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Structural analysis of the transient state of an enzyme active site using NMR relaxation dispersion

Research Project

Project/Area Number 21570170
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionOsaka University

Principal Investigator

IKEGAMI Takahisa  大阪大学, 蛋白質研究所, 准教授 (20283939)

Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2011: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2010: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2009: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywords核磁気共鳴 / NMR / 遷移状態 / induced-fit / 構造解析 / CPMG / 緩和分散 / 残余双極子相互作用
Research Abstract

An enzyme chitinase was aligned along the static magnetic field using Pf1-phage or acrylamide gel as an alignment medium. In this state residual dipolar coupling was observed, confirming that the system was effective for the analysis. To further apply the relaxation dispersion method to the alignment system, a complex system which was well known to be in a conformational exchange was used. Upon changing the stoichiometry in the complex, it was observed that the residual dipolar coupling also changed accordingly.

Report

(4 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (28 results)

All 2012 2011 2010 2009

All Journal Article (9 results) (of which Peer Reviewed: 9 results) Presentation (18 results) Book (1 results)

  • [Journal Article] Binding Energetics of Ferredoxin-NADP^+ Reductase with Ferredoxin and Its Relation to Function2011

    • Author(s)
      Lee, Y. H., Ikegami, T., Standley, D. M., Sakurai, K., Hase, T., and Goto, Y.
    • Journal Title

      Chembiochem

      Volume: 12 Pages: 2062-2070

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis of the recognition of the SAMP motif of adenomatous polyposis coli by the Src-homology 3 domain2010

    • Author(s)
      Kaieda, S., Matsui, C., Mimori-Kiyosue, Y., and Ikegami, T.
    • Journal Title

      Biochemistry

      Volume: 49 Pages: 5143-5153

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis of the recognition of the SAMP motif of adenomatous polyposis coli by the Src-Homology 3 domain.2010

    • Author(s)
      Kaieda, S., Matsui, C., Mimori-Kiyosue, Y., Ikegami, T.
    • Journal Title

      Biochemistry

      Volume: 49 Pages: 5143-5153

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure and functional characterization of Vibrio parahaemolyticus therm ostable direct hemolysin(TDH).2010

    • Author(s)
      Yanagihara, I., Kaieda, S., Ikegami, T., Hashimoto.H., et al.
    • Journal Title

      Journal of Biological Chemistry

      Volume: 285 Pages: 16267-16274

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Immunogenicity of whole-parasite vaccines against Plasmodium falciparum involves malarial hemozoin and host TLR9.2010

    • Author(s)
      Coban, C., Yagi, M., Ikegami, T., Ishii, K.J., Akira, S., et al.
    • Journal Title

      Cell Host Microbe

      Volume: 7 Pages: 50-61

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A robust approach to calculate entropy change based on density functional theory in the energy representation2009

    • Author(s)
      Yokogawa, D. and Ikegami, T.
    • Journal Title

      The Journal of Chemical Physics

      Volume: 131 Pages: 221101-221101

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Arabidopsis Tic62 and ferredoxin-NADP(H) oxidoreductase form light-regulated complexes that are integrated into the chloroplast redox poise2009

    • Author(s)
      Benz, J.P., Stengel, A., Lintala, M., Lee, Y.H., Weber, A., Philippar, K., Gugel, I.L., Kaieda, S., Ikegami, T., Mulo, P., Soll.J., Bolter.B
    • Journal Title

      Plant Cell 21

      Pages: 3965-3983

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A robust approach to calculate entropy change based on density functional theory in the energy representation2009

    • Author(s)
      Yokogawa, D., Ikegami, T.
    • Journal Title

      The Journal of Chemical Physics 131

      Pages: 221101-221104

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Unusual thermal disassembly of the SPFH domain oligomer from Pyrococcus horikoshii2009

    • Author(s)
      Kuwahara, Y., Unzai, Nagata, T., Hiroaki, Y., Yokoyama, H., Matsui, I., Ikegami, T., Fujiyoshi, Y., Hiroaki, H.
    • Journal Title

      Biophysical Journal 97

      Pages: 2034-2043

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Presentation] Is the interaction site with SH2 domains really well-known several residues including phosphotyrosine alone?2012

    • Author(s)
      池上貴久
    • Organizer
      9^<th> Japan-Korea Bilateral Symposium on Biological NMR
    • Place of Presentation
      北海道大学Conference Hall
    • Year and Date
      2012-03-16
    • Related Report
      2011 Final Research Report
  • [Presentation] ダイナミクスを利用したさまざまなNMR相互作用解析法の紹介2012

    • Author(s)
      池上貴久
    • Organizer
      第43回ワークショップ「計算科学とNMRの融合に向けて」
    • Place of Presentation
      理化学研究所横浜研究所交流棟ホール
    • Year and Date
      2012-02-06
    • Related Report
      2011 Final Research Report
  • [Presentation] ダイナミクスを利用したさまざまなNMR相互作用解析法の紹介2012

    • Author(s)
      池上貴久
    • Organizer
      よこはまNMR構造生物学研究会
    • Place of Presentation
      理化学研究所横浜研究所(招待講演)
    • Year and Date
      2012-02-06
    • Related Report
      2011 Annual Research Report
  • [Presentation] 核磁気共鳴の測定や解析の実際2012

    • Author(s)
      池上貴久
    • Organizer
      熊本大学特別講演会
    • Place of Presentation
      熊本大学薬学教育部
    • Year and Date
      2012-01-17
    • Related Report
      2011 Final Research Report
  • [Presentation] NMRによる蛋白質と低分子リガンドとの相互作用の解析法2012

    • Author(s)
      池上貴久
    • Organizer
      NMRによる蛋白-薬剤相互作用検出実験法
    • Place of Presentation
      蛋白質研究所
    • Related Report
      2011 Final Research Report
  • [Presentation] Advantages and disadvantages of a high magnetic field NMR and <13>^C detection(高磁場NMRの利用・13C検出への期待)2012

    • Author(s)
      池上貴久
    • Organizer
      第13回RRR-workshop 2011/ 12
    • Place of Presentation
      首都大学東京秋葉原サテライトキャンパス
    • Related Report
      2011 Final Research Report
  • [Presentation] 図で見る新しいNMR手法の原理2011

    • Author(s)
      池上貴久
    • Organizer
      ISNMR2011チュートリアル講演
    • Place of Presentation
      横浜大桟橋ホール
    • Year and Date
      2011-11-15
    • Related Report
      2011 Final Research Report
  • [Presentation] 図で見る新しいNMR手法の原理2011

    • Author(s)
      池上貴久
    • Organizer
      ISNMR2011チュートリアル講演
    • Place of Presentation
      横浜大桟橋ホール(招待講演)
    • Year and Date
      2011-11-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] 950MHz-NMRマシンの性能を最大限に引き出すことを目指して2011

    • Author(s)
      池上貴久
    • Organizer
      蛋白研セミナー
    • Place of Presentation
      大阪大学蛋白質研究所
    • Year and Date
      2011-07-28
    • Related Report
      2011 Annual Research Report
  • [Presentation] タンパク質のNMR-13C検出への期待-2011

    • Author(s)
      池上貴久
    • Organizer
      平成23年度日本分光学会NMR講習会
    • Place of Presentation
      東京大学薬学部西講義室(西館一階)
    • Year and Date
      2011-07-20
    • Related Report
      2011 Final Research Report
  • [Presentation] タンパク質のNMR-13C検出への期待-2011

    • Author(s)
      池上貴久
    • Organizer
      日本分光学会NMR講習会
    • Place of Presentation
      東京大学薬学部(招待講演)
    • Year and Date
      2011-07-20
    • Related Report
      2011 Annual Research Report
  • [Presentation] 蛋白質解析におけるNMRのより面白い活用法とは2011

    • Author(s)
      池上貴久
    • Organizer
      日本生物物理学会北海道支部講演会
    • Place of Presentation
      北海道大学理学部
    • Year and Date
      2011-02-24
    • Related Report
      2011 Final Research Report
  • [Presentation] 950MHz-NMRマシンの性能を最大限に引き出すことを目指して2011

    • Author(s)
      池上貴久
    • Organizer
      蛋白研セミナー(先端的NMR拠点から生まれる新たな潮流:最新成果、役割、利用)
    • Place of Presentation
      蛋白質研究所
    • Related Report
      2011 Final Research Report
  • [Presentation] Structural analysis of an SH3 domain that also interacts in the same recognition region with a sequence containing no proline-rich motif.2010

    • Author(s)
      池上貴久
    • Organizer
      Korea-Japan Bilateral Symposium on Protein Structure and Folding
    • Place of Presentation
      ソウル大学薬学部,韓国(招待講演)
    • Year and Date
      2010-11-26
    • Related Report
      2010 Annual Research Report
  • [Presentation] プロダクトオペレータの基礎(10hr)、プロダクトオペレータの発展(6hr)2010

    • Author(s)
      池上貴久
    • Organizer
      先導的若手NMRスペシャリスト育成プログラム(第一回研修会)
    • Place of Presentation
      琵琶湖リゾートクラブ
    • Related Report
      2011 Final Research Report
  • [Presentation] Structural analysis of an SH3 domain that also interacts in the same recognition region with a sequence containing no proline-rich motif2010

    • Author(s)
      池上貴久
    • Organizer
      Korea-Japan Bilateral Symposium on Protein Structure and Folding
    • Place of Presentation
      ソウル大学薬学部
    • Related Report
      2011 Final Research Report
  • [Presentation] 950MHz-NMRの設置の経緯、現状、これからの方針2010

    • Author(s)
      池上貴久
    • Organizer
      蛋白研セミナー「超高磁場が拓く生体系NMR :最新技術と応用」
    • Place of Presentation
      大阪大学蛋白質研究所講堂
    • Related Report
      2011 Final Research Report
  • [Presentation] 蛋白質のNMR2009

    • Author(s)
      池上貴久
    • Organizer
      日本分光学会
    • Place of Presentation
      幕張メッセ国際会議場
    • Year and Date
      2009-09-03
    • Related Report
      2009 Annual Research Report
  • [Book] 分光測定入門シリーズ第8巻 核磁気共鳴分光法 タンパク質のNMR2009

    • Author(s)
      池上貴久
    • Total Pages
      42
    • Publisher
      講談社
    • Related Report
      2009 Annual Research Report

URL: 

Published: 2009-04-01   Modified: 2016-04-21  

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