| Project/Area Number |
09480181
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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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 | OKAZAKI NATIONAL RESEARCH INSTITVTES |
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Principal Investigator |
OKAMOTO Yuko Okazaki National Researoh Institvtes, Institvts for Molewlav Science, Associate Professor, 分子科学研究所, 助教授 (70185487)
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| Project Period (FY) |
1997 – 1998
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| Project Status |
Completed (Fiscal Year 1998)
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| Budget Amount *help |
¥800,000 (Direct Cost: ¥800,000)
Fiscal Year 1998: ¥800,000 (Direct Cost: ¥800,000)
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| Keywords | proteiu / nudeic acid / structure determination / X-ray experiment / NMR experiment / murticanonieal algorithm / generalized-eusemble algorithm / マルチカノニカル法 |
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| Research Abstract |
We have been advocating the uses of Monte Carlo simulated annealing and multi-canonical algorithms for the prediction of protein tertiary structures.We have been mainly trying the predictions from the first principles.However, it is the purpose of the present project to show that these methods can also be used for the structural refinement in X-ray and NMR experiments.
In the first year of the project, we first introduced the RISM theory for accurate inclusion of solvent effects and combined RISM and simulated annealing method.As for multicanonical algorithms, it is non-trivial to obtain the probability factor for simulations.It is thus important to develop an efficient method that allows an easy determination of the weight factor.We have invented such a method based on Tsallis statistical mechanics and tested the effectiveness with a penta peptide, Met-enkephalin.
In the second year of the project, we first developed a molecular dynamics version of the above new method that is based on Tsallis statistical mechanics.This is important, since structural refinements in X-ray and NMR experiments are usually based on molecular dynamics method.We further succeeded in the prediction of the tertiary structures of C-peptide of ribonuclease A by multicanonical simulations.We also predicted the tertiary structures of a bovine pancreatic trypsin inhibitor fragment by simulated annealing.It was found that these simulation results are in good agreement with those of X-ray and NMR experiments.
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