1987 Fiscal Year Final Research Report Summary
How to Display Three-dimensional Structures of Proteins by Predictive Methods
| Project/Area Number |
61490009
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| Research Category |
Grant-in-Aid for General Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Research Field |
広領域
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| Research Institution | University of Tokyo |
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Principal Investigator |
NAGANO Kozo Univ. Tokyo, Fac. Pharm. Sci., Associate Prof., 薬学部, 助教授 (30012636)
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| Co-Investigator(Kenkyū-buntansha) |
ITAI Akiko Univ. Tokyo, Fac. Pharm. Sci., Assistant Prof., 薬学部, 助手 (60012647)
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| Project Period (FY) |
1986 – 1987
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| Keywords | protein / amino acid sequence / secondary structure / quaternary structure / HBsAg protein / HGS plastic molecular modol / microcomputer / 3SPACE digitizer / AMBER program / atomic coordinato rofinomont / AMBERプログラム / 原子座標合理化 / 三次元グラフィックス |
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| Research Abstract |
We have chosen the structure of hepatitis B surface antigen. The secondary structure prediction method of Nagano suggested that the region of residues 80-98 could be both <alpha>-helical and <beta>-structural. It is very hydrophobic and playing an important role in forming a small spherical particle and an infectious Dane particle. We assumed that a small spherical particle of 22 nm in diameter can be described as an icosahedron with a triangulation number T=1 covered by 60 copies of the proteins, and that a Dane particle of 42 nm as that of T=4 covered by 240 copies. Since the side length of the smallest unit of the equilateral triangles containg 3 copies is ca. 110 A, the region 80-98 was concluded as <beta>-structural. The sequence comparison of the human proteins with the homologous proteins of woodchuck, ground squirrel and duck suggested that a common dimeric disulphide bridge Cys 48-Cys 48. The HGS plastic models were used to build a 3D molecular model of the quaternary structure satisfying the combination of disulphide bridges, the exposed locations of various subtypic determinant amino acid residues, and the maximally possible main-chain hydrogen bonds of the secondary structure. The model was hung inside a wooden latice attached on the table of a magnetically modulated device for measuring the 3D atomic coordinates, 3SPACE digitizer. A modification of the measurement applying a plastic straw at the head of the induction coil was introduced so that we could make measurements inside a considerably complicated plastic model. The measured coordinates were sent to a large central computer for refining the atomic coordinates by the program AMBER. The model was displayed by a 3D interactive computer graphics.
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