Computer Modelling of an Enzyme Reference Reaction for Empirical Valence Bond Simulation

Abstract

It is extensively recognized that an enzyme functions through reducing the energy of activation of its elemental reaction and the catalytic effect of an enzyme is as a result of a change in activation free energy obtained relative to a reference reaction in water of the same mechanism. In this study, chorismate mutase which is an enzyme that catalyzes biochemical reactions for chorismate conversion to prephenate has been used as the model enzyme and its catalytic effect was investigated using Empirical Valence Bond method with the employment of Density Functional theory calculation to obtain its reference state reaction. It was found in this study that DFT has been able to produce good activation and reaction free energies compared to experimental values that can serve as a reference to investigate the enzymatic reaction of chorismate mutase and the enzyme’s catalytic effect was well analysed with EVB as the method was able to reproduce the enzyme’s activation and reaction free energies.