A hybrid density functional theory molecular mechanics study of nickel-iron hydrogenase: Investigation of the active site redox states

We have investigated using theoretical methods some of the redox states of the active site of Desulfovibrio gigas NiFe hydrogenase, which is a metalloprotein that catalyzes the reversible reaction H-2 <--(-->) 2H(+) + 2 e(-). A hybrid potential that combines ab initio density functional theory and a molecular mechanics energy function was employed. Starting from the X-ray structure of the oxidized form refined at 2.54 Angstrom resolution, we have optimized the structures of the active site redox states, believed to be involved in the activation and the catalytic cycle of the enzyme, and compared them with the available X-ray data. We have also tested various hypotheses concerning the oxidation states of the Ni-Fe bimetallic center and the protonation states of the active site by comparing calculated spin densities and vibrational frequencies with EPR and IR spectroscopic data. The good agreement we have obtained with experiment allows us to identify more precisely those structures that are likely to be important in the enzymatic reaction mechanism.