PDZ domains are one of the most abundant protein-protein interaction modules that mediate protein recognition by binding to short amino acid sequences in the cells. These globular protein domains usually consist of 80-100 amino acid residues that fold into six ß-strands and two a-helices. They are often found in tandem with other interacting modules such as SH3 and GK domains and even with other PDZ containing protein. These domains are involved in signal transduction, synapse formation and receptor translocation and have been implicated in certain diseases such as cervical cancer, Parkinson’s disease and cystic fibrosis.
In this thesis, I have characterized the folding and binding mechanism of three PDZ domains, i.e. SAP97 PDZ2, PSD95 PDZ3 and PTP-BL PDZ2.
I studied the folding mechanism of SAP97 PDZ2, which follows a triangular folding scheme. An intermediate was identified in the folding pathway of this domain, which was populated at equilibrium and may form from denatured or native state depending upon the experimental temperature. The results are suggestive of the plasticity of the folding landscape and reconcile the previous folding studies on PDZ domains (Paper I).
I have also identified allosteric networks in two PDZ domains i.e. PSD95 PDZ3 and PTP-BL PDZ2 by calculating the coupling free energy using the double mutant cycle analysis. Contrary to a previous study, the allosteric network was found to be sequence dependent rather than conserved among the PDZ domains. Moreover, the network identified for one ligand was found to be different from the network for another ligand for the same PDZ domain (Paper II).
Similarly, I have determined the allosteric networks in SAP97 PDZ2 that responds to the binding of peptides derived from the C-terminal end of HPV18 E6 protein. Importantly, the results corroborate the finding in Paper 2, i.e. the residues that are responsive to one peptide ligand are different from the residues that respond to the other peptide ligand (Paper II).
The results thus provide an insight about how the PDZ domain with simple topology and multiple binding partners may retain selectivity within the cell (Paper II and III).
I have also investigated the role of an auxiliary C-terminal helix (α-3) in the allosteric regulation of ligand binding in PSD95 PDZ3. The interaction of α-3 with the peptide Y-5 was found to be direct. Thus we proved in this study that the α-3 contribute towards the regulation of ligand binding in PSD95 PDZ3, and the decrease in affinity of ligand towards α-3 deleted mutant was due to the loss of direct interaction between the α-3 and the peptide ligand (Paper IV). A previous study has suggested that α-3 contributes towards regulation of ligand binding allosterically. But our results suggest that the interaction between the α-3 and Y-5 of the peptide is a direct one and therefore, this helix appears not to allosterically regulate the PDZ3 function.