Characterization of a Nitrogenase Iron Protein Substituted with a Synthetic [Fe4 Se4 ] Cluster

The Fe protein of nitrogenase plays multiple roles in substrate reduction and cluster maturation via its redox-active [Fe₄ S₄ ] cluster. Here we report the synthesis and characterization of a water-soluble [Fe₄ Se₄ ] cluster that is used to substitute the [Fe₄ S₄ ] cluster of the Azotobacter vinelandii Fe protein (AvNifH). Biochemical, EPR and XAS/EXAFS analyses demonstrate the ability of the [Fe₄ Se₄ ] cluster to adopt the super-reduced, all-ferrous state upon its incorporation into AvNifH. Moreover, these studies reveal that the [Fe₄ Se₄ ] cluster in AvNifH already assumes a partial all-ferrous state ([Fe₄ Se₄ ]⁰ ) in the presence of dithionite, where its [Fe₄ S₄ ] counterpart in AvNifH exists solely in the reduced state ([Fe₄ S₄ ]¹⁺ ). Such a discrepancy in the redox properties of the AvNifH-associated [Fe₄ Se₄ ] and [Fe₄ S₄ ] clusters can be used to distinguish the differential redox requirements for the substrate reduction and cluster maturation of nitrogenase, pointing to the utility of chalcogen-substituted FeS clusters in future mechanistic studies of nitrogenase catalysis and assembly.

Uno Ferro, a de novo Designed Protein, Binds Transition Metals with High Affinity and Stabilizes Semiquinone Radical Anion

Metalloenzymes often utilize radicals in order to facilitate chemical reactions. Recently, DeGrado and co-workers have discovered that model proteins can efficiently stabilize semiquinone radical anion produced by oxidation of 3,5-di-tert-butylcatechol (DTBC) in the presence of two zinc ions. Here, we show that the number and the nature of metal ions have relatively minor effect on semiquinone stabilization in model proteins, with a single metal ion being sufficient for radical stabilization. The radical is stabilized by both metal ion, hydrophobic sequestration, and interactions with the hydrophilic residues in the protein interior resulting in a remarkable, nearly 500 mV change in the redox potential of the SQ^{. -} /catechol couple compared to bulk aqueous solution. Moreover, we have created 4G-UFsc, a single metal ion-binding protein with pm affinity for zinc that is higher than any other reported model systems and is on par with many natural zinc-containing proteins. We expect that the robust and easy-to-modify DFsc/UFsc family of proteins will become a versatile tool for mechanistic model studies of metalloenzymes.

Strategies Towards Capturing Nitrogenase Substrates and Intermediates via Controlled Alteration of Electron Fluxes

Nitrogenase utilizes an ATP-dependent reductase to deliver electrons to its catalytic component to enable two important reactions: the reduction of N₂ to NH₄ ⁺ , and the reduction of CO to hydrocarbons. The two nitrogenase-based reactions parallel the industrial Haber-Bosch and Fischer-Tropsch processes, yet they occur under ambient conditions. As such, understanding the enzymatic mechanism of nitrogenase is crucial for the future development of biomimetic strategies for energy-efficient production of valuable chemical commodities. Mechanistic investigations of nitrogenase has long been hampered by the difficulty to trap substrates and intermediates relevant to the nitrogenase reactions. Recently, we have successfully captured CO on the Azotobacter vinelandii V-nitrogenase via two approaches that alter the electron fluxes in a controlled manner: one approach utilizes an artificial electron donor to trap CO on the catalytic component of V-nitrogenase in the resting state; whereas the other employs a mismatched reductase component to reduce the electron flux through the system and consequently accumulate CO on the catalytic component of V-nitrogenase. Here we summarize the major outcome of these recent studies, which not only clarified the catalytic relevance of the one-CO (lo-CO) and multi-CO (hi-CO) bound states of nitrogenase, but also pointed to a potential competition between N₂ and CO for binding to the same pair of reactive Fe sites across the sulfur belt of the cofactor. Together, these results highlight the utility of these strategies in poising the cofactor at a well-defined state for substrate- or intermediate-trapping via controlled alteration of electron fluxes, which could prove beneficial for further elucidation of the mechanistic details of nitrogenase-catalyzed reactions.

Evaluation of the Catalytic Relevance of the CO-Bound States of V-Nitrogenase

Binding and activation of CO by nitrogenase is a topic of interest because CO is isoelectronic to N₂ , the physiological substrate of this enzyme. The catalytic relevance of one- and multi-CO-bound states (the lo-CO and hi-CO states) of V-nitrogenase to C-C coupling and N₂ reduction was examined. Enzymatic and spectroscopic studies demonstrate that the multiple CO moieties in the hi-CO state cannot be coupled as they are, suggesting that C-C coupling requires further activation and/or reduction of the bound CO entity. Moreover, these studies reveal an interesting correlation between decreased activity of N₂ reduction and increased population of the lo-CO state, pointing to the catalytic relevance of the belt Fe atoms that are bridged by the single CO moiety in the lo-CO state. Together, these results provide a useful framework for gaining insights into the nitrogenase-catalyzed reaction via further exploration of the utility of the lo-CO conformation of V-nitrogenase.

Nitrogen Reduction to Ammonia on a Biomimetic Mononuclear Iron Centre: Insights into the Nitrogenase Enzyme

Nitrogenases catalyse nitrogen fixation to ammonia on a multinuclear Fe‐Mo centre, but their mechanism and particularly the order of proton and electron transfer processes that happen during the catalytic cycle is still unresolved. Recently, a unique biomimetic mononuclear iron model was developed using tris(phosphine)borate (TPB) ligands that was shown to convert N₂ into NH₃. Herein, we present a computational study on the [(TPB)FeN₂]⁻ complex and describe its conversion into ammonia through the addition of electrons and protons. In particular, we tested the consecutive proton transfer on only the distal nitrogen atom or alternated protonation of the distal/proximal nitrogen. It is found that the lowest energy pathway is consecutive addition of three protons to the same site, which forms ammonia and an iron‐nitrido complex. In addition, the proton transfer step of complexes with the metal in various oxidation and spin states were tested and show that the pK_a values of biomimetic mononuclear nitrogenase intermediates vary little with iron oxidation states. As such, the model gives several possible NH₃ formation pathways depending on the order of electron/proton transfer, and all should be physically accessible in the natural system. These results may have implications for enzymatic nitrogenases and give insight into the catalytic properties of mononuclear iron centres.

Tuning Electron Flux through Nitrogenase with Methanogen Iron Protein Homologues

Nitrogenase uses a reductase component called Fe protein to deliver electrons to its catalytic partner for substrate reduction. The essential role of Fe protein in catalysis makes it an ideal target for regulating the electron flux and enzymatic activity of nitrogenase without perturbing the cofactor site. This work reports that hybrids between the Fe protein homologs of Methanosarcina acetivorans and the catalytic components of Azotobacter vinelandii can trap substrate CO through reduced electron fluxes. In addition, homology modeling/in silico docking is used to define markers for binding energy and specificity between the component proteins that correlate with the experimentally determined activities. This homologue-based approach could be further developed to allow identification or design of hybrids between homologous nitrogenase components for mechanistic investigations of nitrogenase through capture of substrates/ intermediates or for transgenic expression of nitrogenase through synthetic biology.