Computational Enzymology

University Of California-Santa Barbara, Santa Barbara CA

Investigators

Abstract

0089864 Bruice The desire to understand the primary tenets, which provide the naturally occurring enzyme catalysts such high efficiency, has been pervasive for half a century. Most attention has been paid to the proposals that: (i) the enzyme binds, and thereby stabilizes, the transition state (Pauling, 1946); (ii) that the binding of substrate and transition state by enzyme freezes out molecular motions and thereby increase the entropy of activation (Jencks, 1970); and (iii) the enzyme holds the substrate in a conformation which closely resembles the transition state (Bruice, 1960). Recent experimental and computational data remove tenet (ii) from contention. This project is to differentiate the importance of tenets (i) and (iii). This is made feasible by recent advances in computational chemistry, the increased performance of current computers, and the advancements in determining the structural coordinates of enzyme substrate species (E S) by x-ray crystallography. By application of kinetic isotope effects and combinations of quantum mechanics along with molecular mechanics (QM/MM) one can obtain from E S the coordinates for the enzyme transition state complex (E TS). Long term molecular dynamic simulations (MD) of the motions in E S and ETS provide all the structural variations in time for these two species. For any given enzyme, data analysis allows a choice between preferential enzyme binding of the transition state (i) rather than the ground state and/or conformers of ES which resemble closely the structure of ETS. This procedure has been used this laboratory for a number of enzymes. Our project is to extend these investigations to the enzyme reactions chorismate to prephenate by chorismate mutase, the hydrolysis of NAD+ by diptheria toxin and nucleoside hydrolysis by Crithidia fasciculata nucleoside hydrolase. These enzymes have been chosen on the basis of the simplicity of their catalytic reactions (first order processes without covalent intermediates) and availability of high resolution X-ray structures. The establishment of any generalization requires many explorations. .