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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Substrate Specificity of Lymphoid-specific Tyrosine Phosphatase (Lyp) and Identification of Src Kinase-associated Protein of 55 kDa Homolog (SKAP-HOM) as a Lyp Substrate

A missense single-nucleotide polymorphism in the gene encoding the lymphoid-specific tyrosine phosphatase (Lyp) has been identified as a causal factor in a wide spectrum of autoimmune diseases. Interestingly, the autoimmune-predisposing variant of Lyp appears to represent a gain-of-function mutation, implicating Lyp as an attractive target for the development of effective strategies for the treatment of many autoimmune disorders. Unfortunately, the precise biological functions of Lyp in signaling cascades and cellular physiology are poorly understood. Identification and characterization of Lyp substrates will help define the chain of molecular events coupling Lyp dysfunction to diseases. In the current study, we identified consensus sequence motifs for Lyp substrate recognition using an 'inverse alanine scanning' combinatorial library approach. The intrinsic sequence specificity data led to the discovery and characterization of SKAP-HOM, a cytosolic adaptor protein required for proper activation of the immune system, as a bona fide Lyp substrate. To determine the molecular basis for Lyp substrate recognition, we solved crystal structures of Lyp in complex with the consensus peptide as well as the phosphopeptide derived from SKAP-HOM. Together with the biochemical data, the structures define the molecular determinants for Lyp substrate specificity and provide a solid foundation upon which novel therapeutics targeting Lyp can be developed for multiple autoimmune diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Recovery of edge states of graphene nanoislands on an iridium substrate by silicon intercalation

Finite-sized graphene sheets, such as graphene nanoislands (GNIs), are promising candidates for practical applications in graphene-based nanoelectronics. GNIs with well-defined zigzag edges are predicted to have spin-polarized edge-states similar to those of zigzag-edged graphene nanoribbons, which can achieve graphene spintronics. However, it has been reported that GNIs on metal substrates have no edge states because of interactions with the substrate. In this work, we used a combination of scanning tunneling microscopy, spectroscopy, and density functional theory calculations to demonstrate that the edge states of GNIs on an Ir substrate can be recovered by intercalating a layer of Si atoms between the GNIs and the substrate. We also found that the edge states gradually shift to the Fermi level with increasing island size. This work provides a method to investigate spin-polarized edge states in high-quality graphene nanostructures on a metal substrate.

density functional theory↗
DOE OSTI2020

Evaluation of Gaseous Substrates for Microbial Immobilization of Contaminant Mixtures in Unsaturated Subsurface Sediments

Extensive vadose zone metals and organic contamination remains at many former industrial and defense manufacturing sites, and effective remedial solutions are needed to slow or prevent its migration to groundwater. In this study, the application of gaseous substrates to stimulate microbial respiratory reduction of comingled radioisotopes and nitrate under unsaturated conditions was examined for possible application at the Hanford Site, a former nuclear production facility in southeastern WA, USA. First, screening studies were performed to qualitatively measure the sediment respiratory response to 14 gaseous or volatile organic substrates at two moisture contents, 4% and 8%. Volatile substrates produced the strongest respiratory response, among them were butyrate, pentane, butyl acetate. Ethane and butane were the most effective gaseous substrates but only at 8% water content. Hanford sediment from two waste sites with distinctive chemistries were wetted to 7% moisture content, packed into columns, and treated with ethane or butane. After 4 weeks, columns were then leached to quantify retardation in the mobility of aqueous contaminant concentrations compared to no gas control columns. Treatment with both gases resulted in >80% removal of Cr from the aqueous phase. However, NO3 concentration and a waste sites exposure history to NO3 had a major effect on U and Tc reduction. Incomplete nitrate reduction outcompeted U and Tc in waste site sediments having limited prior exposure to NO3. Conversely, waste site sediments co-contaminated with NO3 were able to achieve highly reduced conditions resulting in complete denitrification of NO3, and delayed leaching of U and Tc. This implied effective reduction of both contaminants to less mobile species. This study demonstrates that unsaturated vadose sediments at Hanford waste sites have the capacity for a sustained respiratory response to gaseous substrate injection, which could potentially be deployed as part of an overall strategy to reduce the flux of long-lived radionuclides to groundwater at Hanford and other legacy waste sites.

Bagwell, Christopher E.↗
DOE OSTI2016

Structural insights into Parkin substrate lysine targeting from minimal Miro substrates

Hereditary Parkinson’s disease is commonly caused by mutations in the protein kinase PINK1 or the E3 ubiquitin ligase Parkin, which function together to eliminate damaged mitochondria. PINK1 phosphorylates both Parkin and ubiquitin to stimulate ubiquitination of dozens of proteins on the surface of the outer mitochondrial membrane. However, the mechanisms by which Parkin recognizes specific proteins for modification remain largely unexplored. Here, we show that the C-terminal GTPase (cGTPase) of the Parkin primary substrate human Miro is necessary and sufficient for efficient ubiquitination. We present several new X-ray crystal structures of both human Miro1 and Miro2 that reveal substrate recognition and ubiquitin transfer to be specific to particular protein domains and lysine residues. We also provide evidence that Parkin substrate recognition is functionally separate from substrate modification. Finally, we show that prioritization for modification of a specific lysine sidechain of the cGTPase (K572) within human Miro1 is dependent on both its location and chemical microenvironment. Activation of Parkin by phosphorylation or by binding of pUb is required for prioritization of K572 for modification, suggesting that Parkin activation and acquisition of substrate specificity are coupled.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Substrate-induced disorder in V{sub 2}O{sub 3} thin films grown on annealed c-plane sapphire substrates

We investigate the structural and electronic properties of V{sub 2}O{sub 3} thin films deposited by oxygen plasma-assisted molecular beam epitaxy onto annealed and unannealed c-plane sapphire substrates. Annealing the substrates before growth to produce ultra-smooth surfaces improved initial epitaxy, according to in situ reflection high-energy electron diffraction. Surprisingly, films deposited on annealed substrates had a more island-like surface, broader x-ray diffraction peaks, and an increased resistivity of V{sub 2}O{sub 3}'s normally metallic high-temperature phase. We attribute these results to enhanced strain coupling at the interface between the substrate and film, highlighting the vulnerability of V{sub 2}O{sub 3}'s strongly correlated metallic phase to crystalline defects and structural disorder.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Effects of boron-nitride substrates on Stone-Wales defect formation in graphene: An ab initio molecular dynamics study

Ab initio molecular dynamics simulations are performed to investigate the effects of a boron nitride (BN) substrate on Stone-Wales (SW) defect formation and recovery in graphene. It is found that SW defects can be created by an off-plane recoil atom that interacts with the BN substrate. A mechanism with complete bond breakage for formation of SW defects in suspended graphene is also revealed for recoils at large displacement angles. In addition, further irradiation can result in recovery of the SW defects through a bond rotation mechanism in both graphene and graphene/BN, and the substrate has little effect on the recovery process. This study indicates that the BN substrate enhances the irradiation resistance of graphene.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2014

In situ measurement of low-Z material coating thickness on high Z substrate for tokamaks

Rutherford backscattering of energetic particles can be used to determine the thickness of a coating of a low-Z material over a heavier substrate. Simulations indicate that 5 MeV alpha particles from an {sup 241}Am source can be used to measure the thickness of a Li coating on Mo tiles between 0.5 and 15 μm thick. Using a 0.1 mCi source, a thickness measurement can be accomplished in 2 h of counting. This technique could be used to measure any thin, low-Z material coating (up to 1 mg/cm{sup 2} thick) on a high-Z substrate, such as Be on W, B on Mo, or Li on Mo. By inserting a source and detector on a moveable probe, this technique could be used to provide an in situ measurement of the thickness of Li coating on NSTX-U Mo tiles. A test stand with an alpha source and an annular solid-state detector was used to investigate the measurable range of low-Z material thicknesses on Mo tiles.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Surface stability and the selection rules of substrate orientation for optimal growth of epitaxial II-VI semiconductors

The surface structures of ionic zinc-blende CdTe (001), (110), (111), and (211) surfaces are systematically studied by first-principles density functional calculations. Based on the surface structures and surface energies, we identify the detrimental twinning appearing in molecular beam epitaxy (MBE) growth of II-VI compounds as the (111) lamellar twin boundaries. To avoid the appearance of twinning in MBE growth, we propose the following selection rules for choosing optimal substrate orientations: (1) the surface should be nonpolar so that there is no large surface reconstructions that could act as a nucleation center and promote the formation of twins; (2) the surface structure should have low symmetry so that there are no multiple equivalent directions for growth. These straightforward rules, in consistent with experimental observations, provide guidelines for selecting proper substrates for high-quality MBE growth of II-VI compounds.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition

Lytic polysaccharide monooxygenases (LPMOs) are a group of recently discovered enzymes that play important roles in the decomposition of recalcitrant polysaccharides. Here, we report the biochemical, structural, and computational characterization of an LPMO from the white-rot fungus Heterobasidion irregulare (HiLPMO9B). This enzyme oxidizes cellulose at the C1 carbon of glycosidic linkages. The crystal structure of HiLPMO9B was determined at 2.1 A resolution using X-ray crystallography. Unlike the majority of the currently available C1-specific LPMO structures, the HiLPMO9B structure contains an extended L2 loop, connecting ..beta..-strands ..beta..2 and ..beta..3 of the ..beta..-sandwich structure. Molecular dynamics (MD) simulations suggest roles for both aromatic and acidic residues in the substrate binding of HiLPMO9B, with the main contribution from the residues located on the extended region of the L2 loop (Tyr20) and the LC loop (Asp205, Tyr207, and Glu210). Asp205 and Glu210 were found to be involved in the hydrogen bonding with the hydroxyl group of the C6 carbon of glucose moieties directly or via a water molecule. Two different binding orientations were observed over the course of the MD simulations. In each orientation, the active-site copper of this LPMO preferentially skewed toward the pyranose C1 of the glycosidic linkage over the targeted glycosidic bond. This study provides additional insight into cellulose binding by C1-specific LPMOs, giving a molecular-level picture of active site substrate interactions.

09 BIOMASS FUELS↗
DOE OSTI2013

Broad Substrate Specificity of the Loading Didomain of the Lipomycin Polyketide Synthase

LipPks1, a polyketide synthase subunit of the lipomycin synthase, is believed to catalyze the polyketide chain initiation reaction using isobutyryl-CoA as a substrate, followed by an elongation reaction with methylmalonyl-CoA to start the biosynthesis of antibiotic alpha-lipomycin in Streptomyces aureofaciens Tu117. Recombinant LipPks1, containing the thioesterase domain from the 6-deoxyerythronolide B synthase, was produced in Escherichia coli, and its substrate specificity was investigated in vitro. Surprisingly, several different acyl-CoAs, including isobutyryl-CoA, were accepted as the starter substrates, while no product was observed with acetyl-CoA. These results demonstrate the broad substrate specificity of LipPks1 and may be applied to producing new antibiotics.

Yuzawa, S↗