Extracellular DNA Promotes Efficient Extracellular Electron Transfer by Pyocyanin in Pseudomonas aeruginosa Biofilms.

Redox cycling of extracellular electron shuttles can enable the metabolic activity of subpopulations within multicellular bacterial biofilms that lack direct access to electron acceptors or donors. How these shuttles catalyze extracellular electron transfer (EET) within biofilms without being lost to the environment has been a long-standing question. Here, we show that phenazines mediate efficient EET through interactions with extracellular DNA (eDNA) in Pseudomonas aeruginosa biofilms. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by eDNA binding. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and can participate directly in redox reactions through DNA. In vivo, biofilm eDNA can also support rapid electron transfer between redox active intercalators. Together, these results establish that PYO:eDNA interactions support an efficient redox cycle with rapid EET that is faster than the rate of PYO loss from the biofilm.

Redox Chemistry in the Genome: Emergence of the [4Fe4S] Cofactor in Repair and Replication.

Many DNA-processing enzymes have been shown to contain a [4Fe4S] cluster, a common redox cofactor in biology. Using DNA electrochemistry, we find that binding of the DNA polyanion promotes a negative shift in [4Fe4S] cluster potential, which corresponds thermodynamically to a ∼500-fold increase in DNA-binding affinity for the oxidized [4Fe4S]3+ cluster versus the reduced [4Fe4S]2+ cluster. This redox switch can be activated from a distance using DNA charge transport (DNA CT) chemistry. DNA-processing proteins containing the [4Fe4S] cluster are enumerated, with possible roles for the redox switch highlighted. A model is described where repair proteins may signal one another using DNA-mediated charge transport as a first step in their search for lesions. The redox switch in eukaryotic DNA primases appears to regulate polymerase handoff, and in DNA polymerase δ, the redox switch provides a means to modulate replication in response to oxidative stress. We thus describe redox signaling interactions of DNA-processing [4Fe4S] enzymes, as well as the most interesting potential players to consider in delineating new DNA-mediated redox signaling networks.

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism.

We report a 100-million atom-scale model of an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium, that reveals the cascade of energy conversion steps culminating in the generation of ATP from sunlight. Molecular dynamics simulations of this vesicle elucidate how the integral membrane complexes influence local curvature to tune photoexcitation of pigments. Brownian dynamics of small molecules within the chromatophore probe the mechanisms of directional charge transport under various pH and salinity conditions. Reproducing phenotypic properties from atomistic details, a kinetic model evinces that low-light adaptations of the bacterium emerge as a spontaneous outcome of optimizing the balance between the chromatophore's structural integrity and robust energy conversion. Parallels are drawn with the more universal mitochondrial bioenergetic machinery, from whence molecular-scale insights into the mechanism of cellular aging are inferred. Together, our integrative method and spectroscopic experiments pave the way to first-principles modeling of whole living cells.

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.

Current machine learning techniques enable robust association of biological signals with measured phenotypes, but these approaches are incapable of identifying causal relationships. Here, we develop an integrated "white-box" biochemical screening, network modeling, and machine learning approach for revealing causal mechanisms and apply this approach to understanding antibiotic efficacy. We counter-screen diverse metabolites against bactericidal antibiotics in Escherichia coli and simulate their corresponding metabolic states using a genome-scale metabolic network model. Regression of the measured screening data on model simulations reveals that purine biosynthesis participates in antibiotic lethality, which we validate experimentally. We show that antibiotic-induced adenine limitation increases ATP demand, which elevates central carbon metabolism activity and oxygen consumption, enhancing the killing effects of antibiotics. This work demonstrates how prospective network modeling can couple with machine learning to identify complex causal mechanisms underlying drug efficacy.

Resting-State Structure and Gating Mechanism of a Voltage-Gated Sodium Channel.

Voltage-gated sodium (NaV) channels initiate action potentials in nerve, muscle, and other electrically excitable cells. The structural basis of voltage gating is uncertain because the resting state exists only at deeply negative membrane potentials. To stabilize the resting conformation, we inserted voltage-shifting mutations and introduced a disulfide crosslink in the VS of the ancestral bacterial sodium channel NaVAb. Here, we present a cryo-EM structure of the resting state and a complete voltage-dependent gating mechanism. The S4 segment of the VS is drawn intracellularly, with three gating charges passing through the transmembrane electric field. This movement forms an elbow connecting S4 to the S4-S5 linker, tightens the collar around the S6 activation gate, and prevents its opening. Our structure supports the classical "sliding helix" mechanism of voltage sensing and provides a complete gating mechanism for voltage sensor function, pore opening, and activation-gate closure based on high-resolution structures of a single sodium channel protein.

Arginine-Enriched Mixed-Charge Domains Provide Cohesion for Nuclear Speckle Condensation.

Low-complexity protein domains promote the formation of various biomolecular condensates. However, in many cases, the precise sequence features governing condensate formation and identity remain unclear. Here, we investigate the role of intrinsically disordered mixed-charge domains (MCDs) in nuclear speckle condensation. Proteins composed exclusively of arginine-aspartic acid dipeptide repeats undergo length-dependent condensation and speckle incorporation. Substituting arginine with lysine in synthetic and natural speckle-associated MCDs abolishes these activities, identifying a key role for multivalent contacts through arginine's guanidinium ion. MCDs can synergize with a speckle-associated RNA recognition motif to promote speckle specificity and residence. MCD behavior is tunable through net-charge: increasing negative charge abolishes condensation and speckle incorporation. Contrastingly, increasing positive charge through arginine leads to enhanced condensation, speckle enlargement, decreased splicing factor mobility, and defective mRNA export. Together, these results identify key sequence determinants of MCD-promoted speckle condensation and link the dynamic material properties of speckles with function in mRNA processing.

Charge barriers in the kidney elimination of engineered nanoparticles.

The renal elimination pathway is increasingly harnessed to reduce nonspecific accumulation of engineered nanoparticles within the body and expedite their clinical applications. While the size of nanoparticles is recognized as crucial for their passive filtration through the glomerulus due to its limited pore size, the influence of nanoparticle charge on their transport and interactions within the kidneys remains largely elusive. Herein, we report that the proximal tubule and peritubular capillary, rather than the glomerulus, serve as primary charge barriers to the transport of charged nanoparticles within the kidney. Employing a series of ultrasmall, renal-clearable gold nanoparticles (AuNPs) with precisely engineered surface charge characteristics as multimodal imaging agents, we have tracked their distribution and retention across various kidney components following intravenous administration. Our results reveal that retention in the proximal tubules is governed not by the nanoparticle's zeta-potential, but by direct Coulombic interactions between the positively charged surface ligands of the AuNPs and the negatively charged microvilli of proximal tubules. However, further enhancing these interactions leads to increased binding of the positively charged AuNPs to the peritubular capillaries during the initial phase of elimination, subsequently facilitating their slow passage through the glomeruli and interaction with tubular components in a charge-selective manner. By identifying these two critical charge-dependent barriers in the renal transport of nanoparticles, our findings offer a fundamental insight for the design of renal nanomedicines tailored for selective targeting within the kidney, laying down a foundation for developing targeting renal nanomedicines for future kidney disease management in the clinics.

Automotive braking is a source of highly charged aerosol particles.

Although the last several decades have seen a dramatic reduction in emissions from vehicular exhaust, nonexhaust emissions (e.g., brake and tire wear) represent an increasingly significant class of traffic-related particulate pollution. Aerosol particles emitted from the wear of automotive brake pads contribute roughly half of the particle mass attributed to nonexhaust sources, while their relative contribution to urban air pollution overall will almost certainly grow coinciding with vehicle fleet electrification and the transition to alternative fuels. To better understand the implications of this growing prominence, a more thorough understanding of the physicochemical properties of brake wear particles (BWPs) is needed. Here, we investigate the electrical properties of BWPs as emitted from ceramic and semi-metallic brake pads. We show that up to 80% of BWPs emitted are electrically charged and that this fraction is strongly dependent on the specific brake pad material used. A dependence of the number of charges per particle on charge polarity and particle size is also demonstrated. We find that brake wear produces both positive and negative charged particles that can hold in excess of 30 elementary charges and show evidence that more negative charges are produced than positive. Our results will provide insights into the currently limited understanding of BWPs and their charging mechanisms, which potentially have significant implications on their atmospheric lifetimes and thus their relevance to climate and air quality. In addition, our study will inform future efforts to remove BWP emissions before entering the atmosphere by taking advantage of their electric charge.

Perpendicular crossing chains enable high mobility in a noncrystalline conjugated polymer.

The nature of interchain π-system contacts, and their relationship to hole transport, are elucidated for the high-mobility, noncrystalline conjugated polymer C16-IDTBT by the application of scanning tunneling microscopy, molecular dynamics, and quantum chemical calculations. The microstructure is shown to favor an unusual packing motif in which paired chains cross-over one another at near-perpendicular angles. By linking to mesoscale microstructural features, revealed by coarse-grained molecular dynamics and previous studies, and performing simulations of charge transport, it is demonstrated that the high mobility of C16-IDTBT can be explained by the promotion of a highly interconnected transport network, stemming from the adoption of perpendicular contacts at the nanoscale, in combination with fast intrachain transport.

HYPK: A marginally disordered protein sensitive to charge decoration.

Intrinsically disordered proteins (IDPs) that lie close to the empirical boundary separating IDPs and folded proteins in Uversky's charge-hydropathy plot may behave as "marginal IDPs" and sensitively switch conformation upon changes in environment (temperature, crowding, and charge screening), sequence, or both. In our search for such a marginal IDP, we selected Huntingtin-interacting protein K (HYPK) near that boundary as a candidate; PKIα, also near that boundary, has lower secondary structure propensity; and Crk1, just across the boundary on the folded side, has higher secondary structure propensity. We used a qualitative Förster resonance energy transfer-based assay together with circular dichroism to simultaneously probe global and local conformation. HYPK shows several unique features indicating marginality: a cooperative transition in end-to-end distance with temperature, like Crk1 and folded proteins, but unlike PKIα; enhanced secondary structure upon crowding, in contrast to Crk1 and PKIα; and a cross-over from salt-induced expansion to compaction at high temperature, likely due to a structure-to-disorder transition not seen in Crk1 and PKIα. We then tested HYPK's sensitivity to charge patterning by designing charge-flipped variants including two specific sequences with identical amino acid composition that markedly differ in their predicted size and response to salt. The experimentally observed trends, also including mutants of PKIα, verify the predictions from sequence charge decoration metrics. Marginal proteins like HYPK show features of both folded and disordered proteins that make them sensitive to physicochemical perturbations and structural control by charge patterning.

CHD7 and SOX2 act in a common gene regulatory network during mammalian semicircular canal and cochlear development.

Inner ear morphogenesis requires tightly regulated epigenetic and transcriptional control of gene expression. CHD7, an ATP-dependent chromodomain helicase DNA-binding protein, and SOX2, an SRY-related HMG box pioneer transcription factor, are known to contribute to vestibular and auditory system development, but their genetic interactions in the ear have not been explored. Here, we analyzed inner ear development and the transcriptional regulatory landscapes in mice with variable dosages of Chd7 and/or Sox2. We show that combined haploinsufficiency for Chd7 and Sox2 results in reduced otic cell proliferation, severe malformations of semicircular canals, and shortened cochleae with ectopic hair cells. Examination of mice with conditional, inducible Chd7 loss by Sox2CreER reveals a critical period (~E9.5) of susceptibility in the inner ear to combined Chd7 and Sox2 loss. Data from genome-wide RNA-sequencing and CUT&Tag studies in the otocyst show that CHD7 regulates Sox2 expression and acts early in a gene regulatory network to control expression of key otic patterning genes, including Pax2 and Otx2. CHD7 and SOX2 directly bind independently and cooperatively at transcription start sites and enhancers to regulate otic progenitor cell gene expression. Together, our findings reveal essential roles for Chd7 and Sox2 in early inner ear development and may be applicable for syndromic and other forms of hearing or balance disorders.

Transient charge-driven 3D conformal printing via pulsed-plasma impingement.

Seamless integration of microstructures and circuits on three-dimensional (3D) complex surfaces is of significance and is catalyzing the emergence of many innovative 3D curvy electronic devices. However, patterning fine features on arbitrary 3D targets remains challenging. Here, we propose a facile charge-driven electrohydrodynamic 3D microprinting technique that allows micron- and even submicron-scale patterning of functional inks on a couple of 3D-shaped dielectrics via an atmospheric-pressure cold plasma jet. Relying on the transient charging of exposed sites arising from the weakly ionized gas jet, the specified charge is programmably deposited onto the surface as a virtual electrode with spatial and time spans of ~mm in diameter and ~µs in duration to generate a localized electric field accordantly. Therefore, inks with a wide range of viscosities can be directly drawn out from micro-orifices and deposited on both two-dimensional (2D) planar and 3D curved surfaces with a curvature radius down to ~1 mm and even on the inner wall of narrow cavities via localized electrostatic attraction, exhibiting a printing resolution of ~450 nm. In addition, several conformal electronic devices were successfully printed on 3D dielectric objects. Self-aligned 3D microprinting, with stacking layers up to 1400, is also achieved due to the electrified surfaces. This microplasma-induced printing technique exhibits great advantages such as ultrahigh resolution, excellent compatibility of inks and substrates, antigravity droplet dispersion, and omnidirectional printing on 3D freeform surfaces. It could provide a promising solution for intimately fabricating electronic devices on arbitrary 3D surfaces.

Thermal suppression of charge disproportionation accelerates interface electron transfer of water electrolysis.

The sluggish electron transfer kinetics in electrode polarization driven oxygen evolution reaction (OER) result in big energy barriers of water electrolysis. Accelerating the electron transfer at the electrolyte/catalytic layer/catalyst bulk interfaces is an efficient way to improve electricity-to-hydrogen efficiency. Herein, the electron transfer at the Sr3Fe2O7@SrFeOOH bulk/catalytic layer interface is accelerated by heating to eliminate charge disproportionation from Fe4+ to Fe3+ and Fe5+ in Sr3Fe2O7, a physical effect to thermally stabilize high-spin Fe4+ (t2g3eg1), providing available orbitals as electron transfer channels without pairing energy. As a result of thermal-induced changes in electronic states via thermal comproportionation, a sudden increase in OER performances was achieved as heating to completely suppress charge disproportionation, breaking a linear Arrhenius relationship. The strategy of regulating electronic states by thermal field opens a broad avenue to overcome the electron transfer barriers in water splitting.

Orbital-selective time-domain signature of nematicity dynamics in the charge-density-wave phase of La1.65Eu0.2Sr0.15CuO4.

Understanding the interplay between charge, nematic, and structural ordering tendencies in cuprate superconductors is critical to unraveling their complex phase diagram. Using pump-probe time-resolved resonant X-ray scattering on the (0 0 1) Bragg peak at the Cu [Formula: see text] and O [Formula: see text] resonances, we investigate nonequilibrium dynamics of [Formula: see text] nematic order and its association with both charge density wave (CDW) order and lattice dynamics in La[Formula: see text]Eu[Formula: see text]Sr[Formula: see text]CuO[Formula: see text]. The orbital selectivity of the resonant X-ray scattering cross-section allows nematicity dynamics associated with the planar O 2[Formula: see text] and Cu 3[Formula: see text] states to be distinguished from the response of anisotropic lattice distortions. A direct time-domain comparison of CDW translational-symmetry breaking and nematic rotational-symmetry breaking reveals that these broken symmetries remain closely linked in the photoexcited state, consistent with the stability of CDW topological defects in the investigated pump fluence regime.

Enhanced charge-carrier dynamics and efficient solar-to-urea conversion on Si-based photocathodes.

Photoelectrochemical (PEC) coupling of CO2 and nitrate can provide a useful and green source of urea, but the process is affected by the photocathodes with poor charge-carrier dynamics and low conversion efficiency. Here, a NiFe diatomic catalysts/TiO2 layer/nanostructured n+p-Si photocathode is rationally designed, achieving a good charge-separation efficiency of 78.8% and charge-injection efficiency of 56.9% in the process of PEC urea synthesis. Compared with the electrocatalytic urea synthesis by using the same catalysts, the Si-based photocathode shows a similar urea yield rate (81.1 mg·h-1·cm-2) with a higher faradic efficiency (24.2%, almost twice than the electrocatalysis) at a lower applied potential under 1 sun illumination, meaning that a lower energy-consumption method acquires more aimed productions. Integrating the PEC measurements and characterization results, the synergistic effect of hierarchical structure is the dominating factor for enhancing the charge-carrier separation, transfer, and injection by the matched band structure and favorable electron-migration channels. This work provides a direct and efficient route of solar-to-urea conversion.

Real-space visualization of a defect-mediated charge density wave transition.

We study the coupled charge density wave (CDW) and insulator-to-metal transitions in the 2D quantum material 1T-TaS2. By applying in situ cryogenic 4D scanning transmission electron microscopy with in situ electrical resistance measurements, we directly visualize the CDW transition and establish that the transition is mediated by basal dislocations (stacking solitons). We find that dislocations can both nucleate and pin the transition and locally alter the transition temperature Tc by nearly ~75 K. This finding was enabled by the application of unsupervised machine learning to cluster five-dimensional, terabyte scale datasets, which demonstrate a one-to-one correlation between resistance-a global property-and local CDW domain-dislocation dynamics, thereby linking the material microstructure to device properties. This work represents a major step toward defect-engineering of quantum materials, which will become increasingly important as we aim to utilize such materials in real devices.

Secondary structure determines electron transport in peptides.

Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green's function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 310 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Charge block-driven liquid-liquid phase separation - mechanism and biological roles.

Liquid-liquid phase separation (LLPS) has increasingly been found to play pivotal roles in a number of intracellular events and reactions, and has introduced a new paradigm in cell biology to explain protein-protein and enzyme-ligand interactions beyond conventional molecular and biochemical theories. LLPS is driven by the cumulative effects of weak and promiscuous interactions, including electrostatic, hydrophobic and cation-π interactions, among polypeptides containing intrinsically disordered regions (IDRs) and describes the macroscopic behaviours of IDR-containing proteins in an intracellular milieu. Recent studies have revealed that interactions between 'charge blocks' - clusters of like charges along the polypeptide chain - strongly induce LLPS and play fundamental roles in its spatiotemporal regulation. Introducing a new parameter, termed 'charge blockiness', into physicochemical models of disordered polypeptides has yielded a better understanding of how the intrinsic amino acid sequence of a polypeptide determines the spatiotemporal occurrence of LLPS within a cell. Charge blockiness might also explain why some post-translational modifications segregate within IDRs and how they regulate LLPS. In this Review, we summarise recent progress towards understanding the mechanism and biological roles of charge block-driven LLPS and discuss how this new characteristic parameter of polypeptides offers new possibilities in the fields of structural biology and cell biology.

Correlated surface-charging behaviors of two electrodes in an electrochemical cell.

It is revealed herein that surface-charging behaviors of the two electrodes constituting an electrochemical cell cannot be described independently by their respective electric double-layer (EDL) properties. Instead, they are correlated in such a way that the surface-charging behavior of each electrode is determined by the EDL and the reaction kinetics at both electrodes. Two fundamental equations describing the correlated surface-charging behaviors are derived, and approximate analytical solutions are obtained at low and high current densities, respectively, to facilitate transparent understanding. Important implications of the presented conceptual analysis for theoretical and computational electrochemistry are discussed. A strategy of modulating the activity of one electrode by tuning EDL parameters of the other in a two-electrode electrochemical cell is demonstrated.

Discovery of charge order in a cuprate Mott insulator.

Copper oxide superconductors universally exhibit multiple forms of electronically ordered phases that break the native translational symmetry of the CuO2 planes. In underdoped cuprates with correlated metallic ground states, charge/spin stripes and incommensurate charge density waves (CDWs) have been experimentally observed over the years, while early theoretical studies also predicted the emergence of a Coulomb-frustrated 'charge crystal' phase in the very lightly doped, insulating limit of CuO2 planes. Here, we search for signatures of CDW order in very lightly hole-doped cuprates from the 123 family RBa2Cu3O7 - δ (RBCO; R: Y or rare earth), by using resonant X-ray scattering, electron transport, and muon spin rotation measurements to resolve the electronic and magnetic ground states fully. Specifically, Pr is used to substitute Y at the R-site to systematically suppress the superconductivity and access the extremely low hole-doping regime of the cuprate phase diagram without changing the oxygen stoichiometry. X-ray scattering data taken on Pr-doped YBCO thin films reveal an in-plane CDW order that follows the same linear evolution of wave vector versus hole concentration as oxygen-underdoped YBCO but extends all the way to the insulating and magnetically ordered Mott limit. Combined with the recent observation of charge crystal phase on an insulating surface of Bi2Sr2CaCu2O8 + z, our results in RBCO suggest that this electronic symmetry breaking is universally present in very lightly doped CuO2 planes. These findings bridge the gap between the Mott insulating state and the underdoped metallic state and underscore the prominent role that Coulomb-frustrated electronic phase separation plays among all cuprates.