220 Search Results

Metalloenzyme superfamilies are typically defined by their protein scaffolds and active sites. Owing to the high tunability of protein structures, members of a single superfamily can catalyze diverse reactions with the same metallocofactor. Some superfamilies, such as amidohydrolase-related dinuclear oxygenases (AROs), display further versatility by utilizing multiple metallocofactors. We have shown that certain AROs catalyze monooxygenation reactions with diiron, dimanganese, and/or mixed manganese−iron cofactors, but the molecular factors governing the selection of a particular cofactor remain unknown, and the extent of this superfamily in biology is unclear. Here, we report bioinformatic analyses that expand the ARO superfamily to approximately 17,000more » unique UniProt sequences, far exceeding the number of previously characterized enzymes. Through the integration of structural, spectroscopic, and thermodynamic analyses of representative proteins with a bioinformatic pipeline that identifies key secondary- and tertiary-sphere residues, we can predict in silico the metal preference for the majority of reported ARO sequences. These annotations were validated via the characterization of multiple new AROs, including ones implicated in key oxidative steps of natural product biosyntheses. This study establishes the key structure−function relationships governing metal preferences in AROs and highlights their vastly underappreciated role in myriad biological processes.« less

Direct air capture (DAC) compatible ionic liquids (ILs) are attractive for integrating CO₂ capture and conversion due to their high CO₂ solubility at low partial pressures, tunable chemisorption mechanisms, low volatility, and wide electrochemical windows. However, very few ILs have high CO₂ uptake at DAC conditions (420 ppm CO₂), and even fewer have been evaluated for chemical compatibility and mechanistic continuity for combined capture and electrochemical CO₂ reduction (eCO₂RR). We demonstrate that two representative DAC-capable ILs, [P₄₄₄₄][Val] (amino acid-based) and [P₆₆₆₁₄][5-Me-Imd] (azolate-based), exhibit favorable electrochemical reduction behavior. CO and H₂ were the dominant gas-phase products by GC, while ¹H andmore » ¹³C NMR confirmed negligible liquid-phase HCOOH. Chronoamperometry at moderate applied potentials (−2.0 to −2.5 V vs Ag/AgCl) in a two-compartment H-cell with a Ag coated carbon paper as the working electrode yielded steady-state current densities of ∼10 mA cm⁻² with CO FE of 96% for [P₄₄₄₄][Val] and 95% for [P₆₆₆₁₄][5-Me-Imd], highlighting the role of viscosity and chemically absorbed CO₂-IL species to provide highly selective CO formation while suppressing H₂ evolution.« less

We report a phase transition in the projected ensemble—the collection of postmeasurement wave functions of a local subsystem obtained by measuring its complement. The transition emerges in systems undergoing random permutation dynamics, a type of quantum time evolution wherein computational basis states are shuffled without creating superpositions. It separates a phase exhibiting deep thermalization, where the projected ensemble is distributed over Hilbert space in a maximally entropic fashion (Haar random), from a phase where it is minimally entropic (“classical bit-string ensemble”). Crucially, this deep thermalization transition is invisible to the subsystem’s density matrix, which always exhibits thermalization to infinite temperaturemore » across the phase diagram. Through a combination of analytical arguments and numerical simulations, we show that the transition is tuned by the total amount of injected by the input state and the measurement basis, and is exhibited robustly across different microscopic models. Our findings represent a novel form of ergodicity-breaking universality in quantum many-body dynamics, characterized not by a failure of regular thermalization, but rather by a failure of deep thermalization.« less

We present nonlinear magnetohydrodynamic (MHD) simulations of high-β Wendelstein 7-X plasmas using the stellarator extension of the M3D-C¹ code, building on the recent work that shows benign saturation of ideal ballooning modes above the designed β limit in the standard configuration [Zhou et al., Phys. Rev. Lett. 133, 135102 (2024)]. First, we examine the results' sensitivity to the parallel thermal conductivity. It is found that while an increased parallel conductivity reduces the linear growth rate, the saturated pressure profile is barely affected. Second, we consider the dependence on the profile shape. It is shown that an equilibrium with a peakedmore » pressure profile and lower β is subject to more significant change than a broad profile with higher β and a larger growth rate, suggesting that benign saturation, or nonlinear stability, is not guaranteed and not dictated by linear growth. Third, we study the influence of the magnetic configuration, with the equilibrium rotational transform varied by adjusting the planar coil current. With similar growth rates, similar magnitudes of profile change are found regardless of the presence of a low-order resonance, which implies that the saturation mechanism is not specific to a resonant or non-resonant mode. These results indicate that MHD stability should still be treated seriously in stellarator operation and design, for which nonlinear modeling using tools like M3D-C¹ can play an instrumental role.« less

Protein ubiquitination is a central regulatory mechanism governing plant growth, development and environmental adaptation. Ubiquitylomic studies have revealed that many enzymes in phenylpropanoid biosynthetic pathways are subject to ubiquitination. Increasing evidence indicates that specific F-box proteins target key enzymes in these pathways, including PAL, CCR, CAD, COMT and peroxidases in the lignin biosynthetic branch, and CHS in the flavonoid biosynthetic branch, thereby promoting their ubiquitination and selective degradation. These F-box proteins act in response to diverse developmental and environmental cues, including cellular carbon status, light quality and intensity, and biotic stresses (e.g., pathogen and insect attack). By regulating the stabilitymore » and activity of both enzymes and regulatory proteins involved in phenylpropanoid biosynthesis, F-box proteins modulate the accumulation of simple phenolics and lignin polymers, ultimately contributing to plant resilience. This review summarizes recent advances in the characterization of F-box proteins involved in phenylpropanoid metabolism and their regulatory roles in response to biotic and abiotic stresses and identifies key knowledge gaps that limit mechanistic understanding of F-box protein-mediated proteolytic regulation of phenylpropanoid metabolism. In conclusion, insights into ubiquitin-mediated proteolytic control of phenylpropanoid metabolism offer promising avenues for enhancing bioactive phenolic production, advancing biofuel feedstock engineering and improving crop stress tolerance.« less

The hydrogen evolution reaction (HER) plays a critical role in enabling large-scale electrolytic hydrogen production and advancing future technologies and fuel production. Among non-precious metals, NiMo-based catalysts are particularly attractive due to their capability to promote both water dissociation and hydrogen adsorption in alkaline media. However, conventional NiMo catalysts often suffer from incomplete alloying, particle aggregation, weak metal–support interactions, and surface oxidation, which significantly limit active site utilization, electronic conductivity, and long-term stability. Herein, we report a scalable, solid-state, two-step ball milling strategy for constructing an efficient NiMo/C catalyst for the HER. Pre-milling the metal precursors prior to carbon incorporationmore » promotes efficient solid-state activation, leading to the formation of uniformly alloyed, ultrafine, and defect-rich Ni–Mo nanoparticles with robust metal–carbon interfacial anchoring. Benefiting from this integrated structural design, the optimized NiMo/C catalyst exhibits low overpotentials and Tafel slopes, reduced charge-transfer resistance, and excellent durability under alkaline conditions. Comprehensive structural and surface analysis reveal that the enhanced HER performance can be attributed to the synergistic interplay of homogeneous Ni–Mo alloying, uniform nanoparticle dispersion on a defect-rich carbon scaffold, enhanced accessibility of catalytically active sites, and optimized electronic coupling that stabilizes the catalyst surface. This work highlights the two-step solid-state ball milling strategy as a simple, robust, and scalable route for the preparation of effective and durable non-precious metal HER electrocatalysts, offering practical insights toward large-scale and inexpensive hydrogen production.« less

We present a novel host galaxy subtraction technique in long-slit spectroscopy for extragalactic transients. Unlike classic methods which generally estimate the background using simple interpolation of local galaxy flux in the 2D spectrum, our approach leverages multi-band archival images of the host galaxies to model the background emission from the galaxy in the 2D spectrum. Such imaging encodes the wavelength-dependent galaxy profile along the slit, and is readily accessible through wide-field imaging surveys. We construct a smooth prior for the 2D galaxy profile with a Gaussian process (GP) based on these reference images, and use another GP to model themore » correlated deviations from the prior in the observed spectrum. This enables accurate inference of the galaxy flux blended with the transient. On synthetic long-slit data of a spiral galaxy extracted from a Multi Unit Spectroscopic Explorer hyper-spectral cube, the GP method remains robust as long as the host galaxy is spatially resolved and consistently outperforms classic methods. We apply the method to archival Keck spectra of two real transients, SN 2019eix and AT 2019qiz, to further demonstrate how the method uniquely recovers weak spectral features amid strong galaxy contamination, enabling refined constraints on the properties of both transients. We have released the software implementation, HostSub_GP, a scalable toolkit that leverages JAX, with an MIT license.« less

Tracking the structural evolution of colloidal nanocrystals (NCs) facilitates the mechanistic studies of their materials chemistry. NC engineering via phase transformation reveals the chemical and physical determinants that drive lattice-scale dynamic processes such as cation exchange. Here, in this study, we employed NCs to demonstrate the cation exchange process from Cu₃As to InAs and GaAs within nanocubes. The symmetry conversion in unit cells from cubic Cu₃As to hexagonal InAs and GaAs can be described using a schematic cellular automaton model, which suggests a simplified cube-to-sphere transition. The strong covalent characteristics of III–V materials highlight the kinetic control that navigates themore » tailorable transformation through either an isotropic trajectory, leading to hollow structures, or a topotaxial trajectory, with abundant stacking faults. The reconstruction of complex covalent bonds is envisioned as the foundation for the synthesis of NCs.« less

Fatty acids are primary components of lipids, which serve as major energy sources in cells and play essential roles in membrane structure, signaling, and metabolic regulation (Shanklin and Cahoon 1998). The degree of fatty acid unsaturation critically influences lipid physicochemical properties, thereby affecting membrane fluidity and biological function (Nguyen et al. 2019). In Arabidopsis thaliana, fatty acid desaturation occurs via 2 parallel pathways: the “prokaryotic pathway” in plastids, involving glycosylglycerides, such as monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), and phospholipid phosphatidylglycerol (PG); and the “eukaryotic pathway” in the endoplasmic reticulum (ER), involving phosphatidylcholine (PC) (Lou et al. 2014) (Supplementary Figure S1).more » Seven fatty acid desaturases (FADs) in Arabidopsis differentially desaturate each glycerolipid class in the plastid and ER (Nguyen et al. 2019). FAD2, an ER-resident ω-6 fatty acid desaturase, catalyzes the conversion of oleic acid (18:1) to linoleic acid (18:2), which can be further desaturated to α-linolenic acid (18:3) by FAD3, an ER-resident ω-3 fatty acid desaturase. In plastids, FAD6 catalyzes the desaturation of 18:1/16:1 to produce 18:2/16:2, while FAD7 and FAD8 redundantly convert 18:2/16:2 to 18:3/16:3 (Li-Beisson et al. 2013; Nguyen et al. 2019). Additionally, fatty acids synthesized in the ER can also be reimported into plastids to their site of de novo synthesis (Xu et al. 2010). All FADs require reducing power, in the form of 2 electrons, for catalysis, but the sources of the electrons vary between their subcellular localizations. In the ER, FAD2 and FAD3 receive electrons from a cytochrome b₅ (CB5)-based electron transfer chain comprising cytochrome b₅ reductase (CBR) and CB5. In contrast, ferredoxin serves as the electron donor for plastid-localized FAD6, FAD7, and FAD8 (Ohlrogge and Browse 1995; Andreu et al. 2007). While the relative contributions of the 2 pathways to total cellular desaturation products vary across tissues and species, most polyunsaturated FA biosynthesis in seeds occurs via ER-resident FAD2 and FAD3 (Miquel and Browse 1992; Ohlrogge and Browse 1995).« less

Electrochemical processes that utilize biomass-derived ethanol as a source of electrons and protons offer a sustainable energy strategy, yet their practical implementation is limited by sluggish ethanol oxidation reaction (EOR) kinetics and catalyst poisoning. Here, in this study, we report a modular multi-interface nanocrystal catalyst comprising core/shell Co₂P/Pd and Pd-Au heterostructured interfaces that exhibit complementary functions for the enhanced EOR catalysis. The Co₂P/Pd interface boosts Pd atom utilization and lowers the kinetic barriers for ethanol-to-acetate conversion, while the Pd-Au interface effectively alleviates CO poisoning caused by C–C bond cleavage of ethanol. In-depth analyses using in situ attenuated total reflectance-surface-enhanced infraredmore » absorption spectroscopy, differential electrochemical mass spectrometry, and density functional theory calculations elucidate the mechanistic roles of these interfaces. The optimized Co₂P/Pd-Au_0.08 nanorods achieve an excellent mass activity, underscoring the potential of modular, multi-interface nanocrystals for advancing EOR catalysis and offering a generalizable strategy for broader catalytic innovations.« less