Modeling the interplay between geometrical and energetic effects in protein folding

A theoretical framework is constructed with the aid of a free-energy functional method that is capable of describing the interplay between geometrical and energetic effects on protein folding. In this paper, we generalize a free-energy functional model based on polymer theory to make it more appropriate for comparison with protein folding simulations and experiments. This generalization is made by introducing cooperativity into the configurational entropy and the internal energy. Modifications to configurational entropy enable the model to account for the loop-loop interactions, a contribution neglected in the original model. Modifications to the internal energy introduce many-body corrections, which are needed to establish quantitative contact to simulations as well as experimental observations. To demonstrate the efficiency of the modified analytical model, we compare our results with C(alpha) structure-based (Go) model simulations of chymotrypsin inhibitor II and the SH3 domain of src.