Low Frequency Motions of a Carboxylesterase and their Relation to Substrate Selectivity and Catalytic Activity

Carboxylesterase (CEs) are ubiquitous enzymes responsible for the detoxification of xenobiotics. CEs can metabolize and hydrolyze a variety of esterified drugs, including the anticancer agent CPT-11. The specificity of CEs for a particular substrate or inhibitor depends on the enzyme's molecular structure and the dynamics of conformational substructures when a substrate is bound. We have used computational techniques to understand differences in substrate selectivity of CEs. First, we used 10ns molecular dynamics simulations (MD) to identify the loop region of high fluctuation in a CE from B. subtilis - pnbCE. Then we used normal mode analysis to find the lowest frequency mode which represented the largest global motion of pnbCE. Both computational methods were able to identify these two flexible loop regions. Our hypothesis is that the molecular dynamics of this loop region is correlated with substrate conversion efficiency for selected CEs. These experiments provide the first data toward testing this hypothesis.