NMR自動解析手法の細胞内蛋白質構造決定への最適化

2015 Fiscal Year Annual Research Report

• Project/Area Number: 25440032
• Research Institution: Tokyo Metropolitan University
• Principal Investigator: PETER GUENTERT 首都大学東京, 理工学研究科, 教授 (20392110)
• Co-Investigator(Kenkyū-buntansha): 池谷 鉄兵 首都大学東京, 理工学研究科, 助教 (30457840)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Keywords: NMR 立体構造計算 / CYANA / NOE自動解析 / eNOE / NMR^2 / ベイズ推定 / 蛋白質-リガンド複合体

Outline of Annual Research Achievements

本課題の最終年度は，CYANAプログラムの自動帰属と立体構造計算の改良に成功し，細胞内蛋白質，創薬の開発に重要な蛋白質-リガンド複合体，蛋白質のダイナミクス解析など，複数の試料に応用し，新たな知見を得ることに成功した．
新規に改良を加えたNOE自動解析法と立体構造計算手法の開発は，J. Biomol. NMR 62, 453-471 (2015)に報告している．また，ベイズ推定を立体構造計算に応用した手法を，J. Phys Conf. Ser. 699, 012005 (2016)に報告した．本手法は，NOEクロスピークの自動解析を実行しながら，水を陰に考慮した物理ポテンシャルから得られる事前確率分布を活用し，構造計算を行うことで，従来法より遙かに高精度に構造解析が可能なことを示した．
また，これらのNMR解析法を，これまでの蛋白質や核酸のみから，任意の有機分子にも適用可能な改良を加え，その有効性を検証した（J. Biomol. NMR 63, 21-37 (2015)）．これにより，特に創薬研究に応用されるような蛋白質-リガンドの構造解析に応用が可能となった．複合体の構造解析では，これに加えて，測定とデータ解析を組み合わせた新手法として，薬の候補分子と蛋白質の構造活性を推定可能な, NMR^2法の開発に成功した. 本法は，複合体の結合部位を原子解像度で決定できる高速・堅牢な手法として，今後の創薬開発に大きく貢献できると期待される．
本年度はさらに，NMRデータから正確な距離情報を見積もることのできるeNOE法(J. Struct. Biol. 191, 306-317 (2015); Biophys. J. 110, 113-126 (2016))やシクロフィリン酵素の2状態解析にも成功した(Angew. Chem. 54, 11657-11661 (2015))．

Research Products

• [Journal Article] NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment. (2016)
  • Author(s): Orts, J., Waelti, M. A., Marsh, M., Vera, L., Gossert, A. D., Guentert, P. & Riek, R.
  • Journal Title: J. Am. Chem. Soc. Volume: 138 Pages: 4393-4400
  • DOI: 10.1021/jacs.5b12391.
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] . Protein NMR structure refinement based on Bayesian inference. (2016)
  • Author(s): Ikeya, T., Ikeda, S., Kigawa, T., Ito, Y. & Guentert, P.
  • Journal Title: J. Phys Conf. Ser. Volume: 699 Pages: 012005:1-14
  • DOI: 10.1088/1742-6596/699/1/012005
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Solid-state NMR sequential assignments of the N-terminal domain of HpDnaB helicase. (2016)
  • Author(s): Wiegand, T., Gardiennet, C., Ravotti, F., Bazin, A., Kunert, B., Lacabanne, D., Cadalbert, R., Guentert, P., Terradot, L., Boeckmann, A. & Meier, B. H.
  • Journal Title: Biomol. NMR Assign. Volume: 10 Pages: 13-23
  • DOI: 10.1007/s12104-015-9629-8.
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] The exact NOE as an alternative in ensemble structure determination. (2016)
  • Author(s): Voegeli, B., Olsson, S., Guentert, P. & Riek, R.
  • Journal Title: Biophys. J. Volume: 110 Pages: 113-126
  • DOI: 10.1016/j.bpj.2015.11.031.
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Compiled data set of exact NOE distance limits, residual dipolar couplings and scalar couplings for the protein GB3. (2015)
  • Author(s): Voegeli, B., Olsson, S., Riek, R. & Guentert, P.
  • Journal Title: Data in Brief Volume: 5 Pages: 99-106
  • DOI: 10.1016/j.dib.2015.08.020.
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A structural ensemble of the enzyme cyclophilin reveals an orchestrated mode of action at atomic resolution. (2015)
  • Author(s): Chi, C. N., Voegeli, B., Bibow, S., Strotz, D., Orts, J., Guentert, P. & Riek, R.
  • Journal Title: Angew. Chem. Volume: 54 Pages: 11657-11661
  • DOI: 10.1002/anie.201503698.
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary. (2015)
  • Author(s): Yilmaz Maden, E. & Guentert, P.
  • Journal Title: J. Biomol. NMR Volume: 63 Pages: 21-37
  • DOI: 10.1007/s10858-015-9959-y.
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics. (2015)
  • Author(s): Voegeli, B., Olsson, S., Riek, R. & Guentert, P.
  • Journal Title: J. Struct. Biol. Volume: 191 Pages: 306-317
  • DOI: 10.1016/j.jsb.2015.07.008.
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Combined automated NOE assignment and structure calculation with CYANA. (2015)
  • Author(s): Guentert, P. & Buchner, L.
  • Journal Title: J. Biomol. NMR Volume: 62 Pages: 453-471
  • DOI: 10.1007/s10858-015-9924-9.
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] NMR Exchange Format: a unified and open standard for representation of NMR restraint data. (2015)
  • Author(s): Gutmanas, A., Adams, P. D., Bardiaux, B., Berman, H. M., Case, D. A., Fogh, R. H. Guentert, P., et.al
  • Journal Title: Nat. Struct. Mol. Biol. Volume: 22 Pages: 433-434
  • DOI: 10.1038/nsmb.3041.
  • Peer Reviewed / Int'l Joint Research
• [Presentation] Automated assignment of NMR spectra with FLYA (2016)
  • Author(s): Guentert, P.
  • Organizer: ライデン大学セミナー
  • Place of Presentation: オランダ ライデン
  • Year and Date: 2016-03-30 – 2016-03-31
  • Invited
• [Presentation] NMR structure analysis with CYANA (2016)
  • Author(s): Guentert, P.
  • Organizer: 2nd G-NMR School
  • Place of Presentation: ドイツ フランクフルト
  • Year and Date: 2016-02-29 – 2016-03-04
  • Invited
• [Presentation] Molecular multibody dynamics (2016)
  • Author(s): Guentert, P.
  • Organizer: 京都大学セミナー
  • Place of Presentation: 京都
  • Year and Date: 2016-02-15 – 2016-02-15
  • Invited
• [Presentation] CYANA: A tool for structure calculation (2016)
  • Author(s): Guentert, P.
  • Organizer: NMR Meets Biology
  • Place of Presentation: インド ケララ
  • Year and Date: 2016-02-14 – 2016-02-19
  • Invited
• [Presentation] Computation methods to study biomolecular systems (2016)
  • Author(s): Guentert, P.
  • Organizer: 京都大学セミナー
  • Place of Presentation: 京都
  • Year and Date: 2016-02-09 – 2016-02-09
  • Invited
• [Presentation] Insight into protein structure and dynamics from solution- and solid-state NMR (2015)
  • Author(s): Guentert, P.
  • Organizer: WPI-NEXT Workshop on High Resolution Cell Biology
  • Place of Presentation: 名古屋
  • Year and Date: 2015-10-01 – 2015-10-01
  • Invited
• [Presentation] Automated NMR resonance assignment and structure calculation (2015)
  • Author(s): Guentert, P.
  • Organizer: 名古屋大学セミナー
  • Place of Presentation: 名古屋
  • Year and Date: 2015-09-30 – 2015-09-30
  • Invited
• [Presentation] Consensus structure bundles and the information content of NMR restraints (2015)
  • Author(s): Guentert, P.
  • Organizer: 第16回若手NMR研究会
  • Place of Presentation: 神奈川
  • Year and Date: 2015-09-27 – 2015-09-29
  • Invited
• [Presentation] NMR structure calculation (2015)
  • Author(s): Guentert, P.
  • Organizer: EMBO Practical Course on Structure Determination of Biological Macromolecules by Solution NMR
  • Place of Presentation: ドイツ
  • Year and Date: 2015-07-31 – 2015-08-07
  • Invited
• [Presentation] Advances in automated assignment and structure determination of difficult proteins (2015)
  • Author(s): Guentert, P.
  • Organizer: Paulo Foundation Symposium
  • Place of Presentation: フィンランド ヘルシンキ
  • Year and Date: 2015-06-09 – 2015-06-09
  • Invited
• [Presentation] Advances in automated assignment and structure determination of difficult proteins (2015)
  • Author(s): Guentert, P.
  • Organizer: Symposium on in-cell NMR studies
  • Place of Presentation: 東京 秋葉原
  • Year and Date: 2015-04-24 – 2015-04-24
  • Invited