Conservation of Electrostatically Mediated Function Across Protein Families and Superfamilies

136 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2000.The molecular association between an enzyme and substrate is highly specific. The overall association reaction is a delicate balance between attractive and repulsive forces. Association occurs at the cost of removing waters from the binding site and reducing side chain degrees of freedom, which is balanced by the energy gained due to non-covalent interactions, burying of hydrophobic surfaces, and other stabilizing factors (most of which are electrostatic in nature). At long distances, electrostatic forces orient and steer the incoming ligand to the receptor, providing the leit-motif for association. This work explores the conserved electrostatic properties across enzyme families and superfamilies that, despite sequence and structural differences, have maintained function. In order to completely understand how function is conserved across a enzyme family or superfamily, we investigate the conserved and varying features of the protein at both the structure and sequence level. First, methods based in statistical mechanics and biophysics have proven robust enough to probe enzyme function. Continuum electrostatics methods (based on the Poisson-Boltzmann equation) provide a cornputationally efficient method for calculating electrostatic properties of biological molecules. The insights from these methods show that the electrostatically mediated function within a variety of enzyme families and superfamilies is conserved. Second, bioinformatic methods are used to show how the sequence plasticity of the enzyme family or superfamily provides the evolutionary origins for the conserved electrostatic mechanism.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD