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Development of Rapid and Accurate Methods for X-ray Crystallography to Study Crystal Structures and Functions of Proteins.

Research Project

Project/Area Number 06305006
Research Category

Grant-in-Aid for Co-operative Research (A)

Allocation TypeSingle-year Grants
Research Field 広領域
Research InstitutionUniversity of Tokyo

Principal Investigator

SATOW Yoshinori  University of Tokyo, Faculty of Pharmaceutical Sciences, Professor, 薬学部, 教授 (30150014)

Co-Investigator(Kenkyū-buntansha) FUKUYAMA Keiichi  Osaka University, Faculty of Science, Professor, 理学部, 教授 (80032283)
TSUKIHARA Tomitake  Osaka University, Institute for Protein Research, Professor, 蛋白質研究所, 教授 (00032277)
MIKI Kunio  University of Kyoto, Graduate School of Science, Professor, 大学院理学研究科, 教授 (10116105)
TANAKA Isao  Hokkaido University, Graduate School of Science, Professor, 理学部, 教授 (70093052)
TANAKA Nobuo  Tokyo Institute of Technology, Faculty of Bioscience and Biotechnology, Professo, 生命理工学部, 教授 (50032024)
山根 隆  名古屋大学, 工学部, 助教授 (80030055)
藤井 敏  大阪大学, 薬学部, 助教授 (10107104)
Project Period (FY) 1994 – 1995
Project Status Completed (Fiscal Year 1995)
Budget Amount *help
¥9,300,000 (Direct Cost: ¥9,300,000)
Fiscal Year 1995: ¥4,400,000 (Direct Cost: ¥4,400,000)
Fiscal Year 1994: ¥4,900,000 (Direct Cost: ¥4,900,000)
KeywordsProteins / X-ray crystallography / Structural biology / Membrane protein / Glycoprotein / Antibody / Crystal structure / Antigen recognition / X線結晶構造解析 / 膜蛋白質 / 蛋白質三次元構造 / 結晶構造 / 生体高分子 / X線回折法 / 分子生物学
Research Abstract

This research project aimed at the development of rapid and accurate methods for macromolecular X-ray crystallography, through collaborative studies of three-dimensional structures and functions of proteins. The project was carried out by 15 investigators.
The proteins studied in the project were, genetically engineered proteins with amino-acid substitutions, proteolytic and glycolytic enzymes as well as their complexes with inhibitors, proteins that recognize nucleic acids, antibodies and their complexes with haptens, membrane proteins, viruses, and glycoproteins. The methods and techniques developed were, for engineering and preparation of protein specimens, for crystallization of proteins, for determination of very large structural units, for diffraction data collection, for utilization of anomalous scattering effects, for automated molecular-replacement solutions, and for utilization of other structural information.
Structure determinations of a membrane protein of bovine cytochrome c oxidase and a glycoprotein of human renal dipeptidase are typical examples of the successful results. The former protein was crystallized and solved with the techniques developed. The later were prepared with genetic engineering and enzymatic deglycosylation techniques. The structures of chimeric enzymes, proteinases of a trypsin family, and unliganded and hapten-liganded forms of Fab and Fv fragments of antibodies were also determined. The developments of hardware and software systems with rapid and accurate data collection capabilities, of techniques for locating anomalous scatterers and for MAD analyzes, and of automated molecular-replacement procedures were carried out.
In each year, a meeting for exchanging information about research activities of investigators was held. A report on research activities, progresses, and achievements was published at the end of each year. The report for the final year was circulated to researchers in related fields.

Report

(3 results)
  • 1995 Annual Research Report   Final Research Report Summary
  • 1994 Annual Research Report
  • Research Products

    (63 results)

All Other

All Publications (63 results)

  • [Publications] Mizutani,Ryuuta他: "Three-dimensional Structures of the Fab Fragment of Murine N1G9 Antibody from the Primary Immune Response and of Its Complex with(4-Hydroxy-3-nitrophenyl)acetate." J. Mol. Biol.254. 208-222 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Noguchi,shuji他: "Crystal Structure of Ustilago sphaerogena Ribonuclease U_2 at 1.8 Å Resolution." Biochemistry. 34. 15583-15591 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Harada,Shigeharu他: "Crystallization and Preliminary X-ray Diffraction Studies of Curculin,A New Type of Sweet Protein Having Taste-Midifying Action." J. Mol. Biol.238. 286-287 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Nakamura,Msahiro他: "Design of Noncovalent Trypsin Inhibitor Based on the X-ray Crystal Structure of the Complex." Biochem. Biopys. Res. Comm.213. 583-587 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Takenaka,Akio他: "Structural Composition of Hammerhead Ribozymes." J. Biochem.117. 850-855 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Kumasaka,Takashi他: "Crystal Structures of H_2C Proteinase from the Venom of Trimeresurus flavoviridis." J. Biochem.119. 49-57 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Harada,Shigeharu他: "Complete Amino Acid Sequence of a Zinc Metalloendoprotease from Streptomyces caespitosus." Eur. J. Biochem.233. 683-686 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Nagata,Chikahiro他: "Crystallization and Preliminary X-ray Analysis of Cytochrome c_<552> from Pseudomonas europae." J. Biochem.116. 946-947 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Tsukihara,Tomitake他: "Structures of Metal Sites of Oxidized Bovine Cytochrome c Oxidase at 2.8 Å." Science. 269. 1069-1074 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Gohda,Keigo他: "Crystal Structure of RNase T_1 Complexed with 3'AMP:Structural Evidence for Direct Interaction of His40 and Glu58 with the 2'-Hydroxyl Group of the Ribose." J. Biol. Chem.269. 17531-17536 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Miyatake,Hideyuki他: "Crystal Structure of the Unliganded Alkaline Protease from Pseudomonas aeruginosa IFO3080 and Its Conformational Changes on Ligand Binding." J. Biochem.118. 474-479 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Takano,Kazufumi他: "Contribution of Hydrophobic Residues to the Stability of Human Lysozyme:Calorimetric Studies and X-ray Structural Analysis of the Five Isoleucine to Valine Mutants." J. Mol. Biol.254. 62-76 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Miki,Kunio他: "Application of Automatic Molecular Replacement Procedure to Ctystal Structure Analysis of Cytochrome c_2 from Rhodopseudomonas viridis." Acta Crystallogr.D50. 271-275 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Yamagata,Yuriko他: "Medel Building of DNA Repair Enzyme 3-Methyladenosine DNA Glycosidase-DNA Complex." Nucleic Acids Symposium Series.

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Yamane,Takashi他: "Crystal Structure of Streptomyces erythraeus Trypsin at 1.9 Å Resolution." J. Biochem.

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Suzuki,Atsuo他: "Crystal Structure Analysis of Phospholipase A2 from Trimeresurus flavoviridis(Habu Snake)at 1.5 Å Resolution." J. Biochem.117. 730-740 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Nitanai,Yasushi他: "Crystallizationand Preliminary X-Ray Investigation of a Glycoprotein,Human Renal Dipeptidase." J. Crystal Growth,. (印刷中). (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Mizutani,Ryuta他: "Crystallization and Crystallographic Studies on Fab Fragments of Anti-Nitrophenol Antibodies from Primary and Secondary Immune Responses." J. Crystal Growth,. (印刷中).

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] 佐藤能雅: ""続医薬品の開発"第17巻「薬物の構造解析」(荒田洋治編集のp.66-97を担当)" 廣川書店, 222 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Mizutani, Ryuta et al.: "Three-dimesional Structures of the Fab Fragment of Murine N1G9 Antibody from the Primary Immune Response and of Its Complex with (4-Hydroxy-3-nitrophenyl) acetate." J.Mol.Biol.254. 208-222 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Noguchi, shiuji et al.: "Crystal Structure of Ustilago sphaerogena Ribonuclease U_2 at 1.8 @90 Resolution." Biochemistry. 34. 15583-15591 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Harada, Shigeharu et al.: "Crystallization and Preliminary X-ray Diffraction Studies of Curculin, A New Type of Sweet Protein Having Taste-Midifying Action." J.Mol.Biol.238. 286-287 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Nakamura, Msahiro et al.: "Design of Noncovalent Trypsin Inhibitor Based on the X-ray Crystal Structure of the Complex." Biochem.Biopys.Res.Comm.213. 583-587 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Takenaka, Akio et al.: "Structural Composition of Hammerhead Ribozymes." J.Biochem.117. 850-855 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Kumasaka, Takashi et al.: "Crystal Structures of H_2C Proteinase from the Venom of Trimeresurus flavoviridis." J.Biochem.119. 49-57 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Nagata, Chikahiro et al.: "Crystallization and Preliminary X-ray. Analysis of Cytochrome c_<552> from Pseudomonas europae." J.Biochem.116. 946-947 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Tsukihara, Tomitake et al.: "Structures of Metal Sites of Oxidized Bovine Cytochrome c Oxidase at 2.8 @90." Science. 269. 1069-1074 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Gohda, Keigo et al.: "Crystal Structure of RNase T_1 Complexed with. 3'AMP : Structural Evidence for Direct Interaction of His 40 and Glu 58 with the 2'-Hydroxyl Group of the Ribose." J.Biol.Chem.269. 17531-17536 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Miyatake, Hideyuki et al.: "Crystal Structure of the Unliganded Alkaline Protease from Pseudomonas aeruginosa IFO3080 and Its Conformational Changes on Ligand Binding." J.Biochem.118. 474-479 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Harada, Shigeharu et al.: "Complete Amino Acid Sequence of a Zinc. Metalloendoprotease from Streptomyces caespitosus." Eur.J.Biochem.233. 683-686 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Takano, Kazufumi et al.: "Contribution of Hydrophobic Residues to the Stability of Human Lysozyme : Calorimetric Studies and X-ray Structural Analysis of the Five Isoleucine to Valine Mutants." J.Mol.Biol.254. 62-76 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Miki, Kunio et al.: "Application of Automatic Molecular Replacement Procedure to Crystal Structure Analysis of Cytochrome c_2 from Rhodopseudomonas viridis." Acta Crystallogr.D50. 271-275 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Suzuki, Atsuo et al.: "Crystal Structure Analysis of Phospholipase A_2 from Trimeresurus flavoviridis (Habu Snake) at 1.5 @90 Resolution." J.Biochem.117. 730-740 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Yamane, Takashi et al.: "Crystal Structure of Streptomyces erythraeus Trypsin at 1.9 @90 Resolution." J.Biochem.118. 882-894 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Yamagata, Yuriko et al.: "Medel Building of DNA Repair Enzyme 3-Methyladenosine DNA Glycosidase-DNA Complex." Nucleic Acids Symposium Series. 34. 7-8 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Nitanai, Yasushi et al.: "Crystallizationand Preliminary X-ray investigation of a Glycoprotein, Human Renal Dipeptidase." J.Crystal Growth. (in press). (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Mizutani, Ryuta et al.: "Crystallization and Crystallographic Studies on Fab Fragments of Anti-Nitrophenol Antibodies from Primary and Secondary Immune Responses." J.Crystal Growth. (in press). (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Mizutani, Ryuuta 他: "Three-dimesional Structures of the Fab Fragment of Murine NIG9 Antibody from the Primary Immune Response and of Its Complex with (4-Hydroxy-3-nitrophenyl) acetate." J. Mol. Biol.254. 208-222 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Noguchi, shuji 他: "Crystal Structure of Ustilago sphaerogena Ribonuclease U_2 at 1.8 Å Resolution." Biochemistry. 34. 15583-15591 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Harada, Shigeharu 他: "Crystallization and Preliminary X-ray Diffraction Studies of Curculin, A New Type of Sweet Protein Having Taste-Midifying Action." J. Mol. Biol.238. 286-287 (1994)

    • Related Report
      1995 Annual Research Report
  • [Publications] Harada, Shigeharu 他: "Complete Amino Acid Sequence of a Zinc Metalloendoprotease from Streptomyces caespitosus." Eur. J. Biochem.233. 683-686 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Nakamura, Msahiro 他: "Design of Noncovalent Trypsin Inhibitor Based on the X-ray Crystal Structure of the Complex." Biochem. Biopys. Res. Comm.213. 583-587 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Takenaka, Akio 他: "Structural Composition of Hammerhead Ribozymes." J. Biochem.119. 49-57 (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] Kumasaka, Takashi 他: "Crystal Structures of H_2C Proteinase from the Venom of Trimeresurus flavoviridis." J. Biochem.119. 49-57 (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] Nagata, Chikahiro 他: "Crystallization and Preliminary X-ray Analysis of Cytochrome c_<552> from Pseudomonas europae." J. Biochem.116. 946-947 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Tsukihara, Tomitake 他: "Structures of Metal Sites of Oxidized Bovine Cytochrome c Oxidase at 2.8 Å." Science. 269. 1069-1074 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Gohda, Keigo 他: "Crystal Structure of RNase T_1 Complexed with 3'AMP: Structural Evidence for Direct Interaction of His 40 and Glu 58 with the 2'-Hydroxyl Group of the Ribose." J. Biol. Chem.269. 17531-17536 (1994)

    • Related Report
      1995 Annual Research Report
  • [Publications] Miyatake, Hideyuki 他: "Crystal Structure of the Unliganded Alkaline Protease from Pseudomonas aeruginosa IFO3080 and Its Conformational Changes on Ligand Binding." J. Biochem.118. 474-479 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Takano, Kazufumi 他: "Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-ray Structural Analysis of the Five Isoleucine to Valine Mutants." J. Mol. Biol.254. 62-76 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Yamane, Takashi 他: "Crystal Structure of Streptomyces erythraeus Trypsin at 1.9 Å Resolution." J. Biochem.118. 882-894 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Nitanai, Yasushi 他: "Crystallizationand Preliminary X-Ray Investigation of a Glycoprotein, Human Renal Dipeptidase." J. Crystal Growth.印刷中. (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] Miki, Kunio 他: "Application of Automatic Molecular Replacement Procedure to Crystal Structure Analysis of Cytochrome c_2 from Rhodopseudomonas viridis." Acta Crystallogr.D50. 271-275 (1994)

    • Related Report
      1995 Annual Research Report
  • [Publications] Suzuki, Atsuo 他: "Crystal Structure Analysis of Phospholipase A2 from Trimeresurus flavoviridis (Habu Snake) at 1.5 Å Resolution." J. Biochem.117. 730-740 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Yamagata, Yuriko 他: "Medel Building of DNA Repair Enzyme 3-Methyladenosine DNA Glycosidase-DNA Complex." Nucleic Acids Symposium Series. 34. 7-8 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Mizuyani, Ryuta 他: "Crystallization and Crystallographic Studies on Fab Fragments of Anti-Nitrophenol Antibodies from Primary and Secondary Immune Responses." J. Crystal Growth. 印刷中. (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] 佐藤能雅: "“続医薬品の開発"第17巻「薬物の構造解析」(荒田洋治編集のp. 66-97を担当)" 廣川書店, 222 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Kunio Miki: "Application of an Automatic Molecular-Replacement Procedure to Crystal Structure Analysis of Cytochrome c_2 from Rhodospeudomonas viridis" Acta Crystallographica. D50. 271-275 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] 濱田賢作: "親規βシートコイル構造をもつセラチアプロテアーゼの構造" 日本結晶学会誌. 36. 327-332 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Chikahiro Nagata: "Crystallization and Preliminary X-ray Analysis of Cytochrome c-552 from Nitrosomonas europaea" J.Biochem.116. 946-947 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Zheng Chaode: "DS- a 3-D Graphics Simulation Program for Single-Crystal Diffractometry" J.Appl.Cryst.(印刷中). (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Yasuo Hata: "Crystallization and Preliminary x-ray Diffraction Studies of an Endoglucanase from Aspergillus aculeatus" J.Mol.Biol.241. 278-280 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Shigeharu Harada: "Crystallization and Preliminary x-ray Diffraction Studies of Curculin:A New Type of Sweet Protein Having Taste-Modifying Action" J.Mol.Biol.238. 286-287 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Yoshiki Matsuura: "Enzyme Chemistry and Molecular Biology of Amylase and Related Enzymes" Amylase Research Soc.Japan,CRC Press, 137-165 (1994)

    • Related Report
      1994 Annual Research Report

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Published: 1994-04-01   Modified: 2016-04-21  

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