Energetic frustration and the nature of the transition state in protein folding

The amino acid sequence and the folding motif are essential in determining the protein folding mechanism. The interplay between energetic (sequence-dependent) and topological (motif dependent) frustrations is investigated for two model beta-barrel proteins of the same native fold but with different interaction Hamiltonians. The nature of the folding transition state ensemble for both models is probed. The extent of structure in the transition state is determined by performing point mutations and recording their effect on the stability of the transition state through their φ values. The transition state shows more structural heterogeneity for the more frustrated sequence, a reflection of the increased roughness of the funneled energy landscape which restricts the number of pathways to the native state. The validity of the φ-analysis approach was assessed to be critically dependent on the degree of frustration of the model. The interpretation of φ values as a measure of the structure of the transition state breaks down for sequences with higher levels of frustration (lower cooperativity) in which a Kramers’ description of the folding reaction is no longer appropriate.