190 Search Results

Wadsley-Roth (WR) niobates have emerged as high-rate anode materials that can combine rapid ionic diffusion with good electronic conductivity. WR compounds have been defect-enhanced by limited annealing, however, such materials often contain multiple types of defects. In particular, both Wadsley defects (variable block size) and transition metal disorder have the potential to modify transport rates, however the corresponding effects are not well understood mechanistically. Here, MoNb₁₂O₃₃ (MNO) was calcined at two different temperatures to compare a defect-rich condition (MNO-800) with a proximal order-rich condition (MNO-900) as assessed through XRD, XANES, EXAFS, and STEM characterizations. Galvanostatically cycled lithium half cells ofmore » MNO-800 exhibited additional capacity (307 mAhg⁻¹ at 0.1C, 4.66% higher) and improved high-rate capacity of 200 mAhg⁻¹ at 10C. ICI-based overpotential analysis identified solid state diffusion as the dominant rate limiting process where MNO-800 correspondingly exhibited ∼3X faster capacity-weighted diffusivity. A machine-learning interatomic potential was trained to density functional theory and then applied with molecular dynamics (MLIP-MD) to examine the possible roles of Wadsley defects and transition metal disorder. For both defect-types, Li was found to populate and activate fast diffusion paths from window sites at lower extents of lithiation as compared to the order-rich model.« less

Maltose is one of the most abundant sugars in brewer’s wort, and its efficient utilization is critical for successful fermentation. However, maltose consumption varies naturally among Saccharomyces eubayanus strains isolated from different host trees, such as Quercus and Nothofagus. To identify the genetic determinants underlying these phenotypic differences, we performed bulk segregant analysis (BSA) and quantitative trait loci (QTL) mapping using an F₂ offspring derived from QC18 (Quercus-associated) and CL467.1 (Nothofagus-associated) strains. QTL mapping identified two significant genomic regions on subtelomeric loci of chromosomes V-R and XVI-L, each containing complete MAL loci composed of MAL32 (encoding maltase), MAL31 (transporter), andmore » MAL33 (transcriptional activator) genes. Comparative polymorphism analyses identified mutations in MAL32 and MAL33 of QC18, including frameshift mutations resulting in premature stop codons. Functional validation demonstrated that the heterologous expression of MAL33_ChrV from CL467.1 fully restored maltose utilization in QC18, indicating the functional presence of MAL33 cis-regulatory sequences and MAL32 and MAL31 genes in QC18. While structural protein predictions identified truncation and impaired functionality in the maltose-responsive activation domain of Mal33p from QC18, overexpression of QC18’s own MAL33_ChrV allele also improved maltose metabolism, suggesting dosage-dependent transcriptional limitations rather than complete functional loss. These results indicate that allelic variations in the maltose-responsive activation domain of Mal33p result in differences in maltose consumption between strains. Here, we hypothesized that reduced maltose metabolism in QC18 is an adaptive response to the distinct sugar composition in Quercus robur bark, contrasting with the starch-rich environment of Nothofagus pumilio. These findings highlight subtelomeric MAL gene diversity as a reservoir of genetic variation, representing a key evolutionary mechanism that influences maltose adaptation among natural Saccharomyces isolates.« less

Apolipoprotein A-V (APOA5) is a critical regulator of circulating triglyceride (TG) levels. Its deletion leads to elevated plasma TG concentrations by altering the metabolism of very low-density lipoprotein (VLDL) particles in vivo. One way APOA5 exerts its effects is through modulation of lipoprotein lipase (LPL) activity, specifically by disrupting inhibitory interactions between LPL and angiopoietin-like proteins (ANGPTLs). However, the impact of APOA5 on VLDL composition and its potential to alter VLDL metabolism in other ways remains poorly understood. To address this, we investigated the influence of APOA5 on the VLDL proteome, LPL activation, and hepatic remnant uptake. Using VLDL frommore » Apoa5 knockout (KO) and wild-type (WT) mice, we found no evidence that APOA5 directly enhances LPL activity in purified or plasma systems. However, VLDL from Apoa5 K mice was cleared significantly more slowly by cultured hepatocytes. Proteomics experiments from two independent laboratories identified consistent depletion of 17 proteins involved in lipoprotein metabolism, inflammation, and immune response in Apoa5 KO VLDL, including APOE and serum amyloid A1 (SAA1). Remarkably, reintroduction of recombinant mouse APOA5 to the KO plasma partially restored the WT VLDL proteome, including APOE, and normalized VLDL uptake by hepatocytes without altering LPL lipolysis. These findings reveal that APOA5 influences hepatic clearance of VLDL remnants by modulating particle composition, particularly APOE content. This study expands the functional scope of APOA5 in TG metabolism and underscores its role in VLDL remodeling and remnant clearance, offering new insights with implications for understanding hypertriglyceridemia and its roles in inflammation and immune response.« less

Acetylcholinesterase (AChE) is an enzyme that hydrolyzes the neurotransmitter acetylcholine (ACh), removing it from the synaptic cleft after the transmission of an electrical signal, making it an essential component of chemical neurotransmission. AChE is a serine hydrolase, containing a catalytic triad of Ser/His/Glu. AChE is a prime target for pharmaceuticals treating a variety of neurological disorders. It is also the target of synthetic organophosphorus (OP) compounds that have been used as pesticides and chemical warfare agents. OP compounds contain a potent leaving group, such as fluorine, and act by forming a covalent adduct with the catalytic serine of the AChEmore » active site. A wealth of structural information is available for AChE, including over 300 structures, including a subset of structures in complex with drugs as well as OP compounds. This review will highlight the interactions between OP compounds and AChE from a structural and computational perspective, with a discussion of access to the active site, as well as side reactions that lead to dealkylation of the OP-catalytic serine adduct, a process known as aging. We conclude that while the majority of the conformational changes needed to accommodate the OP compounds are localized to the acyl loop in the crystal structures, molecular dynamics simulations highlight the potential for a far more dynamic enzyme.« less

Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane, onto which they interact and form two-dimensional (2D) patterns. It is unclear how the membrane’s continuity and dimensionality impact pattern formation. Here, we address this gap using the MinDE system, a prototypical example of pattern-forming membrane proteins. We show that when the lipid substrate is fragmented into submicrometer-sized diffusive liposomes, adenosine triphosphate-driven protein–protein interactions generate three-dimensional (3D) spatially extended patterns, despite the complete loss of membranemore » continuity. Remarkably, these 3D patterns emerge at scales four orders of magnitude larger than the individual liposomes. By systematically varying protein concentration, liposome size, and density, we observed and characterized a variety of 3D dynamical patterns not seen on continuous 2D membranes, including traveling waves, dynamical spirals, and a coexistence phase. Simulations and linear stability analysis of a coarse-grained model revealed that the physical properties of the dispersed membrane effectively rescale both the protein–membrane binding rates and diffusion, two key parameters governing pattern formation and wavelength selection. These findings highlight the robustness of Min’s pattern-forming ability, suggesting that protein–membrane suspensions could serve as an adaptable template for studying out-of-equilibrium self-organization in 3D, beyond in vivo contexts.« less

Stabilizing oil-water interfaces in emulsions by plant-based proteins provides sustainable and tunable ways for designing emulsions with specific properties, for food, healthcare, and pharmaceuticals. Cruciferin, a protein from rapeseed, has great potential as green emulsifier, but details about its structure and mobility at oil-water interfaces are largely unknown. Here, these properties are studied with small angle neutron and x-ray scattering, and neutron spin echo spectroscopy, analyzed by atomistic modelling of scattering curves and coarse-grained modelling, to gain insight into interface coverage, and molecular conformation and mobility at the interface. Cruciferin assumes trimeric conformations at the interface, as in solution, butmore » with its protrusions from the central core of the subunits (“arms”) more compressed. Interfacial mobility is only marginally lower than in solution, indicating the arms still transiently extend and preserve a network, for the first time revealing the mechanism how cruciferin forms highly elastic 2d gel-like oil-water interfaces, as observed in macroscopic rheology. The high interfacial mobility may help in self-repairing non-stabilized interfacial fractions, reducing coalescence. These findings provide a deeper molecular level understanding of proteins at oil-water interfaces, which can stimulate development of new plant-based emulsion products, and contribute to the global protein transition.« less

Large-momentum effective theory (LaMET) provides an approach to directly calculate the x-dependence of generalized parton distributions (GPDs) on a Euclidean lattice through power expansion and a perturbative matching. When a parton’s momentum becomes soft, the corresponding logarithms in the matching kernel become non-negligible at higher orders of perturbation theory, which requires a resummation. But the resummation for the off-forward matrix elements at nonzero skewness ξ is difficult due to their multi-scale nature. In this work, we demonstrate that these logarithms are important only in the threshold limit, and derive the threshold factorization formula for the quasi-GPDs in LaMET. We thenmore » propose an approach to resum all the large logarithms based on the threshold factorization, which is implemented on a GPD model. We demonstrate that the LaMET prediction is reliable for [−1 + x₀, −ξ − x₀] ∪ [−ξ + x₀, ξ − x₀] ∪ [ξ + x₀, 1 − x₀], where x₀ is a cutoff depending on hard parton momenta. Through our numerical tests with the GPD model, we demonstrate that our method is self-consistent and that the inverse matching does not spread the nonperturbative effects or power corrections to the perturbatively calculable regions.« less

Atomic coordinate models are important for the interpretation of 3D maps produced with cryoEM and cryoET (3D electron microscopy; 3DEM). In addition to visual inspection of such maps and models, quantitative metrics can inform about the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, Q-score, was shown to correlate well with the reported resolution of the map for well fitted models. Here, we present new statistical analyses of Q-score based on its application to ∼10 000 maps and models archived in the EMDB (Electron Microscopymore » Data Bank) and PDB (Protein Data Bank). Further, we introduce two new metrics based on Q-score to represent each map and model relative to all entries in the EMDB and those with similar resolution. We explore through illustrative examples of proteins, nucleic acids and small molecules how Q-scores can indicate whether the atomic coordinates are well fitted to 3DEM maps and also whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage and/or conformational heterogeneity. These examples and statistical analyses provide a basis for how Q-scores can be interpreted effectively in order to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving.« less

Incorporating organic bulky cations in the precursor or post-treatment to achieve two-dimensional/three-dimensional (2D/3D) heterojunction is an effective strategy for enhancing the stability of perovskite materials. However, the issue of insufficient charge transport in 2D perovskites limits their development, and the fundamental mechanism of out-of-plane carrier transport remains unclear. This study designed and synthesized seven organic phenyl-core cations, differentiated at the 1- and 1,4-positions, and identified the impacts on the corresponding properties of the 2D crystalline perovskite. Shorter cations facilitated a more compact arrangement of adjacent inorganic layers, aligning to favor charge transport along the vertical direction. In addition, introducing highmore » electronegativity led to increased intermolecular interactions, resulting in enhanced structural stability and improved phenyl ring π-orbital overlap and interlayer electron coupling, yielding efficient charge transport. Resilience to thermal stressing of the perovskite was strongly correlated with the carbon chain length of the spacer cations. Here, the increase in cation length and the reduction in the rigidity of the amino-terminal both aided in the dispersion of thermal stress in the inorganic framework. Additional hydrogen bonding also contributed to mitigating structural disorder.« less

We derive a general formalism that relates the spectrum of two-particle systems in a finite volume to physical scattering amplitudes, taking into account the presence of any left-hand branch cuts due to single-particle exchanges. The method first relates the finite-volume spectrum to an infinite-volume short-range quantity, denoted $${\mathcal{M}}_0$$, and then relates the latter to the physical scattering amplitudes via known integral equations. The derivation of both relations is performed using all-orders perturbation theory and is exact up to neglected exponentially suppressed volume dependence. The relations hold for arbitrary two-particle systems with any number of coupled channels, non-identical and non-degenerate particles,more » and any intrinsic spin.« less