We performed a KS-DFT study of the catalytic cycle of FeNi Hydrogenase where hydrogen is reduced to protons and electrons. From the computational perspective, modeling FeNi Hydrogenase faces extraordinary challenges. The enzyme combines sublet electronic effects of the iron and nickel atoms combined with the large system size that is the active site environment. Therefore, we performed a series of calculations using increasing large models to determine the role that neighboring amino acids have on the geometries and energetics of the reaction intermediates.. Surprisingly, many amino acids near the active site that do not play a role in the proton shuttling channel contribute little to electronic stabilization of the intermediates; therefore, we find the primary role of the environment is to enforce the conformation of the active site. Using these models, we are able to propose a reaction mechanism of this enzyme and elucidate intermediates which unable to be experimentally studied. Specifically, we studied the portion of the catalytic cycle where the hydrogen molecule binds to the active site, which due to the lack of unpaired electrons makes these integral steps in the catalytic cycle EPR silent. We find that the highest free energy intermediate for the catalytic cycle occurs at an intermediate where a proton is coordinated to the Ni center with a μ-hydride bridging between the Ni and Fe centers. Interestingly, this intermediate is often overlooked in the literature due to the close energy difference between it and the H2 bound to Ni intermediate. Additionally, we compare possible pathways for catalysis in the enzyme using a combination of conserved and mutated amino acid residues. It was experimentally determined that mutating the conserved Arg residue to Lys causes the turnover rate of catalysis to shut down, leading to the hypothesis that the splitting of the H2 bond is facilitated by the Arg residue. This was tested by performing a series of calculations on two models, one with the Arg residue and one with the Lys residue. Preliminary data suggests that the presence of either the Arg residue or the mutated Lys residue does not drastically change the stabilization of reaction intermediates and suggests that structural changes in the active site are responsible for the lack of reactivity for the mutated Lys residue.

Elucidating the role of the enzyme environment and mechanism of H2 catalysis in FeNi hydrogenase

2019 Spring National Meeting

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