Abstract: Objective compare PDZs from two homologous simple adaptor proteins PDZK1 and PDZK2 and their binding properties. Method we used yeast two-hybrid screening of a random peptide library and high throughput validation screening of a specialized PDZ ligand candidate library to systematically and comprehensively identify PDZ ligands, consensus-binding sequences were deduced from sequence alignment of positive clones. Two PDZs were compared by structure-guided sequence alignment. The binding properties of the PDZ domains were analyzed. Result the C-terminal consensus sequence for binding to PDZK1-PDZ1 and PDZK2-PDZ1 are -[S/T]-x-Φ and -[S/T]-[K/R/H]-[F/L] respectively. The contacting residues on the PDZ domains are similar, only the amino acids between 37 and 45 are difference, especially at the 42 position (F vs H). Conclusion Homologous PDZK1 and PDZK2 have different contacting residues and different binding properties.

Key words: protein interaction, PDZ, Yeast two-hybrid, bioinformatics.