Many of the biological processes that are governed by electrostatics, such as catalysis, redox reactions, proton and electron transport, photoactivation, ion selectivity, and ligand recognition and binding, take place in environments secluded from solvent, such as in the protein interior or at interfaces between molecules. Calculations of electrostatic effects with existing computational methods fail dramatically in these environments. To address these problems we are studying the energetics of ionization of buried groups. The approach entails experiments to identify the processes that contribute to the polarizability in the protein interior and to obtain the data needed to improve and to test computational methods for structure-based energy calculations.
We are studying the molecular determinants of pKa values of surface ionizable residues. This entails mapping contributions from short-range and long-range coulombic interactions, hydrogen bonding, packing, degree of exposure to solvent, etc. More recently we have begun to explore the hypothesis that local conformational fluctuations are important determinants of pKa values. In a related project we are studying the molecular mechanism of acid denaturation of staphylococcal nuclease. Our goal is to improve understanding of the balance of forces in proteins and of the mechanisms whereby changes in solution conditions trigger conformational transitions in proteins.
Viruses are macromolecular assemblies that can sense and respond to minute changes in the ionic properties of their environment. Changes in pH and ion concentration can trigger conformational transitions essential for the viral life cycle. We study the molecular mechanisms in icosahedral viral capsids whereby changes in environmental signals can trigger conformational transitions required for presentation of the viral genome to the replication machinery of the host cell. This involves mapping the effects of solution conditions on virus stability with a variety of physical and biochemical techniques. Crystallographic structures of viruses are used to interpret the measured energetics structurally.
Algorithms for structure-based energy calculations represent a powerful approach for connecting high resolution structures and functional energetics. We are involved in the design, implementation and testing of semi-empirical algorithms for structure-based calculation of electrostatic energies in proteins. The algorithms for structure-based energy calculations are based on classical electrostatics and on the principles of statistical thermodynamics. One of the specific problems that we are studying concerns the treatment of site-bound waters in pKa calculations and the coupling between changes in pKa values and conformational transitions.