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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids

Expansion of the genetic code with nonstandard amino acids (nsAAs) has enabled biosynthesis of proteins with diverse new chemistries. However, this technology has been largely restricted to proteins containing a single or few nsAA instances. We describe an in vivo evolution approach in a genomically recoded Escherichia coli strain for the selection of orthogonal translation systems capable of multi-site nsAA incorporation. We evolved chromosomal aminoacyl-tRNA synthetases (aaRSs) with up to 25-fold increased protein production for p-acetyl-L-phenylalanine and p-azido-L-phenylalanine (pAzF). We also evolved aaRSs with tunable specificities for 14 nsAAs, including an enzyme that efficiently charges pAzF while excluding 237 other nsAAs. These variants enabled production of elastin-like-polypeptides with 30 nsAA residues at high yields (~50 mg/L) and high accuracy of incorporation (>95%). This approach to aaRS evolution should accelerate and expand our ability to produce functionalized proteins and sequence-defined polymers with diverse chemistries.

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

On the role of α-alumina in the origin of life: Surface-driven assembly of amino acids

We investigate the hypothesis that mineral/water interfaces played a crucial catalytic role in peptide formation by promoting the self-assembly of amino acids. Using classical molecular dynamics simulations, we demonstrate that the α-alumina(0001) surface exhibits an affinity of 4k B Tfor individual glycine or GG dipeptide molecules due to hydrogen bonds. In simulations with multiple glycine molecules, surface-bound glycine enhances further adsorption, leading to the formation of long chains connected by hydrogen bonds between the carboxyl and amine groups of glycine molecules. We find that the likelihood of observing chains longer than 10 glycine units increases by at least five orders of magnitude at the surface compared to the bulk. This surface-driven assembly is primarily due to local high density and alignment with the alumina surface pattern. Together, these results propose a model for how mineral surfaces can induce configuration-specific assembly of amino acids, thereby promoting condensation reactions.

Science & Technology - Other Topics↗
DOE OSTI2018

Influence of isopropylmalate synthase Os IPMS 1 on seed vigour associated with amino acid and energy metabolism in rice

Summary Seed vigour is an imperative trait for the direct seeding of rice. Isopropylmalate synthase ( IPMS ) catalyses the committed step of leucine (Leu) biosynthesis, but its effect on seed vigour remains unclear. In this study, rice Os IPMS 1 and Os IPMS 2 was cloned, and the roles of Os IPMS 1 in seed vigour were mainly investigated. Os IPMS 1 and Os IPMS 2 catalyse Leu biosynthesis, and Leu feedback inhibits their IPMS activities. Disruption of Os IPMS 1 resulted in low seed vigour under various conditions, which might be tightly associated with the reduction of amino acids in germinating seeds. Eleven amino acids that associated with stress tolerance, GA biosynthesis and tricarboxylic acid ( TCA ) cycle were significantly reduced in osipms1 mutants compared with those in wide type ( WT ) during seed germination. Transcriptome analysis indicated that a total of 1209 differentially expressed genes ( DEG s) were altered in osipms1a mutant compared with WT at the early germination stage, wherein most of the genes were involved in glycolysis/gluconeogenesis, protein processing, pyruvate, carbon, fructose and mannose metabolism. Further analysis confirmed that the regulation of Os IPMS 1 in seed vigour involved in starch hydrolysis, glycolytic activity and energy levels in germinating seeds. The effects of seed priming were tightly associated with the mRNA levels of Os IPMS 1 in priming seeds. The Os IPMS 1 might be used as a biomarker to determine the best stop time‐point of seed priming in rice. This study provides novel insights into the function of Os IPMS 1 on seed vigour and should have practical applications in seed priming of rice.

He, Yongqi↗
DOE OSTI2021

Methods of making polypeptides with non-standard amino acids using genomically recoded organisms

A method of making a polypeptide including at least one covalent bond between a pair of reactive side chains of corresponding amino acids, wherein the covalent bond is insensitive to reduction is provided including genetically modifying a genomically recoded organism to express a corresponding synthetase, tRNA or synthetase/tRNA pair for translating mRNA encoding the corresponding amino acids having the reactive side chains into the polypeptide and to express the polypeptide including the at least one pair of the reactive side chains wherein the reactive side chains are oriented near one another when the expressed polypeptide is in a folded configuration, wherein the reactive side chains react to form the covalent bond that is insensitive to reduction.

Church, George M.↗
DOE OSTI2016

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental–Computational Study

Here, we present a joint experimental-computational study to quantitatively describe the thermodynamics of hydrophobic leucine amino acids in aqueous solution. X-ray scattering data were acquired at a series of solute and salt concentrations to effectively measure inter-leucine interactions, indicating that a major scattering peak is observed consistently at q = 0.83 Å -1 . Atomistic molecular dynamics simulations were then performed and compared with the scattering data, achieving high consistency at both small and wider scattering angles (q = 0$-$1.5 Å -1 ). This experimental-computational consistence enables a first glimpse of the leucineleucine interacting landscape, where two leucine molecules are aligned mostly in a parallel fashion, as opposed to anti-parallel, but also allows us to derive effective leucine-leucine interactions in solution. Collectively, this combined approach of employing experimental scattering and molecular simulation enables a quantitative characterization on effective inter-molecular interactions of hydrophobic amino acids, critical for protein function and dynamics such as protein folding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

Summary Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non‐canonical amino acid tagging ( BONCAT ), is based on the in vivo incorporation of the non‐canonical amino acid L ‐azidohomoalanine ( AHA ), a surrogate for l ‐methionine, followed by fluorescent labelling of AHA ‐containing cellular proteins by azide‐alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater and anoxic sediment. We also developed combined assays that couple BONCAT with ribosomal RNA (rRNA)‐targeted fluorescence in situ hybridization ( FISH ), enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT‐FISH to study microbial physiology in situ . A direct comparison of anabolic activity using BONCAT and stable isotope labelling by nano‐scale secondary ion mass spectrometry ( 15 NH 3 assimilation) for individual cells within a sediment‐sourced enrichment culture showed concordance between AHA ‐positive cells and 15 N enrichment. BONCAT‐FISH offers a fast, inexpensive and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single‐cell level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Self‐assembling Peptides with Internal Ionizable Unnatural Amino Acids: A General Approach to pH‐responsive Peptide Materials

Self‐assembled peptides are an emerging family of biomaterials that show great promise for a range of biomedical and biotechnological applications. Introducing and tuning the pH‐responsiveness of the assembly is highly desirable for improving their biological activities. Inspired by proteins with internal ionizable residues, we report a simple but effective approach to constructing pH‐responsive peptide assembly containing unnatural ionic amino acids with an aliphatic tertiary amine side chain. Through a combined experimental and computational investigation, we demonstrate that these residues can be accommodated and stabilized within the internal hydrophobic compartment of the peptide assembly. The hydrophobic microenvironment shifts their pK a significantly from a basic pH typically found for free amines to a more biologically relevant pH in the weakly acidic range. The pH‐induced ionization and ionization‐dependent self‐assembly and disassembly are thoroughly investigated and correlated with the biological activity of the assembly. This new approach has unique advantages in tuning the pH‐responsiveness of self‐assembled peptides across a large pH range in a complex biological environment. We anticipate the ionizable amino acids developed here can be widely applicable to the synthesis and self‐assembly of many amphiphilic peptides with endowed pH‐responsive properties to enhance their biological activities toward applications ranging from targeted therapeutic delivery to proton transport.

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

Site-specific incorporation of redox active amino acids into proteins

Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate redox active amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with redox active amino acids using these orthogonal pairs.

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

Tip-induced domain structures and polarization switching in ferroelectric amino acid glycine

Bioorganic ferroelectrics and piezoelectrics are becoming increasingly important in view of their intrinsic compatibility with biological environment and biofunctionality combined with strong piezoelectric effect and a switchable polarization at room temperature. Here, we study tip-induced domain structures and polarization switching in the smallest amino acid β-glycine, representing a broad class of non-centrosymmetric amino acids. We show that β-glycine is indeed a room-temperature ferroelectric and polarization can be switched by applying a bias to non-polar cuts via a conducting tip of atomic force microscope (AFM). Dynamics of these in-plane domains is studied as a function of an applied voltage and pulse duration. The domain shape is dictated by polarization screening at the domain boundaries and mediated by growth defects. Thermodynamic theory is applied to explain the domain propagation induced by the AFM tip. Our findings suggest that the properties of β-glycine are controlled by the charged domain walls which in turn can be manipulated by an external bias.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Highly efficient inverted organic solar cells using amino acid modified indium tin oxide as cathode

In this paper, we report that highly efficient inverted organic solar cells were achieved by modifying the surface of indium tin oxide (ITO) using an amino acid, Serine (Ser). With the modification of the ITO surface, device efficiency was significantly enhanced from 0.63% to 4.17%, accompanied with an open circuit voltage (Voc) that was enhanced from 0.30 V to 0.55 V. Ultraviolet and X-ray photoelectron spectroscopy studies indicate that the work function reduction induced by the amino acid modification resulting in the decreased barrier height at the ITO/organic interface played a crucial role in the enhanced performances.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Amino acid enantiomers in old and young dissolved organic matter: Implications for a microbial nitrogen pump

Dissolved organic nitrogen (DON) represents the largest reservoir of fixed N in the surface ocean and a significant portion accumulates in the deep sea, where it can persist for millennial time scales. However, like the dissolved organic carbon (DOC) pool, the origin and composition of long-lived, refractory DON remains largely unknown. In recent years, the “microbial carbon pump” hypothesis has emerged from abundant evidence showing that microbial processes are primarily responsible for refractory DOC accumulation. However, a similar mechanism for DON has rarely been investigated. In the study of DON, spectroscopic evidence has indicated a primarily amide composition, implying a dominant contribution from peptides. Therefore, if an analogous “microbial nitrogen pump” controls refractory DON accumulation, the amino acid component should bear increasing signatures of microbial origin with increasing age. Here we investigate the microbial sequestration of N via the production of refractory DON, for the first time considering together DOM Δ 14 C with amino acid (AA) molar abundance (Mol%) and D/L ratio (as a tracer for prokaryotic input). Measurements were made on a unique set of high and low molecular weight (HMW, LMW) DOM isolates with 14 C ages and chemical compositions generally consistent with semi-labile and refractory DOM respectively. The samples were collected in the North Pacific Subtropical Gyre where deep waters contain some of the oldest DOC in the world ocean. We observe higher D/L ratios in older, LMW DOM isolates for almost all analyzed AAs. Using mass spectral data, we also quantify three D-AAs in all samples (D-valine, D-phenylalanine, and D-leucine), which have not previously been confirmed in ocean DOM. These newly identified D-AAs are concentrated in the LMW refractory DOM fraction and have oceanographically consistent depth profiles. Our results suggest that several novel D-AA subgroupings may be unique tracers for different prokaryotic source processes. D-alanine appears to have largely independent cycling from the other D-AAs with a connection to the production of HMW DON, which we hypothesize is linked to water column peptidoglycan. In contrast, D-leucine, D-valine, and D-phenylalanine appear to be most strongly related to the production of LMW DON. Trends in both the HMW and LMW fractions suggest a linkage to sinking particles and local microbial transformations, implying that LMW DON has a direct biological source rather than originating from successive microbial reprocessing of HMW DON. In conclusion, taken together, our observations are consistent with the dominant production of refractory LMW DON by prokaryotic organisms and suggests that different AA sub-groupings that can be used to track different processes within the DON pool.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Crystal structures of Leishmania mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors

Leishmania arginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiates de novo polyamine biosynthesis by catalyzing the hydrolysis of L-arginine to generate L-ornithine and urea. The product L-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis. Polyamines such as spermidine are essential for the growth and survival of the parasite, so inhibition of enzymes in the polyamine-biosynthetic pathway comprises an effective strategy for treating parasitic infections. To this end, two X-ray crystal structures of L. mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors based on the molecular scaffold of 2-( S )-amino-6-boronohexanoic acid are now reported. Structural comparisons with human and parasitic arginase complexes reveal interesting differences in the binding modes of the additional α-substituents, i.e. the D side chains, of these inhibitors. Subtle differences in the three-dimensional contours of the outer active-site rims among arginases from different species lead to different conformations of the D side chains and thus different inhibitor-affinity trends. The structures suggest that it is possible to maintain affinity while fine-tuning intermolecular interactions of the D side chain of α,α-disubstituted boronic amino-acid inhibitors in the search for isozyme-specific and species-specific arginase inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Characterization of amino acid residues within the N-terminal region of Ubc9 that play a role in Ubc9 nuclear localization

As the sole E2 enzyme for SUMOylation, Ubc9 is predominantly nuclear. However, the underlying mechanisms of Ubc9 nuclear localization are still not well understood. Here we show that RNAi-depletion of Imp13, an importin known to mediate Ubc9 nuclear import, reduces both Ubc9 nuclear accumulation and global SUMOylation. Furthermore, Ubc9-R13A or Ubc9-H20D mutation previously shown to interrupt the interaction of Ubc9 with nucleus-enriched SUMOs reduces the nuclear enrichment of Ubc9, suggesting that the interaction of Ubc9 with the nuclear SUMOs may enhance Ubc9 nuclear retention. Moreover, Ubc9-R17E mutation, which is known to disrupt the interaction of Ubc9 with both SUMOs and Imp13, causes a greater decrease in Ubc9 nuclear accumulation than Ubc9-R13A or Ubc9-H20D mutation. Lastly, Ubc9-K74A/S89D mutations that perturb the interaction of Ubc9 with nucleus-enriched SUMOylation-consensus motifs has no effect on Ubc9 nuclear localization. Altogether, our results have elucidated that the amino acid residues within the N-terminal region of Ubc9 play a pivotal role in regulation of Ubc9 nuclear localization. - Highlights: • Imp13-mediated nuclear import of Ubc9 is critical for global SUMOylation. • Ubc9 mutations disrupting Ubc9-SUMO interaction decrease Ubc9 nuclear accumulation. • N-terminal amino acid residues of Ubc9 are critical for Ubc9 nuclear enrichment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Potential transfer of neurotoxic amino acid β-N-methylamino-alanine (BMAA) from mother to infant during breast-feeding: Predictions from human cell lines

β-N-methylamino-alanine (BMAA) is a non-protein amino acid produced by cyanobacteria, diatoms and dinoflagellates. BMAA has potential to biomagnify in a terrestrial food chain, and to bioaccumulate in fish and shellfish. We have reported that administration of [{sup 14}C]L-BMAA to lactating mice and rats results in a mother to off-spring transfer via the milk. A preferential enantiomer-specific uptake of [{sup 14}C]L-BMAA has also been demonstrated in differentiated murine mammary epithelium HC11 cells. These findings, together with neurotoxic effects of BMAA demonstrated both in vitro and in vivo, highlight the need to determine whether such transfer could also occur in humans. Here, we used four cell lines of human origin to examine and compare the transport of the two BMAA enantiomers in vitro. The uptake patterns of [{sup 14}C]L- and [{sup 14}C]D-BMAA in the human mammary MCF7 cell line were in agreement with the results in murine HC11 cells, suggesting a potential secretion of BMAA into human breast milk. The permeability coefficients for both [{sup 14}C]L- and [{sup 14}C]D-BMAA over monolayers of human intestinal Caco2 cells supported an efficient absorption from the human intestine. As a final step, transport experiments confirmed that [{sup 14}C]L-and [{sup 14}C]D-BMAA can be taken up by human SHSY5Y neuroblastoma cells and even more efficiently by human U343 glioblastoma cells. In competition experiments with various amino acids, the ASCT2 specific inhibitor benzylserine was the most effective inhibitor of [{sup 14}C]L-BMAA uptake tested here. Altogether, our results suggest that BMAA can be transferred from an exposed mother, via the milk, to the brain of the nursed infant. - Highlights: • Transport of BMAA in human intestinal, mammary and CNS cell lines was examined. • The transport of L-BMAA over intestinal cell monolayers was unidirectional. • Enantiomer-selective uptake of L-BMAA in breast, neuron and glia cells was evident. • Competition experiments indicate that L-BMAA uptake involved several transporters. • A potential for mother to infant transfer of BMAA is proposed.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

13 C NMR study of amino acid salts in facilitated transport membranes for post-combustion carbon capture

Some of amino acid salts (AASs) have been demonstrated to be effective mobile carriers in facilitated transport membranes (FTMs) to achieve superior CO 2 permeance and CO 2 /N 2 selectivity for CO 2 capture from flue gas. Understandings of how the structures of different AASs affect the chemistry of the amine–CO 2 reaction are essential for the future development of more efficient AAS mobile carriers. In this study, the reaction chemistry of selected AASs with CO 2 was investigated by 13 C nuclear magnetic resonance (NMR) spectroscopy. The CO 2 loading and the distribution of major reaction products, including carbamate and bicarbonate products of each studied AAS were quantitatively analyzed. The positive correlation between the CO 2 loading of AAS (mol CO 2 /g AAS) and the CO 2 permeance of FTMs suggested that AAS with a higher CO 2 loading may improve the performance of FTMs. Our results also showed that increasing the steric hindrance of AAS could be a practical way to promote the bicarbonate reaction pathway and thus potentially increase the CO 2 loading (mol CO 2 /mol AAS). Moreover, 2-(1-piperazinyl)ethylamine (PZEA) was found to be a more effective multi-amine than piperazine (PZ) for synthesizing AASs due to the presence of more effective nitrogen sites per molecule. The superior CO 2 permeance of the PZEA-Sar membrane is also attributed to its more uniform membrane formation. As a result, the knowledge gained from this study will inform the rational design of more effective AAS carriers for CO 2 capture.

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

Chaperone protein HYPK interacts with the first 17 amino acid region of Huntingtin and modulates mutant HTT-mediated aggregation and cytotoxicity

Highlights: • HYPK reduces mutant HTT-mediated aggregate formation and cytotoxicity. • Interaction of HYPK with HTT requires N-terminal 17 amino acid of HTT (HTT-N17). • Deletion of HTT-N17 leads to SDS-soluble, smaller, nuclear aggregates. • These smaller aggregates do not associate with HYPK and are more cytotoxic. • Maybe, interaction of HYPK with amphipathic HTT-N17 block HTT aggregate formation. - Abstract: Huntington’s disease is a polyglutamine expansion disorder, characterized by mutant HTT-mediated aggregate formation and cytotoxicity. Many reports suggests roles of N-terminal 17 amino acid domain of HTT (HTT-N17) towards subcellular localization, aggregate formation and subsequent pathogenicity induced by N-terminal HTT harboring polyQ stretch in pathogenic range. HYPK is a HTT-interacting chaperone which can reduce N-terminal mutant HTT-mediated aggregate formation and cytotoxicity in neuronal cell lines. However, how HYPK interacts with N-terminal fragment of HTT remained unknown. Here we report that specific interaction of HYPK with HTT-N17 is crucial for the chaperone activity of HYPK. Deletion of HTT-N17 leads to formation of tinier, SDS-soluble nuclear aggregates formed by N-terminal mutant HTT. The increased cytotoxicity imparted by these tiny aggregates might be contributed due to loss of interaction with HYPK.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding

Abstract Motivation The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families. Results Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes. Availability and implementation Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license. Supplementary information Supplementary data are available at Bioinformatics Advances online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures

Structure modelling via small-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures. This EDM method is compared with and tested against other CG SAXS computing methods, and the resulting CG SAXS profiles from EDM agree better with all-atom theoretical SAXS data. By including the protein hydration shell represented by explicit CG water molecules and the correction of protein excluded volume, the developed CG form factors also reproduce the selected experimental SAXS profiles with very small deviations. Taken together, these EDM-derived CG form factors present an accurate and efficient computational approach for SAXS computing, especially when higher molecular details (represented by the q range of the SAXS data) become necessary for effective structure modelling.

Tong, Dudu↗