京都大学原子炉実験所
    • Related Report
      2016 Research-status Report
  • [Presentation] 納豆菌由来MK-7の構造特性および納豆菌のガンマ線耐性の研究2017

    • Author(s)
      柳澤泰任、髙根光紗、足立達美、茶竹俊行、齊藤剛 、井上倫太郎、杉山正明、松尾龍人、藤原悟、大杉忠則、須見洋行
    • Organizer
      京都大学原子炉実験所第51回学術講演会
    • Place of Presentation
      京都大学原子炉実験所
    • Related Report
      2016 Research-status Report
  • [Presentation] 中性子タンパク質結晶構造解析での水素高感度検出のための動的核偏極法の予備的結果2016

    • Author(s)
      Naoya Komatsuzaki, Ichiro Tanaka, Takahiro Iwata, Daisuke Miura, Yoshiyuki Miyachi, Genki Nukazuka, Hiroki Matsuda, Toshiyuki Chatake, Katsuhiro Kusaka, Nobuo Niimura
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      エポカル筑波
    • Related Report
      2016 Research-status Report
  • [Presentation] 構造状態と関係したヘモグロビンのピコ秒ダイナミクスの変化2016

    • Author(s)
      Satoru Fujiwara, Toshiyuki Chatake, Tatsuhito Matsuo, Fumiaki Kono, Taiki Tominaga, Kaoru Shibata, Ayana Sato, Naoya Shibayama
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      エポカル筑波
    • Related Report
      2016 Research-status Report
  • [Presentation] 結晶構造中で観察される DNA 構造ゆらぎの網羅解析2016

    • Author(s)
      Tomoko Sunami, Toshiyuki Chatake, Hidetoshi Kono
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      エポカル筑波
    • Related Report
      2016 Research-status Report

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Published: 2016-04-21   Modified: 2020-03-30  

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