Numerous studies have provided large-scale information on human protein-protein interactions. However, many interactions remain to be discovered, and low affinity, conditional and cell type-specific interactions disproportionately under-represented. Most of the missing interactions are most likely mediated by short linear motifs (SLiMs). The SLiM-based interactions are of critical importance for cell function and regulation. Over the last ten years we have developed dedicated experimental methods for large-scale screening of SLiM-based interactions together with tools and guidelines for processing the generated data. I will describe our optimized proteomic peptide-phage display (ProP-PD) library that tiles all disordered regions of the human proteome and allows the screening of ~1,000,000 overlapping peptides in a single binding assay. Using this resource we have identified >2,000 interaction SLiM-based interactions. The amino acid resolution binding site information can be used to pin-point functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the proteome. Following this line, I will describe our novel study focused on uncovering how disease mutations make and break SLiM-based interactions. Finally, I will showcase how we employ ProP-PD to explore host-virus protein-protein interactions, and how this information can be used to identify peptides with antiviral activities.
Published on September 20, 2023