Resolving Complexity in the Interactions of Redox Enzymes and Their Inhibitors: Contrasting Mechanisms for the Inhibition of a Cytochrome c Nitrite Reductase Revealed by Protein Film Voltammetry

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.

Interfacing the enzyme multiheme cytochrome c nitrite reductase with pencil lead electrodes: Towards a disposable biosensor for cyanide surveillance in the environment

The present study reports a novel voltammetric biosensor for cyanide based on its inhibitory effect on cytochrome c nitrite reductase (ccNiR). Interestingly, the earlier development of a point-of-care test for nitrite based on the direct electrochemistry of ccNiR has shown that the cyanide inhibition depends on the type of carbon material employed as transducer (Monteiro et al., 2019). In this work, commercial graphite pencil leads were employed in the construction of both working and pseudo-reference electrodes, with ccNiR being simply drop casted onto the former. In this way, we produced a functional and fully integrated voltammetric biosensor for nitrite quantification that also allows to observe a decrease in the catalytic current due to cyanide addition. Under turnover conditions, the biosensor showed a linear response with the logarithm of cyanide concentration in the 5-76 μM (cyclic voltammetry) and 1-40 μM (square-wave voltammetry) ranges, with a sensitivity of 20-25% ln [cyanide μM]^-1 and a detection limit of 0.86-4.4 μM. The application of the pencil lead as a putative pseudo-reference was very promising, since the potentials profile matched those observed with a true reference electrode (Ag/AgCl). Overall, the direct electron transfer between ccNiR and a pencil lead electrode was demonstrated for the first time, with cyanide-induced inhibition being easily monitored, paving the way for the employment of these low-cost bioelectrodes as cyanide probes for on-site surveillance of aquatic environments.

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.

A quasi-reagentless point-of-care test for nitrite and unaffected by oxygen and cyanide

The ubiquitous nitrite is a major analyte in the management of human health and environmental risks. The current analytical methods are complex techniques that do not fulfil the need for simple, robust and low-cost tools for on-site monitoring. Electrochemical reductase-based biosensors are presented as a powerful alternative, due to their good analytical performance and miniaturization potential. However, their real-world application is limited by the need of anoxic working conditions, and the standard oxygen removal strategies are incompatible with point-of-care measurements. Instead, a bienzymatic oxygen scavenger system comprising glucose oxidase and catalase can be used to promote anoxic conditions in aired environments. Herein, carbon screen-printed electrodes were modified with cytochrome c nitrite reductase together with glucose oxidase and catalase, so that nitrite cathodic detection could be performed by cyclic voltammetry under ambient air. The resulting biosensor displayed good linear response to the analyte (2–200 µM, sensitivity of 326 ± 5 mA M⁻¹ cm⁻² at −0.8 V; 0.8–150 µM, sensitivity of 511 ± 11 mA M⁻¹ cm⁻² at −0.5 V), while being free from oxygen interference and stable up to 1 month. Furthermore, the biosensor’s catalytic response was unaffected by the presence of cyanide, a well-known inhibitor of heme-enzymes.

Opportunities for mesoporous nanocrystalline SnO2 electrodes in kinetic and catalytic analyses of redox proteins

PFV (protein film voltammetry) allows kinetic analysis of redox and coupled-chemical events. However, the voltammograms report on the electron transfer through a flow of electrical current such that simultaneous spectroscopy is required for chemical insights into the species involved. Mesoporous nanocrystalline SnO(2) electrodes provide opportunities for such 'spectroelectrochemical' analyses through their high surface area and optical transparency at visible wavelengths. Here, we illustrate kinetic and mechanistic insights that may be afforded by working with such electrodes through studies of Escherichia coli NrfA, a pentahaem cytochrome with nitrite and nitric oxide reductase activities. In addition, we demonstrate that the ability to characterize electrocatalytically active protein films by MCD (magnetic circular dichroism) spectroscopy is an advance that should ultimately assist our efforts to resolve catalytic intermediates in many redox enzymes.

Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli

The Escherichia coli NapA (periplasmic nitrate reductase) contains a [4Fe-4S] cluster and a Mo-bis-molybdopterin guanine dinucleotide cofactor. The NapA holoenzyme associates with a di-heme c-type cytochrome redox partner (NapB). These proteins have been purified and studied by spectropotentiometry, and the structure of NapA has been determined. In contrast to the well characterized heterodimeric NapAB systems ofalpha-proteobacteria, such as Rhodobacter sphaeroides and Paracoccus pantotrophus, the gamma-proteobacterial E. coli NapA and NapB proteins purify independently and not as a tight heterodimeric complex. This relatively weak interaction is reflected in dissociation constants of 15 and 32 mum determined for oxidized and reduced NapAB complexes, respectively. The surface electrostatic potential of E. coli NapA in the apparent NapB binding region is markedly less polar and anionic than that of the alpha-proteobacterial NapA, which may underlie the weaker binding of NapB. The molybdenum ion coordination sphere of E. coli NapA includes two molybdopterin guanine dinucleotide dithiolenes, a protein-derived cysteinyl ligand and an oxygen atom. The Mo-O bond length is 2.6 A, which is indicative of a water ligand. The potential range over which the Mo(6+) state is reduced to the Mo(5+) state in either NapA (between +100 and -100 mV) or the NapAB complex (-150 to -350 mV) is much lower than that reported for R. sphaeroides NapA (midpoint potential Mo(6+/5+) > +350 mV), and the form of the Mo(5+) EPR signal is quite distinct. In E. coli NapA or NapAB, the Mo(5+) state could not be further reduced to Mo(4+). We then propose a catalytic cycle for E. coli NapA in which nitrate binds to the Mo(5+) ion and where a stable des-oxo Mo(6+) species may participate.

Voltammetry and in situ scanning tunneling microscopy of cytochrome C nitrite reductase on Au(111) electrodes

Escherichia coli cytochrome c nitrite reductase (NrfA) catalyzes the six-electron reduction of nitrite to perform an important role in the biogeochemical cycling of nitrogen. Here we describe NrfA adsorption on single-crystal Au(111) electrodes as an electrocatalytically active film in which the enzyme undergoes direct electron exchange with the electrode. The adsorbed NrfA has been imaged to molecular resolution by in situ scanning tunneling microscopy (in situ STM) under full electrochemical potential control and under conditions where the enzyme is electrocatalytically active. Details of the density and orientational distribution of NrfA molecules are disclosed. The submonolayer coverage resolved by in situ STM is readily reconciled with the failure to detect nonturnover signals in cyclic voltammetry of the NrfA films. The molecular structures show a range of lateral dimensions. These are suggestive of a distribution of orientations that could account for the otherwise anomalously low turnover number calculated for the total population of adsorbed NrfA molecules when compared with that determined for solutions of NrfA. Thus, comparison of the voltammetric signals and in situ STM images offers a direct approach to correlate electrocatalytic and molecular properties of the protein layer, a long-standing issue in protein film voltammetry.

Interpreting the catalytic voltammetry of an adsorbed enzyme by considering substrate mass transfer, enzyme turnover, and interfacial electron transport

Redox active enzymes can be adsorbed onto electrode surfaces to catalyze the interconversion of oxidized and reduced substrates in solution, driven by the supply or removal of electrons by the electrode. The catalytic current is directly proportional to the rate of enzyme turnover, and its dependence on the electrode potential can be exploited to define both the kinetics and thermodynamics of the enzyme's catalytic cycle. However, observed electrocatalytic voltammograms are often complex because the identity of the rate limiting step changes with the electrode potential and under different experimental conditions. Consequently, extracting mechanistic information requires that accurate models be constructed to deconvolute and analyze the observed behavior. Here, a basic model for catalysis by an adsorbed enzyme is described. It incorporates substrate mass transport, enzyme kinetics, and interfacial electron transport, and it accurately reproduces experimentally recorded voltammograms from the oxidation of NADH by subcomplex Ilambda (the hydrophilic subcomplex of NADH:ubiquinone oxidoreductase), under a range of conditions. Mass transport is imposed by a rotating disk electrode and described by the Levich equation. Interfacial electron transport is controlled by the electrode potential and characterized by a dispersion of rate constants, according to the model of Léger and co-workers. Here, the Michaelis-Menten equation is used for the enzyme kinetics, but our methodology can also be readily applied to derive and apply analogous equations relating to alternative enzyme mechanisms. Therefore, our results are highly relevant to the interpretation of electrocatalytic voltammograms for adsorbed enzymes in general.

Elucidating the mechanisms of coupled electron transfer and catalytic reactions by protein film voltammetry

Protein film voltammetry, the direct electrochemistry of redox enzymes and proteins, provides precise and comprehensive information on complicated reaction mechanisms. By controlling the driving force for a reaction (using the applied potential) and monitoring the reaction in real time (using the current), it allows thermodynamic and kinetic information to be determined simultaneously. Two challenges are inherent to protein film voltammetry: (i) to adsorb the protein or enzyme in a native and active configuration on the electrode surface, and (ii) to understand and interpret voltammetric results on both a qualitative and quantitative level, allowing mechanistic models to be proposed and rigorous experiments to test these models to be devised. This review focuses on the second of these two challenges. It describes how to use protein film voltammetry to derive mechanistic and biochemically relevant information about redox proteins and enzymes, and how to evaluate and interpret voltammetric results. Selected key studies are described in detail, to illustrate their underlying principles, strategies and physical interpretations.

Inhibiting Escherichia coli cytochrome c nitrite reductase: voltammetry reveals an enzyme equipped for action despite the chemical challenges it may face in vivo

Escherichia coli cytochrome c nitrite reductase is one of a large family of homologous enzymes that are particularly prevalent in pathogenic enterobacteria. The enzymes are periplasmic and in vivo may find themselves challenged by molecules that could enhance or compromise their performance. In the present study, we describe protein film voltammetry in which the activity of E. coli cytochrome c nitrite reductase is challenged by the presence of a number of small molecules. These results are discussed in light of the environment(s) that the enzyme may face before and after colonization of a human host.

Diode or Tunnel-Diode Characteristics? Resolving the Catalytic Consequences of Proton Coupled Electron Transfer in a Multi-Centered Oxidoreductase

Protein film voltammetry has been employed to define multiple catalytic consequences of proton coupled electron transfer (PCET) in a cytochrome c nitrite reductase. Current-potential profiles reflecting the steady-state rate of nitrite-limited reduction have been defined from pH 4 to 8. Lowering the electrode potential at pH 8 causes the catalytic current to increase and then decrease before it takes a value independent of any further lowering of electrode potential. By comparison, at pH 4, catalysis is initiated at more positive electrode potentials in an approximately sigmoidal fashion with no attenuation of the catalytic rate evident at more negative electrode potentials. The results show that activity is turned on by the coupled transfer of two electrons and one proton to the enzyme. The decreased rate of catalysis at lower electrode potentials under more alkaline conditions shows that this rate attenuation occurs only when reduction is not coupled to compensating protonation(s) of the enzyme. Sites within the enzyme whose reduction and/or protonation may contribute to the definition of these activities are discussed.