The Challenging in silico Description of Carbon Monoxide Oxidation as Catalyzed by Molybdenum-Copper CO Dehydrogenase

Abstract

Carbon monoxide (CO) is a highly toxic gas to many living organisms. However, some microorganisms are able to use this molecule as the sole source of carbon and energy. Soil bacteria such as the aerobic Oligotropha carboxidovorans are responsible for the annual removal of about 2x108 tons of CO from the atmosphere. Detoxification through oxidation of CO to CO2 is enabled by the MoCu-dependent CO-dehydrogenase enzyme (MoCu-CODH) which—differently from other enzyme classes with similar function—retains its catalytic activity in the presence of atmospheric O2. In the last few years, targeted advancements have been described in the field of bioengineering and biomimetics, which is functional for future technological exploitation of the catalytic properties of MoCu-CODH and for the reproduction of its reactivity in synthetic complexes. Notably, a growing interest for the quantum chemical investigation of this enzyme has recently also emerged. This mini-review compiles the current knowledge of the MoCu-CODH catalytic cycle, with a specific focus on the outcomes of theoretical studies on this enzyme class. Rather controversial aspects from different theoretical studies will be highlighted, thus illustrating the challenges posed by this system as far as the application of density functional theory and hybrid quantum-classical methods are concerned.

Unraveling the Reaction Mechanism of Mo/Cu CO Dehydrogenase Using QM/MM Calculations

“…In this work, we present for the first time a reaction mechanism for the oxidation of CO to CO 2 catalyzed by the Mo/Cu-CODH enzyme that agrees with experimental data, in which dissociation of carbon dioxide takes place directly from the product of the nucleophilic attack reaction aided by the temporary coordination of the glutamate residue to the Mo ion and in which the formation of the thiocarbonate intermediate does not constitute a complication for the enzymatic process. This was achieved thanks to the experience gained by previous works that have shown that the computational modeling of this system requires special care. − In particular, accurate modeling of the protein surrounding the active site, the employment of dispersion corrections, and sufficiently large basis sets in the description of the system proved to be crucial for achieving consistent results. Moreover, we employed the BigQM approach , to obtain refined energies of each step in the CO-oxidation catalysis.…”

Synthesis and Cu(I)/Mo(VI) Reactivity of a Bifunctional Heterodinucleating Ligand on a Xanthene Platform

“…The structural motifs that appear to have an effect on the reactivity are (i) coordination of Mo­(VI) by a redox-active dithiolene ligand that stabilizes the formally Mo­(VI) oxidation state, (ii) several ligands multiply bonded to Mo­(VI), which increases the nucleophilic character of the reactive oxo by decreasing the metal–oxo bond order, , (iii) coordinative unsaturation at the Cu­(I) site, consistent with substrate (CO) coordination, , and (iv) the proximity of Mo­(VI) and Cu­(I), enabled by the sulfido bridge. The mechanism of CO oxidation was probed by spectroscopic and computational studies. − One of the leading current mechanistic hypotheses, supported by DFT calculations, suggests that the initial binding of CO to Cu­(I) ( I -CO) is followed by a nucleophilic attack of Mo-oxo on the electrophilic carbon of CO to form intermediate II . The subsequent oxidation of carbon and reduction of Mo (formally oxo transfer) results in the formation of intermediate III , which is reoxidized to I .…”

Functional Expression of a Mo–Cu-Dependent Carbon Monoxide Dehydrogenase (CODH) and Its Use as a Dissolved CO Bio-microsensor

“…coli was found to be a suitable host for the expression of Mo–Cu CODH after the discovery of a molybdopterin-cytosine-dinucleotide-type (MCD-type) Mo cofactor . This MCD-type Mo cofactor is very unique, exclusive, and pivotal to establish the catalytic activity of expressed recombinant Mo–Cu CODH. ,, …”

“…However, its practical applications have been largely hampered by the extreme sensitivities of these prolific CO oxidizing enzymes to oxygen, leading to its inactivation in CO oxidation activity. In contrast, Mo−Cu CODH has a rare and special feature in which it retains its catalytic activity regardless of oxygen presence (or absence), 3 hence opening an opportunity for Mo−Cu CODH to be prospectively used for an application such as a CO sensor catalytic unit.…”

“…6 This MCD-type Mo cofactor is very unique, exclusive, and pivotal to establish the catalytic activity of expressed recombinant Mo−Cu CODH. 3,7,8 Hitherto, challenges are still arising related to the complexity of the expression process in the host organism. The expression of plasmid-borne coxM-coxS-coxL Mo−Cu CODH structural genes from O. carboxidovorans in E. coli resulted in an inactive apoprotein that lacked cofactors, as reported by Kaufmann and colleagues.…”