Free energy barriers in protein folding and unfolding reactions

Protein folding and unfolding reactions are slowed down by free energy barriers that arise when changes in enthalpy and entropy do not compensate for each other during the course of the reaction. The nature of these free energy barriers is poorly understood. The common assumption is that a single dominant barrier (>3 k(B)T), describable in terms of a single reaction coordinate, slows down the structural transition, which then becomes an all-or-none transition. This assumption has allowed the empirical application of transition state theory which has proven to be remarkably successful in describing protein folding reactions. Not surprisingly, much effort, both experimental and computational, has focused on determining the native and non-native interactions that determine the properties of the transition state, in order to determine which residues play crucial roles on the folding and unfolding pathways. The alternative hypothesis is that many small (<3 k(B)T) barriers distributed on the energy landscape slow down the structural transition, which then becomes gradual and diffusive. Experimental, theoretical and computational evidence supporting this alternative hypothesis for describing the folding and unfolding of at least some proteins, has gradually been mounting.