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Investigators and Program Directors

David LeMaster

David LeMaster

Research Scientist, Wadsworth Center,
Computational & Structural Biology Associate Professor, School of Public Health, Biomedical Sciences

Ph.D., Yale University (1980)
Postdoctoral training, Yale University


Research Interests

Our laboratory is using protein nuclear magnetic resonance (NMR) measurements to quantify site-specific interactions to gain clearer insight into catalytic function and conformational dynamics. Electrostatic interactions within the active sites of enzymes are widely believed to provide a dominant contribution to biological catalysis. Similarly, the crucial role of electrostatics in the analysis of protein conformation by molecular dynamics algorithms stimulates ongoing efforts to more accurately represent these forces. However, progress in these areas is impeded, in part, by the paucity of experimental data that accurately characterize specific electrostatic interactions within a protein structure. The utility of sidechain ionizations as monitors of local electrostatic interactions is severely limited by the long (Ás-ms) lifetime of the charged state which allows for potentially extensive protein conformational reorganization to occur in response to that ionization. In contrast, the peptide anion intermediate formed during the hydroxide-catalyzed amide hydrogen exchange reaction has a brief (~10 ps) lifetime. Given the limited conformational motion that can occur in that timeframe, the dielectric shielding of peptide ionization appears to be largely limited to the nearly instantaneous electronic polarizability response.

By focusing on backbone amide hydrogens that are exposed to solvent in high resolution X-ray structures, we have found a billion-fold range in exchange rate constants among four well-characterized proteins. Furthermore, these exchange rates are predictable by continuum dielectric methods to within a factor of 7. The optimal internal dielectric value of 3 for hydrogen exchange analysis points to an inconsistency in how electrostatic energies and electrostatic fields of proteins are standardly predicted using nonpolarizable molecular force fields. In the early days of molecular force field analysis, Richard Feynman noted that parametrizations which are optimized to predict total energies need not accurately predict the forces. Optimizing nonpolarizable force fields to predict the total electrostatic energy requires that the atomic charge values be hyperpolarized in order to match the average electric field energy density 1/2 e(t)E2(t) when e(t) is set to the in vacuo dielectric value of 1. As demonstrated by these hydrogen exchange data, substantial systematic errors in the predicted electrostatic potential that arise when the dielectric shielding due to electronic polarizability is neglected.

The local electrostatic potential that determines the acidity of each solvent-exposed amide in a protein depends upon a large set of interactions ranging from atomic contact distance out to at least 14 ┼. As a result, the accuracy of hydrogen exchange prediction is acutely sensitive to the accuracy of the structural model. We are characterizing the use of hydrogen exchange data in analyzing the quality of models for protein structures in solution.

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Contact Information

Phone: (518) 474-6396
Fax: (518) 473-2900