Electrostatic Contribution to the Transition States Binding Free Energy Using Simplified Coarse Grained Model

Abstract

Simplified coarse-grained (CG) models (of the type originally developed by Levitt and Warshel (1)) can provide an effective way of evaluating the free energies of explicit protein models (2). Here we use such a reference potential strategy in evaluating the transition state electrostatic binding free energies calculations, which are essential for the rational enzyme design. The method is examined and demonstrated in studies of the effects of mutation on the transition state binding free energies of the esterase catalytic substrates (p-nitrophenyl acetate, 1-and 2-naphthyl acetates) of human carbonic anhydrase II (hCAII) and dienelactone hydrolase (DLH). These have been computed using empirical valence bond (EVB) approach in MOLARIS program (3) with and without the use of the CG model as a reference potential. The calculated electrostatic contributions to the transition state binding free energies reproduce the experimental trends (4, 5). This indicates that the method should provide a powerful tool for exploring the esterase activities of hCAII and DLH for understanding the promiscuity of these enzymes.(1) Levitt, M. and Warshel, A., Nature, 1975, vol. 253, no. 5495, pp. 694-698.(2) Messer, M. M., Roca, M., Chu, Z. T., Vicatos, S., Vardi-Kilshtain, A. and Warshel, A., Proteins, 2009, in press.(3) Lee, F. S., Chu, Z. T. and Warshel, A., J. Comp. Chem., 1993, vol. 14 p. 161.(4) Gould, S. M. and Tawfik, D. S., Biochemistry, 2005, vol. 44, no. 14, pp. 5444-5452.(5) Kim, H.-K., Liu, J.-W., Carr, P.D., Ollis, D.L., Acta Cryst., 2005, vol. D61, pp. 920-031.