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 1,495 records · Page 83
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Crystal structure of the flavoenzyme PA4991 from Pseudomonas aeruginosa

PA4991 is a FAD-dependent oxidoreductase from the pathogen P. aeruginosa that is essential for virulence and survival in the infected host. The structure of this enzyme, determined to 2.4 Å resolution, reveals that PA4991 belongs to the GR{sub 2} family of flavoenzymes. The locus PA4991 in Pseudomonas aeruginosa encodes an open reading frame that has been identified as essential for the virulence and/or survival of this pathogenic organism in the infected host. Here, it is shown that this gene encodes a monomeric FAD-binding protein of molecular mass 42.2 kDa. The structure of PA4991 was determined by a combination of molecular replacement using a search model generated with Rosetta and phase improvement by a low-occupancy heavy-metal derivative. PA4991 belongs to the GR{sub 2} family of FAD-dependent oxidoreductases, comprising an FAD-binding domain typical of the glutathione reductase family and a second domain dominated by an eight-stranded mixed β-sheet. Most of the protein–FAD interactions are via the FAD-binding domain, but the isoalloxazine ring is located at the domain interface and interacts with residues from both domains. A comparison with the structurally related glycine oxidase and glycerol-3-phosphate dehydrogenase shows that in spite of very low amino-acid sequence identity (<18%) several active-site residues involved in substrate binding in these enzymes are conserved in PA4991. However, enzymatic assays show that PA4991 does not display amino-acid oxidase or glycerol-3-phosphate dehydrogenase activities, suggesting that it requires different substrates for activity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Method and system for capturing carbon dioxide and/or sulfur dioxide from gas stream

The present invention provides a system for capturing CO.sub.2 and/or SO.sub.2, comprising: (a) a CO.sub.2 and/or SO.sub.2 absorber comprising an amine and/or amino acid salt capable of absorbing the CO.sub.2 and/or SO.sub.2 to produce a CO.sub.2- and/or SO.sub.2-containing solution; (b) an amine regenerator to regenerate the amine and/or amino acid salt; and, when the system captures CO.sub.2, (c) an alkali metal carbonate regenerator comprising an ammonium catalyst capable catalyzing the aqueous alkali metal bicarbonate into the alkali metal carbonate and CO.sub.2 gas. The present invention also provides for a system for capturing SO.sub.2, comprising: (a) a SO.sub.2 absorber comprising aqueous alkali metal carbonate, wherein the alkali metal carbonate is capable of absorbing the SO.sub.2 to produce an alkali metal sulfite/sulfate precipitate and CO.sub.2.

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

Combined effects of lipase and Lactiplantibacillus plantarum 1‐24‐LJ on physicochemical property, microbial succession and volatile compounds formation in fermented fish product

Abstract BACKGROUND Studies have shown that either the addition of starter culture or enzyme can improve fermentation in fish or other products. However, little research has been carried out on the effects of coupling starter cultures with lipase on the microbial community and product quality. Suanzhayu is a Chinese fermented fish product that mainly relies on spontaneous fermentation, resulting in an unstable flavor and quality. The present study investigated the impact of lipase and Lactiplantibacillus plantarum 1‐24‐LJ on the quality of Suanzhayu . RESULTS Inoculation decreased pH and 2‐thiobarbituric acid reactive substances (TBARS) values, and also helped the dominance of the strain in the ecosystem, whereas lipase addition raised TBARS values and had little effect on pH, water activity ( a w ) and microbiota. The addition of lipase and/or Lpb. plantarum increased the content of alcohols, aldehydes, ketones, esters and umami amino acids. The co‐additions with the most significant effect and the total contents of volatile compounds (VCs) and free amino acids (FAAs) were 1801.92 g per 100 g and 21 357.05 mg per 100 g, respectively. Former‐ Lactobacillus was negatively correlated with pH, a w and Prevotella , but positively with VCs (ethyl ester of heptanoic acid, ethyl ester of octanoic acid) and FAAs (Tyr, Phe). Furthermore, adding Lpb. plantarum 1‐24‐LJ alone or in combination with lipase shortened the fermentation process. CONCLUSION The present study provides a recommended Suanzhayu process approach for improving product quality and flavor, as well as shortening fermentation time, by adding Lpb. plantarum 1‐24‐LJ with or without lipase. © 2023 Society of Chemical Industry.

Zhang, Zuoli↗
DOE OSTI2017

Atomic-Scale Quantification of Interfacial Binding between Peptides and Inorganic Crystals: The Case of Calcium Carbonate Binding Peptide on Aragonite

Using a specific explicitly solvated interface model between a calcium carbonate binding peptide and crystalline aragonite, we investigate the electronic structure, atomic bonding, solvation effect, and the role of hydrogen bonding on the cohesion, stability, and functionality of this complex hybrid system using density functional calculation. The large interface model is strategically constructed using a stepwise procedure followed by ab initio molecular dynamics to obtain the optimal conformation. The calculated data on the electronic structure and bonding are analyzed in terms of three structural parts: aragonite, peptide, and water. Next, we focus on the binding between aragonite (001) surface and the peptide mediated by water. Finally, specific interatomic bonding between the amino acids in peptide and the (001) surface of aragonite is quantified. A single quantum mechanical metric, the total bond order density (TBOD), infers the dynamic interplay of different competing interactions. Four amino acids HIS1, ARG6, MET7, and TRP11 in the peptide sequence have strong interfacial Ca–O bonding and O···H hydrogen bonding between aragonite and peptide. The calculated Young’s modulus 33.37 GPa is in line with the measured value for nacre. Our approach for interfacial study between aragonite and a calcium carbonate binding peptide offers a broad perspective for probing complex interactions between the biomimetic interfaces. Finally, TBOD can be used as an effective parameter in ranking the efficacy of peptide–surface interactions and in providing a programmable design for bio-inspired material interfaces based on computational means.

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

How Does Escherichia coli Allocate Proteome?

Microorganisms are shown to actively partition their intracellular resources, such as pro- teins, for growth optimization. Recent experiments have begun to reveal molecular com- ponents unpinning the partition; however, it remains unclear quantitatively how individual parts orchestrate to yield precise resource allocation that is both robust and dynamic. Here we developed a coarse-grained mathematical framework that centers on guanosine pentaphosphate (ppGpp)-mediated regulation, and used it to systematically uncover the design principles of proteome allocation in Escherichia coli. Our results showed that cellular ability of resource partition lies in an ultrasensitive, negative feedback control- ling topology with the ultrasensitivity arising from zero-order amino acid kinetics and the negative feedback from ppGpp-controlled ribosome synthesis. In addition, together with the time-scale separation between slow ribosome kinetics and fast turnovers of ppGpp and amino acids, the network topology confers the organism an optimization mechanism which mimics sliding mode control, a nonlinear optimization strategy that is widely used in man-made systems. We further showed that such a controlling mechanism is robust against parameter variations and molecular fluctuations, and is also efficient for biomass production over time. Furthermore, this work elucidates the fundamental controlling mechanism of E. coli proteome allocation, thereby providing insights into quantitative microbial physiology as well as the design of synthetic gene networks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Establishing the precise evolutionary history of a gene improves prediction of disease-causing missense mutations

Here, predicting the phenotypic effects of mutations has become an important application in clinical genetic diagnostics. Computational tools evaluate the behavior of the variant over evolutionary time and assume that variations seen during the course of evolution are probably benign in humans. However, current tools do not take into account orthologous/paralogous relationships. Paralogs have dramatically different roles in Mendelian diseases. For example, whereas inactivating mutations in the NPC1 gene cause the neurodegenerative disorder Niemann-Pick C, inactivating mutations in its paralog NPC1L1 are not disease-causing and, moreover, are implicated in protection from coronary heart disease. Methods: We identified major events in NPC1 evolution and revealed and compared orthologs and paralogs of the human NPC1 gene through phylogenetic and protein sequence analyses. We predicted whether an amino acid substitution affects protein function by reducing the organism s fitness. As a result, removing the paralogs and distant homologs improved the overall performance of categorizing disease-causing and benign amino acid substitutions. In conclusion, the results show that a thorough evolutionary analysis followed by identification of orthologs improves the accuracy in predicting disease-causing missense mutations. We anticipate that this approach will be used as a reference in the interpretation of variants in other genetic diseases as well.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Predicting 2CS protein pairs with Deep Learning

Neural network was trained on the amino acid sequences of known two-component systems (2CS) pairs. The recommender algorithm uses learned model to select the most likely 2CS pair from an arbitrary set of protein pairs whose amino acid sequences are known.

Balewski, Jan↗
DOE OSTI2023

Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins

Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate the characteristics of TRs in all ten complete Borg genomes. We find that TR regions are rapidly evolving, recently formed, arise independently, and are virtually absent in host Methanoperedens genomes. Flanking partial repeats and A-enriched character constrain the TR formation mechanism. TRs can be in intergenic regions, where they might serve as regulatory RNAs, or in open reading frames (ORFs). TRs in ORFs are under very strong selective pressure, leading to perfect amino acid TRs (aaTRs) that are commonly intrinsically disordered regions. Proteins with aaTRs are often extracellular or membrane proteins, and functionally similar or homologous proteins often have aaTRs composed of the same amino acids. We propose that Borg aaTR-proteins functionally diversify Methanoperedens and all TRs are crucial for specific Borg–host associations and possibly cospeciation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1996

Insect Development in Altered Gravitational Environment

When tobacco hornworm (Manduca sexta) larvae burrow underground (25-30 cm) to pupate, they reorient themselves to a relatively horizontal position indicating an ability to sense gravity. To evaluate their sensitivity to gravitational environment during metamorphosis, Manduca (pharate adults) were placed in a vertical (head-up) position. Distinct morphological changes, each one reflecting ensuing phases, were used to follow adult development. Five days after pupation, the vertical group showed accelerated (P less than 0.05) development and were nearly 4 phases ahead (P less than 0.0001) after 10 days. Differences in development in the vertical group were characterized further by increased (7-48%) hemolymph concentrations of 13 amino acids, but a decrease in cys and pro and no change in arg, his, met and val (trp, undetectable). Decreased (36%) turnover of injected H-3 - phenylalanine suggested slower utilization of amino acids contributed, at least partly, to the increased concentrations. Vertically-oriented Manduca also exhibited a greater (20 %, P less than 0.001) protein content in their flight muscles near the end of development. Analysis of hemolymph sugar levels showed a redistribution of sugars from the monosaccharide glucose to the disaccharide trehalose. Since injection of 20-hydroxyecdysone decreased (49%) turnover of H-3- phenylalanine in pharate adults and since ecdysteroids are known to increase flight muscle size and control adult development, these results are consistent with our measuring a greater (+80%, P less than 0.05) ecdysteroid titer in the vertically-oriented insects. These results suggest that gravity environment influences ecdysone output by the pharate adult. When we evaluated hemolymph flow in the head-up and control positions, we found that injected C-14-inulin was distributed somewhat more rapidly in the head-up group irrespective of the sight of injection (head or abdomen) likely because in the head-up position flow of the hemolymph is facilitated throughout the animal. Other experiments showed that an intact prothoracic gland is needed for the response. Hence vertical, head-up orientation affects release of ecdysone from the prothoracic gland.

Tischler, Marc E.↗
NASA NTRS1996

The Metabolic World: Sugars as an Energized Carbon Substrate for Prebiotic and Biotic Synthesis

To understand the origin of metabolism and biopolymer synthesis we investigated the energy sources that drive anabolic metabolism. We found that biosynthesis of amino acids and lipids from sugars is driven bz the free energy of redox disproportionation of carbon (see discussion or next page). The indispensable role of sugar disproportionation in the biosynthesis of amino acids and lipids suggests that the origin of life uses the same chemical engine, and was therefore based on nonenzymatic redox disproportionation reactions of sugars that occurred in the presence o ammonia and hydrogen sulfide. The chemistry of this 'metabolic' model of the origin of life is described.

Weber, Arthur L.↗
DOE OSTI2023

Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble

T-box riboswitches are multi-domain noncoding RNAs that surveil individual amino acid availabilities in most Gram-positive bacteria. T-boxes directly bind specific tRNAs, query their aminoacylation status to detect starvation, and feedback control the transcription or translation of downstream amino-acid metabolic genes. Most T-boxes rapidly recruit their cognate tRNA ligands through an intricate three-way stem I-stem II-tRNA interaction, whose establishment is not understood. Using single-molecule FRET, SAXS, and time-resolved fluorescence, we find that the free T-box RNA assumes a broad distribution of open, semi-open, and closed conformations that only slowly interconvert. tRNA directly binds all three conformers with distinct kinetics, triggers nearly instantaneous collapses of the open conformations, and returns the T-box RNA to their pre-binding conformations upon dissociation. This scissors-like dynamic behavior is enabled by a hinge-like pseudoknot domain which poises the T-box for rapid tRNA-induced domain closure. This study reveals tRNA-chaperoned folding of flexible, multi-domain mRNAs through a Venus flytrap-like mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1972

Selective condensation of aminoacyl adenylates by nucleoproteinoid microparticles.

Microparticles composed of each of four enzymically synthesized homopolynucleotides and the same lysine-rich proteinoid have been found to influence the condensation of the AMP-anhydrides of each of four amino acids. The conditions of preparation of the particles and other variables of the experiments control the types of reaction. When a period set of conditions was identified empirically, the incorporation favored the amino acids whose present-day codons are related to the homopolynucleotide in the particle.

Nakashima, T.↗
NASA NTRS1979

Effects of gravity on contractile proteins

A method was established for the isolation and purification of nuclei in high yield from the microplasmodia of Physarum flavicomum. Purified nuclei were resistant to breakage by methods commonly employed for isolated plant and animal nuclei. Several methods for the extraction of nuclear protein were compared. Incubation of nuclear lysates with either 2 M NaCl, with or without 5 M urea, or 1 M CaCl2 resulted in the extraction of nuclear action together with histones. The histones were chemically fractionated into the 5 basic groups common to other eucaryotic tissue. Amino acid analyses of the total histone were also performed. Nuclear actin was found to have a molecular weight of 41,000 ? 4,000 daltons as determined by SDS polyacrylamide gel electrophoresis. The amino acid composition of the nuclear action was established.

Henney, H. R., Jr.↗
NASA NTRS1985

Rationalization of some genetic anticodonic assignments

The hydrophobicity of most amino acids correlates well with that of their anticodon nucleotides, with Trp, Tyr, Ile, and Ser being the exceptions to this rule. Using previous data on hydrophobicity and binding constants, and new data on rates of esterification of polyadenylic acid with several N-acetylaminoacyl imidazolides, several of the anticodon assignments are rationalized. Chemical reasons are shown supporting the idea of the inclusion of the Ile in the catalog of biological amino acids late in the evolution, through a mutation of the existing tRNA and its aminoacyl-tRNA-synthetase. It was found that an addition of hexane increases the incorporation of hydrophobic Ac-Phe into poly-A, in support of the Fox (1965) and Oparin (1965) emphasis on the biogenetic importance of phase-separated systems.

Lacey, J. C., Jr.↗
NASA NTRS2015

Magnetite Plaquettes Provide an Extraterrestrial Source of Asymmetric Components

Molecular selectivity is a crucial criterion for life. A possible abiotic mechanism that can produce chiral asymmetry in meteoritic amino acids is their formation with the presence of asymmetric catalysts. Magnetite (Fe3O4), a common mineral in some carbonaceous chondrites (CCs), has been shown to be an effective catalyst for the formation of amino acids that are commonly found in these meteorites. Magnetite sometimes takes the form of plaquettes that consist of barrel-shaped stacks of magnetite disks that resemble a spiral. However, a widely accepted description of the internal morphology of this particular magnetite form is still lacking, which is necessary in order to confirm or disprove the spiral configuration.

Chan, Q. H. S.↗
DOE OSTI2018

Direct air capture of CO 2 via aqueous-phase absorption and crystalline-phase release using concentrated solar power

Using negative emissions technologies for the net removal of greenhouse gases from the atmosphere could provide a pathway to limit global temperature rises. Direct air capture of carbon dioxide offers the prospect of permanently lowering the atmospheric CO 2 concentration, providing that economical and energy-efficient technologies can be developed and deployed on a large scale. Here in this paper, we report an approach to direct air capture, at the laboratory scale, using mostly off-the-shelf materials and equipment. First, CO 2 absorption is achieved with readily available and environmentally friendly aqueous amino acid solutions (glycine and sarcosine) using a household humidifier. The CO 2 -loaded solutions are then reacted with a simple guanidine compound, which crystallizes as a very insoluble carbonate salt and regenerates the amino acid sorbent. Finally, effective CO 2 release and near-quantitative regeneration of the guanidine compound are achieved by relatively mild heating of the carbonate crystals using concentrated solar power.

14 SOLAR ENERGY↗
DOE OSTI2020

Drosophila TRIM32 cooperates with glycolytic enzymes to promote cell growth

Cell growth and/or proliferation may require the reprogramming of metabolic pathways, whereby a switch from oxidative to glycolytic metabolism diverts glycolytic intermediates towards anabolic pathways. Herein, we identify a novel role for TRIM32 in the maintenance of glycolytic flux mediated by biochemical interactions with the glycolytic enzymes Aldolase and Phosphoglycerate mutase. Loss of Drosophila TRIM32, encoded by thin (tn), shows reduced levels of glycolytic intermediates and amino acids. This altered metabolic profile correlates with a reduction in the size of glycolytic larval muscle and brain tissue. Consistent with a role for metabolic intermediates in glycolysis-driven biomass production, dietary amino acid supplementation in tn mutants improves muscle mass. Remarkably, TRIM32 is also required for ectopic growth - loss of TRIM32 in a wing disc-associated tumor model reduces glycolytic metabolism and restricts growth. Overall, our results reveal a novel role for TRIM32 for controlling glycolysis in the context of both normal development and tumor growth.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1973

Prebiotic activation processes.

Questions regarding the combination of amino acids and ribonucleotides to polypeptides and polynucleotides are investigated. Each of the reactions considered occurs in the solid state in plausible prebiotic conditions. Together they provide the basis for a unified scheme of amino acid and nucleotide activation. Urea, imidazole and Mg(++) are essential catalytic components of the reaction mixtures. However, these compounds could probably be replaced by other organic molecules.

Lohrmann, R.↗