Energetics and Dynamics in Protein Recognition

University Of North Carolina At Chapel Hill, Chapel Hill NC

Investigators

Abstract

The dynamic motions in proteins are impressively rich, in terms of both amplitudes and timescales. These fluctuations have a profound impact on protein stability and function. The overall goal of this research is to identify three-dimensional, connective motional networks in a functional protein domain, the second PDZ domain from tyrosine phosphatase 1E (hPTP1E-PDZ2), and relate these networks to PDZ function by characterizing them in the free and ligand-bound PDZ states. Dynamic motions will be characterized using a combination of NMR spin relaxation methods (15N and 2H) and molecular dynamics simulations. To gain insight into the structural and functional context of dynamic perturbations, the dynamic response to single-site mutations will be determined in free and bound PDZ states. Coupling free energies between these residues will be determined with respect to ligand binding and protein unfolding. This combined experimental and theoretical approach may allow determination of the residence of pair-wise residue couplings with respect to functional state. The significance of these studies is to begin to understand how individual, residue motions contribute to larger, multibody, correlated motions that are essential for protein function, such as protein-protein interactions. Key to this effort is a focus on the motions of individual side chains, even those pointing into the protein core, as side chains have large amplitudes of motion, due in part to sampling of multiple rotameric states. The effects of energetic and dynamical coupling and their relation to function investigated here should be fundamental to proteins, and therefore of broad intellectual significance. Integrating this research with the training of minority and women trainees will result in an effort of broad scientific and cultural impact.