Universal free-energy landscape produces efficient and reversible electron bifurcation

The role of an intramolecular hydrogen bond in the redox properties of carboxylic acid naphthoquinones

A bioinspired naphthoquinone model of the quinones in photosynthetic reaction centers but bearing an intramolecular hydrogen-bonded carboxylic acid has been synthesized and characterized electrochemically, spectroscopically, and computationally to provide mechanistic insight into the role of proton-coupled electron transfer (PCET) of quinone reduction in photosynthesis. The reduction potential of this construct is 370 mV more positive than the unsubstituted naphthoquinone. In addition to the reversible cyclic voltammetry, infrared spectroelectrochemistry confirms that the naphthoquinone/naphthoquinone radical anion couple is fully reversible. Calculated redox potentials agree with the experimental trends arising from the intramolecular hydrogen bond. Molecular electrostatic potentials illustrate the reversible proton transfer driving forces, and analysis of the computed vibrational spectra supports the possibility of a combination of electron transfer and PCET processes. The significance of PCET, reversibility, and redox potential management relevant to the design of artificial photosynthetic assemblies involving PCET processes is discussed.

Undulating Free Energy Landscapes Buffer Redox Chains from Environmental Fluctuations

Roller-coaster or undulating free energy landscapes, with alternating high and low potential cofactors, occur frequently in biological redox chains. Yet, there is little understanding of the possible advantages created by these landscapes. We examined the tetraheme subunit associated with Blastochloris viridis reaction centers, comparing the dynamics of the native protein and of hypothetical (in silico) mutants. We computed the variation in the total number of electrons in wild type (WT) and mutant tetrahemes connected to an electron reservoir in the presence of a time-varying potential, as a model for a fluctuating redox environment. We found that roller-coaster free energy landscapes buffer the redox cofactor populations from these fluctuations. The WT roller-coaster landscape slows forward and backward electron transfer in the face of fluctuations, and may offer the advantage of sustaining the reduction of essential cofactors, such as the chlorophyll special pair in photosynthesis, even though an undulating landscape introduces thermodynamically uphill steps in multistep redox chains.

Structures and Electron Transport Paths in the Four Families of Flavin-Based Electron Bifurcation Enzymes

Oxidoreductases facilitating electron transfer between molecules are pivotal in metabolic pathways. Flavin-based electron bifurcation (FBEB), a recently discovered energy coupling mechanism in oxidoreductases, enables the reversible division of electron pairs into two acceptors, bridging exergonic and otherwise unfeasible endergonic reactions. This chapter explores the four distinct FBEB complex families and highlights a decade of structural insights into FBEB complexes. In this chapter, we discuss the architecture, electron transfer routes, and conformational changes across all FBEB families, revealing the structural foundation that facilitate these remarkable functions.

Syntrophic Propionate Oxidation: One of the Rate-Limiting Steps of Organic Matter Decomposition in Anoxic Environments

Syntrophic propionate oxidation is one of the rate-limiting steps during anaerobic decomposition of organic matter in anoxic environments. Syntrophic propionate-oxidizing bacteria (SPOB) are members of the "rare biosphere" living at the edge of the thermodynamic limit in most natural habitats. Hitherto, only 10 bacterial species capable of syntrophic propionate oxidization have been identified. SPOB employ different metabolisms for propionate oxidation (e.g., methylmalonyl-CoA pathway and C6 dismutation pathway) and show diverse life strategies (e.g., obligately and facultatively syntrophic lifestyle). The flavin-based electron bifurcation/confurcation (FBEB/C) systems have been proposed to help solve the thermodynamic dilemma during the formation of the low-potential products H2 and formate. Molecular ecological approaches, such as DNA stable isotope probing (DNA-SIP) and metagenomics, have been used to detect SPOB in natural environments. Furthermore, the biogeographical pattern of SPOB has been recently described in paddy soils. A comprehensive understanding of SPOB is essential for better predicting and managing organic matter decomposition and carbon cycling in anoxic environments. In this review, we described the critical role of syntrophic propionate oxidation in anaerobic decomposition of organic matter, phylogenetic and metabolic diversity, life strategies and ecophysiology, composition of syntrophic partners, and pattern of biogeographic distribution of SPOB in natural environments. We ended up with a few perspectives for future research.

Correlated particle transport enables biological free energy transduction

Studies of biological transport frequently neglect the explicit statistical correlations among particle site occupancies (i.e., they use a mean-field approximation). Neglecting correlations sometimes captures biological function, even for out-of-equilibrium and interacting systems. We show that neglecting correlations fails to describe free energy transduction, mistakenly predicting an abundance of slippage and energy dissipation, even for networks that are near reversible and lack interactions among particle sites. Interestingly, linear charge transport chains are well described without including correlations, even for networks that are driven and include site-site interactions typical of biological electron transfer chains. We examine three specific bioenergetic networks: a linear electron transfer chain (as found in bacterial nanowires), a near-reversible electron bifurcation network (as in complex III of respiration and other recently discovered structures), and a redox-coupled proton pump (as in complex IV of respiration).

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.

Exploring Proton-Coupled Electron Transfer at Multiple Scales

The coupling of electron and proton transfer is critical for chemical and biological processes spanning a wide range of length and time scales and often occurring in complex environments. Thus, diverse modeling strategies, including analytical theories, quantum chemistry, molecular dynamics, and kinetic modeling, are essential for a comprehensive understanding of such proton-coupled electron transfer reactions. Each of these computational methods provides one piece of the puzzle, and all these pieces must be viewed together to produce the full picture.

Q-lipid-containing membranes show high in-plane conductivity using a membrane-on-a-chip setup

The light-driven reactions of photosynthesis as well as the mitochondrial power supply are located in specialized membranes containing a high fraction of redox-active lipids. In-plane charge transfer along such cell membranes is currently thought to be facilitated by the diffusion of redox lipids and proteins. Using a membrane on-a-chip setup, we show here that redox-active model membranes can sustain surprisingly high currents (mA) in-plane at distances of 25 μm. We also show the same phenomenon in free-standing monolayers at the air-water interface once the film is compressed such that the distance between redox centers is below 1 nm. Our data suggest that charge transfer within cell walls hosting electron transfer chains could be enabled by the coupling of redox-lipids via simultaneous electron and proton in-plane hopping, similar to conductive polymers. This has major implications for our understanding of the role of lipid membranes, suggesting that Q-lipid-containing membranes may be essential for evolving the complex redox machineries of life.

Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case

Determining the redox potentials of protein cofactors and how they are influenced by their molecular neighborhoods is essential for basic research and many biotechnological applications, from biosensors and biocatalysis to bioremediation and bioelectronics. The laborious determination of redox potential with current experimental technologies pushes forward the need for computational approaches that can reliably predict it. Although current computational approaches based on quantum and molecular mechanics are accurate, their large computational costs hinder their usage. In this work, we explored the possibility of using more efficient QSPR models based on machine learning (ML) for the prediction of protein redox potential, as an alternative to classical approaches. As a proof of concept, we focused on flavoproteins, one of the most important families of enzymes directly involved in redox processes. To train and test different ML models, we retrieved a dataset of flavoproteins with a known midpoint redox potential (Em) and 3D structure. The features of interest, accounting for both short- and long-range effects of the protein matrix on the flavin cofactor, have been automatically extracted from each protein PDB file. Our best ML model (XGB) has a performance error below 1 kcal/mol (∼36 mV), comparing favorably to more sophisticated computational approaches. We also provided indications on the features that mostly affect the Em value, and when possible, we rationalized them on the basis of previous studies.

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.

Kinetic model for reversible radical transfer in ribonucleotide reductase

The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Å through two protein subunits and the intervening aqueous interface. Herein, a kinetic model is designed to describe reversible radical transfer in Escherichia coli RNR. This model is based on experimentally studied photoRNR systems that allow the photochemical injection of a radical at a specific tyrosine residue, Y356, using a photosensitizer. The radical then transfers across the interface to another tyrosine residue, Y731, and continues until it reaches a cysteine residue, C439, which is primed for catalysis. This kinetic model includes radical injection, an off-pathway sink, radical transfer between pairs of residues along the pathway, and the conformational flipping motion of Y731 at the interface. Most of the input rate constants for this kinetic model are obtained from previous experimental measurements and quantum mechanical/molecular mechanical free-energy simulations. Ranges for the rate constants corresponding to radical transfer across the interface are determined by fitting to the experimentally measured Y356 radical decay times in photoRNR systems. This kinetic model illuminates the time evolution of radical transport along the tyrosine and cysteine residues following radical injection. Further analysis identifies the individual rate constants that may be tuned to alter the timescale and probability of the injected radical reaching C439. The insights gained from this kinetic model are relevant to biochemical understanding and protein-engineering efforts with potential pharmacological implications.

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

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.

Electron bifurcation, an energy-conserving process utilized extensively throughout all domains of life, represents an elegant means of generating high-energy products from substrates with less reducing potential. The coordinated coupling of exergonic and endergonic reactions has been shown to operate over an electrochemical potential of ∼1.3 V through the activity of a unique flavin cofactor in the enzyme NADH-dependent ferredoxin-NADP⁺ oxidoreductase I. The inferred energy landscape has features unprecedented in biochemistry and presents novel energetic challenges, the most intriguing being a large thermodynamically uphill step for the first electron transfer of the bifurcation reaction. However, ambiguities in the energy landscape at the bifurcating site deriving from overlapping flavin spectral signatures have impeded a comprehensive understanding of the specific mechanistic contributions afforded by thermodynamic and kinetic factors. Here, we elucidate an uncharacteristically low two-electron potential of the bifurcating flavin, resolving the energetic challenge of the first bifurcation event.

Interaction of membrane-embedded cytochrome b-complexes with quinols: Classical Q-cycle and murburn model

We recently proposed a diffusible reactive (oxygen) species (DRS/DROS) based function for cytochrome b complexes (CBC) and quinones (Q)/quinols (QH₂ ) in the murburn model of bioenergetics. This proposal is in direct conflict with the classical purview of Q-cycle. Via extensive analyses of the structure-function correlations of membrane-quinones/quinols and proteins, we present qualitative and quantitative arguments to infer that the classical model cannot explain the energetics, kinetics, mechanism and probabilistic considerations. Therefore, it is proposed that Q-cycle is neither necessary nor feasible at CBCs. In contrast, we substantiate that the murburn model explains: (a) crucial structural data of CBCs, (b) why quinones/quinols are utilized in bioenergetic membranes, (c) how trans-membrane potential is generated owing to effective charge separation at CBCs, (d) mobility data of O₂ , DRS, Q/QH₂ , and (e) utility of other reaction/membrane components. Further, the murburn model also accommodates the absence of quinones in anaerobic Archaea, wherein methanophenazines are prevalent. The work mandates that the textbooks and research agendas are refreshed to reflect the new perception. SIGNIFICANCE: The current article must be seen as a critical and detailed analysis of the role and working mechanism of quinone (Q) /quinols (QH₂ ) in bioenergetic membranes. In the classical model, QH₂ are perceived as highly mobile electron-transport agents that bind and donate electrons to cytochrome b complexes (CBCs), using sophisticated electronic circuitries, in order to recycle Q and pump protons. The classical perception sees radicals (such as Q*-, O₂ *-, etc., also called diffusible reactive species, DRS) as wasteful or toxic (patho) physiological manifestations. It is highlighted herein that QH₂ has low mobility and matrix has little protons to pump. New insights from the structural analyses of diverse CBCs and quinols, in conjunction with murburn reaction thermodynamics suggest that the electrons from substrates/quinols are effectively utilized via DRS. This perception fits into a much broader analysis of 1 and 2 electron transfers in overall redox metabolism, as recently brought out by the murburn model, wherein DRS are considered obligatory ingredients of physiology. Thus, the findings mandate a reorientation in the pertinent research field.

Free Energies of Proton-Coupled Electron Transfer Reagents and Their Applications

We present an update and revision to our 2010 review on the topic of proton-coupled electron transfer (PCET) reagent thermochemistry. Over the past decade, the data and thermochemical formalisms presented in that review have been of value to multiple fields. Concurrently, there have been advances in the thermochemical cycles and experimental methods used to measure these values. This Review (i) summarizes those advancements, (ii) corrects systematic errors in our prior review that shifted many of the absolute values in the tabulated data, (iii) provides updated tables of thermochemical values, and (iv) discusses new conclusions and opportunities from the assembled data and associated techniques. We advocate for updated thermochemical cycles that provide greater clarity and reduce experimental barriers to the calculation and measurement of Gibbs free energies for the conversion of X to XH_n in PCET reactions. In particular, we demonstrate the utility and generality of reporting potentials of hydrogenation, E°(V vs H₂), in almost any solvent and how these values are connected to more widely reported bond dissociation free energies (BDFEs). The tabulated data demonstrate that E°(V vs H₂) and BDFEs are generally insensitive to the nature of the solvent and, in some cases, even to the phase (gas versus solution). This Review also presents introductions to several emerging fields in PCET thermochemistry to give readers windows into the diversity of research being performed. Some of the next frontiers in this rapidly growing field are coordination-induced bond weakening, PCET in novel solvent environments, and reactions at material interfaces.

Why Do Most Aromatics Fail to Support Hole Hopping in the Cytochrome c Peroxidase-Cytochrome c Complex?

Electron transport through aromatic species (especially tryptophan and tyrosine) plays a central role in water splitting, redox signaling, oxidative damage protection, and bioenergetics. The cytochrome c peroxidase (CcP)-cytochrome c (Cc) complex (CcP:Cc) is used widely to study interprotein electron transfer (ET) mechanisms. Tryptophan 191 (Trp191) of CcP supports hole hopping charge recombination in the CcP:Cc complex. Experimental studies find that when Trp191 is substituted by tyrosine, phenylalanine, or redox-active aniline derivatives bound in the W191G cavity, enzymatic activity and charge recombination rates both decrease. Theoretical analysis of these CcP:Cc complexes finds that the ET kinetics depend strongly on the chemistry of the modified Trp site. The computed electronic couplings in the W191F and W191G species are orders of magnitude smaller than in the native protein, due largely to the absence of a hopping intermediate and the large tunneling distance. Small molecules bound in the W191G cavity are weakly coupled electronically to the Cc heme, and the structural disorder of the guest molecule in the binding pocket may contribute further to the lack of enzymatic activity. The couplings in W191Y are not substantially weakened compared to the native species, but the redox potential difference for tyrosine vs tryptophan oxidation accounts for the slower rate in the Tyr mutant. Thus, theoretical analysis explains why only the native Trp supports rapid hole hopping in the CcP:Cc complex. Favorable free energies and electronic couplings are essential for establishing an efficient hole hopping relay in this protein-protein complex.

Iron-sulfur flavoenzymes: the added value of making the most ancient redox cofactors and the versatile flavins work together

Iron-sulfur (Fe-S) flavoproteins form a broad and growing class of complex, multi-domain and often multi-subunit proteins coupling the most ancient cofactors (the Fe-S clusters) and the most versatile coenzymes (the flavin coenzymes, FMN and FAD). These enzymes catalyse oxidoreduction reactions usually acting as switches between donors of electron pairs and acceptors of single electrons, and vice versa. Through selected examples, the enzymes' structure−function relationships with respect to rate and directionality of the electron transfer steps, the role of the apoprotein and its dynamics in modulating the electron transfer process will be discussed.

Tunneling and Nonadiabatic Effects on a Proton-Coupled Electron Transfer Model for the Qo Site in Cytochrome bc1

Cytochrome bc₁ is a fundamental enzyme for cellular respiration and photosynthesis. This dimeric protein complex catalyzes a proton-coupled electron transfer (PCET) from the reduced coenzyme-Q substrate (Q) to a bimetallic iron-sulfur cluster in the Q_o active site. Herein, we combine molecular dynamics simulations of the complete cytochrome bc₁ protein with electronic-structure calculations of truncated models and a semiclassical tunneling theory to investigate the electron-proton adiabaticity of the initial reaction catalyzed in the Q_o site. After sampling possible orientations between the Q substrate and a histidine side chain that functions as hydrogen acceptor, we find that a truncated model composed by ubiquinol-methyl and imidazole-iron(III)-sulfide captures the expected changes in oxidation and spin states of the electron donor and acceptor. Diabatic electronic surfaces obtained for this model with multiconfigurational wave function calculations demonstrate that this reaction is electronic nonadiabatic, and proton tunneling is faster than mixing of electronic configurations. These results indicate the formalism that should be used to calculate vibronic couplings and kinetic parameters for the initial reaction in the Q_o site of cytochrome bc₁. This framework for molecular simulation may also be applied to investigate other PCET reactions in the Q-cycle or in various metalloproteins that catalyze proton translocation coupled to redox processes.

The modified Q-cycle: A look back at its development and forward to a functional model

On looking back at a lifetime of research, it is interesting to see, in the light of current progress, how things came to be, and to speculate on how things might be. I am delighted in the context of the Mitchell prize to have that excuse to present this necessarily personal view of developments in areas of my interests. I have focused on the Q-cycle and a few examples showing wider ramifications, since that had been the main interest of the lab in the 20 years since structures became available, - a watershed event in determining our molecular perspective. I have reviewed the evidence for our model for the mechanism of the first electron transfer of the bifurcated reaction at the Q_o-site, which I think is compelling. In reviewing progress in understanding the second electron transfer, I have revisited some controversies to justify important conclusions which appear, from the literature, not to have been taken seriously. I hope this does not come over as nitpicking. The conclusions are important to the final section in which I develop an internally consistent mechanism for turnovers of the complex leading to a state similar to that observed in recent rapid-mix/freeze-quench experiments, reported three years ago. The final model is necessarily speculative but is open to test.

Flavins in the electron bifurcation process

The discovery of a new energy-coupling mechanism termed flavin-based electron bifurcation (FBEB) in 2008 revealed a novel field of application for flavins in biology. The key component is the bifurcating flavin endowed with strongly inverted one-electron reduction potentials (FAD/FAD•^- ≪ FAD•^-/FADH^-) that cooperatively transfers in its reduced state one low and one high-energy electron into different directions and thereby drives an endergonic with an exergonic reduction reaction. As energy splitting at the bifurcating flavin apparently implicates one-electron chemistry, the FBEB machinery has to incorporate prior to and behind the central bifurcating flavin 2e-to-1e and 1e-to-2e switches, frequently also flavins, for oxidizing variable medium-potential two-electron donating substrates and for reducing high-potential two-electron accepting substrates. The one-electron carriers ferredoxin or flavodoxin serve as low-potential (high-energy) electron acceptors, which power endergonic processes almost exclusively in obligate anaerobic microorganisms to increase the efficiency of their energy metabolism. In this review, we outline the global organization of FBEB enzymes, the functions of the flavins therein and the surrounding of the isoalloxazine rings by which their reduction potentials are specifically adjusted in a finely tuned energy landscape.

Functional diversity of prokaryotic HdrA(BC) modules: Role in flavin-based electron bifurcation processes and beyond

In methanogenic archaea, the archetypical complex of heterodisulfide reductase (HdrABC) and hydrogenase (MvhAGD) couples the endergonic reduction of CO₂ by H₂ to the exergonic reduction of the CoB-S-S-CoM heterodisulfide by H₂ via flavin-based electron bifurcation. Presently known enzymes containing HdrA(BC)-like components play key roles in methanogenesis, acetogenesis, respiratory sulfate reduction, lithotrophic reduced sulfur compound oxidation, aromatic compound degradation, fermentations, and probably many further processes. This functional diversity is achieved by a modular architecture of HdrA(BC) enzymes, where a big variety of electron input/output modules may be connected either directly or via adaptor modules to the HdrA(BC) components. Many, but not all HdrA(BC) complexes are proposed to catalyse a flavin-based electron bifurcation/confurcation. Despite the availability of HdrA(BC) crystal structures, fundamental questions of electron transfer and energy coupling processes remain. Here, we address the common properties and functional diversity of HdrA(BC) core modules integrated into electron-transfer machineries of outstanding complexity.

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. We conclude with an outlook for propelling the field toward an integrative understanding of the impact of electron bifurcation.