The development of a method for studying aromatic ring flipping motion in the interior of proteins

• Project/Area Number: 23770109
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Structural biochemistry
• Research Institution: Nagoya University
• Principal Investigator: TAKEDA Mitsuhiro 名古屋大学, 理学研究科, 特任助教 (90508558)
• Project Period (FY): 2011 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2012: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2011: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
• Keywords: NMR / SAIL / 構造生物学 / 蛋白質 / ダイナミクス

Research Abstract

Aromatic rings of phenylalanine and tyrosine residues in the interior of proteins infrequently rotates about their Cb-Cg axis in concert with the large amplitude slow breathing motion of protein molecules. An NMR method for evaluating ring-flipping rate based on a Carr-Purcell Meiboom Gill relaxation experiments and SAIL-NMR method is developed. This method enables the quantitative evaluation of the ring-flipping phenomenon on the micro-second time scales.

Research Products

• [Journal Article] Molecular bases of multimodal regulation of a fungal transient receptor potential (TRP) channel (2013)
  • Author(s): 伊原 誠
  • Journal Title: Journal of Biologial Chemistry Volume: in press
  • Peer Reviewed
• [Journal Article] Cell-Free Protein Synthesis Using E. coli Cell Extract for NMR Studies (2012)
  • Author(s): 武田 光広
  • Journal Title: Advances in Experimental Medicine and Biology Volume: 992 Pages: 167-177
  • DOI: 10.1007/978-94-007-4954-2_9
  • ISBN: 9789400749535, 9789400749542
• [Journal Article] Cell-free protein production for NMR studies (2012)
  • Author(s): 武田 光広
  • Journal Title: Methods molecular biology Volume: 831 Pages: 71-84
  • DOI: 10.1007/978-1-61779-480-3_5
  • ISBN: 9781617794797, 9781617794803
• [Journal Article] Conformational analysis by quantitative NOE measurements of the β-proton pairs across individual disulfide bonds in proteins (2012)
  • Author(s): 武田 光広
  • Journal Title: Journal of Biomolecular NMR Volume: 52 Issue: 2 Pages: 127-139
  • DOI: 10.1007/s10858-011-9587-0
  • Peer Reviewed
• [Journal Article] Stereo-array isotope labeling method for studying protein structure and dynamics (2012)
  • Author(s): 宮ノ入 洋平
  • Journal Title: Advances in Experimental Medicine and Biology Volume: 992 Pages: 83-93
  • DOI: 10.1007/978-94-007-4954-2_5
  • ISBN: 9789400749535, 9789400749542
• [Journal Article] Hydrogen Exchange Study on the Hydroxyl Groups of Serine and Threonine Residues in Proteins and Structure Refinement Using NOE Restraints with Polar Side-Chain Groups (2011)
  • Author(s): M.Takeda, J.-G.Jee, A.M.Ono, T.Terauchi, M.Kainosho
  • Journal Title: J.Am.Chem.Soc. Volume: 133 Issue: 43 Pages: 17420-17427
  • DOI: 10.1021/ja206799v
  • Peer Reviewed
• [Journal Article] Alternative SAIL-Trp for robust aromatic signal assignment and determination of the X(2) conformation by intra-residue NOEs (2011)
  • Author(s): Y.Miyanoiri, M.Takeda, J.-G.Jee, A.M.Ono, K.Okuma, T.Terauchi, M.Kainosho
  • Journal Title: J.Biomol.NMR Volume: 51 Issue: 4 Pages: 425-435
  • DOI: 10.1007/s10858-011-9568-3
  • Peer Reviewed
• [Presentation] SAIL-NMR法によるジスルフィド結合の立体配座決定と動態解析 (2012)
  • Author(s): 武田光広、寺内勉、甲斐荘正恒
  • Organizer: 第51回 NMR 討論会
  • Place of Presentation: ウィンク愛知 (愛知県)
• [Presentation] Analysis of Connectivities and Conformations of Disulfide bonds in Proteins by Quantitative NOE Measurements of the beta-Proton Pairs across the Bonds (2012)
  • Author(s): Takeda M, Terauchi T, Kainosho M
  • Organizer: International Conference of Magnetic Resonance in Biological System
  • Place of Presentation: The Lyon Convention Center(Lyon) France
• [Presentation] Analysis of Connectivities and Conformations of Disulfide bonds in Proteins by Quantitative NOE Measurements of the beta-Proton Pairs across the Bonds (2012)
  • Author(s): 武田 光広
  • Organizer: International Conference of Magnetic Resonance in Biological System
  • Place of Presentation: The Lyon Convention centre (リヨン) フランス
• [Presentation] SAIL-NMR法によるジスルフィド結合の立体配座決定と動態解析 (2012)
  • Author(s): 武田 光広
  • Organizer: 第51回NMR討論会
  • Place of Presentation: ウィンクあいち (愛知県）
• [Presentation] Applications of the SAIL method for studying protein structures and dynamics in solution (2012)
  • Author(s): Mitsuhiro Takeda, Yohei Miyanoiri, Masatsune Kainosho
  • Organizer: International Workshop: from Structure to Dynamics: for Our Understanding of Protein-Protein Interactions
  • Place of Presentation: 名古屋
• [Presentation] SAIL-NMR 法により広がるタンパク質の NMR 研究 (2011)
  • Author(s): 武田光広
  • Organizer: 第6回構造生物学に関する先端技術講演会-NMR、AFM、EM 解析のトピックスー生体防御医学研究所共同利用研究集会
  • Place of Presentation: 九州大学(福岡県)
  • Year and Date: 2011-09-02
• [Presentation] Construction and performance of a sample tube with slot-shaped sample cavity fabricated from magnetic susceptibility-matched glass (2011)
  • Author(s): Takeda M, Hallenga K, Shigezane M, Waelchli MR, Markley JL, Kainosho M
  • Organizer: ISNMR
  • Place of Presentation: 大さん橋ホール (神奈川県)
• [Presentation] SAIL-NMR 法によるタンパク質動態構造の研究 (2011)
  • Author(s): 武田光広、甲斐荘正恒
  • Organizer: 第49回生物物理学会
  • Place of Presentation: 兵庫県立大学(兵庫県)
• [Presentation] 隣接炭素科学シフトへの重水素同位体効果を利用したタンパク質側鎖 OH/SH 基の新しい NMR 研究手法 (2011)
  • Author(s): 武田光広、Chun-Jing Yang、JunGoo Jee、小野明、寺内勉、甲斐荘正恒
  • Organizer: 第49回生物物理学会
  • Place of Presentation: 兵庫県立大学(兵庫県)
• [Presentation] Recent progress in a Stereo-Array Isotope Labeling(SAIL) method for NMR structure determination (2011)
  • Author(s): Mitsuhiro Takeda, Akira M Ono, Tsutomu Terauchi, JunGoo Jee, Masatsune Kainosho
  • Organizer: PDB40 symposium
  • Place of Presentation: New York
• [Presentation] Construction and performance of a sample tube with slot-shaped sample cavity fabricated from magnetic susceptibility-matched glass (2011)
  • Author(s): Mitsuhiro Takeda, Klass Hallenga, Masahiro Shigezane, Markus R.Waelchli, John L. Markley and Masatsune Kainosho
  • Organizer: ISNMR
  • Place of Presentation: 横浜
• [Presentation] SAIL-NMR法によるタンパク質動態構造の研究 (2011)
  • Author(s): 武田光広、甲斐荘正恒
  • Organizer: 第49回生物物理学会
  • Place of Presentation: 姫路
• [Presentation] SAIL-NMR法により広がるタンパク質のNMR研究 (2011)
  • Author(s): 武田光広
  • Organizer: 第６回構造生物学に関する先端技術講演会
  • Place of Presentation: 福岡
• [Presentation] 隣接炭素科学シフトへの重水素同位体効果を利用したタンパク質側鎖OH/SH基の新しいNMR研究手法 (2011)
  • Author(s): 武田光広、Chun-Jing Yang、JunGoo Jee、小野明、寺内勉、甲斐荘正恒
  • Organizer: 第49回生物物理学会
  • Place of Presentation: 姫路
• [Remarks]
  • URL: http://str.bio.nagoya-u.ac.jp:8080/Plone/753265908358
• [Remarks] 名古屋大学理学研究科構造生物学研究センター 甲斐荘グループ
  • URL: http://str.bio.nagoya-u.ac.jp:8080/Plone/753265908358