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1998 Fiscal Year Final Research Report Summary

Analyses of Signal Transduction Mechanisms based on Protein Structures

Research Project

Project/Area Number 06276103
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Research InstitutionYokohama City University

Principal Investigator

NISHIMURA Yoshifumi  Yokohama City University, Professor, 大学院・総合理学研究科, 教授 (70107390)

Co-Investigator(Kenkyū-buntansha) MORIKAWA Kosuke  Biomolecular Engineering Institute, Chief Researcher, 構造解析部門, 部門長 (80012665)
AIMOTO Saburo  Osaka University, Professor, 蛋白質研究所, 教授 (80029967)
INAGAKI Fuyuhiko  Tokyo Metropolitan Institute of Medical Science, Researcher, 生理活性物質研究部門, 部長 (70011757)
SHIRAKAWA Masahiro  Nara Advanced Institute of Science and Technology, Assistant Professor, バイオサイセンス研究科, 助教授 (00202119)
KATAHIRA Masato  Yokohama National University, Assistant Professor, 工学部, 助教授 (70211844)
Project Period (FY) 1994 – 1998
KeywordsStructural Biology / X-ray Crystallography / NMR / Signal Transduction / Transcription / DNA-binding Proteins / RNA-binding Proteins / Molecular Biology
Research Abstract

To encourage collaborative studies between structural and molecular biologists, newsletters containing the research targets and conditions of each member in this project have been published with thirteen issues during 1994 - 1997. To announce research results of this project for other scientists outside the members, many symposia have been held, for example, "Roles of Protein Structures in Signal Transduction and Transcription" in 1994, "Molecular Recognition of Proteins" in 1995, "The Frontiers of Structural Biology", "Molecular Recognition Based on Protein Tertiary Structures" and "Structural Biology on Molecular Recognition of Proteins" in 1996, "Structural Biology of Signal Transduction and Molecular Recognition of DNA/RNA" and "Structural Biology of Reaction Regulation and Molecular Recognition" in 1997, and "Protein Structures in Signal Recognition' in 1998. In addition, we support the "Annual Symposium on Structural Biology" started from 1995. In 1995, a workshop on "Structure Determination of Proteins by X-ray and NMR Methods" was held for young researchers to enter the field of structural biology. For graduate and under graduate students, a Japanese book entitled "The Frontiers of Structural Biology" has been published under the editors that are the members of this project and nearly twenty members of this project have contributed to this book.

  • Research Products

    (58 results)

All Other

All Publications (58 results)

  • [Publications] Nishikawa,T.: "Solution structure of the DNA-binding domain of human telomeric protein,hTRf1."Structure. 6. 1057-1065 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Katahira,M.: "Two metal-binding sites in a lead ribozyme bound to competitively by Pb and Mg.induced structural changes as revealed by NMR."Eur.J.Biochem.. 255. 727-733 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nagadoi,A.: "Solution structure of the transactivation domain of ATF-2 comprising a zinc finger-like subdomain and a flexible subdomain."J.Mol.Biol.. 287. 595-609 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ichikawa,S.: "Solution of Der f2,the Major Mite Allergen for Atopic Diseases"J.Biol.Chem.. 273. 356-360 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Li,X..: "Direct Preparation of Peptide Thioesters Using an Fmoc Solid-Phase Method."Tetrahedron Lett.. 39. 8669-8672 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ikegami,T.: "Solution structure of the DNA-and RPA-binding domain of the human repairfactor XPA."Natrue Structural Biology. 5. 701-706 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Oda,M.: "Investigation of the pytimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence."J.Biol.Chem.. 272. 17966-17971 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Kondo,H.: "Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site."Nature structural biology. 4. 28-31 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Young Ho Jeon: "Flexible Linker in the RNA Polymerase Alpha Subunit Facilitates the Independent Motion of the C-Terminal Activator Contact Domain."J.Mol.Biol.. 267. 953-962 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Iwasaki,W.: "Solution Structure of Midkine,a New Heparin-BindingGrowth Factor."The EMBO J.. 16. 6936-6946 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ogura,K.: "Conformation of Shc-derived Phosphotyrosine Containing Peptide Complexed with Grb2 SH2 Domain."J.Biomolecular NMR. 10. 273-278 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Suzuki,A.: "MKBP,a novel member of the small heat shock protein family,binds and activates the myotonic dystrophy protein kinase(DMPK)."J.Cell Biol.. 140(5). 1113-1124 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ogata,K.: "The Cavity in the Hydrophobic Core of c-Myb DNA-Binding Domain is Reserved for DNA Recognition and trans-Activation."Nature structural biology. 3. 178-187 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Kamada,K.: "Sturucture of a replication-terminator protein complexed with DNA."Nature. 383. 598-603 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Arkin,I.: "Mapping the Lipid-Exposed Surfaces of Membrane Proteins."Nature Struct,Biol.. 3. 240-243 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nagadoi,A.: "Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain."Structure. 3. 1217-1224 (1995)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Hojo,H.: "Preparation of S--Protected Cysteine-Containing Peptide Thioester and Its Use for the Synthesis of the Barnase-Like Domain in DNA-Directed RNA polymarase II of Saccharomyces cerevisiae."Bull.Chem.Soc.Japan. 68. 330-336 (1995)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Mihara,H.: "Peptide Synthesis Mediated by Thiolsubtilisin Using peptide Thioester as Building Block."Chem.Lett.. 397-398 (1995)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Terasawa,H.: "Structure of the N-terminal SH3 domain of GRB2 complexed with a peptide from the guanine nucleotide releasing factor Sos."Nature Struct.Biol.. 1. 891-897 (1994)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Kohda,D.: "Solution structure and ligand-binding site of the carboxy-terminal SH3 domain of GRB2."Structure. 2. 1029-1040 (1994)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Hirao,I.: "Most compact hairpin-turn structure exerted by a short DNA fragment,d(GCGAAGC)in solution:an extraoridinary stable structure resistant to nuclease and heat."Nucleic Acids Res.. 22. 576-582 (1994)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 西村善文 他編: "構造生物学のフロンティア"共立出版. 326 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Hirao, I.: "Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution : an extraoridinary stable structure resistant to nuclease and heat"Nucleic Acids Res.. 22. 576-582 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ogata, K.: "Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices"Cell. 79. 639-648 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Uno, T.: "Resonance Raman and Fourier transform infrared studies on the subunit 1 histidine mutants of the cytochrome bo complex in Escherichia coli"J. Biol. Chem.. 269. 11912-11920 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kondo, H.: "Crystallization and X-ray studies of the DNA-binding domain of OmpR protein, a positive regulator involved in activation of osmoregulatory genes in Esherichia coli"J. Mol. Biol.. 235. 8-782 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Uno, T.: "2-Methylimidazole does not bind to (octaethylporphinato)iron(IIL) chloride in the presence of methanol : A resonance Raman study"J. Amer. Chem. Soc.. 116. 4107-4108 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Katahira, M.: "A Raman spectroscopic study on conformations of DNA oligomers : A dominant effect of an AA:TT sequence over those of AT:AT and TA:TA sequences on determining conformations of DNA duplexes"Nucleosides and Nucleotides. 13. 1467-1481 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ogata,K.: "Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb"Nature Structural Biology. 2. 309-320 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nagadoi, A.: "Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain"Structure. 3. 1217-1224 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Morikawa, S.: "Determination of the nuclear magnetic resonance solution structure of a specific DNA complex of the Myb DNA-binding domain"J. biomol. NMR. 6. 294-305 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Zheng, Z.: "Amide proton exchange rates in c-Myb DNA-binding domain"Quat. Magn. Res. in Biol. Med.. 3. 33-45 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Enari, M.: "Different apoptotic pathways mediated by Fas and the tumore-necrosis-factor receptor"Eur. J. Biochemistry. 236. 533-538 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ogata, K.: "The Cavity in the Hydrophobic Core of c-Myb DNA-Binding Domain is Reserved for DNA Recognition and trans-Activation"Nature structural biology. 3. 178-187 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kondo, H.: "Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site"Nature structural biology. 4. 28-31 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Oda, M.: "Investigation of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence"J. Biol. Chem.. 272. 17966-17971 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Izumi, Y.: "A protein kinase Cdelta-binding protein SRBC whose expression is induced by serum starvation"J. Biol. Chem.. 272. 7381-7389 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Oda, M.: "Identification of indispensable residues for specific DNA-binding in the imperfect tandem repeats of c-Myb R2R3"Protein Engineering. 10. 1407-1414 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Mogi, T.: "Substitutions of conserved aromatic amino acid residues in subunit-l perturb the metal centers of the Escherichia coli bo-type ubiquinol oxidase"Biochemistry. 37. 1632-1639 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nishikawa, T.: "Solution structure of the DNA-binding domain of human telomeric protein, hTRf1"Structure. 6. 1057-1065 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Katahira, M.: "Two metal-binding sites in a lead ribozyme bound to competitively by Pb and Mg. Induced structural changes as revealed by NMR"Eur. J. Biochem.. 255. 727-733 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nagadoi, A.: "Solution structure of the transactivation domain of ATF-2 comprising a zinc finger-like subdomain and a flexible subdomain"J. Mol. Biol.. 287. 595-609 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Shimizu, T.: "Crystallization and preliminary crystallographic data of vitelline membrane outer layer protein, IVMO-1"J. Mol. Biol.. 235. 793-794 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Shimizu, T.: "Crystal structure of vitelline membrane outer layer protein I (VMO-1) : a folding motif with homologous Greek key structures related by an internal three-fold symmetry"EMBO J.. 13. 1003-1010 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ariyoshi, M.: "Preliminary crystallograhic study of Escherichia coli RuvC Protein : an endonuclease specific for Holliday junctions"J. Mol. Biol.. 241. 281-282 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ariyoshi, M.: "Atomic structure of the RuvC resolvase : a Holliday junction-specific endonuclease from E.coli"Cell. 78. 1063-1072 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nureki, O.: "Architectures of class-defining and specific domains of glutamyl-tRNA synthetase"SCIENCE. 267. 1958-1965 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Morikawa, K.: "Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4 : refinement at 1.45* and X-ray analysis of the three active site mutants"J. Mol. Biol.. 249. 360-375 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Saito, A.: "Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase"Proc. Natl. Acad. Sci.. 92. 7470-7474 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Sugiyama, S.: "The 1.8A X-ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding"Protein Science. 5. 1984-1990 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Morita, E. H.: "Implications of the zinc-finger motif found in the DNA-binding domain of the human XPA protein"Genes to Cells. 1. 437-442 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kamada, K.: "Structure of a replication-terminator protein complexed with DNA"Nature. 383. 598-603 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kashiwagi, T.: "Proposal for new catalytic roles for tow invariantresidues in Escherichia coli ribonuclease HI"Protein Engineering. 9. 857-867 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Vassylyev, D. G.: "Precluding uracil from DNA"Structure. 4. 1381-1385 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kashiwagi, T.: "The novel acidophilic structure of the killer toxin from halotolerant yeast demonstrates remarkable folding similarity with a fungal killer toxin"Structure. 5. 81-94 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Aritomi, M.: "Crystal structure of rat Bcl-xL"J. Biol. Chem.. 272. 27886-27892 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nishino, T.: "Functional analyses of the domain structure in the Holliday junction binding protein RuvA"Structure. Vol.6 No.1. 11-21 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Morikawa, K.: "Crystallographyic Study of Proteins involved in recombinational repair and excision repair"Prog. Nuc. Acids. Res.. (in press). (1998)

    • Description
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Published: 2001-10-23  

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