Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein-protein interactions

Motivation: The increasing amount of data on protein-protein interaction needs to be rationalized for deriving guidelines for the alteration or design of an interface between two proteins. Results: We present a detailed structural analysis and comparison of homo- versus heterodimeric protein-protein interfaces. Regular secondary structures (helices and strands) are the main components of the former, whereas non-regular structures (turns, loops, etc.) frequently mediate interactions in the latter. Interface helices get longer with increasing interface area, but only in heterocomplexes. On average, the homodimers have longer helical segments and prominent helix-helix pairs. There is a surprising distinction in the relative orientation of interface helices, with a tendency for aligned packing in homodimers and a clear preference for packing at 90 degrees in heterodimers. Arg and the aromatic residues have a higher preference to occur in all secondary structural elements (SSEs) in the interface. Based or the dominant SSE, the interfaces have been grouped into four classes: alpha, beta, alpha beta and non-regular. Identity between protein and interface classes is the maximum for a proteins, but rather mediocre for the other protein classes. The interface classes of the two chains forming a heterodimer are often dissimilar. Eleven binding motifs can capture the prominent architectural features of most of the interfaces.