Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase

Abstract

The Mo/Cu-dependent CO dehydrogenase from O. carboxydovorans is an enzyme that is able to catalyse CO oxidation to CO 2 ; moreover, it also expresses hydrogenase activity, as it is able to oxidize H 2 . Here, we have studied the dihydrogen oxidation catalysis by this enzyme using QM/MM calculations. Our results indicate that the equatorial oxo ligand of Mo is the best suited base for catalysis. Moreover, extraction of the first proton from H 2 by means of this basic centre leads to the formation of a Mo–OH–Cu I H hydride that allows for the stabilization of the copper hydride, otherwise known to be very unstable. In light of our results, two mechanisms for the hydrogenase activity of the enzyme are proposed. The first reactive channel depends on protonation of the sulphur atom of a Cu-bound cysteine residues, which appears to favour the binding and activation of the substrate. The second reactive channel involves a frustrated Lewis pair, formed by the equatorial oxo group bound to Mo and by the copper centre. In this case, no binding of the hydrogen molecule to the Cu center is observed but once H 2 enters into the active site, it can be split following a low-energy path.

QM/MM study of the binding of H2 to MoCu CO dehydrogenase: development and applications of improved H2 van der Waals parameters

“…In a previous study [ 13 ], we employed the hybrid QM/MM technique to investigate plausible mechanisms for the oxidation of H 2 by MoCu-CODH. Binding of H 2 to the active site was explored considering the enzyme resting state ( 1H ), the presence of a water molecule in proximity to the copper ion ( 2H ) and the hypothetical protonation of the Cu-bound cysteine residue ( 3H ).…”

“…In this paper, we have deepened our insights about the energetics of the putative initial steps for dihydrogen oxidation by MoCu CO dehydrogenase, keeping as a reference the QM/MM results from our previous investigation of the hydrogenase activity [ 13 ]. The energies were refined by using the BigQM approach on the QM/MM optimised geometries, analogously to our previous work on the CO-oxidation catalysis by this enzyme [ 26 ].…”

“…The setup of the protein was the same as in our previous QM/MM studies of MoCu-CODH [ 13 ]. All calculations were based on the crystal structure of CODH in its oxidised form (PDB ID: 1N5W) [ 2 ].…”

“…Many theoretical studies of hydrogenase reactivity have been published, based either on quantum mechanical (QM) cluster or on hybrid quantum mechanics/molecular mechanics (QM/MM) approaches [ 7 – 13 ]. Moreover, H 2 and O 2 gas diffusion inside the various protein matrices has been investigated via molecular dynamics (MD) simulations [ 14 – 17 ].…”

“…In a previous study, we proposed a mechanistic picture for the MoCu-CODH hydrogenase activity on the basis of QM/MM results [ 13 ]. As far as computed energies are concerned, it has been pointed out that both QM-cluster and QM/MM results may depend critically on the size of the QM system [ 19 – 25 ].…”