Mark Paulsen


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Researcher Bio

Mark D. Paulsen

Professor and Department Head

3301A New Science Facility


My research interests are focused on developing and applying computational methods to study reactions of biochemical interest. The reactions of interest include the collapse of a nascent polypeptide chain to its compact native structure, the association of two proteins, for instance different subunits in a multisubunit complex or redox partners in an electron transfer complex, the association of nucleic acids with nucleic acid binding proteins, or the binding of small ligands to either DNA or enzymes. In order to study these reactions, I utilize a variety of computational techniques including ab initio and semi-empirical quantum mechanical calculations, classical molecular mechanics and dynamics calculations, conformer searching, and free energy calculations, as well as sequence alignment and structure prediction techniques. Currently, I am particularly interested in enzymes which play a critical role in detoxification of potentially hazardous compounds. These enzymes include cyctochromes P450 and glutathione S-transferases which metabolize a wide variety of aliphatc and aromatic compound, phosphotriesterases which degrade organophosphate neurotoxins, and haloalkane dehalogenase and haloacid dehalogenase both of which metabolize simple halogenated aliphatics.


PRIME, interdisciplinary, research, Chemistry