The Crystal Structure of a Biological Insulated Transmembrane Molecular Wire.

A growing number of bacteria are recognized to conduct electrons across their cell envelope, and yet molecular details of the mechanisms supporting this process remain unknown. Here, we report the atomic structure of an outer membrane spanning protein complex, MtrAB, that is representative of a protein family known to transport electrons between the interior and exterior environments of phylogenetically and metabolically diverse microorganisms. The structure is revealed as a naturally insulated biomolecular wire possessing a 10-heme cytochrome, MtrA, insulated from the membrane lipidic environment by embedding within a 26 strand ß-barrel formed by MtrB. MtrAB forms an intimate connection with an extracellular 10-heme cytochrome, MtrC, which presents its hemes across a large surface area for electrical contact with extracellular redox partners, including transition metals and electrodes.

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.

Pathway of Actin Folding Directed by the Eukaryotic Chaperonin TRiC.

The hetero-oligomeric chaperonin of eukarya, TRiC, is required to fold the cytoskeletal protein actin. The simpler bacterial chaperonin system, GroEL/GroES, is unable to mediate actin folding. Here, we use spectroscopic and structural techniques to determine how TRiC promotes the conformational progression of actin to the native state. We find that actin fails to fold spontaneously even in the absence of aggregation but populates a kinetically trapped, conformationally dynamic state. Binding of this frustrated intermediate to TRiC specifies an extended topology of actin with native-like secondary structure. In contrast, GroEL stabilizes bound actin in an unfolded state. ATP binding to TRiC effects an asymmetric conformational change in the chaperonin ring. This step induces the partial release of actin, priming it for folding upon complete release into the chaperonin cavity, mediated by ATP hydrolysis. Our results reveal how the unique features of TRiC direct the folding pathway of an obligate eukaryotic substrate.

Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2.

The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, we examined the human respiratory chain megacomplex-I2III2IV2 (MCI2III2IV2) with 140 subunits and a subset of associated cofactors using cryo-electron microscopy. The MCI2III2IV2 forms a circular structure with the dimeric CIII located in the center, where it is surrounded by two copies each of CI and CIV. Two cytochrome c (Cyt.c) molecules are positioned to accept electrons on the surface of the c1 state CIII dimer. Analyses indicate that CII could insert into the gaps between CI and CIV to form a closed ring, which we termed the electron transport chain supercomplex. The structure not only reveals the precise assignment of individual subunits of human CI and CIII, but also enables future in-depth analysis of the electron transport chain as a whole.

Structure of Mammalian Respiratory Supercomplex I1III2IV1.

The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to synthesize ATP. The precise arrangement of SCs is largely unknown. Here, we report a 4.0-Å cryo-electron microscopy (cryo-EM) structure of the major SC in porcine heart, the 1.7-MDa SCI1III2IV1. The complex III (CIII) dimer and complex IV (CIV) bind at the same side of the L-shaped complex I (CI). Several accessory or supernumerary subunits of CI, such as NDUFA11, NDUFB4, NDUFB8, and NDUFB9, directly contribute to the oligomerization of CI, CIII, and CIV. COX7C and COX7A of CIV attach CIV to the concave surface formed by CIII and the distal end of membrane arm of CI. The structure suggests a possible mechanism by which electrons are transferred from NADH to cytochrome c and provides a platform for future functional dissection of respiration.

Structure and energy transfer in photosystems of oxygenic photosynthesis.

Oxygenic photosynthesis is the principal converter of sunlight into chemical energy on Earth. Cyanobacteria and plants provide the oxygen, food, fuel, fibers, and platform chemicals for life on Earth. The conversion of solar energy into chemical energy is catalyzed by two multisubunit membrane protein complexes, photosystem I (PSI) and photosystem II (PSII). Light is absorbed by the pigment cofactors, and excitation energy is transferred among the antennae pigments and converted into chemical energy at very high efficiency. Oxygenic photosynthesis has existed for more than three billion years, during which its molecular machinery was perfected to minimize wasteful reactions. Light excitation transfer and singlet trapping won over fluorescence, radiation-less decay, and triplet formation. Photosynthetic reaction centers operate in organisms ranging from bacteria to higher plants. They are all evolutionarily linked. The crystal structure determination of photosynthetic protein complexes sheds light on the various partial reactions and explains how they are protected against wasteful pathways and why their function is robust. This review discusses the efficiency of photosynthetic solar energy conversion.

Electron Transfer Beyond the Outer Membrane: Putting Electrons to Rest.

Extracellular electron transfer (EET) is the physiological process that enables the reduction or oxidation of molecules and minerals beyond the surface of a microbial cell. The first bacteria characterized with this capability were Shewanella and Geobacter, both reported to couple their growth to the reduction of iron or manganese oxide minerals located extracellularly. A key difference between EET and nearly every other respiratory activity on Earth is the need to transfer electrons beyond the cell membrane. The past decade has resolved how well-conserved strategies conduct electrons from the inner membrane to the outer surface. However, recent data suggest a much wider and less well understood collection of mechanisms enabling electron transfer to distant acceptors. This review reflects the current state of knowledge from Shewanella and Geobacter, specifically focusing on transfer across the outer membrane and beyond-an activity that enables reduction of highly variable minerals, electrodes, and even other organisms.

Protein engineering a PhotoRNR chimera based on a unifying evolutionary apparatus among the natural classes of ribonucleotide reductases.

Ribonucleotide reductases (RNRs) are essential enzymes that catalyze the de novo transformation of nucleoside 5'-di(tri)phosphates [ND(T)Ps, where N is A, U, C, or G] to their corresponding deoxynucleotides. Despite the diversity of factors required for function and the low sequence conservation across RNRs, a unifying apparatus consolidating RNR activity is explored. We combine aspects of the protein subunit simplicity of class II RNR with a modified version of Escherichia coli class la photoRNRs that initiate radical chemistry with light to engineer a mimic of a class II enzyme. The design of this RNR involves fusing a truncated form of the active site containing α subunit with the functionally important C-terminal tail of the radical-generating ß subunit to render a chimeric RNR. Inspired by a recent cryo-EM structure, a [Re] photooxidant is located adjacent to Y356[ß], which is an essential component of the radical transport pathway in class I RNRs. Combination of this RNR photochimera with cytidine diphosphate (CDP), adenosine triphosphate (ATP), and light resulted in the generation of Y356• along with production of deoxycytidine diphosphate (dCDP) and cytosine. The photoproducts reflect an active site chemistry consistent with both the consensus mechanism of RNR and chemistry observed when RNR is inactivated by mechanism-based inhibitors in the active site. The enzymatic activity of the RNR photochimera in the absence of any ß metallocofactor highlights the adaptability of the 10-stranded αß barrel finger loop to support deoxynucleotide formation and accommodate the design of engineered RNRs.

Fenton-like activity and pathway modulation via single-atom sites and pollutants comediates the electron transfer process.

The studies on the origin of versatile oxidation pathways toward targeted pollutants in the single-atom catalysts (SACs)/peroxymonosulfate (PMS) systems were always associated with the coordination structures rather than the perspective of pollutant characteristics, and the analysis of mechanism commonality is lacking. In this work, a variety of single-atom catalysts (M-SACs, M: Fe, Co, and Cu) were fabricated via a pyrolysis process using lignin as the complexation agent and substrate precursor. Sixteen kinds of commonly detected pollutants in various references were selected, and their lnkobs values in M-SACs/PMS systems correlated well (R2 = 0.832 to 0.883) with their electrophilic indexes (reflecting the electron accepting/donating ability of the pollutants) as well as the energy gap (R2 = 0.801 to 0.840) between the pollutants and M-SACs/PMS complexes. Both the electron transfer process (ETP) and radical pathways can be significantly enhanced in the M-SACs/PMS systems, while radical oxidation was overwhelmed by the ETP oxidation toward the pollutants with lower electrophilic indexes. In contrast, pollutants with higher electrophilic indexes represented the weaker electron-donating capacity to the M-SACs/PMS complexes, which resulted in the weaker ETP oxidation accompanied with noticeable radical oxidation. In addition, the ETP oxidation in different M-SACs/PMS systems can be regulated via the energy gaps between the M-SACs/PMS complexes and pollutants. As a result, the Fenton-like activities in the M-SACs/PMS systems could be well modulated by the reaction pathways, which were determined by both electrophilic indexes of pollutants and single-atom sites. This work provided a strategy to establish PMS-based AOP systems with tunable oxidation capacities and pathways for high-efficiency organic decontamination.

Selective adsorption of high ionization potential value organic pollutants in wastewater.

It is imperative to devise effective removal strategies for high ionization potential (IP) organic pollutants in wastewater as their reduced electron-donating capacity challenges the efficiency of advanced oxidation systems in degradation. Against this backdrop, leveraging the metal-based carbon material structure meticulously, we employed metal-pyridine-N (M-N-C, M=Fe, Co, and Ni) as the electron transfer bridge. This distinctive design facilitated the ordered transfer of electrons from the adsorbent surface to the surface of high IP value pollutants, acting as a "supplement" to compensate for their deficient electron-donating capability, thereby culminating in the selective adsorption of these pollutants. Furthermore, this adsorbent also demonstrated effective removal of trace emerging contaminants (2 mg/L), displayed robust resistance to various salts, exhibited reusability, and maintained stability. These findings carry substantial implications for future carbon-based material design, offering a pathway toward exceptional adsorption performance in treating water pollution.

Phosphorothioate RNA Analysis by NETD Tandem Mass Spectrometry.

Therapeutic RNAs are routinely modified during their synthesis to ensure proper drug uptake, stability, and efficacy. Phosphorothioate (PS) RNA, molecules in which one or more backbone phosphates are modified with a sulfur atom in place of standard nonbridging oxygen, is one of the most common modifications because of ease of synthesis and pharmacokinetic benefits. Quality assessment of RNA synthesis, including modification incorporation, is essential for drug selectivity and performance, and the synthetic nature of the PS linkage incorporation often reveals impurities. Here, we present a comprehensive analysis of PS RNA via tandem mass spectrometry (MS). We show that activated ion-negative electron transfer dissociation MS/MS is especially useful in diagnosing PS incorporation, producing diagnostic a- and z-type ions at PS linkage sites, beyond the standard d- and w-type ions. Analysis using resonant and beam-type collision-based activation reveals that, overall, more intense sequence ions and base-loss ions result when a PS modification is present. Furthermore, we report increased detection of b- and x-type product ions at sites of PS incorporation, in addition to the standard c- and y-type ions. This work reveals that the gas-phase chemical stability afforded by sulfur alters RNA dissociation and necessitates inclusion of additional product ions for MS/MS of PS RNA.

Electrochemical interfacial catalysis in Co-based battery electrodes involving spin-polarized electron transfer.

Interfacial catalysis occurs ubiquitously in electrochemical systems, such as batteries, fuel cells, and photocatalytic devices. Frequently, in such a system, the electrode material evolves dynamically at different operating voltages, and this electrochemically driven transformation usually dictates the catalytic reactivity of the material and ultimately the electrochemical performance of the device. Despite the importance of the process, comprehension of the underlying structural and compositional evolutions of the electrode material with direct visualization and quantification is still a significant challenge. In this work, we demonstrate a protocol for studying the dynamic evolution of the electrode material under electrochemical processes by integrating microscopic and spectroscopic analyses, operando magnetometry techniques, and density functional theory calculations. The presented methodology provides a real-time picture of the chemical, physical, and electronic structures of the material and its link to the electrochemical performance. Using Co(OH)2 as a prototype battery electrode and by monitoring the Co metal center under different applied voltages, we show that before a well-known catalytic reaction proceeds, an interfacial storage process occurs at the metallic Co nanoparticles/LiOH interface due to injection of spin-polarized electrons. Subsequently, the metallic Co nanoparticles act as catalytic activation centers and promote LiOH decomposition by transferring these interfacially residing electrons. Most intriguingly, at the LiOH decomposition potential, electronic structure of the metallic Co nanoparticles involving spin-polarized electrons transfer has been shown to exhibit a dynamic variation. This work illustrates a viable approach to access key information inside interfacial catalytic processes and provides useful insights in controlling complex interfaces for wide-ranging electrochemical systems.

Single-atom Mo-Co catalyst with low biotoxicity for sustainable degradation of high-ionization-potential organic pollutants.

Single-atom catalysts (SACs) are a promising area in environmental catalysis. We report on a bimetallic Co-Mo SAC that shows excellent performance in activating peroxymonosulfate (PMS) for sustainable degradation of organic pollutants with high ionization potential (IP > 8.5 eV). Density Functional Theory (DFT) calculations and experimental tests demonstrate that the Mo sites in Mo-Co SACs play a critical role in conducting electrons from organic pollutants to Co sites, leading to a 19.4-fold increase in the degradation rate of phenol compared to the CoCl2-PMS group. The bimetallic SACs exhibit excellent catalytic performance even under extreme conditions and show long-term activation in 10-d experiments, efficiently degrading 600 mg/L of phenol. Moreover, the catalyst has negligible toxicity toward MDA-MB-231, Hela, and MCF-7 cells, making it an environmentally friendly option for sustainable water treatment. Our findings have important implications for the design of efficient SACs for environmental remediation and other applications in biology and medicine.

Boosting CO2 photoreduction by π-π-induced preassembly between a Cu(I) sensitizer and a pyrene-appended Co(II) catalyst.

The design of a highly efficient system for CO2 photoreduction fully based on earth-abundant elements presents a challenge, which may be overcome by installing suitable interactions between photosensitizer and catalyst to expedite the intermolecular electron transfer. Herein, we have designed a pyrene-decorated Cu(I) complex with a rare dual emission behavior, aiming at additional π-interaction with a pyrene-appended Co(II) catalyst for visible light-driven CO2-to-CO conversion. The results of 1H NMR titration, time-resolved fluorescence/absorption spectroscopies, quantum chemical simulations, and photocatalytic experiments clearly demonstrate that the dynamic π-π interaction between sensitizer and catalyst is highly advantageous in photocatalysis by accelerating the intermolecular electron transfer rate up to 6.9 × 105 s-1, thus achieving a notable apparent quantum yield of 19% at 425 nm with near-unity selectivity. While comparable to most earth-abundant molecular systems, this value is over three times of the pyrene-free system (6.0%) and far surpassing the benchmarking Ru(II) tris(bipyridine) (0.3%) and Ir(III) tris(2-phenylpyridine) (1.4%) photosensitizers under parallel conditions.

Generating dual-active species by triple-atom sites through peroxymonosulfate activation for treating micropollutants in complex water.

The peroxymonosulfate (PMS)-triggered radical and nonradical active species can synergistically guarantee selectively removing micropollutants in complex wastewater; however, realizing this on heterogeneous metal-based catalysts with single active sites remains challenging due to insufficient electron cycle. Herein, we design asymmetric Co-O-Bi triple-atom sites in Co-doped Bi2O2CO3 to facilitate PMS oxidation and reduction simultaneously by enhancing the electron transfer between the active sites. We propose that the asymmetric Co-O-Bi sites result in an electron density increase in the Bi sites and decrease in the Co sites, thereby PMS undergoes a reduction reaction to generate SO4•- and •OH at the Bi site and an oxidation reaction to generate 1O2 at the Co site. We suggest that the synergistic effect of SO4•-, •OH, and 1O2 enables efficient removal and mineralization of micropollutants without interference from organic and inorganic compounds under the environmental background. As a result, the Co-doped Bi2O2CO3 achieves almost 99.3% sulfamethoxazole degradation in 3 min with a k-value as high as 82.95 min-1 M-1, which is superior to the existing catalysts reported so far. This work provides a structural regulation of the active sites approach to control the catalytic function, which will guide the rational design of Fenton-like catalysts.

Structure and function of the S. pombe III-IV-cyt c supercomplex.

The respiratory chain in aerobic organisms is composed of a number of membrane-bound protein complexes that link electron transfer to proton translocation across the membrane. In mitochondria, the final electron acceptor, complex IV (CIV), receives electrons from dimeric complex III (CIII2), via a mobile electron carrier, cytochrome c. In the present study, we isolated the CIII2CIV supercomplex from the fission yeast Schizosaccharomyces pombe and determined its structure with bound cyt. c using single-particle electron cryomicroscopy. A respiratory supercomplex factor 2 was found to be bound at CIV distally positioned in the supercomplex. In addition to the redox-active metal sites, we found a metal ion, presumably Zn2+, coordinated in the CIII subunit Cor1, which is encoded by the same gene (qcr1) as the mitochondrial-processing peptidase subunit ß. Our data show that the isolated CIII2CIV supercomplex displays proteolytic activity suggesting a dual role of CIII2 in S. pombe. As in the supercomplex from S. cerevisiae, subunit Cox5 of CIV faces towards one CIII monomer, but in S. pombe, the two complexes are rotated relative to each other by ~45°. This orientation yields equal distances between the cyt. c binding sites at CIV and at each of the two CIII monomers. The structure shows cyt. c bound at four positions, but only along one of the two symmetrical branches. Overall, this combined structural and functional study reveals the integration of peptidase activity with the CIII2 respiratory system and indicates a two-dimensional cyt. c diffusion mechanism within the CIII2-CIV supercomplex.

A multiple Kirkendall strategy for converting nanosized zero-valent iron to highly active Fenton-like catalyst for organics degradation.

Nanosized zero-valent iron (nZVI) is a promising persulfate (PS) activator, however, its structurally dense oxide shell seriously inhibited electrons transfer for O-O bond cleavage of PS. Herein, we introduced sulfidation and phosphorus-doped biochar for breaking the pristine oxide shell with formation of FeS and FePO4-containing mixed shell. In this case, the faster diffusion rate of iron atoms compared to shell components triggered multiple Kirkendall effects, causing inward fluxion of vacancies with further coalescing into radial nanocracks. Exemplified by trichloroethylene (TCE) removal, such a unique "lemon-slice-like" nanocrack structure favored fast outward transfer of electrons and ferrous ions across the mixed shell to PS activation for high-efficient generation and utilization of reactive species, as evidenced by effective dechlorination (90.6%) and mineralization (85.4%) of TCE. [Formula: see text] contributed most to TCE decomposition, moreover, the SnZVI@PBC gradually became electron-deficient and thus extracted electrons from TCE with achieving nonradical-based degradation. Compared to nZVI/PS process, the SnZVI@PBC/PS system could significantly reduce catalyst dosage (87.5%) and PS amount (68.8%) to achieve nearly complete TCE degradation, and was anti-interference, stable, and pH-universal. This study advanced mechanistic understandings of multiple Kirkendall effects-triggered nanocrack formation on nZVI with corresponding rational design of Fenton-like catalysts for organics degradation.

Photoexcited Ru single-atomic sites for efficient biomimetic redox catalysis.

The unsatisfactory catalytic activity of nanozymes owing to their inefficient electron transfer (ET) is the major challenge in biomimetic catalysis-related biomedical applications. Inspired by the photoelectron transfers in natural photoenzymes, we herein report a photonanozyme of single-atom Ru anchored on metal-organic frameworks (UiO-67-Ru) for achieving photoenhanced peroxidase (POD)-like activity. We demonstrate that the atomically dispersed Ru sites can realize high photoelectric conversion efficiency, superior POD-like activity (7.0-fold photoactivity enhancement relative to that of UiO-67), and good catalytic specificity. Both in situ experiments and theoretical calculations reveal that photoelectrons follow the cofactor-mediated ET process of enzymes to promote the production of active intermediates and the release of products, demonstrating more favorable thermodynamics and kinetics in H2O2 reduction. Taking advantage of the unique interaction of the Zr-O-P bond, we establish a UiO-67-Ru-based immunoassay platform for the photoenhanced detection of organophosphorus pesticides.

Shewanella oneidensis MR-1 respires CdSe quantum dots for photocatalytic hydrogen evolution.

Living bio-nano systems for artificial photosynthesis are of growing interest. Typically, these systems use photoinduced charge transfer to provide electrons for microbial metabolic processes, yielding a biosynthetic solar fuel. Here, we demonstrate an entirely different approach to constructing a living bio-nano system, in which electrogenic bacteria respire semiconductor nanoparticles to support nanoparticle photocatalysis. Semiconductor nanocrystals are highly active and robust photocatalysts for hydrogen (H2) evolution, but their use is hindered by the oxidative side of the reaction. In this system, Shewanella oneidensis MR-1 provides electrons to a CdSe nanocrystalline photocatalyst, enabling visible light-driven H2 production. Unlike microbial electrolysis cells, this system requires no external potential. Illuminating this system at 530 nm yields continuous H2 generation for 168 h, which can be lengthened further by replenishing bacterial nutrients.

Generic dynamic molecular devices by quantitative non-steady-state proton/water-coupled electron transport kinetics.

Dynamic molecular devices operating with time- and history-dependent performance raised new challenges for the fundamental study of microscopic non-steady-state charge transport as well as functionalities that are not achievable by steady-state devices. In this study, we reported a generic dynamic mode of molecular devices by addressing the transient redox state of ubiquitous quinone molecules in the junction by proton/water transfer. The diffusion limited slow proton/water transfer-modulated fast electron transport, leading to a non-steady-state transport process, as manifested by the negative differential resistance, dynamic hysteresis, and memory-like behavior. A quantitative paradigm for the study of the non-steady-state charge transport kinetics was further developed by combining the theoretical model and transient state characterization, and the principle of the dynamic device can be revealed by the numerical simulator. On applying pulse stimulation, the dynamic device emulated the neuron synaptic response with frequency-dependent depression and facilitation, implying a great potential for future nonlinear and brain-inspired devices.