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At least 19 records

Uncovering Sequence and Structural Characteristics of Fungal Expansin‐Related Proteins With Potential to Drive Substrate Targeting

Expansins loosen plant cell wall networks through disrupting non-covalent bonds between cellulose microfibrils and matrix polysaccharides. Whereas expansins were first discovered in plants, expansin-related proteins have since been identified in bacteria and fungi. The biological function of microbial expansins remains unclear; however, several studies have shown distinct binding preferences toward different structural polysaccharides. Earlier studies of bacterial expansin-related proteins uncovered sequence and structural features that correlate to substrate binding. Herein, 20 fungal expansin-related sequences were recombinantly produced in Komagataella phaffii, and the purified proteins were compared in terms of substrate binding to cellulosic and chitinous substrates. The impact of pH on the zeta potential of prioritized substrates was also measured, and Principal Component Analysis was performed to uncover correlations between protein characteristics (e.g., pI, hydrophobicity, surface charge distribution) and measured substrate binding preferences. Whereas acidic proteins with a predicted pI less than 5.0 preferentially bound to chitin, basic proteins with pI greater than 8.0 preferentially bound to xylan and xylan-containing fiber. Similar to many cellulases, binding to cellulose was correlated to relatively high aromatic amino acid content in the protein sequence and presence of a carbohydrate binding module (CBM), which in the case of expansins is a C-terminal CBM63. Whereas overall sequence characteristics could be correlated to substrate binding preference, the identity of amino acids occupying conserved positions that impact protein activity was better correlated with loosenin versus expansin classifications.

chitin

Effect of LPBF Processing Parameters on Inconel 718 Lattice Structures: Geometrical Characteristics, Surface Morphology, and Mechanical Properties

Laser Powder Bed Fusion (LPBF) enables the additive manufacturing of complex lattice structures. However, the fabrication of lattice structures via LPBF poses challenges in achieving the intended geometrical accuracy due to their inherent complexity. This study investigates the effects of LPBF processing parameters, specifically laser power and scanning speed, on the geometrical characteristics, surface quality, and mechanical behavior of Inconel 718 lattices structures. The results reveal that processing parameters required for the fabrication of near-full dense structures do not translate effectively to lattice configurations, as variations in energy input influence lattice geometry and surface quality. In this work, strut thickness, open-pore size, open-cell porosity, and surface roughness were measured, and the mechanical properties of the lattices were evaluated under shear loading. The findings indicate that lower energy inputs, achieved by reducing laser power and increasing scanning speed, yield porous structures but lead to mechanical degradation. In contrast, high energy inputs lead to lattices with enhanced strength but result in undesirable open-pore blockage and dimensional inaccuracies. These findings provide insights into tailoring LPBF parameters for dimensional accuracy in lattices and correlating the processing parameters to mechanical performance and surface roughness.

36 MATERIALS SCIENCE

Low leakage current in heteroepitaxial Al 0.7 Sc 0.3 N ferroelectric films on Ga N

Wurtzite ( Al , Sc ) N ferroelectrics are attractive for microelectronics applications due to their chemical and structural compatibility with wurtzite semiconductors, such as Ga N and ( Al , Ga ) N . However, the leakage current in epitaxial stacks reported to date should be reduced for reliable device operation. Here, we demonstrate low leakage current in epitaxial Al 0.7 Sc 0.3 N films on Ga N with well-saturated ferroelectric hysteresis loops that are orders of magnitude lower (i.e., 0.07 A cm − 2 ) than previously reported films (1–19 A cm − 2 ) having similar or better structural characteristics. We also show that, for these high-quality epitaxial ( Al , Sc ) N films, structural quality (edge and screw dislocations), as measured by diffraction techniques, is not the dominant contributor to leakage. Instead, the small leakage in our films is limited by thermionic emission across the interfaces, which is distinct from the large leakage due to trap-mediated bulk transport in the previously reported ( Al , Sc ) N films. To support this conclusion, we show that Al 0.7 Sc 0.3 N on lattice-matched In 0.18 Ga 0.82 N buffers with improved structural characteristics but higher interface roughness exhibit increased leakage characteristics. This demonstration of low leakage current in heteroepitaxial ( Al , Sc ) N films and understanding of the importance of interface barrier and surface roughness can guide further efforts toward improving the reliability of wurtzite ferroelectric devices. Published by the American Physical Society 2025

36 MATERIALS SCIENCE

Resolving local structural motifs across the phase evolution of zinc titanates with computational x-ray absorption spectroscopy

Resolving the local structure motifs that characterize phase evolution as a function of composition is a key challenge in structure characterization of complex materials. Here, in this study, we combine first-principles simulations and x-ray absorption near-edge structures (XANES) analysis to gain insights into the structure evolution revealed by measurements across a combinatorial zinc titanate thin film, which was grown with smoothly varying composition over a wide range of the Ti:Zn ratio. Specifically, we propose a cluster blind-signal-separation (cBSS) method for XANES spectral analysis based on a library of the structures and spectra of representative local motifs. In addition to motifs from zinc titanate crystals, two types of Ti-defect models constructed in this study are key to the understanding of the structure characteristics in the Zn-rich region. The cBSS method makes use of both spectral clustering of the simulated site-XANES spectra library and the BSS procedure to construct high-fidelity spectral basis functions from an experimental spectral sequence. The method provides a rigorous measure of the spectral sensitivity and basis completeness. The results of the XANES analysis are corroborated with other experimental modalities, including x-ray diffraction and spectroscopic ellipsometry, to validate the cBSS method. The calculated motif weights resulting from fitting the XANES spectra with the cBSS basis probe the atomic structure characteristics of both crystalline and amorphous phases as a function of the Ti/Zn composition. The insights of the local structure motif evolution are pivotal to the understanding of the nonmonotonic trend in the optical gap, which may lead to potential applications through tuning the optical properties of zinc titanate. The workflow of the XANES spectral analysis developed in this work can be generalized to construct the structure-property relationship in a broad material space.

36 MATERIALS SCIENCE

Characterizing leaf-scale fluorescence with spectral invariants

Sun-induced chlorophyll fluorescence (SIF) is increasingly recognized as a non-destructive probe for tracking terrestrial photosynthesis. Emerging developments in spectral invariants theory provide an innovative and efficient approach for representing SIF radiative transfer processes at the canopy scale. However, modeling leaf-scale fluorescence based on the spectral invariants properties (SIP) remains underexplored. In this study, the spectral invariants theory is employed for the first time to model the leaf-scale total, backward and forward fluorescence (leaf-SIP SIF). The leaf-SIP SIF model separates the leaf-scale radiative transfer process into two distinct components: the wavelength-dependent one associated with leaf biochemical properties, and the wavelength-independent component linked to leaf structural characteristics. The leaf structure-related effects are characterized by two spectrally invariant parameters: the photon recollision probability (p) and the scattering asymmetry parameter (q), which are parameterized using the directly measurable leaf dry matter. Evaluation against field measurements shows that the proposed leaf-SIP SIF model has a good performance, with coefficient of determination (R 2 ) of 0.89, 0.89, 0.90 and root mean squared errors (RMSE) of 1.28, 0.69, 0.74 Wm -2 µm -1 sr -1 , respectively for the total, backward, and forward fluorescence (660–800 nm). The leaf-SIP SIF model with a more concise formulation demonstrates comparable performance with the widely used Fluspect model. Further, the leaf-SIP SIF model provides a simple and efficient approach for simulating leaf-scale fluorescence, with the potential to be integrated into a unified SIP-based model framework for simulating the radiative transfer processes across the soil-leaf-canopy-atmosphere continuum.

59 BASIC BIOLOGICAL SCIENCES

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State

Three-dimensional photoluminescence imaging of threading dislocations in GaN by sub-band optical excitation

GaN is rapidly gaining attention for implementation in power electronics but is still impacted by its high density of threading dislocations (TDs), which have been shown to facilitate current leakage through devices limiting their performance and reliability. Here, we discuss a novel implementation of photoluminescence (PL) imaging to study TDs in regions within vertically structured p-i-n GaN (PIN) diodes consisting of metalorganic chemical vapor deposition (MOCVD) epitaxial layers grown on ammonothermal GaN (am-GaN) substrates. PL imaging with a sub-bandgap excitation energy (3.1 eV) reveals TDs with excellent clarity in three dimensions within the am-GaN substrate. Galvanometric-driven PL imaging allows the microstructure of hundreds of devices to be characterized in a single session, enhancing the screening process through the addition of device specific TD location tracking and density mapping. The visibility, structural characteristics, luminescent nature and evolution of TDs through the GaN growth process are described, potentially providing the ability to define TD structures associated with leakage current.

36 MATERIALS SCIENCE

Hardenability and microstructural evolution of a precipitation strengthened Ni 50 Ti 21 Hf 25 Al 4 alloy

NiTi-based quaternary alloys are used in a variety of mechanical components, such as bearings, actuators, and dampers, owing to their good hardenability, wear resistance, and corrosion resistance. Additionally, one of the most notable characteristics of NiTi-based alloys is their shape memory effect and pseudoelastic properties. Connecting the macroscopic processing parameters employed in the design of new intermetallic alloys to the nanoscale structural characteristics dictating their behavior is crucial for improving their mechanical properties and expanding the spectrum of potential applications. Here, in this work, an arc melted Ni 50 Ti 21 Hf 25 Al 4 (at%) alloy was solution treated at 1050 °C followed by quenching and aging at 600 °C to investigate the effect of aging time on the microstructure and mechanical properties. Two types of nano-sized precipitates were observed and determined as face-centered orthorhombic H-phase (TiHf)Ni and L2 1 Heusler precipitates Ni 2 TiAl. The morphology and orientation of the H-phase were investigated using scanning and transmission electron microscopy (SEM and TEM), elucidating the coarsening kinetics and strengthening contribution of that phase to the intermetallic mechanical behavior. Following coarsening, the presence of Heusler nanoprecipitates was detected under overaged conditions through TEM imaging and nanobeam electron diffraction patterns. A peak hardness condition of 756 HV was achieved after 70 h of aging, indicating that the co-precipitation of H-phase and Heusler precipitates through a well-designed aging treatment can lead to optimal mechanical performance, thus elevating the alloy’s potential as a viable material for industrial applications.

36 MATERIALS SCIENCE

Growth, discovery and characterization of single crystalline Eu 0.8 Pt 6 Al 16.4

Here, we report the discovery of a ternary compound, Eu 0.8 Pt 6 Al1 6.4 . We determine its chemical and structural characteristics based on energy-dispersive X-ray spectroscopy as well as both powder and single-crystal X-ray diffraction, demonstrating that it crystallizes in a hexagonal structure type EuPt 6 Al 17 with no reported structural analog. The temperature- and field-dependent magnetization, and temperature-dependent resistance measurements, reveal that the Eu 2+ magnetic moments order antiferromagnetically below 2.8 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Interpretation of wide-angle x-ray diffraction patterns from mesophase pitch-based carbon fibers – a simulation and experimental study

Carbon fiber is a critical material in a wide range of industries, where it is highly valued for its high specific strength/stiffness, excellent wear resistance, efficient electrical and thermal transport properties, chemical resistance, and low coefficient of thermal expansion. The properties of a specific carbon fiber are closely tied to its structural characteristics at all length scales. Here, in this work, we applied wide-angle x-ray diffraction to a set of heat-treated mesophase pitch-based carbon fibers, with the goal of elucidating the crystalline structures as a function of fiber orientation. To assist with analysis and interpretation of the experimental data, we employed diffraction pattern simulations using the scalar and vector forms of the Debye scattering equation to determine the influence of basal plane orientation, crystalline ordering (turbostratic-graphitic), and basal plane asymmetry on the diffraction patterns. The results presented here suggest that growth of the transverse crystallites in mesophase pitch-based carbon fiber is fixed until graphitization temperatures are reached. The work completed here provides a framework for the analysis of carbon fiber and other oriented carbon-based materials via diffraction.

36 MATERIALS SCIENCE

Superconducting phase diagram of multilayer square-planar nickelates

The discovery of superconductivity in square-planar nickelates has offered a rich materials platform to explore the origins of high-temperature superconductivity. However, experimental investigations have largely been limited to the infinite-layer R NiO 2 ( R , rare earth) nickelates. For this work we constructed a phase diagram of multilayer square-planar Nd n+1 Ni n O 2n+2 compounds and found signatures of superconductivity for dimensionality n = 4 to 8. Upon decreasing n , the superconducting anisotropy evolves owing to 4ƒ electron effects, and electronic structure characteristics approach cuprate-like behavior. Magnetic fluctuations persist from within the superconducting regime and into the overdoped, nonsuperconducting regime. The superconducting regime overlaps with that of chemically doped infinite-layer nickelates, demonstrating underlying commonalities as well as differences across varying structural realizations of square-planar nickelates. Our work establishes this layered template for creating new nickel-based superconductors.

36 MATERIALS SCIENCE

Noncanonical folding of peptoid oligomers: Formation of a closed conformation in nonpolar solvent

Peptoids provide a versatile platform for foldamer design, yet their conformational behavior in low-dielectric media remains poorly understood. The structural characteristics of N-1-phenylethylglycine (Nspe) homo-oligomers were inves-tigated in chloroform, a solvent that mimics the interior of lipid bilayers, using nuclear magnetic resonance (NMR) spec-troscopy and molecular dynamics (MD) simulations. Nspe7 populated two distinct compact conformations, while Nspe10 adopted a single homogeneous conformation related to the previously reported Nspe9 threaded-loop structure. Integrated experimental and computational analysis reveals that these structures are stabilized by cooperative end-to-end intramo-lecular hydrogen bonding, cis-trans backbone isomerism, and hydrophobic side-chain shielding. The resulting structures minimize exposed polar surface area, demonstrating a closed conformation in the low-dielectric environment. These find-ings establish specific chain-length requirements for achieving well-defined closed conformations. This work provides insights into peptoid folding in nonpolar media, enabling rational design strategies for solvent-directed conformational switching systems.

Oh, Jinyoung

High-Pressure Phase Transition of Metastable Wurtzite-Like CuInSe 2 Nanocrystals

Ternary I–III–VI 2 semiconductors, such as CuInSe 2 , exhibit diverse polymorphs with unique structural characteristics and optoelectronic properties. This study investigates the pressure-induced phase transitions of metastable wurtzite-like CuInSe 2 nanocrystals. Using a combination of synchrotron X-ray diffraction, pair distribution function analysis, and density functional theory calculations, we reveal a transition from cation-ordered wurtzite-like (Pmc2 1 ) to cation-disordered NaCl-like (Fm3̅m) structures at 7.7 GPa. The cation-disordered NaCl-like phase persists upon decompression. Bulk modulus calculations highlight size-dependent deviations from bulk material behavior. These findings deepen our understanding of phase stability in colloidal I–III–VI 2 semiconductor nanocrystals, with implications for tailoring functional materials under extreme conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Structure-performance relationships in lignin-based transesterification vitrimers: The role of lignin structural features

Lignin has been hailed as an ideal renewable alternative for petrochemical-based prepolymers in material synthesis for a sustainable and circular economy, due to its abundant aromatic network and high carbon content. However, the properties and performance of lignin-derived macromolecules are strongly influenced by the lignin itself. While numerous studies have explored the impact of lignin content on the thermomechanical performance of lignin-based vitrimers, literature on how the inherent structural features of lignin affect these properties is scanty. In this study, hardwood organosolv lignin was fractionated in ethyl acetate, ethanol, and acetone to obtain lignin fractions with varying structural characteristics. These fractions were then modified through carboxylation and crosslinked with epoxidized soybean oil (ESO) at a hydroxyl to epoxy group ratio of 1:1 to produce lignin-based transesterification vitrimers (LVs). The thermal properties (i.e. glass transition temperature and thermal stability), tensile strength, storage modulus, and stress relaxation behavior of the LVs were studied and carefully related to the structural features of lignin. The results revealed a positive relationship between strong hydroxyl content in modified lignin and the tensile strength (5.10–9.71 MPa), storage modulus (1099.4 – 1372.8 MPa), crosslinking density, and stress relaxation of the LVs. Additionally, both the storage modulus and tensile strength exhibited a positive relationship with the ratio of rigid linkages in modified lignin, while lignin molecular weight was found to significantly impact the thermal properties of LVs (i.e Tg and thermal stability). This study not only highlights the valorization of lignin in vitrimer synthesis but also provide insights for designing lignin-based materials with tailored properties for specific applications.

Bio-based polymer

Effects of Composition and Oxidation States on the Structures of Chromium-Containing Sodium Silicate Glasses: Molecular Dynamics Simulations using Machine Learning Interatomic Potentials

Chromium represents a significant challenge for the vitrification of high-level nuclear waste into silicate and borosilicate glasses due to its low solubility and variable oxidation states, which can limit the waste loading due to promotion of crystallization or phase separation during processing. In this study, we modeled chromium containing silicate glasses using molecular dynamics simulations with three machine learning interatomic potentials (MLIPs), MACE, CHGNet, and PFP were employed, to gain insights on glass composition and oxidation states on the structures of these glasses. One of the goals is to evaluate their ability of these MLIPs to accurately represent the general structure of silicate glasses and chromium local environments as a function of chromium oxidation states. Density Functional Theory (DFT) based calculations and experimental data such as neutron structure factors were used to validate the structural models. It was found that the foundation models of all three MLIPs are able to reproduce general structural features of the sodium silicate glass structure consistent with experimental and DFT data, but only CHGNet and PFP can accurately capture the oxidation states and local environment of chromium: tetrahedral for Cr6+ and octahedral for Cr3+. Furthermore, we studied the effect of varying Cr3+/ Cr6+ (Cr3+/Crtotal) ratio and total chromium content using PFP. Our results show that Cr6+ enhances network polymerization by reducing non-bridging oxygens through Na? charge compensation required due to the formation of chromate (CrO42-) species, while Cr³? acts as a network modifier that disrupts connectivity. System size effects on the structural characteristics and chromium environments were also tested using the PFP potential. This work highlights the importance of careful validation on the precision, transferability, and potential of MLIPs for modeling glasses containing transition metal elements that can exist in multiple oxidation states. It is also encouraging to see the foundational models are all three MLFFs are able to reproduce the basic sodium silicate glass structures, while suggesting additional training or refining is needed to improve the description of more complex systems containing transition metals.

Puga, Christina L.

The structural basis for the broad aldehyde specificity of the aminoaldehyde dehydrogenase PauC from the human pathogen Pseudomonas aeruginosa

Abstract Despite significant differences in size and formal charge, the aldehyde dehydrogenasePaPauC (PA5312) fromPseudomonas aeruginosaPAO1 efficiently catalyzes the NAD + ‐dependent oxidation of the aminoaldehydes formed in polyamines degradation. We report here thatPaPauC also oxidizes 4‐guanidinebutyraldehyde, formed in one arginine degradation pathway, trimethylaminobutyraldehyde, of unknown metabolic origin, and indole‐3‐acetaldehyde, a precursor of the plant growth‐promoting hormone indoleacetic acid.PaPauC has been proposed as a potential target for combatingP. aeruginosa. However, understanding its structure–function relationships, crucial for developing specific inhibitors, is lacking. Using X‐ray crystallography, we identified the structural characteristics that determinePaPauC broad aldehyde specificity: a spacious aldehyde‐entrance tunnel and six active‐site residues. Docking simulations, site‐directed mutagenesis, and kinetic analyses support the interactions of Lys479 with glutamylated aminoaldehydes; Phe169, Trp176, and Phe467 with amino and guanidinium groups through cation–π interactions and with the indole group via NH–π and CH–π interactions; Asp459 with amino and indole groups; and Thr303 with amide and guanidinium groups. Exploiting the distinctive structural features of thePaPauC active site could aid in developing specific inhibitors to combatP. aeruginosainfections in humans and animals, as well as in preventing its colonization of plants, which are abundantP. aeruginosareservoirs and, therefore, a significant source of human infections.

Biochemistry & Molecular Biology

Strain release by 3D atomic misfit in fivefold twinned icosahedral nanoparticles with amorphization and dislocations

Multiple twinning to form fivefold twinned nanoparticles in crystal growth is common and has attracted broad attention ranging from crystallography research to physical chemistry and materials science. Lattice-misfit strain and defects in multiple twinned nanoparticles (MTP) are key to understand and tailor their electronic properties. However, the structural defects and related strain distributions in MTPs are poorly understood in three dimensions (3D). Here, we show the 3D atomic misfit and strain relief mechanism in fivefold twinned icosahedral nanoparticles with amorphization and dislocations by using atomic resolution electron tomography. We discover a two-sided heterogeneity in variety of structural characteristics. A nearly ideal crystallographic fivefold face is always found opposite to a less ordered face, forming Janus-like icosahedral nanoparticles with two distinct hemispheres. The disordered amorphous domains release a large amount of strain. Molecular dynamics simulations further reveal the Janus-like icosahedral nanoparticles are prevalent in the MTPs formed in liquid-solid phase transition. This work provides insights on the atomistic models for the modelling of formation mechanisms of fivefold twinned structures and computational simulations of lattice distortions and defects. We anticipate it will inspire future studies on fundamental problems such as twin boundary migration and kinetics of structures in 3D at atomic level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic sinefungin

Abstract The essential enzyme messenger RNA (mRNA) (guanine-N7) methyltransferase catalyzes S-adenosylmethionine (SAM)-dependent conversion of GpppRNA ends to the m7GpppRNA cap structure characteristic of eukaryal mRNAs. The antibiotic sinefungin (SFG) is a SAM analog in which the S-CH3 sulfonium moiety of SAM is replaced by a C-NH2 amine. Available evidence indicates that the antifungal activity of SFG is exerted via inhibition of fungal cap methyltransferase Abd1. Here we report that recombinant Kluyveromyces lactis and Saccharomyces cerevisiae Abd1 are 240-fold and 485-fold more sensitive to inhibition by SFG than by the reaction product S-adenosylhomocysteine (SAH). Crystal structures of K. lactis and S. cerevisiae Abd1 as binary complexes with SAH or SFG and ternary complexes with GTP•SFG highlight how SFG makes two hydrogen bonds from its C-NH2 amine to the guanine-O6 and -N7 atoms of GTP that account for its higher affinity vis-à-vis SAH and SAM. Through a genetic screen to isolate SFG-resistant S. cerevisiae strains, a conserved tyrosine (Tyr416) that interacts with the cap guanine in Abd1 was identified as a key determinant of SFG potency. Tyr416 Abd1 variants confer SFG resistance in vitro by weakening cap-assisted SFG interactions with Abd1. Our study illuminates the basis for the exquisite SFG sensitivity of fungal cap methyltransferases.

Biochemistry & Molecular Biology