An entropy criterion to detect minimally frustrated intermediates in native proteins.

Abstract

The analysis of the information flow in a feed-forward neural network suggests that the output of the network can be used to compute a structural entropy for the sequence-to-secondary structure mapping. On this basis, we formulate a minimum entropy criterion for the identification of minimally frustrated traits with helical conformation that correspond to initiation sites of protein folding. The entropy of protein segments can be viewed as a nucleation propensity that is useful to characterize putative regions where folding is likely to be initiated with the formation of stretches of alpha-helices under the predominant influence of local interactions. Our procedure is successfully tested in the search for initiation sites of protein folding for which independent experimental and computational evidence exists. Our results lend support to the view that folding is a hierarchical event in which, in harmony with the minimal frustration principle, the final conformation preserves structural modules formed in the early stages of the process.