2000 Fiscal Year Final Research Report Summary
The dynamic structure of protein molecules based on coupling among normal modes
| Project/Area Number |
11680664
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | Kitasato University |
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Principal Investigator |
ENDO Shigeru Kitasato University, School of Science, Associate Professor, 理学部, 助教授 (00265729)
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| Co-Investigator(Kenkyū-buntansha) |
WAKO Hiroshi Waseda University, School of Social Sciences, Professor, 社会科学部, 教授 (60158607)
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| Project Period (FY) |
1999 – 2000
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| Keywords | molecular dynamics / internal coordinate / dihedral angle / energy transfer / nonlinear effect / 434 repressor |
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| Research Abstract |
This research aims to investigate complicated motions of a protein systematically by the molecular dynamics with the initial velocity in the direction of each normal mode of a protein molecule from the viewpoint that linear movement of normal modes is extended to the nonlinear range. In normal mode analyses, since the number of variables describing the three-dimensional structure of a molecule decreased, internal coordinates like dihedral angles were often used. The dihedral angle coordinate system was also used for the program of molecular dynamics (FEDER/3) which we have developed.
Molecular dynamics were performed in all the directions along about 300 normal modes lower than 200cm^<-1>, respectively for 434Cro and 434 repressor, and P22c2 repressor, which are homologous proteins. When the temperature per each mode was 300K (about 0.7 K for the whole molecule), the movement initialized with a mode faster than 40cm^<-1> resulted in harmonic oscillation with the fiequency expected from the mode. In higher temperature it was observed that the energy in a mode was dissipated to other modes, in which the energy had a tendency to move to modes roughly corresponding to the second harmonic. In the dynamics initialized with a mode slower than 40cm^<-1>, it was observed also in 300K that the tertiary structure was transferred to that around an energy minimum other than the energy minimum where the normal mode analysis was done. Energy minimization from low-energy states in the trajectories, which started from several different normal modes, however converged to the same energy minimum. That is, the number of energy minima near the native structure was not so many, for example of 434Cro, ones which were able to be transferred at 300K and at 1500K were seven and 32, respectively. It was proved that using this protocol the energy minima near the native structure can be systematically explored even in complicated multidimensional structural space of a protein.
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