Ligand-Induced Dynamic Changes in Extended PDZ Domains from NHERF1

Abstract

The multi-domain scaffolding protein NHERF1 modulates the assembly and intracellular trafficking of various transmembrane receptors and ion-transport proteins. The two PDZ domains of NHERF1 possess very different ligand-binding capabilities: PDZ1 recognizes a variety of membrane proteins with high affinity, while PDZ2 only binds limited number of target proteins. Here using NMR, we have determined the structural and dynamic mechanisms that differentiate the binding affinities of the two PDZ domains, for the Type 1 PDZ-binding motif (QDTRL) in the carboxyl-terminus of CFTR. Similar to PDZ2, we have identified a helix-turn-helix subdomain coupled to the canonical PDZ1 domain. The extended PDZ1 domain is highly flexible with correlated backbone motions on fast and slow timescales, while the extended PDZ2 domain is relatively rigid. The malleability of the extended PDZ1 structure facilitates the transmission of conformational changes at the ligand-binding site to the remote helix-turn-helix extension. By contrast, ligand-binding has only modest effects on the conformation and dynamics of the extended PDZ2 domain. The study shows that ligand induced structural and dynamic changes coupled with sequence variation at the putative PDZ binding site dictate ligand selectivity and binding affinity of the two PDZ domains of NHERF1.

Structural Insights into Neutrophilic Migration Revealed by the Crystal Structure of the Chemokine Receptor CXCR2 in Complex with the First PDZ Domain of NHERF1

“…Only the last four residues of CXCR2 make specific contacts to PDZ1, whereas the first threonine adopts a well-defined conformation but is not directly involved in PDZ1 recognition. This indicates that this residue may not contribute to the interaction specificity, consistent with recent finding that the residue at the corresponding peptide position does not have any contacts with PDZ1 in the solution structure of the PDZ1/synthetic CFTR peptide complex [22]. Similar to other PDZ domains [10], the specificity and affinity of the PDZ1-CXCR2 interaction are achieved mainly by the residues at positions 0 and -2 of the peptide (position 0 referring to the very C-terminal residue), whereas residues -1 and -3 appear to be important for ligand-specific interactions (see below).…”

Controllable Activation of Nanoscale Dynamics in a Disordered Protein Alters Binding Kinetics

“…There is no high-resolution structure of the full-length NHERF1. We have determined the atomic structures of the individual PDZ1, PDZ2, as well as the disordered C-tail using high-resolution NMR [41]. With the available SANS data and atomic coordinates of the PDZ domains, structural models of the full-length NHERF1(wt) or NHERF1(S339D/S340D) are first generated using the program EOM [42].…”

The tails of apical scaffolding proteins EBP50 and E3KARP regulate their localization and dynamics

“…Interestingly, binding to the FERM domain of ezrin has been shown to affect allosteric distances between the PDZ domains, and binding to PDZ ligands has been shown to affect conformation and backbone dynamics (Farago et al. , 2010; Bhattacharya et al. , 2013).…”