The broad objective of this research project is to characterize and calculate electrostatic effects in proteins. A semi-continuum electrostatic model will be used, in which the protein is treated as a low-dielectric object containing embedded charges immersed in a high-dielectric solvent. The atomic coordinates and radii of the protein structure determine the shape of the dielectric boundary, which is generally complex and irregular, and the resulting electrostatic equations are solved by finite numerical techniques. Methods will developed to account for the effects of conformational flexibility in the pH titration of proteins, and pH-driven conformational change. The electrostatic model will also be combined with more detailed quantum mechanical calculations for the description of protein active sites. These methods will be applied to studies of the protein tyrosine phosphatases, a class of enzymes involved in the regulation of cell growth and differentiation; and to bacteriorhodopsin, a light-driven proton pump. The protein tyrosine phosphatases must stabilize a large negative charge in a transition state of the catalytic pathway, and have several ionizable sidechains with unusually large pKa shifts of functional or structural importance. In bacteriorhodopsin, the modulation of several pKa values and proton transfer energies within the molecule during its photocycle is crucial to its function as a proton pump.
