Is protein unfolding the reverse of protein folding? A lattice simulation analysis.
Simulations and experiments that monitor protein unfolding under denaturing conditions are commonly employed to study the mechanism by which a protein folds to its native state in a physiological environment. Due to the differences in conditions and the complexity of the reaction, unfolding is not necessarily the reverse of folding. To assess the relevance of temperature initiated unfolding studies to the folding problem, we compare the folding and unfolding of a 125-residue protein model by Monte Carlo dynamics at two temperatures; the lower one corresponds to the range used in T -jump experiments and the higher one to the range used in unfolding simulations of all-atom models. The trajectories that lead from the native state to the denatured state at these elevated temperatures are less diverse than those observed in the folding simulations. At the lower temperature, the system unfolds through a mandatory intermediate that corresponds to a local free energy minimum. At the higher temperature, no such intermediate is observed, but a similar pathway is followed. The structures contributing to the unfolding pathways resemble most closely those that make up the "fast track" of folding. The transition state for unfolding at the lower temperature (above Tm) is determined and is found to be more structured than the transition state for folding below the melting temperature. This shift towards the native state is consistent with the Hammond postulate. The implications for unfolding simulations of higher resolution models and for unfolding experiments of proteins are discussed.
Dinner
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Dept. of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, MA 02138, USA.
Karplus
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D003198:Computer Simulation; D007700:Kinetics; D009010:Monte Carlo Method; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013696:Temperature; D013816:Thermodynamics