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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Energy transduction by reversible electron bifurcation

Electron bifurcation is a biological energy conversion process that oxidizes a two-electron donor at medium potential, coupled to the reduction of a high- and a low-potential acceptor species. This process is often fully reversible (can occur close to ΔG ≈ 0), allowing the creation of strong reductants with minimal free energy cost, using compounds with higher reduction potentials. For many years, the internal workings of electron bifurcating enzymes were poorly understood, especially regarding how short-circuit reactions are prevented. Recently, a conserved energy landscape was proposed to naturally insulate against short-circuit reactions, enabling efficient and reversible electron bifurcation (the reversible EB scheme). Here, we review the physical principles that underpin the EB scheme, describe how the reversible EB scheme is distinct from previous views, and outline questions that remain open.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The role of thermodynamic features on the functional activity of electron bifurcating enzymes

Electron bifurcation is a biological mechanism to drive a thermodynamically unfavorable redox reaction through direct coupling with an exergonic reaction. This process allows microorganisms to generate high energy reducing equivalents in order to sustain life and is often found in anaerobic metabolism, where the energy economy of the cell is poor. Recent work has revealed details of the redox energy landscapes for a variety of electron bifurcating enzymes, greatly expanding the understanding of how energy is transformed by this unique mechanism. Here we highlight the plasticity of these emerging landscapes, what is known regarding their mechanistic underpinnings, and provide a context for interpreting their biochemical activity within the physiological framework. Here, we conclude with an outlook for propelling the field toward an integrative understanding of the impact of electron bifurcation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Site-Differentiated Iron–Sulfur Cluster Ligation Affects Flavin-Based Electron Bifurcation Activity

Electron bifurcation is an elegant mechanism of biological energy conversion that effectively couples three different physiologically relevant substrates. As such, enzymes that perform this function often play critical roles in modulating cellular redox metabolism. One such enzyme is NADH-dependent reduced-ferredoxin: NADP+ oxidoreductase (NfnSL), which couples the thermodynamically favorable reduction of NAD+ to drive the unfavorable reduction of ferredoxin from NADPH. The interaction of NfnSL with its substrates is constrained to strict stoichiometric conditions, which ensures minimal energy losses from non-productive intramolecular electron transfer reactions. However, the determinants for this are not well understood. One curious feature of NfnSL is that both initial acceptors of bifurcated electrons are unique iron–sulfur (FeS) clusters containing one non-cysteinyl ligand each. The biochemical impact and mechanistic roles of site-differentiated FeS ligands are enigmatic, despite their incidence in many redox active enzymes. Herein, we describe the biochemical study of wild-type NfnSL and a variant in which one of the site-differentiated ligands has been replaced with a cysteine. Results of dye-based steady-state kinetics experiments, substrate-binding measurements, biochemical activity assays, and assessments of electron distribution across the enzyme indicate that this site-differentiated ligand in NfnSL plays a role in maintaining fidelity of the coordinated reactions performed by the two electron transfer pathways. Given the commonality of these cofactors, our findings have broad implications beyond electron bifurcation and mechanistic biochemistry and may inform on means of modulating the redox balance of the cell for targeted metabolic engineering approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Spectral Deconvolution of Electron-Bifurcating Flavoproteins

Electron-bifurcating flavoproteins catalyze the tightly coupled reduction of high- and low-potential acceptors using a median-potential electron donor, and are invariably complex systems with multiple redox-active centers in two or more subunits. Methods are described that permit, in favorable cases, the deconvolution of spectral changes associated with reduction of specific centers, making it possible to dissect the overall process of electron bifurcation into individual, discrete steps.

electron bifurcation↗
DOE OSTI2026

Photoinduced Electron Transfer Informs on Pathway Coupling in Flavin-Based Electron Bifurcation

Flavin-based electron bifurcation (FBEB) is an enzymatic mechanism that generates extremely high-energy electrons to drive unfavorable chemical reactions. It is utilized by the NADHdependent ferredoxin:NADP + -oxidoreductase (Nfn) enzyme in hyperthermophile Pyrococcus furiosus to bifurcate electrons from NADPH into the coupled low-potential (endergonic) and highpotential (exergonic) pathways. This process enables P. furiosus to live in harsh and uninviting environments. Despite its biological importance, the mechanisms used by Nfn to facilitate exceptional directional control over short-lived, high-energy electrons and to prevent undesired transfer, particularly along the low-potential pathway, are still not well understood. To elucidate how the protein environment contributes to electronic control in the lowpotential pathway, new techniques must be utilized to probe these unstable intermediates. In this study, we have adapted lowtemperature photoexcitation combined with electron paramagnetic resonance (EPR) to accumulate the short-lived intermediate and place it in the context of the other cofactors involved in the low-potential pathway of Nfn. We observed coincident growth of both the radical intermediate and its nearby [4Fe-4S] cluster over 4.5 h of illumination with NADPH at cryogenic temperatures. The photogenerated paramagnetic species were stable in LN 2 storage indefinitely and recombined when warmed to higher temperatures. The results provide insights into the electron transfer steps and cofactor interactions along the low potential pathway, facilitating a more robust mechanistic understanding of the high-energy events of electron bifurcation. Furthermore, through comparison of cryogenic and room temperature experiments, a potential gating step involving the movement of key residues important for the reversibility of electron flow along this pathway is suggested.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Efficient and reversible electron bifurcation with either normal or inverted potentials at the bifurcating cofactor

A longstanding mystery surrounding electron bifurcation is the significance of inverted (or “crossed”) reduction potentials of the two-electron bifurcating cofactor. Using a many-electron open-system kinetic model, we show that reversible and efficient electron bifurcation is possible without inverted reduction potentials at the bifurcating site if the absolute value of the difference between first and second reduction potentials of the bifurcating species is sufficiently large (on the scale of the redox-potential span of the high- and low-potential branches). Surprisingly, the case with strong, normally ordered potentials at the bifurcating cofactor can produce electron bifurcation that is just as effective as the case with strongly inverted potentials. Lastly, this finding amplifies the puzzle surrounding the recruitment of inverted potentials in the few well-characterized bifurcating systems of nature and suggests that electron bifurcating cofactors without strongly inverted potentials may yet be discovered.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Electron Bifurcating Hydrogenases

The importance of electron-bifurcating enzymes is manifest by their ability to maximize energy efficiency. Specifically, they couple a downhill oxidation-reduction (redox) reaction with an uphill redox reaction. Since the rapid increase in the discovery of bifurcating enzymes starting in 2008, there has been interest in incorporating their mechanistic principles into artificial/semiartificial systems to drive chemically challenging reactions. This has yet to be achieved, partly because the details of electron bifurcation, i.e. mechanisms, are largely elusive. Nevertheless, much progress has been made in understanding reactivities, structures, and some mechanistic aspects of these enzymes. Notable examples are electron-bifurcating hydrogenases, which are the focus of this chapter. The chapter is organized as follows. Section 11.1 provides an overview of hydrogenases and electron bifurcation. In Section 11.2, some physiological roles of electron-bifurcating hydrogenases are highlighted. Additionally, electron-bifurcating subunit compositions and biochemical reactivities are comprehensively tabulated, and some key points/considerations about these are noted. In Section 11.3, we discuss the known structures of these enzymes, which provide insight into their complex arrangements of redox cofactors, such as iron-sulfur clusters. Also provided are tabulations and discussions of some biophysical properties of the cofactors. In Section 11.4, we discuss the mechanistic proposals of these enzymes, which are primarily based on structural information. Areas of research that are much needed are outlined in Section 11.5. We conclude on the note that what is learned from electron-bifurcating hydrogenases has applicability to other bifurcating enzymes, nonbifurcating analogs, and mechanistic enzymology at large.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Universal free-energy landscape produces efficient and reversible electron bifurcation

For decades, it was unknown how electron-bifurcating systems in nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron-bifurcating molecular machines could not be designed and built. The underpinning free-energy landscapes for electron bifurcation were also enigmatic. We predict that a simple and universal free-energy landscape enables electron bifurcation, and we show that it enables high-efficiency bifurcation with limited short-circuiting (the EB scheme). The landscape relies on steep free-energy slopes in the two redox branches to insulate against short-circuiting using an electron occupancy blockade effect, without relying on nuanced changes in the microscopic rate constants for the short-circuiting reactions. The EB scheme thus unifies a body of observations on biological catalysis and energy conversion, and the scheme provides a blueprint to guide future campaigns to establish synthetic electron bifurcation machines.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

An Abundant and Diverse New Family of Electron Bifurcating Enzymes With a Non-canonical Catalytic Mechanism

Microorganisms utilize electron bifurcating enzymes in metabolic pathways to carry out thermodynamically unfavorable reactions. Bifurcating FeFe-hydrogenases (HydABC) reversibly oxidize NADH (E′∼−280 mV, under physiological conditions) and reduce protons to H 2 gas (E°′−414 mV) by coupling this endergonic reaction to the exergonic reduction of protons by reduced ferredoxin (Fd) (E′∼−500 mV). We show here that HydABC homologs are surprisingly ubiquitous in the microbial world and are represented by 57 phylogenetically distinct clades but only about half are FeFe-hydrogenases. The others have replaced the hydrogenase domain with another oxidoreductase domain or they contain additional subunits, both of which enable various third reactions to be reversibly coupled to NAD + and Fd reduction. We hypothesize that all of these enzymes carry out electron bifurcation and that their third substrates can include hydrogen peroxide, pyruvate, carbon monoxide, aldehydes, aryl-CoA thioesters, NADP + , cofactor F 420 , formate, and quinones, as well as many yet to be discovered. Some of the enzymes are proposed to be integral membrane-bound proton-translocating complexes. These different functionalities are associated with phylogenetically distinct clades and in many cases with specific microbial phyla. We propose that this new and abundant class of electron bifurcating enzyme be referred to as the Bfu family whose defining feature is a conserved bifurcating BfuBC core. This core contains FMN and six iron sulfur clusters and it interacts directly with ferredoxin (Fd) and NAD(H). Electrons to or from the third substrate are fed into the BfuBC core via BfuA. The other three known families of electron bifurcating enzyme (abbreviated as Nfn, EtfAB, and HdrA) contain a special FAD that bifurcates electrons to high and low potential pathways. The Bfu family are proposed to use a different electron bifurcation mechanism that involves a combination of FMN and three adjacent iron sulfur clusters, including a novel [2Fe-2S] cluster with pentacoordinate and partial non-Cys coordination. The absolute conservation of the redox cofactors of BfuBC in all members of the Bfu enzyme family indicate they have the same non-canonical mechanism to bifurcate electrons. A hypothetical catalytic mechanism is proposed as a basis for future spectroscopic analyses of Bfu family members.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Differential Ligation Alters Electronic State and Coupling Signals of Iron-Sulfur Clusters in Flavin-Based Electron Bifurcation

Flavin-based electron bifurcation (FBEB) is employed by microorganisms for controlling pools of redox equivalents by reversibly splitting electron pairs into high- and low-energy levels from an initial midpoint potential. Our ability to harness this phenomenon is crucial for biocatalytic design which is limited by our understanding of energy coupling in the bifurcation system. In Pyrococcus furiosus, FBEB is carried out by the NADH-dependent ferredoxin:NADP+-oxidoreductase (NfnSL), coupling the uphill reduction of ferredoxin in NfnL to the downhill reduction of NAD+ in NfnS from oxidation of NADPH. Flanking the bifurcating flavin are two site-differentiated iron-sulfur clusters; the nearest is a glutamate-ligated [4Fe-4S] cluster in NfnL. Recent biochemical experiments substituting the native glutamate with cysteine led to loss of coupling between the uphill and downhill pathways, in contrast to the tight thermodynamic coupling in the native system. To understand how this decoupling is biochemically manifested by the cysteine-substituted [4Fe-4S] in NfnL, we employed electron paramagnetic resonance (EPR) spectroscopy to identify changes in electronic architecture and square wave voltammetry (SWV) to probe thermodynamic shifts produced by the substitution. We observed notable g-value shifts in the EPR for the cysteine-substituted iron-sulfur cluster in addition to significant downward shifts in the redox potential, as well as the disappearance of several low-field signals observed in the native NfnSL complex. These results suggest the site-differentiated glutamate residue facilitates higher spin states in the [4Fesingle bond4S] cluster to bridge energetic gaps in electron transfer to the bifurcating flavin in the native complex, preventing unwanted short-circuiting seen in the cysteine-substituted complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Mechanistic implications of excited high-spin states, spin–spin coupling, and differential [2Fe–2S] + cluster temperature relaxations in the electron-bifurcating NfnABC from Thermococcus sibiricus

Electron bifurcation (EB) is a mechanism of biological energy transduction in which multiple oxidation–reduction (redox) reactions are thermodynamically coupled within a single enzyme, enabling the enzyme to harness the excess free energy from an exergonic process to drive an endergonic process. Because of this unprecedented chemistry, there is interest to translate EB principles to artificial and bioengineered systems, but a hurdle is that knowledge pertaining to the fundamental design principles of EB enzymes remains scarce. Here, we investigated the fundamental physical and electronic properties of electron transfer sites in a spectroscopically uncharacterized member of the BfuABC family of EB enzymes, the NADH-dependent reduced-ferredoxin:NADP + oxidoreductase from Thermococcus sibiricus (Tsi NfnABC). Cryo-EM structures of Tsi NfnABC previously demonstrated that it contains twelve redox cofactors: two flavins (one FAD and one FMN), eight [4Fe–4S] clusters, and two [2Fe–2S] clusters. The FMN, one [4Fe–4S] cluster, and one [2Fe–2S] cluster comprise the bifurcating active site termed the electron-bifurcating flavobicluster (BF-FBC), which is found in all BfuABC family members. By using electron paramagnetic resonance spectroscopy, we identified spectral signatures originating from interactions between the FMN radical and [4Fe–4S] + cluster in the BF-FBC and observed temperature dependent behavior of the BF-FBC's [2Fe–2S] + cluster indicative of moderately slow spin–lattice relaxation. Additionally, we uncovered numerous spectral features corresponding to half-integer, S > ½ spin states of [4Fe–4S] + clusters, including one attributable to the consequences of lysine-ligation of a [4Fe–4S] cluster unique to NfnABC. We contextualize these findings to electron transfer theory and NfnABC's structure. Our insights further the understanding of how enzymes are designed to exert control over electron transfer to conduct thermodynamically challenging reactions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Cryoelectron microscopy structure and mechanism of the membrane-associated electron-bifurcating flavoprotein Fix/EtfABCX

Significance Electron bifurcation is a recently recognized mechanism of biological energy conservation that is widespread in anaerobic microorganisms and provides low-potential, high-energy electrons to drive otherwise nonspontaneous metabolic reactions. Here we describe the structure of a membrane-associated bifurcating enzyme from an aerobic microorganism. Termed Fix/EtfABCX, this enzyme is used by some nitrogen-fixing microbes to drive the low-potential reduction of nitrogen gas to ammonia. Fix/EtfABCX is a superdimer and a catalytic mechanism is proposed involving six flavins, two of which bifurcate, four iron-sulfur clusters, and two menaquinones. Fix/EtfABCX shares structural similarity with mammalian quinone oxidoreductase involved in mitochondrial fatty acid oxidation, suggesting an unexpected evolutionary link between bifurcating and nonbifurcating systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Insight Into the High-Potential Branch of the Alternate Nad+-Dependent NADPH:Ferredoxin Oxidoreductase II (NfnII) from Pyrococcus Furiosus. Evidence for the Gating Step in Electron Bifurcation

We have investigated the rapid-reaction kinetics of the NAD+-dependent NADPH:ferredoxin oxidoreductase II (NfnII) from Pyrococcus furiosus, permitting a comparison with recent work done with the paralog NfnI from the same organism. The half-potentials of the electron-bifurcating L-FAD are highly crossed in both NfnI, meaning the potential for the quinone/semiquinone couple is significantly lower than that for the semiquinone/hydroquinone couple so that the semiquinone oxidation state is thermodynamically unstable. The same appears to be the case with NfnII on the basis of its similar behavior in transient absorption spectroscopy experiments and the absence of any evidence for FAD*- accumulation in the course of reductive titrations (which would be manifested as a transient increase in absorbance at ~380 nm)1. Reductive titrations with both the one-electron donor sodium dithionite and the obligate two-electron donor NADPH demonstrate that, in contrast to NfnI, little FADH* accumulates in the high-potential pathway of NfnII in the course of reduction, as reflected in the absence of a transient increase in absorbance in the 500-600 nm region. This indicates that the half-potentials of the S-FAD are crossed in NfnII by a minimum of 120 mV. Rapid-reaction experiments mixing oxidized NfnII with NADPH also show no evidence of S-FADH* accumulation. Furthermore, the enzyme is only partially reduced at the end of the reaction with NADPH, indicating that there is little electron transfer into the high-potential pathway of NfnII. When the reaction is carried out in the presence of the one-electron carrier ferredoxin, only approximately one equivalent of ferredoxin becomes reduced, in contrast to the maximum of three equivalents seen with NfnI. This is consistent with only a single electron bifurcation event taking place under these conditions with NfnII, with only a single high-potential electron passing into the [2Fe-2S] cluster of the high-potential pathway of NfnII but not progressing further to the S-FAD. This accounts for the observation that NfnII has greatly reduced bifurcating activity compared to NfnI. The lack of electron transfer into the S-FAD of NfnII due to its crossed half-potentials prevents successive bifurcation activity and indicates that electron transfer within the high-potential branch gates bifurcation activity in NfnI.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Electrochemical Observation and pH Dependence of All Three Expected Redox Couples in an Extremophilic Bifurcating Electron Transfer Flavoprotein with Fused Subunits

Bifurcating enzymes employ energy from a favorable electron transfer to drive unfavorable transfer of a second electron, thereby generating a more reactive product. They are therefore highly desirable in catalytic systems, for example, to drive challenging reactions such as nitrogen fixation. While most bifurcating enzymes contain air-sensitive metal centers, bifurcating electron transfer flavoproteins (bETFs) employ flavins. However, they have not been successfully deployed on electrodes. Herein, we demonstrate immobilization and expected thermodynamic reactivity of a bETF from a hyperthermophilic archaeon, Sulfolobus acidocaldarius (SaETF). SaETF differs from previously biochemically characterized bETFs in being a single protein, representing a concatenation of the two subunits of known ETFs. However, SaETF retains the chemical properties of heterodimeric bETFs, including possession of two FADs: one that undergoes sequential 1-electron (1e) reductions at high E° and forms an anionic semiquinone, and another that is amenable to lower-E° 2e reduction, including by NADH. We found homologous monomeric ETF genes in archaeal and bacterial genomes, accompanied by genes that also commonly flank heterodimeric ETFs, and SaETF’s sequence conservation is 50% higher with bETFs than with canonical ETFs. Thus, SaETF is best described as a bETF. Our direct electrochemical trials capture reversible redox couples for all three thermodynamically expected redox events. We document electrochemical activity over a range of pH values and reveal a conformational change coupled to proton acquisition that affects the electrochemical activity of the higher-E° FAD. Thus, this well-behaved monomeric bETF opens the door to bioinspired bifurcating devices or bifurcation on a chip.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

An uncharacteristically low-potential flavin governs the energy landscape of electron bifurcation

Significance Nature has long been an inspiration for materials design, as it exemplifies exquisite control of both matter and energy. Electron bifurcation, a mechanism employed in biological systems to drive thermodynamically unfavorable and energetically challenging chemical reactions, is one such example. A key feature of bifurcating enzymes is the ability of a single redox cofactor to distribute a pair of electrons across two spatially separated electron transfer pathways. Here, we report on the empirical determination of both the one-electron potential and two-electron potential of the bifurcating flavin cofactor in the NADH-dependent ferredoxin-NADP + oxidoreductase I (NfnSL) enzyme. Insights arising from the defined energy landscape of this bifurcation site may underlie the design of synthetic catalysts capable of generating high-energy intermediates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

An electron-bifurcating “plug” to a protein nanowire in tungsten-dependent aldehyde detoxification

Members of the tungsten-containing oxidoreductase (WOR) family, which contain a tungstopyranopterin (Tuco) cofactor, are typically either monomeric (WorL) or heterodimeric (WorLS). These enzymes oxidize aldehydes to the corresponding acids while reducing the redox protein ferredoxin. They have been structurally characterized mainly using WORs from hyperthermophilic archaea. The WORs of some bacteria contain three additional subunits of the BfuABC family and these chimeric WorABCSL enzymes catalyze an electron-bifurcating reaction in which aldehyde oxidation is coupled to the simultaneous reduction of ferredoxin and nicotinamide adenine dinucleotide. In human gut microbes, electron bifurcation by WorABSL is proposed to enable the detoxification of aldehydes generated from cooked foods and in the tungstocentric production of beneficial short chain fatty acids from lactate, potentially impacting health. Herein we present the high-resolution cryogenic electron microscopy (cryo-EM) structure of the WorABCSL purified from the bacteriumAcetomicrobium mobile.The structure reveals a surprising 1:3 stoichiometry between WorABC and WorSL, with the WorSL units forming a nanowire-like architecture leading from three Tuco-containing catalytic sites in WorL via strings of multiple iron-sulfur clusters in WorS to a single bifurcating WorABC core. Our structure uncovers a distinct domain arrangement that links three Tuco-dependent aldehyde oxidation sites with the bifurcation process and potentially facilitates environmental aldehyde oxidation.

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