Abstract
The geometry and vibrational behavior of selenocysteine [NiFeSe] hydrogenase isolated from Desulfovibrio vulgaris Hildenborough have been investigated using a hybrid quantum mechanical (QM)/ molecular mechanical (MM) approach. Structural models have been built based on the three conformers identified in the recent crystal structure resolved at 1.3 Å from X-ray crystallography. In the models, a diamagnetic Ni2+ atom was modeled in combination with both Fe2+ and Fe3+ to investigate the effect of iron oxidation on geometry and vibrational frequency of the nonproteic ligands, CO and CN-, coordinated to the Fe atom. Overall, the QM/MM optimized geometries are in good agreement with the experimentally resolved geometries. Analysis of computed vibrational frequencies, in comparison with experimental Fourier-transform infrared (FTIR) frequencies, suggests that a mixture of conformers as well as Fe2+ and Fe3+ oxidation states may be responsible for the acquired vibrational spectra.
Highlights
The present work addresses the structure of the active site of recombinant [NiFeSe] hydrogenase isolated from Desulfovibrio vulgaris Hildenborough [1]
The quantum mechanical (QM)/molecular mechanical (MM) optimized geometries of each conformer are shown in Figure 5 for both Fe2+ and Fe3+ superimposed on the oxidized structure determined with X-ray crystallography at
(atoms shown in color: nickel atom is depicted in light blue, iron atom in green, sulfur and selenium atoms in yellow, carbon atoms in light blue, oxygen atoms in red, and nitrogen atoms in dark blue; hydrogen atoms are omitted for clarity)
Summary
The present work addresses the structure of the active site of recombinant [NiFeSe] hydrogenase isolated from Desulfovibrio vulgaris Hildenborough [1]. Hydrogenases are metalloenzymes with an active site that contains, under a reducing atmosphere, iron, nickel and sulfur as well as diatomic ligands like CN and CO, which catalyze the reversible oxidation of molecular hydrogen, H2 ↔ 2 H+ + 2 e−. Hydrogenases can be reductively reactivated after exposure to O2 [1]. Due to their potential of producing hydrogen, these enzymes represent a design template for molecular catalysts being applied in electrolyzers, which use electricity to split water into hydrogen and oxygen, as well as in fuel cells [2].
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