Energetics and Dynamics of Proton-Coupled Electron Transfer in the NADH/FMN Site of Respiratory Complex I

Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I

Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is a major enzyme of energy metabolism that couples NADH oxidation and ubiquinone reduction with proton translocation. The NADH oxidation site features different enzymatic activities with various nucleotides. While the kinetics of these reactions are well described, only binding of NAD+ and NADH have been structurally characterized. Here, we report the structures of the electron input module of Aquifex aeolicus complex I with bound ADP-ribose and 3-acetylpyridine adenine dinucleotides at resolutions better than 2.0 Å. ADP-ribose acts as inhibitor by blocking the "ADP-handle" motif essential for nucleotide binding. The pyridine group of APADH is minimally offset from flavin, which could contribute to its poorer suitability as substrate. A comparison with other nucleotide co-structures surprisingly shows that the adenine ribose and the pyrophosphate moiety contribute most to nucleotide binding, thus all adenine dinucleotides share core binding modes to the unique Rossmann-fold in complex I.

The role of the active site lysine residue on FAD reduction by NADPH in glutathione reductase

Glutathione reductase (GR) is a two dinucleotide binding domain flavoprotein (tDBDF) that catalyzes the reduction of glutathione disulfide to glutathione coupled to the oxidation of NADPH to NADP+. An interesting feature of GR and other tDBDFs is the presence of a lysine residue (Lys-66 in human GR) at the active site, which interacts with the flavin group, but has an unknown function. To better understand the role of this residue, the dynamics of GR was studied using molecular dynamics simulations, and the reaction mechanism of FAD reduction by NADPH was studied using QM/MM molecular modeling. The two possible protonation states of Lys-66 were considered: neutral and protonated. Molecular dynamics results suggest that the active site is more structured for neutral Lys-66 than for protonated Lys-66. QM/MM modeling results suggest that Lys-66 should be in its neutral state for a thermodynamically favorable reduction of FAD by NADPH. Since the reaction is unfavorable with protonated Lys-66, the reverse reaction (the reduction of NADP+ by FADH-) is expected to take place. A phylogenetic analysis of various tDBDFs was performed, finding that an active site lysine is present in different the tDBDFs enzymes, suggesting that it has a conserved biological role. Overall, these results suggest that the protonation state of the active site lysine determines the energetics of the reaction, controlling its reversibility.

Magnetic porous microspheres enhancing the anaerobic digestion of sewage sludge: Synergistic free and attached methanogenic consortia

The addition of exogenous materials is a commonly reported method for promoting the anaerobic digestion (AD) of sludge. However, most exogenous materials are nano-sized and their use encounters problems relating to a need for continuous replenishment, uncontrollability and non-recyclability. Here, magnetic porous microspheres (MPMs), which can be controlled by magnetic forces, were prepared and used to enhance the methanogenesis of sludge. It was observed that the MPMs were spherical particles with diameters of approximately 100 µm and had a stable macroporous hybrid structure of magnetic cores and polymeric shells. Furthermore, the MPMs had good magnetic properties and a strong solid-liquid interfacial electron transfer ability, suggesting that MPMs are excellent carriers for methanogenic consortia. Experimental results showed that the addition of MPMs increased methane production and the proportion of methane in biogas from AD by 100.0 % and 21.2 %, respectively, indicating the MPMs notably enhanced the methanogenesis of sludge. Analyses of variations in key enzyme activities and electron transfer in sludge samples with and without MPMs in AD revealed that the MPMs significantly enhanced the activities of key enzymes involved in hydrolysis, acidification and methanation. This was achieved mainly by enhancing the extracellular electron transfer to strengthen the proton motive force on the cell membrane, which provides more energy generation for methanogenic metabolism. A careful examination of the variations in the morphology, pore structure and magnetism of the MPMs before and after AD revealed that the MPMs increased the prevalence of many highly active anaerobes, and that this did not weaken the magnetic performance. The microbial community structure and metatranscriptomic analysis further indicated that the acetotrophic methanogens (i.e., Methanosaeta) were mainly in a free state and that CO2-reducing methanogens (i.e., Methanolinea and Methanobacterium) mainly adhered to the MPMs. The above synergistic metabolism led to efficient methanogenesis, which indicates that the MPMs optimised the spatial ecological niche of methanogenic consortia. These findings provide an important reference for the development of magnetic porous materials promoting AD.

Characterization and antitumor effect of doxorubicin-loaded Fe3O4-Au nanocomposite synthesized by electron beam evaporation for magnetic nanotheranostics

Magnetic nanocomposites (MNC) are promising theranostic platforms with tunable physicochemical properties allowing for remote drug delivery and multimodal imaging. Here, we developed doxorubicin-loaded Fe3O4-Au MNC (DOX-MNC) using electron beam physical vapor deposition (EB-PVD) in combination with magneto-mechanochemical synthesis to assess their antitumor effect on Walker-256 carcinosarcoma under the influence of a constant magnetic (CMF) and electromagnetic field (EMF) by comparing tumor growth kinetics, magnetic resonance imaging (MRI) scans and electron spin resonance (ESR) spectra. Transmission (TEM) and scanning electron microscopy (SEM) confirmed the formation of spherical magnetite nanoparticles with a discontinuous gold coating that did not significantly affect the ferromagnetic properties of MNC, as measured by vibrating-sample magnetometry (VSM). Tumor-bearing animals were divided into the control (no treatment), conventional doxorubicin (DOX), DOX-MNC and DOX-MNC + CMF + EMF groups. DOX-MNC + CMF + EMF resulted in 14% and 16% inhibition of tumor growth kinetics as compared with DOX and DOX-MNC, respectively. MRI visualization showed more substantial tumor necrotic changes after the combined treatment. Quantitative analysis of T2-weighted (T2W) images revealed the lowest value of skewness and a significant increase in tumor intensity in response to DOX-MNC + CMF + EMF as compared with the control (1.4 times), DOX (1.6 times) and DOX-MNC (1.8 times) groups. In addition, the lowest level of nitric oxide determined by ESR was found in DOX-MNC + CMF + EMF tumors, which was close to that of the muscle tissue in the contralateral limb. We propose that the reason for the relationship between the observed changes in MRI and ESR is the hyperfine interaction of nuclear and electron spins in mitochondria, as a source of free radical production. Therefore, these results point to the use of EB-PVD and magneto-mechanochemically synthesized Fe3O4-Au MNC loaded with DOX as a potential candidate for cancer magnetic nanotheranostic applications.

The use of NADH anisotropy to investigate mitochondrial cristae alignment

Life may be expressed as the flow of electrons, protons, and other ions, resulting in large potential difference. It is also highly photo-sensitive, as a large proportion of the redox capable molecules it relies on are chromophoric. It is thus suggestive that a key organelle in eukaryotes, the mitochondrion, constantly adapt their morphology as part of the homeostatic process. Studying unstained in vivo nano-scale structure in live cells is technically very challenging. One option is to study a central electron carrier in metabolism, reduced nicotinamide adenine dinucleotide (NADH), which is fluorescent and mostly located within mitochondria. Using one and two-photon absorption (340-360 nm and 730 nm, respectively), fluorescence lifetime imaging and anisotropy spectroscopy of NADH in solution and in live cells, we show that mitochondria do indeed appear to be aligned and exhibit high anisotropy (asymmetric directionality). Aqueous solution of NADH showed an anisotropy of ~ 0.20 compared to fluorescein or coumarin of < 0.1 and 0.04 in water respectively and as expected for small organic molecules. The anisotropy of NADH also increased further to 0.30 in the presence of proteins and 0.42 in glycerol (restricted environment) following two-photon excitation, suggesting more ordered structures. Two-photon NADH fluorescence imaging of Michigan Cancer Foundation-7 (MCF7) also showed strong anisotropy of 0.25 to 0.45. NADH has a quantum yield of fluorescence of 2% compared to more than 40% for photoionisation (electron generation), when exposed to light at 360 nm and below. The consequence of such highly ordered and directional NADH patterns with respect to electron ejection upon ultra-violet (UV) excitation could be very informative-especially in relation to ascertaining the extent of quantum effects in biology, including electron and photonic cascade, communication and modulation of effects such as spin and tunnelling.

Improving microbial production of value-added products through the intervention of magnetic fields

The magnetic field application is emerging as an auxiliary physical strategy to facilitate rapid biomass accumulation and intracellular production of compounds. However, the underlying mechanisms and principles governing the application of magnetic fields for microbial growth and biotransformation are not yet fully understood. Therefore, a better understanding of interdisciplinary technologies integration, expanded magnetic field application, and scaled-up industrial implementation is crucial. In this review, the magnetic field characteristics, magnetic field-assisted fermentation devices, and the working mechanism of magnetic field have been reviewed comprehensively from both physical and microbiological perspectives. The review suggests that magnetic fields affect the biochemical processes in microorganisms by mediating nutrient transport across membranes, electron transfer during photosynthesis and respiration, enzyme activity and gene expression. Moreover, the recent advances in magnetic field application for microbial fermentation and conversion in biochemical, food and agricultural fields have been summarized.

An Ultrafast Air Self-Charging Zinc Battery

Air self-charging power systems possess the capability of energy harvesting, conversion, and storage simultaneously. However, in general, their self-charging rate is slow and the batteries cannot be oxidized to the fully charged state due to the weak oxidizability of O2 . Herein, an ultrafast air self-charging aqueous zinc battery is designed by constructing a polyaniline@Pt/C (PANI@Pt/C) composite cathode. The introduction of Pt/C catalyst endows the redox reaction between PANI and O2 with fast reaction kinetics and extended redox potential difference. Therefore, the self-charging rate of the Zn/PANI@Pt/C batteries is effectively accelerated and they can be self-charged to fully charged state. Furthermore, the PANI can be recharged by O2 simultaneously during discharging process to compensate the consumed electrical energy, achieving prolonged energy supply. In addition, the PANI@Pt/C cathodes can be directly used as the cathodes of flexible self-charging zinc batteries due to their excellent mechanical properties. As a proof of concept, flexible soft-packaged Zn/PANI@Pt/C batteries are fabricated and displayed stable electrochemical performance and self-rechargeability even at different bending states. A route is provided here to design ultrafast chemical self-charging energy storage devices and the horizons of flexible energy storage devices are broadened.

Aminoglycoside uptake, stress, and potentiation in Gram-negative bacteria: new therapies with old molecules

SUMMARYAminoglycosides (AGs) are long-known molecules successfully used against Gram-negative pathogens. While their use declined with the discovery of new antibiotics, they are now classified as critically important molecules because of their effectiveness against multidrug-resistant bacteria. While they can efficiently cross the Gram-negative envelope, the mechanism of AG entry is still incompletely understood, although this comprehension is essential for the development of new therapies in the face of the alarming increase in antibiotic resistance. Increasing antibiotic uptake in bacteria is one strategy to enhance effective treatments. This review aims, first, to consolidate old and recent knowledge about AG uptake; second, to explore the connection between AG-dependent bacterial stress and drug uptake; and finally, to present new strategies of potentiation of AG uptake for more efficient antibiotic therapies. In particular, we emphasize on the connection between sugar transport and AG potentiation.

A critical review of improving mainstream anammox systems: Based on macroscopic process regulation and microscopic enhancement mechanisms

Full-scale anaerobic ammonium oxidation (anammox) engineering applications are vastly limited by the sensitivity of anammox bacteria to the complex mainstream ambience factors. Therefore, it is of great necessity to comprehensively summarize and overcome performance-related challenges in mainstream anammox process at the macro/micro level, including the macroscopic process variable regulation and microscopic biological metabolic enhancement. This article systematically reviewed the recent important advances in the enrichment and retention of anammox bacteria and main factors affecting metabolic regulation under mainstream conditions, and proposed key strategies for the related performance optimization. The characteristics and behavior mechanism of anammox consortia in response to mainstream environment were then discussed in details, and we revealed that the synergistic nitrogen metabolism of multi-functional bacterial genera based on anammox microbiome was conducive to mainstream anammox nitrogen removal processes. Finally, the critical outcomes of anammox extracellular electron transfer (EET) at the micro level were well presented, carbon-based conductive materials or exogenous electron shuttles can stimulate and mediate anammox EET in mainstream environments to optimize system performance from a micro perspective. Overall, this review advances the extensive implementation of mainstream anammox practice in future as well as shedding new light on the related EET and microbial mechanisms.

Mitochondrial complex I ROS production and redox signaling in hypoxia

Mitochondria are a main source of cellular energy. Oxidative phosphorylation (OXPHOS) is the major process of aerobic respiration. Enzyme complexes of the electron transport chain (ETC) pump protons to generate a protonmotive force (Δp) that drives OXPHOS. Complex I is an electron entry point into the ETC. Complex I oxidizes nicotinamide adenine dinucleotide (NADH) and transfers electrons to ubiquinone in a reaction coupled with proton pumping. Complex I also produces reactive oxygen species (ROS) under various conditions. The enzymatic activities of complex I can be regulated by metabolic conditions and serves as a regulatory node of the ETC. Complex I ROS plays diverse roles in cell metabolism ranging from physiologic to pathologic conditions. Progress in our understanding indicates that ROS release from complex I serves important signaling functions. Increasing evidence suggests that complex I ROS is important in signaling a mismatch in energy production and demand. In this article, we review the role of ROS from complex I in sensing acute hypoxia.

Mitochondrial Cristae Morphology Reflecting Metabolism, Superoxide Formation, Redox Homeostasis, and Pathology

Significance: Mitochondrial (mt) reticulum network in the cell possesses amazing ultramorphology of parallel lamellar cristae, formed by the invaginated inner mitochondrial membrane. Its non-invaginated part, the inner boundary membrane (IBM) forms a cylindrical sandwich with the outer mitochondrial membrane (OMM). Crista membranes (CMs) meet IBM at crista junctions (CJs) of mt cristae organizing system (MICOS) complexes connected to OMM sorting and assembly machinery (SAM). Cristae dimensions, shape, and CJs have characteristic patterns for different metabolic regimes, physiological and pathological situations. Recent Advances: Cristae-shaping proteins were characterized, namely rows of ATP-synthase dimers forming the crista lamella edges, MICOS subunits, optic atrophy 1 (OPA1) isoforms and mitochondrial genome maintenance 1 (MGM1) filaments, prohibitins, and others. Detailed cristae ultramorphology changes were imaged by focused-ion beam/scanning electron microscopy. Dynamics of crista lamellae and mobile CJs were demonstrated by nanoscopy in living cells. With tBID-induced apoptosis a single entirely fused cristae reticulum was observed in a mitochondrial spheroid. Critical Issues: The mobility and composition of MICOS, OPA1, and ATP-synthase dimeric rows regulated by post-translational modifications might be exclusively responsible for cristae morphology changes, but ion fluxes across CM and resulting osmotic forces might be also involved. Inevitably, cristae ultramorphology should reflect also mitochondrial redox homeostasis, but details are unknown. Disordered cristae typically reflect higher superoxide formation. Future Directions: To link redox homeostasis to cristae ultramorphology and define markers, recent progress will help in uncovering mechanisms involved in proton-coupled electron transfer via the respiratory chain and in regulation of cristae architecture, leading to structural determination of superoxide formation sites and cristae ultramorphology changes in diseases. Antioxid. Redox Signal. 39, 635-683.

Enhanced Anaerobic Wastewater Treatment by a Binary Electroactive Material: Pseudocapacitance/Conductance-Mediated Microbial Interspecies Electron Transfer

Anaerobic digestion (AD) is a promising method to treat organic matter. However, AD performance was limited by the inefficient electron transfer and metabolism imbalance between acid-producing bacteria and methanogens. In this study, a novel binary electroactive material (Fe3O4@biochar) with pseudocapacitance (1.4 F/g) and conductance (10.2 μS/cm) was exploited to store-release electrons as well as enhance the direct electron transfer between acid-producing bacteria and methanogens during the AD process. The mechanism of pseudocapacitance/conductance on mediating interspecies electron transfer was deeply studied at each stage of AD. In the hydrolysis acidification stage, the pseudocapacitance of Fe3O4@biochar acting as electron acceptors proceeded NADH/NAD+ transformation of bacteria to promote ATP synthesis by 21% which supported energy for organics decomposition. In the methanogenesis stage, the conductance of Fe3O4@biochar helped the microbes establish direct interspecies electron transfer (DIET) to increase the coenzyme F420 content by 66% and then improve methane production by 13%. In the complete AD experiment, electrons generated from acid-producing bacteria were rapidly transported to methanogens via conductors. Excess electrons were buffered by the pseudocapacitor and then gradually released to methanogens which alleviated the drastic drop in pH. These findings provided a strategy to enhance the electron transfer in anaerobic treatment as well as guided the design of electroactive materials.

Charge Regulation in a Rieske Proton Pump Pinpoints Zero, One, and Two Proton-Coupled Electron Transfer

The degree to which redox-driven proton pumps regulate net charge during electron transfer (ΔZ_ET) remains undetermined due to difficulties in measuring the net charge of solvated proteins. Values of ΔZ_ET can reflect reorganization energies or redox potentials associated with ET and can be used to distinguish ET from proton(s)-coupled electron transfer (PCET). Here, we synthesized protein "charge ladders" of a Rieske [2Fe-2S] subunit from Thermus thermophilus (truncTtRp) and made 120 electrostatic measurements of ΔZ_ET across pH. Across pH 5-10, truncTtRp is suspected of transitioning from ET to PCET, and then to two proton-coupled ET (2PCET). Upon reduction, we found that truncTtRp became more negative at pH 6.0 by one unit (ΔZ_ET = -1.01 ± 0.14), consistent with single ET; was isoelectric at pH 8.8 (ΔZ_ET = -0.01 ± 0.45), consistent with PCET; and became more positive at pH 10.6 (ΔZ_ET = +1.37 ± 0.60), consistent with 2PCET. These ΔZ_ET values are attributed to protonation of H154 and H134. Across pH, redox potentials of TtRp (measured previously) correlated with protonation energies of H154 and H134 and ΔZ_ET for truncTtRp, supporting a discrete proton pumping mechanism for Rieske proteins at the Fe-coordinating histidines.

Electromotive force induced by dynamic magnetic field electrically polarized sediment to aggravate methane emission

As a primary driving force of global methane production, methanogens like other living organisms are exposed to an environment filled with dynamic electromagnetic waves, which might induce electromotive force (EMF) to potentially influence the metabolism of methanogens. However, no reports have been found on the effects of the induced electromotive force on methane production. In this study, we found that exposure to a dynamic magnetic field enhanced bio-methanogenesis via the induced electromotive force. When exposed to a dynamic magnetic field with 0.20 to 0.40 mT of intensity, the methane emission of the sediments increased by 41.71%. The respiration of methanogens and bacteria was accelerated by the EMF, as the ratios of F420H2/F420 and NAD+/NADH of the sediment increased by 44.12% and 55.56%, respectively. The respiratory enzymes in respiration chains might be polarized with the EMF to accelerate the proton-coupled electron transfer to enhance microbial metabolism. Together with the enriched exoelectrogens and electrotrophic methanogens, as well as the increased sediment electro-activities, this study indicated that the EMF could enhance the electron exchange among extracellular respiratory microorganisms to increase the methane emission from sediments.

Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC

Electron bifurcation is a fundamental energy coupling mechanism widespread in microorganisms that thrive under anoxic conditions. These organisms employ hydrogen to reduce CO₂, but the molecular mechanisms have remained enigmatic. The key enzyme responsible for powering these thermodynamically challenging reactions is the electron-bifurcating [FeFe]-hydrogenase HydABC that reduces low-potential ferredoxins (Fd) by oxidizing hydrogen gas (H₂). By combining single-particle cryo-electron microscopy (cryoEM) under catalytic turnover conditions with site-directed mutagenesis experiments, functional studies, infrared spectroscopy, and molecular simulations, we show that HydABC from the acetogenic bacteria Acetobacterium woodii and Thermoanaerobacter kivui employ a single flavin mononucleotide (FMN) cofactor to establish electron transfer pathways to the NAD(P)⁺ and Fd reduction sites by a mechanism that is fundamentally different from classical flavin-based electron bifurcation enzymes. By modulation of the NAD(P)⁺ binding affinity via reduction of a nearby iron-sulfur cluster, HydABC switches between the exergonic NAD(P)⁺ reduction and endergonic Fd reduction modes. Our combined findings suggest that the conformational dynamics establish a redox-driven kinetic gate that prevents the backflow of the electrons from the Fd reduction branch toward the FMN site, providing a basis for understanding general mechanistic principles of electron-bifurcating hydrogenases.

Applying Dynamic Magnetic Field To Promote Anaerobic Digestion via Enhancing the Electron Transfer of a Microbial Respiration Chain

Electrochemical methods have been reported to strengthen anaerobic digestion, but the continuous electrical power supply and the complicated electrode installed inside the digester have restricted it from practical use. In this study, a dynamic magnetic field (DMF) was placed outside a digester to induce an electromotive force to electrically promote anaerobic digestion. With the applied DMF, an electromotive force of 0.14 mV was generated in the anaerobic sludge, and a 65.02% methane increment was obtained from the anaerobic digestion of waste-activated sludge. Experiments on each stage of anaerobic digestion showed that acidification and methanogenesis that involve electron transfer of respiration chains were promoted with the DMF, while solubilization and hydrolysis less related to respiration chains were not enhanced. Further analysis indicated that the induced electromotive force polarized the protein-like substances in the sludge to increase the conductivity and capacitance of the sludge. Electrotrophic methanogens (Methanothrix) and exoelectrogens (Exiguobacterium) were enriched with DMF. The kinetic isotope effect test confirmed that electron transfer was accelerated with DMF. Consistently, the concentration ratio of co-enzymes (NADH/NAD⁺ and F₄₂₀H₂/F₄₂₀₎ that reflects the electron exchange with respiration chains significantly increased. Applying the DMF seemed a more accessible strategy to electrically strengthen anaerobic digestion.

Electro-polarization of protein-like substances accelerates trans-cell-wall electron transfer in microbial extracellular respiration

Electrical stimulation has been used to strengthen microbial extracellular electron transfer (EET), however, the deep-seated reasons remain unclear. Here we reported that Bacillus subtilis, a typical gram-positive bacterium capable of extracellular respiration, obtained a higher EET capacity after the electrical domestication. After the electrical domestication, the current generated by the EET of B. subtilis was 23.4-fold that of the control group without pre-domestication. Multiple lines of evidence in bacterial cells of B. subtilis, their cell walls, and a model tripeptide indicated that the polarization of amide groups after the electrical stimulation forwarded the H-bonds recombination and radical generation of protein-like substances to develop extracellular electron transfer via the proton-coupled pattern. The improved electrochemical properties of protein-like substances benefited the trans-cell-wall electron transfer and strengthen extracellular respiration. This study was the first exploration to promote microbial extracellular respiration by improving the electrochemical properties of protein-like substances in cell envelopes.

Photosynthesis of Acetate by Sporomusa ovata-CdS Biohybrid System

Sporomusa ovata, a typical electroautotrophic microorganism, has been utilized in bioelectrosynthesis for carbon dioxide fixation to multicarbon organic chemicals. However, additional photovoltaic devices are normally needed to convert photo energy to electric energy to power the carbon dioxide fixation, which restricts the overall energy conversion efficiency. Herein, we report Sporomusa ovata-CdS biohybrids for artificial photosynthesis driven by light without any other power source. The quantum yield can reach 16.8 ± 9%, and the active duration time of the system can last for 5 days. During the artificial photosynthesis, carbon dioxide is first reduced to formate and finally converted to acetate via the Wood-Ljungdahl pathway. The carbon dioxide fixation, electron transfer, energy metabolism, and reactive oxygen species damage repair processes in the biohybrid system were characterized by proteomic analysis. Key enzymes, e.g., flavoprotein, ferredoxin, formate-tetrahydrofolate ligase, 5-methyltetrahydrofolate:corrinoid iron-sulfur protein methyltransferase, thioredoxin, and rubrerythrin, were found up-regulated in the biohybrid system. The findings are helpful in understanding the mechanism of the artificial photosynthesis and useful for the development of new biohybrid systems using genetically engineered microbes in the future. The study is expected to boost the development of bioabiotic hybrid system in solar energy harvest.

Theoretical Modeling of Redox Potentials of Biomolecules

The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.

Asymmetric Catalytic Assembly of Triple-Columned and Multiple-Layered Chiral Folding Polymers Showing Aggregation-Induced Emission (AIE)

The first chiral multi-layer 3D folding polymers have been assembled and regulated by both uniformed and differentiated aromatic chromophoric units between naphthyl piers. Screening catalysts, catalytic systems and monomers was proven to be crucial for asymmetric catalytic Suzuki-Miyaura poly-couplings for this assembly. X-ray crystallography of corresponding dimers and trimers revealed the absolute stereochemistry and the intermolecular packing pattern. Up to 61,960 M w /41,900 M n and m / z = 4317 for polymers and oligomers as confirmed by GPC and MALDI-TOF MS indicated that the present frameworks were composed of multiple layers stacked. The resulting multiple π-assemblies exhibited remarkable optical properties in aggregated states (PL in solids and AIE in solutions), as well as reversible redox properties in electrochemical performance.

Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I

Biological energy conversion is catalyzed by membrane-bound proteins that transduce chemical or light energy into energy forms that power endergonic processes in the cell. At a molecular level, these catalytic processes involve elementary electron-, proton-, charge-, and energy-transfer reactions that take place in the intricate molecular machineries of cell respiration and photosynthesis. Recent developments in structural biology, particularly cryo-electron microscopy (cryoEM), have resolved the molecular architecture of several energy transducing proteins, but detailed mechanistic principles of their charge transfer reactions still remain poorly understood and a major challenge for modern biochemical research. To this end, multiscale molecular simulations provide a powerful approach to probe mechanistic principles on a broad range of time scales (femtoseconds to milliseconds) and spatial resolutions (10¹–10⁶ atoms), although technical challenges also require balancing between the computational accuracy, cost, and approximations introduced within the model. Here we discuss how the combination of atomistic (aMD) and hybrid quantum/classical molecular dynamics (QM/MM MD) simulations with free energy (FE) sampling methods can be used to probe mechanistic principles of enzymes responsible for biological energy conversion. We present mechanistic explorations of long-range proton-coupled electron transfer (PCET) dynamics in the highly intricate respiratory chain enzyme Complex I, which functions as a redox-driven proton pump in bacterial and mitochondrial respiratory chains by catalyzing a 300 Å fully reversible PCET process. This process is initiated by a hydride (H^–) transfer between NADH and FMN, followed by long-range (>100 Å) electron transfer along a wire of 8 FeS centers leading to a quinone biding site. The reduction of the quinone to quinol initiates dissociation of the latter to a second membrane-bound binding site, and triggers proton pumping across the membrane domain of complex I, in subunits up to 200 Å away from the active site. Our simulations across different size and time scales suggest that transient charge transfer reactions lead to changes in the internal hydration state of key regions, local electric fields, and the conformation of conserved ion pairs, which in turn modulate the dynamics of functional steps along the reaction cycle. Similar functional principles, which operate on much shorter length scales, are also found in some unrelated proteins, suggesting that enzymes may employ conserved principles in the catalysis of biological energy transduction processes.

Quantitative Estimation of the Hydrogen-Atom-Donating Ability of 4-Substituted Hantzsch Ester Radical Cations

The purpose of this study is to investigate thermodynamic and kinetic properties on the hydrogen-atom-donating ability of 4-substituted Hantzsch ester radical cations (XRH•+), which are excellent NADH coenzyme models. Gibbs free energy changes and activation free energies of 17 XRH•+ releasing H• [denoted as ΔG HD o(XRH•+) and ΔG HD ≠(XRH•+)] were calculated using density functional theory (DFT) and compared with that of Hantzsch ester (HEH2) and NADH. ΔG HD o(XRH•+) range from 19.35 to 31.25 kcal/mol, significantly lower than that of common antioxidants (such as ascorbic acid, BHT, the NADH coenzyme, and so forth). ΔG HD ≠(XRH•+) range from 29.81 to 39.00 kcal/mol, indicating that XRH•+ spontaneously releasing H• are extremely slow unless catalysts or active intermediate radicals exist. According to the computed data, it can be inferred that the Gibbs free energies and activation free energies of the core 1,4-dihydropyridine radical cation structure (DPH•+) releasing H• [ΔG HD o(DPH•+) and ΔG HD ≠(DPH•+)] should be 19-32 kcal/mol and 29-39 kcal/mol in acetonitrile, respectively. The correlations between the thermodynamic driving force [ΔG HD o(XRH•+)] and the activation free energy [ΔG HD ≠(XRH•+)] are also explored. Gibbs free energy is the important and decisive parameter, and ΔG HD ≠(XRH•+) increases in company with the increase of ΔG HD o(XRH•+), but no simple linear correlations are found. Even though all XRH•+ are judged as excellent antioxidants from the thermodynamic view, the computed data indicate that whether XRH•+ is an excellent antioxidant in reaction is decided by the R substituents in 4-position. XRH•+ with nonaromatic substituents tend to release R• instead of H• to quench radicals. XRH•+ with aromatic substituents tend to release H• and be used as antioxidants, but not all aromatic substituted Hantzsch esters are excellent antioxidants.

An interesting possibility of forming special hole stepping stones with high-stacking aromatic rings in proteins: three-π five-electron and four-π seven-electron resonance bindings

Long-range hole transfer of proteins plays an important role in many biological processes of living organisms. Therefore, it is highly useful to examine the possible hole stepping stones, which can facilitate hole transfer in proteins. However, the structures of stepping stones are diverse because of the complexity of the protein structures. In the present work, we proposed a series of special stepping stones, which are instantaneously formed by three and four packing aromatic side chains of amino acids to capture a hole, corresponding to three-π five-electron (π:π∴π↔π∴π:π) and four-π seven-electron (π:π∴π:π↔π:π:π∴π) resonance bindings with appropriate binding energies. The aromatic amino acids include histidine (His), phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp). The formations of these special stepping stones can effectively reduce the local ionization potential of the high π-stacking region to efficiently capture the migration hole. The quick formations and separations of them promote the efficient hole transfer in proteins. More interestingly, we revealed that a hole cannot delocalize over infinite aromatic rings along the high π-π packing structure at the same time and the micro-surroundings of proteins can modulate the formations of π:π∴π↔π∴π:π and π:π∴π:π↔π:π:π∴π bindings. These results may contribute a new avenue to better understand the potential hole transfer pathway in proteins.

Triple-Columned and Multiple-Layered 3D Polymers: Design, Synthesis, Aggregation-Induced Emission (AIE), and Computational Study

Conjugated polymers and oligomers have great potentials in various fields, especially in materials and biological sciences because of their intriguing electronic and optoelectronic properties. In recent years, the through-space conjugation system has emerged as a new assembled pattern of multidimensional polymers. Here, a novel series of structurally condensed multicolumn/multilayer 3D polymers and oligomers have been designed and synthesized through one-pot Suzuki polycondensation (SPC). The intramolecularly stacked arrangement of polymers can be supported by either X-ray structural analysis or computational analysis. In all cases, polymers were obtained with modest to good yields, as determined by GPC and ¹H-NMR. MALDI-TOF analysis has proven the speculation of the step-growth process of this polymerization. The computational study of ab initio and DFT calculations based on trimer and pentamer models gives details of the structures and the electronic transition. Experimental results of optical and AIE research confirmed by calculation indicates that the present work would facilitate the research and applications in materials.

Coenzyme-dependent nanozymes playing dual roles in oxidase and reductase mimics with enhanced electron transport

Although nanozymes overcome a series of shortcomings of natural enzymes, their wide applications are hampered due to their limited varieties. In this work, we propose a coenzyme-dependent nanozyme, a synergistic composite comprising zeolitic imidazolate frameworks encapsulated with polyethylenimine (PEI) and functionalized with a flavin mononucleotide (PEI/ZIF-FMN). The flavin mononucleotide (FMN) plays the role of a prosthetic group, and the positively charged NH2 groups in PEI readily provide the binding affinity to nicotinamide adenine dinucleotide (NADH), which facilitates the electron transfer from NADH to FMN and terminal electron acceptors (such as O2) with a greatly enhanced (80 times) catalytic performance. The integrated nanoparticle-coenzyme composite works as an NADH oxidase mimic and couples with dehydrogenases for the tandem enzymatic reaction. PEI/ZIF-FMN also mediated the electron transfer from NADH to cytochrome c (Cyt c), thereby exhibiting Cyt c reductase-like activity.

Water-Gated Proton Transfer Dynamics in Respiratory Complex I

The respiratory complex I transduces redox energy into an electrochemical proton gradient in aerobic respiratory chains, powering energy-requiring processes in the cell. However, despite recently resolved molecular structures, the mechanism of this gigantic enzyme remains poorly understood. By combining large-scale quantum and classical simulations with site-directed mutagenesis and biophysical experiments, we show here how the conformational state of buried ion-pairs and water molecules control the protonation dynamics in the membrane domain of complex I and establish evolutionary conserved long-range coupling elements. We suggest that an electrostatic wave propagates in forward and reverse directions across the 200 Å long membrane domain during enzyme turnover, without significant dissipation of energy. Our findings demonstrate molecular principles that enable efficient long-range proton–electron coupling (PCET) and how perturbation of this PCET machinery may lead to development of mitochondrial disease.

Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I

The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron-sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron-sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol form-a design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.

Redox-Active Guanidines in Proton-Coupled Electron-Transfer Reactions: Real Alternatives to Benzoquinones?

Guanidino-functionalized aromatics (GFAs) are readily available, stable organic redox-active compounds. In this work we apply one particular GFA compound, 1,2,4,5-tetrakis(tetramethylguanidino)benzene, in its oxidized form in a variety of oxidation/oxidative coupling reactions to demonstrate the scope of its proton-coupled electron transfer (PCET) reactivity. Addition of an excess of acid boosts its oxidation power, enabling the oxidative coupling of substrates with redox potentials of at least +0.77 V vs. Fc⁺ /Fc. The green recyclability by catalytic re-oxidation with dioxygen is also shown. Finally, a direct comparison indicates that GFAs are real alternatives to toxic halo- or cyano-substituted benzoquinones.