Allosteric Communication In Pdz3 Is Orchestrated By The Charged N-Terminus

PDZ domains constitute common models to study single domain allostery, and the third PDZ domain of PSD-95(PDZ3) is known to have selective features that mediate this unit. In this model system, H372 directly connected to the binding site and G330 holding an off-binding-site position, were designated to assess effect of mutations on binding selectivity. H372A and G330T/H372A(DM) mutations change ligand preferences from class-I to class-II, while G330T mutation leads to the recognition of both ligand classes. We have performed a series of molecular dynamics(MD) simulations for wild-type, H372A, G330T single mutants and DM of PDZ3 in the absence and presence of both ligand types. Along with free energy difference calculations and in-depth analysis of MD trajectories, ‘class-switching’ and ‘class-bridging’ behavior of PDZ3 mutants, as well as their effects on binding affinities are explained. We show that the dynamics of the charged N-terminus plays a fundamental role in determining the binding preferences in PDZ3 by altering the electrostatic energy. These findings are corroborated by simulations on N-termini truncated versions of these systems. Furthermore, we employed centrality measures from graph theory to investigate the relation between the previously emphasized structural segments of PDZ3, such as N/C termini, second/third helices and ligands. Modularity of PDZ3 is scrutinized by assessing the dynamic community structures throughout collected MD snapshots. This investigation displays the impact of N-terminus in allosteric communication of selective binding behavior. Take home message is that, dynamical allostery modulated by the charged N-terminus offers a fresh perspective to the study of communication pathways in a wide-range of proteins.