Development of NMR methodology for soft interaction of proteins

• Project/Area Number: 15083202
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The University of Tokyo
• Principal Investigator: SHIMADA Ichio The University of Tokyo, 大学院・薬学系研究科, 教授 (70196476)
• Co-Investigator(Kenkyū-buntansha): TERASAWA Hiroaki 東京大学, 大学院・薬学系研究科, 助手 (10300956)
• Project Period (FY): 2003 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥142,000,000 (Direct Cost: ¥142,000,000); Fiscal Year 2008: ¥17,000,000 (Direct Cost: ¥17,000,000); Fiscal Year 2007: ¥17,000,000 (Direct Cost: ¥17,000,000); Fiscal Year 2006: ¥66,000,000 (Direct Cost: ¥66,000,000); Fiscal Year 2005: ¥16,500,000 (Direct Cost: ¥16,500,000); Fiscal Year 2004: ¥17,000,000 (Direct Cost: ¥17,000,000); Fiscal Year 2003: ¥8,500,000 (Direct Cost: ¥8,500,000)
• Keywords: 膜タンパク質 / 相互作用 / 核磁気共鳴法 / NMR / 分子認識 / 構造生物学

Research Abstract

本研究では生体機能の発現に重要かつ創薬開発における標的タンパク質である膜タンパク質を研究対象とし、その機能解明を行うことが可能な核磁気共鳴法の測定法開発を行い、複数の系において機能解明を行った。

Research Products

• [Journal Article] Cross-saturation and transferred cross-saturation experiments (2009)
  • Author(s): Ichio Shimada, Takumi Ueda, Masahiko Matsumoto, Masayoshi Sakakura, Masanori Osawa, Koh Takeuchi, Noritaka Nishida, Hideo Takahashi
  • Journal Title: Prog. Nuc. Magn. Reson. Spect. 54 Pages: 123-140
  • Peer Reviewed
• [Journal Article] Backbone resonance assignments for the cytoplasmic regions of G protein-activated inwardly rectifying potassium channel 1(GIRK1) (2009)
  • Author(s): Yokogawa M.
  • Journal Title: Biomolecular NMR Assignments (In press)
  • Peer Reviewed
• [Journal Article] Stable isotope labeling of protein by Kluyveromyces laais for NMR study (2008)
  • Author(s): Sugiki T.
  • Journal Title: J Biomol NMR. 42 Pages: 159-162
  • Peer Reviewed
• [Journal Article] Carbohydrate binding mechanism of the macrophage galactose-type C-type lectin 1 revealed by saturation transfer experiments (2008)
  • Author(s): Sakakura M.
  • Journal Title: J Biol Chem. 283 Pages: 33665-33673
  • Peer Reviewed
• [Journal Article] Chondroitin sulfate E fragments enhance CD44 cleavage and CD44-dependent motility in tumor cells (2008)
  • Author(s): Sugahara K. N.
  • Journal Title: Cancer Res. 68 Pages: 7191-7199
  • Peer Reviewed
• [Journal Article] Amino acid selective cross-saturation method for identification of proximal residue pairs in a protein-protein complex (2008)
  • Author(s): Igarashi S.
  • Journal Title: J. Am. Chem. Soc. 130 Pages: 12168-12176
  • Peer Reviewed
• [Journal Article] The amino acids involved in the distinct carbohydrate specificities between macrophage galactose-type C-type lectins 1 and 2 (CD301a and b) of mice. (2008)
  • Author(s): Oo-Puthinan Sarawut
  • Journal Title: Biochim. Biophys. Acta. 1780 Pages: 89-100
  • Peer Reviewed
• [Journal Article] Structural Basis of the Collagen-binding Mode of Discoidin Domain Receptor 2 (2007)
  • Author(s): Osamu Ichikawa, Masanori Osawa, Noritaka Nishida, Naoki Goshima, Nobuo Nomura, and Ichio Shimada
  • Journal Title: EMBO J. 26 Pages: 4168-4176
  • Peer Reviewed
• [Journal Article] Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis. (2007)
  • Author(s): Masayuki Oda
  • Journal Title: J. Mol. Biol. 369 Pages: 198-209
  • Peer Reviewed
• [Journal Article] Backbone resonance assignment for the outer membrane lipoprotein receptor LolB from Escherichia coli (2007)
  • Author(s): Shingo Nakada
  • Journal Title: Biomol. NMR Assign. 1 Pages: 121-123
  • Peer Reviewed
• [Journal Article] Nickel binding to NikA : an additional binding site reconciles spectroscopy, calorimetry and crystallography. (2007)
  • Author(s): Addy C.
  • Journal Title: Acta Crystallogr D Biol Crystallogr. 64 Pages: 221-229
• [Journal Article] Pairwise NMR experiments for the determination of protein backbone dihedral angle Phi based on cross-correlated spin relaxation. (2007)
  • Author(s): Takahashi H.
  • Journal Title: J Biomol NMR 37・3 Pages: 179-185
• [Journal Article] Ligand-induce structure changes of the CD44 hyaluronan-binding domain revealed by NMR. (2007)
  • Author(s): Takeda M.
  • Journal Title: J Biol Chem. 281 Pages: 40089-40095
• [Journal Article] Identification and characterization of the slow-exchanging pH-dependent conformational rearrangement in KcsA. (2007)
  • Author(s): Takeuchi K.
  • Journal Title: J Biol Chem. (In press)
• [Journal Article] Ligand-induced structural change of the CD44 hyaluronan-binding domain revealed by NMR (2006)
  • Author(s): Mitsuhiro Takeda, Shinji Ogino, Ryo Umemoto, Masayoshi Sakakura, Masahiro Kajiwara, Kazuki Sugahara, Hiroto Kawashima, Masayuki Miyasaka, Hiroaki Terasawa, and Ichio Shimada
  • Journal Title: J Biol Chem. 281 Pages: 40089-40095
  • Peer Reviewed
• [Journal Article] Structural Basis of the Transition-state Stabilization in Antibody-catalyzed Hydrolysis. (2006)
  • Author(s): Sakakura M.
  • Journal Title: J. Mol. Biol. 367・1 Pages: 133-147
• [Journal Article] Probing dynamics an conformational change of the GroEL-GroES complex by 13C NMR spectroscopy. (2006)
  • Author(s): Nishida N.
  • Journal Title: J Biochem (Tokyo). 140 Pages: 591-598
• [Journal Article] Utilization of methyl proton resonances in cross-saturation measurement for determining the interfaces of large protein-protein complexes. (2006)
  • Author(s): Takahashi H.
  • Journal Title: J Biomol NMR 34 Pages: 167-177
• [Journal Article] Bead-linked proteoliposomes : a reconstitution method for NMR analyses of membrane protein-ligand interactions (2005)
  • Author(s): Mariko Yokogawa, Koh Takeuchi, and Ichio Shimada
  • Journal Title: J. Am. Chem. Soc. 127 Pages: 12021-12027
  • Peer Reviewed
• [Journal Article] An NMR Method for the Determination of Protein Binding Interfaces Using Dioxygen-Induced Spin-Lattice Relaxation Enhancement (2005)
  • Author(s): M.Sakakura, I.Shimada 他
  • Journal Title: J.Am.Chem.Soc. 127 Pages: 5826-5832
• [Journal Article] Conformational dynamics of complementary determining region H3 of an anti-dansyl Fvfragment in the presence of its hapten (2005)
  • Author(s): M.Nakasako, I.Shimada 他
  • Journal Title: J.Mol.Biol 351 Pages: 627-640
• [Journal Article] Bead-linked proteoliposomes : a reconstitution method for NMR analyses of membrane protein-ligand interactions (2005)
  • Author(s): M.Yokogawa, I.Shimada 他
  • Journal Title: J.Am.Chem.Soc. 127 Pages: 12021-12027
• [Journal Article] NMR techniques for identifying the interface of a larger protein-protein complex : cross-salutation and transferred cross-saturation experiments. (2004)
  • Author(s): Ichio Shimada
  • Journal Title: Method. Enzymol. 394 Pages: 483-506
  • Peer Reviewed
• [Journal Article] 1H, 13C, and 15N backbone resonance assignments of the hyaluronan-binding (2004)
  • Author(s): Mitsuhiro Takeda
  • Journal Title: J.Biomol.NMR 29 Pages: 97-98
• [Journal Article] Optimization of 13C Direct Detection NMR Methods (2004)
  • Author(s): Nobuhisa Shimba
  • Journal Title: J.Biomol.NMR 30 Pages: 175-179
• [Journal Article] Investigation of the CPD photolyase DNA Recognition Mechanism by NMR Analyses (2004)
  • Author(s): Takuya Torizawa
  • Journal Title: J.Biol.Chem. 279 Pages: 32950-32956
• [Journal Article] NMR Study of Repair Mechanism of DNA Photolyase by FAD-Induced Paramagnetic Relaxation Enhancement (2004)
  • Author(s): Takumi Ueda
  • Journal Title: J.Biol.Chem. 279 Pages: 52574-52579
• [Journal Article] Novel Collagen-Binding Mode of the VWA Domain Determined by a Transferred Cross-Saturation Experiment (2003)
  • Author(s): Noritaka Nishida, Hiromi Sumikawa, Masayoshi Sakakura, Nobuhisa Shimba, Hideo Takahashi, Hiroaki Terasawa, Ei-ichiro Suzuki, Ichio Shimada
  • Journal Title: Nature Struct. Biol. 10 Pages: 53-58
  • Peer Reviewed
• [Journal Article] Identification and characterization of a second chromophore of DNA photolyase from Thermus thermophilus HB27
  • Author(s): T.Ueda, I.Shiamda 他
  • Journal Title: J.Biol.Chem (in press.)
• [Journal Article] Direct determination of interface between membrane and peptide using NMR cross-saturation method
  • Author(s): T.Nakamura, I.Shimada 他
  • Journal Title: Biophys.J. (in press)
• [Journal Article] Backbone resonance assignments for the Fv fragment of catalytic antibody 6D9 complexed with a transition state analogue
  • Author(s): M.Sakakura, I.Shimada 他
  • Journal Title: J.Biomol.NMR (in press)
• [Journal Article] Utilization of Methyl Proton Resonances in Cross-saturation Measurements
  • Author(s): H.Takahashi, I.Shimada 他
  • Journal Title: J.Biomol.NMR. (in press)
• [Journal Article] Rapid preparation of stable isotope labeled peptides that bind to target proteins by a phage library system
  • Author(s): Y.Mizukoshi, I.Shimada 他
  • Journal Title: J.Biomol.NMR. (in press.)
• [Journal Article] NMR techniques for identifying the interface of a larger protein -protein complex : cross-salutation and transferred cross-saturation experiments
  • Author(s): Ichio Shimada
  • Journal Title: Method.Enzymol (In press)
• [Journal Article] An NMR Method for the Determination of Protein Binding Interfaces Using Dioxygen-Induced Spin-Lattice Relaxation Enhancement
  • Author(s): M.Sakakura
  • Journal Title: J.Am.Chem.Soc (In press)
• [Presentation] 生体超分子における分子認識機構解明に向けたHR-MASの適用 (2008)
  • Author(s): 豊永翔
  • Organizer: 第47回NMR討論会
  • Place of Presentation: 茨城県つくば市
  • Year and Date: 2008-11-13
• [Presentation] 巨大タンパク質複合体のモデル構築を目的とした残基選択的交差飽和法の開発 (2008)
  • Author(s): 小澤新一郎
  • Organizer: 第47回NMR討論会
  • Place of Presentation: 茨城県つくば市
  • Year and Date: 2008-11-13
• [Presentation] Structural studies on the interaction of spermine with inwardly rectifying potassium channel (2008)
  • Author(s): Osawa M.
  • Organizer: XXIIIrd International Conference on Magnetic Resonance in Biological Systems
  • Place of Presentation: San Diego, CA, USA
  • Year and Date: 2008-08-24
• [Presentation] Structural basis of the gating of G protein (2008)
  • Author(s): Yokogawa M.
  • Organizer: XXIIIrd International Conference on Magnetic Resonance in Biological Systems
  • Place of Presentation: San Diego, CA, USA
  • Year and Date: 2008-08-24
• [Presentation] 常磁性シフトと立体整列同位体標識を利用した、タンパク質間相互作用解析法の開発 (2008)
  • Author(s): 徳永 裕二
  • Organizer: 日本薬学会
  • Place of Presentation: 横浜(パシフィコ横浜)
  • Year and Date: 2008-03-28
• [Presentation] Carbohydrate binding mechanism of the macrophage galactose-type C-type lectin1 revealed by the saturation transfer experiments (2007)
  • Author(s): 坂倉 正義
  • Organizer: 平成19年度 社団法人 日本分光学会 年次講演会
  • Place of Presentation: 東京工業大学百年記念館
  • Year and Date: 2007-11-14
• [Presentation] An NMR Method for the Determination of Protein Binding Interfaces using TEMPOL-induced Chemical Shift Perturbations (2007)
  • Author(s): 坂倉 正義
  • Organizer: ISMAR 2007
  • Place of Presentation: Kenting, Taiwan
  • Year and Date: 2007-10-18
• [Presentation] NMR study on protein-protein interactions using paramagnetic probe (2007)
  • Author(s): 嶋田一夫
  • Organizer: International Workshop on Perspectives on Stable Isotope Aided NMR Methods for Protein Structural Analysis
  • Place of Presentation: Osaka, Japan
• [Presentation] NMR Study on Membrane proteins-ligands (2007)
  • Author(s): 嶋田一夫
  • Organizer: Interactions-Application of Transferred Cross Saturation- AIMECS 07, the 6th International Medicinal Chemistry Symposium
  • Place of Presentation: Istanbul, Turkey
• [Remarks]
  • URL: http://ishimada.f.u-toko.ac.jp/ublic_html/
• [Remarks]
  • URL: http://ishimada.f.u-tokyo.ac.jp/public_html/
• [Publications] Noritaka Nishida: "Novel Collagen-Binding Mode of the VWA Domain Determined by a Transferred Cross-Saturation Experiment"Nature Struct.Biol.. 10. 53-58 (2003)
• [Publications] Yoshimasa Kyogoku: "Structural Genomics of Membrane Proteins"Accounts.Chem.Res. 36. 199-206 (2003)
• [Publications] Koh Takeuchi: "Structural basis of the KcsA K^+ channel and agitoxin2 pore-blocking toxin interaction by using the transferred cross-saturation method"Structure. 11. 1381-1392 (2003)
• [Publications] Lee CW: "Molecular basis of the high-affinity activation of type 1 ryanodine receptors by imperatoxin A."Biochem J.. 377. 385-394 (2003)
• [Publications] Mitsuhiro Takeda: "Hyaluronan-recognition mode of CD44 revealed by cross-saturation and chemical shift perturbation experiments"J.Biol.Chem. 278. 43550-43555 (2003)
• [Publications] Hiroto Kawashima: "^1H, ^<13>C, and ^<15>N backbone resonance assignments of the hyaluronan-binding domain of CD44"J.Biomol.NMR. In Press. (2003)