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Electrochemistry of flavin-based electron bifurcation: ‘Current’ past and ‘potential’ futures
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Correlating Conformational Equilibria with Catalysis in the Electron Bifurcating EtfABCX of Thermotoga maritima
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Cryo-EM reveals a composite flavobicluster electron bifurcation site in the Bfu family member NfnABC
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Extended conformations of bifurcating electron transfer flavoprotein constitute up to half the population, possibly mediating conformational change
Small-angle neutron scattering shows that electron transfer flavoprotein in solution populates extended conformations that are distinct from crystal structures. Extended conformations could mediate conformation changes that gate electron transfer.
Interactions that shape the complementary reactivities of the flavins of bifurcating electron transfer flavoproteins
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Very-Low-Frequency transmitters bifurcate energetic electron belt in near-earth space
Very-Low-Frequency (VLF) transmitters operate worldwide mostly at frequencies of 10–30 kilohertz for submarine communications. While it has been of intense scientific interest and practical importance to understand whether VLF transmitters can affect the natural environment of charged energetic particles, for decades there remained little direct observational evidence that revealed the effects of these VLF transmitters in geospace. Here we report a radially bifurcated electron belt formation at energies of tens of kiloelectron volts (keV) at altitudes of ~0.8–1.5 Earth radii on timescales over 10 days. Using Fokker-Planck diffusion simulations, we provide quantitative evidence that VLF transmitter emissions that leak from the Earth-ionosphere waveguide are primarily responsible for bifurcating the energetic electron belt, which typically exhibits a single-peak radial structure in near-Earth space. Since energetic electrons pose a potential danger to satellite operations, our findings demonstrate the feasibility of mitigation of natural particle radiation environment.
Understanding flavin electronic structure and spectra
Abstract Flavins have emerged as central to electron bifurcation, signaling, and countless enzymatic reactions. In bifurcation, two electrons acquired as a pair are separated in coupled transfers wherein the energy of both is concentrated on one of the two. This enables organisms to drive demanding reactions based on abundant low‐grade chemical fuel. To enable incorporation of this and other flavin capabilities into designed materials and devices, it is essential to understand fundamental principles of flavin electronic structure that make flavins so reactive and tunable by interactions with protein. Emerging computational tools can now replicate spectra of flavins and are gaining capacity to explain reactivity at atomistic resolution, based on electronic structures. Such fundamental understanding can moreover be transferrable to other chemical systems. A variety of computational innovations have been critical in reproducing experimental properties of flavins including their electronic spectra, vibrational signatures, and nuclear magnetic resonance (NMR) chemical shifts. A computational toolbox for understanding flavin reactivity moreover must be able to treat all five oxidation and protonation states, in addition to excited states that participate in flavoprotein's light‐driven reactions. Therefore, we compare emerging hybrid strategies and their successes in replicating effects of hydrogen bonding, the surrounding dielectric, and local electrostatics. These contribute to the protein's ability to modulate flavin reactivity, so we conclude with a survey of methods for incorporating the effects of the protein residues explicitly, as well as local dynamics. Computation is poised to elucidate the factors that affect a bound flavin's ability to mediate stunningly diverse reactions, and make life possible. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Theoretical and Physical Chemistry > Spectroscopy
Effect of controlled magnetic island bifurcation on electron diffusion
Magnetic islands strongly influence cross-field electron transport in magnetized plasmas. In particular, bifurcations of the island topology modify the number and location of O-points, X-points, and separatrix boundaries, thereby altering diffusion pathways. In recent DIII-D experiments, external magnetic perturbations were used to rotate and periodically bifurcate the island on the q = 2 surface, causing a switchback between a q = 2/1-dominated structure and a narrower q = 4/2-dominated structure. To investigate how this topological change affects electron transport, we employ the field line tracing code TRIP3D with an implemented collisional operator. Thermal, tracer electrons launched from O-points, X-points, and outside separatrix boundaries reveal distinct diffusion regimes, including classical, subdiffusive, and superdiffusive behavior, depending on both the dominant island mode and launch location. These results suggest that island bifurcation can alter electron diffusion across rational surfaces, with direct implications for particle confinement. While the present work emphasizes diffusion as a general framework, the findings provide insight into the conditions under which electron trapping into an island or stochastization of the island's separatrix can enable additional mechanisms, such as the generation of energetic electrons.
E × B flow driven electron temperature bifurcation in a closed slot divertor with ion B × ∇ B away from the X-point in the DIII-D tokamak
An electron temperature bifurcation is observed in the small angle slot divertor, which has been developed to enhance neutral cooling across the divertor target by coupling a closed slot structure with appropriate target shaping. Experiments in the DIII-D tokamak and associated SOLPS-ITER modeling with full drifts find a strong interplay between drifts and divertor geometry on divertor dissipation. The coupling of divertor geometry and drift flows can strongly affect the path towards divertor detachment onset as the plasma density is raised. With the strike point on the inner slanted surface and ion B × ∇B away from the magnetic X-point, bifurcative transitions were observed with sharp decrease of T e towards detachment onset both experimentally and computationally. This differs from the situation for the open divertor where the T e cliff was only observed for ion B × ∇B towards the X-point. SOLPS-ITER modeling with full drifts demonstrates that the magnitude of the E × B drift flow is comparable with the main plasma flow. The reversal of both the poloidal and radial E × B flows near the strike point leads to rapid density accumulation right near the separatrix, which results in bifurcative step transition of divertor conditions with cold plasma across the entire divertor target plate. Furthermore, these results indicate that the interplay between geometry and drifts should be fully taken into account in future fusion reactor divertor designs.
Catalytic Bias of NADH-Dependent Reduced Ferredoxin: NADP+ Oxidoreductase (Nfn) and its Relevance to Ethanol Production in Thermoanaerobacterium Saccharolyticum
NADH-dependent reduced ferredoxin: NADP+ oxidoreductase (Nfn) enzyme catalyzes an energy-conserving flavin-based electron bifurcation (FBEB) reaction. In microbial metabolism, Nfn links redox pools of three electron carriers - ferredoxin (Fd), NAD(H), and NADP(H) - through the following FBEB reaction: 2 NADPH + NAD+ + 2 Fdox 2 NADP+ + NADH + 2 Fdred + H+ The forward reaction is termed electron bifurcation, and the reverse reaction is electron confurcation. Catalytic bias describes an enzyme's tendency to favor one direction of a reversible reaction over the other and is expressed as the ratio of activities in the two directions. Thermoanaerobacterium saccharolyticum (Tsac) is a thermophilic, ethanologenic bacterium that ferments hemicellulose to ethanol at yields above 90%. Its Nfn enzyme is known to support ethanol production, presumably by operating in the confurcating direction to balance cellular cofactors, but this has not previously been demonstrated. To investigate the Tsac Nfn further, we heterologously expressed, purified, and reconstituted the proteins NfnS (NfnA), NfnL (NfnB), and the putative partner Fd with iron-sulfur cluster and/or FAD cofactors. Activity assays monitoring the oxidation or reduction of Fd showed that, across pH 5-10, Tsac Nfn is catalytically biased towards the confurcating direction, favoring NADPH generation over NADPH oxidation by at least fivefold. Using protein electrochemistry, we also determined the reduction potentials of the cofactors in NfnL and Fd. These results indicate that the energetic landscape of FBEB in Tsac Nfn is similar to that in an ortholog. However, Tsac Fd has redox properties distinct from previously assayed Fds, suggesting that the identity and redox properties of Fd may help determine the catalytic bias of Nfn. Additionally, we confirmed the standalone ferredoxin: NADP+ oxidoreductase (FNOR) activity of NfnL but found it to be low and likely insignificant for in vivo redox conversion. We also show how the catalytic bias of Nfn integrates with the hydrogen cycling mechanism proposed in Tsac to better explain cofactor balancing for ethanol production. Our work advances the understanding of electron transfer processes within metabolic networks for the generation of valuable bioproducts.
Unusual reactivity of a flavin in a bifurcating electron-transferring flavoprotein leads to flavin modification and a charge-transfer complex
From the outset, canonical electron transferring flavoproteins (ETFs) earned a reputation for containing modified flavin. We now show that modification occurs in the recently recognized bifurcating (Bf) ETFs as well. In Bf ETFs, the ’electron transfer’ (ET) flavin mediates single electron transfer via a stable anionic semiquinone state, akin to the FAD of canonical ETFs, whereas a second flavin mediates bifurcation (the Bf FAD). We demonstrate that the ET FAD undergoes trans- formation to two different modified flavins by a sequence of protein-catalyzed reactions that occurs specifically in the ET site, when the enzyme is maintained at pH 9 in an amine-based buffer. Our optical and mass spectrometric characterizations identify 8-formyl flavin early in the process and 8-amino flavins (8AFs) at later times. The latter have not previously been documented in an ETF to our knowledge. Mass spectrometry of flavin products formed in Tris or bis-tris-aminopropane solutions demonstrates that the source of the amine adduct is the buffer. Stepwise reduction of the 8AF demonstrates that it can explain a charge transfer band observed near 726 nm in Bf ETF, as a complex involving the hydroquinone state of the 8AF in the ET site with the oxidized state of unmodified flavin in the Bf site. This supports the possibility that Bf ETF can populate a conformation enabling direct electron transfer between its two flavins, as has been proposed for cofactors brought together in complexes between ETF and its partner proteins.
Better Living Through Biology: Studying Enzymes to Make Industrial Processes More Efficient
In biology, enzymes are the molecular machinery needed to speed up slow chemical reactions for life to occur. These molecular machines enhance chemical processes to a large degree, allowing for improbable and challenging chemical reactions to efficiently happen in water at room temperature. Many microorganisms have specialized enzymes used to tackle particularly challenging chemistry that they experience in their own environment. Our group is studying a specific enzyme using a reaction called "electron bifurcation" that energetically pairs electrons and is analogous to a trampoline, using one person's jump to propel another person higher than they could by themselves. We have learned that certain metal- and vitamin-containing pathways in this protein funnel electrons in specific directions. Our investigation into this enzyme is the foundation for future industrial applications, ranging from biological production of sustainable aviation fuel from CO2, production of nitrogen-based fertilizers, and biologically remediating environmental contamination.
How a Formate Dehydrogenase Responds to Oxygen: Unexpected O 2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters
The reversible two-electron interconversion of formate and CO 2 is catalyzed by both nonmetallo- and metallo-formate dehydrogenases (FDHs). The latter group comprises molybdenum- or tungsten-containing enzymes with the metal coordinated by two equivalents of a pyranopterin cofactor, a cysteinyl or selenocysteinyl (Sec) ligand supplied by the polypeptide, and a catalytically essential terminal sulfido ligand. In addition, these biocatalysts incorporate one or more [4Fe–4S] clusters for facilitating long-distance electron transfer. However, an interesting dichotomy arises when attempting to understand how the metallo-FDHs react with O 2 . Whereas existing scholarship portrays these enzymes as being unable to perform in air due to extreme O 2 lability of their metal centers, studies dating as far back as the 1930s emphasize that some of these systems exhibit formate oxidase (FOX) activity, coupling formate oxidation to O 2 reduction. Therefore, to reconcile these conflicting views, we explored context-dependent functional linkages between metallo-FDHs and their cognate electron acceptors within the same organism vis-à-vis catalysis under atmospheric O 2 . Here, we report the discovery and characterization of an O 2 -insensitive FDH2 from the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) that ligates tungsten, Sec, and four [4Fe–4S] clusters. By advancing a robust expression platform for its recombinant production, we eliminate both the requirement of nitrate or azide during purification and reductive activation with thiols and/or formate prior to catalysis. Because the distinctive spectral signatures of formate-reduced DvH-FDH2 remain invariant under anaerobic and aerobic conditions, we benchmarked the enzyme activity in air, identifying CO 2 as the catalytic product. Full reaction progress curve analysis discloses a high catalytic efficiency when probed with a high-potential artificial electron acceptor. Furthermore, we show that DvH-FDH2 enables near-stoichiometric hydrogen peroxide production without superoxide release to achieve O 2 insensitivity. Notably, simultaneous electron transfer to cytochrome c and O 2 reveals that metal-based electron bifurcation is operational in this system. Taken together, our work proves the co-occurrence of redox bifurcated FDH and FOX activities within a metalloenzyme scaffold. These findings set the stage for uncovering previously unknown O 2 -insensitive flavin-based electron bifurcation mechanisms, as well as for developing authentic formate/air biofuel cells, engineering O 2 -stable FDHs and biohybrid metallocatalysts, and discerning formate bioenergetics of gut microbiota.
Evolving a New Electron Transfer Pathway for Nitrogen Fixation Uncovers an Electron Bifurcating-Like Enzyme Involved in Anaerobic Aromatic Compound Degradation
There is increasing evidence that protein electron carriers like Fd evolved to form specific partnerships with select electron donors and acceptors to keep native electron transfer pathways insulated from one another. This makes it challenging to integrate a Fd-dependent pathway such as biological nitrogen fixation into non-nitrogen-fixing organisms and provide the high-energy reducing power needed to fix nitrogen.
Biological Electron Transfer and Catalysis EFRC
The focus of the Biological Electron Transfer and Catalysis (BETCy) EFRC research is elucidating mechanisms of conversion of electrochemical potential into chemical bond energy and is organized into two integrated Thrusts: Electron Bifurcation Catalysis and Electron Transfer Kinetics. We are developing a collective knowledge of metalloenzymes as models for redox reactions by applying physical science and computational tools to characterize biochemical reactions catalyzed by multi- subunit enzymes harboring arrays of iron-sulfur clusters and flavin cofactors. Understanding these mechanisms is central to overcoming the thermodynamic barriers that currently limit production of reduced products and fuels. Biological systems have elegant strategies for converting electrochemical potential energy into chemical bond energy (e.g., C-H, H-H, and N-H) stored in reduced compounds that can serve as advanced biofuels. One significant limitation for the production of highly reduced compounds is that their production in natural and industrial processes relies on low oxidation-reduction potential chemicals as feedstocks.
A comparative genome analysis of the Bacillota ( Firmicutes ) class Dehalobacteriia
Dehalobacterium formicoaceticum is recognized for its ability to anaerobically ferment dichloromethane (DCM), and a catabolic model has recently been proposed. D. formicoaceticum is currently the only axenic representative of its class, the Dehalobacteriia, according to the Genome Taxonomy Database. However, substantial additional diversity has been revealed in this lineage through culture-independent exploration of anoxic habitats. Here we performed a comparative analysis of 10 members of the Dehalobacteriia, representing three orders, and infer that anaerobic DCM degradation appears to be a recently acquired trait only present in some members of the order Dehalobacteriales. Inferred traits common to the class include the use of amino acids as carbon and energy sources for growth, energy generation via a remarkable range of putative electron-bifurcating protein complexes and the presence of S-layers. The ability of D. formicoaceticum to grow on serine without DCM was experimentally confirmed and a high abundance of the electron-bifurcating protein complexes and S-layer proteins was noted when this organism was grown on DCM. We suggest that members of the Dehalobacteriia are low-abundance fermentative scavengers in anoxic habitats.