Engineering Papers⌕ Search

SEARCH · Engineering Papers

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Life-cycle analysis of soybean meal, distiller-dried grains with solubles, and synthetic amino acid-based animal feeds for swine and poultry production

Swine and poultry meat production are two important sectors in the U.S. economy. They play an important role in environmental sustainability because they contribute to the greenhouse gas (GHG) emissions as the result of agricultural and production activities. To improve the sustain ability of swine and poultry meat production, it is important to understand the environmental effects and identify the key drivers of the production activities. In this work, we presented an environmental assessment of the production of swine (i.e., pork) and poultry (i.e., broiler chicken). We conducted a life-cycle analysis of formulating animal feeds using soybean meal, corn, distiller-dried grains with solubles (DDGS), and synthetic amino acids as candidate ingredients to produce swine and poultry. We evaluated GHG emissions, fossil fuel consumption, and water consumption from formulating and utilizing a variety of animal feeds based on these ingredients for swine and poultry production, using an expanded version of the Greenhouse gases, Regulated Emissions, and Energy use in Transportation (GREET (R)) model. With pork and broiler chicken as the finished products, the functional unit was defined as one kg of live-weight animal at the farm gate. Feed production was the major contributor to the life-cycle GHG emissions (88 % and 91 % of the total GHG emissions for swine and poultry production, respectively) and fossil fuel consumption (79 % and 84 % of the total fossil fuel consumption for swine and poultry process, respectively). Among the four ingredient types, amino acids had the biggest GHG emission footprint; however, DDGS had the largest effect on increasing GHG emissions of swine and poultry production.

animal feed production↗
DOE OSTI2018

Upgrading aminoacyl-tRNA synthetases for genetic code expansion

Synthesis of proteins with non-canonical amino acids via genetic code expansion is at the forefront of synthetic biology. Progress in this field has enabled site-specific incorporation of over 200 chemically and structurally diverse amino acids into proteins in an increasing number of organisms. This has been facilitated by our ability to repurpose aminoacyl-tRNA synthetases to attach non-canonical amino acids to engineered tRNAs. Current efforts in the field focus on overcoming existing limitations to the simultaneous incorporation of multiple non-canonical amino acids or amino acids that differ from the l-α-amino acid structure (e.g. d-amino acid or β-amino acid). Here, we summarize the progress and challenges in developing more selective and efficient aminoacyl-tRNA synthetases for genetic code expansion.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Comet impacts and chemical evolution on the bombarded earth

Amino acids yields for previously published shock tube experiments are used with minimum Cretaceous-Tertiary (K/T) impactor mass and comet composition to predict AIB amino acid K/T boundary sediment column density. The inferred initial concentration of all amino acids in the K/T sea and in similar primordial seas just after 10 km comet impacts would have been at least 10 exp -7 M. However, sinks for amino acids must also be considered in calculating amino acid concentrations after comet impacts and in assessing the contribution of comets to the origin of life. The changing concentration of cometary amino acids due to ultraviolet light is compared with the equilibrium concentration of amino acids produced in the sea from corona discharge in the atmosphere, deposition in water, and degradation by ultraviolet light. Comets could have been more important than endogenous agents for initial evolution of amino acids. Sites favorable for chemical evolution of amino acids are examined, and it is concluded that chemical evolution could have occurred at or above the surface even during periods of intense bombardment of earth before 3.8 billion years ago.

Oberbeck, Verne R.↗
NASA NTRS1998

Prebiotic Polymer Synthesis and the Origin of Glycolytic Metabolism

Our research resulted in several discoveries which contributed to understanding the origin and operation of life. (1) Most importantly, we discovered a new pathway of prebiotic amino acid synthesis in which formaldehyde and glycolaldehyde (formose reaction substrates) react with ammonia to give alanine and homoserine in the presence of thiol catalysts. The thiol-dependent synthesis of amino acids undoubtedly occurs via amino acid thioester intermediates capable of forming peptides. This 'one-pot' reaction system operates under mild aqueous conditions, and like modern amino acid biosynthesis, uses sugar intermediates which are converted to amino acids by energy-yielding redox disproportionation. Preliminary evidence suggests that this type of process can be "evolved" by a serial transfer methods that lead to enrichment of autocatalytic molecules. (2) We established that prebiotic peptide polymers can be made by condensation of amino acid thioesters (homocysteine thiolactone and S-(N-beta-orotidyl- diaminopropionic acid) ethanethiol), and that prebiotic polydisulfide polymers can be generated by oxidation of dithiols with iron(III) in minerals. (3) In our analysis of metabolism we discovered the primary energy source of biosynthesis -- chemical energy made available by the redox disproportionation of substrate carbon groups. We concluded that the energy and reactivity of sugars make them the optimal substrate for the origin and operation of terrestrial (or extraterrestrial) life. (4) Since it is likely that the use of optimal sugar substrates in biosynthesis sets the average oxidation number of functional biocarbon throughout the Universe near 0.0 (the reduction level of formaldehyde), we proposed that a line(s) in the microwave spectrum of formaldehyde could be rationally selected as a frequency for interstellar communication that symbolizes life. (5) Finally, in preparation for the analysis of Martian meteorite samples, we upgraded our HPLC system to one femtomole sensitivity, and developed a new electrophoretic method of sample preparation for HPLC analysis of the meteoritic amino acids. In a sample of the KT boundary layer from Sussex Wyoming, we found about 300 picomoles per gram of meteoritic alpha-aminoisobutyric acid per gram of KT layer.

Weber, Arthur L.↗
NASA NTRS1992

Impact contribution of prebiotic reactants to Earth

It is proposed that the AIB amino acid at the K/T boundary were synthesized during entry of a comet. However, whether they were synthesized or supplied directly from space, the concentration of amino acids in the shallow K/T sea would have been about 10(exp -7) M. It is probable that clays were the dominant sinks for the amino acids in the K/T sea and in the primordial ocean. Because clay removed amino acids from sea water quickly, the amino acid contribution must be studied from individual comets in order to evaluate the effectiveness of comets for chemical evolution. Such an evaluation shows that comets would have produced amino acid concentration higher than equilibrium concentrations of amino acid from corona discharge at all times preceding the age of the oldest fossils. The perferred sites for chemical evolution of cometary amino acids are in cloud drops and tide pools where the concentration of amino acids would have been the highest. Life could have originated at the surface even during periods of intense bombardment of the earth before 3.8 billion years ago.

Aggarwal, Hans R.↗
DOE OSTI2022

Isotope effects at the origin of life: Fingerprints of the Strecker synthesis

We report strecker synthesis creates α-amino acids from prebiotically plausible substrates (cyanide, ammonia, and aldehydes) and is widely hypothesized to be a key mechanism in the chemistry that led to life on Earth and on other planets. To better constrain the synthetic environments and precursors of abiotic α-amino acids, and to determine unique signatures of abiogenic amino acids, we measured the molecular-averaged and site-specific carbon and nitrogen isotope effects for the Strecker synthesis of alanine. The reaction steps of the Strecker synthesis can be divided into two groups: an initial series of reversible amination and nitrile-addition reactions (‘equilibration’) and a second series of irreversible hydrolysis reactions (‘hydrolysis’). The equilibration of cyanide, acetaldehyde, and ammonia with the intermediate, α-aminopropionitrile (α-APN), has a measured 55.1‰ equilibrium nitrogen isotope effect between the 15 N-rich amine nitrogen in α-aminopropionitrile and the 15 N-poor ammonia and a 20.0‰ equilibrium carbon isotope effect between the 13 C-poor C-2 site in α-aminopropionitrile and the 13 C-rich carbonyl carbon in acetaldehyde. The first irreversible hydrolysis step is inferred to have an up to 10‰ normal carbon fractionation (i.e., faster for 12 C, slower for 13 C) for the whole molecule, but it also has one or more side reactions that deplete the reactive α-APN reservoir by up to 15‰. The second hydrolysis step has a 15.4‰ normal kinetic isotope effect on the amide (C-1) site of alaninamide, which becomes the carboxyl site of alanine. Other α-amino acids will likely experience similar nitrogen isotope fractionations between ammonia and their amine sites, and similar carbon isotope fractionations between the carbonyl carbon in reactant aldehydes or ketones and the intermediate α-aminonitrile, and between cyanide and the carboxyl site. Therefore, these isotope effects allow us to predict the carbon and nitrogen isotopic contents and intramolecular structures of α-amino acids formed by Strecker synthesis based on their substrates’ isotopic compositions, or to infer the isotopic compositions of substrates from which amino acids formed, for example in the case of the amino-acid-rich carbonaceous chondrites. The site-specific C and N isotopic compositions of amino acids formed by Strecker chemistry contrast with those typical of terrestrial biosynthetic amino acids, so these data also provide a means of discriminating between biogenic and abiogenic α-amino acids.

58 GEOSCIENCES↗
DOE OSTI2013

Selective posttranslational modification of phage-displayed polypeptides

The invention relates to posttranslational modification of phage-displayed polypeptides. These displayed polypeptides comprise at least one unnatural amino acid, e.g., an aryl-azide amino acid such as p-azido-L-phenylalanine, or an alkynyl-amino acid such as para-propargyloxyphenylalanine, which are incorporated into the phage-displayed fusion polypeptide at a selected position by using an in vivo orthogonal translation system comprising a suitable orthogonal aminoacyl-tRNA synthetase and a suitable orthogonal tRNA species. These unnatural amino acids advantageously provide targets for posttranslational modifications such as azide-alkyne [3+2]cycloaddition reactions and Staudinger modifications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Selective posttranslational modification of phage-displayed polypeptides

The invention relates to posttranslational modification of phage-displayed polypeptides. These displayed polypeptides comprise at least one unnatural amino acid, e.g., an aryl-azide amino acid such as p-azido-L-phenylalanine, or an alkynyl-amino acid such as para-propargyloxyphenylalanine, which are incorporated into the phage-displayed fusion polypeptide at a selected position by using an in vivo orthogonal translation system comprising a suitable orthogonal aminoacyl-tRNA synthetase and a suitable orthogonal tRNA species. These unnatural amino acids advantageously provide targets for posttranslational modifications such as azide-alkyne [3+2] cycloaddition reactions and Staudinger modifications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Co‐culture engineering for microbial biosynthesis of 3‐amino‐benzoic acid in Escherichia coli

Abstract 3‐amino‐benzoic acid (3AB) is an important building block molecule for production of a wide range of important compounds such as natural products with various biological activities. In the present study, we established a microbial biosynthetic system for de novo 3AB production from the simple substrate glucose. First, the active 3AB biosynthetic pathway was reconstituted in the bacterium Escherichia coli , which resulted in the production of 1.5 mg/L 3AB. In an effort to improve the production, an E. coli ‐ E. coli co‐culture system was engineered to modularize the biosynthetic pathway between an upstream strain and an downstream strain. Specifically, the upstream biosynthetic module was contained in a fixed E. coli strain, whereas a series of E. coli strains were engineered to accommodate the downstream biosynthetic module and screened for optimal production performance. The best co‐culture system was found to improve 3AB production by 15 fold, compared to the mono‐culture approach. Further engineering of the co‐culture system resulted in biosynthesis of 48 mg/L 3AB. Our results demonstrate co‐culture engineering can be a powerful new approach in the broad field of metabolic engineering.

Zhang, Haoran↗
DOE OSTI2013

Characterization of the nuclear localization signal of the mouse TET3 protein

Highlights: •Amino acid sequence KKRK is responsible for nuclear localization of TET3. •Amino acid sequence KKRK are capable of targeting the cytoplasmic proteins to the nucleus. •Amino acid sequence KKRK are conserved in TET3 orthologs. -- Abstract: DNA demethylation is associated with gene activation and is mediated by a family of ten-eleven translocation (TET) dioxygenase. The TET3 protein is a 1668-amino-acid DNA demethylase that is predicted to possess five nuclear localization signals (NLSs). In this paper, we used a series of green fluorescent protein-tagged and mutation constructs to identify a conserved NLS (KKRK) embedded between amino acid 1615 and 1618 of mouse TET3. The KKRK sequence facilitates the cytoplasmic protein’s translocation into the nucleus. Additionally TET3 may be imported into the nucleus by importin-α and importin-β.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Aza-proline effectively mimics L -proline stereochemistry in triple helical collagen

The prevalence of L -amino acids in biomolecules has been shown to have teleological importance in biomolecular structure and self-assembly. Recently, biophysical studies have demonstrated that natural L -amino acids can be replaced with non-natural achiral aza-amino acids in folded protein structures such as triple helical collagen. However, the structural consequences of achiral aza-amino acid incorporation has not been elucidated in the context of any relevant folded biomolecule. Herein, we use X-ray crystallography to provide the first atomic resolution crystal structure of an achiral aza-amino acid residue embedded within a folded protein structure, definitively illustrating that achiral aza-proline has the capacity to effectively mimic the stereochemistry of natural amino acids within the context of triple helical collagen. We further corroborate this finding with density functional theory computational analysis showing that the natural L -amino acid stereochemistry for aza-proline is energetically favored when arranged in the aza-proline-hydroxyproline-glycine motif. In addition to providing fundamental insight into peptide and protein structure, the incorporation of achiral stereochemical mimics such as aza-amino acids could have far reaching impacts in areas ranging from synthetic materials to drug design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Increased urine acylcarnitines in diabetic ApoE-/- mice: Hydroxytetradecadienoylcarnitine (C14:2-OH) reflects diabetic nephropathy in a context of hyperlipidemia

Hyperlipidemia is a risk factor for initiation and progression of diabetic nephropathy but the metabolic pathways altered in the diabetic kidney in a context of hyperlipidemia remain incompletely described. Assuming that changes in urine composition reflect the alteration of renal metabolism and function, we analyzed the urine metabolite composition of diabetic (streptozotocin-treatment) and control (non diabetic) ApoE−/− mice fed a high cholesterol diet using targeted quantitative metabolomics. Urine metabolome was also compared to the plasma metabolome of the same animals. As previously shown, urine albuminuria/urine creatinine ratio (uACR) and glomerular area and plasma lipids (cholesterol, triglycerides) were more elevated in diabetic mice compared to control. After adjustment to urine creatinine, the abundance of 52 urine metabolites was significantly different in diabetic mice compared to control. Among them was a unique metabolite, C14:2-OH (3-hydroxytetradecadienoylcarnitine) that, in diabetic mice, was positively and significantly correlated with uACR, glomerular hypertrophy, blood glucose and plasma lipids. That metabolite was not detected in plasma. C14:2-OH is a long-chain acylcarnitine reminiscent of altered fatty acid beta oxidation. Other acylcarnitines, particularly the short chains C3-OH, C3-DC, C4:1, C5-DC, C5-M-DC, C5-OH that are reminiscent of altered oxidation of branched and aromatic amino acids were also exclusively detected in urine but were only correlated with plasma lipids. Finally, the renal gene expression of several enzymes involved in fatty acid and/or amino acid oxidation was significantly reduced in diabetic mice compared to control. This included the bifunctional enoyl-CoA hydratase/3-hydroxyacyl-CoA (Ehhadh) that might play a central role in C14:2-OH production. This study indicate that the development of diabetes in a context of hyperlipidemia is associated with a reduced capacity of kidney to oxidize fatty acids and amino acids with the consequence of an elevation of urinary acetylcarnitines including C14:2-OH that specifically reflects diabetic nephropathy.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1997

Redox Energy and Sulfur Chemistry in Prebiotic Polymer Synthesis and Replication

In the past year we have made significant progress in three research areas: (1) Most importantly, we discovered a new pathway of prebiotic amino acid synthesis in which formaldehyde and glycolaldehyde (substrates of the formose reaction) react with ammonia yielding alanine and homoserine in the presence of thiol catalysts. This thiol-dependent synthesis of amino acids undoubtedly occurs via amino acid thioester intermediates capable of forming peptides. This 'one-pot' reaction system operates under mild aqueous conditions, and like modern amino acid biosynthesis, uses sugar intermediates which are converted to amino acids by energy-yielding redox disproportionation. (2) Finally, in preparation for the analysis of Martian meteorite samples, we upgraded our HPLC system and developed an improved method capable of detecting a I femtomole of amino acid enantiomers. (3) We completed our analysis of the energetics of metabolism that revealed that life depends on biosynthetic processes driven by chemical energy made available by the redox disproportionation of carbon groups of sugars. We established that the favorable energy of redox disproportionation is based on the universal reduction potentials of carbon groups. We concluded that it is hard to imagine any other organic molecule besides sugars (formaldehyde oligomers) having the energy and reactivity needed to drive either modem biosynthesis or the chemical processes behind its origin.

Weber, Arthur L.↗
DOE OSTI2018

A novel strategy to improve the thermostability of Penicillium camembertii mono- and di-acylglycerol lipase

Highlights: • A new protein engineering method has been developed to tailor enzyme with high thermostability. • The optimum catalytic temperature of mutant D25R was increased by 5 °C. • Tm value of mutant D25R was increase by 3 °C. • Mutant D25R showed the increase in t{sub 1/2} with a nearly 4-fold. Penicillium camembertii (PCL), a mono- and di-acylglycerol lipase (DGL), has the vital potential in the oil chemistry for food industry. However, known DGLs are mesophilic enzymes which restricts its application in the industry. To improve thermostability of PCL, we used amino acid substitution by comparison of amino acids compositions of PCL and protein sequences from typical thermophilic bacteria. Then, some conservative residues around active center were avoided to mutate according to homologous alignment analyses. Furthermore, the list was narrowed down to 28 candidate mutational sites of PCL by analyzing the hydrophobic interaction of amino acids in the structure. And among them only the mutant PCL-D25R had formed an additional salt bridge between R25-D32 and increased more hydrogen bonds interaction. Therefore, mutant PCL-D25R were constructed and expressed. Thermal inactivation assay showed that the half-life of mutant PCL-D25R at 45 °C increased 4-fold compared to that of PCL-WT. Melting temperature of mutant PCL-D25R increased to 49.5 °C from 46.5 °C by fluorescence-based thermal stability assay. This study provides a valuable strategy for engineering DGL thermostability.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1992

Impact contribution of prebiotic reactants to Earth

It is proposed that the AIB amino acids at the K/T boundary were synthesized during entry of a comet. However, whether they were synthesized or supplied directly from space, the concentration of amino acids in the shallow K/T sea would have been about 10(exp -7) M. It is probable that clays were the dominant sinks for the amino acids in the K/T sea and in the primordial ocean. Because clay removed amino from the sea so quickly, we must study the amino acid contribution from individual comets in order to evaluate the effectiveness of comets for chemical evolution. Such an evaluation shows that comets would have produced amino acid concentrations higher than equilibrium concentrations of amino acids from corona discharge at all times preceding the age of the oldest fossils. The preferred sites for chemical evolution of cometary amino acids are in cloud drops and tide pools where the concentration of amino acids would have been the highest. Life could have originated at the surface even during periods of intense bombardment of the earth before 3.8 billion years ago.

Aggarwal, Hans R.↗
NASA NTRS2014

Magnetite as Possible Template for the Synthesis of Chiral Organics in Carbonaceous Chondrites

The main goal of the Japanese Aerospace Ex-ploration Agency (JAXA) Hayabusa-2 mission is to visit and return to Earth samples of a C-type asteroid (162173) 1999 JU3 in order to understand the origin and nature of organic materials in the Solar System. Life on Earth shows preference towards the set of organics with particular spatial arrangements, this 'selectivity' is a crucial criterion for life. With only rare exceptions, life 'determines' to use the left- (L-) form over the right- (D-) form of amino acids, resulting in a L-enantiomeric excess (ee). Recent studies have shown that L-ee is found within the alpha-methyl amino acids in meteorites [1, 2], which are amino acids with rare terrestrial occurrence, and thus point towards a plausible abiotic origin for ee. One of the proposed origins of chiral asymmetry of amino acids in meteorites is their formation with the presence of asymmetric catalysts [3]. The catalytic mineral grains acted as a surface at which nebular gases (CO, H2 and NH3) were allowed to condense and react through Fisher Tropsch type (FTT) syntheses to form the organics observed in meteorites [4]. Magnetite is shown to be an effective catalyst of the synthesis of amino acids that are commonly found in meteorites [5]. It has also taken the form as spiral magnetites (a.k.a. 'plaquettes'), which were found in various carbonaceous chondrites (CCs), including C2s Tagish Lake and Esseibi, CI Orgueil, and CR chondrites [e.g., 6, 7, 8]. In addition, L-ee for amino acids are common in the aqueously altered CCs, as opposed to the unaltered CCs [1]. It seems possible that the synthesis of amino acids with chiral preferences is correlated to the alteration process experienced by the asteroid parent body, and related to the configuration of spiral magnetite catalysts. Since C-type asteroids are considered to be enriched in organic matter, and the spectral data of 1999 JU3 indicates a certain de-gree of aqueous alteration [9], the Hayabusa-2 mission serves as a perfect chance to attest this argument. In order to understand the distribution of spiral magnetites among different meteorite classes, as well as to investigate their spiral configurations and correlation to molecular asymmetry, we observed polished thin sections of CCs using scanning electron microscope (SEM) imaging. Individual magnetite grains were picked, embedded in epoxy, thin-sectioned using an ultra-microtome, and studied with electron backscatter diffraction (EBSD) in order to reconstruct the crystal orientation along the stack of magnetite disks.

Chan, Q. H. S.↗
NASA NTRS1992

Esterification of all four monoribonucleotides with acetyl-D-L-valine proceeds with a preference for the D-isomer but the D/L ratio in the products declines as a function of the hydrophobicity of the nucleotide

We recently reported that esterification of 5'-AMP with N-acetyl amino acids proceeds with a preference for D-amino acids, and the D/L ratio in products declines as the hydrophobicity of the amino acid declines. Using one amino acid, Ac-Val, we now show that esterification of all four nucleotides proceeds with a preference for the D-isomer and the preference declines as the hydrophobicity of the nucleotide declines. So, in both types of experiments, the preferences seem determined by hydrophobic interactions.

NASA Discipline Exobiology↗
NASA NTRS2019

Size and Structure of the Sequence Space of Repeat Proteins

The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family— the total number of sequences in that family—can be estimated using models of maximum entropy trained on multiple sequence alignments of naturally occurring amino acid sequences. We analyzed and calculated the size of three abundant repeat proteins families, whose members are large proteins made of many repetitions of conserved portions of *30 amino acids. While amino acid conservation at each position of the alignment explains most of the reduction of diversity relative to completely random sequences, we found that correlations between amino acid usage at different positions significantly impact that diversity. We quantified the impact of different types of correlations, functional and evolutionary, on sequence diversity. Analysis of the detailed structure of the coding space of the families revealed a rugged landscape, with many local energy minima of varying sizes with a hierarchical structure, reminiscent of frustrated energy landscapes of spin glass in physics. This clustered structure indicates a multiplicity of subtypes within each family and suggests new strategies for protein design.

Jacopo Marchi↗