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 metallo protein 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 i nvolved in the activation and the catalytic cycle of the enzyme, and compar ed them with the available X-ray data. We have also tested various hypothes es concerning the oxidation states of the Ni-Fe bimetallic center and the p rotonation states of the active site by comparing calculated spin densities and vibrational frequencies with EPR and IR spectroscopic data. The good a greement we have obtained with experiment allows us to identify more precis ely those structures that are likely to be important in the enzymatic react ion mechanism.