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Structure analysis of high-molecular weight intrinsically disordered proteins using 13C detection NMR approach

Research Project

Project/Area Number 23659024
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Physical pharmacy
Research InstitutionHiroshima University

Principal Investigator

TATE Shinichi  広島大学, 大学院・理学研究科, 教授 (20216998)

Project Period (FY) 2011 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2011: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords構造生物学 / 過渡的構造形成 / 13C検知 / 安定同位体 / NMR / 天然変性タンパク質 / 蛋白質 / 生体高分子 / 生物物理
Research Abstract

We analyzed one of the general transcription factors in yeast cell, Tfa2, with the 13C and 1H detection NMR methods. In this work, we particularly focused on the intrinsically disordered part in Tfa2, which binds to Gal11 subunit in the Mediator complex. The severe signal overlaps typically found for the ID segment were solved using the 13C and 15N evolution axes, whose chemical shifts have significant dispersions over the other nuclear spins in protein.We found the Mediator binding domain of Tfa2, Tfa2-mbd, transiently forms three-helix structure. The transient structure formation was mediated by its homo-dimer formation. We also found that the transiently folded structure has binding ability to Gal11; the mutant that lacks the transient folding ability does not bind to Gal11. Over all, the present research has demonstrated the unique structural and functional properties associated with the ID part in Tfa2.

Report

(3 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Research-status Report
  • Research Products

    (60 results)

All 2013 2012 2011 Other

All Journal Article (18 results) (of which Peer Reviewed: 18 results) Presentation (37 results) (of which Invited: 6 results) Book (1 results) Remarks (2 results) Patent(Industrial Property Rights) (2 results)

  • [Journal Article] Phosphorylation-coupled intramolecular dynamics of unstructured regions in chromatin remodeler FACT2013

    • Author(s)
      Hashimoto,M., Kodera,N., Tsunaka,Y., Oda,M., Tanimoto,M., Ando,T., Morikawa,K., and Tate,S.
    • Journal Title

      Biophys. J

      Volume: 104 Pages: 2222-2234

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Preferential domain orientation of HMGB2 determined by the weak intramokecular interactions mediated by the interdomain linker2013

    • Author(s)
      Uewaki,J., Kamikubo,H., Kurita,J., Hiroguchi,N., Moriuchi,H., Yoshida,M., Kataoka,M., Utsunomiya-Tate,N., and Tate,S
    • Journal Title

      Chem.Phys

      Volume: 419 Pages: 212-223

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Preferential domain orientation of HMGB2 determined by the weak intramolecular interactions mediated by the interdomain linker2013

    • Author(s)
      J. Uewaki, H. Kamikubo, J. Kurita, N. Hiroguchi, H. Moriuchi, M. Yoshida, M. Kataoka, N. U.-Tate, S. Tate
    • Journal Title

      Chem.Phys

      Volume: 419 Pages: 212

    • DOI

      10.1016/j.chemphys.2013.02.004

    • URL

      https://pure.teikyo.jp/en/publications/d5a2b53c-f986-4ac3-b994-d5a09681cf5f

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Phosphorylation-coupled intramolecular dynamics of unstructured region in chromatin remodeler FACT2013

    • Author(s)
      Hashimoto,M.
    • Journal Title

      Biophys. J.

      Volume: in press

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Pressure dependence of activity and stability of dihydrofolate reductases of the deep-sea bacterium Moritella profunda and Escherichia coli2012

    • Author(s)
      Ohmae, E., Murakami, C., Tate, S., Gekko, K., Hata, K., Akasaka, K. and Kato,C.
    • Journal Title

      Biochim. Biophys. Acta

      Volume: 1824 Pages: 511-519

    • NAID

      120005308242

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural implication for the impaired binding of W150A mutant LOX-1 to oxidized low density lipoprotein, OxLDL2012

    • Author(s)
      Nakano,S., Sugihara,M., Yamada,R., Katayanagi,K., Tate,S
    • Journal Title

      Biochim. Biophys. Acta.

      Volume: 1824 Pages: 739-749

    • NAID

      120005308231

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Pressure dependence of activity and stability of dihydrofoalte reductase of the deep-sea bacterium Moritella profunda and Escherichia coli.2012

    • Author(s)
      Ohmae,E., Murakami,C., Tate,S.,Gekko,K., Hata,K., Akasaka,K., and Kato,C
    • Journal Title

      Biochim. Biophys. Acta

      Volume: 1824 Pages: 511-519

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Secondary-structure of alcohol-denatured proteins by vaccum-ultraviolet cicular dichroism spectroscopy2012

    • Author(s)
      Koichi,M., Sakurada,Y., Tate,S.,Namatame,H., Taniguchi,M., Gekko,K
    • Journal Title

      PROTEINS

      Volume: 80 Pages: 281-193

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural implication for the impaired binding of W150A mutant LOX-1 to oxidized low density lipoprotein, OxLDL2012

    • Author(s)
      S.Nakano, M.Sugiliara, R.Yamada, K.Katayanagi, S.Tate
    • Journal Title

      Biochim.et Biophys.Acta.

      Volume: (In press) Issue: 5 Pages: 739-749

    • DOI

      10.1016/j.bbapap.2012.02.003

    • NAID

      120005308231

    • Related Report
      2012 Annual Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Pressure dependence of activity and stability of dihydrofolate reductase of the deep-sea bacterium Moritella profunda and Eschericha coli2012

    • Author(s)
      E.Ohmae, C.Murakami, S.Tate, K.Gekko, K.Hata, K.Akasaka, C.Kato
    • Journal Title

      Biochim.et Biophys.Acta.

      Volume: 1824 Issue: 3 Pages: 511-519

    • DOI

      10.1016/j.bbapap.2012.01.001

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Pressure dependence of activity and stability of dihydrofolate reductase of the deep-sea bacterium Moritella profunda and Escherichia coli.2012

    • Author(s)
      E.Ohmae, C.Murakami, S.Tate, K.Gekko, K.Hata, K.Akasaka, C.Kato
    • Journal Title

      Biochim. et Biophys. Acta.

      Volume: 1824 Pages: 511-519

    • NAID

      120005308242

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Secondary-structure analysis of alcohol-denatured proteins by vacuum-ultraviolet circular dichroism spectroscopy2012

    • Author(s)
      M.Koichi, Y.Sakurada, S.Tate, H.Namatame, M.Taniguchi, K.Gekko
    • Journal Title

      PROTEINS

      Volume: 80 Issue: 1 Pages: 281-293

    • DOI

      10.1002/prot.23206

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] The NMR structure of FliK, the trigger for the switch of substrate specificity in the flagellar type III secretion apparatus2011

    • Author(s)
      Mizuno,S., Amida,H., Kobayashi,N.,Aizawa,S., and Tate,S.
    • Journal Title

      J.Mol.Biol

      Volume: 409 Pages: 558-573

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] "Complementary use of NMR to X-ray crystallography for the analysis of protein morphological change in solution" in ,Current trends in X-ray crystallography (ed. Chandrasekaran, A.)2011

    • Author(s)
      Tate,S. Imada,A., and Hiroguchi,N.
    • Journal Title

      InTech, Cloatia

      Volume: 18 Pages: 409-436

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Surface plasmon resonance study on functional significance of clustered organization of lectin-like oxidized LDL (LOX-1)2011

    • Author(s)
      Ohki, I., Amida, H., Yamada, R., Sugihara, M., Ishigaki, T. and Tate, S.
    • Journal Title

      Biochimica. Biophysica Acta

      Volume: 1814 Pages: 345-354

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Comparative study on dihydrofolate reductases from Shewanella species living in deep-sea and ambient atmospheric-pressure environments2011

    • Author(s)
      Murakami, C., Ohame, E., Tate, S., Gekko, K., Nakasone, K. and Kato, C
    • Journal Title

      Extremophiles

      Volume: 15 Pages: 165-175

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] NMRで観測する超高分子量タンパク質の分子形態2011

    • Author(s)
      楯 真一
    • Journal Title

      生物物理

      Volume: 51 Pages: 84-87

    • NAID

      10028105827

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] The NMR structure of FliK, the trigger for the switch of substrate specificity in the flagellar type III secretion appratus2011

    • Author(s)
      S.Mizuno, H.Amida, N.Kobayashi, S.Aizawa, S.Tate
    • Journal Title

      J.Mol.Biol.

      Volume: 409 Issue: 4 Pages: 558-573

    • DOI

      10.1016/j.jmb.2011.04.008

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Presentation] Gene regulation in thechromatin context seen from the protein structural dynamics point of view2013

    • Author(s)
      Tate,S.
    • Organizer
      1stInt. symposium of the Mathematics on chromatin live dynamics
    • Place of Presentation
      広島
    • Year and Date
      2013-03-15
    • Related Report
      2012 Final Research Report
  • [Presentation] Gene regulation in the chromatin context seen from the protein structural dynamics point of view2013

    • Author(s)
      Shin-ichi Tate
    • Organizer
      1st International Symposium of the Mathematics on Chromatin Live Dynamics
    • Place of Presentation
      広島
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 核内受容体タンパク質 PPARgの基質依存的構造変化とコアクティベーター認識機構2012

    • Author(s)
      楯 真一
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      福岡
    • Year and Date
      2012-12-12
    • Related Report
      2012 Final Research Report
  • [Presentation] NMR によるタンパク質構造揺動の検出-タンパク質分子の動的構造と機能の相関解明に向けて2012

    • Author(s)
      楯 真一
    • Organizer
      日本生化学会西日本大会
    • Place of Presentation
      佐賀
    • Year and Date
      2012-11-11
    • Related Report
      2012 Final Research Report
  • [Presentation] 「タンパク質構造の揺らぎと機能の相関」広島大学・数理分子生命理学専攻2012

    • Author(s)
      楯 真一
    • Organizer
      第4回公開シンポジウム
    • Place of Presentation
      広島
    • Year and Date
      2012-09-06
    • Related Report
      2012 Final Research Report
  • [Presentation] Functionally detuning motion for the hydride transfer step, which is intrinsically active loop dynamics of dihydrofolate reductase2012

    • Author(s)
      Tate,S
    • Organizer
      DHFR"Euromer2012
    • Place of Presentation
      Dublin, Ireland
    • Year and Date
      2012-07-01
    • Related Report
      2012 Final Research Report
  • [Presentation] タンパク質構造の揺らぎによる機能制御-NMR により明らかになった msec 時間域の構造揺らぎの役割2012

    • Author(s)
      楯 真一
    • Organizer
      スーパーコンピューター京と生命科学
    • Place of Presentation
      岡山
    • Year and Date
      2012-06-01
    • Related Report
      2012 Final Research Report
  • [Presentation] TAL effector の結晶構造から明らかになった DNA 認識機構2012

    • Author(s)
      楯 真一
    • Organizer
      第1回ゲノム編集研究会
    • Place of Presentation
      広島
    • Year and Date
      2012-02-28
    • Related Report
      2012 Final Research Report
  • [Presentation] NMR 用いた新しい膜タンパク質構造研究のアプローチ2012

    • Author(s)
      楯 真一
    • Organizer
      高次系分子化学ミニシンポジウム
    • Place of Presentation
      大阪
    • Year and Date
      2012-01-24
    • Related Report
      2012 Final Research Report
  • [Presentation] アミノ酸変異によるタンパク質構造揺らぎの変化と機能変調の相関2012

    • Author(s)
      楯 真一
    • Organizer
      日本生物物理学会第4回中国四国支部大会
    • Place of Presentation
      山口
    • Related Report
      2012 Annual Research Report
  • [Presentation] 動的平行を利用したタンパク質のDNA認識過程のNMR解析2012

    • Author(s)
      竹内 彩
    • Organizer
      日本生物物理学会第4回中国四国支部大会
    • Place of Presentation
      山口
    • Related Report
      2012 Annual Research Report
  • [Presentation] ジヒドロ葉酸還元酵素42位変異体の酵素機能に対する塩の効果2012

    • Author(s)
      宮下由里奈
    • Organizer
      日本生物物理学会第4回中国四国支部大会
    • Place of Presentation
      山口
    • Related Report
      2012 Annual Research Report
  • [Presentation] タンパク質構造の「揺らぎ」と「機能」の相関2012

    • Author(s)
      楯 真一
    • Organizer
      広島大学・数理分子生命理学専攻 第4回公開シンポジウム
    • Place of Presentation
      広島
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 天然変性領域の多重リン酸化を利用したFACTの動的機能調節2012

    • Author(s)
      橋本愛美
    • Organizer
      第12回 日本タンパク質化学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] Functional modulation of protein through the change in its structure dynamics2012

    • Author(s)
      Tate,S.
    • Organizer
      第51回NMR討論会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] タンパク質リンカー変異を用いた残基特異的化学シフト異方性テンソル決定技術2012

    • Author(s)
      玉利 裕
    • Organizer
      第51回NMR討論会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] SRC1によるPPARgのアゴニスト依存的な構造変化の認識2012

    • Author(s)
      橋本愛美
    • Organizer
      第85回日本生化学会大会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] 酵母の転写因子TFIIEβのC末端における立体構造解析2012

    • Author(s)
      野坂佳加
    • Organizer
      第85回日本生化学会大会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] TAL effectorの結晶構造から明らかになったDNA認識機構2012

    • Author(s)
      楯 真一
    • Organizer
      第1回 ゲノム編集研究会(招待講演)
    • Place of Presentation
      広島
    • Related Report
      2011 Research-status Report
  • [Presentation] NMRを用いた新しいタンパク質構造研究のアプローチ2012

    • Author(s)
      楯 真一
    • Organizer
      特定領域研究・高次系分子科学 ミニシンポジウム(招待講演)
    • Place of Presentation
      大阪
    • Related Report
      2011 Research-status Report
  • [Presentation] Protein structural dynamics modulation induced by a mutation to flexible loop2011

    • Author(s)
      Tate,S
    • Organizer
      日本生物物理学会第49回年会
    • Place of Presentation
      兵庫
    • Year and Date
      2011-11-16
    • Related Report
      2012 Final Research Report
  • [Presentation] タンパク質の内部運動性と機能制御2011

    • Author(s)
      楯 真一
    • Organizer
      理論と実験研究会 2011
    • Place of Presentation
      広島
    • Year and Date
      2011-10-07
    • Related Report
      2012 Final Research Report
  • [Presentation] Functional regulation through phosphorylation to acidic intrinsically disordered region in FACT as a chromatin remodeling factor2011

    • Author(s)
      Tate,S
    • Organizer
      Ann. Meeting of Protein Science Japan, cosponsored Asia Pacific Protein Association
    • Place of Presentation
      大阪
    • Year and Date
      2011-06-07
    • Related Report
      2012 Final Research Report
  • [Presentation] Functional regulation through phosphorylation to acidic intrinsically disordered region in FACT as a chromatin remodeling factor2011

    • Author(s)
      S.Tate
    • Organizer
      Annual meeting of Protein Science Japan(招待講演)
    • Place of Presentation
      大阪
    • Related Report
      2011 Research-status Report
  • [Presentation] Protein structural dynamics modulation induced by a mutation to flexible loop2011

    • Author(s)
      S.Tate
    • Organizer
      日本生物物理学会第49回年会(招待講演)
    • Place of Presentation
      兵庫
    • Related Report
      2011 Research-status Report
  • [Presentation] 蛋白質の内部運動性と機能制御2011

    • Author(s)
      楯 真一
    • Organizer
      「理論と実験」研究会2011(招待講演)
    • Place of Presentation
      広島
    • Related Report
      2011 Research-status Report
  • [Presentation] Domain orientation dynamics revealed by alignment induced TROSY shift changes2011

    • Author(s)
      S.Tate, J.Uewaki, N.Utsunomiya-Tate
    • Organizer
      ISNMR2011
    • Place of Presentation
      横浜
    • Related Report
      2011 Research-status Report
  • [Presentation] Determination of the alignment tensor of protein by orientation induced TROSY shift changes2011

    • Author(s)
      S.Tate
    • Organizer
      Gordon Research Conference
    • Place of Presentation
      Lucca, Italy
    • Related Report
      2011 Research-status Report
  • [Presentation] 酸化LDL受容体タンパク質LOX-1の基質認識機構の解明2011

    • Author(s)
      杉原守,山田梨紗都,編田宏一,楯 真一
    • Organizer
      日本生物物理学会 第3回中国四国支部大会
    • Place of Presentation
      広島
    • Related Report
      2011 Research-status Report
  • [Presentation] クロマチンリモデリングタンパク質のリン酸化による機能制御機構の解明2011

    • Author(s)
      橋本愛美,松井理恵子,上脇隼一,津中康央,森川耿右,楯 真一
    • Organizer
      第52回 日本生化学会 中国四国支部例会
    • Place of Presentation
      広島
    • Related Report
      2011 Research-status Report
  • [Presentation] Prepared domain orientation of tandem HMG boxes defined by the inter-domain linker in HMGB22011

    • Author(s)
      J.Uewaki, J.Kurita, N-U.Tate, S.Tate
    • Organizer
      日本生物物理学会第49回年会
    • Place of Presentation
      兵庫
    • Related Report
      2011 Research-status Report
  • [Presentation] CH-p相互作用が規定するタンパク質の動的平衡2011

    • Author(s)
      上脇隼一,楯 直子,楯 真一
    • Organizer
      2011年 日本化学会西日本大会
    • Place of Presentation
      徳島
    • Related Report
      2011 Research-status Report
  • [Presentation] DNA結合により誘導されるタンパク質のドメイン配向変化の定量的観測2011

    • Author(s)
      竹内 彩,上脇隼一,楯 真一
    • Organizer
      2011年 日本化学会西日本大会
    • Place of Presentation
      徳島
    • Related Report
      2011 Research-status Report
  • [Presentation] タンパク質構造の揺らぎによる機能制御機構-NMRより明らかになったmsec時間域の構造揺らぎの役割

    • Author(s)
      楯 真一
    • Organizer
      スーパーコンピューター「京」と生命科学
    • Place of Presentation
      岡山
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Functionally detuning motion for the hydride transfer step, which is intrinsically encoded in the active loop dynamics of dihydrofolate reductase, DHFR

    • Author(s)
      Tate,S.
    • Organizer
      Euromar 2012
    • Place of Presentation
      Dublin,Ireland
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] NMRによるタンパク質構造揺動の検出-タンパク質分子の動的構造と機能の相関解明に向けて

    • Author(s)
      楯 真一
    • Organizer
      日本化学会西日本大会
    • Place of Presentation
      佐賀
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 核内受容体タンパク質PPARgの基質依存的構造変化とコアクティベーター認識機構

    • Author(s)
      楯 真一
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Book] Current Trends in X-ray crystallography2011

    • Author(s)
      S.Tate, A.Imada, N.Hiroguchi
    • Total Pages
      436
    • Publisher
      InTech (chap. 18, pp 409-436)
    • Related Report
      2011 Research-status Report
  • [Remarks]

    • URL

      http://www.mls.sci.hiroshima-u.ac.jp/biophys/index.html

    • Related Report
      2012 Final Research Report
  • [Remarks] TateLab Home

    • URL

      http://www.mls.sci.hiroshima-u.ac.jp/biophys/index.html

    • Related Report
      2012 Annual Research Report
  • [Patent(Industrial Property Rights)] 酸化 LDL 受容体に作用するリポソーム2012

    • Inventor(s)
      町田幸子,倉持みゆき,楯 真一,山田梨紗都
    • Industrial Property Rights Holder
      町田幸子,倉持みゆき,楯 真一,山田梨紗都
    • Industrial Property Number
      2012-072404
    • Filing Date
      2012-03-27
    • Related Report
      2012 Final Research Report
  • [Patent(Industrial Property Rights)] 酸化LDL受容体に作用するリポソーム2012

    • Inventor(s)
      町田幸子,倉持みゆき,楯真一,山田梨紗都
    • Industrial Property Rights Holder
      町田幸子,倉持みゆき,楯真一,山田梨紗都
    • Industrial Property Number
      2012-072404
    • Filing Date
      2012
    • Related Report
      2011 Research-status Report

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Published: 2011-08-05   Modified: 2019-07-29  

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