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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Phase Field Dislocation Dynamics (PFDD) version 2.x

This disclosure is for version 2.x of a mesoscale model called Phase Field Dislocation Dynamics (PFDD). PFDD is used for investigating deformation in nanoscale (grain sizes of ~300 nm and less) materials, such as metals and alloys. This approach models the motion and interaction of individual defects, namely dislocations, in the material using scalar-valued phase field variables, also called order parameters. The system is evolved through energy minimization thus the model calculates the total energy density in terms of the phase field variables. The energy minimization is completed using the Ginzburg-Landau equation, and is implemented with explicit time integration. The total system energy can be comprised of several terms, including the strain energy (which describes dislocation-dislocation interactions), the energy due to an applied stress (dislocation interactions with the applied stress), and a core/lattice (perfect dislocations) or generalized stacking fault (partial dislocations) energy (described the dislocation core structure). The latter term in particular may vary based on the crystal structure being modeled and is typically informed using lower length scale (e.g., atomistic) approaches, although no such (atomistic) calculations are completed within the PFDD algorithm. This basic formulation was previously reviewed by Los Alamos National Laboratory and released under license number C17113. This previously reviewed version we will henceforth refer to as PFDD v1.0. PFDD v1.0 consisted of 2 codes (one parallel and one serial) plus input files, all written in the C language. This new disclosure is addressing the next versions of the PFDD, versions 2.x. There have been several enhancements of PFDD v1.0, which are described here and included in the attached code, which we will refer to as PFDD v2.0. There are also several new features described here that are either planned or already in process and are expected to be subsequent releases, i.e., v2.1, v2.2, ...v2.x.

Hunter, Abigail↗
DOE OSTI2025

Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H 2 O 2 and O 2 . This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Fleetite, Cu 2 RhIrSb 2 , a New Species of Platinum-Group Mineral from the Miass Placer Zone, Southern Urals, Russia

Fleetite, Cu 2 RhIrSb 2 , a new species of platinum-group mineral (PGM), was discovered intergrown with an Os–Ir–Ru alloy in the Miass Placer Zone (Au–PGE), southern Urals, Russia. A single grain 50 μm across was found. Osmium, ruthenium, and iridium are the main associated minerals; also present are Pt–Fe alloys, laurite, Sb-rich irarsite, Rh-rich tolovkite, kashinite, anduoite, ferronickelplatinum, heazlewoodite, PGE-bearing pentlandite and digenite, as well as micrometric inclusions of forsterite (Fo 93.7 ), chromite–magnesiochromite, and Mg-rich edenite. In reflected light, fleetite is light gray; it is opaque, isotropic, non-pleochroic, and non-bireflectant. We report reflectance values measured in air. A mean of seven point-analyses (wavelength-dispersive spectrometry) gave Cu 13.93, Ni 8.60, Fe 0.10, Ir 28.07, Rh 7.91, Ru 1.96, Sb 39.28, total 99.85 wt.%, corresponding to (Cu 1.41 Ni 0.58 Fe 0.01 ) Σ2.00 (Rh 0.49 Ni 0.36 Ru 0.12 ) Σ0.97 Ir 0.95 Sb 2.08 on the basis of six atoms per formula unit, taking into account the structural results. The calculated density is 10.83 g/cm 3 . Single-crystal X-ray studies show that fleetite is cubic, space group Fdm (#227), a = 11.6682(8) Å, V = 1588.59(19) Å 3 , and Z = 16. A least-squares refinement of X-ray powder-diffraction data gave a = 11.6575(5) Å and V = 1584.22(19) Å 3 . The strongest five reflections in the powder pattern [d in Å(I)(hkl)] are: 6.70(75)(111), 4.13(100)(220), 3.52(30)(311), 2.380(50)(422), 2.064(40)(440). Results of synchrotron micro-Laue diffraction experiments are consistent [a = 11.66(2) Å]. The crystal structure of fleetite was solved and refined to R = 0.0340 based upon 153 reflections with F o > 4σ(F o ). It is isotypic with Pd 11 Bi 2 Se 2 and best described as intermetallic, with all metal atoms in 12-fold coordination. Fleetite and other late exotic phases were formed by reaction of the associated alloy phases with a fluid phase enriched in Sb, As, and S in circulation in the cooling ophiolite source-rock. The mineral is named after Michael E. Fleet (1938–2017) in recognition of his significant contributions to the Earth Sciences.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Chemical Bonding Governs Complex Magnetism in MnPt 5 P

Subtle changes in chemical bonds may result in dramatic revolutions in magnetic properties in solid-state materials. MnPt 5 P, a derivative of the rare-earth-free ferromagnetic MnPt 5 As, was discovered and is presented in this work. Specifically, MnPt 5 P was synthesized, and its crystal structure and chemical composition were characterized by X-ray diffraction as well as energy-dispersive X-ray spectroscopy. Accordingly, MnPt 5 P crystallizes in the layered tetragonal structure with the space group P4/mmm (No. 123), in which the face-shared Mn@Pt 12 polyhedral layers are separated by P layers. In contrast to the ferromagnetism observed in MnPt 5 As, the magnetic properties measurements on MnPt 5 P show antiferromagnetic ordering occurs at ~188 K with a strong magnetic anisotropy in and out of the ab-plane. Moreover, a spin-flop transition appears when a high magnetic field is applied. An A-type antiferromagnetic structure was obtained from the analysis of powder neutron diffraction (PND) patterns collected at 150 and 9 K. Calculated electronic structures imply that hybridization of Mn-3d and Pt-5d orbitals is critical for both the structural stability and observed magnetic properties. Semiempirical molecular orbitals calculations on both MnPt 5 P and MnPt 5 As indicate that the lack of 4p character on the P atoms at the highest occupied molecular orbital (HOMO) in MnPt 5 P may cause the different magnetic behavior in MnPt 5 P compared to MnPt 5 As. The discovery of MnPt 5 P, along with our previously reported MnPt5As, parametrizes the end points of a tunable system to study the chemical bonding which tunes the magnetic ordering from ferromagnetism to antiferromagnetism with the strong spin–orbit coupling (SOC) effect.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Multifunctional Cu 2 TSiS 4 (T = Mn and Fe): Polar Semiconducting Antiferromagnets with Nonlinear Optical Properties

In this work, Cu 2 TSiS 4 (T = Mn and Fe) polycrystalline and single-crystal materials were prepared with high-temperature solid-state and chemical vapor transport methods, respectively. The polar crystal structure (space group Pmn2 1 ) consists of chains of corner-sharing and distorted CuS 4 , Mn/FeS 4 , and SiS 4 tetrahedra, which is confirmed by Rietveld refinement using neutron powder diffraction data, X-ray single-crystal refinement, electron diffraction, energy-dispersive X-ray spectroscopy, and second harmonic generation (SHG) techniques. Magnetic measurements indicate that both compounds order antiferromagnetically at 8 and 14 K, respectively, which is supported by the temperature-dependent (100–2 K) neutron powder diffraction data. Additional magnetic reflections observed at 2 K can be modeled by magnetic propagation vectors k = (1/2,0,1/2) and k = (1/2,1/2,1/2) for Cu 2 MnSiS 4 and Cu 2 FeSiS 4 , respectively. The refined antiferromagnetic structure reveals that the Mn/Fe spins are canted away from the ac plane by about 14°, with the total magnetic moments of Mn and Fe being 4.1(1) and 2.9(1) μ B , respectively. Both compounds exhibit an SHG response with relatively modest second-order nonlinear susceptibilities. Density functional theory calculations are used to describe the electronic band structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Assessing Metal Ion Assignment Accuracy in Protein Data Bank Models via Elemental Spectroscopy

Accurate representation of metal ions in macromolecular structures is critical for chemical interpretation, computational modeling, and machine-learning methods that rely on Protein Data Bank (PDB) entries. However, the elemental identity of metals modeled in crystallographic structures is often inferred indirectly and rarely validated experimentally. Here, we combine Particle Induced X-ray Emission (PIXE) and X-ray Fluorescence Spectroscopy (XRFS) to determine the elemental composition of protein samples used to generate 70 deposited metalloprotein crystal structures. By analyzing the original protein material employed for crystallization, but before the addition of crystallization buffer solutions, we assess whether the modeled metal ions in deposited structures are consistent with experimentally detectable elemental content. We find that in a majority of cases, the metals modeled in the corresponding PDB entries are inconsistent with the metals present in the protein samples before crystallization, or that additional metals are present but not represented in the structural models. Spectroscopic results were integrated with automated crystallographic validation metrics, including real-space Z-difference (RSZD) analysis and systematic rerefinement, to evaluate atomic-number mismatch at metal sites. PIXE and XRFS show strong agreement for dominant elemental signals and provide complementary, scalable approaches for identifying suspect metal assignments. This work does not address physiological or functional metalation but instead highlights a widespread data integrity issue in deposited macromolecular structures, PDB-wide. These results establish an experimentally corroborated link between elemental identity and crystallographic validation metrics, enabling the large-scale detection of chemically inconsistent annotations in structural databases used for computational modeling and machine learning.

Crystallization↗
DOE OSTI2020

Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression

Abstract Background Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. Results Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh ( Sm Bdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34–2.87 µmol/min/mg). The Sm Bdh crystal structure was determined through crystallization with cofactor (NAD + ) and substrate (acetoin) molecules bound in the active site. Active Sm Bdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. Sm Bdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae ( Ec Bdh) enzyme resulted in reduction of Sm Bdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the Ec Bdh to mimic the Sm Bdh structure resulted in ~ 70% increase in its activity. Conclusions This study has demonstrated that Sm Bdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. Sm Bdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.

09 BIOMASS FUELS↗
DOE OSTI2025

The structure and migration of twin boundaries in tetragonal β -Sn: An application of machine learning based interatomic potentials

Although atomistic simulations have contributed significantly to our understanding of twin boundary structure and migration in metals and alloys with hexagonal close packed (HCP) crystal structures, few direct atomistic studies of twinning have been conducted for other types of low symmetry materials, in large part due to a lack of reliable interatomic potentials. In this work, we examine twin boundary structure and migration in a tetragonal material, β-Sn, comparing high resolution Transmission Electron Microscopy (TEM) images of deformation twins in β-Sn to the results of direct atomistic simulations using multiple interatomic potentials. ML-based potentials developed in this work are found to give results consistent with our experimental data, revealing faceted twin boundary structures formed by the nucleation and motion of twinning disconnections. We use bicrystallographic methods in combination with atomistic simulations to analyze the structure, energy and shear coupled migration of observed twin facets in β-Sn. In analogy to Prismatic-Basal (PB/BP) interfaces in HCP metals, we discover low energy asymmetric Prismatic-A-plane (PA/AP) interfaces important to twin growth in β-Sn. Finally, a Moment Tensor Potential (MTP) and Rapid Artificial Neural Network (RANN) interatomic potential suitable for studying twinning and phase transformations in Sn are made publicly available as part of this work.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Thermochemistry of Layered and Two-Dimensional Niobium Carbo-Chalcogenides

Two-dimensional transition metal carbo-chalcogenides (TMCCs) represent a novel class of layered materials with tunable electronic structures and high chemical versatility, making them promising candidates for energy and environmental applications. In this work, the structural and thermochemical properties of a series of TMCCs are investigated. High-temperature oxidative solution calorimetry, conducted at 800 °C in molten sodium molybdate (3Na2O·4MoO3), was used to determine the enthalpies of oxidation and formation from the elements at 25 °C, enabling a comprehensive thermodynamic assessment. Comparison of these enthalpies reveals distinct stability trends across the series. Cu0.67Nb2S2C exhibits the most exothermic oxidation enthalpy, indicating a strong thermodynamic driving force for oxidation and reduced resistance to oxidative degradation. Its positive enthalpy of formation from the elements suggests lower thermodynamic stabilization relative to the other compositions, consistent with the energetic influence of Cu and residual Fe within the Nb–S–C framework. In contrast, delaminated Nb2S2C exhibits poor oxidative stability but a highly exothermic enthalpy of formation, consistent with a defect-rich, metastable structural state rather than enhanced lattice stability. These findings establish correlations between crystal structure and energetic stability, providing insights into the design of robust TMCC-based materials for advanced energy and environmental technologies.

Cassell, Nakeshma [Clemson University]↗
DOE OSTI2024

Ultrafast Yttrium Hydride Chemistry at High Pressures via Non-equilibrium States Induced by an X-ray Free Electron Laser

Controlling the formation and stoichiometric content of the desired phases of materials has become of central interest for a variety of fields. The possibility of accessing metastable states by initiating reactions by X-ray-triggered mechanisms over ultrashort time scales has been enabled by the development of X-ray free electron lasers (XFELs). Utilizing the exceptionally high-brilliance X-ray pulses from the EuXFEL, we report the synthesis of a previously unobserved yttrium hydride under high pressure, along with nonstoichiometric changes in hydrogen content as probed at a repetition rate of 4.5 MHz using time-resolved X-ray diffraction. Furthermore, exploiting non-equilibrium pathways, we synthesize and characterize a hydride in a Weaire–Phelan structure type at pressures as low as 125 GPa, predicted using a crystal structure search, with a hydrogen content of 4.0–5.75 hydrogens per cation, that is enthalpically metastable on the convex hull.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Delocalization of dark and bright excitons in flat-band materials and the optical properties of V2O5

Abstract The simplest picture of excitons in materials with atomic-like localization of electrons is that of Frenkel excitons, where electrons and holes stay close together, which is associated with a large binding energy. Here, using the example of the layered oxide V 2 O 5 , we show how localized charge-transfer excitations combine to form excitons that also have a huge binding energy but, at the same time, a large electron-hole distance, and we explain this seemingly contradictory finding. The anisotropy of the exciton delocalization is determined by the local anisotropy of the structure, whereas the exciton extends orthogonally to the chains formed by the crystal structure. Moreover, we show that the bright exciton goes together with a dark exciton of even larger binding energy and more pronounced anisotropy. These findings are obtained by combining first principles many-body perturbation theory calculations, ellipsometry experiments, and tight binding modelling, leading to very good agreement and a consistent picture. Our explanation is general and can be extended to other materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Correlative chemical and elemental nano-imaging of morphology and disorder at the nacre-prismatic region interface in Pinctada margaritifera

Abstract Understanding biomineralization relies on imaging chemically heterogeneous organic–inorganic interfaces across a hierarchy of spatial scales. Further, organic minority phases are often responsible for emergent inorganic structures from the atomic arrangement of different polymorphs, to nano- and micrometer crystal dimensions, up to meter size mollusk shells. The desired simultaneous chemical and elemental imaging to identify sparse organic moieties across a large field-of-view with nanometer spatial resolution has not yet been achieved. Here, we combine nanoscale secondary ion mass spectroscopy (NanoSIMS) with spectroscopic IR s -SNOM imaging for simultaneous chemical, molecular, and elemental nanoimaging. At the example of Pinctada margaritifera mollusk shells we identify and resolve ~ 50 nm interlamellar protein sheets periodically arranged in regular ~ 600 nm intervals. The striations typically appear ~ 15 µm from the nacre-prism boundary at the interface between disordered neonacre to mature nacre. Using the polymorph distinctive IR-vibrational carbonate resonance, the nacre and prismatic regions are consistently identified as aragonite ( $${\overline{\nu }}_{a}=860$$ ν ¯ a = 860 cm −1 ) and calcite ( $${\overline{\nu }}_{c}=880$$ ν ¯ c = 880 cm −1 ), respectively. We observe previously unreported morphological features including aragonite subdomains encapsulated in extensions of the prism-covering organic membrane and regions of irregular nacre tablet formation coincident with dispersed organics. We also identify a ~ 200 nm region in the incipient nacre region with less well-defined crystal structure and integrated organics. These results show with the identification of the interlamellar protein layer how correlative nano-IR chemical and NanoSIMS elemental imaging can help distinguish different models proposed for shell growth in particular, and how organic function may relate to inorganic structure in other biomineralized systems in general.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Structural insights into photoactivation of plant Cryptochrome-2

Cryptochromes (CRYs) are evolutionarily conserved photoreceptors that mediate various light-induced responses in bacteria, plants, and animals. Plant cryptochromes govern a variety of critical growth and developmental processes including seed germination, flowering time and entrainment of the circadian clock. CRY’s photocycle involves reduction of their flavin adenine dinucleotide (FAD)-bound chromophore, which is completely oxidized in the dark and semi to fully reduced in the light signaling-active state. Despite the progress in characterizing cryptochromes, important aspects of their photochemistry, regulation, and light-induced structural changes remain to be addressed. In this study, we determine the crystal structure of the photosensory domain of Arabidopsis CRY2 in a tetrameric active state. Systematic structure-based analyses of photo-activated and inactive plant CRYs elucidate distinct structural elements and critical residues that dynamically partake in photo-induced oligomerization. Our study offers an updated model of CRYs photoactivation mechanism as well as the mode of its regulation by interacting proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Novel fold of rotavirus glycan-binding domain predicted by AlphaFold2 and determined by X-ray crystallography

The VP8* domain of spike protein VP4 in group A and C rotaviruses, which cause epidemic gastroenteritis in children, exhibits a conserved galectin-like fold for recognizing glycans during cell entry. In group B rotavirus, which causes significant diarrheal outbreaks in adults, the VP8* domain (VP8*B) surprisingly lacks sequence similarity with VP8* of group A or group C rotavirus. Here, by using the recently developed AlphaFold2 for ab initio structure prediction and validating the predicted model by determining a 1.3-Å crystal structure, we show that VP8*B exhibits a novel fold distinct from the galectin fold. This fold with a β-sheet clasping an α-helix represents a new fold for glycan recognition based on glycan array screening, which shows that VP8*B recognizes glycans containing N-acetyllactosamine moiety. Although uncommon, our study illustrates how evolution can incorporate structurally distinct folds with similar functionality in a homologous protein within the same virus genus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure-driven development of a biomimetic rare earth artificial metalloprotein

The 2011 discovery of the first rare earth–dependent enzyme in methylotrophic Methylobacterium extorquens AM1 prompted intensive research toward understanding the unique chemistry at play in these systems. This enzyme, an alcohol dehydrogenase (ADH), features a La 3+ ion closely associated with redox-active coenzyme pyrroloquinoline quinone (PQQ) and is structurally homologous to the Ca 2+ -dependent ADH from the same organism. AM1 also produces a periplasmic PQQ-binding protein, PqqT, which we have now structurally characterized to 1.46-Å resolution by X-ray diffraction. This crystal structure reveals a Lys residue hydrogen-bonded to PQQ at the site analogously occupied by a Lewis acidic cation in ADH. Accordingly, we prepared K 142 A- and K 142 D-PqqT variants to assess the relevance of this site toward metal binding. Isothermal titration calorimetry experiments and titrations monitored by UV–Vis absorption and emission spectroscopies support that K 142 D-PqqT binds tightly (Kd = 0.6 ± 0.2 μM) to La 3+ in the presence of bound PQQ and produces spectral signatures consistent with those of ADH enzymes. These spectral signatures are not observed for WT- or K 142 A-variants or upon addition of Ca 2+ to PQQ ⸦ K 142 D-PqqT. Addition of benzyl alcohol to La 3+ -bound PQQ ⸦ K 142 D-PqqT (but not Ca 2+ -bound PQQ ⸦ K 142 D-PqqT, or La 3+ -bound PQQ ⸦ WT-PqqT) produces spectroscopic changes associated with PQQ reduction, and chemical trapping experiments reveal the production of benzaldehyde, supporting ADH activity. By creating a metal binding site that mimics native ADH enzymes, we present a rare earth-dependent artificial metalloenzyme primed for future mechanistic, biocatalytic, and biosensing applications.

Science & Technology - Other Topics↗
DOE OSTI2025

Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition

Ethanolamine signaling through the transmembrane quorum-sensing receptor CqsR influencesVibrio choleraeniche recognition and host colonization. In this study, we present a comprehensive structure-function analysis of CqsR. Specifically, we have determined X-ray crystal structures of the CqsR periplasmic domain bound to the signaling agonist ethanolamine and its analogs, serinol and L-alaninol, as well as the ligand-free (apo) form of CqsR. The periplasmic ligand-binding domain of CqsR is a Cache domain, the most prevalent extracellular sensory module in prokaryotes. Our findings provide a rare structural comparison of ligand-bound and unbound states of a Cache domain receptor. Coupled with thermodynamic binding assays and genetic analyses, these structures elucidate the molecular basis of CqsR ligand specificity. This study not only advances the understanding of Cache domain function but also informs the identification of ligands for orphan Cache receptors and the rational design of signaling agonists and antagonists. Lastly, we discuss ligand-induced conformational changes in the CqsR Cache domains and explore the potential for the existence of additional regulatory ligands.

Microbiology↗
DOE OSTI2021

Defining the Structural Stability Field of Disordered Fluorite Oxides

Fluorite-structured oxides constitute an important class of materials for energy technologies. Despite their high level of structural symmetry and simplicity, these materials can accommodate atomic disorder without losing crystallinity, making them indispensable for uses in environments with high temperature, changing chemical compositions, or intense radiation fields. In this contribution, we present a set of simple rules that predict whether a compound may adopt a disordered fluorite structure. This approach is closely aligned with Pauling’s rules for ionic crystal structures and Goldschmidt’s rules for ionic substitution.

36 MATERIALS SCIENCE↗
DOE OSTI2021

The Ephb2 Receptor Uses Homotypic, Head-to-Tail Interactions within Its Ectodomain as an Autoinhibitory Control Mechanism

The Eph receptor tyrosine kinases and their ephrin ligands direct axon pathfinding and neuronal cell migration, as well as mediate many other cell–cell communication events. Their dysfunctional signaling has been shown to lead to various diseases, including cancer. The Ephs and ephrins both localize to the plasma membrane and, upon cell–cell contact, form extensive signaling assemblies at the contact sites. The Ephs and the ephrins are divided into A and B subclasses based on their sequence conservation and affinities for each other. The molecular details of Eph–ephrin recognition have been previously revealed and it has been documented that ephrin binding induces higher-order Eph assemblies, which are essential for full biological activity, via multiple, distinct Eph–Eph interfaces. One Eph–Eph interface type is characterized by a homotypic, head-to-tail interaction between the ligand-binding and the fibronectin domains of two adjacent Eph molecules. While the previous Eph ectodomain structural studies were focused on A class receptors, we now report the crystal structure of the full ectodomain of EphB2, revealing distinct and unique head-to-tail receptor–receptor interactions. The EphB2 structure and structure-based mutagenesis document that EphB2 uses the head-to-tail interactions as a novel autoinhibitory control mechanism for regulating downstream signaling and that these interactions can be modulated by posttranslational modifications.

59 BASIC BIOLOGICAL SCIENCES↗