Native State Conformational Ensemble of SEM5 SH3 Domain

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Molecular recognition is one of the most important problems in structural biology. This issue is not just academic, as a clear understanding of the mechanism of recognition will facilitate development of rational design strategies to produce agonistic or antagonistic variants or ligand for clinically important proteins. Although it is clear that the conformational fluctuations (or dynamics) of proteins both affect and are affected by binding, no quantitative, predictive model for the role of dynamics in recognition is available. As a model system, this project investigates the nature and energetics of the native stage conformational ensemble of the SEM5 Sh3 domain from C. elegans. Our Specific Aims are: 1) experimental characterization of its region stability and dynamics, using NMR-detected hydrogen exchange and 15N relaxation; 2) determining the cooperativity of the conformational fluctuations, by measuring the effects of ALA to GLY mutations at positions showing differential stability in Aim 1; 3) correlating the mutations' effects on stability with those on ligand binding, to provide a quantitative description for the role of fluctuations in the recognition process; and 4) structural thermodynamic analysis of selected mutants to determine the energy of the different states, by solving the mutants' solution structures and modeling their flexible regions to the observed changes in their NOE constraints. These experiments are an essential step toward our long-term goal, a structure-based model for quantitatively describing the role of conformational heterogeneity in molecular recognition.