Structural basis for PDZ domain interactions in the post-synaptic density scaffolding protein Shank3

Area of Science:

• Neuroscience
• Structural Biology
• Molecular Biology

Background:

• Shank proteins function as essential scaffolding molecules within the post-synaptic density (PSD), a critical structure in neuronal synapses.
• The PDZ domain of Shank proteins is well-characterized for its ability to bind C-terminal segments of various PSD proteins, mediating crucial protein-protein interactions.

Purpose of the Study:

• To conduct a detailed structural analysis of Shank3 PDZ domain-peptide complexes.
• To elucidate the determinants of binding affinity between the Shank3 PDZ domain and different ligand proteins.
• To investigate the structural and functional implications of the SH3-PDZ tandem construct and a schizophrenia-associated mutation.

Main Methods:

• Co-crystallization of Shank3 PDZ domain with peptides from four different proteins.
• Determination of binding affinities using isothermal titration calorimetry.
• Solution structure determination of a tandem Shank3 construct (SH3-PDZ domains).
• Structural analysis of the R536W mutation in the Shank3 SH3-PDZ unit.

Main Results:

• Binding affinity is influenced by conserved class I interactions and additional side chain interactions between peptide residues and the PDZ domain.
• Structural conservation across Shank PDZ domains suggests similar binding specificities.
• Two conserved buried water molecules within PDZ domains may play a role in the local folding of ligand recognition sites.
• The SH3 and PDZ domains in the tandem construct are spatially proximate, potentially impacting the recognition of full-length target proteins.
• The R536W mutation linked to schizophrenia did not alter the structure or peptide binding of the Shank3 SH3-PDZ unit.

Conclusions:

• The study identifies key determinants of binding affinity for short PDZ domain ligands with limited sequence homology.
• The proximity of the SH3 and PDZ domains suggests potential cooperative roles in protein binding.
• The findings provide insights into the structural basis of Shank protein function in synaptic scaffolding and potential implications for neurological disorders.