PDZ domains are one of the most abundant proteins in the human proteome and are essential to normal cellular physiology. Not surprisingly, errors in either sequence or expression lead to a number of disease states ranging from the rare Usher's Syndrome to Colon Cancer. Yet, we struggle to understand the promiscuous protein-protein interactions which PDZ domains drive and there remains no clear molecular mechanism which details PDZ domain ligand recognition. Domains show a higher diversity in partners than predicted, access a wide range of affinities, and might engage in previously unknown allosteric signaling. As our knowledge of PDZ domain binding preferences increases, ideas about PDZ domains specificity from x-ray structure prove incomplete. This is because proteins are not static structures from which function might be immediately derived. Instead, folded proteins are dynamic around an average structure producing an ensemble of native state conformations. Increasing evidence demonstrates that the motions, or dynamics, of the native state are essential for function. Like other facets of protein architecture, protein dynamics may be under evolutionary pressure to optimize or fine tune a specific task. In this proposal, we have the objective of expanding the traditional notion of a structure-function axis to include dynamics. We put forth the following hypothesis: PDZ domain ligand recognition is modulated by the specific distribution of side-chain dynamics (SCD) of its structure, i.e. its 'dynamics motif'. We test our hypothesis with three aims.
In Aim #1, we will access the evolutionary pressure on SCD and relate this to functional differences observed across the PDZ domain family.
In Aim #2, we seek to find correlated motions as they are a plausible mechanism for long distance communication in proteins without the need for conformational change. And finally, in Aim #3, we design a 'hybrid'PDZ domain and test how long distance alterations in dynamics may alter the interface binding preferences. In this proposal, we expect to determine if SCD have a role in determining PDZ domain specificity, and further, the mechanism with which dynamics convey specificity. We are driven by the rationale that better understanding of PDZ domain binding allows for rational drug design and protein design. And further, PDZ domain interaction may serve as a model system for many promiscuous protein-protein interactions.
- Fundamental to successful drug targeting of protein-protein interactions is the ability to understand the promiscuous nature of these interfaces. This proposed line of research addresses the promiscuity of arguably one of the cells'most important class of protein-protein interactions, those of the PDZ domain family. We expect to define a role for side-chain dynamics in determining specificity in the PDZ domain family, thus providing a framework for improved theoretical prediction of drug and overall ligand binding.