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Published June 2014 | public
Journal Article Open

PDZ affinity chromatography: A general method for affinity purification of proteins based on PDZ domains and their ligands


PDZ (PSD-95, DiscsLarge, ZO1) domains function in nature as protein binding domains within scaffold and membrane-associated proteins. They comprise ∼90 residues and make specific, high affinity interactions with complementary C-terminal peptide sequences, with other PDZ domains, and with phospholipids. We hypothesized that the specific, strong interactions of PDZ domains with their ligands would make them well suited for use in affinity chromatography. Here we describe a novel affinity chromatography method applicable for the purification of proteins that contain PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We created a series of affinity resins comprised of PDZ domains from the scaffold protein PSD-95, or from neuronal nitric oxide synthase (nNOS), coupled to solid supports. We used them to purify heterologously expressed neuronal proteins or protein domains containing endogenous PDZ domain ligands, eluting the proteins with free PDZ domain peptide ligands. We show that Proteins of Interest (POIs) lacking endogenous PDZ domain ligands can be engineered as fusion products containing C-terminal PDZ domain ligand peptides or internal, N- or C-terminal PDZ domains and then can be purified by the same method. Using this method, we recovered recombinant GFP fused to a PDZ-domain ligand in active form as verified by fluorescence yield. Similarly, chloramphenicol acetyltransferase (CAT) and β-Galactosidase (LacZ) fused to a C-terminal PDZ domain ligand or an N-terminal PDZ domain were purified in active form as assessed by enzymatic assay. In general, PDZ domains and ligands derived from PSD-95 were superior to those from nNOS for this method. PDZ Domain Affinity Chromatography promises to be a versatile and effective method for purification of a wide variety of natural and recombinant proteins.

Additional Information

© 2014 Elsevier Inc. Received 25 December 2013. and in revised form 24 February 2014. Available online 6 March 2014. This work was supported by grants from the Gordon and Betty Moore Foundation, the Hicks Foundation for Alzheimer's Research, the Allen and Lenabelle Davis Foundation, and from National Institutes of Health Grant MH095095 to MBK. WGW IV was supported by the National Science Foundation Graduate Research Fellowship under Grant No. 2006019582 and the National Institutes of Health under Grant No. NIH/NRSA 5 T32 GM07616. We thank Kathryn M. Ivanetich for her careful editing and review of the manuscript, Jost Vielmetter and Mark Welch for technical discussions and Leslie Schenker for technical assistance.

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August 22, 2023
August 22, 2023