A Systematic Family-wide Investigation Reveals that ∼30% of Mammalian PDZ Domains Engage in PDZ-PDZ Interactions

PDZ domains are independently folded modules that typically mediate protein-protein interactions by binding to the C termini of their target proteins. However, in a few instances, PDZ domains have been reported to dimerize with other PDZ domains. To investigate this noncanonical-binding mode further, we used protein microarrays comprising virtually every mouse PDZ domain to systematically query all possible PDZ-PDZ pairs. We then used fluorescence polarization to retest and quantify interactions and coaffinity purification to test biophysically validated interactions in the context of their full-length proteins. Overall, we discovered 37 PDZ-PDZ interactions involving 46 PDZ domains (∼30% of all PDZ domains tested), revealing that dimerization is a more frequently used binding mode than was previously appreciated. This suggests that many PDZ domains evolved to form multiprotein complexes by simultaneously interacting with more than one ligand. [Display omitted] ► PDZ-PDZ interactions were investigated on a proteome-wide scale by combining the throughput of protein microarray technology with the fidelity of solution-phase fluorescence polarization ► Thirty-seven PDZ-PDZ interactions were identified, and a representative subset of these interactions was investigated biochemically and found to mediate protein-protein interactions in the context of their full-length proteins ► Overall, PDZ-PDZ dimerization was found to be a much more frequently used binding mode than was previously appreciated