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Development of NMR measurement and analysis method for protein structural study in 2H2O solution.

Research Project

Project/Area Number 22570109
Research Category

Grant-in-Aid for Scientific Research (C)

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

Principal Investigator

OGURA Kenji  北海道大学, 大学院・先端生命科学研究院, 特任准教授 (50270682)

Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2012: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2011: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2010: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
KeywordsNMR / タンパク質 / 立体構造解析
Research Abstract

We developed an NMR pulse sequence, 3D HCA(N)CO, to correlate the chemical shifts of protein backbone 1H and 13C to those of 13C' in the preceding residue. When combined with HCACO, HCAN and HCA(CO)N, the HCA(N)CO sequence allows the sequential assignment using backbone 13C' and amide 15N chemical shifts without resort to backbone amide protons. This assignment strategy was demonstrated for 13C/15N-labeled GB1 dissolved in 2H2O. The quality of the GB1 structure determined in 2H2O was similar to that determined in H2O in spite of significantly smaller number of NOE correlations. Thus this strategy enables the determination of protein structures in 2H2O or H2O at high pH values.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (45 results)

All 2013 2012 2011 2010

All Journal Article (20 results) (of which Peer Reviewed: 19 results) Presentation (25 results) (of which Invited: 2 results)

  • [Journal Article] NMR structure note: a defective isoform and its activity-improved variant of a type III antifreeze protein from Zoarces elongates Kner2013

    • Author(s)
      Kumeta H, Ogura K, Nishimiya Y, Miura A, Inagaki F, Tsuda S.
    • Journal Title

      Journal of Biomolecular NMR 55

      Pages: 225-230

    • NAID

      120005228323

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Practical applications of hydrostatic pressure to refold proteins from inclusion bodies for NMR structural studies.2013

    • Author(s)
      Ogura K., Kobashigawa Y., Saio T., Kumeta H., Torikai S., Inagaki F.
    • Journal Title

      Protein Eng Des Sel.

      Volume: 26(6) Issue: 6 Pages: 409-16

    • DOI

      10.1093/protein/gzt012

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] NMR analyses of the interaction between the EEA1 FYVE domain and phosphoinositide embedded in lipid bilayer2012

    • Author(s)
      Yokogawa M, Kobashigawa Y, Yoshida N, Ogura K, Harada K, Inagaki F
    • Journal Title

      Journal of Biological Chemistry 287

      Pages: 34936-452012

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Conformational dynamics of yeast calmodulin in the Ca(2+)-bound state probed using NMR relaxation dispersion2012

    • Author(s)
      Ogura K, Okamura H, Katahira M, Katoh E, Inagaki F
    • Journal Title

      FEBS Letters 586

      Pages: 2548-2554

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Convenient method for resolving degeneracies due to symmetry of the magnetic susceptibility tensor and its application to pseudo contact shift-based protein-protein complex structure determination2012

    • Author(s)
      Kobashigawa Y, Saio T, Ushio M, Sekiguchi M, Yokochi M, Ogura K, Inagaki F
    • Journal Title

      Journal of Biomolecular NMR 53

      Pages: 53-63

    • NAID

      120005946609

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Solution structures of yeast Saccharomyces cerevisiae calmodulin in calcium-and target peptide-bound states reveal similarities and differences to vertebrate calmodulin2012

    • Author(s)
      Ogura K, Kumeta H, Takahasi K, Kobashigawa Y, Yoshida R, Itoh H, Yazawa M, Inagaki F
    • Journal Title

      Genes to Cells 17

      Pages: 159-172

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] NMR analyses of the interaction between the FYVE domain of early endosome antigen 1 (EEA1) and phosphoinositide embedded in a lipid bilayer2012

    • Author(s)
      Mariko Yokogawa, Yoshihiro Kobashigawa, Naoki Yoshida, Kenji Ogura, Kohsuke Harada and Fuyuhiko Inagaki
    • Journal Title

      Journal of Biological Chemistry

      Volume: 287 Issue: 42 Pages: 34936-34945

    • DOI

      10.1074/jbc.m112.398255

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Conformational dynamics of yeast calmodulin in the Ca(2+)-bound state probed using NMR relaxation dispersion2012

    • Author(s)
      Kenji Ogura, Hideyasu Okamura, Masato Katahira, Etsuko Katoh, and Fuyuhiko Inagaki
    • Journal Title

      FEBS Letters

      Volume: 586 Issue: 16 Pages: 2548-2554

    • DOI

      10.1016/j.febslet.2012.06.031

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Convenient method for resolving degeneracies due to symmetry of the magnetic susceptibility tensor and its application to pseudo contact shift-based protein-protein complex structure determination2012

    • Author(s)
      Yoshihiro Kobashigawa, Tomohide Saio, Masahiro Ushio, Mitsuhiro Sekiguchi, Masashi Yokochi, Kenji Ogura, and Fuyuhiko Inagaki
    • Journal Title

      Journal of Biomolecular NMR

      Volume: 53 Issue: 1 Pages: 53-63

    • DOI

      10.1007/s10858-012-9623-8

    • NAID

      120005946609

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] NMR structure note: a defective isoform and its activity-improved variant of a type III antifreeze protein from Zoarces elongates Kner2012

    • Author(s)
      Hiroyuki Kumeta, Kenji Ogura, Yoshiyuki Nishimiya, Ai Miura, Fuyuhiko Inagaki, and Sakae Tsuda
    • Journal Title

      Journal of Biomolecular NMR

      Volume: 55 Issue: 2 Pages: 225-230

    • DOI

      10.1007/s10858-012-9703-9

    • NAID

      120005228323

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Solution structures of yeast Saccharomyces cerevisiae calmodulin in calcium- and target peptide-bound states reveal similarities and differences to vertebrate calmodulin2012

    • Author(s)
      Ogura, K.
    • Journal Title

      Genes to Cells

      Volume: 17 Issue: 3 Pages: 159-172

    • DOI

      10.1111/j.1365-2443.2012.01580.x

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis of atg8 activation by a homodimeric e1, atg72011

    • Author(s)
      Noda NN, Satoo K, Fujioka Y, Kumeta H, Ogura K, Nakatogawa H, Ohsumi Y, Inagaki
    • Journal Title

      Molecular Cells 44

      Pages: 462-475

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe2011

    • Author(s)
      Saio T, Ogura K, Shimizu K, Yokochi M, Burke TR Jr, Inagaki F.
    • Journal Title

      Journal of Biomolecular NMR 51

      Pages: 395-408

    • NAID

      120003464639

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Phosphoinositide-incorporated lipid-protein Nanodiscs: A tool for studying protein-lipid interactions2011

    • Author(s)
      Kobashigawa Y, Harada K, Yoshida N, Ogura K, Inagaki F.
    • Journal Title

      Analytical Biochemistry 410

      Pages: 77-83

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] An NMR strategy for fragment-based ligand screening utilizing a param agnetic lanthanide probe2011

    • Author(s)
      Saio, T.
    • Journal Title

      Journal of Biomolecular NMR

      Volume: 51 Issue: 3 Pages: 395-408

    • DOI

      10.1007/s10858-011-9566-5

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis of Atg8 activation by a homodimeric E1, Atg72011

    • Author(s)
      Noda N.N., Satoo K., Fujioka Y., Kumeta H., Ogura K., Nakatogawa H., Ohsumi Y., Inagaki F.
    • Journal Title

      Molecular Cell

      Volume: 44 Issue: 3 Pages: 462-475

    • DOI

      10.1016/j.molcel.2011.08.035

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure determination of protein2010

    • Author(s)
      Ogura K, Kumeta H, Inagaki F
    • Journal Title

      Journal of Biomolecular NMR 47

      Pages: 243-248

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] The NMR structure of the autophagy-related protein Atg82010

    • Author(s)
      Kumeta H, Watanabe M, Nakatogawa H, Yamaguchi M, Ogura K, Adachi W, Fujioka Y, Noda NN, Ohsumi Y, Inagaki F
    • Journal Title

      Journal of Biomolecular NMR 47

      Pages: 237-24

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Solution structure of a novel Cdc42-binding module of Bem1 and its interaction with Ste20 and Cdc422010

    • Author(s)
      Takaku T, Ogura K, Kumeta H, Yoshida N, Inagaki F
    • Journal Title

      Journal of Biological Chemistry 285

      Pages: 19346-19353

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure determination of proteins in ^2H_2O solution aided by a deuterium-decoupled 3D HCA(N)CO experiment.2010

    • Author(s)
      Ogura, K, Kumeta, H, Inagaki, F
    • Journal Title

      Journal of Biomolecular NMR

      Volume: Vol.47 Pages: 243-248

    • Related Report
      2010 Annual Research Report
  • [Presentation] 出芽酵母カルモジュリンの立体構造とダイナミクス2013

    • Author(s)
      小椋賢治,岡村英保,久米田博之,矢澤道生,稲垣冬彦
    • Organizer
      2012年度日本生物物理学会北海道支部例会
    • Place of Presentation
      北海道大学(札幌市)
    • Year and Date
      2013-03-05
    • Related Report
      2012 Final Research Report
  • [Presentation] 常磁性NMR法の創薬への応用2013

    • Author(s)
      小椋賢治
    • Organizer
      第19回未来創薬・医療イノベーションセミナー
    • Place of Presentation
      北海道大学(札幌市)
    • Year and Date
      2013-01-16
    • Related Report
      2012 Final Research Report
  • [Presentation] タンパク質NMRの新展開ーダイナミクスと創薬ー2013

    • Author(s)
      小椋賢治
    • Organizer
      高知大学大学院博士課程医学専攻DCセミナー
    • Place of Presentation
      高知大学(高知市)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] NMRによるp47phox PXドメインとホスファチジルイノシトールの相互作用の解析2013

    • Author(s)
      小椋賢治,小橋川敬博,吉田直樹,住本英樹,稲垣冬彦
    • Organizer
      第13回日本蛋白質科学会年会
    • Place of Presentation
      とりぎん文化会館(鳥取市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] NADPHオキシダーゼ細胞質因子p47phoxの柔軟な構造と機能2012

    • Author(s)
      小椋賢治,住本英樹,稲垣冬彦
    • Organizer
      第85回日本生化学会大会
    • Place of Presentation
      福岡国際会議場(福岡市)
    • Year and Date
      2012-12-14
    • Related Report
      2012 Final Research Report
  • [Presentation] Structure and dynamics of yeast calmodulin2012

    • Author(s)
      小椋賢治,岡村英保,久米田博之,矢澤道生,稲垣冬彦
    • Organizer
      第51回NMR討論会
    • Place of Presentation
      ウインクあいち(名古屋市)
    • Year and Date
      2012-11-08
    • Related Report
      2012 Final Research Report
  • [Presentation] Pseudo Contact Shift が生み 出す構造情報とその取り扱い2012

    • Author(s)
      小椋賢治
    • Organizer
      平成24年度日本分光学会 NMR 分光部会集中講義
    • Place of Presentation
      東京大学(東京都)
    • Year and Date
      2012-10-24
    • Related Report
      2012 Final Research Report
  • [Presentation] Structure and dynamics of yeast calmodulin2012

    • Author(s)
      Ogura K, Okamura H, Kumeta H, Yazawa M, Inagaki F
    • Organizer
      The 10th International Symposium for Future Drug Discovery and Medical Care
    • Place of Presentation
      北海道大学(札幌市)
    • Year and Date
      2012-10-02
    • Related Report
      2012 Final Research Report
  • [Presentation] Structure and dynamics of yeast calmodulin2012

    • Author(s)
      Ogura K, Okamura H, Kumeta H, Yazawa M, Inagaki F
    • Organizer
      25th ICMRBS
    • Place of Presentation
      Lyon Convention Centre, (France)
    • Year and Date
      2012-08-19
    • Related Report
      2012 Final Research Report
  • [Presentation] Structure and dynamics of yeast calmodulin2012

    • Author(s)
      小椋賢治,岡村英保,久米田博之,矢澤道生,稲垣冬彦
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場(名古屋市)
    • Year and Date
      2012-06-22
    • Related Report
      2012 Final Research Report
  • [Presentation] NADPHオキシダーゼ細胞質因子p47phoxの柔軟な構造と機能2012

    • Author(s)
      小椋賢治,住本英樹,稲垣冬彦
    • Organizer
      第85回日本生化学会大会
    • Place of Presentation
      福岡国際会議場(福岡市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Pseudo Contact Shiftが生み出す構造情報とその取り扱い2012

    • Author(s)
      小椋賢治
    • Organizer
      平成24年度日本分光学会NMR分光部会集中講義
    • Place of Presentation
      東京大学(東京都)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Structure and dynamics of yeast calmodulin2011

    • Author(s)
      小椋賢治,岡村英保,久米田博之,矢澤道生,稲垣冬彦
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(横浜市)
    • Year and Date
      2011-12-14
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
  • [Presentation] Structure and dynamics of yeast calmodulin2011

    • Author(s)
      Ogura K, Okamura H, Kumeta H, Yazawa M, Inagaki F
    • Organizer
      第50回 NMR 討論会記念国際シンポジウム
    • Place of Presentation
      大さんばしホール(横浜市)
    • Year and Date
      2011-11-15
    • Related Report
      2012 Final Research Report
  • [Presentation] Structure and dynamics of yeast calmodulin2011

    • Author(s)
      Ogura, K.
    • Organizer
      第50回NMR討論会記念国際シンポジウム
    • Place of Presentation
      大さんばしホール(横浜市)
    • Year and Date
      2011-11-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] 高圧リフォールディングによるタンパク質立体構造解析試料の調製法2011

    • Author(s)
      小椋賢治,斎尾智英,小橋川敬博,稲垣冬彦
    • Organizer
      第52回高圧討論会
    • Place of Presentation
      沖縄キリスト教学院大学(沖縄県西原町)
    • Year and Date
      2011-11-09
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
  • [Presentation] Characterizing conformational change in yeast calmodulin using NMR relaxation dispersion and SAXS2011

    • Author(s)
      Ogura K, Okamura H, Kumeta H, Inagaki F
    • Organizer
      第49回日本生物物理学会年会
    • Place of Presentation
      兵庫県立大学(兵庫県姫路市)
    • Year and Date
      2011-09-18
    • Related Report
      2012 Final Research Report
  • [Presentation] Characterizing conformational change in yeast calmodulin using NMR relaxation dispersion and SAXS2011

    • Author(s)
      Ogura, K.
    • Organizer
      第49回日本生物物理学会年会
    • Place of Presentation
      姫路工業大学(兵庫県姫路市)
    • Year and Date
      2011-09-18
    • Related Report
      2011 Annual Research Report
  • [Presentation] プロリンリッチペプチドの構造とダイナミクス2011

    • Author(s)
      小椋賢治,久米田博之,稲垣冬彦
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      ホテル阪急エキスポパーク(大阪府吹田市)
    • Year and Date
      2011-06-08
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
  • [Presentation] 重水溶媒中におけるタンパク質立体構造解析2011

    • Author(s)
      小椋賢治
    • Organizer
      よこはまNMR構造生物学研究会第41回ワークショップ
    • Place of Presentation
      理化学研究所横浜研究所(横浜市)
    • Year and Date
      2011-03-02
    • Related Report
      2012 Final Research Report
  • [Presentation] 重水溶媒中におけるタンパク質立体構造解析2011

    • Author(s)
      小椋賢治
    • Organizer
      よこはまNMR構造生物学研究会第41回ワークショップ
    • Place of Presentation
      理化学研究所横浜研究所(横浜市) 招待講演
    • Year and Date
      2011-03-02
    • Related Report
      2010 Annual Research Report
  • [Presentation] 出芽酵母Bem1およびCdc24のPB1ドメインヘテロダイマーのNMR構造2010

    • Author(s)
      小椋賢治,丹代翼,吉永壮佐,小橋川敬博,久米田博之,伊藤隆司,稲垣冬彦
    • Organizer
      BMB2010
    • Place of Presentation
      神戸国際会議場(神戸市)
    • Year and Date
      2010-12-07
    • Related Report
      2012 Final Research Report
  • [Presentation] Deuterium-decoupled 3D HCA(N)COに支援された重水溶媒中におけるタンパク質の立体構造解析2010

    • Author(s)
      小椋賢治,久米田博之,稲垣冬彦
    • Organizer
      第49回NMR討論会
    • Place of Presentation
      タワーホール船堀(東京都)
    • Year and Date
      2010-11-15
    • Related Report
      2012 Final Research Report 2010 Annual Research Report
  • [Presentation] Structure determination of proteins in 2H2O solution aided by a deuterium-decoupled HCA(N)CO experiment2010

    • Author(s)
      Ogura K, Kumeta H, and Inagaki F
    • Organizer
      24th ICMRBS
    • Place of Presentation
      Cairns Convention Centre, Cairns,Australia
    • Year and Date
      2010-08-22
    • Related Report
      2012 Final Research Report
  • [Presentation] 酵母カルモジュリンの特異な標的認識機構2010

    • Author(s)
      小椋賢治,久米田博之,高橋清大,小橋川敬博,吉田良輔,伊藤浩之,矢澤道生,稲垣冬彦
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター(札幌市)
    • Year and Date
      2010-06-16
    • Related Report
      2012 Final Research Report

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Published: 2010-11-30   Modified: 2019-07-29  

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