Protein-protein recognition: Structure, energetics and drug design

Protein-protein interactions are ubiquitous and essential to almost all known cellular and physiological processes. Many of such interactions are validated targets for chemical therapeutics, and aberrant associations can lead to severe disorders. The importance of such interactions in biology has made the protein-protein recognition process an area of considerable interest. The dissertation focuses on structural and energetic analysis of protein-protein recognition sites, and development of new classes of small molecules inhibiting protein-protein association based on the hypothesis that the binding energies driving protein-protein interactions can also be applied to drive protein-drug interactions.; By analyzing the structural-energetic relationship of protein-protein interactions, we proposed a simple empirical scoring function based on the structural knowledge of protein complexes. It could predict binding modes of protein-protein associations given only the unbound protein structures, and estimates “hot spots” on protein-protein interfaces given the complex structures.; Based on the privileged template model, that the pharmacophore of the recognition sites for peptides/proteins could be transferred onto another template with similar C_α-C_β vectors and still retain the binding specificity, new classes of small molecules have been designed to inhibit three different types of protein-protein recognition sites. (i) The cis-amide bond: a rare but biologically important recognition and regulatory site. (ii) The reverse-turn motif: a popular scaffold mainly sitting on protein surfaces mediating many examples of protein recognition. (iii) The helix: the most abundant secondary structure in protein involving all kinds of recognition processes. Experimental studies on CheY protein and others support the model.; The concepts presented herein will help to experimentally identify protein-protein interactions based on their recognition specificity in the whole genome. This should enrich our knowledge about cellular processes in the post-genomic era.