Analysis of PDZ domain-ligand interactions using carboxyl-terminal phage display

PDZ domains mediate protein-protein interactions at specialized subcellular sites, such as epithelial cell tight junctions and neuronal post-synaptic densities. Because most PDZ domains bind extreme carboxyl-terminal sequence s, the phage display method has not been amenable to the study of PDZ domai n binding specificities. For the first time, we demonstrate the functional display of a peptide library fused to the carboxyl terminus of the M13 majo r coat protein. We used this library to analyze carboxyl-terminal peptide r ecognition by two PDZ domains. For each PDZ domain, the library provided sp ecific ligands with sub-micromolar binding affinities. Synthetic peptides a nd homology modeling were used to dissect and rationalize the binding inter actions. Our results establish carboxyl-terminal phage display as a powerfu l new method for mapping PDZ domain binding specificity.