Development of siginal processing and proten structure determination methods for low qulaity NMR data

• Project/Area Number: 18K06160
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 43040:Biophysics-related
• Research Institution: Tokyo Metropolitan University
• Principal Investigator: IKEYA Teppei 東京都立大学, 理学研究科, 助教 (30457840)
• Project Period (FY): 2018-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2018: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: NMR / 蛋白質 / 立体構造計算 / 立体構造決定 / 常磁性効果 / 溶液NMR / 蛋白質立体構造 / 信号処理 / ベイズ推定 / 蛋白質立体構造決定 / スパースモデリング

Outline of Final Research Achievements

We achieved the first de novo protein structure determinations in eukaryotes with the sf9 cell that are based exclusively on NMR data from living cells. As model systems, we applied this method to three proteins and determined well-converged 3D structures. A new method for structure determination with Bayesian inference was particularly effective for determining 3D structures with sufficient precision to detect conformational differences between the structures in sf9 cells and in diluted solution. We also developed another new NMR protein structure determination method for the inference of multi-state conformations using multiple types of NMR data. Applying the method to the protein YUH1, we find large dynamics of two loops surrounding the active site for ubiquitin-recognition and proteolysis. Our results, including those from biochemical analysis, showed that large motion surrounding the active site contributes strongly to the efficiency of the enzymatic activity.

Academic Significance and Societal Importance of the Research Achievements

創薬研究分野では，蛋白質立体構造情報を利用した構造基盤薬物設計(Structural Based-Drug Discovery; SBDD)が，効率的な薬剤設計法として確立している．本課題のアンサンブル構造解析が確立できれば，生体分子の揺らぎを含めた形で，蛋白質ー低分子化合物，蛋白質間相互作用等を解析可能となり，こうした情報の蓄積によりSBDD研究にも全く新しい知見を提供できる．また,ここで開発した統計解析のソフトウェアの世界への普及、全世界の生体系NMRのグループが本技術を共有できるよう世界に還元していく．

Research Products

• [Int'l Joint Research] スイス連邦工科大学(スイス)
• [Int'l Joint Research] レスター大学(英国)
• [Int'l Joint Research] フランクフルトゲーテ大学(ドイツ)
• [Int'l Joint Research] スイス連邦工科大学(スイス)
• [Int'l Joint Research] レスター大学(英国)
• [Int'l Joint Research] フランクフルトゲーテ大学(ドイツ)
• [Int'l Joint Research] スイス連邦工科大学(スイス)
• [Int'l Joint Research] レスター大学(英国)
• [Journal Article] Multi-state structure determination and dynamics analysis reveals a new ubiquitin-recognition mechanism in yeast ubiquitin C-terminal hydrolase (2021)
  • Author(s): Okada, M., Tateishia, Y., Nojiri, E., Mikawa, T., Rajesh, S., Ogasa, H., Ueda, T., Yagi, H., Kohno, T., Kigawa, T., Shimada, I., Guentert, P., Ito, Y., & Ikeya, T.
  • Journal Title: biorxiv Volume: 2021.04.22.440356 Pages: 1-39
  • DOI: 10.1101/2021.04.22.440356
  • Open Access / Int'l Joint Research
• [Journal Article] Paramagnetic relaxation enhancement-assisted structural determination of a partially disordered conformation of ubiquitin (2019)
  • Author(s): Takuro Wakamoto, Teppei Ikeya, Soichiro Kitazawa, Nicola J. Baxter, Mike P. Williamson, Ryo Kitahara
  • Journal Title: Protein Science Volume: 28 Issue: 11 Pages: 1993-2003
  • DOI: 10.1002/pro.3734
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Protein Structure Determination in Living Cells. (2019)
  • Author(s): Teppei Ikeya, Peter Guentert, Yutaka Ito
  • Journal Title: international journal of molecular sciences Volume: 20 Issue: 10 Pages: 2442-2442
  • DOI: 10.3390/ijms20102442
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] NMRによる生体高分子立体構造計算の基礎と最近の進展 (2019)
  • Author(s): 池谷鉄兵
  • Journal Title: 日本核磁気共鳴学会学会誌 Volume: 10 Pages: 82-96
  • Peer Reviewed / Open Access
• [Journal Article] High resolution protein 3D structure determination in living eukaryotic cells (2019)
  • Author(s): Tanaka, T., Ikeya, T., Kamoshida, H., Suemoto, Y., Mishima, M., Shirakawa, M., Guentert, P., Ito, Y.
  • Journal Title: Angewandte Chemie International Edition Volume: in press Issue: 22 Pages: 1-7
  • DOI: 10.1002/anie.201900840
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Solution NMR views of dynamical ordering of biomacromolecules (2018)
  • Author(s): Ikeya Teppei、Ban David、Lee Donghan、Ito Yutaka、Kato Koichi、Griesinger Christian
  • Journal Title: Biochim. Biophys. Acta-General Subjects Volume: 1862 Issue: 2 Pages: 287-306
  • DOI: 10.1016/j.bbagen.2017.08.020
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Protein NMR Structure Refinement Based on Bayesian Inference for Dynamical Ordering of Biomacromolecules (2018)
  • Author(s): Teppei Ikeya and Yutaka Ito
  • Journal Title: Journal of Computer Chemistry, Japan Volume: 17 Issue: 1 Pages: 65-75
  • DOI: 10.2477/jccj.2018-0009
  • NAID: 130006555815
  • ISSN: 1347-1767, 1347-3824
  • Peer Reviewed / Open Access
• [Presentation] 複数の異なるNMR データの統合解析によるタンパク質multi-state 立体構造解析 (2020)
  • Author(s): 池谷鉄兵 & 伊藤隆
  • Organizer: 第58回日本生物物理学会
  • Invited
• [Presentation] アコヤガイ靭帯の石灰化に関わる有機物の機能・構造解析 (2020)
  • Author(s): 森岡太一，岩橋晴香，池谷鉄兵，伊藤隆，片山秀和，降旗一夫，永田宏次 & 鈴木道生
  • Organizer: 第15回バイオミネラリゼーションワークショップ
• [Presentation] NMRを用いたアダプター蛋白質Drkの動態解析 (2020)
  • Author(s): 渡邉吏輝，プバティ マキシン サイーシュ，末元雄介，木川隆則，三島正規，猪股晃介，池谷鉄兵 & 伊藤隆
  • Organizer: 第59回NMR討論会
• [Presentation] PRE, PCSを用いたマルチドメイン蛋白質Grb2の立体構造解析 (2020)
  • Author(s): 田端真彩子，池谷鉄兵，美川務，川端庸平，安藤考史，館野桂太，三島正規 & 伊藤隆
  • Organizer: 第59回NMR討論会
• [Presentation] Solution NMR approaches to investigating protein behaviours under intracellular crowding environments (2020)
  • Author(s): Yutaka Ito & Teppei Ikeya
  • Organizer: The International Chemical Congress of Pacific Basin Societies 2020
  • Invited
• [Presentation] 生細胞内のタンパク質立体構造解析 (2020)
  • Author(s): 池谷鉄兵，田中孝，立石泰，岡田真由，Peter Guentert，伊藤隆
  • Organizer: 日本化学会第100春季年会
  • Int'l Joint Research
• [Presentation] Solution NMR approaches to 3D structure determination of proteins in living eukaryotic cells (2019)
  • Author(s): Yutaka Ito, Teppei Ikeya
  • Organizer: 33rd Annual Symposium of the Protein Society
  • Int'l Joint Research
• [Presentation] High resolution protein 3D structure determination in living eukaryotic cells (2019)
  • Author(s): Teppei Ikeya, Yutaka Ito
  • Organizer: the 8th Asia Pacific NMR Symposium, Singapore
  • Int'l Joint Research / Invited
• [Presentation] MDシミュレーション vs NMR立体構造計算(multi-state 立体構造計算) (2019)
  • Author(s): 池谷鉄兵
  • Organizer: 第20回若手NMR研究会
  • Invited
• [Presentation] 溶液NMRを用いたin situ構造生物学 (2019)
  • Author(s): 伊藤隆，池谷鉄兵
  • Organizer: 第13回バイオ関連化学シンポジウム2019
• [Presentation] Dynamics and interdomain interactions in a Drosophila adapter protein (Drk) and theircorrelation to the unfolding of the N-SH3 domain (2019)
  • Author(s): Hisham Dokainish, Yusuke Suemoto, Teppei Ikeya, Takuma Kasai, Takanori Kigawa, Yutaka Ito, Yuji Sugita
  • Organizer: 第57回日本生物物理学会年会
• [Presentation] 磁性効果による遠距離構造情報を利用したタンパク質multi-state立体構造解析 (2019)
  • Author(s): 池谷鉄兵
  • Organizer: 第58回NMR討論会
  • Int'l Joint Research
• [Presentation] 分子クラウディング環境下の蛋白質の緩和解析 (2019)
  • Author(s): 田岸亮馬, 田中孝, 三島正規, 池谷鉄兵, 伊藤隆
  • Organizer: 第58回NMR討論会
• [Presentation] PRE,PCSを用いた蛋白質立体構造解析のための常磁性金属タグの性能評価 (2019)
  • Author(s): 田端真彩子, 池谷鉄兵, 彦根佑哉, 岡田真由, 田岸亮馬, 八木宏昌, 木川隆則, 三島正規, 伊藤隆
  • Organizer: 第58回NMR討論会
• [Presentation] 分子混雑環境下のRas蛋白質の動態解析 (2019)
  • Author(s): 亀井駿, 池谷鉄兵, 田仲加代子, 伊藤隆
  • Organizer: 第58回NMR討論会
• [Presentation] 常磁性NMRを用いたYeast Ubiquitin hydrolase 1 (YUH1) の構造決定及びダイナミクス解析 (2019)
  • Author(s): 立石泰, 池谷鉄兵, 岡田真由, 三島正規, 美川務, 八木宏昌, 河野俊之, 木川隆則, 伊藤隆
  • Organizer: 第58回NMR討論会
• [Presentation] Multi-state protein structure determination by integrated analysis of several NMR data sets (2019)
  • Author(s): Teppei Ikeya
  • Organizer: IPR seminar
  • Int'l Joint Research / Invited
• [Presentation] High-resolution protein 3D structure determination in living eukaryotic cells (2019)
  • Author(s): Takashi Tanaka, Teppei Ikeya, Masaki Mishima, Peter Guentert, Yutaka Ito
  • Organizer: The 12th Australian and New Zealand Society for Magnetic Resonance (ANZMAG)
  • Int'l Joint Research
• [Presentation] Solution NMR approaches to 3D structure determination of proteins in living eukaryotic cells (2019)
  • Author(s): Yutaka Ito, Teppei Ikeya
  • Organizer: 第42回日本分子生物学会年会
• [Presentation] High resolution protein 3D structure determination in living eukaryotic cells (2018)
  • Author(s): Teppei Ikeya, Yusuke Suemoto, Takashi Tanaka, Hajime Kamoshida, Masaki Mishima, Masahiro Shirakawa, Peter Guentert, Yutaka Ito
  • Organizer: XXVIII International Conference on Magnetic Resonance in Biological Systems (ICMRBS 2018)
  • Int'l Joint Research
• [Presentation] Structural and Dynamics Analysis of Yeast Ubiquitin Hydrolase 1 (YUH1) Using Paramagnetic NMR Spectroscopy (2018)
  • Author(s): Mayu Okada, Teppei Ikeya, Sundaresan Rajesh, Eri Nojir, Tsutomu Mikawa Yutaka Ito
  • Organizer: XXVIII International Conference on Magnetic Resonance in Biological Systems (ICMRBS 2018)
  • Int'l Joint Research
• [Presentation] 常磁性効果を用いたYeast Ubiquitin hydrolase 1 (YUH1) の構造決定及びダイナミクス解析 (2018)
  • Author(s): 岡田真由，池谷鉄兵，Rajesh Sundaresan，野尻英里，美川務，伊藤隆
  • Organizer: 第57回NMR討論会
• [Presentation] NMRによるタンパク質のミトコンドリア内動態の解析 (2018)
  • Author(s): 清水涼香，美川務，福島瑞穂，池谷鉄兵，鴨志田一，木川隆則，三島正規，伊藤隆
  • Organizer: 第57回NMR討論会
• [Presentation] 生きた真核細胞中での蛋白質立体構造決定 (2018)
  • Author(s): 池谷鉄兵，田中孝，鴨志田一，三島正規，白川昌宏，Peter Guentert，伊藤隆
  • Organizer: 第57回NMR討論会
• [Presentation] 生きた真核細胞内の蛋白質の高分解能立体構造解析 (2018)
  • Author(s): 伊藤隆，池谷鉄兵
  • Organizer: 第41回日本分子生物学会年会
• [Book] 生命金属ダイナミクス: 生体内における金属の挙動と制御 (2021)
  • Author(s): 伊藤隆，猪股晃介，三島正規 & 池谷鉄兵
  • Total Pages: 12
  • Publisher: エヌ・ティー・エス出版
  • ISBN: 9784860437060
• [Book] In-cell NMR Spectroscopy: From Molecular Sciences to Cell Biology (2019)
  • Author(s): Teppei Ikeya, Peter Guentert and Yutaka Ito
  • Total Pages: 305
  • Publisher: The Royal Society of Chemistry
  • ISBN: 9781788012171
• [Remarks] 生きた真核細胞内でたんぱく質の立体構造を詳細に観測 ～構造変化を0.05ナノメートルの精度で捉える～
  • URL: https://www.tmu.ac.jp/news/topics/19272.html
• [Remarks] 生きた真核細胞内でたんぱく質の立体構造を詳細に観測 ～構造変化を0.05ナノメートルの精度で捉える～
  • URL: http://www.jst.go.jp//pr/announce/20190426/index.html