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1990 Fiscal Year Final Research Report Summary

A Rapid Analysis System of Protein Crystal Structures

Research Project

Project/Area Number 01880019
Research Category

Grant-in-Aid for Developmental Scientific Research (B).

Allocation TypeSingle-year Grants
Research Field 物質生物化学
Research InstitutionNagaoka University of Technology (1990)
The University of Tokyo (1989)

Principal Investigator

NAKAMURA Kazuo  Nagaoka Univ. of Technology Associate Prof., 工学部, 助教授 (00012675)

Co-Investigator(Kenkyū-buntansha) MITSUI Yukio  Nagaoka Univ. of Technology Professor, 工学部, 教授 (40012637)
Project Period (FY) 1989 – 1990
KeywordsMolecular graphics / Protein / Three-dimensional structure / X-ray analysis / Refinement
Research Abstract

1. After a personal IRIS graphics workstation was introduced into our laboratory, we checked its graphic and arithmetic performances at first. In result, we found that it has enough performance to realize the object of this project. Then we adapted the TOM program, a graphics fitting program for macromolecules originally coded by Cambillau (1987), to the Personal IRIS workstation. 2. Using a mainframe computer, we optimized thoroughly the stereochemically restrained least-squares refinement program PROLSQ (Hendrickson and Konnert, 1980) modified by us so that the execution time might become as short as possible. After the optimization we adapted the PROLSQ program to the Personal IRIS workstation, and improved the interface between the PROLSQ and TOM programs so that crystallographers might refine protein structures easily and quickly. 3. In order to see if this refinement system works well, we refined the crystal structure of the complex between microbial ribonuclease Ms and its inhibitor, 3'-guanylic acid, using the system. Its coarse atomic coordinates had been obtained by molecular replacement methods. The refinement system worked quite efficiently. It is the proof of the efficiency of the refinement system that for the past only one year we have finished refining seven kinds of protein structures, (1) RNase Ms*3'-GMP complex (2) Subtilisin-SSI complex (3) RNase Ms*2'-GMP complex (4) RNase Ms*GfpC complex (5) Trypsin-SSI complex (6) Interferon-beta and (7) RNase Rh, using this refinement system.

  • Research Products

    (25 results)

All Other

All Publications (25 results)

  • [Publications] 中村 和郎: "分子グラフィックスの現状" 日本結晶学会誌. 32. 31-38 (1990)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Toshiya Senda: "Threeーdimensional Structure of Recombimant Murine Interferonーβ" Proceedings of the Japan Academy. 66. 77-80 (1990)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 中村 和郎: "タンパク質結晶構造の精密化における分子動力学の利用" 化学と工業. 43. 1286-1287 (1990)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Kazuo T.Nakamura: "Threeーdimensional Structres of the complexes between ribonuclease Ms and inhibitors,3'ーGMP and 2'ーGMP" Proceedings of the Second International Meething on Structure, Function and Chemistry (Barcelona). (1991)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Takamasa Nonaka: "Preliminary Crystallographic Study of the Complex between ribonuclease Ms and GfpC" Proceedings of the Second International Meething on Structure,Function and Chemisty (Barcelona). (1991)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Yasuo Takeuchi: "Refined Crystal Structure of the Complex of Subtilisim BPN' and Streptomyces Subtilisin Inhibitor at 1.8A Rosolution" J. Mol. Biol.(1991)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Yasuo Takeuchi: "Moleculer Recognition at the Active Site of Subtilisin BPN'" Protein Engineering. (1991)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Takamasa Nonaka: "Crystal Structure of the complex between ribonuclease Ms and a substrate amalogus,GfpC" KEK Photon Factory Active Report. (1991)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Takamasa Nonaka: "Threeーdimensional Structures of the Complexes between Ribonuclease Ms and Inhibitors,3'ーGMP and 2'ーGMP" KEK Photon Factory Active Report. (1991)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Takamasa Nonaka: "Threeーdimensional Structure of Ribonuclease Ms* 3'ーGnenylic Acid Complex at 2.5A resolution" FEBS Letters. (1991)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 中村 和郎: "新しい実験化学講座 10「回折」4章5節「モデル作成」" 丸善(株), (1992)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Hiroyuki Kurihara: "Crystallization of a New Class of Microbial Ribonuclease from Rhizopus niveus" J. Mol. Biol.,. Vol. 206. 791-792 (1989)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Takamasa Nonaka: "Crystallization of a Complex between Ribonuclease Ms and 3'-Guanylic Acid" J. Mol. Biol.Vol. 207. 853-854 (1989)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kazuo T. Nakamura: "Refined Crystal Structure of Ribonuclease St" Proceedings of the First International Meeting on Structure and Chemistry of Ribonuclease (Moscow). 434-439

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Hiroyuki Kurihara: "Polymorphism of Ribonuclease Rh Crystals which is enhanced through Exposure to Synchrotron beam and its remedy" KEK Photon Factory Activity Report. Vol. 7. 103 (1989)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kazuo T. Nakamura: "Molecular graphics programs on engineering work-stations" J. Cryst. Soc. Japan (in Japanese). 32. 31-38 (1990)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Toshiya Senda: "Three-dimensional Structure of Recombinant Murine Interferon-beta" Proceedings of the Japan Academy. Vol. 66. 77-80 (1990)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] KAzuo T. Nakamura: "Utilizing molecular dynamics in the refinement of protein structures" Kagaku to Kogyo (in Japanese). 43. 1286-1287 (1990)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kazuo T. Nakamura: "Three-dimensional Structures of the complexes between ribonuclease Ms and inhibitors, 3'-GMP and 2'-GMP" Proceedings of the Second International Meeting on Structure, Function and Chemistry (Barcelona). (1991)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Takamasa Nonaka: "Preliminary Crystallographic Study of the complexes between ribonuclease Ms and GfpC" Proceedings of the Second International Meeting on Structure, Function and Chemistry (Barcelona). (1991)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Yasuo Takeuchi: "Refined Crystal Structure of the Complex of Subtilisin BPN' and Streptomyces Subtilisin Inhibitor at 1.8ALPHA Resolution" J. Mol. Biol.,. (1991)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Yasuo Takeuchi: "Molecular Recognition at the Active Site of Subtilisin" Protein Engineering. (1991)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Takamasa Nonaka: "Crystal Structure of the Complex between Ribonuclease Ms and a Substrate Analogue" GfpC, KEK Photon Factory Active Report. (1991)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Takamasa Nonaka: "Three-dimensional Structures of the Complexes between Ribonuclease Ms and inhibitors, 3'-GMP and 2'-GMP" KEK Photon Factory Active Report. (1991)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Takamasa Nonaka: "Three-dimensional Structure of Ribonuclease Ms*3'-Guanylic Acid Complex at 2.5ALPHA Resolution" FEBS Letters. (1991)

    • Description
      「研究成果報告書概要(欧文)」より

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Published: 1993-08-12  

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