Doctor Stanley K. Burt
Advanced Biomedical Computing Center
Frederick, Maryland

Monday, April 10, 2000
3:00 pm (CT)
3269 Beckman Institute

Abstract

Density functional theory (DFT) is an ab initio quantum method that allows one to investigate enzyme catalytic mechanisms using larger models of the active site than are currently computationally feasible by traditional Hartree Fock methods. In this presentation, the enzymatic mechanism of two enzymes, thymidine phosphorylase and DNA polymerase beta that are potential targets for anti-cancer and anti-AIDS therapies are investigated. Thymidine phosphorylase is a dual substrate enzyme with two domains whose published crystal structures do not appear to be in a catalytically active conformation. Molecular dynamics simulations reveal a different structure of the enzyme in which the two domains of the enzyme have moved to place the substrates in close contact, and allow a reaction to occur by a direct nucleophilic attack with a low barrier. DNA polymerases are essential for evolution and the maintenance of life. Despite numerous structural, biochemical, and genetic studies their catalytic mechanism is not understood. Crystal structures support a universal two metal ion mechanism of nucleotide addition due to the two Mg++ and two aspartic acids that are strongly conserved in all polymerases. We present our results for the catalytic mechanism of DNA polymerase beta and discuss the contribution of numerous active site residues to the catalysis.

Tea and coffee will be served in R3151 Beckman Institute at 2:15pm.