Structural features and evolution of protein-protein interactions.

Solved structures of protein-protein complexes give fundamental insights into protein function and molecular recognition. Although the determination of protein-protein complexes is generally more difficult than solving individual proteins, the number of experimentally determined complexes increased conspicuously during the last decade. Here, the interfaces of 750 transient protein-protein interactions as well as 2,000 interactions between domains of the same protein chain (obligate interactions) were analyzed to obtain a better understanding of molecular recognition and to identify features applicable for protein binding site prediction. Calculation of knowledge-based potentials showed a preference of contacts between amino acids having complementary physicochemical properties. The analysis of amino acid conservation of the entire interface area showed a weak but significant tendency to a higher evolutionary conservation of protein binding sites compared to surface areas that are permanently exposed to solvent. Remarkably, contact frequencies between outstandingly conserved residues are much higher than expected confirming the so-called "hot spot" theory. The comparisons between obligate and transient domain contacts reveal differences and point out that structural diversification and molecular recognition of protein-protein interactions are subjected to other evolutionary aspects than obligate domain-domain interactions.