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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS1998

Prebiotic Amino Acid Thioester Synthesis: Thiol-Dependent Amino Acid Synthesis from Formose substrates (Formaldehyde and Glycolaldehyde) and Ammonia

Formaldehyde and glycolaldehyde (substrates of the formose autocatalytic cycle) were shown to react with ammonia yielding alanine and homoserine under mild aqueous conditions in the presence of thiol catalysts. Since similar reactions carried out without ammonia yielded alpha-hydroxy acid thioesters, the thiol-dependent synthesis of alanine and homoserine is presumed to occur via amino acid thioesters-intermediates capable of forming peptides. A pH 5.2 solution of 20 mM formaldehyde, 20 mM glycolaldehyde, 20 mM ammonium chloride, 23 mM 3-mercaptopropionic acid, and 23 mM acetic acid that reacted for 35 days at 40 C yielded (based on initial formaldehyde) 1.8% alanine and 0.08% homoserine. In the absence of thiol catalyst, the synthesis of alanine and homoserine was negligible. Alanine synthesis required both formaldehyde and glycolaldehyde, but homoserine synthesis required only glycolaldehyde. At 25 days the efficiency of alanine synthesis calculated from the ratio of alanine synthesized to formaldehyde reacted was 2.1%, and the yield (based on initial formaldehyde) of triose and tetrose intermediates involved in alanine and homoserine synthesis was 0.3 and 2.1%, respectively. Alanine synthesis was also seen in similar reactions containing only 10 mM each of aldehyde substrates, ammonia, and thiol. The prebiotic significance of these reactions that use the formose reaction to generate sugar intermediates that are converted to reactive amino acid thioesters is discussed.

Weber, Arthur L.↗
NASA NTRS2021

Low total abundances and a predominance of n-ω-amino acids in enstatite chondrites: Implications for thermal stability of amino acids in the inner solar system

Investigating the organic contents of enstatite chondrite meteorites may offer insights into both early inner solar system and early Earth chemistry. Enstatite chondrite meteorites have highly reduced and anhydrous compositions, and their bulk isotopic compositions closely resemble terrestrial values, suggesting that their parent body asteroids accreted within the inner protoplanetary disk and were a primary contributor during Earth’s late accretion (Javoy, 1995; Piani et al., 2020). Here, we present the first report of amino acids in enstatite chondrite meteorite samples. Three EH3 meteorites were analyzed (Dominion Range [DOM] 14021, Larkman Nunatak [LAR] 12001, and Larkman Nunatak 06252). The acid-hydrolyzed water extracts of the meteorites contained low abundances (1.5–215.9 pmol per g) of n-ω-amino acids (glycine, β-alanine, γ-amino-n-butyric acid [γ- ABA], δ-amino-n-valeric acid [δ-AVA], and ϵ-amino-n-caproic acid [ϵ-ACA]), but amino acids were not present above detection limits in the nonhydrolyzed samples. The low amino acid abundances and the predominance of n-ω-amino acids resemble amino acid distributions previously observed for thermally altered chondrites. These results suggest that the parent body asteroid was not conducive to the synthesis and/or preservation of α-amino acids, or free amino acids in general, and that EH3 chondrite-like material may not have been a primary contributor of diverse or abundant free amino acids to the early Earth.

Danielle N. Simkus↗
NASA NTRS2021

Low Total Abundances and a Predominance of n-ω-Amino Acids in Enstatite Chondrites: Implications for Thermal Stability of Amino Acids in the Inner Solar System

Investigating the organic contents of enstatite chondrite meteorites may offer insights into both early inner solar system and early Earth chemistry. Enstatite chondrite meteorites have highly reduced and anhydrous compositions, and their bulk isotopic compositions closely resemble terrestrial values, suggesting that their parent body asteroids accreted within the inner protoplanetary disk and were a primary contributor during Earth’s late accretion (Javoy et al., 1995; Piani et al., 2020). Here, we present the first report of amino acids in enstatite chondrite meteorite samples. Three EH3 meteorites were analyzed (Dominion Range 14021, Larkman Nunatak 12001, and Larkman Nunatak 06252). The acid-hydrolyzed water extracts of the meteorites contained low abundances (1.5 – 215.9 pmol/g) of n-ω-amino acids (glycine, β-alanine, γ-amino-n-butyric acid (γ-ABA), δ-amino-n-valeric acid (δ-AVA), and ε-amino-n-caproic acid (ε-ACA)), but amino acids were not present above detection limits in the non-hydrolyzed samples. The low amino acid abundances and the predominance of n-ω-amino acids resembles amino acid distributions previously observed for thermally altered chondrites. These results suggest that the parent body asteroid was not conducive to the synthesis and/or preservation of α-amino acids, or free amino acids in general, and that EH3 chondrite-like material may not have been a primary contributor of diverse or abundant free amino acids to the early Earth.

Danielle N Simkus↗
NASA NTRS1999

Formation of Amino Acid Thioesters for Prebiotic Peptide Synthesis: Catalysis By Amino Acid Products

The origin of life can be described as a series of events in which a prebiotic chemical process came increasingly under the control of its catalytic products. In our search for this prebiotic process that yielded catalytic takeover products (such as polypeptides), we have been investigating a reaction system that generates peptide-forming amino acid thioesters from formaldehyde, glycolaldehyde, and ammonia in the presence of thiols. As shown below, this model process begins by aldol condensation of formaldehyde and glycolaldehyde to give trioses and releases. These sugars then undergo beta-dehydration yielding their respective alpha-ketoaldehydes. Addition of ammonia to the alpha-ketoaldehydes yields imines which can either: (a) rearrange in the presence of thesis to give amino acid thioesters or (be react with another molecule of aldehyde to give imidazoles. This 'one-pot' reaction system operates under mild aqueous conditions, and like modem amino acid biosynthesis, uses sugar intermediates which are converted to products by energy-yielding redox reactions. Recently, we discovered that amino acids, such as the alanine reaction product, catalyze the first and second steps of the process. In the presence of ammonia the process also generates other synthetically useful products, like the important biochemical -- pyruvic acid.

Weber, Arthur L.↗
NASA NTRS1992

Preferential hydrophobic interactions are responsible for a preference of D-amino acids in the aminoacylation of 5'-AMP with hydrophobic amino acids

We have studied the chemistry of aminoacyl AMP to model reactions at the 3' terminus of aminoacyl tRNA for the purpose of understanding the origin of protein synthesis. The present studies relate to the D, L preference in the esterification of 5'-AMP. All N-acetyl amino acids we studied showed faster reaction of the D-isomer, with a generally decreasing preference for D-isomer as the hydrophobicity of the amino acid decreased. The beta-branched amino acids, Ile and Val, showed an extreme preference for D-isomer. Ac-Leu, the gamma-branched amino acid, showed a slightly low D/L ratio relative to its hydrophobicity. The molecular basis for these preferences for D-isomer is understandable in the light of our previous studies and seems to be due to preferential hydrophobic interaction of the D-isomer with adenine. The preference for hydrophobic D-amino acids can be decreased by addition of an organic solvent to the reaction medium. Conversely, peptidylation with Ac-PhePhe shows a preference for the LL isomer over the DD isomer.

Non-NASA Center↗
DOE OSTI2017

Evaluating the role of acidic, basic, and polar amino acids and dipeptides on a molecular electrocatalyst for H 2 oxidation

Amino acids and peptides have been shown to have a significant influence on the H2 production and oxidation reactivity of Ni(P R 2 N R’ 2 ) 2 , where P R 2 N R’ 2 = 1,5-diaza-3,7-diphosphacyclooctane, R is either phenyl (Ph) or cyclohexyl (Cy), and R’ is either an amino acid or peptide. Most recently, the Ni(P Cy 2 Naminoacid 2 ) 2 complexes (CyAA) have shown enhanced H 2 oxidation rates, water solubility, and in the case of arginine (CyArg) and phenylalanine (CyPhe), electrocatalytic reversibility. Both the backbone –COOH and side chain interactions were shown to be critical to catalytic performance. Here we further investigate the roles of the outer coordination sphere by evaluating amino acids with acidic, basic, and hydrophilic side chains, as well as dipeptides which combine multiple successful features from previous complexes. Six new complexes were prepared, three containing single amino acids: aspartic acid (CyAsp), lysine (CyLys), and serine (CySer) and three containing dipeptides: glycine-phenylalanine (Cy(GlyPhe)), phenylalanine-glycine (Cy(PheGly)), and aspartic acid-phenylananine (Cy(AspPhe)). The resulting catalytic performance demonstrates that complexes need both interactions between side chain and –COOH groups for fast, efficient catalysis. The fastest of all of the catalysts, Cy(AspPhe), had both of these features, while the other dipeptide complexes with an amide replacing the -COOH were both slower; however, the amide group was demonstrated to participate in the proton pathway when side chain interactions are present to position it. Both the hydrophilic and basic side chains, notably lacking in side chain interactions, significantly increased the overpotential, with only modest increases in TOF. Of all of the complexes, only CyAsp was reversible at room temperature, and only in water, the first of these complexes to demonstrate room temperature reversibility in water. These results continue to provide and solidify design rules for controlling reactivity and efficiency of Ni(P 2 N 2 ) 2 complexes with the outer coordination sphere.

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

Distinguishing enantiomeric amino acids with chiral cyclodextrin adducts and structures for lossless ion manipulations

Enantiomeric molecular evaluations remain an enormous challenge for current analytical techniques. To date, derivatizations strategies and long separation times are generally required in these studies, and the development and implementation of new approaches is greatly desired to increase speed and distinguish currently unresolvable compounds. Herein, we describe a method using chiral cyclodextrin adducts and structures for lossless ion manipulations (SLIM) ion mobility to achieve rapid, high resolution separations of D and L enantiomeric amino acids. In the analyses, chiral cyclodextrin adducts are added to each sample. Two cyclodextrins were found to sandwich each amino acid and form host-guest noncovalent complexes that were distinct for each D and L amino acid pair studied and thus separable with ion mobility (IM) in SLIM devices. The SLIM was also used to accumulate much larger ion populations than previously feasible for evaluation and therefore allow enantiomeric measurements of higher sensitivity and resolution than previously reported by any other IM-based approach.

chiral separations, cyclodextrins, enantiomers, io↗
DOE OSTI2026

Contrasting effects of glutamate and branched-chain amino acid metabolism on acid tolerance in a Castellaniella isolate from acidic groundwater

Groundwater acidification co-occurring with nitrate pollution is a common, global environmental health hazard. Denitrifying bacteria have been leveraged for the in situ removal of nitrate in groundwater. However, co-existing stressors—such as low pH—reduce the efficacy of biological removal processes. Castellaniella sp. str. MT123 is a complete denitrifier that was isolated from acidic, nitrate-contaminated groundwater. The strain grows robustly by nitrate respiration at pH < 6.0, completely reducing nitrate to dinitrogen gas. Genomic analyses of MT123 revealed few previously characterized acid tolerance genes. Thus, we utilized a combination of proteomics, metabolomics, and competitive mutant fitness to characterize the genetic mechanisms of MT123 acclimation to growth under mildly acidic conditions. We found that glutamate accumulation is critical in the acid acclimation of MT123, possibly through consumption of intracellular protons via glutamate decarboxylation to GABA. This is despite the fact that MT123 lacks the canonical glutamate decarboxylase-glutamate/GABA antiporter system implicated in acid tolerance in other bacteria. In contrast, branched-chain amino acid (BCAA) accumulation was detrimental to cell growth at lower pHs, possibly through indirect mechanisms impacting the cellular glutamate pool. Genetic analysis previously linked MT123 to a population of Castellaniella that bloomed—concurrent to nitrate removal—during a biostimulation effort to reduce groundwater nitrate concentrations at MT123’s location of origin. Thus, our analyses provide novel insight into mechanisms of acclimation to acidic conditions in a strain with significant potential for nitrate bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Potential Foldamers Based on an ortho- Terphenyl Amino Acid

We describe the synthesis and characterization of a new class of oligomers built from a terphenyl-based amino acid. Here, these oligomeric amides are of interest because the adoption of specific conformations could potentially be driven by the coordinated formation of inter-residue hydrogen bonds and aromatic interactions. Although high-resolution structural data have proven inaccessible, circular dichroism and nuclear magnetic resonance studies suggest that the new oligomers fold concomitantly with discrete self-association in chloroform. Molecular simulations find no sign of folding as a monomer, and in fact suggest that hydrogen bond patterning is anti-cooperative, inhibiting longer helices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions

Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here in this paper, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box–tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate ‘discriminator’ structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1983

Complexes of polyadenylic acid and the methyl esters of amino acids

A study of amino acid methyl esters binding to polyadenylic acid supports the theory that the genetic code originated through weak but selective affinities between amino acids and nucleotides. NMR, insoluble complex analysis, and ultraviolet spectroscopy are used to illustrate a correlation between the hydrophybicities of A amino acids and their binding constants, which, beginning with the largest, are in the order of Phe (having nominally a hydrophobic AAA anticodon), Ile, Leu, Val and Gly (having a hydrophilic anticodon with no A). In general, the binding constants are twice the values by Reuben and Polk (1980) for monomeric AMP, which suggests that polymer amino acids are interacting with only one base. No real differences are found betwen poly A binding for free Phe, Phe methyl ester or Phe amide, except that the amide value is slightly lower.

Khaled, M. A.↗
DOE OSTI2020

Electron Spin-Polarization Dependent Damage to Chiral Amino Acid l-Histidine

The damage of approximately monolayer films of L-histidine by low-energy spin-polarized electrons (SPE) ejected from a magnetized cobalt substrate has been probed using X-ray photoelectron spectroscopy (XPS). Average damage cross sections for N-containing motifs of L-histidine are 25-30 and 2-5 Mb for zwitterions and neutral molecules, respectively. Here, the magnetization direction of the substrate, which controls the ejected SPE helicity, was reversed in situ, and statistically significant differences in the damage cross sections of 10-30% were measured between positive and negative electron helicities. This is the first measurement of spin dichroism (SD) in an amino acid. The differential cross sections suggest that inelastic scattering of SPE with chiral molecules could contribute to the persistence of one enantiomer vs the other under certain irradiation conditions, particularly for the zwitterionic species.

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

Cryo-EM structure of the human neutral amino acid transporter ASCT2

Human ASCT2 belongs to the SLC1 family of secondary transporters and is specific for the transport of small neutral amino acids. ASCT2 is upregulated in cancer cells and serves as the receptor for many retroviruses; hence, it has importance as a potential drug target. Here we used single-particle cryo-EM to determine a structure of the functional and unmodified human ASCT2 at 3.85-Å resolution. ASCT2 forms a homotrimeric complex in which each subunit contains a transport and a scaffold domain. Prominent extracellular extensions on the scaffold domain form the predicted docking site for retroviruses. Relative to structures of other SLC1 members, ASCT2 is in the most extreme inward-oriented state, with the transport domain largely detached from the central scaffold domain on the cytoplasmic side. In conclusion, this domain detachment may be required for substrate binding and release on the intracellular side of the membrane.

59 BASIC BIOLOGICAL SCIENCES↗