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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 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
NASA NTRS2003

The Thiamin Pyrophosphate-Motif

Using databases the authors have identified a common thiamin pyrophosphate (TPP)-motif in the family of functionally diverse TPP-dependent enzymes. This common motif consists of multimeric organization of subunits and two catalytic centers. Each catalytic center (PP:PYR) is formed at the interface of the PP-domain binding the magnesium ion, pyrophosphate and amhopyrimidine ring of TPP, and the PYR-domain binding the aminopyrimidine ring of that cofactor. A pair of these catalytic centers constitutes the catalytic core (PP:PYR)(sub 2) within these enzymes. Analysis of the structural elements of this catalytic core reveals novel definition of the common amino acid sequences, which are GXPhiX(sub 4)(G)PhiXXGQ and GDGX(sub 25-30)NN in the PP-domain, and the EX(sub 4)(G)PhiXXGPhi in the PYR-domain, where Phi corresponds to a hydrophobic amino acid. This TPP-motif provides a novel tool for annotation of TPP-dependent enzymes useful in advancing functional proteomics.

Dominiak, P.↗
DOE OSTI2015

Reconstruction and analysis of the genome-scale metabolic model of schizochytrium limacinum SR21 for docosahexaenoic acid production

Schizochytrium limacinum SR21 is a potential industrial strain for docosahexaenoic acid (DHA) production that contains more than 30–40 % DHA among its total fatty acids. To resolve the DHA biosynthesis mechanism and improve DHA production at a systematic level, a genomescale metabolic model (GSMM), named iCY1170_DHA, which contains 1769 reactions, 1659 metabolites, and 1170 genes, was reconstructed. Results: Based on genome annotation results and literature reports, a new DHA synthesis pathway based on a polyketide synthase (PKS) system was detected in S. limacinum. Similarly to conventional fatty acid synthesis, the biosynthesis of DHA via PKS requires abundant acetyl-CoA and NADPH. The in silico addition of malate and citrate led to increases of 24.5 % and 37.1 % in DHA production, respectively. Moreover, based on the results predicted by the model, six amino acids were shown to improve DHA production by experiment. Finally, 30 genes were identified as potential targets for DHA over-production using a Minimization of Metabolic Adjustment algorithm. The reconstructed GSMM, iCY1170_DHA, could be used to elucidate the mechanism by which DHA is synthesized in S. limacinum and predict the requirements of abundant acetyl-CoA and NADPH for DHA production as well as the enhanced yields achieved via supplementation with six amino acids, malate, and citrate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Top-Down Mass Spectrometry Analysis of Membrane-Bound Light-Harvesting Complex 2 from Rhodobacter sphaeroides

We show a top-down proteomic analysis of the membrane-bound peripheral light-harvesting complex LH2 isolated from the purple photosynthetic bacterium Rhodobacter sphaeroides. The LH2 complex is coded for by the puc operon. The Rb. sphaeroides genome contains two puc operons, designated puc1BAC and puc2BA. Although previous work has shown consistently that the LH2 β polypeptide coded by the puc2B gene was assembled into LH2 complexes, there are contradictory reports as to whether the Puc2A polypeptides are incorporated into LH2 complexes. Furthermore, post-translational modifications of this protein offer the prospect that it could coordinate bacteriochlorophyll a (Bchl a) by a modified N-terminal residue. Here, we describe the components of the LH2 complex on the basis of electron-capture dissociation fragmentation to confirm the identity and sequence of the protein’s subunits. We found that both gene products of the β polypeptides are expressed and assembled in the mature LH2 complex, but only the Puc1A-encoded polypeptide α is observed here. The methionine of the Puc2B-encoded polypeptide is missing, and a carboxyl group is attached to the threonine at the N-terminus. Surprisingly, one amino acid encoded as an isoleucine in both the puc2B gene and the mRNA is found as valine in the mature LH2 complex, suggesting an unexpected and unusual post-translational modification or a specific tRNA recoding of this one amino acid.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models

Background: Identification of the epitopes targeted by antibodies that can neutralize diverse HIV-1 strains can provide important clues for the design of a preventative vaccine. Methods: We have developed a computational approach that can identify key amino acids within the HIV-1 envelope glycoprotein that influence sensitivity to broadly cross-neutralizing antibodies. Given a sequence alignment and neutralization titers for a panel of viruses, the method works by fitting a phylogenetic model that allows the amino acid frequencies at each site to depend on neutralization sensitivities. Sites at which viral evolution influences neutralization sensitivity were identified using Bayes factors (BFs) to compare the fit of this model to that of a null model in which sequences evolved independently of antibody sensitivity. Conformational epitopes were identified with a Metropolis algorithm that searched for a cluster of sites with large Bayes factors on the tertiary structure of the viral envelope. Results: We applied our method to ID 50 neutralization data generated from seven HIV-1 subtype C serum samples with neutralization breadth that had been tested against a multi-clade panel of 225 pseudoviruses for which envelope sequences were also available. For each sample, between two and four sites were identified that were strongly associated with neutralization sensitivity (2ln(BF) > 6), a subset of which were experimentally confirmed using site-directed mutagenesis. Conclusions: Our results provide strong support for the use of evolutionary models applied to cross-sectional viral neutralization data to identify the epitopes of serum antibodies that confer neutralization breadth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Mechanochemical Genesis of Prebiotics (18-LW-36) (Final Report)

In this project we explored the athermal condensation of simple amino acids towards the formation of peptides under high-pressure conditions. Our main aim was to address the provocative question that science continues explore: “Does life exists beyond Earth?”. We followed a combined experimental and theoretical investigation of simple amino acids under static high pressure and also under simultaneous application of high pressure and plastic shear. Surprisingly, we find that the ambient crystal structure of a-glycine has an extensive pressure resilience and stability up to at least 50 GPa. In the case glycylglycine (the simplest polypeptide) an isosymmetric phase transition was observed at ~7GPa. In the framework of this project a novel QMD approach was developed aiming to simulate the response of organic, molecules (with focus on glycine) under the simultaneous application of high pressure and plastic shear (V-RDAC). The V-RDAC simulations predict that glycine readily reacts when subject to high strain rate shearing under applied compressive loads greater than 7 GPa.

36 MATERIALS SCIENCE↗
DOE OSTI2019

ToF-SIMS Depth Profiling of Organic Delta Layers with Low-Energy Cesium Ions: Depth Resolution Assessment

The advent of cluster ion beams has paved the way to the routine 3D analysis of organic heterojunctions. Alternatively, organic thin layers have also been successfully depth profiled with a low-energy cesium ion beam (Cs{sup +}), to exploit the high chemical reactivity of cesium atoms, acting as free-radical scavengers. Despite of this, little is known about the depth resolution associated with low-energy Cs{sup +} sputtering on organic multilayers. In this work, amino acids multilayers, consisting of phenylalanine delta layers alternated with tyrosine spacers, were used as model systems to assess the depth resolution associated with 500 eV Cs{sup +} depth profiles. High yields were obtained for quasi-molecular ions from both amino acids, and no significant chemical alteration was noticed under the monoatomic bombardment. A depth resolution as low as 4 nm is demonstrated without sensible degradation on a rather long profile depth (300 nm). Limited depth resolution (> 10 nm) along with high molecular degradation was previously reported on similar systems by combining low-energy Cs{sup +} with Ga{sup +} analysis beam. The use of the Bi{sub 3}{sup +} analysis beam results in a dramatic improvement of both the characteristic molecular signal intensities and the depth resolution. Even though the analysis beam fluence is very low compared to the sputtering beam fluence, data suggest that further reducing the analysis Bi{sub 3}{sup +} fluence could improve the depth resolution by ~ 1 nm. .

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

Structural basis for regulation of human calcium-sensing receptor by magnesium ions and an unexpected tryptophan derivative co-agonist

Ca 2+ -sensing receptors (CaSRs) modulate calcium and magnesium homeostasis and many (patho)physiological processes by responding to extracellular stimuli, including divalent cations and amino acids. We report the first crystal structure of the extracellular domain (ECD) of human CaSR bound with Mg 2+ and a tryptophan derivative ligand at 2.1 Å. The structure reveals key determinants for cooperative activation by metal ions and aromatic amino acids. The unexpected tryptophan derivative was bound in the hinge region between two globular ECD subdomains, and represents a novel high-affinity co-agonist of CaSR. The dissection of structure-function relations by mutagenesis, biochemical, and functional studies provides insights into the molecular basis of human diseases arising from CaSR mutations. The data also provide a novel paradigm for understanding the mechanism of CaSR-mediated signaling that is likely shared by the other family C GPCR [G protein (heterotrimeric guanine nucleotide–binding protein)–coupled receptor] members and can facilitate the development of novel CaSR-based therapeutics.

Binding Affinity↗
NASA NTRS2002

A site-directed mutagenesis analysis of tNOX functional domains

Constitutive NADH oxidase proteins of the mammalian cell surface exhibit two different activities, oxidation of hydroquinones (or NADH) and protein disulfide-thiol interchange which alternate to yield oscillatory patterns with period lengths of 24 min. A drug-responsive tNOX (tumor-associated NADH oxidase) has a period length of about 22 min. The tNOX cDNA has been cloned and expressed. These two proteins are representative of cycling oxidase proteins of the plant and animal cell surface. In this report, we describe a series of eight amino acid replacements in tNOX which, when expressed in Escherichia coli, were analyzed for enzymatic activity, drug response and period length. Replacement sites selected include six cysteines that lie within the processed plasma membrane (34 kDa) form of the protein, and amino acids located in putative drug and adenine nucleotide (NADH) binding domains. The latter, plus two of the cysteine replacements, resulted in a loss of enzymatic activity. The recombinant tNOX with the modified drug binding site retained activity but the activity was no longer drug-responsive. The four remaining cysteine replacements were of interest in that both activity and drug response were retained but the period length for both NADH oxidation and protein disulfide-thiol interchange was increased from 22 min to 36 or 42 min. The findings confirm the correctness of the drug and adenine nucleotide binding motifs within the tNOX protein and imply a potential critical role of cysteine residues in determining the period length.

Non-NASA Center↗
DOE OSTI2022

A mutagenic analysis of NahE, a hydratase-aldolase in the naphthalene degradative pathway

NahE is a hydratase-aldolase that converts o-substituted trans-benzylidenepyruvates (H, OH, or CO 2 - ) to benzaldehyde, salicylaldehyde, or 2-carboxybenzaldehyde, respectively, and pyruvate. The enzyme is in a bacterial degradative pathway for naphthalene, which is a toxic and persistent environmental contaminant. Sequence, crystallographic, and mutagenic analysis identified the enzyme as a member of the N-acetylneuraminate lyase (NAL) subgroup in the aldolase superfamily. As such, it has a conserved lysine (Lys183) and tyrosine (Tyr155), for Schiff base formation, as well as a GXXGE motif for binding of the pyruvoyl carboxylate group. A crystal structure of the selenomethionine derivative of NahE shows these active site elements along with nearby residues that might be involved in the mechanism and/or specificity. Mutations of five active site amino acids (Thr65, Trp128, Tyr155, Asn157, and Asn281) were constructed and kinetic parameters measured in order to assess the effect(s) on catalysis. Here, the results show that the two Trp128 mutants (Phe and Tyr) have the least effect on catalysis, whereas amino acids with bulky side chains at Thr65 (Val) and Asn281 (Leu) have the greatest effect. Changing Tyr155 to Phe and Asn157 to Ala also hinders catalysis, and the effects fall in between these extremes. These observations are put into a structural context using a crystal structure of the Schiff base of the reaction intermediate. Trapping experiments with substrate, Na(CN)BH 3 , and wild type enzyme and selected mutants mostly paralleled the kinetic analysis, and identified two salicylaldehyde-modified lysines: the active site lysine (Lys183) and one outside the active site (Lys279). The latter could be responsible for the observed inhibition of NahE by salicylaldehyde. Together, the results provide new insights into the NahE-catalyzed reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Region of Nipah virus C protein responsible for shuttling between the cytoplasm and nucleus

Nipah virus (NiV) causes severe encephalitis in humans, with high mortality. NiV nonstructural C protein (NiV-C) is essential for its pathogenicity, but its functions are unclear. In this study, we focused on NiV-C trafficking in cells and found that it localizes predominantly in the cytoplasm but partly in the nucleus. An analysis of NiV-C mutants showed that amino acids 2, 21–24 and 110–139 of NiV-C are important for its localization in the cytoplasm. Inhibitor treatment indicates that the nuclear export determinant is not a classical CRM1-dependent nuclear export signal. We also determined that amino acids 60–75 and 72–75 were important for nuclear localization of NiV-C. Furthermore, NiV-C mutants that had lost their capacity for nuclear localization inhibited the interferon (IFN) response more strongly than complete NiV-C. These results indicate that the IFN-antagonist activity of NiV-C occurs in the cytoplasm. -- Highlights: •Nipah virus (NiV) infection resulted in high mortality, but effective treatment has not been established. •Several reports revealed that NiV nonstructural C protein (NiV-C) was essential for NiV pathogenicity, however, whole of NiV-C function is still unknown. •Although nonstructural C proteins of other Paramyxoviruses are expressed in similar mechanism and exert similar activity, subcellular localization and cellular targets are different. In this study, we evaluated the subcellular localization of NiV-C. •To our knowledge, this is the first report showing that NiV-C shuttles between the nucleus and cytoplasm. We also clarified that NiV-C has nuclear export signal and nuclear localization signal using NiV-C deleted, alanine substitution mutants and enhanced green fluorescent protein (EGFP) fused proteins. •And we also showed that interferon (IFN) antagonist activity of NiV-C related to its subcellular localization. Our results indicate that NiV-C exert IFN antagonist activity in the cytoplasm.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Molecular Weight Calculator

This program can calculate the molecular weight and percent composition of chemical formulas and amino acids, providing a graphical user interface to edit the formulas and parsing options. It recognizes user-definable abbreviations, custom elemental isotopes, and can display up to 20 compounds simultaneously. It also includes a Mole/Mass Converter, Formula Finder, Capillary Flow Modeller, Amino Acid Notation Converter, Peptide Sequence Fragmentation Modeler, Isotopic Distribution Calculator, and built-in calculator. Full program documentation is available by pressing F1 during program operation.

Monroe, Matthew↗
NASA NTRS1993

Sequence and Genetic Characterization of etrA, an fnr Analog that Regulates Anaerobic Respiration in Shewanella putrefaciens MR-1

An electron transport regulatory gene, etrA, has been isolated and characterized from the obligate respiratory bacterium Shewanella putrefaciens MR-l. The deduced amino acid sequence of etrA (EtrA) shows a high degree of identity to both the Fnr of Escherichia coli (73.6%) and the analogous protein (ANR) of Pseudomonas aeruginosa (50.8%). The four active cysteine residues of Fnr are conserved in EtrA, and the amino acid sequence of the DNA-binding domains of the two proteins are identical. Further, S.putrefaciens etrA is able to complement an fnr mutant of E.coli. In contrast to fnr, there is no recognizable Fnr box upstream of the etrA sequence. Gene replacement etr.A mutants of MR-1 were deficient in growth on nitrite, thiosulfate, sulfite, trimethylamine-N-oxide, dimethyl sulfoxide, Fe(III), and fumarate, suggesting that EtrA is involved in the regulation of the corresponding reductase genes. However, the mutants were all positive for reduction of and growth on nitrate and Mn(IV), indicating that EtrA is not involved in the regulation of these two systems. Southern blots of S.putrefaciens DNA with use of etrA as a probe revealed the expected etrA bands and a second set of hybridization signals whose genetic and functional properties remain to be determined.

Saffarini, Daad A.↗
DOE OSTI2022

The Fe 2 O 3 (0001) Surface Under Electroreduction Conditions: A DFT Study of L-Cysteine Adsorption

Local catalyst surface structure and environment can play a significant role towards catalytic activity and selectivity. Surface functionalization using organic additives, such as amino acid chains or peptides, can alter surface properties. Density Functional Theory calculations are used to evaluate the potential dependent surface stability of different terminations of the Fe 2 O 3 (0001) surface. Adsorption of L-Cysteine in different redox states and through different binding modes (carboxylic: O-Fe, amine: N-Fe and thiol: S-Fe) is evaluated. At moderate electrochemical reducing conditions, Fe 2 O 3 (0001) exposes a partially reduced termination with both surface H atoms and undercoordinated Fe atoms in the outermost layer. L-Cysteine adsorption occurs most preferentially through carboxylic acid, O-Fe, binding and does not significantly alter the relative surface stability of different surface terminations. A partially reduced surface with L-Cysteine functionalization will be stable under electroreduction conditions. As a result, stable functionalization of an oxide material through amino acid chains or peptide adsorption may provide an additional design lever to develop improved catalytic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Taurine and β-alanine intraperitoneal injection in lactating mice modifies the growth and behavior of offspring

Highlights: • Taurine concentration in milk was decreased by the administration of β-alanine. • β-Alanine administration in lactating dams lowered the body weight of offspring. • Decreased taurine concentration in the brain induced hyperactivity in offspring. Taurine, one of the sulfur-containing amino acids, has several functions in vivo. It has been reported that taurine acts on γ-aminobutyric acid receptors as an agonist and to promote inhibitory neurotransmission. Milk, especially colostrum, contains taurine and it is known that milk taurine is essential for the normal development of offspring. β-Alanine is transported via a taurine transporter and a protein-assisted amino acid transporter, the same ones that transport taurine. The present study aimed to investigate whether the growth and behavior of offspring could be altered by modification of the taurine concentration in milk. Pregnant ICR mice were separated into 3 groups: 1) a control group, 2) a taurine group, and 3) a β-alanine group. During the lactation periods, dams were administered, respectively, with 0.9% saline (10 ml/kg, i.p.), taurine dissolved in 0.9% saline (43 mg/10 ml/kg, i.p.), or β-alanine dissolved in 0.9% saline (31 mg/10 ml/kg, i.p.). Interestingly, the taurine concentration in milk was significantly decreased by the administration of β-alanine, but not altered by the taurine treatment. The body weight of offspring was significantly lower in the β-alanine group. β-Alanine treatment caused a significant decline in taurine concentration in the brains of offspring, and it was negatively correlated with total distance traveled in the open field test at postnatal day 15. Thus, decreased taurine concentration in the brain induced hyperactivity in offspring. These results suggested that milk taurine may have important role of regulating the growth and behavior of offspring.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

High Genetic Potential for Proteolytic Decomposition in Northern Peatland Ecosystems

Nitrogen (N) is a common limitation on primary productivity, and its source remains unresolved in northern peatlands that are vulnerable to environmental change. Decomposition of complex organic matter into free amino acids has been proposed as an important N source, but the genetic potential of microorganisms mediating this process has not been examined. Such information can inform possible responses of northern peatlands to environmental change. We show high genetic potential for microbial production of free amino acids across a range of microbial guilds in northern peatlands. In particular, the abundance and diversity of bacterial genes encoding proteolytic activity suggest a predominant role for bacteria in regulating productivity and contrasts with a paradigm of fungal dominance of organic N decomposition. Our results expand our current understanding of coupled carbon and nitrogen cycles in northern peatlands and indicate that understudied bacterial and archaeal lineages may be central in this ecosystem’s response to environmental change.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Reduced Organic Outgassing in the NASA Osiris-Rex and Hayabusa2 Curation Facility by Careful Selection and Implementation of Cleanroom Construction Materials

In October 2021, NASA Johnson Space Center (JSC) Astromaterials Acquisition and Cu-ration Office in JSC bldg. 31 completed construction and commissioning of the OSIRIS-REx and Hayabusa2cleanroom laboratory suites along with new precision cleaning and advanced curation laboratories: •OSIRIS-REx Curation Cleanroom: ISO Class 5•Hayabusa2 Curation Cleanroom: ISO Class 5•Final Precision Cleaning Cleanroom: ISO Class 5•Advanced Precision Cleaning Cleanroom: ISO Class 6•PreClean Precision Cleaning Cleanroom: ISO Class 6•Advanced Curation Cleanroom: ISO Class 7The new curation facilities are designed for initial receiving, basic characterization, curation processing, and preliminary examination of carbonaceous asteroidal material. The facilities are also designed to enable long-term pristine sample storage to preserve the scientific integrity of each sample to enable decades of future re-search by the international science community. The scientific study of organics in general is critical for both missions. The OSIRIS-REx mission executed a stringent contamination control plan [1] where all sample hardware at time of sample acquisition would be at Level 100 A/2 per IEST-STD-CC1246D (non-volatile residue (NVR) < 500 ng/cm2). In addition, the mission imposed a requirement of <180 ng/cm2 for amino acids (and hydrazine) [1]. Given these mission requirements, long-term storage preservation requirements, and information from the Organic Contamination Baseline Study at JSC [2], the JSC Curation team decided to carefully select cleanroom construction materials that would not hinder the scientific search for amino acids and the study of organics in the samples [3].

astromaterials curation↗
NASA NTRS2004

Lunar and Planetary Science XXXV: Astrobiology

The presentations in this session are: 1. A Prototype Life Detection Chip 2. The Geology of Atlantis Basin, Mars, and Its Astrobiological Interest 3. Collecting Bacteria Together with Aerosols in the Martian Atmosphere by the FOELDIX Experimental Instrument Developed with a Nutrient Detector Pattern: Model Measurements of Effectivity 4. 2D and 3D X-ray Imaging of Microorganisms in Meteorites Using Complexity Analysis to Distinguish Field Images of Stromatoloids from Surrounding Rock Matrix in 3.45 Ga Strelley Pool Chert, Western Australia 4. Characterization of Two Isolates from Andean Lakes in Bolivia Short Time Scale Evolution of Microbiolites in Rapidly Receding Altiplanic Lakes: Learning How to Recognize Changing Signatures of Life 5. The Effect of Salts on Electrospray Ionization of Amino Acids in the Negative Mode 6. Determination of Aromatic Ring Number Using Multi-Channel Deep UV Native Fluorescence 7. Microbial D/H Fractionation in Extraterrestrial Materials: Application to Micrometeorites and Mars 8. Carbon Isotope Characteristics of Spring-fed Iron-precipitating Microbial Mats 9. Amino Acid Survival Under Ambient Martian Surface UV Lighting Extraction of Organic Molecules from Terrestrial Material: Quantitative Yields from Heat and Water Extractions 10. Laboratory Detection and Analysis of Organic Compounds in Rocks Using HPLC and XRD Methods 11. Thermal Decomposition of Siderite-Pyrite Assemblages: Implications for Sulfide Mineralogy in Martian Meteorite ALH84001 Carbonate Globules 12. Determination of the Three-Dimensional Morphology of ALH84001 and Biogenic MV-1 Magnetite: Comparison of Results from Electron Tomography and Classical Transmission Electron Microscopy 13. On the Possibility of a Crypto-Biotic Crust on Mars Based on Northern and Southern Ringed Polar Dune Spots 14. Comparative Planetology of the Terrestrial Inner Planets: Implications for Astrobiology 15. A Possible Europa Exobiology 16. A Possible Biogeochemical Model for Titan

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