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At least 541 records · Page 30

Structural signatures in EPR3 define a unique class of plant carbohydrate receptors

Abstract Receptor-mediated perception of surface-exposed carbohydrates like lipo- and exo-polysaccharides (EPS) is important for non-self recognition and responses to microbial associated molecular patterns in mammals and plants. In legumes, EPS are monitored and can either block or promote symbiosis with rhizobia depending on their molecular composition. To establish a deeper understanding of receptors involved in EPS recognition, we determined the structure of the Lotus japonicus ( Lotus ) exopolysaccharide receptor 3 (EPR3) ectodomain. EPR3 forms a compact structure built of three putative carbohydrate-binding modules (M1, M2 and LysM3). M1 and M2 have unique βαββ and βαβ folds that have not previously been observed in carbohydrate binding proteins, while LysM3 has a canonical βααβ fold. We demonstrate that this configuration is a structural signature for a ubiquitous class of receptors in the plant kingdom. We show that EPR3 is promiscuous, suggesting that plants can monitor complex microbial communities though this class of receptors.

59 BASIC BIOLOGICAL SCIENCES↗

Two VHH Antibodies Neutralize Botulinum Neurotoxin E1 by Blocking Its Membrane Translocation in Host Cells

Botulinum neurotoxin serotype E (BoNT/E) is one of the major causes of human botulism, which is a life-threatening disease caused by flaccid paralysis of muscles. After receptor-mediated toxin internalization into motor neurons, the translocation domain (HN) of BoNT/E transforms into a protein channel upon vesicle acidification in endosomes and delivers its protease domain (LC) across membrane to enter the neuronal cytosol. It is believed that the rapid onset of BoNT/E intoxication compared to other BoNT serotypes is related to its swift internalization and translocation. We recently identified two neutralizing single-domain camelid antibodies (VHHs) against BoNT/E1 termed JLE-E5 and JLE-E9. Here, we report the crystal structures of these two VHHs bound to the LCHN domain of BoNT/E1. The structures reveal that these VHHs recognize two distinct epitopes that are partially overlapping with the putative transmembrane regions on HN, and therefore could physically block membrane association of BoNT/E1. This is confirmed by our in vitro studies, which show that these VHHs inhibit the structural change of BoNT/E1 at acidic pH and interfere with BoNT/E1 association with lipid vesicles. Therefore, these two VHHs neutralize BoNT/E1 by preventing the transmembrane delivery of LC. Furthermore, structure-based sequence analyses show that the 3-dimensional epitopes of these two VHHs are largely conserved across many BoNT/E subtypes, suggesting a broad-spectrum protection against the BoNT/E family. In summary, this work improves our understanding of the membrane translocation mechanism of BoNT/E and paves the way for developing VHHs as diagnostics or therapeutics for the treatment of BoNT/E intoxication.

60 APPLIED LIFE SCIENCES↗

NMR Studies of Block Copolymer-Based Supramolecules in Solution

Hierarchical assemblies from block copolymer (BCP)-based supramolecules have shown immense potential as programmable materials owing to their versatility for incorporating functional molecules and provide access to arrays of hierarchical structures. However, there remains a knowledge gap on the formation of the supramolecule in solution. Here, we applied NMR techniques to investigate the solution-phase behavior of the most studied supramolecular systems, polystyrene-block-poly(4-vinylpyridine)(3-pentadecylphenol) (PS-b-P4VP(PDP) r ). The results show that the supramolecule likely adopts a coil-comb conformation, despite the small molecule's (PDP) rapid exchange between the bonded and free states. The exchange rate (>10 4 s -1 ) exceeds the NMR time scale at the frequency of interest. The supramolecules form under dilute conditions (~2 vol %) and are attributed to the enthalpic gain of the hydrogen bonding between the PDP and 4VP. As the solute concentration increases (>10 vol %), the supramolecule forms micelle-like aggregates with PDP accumulated within the comb-block's pervaded volume based on analysis of the apparent molecular weight, viscosity, and chain dynamics. Overall, this work sheds light on the long-standing question regarding the evolution of the constituents in the BCP-based supramolecule in solution and provides valuable guidance toward their solution-based processing and morphological control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A unified neural-network framework for nucleon imaging from numerical simulations of QCD

Parton distributions encode the momentum-space structure and, in their generalizations, the spatial tomography of quarks and gluons inside hadrons, the building blocks of visible matter. We present a unified neural-network approach that learns these distributions directly from matrix elements calculated via numerical simulations of quantum chromodynamics (QCD) on the lattice by fitting two complementary inputs simultaneously: data matched to physical quantities via known momentum-space and coordinate-space formalisms. Utilizing data from both methods stabilizes the extraction and mitigates biases that can arise when either is used alone. We validate the method on controlled mock data and apply it to lattice-QCD matrix elements to extract parton distribution functions (PDFs). We show benefits of such an approach for determining the physical quantities. We further extend the framework to zero-skewness generalized parton distributions and demonstrate nucleon tomography within the same neural-network parameterization. Our results provide an adaptable and systematically improvable approach for extracting partonic distributions from Euclidean correlators. It can incorporate polarization, additional channels, and future experimental constraints from current and future facilities, such as the Electron-Ion Collider.

Hadronic Spectroscopy↗

Reconfiguring DNA Nanotube Architectures via Selective Regulation of Terminating Structures

Molecular assemblies inside cells often undergo structural reconfiguration in response to stimuli to alter their function. Adaptive reconfiguration of cytoskeletal networks, for example, enables cellular shape change, movement, and cargo transport and plays a key role in driving complex processes such as division and differentiation. The cellular cytoskeleton is a self-assembling polymer network composed of simple filaments, so reconfiguration often occurs through the rearrangement of its component filaments’ connectivities. DNA nanotubes have emerged as promising building blocks for constructing programmable synthetic analogs of cytoskeletal networks. Nucleating seeds can control when and where nanotubes grow and capping structures can bind nanotube ends to stop growth. Such seeding and capping structure, collectively called termini, can organize nanotubes into larger architectures. However, these structures cannot be selectively activated or inactivated in response to specific stimuli to rearrange nanotube architectures, a key property of cytoskeletal networks. Here we demonstrate how selective regulation of the binding affinity of DNA nanotube termini for DNA nanotube monomers or nanotube ends can direct the reconfiguration of nanotube architectures. Using DNA hybridization and strand displacement reactions that specifically activate or inactivate four orthogonal nanotube termini, we demonstrate that nanotube architectures can be reconfigured by selective addition or removal of unique termini. Lastly, we show how terminus activation could be a sensitive detector and amplifier of a DNA sequence signal. These results could enable the development of adaptive and multifunctional materials or diagnostic tools.

59 BASIC BIOLOGICAL SCIENCES↗

Cryo-EM structure of a methanogen nitrogenase-PII protein supercomplex

Abstract Nitrogenases are metalloenzymes that catalyze the reduction of atmospheric dinitrogen to ammonia, sustaining the global nitrogen cycle. While bacterial nitrogenase has been extensively characterized, the architecture and regulation of archaeal nitrogenases remain unknown despite longstanding evidence of nitrogen fixation in methanogens. Here we report a 3.1 Å cryo-electron microscopy structure of a native nitrogenase–PII protein supercomplex from Methanosarcina acetivorans. The structure reveals an unprecedented assembly of three NifDK heterotetramers bridged by six NifI1,2 heterotrimeric PII complexes, which sterically block NifH association and lock the enzyme in an inactive state. The NifI complexes display asymmetric binding of ADP and 2-oxoglutarate, coupling nitrogenase inhibition directly to cellular energy and nitrogen status. Addition of 2-oxoglutarate and ATP releases the NifI complexes, stimulating a threefold increase in NifDK activity in vitro. This higher-order architecture uncovers a previously unrecognized regulatory strategy in methanogens, in which PII proteins drive nitrogenase oligomerization to control activity. The discovery that nitrogenase activity may be modulated through direct assembly into higher-order structures opens new avenues for exploring nitrogenase evolution, regulation, and biotechnological applications. One sentence summary Discovery of a nitrogenase-PII protein supercomplex in methanogens, uncovering a metabolite-gated assembly mechanism for nitrogenase inhibition.

Nitrogenase, Electron Transfer, Methanogen↗

Molecular Modifications of Crystalline Poly(triazine imide) for Advancing Its Structure–Property Relationships in Light-Driven Catalysis

Carbon-nitride materials represent light-absorbing structures composed of earth-abundant elements capable of being leveraged for semiconductor photocatalysis at their surfaces. This study systematically investigates the addition of molecular modifiers to the synthesis of crystalline carbon nitrides to assess their effects on the materials’ structure, optical bandgap, and photocatalytic activity for hydrogen (H 2 ) and oxygen (O 2 ) evolution under ultraviolet and visible-light irradiation. Melamine and five pyrimidine-centered analogs were employed as building blocks to modify various heteroatoms within the polymeric framework. The modified materials were characterized with attention to the differences introduced by the monomeric modifiers and their influence on the resulting structures and compositions. The findings indicate that these changes significantly broaden the visible-light absorption range, albeit with the gradual loss of the bulk crystalline structure. As the loading of modifiers increased beyond 50%, a predominantly amorphous form of carbon nitride emerged. XPS, 13 C solid-state NMR, and SEM analyses corroborated the changes, which were attributed to modifications of the elemental composition and a reduced amount of Li cations and charge-balancing Cl anions owing to fewer binding sites in the intralayer cavities. In photocatalytic measurements under an ultraviolet 390 nm LED, and aided by photodeposited nanoparticle cocatalysts, the unmodified PTI-LiCl framework demonstrated the highest H 2 evolution rate (HER; 3.44 mmol·g –1 ·h –1 ) with an apparent quantum yield of 5.4%, along with total water splitting at rates of 163 μmol of H 2 ·g –1 ·h –1 and 75.6 μmol·O 2 g –1 ·h –1 . While PTI-LiCl showed trace activity under a visible-light 440 nm LED, all modified materials exhibited enhanced reactivity with as low as 5% molecular modifiers. The photocatalytic rates peaked at a 15% modification level when using 2,4,6-triaminopyrimidine, with rates of 33 μmol·g –1 ·h –1 for HER, along with 19.7 μmol of H 2 ·g –1 ·h –1 and 8.7 μmol of O 2 ·g –1 ·h –1 for total water splitting. Density functional theory calculations were used to probe electronic structure changes resulting from the modifications. Furthermore, these results elucidate the structural, optical, and electronic changes arising from the five selected molecular modifiers and their impact on the semiconductors’ photocatalytic properties.

Electrical conductivity↗

ABC -Auxetics: An Implicit Design Approach for Negative Poisson's Ratio Materials

A novel methodology is introduced for designing auxetic (negative Poisson's ratio) structures based on topological principles and is demonstrated by investigating a new class of auxetics based on two-dimensional (2D) textile weave patterns. Conventional methodology for designing auxetic materials typically involves determining a single deformable block (a unit cell) of material whose shape results in auxetic behavior. Consequently, patterning such a unit cell in a 2D (or 3D) domain results in a larger structure that exhibits overall auxetic behavior. Such an approach naturally relies on some prior intuition and experience regarding which unit cells may be auxetic. Second, tuning the properties of the resulting structures is typically limited to parametric variations of the geometry of a specific type of unit cell. Thus, most of the currently known auxetic structures belong to a selected few classes of unit cell geometries that are explicitly defined in accordance with a specified topological (i.e., grid structure). Herein, a new class of auxetic structures is demonstrated that, while periodic, can be generated implicitly, i.e., without reference to a specific unit cell design. The approach leverages weave-based parameters (A–B–C), resulting in a rich design space for auxetics that is previously unexplored.

36 MATERIALS SCIENCE↗

First Measurement of the Isospin-Dependence of Nuclear Structure Functions at 12 GeV Jefferson Lab

The structure functions of protons and neutrons provide crucial insight into how the strong nuclear force, as described by Quantum Chromodynamics (QCD), manifests at everyday energies, allowing us to better understand precisely how quarks and gluons interact to form the basic building blocks of almost all visible mass in our universe. Despite more than 40 years of experimental and theoretical effort, the EMC effect – the observation that nuclear structure functions appear to be modified from those of free nucleons – is still not fully understood. One open question that remains is whether or not the modification of quark distributions is the same for all quark flavors. Determining the flavor (isospin) dependence of the EMC effect, which is predicted by several models, is essential for coming to a complete understanding of how QCD manifests in nuclei. To this end, inclusive electron Deep Inelastic Scattering (DIS) from nuclei with approximately constant atomic mass number A and variable proton-to-neutron ratio N/Z was measured in Jefferson Lab experiment E12-10-008 to look for isospin-dependent modification of nuclear structure functions. The preliminary EMC ratios presented here cover a kinematic range of 2.8 < Q2 < 8.1 GeV2 and 0.18 < xBj < 1.0. The size of the EMC effect in these nuclei is extracted by calculating the slope of the EMC ratio as a function of Bjorken x (xBj ) over the ranges 0.3 < xBj < 0.6 and 0.3 < xBj < 0.7; these slopes then are compared with existing world data. Our preliminary results do not appear to indicate significant isospin-dependence of the EMC effect, though a more careful study is needed once all results are confirmed.

Cotton, Cameron William [Univ. of Virginia, Charlo↗

Transforming an Ionic Conductor into an Electronic Conductor via Crystallization: In Situ Evolution of Transference Numbers and Structure in (La,Sr)(Ga,Fe)O 3–x Perovskite Thin Films

Mixed-conducting perovskites are workhorse electrochemically active materials, but typical high-temperature processing compromises their catalytic activity and chemo-mechanical integrity. Low-temperature pulsed laser deposition of amorphous films plus mild thermal annealing is an emerging route to form homogeneous mixed conductors with exceptional catalytic activity, but little is known about the evolution of the oxide-ion transport and transference numbers during crystallization. Here the coupled evolution of ionic and electronic transport behavior and structure in room-temperature-grown amorphous (La,Sr)(Ga,Fe)O 3-x films as they crystallize is explored. In situ ac-impedance spectroscopy with and without blocking electrodes, simultaneous capturing-synchrotron-grazing-incidence X-ray diffraction, dc polarization, transmission electron microscopy, and molecular dynamics simulations to evaluate isothermal and non-isothermal crystallization effects and the role of grain boundaries on transference numbers is combined. Ionic conductivity increases by ≈2 orders of magnitude during crystallization, with even larger increases in electronic conductivity. Consequently, as crystallinity increases, LSGF transitions from a predominantly ionic conductor to a predominantly electronic conductor. The roles of evolving lattice structural order, microstructure, and defect chemistry are examined. Grain boundaries appear relatively nonblocking electronically but significantly blocking ionically. The results demonstrate that ionic transference numbers can be tailored over a wide range by tuning crystallinity and microstructure without having to change the cation composition.

36 MATERIALS SCIENCE↗

A Structural Basis for Inhibition of the Complement Initiator Protease C1r by Lyme Disease Spirochetes

Abstract Complement evasion is a hallmark of extracellular microbial pathogens such as Borrelia burgdorferi, the causative agent of Lyme disease. Lyme disease spirochetes express nearly a dozen outer surface lipoproteins that bind complement components and interfere with their native activities. Among these, BBK32 is unique in its selective inhibition of the classical pathway. BBK32 blocks activation of this pathway by selectively binding and inhibiting the C1r serine protease of the first component of complement, C1. To understand the structural basis for BBK32-mediated C1r inhibition, we performed crystallography and size-exclusion chromatography–coupled small angle X-ray scattering experiments, which revealed a molecular model of BBK32-C in complex with activated human C1r. Structure-guided site-directed mutagenesis was combined with surface plasmon resonance binding experiments and assays of complement function to validate the predicted molecular interface. Analysis of the structures shows that BBK32 inhibits activated forms of C1r by occluding substrate interaction subsites (i.e., S1 and S1’) and reveals a surprising role for C1r B loop–interacting residues for full inhibitory activity of BBK32. The studies reported in this article provide for the first time (to our knowledge) a structural basis for classical pathway–specific inhibition by a human pathogen.

Garrigues, Ryan J. (ORCID:0000000259233250)↗

Complex Phase Transitions of Fully Rigid Sphere–Rod Amphiphiles Induced by Solvent Polarity in Dilute Solutions

Here we report complex macrophase and microphase transitions of rigid amphiphiles with spherical Keggin molecular clusters as the solvophilic block and rod-like rigid oligofluorene (OF) as the solvophobic block in mixed solvents of water and polar organic solvent. By properly adjusting the solvent polarity, the amphiphiles are found to respond accordingly by self-assembling into multilayered incomplete onion-like structures (10–25 vol % THF), single-layered vesicular structures (60 vol % THF), and an unexpected macrophase separation in the middle (40–50 vol % THF), which is due to the anomalous trends in Keggin solubility as a result of the nature of TBA + counterions. The rigidity of the OF block prevents the amphiphile from assembling by following the rule of packing parameters; instead, interdigitation among different rods leads to the formation of the solvophobic domain to achieve self-assembly. The incomplete onion structures are controlled by the interdigitation of rigid rods for the number of layers and the electrostatic interaction among Keggin head groups for the interlayer distance. When the degree of interdigitation becomes lower, the self-assembly process shows a trend that can be explained by the traditional rule of packing parameter. This study demonstrates the formation of different self-assembled structures by rigid amphiphiles and their transitions induced by solvent composition. The self-assembly (microphase separation) of rigid amphiphiles in a dilute solution could indeed represent a broad area containing complicated, uncharted rules.

36 MATERIALS SCIENCE↗

Hex-C 558 : A new porous metallic carbon allotrope for lithium-ion battery anode

Due to the limited specific capacity of graphite anodes in lithium-ion batteries (LIBs), it is imperative to find alternatives with better performance. Here in this work, we propose, for the first time, a three dimensional (3D) porous metallic 5-5-8 carbon monolith with hexagonal lattice as a potential candidate. With 5-5-8 carbon nanoribbon as the building block, this material, named Hex-C558, goes beyond graphene-nanoribbon-based 3D porous carbon structures. Using first-principles calculations, we show that Hex-C 558 is not only dynamically and thermally stable, but also is energetically more favorable than many other theoretically predicted carbon allotropes. More importantly, Hex-C 558 is metallic with ordered ionic conducting channels and possesses a low mass density of 1.05 gcm -3 , exhibiting great potential for ion-battery applications. As an anode for LIBs, Hex-C558 possesses a large specific capacity of 591 mAhg -1 , low diffusion energy barrier of 0.27 eV (at low Li concentration) and 0.52 eV (at high Li concentration), a low open-circuit voltage of 0.51 V, and a small volume change of 2.4%. This work provides a new route for the design and synthesis of novel carbon materials for battery applications by using pentagon-based building units.

36 MATERIALS SCIENCE↗

A substrate-induced gating mechanism is conserved among Gram-positive IgA1 metalloproteases

The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by producing IgA1 proteases (IgA1Ps). Our lab was the first to describe the structures of a metal-dependent IgA1P (metallo-IgA1P) produced from Gram-positive Streptococcus pneumoniae both in the absence and presence of its IgA1 substrate through cryo-EM single particle reconstructions. This prior study revealed an active-site gating mechanism reliant on substrate-induced conformational changes to the enzyme that begged the question of whether such a mechanism is conserved among the wider Gram-positive metallo-IgA1P subfamily of virulence factors. Here, we used cryo-EM to characterize the metallo-IgA1P of a more distantly related family member from Gemella haemolysans, an emerging opportunistic pathogen implicated in meningitis, endocarditis, and more recently bacteremia in the elderly. While the substrate-free structures of these two metallo-IgA1Ps exhibit differences in the relative starting positions of the domain responsible for gating substrate, the enzymes have similar domain orientations when bound to IgA1. Together with biochemical studies that indicate these metallo-IgA1Ps have similar binding affinities and activities, these data indicate that metallo-IgA1P binding requires the specific IgA1 substrate to open the enzymes for access to their active site and thus, largely conform to an “induced fit” model.

59 BASIC BIOLOGICAL SCIENCES↗

Behavior of strain stripe networks in barium titanate nanocrystals on crossing its ferroelectric phase transition

Nanoscale strain networks are reported in BaTi O 3 (BTO) crystals of 300 nm size using Bragg coherent diffractive imaging. BTO nanocrystals with clear facets were chosen to identify the crystallographic directions, allowing the strain field direction and periodicity to be studied in detail. Stripes of strain were observed, which were both stable and preserved in tetragonal and cubic phases at elevated temperatures, above the tetragonal-to-cubic phase transition. A finite element analysis approach was used to simulate the domain structures inside a BTO crystal and to understand the origins of the strain stripes as piezoelectric blocks. A 180 ∘ domain model gives a better qualitative match to the experimental images. Published by the American Physical Society 2024

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Control Design of Passive Grid-Forming Inverters in Port-Hamiltonian Framework

This article presents a modified dispatchable virtual oscillator control approach for achieving the passivity of gridforming inverters (GFMs), without assuming constant voltage and constant frequency. The proposed control framework utilizes the Port-Hamiltonian (PH) based structure that mimics the behaviors of coupled harmonic oscillators, along with an energy ‘pumpingor-damping’ block and the Control by Interconnection (CbI) technique, to render the inverter passive. Once passivity is achieved, transient stability of the system will be guaranteed. The proposed control framework is composed of three loops: an outer power dispatching loop that generates the voltage and frequency references, a virtual oscillator loop that emulates the spontaneous synchronization of oscillators, and an inductor current loop that maintains lossless interconnection in PH systems. In conclusion, the study shows that the proposed control approach ensures the passivity of GFMs, facilitating the transient stability design of multi-inverter systems, as interconnections of passive systems remain passive and stable.

42 ENGINEERING↗

The structure of the RCAN1:CN complex explains the inhibition of and substrate recruitment by calcineurin

Regulator of calcineurin 1 (RCAN1) is an endogenous inhibitor of the Ser/Thr phosphatase calcineurin (CN). It has been shown that excessive inhibition of CN is a critical factor for Down syndrome and Alzheimer’s disease. Here, we determined RCAN1’s mode of action. Using a combination of structural, biophysical, and biochemical studies, we show that RCAN1 inhibits CN via multiple routes: first, by blocking essential substrate recruitment sites and, second, by blocking the CN active site using two distinct mechanisms. We also show that phosphorylation either inhibits RCAN1-CN assembly or converts RCAN1 into a weak inhibitor, which can be reversed by CN via dephosphorylation. This highlights the interplay between posttranslational modifications in regulating CN activity. Last, this work advances our understanding of how active site inhibition of CN can be achieved in a highly specific manner. Together, these data provide the necessary road map for targeting multiple neurological disorders.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗