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Characterization of diverse internal binding sequences to PDZ domains by screening special random peptide library in yeast two‐hybrid system

There are probably more ways of protein interaction than we currently realize. PDZ domains are flexible protein interaction modules that are considered mainly recognize C‐termini. However, the binding characteristics of PDZ domains to internal sequences have not been systematically studied. In this study, a nearly random octapeptide library with no stop codon designed in the insert was constructed in the yeast two‐hybrid vector. A total of twenty PDZ domains were used as baits to screen the library. They were either previously reported to bind internal sequences or had no known C‐terminal ligand. Among the twenty PDZ domains, eleven were found to bind internal sequences, including three PDZ domains that were not previously reported to bind internal sequences. Eight PDZ domains showed strong amino acids preferences; one of the consensuses was similar to its C‐terminal ligand, but the other consensuses were more diverse than those of common C‐terminal ligands. In addition, one PDZ domain with no strong consensus recognized extended hydrophobic peptides. The results suggest that PDZ domains binding abilities to internal sequences may have been underestimated. Moreover, this data can help us to find potential binding partners which are currently under validation.