CALCULATING ACCURATE REDOX POTENTIALS IN ENZYMES WITH A COMBINED QM/MM FREE ENERGY PERTURBATION APPROACH

Abstract

An approach for computing accurate redox potentials in enzymes is developed based on the free energy perturbation technique in a QM/MM framework. With an appropriate choice of the QM level and QM/MM coupling scheme, the intermolecular interaction between the redox center and the protein environment can be adequately described; the speed of QM/MM methods also allows a sufficient configurational sampling for the convergence of free energy derivatives. Following the implementation into the simulation package CHARMM, the method was tested with an application to the first reduction potential of FAD in cholesterol oxidase (Chox). In addition to an accurate QM level and adequate conformational samplings, the effect of long-range electrostatic interactions due to the bulk solvent was also found to be essential. Using a semi-empirical density functional theory (SCC-DFTB) as the QM level, and a multi-stage charge-scaling scheme based on Poisson–Boltzmann calculations for the solvation effect, satisfactory agreements with experimental measurements were obtained. The study of Chox also indicates that large errors in the calculated redox potential might arise if changes in the conformational properties of the protein during the redox process are not taken into account, such as in energy minimization type of studies based on only the X-ray structure of the enzyme in one redox state.