Molecular Determinants for the Complex Binding Specificity of the PDZ Domain in PICK1

Abstract

PICK1 (protein interacting with C kinase 1) contains a single PDZ domain known to mediate interaction with the C termini of several receptors, transporters, ion channels, and kinases. In contrast to most PDZ domains, the PICK1 PDZ domain interacts with binding sequences classifiable as type I (terminating in (S/T)X⌽; X, any residue) as well as type II (⌽X⌽; ⌽, any hydrophobic residue). To enable direct assessment of the affinity of the PICK1 PDZ domain for its binding partners we developed a purification scheme for PICK1 and a novel quantitative binding assay based on fluorescence polarization. Our results showed that the PICK1 PDZ domain binds the type II sequence presented by the human dopamine transporter (-WLKV) with an almost 15-fold and >100-fold higher affinity than the type I sequences presented by protein kinase C␣ (-QSAV) and the ␤ 2 -adrenergic receptor (-DSLL), respectively. Mutational analysis of Lys 83 in the ␣B1 position of the PDZ domain suggested that this residue mimics the function of hydrophobic residues present in this position in regular type II PDZ domains. The PICK1 PDZ domain was moreover found to prefer small hydrophobic residues in the C-terminal P(0) position of the ligand. Molecular modeling predicted a rank order of (Val > Ile > Leu) that was verified experimentally with up to a ϳ16-fold difference in binding affinity between a valine and a leucine in P(0). The results define the structural basis for the unusual binding pattern of the PICK1 PDZ domain by substantiating the critical role of the ␣B1 position (Lys 83 ) and of discrete side chain differences in position P(0) of the ligands.With over 540 domains in more than 300 different proteins, PDZ (PSD-95/Disc-large/ZO-1 homology) 1 domains are among the most common protein domains in the human genome (1-3). They mediate cellular protein-protein interactions and serve important roles in protein targeting and in the assembly of protein complexes (1, 2). PICK1 (protein interacting with C kinase 1) contains a single N-terminal PDZ domain and was originally identified as an interaction partner for protein kinase C␣ (PKC␣) (5). In addition to its N-terminal PDZ domain, PICK1 contains a coiled-coil domain (residue 145-165 in rat PICK1) that is believed to mediate dimerization of PICK1 (6), followed by a region bearing homology to Arfaptin 1 and 2 (residue 152-362), and a C-terminal acidic cluster (residue 381-389). Although PICK1 was named for its interaction with PKC␣, it rapidly became clear that it had multiple interaction partners. At the current stage, the PDZ domain of PICK1 has been shown to mediate interaction with a broad range of proteins including receptor tyrosine kinases, ionotropic glutamate receptors of the L-␣-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) and kainate subtypes, metabotropic glutamate receptors, ion channels, G protein-coupled receptors, aquaporins, transmembrane transporters, and ADPribosylation factors (see Table I and Ref. 7). PICK1 has been proposed to play a key role in clustering several o...

A flexible docking scheme to explore the binding selectivity of PDZ domains

“…On the other hand, docking Class II peptide to of Cipp-PDZ9 using our flexible approach gives consistently lower RMSD of 0.23 Å . As observed in earlier PDZ docking cases, the inclusion of backbone flexibility through ENM-REMD snapshots does a better job in discriminating that that Lrcc7 has affinity towards Class I peptide, and [87][88][89] Yet, there are several mutations that have been reported previously, such as the mutation of lysine 27 (K27E) to glutamic acid alone or together with aspartic acid 28 (D28A) to alanine, which completely disrupt the interaction with both GluR2 and PKCa. 89 Moreover, the experimental study of Dev et al 87 has shown that mutating lysine 27 to glutamic acid, a point mutation on the bA-bB loop, changes the binding selectivity of PICK1 to exhibit only Class I behavior.…”

“…89 Moreover, the experimental study of Dev et al 87 has shown that mutating lysine 27 to glutamic acid, a point mutation on the bA-bB loop, changes the binding selectivity of PICK1 to exhibit only Class I behavior. Another mutation study that replaces the residue in aB helix (lysine 83 to histidine) by Madsen et al 88 showed that the preference of PICK1 reverts to that of a Class I motif. Docking Class I and Class II peptides to the unbound conformation of wild and mutant PICK1 does not show the change in selectivity upon mutation [brown and red dots in the Figure 4(A-C)].…”

Parkin-mediated Monoubiquitination of the PDZ Protein PICK1 Regulates the Activity of Acid-sensing Ion Channels

“…Through its single PDZ domain, PICK1 binds numerous synaptic proteins, including several neurotransmitter receptors, transporters, and ion channels (Madsen et al, 2005). Furthermore, PICK1 can dimerize via its central coiled-coil motif and thereby promote protein complex formation between its binding partners.…”

“…PICK1 is a synaptic scaffolding protein known to functionally interact with an assortment of neurotransmitter receptors, transporters, and ion channels (Madsen et al, 2005). Unlike CASK, however, PICK1 is a substrate for parkin-mediated ubiquitination.…”

“…This mutation is particularly interesting because it truncates only the last 13 amino acids of parkin, eliminating its PDZ-binding motif, but leaves the critical E2-binding RING domain intact (Lucking et al, 2000;Zhang et al, 2000). Interestingly, although CASK contains a wellcharacterized class II PDZ domain, the PDZ domain of PICK1 can interact with both type I and type II as well as with atypical PDZ ligands (Staudinger et al, 1997;Dev et al, 1999;Williams et al, 2003;Madsen et al, 2005). In contrast, both PSD95 and Veli-1 contain distinct type I PDZ domains and, accordingly, these do not bind to the GST-IR WT construct.…”