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At least 1,189 records · Page 66
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Comparative study of surface modification and D retention between beryllium and beryllides under high flux plasma exposure

The microstructures and deuterium (D) retention properties were investigated for beryllium intermetallic compounds (beryllides), such as Be 12 Ti and Be 12 V, compared to pure beryllium (Be), exposed to high density pure D and helium (He) mixed plasmas. TEM cross-sectional observations revealed the formation of cone structures on the Be surface exposed to the plasmas at a moderate temperature of 573 K. The crystal structure of the cones and the mass loss caused by the plasma exposure implied that the cone structures were generated by sputtering. The Ti or V surface enrichment was observed on both beryllides with no cone structures developed. TDS measurements indicated that He seeding to D plasma caused a ~ 4 times reduction of the D retention for both beryllides, while no reduction was observed for Be. As a result, the beryllide samples exposed to D + He mixture plasmas showed a lower total D retention than in Be.

Hydrogen retention↗
DOE OSTI2021

Influence of Surface and Structural Variations in Donor–Acceptor–Donor Sensitizers on Photoelectrocatalytic Water Splitting

Conjugated organic chromophores composed of linked donor (D) and acceptor (A) moieties have attracted considerable attention for photoelectrochemical applications. In this work, we compare the optoelectronic properties and photoelectrochemical performance of two D–A–D structural isomers with thiophene-X-carboxylic acid (X denotes 3 and 2 positions) derivatives and 2,1,3-benzothiadiazole as the D and A moieties, respectively. 5,5′-(Benzo[c][1,2,5]thiadiazole-4,7-diyl)bis(thiophene-3-carboxylic acid), BTD1, and 5,5′-(benzo[c][1,2,5]thiadiazole-4,7-diyl)bis(thiophene-2-carboxylic acid), BTD2, were employed in the study to understand how structural isomers affect surface attachments within chromophore–catalyst assemblies and their influence on charge-transfer dynamics. Crystal structures revealed that varying the position of the −COOH anchoring group causes the molecules to either contort out of a plane (BTD1) or adopt a near-perfect planar conformation (BTD2). BTD1 and BTD2 were co-loaded with either a water oxidation catalyst, [Ru(2,6-bis(1-methylbenzimidazol-2-yl)pyridine)-(4,4′-((HO) 2 OPCH 2 )2-2,2′-bipyridine)(OH 2 )] 2 , RuCt 2+ , or proton reduction catalyst [Ni(P 2 Ph N 2 C 6 H 4 CH 2 PO 3 H 2 ) 2 ] 2+ , NiCt 2+ , on oxide electrodes to facilitate photodriven water splitting reactions. Emission quenching measurements indicate that both BTD1 and BTD2 inject electrons into n-type SnO 2 |TiO 2 electrodes and holes into p-type NiO semiconductors from their respective excited states at high efficiencies >60%. Photocurrent densities of chromophore–catalyst assemblies obtained using linear sweep voltammetry (LSV) show that BTD2-sensitized photoanodes generate significantly more photocurrent than BTD1-sensitized electrodes; however, both exhibit similar performances at the photocathode. Photoelectrocatyltic measurements demonstrate that both BTD1 and BTD2 performed similarly, generating Faradaic efficiencies of 39 and 38% at the anode or 61 and 79% at the cathode. Transient absorption measurements suggest that the differences between the LSV and photoelectrocatalytic measurements result from the differences in quantum yields of the photogenerated redox equivalents, which is also a reflection of the varying metal oxide surface conformation. Our findings suggest that BTD2 should be investigated further in photocathodic studies since it has the structural advantage of being incorporated into diverse types of chromophore–catalyst assemblies.

Chromophores↗
DOE OSTI2023

Hallucination of closed repeat proteins containing central pockets

In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity that can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep-learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in Escherichia coli are consistent with the design models, and the three crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small-molecule binders and enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

PE5–PPE4–EspG 3 heterotrimer structure from mycobacterial ESX-3 secretion system gives insight into cognate substrate recognition by ESX systems

Mycobacterium tuberculosis has evolved numerous type VII secretion (ESX) systems to secrete multiple factors important for both growth and virulence across their cell envelope. ESX-1, ESX-3, and ESX-5 systems have been shown to each secrete a distinct set of substrates, including PE and PPE families of proteins, named for conserved Pro-Glu and Pro-Pro-Glu motifs in their N termini. Proper secretion of the PE–PPE proteins requires the presence of EspG, with each system encoding its own unique copy. There is no cross-talk between any of the ESX systems, and how each EspG recognizes its subset of PE–PPE proteins is currently unknown. The only current structural characterization of PE–PPE–EspG heterotrimers is from the ESX-5 system. Here we present the crystal structure of the PE5 mt –PPE4 mt –EspG 3mm heterotrimer from the ESX-3 system. Our heterotrimer reveals that EspG 3mm interacts exclusively with PPE4 mt in a similar manner to EspG 5 , shielding the hydrophobic tip of PPE4 mt from solvent. The C-terminal helical domain of EspG 3mm is dynamic, alternating between “open” and “closed” forms, and this movement is likely functionally relevant in the unloading of PE–PPE heterodimers at the secretion machinery. In contrast to the previously solved ESX-5 heterotrimers, the PE–PPE heterodimer of our ESX-3 heterotrimer is interacting with its chaperone at a drastically different angle and presents different faces of the PPE protein to the chaperone. We conclude that the PPE–EspG interface from each ESX system has a unique shape complementarity that allows each EspG to discriminate among noncognate PE–PPE pairs.

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

PDBspheres: a method for finding 3D similarities in local regions in proteins

Abstract We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (‘spheres’) adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. PDBspheres uses the LGA (Local–Global Alignment) structure alignment algorithm as the main engine for detecting structural similarities between the protein of interest and template spheres from the library, which currently contains >2 million spheres. To assess confidence in structural matches, an all-atom-based similarity metric takes side chain placement into account. Here, we describe the PDBspheres method, demonstrate its ability to detect and characterize binding sites in protein structures, show how PDBspheres—a strictly structure-based method—performs on a curated dataset of 2528 ligand-bound and ligand-free crystal structures, and use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of 4876 structures in the ‘refined set’ of the PDBbind 2019 dataset.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Tuning structural, transport, and magnetic properties of epitaxial SrRu O 3 through Ba substitution

The perovskite ruthenates (A RuO 3 , A=Ca, Ba, or Sr) exhibit unique properties owing to a subtle interplay of crystal structure and electronic-spin degrees of freedom. Here, in this study, we demonstrate an intriguing continuous tuning of crystal symmetry from orthorhombic to tetragonal (no octahedral rotations) phases in epitaxial SrRuO 3 achieved via Ba substitution (Sr 1-x Ba x RuO 3 with 0 ≤ x ≤ 0.7 ). An initial Ba substitution to SrRuO 3 not only changes the ferromagnetic properties, but also tunes the perpendicular magnetic anisotropy via flattening the Ru–O–Ru bond angle (to 180°), resulting in the maximum Curie temperature and an extinction of RuO 6 rotational distortions at x≈0.20. For x ≤ 0.2, the reduction of RuO 6 octahedral rotational distortion dominantly enhances the ferromagnetism in the system, though competing with the effect of the RuO 6 tetragonal distortion. Further increasing Ba substitution (x > 0.2) gradually enhances the tetragonal-type distortion, resulting in the tuning of Ru-4d orbital occupancy and suppression of ferromagnetism. Our results demonstrate that isovalent substitution of the A-site cations significantly and controllably impacts both electronic and magnetic properties of perovskite oxides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Mechanochemically Assisted Synthesis of High-Entropy Layer-Structured Dittmarite Analogues

High-entropy solid-solution materials, especially layered ones incorporating five or more near-equimolar components into single-phase crystal structures, may spark functional synergism toward the electrochemistry area because of their unique antisite disordering structures and the synergistic effect of multiple active sites. Herein, high-entropy dittmarite analogues (HEDAs) were synthesized via a mechanochemistry-assisted hydrothermal method. Furthermore, the as-prepared HEDAs have single dittmarite phases with five homogeneously distributed metal elements, exhibiting enhanced activities in oxygen evolution catalysis compared to the single metal counterparts.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure of VanS from vancomycin-resistant enterococci: A sensor kinase with weak ATP binding

The VanRS two-component system regulates the resistance phenotype of vancomycin-resistant enterococci. VanS is a sensor histidine kinase that responds to the presence of vancomycin by autophosphorylating and subsequently transferring the phosphoryl group to the response regulator, VanR. The phosphotransfer activates VanR as a transcription factor, which initiates the expression of resistance genes. Structural information about VanS proteins has remained elusive, hindering the molecular-level understanding of their function. Here, we present X-ray crystal structures for the catalytic and ATP-binding (CA) domains of two VanS proteins, derived from vancomycin-resistant enterococci types A and C. Both proteins adopt the canonical Bergerat fold that has been observed for CA domains of other prokaryotic histidine kinases. We attempted to determine structures for the nucleotide-bound forms of both proteins; however, despite repeated efforts, these forms could not be crystallized, prompting us to measure the proteins' binding affinities for ATP. Unexpectedly, both CA domains displayed low affinities for the nucleotide, with K D values in the low millimolar range. Since these K D values are comparable to intracellular ATP concentrations, this weak substrate binding could reflect a way of regulating expression of the resistance phenotype.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Opportunities in electrically tunable 2D materials beyond graphene: Recent progress and future outlook

The interest in two-dimensional and layered materials continues to expand, driven by the compelling properties of individual atomic layers that can be stacked and/or twisted into synthetic heterostructures. The plethora of electronic properties as well as the emergence of many different quasiparticles, including plasmons, polaritons, trions, and excitons with large, tunable binding energies that all can be controlled and modulated through electrical means, has given rise to many device applications. In addition, these materials exhibit both room-temperature spin and valley polarization, magnetism, superconductivity, piezoelectricity that are intricately dependent on the composition, crystal structure, stacking, twist angle, layer number, and phases of these materials. Initial results on graphene exfoliated from single bulk crystals motivated the development of wide-area, high purity synthesis and heterojunctions with atomically clean interfaces. Now by opening this design space to new synthetic two-dimensional materials “beyond graphene,” it is possible to explore uncharted opportunities in designing novel heterostructures for electrically tunable devices. To fully reveal the emerging functionalities and opportunities of these atomically thin materials in practical applications, this review highlights several representative and noteworthy research directions in the use of electrical means to tune these aforementioned physical and structural properties, with an emphasis on discussing major applications of beyond graphene 2D materials in tunable devices in recent years and an outlook of what is to come in the next decade.

Vincent, Tom (ORCID:0000000159749137)↗
DOE OSTI2021

Anisotropic Transient Disordering of Colloidal, Two-Dimensional CdSe Nanoplatelets upon Optical Excitation

Nanoplatelets (NPLs)-colloidally synthesized, spatially anisotropic, two-dimensional semiconductor quantum wells-are of intense interest owing to exceptionally narrow transition line widths, coupled with solution processability and bandgap tunability. However, given large surface areas and undercoordinated bonding at facet corners and edges, excitation under sufficient intensities may induce anisotropic structural instabilities that impact desired properties. We employ time-resolved X-ray diffraction to study the crystal structure of CdSe NPLs in response to optical excitation. Photoexcitation induces greater out-of-plane than in-plane disordering in 4 and 5 monolayer (ML) NPLs, while 3 ML NPLs display the opposite behavior. Recovery dynamics suggest that out-of-plane cooling slightly outpaces in-plane cooling in 5 ML NPLs with recrystallization occurring on indistinguishable time scales. In comparison, for zero-dimensional CdSe nanocrystals, disordering is isotropic and recovery is faster. These results favor the use of NPLs in optoelectronic applications, where they are likely to exhibit superior performance over traditional, zero-dimensional nanocrystals.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Discovery of first-in-class inhibitors of ASH1L histone methyltransferase with anti-leukemic activity

ASH1L histone methyltransferase plays a crucial role in the pathogenesis of different diseases, including acute leukemia. While ASH1L represents an attractive drug target, developing ASH1L inhibitors is challenging, as the catalytic SET domain adapts an inactive conformation with autoinhibitory loop blocking the access to the active site. Here, by applying fragment-based screening followed by medicinal chemistry and a structure-based design, we developed first-in-class small molecule inhibitors of the ASH1L SET domain. The crystal structures of ASH1L-inhibitor complexes reveal compound binding to the autoinhibitory loop region in the SET domain. When tested in MLL leukemia models, our lead compound, AS-99, blocks cell proliferation, induces apoptosis and differentiation, downregulates MLL fusion target genes, and reduces the leukemia burden in vivo. This work validates the ASH1L SET domain as a druggable target and provides a chemical probe to further study the biological functions of ASH1L as well as to develop therapeutic agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A structured RNA motif locks Argonaute2:miR-122 onto the 5’ end of the HCV genome

microRNAs (miRNAs) form regulatory networks in metazoans. Viruses engage miRNA networks in numerous ways, with Flaviviridae members exploiting direct interactions of their RNA genomes with host miRNAs. For hepatitis C virus (HCV), binding of liver-abundant miR-122 stabilizes the viral RNA and regulates viral translation. Here, we investigate the structural basis for these activities, taking into consideration that miRNAs function in complex with Argonaute (Ago) proteins. The crystal structure of the Ago2:miR-122:HCV complex reveals a structured RNA motif that traps Ago2 on the viral RNA, masking its 5’ end from enzymatic attack. The trapped Ago2 can recruit host factor PCBP2, implicated in viral translation, while binding of a second Ago2:miR-122 competes with PCBP2, creating a potential molecular switch for translational control. Combined results reveal a viral RNA structure that modulates Ago2:miR-122 dynamics and repurposes host proteins to generate a functional analog of the mRNA cap-binding complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Demonstrating the importance of porcine reproductive and respiratory syndrome virus papain-like protease 2 deubiquitinating activity in viral replication by structure-guided mutagenesis

Deubiquitination of cellular substrates by viral proteases is a mechanism used to interfere with host cellular signaling processes, shared between members of the coronavirus- and arterivirus families. In the case of Arteriviruses, deubiquitinating and polyprotein processing activities are accomplished by the virus-encoded papain-like protease 2 (PLP2). Several studies have implicated the deubiquitinating activity of the porcine reproductive and respiratory syndrome virus (PRRSV) PLP2 in the downregulation of cellular interferon production, however to date, the only arterivirus PLP2 structure described is that of equine arteritis virus (EAV), a distantly related virus. Here we describe the first crystal structure of the PRRSV PLP2 domain both in the presence and absence of its ubiquitin substrate, which reveals unique structural differences in this viral domain compared to PLP2 from EAV. To probe the role of PRRSV PLP2 deubiquitinating activity in host immune evasion, we selectively removed this activity from the domain by mutagenesis and found that the viral domain could no longer downregulate cellular interferon production. Interestingly, unlike EAV, and also unlike the situation for MERS-CoV, we found that recombinant PRRSV carrying PLP2 DUB-specific mutations faces significant selective pressure to revert to wild-type virus in MARC-145 cells, suggesting that the PLP2 DUB activity, which in PRRSV is present as three different versions of viral protein nsp2 expressed during infection, is critically important for PRRSV replication.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Structural Characterization of Linker Shielding in ADC Site-Specific Conjugates

Background/Objectives: Antibody–Drug Conjugates (ADCs) have rapidly evolved from early, rudimentary conjugates to highly targeted and precisely engineered molecules. Despite notable clinical successes, ADCs continue to face significant challenges, including aggregation and high hydrophobicity driven by high drug-to-antibody ratios (DARs), premature payload release, dose-limiting toxicities, and suboptimal pharmacokinetics. While site-specific linker–payload conjugation has improved ADC homogeneity and stability, the structural basis of antibody–linker interactions at specific sites remains underexplored. Methods: In this work, we present the crystal structures of trastuzumab Fab and Fc domains site-specifically conjugated with a cleavable linker–payload. Results: Our findings suggest that pockets within both Fab and Fc regions may interact with and shield the linker portion of the conjugate. Conclusions: These insights highlight the previously underappreciated potential of structure-based design to drive the optimization of ADC linker chemistry and facilitate the co-design of bespoke linker–payloads tailored to individual antibody conjugation sites.

Jaime-Garza, Maru [Discovery Chemistry, Merck & Co↗
DOE OSTI2023

Does photoinduced structural change by β-rhombohedral boron occur at room temperature?

β-rhombohedral boron (β-B) is an intriguing solid among the elements. The crystal structure of β-B is widely accepted as a complex structure based on the B 12 clusters, and with a lot of intrinsic structural defects. In the last decade, β-B was proved to be the only elemental semiconductor that exhibits the self-compensation property accompanied by changing structural defects during atom doping. Moreover, it is reported that various physical properties of β-B change discontinuously around 550 K, which may originate from defect diffusion [S. Hoffmann and H. Werheit, Solid State Sciences 14, 1572 (2012)]. We previously reported that a volume expansion of about 1.5% takes place above this temperature (between 650 K and 850 K). On the other hand, this expanded structure is stable in dark conditions for more than 4.5 months. Finally, light irradiation at room temperature reverses the volume back to the initial state, and a possible scenario will be discussed in this paper.

36 MATERIALS SCIENCE↗