Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes

Abstract

Significance: Although knowledge about the human interactome is increasing in coverage because of the development of high-throughput technologies, fundamental gaps remain. In particular, interactions mediated by short linear motifs are of great importance for signaling, but systematic experimental approaches for their detection are missing. We fill this important gap by developing a dedicated approach that combines bioinformatics, custom oligonucleotide arrays and peptide-phage display. We computationally design a library of all possible motifs in a given proteome, print representatives of these on custom oligonucleotide arrays, and identify natural peptide binders for a given protein using phage display. Our approach is scalable and has broad application. Here, we present a proof-of-concept study using both designed human and viral peptide libraries.