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The development of NMR methods for drug discovery targeting on ribosome recycling.

Research Project

Project/Area Number 14370756
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field 医薬分子機能学
Research InstitutionOsaka University

Principal Investigator

KOBAYASHI Yuji  Osaka University, Graduate School of Pharmaceutical Sciences, Professor, 薬学研究科, 教授 (20127228)

Co-Investigator(Kenkyū-buntansha) YOSHIDA Takuya  Osaka Univ., Graduate School of Pharmaceutical Sciences, Research Associate, 薬学研究科, 助手 (00294116)
OHKUBO Tadayasu  Osaka Univ., Graduate School of Pharmaceutical Sciences, Associate Professor, 薬学研究科, 助教授 (90272997)
Project Period (FY) 2002 – 2003
Project Status Completed (Fiscal Year 2003)
Budget Amount *help
¥12,700,000 (Direct Cost: ¥12,700,000)
Fiscal Year 2003: ¥3,700,000 (Direct Cost: ¥3,700,000)
Fiscal Year 2002: ¥9,000,000 (Direct Cost: ¥9,000,000)
KeywordsRibosome / RRF / NMR / Interaction / Antibiotics / Drug design / 分子間相互作用
Research Abstract

We established NMR assignments of RRFs originated from five bacteria. Resulting assignments bring not only the basis of following structural study, but also the set of interaction probes at an atomic resolution for drug discovery. We investigated inter-molecular dynamics of RRF by NMR relaxation analyses and nanosecond molecular dynamics simulations. The results revealed characteristic flexibility in inter-domain orientation of RRF molecule experimentally, indicating that a compound bound to hinge region would inhibit RRF function. In order to obtain structural information for CARDD, we carried out an X-ray analysis on RRF from Vibrio parahaemolyticus. To elucidate the ribosome binding site of RRF, the peptide fragment corresponding to domain I of RRF (RRF-DI) was expressed and characterized. RRF-DI is bound to 70S ribosome and the 50S subunit with an affinity similar to that of wild-type RRF. But it does not bind to the 30S subunit. Moreover, we carried out a cryo-EM analyses and chemical probing experiments on RRF-ribosome complex. By the virtual screening based on the determined structure and interaction mode of RRF, some candidates for RRF inhibitor were obtained. To assay such compounds, novel screening system in vitro was developed.

Report

(3 results)
  • 2003 Annual Research Report   Final Research Report Summary
  • 2002 Annual Research Report
  • Research Products

    (63 results)

All Other

All Publications (63 results)

  • [Publications] Nakano, H. et al.: "Crystallization and preliminary X-ray crystallographic studies of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly"Acta Crystallogr.Sect.D. 58. 124-126 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Yoshida, T. et al.: "Backbone NMR assignments of Ribosome Recycling Factors (RRFs) from Escherichia coli and Thermotoga maritime"J.Biomol.NMR. 22. 195-196 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Uchiyama, S. et al.: "Thermodynamic characterization of variants of mesophilic cytochrome c and its thermophilic counterpart"Protein Eng.. 15. 455-461 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Shimizu, T. et al.: "Interaction among silkworm ribosomal proteins P1, P2 and P0 required for functional protein binding to the GTPase-associated domain of 28S rRNA"Nucleic Acids Research. 30. 2620-2627 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Hemmi, H. et al.: "Solution Structure of Ascidian Trypsin Inhibitor Determined by Nuclear Magnetic Resonance Spectroscopy"Biochemistry. 41. 10657-10664 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Otaka, A. et al.: "Remodeling of gp41-C34 Peptide Leads to Highly Effective Inhibitors of the Fusion of HIV-1 with Target Cells"Angewante Chemie. 41. 2937-2940 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Doi, M.et al.: "Simple and efficient syntheses of Boc- and Fmoc-protected 4(R)-and 4(S)-fluoroproline solely from 4(R)-hydroxyproline"Tetrahedron. 58. 8453-8459 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Okajima, T. et al.: "Novel Trimeric Adenylate Kinase from an Extremely Thermoacidophilic Archaeon, Sulfolobus solfataricus : Molecular Cloning, Nucleotide Sequencing, Expression in Escherichia coil, and Characterization of the Recombinant Enzyme"Biosci.Biotechnol.Biochem.. 66. 2112-2124 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Yamamoto, Y. et al.: "Influence of Amino Acid Side Chain Packing on Fe-Methionine Coordination in Thermostable Cytochrome c"J.Am.Chem.Soc.. 124. 11574-11575 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Sambongi, Y.: "Cytochrome c from a thermophilic bacterium has provided insights into the mechanisms of protein maturation, folding, and stability"Eur.J.Biochem.. 269. 3355-3361 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Nakano, H. et al.: "Structure and Binding Mode of a Ribosome Recycling Factor (RRF) from Mesophilic Bacterium"J.Biol.Chem.. 278. 3427-3436 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Minamino, T. et al.: "Effect of Intracellular pH on Rotational Speed of Bacterial Flagellar Motors"J.Bacteriol.. 185. 1190-1194 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Yoshida, T. et al.: "Characteristic domain motion in the ribosome recycling factor revealed by 15N NMR relaxation experiments and molecular dynamics simulations."Biochemistry. 42. 4101-4107 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Hemmi, H. et al.: "Inhibittory Specificity Change of the Ovomucoid Third Domain of the Silver Pheasant upon Introduction of an Engineered Cys14-Cys39 Bond"Biochemistry. 42. 2524-2534 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Doi, M.et al.: "Characterization of Collagen Model Peptides Containing 4-Fluoroproline ; (4(S)-Fluoroproline-Pro-Gly)10 Forms a Triple Helix, but (4(R)-Fluoroproline-Pro-Gly)10 Dose Not"J.Am.Chem.Soc.. 125. 9922-9923 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Terui, N. et al.: "Relationship between Redox Function and Protein Stability of Cytochromes c"J.Am.Chem.Soc.. 125. 13650-13651 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Ohwada, T. et al.: "α,α-Disubstituted Glycines Bearing a Large Hydrocarbon Ring : Peptide Self-Assembly through Hydrophobic Recognition"Chem.Eur.J.. 10. 617-626 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Takashima, K. et al.: "Distribution Computing and NMR Constraint Based High Resolution Structure Determination : Applied for Bioactive Peptide Endothelin-1 to Determine C-terminal Folding"J.Am.Chem.Soc.. 126. 4504-4505 (2004)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Takinowaki, H. et al.: "1H, 13C and 15N resonance assignments of the N-terminal 16kDa domain of Escherichia coli Ada protein."J.Biomol.NMR. in press. (2004)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Nakano, H. et al.: "Crystallization and preliminary X-ray crystallographic studies of a mutant of ribosome recycling factor from Escherichia coli, Argl32 Gly"Acta crystallogr.Sect.D. 58. 124-126 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Yoshida, T. et al.: "Backbone NMR assignments of Ribosome Recycling Factors (RRFs) from Escherichia coli and Thermotoga maritime"J.Biomol.NMR. 22. 195-196 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Uchiyama, S. et al.: "Thermodynamic characterization of variants of mesophilic cytochrome c and its thermophilic counterpart"Protein Eng.. 15. 455-461 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Shimizu, T. et al.: "Interaction among silkworm ribosomal proteins PI, P2 and PO required for functional protein binding to the GTPase-associated domain of 28S rRNA"Nucleic Acids Research. 30. 2620-2627 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Hemmi, H. et al.: "Solution Structure of Ascidian Trypsin Inhibitor Determined by Nuclear Magnetic Resonance Spectroscopy"Biochemistry. 41. 10657-10664 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Otaka, A. et al.: "Remodeling of gp41-C34 Peptide Leads to Highly Effective Inhibitors of the Fusion of HIV-1 with Target Cells"Angewante Chemie. 41. 2937-2940 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Doi, M.et al.: "Simple and efficient syntheses of Boc-and Fmoc-protected 4(R)-and 4(S)-fluoroproline solely from 4(R)-hydroxyproline"Tetrahedron. 58. 8453-8459 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Yamamoto, Y. et al.: "Influence of Amino Acid Side Chain Packing on Fe-Methionine Coordiriation in Themiostable Cytochrome c"J.Am.Chem.Soc.. 124. 11574-11575 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Okajima, T. et al.: "Novel Trimeric Aderiylate Kinase from an Extremely Thermoacidop hilic Archaeon, Sulfolobus solfataricus: Molecular Cloning, Nucleotide Sequencing, Expression in Escherichia coli, and Characterization of the Recombinant Enzyme"Biosci. Biotechnol. Biochem.. 66. 2112-2124 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Sambongi, Y.: "Cytochrome c from a thermophilic bacterium has provided insights into the mechanisms of protein maturation, folding, and stability"Eur.J.Biochem.. 269. 3355-3361 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Nakano, H. et al.: "Structure and Binding Mode of a Ribosome Recycling Factor (RRF) from Mesophilic Bacterium"J.Biol.Chem.. 278. 3427-3436 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Minamino, T. et al.: "Effect of Intracellular pH on Rotational Speed of Bacterial Flagellar Motors"J.Bacteriol.. 185. 1190-1194 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Yoshida, T. et al.: "Characteristic domain motion in the ribosome recycling factor revealed by 15N NMR relaxation experiments and molecular dynamics simulations."Biochemistry. 42. 4101-4107 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Hemmi, H. et al.: "Inhibitory Specificity Change of the Ovomucoid Third Domain of the Silver Pheasant upon Introduction of an Engineered Cys14-Cys39 Bond"Biochemistry. 42. 2524-2534 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Doi, M.et al.: "Characterization of Collagen Model Peptides Containing 4-Fluoroproline; (4(S)-Fluoroproline-Pro-Gly)10 Forms a Triple Helix, but (4(R)-Fluoroprolme-Pro-Gly)10 Dose Not"J.am.Chem.Soc.. 125. 9922-9923 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Terui, N. et al.: "Relationship between Redox Function and Protein Stability of Cytochromes c"J.Am.Chem.Soc.. 125. 13650-13651 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Ohwada, T. et al.: "α,α-Disubstituted Glycines Bearing a Large Hydrocarbon Ring: Peptide Self-Assembly through Hydrophobic Recognition"Chem.Eur.J.. 10. 617-626 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Takashima, K. et al.: "Distribution Computing and NMR Constraint Based High Resolution Structure Determination: Applied for Bioactive Peptide Endothelin-1 to Determine C-terminal Folding"J.Am.Chem.Soc.. 126. 4504-4505 (2004)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Nakano, H. et al.: "Crystallization and preliminary X-ray crystallographic studies of a mutant of ribosome recycling factor from Escherichia coli, Arg132G1y"Acta Crystallogr. Sect. D. 58. 124-126 (2002)

    • Related Report
      2003 Annual Research Report
  • [Publications] Yoshida, T. et al.: "Backbone NMR assignments of Ribosome Recycling Factors (RRFs) from Escherichia coli and Thermotoga maritime"J.Biomol.NMR. 22. 195-196 (2002)

    • Related Report
      2003 Annual Research Report
  • [Publications] Uchiyama, S. et al.: "Thermodynamic characterization of variants of mesophilic cytochrome c and its thermophilic counterpart"Protein Eng.. 15. 455-461 (2002)

    • Related Report
      2003 Annual Research Report
  • [Publications] Shimizu, T. et al.: "Interaction among silkworm ribosomal proteins P1, P2 and PO required for functional protein binding to the GTPase-associated domain of 28S rRNA"Nucleic Acids Research. 30. 2620-2627 (2002)

    • Related Report
      2003 Annual Research Report
  • [Publications] Hemmi, H. et al.: "Solution Structure of Ascidian Trypsin Inhibitor Determined by Nuclear Magnetic Resonance Spectroscopy"Biochemistry. 41. 10657-10664 (2002)

    • Related Report
      2003 Annual Research Report
  • [Publications] Otaka, A. et al.: "Remodeling of gp41-C34 Peptide Leads to Highly Effective Inhibitors of the Fusion of HIV-1 with Target Cells"Angewante Chemie. 41. 2937-2940 (2002)

    • Related Report
      2003 Annual Research Report
  • [Publications] Doi, M.et al.: "Simple and efficient syntheses of Boc- and Fmoc-protected 4(R)-and 4(S)-fluoroproline solely from 4(R)-hydroxyproline"Tetrahedron. 58. 8453-8459 (2002)

    • Related Report
      2003 Annual Research Report
  • [Publications] Yamamoto, Y. et al.: "Influence of Amino Acid Side Chain Packing on Fe-Methionine Coordination in Thermostable Cytochrome c"J.Am.Chem.Soc.. 124. 11574-11575 (2002)

    • Related Report
      2003 Annual Research Report
  • [Publications] Okajima, T. et al.: "Novel Trimeric Adenylate Kinase from an Extremely Thermoacidophilic Archaeon, Sulfolobus solfataricus : Molecular Cloning, Nucleotide Sequencing, Expression in Escherichia coli, and Characterization of the Recombinant Enzyme"Biosci.Biotechnol.Biochem.. 66. 2112-2124 (2002)

    • Related Report
      2003 Annual Research Report
  • [Publications] Yamamoto, Y. et al.: "Influence of Amino Acid Side Chain Packing on Fe-Methionine Coordination in Thermostable Cytochrome c"J.Am.Chem.Soc.. 124. 11574-11575 (2002)

    • Related Report
      2003 Annual Research Report
  • [Publications] Sambongi, Y.: "Cytochrome c from a thermophilic bacterium has provided insights into the mechanisms of protein maturation, folding, and stability"Eur.J.Biochem.. 269. 3355-3361 (2002)

    • Related Report
      2003 Annual Research Report
  • [Publications] Nakano, H. et al.: "Structure and Binding Mode of a Ribosome Recycling Factor (RRF) from Mesophilic Bacterium"J.Biol.Chem.. 278. 3427-3436 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Minamino, T. et al.: "Effect of Intracellular pH on Rotational Speed of Bacterial Flagellar Motors"J.Bacteriol.. 185. 1190-1194 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Yoshida, T. et al.: "Characteristic domain motion in the ribosome recycling factor revealed by 15N NMR relaxation experiments and molecular dynamics simulations"Biochemistry. 42. 4101-4107 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Hemmi, H. et al.: "Inhibittory Specificity Change of the Ovomucoid Third Domain of the Silver Pheasant upon Introduction of an Engineered Cys14-Cys39 Bond"Biochemistry. 42. 2524-2534 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Doi, M.et al.: "Characterization of Collagen Model Peptides Containing 4-Fluoroproline ; (4(S)-Fluoroproline-Pro-Gly)10 Forms a Triple Helix, but (4(R)-Fluoroproline-Pro-Gly)10 Dose Not"J.Am.Chem.Soc.. 125. 9922-9923 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Terui, N. et al.: "Relationship between Redox Function and Protein Stability of Cytochromes c"J.Am.Chem.Soc.. 125. 13650-13651 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Ohwada, T. et al.: "α,α-Disubstituted Glycines Bearing a Large Hydrocarbon Ring Peptide Self-Assembly through Hydrophobic Recognition"Chem.Eur.J.. 10. 617-626 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Takashima, K. et al.: "Distribution Computing and NMR Constraint Based High Resolution Structure Determination: Applied for Bioactive Peptide Endothelin-1 to Determine C-terminal Folding"Chem.Eur.J.. (in press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Takinowaki, H. et al.: "1H, 13C and 15N resonance assignments of the N-terminal 16kDa domain of Escherichia coli Ada protein."J.Biomol.NMR. (in press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Nakano, H. et al.: "Structure and binding mode of a ribosome recycling factor(RRF)from mesophilic bacterium"J. Biol. Chem.. 278. 3427-3436 (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Inui, T. et al.: "Characyerization of the unfolding process of lipocalin-type prostaglandin D synthase"J. Biol. Chem.. 278. 2845-2852 (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Hemmi, H. et al.: "Inhibitory specificity change of ovomucoid third domain of the silver pheasant upon introduction of an engineered Cys14-Cys39 bond"Biochemistry. 42. 2524-2534 (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Hemmi, H. et al.: "Solution structure of ascidian trypsin inhibitor determined by nuclear magnetic resonance spectroscopy"Biochemistry. 41. 10657-10664 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Nakano, H. et al.: "Crystallization and preliminary X-ray crystallographic studies of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly"Acta Crystallogr. Sect. D Biol.. 58. 124-126 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Yoshida, T.: "Backbone NMR assignments of ribosome recycling factors(RRFs)from Escherichia coli and Thermotoga maritima"J. Biomol. NMR. 22. 195-196 (2002)

    • Related Report
      2002 Annual Research Report

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Published: 2002-04-01   Modified: 2016-04-21  

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