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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Practical considerations for amino acid isotope analysis

Over the last few decades, isotopic analysis of amino acids at the compound- and position-specific levels has been rapidly advancing across diverse fields. As these techniques progress, evaluation of isotopic fractionation associated with sample workup is essential. This critical review of analytical methods through the lens of isotope geochemistry provides a benchmark for researchers across disciplines seeking to make compound- and position-specific amino acid isotope measurements. We focus on preparation, acid hydrolysis, clean-up, derivatization, separation, and C, H, N, and S isotope measurement. Despite substantial customizability across these steps, the following general recommendations should maximize recovery while minimizing isotopic fractionation. Samples should be freeze-dried and stored anoxically at ≤ –20 °C prior to conventional acid hydrolysis (6N HCl, 110 °C, 20–24 h, anoxic), which suffices for many residues. Both gas and liquid chromatographic (GC and LC, respectively) techniques are well-established and separate about 15 amino acids; LC bypasses the need for derivatization, while GC provides higher sensitivity. Furthermore, when derivatization is needed, n-acetyl and alkoxycarbonyl esters provide the most reproducible C isotope ratios. For compound-specific analyses, online GC–IRMS and LC–IRMS systems offer the easiest workflow, but EA–IRMS enables potential multi-element isotope analysis. Emerging techniques like high-resolution mass spectrometry are also promising for multi-element analysis and recover position-specific isotopic information. Looking forward to the next decade of innovation, isotope geochemists and ecologists can improve amino acid isotope analysis by focusing on streamlining multi-element analysis and standardizing calibration practices across laboratories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Abstract Many microorganisms are auxotrophic—unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial genomes spanning 12 phyla using a metabolic pathway model validated with empirical data. Amino acid auxotrophy is widespread across bacterial phyla, but we conservatively estimate that the majority of taxa (78.4%) are able to synthesize all amino acids. Our estimates indicate that amino acid auxotrophies are more prevalent among obligate intracellular parasites and in free-living taxa with genomic attributes characteristic of ‘streamlined’ life history strategies. We predicted the amino acid biosynthetic capabilities of bacterial communities found in 12 unique habitats to investigate environmental associations with auxotrophy, using data compiled from 3813 samples spanning major aquatic, terrestrial, and engineered environments. Auxotrophic taxa were more abundant in host-associated environments (including the human oral cavity and gut) and in fermented food products, with auxotrophic taxa being relatively rare in soil and aquatic systems. Overall, this work contributes to a more complete understanding of amino acid auxotrophy across the bacterial tree of life and the ecological contexts in which auxotrophy can be a successful strategy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Amino acids as performance-controlling additives in carbonation-activated cementitious materials

This article presents an investigation on the application of amino acids to control the CaCO{sub 3} crystallization in carbonation cured wollastonite composites. It was observed that wollastonite carbonated without any amino acid formed calcite as the primary polymorph of CaCO{sub 3}. In contrast, the use of amino acids as admixtures resulted in the formation of stable amorphous calcium carbonate (ACC), vaterite, and aragonite during the carbonation of wollastonite. The carbonated composites produced with amino acids were observed to have a lower critical pore size, but a higher total porosity, compared to the control batch. Additionally, the utilization of amino acids was observed to increase the flexural strength and compressive strength of the composites up to 106% and 48%, respectively, compared to the control batch. Such performance enhancement of the carbonated composites in the presence of amino acids was attributed to the reduced critical pore size and the formation of organic-inorganic hybrid phases in the matrix.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Methods of making proteins with non-standard amino acids

The disclosure provides methods of making a protein having a desired non-standard amino acid incorporated at its N-terminus in a cell and methods of screening for an amino acyl tRNA synthetase variant that preferentially selects a non-standard amino acid against its standard amino acid counterpart or undesired non-standard amino acids for incorporation into a protein in a cell.

Kunjapur, Aditya Mohan↗
DOE OSTI2020

Regulatory interventions improve the biosynthesis of limiting amino acids from methanol carbon to improve synthetic methylotrophy in Escherichia coli

Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methylotrophs have proved successful, autonomous methylotrophy, that is, the ability to utilize methane or methanol as sole carbon and energy substrates, has not yet been realized. Here, we address an important limitation of autonomous methylotrophy in E. coli: the inability of the organism to synthesize several amino acids when grown on methanol. We targeted global and local amino acid regulatory networks. Those include removal of amino acid allosteric feedback inhibition (argA H15Y , ilvA L447F , hisG E271K , leuA G462D , proB D107N , thrA S345F, trpE S40F ), knockouts of transcriptional repressors (ihfA, metJ); and overexpression of amino acid biosynthetic operons (hisGDCBHAFI, leuABCD, thrABC, trpEDCBA) and transcriptional regulators (crp, purR). Compared to the parent methylotrophic E. coli strain that was unable to synthesize these amino acids from methanol carbon, these strategies resulted in improved biosynthesis of limiting proteinogenic amino acids (histidine, leucine, lysine, methionine, phenylalanine, threonine, tyrosine) from methanol carbon. In several cases, improved amino acid biosynthesis from methanol carbon led to improvements in methylotrophic growth in methanol minimal medium supplemented with a small amount of yeast extract. Here, this study addresses a key limitation currently preventing autonomous methylotrophy in E. coli and possibly other synthetic methylotrophs and provides insight as to how this limitation can be alleviated via global and local regulatory modifications.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Amino Acids Dominate Diffusive Nitrogen Fluxes in Acidic Tussock Tundra

Organic nitrogen (N) is abundant in soils, but early conceptual frameworks considered it nonessential for plant growth. It is now well recognised that plants have the potential to take up organic N. However, it is still unclear whether plants supplement their N requirements by taking up organic N in situ: at what rate is organic N diffusing towards roots and are plants taking it up? In this work, we combined microdialysis with live-root uptake experiments to measure amino acid speciation and diffusion rates towards roots of Eriophorum vaginatum. Amino acid diffusion rates (321 ng N cm -2 h -1 ) were c. 3× higher than those for inorganic N. Positively charged amino acids made up 68% of the N diffusing through soils compared with neutral and negatively charged amino acids. Live-root uptake experiments confirmed that amino acids are taken up by plants (up to 1 µg N g -1 min -1 potential net uptake). Amino acids must be considered when forecasting plant-available N, especially when they dominate the N supply, and when acidity favours proteolysis over net N mineralisation. Determining amino acid production pathways and supply rates will become increasingly important in projecting the extent and consequences of shrub expansion, especially considering the higher C : N ratio of plants relative to soil.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Examining Interactions of Uranyl(VI) Ions with Amino Acids in the Gas Phase

Gas-phase experiments, using electrospray ionization quadrupole ion trap mass spectrometry (ESI-QIT/MS), were conducted to probe basic interactions of the uranyl(VI) ion, UO 2 2+ , with selected natural amino acids, namely, L-cysteine (Cys), L-histidine (His), and L-aspartic acid (Asp), which strongly bind to metal ions. The simplest amino acid, glycine (Gly), was also studied for comparison. Cys, His, and Asp have additional potentially coordinating groups beyond the amino and carboxylic acid functional groups, specifically thiol in Cys, imidazole in His, and a second carboxylate in Asp. Gas-phase experiments comprised collision-induced dissociation (CID) of uranyl–amino acid complexes and competitive CID to assess the relative binding strength of different amino acids in the same uranyl complex. Reactivity of selected uranyl–amino acid complexes with water provided further insights into relative stabilities. In positive ion mode, CID and ensuing reactions with water suggested that uranyl–neutral AA binding strength decreased in the order His > Asp > Cys > Gly, which is similar to amino acid proton affinities. In negative ion mode, CID revealed a decreasing dissociation tendency in the order Gly >> His ≈ Cys > Asp, presumably reflecting a reverse enhanced binding to uranyl of the doubly deprotonated amino acids formed in CID.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2021

A Process Intensification Approach for CO 2 Absorption Using Amino Acid Solutions and a Guanidine Compound

Environmentally friendly amino-acid salt solutions are used for the absorption of carbon dioxide from concentrated flue-gas streams via chemical absorption. Process intensification reduces operating and capital costs by combining chemical reactions and separation operations. Here, we present a new process-intensification approach that combines the CO 2 capture and the amino-acid regeneration steps into a single process carried out in a slurry three-phase reactor. The absorbed CO 2 precipitates as a solid carbonated guanidine compound. The cycle is completed by separation of the solid precipitate to strip the CO 2 and regenerate the guanidine compound, while the liquid solution is recycled to the slurry reactor. The process was studied by modifying a model developed by the authors for a gas-liquid bubble column without the presence of the guanidine compound. The guanidine precipitation reaction was accounted for using kinetic parameters calculated by the authors in another study. The proposed model was implemented by modifying an existing computer code used for the simulation of gas-liquid bubble columns. The calculated results showed that the proposed cycle can significantly reduce energy, equipment, and operating costs and can make an important contribution to developing a competitive cost-effective large-scale process for CO 2 capture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

Radiation of the plant pyridoxal 5'-phosphate (PLP)-dependent aromatic L -amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic L -amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. In this paper, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dual incorporation of non-canonical amino acids enables production of post-translationally modified selenoproteins

Post-translational modifications (PTMs) can occur on almost all amino acids in eukaryotes as a key mechanism for regulating protein function. The ability to study the role of these modifications in various biological processes requires techniques to modify proteins site-specifically. One strategy for this is genetic code expansion (GCE) in bacteria. The low frequency of post-translational modifications in bacteria makes it a preferred host to study whether the presence of a post-translational modification influences a protein’s function. Genetic code expansion employs orthogonal translation systems engineered to incorporate a modified amino acid at a designated protein position. Selenoproteins, proteins containing selenocysteine, are also known to be post-translationally modified. Selenoproteins have essential roles in oxidative stress, immune response, cell maintenance, and skeletal muscle regeneration. Their complicated biosynthesis mechanism has been a hurdle in our understanding of selenoprotein functions. As technologies for selenocysteine insertion have recently improved, we wanted to create a genetic system that would allow the study of post-translational modifications in selenoproteins. By combining genetic code expansion techniques and selenocysteine insertion technologies, we were able to recode stop codons for insertion of N ε -acetyl- l -lysine and selenocysteine, respectively, into multiple proteins. The specificity of these amino acids for their assigned position and the simplicity of reverting the modified amino acid via mutagenesis of the codon sequence demonstrates the capacity of this method to study selenoproteins and the role of their post-translational modifications. Moreover, the evidence that Sec insertion technology can be combined with genetic code expansion tools further expands the chemical biology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Synthesis of β-Deuterated Amino Acids via Palladium-Catalyzed H/D Exchange

Despite several synthetic approaches that have been developed for α-deuterated amino acids, the synthesis of β-deuterated amino acids has remained a challenge. Herein, we disclose a palladium catalyzed H/D exchange protocol for a β-deuterated N-protected amino amide, which can be converted to a β-deuterated amino acid simply by removal of protecting groups. Further, this protocol is highly efficient, simply manipulated, and appliable for deuterium-labeling of many amino amides. In addition, deuterium labeling of phenylalanine derivatives was also successful when pivalic acid served as an additive to promote the H/D exchange process.

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

Empirical evidence that glucan-interacting amino acid side chains within the transmembrane channel collectively facilitate cellulose synthase function

The fundamental mechanism of cellulose synthesis is widely conserved across Kingdoms and depends on cellulose synthases, which are processive, dual-function, family 2 glycosyltransferases (GT-2). These enzymes polymerize glucose on the cytoplasmic side of the plasma membrane and export the glucan chain to the cell surface through an integral transmembrane (TM) channel. Structural studies of active plant cellulose synthases (CESAs) have revealed interactions between the nascent glucan chain and the side chains of polar, charged, and aromatic amino acid residues that line the TM channel. However, the functional consequences of modifying these side chains have not been tested in vivo in CESAs or other processive GT-2s. To test this, we used an established in vivo assay based on genetic complementation of CESA5 in the moss, Physcomitrium patens. For accurate prediction of glucan-interacting amino acid residues, we generated a complete homotrimeric molecular model of PpCESA5 using a combination of homology and de novo modeling. All-atom molecular dynamics-based analyses of contact metrics and interaction energy identified 23 amino acid residues with high propensity to interact with the nascent glucan chain within the TM channel or on the apoplastic surface of PpCESA5. Mutating any one of 18 of these amino acid residues to alanine, thereby removing their side chains, abolished or impaired CESA function, with the strongest effects observed upon the loss of charged amino acid side chains. This provides direct evidence to support the hypothesis that multiple amino acid residues collectively maintain a smooth energy landscape within the TM channel to facilitate glucan translocation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Analysis of the cyanobacterial amino acid metabolism with a precise genome-scale metabolic reconstruction of Anabaena sp. UTEX 2576

Filamentous cyanobacteria such as Anabaena sp. UTEX 2576 (a.k.a., Nostoc sp. PCC 7120) are a sustainable platform for commodity and specialty chemical production. Anabaena is a model cyanobacterium adopted to study production of nitrogen-containing metabolites useful for chemical, cosmetic, and pharmaceutical industries. Therefore, a precise description of the Anabaena metabolic network is desired to analyze their amino-acid metabolism and elucidate potential applications of these cyanobacteria as host organisms for biotechnological production. Secondary metabolite production depends on the metabolic availability of amino acids. We provide new insight on the biotechnological utilization of Anabaena after predicting phycocyanobilin and amino-acid production rates, using a genome-scale metabolic model (iDN1004). This metabolic reconstruction is a highly comprehensive representation of the global metabolism of Anabaena, which also contains experimental biomass equations and constraints under photoautotrophic and photodiazotrophic growth. Modelling results ranked proteinogenic amino acids based on predicted metabolic fluxes through amino-acid producing reactions. From these, l-aspartate, glycine, l-serine, l-valine, l-alanine, l-threonine, and l-leucine were selected as the best branching points to conduct metabolic engineering, where l-aspartate, l-serine, l-valine and glycine serve as potential precursors of the secondary metabolites Schizokinen (a siderophore), Sphingosine (a ceramide), Lyngbyatoxin A (an alkaloid), and Shinorine (a sunscreen).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Host cells and methods for oxidizing aromatic amino acids

The present invention provides for a method of producing an oxidation product of an aromatic amino acid in a genetically modified host cell. The method comprises culturing the genetically modified host cell under a suitable condition such that the culturing results in the genetically modified host cell producing oxidation product of an aromatic amino acid. The host cell comprises an enzyme capable of catalyzing the oxidation of aromatic amino acid. In some embodiments, the host cell is capable of biosynthesizing BH4 or MH4 from GTP.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Adaptive laboratory evolution of methylotrophic Escherichia coli enables synthesis of all amino acids from methanol-derived carbon

Recent attempts to create synthetic Escherichia coli methylotrophs identified that de novo biosynthesis of amino acids, in the presence of methanol, presents significant challenges in achieving autonomous methylotrophic growth. Previously engineered methanol-dependent strains required co-utilization of stoichiometric amounts of co-substrates and methanol. As such, these strains could not be evolved to grow on methanol alone. In this work, we have explored an alternative approach to enable biosynthesis of all amino acids from methanol-derived carbon in minimal media without stoichiometric coupling. First, we identified that biosynthesis of threonine was limiting the growth of our methylotrophic E. coli. To address this, we performed adaptive laboratory evolution to generate a strain that grew efficiently in minimal medium with methanol and threonine. Methanol assimilation and growth of the evolved strain were analyzed and, interestingly, we found that the evolved strain synthesized all amino acids, including threonine, from methanol-derived carbon. Here, the evolved strain was then further engineered through overexpression of an optimized threonine biosynthetic pathway. We show that the resulting methylotrophic E. coli strain has a methanol-dependent growth phenotype with homoserine as co-substrate. In contrast to previous methanol-dependent strains, co-utilization of homoserine is not stoichiometrically linked to methanol assimilation. As such, future engineering of this strain and successive adaptive evolution could enable autonomous growth on methanol as the sole carbon source.

13C-labeling analysis↗
DOE OSTI2020

Amino acid interacting network in the receptor-binding domain of SARS-CoV-2 spike protein

The relation between amino acid (AA) sequence and biologically active conformation controls the process of polypeptide chains folding into three-dimensional (3d) protein structures. The recent achievements in the resolution achieved in cryo-electron microscopy coupled with improvements in computational methodologies have accelerated the analysis of structures and properties of proteins. However, the detailed interaction between AAs has not been fully elucidated. Herein, we present a de novo method to evaluate inter-amino acid interactions based on the concept of accurately evaluating the amino acid bond pairs (AABP). The results obtained enabled the identification of complex 3d long-range interconnected AA interacting network in proteins. The method is applied to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. We show that although nearest-neighbor AAs in the primary sequence have large AABP, other nonlocal AAs make substantial contribution to AABP with significant participation of both covalent and hydrogen bonding. Detailed analysis of AABP in RBD reveals the pivotal role they play in sequence conservation with profound implications on residue mutations and for therapeutic drug design. This approach could be easily applied to many other proteins of biomedical interest in life sciences.

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

The Photochemistry of Amino Acids Produced on the Polar Cryovolcanic Regions of Titan

The cryovolcanic regions of Titan offer transient opportunities for prebiotic molecules to exist in water–ammonia solutions on the surface of the Saturnian moon. The upcoming NASA’s Dragonfly mission will search for high nitrogen concentrations and amino acids on Titan’s equatorial terrains. Cryovolcanic features, however, are most common on the polar regions. To mitigate the distance, bubble bursting may encapsulate the prebiotic molecules into aerosols, which Titan’s Hadley circulation would subsequently transport to the equator. Here we investigate whether alanine and glycine survive this meridional journey. Despite the unconstrained meridional wind velocities, our results suggest that the amino acids can survive the transport through the mesosphere. Dragonfly may find cryo-volcanogenic amino acids on Titan’s equator. Further, the interaction between the two amino acids increased 10-fold the photodegradation rate of glycine. We justify it based on changes in the environment polarity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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.↗