Computation of the protein structure entropy and its applications to protein folding processes

Abstract

We have developed a general method to compute the structure, entropies of protein sequences. Structure entropy gives a quantitative measure of structure, conservation. This relationship is similar to that between sequence entropy and sequence conservation. Experimental studies in protein folding have suggested that residues relevant to protein folding, or the so-called "hot spot" residues, are usually structurally conserved, though not necessarily conserved in sequences. Hence, the ability to compute structure entropy can help identify important residues related to protein folding. In this work, we have applied our approach to several model proteins frequently used in protein folding experiments. Our results suggest a close relationship between the structure entropies of residues and their rates of amide proton exchange, and we are able to identity regions of residues that are important in protein folding.