Prediction of protein domain boundaries from sequence alone

We present here a simple approach to identify domain boundaries in proteins of an unknown three-dimensional structure. Our method is based on the hypothesis that a high-side chain entropy of a region in a protein chain must be compensated by a high-residue interaction energy within the region, which could correlate with a well-structured part of the globule, that is, with a domain unit. For protein domains, this means that the domain boundary is conditioned by amino acid residues with a small value of side chain entropy, which correlates with the side chain size. On the one hand, relatively high Ala and Gly content on the domain boundary results in high conformational entropy of the backbone chain between the domains. On the other hand, the presence of Pro residues leads to the formation of hinges for a relative orientation of domains. The method was applied to 646 proteins with two contiguous domains extracted from the SCOP database with a success rate of 63%. We also report the prediction of domain boundaries for CASP5 targets obtained with the same method.