Development of methods for studying conformational dynamics of ubiquitin-ubiquitin binding protein complex

• Project/Area Number: 16K08191
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Physical pharmacy
• Research Institution: The University of Tokyo
• Principal Investigator: Ueda Takumi 東京大学, 大学院薬学系研究科(薬学部), 助教 (20451859)
• Co-Investigator(Kenkyū-buntansha): 嶋田 一夫 東京大学, 大学院薬学系研究科(薬学部), 教授 (70196476)
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2018: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2017: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: NMR / 蛋白質-蛋白質複合体 / 蛋白質ー蛋白質相互作用 / 動的構造平衡 / ユビキチン / 蛋白質-蛋白質相互作用 / 構造生物学

Outline of Final Research Achievements

We developed an NMR method for determination of the distances between the observed atoms and the paramagnetic probes in the protein-protein complexes that undergo exchange between multiple conformations. We applied the developed method to the interaction between ubiquitin and a ubiquitin-binding protein, and revealed that these proteins transiently form a complex in which each protein adopts multiple conformations. The transient complex leads to rapid formation of the functional complex in the conformational selection manner.

Academic Significance and Societal Importance of the Research Achievements

ユビキチン修飾による蛋白質の機能制御、および様々なマルチドメイン蛋白質による細胞ないシグナル伝達の制御において、動的構造が重要な役割を持つことが予想されている。一方、蛋白質-蛋白質複合体の動的構造平衡の知見は極めて乏しい。したがって、本研究で開発した手法は、従来にない新たな視点から機能制御のメカニズムの手掛かりを与えることを可能とすることが予想され、意義深い。

Research Products

• [Int'l Joint Research] Institute of Biotechnology/University of Helsinki(Finland)
• [Journal Article] GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures (2018)
  • Author(s): Shimada Ichio、Ueda Takumi、Kofuku Yutaka、Eddy Matthew T.、Wuthrich Kurt
  • Journal Title: Nature Reviews Drug Discovery Volume: 18 Issue: 1 Pages: 59-82
  • DOI: 10.1038/nrd.2018.180
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Deuteration and Selective Labeling of Alanine Methyl Groups of β 2-Adrenergic Receptor Expressed in a Baculovirus-Insect Cell Expression System (2018)
  • Author(s): Yutaka Kofuku, Tomoki Yokomizo, Shunsuke Imai, Yutaro Shiraishi, Mei Natsume, Hiroaki Itoh, Masayuki Inoue, Kunio Nakata, Shunsuke Igarashi, Hideyuki Yamaguchi, Toshimi Mizukoshi, Ei-Ichiro Suzuki, Takumi Ueda, Ichio Shimada
  • Journal Title: Journal of Biomolecular NMR Volume: 印刷中 Issue: 3 Pages: 185-192
  • DOI: 10.1007/s10858-018-0174-5
  • Peer Reviewed / Open Access
• [Journal Article] Endogenous Membrane Receptor Labeling by Reactive Cytokines and Growth Factors to Chase Their Dynamics in Live Cells (2018)
  • Author(s): Takaoka Yousuke、Uchinomiya Shohei、Kobayashi Daichi、Endo Masataka、Hayashi Takahiro、Fukuyama Yoshiaki、Hayasaka Haruko、Miyasaka Masayuki、Ueda Takumi、Shimada Ichio、Hamachi Itaru
  • Journal Title: Chem Volume: 4 Issue: 6 Pages: 1451-1464
  • DOI: 10.1016/j.chempr.2018.03.021
  • Peer Reviewed / Open Access
• [Journal Article] Phosphorylation-induced conformation of β2-adrenoceptor related to arrestin recruitment revealed by NMR (2018)
  • Author(s): Yutaro Shiraishi, Mei Natsume, Yutaka Kofuku, Shunsuke Imai, Kunio Nakata, Toshimi Mizukoshi, Takumi Ueda, Hideo Iwai, Ichio Shimada
  • Journal Title: Nature Communications Volume: 9 Issue: 1 Pages: 164-164
  • DOI: 10.1038/s41467-017-02632-8
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Dynamic domain arrangement of CheA-CheY complex regulates bacterial thermotaxis, as revealed by NMR (2017)
  • Author(s): YuYuichi Minato, Takumi Ueda, Asako Machiyama, Hideo Iwai, Ichio Shimada
  • Journal Title: as revealed by NMR Scientific Reports Volume: 7 Issue: 1 Pages: 16462-16462
  • DOI: 10.1038/s41598-017-16755-x
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Conductance of P2X4 receptor is determined by conformational equilibrium in the transmembrane region (2016)
  • Author(s): Minato Y, Suzuki S , Hara T, Kofuku Y, Kasuya G, Fujiwara Y, Igarashi S, Suzuki E, Nureki O, Hattori M, Ueda T, Shimada I
  • Journal Title: Proc. Natl. Acad. Sci. Volume: 発行中 Issue: 17 Pages: 4741-4746
  • DOI: 10.1073/pnas.1600519113
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Presentation] Conductance of P2X4 receptor is determined by conformational equilibrium in the transmembrane region (2017)
  • Author(s): Takumi Ueda, Yuichi Minato, Shiho Suzuki, Tomoaki Hara, Yutaka Kofuku, Go Kasuya, Yuichiro Fujiwara, Shunsuke Igarashi, Ei-ichiro Suzuki, Osamu Nureki, Motoyuki Hattori, Ichio Shimada
  • Organizer: 58th Experimental Nuclear Magnetic Resonance Conference
  • Place of Presentation: Asilomar Conference Grounds, Pacific Grove, CA, USA
  • Year and Date: 2017-03-26
  • Int'l Joint Research / Invited
• [Presentation] Functional dynamics of membrane proteins revealed by NMR (2017)
  • Author(s): 上田 卓見、嶋田 一夫
  • Organizer: 第55回日本生物物理学会年会
  • Invited
• [Presentation] 安定同位体標識法の応用による、蛋白質の動的構造の解明 (2017)
  • Author(s): 上田 卓見、嶋田 一夫
  • Organizer: 第56回NMR討論会
  • Invited
• [Remarks]
  • URL: http://ishimada.f.u-tokyo.ac.jp/public_html/
• [Remarks]
  • URL: http://ishimada.f.u-tokyo.ac.jp/public_html/