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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Mass energy-absorption coefficients and average atomic energy-absorption cross-sections for amino acids in the energy range 0.122-1.330 MeV

Mass attenuation coefficients of amino acids such as n-acetyl-l-tryptophan, n-acetyl-l-tyrosine and d-tryptophan were measured in the energy range 0.122-1.330 MeV. NaI (Tl) scintillation detection system was used to detect gamma rays with a resolution of 8.2% at 0.662 MeV. The measured attenuation coefficient values were then used to determine the mass energy-absorption coefficients (σ{sub a,en}) and average atomic energy-absorption cross sections (μ{sub en}/ρ) of the amino acids. Theoretical values were calculated based on XCOM data. Theoretical and experimental values are found to be in good agreement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Hybride magnetic nanostructure based on amino acids functionalized polypyrrole

Conducting polypyrrole is especially promising for many commercial applications because of its unique optical, electric, thermal and mechanical properties. We report the synthesis and characterization of novel pyrrole functionalized monomers and core-shell hybrid nanostructures, consisting of a conjugated polymer layer (amino acids functionalized pyrrole copolymers) and a magnetic nanoparticle core. For functionalization of the pyrrole monomer we used several amino acids: tryptophan, leucine, phenylalanine, serine and tyrosine. These amino acids were linked via different types of hydrophobic linkers to the nitrogen atom of the pyrrole monomer. The magnetic core-shell hybrid nanostructures are characterized by various methods such as FTIR spectroscopy, transmission electron microscopy (TEM) and magnetic measurements.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Bio-treatment of poplar via amino acid for interface control in biocomposites

Advanced biocomposites reinforced by abundant biomass-derived fillers can add a revenue stream to enhance the economic viability of biofuel production chains and the energy efficiency of the composite industry. However, the low stiffness of biopolymers limits their use in structural applications. Poplar fibers (mesh size: <180 μm, Populus spp.), an abundant waste from the wood industry, were used as bio-filler to fabricate high-performance biocomposites based on polylactic acid (PLA), in which the poplar fibers were modified by an amino acid (l-lysine). As a benefit of the amino acid treatment, the tensile Young's moduli of the lysine/poplar/PLA composites increased by up to 68% with the addition of a small amount of lysine, compared with neat PLA. At the same time, the tensile strength, failure strain, and Young's modulus of the poplar/PLA composites all increased after adding only 0.1 wt % of lysine. It has been observed that the lysine content has a significant effect on the decomposition temperature, complex viscosity, storage modulus, crystallization temperature, and crystallinity of composites. The fracture surfaces of the composites with an optimum lysine content had fewer voids and were more compact compared with composites without any lysine. The pores on the surfaces of poplar fibers became more available for the penetration of PLA molecules as a result of lysine addition. Finally, this study presents a facile method for reinforcing biocomposites with extremely low-cost and environmentally friendly biofillers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Binding mechanism and binding free energy of amino acids and citrate to hydroxyapatite surfaces as a function of crystallographic facet, pH, and electrolytes

Hydroxyapatite (HAP) is the major mineral phase in bone and teeth. The interaction of individual amino acids and citrate ions with different crystallographic HAP surfaces has remained uncertain for decades, creating a knowledge gap to rationally design interactions with peptides, proteins, and drugs. In this contribution, we quantify the binding mechanisms and binding free energies of the 20 end-capped natural amino acids and citrate ions on the basal (001) and prismatic (010)/(020) planes of hydroxyapatite at pH values of 7 and 5 for the first time at the molecular scale. We utilized over 1500 steered molecular dynamics simulations with highly accurate potentials that reproduce surface and hydration energies of (hkl) hydroxyapatite surfaces at different pH values. Charged residues demonstrate a much higher affinity to HAP than charge-neutral species due to the formation of superficial ion pairs and ease of penetration into layers of water molecules on the mineral surface. Binding free energies range from 0 to -60 kJ/mol and were determined with ~10% uncertainty. The highest affinity was found for citrate, followed by Asp(-) and Glu(-), and followed after a gap by Arg(+), Lys(+), as well as by His(+) at pH 5. The (hkl)-specific area density of calcium ions, the protonation state of phosphate ions, and subsurface directional order of the ions in HAP lead to surface-specific binding patterns. Amino acids without ionic side groups exhibit weak binding, between -3 and 0 kJ/mol, due to difficulties to penetrate the first layer of water molecules on the apatite surfaces. We explain recognition processes that remained elusive in experiments, in prior simulations, discuss agreement with available data, and reconcile conflicting interpretations. In conclusion, the findings can serve as useful input for the design of peptides, proteins, and drug molecules for the modification of bone and teeth-related materials, as well as control of apatite mineralization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Designing Light-Activated Charge-Separating Proteins with a Naphthoquinone Amino Acid

The first principles design of manmade redox-protein maquettes is used to clarify the physical/chemical engineering supporting the mechanisms of natural enzymes with a view to recapitulate and surpass natural performance. Herein, we use intein-based protein semisynthesis to pair a synthetic naphthoquinone amino acid (Naq) with histidine-ligated photoactive metal–tetrapyrrole cofactors, creating a 100 μs photochemical charge separation unit akin to photosynthetic reaction centers. By using propargyl groups to protect the redox-active para-quinone during synthesis and assembly while permitting selective activation, we gain the ability to employ the quinone amino acid redox cofactor with the full set of natural amino acids in protein design. Direct anchoring of quinone to the protein backbone permits secure and adaptable control of intraprotein electron-tunneling distances and rates.

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

Exploring pH Dynamics in Amino Acid Solutions Under Low-Temperature Plasma Exposure

Low-temperature plasma (LTP) offers a promising alternative for cancer therapy, as it targets malignant cells selectively while minimizing damage to healthy tissues. Upon interaction with an aqueous solution, LTP generates reactive oxygen and nitrogen species and thereby influences the solution’s pH, which is a crucial factor in cancer proliferation and response to treatment. This study investigated the effects of LTP on the pH of aqueous solutions, with a focus on the effect of LTP parameters such as voltage, frequency, and irradiation time. In addition, it explored the influence of solution composition, specifically the presence of the amino acids, glycine and serine, on pH changes; these amino acids are known to play significant roles in cancer proliferation. Our results indicated that LTP induces acidification in deionized water, in which the extent of acidification increased proportionally with plasma parameters. In glycine-containing solutions, pH changes were concentration-dependent, whereas serine-containing solutions maintained a constant pH across all tested concentrations. To investigate potential changes to the structural properties of glycine and serine exposed to LTP that could be responsible for different pH responses, we analyzed the samples using FTIR spectroscopy. A significant decrease in absorbance was observed for solutions with low concentrations of amino acids, suggesting their degradation.

Biochemistry & Molecular Biology↗
DOE OSTI2018

Evaluating the impacts of amino acids in the second and outer coordination spheres of Rh-bis(diphosphine) complexes for CO 2 hydrogenation

To explore the influence of a biologically inspired second and outer coordination sphere on Rh-bis(diphosphine) CO 2 hydrogenation catalysts, a series of five complexes were prepared by varying the substituents on the pendant amine in the P(Et) 2 CH 2 N R CH 2 P(Et) 2 ligands (P Et N R P Et ), where R consists of methyl ester modified amino acids, including three neutral (glycine methyl ester (GlyOMe), leucine methyl ester (LeuOMe), and phenylalanine methyl ester (PheOMe)), one acidic (aspartic acid dimethyl ester (AspOMe)) and one basic (histidine methyl ester (MeHisOMe)) amino acid esters. The turnover frequencies (TOFs) for CO 2 hydrogenation for each of these complexes were compared to those of the non-amino acid containing [Rh(depp) 2 ] + (depp) and [Rh(P Et N Me P Et ) 2 ] + (NMe) complexes. Each complex is catalytically active for CO 2 hydrogenation to formate under mild conditions in THF. Catalytic activity spanned a factor of four, with the most active species being the NMe catalyst, while the slowest were the GlyOMe and the AspOMe complexes. Finally, when compared to a similar set of catalysts with phenyl-substituted phosphorous groups, a clear contribution of the outer coordination sphere is seen for this family of CO 2 hydrogenation catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Innovative use of CaO in combination with amino acid salt to convert CO 2 as CaCO 3 nanoparticles under mild pH and low temperature

The increasing demand for sustainable CO 2 management has driven the development of innovative methods that can convert point source CO 2 into value-added products. In this study, CaO in combination with amino acid salt was used to convert CO 2 into CaCO 3 nanoparticles. Different from the conventional method where CO 2 diffusion presents a major challenge in reacting with CaO to form CaCO 3 , amino acid salt solvent was applied to absorb CO 2 first and then rapidly reacted with CaO to form CaCO 3 nanoparticles (∼50 nm) at a low temperature (e.g., 60 °C). Our experiments showed that at a glycine (Gly)/NaOH ratio of 2:1 or 3:1, the solution pH values during the CO 2 absorption and conversion were about 8–9 at 60 °C, while at a ratio of 1:1, the solution pH values were about 9–11; without Gly, the solution pH values were about 12. Gly-optimized solvent substantially reduced corrosion risk to reactors. In addition, the use of amino acid (i.e., Gly) led to much smaller CaCO 3 particles, distinctly different chemical phases, and fundamentally different chemical reactions. Moreover, in the presence of Gly, the solution pH was completely reversed and the solution was regenerated for cyclic use when CaO was added. The solvent was recyclable and reusable, highlighting the cost-effectiveness and sustainability of this approach. The Gly-modulated CaCO 3 nanoparticles may have significant potential for industrial applications in the biomedicine, construction, plastics, and rubber industries.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Solvation thermodynamics of amino acid side chains on a short peptide backbone

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Branched-chain amino acid specialization drove diversification within Calditenuaceae ( Caldarchaeia ) and enables their cultivation

Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10 6 cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.

Biological and medical sciences↗
DOE OSTI2014

High resolution NMR study of T{sub 1} magnetic relaxation dispersion. IV. Proton relaxation in amino acids and Met-enkephalin pentapeptide

Nuclear Magnetic Relaxation Dispersion (NMRD) of protons was studied in the pentapeptide Met-enkephalin and the amino acids, which constitute it. Experiments were run by using high-resolution Nuclear Magnetic Resonance (NMR) in combination with fast field-cycling, thus enabling measuring NMRD curves for all individual protons. As in earlier works, Papers I–III, pronounced effects of intramolecular scalar spin-spin interactions, J-couplings, on spin relaxation were found. Notably, at low fields J-couplings tend to equalize the apparent relaxation rates within networks of coupled protons. In Met-enkephalin, in contrast to the free amino acids, there is a sharp increase in the proton T{sub 1}-relaxation times at high fields due to the changes in the regime of molecular motion. The experimental data are in good agreement with theory. From modelling the relaxation experiments we were able to determine motional correlation times of different residues in Met-enkephalin with atomic resolution. This allows us to draw conclusions about preferential conformation of the pentapeptide in solution, which is also in agreement with data from two-dimensional NMR experiments (rotating frame Overhauser effect spectroscopy). Altogether, our study demonstrates that high-resolution NMR studies of magnetic field-dependent relaxation allow one to probe molecular mobility in biomolecules with atomic resolution.

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

NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials

Noncanonical Amino Acids (NCAAs) provide numerous avenues for introduction of novel functionality to peptides and proteins. NCAAs can be incorporated through solid phase synthesis or genetic code expansion in conjugation with heterologous expression of the encoded protein modification. Due to the difficulty of synthesis, wide chemical space and lack of empirically resolved structures modeling the effects of NCAA mutation is critical for rational protein design. To evaluate the structural and functional perturbations NCAAs introduce we utilize molecular potentials that describe the forces in protein structure. Most potentials such as CHARMM are designed to model canonical residues but can be parameterized in include novel NCAAs. Here, in this work, we introduce NCAP a software package to generate CHARMM compatible parameters from quantum chemical calculation. Unlike currently available tools NCAP is designed to recognize NCAA structure and automatically bridge the gap between DFT calculations and potential parameters. For our software we discuss workflow, validation against canonical parameter sets and comparison to published NCAA-protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

miR-124-3p affects the formation of intramuscular fat through alterations in branched chain amino acid consumption in sheep

Highlights: • BCKDHA gene is a target gene of miR-124-3p. • miR-124-3p inhibits the adipogenic differentiation of stromal vascular fractions. • Branched chain amino acids consumption is vital for the adipogenic differentiation of stromal vascular fractions. Intramuscular fat is used to determine meat quality in animals; however, factors affecting branched chain amino acid (BCAA) catabolism, which fuels adipogenesis and lipogenesis, remain unclear. To better understand the post-transcriptional influence on BCAA catabolism during adipogenesis, we investigated the role of miR-124-3p. Stromal vascular fraction (SVF) cells were isolated from skeletal muscle of sheep, and induced to differentiate. We determined the roles of miR-124-3p and its predicted target, branched chain keto acid dehydrogenase E1, alpha polypeptide (BCKDHA), in adipogenic differentiation and lipogenesis of SVFs after overexpressing or inhibiting miR-124-3p or BCKDHA, respectively. miR-124-3p altered the luciferase activity of constructs containing 3′-UTR of BCKDHA and the formation of lipid droplets, along with the adipogenic markers and BCAA consumption. Besides, the adipogenic performance and BCAA consumption in BCKDHA-overexpressing or knocked-down SVFs and the expression of adipogenic marker genes were altered. We demonstrate that miR-124-3p is an important factor for adipogenesis and provide insights into the formation of intramuscular fat in animals.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

In vivo unnatural amino acid expression in the methylotrophic yeast Pichia pastoris

The invention provides orthogonal translation systems for the production of polypeptides comprising unnatural amino acids in methylotrophic yeast such as Pichia pastoris. Methods for producing polypeptides comprising unnatural amino acids in methylotrophic yeast such as Pichia pastoris are also provided.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Orthogonal translation components for the in vivo incorporation of unnatural amino acids

The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetase that can incorporate unnatural amino acid into proteins produced in eubacterial host cells such as E. coli, or in a eukaryotic host such as a yeast cell. The invention provides, for example but not limited to, novel orthogonal synthetases, methods for identifying and making the novel synthetases, methods for producing proteins containing unnatural amino acids, and translation systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Effect of essential amino acids on enteroids: Methionine deprivation suppresses proliferation and affects differentiation in enteroid stem cells

We investigated the effects of essential amino acids on intestinal stem cell proliferation and differentiation using murine small intestinal organoids (enteroids) from the jejunum. By selectively removing individual essential amino acids from culture medium, we found that 24 h of methionine (Met) deprivation markedly suppressed cell proliferation in enteroids. This effect was rescued when enteroids cultured in Met deprivation media for 12 h were transferred to complete medium, suggesting that Met plays an important role in enteroid cell proliferation. In addition, mRNA levels of the stem cell marker leucine-rich repeat-containing G protein-coupled receptor 5 (Lgr5) decreased in enteroids grown in Met deprivation conditions. Consistent with this observation, Met deprivation also attenuated Lgr5-EGFP fluorescence intensity in enteroids. In contrast, Met deprivation enhanced mRNA levels of the enteroendocrine cell marker chromogranin A (ChgA) and markers of K cells, enterochromaffin cells, goblet cells, and Paneth cells. Immunofluorescence experiments demonstrated that Met deprivation led to an increase in the number of ChgA-positive cells. These results suggest that Met deprivation suppresses stem cell proliferation, thereby promoting differentiation. In conclusion, Met is an important nutrient in the maintenance of intestinal stem cells and Met deprivation potentially affects cell differentiation. - Highlights: • Met influences the proliferation of enteroids. • Met plays a crucial role in the maintenance of stem cells. • Met deprivation potentially promotes differentiation into secretory cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

A Single Amino Acid Change in Nramp6 from Sedum Alfredii Hance Affects Cadmium Accumulation

SaNramp6 in Sedum alfredii encodes a membrane-localized metal transporter. We isolated the SaNramp6h allele from the hyperaccumulating ecotype (HE) of S. alfredii . When this allele was expressed in transgenic yeast and Arabidopsis thaliana , it enhanced their cadmium (Cd) sensitivity by increased Cd transport and accumulation. We isolated another allele, SaNramp6n , from a nonhyperaccumulating ecotype (NHE) of S. alfredii . Amino acid sequence comparisons revealed three amino acid differences between SaNramp6h and SaNramp6n. We investigated the Cd transport activity of the Nramp6 allele, and determined which residues are essential for the transport activity. We conducted structure-function analyses of SaNramp6 based on site-directed mutagenesis and functional assays of the mutants in yeast and Arabidopsis . The three residues that differed between SaNramp6h and SaNramp6n were mutated. Only the L157P mutation of SaNramp6h impaired Cd transport. The other mutations, S218N and T504A, did not affect the transport activity of SaNramp6h, indicating that these residues are not essential for metal selectivity. Transgenic plants overexpressing SaNramp6h L157P showed altered metal accumulation in shoots and roots. Our results suggest that the conserved site L157 is essential for the high metal transport activity of SaNramp6h. This information may be useful for limiting or increasing Cd transport by other plant natural resistance associated macrophage protein (NRAMP) proteins.

59 BASIC BIOLOGICAL SCIENCES↗