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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Biosynthesis of Strained Amino Acids by a PLP‐Dependent Enzyme through Cryptic Halogenation

Abstract Amino acids (AAs) are modular building blocks which nature uses to synthesize both macromolecules, such as proteins, and small molecule natural products, such as alkaloids and non‐ribosomal peptides. While the 20 main proteinogenic AAs display relatively limited side chain diversity, a wide range of non‐canonical amino acids (ncAAs) exist that are not used by the ribosome for protein synthesis, but contain a broad array of structural features and functional groups. In this communication, we report the discovery of the biosynthetic pathway for a new ncAA, pazamine, which contains a cyclopropane ring formed in two steps. In the first step, a chlorine is added onto the C 4 position of lysine by a radical halogenase, PazA. The cyclopropane ring is then formed in the next step by a pyridoxal‐5′‐phosphate‐dependent enzyme, PazB, via an S N 2‐like attack at C 4 to eliminate chloride. Genetic studies of this pathway in the native host, Pseudomonas azotoformans , show that pazamine potentially inhibits ethylene biosynthesis in growing plants based on alterations in the root phenotype of Arabidopsis thaliana seedlings. We further show that PazB can be utilized to make an alternative cyclobutane‐containing AA. These discoveries may lead to advances in biocatalytic production of specialty chemicals and agricultural biotechnology.

Sosa, Max B.↗
NASA NTRS1972

GLC of amino acids - A survey of contamination.

Analyses of biological substances and geochemical samples, of both terrestrial and extraterrestrial origin, are reported for amino acids at the 1-10 nanogram per gram level achieved by gas-liquid and ion-exchange chromatographic methods. These studies have shown that nanogram quantities of amino acids, present in water extracts of geochemical samples or in other samples of low amino acid concentration, can be successfully determined only if the researcher is well aware of the possible sources of contamination.

Rash, J. J.↗
DOE OSTI2019

Simulation of carbon dioxide absorption by amino acids in two-phase batch and bubble column reactors

The absorption of carbon dioxide (CO 2 ) is a critical process in many practical applications. The use of amino acid solutions as absorption solvents has the potential to reduce the amount of energy required by the regeneration process. The goal of this research project is to develop dynamic models to simulate CO 2 absorption by using amino acid solutions as absorption solvents. A reaction scheme is introduced to represent the chemical reactions between the amino acid and CO 2 . Two reaction models, for a two-phase batch reactor and a bubble column, based upon transient mass and energy balances for the chemical species found in CO 2 gas-liquid absorption are presented. Computer codes have been written to implement the proposed models. Simulation results are presented and discussed. The proposed models can be used to optimize and control CO 2 absorption in practical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2021

Extraterrestrial Hydroxy Amino Acids in CM and CR Carbonaceous Chondrites

7 The abundances, distributions, and enantiomeric ratios of a family of three- and four- 8 9 10 carbon hydroxy amino acids (HAAs) were investigated in extracts of five CM and four 11 12 13 CR carbonaceous chondrites by gas chromatography-mass spectrometry (GC-MS) 14 15 16 analyses. Hydroxy amino acids were detected in both the acid hydrolysates of the hot 17 18 19 water extracts and the 6 M HCl extracts of all the CM and CR chondrites analyzed 20 21 22 here with total hot water and HCl extractable HAA concentrations ranging from 6.94 23 24 25 to 315 nmol per gram. The HAA analyses performed in this study revealed: 1) the 26 27 28 combined (hot water + HCl) extracts of CR2 chondrites contained greater abundances 29 30 31 of -HAAs than that of CM2 chondrites and 2) the combined extracts of CM and CR 32 33 34 chondrites contained roughly similar abundances of β- and γ-HAAs. Application of the 35 36 37 new GC-MS method developed here resulted in the first successful chromatographic 38 39 40 resolution of the enantiomers of an -dialkyl HAA, D,L--methylserine, in 41 42 43 carbonaceous chondrite extracts. Meteoritic -methylserine was found to be mostly 44 45 46 racemic within error and did not show L-enantiomeric excesses correlating with the 47 48 49 degree of aqueous alteration, a phenomenon observed in meteoritic isovaline, another 50 51 52 -dialkyl amino acid. The HAAs identified in CM and CR chondrite extracts could have 53 54 55 been produced during parent body alteration from the Strecker cyanohydrin reaction 56 57 58 (for -HAAs) and an ammonia-involved formose-like reaction (for β-, and γ-HAAs).

Amino acid(s), CM carbonaceous chondrite < Meteori↗
DOE OSTI2012

Identification of Amino Acids that Account for Long-Range Interactions in Two Triosephosphate Isomerases from Pathogenic Trypanosomes

For a better comprehension of the structure-function relationship in proteins it is necessary to identify the amino acids that are relevant for measurable protein functions. Because of the numerous contacts that amino acids establish within proteins and the cooperative nature of their interactions, it is difficult to achieve this goal. Thus, the study of protein-ligand interactions is usually focused on local environmental structural differences. Here, using a pair of triosephosphate isomerase enzymes with extremely high homology from two different organisms, we demonstrate that the control of a seventy-fold difference in reactivity of the interface cysteine is located in several amino acids from two structurally unrelated regions that do not contact the cysteine sensitive to the sulfhydryl reagent methylmethane sulfonate, nor the residues in its immediate vicinity. The change in reactivity is due to an increase in the apparent pKa of the interface cysteine produced by the mutated residues. Our work, which involved grafting systematically portions of one protein into the other protein, revealed unsuspected and multisite long-range interactions that modulate the properties of the interface cysteines and has general implications for future studies on protein structure-function relationships.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Amino acid modified Ni catalyst exhibits reversible H 2 oxidation/production over a broad pH range at elevated temperatures

Hydrogenases interconvert H 2 and protons at high rates and with high energy efficiencies, providing inspiration for the development of molecular catalysts. Studies designed to determine how the protein scaffold can influence a catalytically active site has led to the synthesis of amino acid derivatives, [Ni(P Cy 2 N Amino acid 2) 2 ] 2+ (CyAA), of [Ni(P R 2 N R' 2 ) 2 ] 2+ complexes. It is shown that these CyAA derivatives can catalyze fully reversible H 2 production/oxidation, a feature reminiscent of enzymes. The reversibility is achieved in acidic aqueous solutions, 0.25% H 2 /Ar, and elevated temperatures (tested up to 348 K) for the glycine (CyGly), arginine (CyArg), and arginine methyl ester (CyArgOMe) derivatives. As expected for a reversible process, the activity is dependent upon H 2 and proton concentration. CyArg is significantly faster in both directions than the other two derivatives (~300 s -1 H 2 production and 20 s -1 H 2 oxidation; pH = 1, 348 K). The significantly slower rates for CyArgOMe (35 s -1 production and 7 s -1 oxidation) compared to CyArg suggests an important role for the COOH group during catalysis. That CyArg is faster than CyGly (3 s -1 production and 4 s -1 oxidation under the same conditions) suggests that the additional structural features imparted by the guanidinium groups facilitate fast and reversible H 2 addition/release. Furthermore, these observations demonstrate that appended, outer coordination sphere amino acids work in synergy with the active site and can play an equally important role for synthetic molecular electrocatalysts as the protein scaffold does for redox active enzymes.

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

Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana

Plants produce diverse low-molecular-weight compounds via specialized metabolism. Discovery of the pathways underlying production of these metabolites is an important challenge for harnessing the huge chemical diversity and catalytic potential in the plant kingdom for human uses, but this effort is often encumbered by the necessity to initially identify compounds of interest or purify a catalyst involved in their synthesis. Here, as an alternative approach, we have performed untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions of Arabidopsis thaliana . This approach allowed us to establish genetic linkages between metabolites and genes. Investigation of one of the metabolite-gene associations led to the identification of N-malonyl-D-allo-isoleucine, and the discovery of a novel amino acid racemase involved in its biosynthesis. This finding provides, to our knowledge, the first functional characterization of a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family. Unlike most of known eukaryotic amino acid racemases, the newly discovered enzyme does not require pyridoxal 5'-phosphate for its activity. In conclusion, this study thus identifies a new d-amino acid racemase gene family and advances our knowledge of plant d-amino acid metabolism that is currently largely unexplored. As a result, it also demonstrates that exploitation of natural metabolic variation by integrating metabolomics with genome-wide association is a powerful approach for functional genomics study of specialized metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

The stability of amino acids at submarine hydrothermal vent temperatures

It has been postulated that amino acid stability at hydrothermal vent temperatures is controlled by a metastable thermodynamic equilibrium rather than by kinetics. Experiments reported here demonstrate that the amino acids are irreversibly destroyed by heating at 240 C and that quasi-equilibrium calculations give misleading descriptions of the experimental observations. Equilibrium thermodynamic calculations are not applicable to organic compounds under high-temperature submarine vent conditions.

Bada, Jeffrey L.↗
DOE OSTI2017

Laser-Induced Acoustic Desorption/Electron Ionization of Amino Acids and Small Peptides

Laser-induced acoustic desorption (LIAD) allows for desorption of neutral nonvolatile compounds independent of their volatility or thermal stability. Many different ionization methods have been coupled with LIAD. Hence, this setup provides a better control over the types of ions formed than other mass spectrometry evaporation/ionization methods commonly used to characterize biomolecules, such as ESI or MALDI. In this study, the utility of LIAD coupled with electron ionization (EI) was tested for the analysis of common amino acids with no derivatization. The results compared favorably with previously reported EI mass spectra obtained using thermal desorption/EI. Further, LIAD/EI mass spectra collected for hydrochloride salts of two amino acids were found to be similar to those measured for the neutral amino acids with the exception of the appearance of an HCl{sup +●} ion. However, the hydrochloride salt of arginine showed a distinctly different LIAD/EI mass spectrum than the previously published literature EI mass spectrum, likely due to its highly basic side chain that makes a specific zwitterionic form particularly favorable. Finally, EI mass spectra were measured for seven small peptides, including di-, tri-, and tetrapeptides. These mass spectra show a variety of ion types. However, a{sub n} type ions are prevalent. Also, electron-induced dissociation (EID) of protonated peptides has been reported to form primarily a{sub n} type ions. In addition, the loss of small neutral molecules and side-chain cleavages were observed that are reminiscent of other high-energy fragmentation methods, such as EID. Finally, the isomeric dipeptides LG and IG were found to produce drastically different EI mass spectra, thus allowing differentiation of the leucine and isoleucine amino acids in these dipeptides. .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2011

Oncogenicity of L-type amino-acid transporter 1 (LAT1) revealed by targeted gene disruption in chicken DT40 cells: LAT1 is a promising molecular target for human cancer therapy

Highlights: {yields} We established LAT1 amino-acid transporter-disrupted DT40 cells. {yields} LAT1-disrupted cells showed slow growth and lost the oncogenicity. {yields} siRNA and mAb inhibited human tumor growth in vitro and in vivo. {yields} LAT1 is a promising target molecule for cancer therapy. -- Abstract: L-type amino-acid transporter 1 (LAT1) is the first identified light chain of CD98 molecule, disulfide-linked to a heavy chain of CD98. Following cDNA cloning of chicken full-length LAT1, we have constructed targeting vectors for the disruption of chicken LAT1 gene from genomic DNA of chicken LAT1 consisting of 5.4 kb. We established five homozygous LAT1-disrupted (LAT1{sup -/-}) cell clones, derived from a heterozygous LAT1{sup +/-} clone of DT40 chicken B cell line. Reactivity of anti-chicken CD98hc monoclonal antibody (mAb) with LAT1{sup -/-} DT40 cells was markedly decreased compared with that of wild-type DT40 cells. All LAT1{sup -/-} cells were deficient in L-type amino-acid transporting activity, although alternative-splice variant but not full-length mRNA of LAT1 was detected in these cells. LAT1{sup -/-} DT40 clones showed outstandingly slow growth in liquid culture and decreased colony-formation capacity in soft agar compared with wild-type DT40 cells. Cell-cycle analyses indicated that LAT1{sup -/-} DT40 clones have prolonged cell-cycle phases compared with wild-type or LAT1{sup +/-} DT40 cells. Knockdown of human LAT1 by small interfering RNAs resulted in marked in vitro cell-growth inhibition of human cancer cells, and in vivo tumor growth of HeLa cells in athymic mice was significantly inhibited by anti-human LAT1 mAb. All these results indicate essential roles of LAT1 in the cell proliferation and occurrence of malignant phenotypes and that LAT1 is a promising candidate as a molecular target of human cancer therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Effect of specific amino acid substitutions in the putative fusion peptide of structural glycoprotein E2 on Classical Swine Fever Virus replication

E2, along with E{sup rns} and E1, is an envelope glycoprotein of Classical Swine Fever Virus (CSFV). E2 is involved in several virus functions: cell attachment, host range susceptibility and virulence in natural hosts. Here we evaluate the role of a specific E2 region, {sup 818}CPIGWTGVIEC{sup 828}, containing a putative fusion peptide (FP) sequence. Reverse genetics utilizing a full-length infectious clone of the highly virulent CSFV strain Brescia (BICv) was used to evaluate how individual amino acid substitutions within this region of E2 may affect replication of BICv. A synthetic peptide representing the complete E2 FP amino acid sequence adopted a β-type extended conformation in membrane mimetics, penetrated into model membranes, and perturbed lipid bilayer integrity in vitro. Similar peptides harboring amino acid substitutions adopted comparable conformations but exhibited different membrane activities. Therefore, a preliminary characterization of the putative FP {sup 818}CPIGWTGVIEC{sup 828} indicates a membrane fusion activity and a critical role in virus replication. - Highlights: • A putative fusion peptide (FP) region in CSFV E2 protein was shown to be critical for virus growth. • Synthetic FPs were shown to efficiently penetrate into lipid membranes using an in vitro model. • Individual residues in the FP affecting virus replication were identified by reverse genetics. • The same FP residues are also responsible for mediating membrane fusion.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

A Single Amino Acid Switch Alters the Isoprene Donor Specificity in Ribosomally Synthesized and Post-Translationally Modified Peptide Prenyltransferases

Mutation at a single amino acid alters the isoprene donor specificity of prenyltransferases involved in the modification of ribosomally synthesized and post-translationally modified peptides (RiPPs). Though most characterized RiPP prenyltransferases carry out the regiospecific transfer of C 5 dimethylallyl donor to the side chain atoms on macrocyclic acceptor substrates, the elucidation of the cyanobactin natural product piricyclamide 70005E1 identifies an O-geranyl modification on Tyr, a reaction with little prior biochemical precedence. Reconstitution and kinetic studies of the presumptive geranyltransferase PirF shows that the enzyme utilizes a C 10 donor, with no C 5 transferase activity. The crystal structure of PirF reveals a single amino acid difference in the vicinity of the isoprene-binding pocket, relative to the C 5 utilizing enzymes. Remarkably, only a single amino acid mutation is necessary to completely switch the donor specificity from a C 5 to a C 10 prenyltransferase, and vice versa. Lastly, we demonstrate that these enzymes may be used for the chemospecific attachment of C 5 or C 10 lipid groups on lanthipeptides, an unrelated class of RiPP natural products. Overall, these studies represent a rare example where prenyl donor specificity can be discretely altered, which expands the arsenal of synthetic biology tools for tuning biological activities of peptide natural products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1995

Amino acid racemization on Mars: implications for the preservation of biomolecules from an extinct martian biota

Using kinetic data, we have estimated the racemization half-lives and times for total racemization of amino acids under conditions relevant to the surface of Mars. Amino acids from an extinct martian biota maintained in a dry, cold (<250 K) environment would not have racemized significantly over the lifetime of the planet. Racemization would have taken place in environments where liquid water was present even for time periods of only a few million years following biotic extinction. The best preservation of both amino acid homochirality and nucleic acid genetic information associated with extinct martian life would be in the polar regions.

NASA Discipline Exobiology↗
NASA NTRS1981

Formation of peptides from amino acids by single or multiple additions of ATP to suspensions of nucleoproteinoid microparticles

The synthesis of peptides from individual amino acids or pairs of amino acids and ATP in the presence of catalysis by nucleoproteinoid microparticles is investigated. Experiments were performed with suspensions formed from the condensation of lysine-rich and acidic proteinoids with polyadenylic acid, to which were added glycine, phenylalanine, proline, lysine or glycine-phenylalanine mixtures, and ATP either at once or serially. Peptide yields are found to be greatest for equal amounts of acidic and basic proteinoids. The addition of imidazole is found to alter the preference of glycine-phenylalanine mixtures to form mixed heteropeptides rather than homopeptides. A rapid ATP decay in the peptide synthesis reaction is observed, and a greater yield is obtained for repeated small additions than for a single addition of ATP. The experimental system has properties similar to modern cells, and represents an organizational unit ready for the evolution of associated biochemical pathways.

Nakashima, T.↗
DOE OSTI2011

In vivo incorporation of unnatural amino acids

The invention provides methods and compositions for in vivo incorporation of unnatural amino acids. Also provided are compositions including proteins with unnatural amino acids.

59 BASIC BIOLOGICAL SCIENCES↗