Unfolding of the cold shock protein studied with biased molecular dynamics.
The cold shock protein from Bacillus caldolyticus is a small beta-barrel protein that folds in a two-state mechanism. For the native protein and for several mutants, a wealth of experimental data are available on stability and folding, so that it is an optimal system to study this process. We compare data from unfolding simulations (trajectories of 5 and up to 12 ns) obtained with a bias potential at room temperature and from unbiased thermal unfolding simulations with experimental data. The unfolding patterns derived from the trajectories starting from different native-like conformations and subject to different unfolding conditions agree. The transition state found in the simulations of unfolding is close to the native structure in agreement with experiment. Moreover, a lower value of the free energy barrier of unfolding was found for the mutant R3E than for the mutant E46A and the native protein, as indicated by experimental data. The first unfolding event involves the three-stranded beta-sheet whose decomposition corresponds to the transition state. In contrast to conclusions drawn from experiments, we found that the two-stranded beta-strand forms the most stable substructure, which decomposes very late in the unfolding process. However, assuming that this structure forms very early in the folding process, our findings would not contradict the experiments but require a different interpretation of them.
Morra
Giulia
G
Free University of Berlin, Department of Biology, Chemistry and Pharmacy, Institute of Chemistry, Berlin, Germany.
Hodoscek
Milan
M
Knapp
Ernst-Walter
EW
D001426:Bacterial Proteins; D003198:Computer Simulation; D006360:Heat-Shock Proteins / Q000737:chemistry* / Q000235:genetics; D007700:Kinetics; D008958:Models, Molecular; D009154:Mutation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013696:Temperature
D001426:Bacterial Proteins; D006360:Heat-Shock Proteins; C407094:cold shock protein, Bacillus