Six-Electron Reduction of Nitrite to Ammonia by Cytochrome c Nitrite Reductase: Insights from Density Functional Theory Studies

Recent mechanistic developments for cytochrome c nitrite reductase, the key enzyme in the dissimilatory nitrate reduction to ammonium pathway

Cytochrome c nitrite reductase, NrfA, is a soluble, periplasmic pentaheme cytochrome responsible for the reduction of nitrite to ammonium in the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway, a vital reaction in the global nitrogen cycle. NrfA catalyzes this six-electron and eight-proton reduction of nitrite at a single active site with the help of its quinol oxidase partners. In this review, we summarize the latest progress in elucidating the reaction mechanism of ammonia production, including new findings about the active site architecture of NrfA, as well as recent results that elucidate electron transfer and storage in the pentaheme scaffold of this enzyme.

Role of distal arginine residue in the mechanism of heme nitrite reductases

Heme nitrite reductases reduce NO₂^- by 1e^-/2H⁺ to NO or by 6e^-/8H⁺ to NH₄⁺ which are key steps in the global nitrogen cycle. Second-sphere residues, such as arginine (with a guanidine head group), are proposed to play a key role in the reaction by assisting substrate binding and hydrogen bonding and by providing protons to the active site for the reaction. The reactivity of an iron porphyrin with a NO₂^- covalently attached to a guanidinium arm in its 2nd sphere was investigated to understand the role of arginine residues in the 2nd sphere of heme nitrite reductases. The presence of the guanidinium residue allows the synthetic ferrous porphyrin to reduce NO₂^- and produce a ferrous nitrosyl species ({FeNO}⁷), where the required protons are provided by the guanidinium group in the 2nd sphere. However, in the presence of additional proton sources in solution, the reaction of ferrous porphyrin with NO₂^- results in the formation of ferric porphyrin and the release of NO. Spectroscopic and kinetic data indicated that re-protonation of the guanidine group in the 2nd sphere by an external proton source causes NO to dissociate from a ferric nitrosyl species ({FeNO}⁶) at rates similar to those observed for enzymatic sites. This re-protonation of the guanidine group mimics the proton recharge mechanism in the active site of NiR. DFT calculations indicated that the lability of the Fe-NO bond in the {FeNO}⁶ species is derived from the greater binding affinity of anions (e.g. NO₂^-) to the ferric center relative to neutral NO due to hydrogen bonding and electrostatic interaction of these bound anions with the protonated guanidium group in the 2nd sphere. The reduced {FeNO}⁷ species, once formed, is not affected significantly by the re-protonation of the guanidine residue. These results provide direct insight into the role of the 2nd sphere arginine residue present in the active sites of heme-based NiRs in determining the fate of NO₂^- reduction. Specifically, the findings using the synthetic model suggest that rapid re-protonation of these arginine residues may trigger the dissociation of NO from the {FeNO}⁶, which may also be the case in the protein active site.

An unusual active site architecture in cytochrome c nitrite reductase NrfA-1 from Geobacter metallireducens

Dissimilatory nitrate reduction to ammonia (DNRA) is a central pathway in the biogeochemical nitrogen cycle, allowing for the utilization of nitrate or nitrite as terminal electron acceptors. In contrast to the competing denitrification to N2, a major part of the essential nutrient nitrogen in DNRA is retained within the ecosystem and made available as ammonium to serve as a nitrogen source for other organisms. The second step of DNRA is mediated by the pentahaem cytochrome c nitrite reductase NrfA that catalyzes the six-electron reduction of nitrite to ammonium and is widely distributed among bacteria. A recent crystal structure of an NrfA ortholog from Geobacter lovleyi was the first characterized representative of a novel subclass of NrfA enzymes that lacked the canonical Ca2+ ion close to the active site haem 1. Here, we report the structural and functional characterization of NrfA from the closely related G. metallireducens. We established the recombinant production of catalytically active NrfA with its unique, lysine-coordinated active site haem heterologously in Escherichia coli and determined its three-dimensional structure by X-ray crystallography to 1.9 Å resolution. The structure confirmed GmNrfA as a further calcium-independent NrfA protein, and it also shows an altered active site that contained an unprecedented aspartate residue, D80, close to the substrate-binding site. This residue formed part of a loop that also caused a changed arrangement of the conserved substrate/product channel relative to other NrfA proteins and rendered the protein insensitive to the inhibitor sulphate. To elucidate the relevance of D80, we produced and studied the variants D80A and D80N that showed significantly reduced catalytic activity.

Kinetic Analysis of Nitrite Reduction Reactions by Nitrite Reductase Derived from Spinach in the Presence of One-Electron Reduced Riboflavin

The development of methods for converting nitrogen oxides in water into valuable resources such as ammonia and hydrazine has been given some attention. By utilizing the nitrite-reducing catalytic activity of nitrite reductase (NiR), nitrite in water can be converted into ammonium. However, there are few reports in the research that synthesized ammonium from nitrite using nitrite reductase. Therefore, we aimed to investigate the effect of temperature on the nitrite-reducing catalytic activity of NiR from spinach in the presence of one-electron reduced riboflavin by kinetic analysis to find the optimum temperature conditions. The results of this study showed that the reaction temperature does not need to be higher than 296.15 K in order to improve the efficiency of ammonium production from nitrite using NiR.

Recent advances in electrocatalytic nitrite reduction

Electrocatalytic nitrite reduction is of great significance for wastewater treatment and value-added chemicals synthesis. This review highlights the latest progress in electrochemical nitrite reduction to produce two types of products, including gaseous products (NO, N₂O, N₂) and liquid products (NH₂OH and NH₄⁺). The heterogeneous and homogeneous catalysts used in the corresponding reduction processes are introduced, with emphasis on the product selectivity regulation and reaction mechanism understanding. Finally, the challenges and opportunities in this field are analyzed as well. This review can provide guidelines for designing electrochemical systems with high efficiency and specificity for nitrite reduction.

Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II

Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling techniques represent the two workhorses in mechanistic understanding of enzyme catalysis. One of the stringent tests for QM/MM and/or QM approaches is to provide quantitative answers to real-world biochemical questions, such as the effect of single-point mutations on enzyme kinetics. This translates into predicting the relative activation energies to 1-2 kcal·mol^-1 accuracy; such predictions can be used for the rational design of novel enzyme variants with desired/improved characteristics. Herein, we employ glutamate carboxypeptidase II (GCPII), a dizinc metallopeptidase, also known as the prostate specific membrane antigen, as a model system. The structure and activity of this major cancer antigen have been thoroughly studied, both experimentally and computationally, which makes it an ideal model system for method development. Its reaction mechanism is quite well understood: the reaction coordinate comprises a "tetrahedral intermediate" and two transition states and experimental activation Gibbs free energy of ∼17.5 kcal·mol^-1 can be inferred for the known k_cat ≈ 1 s^-1. We correlate experimental kinetic data (including the E424H variant, newly characterized in this work) for various GCPII mutants (k_cat = 8.6 × 10^-5 s^-1 to 2.7 s^-1) with the energy profiles calculated by QM/MM and QM-only (cluster model) approaches. We show that the near-quantitative agreement between the experimental values and the calculated activation energies (ΔH^⧧) can be obtained and recommend the combination of the two protocols: QM/MM optimized structures and cluster model (QM) energetics. The trend in relative activation energies is mostly independent of the QM method (DFT functional) used. Last but not least, a satisfactory correlation between experimental and theoretical data allows us to provide qualitative and fairly simple explanations of the observed kinetic effects which are thus based on a rigorous footing.

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen

Since the characterization of cytochrome c₅₅₂ as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH₄⁺ produced from NO₂^- is released as NH₃ leading to nitrogen loss, similar to denitrification which generates NO, N₂O, and N₂. NH₄⁺ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO₂^- to NH₄⁺, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.

Low C/N Ratios Promote Dissimilatory Nitrite Reduction to Ammonium in Pseudomonas putida Y-9 under Aerobic Conditions

The biogeochemical consequences of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) have a significant influence on nitrogen (N) cycling in the ecosystem. Many researchers have explored these two pathways in soil and sediment ecosystems under anaerobic conditions. However, limited information is available regarding the influence of external environmental conditions on these two pathways in a well-defined experimental system under aerobic conditions. In this study, the impacts of the external environmental factors (carbon source, C/N ratio, pH, and dissolved oxygen) on nitrite reduction through the denitrification and DNRA routes in Pseudomonas putida Y-9 were studied. Results found that sodium citrate and sodium acetate favored denitrification and DNRA, respectively. Furthermore, neutral pH and aerobic conditions both facilitated DNRA and denitrification. Especially, low C/N ratios motivated the DNRA while high C/N ratios stimulated the denitrification, which was opposite to the observed phenomena under anaerobic conditions.

A Kinetic Investigation of the Early Steps in Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite

The decaheme enzyme cytochrome c nitrite reductase (ccNiR) catalyzes reduction of nitrite to ammonium in a six-electron, eight-proton process. With a strong reductant as the electron source, ammonium is the sole product. However, intermediates accumulate when weaker reductants are employed, facilitating study of the ccNiR mechanism. Herein, the early stages of Shewanella oneidensis ccNiR-catalyzed nitrite reduction were investigated by using the weak reductants N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) and ferrocyanide. In stopped-flow experiments, reduction of nitrite-loaded ccNiR by TMPD generated a transient intermediate, identified as Fe_H1^II(NO₂^-), where Fe_H1 represents the ccNiR active site. Fe_H1^II(NO₂^-) accumulated rapidly and was then more slowly converted to the two-electron-reduced moiety {Fe_H1NO}⁷; ccNiR was not reduced beyond the {Fe_H1NO}⁷ state. The midpoint potentials for sequential reduction of Fe_H1^III(NO₂^-) to Fe_H1^II(NO₂^-) and then to {Fe_H1NO}⁷ were estimated to be 130 and 370 mV versus the standard hydrogen electrode, respectively. Fe_H1^II(NO₂^-) does not accumulate at equilibrium because its reduction to {Fe_H1NO}⁷ is so much easier than the reduction of Fe_H1^III(NO₂^-) to Fe_H1^II(NO₂^-). With weak reductants, free NO• was released from nitrite-loaded ccNiR. The release of NO• from {Fe_H1NO}⁷ is exceedingly slow (k ∼ 0.001 s^-1), but it is somewhat faster (k ∼ 0.050 s^-1) while Fe_H1^III(NO₂^-) is being reduced to {Fe_H1NO}⁷; then, the release of NO• from the undetectable transient {Fe_H1NO}⁶ can compete with reduction of {Fe_H1NO}⁶ to {Fe_H1NO}⁷. CcNiR appears to be optimized to capture nitrite and minimize the release of free NO•. Nitrite capture is achieved by reducing bound nitrite with even weak electron donors, while NO• release is minimized by stabilizing the substitutionally inert {Fe_H1NO}⁷ over the more labile {Fe_H1NO}⁶.

Elucidating Electron Storage and Distribution within the Pentaheme Scaffold of Cytochrome c Nitrite Reductase (NrfA)

Cytochrome c nitrite reductases (CcNIR or NrfA) play important roles in the global nitrogen cycle by conserving the usable nitrogen in the soil. Here, the electron storage and distribution properties within the pentaheme scaffold of Geobacter lovleyi NrfA were investigated via electron paramagnetic resonance (EPR) spectroscopy coupled with chemical titration experiments. Initially, a chemical reduction method was established to sequentially add electrons to the fully oxidized protein, 1 equiv at a time. The step-by-step reduction of the hemes was then followed using ultraviolet-visible absorption and EPR spectroscopy. EPR spectral simulations were used to elucidate the sequence of heme reduction within the pentaheme scaffold of NrfA and identify the signals of all five hemes in the EPR spectra. Electrochemical experiments ascertain the reduction potentials for each heme, observed in a narrow range from +10 mV (heme 5) to -226 mV (heme 3) (vs the standard hydrogen electrode). On the basis of quantitative analysis and simulation of the EPR data, we demonstrate that hemes 4 and 5 are reduced first (before the active site heme 1) and serve the purpose of an electron storage unit within the protein. To probe the role of the central heme 3, an H108M NrfA variant was generated where the reduction potential of heme 3 is shifted positively (from -226 to +48 mV). The H108M mutation significantly impacts the distribution of electrons within the pentaheme scaffold and the reduction potentials of the hemes, reducing the catalytic activity of the enzyme to 1% compared to that of the wild type. We propose that this is due to heme 3's important role as an electron gateway in the wild-type enzyme.

Theoretical Study on the Mechanism of the Acylate Reaction of β-Lactamase

Using density functional theory and a cluster approach, we study the reaction potential surface and compute Gibbs free energies for the acylate reaction of β-lactamase with penicillin G, where the solvent effect is important and taken into consideration. Two reaction paths are investigated: one is a multi-step process with a rate-limit energy barrier of 19.1 kcal/mol, which is relatively small, and the reaction can easily occur; the other is a one-step process with a barrier of 45.0 kcal/mol, which is large and thus makes the reaction hard to occur. The reason why the two paths have different barriers is explained.

Characterization of a nitrite-reducing octaheme hydroxylamine oxidoreductase that lacks the tyrosine cross-link

The hydroxylamine oxidoreductase (HAO) family consists of octaheme proteins that harbor seven bis-His ligated electron-transferring hemes and one 5-coordinate catalytic heme with His axial ligation. Oxidative HAOs have a homotrimeric configuration with the monomers covalently attached to each other via a unique double cross-link between a Tyr residue and the catalytic heme moiety of an adjacent subunit. This cross-linked active site heme, termed the P460 cofactor, has been hypothesized to modulate enzyme reactivity toward oxidative catalysis. Conversely, the absence of this cross-link is predicted to favor reductive catalysis. However, this prediction has not been directly tested. In this study, an HAO homolog that lacks the heme-Tyr cross-link (HAOr) was purified to homogeneity from the nitrite-dependent anaerobic ammonium-oxidizing (anammox) bacterium Kuenenia stuttgartiensis, and its catalytic and spectroscopic properties were assessed. We show that HAOr reduced nitrite to nitric oxide and also reduced nitric oxide and hydroxylamine as nonphysiological substrates. In contrast, HAOr was not able to oxidize hydroxylamine or hydrazine supporting the notion that cross-link-deficient HAO enzymes are reductases. Compared with oxidative HAOs, we found that HAOr harbors an active site heme with a higher (at least 80 mV) midpoint potential and a much lower degree of porphyrin ruffling. Based on the physiology of anammox bacteria and our results, we propose that HAOr reduces nitrite to nitric oxide in vivo, providing anammox bacteria with NO, which they use to activate ammonium in the absence of oxygen.

Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis

Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.

The Metaphosphite (PO2 - ) Anion as a Ligand

The utilization of monomeric, lower phosphorous oxides and oxoanions, such as metaphosphite (PO2 - ), which is the heavier homologue of the common nitrite anion but previously only observed in the gas phase and by matrix isolation, requires new synthetic strategies. Herein, a series of rhenium(I-III) complexes with PO2 - as ligand is reported. Synthetic access was enabled by selective oxygenation of a terminal phosphide complex. Spectroscopic and computational examination revealed slightly stronger σ-donor and comparable π-acceptor properties of PO2 - compared to homologous NO2 - , which is one of the archetypal ligands in coordination chemistry.

Octaheme nitrite reductase: The mechanism of intramolecular electron transfer and kinetics of nitrite bioelectroreduction

Detailed impedance and voltammetric studies of hexameric octaheme nitrite reductase immobilized on carbon-based nanomaterials, specifically nanotubes and nanoparticles, were performed. Well-pronounced bioelectrocatalytic reduction of nitrite on enzyme-modified electrodes was obtained. Analysis of the impedance data indicated the absence of long-lived intermediates involved in the nitrite reduction. Cyclic voltammograms of biomodified electrodes had a bi-sigmoidal shape, which pointed to the presence of two enzyme orientations on carbon supports. The maximum (limiting) catalytic currents were determined and, by applying the correction by the mixed kinetics equation, the Tafel dependences were plotted for each catalytic wave/each enzyme orientation. Finally, two schemes for the rate-limiting processes during bioelectrocatalysis were proposed, viz. for low- and high-potential orientations.

Exploring the Limits of Dative Boratrane Bonding: Iron as a Strong Lewis Base in Low-Valent Non-Heme Iron-Nitrosyl Complexes

We previously reported the synthesis and preliminary characterization of a unique series of low-spin (ls) {FeNO}8-10 complexes supported by an ambiphilic trisphosphineborane ligand, [Fe(TPB)(NO)]+/0/-. Herein, we use advanced spectroscopic techniques and density functional theory (DFT) calculations to extract detailed information as to how the bonding changes across the redox series. We find that, in spite of the highly reduced nature of these complexes, they feature an NO+ ligand throughout with strong Fe-NO π-backbonding and essentially closed-shell electronic structures of their FeNO units. This is enabled by an Fe-B interaction that is present throughout the series. In particular, the most reduced [Fe(TPB)(NO)]- complex, an example of a ls-{FeNO}10 species, features a true reverse dative Fe → B bond where the Fe center acts as a strong Lewis-base. Hence, this complex is in fact electronically similar to the ls-{FeNO}8 system, with two additional electrons "stored" on site in an Fe-B single bond. The outlier in this series is the ls-{FeNO}9 complex, due to spin polarization (quantified by pulse EPR spectroscopy), which weakens the Fe-NO bond. These data are further contextualized by comparison with a related N2 complex, [Fe(TPB)(N2)]-, which is a key intermediate in Fe(TPB)-catalyzed N2 fixation. Our present study finds that the Fe → B interaction is key for storing the electrons needed to achieve a highly reduced state in these systems, and highlights the pitfalls associated with using geometric parameters to try to evaluate reverse dative interactions, a finding with broader implications to the study of transition metal complexes with boratrane and related ligands.

Nitrate assimilation, dissimilatory nitrate reduction to ammonium, and denitrification coexist in Pseudomonas putida Y-9 under aerobic conditions

The specific nitrate reduction pathway in Pseudomonas putida Y-9 under aerobic conditions was studied. Strain Y-9 removed 82% of the nitrate accompanied by an accumulation of ammonium and a decrease of total nitrogen. Ammonium inhibited nitrate transformation (removal efficiency was 22.65%), illustrating that nitrate assimilation exists in strain Y-9. The detectable ammonium in the supernatant during the nitrate reduction process came from intracellular locations in strain Y-9. The nirBD that encodes nitrite reductase had an important role in strain growth and ammonium production. A ¹⁵N isotope experiment demonstrated that strain Y-9 can conduct dissimilatory nitrate reduction to ammonium (DNRA) and nirBD controls this process. This further indicated that the loss of total nitrogen is due to denitrification. All results highlighted that strain Y-9 performs simultaneous nitrate assimilation, DNRA, and denitrification under aerobic conditions, and nirBD controls the assimilation and DNRA process. Thereinto, nitrate assimilation dominates the removal of nitrate.

Cytochrome c nitrite reductase from the bacterium Geobacter lovleyi represents a new NrfA subclass

Cytochrome c nitrite reductase (NrfA) catalyzes the reduction of nitrite to ammonium in the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a process that competes with denitrification, conserves nitrogen, and minimizes nutrient loss in soils. The environmental bacterium Geobacter lovleyi has recently been recognized as a key driver of DNRA in nature, but its enzymatic pathway is still uncharacterized. To address this limitation, here we overexpressed, purified, and characterized G. lovleyi NrfA. We observed that the enzyme crystallizes as a dimer but remains monomeric in solution. Importantly, its crystal structure at 2.55-Å resolution revealed the presence of an arginine residue in the region otherwise occupied by calcium in canonical NrfA enzymes. The presence of EDTA did not affect the activity of G. lovleyi NrfA, and site-directed mutagenesis of this arginine reduced enzymatic activity to <3% of the WT levels. Phylogenetic analysis revealed four separate emergences of Arg-containing NrfA enzymes. Thus, the Ca²⁺-independent, Arg-containing NrfA from G. lovleyi represents a new subclass of cytochrome c nitrite reductase. Most genera from the exclusive clades of Arg-containing NrfA proteins are also represented in clades containing Ca²⁺-dependent enzymes, suggesting convergent evolution.

The Fe2 (NO)2 Diamond Core: A Unique Structural Motif In Non-Heme Iron-NO Chemistry

Non-heme high-spin (hs) {FeNO}⁸ complexes have been proposed as important intermediates towards N₂ O formation in flavodiiron NO reductases (FNORs). Many hs-{FeNO}⁸ complexes disproportionate by forming dinitrosyl iron complexes (DNICs), but the mechanism of this reaction is not understood. While investigating this process, we isolated a new type of non-heme iron nitrosyl complex that is stabilized by an unexpected spin-state change. Upon reduction of the hs-{FeNO}⁷ complex, [Fe(TPA)(NO)(OTf)](OTf) (1), the N-O stretching band vanishes, but no sign of DNIC or N₂ O formation is observed. Instead, the dimer, [Fe₂ (TPA)₂ (NO)₂ ](OTf)₂ (2) could be isolated and structurally characterized. We propose that 2 is formed from dimerization of the hs-{FeNO}⁸ intermediate, followed by a spin state change of the iron centers to low-spin (ls), and speculate that 2 models intermediates in hs-{FeNO}⁸ complexes that precede the disproportionation reaction.

Proton Transfer versus Hydrogen Bonding in a Reduced Iron Porphyrin Nitrosyl Complex

The ¹H NMR spectra of Fe(OEP)(HNO), which was formed from Fe(OEP)(NO)^- in the presence of 3,5-dichlorophenol, were studied as a function of temperature. The chemical shift of the HNO proton showed a unique behavior which could be explained based on the equilibrium between the protonated complex, Fe(OEP)(HNO), and the hydrogen-bonded complex, Fe(OEP)(NO)^-···HOPh. This equilibrium was consistent with UV/visible spectroscopy and the voltammetric data. UV/visible stopped-flow experiments showed that the hydrogen-bonded complex, which was formed when weak acids such as phenol were added, and the Fe(OEP)(HNO) complex were quite similar. In addition to the HNO proton resonance, the meso-resonances were consistent with the proposed equilibrium. Density functional theory calculations of various Fe(OEP)(NO)^-/Fe(OEP)(HNO) species were calculated, and the results were consistent with experimental data.

Cobalt Metallopeptide Electrocatalyst for the Selective Reduction of Nitrite to Ammonium

A cobalt-tripeptide complex (CoGGH) is developed as an electrocatalyst for the selective six-electron, eight-proton reduction of nitrite to ammonium in aqueous buffer near neutral pH. The onset potential for nitrite reduction occurs at -0.65 V vs Ag/AgCl (1 M KCl). Controlled potential electrolysis at -0.90 V generates ammonium with a faradaic efficiency of 90 ± 3% and a turnover number of 3550 ± 420 over 5.5 h. CoGGH also catalyzes the reduction of the proposed intermediates nitric oxide and hydroxylamine to ammonium. These results reveal that a simple metallopeptide is an active functional mimic of the complex enzymes cytochrome c nitrite reductase and siroheme-containing nitrite reductase.

Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets

The globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide (NO) and nitrite, have been known for decades, but the physiological relevance has only recently become more fully appreciated. We previously reported the O-nitrito mode of binding of nitrite to ferric horse heart wild-type (wt) Mb^III and human hemoglobin. We have expanded on this work and report the interactions of nitrite with wt sperm whale (sw) Mb^III and its H64A, H64Q, and V68A/I107Y mutants whose dissociation constants increase in the following order: H64Q < wt < V68A/I107Y < H64A. We also report their X-ray crystal structures that reveal the O-nitrito mode of binding of nitrite to these derivatives. The Mb^II-mediated reductions of nitrite to NO and structural data for the wt and mutant Mb^II-NOs are described. We show that their FeNO orientations vary with distal pocket identity, with the FeNO moieties pointing toward the hydrophobic interiors when the His64 residue is present but toward the hydrophilic exterior when this His64 residue is absent in this set of mutants. This correlates with the nature of H-bonding to the bound NO ligand (nitrosyl O vs N atom). Quantum mechanics and hybrid quantum mechanics and molecular mechanics calculations help elucidate the origin of the experimentally preferred NO orientations. In a few cases, the calculations reproduce the experimentally observed orientations only when the whole protein is taken into consideration.

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT

Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647^T (here referred to as Leptospirillum ferriphilum ^T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum ^T obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS₂). Adaptations of Leptospirillum ferriphilum ^T to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced.IMPORTANCE Leptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilum ^T coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilum ^T for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction.

Nitrite Reduction Cycle on a Dinuclear Ruthenium Complex Producing Ammonia

The fundamental biogeochemical cycle of nitrogen includes cytochrome c nitrite reductase, which catalyzes the reduction of nitrite ions to ammonium with eight protons and six electrons (NO₂^- + 8H⁺ + 6e^- → NH₄⁺ + 2H₂O). This reaction has motivated researchers to explore the reduction of nitrite. Although a number of electrochemical reductions of NO₂^- have been reported, the synthetic nitrite reduction reaction remains limited. To the best of our knowledge, formation of ammonia has not been reported. We report a three-step nitrite reduction cycle on a dinuclear ruthenium platform {(TpRu)₂(μ-pz)} (Tp = HB(pyrazol-1-yl)₃), producing ammonia. The cycle comprises conversion of a nitrito ligand to a NO ligand using 2H⁺ and e^-, subsequent reduction of the NO ligand to a nitrido and a H₂O ligand by consumption of 2H⁺ and 5e^-, and recovery of the parent nitrito ligand. Moreover, release of ammonia was detected.

Over or under: hydride attack at the metal versus the coordinated nitrosyl ligand in ferric nitrosyl porphyrins

Hydride attack at a ferric heme-NO to give an Fe-HNO intermediate is a key step in the global N-cycle. We demonstrate differential reactivity when six- and five-coordinate ferric heme-NO models react with hydride. Although Fe-HNO formation is thermodynamically favored from this reaction, Fe-H formation is kinetically favored for the 5C case.

Recent Trends in Quantum Chemical Modeling of Enzymatic Reactions

The quantum chemical cluster approach is a powerful method for investigating enzymatic reactions. Over the past two decades, a large number of highly diverse systems have been studied and a great wealth of mechanistic insight has been developed using this technique. This Perspective reviews the current status of the methodology. The latest technical developments are highlighted, and challenges are discussed. Some recent applications are presented to illustrate the capabilities and progress of this approach, and likely future directions are outlined.

Enzymatic Bioelectrosynthetic Ammonia Production: Recent Electrochemistry of Nitrogenase, Nitrate Reductase, and Nitrite Reductase

As an essential component of amino acids and nucleic acids, nitrogen (N) is a key element of life. For atmospheric (dinitrogen, N₂ ) and environmental (nitrate and nitrite, NO₃ ^- and NO₂ ^- ) sources of N to be utilized in amino acid synthesis in various forms of life, it must first be reduced to ammonia (NH₃ ). The Haber-Bosch process, in which N₂ is reduced to NH₃ at elevated temperature and pressure, represents a major NH₃ production process that has had a great impact on the agricultural crop industry. This Minireview discusses the recent electrochemistry of three key enzymes of the global biogeochemical N cycle (nitrogenase, nitrate reductase, and nitrite reductase), in view of moving toward the creation of alternative NH₃ production biotechnologies.

Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete

Hydrogen sulfide produced by sulfate-reducing bacteria (SRB) in sewers causes odor problems and asset deterioration due to the sulfide-induced concrete corrosion. Free nitrous acid (FNA) was recently demonstrated as a promising antimicrobial agent to alleviate hydrogen sulfide production in sewers. However, details of the antimicrobial mechanisms of FNA are largely unknown. Here, we report the multiple-targeted antimicrobial effects of FNA on the SRB Desulfovibrio vulgaris Hildenborough by determining the growth, physiological, and gene expression responses to FNA exposure. The activities of growth, respiration, and ATP generation were inhibited when exposed to FNA. These changes were reflected in the transcript levels detected during exposure. The removal of FNA was evident by nitrite reduction that likely involved nitrite reductase and the poorly characterized hybrid cluster protein, and the genes coding for these proteins were highly expressed. During FNA exposure, lowered ribosome activity and protein production were detected. Additionally, conditions within the cells were more oxidizing, and there was evidence of oxidative stress. Based on an interpretation of the measured responses, we present a model depicting the antimicrobial effects of FNA on D. vulgaris These findings provide new insight for understanding the responses of D. vulgaris to FNA and will provide a foundation for optimal application of this antimicrobial agent for improved control of sewer corrosion and odor management.IMPORTANCE Hydrogen sulfide produced by SRB in sewers causes odor problems and results in serious deterioration of sewer assets that requires very costly and demanding rehabilitation. Currently, there is successful application of the antimicrobial agent free nitrous acid (FNA), the protonated form of nitrite, for the control of sulfide levels in sewers (G. Jiang et al., Water Res 47:4331-4339, 2013, http://dx.doi.org/10.1016/j.watres.2013.05.024). However, the details of the antimicrobial mechanisms of FNA are largely unknown. In this study, we identified the key responses (decreased anaerobic respiration, reducing FNA, combating oxidative stress, and shutting down protein synthesis) of Desulfovibrio vulgaris Hildenborough, a model sewer corrosion bacterium, to FNA exposure by examining the growth, physiological, and gene expression changes. These findings provide new insight and underpinning knowledge for understanding the responses of D. vulgaris to FNA exposure, thereby benefiting the practical application of FNA for improved control of sewer corrosion and odor.

Intramolecular, Exciplex-Mediated, Proton-Coupled, Charge-Transfer Processes in N,N-Dimethyl-3-(1-pyrenyl)propan-1-ammonium Cations: Influence of Anion, Solvent Polarity, and Temperature

An intramolecular exciplex-mediated, proton-coupled, charge-transfer (PCCT) process has been investigated for a series of N,N-dimethyl-3-(1-pyrenyl)propan-1-ammonium cations with different anions (PyS) in solvents of low to intermediate polarity over a wide temperature range. Solvent mediates both the equilibrium between conformations of the cation that place the pyrenyl and ammonium groups in proximity (conformation C) or far from each other (conformation O) and the ability of the ammonium group to transfer a proton adiabatically in the PyS excited singlet state. Thus, exciplex emission, concurrent with the PCCT process, was observed only in hydrogen-bond accepting solvents of relatively low polarity (tetrahydrofuran, ethyl acetate, and 1,4-dioxane) and not in dichloromethane. From the exciplex emission and other spectroscopic and thermodynamic data, the acidity of the ammonium group in conformation C of the excited singlet state of PyS (pKa*) has been estimated to be ca. -3.4 in tetrahydrofuran. The ratios between the intensities of emission from the exciplex and the locally excited state (IEx/ILE) appear to be much more dependent on the nature of the anion than are the rates of exciplex formation and decay, although the excited state data do not provide a quantitative measure of the anion effect on the C-O equilibrium. The activation energies associated with exciplex formation in THF are calculated to be 0.08 to 0.15 eV lower than for the neutral amine, N,N-dimethyl-3-(1-pyrenyl)propan-1-amine. Decay of the exciplexes formed from the deprotonation of PyS is hypothesized to occur through charge-recombination processes. To our knowledge, this is the first example in which photoacidity and intramolecular exciplex formation (i.e., a PCCT reaction) are coupled.

Prebiotic NH3 Formation: Insights from Simulations

Simulations of prebiotic NH₃ synthesis from NO₃⁻ and NO₂⁻ on pyrite surfaces under hydrothermal conditions are reported. Ab initio metadynamics calculations have successfully explored the full reaction path which explains earlier experimental observations. We have found that the reaction mechanism can be constructed from stepwise single atom transfers which are compatible with the expected reaction time scales. The roles of the hot-pressurized water and of the pyrite surfaces have been addressed. The mechanistic picture that emerged from the simulations strengthens the theory of chemoautotrophic origin of life by providing plausible reaction pathways for the formation of ammonia within the iron-sulfur-world scenario.

Hydride Attack on a Coordinated Ferric Nitrosyl: Experimental and DFT Evidence for the Formation of a Heme Model-HNO Derivative

Heme-HNO species are crucial intermediates in several biological processes. To date, no well-defined Fe heme-HNO model compounds have been reported. Hydride attack on the cationic ferric [(OEP)Fe(NO)(5-MeIm)]OTf (OEP = octaethylporphyrinato dianion) generates an Fe-HNO product that has been characterized by IR and (1)H NMR spectroscopy. Results of DFT calculations reveal a direct attack of the hydride on the N atom of the coordinated ferric nitrosyl.