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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 1,351 records · Page 75
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structure of the glucosyltransferase domain of TcdA in complex with RhoA provides insights into substrate recognition

Clostridioides difficile is one of the most common causes of antibiotic-associated diarrhea in developed countries. As key virulence factors of C. difficile, toxin A (TcdA) and toxin B (TcdB) act by glucosylating and inactivating Rho and Ras family small GTPases in host cells, which leads to actin cytoskeleton disruption, cell rounding, and ultimately cell death. Here we present the co-crystal structure of the glucosyltransferase domain (GTD) of TcdA in complex with its substrate human RhoA at 2.60-angstrom resolution. This structure reveals that TcdA GTD grips RhoA mainly through its switch I and switch II regions, which is complemented by interactions involving RhoA’s pre-switch I region. Comprehensive structural comparisons between the TcdA GTD–RhoA complex and the structures of TcdB GTD in complex with Cdc42 and R-Ras reveal both the conserved and divergent features of these two toxins in terms of substrate recognition. Taken together, these findings establish the structural basis for TcdA recognition of small GTPases and advance our understanding of the substrates selectivity of large clostridial toxins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Effective and accurate approach for modeling of commensurate–incommensurate transition in krypton monolayer on graphite

Commensurate–incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs–Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton–graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton–carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas–solid and solid–solid system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Magnesium-Dependent RNA Binding to the PA Endonuclease Domain of the Avian Influenza Polymerase

Influenza A viruses are highly pathogenic and pose an unpredictable public health danger to humans. An attractive target for developing new antiviral drugs is the PA N-terminal domain (PAN) of influenza polymerase, which is responsible for the endonuclease activity and essential for viral replication. Recently, the crystal structures of the holo form of PAN as well as PAN bound to different inhibitors have been reported, but the potency and selectivity of these inhibitors still need to be improved. New drug design can be guided by a better understanding of the endonuclease activity of PAN. However, this requires the structure of PAN in complex with the host mRNA, which has not been determined yet. In particular, divalent metal ions are known to be essential for RNA cleavage, but it is not clear whether there is either one or two Mg ions in the PAN active site. In the present work, we have modeled the complex of the PAN endonuclease domain with the host mRNA in the presence of either one or two Mg2+ by using all-atom molecular dynamics. These simulations identify crucial interactions between the enzyme and the nucleic acid. Moreover, they validate a previous hypothesis that a second metal ion binds in the presence of the RNA substrate and therefore support a two-metal ion mechanism, in which K134 decreases the pKa of the nucleophilic water. Nevertheless, at low Mg concentrations an alternative, one-metal ion mechanism is possible, with K137 as the catalytic lysine and H41 as the general base, rationalizing previous unexpected mutagenesis results. The RNA–enzyme interactions determined here could likely be used to design more specific endonuclease inhibitors to fight influenza viral infections.

Chemistry↗
DOE OSTI2014

Role of κ→λ light-chain constant-domain switch in the structure and functionality of A17 reactibody

Catalytic antibody variants with κ and λ light-chain constant domains show differences in their crystal structures which lead to subtle changes in catalytic efficiency and thermodynamic parameters as well as in their affinity for peptide substrates. The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophosphate-metabolizing reactibody A17 has been re-engineered by replacing its constant κ light chain by the λ chain (A17λ), and the X-ray structure of A17λ has been determined at 1.95 Å resolution. It was found that compared with A17κ the active centre of A17λ is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the V{sub L} and V{sub H} domains. These V{sub L}/V{sub H} domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126° compared with 138° in A17κ. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17κ and A17λ variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Investigation of the release of Si from SiO{sub 2} during the formation of manganese/ruthenium barrier layers

The thermodynamic and structural stability of ruthenium-manganese diffusion barriers on SiO{sub 2} is assessed. A {approx}2 nm film composed of partially oxidized manganese (MnO{sub x} where x < 1) was deposited on a 3 nm thick Ru film and the Mn-MnO{sub x}/Ru/SiO{sub 2} structure was subsequently thermally annealed. X-ray photoelectron spectroscopy and secondary ion mass spectroscopy studies suggest the release and upward diffusion of Si from the dielectric substrate as a result of manganese-silicate formation at the Ru/SiO{sub 2} interface. The migration of Si up through the Ru film results in further manganese-silicate formation upon its interaction with the Mn-MnO{sub x} deposited layer.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

NDR1 modulates the UV-induced DNA-damage checkpoint and nucleotide excision repair

Nucleotide excision repair (NER) is the sole mechanism of UV-induced DNA lesion repair in mammals. A single round of NER requires multiple components including seven core NER factors, xeroderma pigmentosum A–G (XPA–XPG), and many auxiliary effector proteins including ATR serine/threonine kinase. The XPA protein helps to verify DNA damage and thus plays a rate-limiting role in NER. Hence, the regulation of XPA is important for the entire NER kinetic. We found that NDR1, a novel XPA-interacting protein, modulates NER by modulating the UV-induced DNA-damage checkpoint. In quiescent cells, NDR1 localized mainly in the cytoplasm. After UV irradiation, NDR1 accumulated in the nucleus. The siRNA knockdown of NDR1 delayed the repair of UV-induced cyclobutane pyrimidine dimers in both normal cells and cancer cells. It did not, however, alter the expression levels or the chromatin association levels of the core NER factors following UV irradiation. Instead, the NDR1-depleted cells displayed reduced activity of ATR for some set of its substrates including CHK1 and p53, suggesting that NDR1 modulates NER indirectly via the ATR pathway. - Highlights: • NDR1 is a novel XPA-interacting protein. • NDR1 accumulates in the nucleus in response to UV irradiation. • NDR1 modulates NER (nucleotide excision repair) by modulating the UV-induced DNA-damage checkpoint response.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Crystal structures of two bacterial HECT-like E3 ligases in complex with a human E2 reveal atomic details of pathogen-host interactions

In eukaryotes, ubiquitination is an important posttranslational process achieved through a cascade of ubiquitin-activating (E1), conjugating (E2), and ligase (E3) enzymes. Many pathogenic bacteria deliver virulence factors into the host cell that function as E3 ligases. How these bacterial 'Trojan horses' integrate into the eukaryotic ubiquitin system has remained a mystery. Here we report crystal structures of two bacterial E3s, Salmonella SopA and Escherichia coli NleL, both in complex with human E2 UbcH7. These structures represent two distinct conformational states of the bacterial E3s, supporting the necessary structural rearrangements associated with ubiquitin transfer. The E2-interacting surface of SopA and NleL has little similarity to those of eukaryotic E3s. However, both bacterial E3s bind to the canonical surface of E2 that normally interacts with eukaryotic E3s. Furthermore, we show that a glutamate residue on E3 is involved in catalyzing ubiquitin transfer from E3 to the substrate, but not from E2 to E3. Together, these results provide mechanistic insights into the ubiquitin pathway and a framework for understanding molecular mimicry in bacterial pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2015

Calcium-magnesium Aluminosilicate (CMAS) Interactions with Advanced Environmental Barrier Coating Material

Particulates, like sand and volcanic ash, threaten the development of robust environmental barrier coatings (EBCs) that protect next-generation silicon-based ceramic matrix composite (CMC) turbine engine components from harsh combustion environments during service. The siliceous particulates transform into molten glassy deposits of calcium-magnesium aluminosilicate (CMAS) when ingested by an aircraft engine operating at temperatures above 1200C. In this study, a sample of desert sand was melted into CMAS glass to evaluate high-temperature interactions between the sand glass and an advanced EBC material. Desert sand glass was added to the surface of hot-pressed EBC substrates, which were then heated in air at temperatures ranging from 1200C to 1500C. Scanning electron microscopy and X-ray energy-dispersive spectroscopy were used to evaluate microstructure and phase compositions of specimens and the CMASEBC interface after heat treatments.

CMAS-coating interactions↗
DOE OSTI2019

Transcription preinitiation complex structure and dynamics provide insight into genetic diseases

Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered by incompletely modeled regions. Here we integrate all available cryo-EM data to build a practically complete human PIC structural model. This enables simulations that reveal the assembly’s global motions, define PIC partitioning into dynamic communities and delineate how structural modules function together to remodel DNA. We identify key TFIIE–p62 interactions that link core-PIC to TFIIH. p62 rigging interlaces p34, p44 and XPD while capping the DNA-binding and ATP-binding sites of XPD. PIC kinks and locks substrate DNA, creating negative supercoiling within the Pol II cleft to facilitate promoter opening. Mapping disease mutations associated with xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome onto defined communities reveals clustering into three mechanistic classes that affect TFIIH helicase functions, protein interactions and interface dynamics.

Biochemistry & Molecular Biology↗
DOE OSTI2016

Platinum-Coated Hollow Graphene Nanocages as Cathode Used in Lithium-Oxygen Batteries

One of the formidable challenges facing aprotic lithium-oxygen (Li-O-2) batteries is the high charge overpotential, which induces the formation of byproducts, loss in efficiency, and poor cycling performance. Herein, the synthesis of the ultrasmall Pt-coated hollow graphene nano cages as cathode in Li-O-2 batteries is reported. The charge voltage plateau can reduce to 3.2 V at the current density of 100 mA g(-1), even maintain below 3.5 V when the current density increased to 500 mA g(-1). The unique hollow graphene nanocages matrix can not only provide numerous nanoscale tri-phase regions as active sites for efficient oxygen reduction, but also offer sufficient amount of mesoscale pores for rapid oxygen diffusion. Furthermore, with strong atomic-level oxygen absorption into its subsurface, ultrasmall Pt catalytically serves as the nucleation site for Li2O2 growth. The Li2O2 is subsequently induced into a favorable form with small size and amorphous state, decomposed more easily during recharge. Meanwhile, the conductive hollow graphene substrate can enhance the catalytic activity of noble metal Pt catalysts due to the graphene-metal interfacial interaction. Benefiting from the above synergistic effects between the hollow graphene nanocages and the nanosized Pt catalysts, the ultrasmall Pt-decorated graphene nanocage cathode exhibits enhanced electrochemical performances.

Wu, Feng↗
DOE OSTI2022

Synthesizing Carbon‐Supported, High‐Loading, Ultra‐Small Pt 3 Ni Nanoparticles via Tuning the Surface Electrostatic Effect

Carbon‐supported nanoparticles (NPs) are widely used as catalysts in fuel cells and electrolyzers. While it is well known that NPs with smaller size and higher loading often lead to better catalytic activity, they remain challenging to synthesize due to the weak control over the surface properties of the support. Herein, a facile approach to synthesize carbon‐supported, high‐loading, and ultra‐small Pt 3 Ni NPs via applying thermal shock on strongly interacted carbon support with metal salt is reported. Specifically, sodium citrate is introduced into the precursor solution and substrate mixture, which induces strong electrostatic effect between metal salts and carbon particles that markedly improves precursor anchoring and dispersion, thereby achieving high particle loading as well as small size and distribution. As a proof‐of‐concept, the synthesis of Pt 3 Ni NPs supported on carbon black with particle size of 1.56 ± 0.36 nm at 30 wt% loading and 1.66 ± 0.56 nm at 40 wt% loading is reported, where the sizes are among the smallest while the loadings are among the highest in the literature. This approach can be readily extended to many compositions and substrates, with tunable particle size and loading, thereby substantially expanding the synthesis space for NP catalysts in various electrochemical applications.

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

Toward single cell traction microscopy within 3D collagen matrices

Mechanical interaction between the cell and its extracellular matrix (ECM) regulates cellular behaviors, including proliferation, differentiation, adhesion, and migration. Cells require the three-dimensional (3D) architectural support of the ECM to perform physiologically realistic functions. However, current understanding of cell–ECM and cell–cell mechanical interactions is largely derived from 2D cell traction force microscopy, in which cells are cultured on a flat substrate. 3D cell traction microscopy is emerging for mapping traction fields of single animal cells embedded in either synthetic or natively derived fibrous gels. We discuss here the development of 3D cell traction microscopy, its current limitations, and perspectives on the future of this technology. Emphasis is placed on strategies for applying 3D cell traction microscopy to individual tumor cell migration within collagen gels. - Highlights: • Review of the current state of the art in 3D cell traction force microscopy. • Bulk and micro-characterization of remodelable fibrous collagen gels. • Strategies for performing 3D cell traction microscopy within collagen gels.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Two-State Reactivity in Iron-Catalyzed Alkene Isomerization Confers σ-Base Resistance

A low-coordinate, high spin (S = 3/2) organometallic iron(I) complex is a catalyst for the isomerization of alkenes. A combination of experimental and computational mechanistic studies supports a mechanism in which alkene isomerization occurs by the allyl mechanism. Importantly, while substrate binding occurs on the S = 3/2 surface, oxidative addition to an η 1 -allyl intermediate only occurs on the S = 1/2 surface. In conclusion, since this spin state change is only possible when the alkene substrate is bound, the catalyst has high immunity to typical σ-base poisons due to the antibonding interactions of the high spin state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Leveraging Triphenylphosphine-Containing Polymers to Explore Design Principles for Protein-Mimetic Catalysts

Complex interactions between noncoordinating residues are significant yet commonly overlooked components of macromolecular catalyst function. While these interactions have been demonstrated to impact binding affinities and catalytic rates in metalloenzymes, the roles of similar structural elements in synthetic polymeric catalysts remain underexplored. Using a model Suzuki–Miyuara cross-coupling reaction, we performed a series of systematic studies to probe the interconnected effects of metal–ligand cross-links, electrostatic interactions, and local rigidity in polymer catalysts. To achieve this, a novel bifunctional triphenylphosphine acrylamide (BisTPPAm) monomer was synthesized and evaluated alongside an analogous monofunctional triphenylphosphine acrylamide (TPPAm). In model copolymer catalysts, increased initial reaction rates were observed for copolymers untethered by Pd complexation (BisTPPAm-containing) compared to Pd-cross-linked catalysts (TPPAm-containing). Further, incorporating local rigidity through secondary structure-like and electrostatic interactions revealed nonmonotonic relationships between composition and the reaction rate, demonstrating the potential for tunable behavior through secondary-sphere interactions. Lastly, through rigorous cheminformatics featurization strategies and statistical modeling, we quantitated relationships between chemical descriptors of the substrate and reaction conditions on catalytic performance. Collectively, these results provide insights into relationships among the composition, structure, and function of protein-mimetic catalytic copolymers.

Catalysts↗
DOE OSTI2026

The oleaginous yeast Cutaneotrichosporon oleaginosum modifies corn stover alkali lignin

The current paradigm in synthetic biology for lignin bioconversion platforms includes primarily bacteria and filamentous fungi. Yeast are notoriously understudied for their role in lignin degradation and utilization, despite their ubiquity in saprophytic microbial communities. A few publications report lignin-modifying yeasts, but investigations to date have relied on model aromatic compounds or lignin-containing substrates replete with other carbon sources. In this work, we use a suite of analytical tools to evaluate interactions between corn stover-extracted lignin and the oleaginous yeast Cutaneotrichosporon oleaginosum. Notably, 2D-NMR analysis showed a significant decrease in the H-lignin component as well as resinol (β-β) and phenylcoumaran (β-5) linkages. Using super-resolution fluorescence microscopy, we demonstrated that this yeast may uptake polymeric lignin and/or undertakes interactions at the cellular envelope. To explore mechanisms of lignin modification, transport, and aromatics catabolism, extensive secretomics and proteomics analyses were conducted. Compared to carbon-limited glucose and “No Carbon” controls, several putative laccases, quinone reductases, superoxide dismutases, and glyoxal/oxalate oxidases were upregulated in the lignin condition. Excitingly, two ferric reductases and an oxalate exchanger were only observed in the lignin condition. These results indicate that C. oleaginosum may perform extracellular quinone redox cycling to generate lignin-modifying reactive oxygen species. These findings enhance our understanding of yeast-lignin interactions and provide valuable insights for validation studies and metabolic engineering.

09 BIOMASS FUELS↗
DOE OSTI2023

Influence of Microstructure on the Absorption of Tritium into Gold-Plated 316 Stainless Steel

The interaction of tritium with metal surfaces is the initial step in the overall absorption of tritium by the substrate metal. As a result, limiting the adsorption of tritium to the surface may effectively reduce the quantity of tritium absorbed by a metal when it is in contact with tritium gas. To limit tritium adsorption, many tritium users electroplate gold onto the substrate metal. The gold layer is expected to reduce tritium adsorption, and subsequently absorption, by reducing water adsorption. The present work shows a comparison between tritium inventories in nonplated 316 stainless steel to the inventories in 316 stainless-steel samples electroplated with gold by various commercial vendors and laboratories. Of the various gold-plated samples, only one type of plating shows ~25% reduction in tritium inventory, relative to non-plated steel samples. The degree of tritium absorption appears to be significantly influenced by the porosity, texture, and completeness of the gold layer. Incomplete and/or porous layers lead to increased absorption, while gold layers with smaller surface features lead to similar tritium inventories as non-plated samples. Furthermore, reduced tritium absorption was observed only for complete gold layers with small surface features.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Orbital control of metal-to-insulator transition in high-entropy nickelates

High-entropy materials have emerged as a promising platform for exploring unique electronic and structural properties. In this study, we investigated the orbital control of the metal-to-insulator transition in thin films of high-entropy nickelates, which are composed of five rare-earth elements in equi-atomic concentrations. By manipulating the levels of misfit strain through substrate choice and film thickness, we modulated the electronic properties and examined the intricate interplay between strain, orbital interactions, and the metal-to-insulator transition. Compared to other nickelates thin films like NdNi O 3 and SmNi O 3 , thin films of high-entropy nickelates exhibited remarkable resilience in maintaining control over their transport properties and orbital polarization, even in the presence of considerable A-site disorder. Further, this finding suggests that the electronic properties of A-site disordered high-entropy nickelates are still governed by the electronic bandwidth, primarily influenced by the Ni-O bonding geometry. This study provides valuable insights into the complex interplay among composition, structure, and electronic properties in perovskite oxides. These insights have the potential to guide the development of perovskite oxide materials with tailored electronic properties for a wide range of applications.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Single Platinum Atoms Electrocatalysts: Oxygen Reduction and Hydrogen Oxidation Reactions

We prepared atomically dispersed catalyst consisting of Pt atoms arranged in a c(2 × 2) array on RuO2(110) substrate. A large interatomic distance of Pt atoms in a c(2 × 2) phase precludes the reactants to interact with more than one Pt atoms. A strong bond of Pt atoms with RuO2 prevents agglomeration of Pt atoms to form 2D-islands or 3D-clusters. The activities of single Pt atom catalyst for the oxygen reduction and hydrogen oxidation reactions were determined and compared with those of bulk Pt. It has lower catalytic activity for the oxygen reduction reaction and similar activity for hydrogen oxidation reaction compared to Pt(111). This was explained by a large calculated up-shift of the dband center of Pt atoms and larger Pt-Pt interatomic distance than that of Pt(111). Our information is of considerable interest for further development of electrocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗