Structural basis of hierarchical multiple substates of a protein. II: Monte Carlo simulation of native thermal fluctuations and energy minimization.
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. Multiple energy 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.
Noguti
T
T
Computation Center, Faculty of Engineering, Kyushu University, Fukuoka, Japan.
Go
N
N
D000818:Animals; D002417:Cattle; D003198:Computer Simulation; D015394:Molecular Structure; D009010:Monte Carlo Method; D011487:Protein Conformation; D013696:Temperature; D013816:Thermodynamics; D014361:Trypsin Inhibitors
D014361:Trypsin Inhibitors