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 sequences, the phage display method has not been amenable to the study of PDZ domain binding specificities. For the first time, we demonstrate the functional display of a peptide library fused to the carboxyl terminus of the M13 major coat protein. We used this library to analyze carboxyl-terminal peptide recognition by two PDZ domains. For each PDZ domain, the library provided specific ligands with sub-micromolar binding affinities. Synthetic peptides and homology modeling were used to dissect and rationalize the binding interactions. Our results establish carboxyl-terminal phage display as a powerful new method for mapping PDZ domain binding specificity.
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Departments of Protein Engineering, Molecular Oncology, and Bioorganic Chemistry, Genentech, Inc., South San Francisco, California 94080, USA.
Pisabarro
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Li
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Quan
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Lasky
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Sidhu
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D000595:Amino Acid Sequence; D017104:Bacteriophage M13; D001665:Binding Sites; D002213:Capsid / Q000737:chemistry*; D036022:Capsid Proteins; D017124:Conserved Sequence; D006801:Humans; D007700:Kinetics; D008024:Ligands; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D019151:Peptide Library; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
D036022:Capsid Proteins; D008024:Ligands; D008565:Membrane Proteins; D009419:Nerve Tissue Proteins; D019151:Peptide Library; D011994:Recombinant Proteins; C025668:coat protein, Bacteriophage M13; C033652:postsynaptic density proteins