Redistribution of sidechain-sidechain interactions govern ligand-specific binding affinity changes in missense Shank1 PDZ mutants

Shank proteins represent a family of abundant scaffolds in the postsynaptic density. Their dysfunctions had been identified as possible causes behind autism spectrum disorders and various types of cancer. The remarkably promiscuous PDZ domain of the Shank family is highly conserved through isoforms, and contains a unique dynamic segment, the {beta}2-{beta}3 loop, which is likely to play an important role in ligand selectivity. We used the Shank1 PDZ as a model system to analyze the perturbing effects of five disease-associated missense mutations on the binding of different partner peptides. Using experimental methods and molecular dynamics simulations, we characterized the interactions in detail, focusing on their dynamic aspect. While the investigated mutations in general weaken most interactions, the R736Q mutant, unique in having increased thermal stability, also binds the GKAP peptide with higher affinity than the wild type. Overall, our results show that the perturbing effect of mutations is highly partner-specific and depends on the dynamic rearrangements of both uniformly occurring and ligand-specific residue-residue interactions. StatementThe Shank1 protein plays a possible role in autism spectrum disorders and also cancer, two conditions that affect many lives. Our paper provides a more-detailed-than-ever model of Shank1 PDZ - including disease-associated mutants - bound to its ligands, and we highlight the importance of flexibility and dynamics, which appear to be the main driving force behind its ligand selectivity, and reveal remarkable complexity hiding within this small protein domain.