On the catalytic role of structural fluctuations in enzyme reactions: computational evidence on the formation of compound 0 in horseradish peroxidase

Abstract

In this study the question as to whether and to what extent horseradish peroxidase (HRP) enzyme structural flexibility affects the free energy barrier for the formation of the key intermediate compound 0 (Cpd0) is addressed by the use of a combined application of molecular dynamics simulations and perturbed matrix method calculations. Results are intriguing and indicate that, within the simulated conditions, free energy profiles are substantially affected by structural fluctuations of the whole surrounding biological environment (i.e. HRP enzyme and solvent). In this respect our results show that the combined effect of enzyme and solvent provides a substantial lowering of the free energy barrier to the formation of Cpd0, with respect to both gas-phase and QM/MM results carried out at a comparable level of theory. A careful inspection of such observations and their general implications in currently employed methodological approaches to the modelling of enzyme reactions, is also discussed.