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Results for “AMINO ACID”

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 OSTI2016

Differential sensitivity of Chironomus and human hemoglobin to gamma radiation

Chironomus ramosus is known to tolerate high doses of gamma radiation exposure. Larvae of this insect possess more than 95% of hemoglobin (Hb) in its circulatory hemolymph. This is a comparative study to see effect of gamma radiation on Hb of Chironomus and humans, two evolutionarily diverse organisms one having extracellular and the other intracellular Hb respectively. Stability and integrity of Chironomus and human Hb to gamma radiation was compared using biophysical techniques like Dynamic Light Scattering (DLS), UV-visible spectroscopy, fluorescence spectrometry and CD spectroscopy after exposure of whole larvae, larval hemolymph, human peripheral blood, purified Chironomus and human Hb. Sequence- and structure-based bioinformatics methods were used to analyze the sequence and structural similarities or differences in the heme pockets of respective Hbs. Resistivity of Chironomus Hb to gamma radiation is remarkably higher than human Hb. Human Hb exhibited loss of heme iron at a relatively low dose of gamma radiation exposure as compared to Chironomus Hb. Unlike human Hb, the heme pocket of Chironomus Hb is rich in aromatic amino acids. Higher hydophobicity around heme pocket confers stability of Chironomus Hb compared to human Hb. Previously reported gamma radiation tolerance of Chironomus can be largely attributed to its evolutionarily ancient form of extracellular Hb as evident from the present study. -- Highlights: •Comparison of radiation tolerant Chironomus Hb and radiation sensitive Human Hb. •Amino acid composition of midge and human heme confer differential hydrophobicity. •Heme pocket of evolutionarily ancient midge Hb provide gamma radiation resistivity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

The allosteric switching mechanism in bacteriophage MS2

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

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

CBH1 homologs and varian CBH1 cellulase

Disclosed are a number of homologs and variants of Hypocrea jecorina Cel7A (formerly Trichoderma reesei cellobiohydrolase I or CBH1), nucleic acids encoding the same and methods for producing the same. The homologs and variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted and/or deleted.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Variants of cellobiohydrolases

Disclosed are a number of homologs and variants of Hypocrea jecorina Ce17A (formerly Trichoderma reesei cellobiohydrolase I or CBH1), nucleic acids encoding the same and methods for producing the same. The homologs and variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted and/or deleted.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Identification of the Raptor-binding motif on Arabidopsis S6 kinase and its use as a TOR signaling suppressor

TOR (target of rapamycin) kinase signaling plays central role as a regulator of growth and proliferation in all eukaryotic cells and its key signaling components and effectors are also conserved in plants. Unlike the mammalian and yeast counterparts, however, we found through yeast two-hybrid analysis that multiple regions of the Arabidopsis Raptor (regulatory associated protein of TOR) are required for binding to its substrate. We also identified that a 44-amino acid region at the N-terminal end of Arabidopsis ribosomal S6 kinase 1 (AtS6K1) specifically interacted with AtRaptor1, indicating that this region may contain a functional equivalent of the TOS (TOR-Signaling) motif present in the mammalian TOR substrates. Transient over-expression of this 44-amino acid fragment in Arabidopsis protoplasts resulted in significant decrease in rDNA transcription, demonstrating a feasibility of developing a new plant-specific TOR signaling inhibitor based upon perturbation of the Raptor-substrate interaction. - Highlights: • Multiple regions on the Arabidopsis Raptor protein were found to be involved in substrate binding. • N-terminal end of the Arabidopsis ribosomal S6 kinase 1 (AtS6K1) was responsible for interacting with AtRaptor1. • The Raptor-interacting fragment of AtS6K1 could be utilized as an effective inhibitor of plant TOR signaling.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Elovl4 can effectively elongate C18 polyunsaturated fatty acids in loach Misgurnus anguillicaudatus

Highlights: • The full-length cDNAs of loach elovl4a and elovl4b were obtained by a RACE PCR method. • Phylogenetic and protein characterizations of these two genes were predicted. • Elovl4a differentially expressed at different tissues in loach, so did elovl4b. • Loach elovl4 could effectively elongate C18 PUFAs, which provided an alternative pathway for C20 biosynthesis in fish. In this study, full-length cDNA sequences of elovl4a and elovl4b from loach Misgurnus anguillicaudatus were cloned. The full-length cDNAs of loach elovl4a and elovl4b were 2423 and 2054bp, encoding 315 and 300 amino acids, respectively. The deduced amino acid sequences of elovl4a and elovl4b in loach both shared the highest identity with those of Danio rerio, whereas lower identity score between loach elovl4a and elovl4b was present. Temporal expression and tissue expression of loach elovl4a and elovl4b were studied by reverse transcriptase PCR. Results of the tissue expression analyses suggested different functions of loach elovl4a and elovl4b. Functional characterizations of loach elovl4a and elovl4b on synthesis of fatty acids, especially elongating C18 polyunsaturated fatty acids (PUFAs) to longer-chain fatty acids, were studied by heterologous expression in Saccharomyces cerevisiae. Loach elovl4a and elvol4b enzymes were able to elongate all fatty acids tested including 18:2n-6, 18:3n-3, 18:3n-6, 20:4n-6 and 20:5n-3. At last, expression levels of the two elovl4 genes of loach fin cells incubated with 18:2n-6 and 18:3n-3 of different concentrations were measured. Expressions of elovl4a and elovl4b of loach fin cells were significantly up-regulated by 18:2n-6 and 18:3n-3. The results obtained here indicated that loach elovl4 could effectively elongate C18 PUFAs. This was a systematic report of elovl4's elongating functions towards C18 and provided an alternative pathway for C20 biosynthesis in fish species.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Biochemical Properties and Catalytic Specificity of a Novel Neutral Serine Peptidase Secreted by Fungus Pyrenochaetopsis sp

The fungal genus Pyrenochaetopsis has received particular attention because of its different lifestyles, such as numerous plant pathogenic, saprophytic, and endophytic species. Its ability to infect plant cells relies heavily upon secreted peptidases. Here, we investigated the biochemical properties and catalytic specificity of a new serine peptidase secreted by the filamentous fungus Pyrenochaetopsis sp. We found that while this neutral serine peptidase displayed optimal activity at a pH of 7.0 and temperature of 45 °C, it tolerated a wide range of pH conditions and temperatures lower than 45 °C. Its peptidase activity was depressed by some metallic ions (such as aluminum, cobalt, and copper (II) chloride) and enhanced by others (such as sodium, lithium, magnesium, potassium, calcium, and manganese). Lastly, the enzyme showed the greatest specificity for non-polar amino acids, particularly leucine and isoleucine, and moderate specificity for basic and neutral polar amino acids. It displayed the least specificity for acidic residues.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Microenvironment control of porphyrin binding, organization, and function in peptide nanofiber assemblies

To take peptide materials from predominantly structural to functional assemblies, variations in cofactor binding sites must be engineered and controlled. Here, we have employed the peptide sequence c16-AHX 3 K 3 -CO 2 H where X 3 represents the aliphatic structural component of the peptide design that dictates β-sheet formation and upon self-assembly yields a change in the overall microenvironment surrounding the Zn protoporphyrin IX ((PPIX)Zn) binding site. All peptides studied yield β-sheet rich nanofibers highlighting the materials’ resiliency to amino acid substitution. We highlight that the (PPIX)Zn binding constants correlate strongly with amino acid side chain volume, where X = L or I yields the lowest dissociation constant values (K D ). The resulting microenvironment highlights the materials’ ability to control interchromophore electronic interactions such that slip-stacked cofacial arrangements are observed via exciton splitting in UV/visible and circular dichroism spectroscopy. Steady state and time-resolved photoluminescence suggests that greater interchromophore packing yields larger excimer populations and corresponding longer excimer association lifetimes (τ A ) which directly translates to shorter exciton diffusion lengths. In comparison to synthetic porphyrin molecular assemblies, this work demonstrates the ability to employ the peptide assembly to modulate the degree of cofactor arrangement, extent of excimer formation, and the exciton hopping rates all while in a platform amenable for producing polymer-like material

14 SOLAR ENERGY↗
NASA NTRS1984

Inhibition of intracellular proteolysis in muscle cultures by multiplication-stimulating activity

The effects of the insulin-like growth factor, multiplication-stimulating activity (MSA), on chick myotube cultures are studied. The results indicate that MSA is an effective anabolic agent regulating protein metabolism and amino acid uptake, but not sugar transport. Similar size effects on protein metabolism and amino acid uptake in serum-free media were observed in parallel studies with insulin, although insulin levels well in excess of the normal physiological range are required to produce significant effects. It is suggested that there is a generally low insulin sensitivity in cultured chick myotubes relative to adult tissues.

Janeczko, Richard A.↗
NASA NTRS1999

Tholins: Can They Provide a Substrate, Carbon and Nitrogen for Plant Production?

Tholin is a word coined to describe the entire class of complex organic solids produced in laboratory experiments where pre-biotic gaseous chemicals are subject to bombardment by high energy. The atomic composition of Titan tholin produced from 10 percent CH4 and 90 percent N2 in a simulation of Titan atmosphere irradiated by charged particles trapped in the magnetosphere of Saturn gave 67 percent C and 33 percent N. Hydrolysis of Titan tholin with 6N HCl produced a racemic mixture of biological and non-biological amino acids that was confirmed by GC/MS. Other tholins, that revealed the presence of amino acids, were UV tholin produced under possible primitive Earth conditions by irradiation of a mixture of gases (CH4, C2H6, NH3, H2S and liquid H2O) with long-wavelength ultraviolet light, representing the most abundant useful energy source for prebiological organic synthesis; Spark tholin in a crude simulation of Jupiter atmosphere using electrical discharge through a mixture of CH4, NH3, and H2O vapor. Pyrolytic GC/MS of Titan tholin produced more than one hundred organic compounds including saturated and unsaturated aliphatic hydrocarbons, substituted polycyclic aromatics, nitriles, amines, pyrroles, pyrazines, pyridines, pyrimidines, and the purine, adenine. Similar rich pyrolytic products were obtained with UV as well as Spark tholins. A range of two to four ring PAHs (Polycyclic Aromatic Hydrocarbons) in Spark as well as Titan tholins, some with one to four alkylation sites, were identified by two-step laser desorption/multiphoton ionization mass spectrometry and also confirmed by the synchronous fluorescence technique. Previous studies have demonstrated the potential for use of tholins as a source of carbon and energy by microbes. This paper describes studies that evaluate the potential for using different types of tholins as (a) a substrate for growing plants and (b) a source of carbon and nitrogen for plants. The data are interpreted in terms of the potential for using such tholins to grow plants for food in extraterrestrial habitats and also to speculate on the possibilities of abiotic evolution of plants.

Wignarajah, Kanapathipillai↗
DOE OSTI2015

Exploring the potential impact of an expanded genetic code on protein function

Significance We describe a general strategy that begins to allow us to address the question of whether an expanded genetic code provides an evolutionary advantage to an organism. A large library of β-lactamase variants with distinct noncanonical amino acids substituted randomly at single sites throughout the protein was generated and then subjected to an antibiotic growth-based screen to identify mutants with enhanced catalytic activity. We show that a unique noncanonical mutation in the enzyme β-lactamase significantly increases catalytic activity by unexpected mechanisms. These effects cannot be recapitulated by other canonical amino acids at this site, suggesting that an expanded set of building blocks beyond the canonical 20 may offer unique solutions to organisms in the evolution of new functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Plasticity and Constraints of tRNA Aminoacylation Define Directed Evolution of Aminoacyl-tRNA Synthetases

Genetic incorporation of noncanonical amino acids (ncAAs) has become a powerful tool to enhance existing functions or introduce new ones into proteins through expanded chemistry. This technology relies on the process of nonsense suppression, which is made possible by directing aminoacyl-tRNA synthetases (aaRSs) to attach an ncAA onto a cognate suppressor tRNA. However, different mechanisms govern aaRS specificity toward its natural amino acid (AA) substrate and hinder the engineering of aaRSs for applications beyond the incorporation of a single l-α-AA. Directed evolution of aaRSs therefore faces two interlinked challenges: the removal of the affinity for cognate AA and improvement of ncAA acylation. Here we review aspects of AA recognition that directly influence the feasibility and success of aaRS engineering toward d- and β-AAs incorporation into proteins in vivo. Emerging directed evolution methods are described and evaluated on the basis of aaRS active site plasticity and its inherent constraints.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Encephalomyocarditis virus Leader protein hinge domain is responsible for interactions with Ran GTPase

Encephalomyocarditis virus (EMCV), a Cardiovirus, initiates its polyprotein with a short 67 amino acid Leader (L) sequence. The protein acts as a unique pathogenicity factor, with anti-host activities which include the triggering of nuclear pore complex hyperphosphorylation and direct binding inhibition of the active cellular transport protein, Ran GTPase. Chemical modifications and protein mutagenesis now map the Ran binding domain to the L hinge-linker region, and in particular, to amino acids 35–40. Large deletions affecting this region were shown previously to diminish Ran binding. New point mutations, especially K35Q, D37A and W40A, preserve the intact L structure, abolish Ran binding and are deficient for nucleoporin (Nup) hyperphosphorylation. Ran itself morphs through multiple configurations, but reacts most effectively with L when in the GDP format, preferably with an empty nucleotide binding pocket. Therefore, L:Ran binding, mediated by the linker-hinge, is a required step in L-induced nuclear transport inhibition. - Highlights: • The hinge domain provides critical residues in Cardiovirus L:Ran complex formation. • Leader prefers to bind Ran in a nucleotide free, GDP-conformation. • L-induced Nup62 phosphorylation is reduced with Ran-deficient binding mutations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Discriminating between adaptive and carcinogenic liver hypertrophy in rat studies using logistic ridge regression analysis of toxicogenomic data: The mode of action and predictive models

Chemical exposure often results in liver hypertrophy in animal tests, characterized by increased liver weight, hepatocellular hypertrophy, and/or cell proliferation. While most of these changes are considered adaptive responses, there is concern that they may be associated with carcinogenesis. In this study, we have employed a toxicogenomic approach using a logistic ridge regression model to identify genes responsible for liver hypertrophy and hypertrophic hepatocarcinogenesis and to develop a predictive model for assessing hypertrophy-inducing compounds. Logistic regression models have previously been used in the quantification of epidemiological risk factors. DNA microarray data from the Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System were used to identify hypertrophy-related genes that are expressed differently in hypertrophy induced by carcinogens and non-carcinogens. Data were collected for 134 chemicals (72 non-hypertrophy-inducing chemicals, 27 hypertrophy-inducing non-carcinogenic chemicals, and 15 hypertrophy-inducing carcinogenic compounds). After applying logistic ridge regression analysis, 35 genes for liver hypertrophy (e.g., Acot1 and Abcc3) and 13 genes for hypertrophic hepatocarcinogenesis (e.g., Asns and Gpx2) were selected. The predictive models built using these genes were 94.8% and 82.7% accurate, respectively. Pathway analysis of the genes indicates that, aside from a xenobiotic metabolism-related pathway as an adaptive response for liver hypertrophy, amino acid biosynthesis and oxidative responses appear to be involved in hypertrophic hepatocarcinogenesis. Early detection and toxicogenomic characterization of liver hypertrophy using our models may be useful for predicting carcinogenesis. In addition, the identified genes provide novel insight into discrimination between adverse hypertrophy associated with carcinogenesis and adaptive hypertrophy in risk assessment. - Highlights: • Hypertrophy (H) and hypertrophic carcinogenesis (C) were studied by toxicogenomics. • Important genes for H and C were selected by logistic ridge regression analysis. • Amino acid biosynthesis and oxidative responses may be involved in C. • Predictive models for H and C provided 94.8% and 82.7% accuracy, respectively. • The identified genes could be useful for assessment of liver hypertrophy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Revalidation of recombinant aequorin as a light emission standard: Estimation of specific activity of Gaussia luciferase

Highlights: • Recombinant aequorin (reAequorin) was evaluated for use as a light emission standard. • reAequorin protein concentration was determined by amino acid composition analysis. • The presence of active reAequorin was confirmed by the absorption peak ratio at 280/460 nm. • The I{sub max} value of Gaussia luciferase was 7.5-fold higher than that of reAequorin. • reAequorin can generally be used as a light emission standard. To validate the use of recombinant aequorin (reAequorin) as a light emission standard, the protein concentrations of highly purified reAequorin were determined by amino acid composition analysis, and the presence of active reAequorin was confirmed by the ratio of absorbance peak at 460 nm to that at 280 nm. The high correlation of the luminescence intensity with the protein concentration showed that reAequorin could be used for a light emission standard to study the luminescence properties of luciferases and to evaluate the detection sensitivity of luminometers. The specific activity of Gaussia luciferase with I{sub max} was 7.5-fold higher than that of reAequorin and was calculated to be 3.8 × 10{sup 16} quanta/mg protein.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

SJL bone marrow-derived macrophages do not have IRF3 mutations and are highly susceptible to Theiler's virus infection

It is well known that SJL mice are susceptible to Theiler's murine encephalomyelitis virus (TMEV)-induced demyelinating disease while C57BL6 (B6) and B10 mice are resistant, and H-2{sup s} on a B10 background (B10.S) contributes modestly to susceptibility. A recent study linked two IRF3 non-conservative mutations in SJL compared to B10.S mice to resistance to TMEV infection of SJL peritoneal-derived macrophages, an observation of practical interest in light of the central role of IRF3 transcription factor in the type I interferon (IFN) response. However, we did not find these non-conservative mutations among SJL, B10.S, B6 and B10 mice in the IRF3 amino acid sequence, and show SJL bone marrow-derived macrophages infected with TMEV exhibit increased virus RNA replication and infectious virus yields as well as greater IL-6 production than C57Bl strain (including B10.S) cultures. - Highlights: • We confirmed that Theiler's murine encephalomyelitis virus (TMEV)-infection in bone marrow-derived macrophages is significantly greater in susceptible SJL macrophages than in resistant C57BL macrophages. • We failed to confirm two non-conservative amino acid changes in IRF3 identified previously in SJL mice or differences in IRF3 activation after infection between the two mouse strain. However, IL-6 levels were significantly greater in infected SJL macrophages late in the infectious cycle. • The data also suggest that addition of the cytokine IL-6 to infected macrophage cultures is modestly antiviral.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Biomimetic peptide-based models of [FeFe]-hydrogenases: utilization of phosphine-containing peptides

Two synthetic strategies for incorporating diiron analogues of [FeFe]-hydrogenases into short peptides via phosphine functional groups are described in this paper. First, utilizing the amine side chain of lysine as an anchor, phosphine carboxylic acids can be coupled via amide formation to resin-bound peptides. Second, artificial, phosphine-containing amino acids can be directly incorporated into peptides via solution phase peptide synthesis. The second approach is demonstrated using three amino acids each with a different phosphine substituent (diphenyl, diisopropyl, and diethyl phosphine). In total, five distinct monophosphine-substituted, diiron model complexes were prepared by reaction of the phosphine-peptides with diiron hexacarbonyl precursors, either (μ-pdt)Fe 2 (CO) 6 or (μ-bdt)Fe 2 (CO) 6 (pdt = propane-1,3-dithiolate, bdt = benzene-1,2-dithiolate). Formation of the complexes was confirmed by UV/Vis, FTIR and 31 P NMR spectroscopy. Electrocatalysis by these complexes is reported in the presence of acetic acid in mixed aqueous-organic solutions. Addition of water results in enhancement of the catalytic rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗