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

• Project/Area Number: 23659024
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Physical pharmacy
• Research Institution: Hiroshima 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: ¥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.

Research Products

• [Journal Article] Phosphorylation-coupled intramolecular dynamics of unstructured regions in chromatin remodeler FACT (2013)
  • 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
  • Peer Reviewed
• [Journal Article] Preferential domain orientation of HMGB2 determined by the weak intramokecular interactions mediated by the interdomain linker (2013)
  • 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
  • Peer Reviewed
• [Journal Article] Preferential domain orientation of HMGB2 determined by weak intramolecular interactions mediated by the interdomain linker (2013)
  • 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: 212-223
  • DOI: 10.1016/j.chemphys.2013.02.004
  • Peer Reviewed
• [Journal Article] Phosphorylation-coupled intramolecular dynamics of unstructured region in chromatin remodeler FACT (2013)
  • Author(s): Hashimoto,M.
  • Journal Title: Biophys. J. Volume: in press
  • Peer Reviewed
• [Journal Article] Pressure dependence of activity and stability of dihydrofolate reductases 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
  • NAID: 120005308242
  • Peer Reviewed
• [Journal Article] Structural implication for the impaired binding of W150A mutant LOX-1 to oxidized low density lipoprotein, OxLDL (2012)
  • Author(s): Nakano,S., Sugihara,M., Yamada,R., Katayanagi,K., Tate,S
  • Journal Title: Biochim. Biophys. Acta. Volume: 1824 Pages: 739-749
  • NAID: 120005308231
  • 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
  • Peer Reviewed
• [Journal Article] Secondary-structure of alcohol-denatured proteins by vaccum-ultraviolet cicular dichroism spectroscopy (2012)
  • Author(s): Koichi,M., Sakurada,Y., Tate,S.,Namatame,H., Taniguchi,M., Gekko,K
  • Journal Title: PROTEINS Volume: 80 Pages: 281-193
  • Peer Reviewed
• [Journal Article] Structural implication for the impaired binding of W150A mutant LOX-1 to oxidized low density lipoprotein, OxLDL (2012)
  • 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
  • Peer Reviewed
• [Journal Article] Pressure dependence of activity and stability of dihydrofolate reductase of the deep-sea bacterium Moritella profunda and Eschericha 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 Issue: 3 Pages: 511-519
  • DOI: 10.1016/j.bbapap.2012.01.001
  • 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
  • Peer Reviewed
• [Journal Article] Secondary-structure analysis of alcohol-denatured proteins by vacuum-ultraviolet circular dichroism spectroscopy (2012)
  • 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
  • Peer Reviewed
• [Journal Article] The NMR structure of FliK, the trigger for the switch of substrate specificity in the flagellar type III secretion apparatus (2011)
  • Author(s): Mizuno,S., Amida,H., Kobayashi,N.,Aizawa,S., and Tate,S.
  • Journal Title: J.Mol.Biol Volume: 409 Pages: 558-573
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Comparative study on dihydrofolate reductases from Shewanella species living in deep-sea and ambient atmospheric-pressure environments (2011)
  • Author(s): Murakami, C., Ohame, E., Tate, S., Gekko, K., Nakasone, K. and Kato, C
  • Journal Title: Extremophiles Volume: 15 Pages: 165-175
  • 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
  • Peer Reviewed
• [Journal Article] The NMR structure of FliK, the trigger for the switch of substrate specificity in the flagellar type III secretion appratus (2011)
  • 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
  • Peer Reviewed
• [Presentation] Gene regulation in thechromatin context seen from the protein structural dynamics point of view (2013)
  • 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
• [Presentation] Gene regulation in the chromatin context seen from the protein structural dynamics point of view (2013)
  • Author(s): Shin-ichi Tate
  • Organizer: 1st International Symposium of the Mathematics on Chromatin Live Dynamics
  • Place of Presentation: 広島
  • 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
• [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
• [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
• [Presentation] Functionally detuning motion for the hydride transfer step, which is intrinsically active loop dynamics of dihydrofolate reductase (2012)
  • Author(s): Tate,S
  • Organizer: DHFR"Euromer2012
  • Place of Presentation: Dublin, Ireland
  • Year and Date: 2012-07-01
• [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
• [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
• [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
• [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
• [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
• [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
• [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
  • 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
• [Presentation] Functional modulation of protein through the change in its structure dynamics (2012)
  • Author(s): Tate,S.
  • Organizer: 第51回NMR討論会
  • Place of Presentation: 名古屋
• [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
• [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
• [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
• [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
• [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
• [Presentation] Protein structural dynamics modulation induced by a mutation to flexible loop (2011)
  • 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
• [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
• [Presentation] Functional regulation through phosphorylation to acidic intrinsically disordered region in FACT as a chromatin remodeling factor (2011)
  • 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
• [Presentation] Functional regulation through phosphorylation to acidic intrinsically disordered region in FACT as a chromatin remodeling factor (2011)
  • Author(s): S.Tate
  • Organizer: Annual meeting of Protein Science Japan(招待講演)
  • Place of Presentation: 大阪
• [Presentation] Protein structural dynamics modulation induced by a mutation to flexible loop (2011)
  • 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
• [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
• [Presentation] Domain orientation dynamics revealed by alignment induced TROSY shift changes (2011)
  • Author(s): S.Tate, J.Uewaki, N.Utsunomiya-Tate
  • Organizer: ISNMR2011
  • Place of Presentation: 横浜
• [Presentation] Determination of the alignment tensor of protein by orientation induced TROSY shift changes (2011)
  • Author(s): S.Tate
  • Organizer: Gordon Research Conference
  • Place of Presentation: Lucca, Italy
• [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
• [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
• [Presentation] Prepared domain orientation of tandem HMG boxes defined by the inter-domain linker in HMGB2 (2011)
  • 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
• [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
• [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
• [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
  • 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
  • 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
  • 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
  • Invited
• [Book] Current Trends in X-ray crystallography (2011)
  • Author(s): S.Tate, A.Imada, N.Hiroguchi
  • Total Pages: 436
  • Publisher: InTech (chap. 18, pp 409-436)
• [Remarks]
  • URL: http://www.mls.sci.hiroshima-u.ac.jp/biophys/index.html
• [Remarks] TateLab Home
  • URL: http://www.mls.sci.hiroshima-u.ac.jp/biophys/index.html
• [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
• [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