Two Conserved Residues Govern the Salt and pH Dependencies of the Binding Reaction of a PDZ Domain

Abstract

PDZ domains are protein-protein interaction modules found in hundreds of human proteins. Their binding reactions are sensitive to variations in salt and pH but the basis of the respective dependence has not been clear. We investigated the binding reaction between PSD-95 PDZ3 and a peptide corresponding to a native ligand with protein engineering in conjunction with stopped-flow and equilibrium fluorimetry and found that the two conserved residues Arg-318 and His-372 were responsible for the salt and pH dependencies, respectively. The basis of the salt-dependent variation of the affinity was explored by mutating all charged residues in and around the peptide-binding pocket. Arg-318 was found to be crucial, as mutation to alanine obliterated the effect of chloride on the binding constants. The direct interaction of chloride with Arg-318 was demonstrated by time-resolved urea denaturation experiments, where the Arg-318 3 Ala mutant was less stabilized by addition of chloride as compared with wild-type PDZ3. We also demonstrated that protonation of His-372 was responsible for the increase of the equilibrium dissociation constant at low pH. Both chloride concentration and pH (during ischemia) vary in the postsynaptic density, where PSD-95 is present, and the physiological buffer conditions may thus modulate the interaction between PSD-95 and its ligands through binding of chloride and protons to the "molecular switches" Arg-318 and His-372, respectively.In the post-genomic era there will be ever-increasing focus on protein-protein interactions (1-3) because of their critical role in cellular function and the growing sequence and structure databases. Indeed, most processes in the cell are governed by more or less specific protein-protein interactions. Often the binding is tuned by cellular or extracellular conditions such as pH, ionic strength, and molecular crowding, and also by specific molecules acting allosterically on the protein or competing with the "natural" ligand. Many proteins or protein domains, have evolved to interact with other proteins and form complexes, and one of the most common of these protein-protein interaction modules is the PDZ domain, which is present in several hundred human proteins (4, 5). PDZ domains are often found within multi-domain scaffolding proteins, and they bind mainly to the C termini of their target proteins (6 -8) but also internally (9, 10). PDZ domains have been shown to be rather promiscuous with regard to their ligand, and they have overlapping ligand specificities (6, 7).One of the most well studied PDZ domains is PDZ3 from PSD-95.3 The three-dimensional structure of this protein with and without its target ligand has been solved (11). The canonical PDZ domain consists of about 90 -100 amino acids forming six ␤ strands (␤A to ␤F) and two ␣ helices; ␣A and ␣B neatly arranged in a spherical structure (Fig. 1a). Peptide binding takes place between the ␤B strand and ␣B helix in an antiparallel manner as shown in Fig. 1a. As judged by the crystal structure, PDZ3 binds its targ...

Reassessing a sparse energetic network within a single protein domain

“…The PSD95 PDZ3 used in this study was similar to that in Chi et al (20). The numbering of residues in this article is in accordance with the crystal structure of PSD95 PDZ3 (13) (PDB entry 1BE9).…”

“…We chose to use the same reference mutation, H372Y, as in the previous study (7). The decrease in affinity for the H372Y mutation (two orders of magnitude) was similar to that for the deletion mutation H372A (20), suggesting that the hydrogen bond present in the wild-type complex (13) is not formed between the mutant H372Y and the peptide. It is clear that the PDZ domain pays a thermodynamic penalty for this functional His residue because mutation to either Ala or Tyr stabilizes the protein by Ϸ2 kcal⅐mol Ϫ1 .…”

“…Protein expression and purification were as described in ref. 20. All purified samples were dialyzed against 25 mM Tris⅐HCl (pH 7.5).…”

Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins

“…43) as well as a short His-tag, which does not influence the folding of PDZ3 (21). Expression and purification were as described earlier (37,46). The purity was checked by SDS/PAGE and the identity, by MALDI-TOF mass spectrometry.…”

Extensions of PDZ domains as important structural and functional elements

“…Furthermore, it is well-documented that the binding affinity can also depend on the phosphorylation state of the target (Cohen et al, 1998;Chung et al, 2000;Hegedüs et al, 2003), as well as the conditions of the surrounding solution, such as the ionic strength, pH, and redox potential (Chi et al, 2006;Mishra et al, 2007). It was surprising when studies suggested that, in the canonical PDZ domain, residues away from the binding pocket can affect the binding affinity (Lockless and Ranganathan, 1999), because such residues were previously thought to have only a supporting structural role.…”