Search NASA⌕ Search

SEARCH · Search NASA

Results for “Structural variant”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Sn 0.24 WO 3 hexagonal tungsten bronze prepared via the metal chloride route

In this work, we report the synthesis of Sn 0.24 WO 3 single crystals via an alternative, less well-known, solid-state synthetic approach that involves the use of tin chloride as a starting material. The compound adopts an unusual variant of the hexagonal tungsten bronze structure in space group P6/mmm (a = 7.4264(7) Å and c = 3.7843(4) Å) with a previously unreported distribution of Sn cations, disordered over two distinct sites in the tunnels. Sn 0.24 WO 3 shows no signs of superconductivity down to 170 mK and exhibits weakly-metallic conducting behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture

Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Materializing rival ground states in the barlowite family of kagome magnets: quantum spin liquid, spin ordered, and valence bond crystal states

The spin- 1 2 kagome antiferromagnet is considered an ideal host for a quantum spin liquid ground state. We find that when the bonds of the kagome lattice are modulated with a periodic pattern, new quantum ground states emerge. Newly synthesized crystalline barlowite (Cu 4 (OH) 6 FBr) and Zn-substituted barlowite demonstrate the delicate interplay between singlet states and spin order on the spin- 1 2 kagome lattice. Comprehensive structural measurements demonstrate that our new variant of barlowite maintains hexagonal symmetry at low temperatures with an arrangement of distorted and undistorted kagome triangles, for which numerical simulations predict a pinwheel va- lence bond crystal (VBC) state instead of a quantum spin liquid (QSL). The presence of interlayer spins eventually leads to an interesting pinwheel q=0 magnetic order. Partially Zn-substituted bar- lowite (Cu 3.44 Zn 0.56 (OH) 6 FBr) has an ideal kagome lattice and shows QSL behavior, indicating a surprising robustness of the QSL against interlayer impurities. The magnetic susceptibility is simi- lar to that of herbertsmithite, even though the Cu 2+ impurities are above the percolation threshold for the interlayer lattice and they couple more strongly to the nearest kagome moment. This system is a unique playground displaying QSL, VBC, and spin order, furthering our understanding of these highly competitive quantum states.

36 MATERIALS SCIENCE↗
DOE OSTI2026

A conserved glycan motif induces broadly reactive functional antibodies against the zoonotic pathogen Streptococcus suis

Streptococcus suis is a largely neglected but emerging bacterial zoonotic pathogen of global concern for animal welfare, antibiotic resistance development, and human health. No effective vaccines are now available. Here, we identified and characterized the function and structure of two cell wall polysaccharide variants in pathogenic S. suis strains using genetic deletion and (heterologous) complementation, lectin staining, glycan composition analysis, and specialized NMR spectroscopy. Both glycan variants were anionic polymers that differed in the presence of glucose in the side chain as a result of allelic variation in a glycosyltransferase gene. Deletion of this variable glycosyltransferase revealed an identical glycan “core” and affected S. suis morphology and lysozyme resistance. Immunization of pigs with this core domain elicited antibodies that recognized antigenically diverse pathogenic S. suis strains and induced complement deposition on encapsulated pathogenic S. suis strains. This study provides valuable insights for developing next-generation glycoconjugate vaccines, whereby a single-glycan target could protect against the emerging zoonotic pathogen S. suis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Reaching High Momenta using Distillation

We present a study of the use of a momentum-smeared variant of distillation for studying the structure of baryons at high momentum from lattice QCD. In particular, we focus on the dispersion relation and the nucleon currents and compare with results for the nucleon at rest.

Richards, David↗
DOE OSTI2022

Deamidation of the human eye lens protein $\gamma$S-crystallin accelerates oxidative aging

Cataract, a clouding of the eye lens from protein precipitation, affects millions of people every year. The lens proteins, the crystallins, show extensive post-translational modifications (PTMs) in cataractous lenses. The most common PTMs, deamidation and oxidation, promote crystallin aggregation; however, it is not clear precisely how these PTMs contribute to crystallin insolubilization. Here, we report six crystal structures of the lens protein γS-crystallin (γS): one of the wild-type and five of deamidated γS variants, from three to nine deamidation sites, after sample aging. The deamidation mutations do not change the overall fold of γS; however, increasing deamidation leads to accelerated disulfide-bond formation. Addition of deamidated sites progressively destabilized protein structure, and the deamidated variants display an increased propensity for aggregation. Here these results suggest that the deamidated variants are useful as models for accelerated aging; the structural changes observed provide support for redox activity of γS-crystallin in the lens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microsecond dynamics control the HIV-1 Envelope conformation

The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the structures of various Env conformations, microsecond timescale dynamics have not been studied experimentally. Here, we used time-resolved, temperature-jump small-angle x-ray scattering to monitor structural rearrangements in an HIV-1 Env SOSIP ectodomain construct with microsecond precision. In two distinct Env variants, we detected a transition that correlated with known Env structure rearrangements with a time constant in the hundreds of microseconds range. A previously unknown structural transition was also observed, which occurred with a time constant below 10 μs, and involved an order-to-disorder transition in the trimer apex. Using this information, we engineered an Env SOSIP construct that locks the trimer in the prefusion closed state by connecting adjacent protomers via disulfides. Our findings show that the microsecond timescale structural dynamics play an essential role in controlling the Env conformation with impacts on vaccine design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Chirality Transfer to the Magnetic Sublattice in the Hybrid Perovskite (R)-/(S)-3-Fluoropyrrolidinium Copper(II) Chloride

Incorporating chiral organic cations into organic–inorganic hybrid materials has been shown to enable the inorganic sublattice to display chiroptical properties. We report a new two-dimensional magnetic (S = 1/2) chiral metal halide perovskite, (R)- and (S)-(C 4 H 9 FN) 2 CuCl 4 (where (C 4 H 9 FN) + is 3-fluoropyrrolidinium), which consists of Cu–Cl inorganic layers separated by (C 4 H 9 FN) + organic cations. The presence of the chiral (C 4 H 9 FN) + organic cation induces the formation of chiral magnetic order, even though the inorganic sublattice itself is nearly structurally centrosymmetric. We also report the racemic variant, containing an equal amount of (R)- and (S)- cations, which shows no evidence of chiral magnetic order. When the magnetic susceptibility is measured perpendicular to the inorganic Cu–Cl layer propagation direction, an antiferromagnetic phase transition at Néel temperature T N = 2.23 K is observed in both the chiral and racemic materials, and the existence of the magnetic phase transition is supported by specific heat capacity measurements. Field-induced magnetic chirality is observed through the existence of a second-order magnetoelectric effect in the chiral variant, while no magnetoelectric signal is observed for the racemic material, indicating the absence of magnetic chirality. Our findings demonstrate that materials exhibiting chiral magnetic order can be created through the incorporation of a chiral cation into an organic–inorganic hybrid magnetic material, potentially allowing for the design of tailored materials that combine chiral magnetism with other desirable optical and electronic properties that come from structural chirality.

Cations↗
DOE OSTI2023

Theory of electric, magnetic, and toroidal polarizations in crystalline solids with applications to hexagonal lonsdaleite and cubic diamond

Multipolar order in bulk crystalline solids is characterized by multipole densities-denoted as polarizations in this work-that cannot be cleanly defined using the concepts of classical electromagnetism. Here we use group theory to overcome this difficulty and present a systematic study of electric, magnetic, and toroidal multipolar order in crystalline solids. Based on our symmetry analysis, we identify five categories of polarized matter, each of which is characterized by distinct features in the electronic band structure. For example, Rashba spin splitting in electropolar bulk materials like wurtzite represents the electric dipolarization in these materials. We also develop a general formalism of indicators for individual multipole densities that provide a physical interpretation and quantification of multipolar order. Our work clarifies the relation between patterns of localized multipoles and macroscopic multipole densities they give rise to. To illustrate the general theory, we discuss its application to polarized variants of hexagonal lonsdaleite and cubic diamond structures. In conclusion, our work provides a general framework for classifying and expanding current understanding of multipolar order in complex materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins

The human metapneumovirus (hMPV) fusion (F) protein is essential for viral entry and is a key target of neutralizing antibodies and vaccine development. The prefusion conformation is thought to be the optimal vaccine antigen, but previously described prefusion F proteins expressed poorly and were not well stabilized. Here, we use structures of hMPV F to guide the design of 42 variants containing stabilizing substitutions. Through combinatorial addition of disulfide bonds, cavity-filling substitutions, and improved electrostatic interactions, we describe a prefusion-stabilized F protein (DS-CavEs2) that expresses at 15mg/L and has a melting temperature of 71.9°C. Crystal structures of two prefusion-stabilized hMPV F variants reveal that antigenic surfaces are largely unperturbed. Importantly, immunization of mice with DS-CavEs2 elicits significantly higher neutralizing antibody titers against hMPV A1 and B1 viruses than postfusion F. The improved properties of DS-CavEs2 will advance the development of hMPV vaccines and the isolation of therapeutic antibodies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

HIV-1 protease inhibitors with a P1 phosphonate modification maintain potency against drug-resistant variants by increased interactions with flap residues

Protease inhibitors are the most potent antivirals against HIV-1, but they still lose efficacy against resistant variants. Improving the resistance profile is key to developing more robust inhibitors, which may be promising candidates for simplified next-generation antiretroviral therapies. Here, in this study, we explored analogs of darunavir with a P1 phosphonate modification in combination with increasing size of the P1′ hydrophobic group and various P2′ moieties to improve potency against resistant variants. The phosphonate moiety substantially improved potency against highly mutated and resistant HIV-1 protease variants, but only when combined with more hydrophobic moieties at the P1′ and P2′ positions. Phosphonate analogs with a larger hydrophobic P1′ moiety maintained excellent antiviral potency against a panel of highly resistant HIV-1 variants, with significantly improved resistance profiles. The cocrystal structures indicate that the phosphonate moiety makes extensive hydrophobic interactions with the protease, especially with the flap residues. Many residues involved in these protease-inhibitor interactions are conserved, enabling the inhibitors to maintain potency against highly resistant variants. These results highlight the need to balance inhibitor physicochemical properties by simultaneous modification of chemical groups to further improve resistance profiles.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Serodominant SARS-CoV-2 Nucleocapsid Peptides Map to Unstructured Protein Regions

The SARS-CoV-2 nucleocapsid (N) protein is highly immunogenic, and anti-N antibodies are commonly used as markers for prior infection. While several studies have examined or predicted the antigenic regions of N, these have lacked consensus and structural context. Using COVID-19 patient sera to probe an overlapping peptide array, we identified six public and four private epitope regions across N, some of which are unique to this study. We further report the first deposited X-ray structure of the stable dimerization domain at 2.05 Å as similar to all other reported structures. Structural mapping revealed that most epitopes are derived from surface-exposed loops on the stable domains or from the unstructured linker regions. An antibody response to an epitope in the stable RNA binding domain was found more frequently in sera from patients requiring intensive care. Since emerging amino acid variations in N map to immunogenic peptides, N protein variation could impact detection of seroconversion for variants of concern.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

30S subunit recognition and G1405 modification by the aminoglycoside-resistance 16S ribosomal RNA methyltransferase RmtC

Acquired ribosomal RNA (rRNA) methylation has emerged as a significant mechanism of aminoglycoside resistance in pathogenic bacterial infections. Modification of a single nucleotide in the ribosome decoding center by the aminoglycoside-resistance 16S rRNA (m 7 G1405) methyltransferases effectively blocks the action of all 4,6-deoxystreptamine ring-containing aminoglycosides, including the latest generation of drugs. To define the molecular basis of 30S subunit recognition and G1405 modification by these enzymes, we used a S-adenosyl-L-methionine analog to trap the complex in a postcatalytic state to enable determination of a global 3.0 Å cryo-electron microscopy structure of the m 7 G1405 methyltransferase RmtC bound to the mature Escherichia coli 30S ribosomal subunit. This structure, together with functional analyses of RmtC variants, identifies the RmtC N-terminal domain as critical for recognition and docking of the enzyme on a conserved 16S rRNA tertiary surface adjacent to G1405 in 16S rRNA helix 44 (h44). To access the G1405 N7 position for modification, a collection of residues across one surface of RmtC, including a loop that undergoes a disorder-to order transition upon 30S subunit binding, induces significant distortion of h44. This distortion flips G1405 into the enzyme active site where it is positioned for modification by two almost universally conserved RmtC residues. Further, these studies expand our understanding of ribosome recognition by rRNA modification enzymes and present a more complete structural basis for future development of strategies to inhibit m 7 G1405 modification to resensitize bacterial pathogens to aminoglycosides.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Role of dislocations on martensitic transformation temperatures and microstructure: A molecular dynamics study

Microstructure and defects strongly affect martensitic transformations in metallic alloys. Significant progress has been made in understanding the atomic-level processes that control the role of grain boundaries and precipitates in these solid-to-solid phase transformations. Yet, the role of dislocations and their structures on martensitic transformation temperature and the resulting microstructure remains unclear. Therefore, we used large-scale molecular dynamics simulations to study the forward and reverse transformation of a martensitic material modeled after Ni63Al37 under cyclic thermal loading. The simulations reveal that dislocations in the austenite phase act as one-dimensional seeds for the martensite phase, which is present at temperatures significantly above the martensite start value. We find a reduction in the dislocation density during cyclic thermal loading, which results in the increase in martensite and austenite transition temperatures, in agreement with experiments. Importantly, we extracted a critical martensitic nuclei size for developing stable domains and found that relatively low dislocation densities are needed to grow independent martensitic variants resulting in a multi-domain structure.

Physics↗
DOE OSTI2025

Asymmetric loading of TnsE regulates Tn7 targeting of DNA replication structures

Abstract Tn7 transposable elements are known for their sophisticated target-site selection mechanisms. For the prototypical Tn7 element, dedicated transposon-encoded proteins direct insertions to either a conserved site in the chromosome or replicating DNA structures in conjugal plasmids, ensuring the vertical and horizontal spread of the element. While the pathway targeting the attTn7 site in the bacterial chromosome has been extensively studied, the pathway targeting DNA replication structures remains poorly understood. We have used an integrative structural biology approach to elucidate how the Tn7-encoded protein TnsE recognizes replication sites. Using native mass spectrometry, we found that TnsE forms 1:1 and 2:1 (TnsE:DNA) complexes on 3′-recessed DNA, with gain-of-function TnsE variants favoring the formation of 2:1 complexes. Structural characterization confirms that two TnsE molecules bind to DNA with the C-terminal domain of the protein recognizing duplex DNA, leaving the N-terminal domain to impose DNA substrate specificity and recruit the core transposition machinery. Collectively, our work is consistent with a model where TnsE-mediated target-site selection relies on the formation of an asymmetric TnsE:DNA complex to recruit the Tn7 transposase to DNA replication structures.

Biochemistry & Molecular Biology↗
DOE OSTI2025

When more data hurts: Optimizing data coverage while mitigating diversity-induced underfitting in an ultrafast machine-learned potential

Machine-learned interatomic potentials (MLIPs) are becoming an essential tool in materials modeling. However, optimizing the generation of training data used to parametrize the MLIPs remains a significant challenge. This is because MLIPs can fail when encountering local environments too different from those present in the training data. The difficulty of determining a priori the environments that will be encountered during molecular dynamics simulation necessitates diverse, high-quality training data. Here, this study investigates how training data diversity affects the performance of MLIPs using the Ultra-Fast force field (UF 3 ) to model amorphous silicon nitride. We employ expert and autonomously generated data to create the training data and fit four force field variants to subsets of the data. Our findings reveal a critical balance in training data diversity: insufficient diversity hinders generalization, while excessive diversity can exceed the MLIP's learning capacity, reducing simulation accuracy. Specifically, we found that the UF 3 variant trained on a subset of the training data, in which nitrogen-rich structures were removed, offered vastly better prediction and simulation accuracy than any other variant. By comparing these UF 3 variants, we highlight the nuanced requirements for creating accurate MLIPs, emphasizing the importance of application-specific training data to achieve optimal performance in modeling complex material behaviors.

ab initio molecular dynamics↗
DOE OSTI2025

Cooling-Rate-Driven Polymorphism and Vacancy Ordering in Ce 2 MnGe 6 Intergrowth Phases

Intergrowth phases in intermetallic systems provide a compelling framework for investigating structure–property relationships as a function of crystallographic subunit stacking. In this study, we examine the influence of Mn vacancy ordering on subunit stacking and reassign the structure of Ce 2 MnGe 6 to a monoclinic C2/m space group (a = 8.3486(17) Å, b = 8.6181(18) Å, c = 10.778(2) Å, β = 101.17(2)°). Additionally, we report a monoclinic polymorph of the Ln 2 MGe 6 family characterized as a tripled c-axis supercell derivative of monoclinic Ce 2 MnGe 6 , 3×c-Ce 2 MnGe 6 (a = 8.3482(16) Å, b = 8.6179(18) Å, c = 31.813(6) Å, β = 93.763(7)°). This polymorph emerges under rapid cooling conditions during the synthesis and offers insight into the structural relationship between the orthorhombic and monoclinic variants of the Ln 2 MGe 6 phases. Notably, the supercell form of Ce 2 MnGe 6 (3×c-Ce 2 MnGe 6 ) exhibits increased electrical resistivity and suggests enhanced Zintl-like behavior, potentially indicating greater thermodynamic stability relative to the parent monoclinic phase.

36 MATERIALS SCIENCE↗