Deciphering PDZ mediated protein complexes by Affinity Chromatography and Mass Spectrometry

Small modular binding domains mediate protein-protein interactions by conferring specificity in multiprotein complex formation. The variability of PDZ (PSD-95/Dlg/ZO-1) domains primary sequences and the structural adaptability of their fold results in different binding modalities. PDZs generally bind to the target carboxyl terminus, but they can also bind to internal sequences of other PDZ or other interaction modules. The eight PDZ domains of the protein PATJ (Protein Associated to Tight Junctions) have been assayed with protein extracts by affinity chromatography followed by mass spectrometry in order to find their protein interactors. Fifteen different proteins were indentified and the interactions of some of them with the PDZ domains of PATJ were further investigated