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Structural basis of hierarchical multiple substates of a protein. II: Monte carlo simulation of native thermal fluctuations and energy minimization
Author(s) -
Noguti Tosiyuki,
Gō Nobuhiro
Publication year - 1989
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340050204
Subject(s) - nanosecond , maxima and minima , monte carlo method , statistical physics , molecular dynamics , superposition principle , energy landscape , cluster (spacecraft) , chemical physics , globular protein , energy minimization , picosecond , chemistry , molecular physics , range (aeronautics) , globular cluster , physics , crystallography , computational chemistry , materials science , thermodynamics , computer science , mathematics , quantum mechanics , galaxy , composite material , mathematical analysis , laser , statistics , programming language , optics
Conformational fluctuations in a globular protein, bovine pancreatic trypsin inhibitor, in the time range between picoseconds and nanoseconds are studied by a Monte Carlo simulation method. Multipleenergy minima are derived from sampled conformations by minimizing their energy. They are distributed in clusters in the conformational space. A hierarchical structure is observed in the simulated dynamics. In the time range between 10 −14 and 10 −10 seconds dynamics is well represented by a superposition of vibrational motions within an energy well with transitions among minima within each cluster. Transitions among clusters take place in the time range of nanoseconds or longer.