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

2012 Fiscal Year Final Research Report

• 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
• Keywords: 構造生物学

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] 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
  • 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
  • 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] 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
  • 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] 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] 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
• [Remarks]
  • 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: 特願2012-72404
  • Filing Date: 2012-03-27