A class III ligand oscillates between internal and terminal binding modes as it engages with the Dishevelled PDZ domain

Area of Science:

• Molecular Biology
• Structural Biology
• Biochemistry

Background:

• Protein-protein interaction Domain (PDZ) domains mediate crucial cellular functions.
• The PDZ interactome is extensive, but the dynamics of PDZ-ligand interactions remain unclear.

Purpose of the Study:

• To elucidate the functional dynamics of PDZ-ligand interactions, particularly for class III ligands.
• To characterize a novel dual binding mode in PDZ domain recognition.

Main Methods:

• X-ray crystallography to determine the structural basis of binding.
• NMR relaxation dispersion experiments to probe conformational dynamics.
• Site-directed mutagenesis of class III ligands.

Main Results:

• A dual PDZ-binding mode was identified for class III ligands, recognizing either terminal or internal carboxylate groups.
• Specific register rules governing this dual recognition were established.
• Ligand variants retaining a single carboxylate group were sufficient for PDZ binding.
• NMR data revealed dynamic shuffling between binding modes during PDZ engagement.

Conclusions:

• Class III ligand recognition by PDZ domains exhibits unique plasticity due to a dual binding mode.
• This plasticity involves dynamic shuffling between different binding conformations.
• Findings deepen the mechanistic understanding of PDZ binding and protein interactions.