Methods and models for studying mechanisms of redox-active enzymes

Source abstract

Abstract Methods and models used in recent quantum chemical studies of redox-active enzymes are described. Only density functional methods are able to treat these systems with sufficient accuracy. For the most accurate of these methods, the so-called hybrid methods, a fraction of exact exchange is included and the deviation from experimental energies is usually not higher than 5 kcal mol−1. The size of the models depends on the problem studied, but is usually in the range 60–100 atoms. To keep the optimized structures sufficiently close to the experimental ones, one atom in each amino acid residue is kept frozen to its position in the X-ray structure. Examples from different recent studies are given with emphasis on dioxygen evolution in photosystem II and proton pumping in cytochrome oxidase. The main advantage of using theoretical methods to study these systems is that short-lived intermediates and transition states can be investigated as easily as stable structures.