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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.

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At least 1,441 records · Page 80
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Symmetry based assembly of a 2 dimensional protein lattice

The design of proteins that self-assemble into higher order architectures is of great interest due to their potential application in nanotechnology. Specifically, the self-assembly of proteins into ordered lattices is of special interest to the field of structural biology. Here we designed a 2 dimensional (2D) protein lattice using a fusion of a tandem repeat of three TelSAM domains (TTT) to the Ferric uptake regulator (FUR) domain. We determined the structure of the designed (TTT-FUR) fusion protein to 2.3 Å by X-ray crystallographic methods. In agreement with the design, a 2D lattice composed of TelSAM fibers interdigitated by the FUR domain was observed. As expected, the fusion of a tandem repeat of three TelSAM domains formed 21 screw axis, and the self-assembly of the ordered oligomer was under pH control. We demonstrated that the fusion of TTT to a domain having a 2-fold symmetry, such as the FUR domain, can produce an ordered 2D lattice. The TTT-FUR system combines features from the rotational symmetry matching approach with the oligomer driven crystallization method. This TTT-FUR fusion was amenable to X-ray crystallographic methods, and is a promising crystallization chaperone.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Nanoscale phase separation in epitaxial Cr-Mo and Cr-V alloy thin films studied using atom probe tomography: Comparison of experiments and simulation

Tailored metal alloy thin film-oxide interfaces generated using molecular beam epitaxy (MBE) deposition of alloy thin films on a single crystalline oxide substrate can be used for detailed studies of irradiation damage response on the interface structure. However, the presence of nanoscale phase separation in the MBE grown alloy thin films can impact the metal-oxide interface structure. Due to nanoscale domain size of such phase separation, it is very challenging to characterize by conventional techniques. Therefore, laser assisted atom probe tomography (APT) was utilized to study the phase separation in epitaxial Cr{sub 0.61}Mo{sub 0.39}, Cr{sub 0.77}Mo{sub 0.23}, and Cr{sub 0.32}V{sub 0.68} alloy thin films grown by MBE on MgO(001) single crystal substrates. Statistical analysis, namely frequency distribution analysis and Pearson coefficient analysis of experimental data was compared with similar analyses conducted on simulated APT datasets with known extent of phase separation. Thus, the presence of phase separation in Cr-Mo films, even when phase separation was not clearly observed by x-ray diffraction, and the absence of phase separation in the Cr-V film were confirmed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Crystal Structure of the FERM-SH2 Module of Human Jak2

Jak-family tyrosine kinases mediate signaling from diverse cytokine receptors. Binding of Jaks to their cognate receptors is mediated by their N-terminal region, which contains FERM and SH2 domains. Here we describe the crystal structure of the FERM-SH2 region of Jak2 at 3.0Å resolution. The structure reveals that these domains and their flanking linker segments interact intimately to form an integrated structural module. The Jak2 FERM-SH2 structure closely resembles that recently described for Tyk2, another member of the Jak family. While the overall architecture and interdomain orientations are preserved between Jak2 and Tyk2, we identify residues in the putative receptor-binding groove that differ between the two and may contribute to the specificity of receptor recognition. Analysis of Jak mutations that are reported to disrupt receptor binding reveals that they lie in the hydrophobic core of the FERM domain, and are thus expected to compromise the structural integrity of the FERM-SH2 unit. Similarly, analysis of mutations in Jak3 that are associated with severe combined immunodeficiency suggests that they compromise Jak3 function by destabilizing the FERM-SH2 structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Density characterization of discharged gas-filled capillaries through common-path two-color spectral-domain interferometry

Electrically discharged plasma structures, typically several centimeters in length and sub-millimeter in diameter, have been applied to guide laser pulses in laser plasma accelerators and to focus ion and relativistic electron beams in compact, radially symmetric transport configurations. Knowledge of the on-axis plasma density is critical. Traditional density interferometry has been ineffective for these laser-machined structures, while group velocity delay (GVD) techniques involve combining two laser paths with corresponding alignment complexities and stability sensitivities. Here the GVD technique is advanced to a common-path two-color interferometer configuration performed in the spectral domain of a broad-bandwidth femtosecond laser. Multi-shot tracking of the phase is not required, and the common path assures improved stability. Here, this in situ technique was validated on 15 mm long plasma structures, measuring electron densities of 10 17 -10 18 cm -3 for various fill pressures.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
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 OSTI2025

Local control of perpendicular magnetic anisotropy of Pd/Co multilayers via ion bombardment

In this work, we have controlled locally the magnetic anisotropy of PdCo multilayers using ion beam modification. First, we have used techniques with different probing depths to confirm that cobalt is partially oxidized in the Pd/Co multilayers exhibiting PMA fabricated by sputtering, presumably due to the diffusion of atmospheric oxygen migrated through the Pd capping layer. Then, low energy ion bombardment has been employed to induce a structural disorder in the upper layers of the multilayer, gradually reducing the PMA at local scale with increasing ion doses. Medium ion doses lead to a marked decline in PMA, resulting in equivalent magnetic anisotropy directions and the loss of characteristic labyrinthine magnetic domain morphology. High ion doses completely suppress PMA, yielding a typical in-plane shape anisotropy. Furthermore, by combining controlled PMA reduction via lithographic techniques, we create elongated structures displaying distinct magnetic responses; bombarded regions exhibit reduced PMA, whereas adjacent regions maintain their PMA. Notably, regions with reduced PMA do not disrupt the distribution of perpendicular magnetic domains in neighboring PMA regions, even at widths as narrow as 500 nm, demonstrating the robustness of the PMA domain structure.

Sebastiani-Tofano, Eugenia [Universidad Complutens↗
DOE OSTI2025

A quantitative comparison of the fingerprint of twinned microstructures through surface and three-dimensional techniques

Assessing the fingerprint of a material’s microstructure is key for supporting materials design. With the emergence of a wide range of 3D characterization techniques, it is critical to understand the main differences in fingerprints reconstructed from 2D and 3D datasets. To this end, we introduce a graph-based microstructure reconstruction framework that enables structural comparisons of twin domain networks in high purity Ti using 3D and 2D electron backscatter diffraction. Insights into the structure of the twin networks are facilitated by combining statistical analysis of twin crystallography with visual and graphical analysis of the novel graph abstractions of the twins. We demonstrate that compared to 3D reconstructions, conventional 2D views of twinning miss key aspects of the microstructure including the high interconnectivity of domains into networks that span the full reconstruction volume. The reduced cross-grain and in-grain twin connectivity typically observed in 2D has notable implications on our understanding of how twinning mediates the plastic response of microstructures and how twin networks evolve. It is thus clear that 3D characterization is critical for accurately inferring both twin network morphologies as well as the key unit processes facilitating network formation.

36 MATERIALS SCIENCE↗
DOE OSTI2015

DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions

FOXP3 is a lineage-specific transcription factor that is required for regulatory T cell development and function. In this study, we determined the crystal structure of the FOXP3 forkhead domain bound to DNA. The structure reveals that FOXP3 can form a stable domain-swapped dimer to bridge DNA in the absence of cofactors, suggesting that FOXP3 may play a role in long-range gene interactions. To test this hypothesis, we used circular chromosome conformation capture coupled with high throughput sequencing (4C-seq) to analyze FOXP3-dependent genomic contacts around a known FOXP3-bound locus, Ptpn22. Our studies reveal that FOXP3 induces significant changes in the chromatin contacts between the Ptpn22 locus and other Foxp3-regulated genes, reflecting a mechanism by which FOXP3 reorganizes the genome architecture to coordinate the expression of its target genes. Our results suggest that FOXP3 mediates long-range chromatin interactions as part of its mechanisms to regulate specific gene expression in regulatory T cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structural Analysis and Electrochemical Properties of Bimetallic Palladium-Platinum Aerogels Prepared by a Two-Step Gelation Process

Multimetallic aerogels have emerged as promising unsupported and high-surface-area metal materials for different applications in heterogeneous catalysis and electrochemistry, which are fabricated using a gelation process characterized by the controlled aggregation of metallic nanoparticles to form a macroscopic network structure in aqueous solution. However, the achievement of the structural homogeneity of the multimetallic aerogels in terms of the diameter of the nanochains and the chemical composition at the nano- and the macro-scale is still a great challenge. In this paper, we investigated two Pd-Pt aerogels prepared by the two-step gelation method. The structural homogeneity and chemical distribution of both metals inside the aerogels were analyzed by using high-resolution (scanning) transmission microscopy, energy-dispersive X-ray spectroscopy, extended X-ray absorption fine structure spectroscopy and cyclic voltammetry. The Pd-Pt aerogels show the presence of Pd/Pt-rich domains inside the long-range framework. It is evident that the initial monometallic features dominate over alloying during the gelation process. Although the same synthetic approach for Pd-Pt aerogels with different atomic ratios was used, we observed that the sizes of these monometallic domains varied strongly between the Pd-rich and Pt-rich aerogels. The presence of such metal clusters influenced the electrochemical robustness of the Pd-Pt aerogels dramatically. Further, electrochemical durability investigations revealed that the aerogels with a high content of Pd are less stable because of the gradual dissolution of the less noble metal particularly inside the Pd-rich domains. A chemical and structural homogeneity might improve the lifetime of the Pd-Pt aerogels under electrochemical conditions. In this work, we provide a better understanding of the structure and chemical distribution of the bimetallic aerogel framework prepared by the two-step gelation process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Structural basis for the antibody neutralization of Herpes simplex virus

The gD–E317-Fab complex crystal revealed the conformational epitope of human mAb E317 on HSV gD, providing a molecular basis for understanding the viral neutralization mechanism. Glycoprotein D (gD) of Herpes simplex virus (HSV) binds to a host cell surface receptor, which is required to trigger membrane fusion for virion entry into the host cell. gD has become a validated anti-HSV target for therapeutic antibody development. The highly inhibitory human monoclonal antibody E317 (mAb E317) was previously raised against HSV gD for viral neutralization. To understand the structural basis of antibody neutralization, crystals of the gD ectodomain bound to the E317 Fab domain were obtained. The structure of the complex reveals that E317 interacts with gD mainly through the heavy chain, which covers a large area for epitope recognition on gD, with a flexible N-terminal and C-terminal conformation. The epitope core structure maps to the external surface of gD, corresponding to the binding sites of two receptors, herpesvirus entry mediator (HVEM) and nectin-1, which mediate HSV infection. E317 directly recognizes the gD–nectin-1 interface and occludes the HVEM contact site of gD to block its binding to either receptor. The binding of E317 to gD also prohibits the formation of the N-terminal hairpin of gD for HVEM recognition. The major E317-binding site on gD overlaps with either the nectin-1-binding residues or the neutralizing antigenic sites identified thus far (Tyr38, Asp215, Arg222 and Phe223). The epitopes of gD for E317 binding are highly conserved between two types of human herpesvirus (HSV-1 and HSV-2). This study enables the virus-neutralizing epitopes to be correlated with the receptor-binding regions. The results further strengthen the previously demonstrated therapeutic and diagnostic potential of the E317 antibody.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

The Role of Interfacial Interactions and Oxygen Vacancies in Tuning Magnetic Anisotropy in LaCrO 3 /LaMnO 3 Heterostructures

The interplay of lattice, electronic, and spin degrees of freedom at epitaxial complex oxide interfaces provides a route to tune their magnetic ground states. Unraveling the competing contributions is critical for tuning their functional properties. The relationship between magnetic ordering and magnetic anisotropy and the lattice symmetry, oxygen content, and film thickness in compressively strained LaMnO 3 (LMO)/LaCrO 3 (LCO) superlattices is investigated. Mn–O–Cr antiferromagnetic superexchange interactions across the heterointerface result in a net ferrimagnetic magnetic structure. Bulk magnetometry measurements reveal isotropic in-plane magnetism for as-grown oxygen-deficient thin samples due to equal fractions of orthorhombic a+a-c-, and a-a+c- twin domains. As the superlattice thickness is increased, in-plane magnetic anisotropy emerges as the fraction of the a+a-c- domain increases. On annealing in oxygen, the suppression of oxygen vacancies results in a contraction of the lattice volume, and an orthorhombic to rhombohedral transition leads to isotropic magnetism independent of the film thickness. The complex interactions are investigated using high-resolution synchrotron diffraction and X-ray absorption spectroscopy. These results highlight the role of the evolution of structural domains with film thickness, interfacial spin interactions, and oxygen-vacancy-induced structural phase transitions in tuning the magnetic properties of complex oxide heterostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Human IFIT3 Modulates IFIT1 RNA Binding Specificity and Protein Stability

Although interferon-induced proteins with tetratricopeptide repeats (IFIT proteins) inhibit infection of many viruses by recognizing their RNA, the regulatory mechanisms involved remain unclear. Here, in this paper, we report a crystal structure of cap 0 (m 7 GpppN) RNA bound to human IFIT1 in complex with the C-terminal domain of human IFIT3. Structural, biochemical, and genetic studies suggest that IFIT3 binding to IFIT1 has dual regulatory functions: (1) extending the half-life of IFIT1 and thereby increasing its steady-state amounts in cells; and (2) allosterically regulating the IFIT1 RNA-binding channel, thereby enhancing the specificity of recognition for cap 0 but not cap 1 (m 7 GpppNm) or 5'-ppp RNA. Mouse Ifit3 lacks this key C-terminal domain and does not bind mouse Ifit1. The IFIT3 interaction with IFIT1 is important for restricting infection of viruses lacking 2'-O methylation in their RNA cap structures. Our experiments establish differences in the regulation of IFIT1 orthologs and define targets for modulation of human IFIT protein activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Kainate receptor channel opening and gating mechanism

Kainate receptors, a subclass of ionotropic glutamate receptors, are tetrameric ligand-gated ion channels that mediate excitatory neurotransmission. Kainate receptors modulate neuronal circuits and synaptic plasticity during the development and function of the central nervous system and are implicated in various neurological and psychiatric diseases, including epilepsy, depression, schizophrenia, anxiety and autism. Although structures of kainate receptor domains and subunit assemblies are available, the mechanism of kainate receptor gating remains poorly understood. Here we present cryo-electron microscopy structures of the kainate receptor GluK2 in the presence of the agonist glutamate and the positive allosteric modulators lectin concanavalin A and BPAM344. Concanavalin A and BPAM344 inhibit kainate receptor desensitization and prolong activation by acting as a spacer between the amino-terminal and ligand-binding domains and a stabilizer of the ligand-binding domain dimer interface, respectively. Channel opening involves the kinking of all four pore-forming M3 helices. Our structures reveal the molecular basis of kainate receptor gating, which could guide the development of drugs for treatment of neurological disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Nanoscale structure and morphology of sulfonated polyphenylenes via atomistic simulations

We performed atomistic simulations on a series of sulfonated polyphenylenes systematically varying the degree of sulfonation and water content to determine their effect on the nanoscale structure, particularly for the hydrophilic domains formed by the ionic groups and water molecules. We found that the local structure around the ionic groups depended on the sulfonation and hydration levels, with the sulfonate groups and hydronium ions less strongly coupled at higher water contents. In addition, we characterized the morphology of the ionic domains employing two complementary clustering algorithms. At low sulfonation and hydration levels, clusters were more elongated in shape and poorly connected throughout the system. As the degree of sulfonation and water content were increased, the clusters became more spherical, and a fully percolated ionic domain was formed. As a result, these structural details have important implications for ion transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Examining Electron-Boson Coupling Using Time-Resolved Spectroscopy

Nonequilibrium pump-probe time-domain spectroscopies can become an important tool to disentangle degrees of freedom whose coupling leads to broad structures in the frequency domain. Here, using the time-resolved solution of a model photoexcited electron-phonon system, we show that the relaxational dynamics are directly governed by the equilibrium self-energy so that the phonon frequency sets a window for “slow” versus “fast” recovery. The overall temporal structure of this relaxation spectroscopy allows for a reliable and quantitative extraction of the electron-phonon coupling strength without requiring an effective temperature model or making strong assumptions about the underlying bare electronic band dispersion.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

The N‐terminal intrinsically disordered region of Ncb5or docks with the cytochrome b 5 core to form a helical motif that is of ancient origin

Abstract NADH cytochromeb 5 oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochromeb 5 (b 5 ) and cytochromeb 5 reductase (b 5 R) domains separated by a CHORD‐Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter‐domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full‐length human Ncb5or has proven resistant to crystallization, we have succeeded in obtaining high‐resolution atomic structures of theb 5 domain and a construct containing the CS andb 5 R domains (CS/b 5 R). Ncb5or also contains an N‐terminal intrinsically disordered region of 50 residues that has no homologs in other protein families in animals but features a distinctive, conserved L 34 MDWIRL 40 motif also present in reduced lateral root formation (RLF) protein in rice and increased recombination center 21 in baker's yeast, all attaching to ab 5 domain. After unsuccessful attempts at crystallizing a human Ncb5or construct comprising the N‐terminal region naturally fused to theb 5 domain, we were able to obtain a high‐resolution atomic structure of a recombinant rice RLF construct corresponding to residues 25–129 of human Ncb5or (52% sequence identity; 74% similarity). The structure reveals Trp 120 (corresponding to invariant Trp 37 in Ncb5or) to be part of an 11‐residue α‐helix (S 116 QMDWLKLTRT 126 ) packing against two of the four helices in theb 5 domain that surround heme (α2 and α5). The Trp 120 side chain forms a network of interactions with the side chains of four highly conserved residues corresponding to Tyr 85 and Tyr 88 (α2), Cys 124 (α5), and Leu 47 in Ncb5or. Circular dichroism measurements of human Ncb5or fragments further support a key role of Trp 37 in nucleating the formation of the N‐terminal helix, whose location in the N/b 5 module suggests a role in regulating the function of this multi‐domain redox enzyme. This study revealed for the first time an ancient origin of a helical motif in the N/b 5 module as reflected by its existence in a class of cytochromeb 5 proteins from three kingdoms among eukaryotes.

Biochemistry & Molecular Biology↗