Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Crystal structures”

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 1,387 records · Page 77

Stabilization of glucose-6-phosphate dehydrogenase oligomers enhances catalytic activity and stability of clinical variants

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a genetic trait that can cause hemolytic anemia. To date, over 150 nonsynonymous mutations have been identified in G6PD, with pathogenic mutations clustering near the dimer and/or tetramer interface and the allosteric NADP + -binding site. Recently, our lab identified a small molecule that activates G6PD variants by stabilizing the allosteric NADP + and dimer complex, suggesting therapeutics that target these regions may improve structural defects. Here, we elucidated the connection between allosteric NADP + binding, oligomerization, and pathogenicity to determine whether oligomer stabilization can be used as a therapeutic strategy for G6PD deficiency (G6PD def ). We first solved the crystal structure for G6PD K403Q , a mutant that mimics the physiological acetylation of wild-type G6PD in erythrocytes and demonstrated that loss of allosteric NADP + binding induces conformational changes in the dimer. These structural changes prevent tetramerization, are unique to Class I variants (the most severe form of G6PD def ), and cause the deactivation and destabilization of G6PD. We also introduced nonnative cysteines at the oligomer interfaces and found that the tetramer complex is more catalytically active and stable than the dimer. Furthermore, stabilizing the dimer and tetramer improved protein stability in clinical variants, regardless of clinical classification, with tetramerization also improving the activity of G6PD K403Q and Class I variants. These findings were validated using enzyme activity and thermostability assays, analytical size-exclusion chromatography (SEC), and SEC coupled with small-angle X-ray scattering (SEC-SAXS). Taken together, our findings suggest a potential therapeutic strategy for G6PD def and provide a foundation for future drug discovery efforts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural basis for the allosteric modulation of rhodopsin by nanobody binding to its extracellular domain

Rhodopsin is a prototypical G protein-coupled receptor (GPCR) critical for vertebrate vision. Research on GPCR signaling states has been facilitated using llama-derived nanobodies (Nbs), some of which bind to the intracellular surface to allosterically modulate the receptor. Extracellularly binding allosteric nanobodies have also been investigated, but the structural basis for their activity has not been resolved to date. Here, we report a library of Nbs that bind to the extracellular surface of rhodopsin and allosterically modulate the thermodynamics of its activation process. Crystal structures of Nb2 in complex with native rhodopsin reveal a mechanism of allosteric modulation involving extracellular loop 2 and native glycans. Nb2 binding suppresses Schiff base deprotonation and hydrolysis and prevents intracellular outward movement of helices five and six – a universal activation event for GPCRs. Nb2 also mitigates protein misfolding in a disease-associated mutant rhodopsin. Our data show the power of nanobodies to modulate the photoactivation of rhodopsin and potentially serve as therapeutic agents for disease-associated rhodopsin misfolding.

59 BASIC BIOLOGICAL SCIENCES↗

Ferroic phase transitions and magnetoelectric coupling in cobalt doped BaTiO 3

Magnetoelectric (ME) materials exhibit interesting physics with cross coupling between ferroelectric and magnetic order parameters and thus strong potential to be utilized in memory, spintronics and other multifunctional electronic/magnetic devices. Doping of suitable transition metals in ferroelectrics can induce magnetism and ME coupling and modify the physical properties. Here, we report the structural, electronic, magnetic and ME coupling of 3.5, 5 and 7.5 mol% cobalt doped BaTiO 3 (BTO) ceramics. X-ray diffraction and Raman spectroscopy indicate that the samples are single phase having a tetragonal crystal structure with P4mm symmetry. The tetragonality ratio is found to decrease with increasing cobalt content. We observed a Fano-like asymmetric peak in the [A 1 (LO 1 )] Raman mode at ~173 cm -1 in all the cobalt doped BTO samples. The cobalt dopants are shown to be uniformly distributed throughout the surface of the samples. We observed a lowering of the ferroelectric transition temperature and increasing diffusivity parameter with increasing cobalt concentration. The electrical properties of all the samples have been investigated in detail by impedance spectroscopy and ac conductivity studies before and after the ferroelectric phase transitions. All the samples show hysteretic ferroelectric behavior with a clear saturation state that decreases with increasing cobalt content. The observed ferroelectricity in these samples is intrinsic in nature. The 3.5% cobalt doped BTO sample exhibits paramagnetic behavior whereas the 5 and 7.5% cobalt doped BTO samples show ferromagnetic ordering below 43 K. The 7.5% cobalt doped BTO samples show significant ME coupling.

36 MATERIALS SCIENCE↗

Local structure of Sr 2 CuO 3.3 , a 95 K cuprate superconductor without CuO 2 planes

The local structure of the highly “overdoped” 95 K superconductor Sr 2 CuO 3.3 determined by Cu K X-ray absorption fine structure (XAFS) at 62 K in magnetically oriented samples shows that 1) the magnetization is perpendicular to the c axis; 2) at these levels of precision the Cu sublattice is tetragonal in agreement with the crystal structure; the O sublattice has 3) continuous -Cu-O- chains that orient perpendicular to an applied magnetic field; 4) approximately half-filled -Cu-O- chains that orient parallel to this field; 5) a substantial number of apical O vacancies; 6) O ions at some apical positions with expanded Cu-O distances; and 7) interstitial positions that imply highly displaced Sr ions. These results contradict the universally accepted features of cuprates that require intact CuO 2 planes, magnetization along the c axis, and a termination of the superconductivity when the excess charge on the CuO 2 Cu ions exceeds 0.27. These radical differences in charge and structure demonstrate that this compound constitutes a separate class of Cu-O–based superconductors in which the superconductivity originates in a different, more complicated structural unit than CuO 2 planes while retaining exceptionally high transition temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Tight-Binding-Based Method for Simulations of Complex Materials with Accompanying Database

The NRL-Tight-Binding (NRL-TB) method has been applied successfully to many monatomic, binary, and a few ternary systems. The method consists of a fit to Density Functional Theory (DFT) results and has transferability beyond the fitted DFT database including performing tight-binding molecular dynamics simulations. We are working on a new website with a detailed guide of how to use the method in performing the fit to DFT results (Fitting Code) and obtaining non-orthogonal TB parameters expressed in a polynomial form as environment-dependent Slater-Koster parameters (on-site terms), and neighbor distance-dependent Hamiltonian and Overlap terms. These parameters are then used in a Static Code to verify or make predictions for large systems often beyond the computational capabilities of standard DFT codes. Our starting point was a website developed at NRL some years ago which NRL no longer supports. We have now been augmenting that website with new examples of expanding the original capabilities of the method such as incorporating in the codes f-electron states. Our website (esd.cos.gmu.edu/tb) contains two separate branches: One named NRL-TB with the full documentation of the method including source codes and examples. The other branch, named ESD-dB, is a library of electronic structure calculations for all the monatomic elements (a subset of the elements also found in a recent book by the author of this proposal. See reference 22) and an approximately 700 hundred compounds in specific crystal structures. We discuss below the progress made so far in improving and expanding the capabilities of our TB method and the plans for further extensions of our approach.

36 MATERIALS SCIENCE↗

Nanoparticle Superlattices through Template-Encoded DNA Dendrimers

The chemical interactions that lead to the emergence of hierarchical structures are often highly complex and difficult to program. In this paper, the synthesis of a series of superlattices based upon 30 different structurally reconfigurable DNA dendrimers is reported, each of which presents a well-defined number of single-stranded oligonucleotides (i.e., sticky ends) on its surface. Such building blocks assemble with complementary DNA-functionalized gold nanoparticles (AuNPs) to yield five distinct crystal structures, depending upon choice of dendrimer and defined by phase symmetry. These DNA dendrimers can associate to form micelle-dendrimers, whereby the extent of association can be modulated based upon surfactant concentration and dendrimer length to produce a low-symmetry Ti5Ga4-type phase that has yet to be reported in the field of colloidal crystal engineering. Taken together, colloidal crystals that feature three different types of particle bonding interactions.template-dendron, dendrimer-dendrimer, and DNA-modified AuNP-dendrimer.are reported, illustrating how sequence-defined recognition and dynamic association can be combined to yield complex hierarchical materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular and structural basis of olfactory sensory neuron axon coalescence by Kirrel receptors

Projections from sensory neurons of olfactory systems coalesce into glomeruli in the brain. The Kirrel receptors are believed to homodimerize via their ectodomains and help separate sensory neuron axons into Kirrel2- or Kirrel3-expressing glomeruli. Here, we present the crystal structures of homodimeric Kirrel receptors and show that the closely related Kirrel2 and Kirrel3 have evolved specific sets of polar and hydrophobic interactions, respectively, disallowing heterodimerization while preserving homodimerization, likely resulting in proper segregation and coalescence of Kirrel-expressing axons into glomeruli. We show that the dimerization interface at the N-terminal immunoglobulin (IG) domains is necessary and sufficient to create homodimers and fail to find evidence for a secondary interaction site in Kirrel ectodomains. Furthermore, we show that abolishing dimerization of Kirrel3 in vivo leads to improper formation of glomeruli in the mouse accessory olfactory bulb as observed in Kirrel3 –/– animals. Our results provide evidence for Kirrel3 homodimerization controlling axonal coalescence.

59 BASIC BIOLOGICAL SCIENCES↗

Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations

Abstract Molecular analysis of interactions between IgE antibody and allergen allows the structural basis of IgE recognition to be defined. Human IgE (hIgE) epitopes of respiratory lipocalin allergens, including Can f 1, remain elusive due to a lack of IgE‐allergen complexes. This study aims to map the structure of allergenic epitopes on Can f 1. The fragment antigen‐binding (Fab) regions of Can f 1 specific human IgE monoclonal antibodies (hIgE mAb) were used to determine the structures of IgE epitopes. Epitope mutants were designed to target Can f 1 epitopes. Immunoassays and a human FcεRIαtransgenic mouse model of passive anaphylaxis in vivo were used to assess the functional activity of epitope mutants. Crystal structures of natural or recombinant Can f 1 complexed with two hIgE mAb 1J11 and 12F3 Fabs, respectively, were determined. The hIgE mAb bound to two partially overlapping epitopes and recognized two different Can f 1 conformations. The hIgE mAb 12F3 showed an unusual mode of binding by protruding its heavy chain CDR3 inside the Can f 1 calyx. Epitope mutants generated based on the structural analyses displayed a 64%–89% reduction in IgE antibody binding and failed to induce passive anaphylaxis in a human FcεRIαtransgenic mouse model. In summary, the structures of Can f 1‐hIgE Fab complexes revealed two unique and partially overlapping epitopes on Can f 1. The modification of the identified IgE epitopes provides a pathway for the design of hypoallergens to treat dog allergies.

Biochemistry & Molecular Biology↗

A snapshot of high-entropy alloy processing techniques and their effects on resulting mechanical properties

High-entropy alloys (HEAs) exhibit exceptional strength, corrosion resistance, and thermal stability, making them promising candidates for nuclear, aerospace, and other extreme applications. While most prior work has focused on compositional design, manufacturing techniques themselves can alter microstructure and mechanical properties as dramatically as alloy chemistry. This review compiles and compares the effects of processing routes—including arc melting, induction melting, mechanical alloying with spark plasma sintering, and additive manufacturing—on the structure and properties of HEAs. Quantitative comparisons highlight, for example, that SPS-processed alloys can achieve ∼20–45 % higher yield and tensile strength than arc-melted counterparts, while Bridgman solidification produces nearly single-crystal structures with elongation to failure exceeding 80 %. Additive manufacturing routes such as selective laser melting offer fine microstructures but also introduce anisotropy and porosity, leading to yield strengths spanning 100–600 MPa for the same composition. By synthesizing such results, this review provides actionable insight into how processing routes interact with HEA core effects (high entropy, lattice distortion, sluggish diffusion, and cocktail effect) to determine performance, thereby offering a practical guide for optimizing manufacturing strategies.

36 MATERIALS SCIENCE↗

Lattice distortions and the metal–insulator transition in pure and Ti-substituted Ca 3 Ru 2 O 7

Here, we report pair distribution function studies on the relationship between the metal–insulator transition (MIT) and lattice distortions in pure and Ti-substituted bilayer Ca 3 Ru 2 O 7 . Structural refinements performed as a function of temperature, magnetic field and length scale reveal the presence of lattice distortions not only within but also orthogonal to the bilayers. Because of the distortions, the local and average crystal structure differ across a broad temperature region extending from room temperature to temperatures below the MIT. The coexistence of distinct lattice distortions is likely to be behind the marked structural flexibility of Ca 3 Ru 2 O 7 under external stimuli. This observation highlights the ubiquity of lattice distortions in an archetypal Mott system and calls for similar studies on other families of strongly correlated materials.

36 MATERIALS SCIENCE↗

Octahedral rotations in Ruddlesden-Popper layered oxides under pressure from first principles

The combination of reduced dimensionality and tunable structural distortions in layered perovskite oxides makes these materials ideal platforms for designing novel properties and functionalities. One example is hybrid improper ferroelectricity in n = 2 Ruddlesden-Popper oxides, where the combination of a layered crystal structure and rotations of the metal-oxide octahedra break symmetry and induce a polarization. Precisely controlling the octahedral rotation distortions, for example by the application of hydrostatic pressure, provides a pathway to tune and optimize the properties of these materials. Here we combine group theoretic methods, density functional theory calculations, and Landau theory analysis to investigate how octahedral rotations respond to pressure in the hybrid improper ferroelectrics Sr 3 Zr 2 O 7 , Ca 3 Ti 2 O 7 , and Sr 3 Sn 2 O 7 . We find that factors that are known to control the pressure response of ABO 3 perovskites—the formal charge of the A- and B-site cations, tolerance factor, and B-site chemistry—also impact the pressure response of these layered perovskites. We also show that coupling between the octahedral rotation and strain order parameters plays a key role in determining the overall pressure response. Despite some similarities, we find that these layered perovskites display a distinct pressure response compared to their ABO 3 perovskite analogs. By identifying trends and underlying mechanisms that control octahedral rotations in Ruddlesden-Popper oxides under pressure, this work lays the foundation for tailoring the structure and properties of these materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Ferroelectric switching pathways and domain structure of SrBi 2 ⁢(Ta,Nb) 2 ⁢O 9 from first principles

Several families of layered perovskite oxide ferroelectrics exhibit a coupling between polarization and structural order parameters, such as octahedral rotation distortions. This coupling provides opportunities for novel electric field-based manipulation of material properties, and it also stabilizes complex domain patterns and domain-wall vortices. Among layered perovskites with such coupled orders, the Aurivillius-phase oxides SrBi 2 ⁢B 2 ⁢O 9 (B = Ta,Nb) are well-known for their excellent room-temperature ferroelectric performance. This work combines group theoretic analysis with density functional theory calculations to examine the ferroelectric switching processes of SrBi2⁢B2⁢O9. Low-energy two-step ferroelectric switching paths are identified, with polarization reversal facilitated by structural order-parameter rotations. Analysis of the domain structure reveals how the relative energetics of the coupled order parameters translates into a network of several distinct domain-wall types linked by domain-wall vortex structures. Comparisons are made between the ferroelectric switching and domain structure of SrBi 2 ⁢B 2 ⁢O 9 and those of the layered n = 2 Ruddlesden-Popper hybrid improper ferroelectrics. The results provide insight into how ferroelectric properties may be optimized by engineering the complex crystal structures of Aurivillius-phase oxides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Functional Characterization and Structural Insights Into Stereoselectivity of Pulegone Reductase in Menthol Biosynthesis

Monoterpenoids are the main components of plant essential oils and the active components of some traditional Chinese medicinal herbs like Mentha haplocalyx Briq ., Nepeta tenuifolia Briq ., Perilla frutescens (L.) Britt and Pogostemin cablin (Blanco) Benth. Pulegone reductase is the key enzyme in the biosynthesis of menthol and is required for the stereoselective reduction of the Δ 2,8 double bond of pulegone to produce the major intermediate menthone, thus determining the stereochemistry of menthol. However, the structural basis and mechanism underlying the stereoselectivity of pulegone reductase remain poorly understood. In this study, we characterized a novel (-)-pulegone reductase from Nepeta tenuifolia ( Nt PR), which can catalyze (-)-pulegone to (+)-menthone and (-)-isomenthone through our RNA-seq, bioinformatic analysis in combination with in vitro enzyme activity assay, and determined the structure of (+)-pulegone reductase from ( Mp PR) by using X-ray crystallography, molecular modeling and docking, site-directed mutagenesis, molecular dynamics simulations, and biochemical analysis. We identified and validated the critical residues in the crystal structure of Mp PR involved in the binding of the substrate pulegone. We also further identified that residues Leu56, Val282, and Val284 determine the stereoselectivity of the substrate pulegone, and mainly contributes to the product stereoselectivity. This work not only provides a starting point for the understanding of stereoselectivity of pulegone reductases, but also offers a basis for the engineering of menthone/menthol biosynthetic enzymes to achieve high-titer, industrial-scale production of enantiomerically pure products.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Structure and Characterization of Crimean-Congo Hemorrhagic Fever Virus GP38

Crimean-Congo hemorrhagic fever virus (CCHFV) is a priority pathogen that poses a high risk to public health. Due to the high morbidity and mortality rates associated with CCHFV infection, there is an urgent need to develop medical countermeasures for disease prevention and treatment. CCHFV GP38, a secreted glycoprotein of unknown function unique to the Nairoviridae family, was recently shown to be the target of a protective antibody against CCHFV. Here, we present the crystal structure of GP38, which revealed a novel fold with distant homology to another CCHFV glycoprotein that is suggestive of a gene duplication event. We also demonstrate that antibody 13G8 protects STAT1-knockout mice against heterologous CCHFV challenge using a clinical isolate from regions where CCHFV is endemic. Collectively, these data advance our understanding of GP38 structure and antigenicity and should facilitate future studies investigating its function.

59 BASIC BIOLOGICAL SCIENCES↗

Insights into pyrrolysine function from structures of a trimethylamine methyltransferase and its corrinoid protein complex

The 22nd genetically encoded amino acid, pyrrolysine, plays a unique role in the key step in the growth of methanogens on mono-, di-, and tri-methylamines by activating the methyl group of these substrates for transfer to a corrinoid cofactor. Previous crystal structures of the Methanosarcina barkeri monomethylamine methyltransferase elucidated the structure of pyrrolysine and provide insight into its role in monomethylamine activation. Herein, we report the second structure of a pyrrolysine-containing protein, the M. barkeri trimethylamine methyltransferase MttB, and its structure bound to sulfite, a substrate analog of trimethylamine. We also report the structure of MttB in complex with its cognate corrinoid protein MttC, which specifically receives the methyl group from the pyrrolysine-activated trimethylamine substrate during methanogenesis. Together these structures provide key insights into the role of pyrrolysine in methyl group transfer from trimethylamine to the corrinoid cofactor in MttC.

60 APPLIED LIFE SCIENCES↗

Structure and functional determinants of Rad6–Bre1 subunits in the histone H2B ubiquitin-conjugating complex

The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 ‘backside’. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6–Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6–Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6–Bre1 interaction through a novel interface that is important for their biochemical and biological responses.

59 BASIC BIOLOGICAL SCIENCES↗

Insights into the thermal decomposition of plutonium(IV) oxalate – a DFT study of the intermediate structures

The thermal decomposition of plutonium oxalate to oxide is one of the most studied reactions in actinide chemistry but the intermediates have been the subject of debate for decades. Recent experimental data suggest that the decomposition of Pu(IV) oxalate in air undergoes dehydration first, then reduction to Pu(III) oxalate. The precise structural modifications that take place are unknown as experiments have not been able to fully characterize the intermediates at the microscopic level. To rectify this, we employed solid state density functional theory calculations at the PBE-D3 level with a Hubbard U correction to model the structures and energetics of potential dehydrated Pu(IV) and Pu(III) oxalate intermediate compounds. Based on the theoretical study presented here, the anhydrous analogues of the known hydrated Pu(IV) and Pu(III) oxalates are the preferred crystal structures formed through an overall exothermic reaction process. However, decomposition could proceed through the formation of a higher energy, more complicated 3D lattice structure with frustrated oxalate binding. It is expected that the intermediates presented here could be identified using spectroscopic techniques to enable further insight into the reaction mechanism.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Solutions to Droop and the Green Gap by Novel Carrier Injection

Long-wavelength (green, yellow, red) visible light-emitting diodes (LEDs) have historically been inefficient compared to blue light-emitters in the III-nitrides. This is due to many factors, including poor material quality due to the low growth temperatures required for high Incomposition InGaN quantum wells (QWs), and the polar nature of the III-nitride crystal structure. Spontaneous and piezoelectric polarization in the III-nitrides causes enhanced quantum-confined Stark effect (QCSE), which spatially separates electrons and holes and reduces radiative recombination (ie: light output) from the devices. Polarization in the crystal also induces additional potential barriers that electrons and holes must cross over before entering the QWs where they can recombine to emit light. Both of these polarization effects worsen as emission wavelength increases, making blue III-nitride LEDs are the most efficient and red III-nitride LEDs the least efficient. The focus of this project has been solving the latter polarization-related issue through the implementation of V-defects in long wavelength LEDs. V-defects are morphological defects which are commonly observed in c-plane III-nitrides. They are observed as hexagonal pyramid-shaped depressions on the c-plane surface, with six semipolar sidewalls. They typically form at the apex of threading dislocations (TDs) under conditions of kinetically-limited growth and low growth-temperature. They were initially thought to be detrimental to LED performance and much early work focused on eliminating them entirely from III-nitride devices. However, over the past decade work has emerged that indicate that they can improve LED performance by allowing electrons and holes to bypass the polarization-induced barriers present in the c-plane and directly enter the QWs of an LED. This is due to the semipolar nature of the V-defect sidewall: these sidewalls are thin and lack the polarization-induced barriers which prevent carriers easily moving between layers. V-defects have since been determined to be an efficient avenue by which to inject electrons and holes into the c-plane QWs where they can recombine to emit light. Throughout this project we have explored lateral injection through a variety of methods: simulation (Task 2), epitaxial growth of V-defect and non-V-defect LEDs (Tasks 1, 3, 4, 5, 6), and advanced characterization methods (Task 7). All tasks have been completed. A description of each task completed follows from this section.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗