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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

In Situ X-ray Diffraction of High Density Polyethylene During Dynamic Compression: Polymer Chain Compression and Phase Transformations

Polymers are widely implemented materials often used for safety and security in our daily lives. However, we do not have a thorough understanding of the phase transformations of these materials when exposed to extreme condition, high strain rate, events. To study polymers in these severe environments, we performed plate impact experiments that impart a one-dimensional shock wave, at high pressures and temperatures, to observe the materials response. Generally, velocimetry is the experimental diagnostic used to capture the movement of high velocity interfaces to then calculate the mechanical variables associated with shock compression. However, when a material undergoes a phase transition, such as between two crystalline phases or melting to decomposition during shock compression, velocimetry does not explicitly indicate what structural change occurred. At the Dynamic Compression Sector at the Advanced Photon Source gas gun driven compression has been paired with x-ray diffraction, providing the ability to study both the shock parameters and structural changes concurrently. We explored high density polyethylene (HDPE) both on its reactants Hugoniot (<10.12 GPa) and within its transition region (24.3 GPa) where HDPE is hypothesized to decompose from reactants to products. With x-ray diffraction we observed both polymer chain compression and crystal structure reorientation from orthorhombic to monoclinic above 6 GPa, as well as either a possible phase change or chemical decomposition at 24.3 GPa. With these experiments we were able to determine the crystalline and amorphous Hugoniot loci at pressures below the polymer transition region.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure and enzymatic characterization of CelD endoglucanase from the anaerobic fungus Piromyces finnis

Anaerobic fungi found in the guts of large herbivores are prolific biomass degraders whose genomes harbor a wealth of carbohydrate-active enzymes (CAZymes), of which only a handful are structurally or biochemically characterized. Here, we report the structure and kinetic rate parameters for a glycoside hydrolase (GH) family 5 subfamily 4 enzyme (CelD) from Piromyces finnis, a modular, cellulosome-incorporated endoglucanase that possesses three GH5 domains followed by two C-terminal fungal dockerin domains (double dockerin). We present the crystal structures of an apo wild-type CelD GH5 catalytic domain and its inactive E154A mutant in complex with cellotriose at 2.5 and 1.8 Å resolution, respectively, finding the CelD GH5 catalytic domain adopts the (β/α) 8 -barrel fold common to many GH5 enzymes. Structural superimposition of the apo wild-type structure with the E154A mutant-cellotriose complex supports a catalytic mechanism in which the E154 carboxylate side chain acts as an acid/base and E278 acts as a complementary nucleophile. Further analysis of the cellotriose binding pocket highlights a binding groove lined with conserved aromatic amino acids that when docked with larger cellulose oligomers is capable of binding seven glucose units and accommodating branched glucan substrates. Activity analyses confirm P. finnis CelD can hydrolyze mixed linkage glucan and xyloglucan, as well as carboxymethylcellulose (CMC). Measured kinetic parameters show the P. finnis CelD GH5 catalytic domain has CMC endoglucanase activity comparable to other fungal endoglucanases with k cat = 6.0 ± 0.6 s –1 and K m = 7.6 ± 2.1 g/L CMC. Enzyme kinetics were unperturbed by the addition or removal of the native C-terminal dockerin domains as well as the addition of a non-native N-terminal dockerin, suggesting strict modularity among the domains of CelD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Derivatization of Mirror-Image L -Nucleic Acids with 2'-OMe Modification for Thermal and Structural Stabilization

To further expand the functionality and enhance the stability of mirror-image nucleic acids as advanced agents for basic research and therapeutic design, we have synthesized 2'-deoxy-2'-methoxy- L -uridine phosphoramidite and incorporated it into L -DNA and L -RNA by solid-phase synthesis quantitatively. We found that the thermostability of L -nucleic acids is dramatically improved after introducing the modifications. Moreover, we successfully crystallized both L -DNA and L -RNA duplexes containing the 2'-OMe modifications and sharing identical sequences. Crystal structure determination and analysis revealed the overall structures of the mirror-image nucleic acids, and for the first time it was possible to interpret the structural deviations caused by 2'-OMe and 2'-OH groups in the oligonucleotides, which are very similar. In conclusion, this novel chemical nucleic acid modification has the potential to be used to design nucleic acid-based therapeutics and materials in the future.

2'-OMe-modifications↗
DOE OSTI2025

An alternative pocket for binding the N‐degrons by the UBR1 and UBR2 ubiquitin E3 ligases

The UBR family of ubiquitin ligases binds to N-termini of their targets (known as N-degron) to induce their ubiquitination and degradation via a conserved domain known as UBR-box. UBR1 and UBR2 share the highest sequence homology among the family, and substantial structural studies were previously performed for substrate binding by the UBR-boxes of UBR1 and UBR2. Here, we describe a new pocket in the UBR-boxes of UBR1 and UBR2 for binding the second residues of N-degrons through determining five co-crystal structures of the UBR-boxes with various N-degron peptides. Together with binding affinities measured by fluorescence polarization, we show that the two highly homologous UBR-boxes can interact with the second residue of an N-degron differently. In addition, the UBR-boxes undergo different conformational changes when binding N-degrons. Furthermore, we demonstrate that the sidechain of the third amino acid of an N-degron has no contribution to binding the UBR-boxes. These findings represent a new conceptual advancement for the UBR E3 ligases and the new insights described here can be leveraged for developing their selective ligands for research and potential therapies.

N-end rule↗
DOE OSTI2025

Interstitial Atoms and the Frustrated and Allowed Structural Transitions Principle: Tunability in the Electronic Structure of AuCu 3 ‐type Frameworks in Dy 4 T 1− x Ga 12 (T = Ag, Ir)

In this Article, we explore how the chemical pressure (CP) features of an intermetallic phase may provide opportunities to couple perturbations in electron count with the stabilization of the underlying geometrical structure. AuCu 3 ‐type LnGa 3 (Ln = lanthanide or group 3 metal) phases contain octahedral cavities of negative CP held open by overly compressed Ln–Ga interactions, leading to a series of transition metal‐stuffed derivatives. We present new additions to this family with the synthesis and crystal structures of Dy 4 T 1−x Ga 12 with (T, x) = (Ag, 0.29) and (Ir, 0.15), adopting Y 4 PdGa 12 ‐type superstructures of the AuCu 3 ‐type. density functional Ttheory (DFT)‐CP calculations, when adjusted to avoid dipolar CP features, affirm that T atom incorporation provides a mechanism for the relief of packing tensions, while electronic density of states distributions illustrate that the T atoms serve largely as electron or hole donors to the band structure, as needed for them to attain d 10 configurations. The maximum obtainable value for x may be limited by a mismatch between the Fermi energy and pseudogap, in line with the balance of factors envisioned by the frustrated and allowed structural transitions principle. Furthermore, trends in resistivity measurements on T = Ir, Pd, and Ag compounds are interpretable in terms of the varying degrees of disorder arising from x < 1.0.

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

Characterization and structure of the human lysine-2-oxoglutarate reductase domain, a novel therapeutic target for treatment of glutaric aciduria type 1

In humans, a single enzyme 2-aminoadipic semialdehyde synthase (AASS) catalyses the initial two critical reactions in the lysine degradation pathway. This enzyme evolved to be a bifunctional enzyme with both lysine-2-oxoglutarate reductase (LOR) and saccharopine dehydrogenase domains (SDH). Moreover, AASS is a unique drug target for inborn errors of metabolism such as glutaric aciduria type 1 that arise from deficiencies downstream in the lysine degradation pathway. While work has been done to elucidate the SDH domain structurally and to develop inhibitors, neither has been done for the LOR domain. Here, we purify and characterize LOR and show that it is activated by alkylation of cysteine 414 by N-ethylmaleimide. We also provide evidence that AASS is rate-limiting upon high lysine exposure of mice. Finally, we present the crystal structure of the human LOR domain. Our combined work should enable future efforts to identify inhibitors of this novel drug target.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Anisotropic Ferromagnetism in CrAu 3 Sb 6

The crystal structure and properties of CrAu 3 Sb 6 are presented, determined by measurements on single crystal and polycrystalline samples and first-principles calculations. The trigonal structure (space group P$\overline{3}$1m) comprises a CdI 2 -like sublattice of AuSb 2 with Cr occupying octahedral holes in a fully ordered triangular array. It can be viewed as a variation of the interesting and well-known families of partially intercalated transition metal dichalcogenides, but with stronger interactions along the stacking direction evidenced by short Cr–Au distances. The compound is metallic and ferromagnetic with a Curie temperature of 164 K. A strong anomalous contribution to the Hall effect is seen in the ferromagnetic state, and quantum oscillations are observed in magnetization at 2 K. Magnetization measurements show that the ordered moments of 1.5 μ B per Cr are oriented along the c-axis with relatively strong magnetocrystalline anisotropy. Electronic structure calculations confirm this uniaxial anisotropy and the important role of spin–orbit coupling in CrAu 3 Sb 6 and reveal strongly favored ferromagnetic ground state consistent with the measured Curie temperature. Through combined experiment and theory, this work provides a detailed picture of the basic properties and behaviors of this uniquely structured, Cr-based, anisotropic ferromagnet.

Crystal structure↗
DOE OSTI2023

Structure of Rhizobium sp. 4-9 histamine dehydrogenase and analysis of the electron transfer pathway to an abiological electron acceptor

Histamine dehydrogenase from the gram-negative bacterium Rhizobium sp. 4-9 (HaDHR) is a member of a small family of dehydrogenases containing a covalently attached FMN, and the only member so far identified to date that does not exhibit substrate inhibition. Here, in this study, we present the 2.1 Å resolution crystal structure of HaDHR. This new structure allowed for the identification of the internal electron transfer pathway to abiological ferrocene-based mediators. Alanine 437 was identified as the exit point of electrons from the Fe 4 S 4 cluster. The enzyme was modified with a Ser436Cys mutation to facilitate covalent attachment of a ferrocene moiety. When modified with Fc-maleimide, this new construct demonstrated direct electron transfer from the enzyme to a gold electrode in a histamine concentration-dependent manner without the need for any additional electron mediators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN

High-fidelity replication of the large RNA genome of coronaviruses (CoVs) is mediated by a 3'-to-5' exoribonuclease (ExoN) in nonstructural protein 14 (nsp14), which excises nucleotides including antiviral drugs misincorporated by the low-fidelity viral RNA-dependent RNA polymerase (RdRp) and has also been implicated in viral RNA recombination and resistance to innate immunity. Here, we determined a 1.6-Å resolution crystal structure of severe acute respiratory syndrome CoV 2 (SARS-CoV-2) ExoN in complex with its essential cofactor, nsp10. The structure shows a highly basic and concave surface flanking the active site, comprising several Lys residues of nsp14 and the N-terminal amino group of nsp10. Modeling suggests that this basic patch binds to the template strand of double-stranded RNA substrates to position the 3' end of the nascent strand in the ExoN active site, which is corroborated by mutational and computational analyses. We also show that the ExoN activity can rescue a stalled RNA primer poisoned with sofosbuvir and allow RdRp to continue its extension in the presence of the chain-terminating drug, biochemically recapitulating proofreading in SARS-CoV-2 replication. Molecular dynamics simulations further show remarkable flexibility of multidomain nsp14 and suggest that nsp10 stabilizes ExoN for substrate RNA binding to support its exonuclease activity. Our high-resolution structure of the SARS-CoV-2 ExoN–nsp10 complex serves as a platform for future development of anticoronaviral drugs or strategies to attenuate the viral virulence.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structure, dynamics, and redox reactivity of an all-purpose flavodoxin

The flavodoxin of Rhodopseudomonas palustris CGA009 (Rp9Fld) supplies highly reducing equivalents to crucial en- zymes such as hydrogenase, especially when the organism is iron-restricted. By acquiring those electrons from photodriven electron flow via the bifurcating electron transfer flavoprotein, Rp9Fld provides solar power to vital metabolic processes. To understand Rp9Fld’s ability to work with diverse partners, we solved its crystal structure. We observed the canonical fla- vodoxin (Fld) fold and features common to other long-chain Flds but not all the surface loops thought to recognize part- ner proteins. Moreover, some of the loops display alternative structures and dynamics. To advance studies of protein– protein associations and conformational consequences, we assigned the 19F NMR signals of all five tyrosines (Tyrs). Our electrochemical measurements show that incorporation of 3- 19 F-Tyr in place of Tyr has only a modest effect on Rp9Fld’s redox properties even though Tyrs flank the flavin on both sides. Meanwhile, the 19 F probes demonstrate the expected paramagnetic effect, with signals from nearby Tyrs becoming broadened beyond detection when the flavin semiquinone is formed. However, the temperature dependencies of chemical shifts and linewidths reveal dynamics affecting loops close to the flavin and regions that bind to partners in a variety of systems. These coincide with patterns of amino acid type conservation but not retention of specific residues, arguing against detailed specificity with respect to partners. We pro- pose that the loops surrounding the flavin adopt altered con- formations upon binding to partners and may even participate actively in electron transfer.

19F NMR↗
DOE OSTI2020

Trigonal polymorph of Li 2 MnO 3

We report the discovery of a trigonal polymorph of the prospective Li ion battery material Li 2 MnO 3 and its synthesis in bulk, single crystal form. Crystal growth of trigonal Li 2 MnO 3 is strongly dependent upon the quality of a polycrystalline LiMnO 2 precursor consumed in the synthesis process. The crystal structure of the new trigonal phase is composed of ordered honeycomb layers of LiO 6 and MnO 6 octahedra segregated by layers of LiO 6 octahedra and represents an ordered stacking variant of the known monoclinic polymorph. Diffuse reflectance spectroscopy reveals a direct optical gap of 2.47 ± 0.11 eV and a series of charge excitations that are well explained by the expected Mn 4+ 3d 3 valence. Density functional theory calculations are in excellent agreement with the spectroscopic measurements and find a near degeneracy in the formation energies of the two polymorphs. Furthermore, our results suggest that the trigonal structure resolves the compositional and structural disorder often manifested in the monoclinic phase.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural Basis for EPC1-Mediated Recruitment of MBTD1 into the NuA4/TIP60 Acetyltransferase Complex

MBTD1, a H4K20me reader, has recently been identified as a component of the NuA4/TIP60 acetyltransferase complex, regulating gene expression and DNA repair. NuA4/TIP60 inhibits 53BP1 binding to chromatin through recognition of the H4K20me mark by MBTD1 and acetylation of H2AK15, blocking the ubiquitination mark required for 53BP1 localization at DNA breaks. The NuA4/TIP60 non-catalytic subunit EPC1 enlists MBTD1 into the complex, but the detailed molecular mechanism remains incompletely explored. Here, we present the crystal structure of the MBTD1-EPC1 complex, revealing a hydrophobic C-terminal fragment of EPC1 engaging the MBT repeats of MBTD1 in a site distinct from the H4K20me binding site. Different cellular assays validate the physiological significance of the key residues involved in the MBTD1-EPC1 interaction. Our study provides a structural framework for understanding the mechanism by which MBTD1 recruits the NuA4/TIP60 acetyltransferase complex to influence transcription and DNA repair pathway choice.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Design, synthesis, evaluation and X-ray structural studies of potent HIV-1 protease inhibitors containing substituted oxaspirocyclic carbamates as the P2 ligands

Here, we report here the design, synthesis and evaluation of a series of HIV-1 protease inhibitors that incorporate substituted oxaspirocyclic carbamate derivatives to serve as the P2 ligands. Various substituted ligand derivatives were synthesized in a racemic manner, using a tandem Prins/pinacol reaction as the key reaction. This reaction sets the relative stereochemistry of the oxaspirocyclic template in a highly diastereoselective manner. Reaction of the resulting ketone with enantiopure (S)-tert-butyl sulfinamide provided a convenient pathway to resolve the oxaspirocyclic ketone derivatives. The absolute stereochemical identity was determined by X-ray crystallography. The structure-activity studies demonstrate the effect of the stereochemistry of the oxaspirocyclic ring systems as well as the substitution effect on the aromatic ring. Several inhibitors exhibited potent HIV-1 protease inhibitory activity. One of these inhibitors displayed subnanomolar HIV-1 protease affinity and also exhibited potent antiviral activity. A high-resolution X-ray crystal structure of this inhibitor-bound HIV-1 protease show that the oxaspirocyclic P2 ligand forms an unconventional C–H⋯O bond with the backbone carboxyl group of Gly48’ and an interesting N–H … π interaction with the aromatic ring in the S2 subsite of HIV-1 protease active site.

Antiviral↗
DOE OSTI2021

Fast and Scalable Synthesis of LiNi 0.5 Mn 1.5 O 4 Cathode by Sol–Gel-Assisted Microwave Sintering

High-voltage spinel LiNi 0.5 Mn 1.5 O 4 (LNMO) is a promising cathode material for high-energy-density and high-power-density lithium-ion batteries (LIBs). The high cost of the currently available LIBs needs to be addressed urgently for wide application in the transport sector (electric vehicles, buses) and large-scale energy storage systems (ESS). Of significance, herein, novel fast and scalable microwave-assisted synthesis of LNMO is reported, which leads to a production cost cut. X-ray diffraction (XRD) analysis confirms the formation of the desired phase with high crystallinity. Field emission scanning (FE-SEM) and transmission electron microscopy (TEM) analyses indicate that the synthesized phase is of nanometric size (50–150 nm) due to an extremely short sintering time (20 min). The material synthesized at 750 °C shows a higher initial discharge capacity (130 mA h g -1 ) than that synthesized at 650 °C (115 mA h g -1 ). The materials heat treated at higher temperatures show better electrochemical performance in terms of initial capacity, rate capability, and improved cycling. The improved electrochemical performance of LNMO at 750 °C is attributed to the formation of a stable crystal structure, low charge transfer resistance at the electrode/electrolyte interface, high electrical conductivity due to the presence of a disorder structure, and improved ionic diffusivity.

25 ENERGY STORAGE↗
DOE OSTI2021

Binary and Ternary Colloidal Cu–Sn–Te Nanocrystals for Thermoelectric Thin Films

Recent advances in copper chalcogenide-based nanocrystals (NCs), copper sulfide, and copper selenide derived nanostructures, have drawn considerable attention. However, reports of crystal phase and shape engineering of binary or ternary copper telluride NCs remain rare. Here, a colloidal hot-injection approach for producing binary copper/tin telluride, and ternary copper tin telluride NCs with controllable compositions, crystal structures, and morphologies is reported. Here, the crystal phase and growth behavior of these tellurides are systematically studied from both experimental and theoretical perspectives.

30 DIRECT ENERGY CONVERSION↗