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Sample records for amino acid positions

  1. Detecting Amino Acid Sites Under Positive Selection and Purifying Selection

    PubMed Central

    Massingham, Tim; Goldman, Nick

    2005-01-01

    An excess of nonsynonymous over synonymous substitution at individual amino acid sites is an important indicator that positive selection has affected the evolution of a protein between the extant sequences under study and their most recent common ancestor. Several methods exist to detect the presence, and sometimes location, of positively selected sites in alignments of protein-coding sequences. This article describes the “sitewise likelihood-ratio” (SLR) method for detecting nonneutral evolution, a statistical test that can identify sites that are unusually conserved as well as those that are unusually variable. We show that the SLR method can be more powerful than currently published methods for detecting the location of positive selection, especially in difficult cases where the strength of selection is low. The increase in power is achieved while relaxing assumptions about how the strength of selection varies over sites and without elevated rates of false-positive results that have been reported with some other methods. We also show that the SLR method performs well even under circumstances where the results from some previous methods can be misleading. PMID:15654091

  2. CKAAPs DB: a conserved key amino acid positions database.

    PubMed

    Li, W W; Reddy, B V; Shindyalov, I N; Bourne, P E

    2001-01-01

    The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. The derivation and significance of CKAAPs starting from pairwise structure alignments is described fully in Reddy et al. [Reddy,B.V.B., Li,W.W., Shindyalov,I.N. and Bourne,P.E. (2000) PROTEINS:, in press]. The CKAAPs identified from this theoretical analysis are provided to experimentalists and theoreticians for potential use in protein engineering and modeling. It has been suggested that CKAAPs may be crucial features for protein folding, structural stability and function. Over 170 substructures, as defined by the Combinatorial Extension (CE) database, which are found in approximately 3000 representative polypeptide chains have been analyzed and are available in the CKAAPs DB. CKAAPs DB also provides CKAAPs of the representative set of proteins derived from the CE and FSSP databases. Thus the database contains over 5000 representative poly-peptide chains, covering all known structures in the PDB. A web interface to a relational database permits fast retrieval of structure-sequence alignments, CKAAPs and associated statistics. Users may query by PDB ID, protein name, function and Enzyme Classification number. Users may also submit protein alignments of their own to obtain CKAAPs. An interface to display CKAAPs on each structure from a web browser is also being implemented. CKAAPs DB is maintained by the San Diego Supercomputer Center and accessible at the URL http://ckaaps.sdsc.edu.

  3. C5-amino acid functionalized LNA: positively poised for antisense applications.

    PubMed

    Guenther, Dale C; Kumar, Pawan; Anderson, Brooke A; Hrdlicka, Patrick J

    2014-08-18

    Incorporation of positively charged C5-amino acid functionalized LNA uridines into oligodeoxyribonucleotides (ONs) results in extraordinary RNA affinity, binding specificity and stability towards 3'-exonucleases.

  4. Amino acids

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/002222.htm Amino acids To use the sharing features on this page, please enable JavaScript. Amino acids are organic compounds that combine to form proteins . ...

  5. Identifying the ligated amino acid of archaeal tRNAs based on positions outside the anticodon

    PubMed Central

    Galili, Tal; Gingold, Hila; Shaul, Shaul; Benjamini, Yoav

    2016-01-01

    Proper recognition of tRNAs by their aminoacyl-tRNA synthetase is essential for translation accuracy. Following evidence that the enzymes can recognize the correct tRNA even when anticodon information is masked, we search for additional nucleotide positions within the tRNA molecule that potentially contain information for amino acid identification. Analyzing 3936 sequences of tRNA genes from 86 archaeal species, we show that the tRNAs’ cognate amino acids can be identified by the information embedded in the tRNAs’ nucleotide positions without relying on the anticodon information. We present a small set of six to 10 informative positions along the tRNA, which allow for amino acid identification accuracy of 90.6% to 97.4%, respectively. We inspected tRNAs for each of the 20 amino acid types for such informative positions and found that tRNA genes for some amino acids are distinguishable from others by as few as one or two positions. The informative nucleotide positions are in agreement with nucleotide positions that were experimentally shown to affect the loaded amino acid identity. Interestingly, the knowledge gained from the tRNA genes of one archaeal phylum does not extrapolate well to another phylum. Furthermore, each species has a unique ensemble of nucleotides in the informative tRNA positions, and the similarity between the sets of positions of two distinct species reflects their evolutionary distance. Hence, we term this set of informative positions a “tRNA cipher.” It is tempting to suggest that the diverging code identified here might also serve the aminoacyl tRNA synthetase in the task of tRNA recognition. PMID:27516383

  6. Positive Darwinian selection at single amino acid sites conferring plant virus resistance

    USDA-ARS?s Scientific Manuscript database

    Explicit evaluation of the accuracy and power of Maximum Likelihood and Bayesian methods for detecting site-specific positive Darwinian selection presents a challenge because selective consequences of single amino acid changes are generally unknown. We exploit extensive molecular and functional cha...

  7. Functional role of positively selected amino acid substitutions in mammalian rhodopsin evolution.

    PubMed

    Fernández-Sampedro, Miguel A; Invergo, Brandon M; Ramon, Eva; Bertranpetit, Jaume; Garriga, Pere

    2016-02-11

    Visual rhodopsins are membrane proteins that function as light photoreceptors in the vertebrate retina. Specific amino acids have been positively selected in visual pigments during mammal evolution, which, as products of adaptive selection, would be at the base of important functional innovations. We have analyzed the top candidates for positive selection at the specific amino acids and the corresponding reverse changes (F13M, Q225R and A346S) in order to unravel the structural and functional consequences of these important sites in rhodopsin evolution. We have constructed, expressed and immunopurified the corresponding mutated pigments and analyzed their molecular phenotypes. We find that position 13 is very important for the folding of the receptor and also for proper protein glycosylation. Position 225 appears to be important for the function of the protein affecting the G-protein activation process, and position 346 would also regulate functionality of the receptor by enhancing G-protein activation and presumably affecting protein phosphorylation by rhodopsin kinase. Our results represent a link between the evolutionary analysis, which pinpoints the specific amino acid positions in the adaptive process, and the structural and functional analysis, closer to the phenotype, making biochemical sense of specific selected genetic sequences in rhodopsin evolution.

  8. Functional role of positively selected amino acid substitutions in mammalian rhodopsin evolution

    PubMed Central

    Fernández-Sampedro, Miguel A.; Invergo, Brandon M.; Ramon, Eva; Bertranpetit, Jaume; Garriga, Pere

    2016-01-01

    Visual rhodopsins are membrane proteins that function as light photoreceptors in the vertebrate retina. Specific amino acids have been positively selected in visual pigments during mammal evolution, which, as products of adaptive selection, would be at the base of important functional innovations. We have analyzed the top candidates for positive selection at the specific amino acids and the corresponding reverse changes (F13M, Q225R and A346S) in order to unravel the structural and functional consequences of these important sites in rhodopsin evolution. We have constructed, expressed and immunopurified the corresponding mutated pigments and analyzed their molecular phenotypes. We find that position 13 is very important for the folding of the receptor and also for proper protein glycosylation. Position 225 appears to be important for the function of the protein affecting the G-protein activation process, and position 346 would also regulate functionality of the receptor by enhancing G-protein activation and presumably affecting protein phosphorylation by rhodopsin kinase. Our results represent a link between the evolutionary analysis, which pinpoints the specific amino acid positions in the adaptive process, and the structural and functional analysis, closer to the phenotype, making biochemical sense of specific selected genetic sequences in rhodopsin evolution. PMID:26865329

  9. d-Amino Acid Position Influences the Anticancer Activity of Galaxamide Analogs: An Apoptotic Mechanism Study

    PubMed Central

    Bai, Defa; Yu, Siming; Zhong, Shenghui; Zhao, Bingxin; Qiu, Shaoling; Chen, Jianwei; Lunagariya, Jignesh; Liao, Xiaojian; Xu, Shihai

    2017-01-01

    Galaxamide, an extract from Galaxaura filamentosa, is a cyclic pentapeptide containing five l-leucines. Due to the particular cyclic structure and the excellent anticancer activity, synthesis of Galaxamide and its analogs and their subsequent bio-applications have attracted great attention. In the present work, we synthesized six Galaxamide analogs by replacing one of the l-leucines with phenylalanine and varying the d-amino acid position. The anticancer effect of the synthesized Galaxamide analogs was tested against four in vitro human cancer cell lines, human hepatocellular cells (HepG2), human breast cancer cell (MCF-7), human breast adenocarcinoma cells (MDA-MB-435) and a human cervical carcinoma cell line (Hela). Results showed that Galaxamide analogs with different d-amino acid positions displayed distinct anticancer potential. The Galaxamide analog containing d-amino acid at position 5 (Analog-6) presented the strongest anticancer activity. The mechanism study revealed that Analog-6 could cause the early apoptosis of HepG2 cells by inhibiting their growth in the sub-G1 stage of the cell cycle and induce the chromatin condensation and fragmentation, which can be seen as 68% of HepG2 cells inhibited in the sub-G1 stage. Moreover, a mitochondria-mediated pathway was found to be involved in the apoptotic process of Analog-6 on HepG2 cells. PMID:28287429

  10. d-Amino Acid Position Influences the Anticancer Activity of Galaxamide Analogs: An Apoptotic Mechanism Study.

    PubMed

    Bai, Defa; Yu, Siming; Zhong, Shenghui; Zhao, Bingxin; Qiu, Shaoling; Chen, Jianwei; Lunagariya, Jignesh; Liao, Xiaojian; Xu, Shihai

    2017-03-10

    Galaxamide, an extract from Galaxaura filamentosa, is a cyclic pentapeptide containing five l-leucines. Due to the particular cyclic structure and the excellent anticancer activity, synthesis of Galaxamide and its analogs and their subsequent bio-applications have attracted great attention. In the present work, we synthesized six Galaxamide analogs by replacing one of the l-leucines with phenylalanine and varying the d-amino acid position. The anticancer effect of the synthesized Galaxamide analogs was tested against four in vitro human cancer cell lines, human hepatocellular cells (HepG₂), human breast cancer cell (MCF-7), human breast adenocarcinoma cells (MDA-MB-435) and a human cervical carcinoma cell line (Hela). Results showed that Galaxamide analogs with different d-amino acid positions displayed distinct anticancer potential. The Galaxamide analog containing d-amino acid at position 5 (Analog-6) presented the strongest anticancer activity. The mechanism study revealed that Analog-6 could cause the early apoptosis of HepG₂ cells by inhibiting their growth in the sub-G1 stage of the cell cycle and induce the chromatin condensation and fragmentation, which can be seen as 68% of HepG₂ cells inhibited in the sub-G1 stage. Moreover, a mitochondria-mediated pathway was found to be involved in the apoptotic process of Analog-6 on HepG₂ cells.

  11. Computational predictors fail to identify amino acid substitution effects at rheostat positions

    PubMed Central

    Miller, M.; Bromberg, Y.; Swint-Kruse, L.

    2017-01-01

    Many computational approaches exist for predicting the effects of amino acid substitutions. Here, we considered whether the protein sequence position class – rheostat or toggle – affects these predictions. The classes are defined as follows: experimentally evaluated effects of amino acid substitutions at toggle positions are binary, while rheostat positions show progressive changes. For substitutions in the LacI protein, all evaluated methods failed two key expectations: toggle neutrals were incorrectly predicted as more non-neutral than rheostat non-neutrals, while toggle and rheostat neutrals were incorrectly predicted to be different. However, toggle non-neutrals were distinct from rheostat neutrals. Since many toggle positions are conserved, and most rheostats are not, predictors appear to annotate position conservation better than mutational effect. This finding can explain the well-known observation that predictors assign disproportionate weight to conservation, as well as the field’s inability to improve predictor performance. Thus, building reliable predictors requires distinguishing between rheostat and toggle positions. PMID:28134345

  12. Amino acid substitutions at position 95 in GyrA can add fluoroquinolone resistance to Mycobacterium leprae.

    PubMed

    Yokoyama, Kazumasa; Kim, Hyun; Mukai, Tetsu; Matsuoka, Masanori; Nakajima, Chie; Suzuki, Yasuhiko

    2012-02-01

    Amino acid substitutions at position 89 or 91 in GyrA of fluoroquinolone-resistant Mycobacterium leprae clinical isolates have been reported. In contrast, those at position 94 in M. tuberculosis, equivalent to position 95 in M. leprae, have been identified most frequently. To verify the possible contribution of amino acid substitutions at position 95 in M. leprae to fluoroquinolone resistance, we conducted an in vitro assay using wild-type and mutant recombinant DNA gyrases. Fluoroquinolone-mediated supercoiling activity inhibition assay and DNA cleavage assay revealed the potent contribution of an amino acid substitution of Asp to Gly or Asn at position 95 to fluoroquinolone resistance. These results suggested the possible future emergence of quinolone-resistant M. leprae isolates with these amino acid substitutions and the usefulness of detecting these mutations for the rapid identification of fluoroquinolone resistance in leprosy.

  13. Nonnatural amino acid incorporation into the methionine 214 position of the metzincin Pseudomonas aeruginosa alkaline protease

    PubMed Central

    Walasek, Paula; Honek, John F

    2005-01-01

    Background The alkaline protease from Pseudomonas aeruginosa (AprA) is a member of the metzincin superfamily of metalloendoproteases. A key feature of these proteases is a conserved methionine-containing 1,4-tight β turn at the base of the active site zinc binding region. Results To explore the invariant methionine position in this class of protease, incorporation of a nonnatural fluorinated methionine, L-difluoromethionine (DFM), into this site was accomplished. Although overproduction of the N-terminal catalytic fragment of AprA resulted in protein aggregates which could not be resolved, successful heterologous production of the entire AprA was accomplished in the presence and absence of the nonnatural amino acid. DFM incorporation was found to only slightly alter the enzyme kinetics of AprA. In addition, differential scanning calorimetry indicated no significant alteration in the thermal stability of the modified enzyme. Conclusion Although invariant in all metzincin proteases, the methionine 214 position in AprA can be successfully replaced by the nonnatural amino acid DFM resulting in little effect on protein structure and function. This study indicates that the increased size of the methyl group by the introduction of two fluorines is still sufficiently non-sterically demanding, and bodes well for the application of DFM to biophysical studies of protein structure and function in this class of protease. PMID:16221305

  14. High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2)

    PubMed Central

    2010-01-01

    Background Genes involved in immune functions, including pathogen recognition and the activation of innate defense pathways, are among the most genetically variable known, and the proteins that they encode are often characterized by high rates of amino acid substitutions, a hallmark of positive selection. The high levels of variation characteristic of immunity genes make them useful tools for conservation genetics. To date, highly variable immunity genes have yet to be found in corals, keystone organisms of the world's most diverse marine ecosystem, the coral reef. Here, we examine variation in and selection on a putative innate immunity gene from Oculina, a coral genus previously used as a model for studies of coral disease and bleaching. Results In a survey of 244 Oculina alleles, we find high nonsynonymous variation and a signature of positive selection, consistent with a putative role in immunity. Using computational protein structure prediction, we generate a structural model of the Oculina protein that closely matches the known structure of tachylectin-2 from the Japanese horseshoe crab (Tachypleus tridentatus), a protein with demonstrated function in microbial recognition and agglutination. We also demonstrate that at least three other genera of anthozoan cnidarians (Acropora, Montastrea and Nematostella) possess proteins structurally similar to tachylectin-2. Conclusions Taken together, the evidence of high amino acid diversity, positive selection and structural correspondence to the horseshoe crab tachylectin-2 suggests that this protein is 1) part of Oculina's innate immunity repertoire, and 2) evolving adaptively, possibly under selective pressure from coral-associated microorganisms. Tachylectin-2 may serve as a candidate locus to screen coral populations for their capacity to respond adaptively to future environmental change. PMID:20482872

  15. Synthesis of oxytocin antagonists containing conformationally constrained amino acids in position 2.

    PubMed

    Tóth, G K; Bakos, K; Penke, B; Pávó, I; Varga, C; Török, G; Péter, A; Fülöp, F

    1999-03-08

    Analogues of oxytocin containing D-Trp, 2-amino-1,2,3,4-tetrahydronaphthalene-1-carboxylic acid (Atc) or 1,2,3,4-tetrahydro-beta-carboline-1-carboxylic acid (Car) with R or S configurations in position 2 were synthetized, and their receptor bindings were tested on isolated guinea-pig uterus, rat liver and rat kidney inner medulla plasma membranes. The peptides were synthetized in the solid phase by using racemates of Car and Atc. The resulting diastereomeric mixtures were separated by means of RP-HPLC. The binding to the oxytocin receptor was somewhat decreased for the Atc isomers and dramatically decreased for both R- and S-Car, while the D-Trp-containing analogue displayed a relatively high receptor affinity. However, the V1 receptor affinities were almost the same as those of the parent peptide for the Car-containing analogues and dramatically decreased for the S-Atc substituted analogue, which has a relatively high OT/V1 receptor selectivity of 44.5.

  16. Chirality effects at each amino acid position on tripeptide self-assembly into hydrogel biomaterials

    NASA Astrophysics Data System (ADS)

    Marchesan, S.; Easton, C. D.; Styan, K. E.; Waddington, L. J.; Kushkaki, F.; Goodall, L.; McLean, K. M.; Forsythe, J. S.; Hartley, P. G.

    2014-04-01

    Hydrogels formed by ultrashort peptides are emerging as cost-effective materials for cell culture. However, l-peptides are labile to proteases, while their d-isomers are thought to not support cell growth as well. In contrast, the self-assembly behaviour and biological performance of heterochiral peptides (i.e., made of both d and l amino acids) are largely unknown. In this study, we evaluate the effects of amino acid chirality on tripeptide self-assembly and hydrogelation at physiological pH, and cytocompatibility in fibroblast cell culture. A series of uncapped hydrophobic tripeptides with all combinations of d, l amino acids was prepared, tested for self-assembly under physiological conditions, and analysed by circular dichroism, FT-IR, cryo-TEM, AFM, and Thioflavin T fluorescence imaging. Amino acid chirality has a profound effect on the peptides' supramolecular behaviour. Only selected isomers form hydrogels, and of amyloid structure, as confirmed by rheology and XRD. Importantly, they are able to maintain the viability and proliferation of fibroblasts in vitro. This study identifies two heterochiral gels that perform well in cell culture and will assist in the design of innovative and cost-effective peptide gel biomaterials.Hydrogels formed by ultrashort peptides are emerging as cost-effective materials for cell culture. However, l-peptides are labile to proteases, while their d-isomers are thought to not support cell growth as well. In contrast, the self-assembly behaviour and biological performance of heterochiral peptides (i.e., made of both d and l amino acids) are largely unknown. In this study, we evaluate the effects of amino acid chirality on tripeptide self-assembly and hydrogelation at physiological pH, and cytocompatibility in fibroblast cell culture. A series of uncapped hydrophobic tripeptides with all combinations of d, l amino acids was prepared, tested for self-assembly under physiological conditions, and analysed by circular dichroism, FT

  17. Amino Acid Metabolism Disorders

    MedlinePlus

    ... this process. One group of these disorders is amino acid metabolism disorders. They include phenylketonuria (PKU) and maple syrup urine disease. Amino acids are "building blocks" that join together to form ...

  18. Chirality effects at each amino acid position on tripeptide self-assembly into hydrogel biomaterials.

    PubMed

    Marchesan, S; Easton, C D; Styan, K E; Waddington, L J; Kushkaki, F; Goodall, L; McLean, K M; Forsythe, J S; Hartley, P G

    2014-05-21

    Hydrogels formed by ultrashort peptides are emerging as cost-effective materials for cell culture. However, L-peptides are labile to proteases, while their D-isomers are thought to not support cell growth as well. In contrast, the self-assembly behaviour and biological performance of heterochiral peptides (i.e., made of both d and l amino acids) are largely unknown. In this study, we evaluate the effects of amino acid chirality on tripeptide self-assembly and hydrogelation at physiological pH, and cytocompatibility in fibroblast cell culture. A series of uncapped hydrophobic tripeptides with all combinations of d, l amino acids was prepared, tested for self-assembly under physiological conditions, and analysed by circular dichroism, FT-IR, cryo-TEM, AFM, and Thioflavin T fluorescence imaging. Amino acid chirality has a profound effect on the peptides' supramolecular behaviour. Only selected isomers form hydrogels, and of amyloid structure, as confirmed by rheology and XRD. Importantly, they are able to maintain the viability and proliferation of fibroblasts in vitro. This study identifies two heterochiral gels that perform well in cell culture and will assist in the design of innovative and cost-effective peptide gel biomaterials.

  19. The HLA-DRβ1 amino acid positions 11-13-26 explain the majority of SLE-MHC associations.

    PubMed

    Kim, Kwangwoo; Bang, So-Young; Lee, Hye-Soon; Okada, Yukinori; Han, Buhm; Saw, Woei-Yuh; Teo, Yik-Ying; Bae, Sang-Cheol

    2014-12-23

    Genetic association of the major histocompatibility complex (MHC) locus is well established in systemic lupus erythematosus (SLE), but the causal functional variants in this region have not yet been discovered. Here we conduct the first fine-mapping study, which thoroughly investigates the SLE-MHC associations down to the amino acid level of major HLA genes in 5,342 unrelated Korean case-control subjects, taking advantages of HLA imputation with a newly constructed Asian HLA reference panel. The most significant association is mapped to amino acid position 13 of HLA-DRβ1 (P=2.48 × 10(-17)) and its proxy position 11 (P=4.15 × 10(-17)), followed by position 26 in a stepwise conditional analysis (P=2.42 × 10(-9)). Haplotypes defined by amino acid positions 11-13-26 support the reported effects of most classical HLA-DRB1 alleles in Asian and European populations. In conclusion, our study identifies the three amino acid positions at the epitope-binding groove of HLA-DRβ1 that are responsible for most of the association between SLE and MHC.

  20. Global trophic position comparison of two dominant mesopelagic fish families (Myctophidae, Stomiidae) using amino acid nitrogen isotopic analyses

    USGS Publications Warehouse

    Choy, C. Anela; Davison, Peter C.; Drazen, Jeffrey C.; Flynn, Adrian; Gier, Elizabeth J.; Hoffman, Joel C.; McClain-Counts, Jennifer P.; Miller, Todd W.; Popp, Brian N.; Ross, Steve W.; Sutton, Tracey T.

    2012-01-01

    The δ15N values of organisms are commonly used across diverse ecosystems to estimate trophic position and infer trophic connectivity. We undertook a novel cross-basin comparison of trophic position in two ecologically well-characterized and different groups of dominant mid-water fish consumers using amino acid nitrogen isotope compositions. We found that trophic positions estimated from the δ15N values of individual amino acids are nearly uniform within both families of these fishes across five global regions despite great variability in bulk tissue δ15N values. Regional differences in the δ15N values of phenylalanine confirmed that bulk tissue δ15N values reflect region-specific water mass biogeochemistry controlling δ15N values at the base of the food web. Trophic positions calculated from amino acid isotopic analyses (AA-TP) for lanternfishes (family Myctophidae) (AA-TP ~2.9) largely align with expectations from stomach content studies (TP ~3.2), while AA-TPs for dragonfishes (family Stomiidae) (AA-TP ~3.2) were lower than TPs derived from stomach content studies (TP~4.1). We demonstrate that amino acid nitrogen isotope analysis can overcome shortcomings of bulk tissue isotope analysis across biogeochemically distinct systems to provide globally comparative information regarding marine food web structure.

  1. Global trophic position comparison of two dominant mesopelagic fish families (Myctophidae, Stomiidae) using amino acid nitrogen isotopic analyses.

    PubMed

    Choy, C Anela; Davison, Peter C; Drazen, Jeffrey C; Flynn, Adrian; Gier, Elizabeth J; Hoffman, Joel C; McClain-Counts, Jennifer P; Miller, Todd W; Popp, Brian N; Ross, Steve W; Sutton, Tracey T

    2012-01-01

    The δ(15)N values of organisms are commonly used across diverse ecosystems to estimate trophic position and infer trophic connectivity. We undertook a novel cross-basin comparison of trophic position in two ecologically well-characterized and different groups of dominant mid-water fish consumers using amino acid nitrogen isotope compositions. We found that trophic positions estimated from the δ(15)N values of individual amino acids are nearly uniform within both families of these fishes across five global regions despite great variability in bulk tissue δ(15)N values. Regional differences in the δ(15)N values of phenylalanine confirmed that bulk tissue δ(15)N values reflect region-specific water mass biogeochemistry controlling δ(15)N values at the base of the food web. Trophic positions calculated from amino acid isotopic analyses (AA-TP) for lanternfishes (family Myctophidae) (AA-TP ∼2.9) largely align with expectations from stomach content studies (TP ∼3.2), while AA-TPs for dragonfishes (family Stomiidae) (AA-TP ∼3.2) were lower than TPs derived from stomach content studies (TP∼4.1). We demonstrate that amino acid nitrogen isotope analysis can overcome shortcomings of bulk tissue isotope analysis across biogeochemically distinct systems to provide globally comparative information regarding marine food web structure.

  2. Proteins and Amino Acids

    USDA-ARS?s Scientific Manuscript database

    Proteins are the most abundant substances in living organisms and cells. All proteins are constructed from the same twenty amino acids that are linked together by covalent bonds. Shorter chains of two or more amino acids can be linked by covalent bonds to form polypeptides. There are twenty amino...

  3. Amino acid analysis

    NASA Technical Reports Server (NTRS)

    Winitz, M.; Graff, J. (Inventor)

    1974-01-01

    The process and apparatus for qualitative and quantitative analysis of the amino acid content of a biological sample are presented. The sample is deposited on a cation exchange resin and then is washed with suitable solvents. The amino acids and various cations and organic material with a basic function remain on the resin. The resin is eluted with an acid eluant, and the eluate containing the amino acids is transferred to a reaction vessel where the eluant is removed. Final analysis of the purified acylated amino acid esters is accomplished by gas-liquid chromatographic techniques.

  4. Food ingestion in an upright sitting position increases postprandial amino acid availability when compared with food ingestion in a lying down position.

    PubMed

    Holwerda, Andrew M; Lenaerts, Kaatje; Bierau, Jörgen; Wodzig, Will K W H; van Loon, Luc J C

    2017-07-01

    Dietary protein digestion and absorption kinetics determine the postprandial increase in muscle protein synthesis. We recently demonstrated that body position during feeding can modulate the postprandial rise in plasma amino acid availability. Here we investigated whether protein ingestion in an upright sitting body position accelerates gastric emptying and improves dietary protein digestion and subsequent amino acid absorption compared with feeding in a supine lying body position. In a crossover design, 8 young males (age, 26 ± 1 years; body mass index, 24.0 ± 0.9 kg·m(-2)) ingested 20 g intrinsically l-[1-(13)C]-phenylalanine-labeled milk protein plus 1.5 g paracetamol while sitting in an upright position or lying down in a supine position. Blood samples were collected frequently during a 5-h postprandial period. Gastric emptying rates and dietary protein digestion and absorption were assessed using plasma paracetamol and amino acid concentrations as well as plasma l-[1-(13)C]-phenylalanine enrichments. Peak plasma leucine concentrations were higher when protein was ingested in an upright sitting versus lying position (213 ± 15 vs 193 ± 12 μmol·L(-1), P < 0.05), which was accompanied by a trend for a greater overall leucine response (13 989 ± 720 vs 11 875 ± 1073 AU, respectively; P = 0.05). Peak plasma paracetamol concentrations were higher in the sitting versus lying treatment (11.6 ± 0.5 vs 9.3 ± 0.6 mg·L(-1), P < 0.05). Protein ingestion in an upright sitting position accelerates gastric emptying and increases the postprandial rise in plasma amino acid availability by increasing protein digestion and amino acid absorption rates. Therefore, feeding in an upright body position as opposed to a lying position is an important prerequisite to allow proper postprandial muscle protein accretion.

  5. Parenteral Nutrition: Amino Acids.

    PubMed

    Hoffer, Leonard John

    2017-03-10

    There is growing interest in nutrition therapies that deliver a generous amount of protein, but not a toxic amount of energy, to protein-catabolic critically ill patients. Parenteral amino acids can achieve this goal. This article summarizes the biochemical and nutritional principles that guide parenteral amino acid therapy, explains how parenteral amino acid solutions are formulated, and compares the advantages and disadvantages of different parenteral amino acid products with enterally-delivered whole protein products in the context of protein-catabolic critical illness.

  6. Parenteral Nutrition: Amino Acids

    PubMed Central

    Hoffer, Leonard John

    2017-01-01

    There is growing interest in nutrition therapies that deliver a generous amount of protein, but not a toxic amount of energy, to protein-catabolic critically ill patients. Parenteral amino acids can achieve this goal. This article summarizes the biochemical and nutritional principles that guide parenteral amino acid therapy, explains how parenteral amino acid solutions are formulated, and compares the advantages and disadvantages of different parenteral amino acid products with enterally-delivered whole protein products in the context of protein-catabolic critical illness. PMID:28287411

  7. Amino Acid Crossword Puzzle

    ERIC Educational Resources Information Center

    Sims, Paul A.

    2011-01-01

    Learning the 20 standard amino acids is an essential component of an introductory course in biochemistry. Later in the course, the students study metabolism and learn about various catabolic and anabolic pathways involving amino acids. Learning new material or concepts often is easier if one can connect the new material to what one already knows;…

  8. Amino Acid Crossword Puzzle

    ERIC Educational Resources Information Center

    Sims, Paul A.

    2011-01-01

    Learning the 20 standard amino acids is an essential component of an introductory course in biochemistry. Later in the course, the students study metabolism and learn about various catabolic and anabolic pathways involving amino acids. Learning new material or concepts often is easier if one can connect the new material to what one already knows;…

  9. An amino acid at position 512 in β-glucosidase from Clavibacter michiganensis determines the regioselectivity for hydrolyzing gypenoside XVII.

    PubMed

    Shin, Kyung-Chul; Hong, Seung-Hye; Seo, Min-Ju; Oh, Deok-Kun

    2015-10-01

    A recombinant β-glucosidase from Clavibacter michiganensis specifically hydrolyzed the outer and inner glucose linked to the C-3 position in protopanaxadiol (PPD)-type ginsenosides and the C-6 position in protopanaxatriol (PPT)-type ginsenosides except for the hydrolysis of gypenoside LXXV (GypLXXV). The enzyme converted gypenoside XVII (GypXVII) to GypLXXV by hydrolyzing the inner glucose linked to the C-3 position. The substrate-binding residues obtained from the GypXVII-docked homology models of β-glucosidase from C. michiganensis were replaced with alanine, and the amino acid residue at position 512 was selected because of the changed regioselectivity of W512A. Site-directed mutagenesis for the amino acid residue at position 512 was performed. W512A and W512K hydrolyzed the inner glucose linked to the C-3 position and the outer glucose linked to the C-20 position of GypXVII to produce GypLXXV and F2. W512R hydrolyzed only the outer glucose linked to the C-20 position of GypXVII to produce F2. However, W512E and W512D exhibited no activity for GypXVII. Thus, the amino acid at position 512 is a critical residue to determine the regioselectivity for the hydrolysis of GypXVII. These wild-type and variant enzymes produced diverse ginsenosides, including GypXVII, GypLXXV, F2, and compound K, from ginsenoside Rb1. To the best of our knowledge, this is the first report of the alteration of regioselectivity on ginsenoside hydrolysis by protein engineering.

  10. Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations.

    PubMed

    Hermida-Carrera, Carmen; Fares, Mario A; Fernández, Ángel; Gil-Pelegrín, Eustaquio; Kapralov, Maxim V; Mir, Arnau; Molins, Arántzazu; Peguero-Pina, José Javier; Rocha, Jairo; Sancho-Knapik, Domingo; Galmés, Jeroni

    2017-01-01

    Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity. It has been hypothesized that RuBisCO has evolved differentially depending on the environmental conditions and leaf traits governing internal gas diffusion patterns. Here, we show, using PAML, that amino acid replacements at the residue positions 95, 145, 251, 262 and 328 of the RuBisCO large subunit have been the subject of positive selection along particular Quercus lineages associated with the leaf traits and climate characteristics. In parallel, the DT model identified amino acid replacements at sites 95, 219, 262 and 328 being associated with the leaf traits and climate characteristics, exhibiting partial overlap with the results obtained using PAML.

  11. [Saturation mutagenesis of three amino acid positions consisting of the active site of an endoglucanase from termite Coptotermes formosanus].

    PubMed

    Lin, Lihua; Qin, Guomei; Wei, Yutuo; Du, Liqin; Pang, Zongwen; Huang, Ribo

    2009-06-01

    Functional improvement to one component of the cellulase, endo-beta-1, 4-glucanase, has been a focus of the recent research in this area. We report here the saturation mutagenesis of the active site of an endoglucanase (CfEG) from termite Coptotermes formosanus. First, three dimensional structure of CfEG was built via homology modeling by using a close-related (79% homology in sequence) endo-beta-1,4-glucanase (NtEG PDB id = 1ks8) from higher termite Nasutitermes takasagoensis as a template. Second, we identified three corresponding amino acid positions at the active site of CfEG by structural superposition onto NtEG. These three putative amino acids for the active site of CfEG, i.e., Asp53, Asp56 and Glu411, were subjected to saturation mutagenesis using degenerate primers. Among the mutants, Asp53Glu and Asp56Cys showed somewhow higher activities than the wildtype, with the latter having more than 3-fold decrease in Km. Double mutation Asp53Leu/Asp56IIe showed nearly 2-fold increase in specific activity and in the same time 2-fold decrease in Km. Saturation mutagenesis to the position Glu411 produced no active mutant, even changing Glu411 explicitly into its similar amino acids such as Glu411Asp and Glu411Gln could not result in any active mutant. These imply that position Glu411 could be extremely important and therefore indispensable for CfEG functionality.

  12. Ionic interaction of positive amino acid residues of fungal hydrophobin RolA with acidic amino acid residues of cutinase CutL1.

    PubMed

    Takahashi, Toru; Tanaka, Takumi; Tsushima, Yusei; Muragaki, Kimihide; Uehara, Kenji; Takeuchi, Shunsuke; Maeda, Hiroshi; Yamagata, Youhei; Nakayama, Mayumi; Yoshimi, Akira; Abe, Keietsu

    2015-04-01

    Hydrophobins are amphipathic proteins secreted by filamentous fungi. When the industrial fungus Aspergillus oryzae is grown in a liquid medium containing the polyester polybutylene succinate co-adipate (PBSA), it produces RolA, a hydrophobin, and CutL1, a PBSA-degrading cutinase. Secreted RolA attaches to the surface of the PBSA particles and recruits CutL1, which then condenses on the particles and stimulates the hydrolysis of PBSA. Here, we identified amino acid residues that are required for the RolA-CutL1 interaction by using site-directed mutagenesis. We quantitatively analyzed kinetic profiles of the interactions between RolA variants and CutL1 variants by using a quartz crystal microbalance (QCM). The QCM analyses revealed that Asp142, Asp171 and Glu31, located on the hydrophilic molecular surface of CutL1, and His32 and Lys34, located in the N-terminus of RolA, play crucial roles in the RolA-CutL1 interaction via ionic interactions. RolA immobilized on a QCM electrode strongly interacted with CutL1 (K(D)  = 6.5 nM); however, RolA with CutL1 variants, or RolA variants with CutL1, showed markedly larger KD values, particularly in the interaction between the double variant RolA-H32S/K34S and the triple variant CutL1-E31S/D142S/D171S (K(D)  = 78.0 nM). We discuss a molecular prototype model of hydrophobin-based enzyme recruitment at the solid-water interface. © 2015 John Wiley & Sons Ltd.

  13. Amino Acids and Chirality

    NASA Technical Reports Server (NTRS)

    Cook, Jamie E.

    2012-01-01

    Amino acids are among the most heavily studied organic compound class in carbonaceous chondrites. The abundance, distributions, enantiomeric compositions, and stable isotopic ratios of amino acids have been determined in carbonaceous chondrites fi'om a range of classes and petrographic types, with interesting correlations observed between these properties and the class and typc of the chondritcs. In particular, isomeric distributions appear to correlate with parent bodies (chondrite class). In addition, certain chiral amino acids are found in enantiomeric excess in some chondrites. The delivery of these enantiomeric excesses to the early Earth may have contributed to the origin of the homochirality that is central to life on Earth today. This talk will explore the amino acids in carbonaceous chondritcs and their relevance to the origin of life.

  14. Position dependence of amino acid intrinsic helical propensities II: non-charged polar residues: Ser, Thr, Asn, and Gln.

    PubMed Central

    Petukhov, M.; Uegaki, K.; Yumoto, N.; Yoshikawa, S.; Serrano, L.

    1999-01-01

    The assumption that the intrinsic alpha-helical propensities of the amino acids are position independent was critical in several helix/coil transition theories. In the first paper of these series, we reported that this is not the case for Gly and nonpolar aliphatic amino acids (Val, Leu, Met, and Ile). Here we have analyzed the helical intrinsic propensities of noncharged polar residues (Ser, Thr, Asn, and Gln) at different positions of a model polyalanine-based peptide. We found that Thr is more favorable (by approximately 0.3 kcal/mol) at positions N1 and N2 than in the helix center, although for Ser, Asn, and Gln the differences are smaller (+/-0.2 kcal/mol), and in many cases within the experimental error. There is a reasonable agreement (+/-0.2 kcal/mol) between the calculated free energies, using the ECEPP/2 force field equipped with a hydration potential, and the experimental data, except at position N1. PMID:10548060

  15. Risk for ACPA-positive rheumatoid arthritis is driven by shared HLA amino acid polymorphisms in Asian and European populations.

    PubMed

    Okada, Yukinori; Kim, Kwangwoo; Han, Buhm; Pillai, Nisha E; Ong, Rick T-H; Saw, Woei-Yuh; Luo, Ma; Jiang, Lei; Yin, Jian; Bang, So-Young; Lee, Hye-Soon; Brown, Matthew A; Bae, Sang-Cheol; Xu, Huji; Teo, Yik-Ying; de Bakker, Paul I W; Raychaudhuri, Soumya

    2014-12-20

    Previous studies have emphasized ethnically heterogeneous human leukocyte antigen (HLA) classical allele associations to rheumatoid arthritis (RA) risk. We fine-mapped RA risk alleles within the major histocompatibility complex (MHC) in 2782 seropositive RA cases and 4315 controls of Asian descent. We applied imputation to determine genotypes for eight class I and II HLA genes to Asian populations for the first time using a newly constructed pan-Asian reference panel. First, we empirically measured high imputation accuracy in Asian samples. Then we observed the most significant association in HLA-DRβ1 at amino acid position 13, located outside the classical shared epitope (Pomnibus = 6.9 × 10(-135)). The individual residues at position 13 have relative effects that are consistent with published effects in European populations (His > Phe > Arg > Tyr ≅ Gly > Ser)--but the observed effects in Asians are generally smaller. Applying stepwise conditional analysis, we identified additional independent associations at positions 57 (conditional Pomnibus = 2.2 × 10(-33)) and 74 (conditional Pomnibus = 1.1 × 10(-8)). Outside of HLA-DRβ1, we observed independent effects for amino acid polymorphisms within HLA-B (Asp9, conditional P = 3.8 × 10(-6)) and HLA-DPβ1 (Phe9, conditional P = 3.0 × 10(-5)) concordant with European populations. Our trans-ethnic HLA fine-mapping study reveals that (i) a common set of amino acid residues confer shared effects in European and Asian populations and (ii) these same effects can explain ethnically heterogeneous classical allelic associations (e.g. HLA-DRB1*09:01) due to allele frequency differences between populations. Our study illustrates the value of high-resolution imputation for fine-mapping causal variants in the MHC.

  16. Amino acid positions subject to multiple co-evolutionary constraints can be robustly identified by their eigenvector network centrality scores

    PubMed Central

    Parente, Daniel J.; Ray, J. Christian J.; Swint-Kruse, Liskin

    2015-01-01

    As proteins evolve, amino acid positions key to protein structure or function are subject to mutational constraints. These positions can be detected by analyzing sequence families for amino acid conservation or for co-evolution between pairs of positions. Co-evolutionary scores are usually rank-ordered and thresholded to reveal the top pairwise scores, but they also can be treated as weighted networks. Here, we used network analyses to bypass a major complication of co-evolution studies: For a given sequence alignment, alternative algorithms usually identify different, top pairwise scores. We reconciled results from five commonly-used, mathematically divergent algorithms (ELSC, McBASC, OMES, SCA, and ZNMI), using the LacI/GalR and 1,6-bisphosphate aldolase protein families as models. Calculations used unthresholded co-evolution scores from which column-specific properties such as sequence entropy and random noise were subtracted; “central” positions were identified by calculating various network centrality scores. When compared among algorithms, network centrality methods, particularly eigenvector centrality, showed markedly better agreement than comparisons of the top pairwise scores. Positions with large centrality scores occurred at key structural locations and/or were functionally sensitive to mutations. Further, the top central positions often differed from those with top pairwise co-evolution scores: Instead of a few strong scores, central positions often had multiple, moderate scores. We conclude that eigenvector centrality calculations reveal a robust evolutionary pattern of constraints – detectable by divergent algorithms – that occur at key protein locations. Finally, we discuss the fact that multiple patterns co-exist in evolutionary data that, together, give rise to emergent protein functions. PMID:26503808

  17. Functional specificity of amino acid at position 246 in the tRNA mimicry domain of bacterial release factor 2.

    PubMed

    Uno, M; Ito, K; Nakamura, Y

    1996-01-01

    The termination of protein synthesis in bacteria requires codon-specific polypeptide release factors RF-1 (UAG/UAA specific) and RF-2 (UGA/UAA specific). We have proposed that release factors mimic tRNA and recognize the stop codon for polypeptide release (Nakamura et al (1996) Cell 87, 147-150). In contrast to the textbook view, genetic experiments have indicated that Escherichia coli RF-2 terminates translation very weakly at UAA while Salmonella RF-2 decodes this signal efficiently. Moreover, an excess of E coli RF-2 was toxic to cells while an excess of Salmonella RF-2 was not. These two RF-2 proteins are identical except for 16 out of 365 amino acids. Fragment swap experiments and site-directed mutagenesis revealed that a residue at position 246 is solely responsible for these two phenotypes. Upon substituting Ala (equivalent to Salmonella RF-2) for Thr-246 of E coli RF-2, the protein acquired increased release activity for UAA as well as for UGA. These results led us to conclude that E coli RF-2 activity is potentially weak and that the amino acid at position 246 plays a crucial role, not for codon discrimination, but for stop codon recognition or polypeptide release, presumably constituting an essential moiety of tRNA mimicry or interacting with peptidyltransferase centers of the ribosome.

  18. An amino acid at position 142 in nitrilase from Rhodococcus rhodochrous ATCC 33278 determines the substrate specificity for aliphatic and aromatic nitriles

    PubMed Central

    Yeom, Soo-Jin; Kim, Hye-Jung; Lee, Jung-Kul; Kim, Dong-Eun; Oh, Deok-Kun

    2008-01-01

    Nitrilase from Rhodococcus rhodochrous ATCC 33278 hydrolyses both aliphatic and aromatic nitriles. Replacing Tyr-142 in the wild-type enzyme with the aromatic amino acid phenylalanine did not alter specificity for either substrate. However, the mutants containing non-polar aliphatic amino acids (alanine, valine and leucine) at position 142 were specific only for aromatic substrates such as benzonitrile, m-tolunitrile and 2-cyanopyridine, and not for aliphatic substrates. These results suggest that the hydrolysis of substrates probably involves the conjugated π-electron system of the aromatic ring of substrate or Tyr-142 as an electron acceptor. Moreover, the mutants containing charged amino acids such as aspartate, glutamate, arginine and asparagine at position 142 displayed no activity towards any nitrile, possibly owing to the disruption of hydrophobic interactions with substrates. Thus aromaticity of substrate or amino acid at position 142 in R. rhodochrous nitrilase is required for enzyme activity. PMID:18412544

  19. Brain amino acid sensing.

    PubMed

    Tsurugizawa, T; Uneyama, H; Torii, K

    2014-09-01

    The 20 different amino acids, in blood as well as in the brain, are strictly maintained at the same levels throughout the day, regardless of food intake. Gastric vagal afferents only respond to free glutamate and sugars, providing recognition of food intake and initiating digestion. Metabolic control of amino acid homeostasis and diet-induced thermogenesis is triggered by this glutamate signalling in the stomach through the gut-brain axis. Rats chronically fed high-sugar and high-fat diets do not develop obesity when a 1% (w/v) monosodium glutamate (MSG) solution is available in a choice paradigm. Deficiency of the essential amino acid lysine (Lys) induced a plasticity in rats in response to Lys. This result shows how the body is able to identify deficient nutrients to maintain homeostasis. This plastic effect is induced by activin A activity in the brain, particularly in certain neurons in the lateral hypothalamic area (LHA) which is the centre for amino acid homeostasis and appetite. These neurons respond to glutamate signalling in the oral cavity by which umami taste is perceived. They play a quantitative role in regulating ingestion of deficient nutrients, thereby leading to a healthier life. After recovery from malnutrition, rats prefer MSG solutions, which serve as biomarkers for protein nutrition. © 2014 John Wiley & Sons Ltd.

  20. TOR complex 2-Ypk1 signaling is an essential positive regulator of the general amino acid control response and autophagy.

    PubMed

    Vlahakis, Ariadne; Graef, Martin; Nunnari, Jodi; Powers, Ted

    2014-07-22

    The highly conserved Target of Rapamycin (TOR) kinase is a central regulator of cell growth and metabolism in response to nutrient availability. TOR functions in two structurally and functionally distinct complexes, TOR Complex 1 (TORC1) and TOR Complex 2 (TORC2). Through TORC1, TOR negatively regulates autophagy, a conserved process that functions in quality control and cellular homeostasis and, in this capacity, is part of an adaptive nutrient deprivation response. Here we demonstrate that during amino acid starvation TOR also operates independently as a positive regulator of autophagy through the conserved TORC2 and its downstream target protein kinase, Ypk1. Under these conditions, TORC2-Ypk1 signaling negatively regulates the Ca(2+)/calmodulin-dependent phosphatase, calcineurin, to enable the activation of the amino acid-sensing eIF2α kinase, Gcn2, and to promote autophagy. Our work reveals that the TORC2 pathway regulates autophagy in an opposing manner to TORC1 to provide a tunable response to cellular metabolic status.

  1. Global trophic position comparison of two dominant mesopelagic fish families (Myctophidae, Stomiidae) using amino acid nitrogen isotopicanalyses

    EPA Science Inventory

    We examined the biogeochemical and ecological mechanisms responsible for variability in bulk tissue and amino acid (AA) stable nitrogen isotope compositions in two groups of important mesopelagic fish families, Myctophidae (lanternfishes) and Stomiidae (dragonfishes), from five d...

  2. Global trophic position comparison of two dominant mesopelagic fish families (Myctophidae, Stomiidae) using amino acid nitrogen isotopicanalyses

    EPA Science Inventory

    We examined the biogeochemical and ecological mechanisms responsible for variability in bulk tissue and amino acid (AA) stable nitrogen isotope compositions in two groups of important mesopelagic fish families, Myctophidae (lanternfishes) and Stomiidae (dragonfishes), from five d...

  3. Novel renal amino acid transporters.

    PubMed

    Verrey, François; Ristic, Zorica; Romeo, Elisa; Ramadan, Tamara; Makrides, Victoria; Dave, Mital H; Wagner, Carsten A; Camargo, Simone M R

    2005-01-01

    Reabsorption of amino acids, similar to that of glucose, is a major task of the proximal kidney tubule. Various amino acids are actively transported across the luminal brush border membrane into proximal tubule epithelial cells, most of which by cotransport. An important player is the newly identified cotransporter (symporter) B0AT1 (SLC6A19), which imports a broad range of neutral amino acids together with Na+ across the luminal membrane and which is defective in Hartnup disorder. In contrast, cationic amino acids and cystine are taken up in exchange for recycled neutral amino acids by the heterodimeric cystinuria transporter. The basolateral release of some neutral amino acids into the extracellular space is mediated by unidirectional efflux transporters, analogous to GLUT2, that have not yet been definitively identified. Additionally, cationic amino acids and some other neutral amino acids leave the cell basolaterally via heterodimeric obligatory exchangers.

  4. HLA-DRB1 rheumatoid arthritis risk in African Americans at multiple levels: Hierarchical classification systems, amino acid positions and residues

    PubMed Central

    Reynolds, Richard J.; Ahmed, Altan F.; Danila, Maria I.; Hughes, Laura B.; Gregersen, Peter K.; Raychaudhuri, Soumya; Plenge, Robert M.; Bridges, S. Louis

    2014-01-01

    Objective To evaluate African American rheumatoid arthritis HLA-DRB1 genetic risk by three validated allele classification systems, and by amino acid position and residue. To compare the genetic risk between African American and European ancestries. Methods Four-digit HLA-DRB1 genotyping was performed on 561 autoantibody-positive African American cases and 776 African American controls. Association analysis was performed on Tezenas du Montcel (TdM); de Vries (DV); and Mattey classification system alleles and separately by amino acid position and individual residues. Results TdM S2 and S3P alleles were associated with RA (odds ratios (95% CI) 2.8 (2.0, 3.9) and 2.1 (1.7, 2.7), respectively). The DV (P-value=3.2 x 10−12) and Mattey (P-value=6.5 x 10−13) system alleles were both protective in African Americans. Amino acid position 11 (permutation P-value < 0.00001) accounted for nearly all variability explained by HLA-DRB1, although conditional analysis demonstrated that position 57 was also significant (0.01<= permutation P-val <=0.05). The valine and aspartic acid residues at position 11 conferred the highest risk for RA in African Americans. Conclusion With some exceptions, the genetic risk conferred by HLA-DRB1 in African Americans is similar to European ancestry at multiple levels: classification system (e.g., TdM), amino acid position (e.g. 11) and residue (Val 11). Unlike that reported from European ancestry, amino acid position 57 was associated with RA in African Americans, but positions 71 and 74 were not. Asp11 (OR = 1 in European ancestry) corresponds to the four digit classical allele, *09:01, also a risk allele for RA in Koreans. PMID:25524867

  5. HLA-DRB1-associated rheumatoid arthritis risk at multiple levels in African Americans: hierarchical classification systems, amino acid positions, and residues.

    PubMed

    Reynolds, Richard J; Ahmed, Altan F; Danila, Maria I; Hughes, Laura B; Gregersen, Peter K; Raychaudhuri, Soumya; Plenge, Robert M; Bridges, S Louis

    2014-12-01

    To evaluate HLA-DRB1 genetic risk of rheumatoid arthritis (RA) in African Americans by 3 validated allele classification systems and by amino acid position and residue, and to compare genetic risk between African American and European ancestries. Four-digit HLA-DRB1 genotyping was performed on 561 autoantibody-positive African American cases and 776 African American controls. Association analysis was performed on Tezenas du Montcel (TdM), de Vries (DV), and Mattey classification system alleles and separately by amino acid position and individual residues. TdM S2 and S3P alleles were associated with RA (odds ratio [95% confidence interval] 2.8 [2.0-3.9] and 2.1 [1.7-2.7], respectively). The DV (P = 3.2 × 10(-12)) and Mattey (P = 6.5 × 10(-13)) system alleles were both protective in African Americans. Amino acid position 11 (permutation P < 0.00001) accounted for nearly all variability explained by HLA-DRB1, although conditional analysis demonstrated that position 57 was also significant (0.01 ≤ permutation P ≤ 0.05). The valine and aspartic acid residues at position 11 conferred the highest risk of RA in African Americans. With some exceptions, the genetic risk conferred by HLA-DRB1 in African Americans is similar to that in individuals of European ancestry at multiple levels: classification system (e.g., TdM), amino acid position (e.g., 11), and residue (Val11). Unlike that reported for individuals of European ancestry, amino acid position 57 was associated with RA in African Americans, but positions 71 and 74 were not. Asp11 (odds ratio 1 in European ancestry) corresponds to the 4-digit classical allele *09:01, which is also a risk allele for RA in Koreans. Copyright © 2014 by the American College of Rheumatology.

  6. Biphalin analogs containing β(3)-homo-amino acids at the 4,4' positions: Synthesis and opioid activity profiles.

    PubMed

    Frączak, Oliwia; Lasota, Anika; Kosson, Piotr; Leśniak, Anna; Muchowska, Adriana; Lipkowski, Andrzej W; Olma, Aleksandra

    2015-04-01

    Biphalin, a synthetic opioid octapeptide with a palindromic sequence has high analgesic activity. Biphalin displays a strong affinity for μ and δ-opioid receptors, and a significant to κ-receptor. The paper reports the synthesis of novel analogs of biphalin containing β(3)-homo-amino acid residues at the 4,4' positions and a hydrazine or 1,2-phenylenediamine linker. The potency and selectivity of the peptides were evaluated by a competitive receptor-binding assay in rat brain homogenate using [(3)H]DAMGO (a μ ligand) and [(3)H]DELT (a δ ligand). Analogs with β(3)-h-p-NO2Phe in positions 4 and 4' are the most active compounds. Selectivity depends on the degree of freedom between the two pharmacophore moieties. Analogs with a hydrazine linker show noticeable binding selectivity to μ receptors (IC50(μ)=0.72nM; IC50(δ)=4.66nM), while the peptides with a 1,2-phenylenediamine linker show slight δ selectivity (IC50(μ)=10.97nM; IC50(δ)=1.99nM). Tyr-d-Ala-Gly-β(3)-h-p-NO2PheNHNH-β(3)-h-p-NO2Phe (1) and (Tyr-d-Ala-Gly-β(3)-h-p-NO2PheNH)2 (2) produced greater antinociceptive effect compared to morphine after i.t. administration.

  7. Amino acids in Arctic aerosols

    NASA Astrophysics Data System (ADS)

    Scalabrin, E.; Zangrando, R.; Barbaro, E.; Kehrwald, N. M.; Gabrieli, J.; Barbante, C.; Gambaro, A.

    2012-11-01

    Amino acids are significant components of atmospheric aerosols, affecting organic nitrogen input to marine ecosystems, atmospheric radiation balance, and the global water cycle. The wide range of amino acid reactivities suggest that amino acids may serve as markers of atmospheric transport and deposition of particles. Despite this potential, few measurements have been conducted in remote areas to assess amino acid concentrations and potential sources. Polar regions offer a unique opportunity to investigate atmospheric processes and to conduct source apportionment studies of such compounds. In order to better understand the importance of amino acid compounds in the global atmosphere, we determined free amino acids (FAAs) in seventeen size-segregated aerosol samples collected in a polar station in the Svalbard Islands from 19 April until 14 September 2010. We used an HPLC coupled with a tandem mass spectrometer (ESI-MS/MS) to analyze 20 amino acids and quantify compounds at fmol m-3 levels. Mean total FAA concentration was 1070 fmol m-3 where serine and glycine were the most abundant compounds in almost all samples and accounted for 45-60% of the total amino acid relative abundance. The other eighteen compounds had average concentrations between 0.3 and 98 fmol m-3. The higher amino acid concentrations were present in the ultrafine aerosol fraction (< 0.49 μm) and accounted for the majority of the total amino acid content. Local marine sources dominate the boreal summer amino acid concentrations, with the exception of the regional input from Icelandic volcanic emissions.

  8. Amino acids in Arctic aerosols

    NASA Astrophysics Data System (ADS)

    Scalabrin, E.; Zangrando, R.; Barbaro, E.; Kehrwald, N. M.; Gabrieli, J.; Barbante, C.; Gambaro, A.

    2012-07-01

    Amino acids are significant components of atmospheric aerosols, affecting organic nitrogen input to marine ecosystems, atmospheric radiation balance, and the global water cycle. The wide range of amino acid reactivities suggest that amino acids may serve as markers of atmospheric transport and deposition of particles. Despite this potential, few measurements have been conducted in remote areas to assess amino acid concentrations and potential sources. Polar regions offer a unique opportunity to investigate atmospheric processes and to conduct source apportionment studies of such compounds. In order to better understand the importance of amino acid compounds in the global atmosphere, we determined free amino acids (FAAs) in seventeen size-segregated aerosol samples collected in a polar station in the Svalbard Islands from 19 April until 14 September 2010. We used an HPLC coupled with a tandem mass spectrometer (ESI-MS/MS) to analyze 20 amino acids to quantify compounds at fmol m-3 levels. Mean total FAA concentration was 1070 fmol m-3 where serine and glycine were the most abundant compounds in almost all samples and accounted for 45-60% of the total amino acid relative abundance. The other eighteen compounds had average concentrations between 0.3 and 98 fmol m-3. The higher amino acid concentrations were present in the ultrafine aerosol fraction (<0.49 μm) and accounted for the majority of the total amino acid content. Local marine sources dominate the boreal summer amino acid concentrations, with the exception of the regional input from Icelandic volcanics.

  9. Synthesis of amino acids

    DOEpatents

    Davis, J.W. Jr.

    1979-09-21

    A method is described for synthesizing amino acids preceding through novel intermediates of the formulas: R/sub 1/R/sub 2/C(OSOC1)CN, R/sub 1/R/sub 2/C(C1)CN and (R/sub 1/R/sub 2/C(CN)O)/sub 2/SO wherein R/sub 1/ and R/sub 2/ are each selected from hydrogen and monovalent hydrocarbon radicals of 1 to 10 carbon atoms. The use of these intermediates allows the synthesis steps to be exothermic and results in an overall synthesis method which is faster than the synthesis methods of the prior art.

  10. The complete amino acid sequence of prochymosin.

    PubMed Central

    Foltmann, B; Pedersen, V B; Jacobsen, H; Kauffman, D; Wybrandt, G

    1977-01-01

    The total sequence of 365 amino acid residues in bovine prochymosin is presented. Alignment with the amino acid sequence of porcine pepsinogen shows that 204 amino acid residues are common to the two zymogens. Further comparison and alignment with the amino acid sequence of penicillopepsin shows that 66 residues are located at identical positions in all three proteases. The three enzymes belong to a large group of proteases with two aspartate residues in the active center. This group forms a family derived from one common ancestor. PMID:329280

  11. Identification of amino acids by material enhanced laser desorption/ionisation mass spectrometry (MELDI-MS) in positive- and negative-ion mode

    NASA Astrophysics Data System (ADS)

    Hashir, Muhammad Ahsan; Stecher, Guenther; Mayr, Stefan; Bonn, Guenther K.

    2009-01-01

    In the present study, different silica gel modifications were evaluated for their application as target surface for material enhanced laser desorption/ionisation mass spectrometric (MELDI-MS) investigation of amino acids. 4,4'-Azodianiline (ADA-silica) modified silica gel was successfully employed for the qualitative analysis of amino acids in positive- and in negative-ion mode. Further no derivatisation of amino acids was necessary, as the introduced system allowed the direct analysis of targets and delivered spectra with excellent signal intensity and signal-to-noise ratio within a few minutes. The influence of surface chemistry, ionisation mode and the nature of analytes on signal intensity was studied and discussed. Detection limit of 2.10 pg (10 fmol) was achieved by employing ADA-silica in positive-ion mode. Finally, xylem saps from different types of trees were analysed. This proved the high performance and excellent behaviour of the introduced target surface material.

  12. Amino acids in carbonaceous chondrites

    NASA Technical Reports Server (NTRS)

    Lawless, J. G.; Peterson, E.

    1975-01-01

    Studies with the combined gas chromatograph-mass spectrometer were conducted to characterize further the amino acids found in extracts of the Murchison meteorite. With the exception of beta-aminoisobutyric acid, all of the amino acids which were found in previous studies of the Murchison meteorite and the Murray meteorite have been identified. The results obtained lend further support to the hypothesis that amino acids are present in the Murchison meteorite as the result of an extraterrestrial abiotic synthesis.

  13. Enhancement of myofibrillar proteolysis following infusion of amino acid mixture correlates positively with elevation of core body temperature in rats.

    PubMed

    Yamaoka, Ippei; Mikura, Mayumi; Nishimura, Masuhiro; Doi, Masako; Kawano, Yuichi; Nakayama, Mitsuo

    2008-12-01

    Administration of an amino acid (AA) mixture stimulates muscle protein synthesis and elevates core body temperature (T(b)), as characteristically found under anesthetic conditions. We tested the hypothesis that not only AA given, but also AA produced by degradation of endogenous muscular protein are provided for muscle protein synthesis, which is further reflected in T(b) modifications. Rats were intravenously administered an AA mixture or saline in combination with the anesthetic propofol or lipid emulsion. We measured plasma 3-methylhistidine (MeHis) concentrations as an index of myofibrillar protein degradation, rectal temperature and mRNA expression of atrogin-1, MuRF-1 and ubiquitin in gastrocnemius and soleus muscles of rats following 3 h infusion of test solutions. T(b) did not differ significantly between conscious groups, but was higher in the AA group than in the saline group among anesthetized rats. Plasma MeHis concentrations were higher in the AA group than in the saline group under both conditions. Plasma MeHis levels correlated positively with T(b) of rats under both conditions. AA administration decreased mRNA levels of atrogin-1 and ubiquitin in gastrocnemius muscle and all mRNA levels in soleus muscle. These results suggest that AA administration enhances myofibrillar protein degradation and that the change is a determinant of T(b) modification by AA administration. However, the mechanisms underlying AA administration-associated enhancement of myofibrillar proteolysis remains yet to be determined.

  14. Meta-analysis of amino acid stable nitrogen isotope ratios for estimating trophic position in marine organisms.

    PubMed

    Nielsen, Jens M; Popp, Brian N; Winder, Monika

    2015-07-01

    Estimating trophic structures is a common approach used to retrieve information regarding energy pathways, predation, and competition in complex ecosystems. The application of amino acid (AA) compound-specific nitrogen (N) isotope analysis (CSIA) is a relatively new method used to estimate trophic position (TP) and feeding relationships in diverse organisms. Here, we conducted the first meta-analysis of δ(15)N AA values from measurements of 359 marine species covering four trophic levels, and compared TP estimates from AA-CSIA to literature values derived from food items, gut or stomach content analysis. We tested whether the AA trophic enrichment factor (TEF), or the (15)N enrichment among different individual AAs is constant across trophic levels and whether inclusion of δ(15)N values from multiple AAs improves TP estimation. For the TEF of glutamic acid relative to phenylalanine (Phe) we found an average value of 6.6‰ across all taxa, which is significantly lower than the commonly applied 7.6‰. We found that organism feeding ecology influences TEF values of several trophic AAs relative to Phe, with significantly higher TEF values for herbivores compared to omnivores and carnivores, while TEF values were also significantly lower for animals excreting urea compared to ammonium. Based on the comparison of multiple model structures using the metadata of δ(15)N AA values we show that increasing the number of AAs in principle improves precision in TP estimation. This meta-analysis clarifies the advantages and limitations of using individual δ(15)N AA values as tools in trophic ecology and provides a guideline for the future application of AA-CSIA to food web studies.

  15. Amino Acid Uptake in Arbuscular Mycorrhizal Plants

    PubMed Central

    Whiteside, Matthew D.; Garcia, Maria O.; Treseder, Kathleen K.

    2012-01-01

    We examined the extent to which arbuscular mycorrhizal (AM) fungi root improved the acquisition of simple organic nitrogen (ON) compounds by their host plants. In a greenhouse-based study, we used quantum dots (fluorescent nanoparticles) to assess uptake of each of the 20 proteinaceous amino acids by AM-colonized versus uncolonized plants. We found that AM colonization increased uptake of phenylalanine, lysine, asparagine, arginine, histidine, methionine, tryptophan, and cysteine; and reduced uptake of aspartic acid. Arbuscular mycorrhizal colonization had the greatest effect on uptake of amino acids that are relatively rare in proteins. In addition, AM fungi facilitated uptake of neutral and positively-charged amino acids more than negatively-charged amino acids. Overall, the AM fungi used in this study appeared to improve access by plants to a number of amino acids, but not necessarily those that are common or negatively-charged. PMID:23094070

  16. Protein and amino acid nutrition

    USDA-ARS?s Scientific Manuscript database

    Dairy cow protein and amino acid nutrition have a significant role in sustainable dairying. Protein, amino acids, and nitrogen are inextricably linked through effects in the rumen, metabolism of the cow, and environmental nutrient management. Feeding systems have been making progress toward emphasiz...

  17. Hydrothermal synthesis of amino acids

    NASA Astrophysics Data System (ADS)

    Marshall, William L.

    1994-05-01

    This study presents further evidence that amino acids can be synthesized rapidly in hydrothermal solutions from reactants that may have been present in primitive environments. Aqueous NH 4HCO 3 solutions were reacted with C 2H 2, H 2, and O 2 (formed in situ from CaC 2, Ca, and H 2O 2) at 200-275°C over 0.2-2 h periods to synthesize several amino acids and abundant amines. These amino acid and amine producing reactions were not observed to occur below 150°C. Amino acids and amines also were synthesized at 210°C from solutions of NH 4OH, HCHO, NaCN, and H 2. When NH 4OH was replaced by NH 4HCO 3, the syntheses predominantly confirmed the recent results of RENNET et al. (1992). Additionally, amino acids and amines were observed to form by reactions among NH 4OH, HCHO, and H 2 at hydrothermal conditions, essentially confirming the results of FOX and WINDSOR (1970). Inclusion of both carbonate and O 2 in these latter solutions greatly enhanced the production rate of amino acids. The amines synthesized hydrothermally could be significant if they are precursors in the amino acid syntheses either at hydrothermal or later at lower temperatures. These observations provide additional input to the current questions of synthesis, stability, and decomposition of amino acids at hydrothermal conditions, and their possible relevance to the origin of life.

  18. Single substitutions to closely related amino acids contribute to the functional diversification of an insect-inducible, positively selected plant cystatin.

    PubMed

    Rasoolizadeh, Asieh; Goulet, Marie-Claire; Sainsbury, Frank; Cloutier, Conrad; Michaud, Dominique

    2016-04-01

    A causal link has been reported between positively selected amino acids in plant cystatins and the inhibitory range of these proteins against insect digestive cysteine (Cys) proteases. Here we assessed the impact of single substitutions to closely related amino acids on the contribution of positive selection to cystatin diversification. Cystatin sequence alignments, while confirming hypervariability, indicated a preference for related amino acids at positively selected sites. For example, the non-polar residues leucine (Leu), isoleucine (Ile) and valine (Val) were shown to predominate at positively selected site 2 in the N-terminal region, unlike selected sites 6 and 10, where polar residues are preferred. The model cystatin SlCYS8 and single variants with Leu, Ile or Val at position 2 were compared with regard to their ability to bind digestive proteases of the coleopteran pest Leptinotarsa decemlineata and to induce compensatory responses in this insect. A functional proteomics procedure to capture target Cys proteases in midgut extracts allowed confirmation of distinct binding profiles for the cystatin variants. A shotgun proteomics procedure to monitor whole Cys protease complements revealed protease family specific compensatory responses in the insect, dependent on the variant ingested. Our data confirm the contribution of closely related amino acids to the functional diversity of positively selected plant cystatins in a broader structure/function context imposing physicochemical constraints to primary structure alterations. They also underline the complexity of protease/inhibitor interactions in plant-insect systems, and the challenges still to be met in order to harness the full potential of ectopically expressed protease inhibitors in crop protection.

  19. Amino Acid Derangements in Patients With Sepsis: Treatment With Branched Chain Amino Acid Rich Infusions

    PubMed Central

    Freund, Herbert R.; Ryan, John A.; Fischer, Josef E.

    1978-01-01

    reversal of encephalopathy was observed. The following sequence of events may be postulated: The septic patient develops insulin resistance in the peripheral tissues, primarily muscle, while the adipose tissue is much less affected. The insulin resistance and the inability to utilize fat leads to increased muscle proteolysis. Muscle breakdown results in release into the blood of enormous amounts of various amino acids; the muscle itself is able to oxidize the branched chain amino acids, supplying the muscles' own energy requirements and alanine for gluconeogenesis. The extensive muscle proteolysis coupled with relative hepatic insufficiency occurring early in sepsis results in the appearance in the plasma of high levels of most of the amino acids present in muscle, particularly the aromatic and the sulfur-containing amino acids. The outcome of patients with sepsis might be positively affected by combined therapy with glucose, insulin and branched chain amino acids. PMID:99098

  20. Synthesis and biological activity of oxytocin analogues containing unnatural amino acids in position 9: structure activity study.

    PubMed

    Magafa, Vassiliki; Borovicková, Lenka; Slaninová, Jirina; Cordopatis, Paul

    2010-05-01

    We report the solid phase synthesis and some pharmacological properties of 24 oxytocin (OT) analogues. Basic modifications at position 9 (introduction of L- or D-beta-(2-thienyl)-alanine [L- or D-Thi], or L- or D-3-Pyridylalanine [L- or D-3-Pal]) were combined with D-tyrosine(OEthyl) [D-Tyr(Et)] or D-1-naphthylalanine [D-1-Nal] in position 2 and beta-mercaptopropionic acid (Mpa) in position 1 modifications in altogether 14 analogues. Additionally, 8 analogues having alpha-aminoisobutyric acid [Aib] or D-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (D-Tic) or diethylglycine (Deg) in position 9 and D-Tyr(Et) or D-1-Nal or D-Tic in position 2 and Mpa or Pen (beta beta-dimethylcysteine) in position 1 were prepared. Two of these analogues have one more modification in position 6, i.e. Pen. Furthermore, two analogues having Mpa in position 1 and D-Tyr(Et) or D-1-Nal in position 2 were prepared for comparison purposes. The analogues were tested for rat uterotonic activity in vitro, in the rat pressor assay and for binding affinity to human OT receptor. The analogue having the highest anti-oxytocic activity was [Mpa(1), D-Tyr(Et)(2), Deg(9)]OT (pA(2) = 8.68 +/- 0.26); this analogue was also selective.

  1. K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets

    PubMed Central

    Grad, Yonatan; Cobey, Sarah; Puranen, Juha Santeri; Corander, Jukka

    2015-01-01

    The recent growth in publicly available sequence data has introduced new opportunities for studying microbial evolution and spread. Because the pace of sequence accumulation tends to exceed the pace of experimental studies of protein function and the roles of individual amino acids, statistical tools to identify meaningful patterns in protein diversity are essential. Large sequence alignments from fast-evolving micro-organisms are particularly challenging to dissect using standard tools from phylogenetics and multivariate statistics because biologically relevant functional signals are easily masked by neutral variation and noise. To meet this need, a novel computational method is introduced that is easily executed in parallel using a cluster environment and can handle thousands of sequences with minimal subjective input from the user. The usefulness of this kind of machine learning is demonstrated by applying it to nearly 5000 haemagglutinin sequences of influenza A/H3N2.Antigenic and 3D structural mapping of the results show that the method can recover the major jumps in antigenic phenotype that occurred between 1968 and 2013 and identify specific amino acids associated with these changes. The method is expected to provide a useful tool to uncover patterns of protein evolution. PMID:28348810

  2. Amino Acids from a Comet

    NASA Technical Reports Server (NTRS)

    Cook, Jamie Elisla

    2009-01-01

    NASA's Stardust spacecraft returned samples from comet 81P/Wild 2 to Earth in January 2006. Examinations of the organic compounds in cometary samples can reveal information about the prebiotic organic inventory present on the early Earth and within the early Solar System, which may have contributed to the origin of life. Preliminary studies of Stardust material revealed the presence of a suite of organic compounds including several amines and amino acids, but the origin of these compounds (cometary- vs. terrestrial contamination) could not be identified. We have recently measured the carbon isotopic ratios of these amino acids to determine their origin, leading to the first detection of a coetary amino acid.

  3. Amino Acids from a Comet

    NASA Technical Reports Server (NTRS)

    Cook, Jamie Elisla

    2009-01-01

    NASA's Stardust spacecraft returned samples from comet 81P/Wild 2 to Earth in January 2006. Examinations of the organic compounds in cometary samples can reveal information about the prebiotic organic inventory present on the early Earth and within the early Solar System, which may have contributed to the origin of life. Preliminary studies of Stardust material revealed the presence of a suite of organic compounds including several amines and amino acids, but the origin of these compounds (cometary- vs. terrestrial contamination) could not be identified. We have recently measured the carbon isotopic ratios of these amino acids to determine their origin, leading to the first detection of a coetary amino acid.

  4. Positive net movements of amino acids in the hindlimb after overnight food deprivation contribute to sustaining the elevated anabolism of neonatal pigs.

    PubMed

    Thivierge, M Carole; Bush, Jill A; Suryawan, Agus; Nguyen, Hanh V; Orellana, Renan A; Burrin, Douglas G; Jahoor, Farook; Davis, Teresa A

    2008-12-01

    During the neonatal period, high protein breakdown rate is a metabolic process inherent to elevated rates of protein accretion in skeletal muscle. To determine the relationship between hindlimb net movements of essential and nonessential amino acids in the regulation of hindlimb protein breakdown during an overnight fasting-feeding cycle, we infused overnight-food-deprived 10- and 28-day-old piglets with [1-(13)C]phenylalanine and [ring-(2)H(4)]tyrosine over 7 h (during 3 h of fasting and then during 4 h of feeding). Extraction rates for aspartate and glutamate after an overnight fast were 15% and 51% in the 10-day-old compared with 6% and 25% in the 28-day-old (P < 0.05) piglets, suggesting an altered requirement for precursors of amino acids to shuttle nitrogen to the liver as early life progresses. This occurred simultaneously with marginal positive hindlimb net balance of essential amino acids after an overnight fast, with negative net release of many nonessential amino acids, such as alanine, asparagine, glutamine, glycine, and proline. This suggests that newborn muscle does not undergo significant protein mobilization after a short period of fasting in support of an elevated rate of protein accretion. Furthermore, tyrosine efflux from hindlimb breakdown between overnight fasting and feeding periods was not different in the 10-day-old piglets, for which tyrosine was limiting, but when tyrosine supply balanced requirements in the 28-day-old piglet, hindlimb efflux was increased (P = 0.01). The results of the present study indicate that proteolysis and net movements of amino acids are coordinated mechanisms that sustain the elevated rate of net protein accretion during overnight feeding-fasting cycles in the neonate.

  5. Studies on naturally occurring infectious bursal disease viruses suggest that a single amino acid substitution at position 253 in VP2 increases pathogenicity.

    PubMed

    Jackwood, D J; Sreedevi, B; LeFever, L J; Sommer-Wagner, S E

    2008-07-20

    should be noted that some of the classic virus vaccines were not being used according to the manufacturer's recommendations at the time the GA-1, H-30 and CS-2-35 strains were isolated. Together, the molecular and pathogenicity data indicate that a single amino acid mutation from Histidine (H) to Glutamine (Q) or Asparagine (N) at position 253 in VP2 will markedly increase the virulence of an attenuated IBDV.

  6. Determination of the relative positions of amino acids by partial specific cleavages of end-labeled proteins.

    PubMed

    Jue, R A; Doolittle, R F

    1985-01-01

    We have developed a new method for obtaining information about protein sequences that uses an approach analogous to that used to determine DNA sequences. In essence, three steps are involved. First, a detectable label is attached exclusively to the amino terminus of a polypeptide. Next, the labeled chain is subjected to partial specific cleavage in a way that produces roughly equimolar amounts of fragments of different sizes. Cleavages for methionine, tryptophan, arginine, aspartyl-proline bonds, and asparaginyl-glycine bonds have been employed. Lastly, the labeled fragments are separated according to size by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The distribution of target amino acids along the polypeptide chain can be deduced from the specific pattern of labeled bands by reading the "ladder" in the same way that DNA sequencing gels are read. Although the method can be conducted with a radioactive label, we have chosen to use a fluorescent label. We have applied the method successfully to the three subunit chains of two different fibrinogens.

  7. Treatment of Amino Acid Metabolism Disorders

    MedlinePlus

    ... Treatment of amino acid metabolism disorders Treatment of amino acid metabolism disorders E-mail to a friend Please ... this page It's been added to your dashboard . Amino acid metabolism disorders are rare health conditions that affect ...

  8. Amino acid isotopic analysis in agricultural systems

    USDA-ARS?s Scientific Manuscript database

    A relatively new approach to stable isotopic analysis—referred to as compound-specific isotopic analysis (CSIA)—has emerged, centering on the measurement of 15N:14N ratios in amino acids (glutamic acid and phenylalanine). CSIA has recently been used to generate trophic position estimates among anima...

  9. Amino acids of the Murchison meteorite. III - Seven carbon acyclic primary alpha-amino alkanoic acids

    NASA Technical Reports Server (NTRS)

    Cronin, John R.; Pizzarello, Sandra

    1986-01-01

    All of the eighteen possible seven-carbon acyclic primary alpha-amino alkanoic acids have been positively identified in a hot-water extract of the Murchison meteorite by the combined use of gas chromatography-mass spectrometry, ion exchange chromatography and reversed-phase chromatography. None of these amino acids has previously been found in meteorites or in any other natural material. They range in concentration from less than or equal to 0.5 to 5.3 nmol/g. Configuration assignments were made for 2-amino-3,4-dimethylpentanoic acid and allo-2-amino-3,4-dimethylpentanoic acid and the diasteromer ratio was determined. Fifty-five amino acids have now been positively identified in the Murchison meteorite, 36 of which are unknown in terrestrial materials. This unique suite of amino acids is characterized by the occurrence of all structural isomers within the two major classes of amino acids represented, by the predominance of branched chain isomers, and by an exponential decline in amount with increasing carbon chain length within homologous series. These characteristics of the Murchison amino acids are suggestive of synthesis before incorporation into a parent body.

  10. Amino acids and cell regulation.

    PubMed Central

    Forster, R. P.; Goldstein, L.

    1979-01-01

    Free amino play an important role in regulating cell volume in fishes. Four tissues/cells (skeletal muscle, RBC, brain, and myocardium) of the little skate, Raja erinacea, were selected for detailed study because of their special importance or unique advantage as experimental models. Three particular amino acids, beta-alanine, taurine, and sarcosine play a predominant role in all four tissues. As in higher vertebrates, amino acid uptake in skate brain, heart, and RBC is mediated via a Na+-dependent process. Amino acids leave the skate brain rapidly in response to a sudden decrease in plasma osmolality and/or to a simultaneous drop in extracellular Na+ concentration. However, although amino acids are important for volume regulation in normal brain cells, they do not appear to be likely candidates for the unidentified "idiogenic" osmolytes in mammalian brain cells. The high concentration of taurine in skate myocardium is of special interest because of the special role of this amino acid in myocardial contractility. Thus, unlike beta-alanine and sarcosine, taurine may play a dual role in regulating both cell volume and contractility of myocardial cells. The isolated skate atrium is well suited for in vitro studies of these two processes. PMID:395764

  11. Evolution of aromatic amino acid biosynthesis and application to the fine-tuned phylogenetic positioning of enteric bacteria.

    PubMed

    Ahmad, S; Weisburg, W G; Jensen, R A

    1990-02-01

    A comprehensive phylogenetic tree for virtually the entire assemblage of enteric bacteria is presented. Character states of aromatic amino acid biosynthesis are used as criteria, and the results are compared with partial trees based upon sequencing of 16S rRNA, 5S rRNA, and tryptophan leader peptide. Three major clusters are apparent. Enterocluster 1 possesses a gene fusion (trpG-trpD) encoding anthranilate synthase: anthranilate 5-phosphoribosylpyrophosphate phosphoribosyltransferase of tryptophan biosynthesis. This cluster includes the genera Escherichia, Shigella, Citrobacter, Salmonella, Klebsiella, and Enterobacter. The remaining two clusters lack the trpG-trpD gene fusion, but differ in the presence (enterocluster 2) or absence (enterocluster 3) of the three-step overflow pathway to L-phenylalanine. Enterocluster 2 consists of the genera Serratia and Erwinia. Enterocluster 3 includes the genera Cedecea, Kluyvera, Edwardsiella, Hafnia, Yersinia, Proteus, Providencia, and Morganella. Within these three major clusters, a tentative hierarchy of subcluster ordering is formulated on the basis of all data available. This hierarchical framework is proposed as a general working basis for continued refinement of the phylogenetic relationships of enteric bacteria.

  12. Position dependence of the 13C chemical shifts of α-helical model peptides. Fingerprint of the 20 naturally occurring amino acids

    PubMed Central

    Vila, Jorge A.; Baldoni, Héctor A.; Scheraga, Harold A.

    2004-01-01

    The position dependence of the 13C chemical shifts was investigated at the density functional level for α-helical model peptides represented by the sequence Ac-(Ala)i-X-(Ala)j-NH2, where X represents any of the 20 naturally occurring amino acids, with 0 ≤ i ≤ 8 and i + j = 8. Adoption of the locally dense basis approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 20 naturally occurring amino acids in α-helices, there is (1) significant variability of the computed 13C shielding as a function of both the guest residue (X) and the position along the sequence; for example, at the N terminus, the 13Cα and 13Cβ shieldings exhibit a uniform pattern of variation with respect to both the central or the C-terminal positions; (2) good agreement between computed and observed 13Cα and 13Cβ chemical shifts in the interior of the helix, with correlation coefficients of 0.98 and 0.99, respectively; for 13Cα chemical shifts, computed in the middle of the helix, only five residues, namely Asn, Asp, Ser, Thr, and Leu, exhibit chemical shifts beyond the observed standard deviation; and (3) better agreement for four of these residues (Asn, Asp, Ser, and Thr) only for the computed values of the 13Cα chemical shifts at the N terminus. The results indicate that 13Cβ, but not 13Cβ, chemical shifts are sensitive enough to reflect the propensities of some amino acids for specific positions within an α-helix, relative to the N and C termini of peptides and proteins. PMID:15498939

  13. 21 CFR 172.320 - Amino acids.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Amino acids. 172.320 Section 172.320 Food and Drugs... Dietary and Nutritional Additives § 172.320 Amino acids. The food additive amino acids may be safely used... consists of one or more of the following individual amino acids in the free, hydrated or anhydrous form or...

  14. 21 CFR 172.320 - Amino acids.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Amino acids. 172.320 Section 172.320 Food and... Dietary and Nutritional Additives § 172.320 Amino acids. The food additive amino acids may be safely used... consists of one or more of the following individual amino acids in the free, hydrated or anhydrous form or...

  15. 21 CFR 172.320 - Amino acids.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Amino acids. 172.320 Section 172.320 Food and....320 Amino acids. The food additive amino acids may be safely used as nutrients added to foods in... individual amino acids in the free, hydrated, or anhydrous form, or as the hydrochloride, sodium, or...

  16. 21 CFR 172.320 - Amino acids.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Amino acids. 172.320 Section 172.320 Food and... Dietary and Nutritional Additives § 172.320 Amino acids. The food additive amino acids may be safely used... consists of one or more of the following individual amino acids in the free, hydrated or anhydrous form or...

  17. 21 CFR 172.320 - Amino acids.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Amino acids. 172.320 Section 172.320 Food and... Dietary and Nutritional Additives § 172.320 Amino acids. The food additive amino acids may be safely used... consists of one or more of the following individual amino acids in the free, hydrated or anhydrous form or...

  18. Interaction of Adjacent Amino Acids

    NASA Astrophysics Data System (ADS)

    Sheu, Sheh-Yi; Yang, Dah-Yen

    2008-02-01

    Ramachandran plots display the dihedral angles of a single protein residue. We here propose a crossed torsion angle plot called SSY-plot between two neighboring amino acids and demonstrate that a special coherence motion can exist between some very special amino acid pairs leading to spontaneous unusual structures. We also suggest that the existence of two domains corresponds to a bifurcation between two different protein structures and that the special pair is the key to producing these two structures. These are two different structures and are produced spontaneously without an external agent.

  19. Temperature dependence of amino acid hydrophobicities.

    PubMed

    Wolfenden, Richard; Lewis, Charles A; Yuan, Yang; Carter, Charles W

    2015-06-16

    The hydrophobicities of the 20 common amino acids are reflected in their tendencies to appear in interior positions in globular proteins and in deeply buried positions of membrane proteins. To determine whether these relationships might also have been valid in the warm surroundings where life may have originated, we examined the effect of temperature on the hydrophobicities of the amino acids as measured by the equilibrium constants for transfer of their side-chains from neutral solution to cyclohexane (K(w > c)). The hydrophobicities of most amino acids were found to increase with increasing temperature. Because that effect is more pronounced for the more polar amino acids, the numerical range of K(w > c) values decreases with increasing temperature. There are also modest changes in the ordering of the more polar amino acids. However, those changes are such that they would have tended to minimize the otherwise disruptive effects of a changing thermal environment on the evolution of protein structure. Earlier, the genetic code was found to be organized in such a way that--with a single exception (threonine)--the side-chain dichotomy polar/nonpolar matches the nucleic acid base dichotomy purine/pyrimidine at the second position of each coding triplet at 25 °C. That dichotomy is preserved at 100 °C. The accessible surface areas of amino acid side-chains in folded proteins are moderately correlated with hydrophobicity, but when free energies of vapor-to-cyclohexane transfer (corresponding to size) are taken into consideration, a closer relationship becomes apparent.

  20. Position-specific incorporation of fluorescent non-natural amino acids into maltose-binding protein for detection of ligand binding by FRET and fluorescence quenching.

    PubMed

    Iijima, Issei; Hohsaka, Takahiro

    2009-04-17

    Position-specific incorporation of fluorescent groups is a useful method for analysis of the functions and structures of proteins. We have developed a method for the incorporation of visible-wavelength-fluorescent non-natural amino acids into proteins in a cell-free translation system. Using this technique, we introduced one or two BODIPY-linked amino acids into maltose-binding protein (MBP) to obtain MBP derivatives showing ligand-dependent changes in fluorescence intensity or intensity ratio. BODIPY-FL-aminophenylalanine was incorporated in place of 15 tyrosines, as well as the N-terminal Lys1, and the C-terminal Lys370 of MBP. Fluorescence measurements revealed that MBP containing a BODIPY-FL moiety in place of Tyr210 showed a 13-fold increase in fluorescence upon binding of maltose. Tryptophan-to-phenylalanine substitutions suggest that the increase in fluorescence was the result of a decrease in the quenching of BODIPY-FL by tryptophan located around the binding site. MBP containing a BODIPY-558 moiety also showed a maltose-dependent increase in fluorescence. BODIPY-FL was then additionally incorporated in place of Lys1 of the BODIPY-558-containing MBP as a response to the amber codon. Fluorescence measurements with excitation of BODIPY-FL showed a large change in fluorescence intensity ratio (0.13 to 1.25) upon binding of maltose; this change can be attributed to fluorescence resonance energy transfer (FRET) and maltose-dependent quenching of BODIPY-558. These results demonstrate the usefulness of the position-specific incorporation of fluorescent amino acids in the fluorescence-based detection of protein functions.

  1. Signal peptidase I processed secretory signal sequences: Selection for and against specific amino acids at the second position of mature protein.

    PubMed

    Zalucki, Yaramah M; Jennings, Michael P

    2017-02-12

    Signal peptides direct proteins from the cytoplasm to the periplasm. These N-terminal peptides are cleaved upon entry to the periplasm by either signal peptidase I, or signal peptidase II for lipoproteins. Signal peptidase I is a serine protease that has either a serine-lysine or serine-histidine catalytic dyad present in the active site. The recognition site for signal peptide cleavage by signal peptidase I has been defined primarily by an Ala-X-Ala motif at the C-terminal end of the signal peptide, one amino acid away from the cleavage site. We used a verified set of signal peptidase I cleaved proteins from E. coli to look for novel conserved features, focusing on the N-terminus of the mature protein. We observed a striking bias for the presence of acidic residues at second position of the mature protein (P2'), and a complete absence of aromatic amino acids at the same position. Whole genome analysis of the predicted set of all E. coli and B. subtilis secreted proteins confirmed the same strong bias for acidic residues at P2' of the mature protein, and against aromatic amino acids at the same position. When these studies were extended to archaeal genomes (M. voltae and S. tokodaii) and the yeast genome from S. cerevisiae, this bias was not observed. E. coli and B. subtilis primarily express a signal peptidase I contains a serine-lysine catalytic dyad, whilst those of archaeal and eukaryotic origin generally have a serine-histidine catalytic dyad. This difference may explain the differential bias for acidic residues and against aromatic residues at P2'. These observations suggest additional key residues that may favor or prevent signal sequence recognition or cleavage by signal peptidase I, and thereby facilitate more accurate in silico prediction of signal peptidase I cleavage sites. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  2. Conformations of amino acids in proteins.

    PubMed

    Hovmöller, Sven; Zhou, Tuping; Ohlson, Tomas

    2002-05-01

    The main-chain conformations of 237 384 amino acids in 1042 protein subunits from the PDB were analyzed with Ramachandran plots. The populated areas of the empirical Ramachandran plot differed markedly from the classical plot in all regions. All amino acids in alpha-helices are found within a very narrow range of phi, psi angles. As many as 40% of all amino acids are found in this most populated region, covering only 2% of the Ramachandran plot. The beta-sheet region is clearly subdivided into two distinct regions. These do not arise from the parallel and antiparallel beta-strands, which have quite similar conformations. One beta region is mainly from amino acids in random coil. The third and smallest populated area of the Ramachandran plot, often denoted left-handed alpha-helix, has a different position than that originally suggested by Ramachandran. Each of the 20 amino acids has its own very characteristic Ramachandran plot. Most of the glycines have conformations that were considered to be less favoured. These results may be useful for checking secondary-structure assignments in the PDB and for predicting protein folding.

  3. Excitatory amino acid neurotransmission.

    PubMed

    Parsons, C G; Danysz, W; Zieglgänsberger, W

    2005-01-01

    In recent years great progress has been made in understanding the function of ionotropic and metabotropic glutamate receptors; their pharmacology and potential therapeutic applications. It should be stressed that there are already N-methyl-D-aspartate (NMDA) antagonists in clinical use, such as memantine, which proves the feasibility of their therapeutic potential. It seems unlikely that competitive NMDA receptor antagonists and high-affinity channel blockers will find therapeutic use due to limiting side-effects, whereas agents acting at the glycineB site, NMDA receptor subtype-selective agents and moderate-affinity channel blockers are far more promising. This is supported by the fact that there are several glycineB antagonists, NMDA moderate-affinity channel blockers and NR2B-selective agents under development. Positive and negative modulators of AMPA receptors such as the AMPAkines and 2,3-benzodiazepines also show more promise than e.g. competitive antagonists. Great progress has also been made in the field of metabotropic glutamate receptors since the discovery of novel, allosteric modulatory sites for these receptors. Selective agents acting at these transmembrane sites have been developed that are more drug-like and have a much better access to the central nervous system than their competitive counterparts. The chapter will critically review preclinical and scarce clinical experience in the development of new ionotropic and metabotropic glutamate receptor modulators according to the following scheme: rational, preclinical findings in animal models and finally clinical experience, where available.

  4. Hereditary folate malabsorption: A positively charged amino acid at position 113 of the proton-coupled folate transporter (PCFT/SLC46A1) is required for folic acid binding

    SciTech Connect

    Lasry, Inbal; Berman, Bluma; Glaser, Fabian; Jansen, Gerrit; Assaraf, Yehuda G.

    2009-08-28

    The proton-coupled folate transporter (PCFT/SLC46A1) mediates intestinal folate uptake at acidic pH. Some loss of folic acid (FA) transport mutations in PCFT from hereditary folate malabsorption (HFM) patients cluster in R113, thereby suggesting a functional role for this residue. Herein, unlike non-conservative substitutions, an R113H mutant displayed 80-fold increase in the FA transport Km while retaining parental Vmax, hence indicating a major fall in folate substrate affinity. Furthermore, consistent with the preservation of 9% of parental transport activity, R113H transfectants displayed a substantial decrease in the FA growth requirement relative to mock transfectants. Homology modeling based on the crystal structures of the Escherichia coli transporter homologues EmrD and glycerol-3-phosphate transporter revealed that the R113H rotamer properly protrudes into the cytoplasmic face of the minor cleft normally occupied by R113. These findings constitute the first demonstration that a basic amino acid at position 113 is required for folate substrate binding.

  5. Inhibition of D-amino acid oxidase by alpha-keto acids analogs of amino acids.

    PubMed

    Moreno, J A; Montes, F J; Catalán, J; Galán, M A

    1996-04-01

    The inhibition of D-amino acid oxidase by certain alpha-keto acids products of the reaction with D-amino acids, in particular alpha-keto acids that are analogs of the amino acids alanine, valine, leucine, phenylanaline, phenylglycine, tyrosine and tryptophan, is reported. All the alpha-keto acids assayed behaved as substrate competitive inhibitors of the enzyme. The relationship between the degree of inhibition and the structure of the inhibitor is discussed.

  6. A patch of positively charged amino acids surrounding the human immunodeficiency virus type 1 Vif SLVx4Yx9Y motif influences its interaction with APOBEC3G.

    PubMed

    Chen, Gongying; He, Zhiwen; Wang, Tao; Xu, Rongzhen; Yu, Xiao-Fang

    2009-09-01

    The amino-terminal region of the Vif molecule in human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus (SIV) contains a conserved SLV/Ix4Yx9Y motif that was first described in 1992, but the importance of this motif for Vif function has not yet been examined. Our characterization of the amino acids surrounding this motif in HIV-1 Vif indicated that the region is critical for APOBEC3 suppression. In particular, amino acids K22, K26, Y30, and Y40 were found to be important for the Vif-induced degradation and suppression of cellular APOBEC3G (A3G). However, mutation of these residues had little effect on the Vif-mediated suppression of A3F, A3C, or A3DE, suggesting that these four residues are not important for Vif assembly with the Cul5 E3 ubiquitin ligase or protein folding in general. The LV portion of the Vif SLV/Ix4Yx9Y motif was found to be required for optimal suppression of A3F, A3C, or A3DE. Thus, the SLV/Ix4Yx9Y motif and surrounding amino acids represent an important functional domain in the Vif-mediated defense against APOBEC3. In particular, the positively charged K26 of HIV-1 Vif is invariably conserved within the SLV/Ix4Yx9Y motif of HIV/SIV Vif molecules and was the most critical residue for A3G inactivation. A patch of positively charged and hydrophilic residues (K(22)x(3)K(26)x(3)Y(30)x(9)YRHHY(44)) and a cluster of hydrophobic residues (V(55)xIPLx(4-5)LxPhix2YWxL(72)) were both involved in A3G binding and inactivation. These structural motifs in HIV-1 Vif represent attractive targets for the development of lead inhibitors to combat HIV infection.

  7. [Study on basic amino acid contents in Dendrobium officinale].

    PubMed

    Zhang, Ailian; Wei, Tao; Si, Jinping'; Jin, Luying; Mo, Yina

    2011-10-01

    To investigate the contents of 16 basic amino acid and find out the variation of them in Dendrobium officinale with different germplasms and physiological ages, and then provide scientific basis for the quality evaluation and the breeding of D. officinale. Thirty-three samples with 1-3 ages were collected from cultivated fields of Zhejiang. The samples were acid hydrolyzed, and then 16 basic amino acid contents of samples were determined by amino acid analyzer. The average contents of 7 necessary amino acid were in 0.28 - 2.96 mg x g(-1), the average contents of other 9 basic amino acid were in 0.53 - 4.20 mg x g(-1). The contents of many amino acids were impacted by germplasms significantly, and contents of several amino acids were impacted by physiological ages significantly. There were rich basic amino acids in D. officinale. The breeding of D. officinale can increase the contents of essential amino acids and other basic amino acids. The relations among physiological age and amino acid contents were as follows: three years > two years > one year. The contents of Asp and Tyr have significantly negative correlation with magnesium, the content of Pro has significantly positive correlation with copper.

  8. Bovine testis acylphosphatase: purification and amino acid sequence.

    PubMed

    Pazzagli, L; Cappugi, G; Camici, G; Manao, G; Ramponi, G

    1993-10-01

    Two acylphosphatase molecular forms have been isolated from bovine testis. Their amino acid sequence was determined. One (ACY1) consists of 98 amino acid residues, while the other one (ACY2) consists of 100 amino acid residues. Both molecular forms are N-acetylated and differ only in the amino terminus. ACY2 has an additional Ser-Met tail with respect to ACY1. Both ACY1 and ACY2 are organ-common type isoenzymes and thus differ for about half of the amino acid positions from the previously sequenced bovine muscle isoenzyme.

  9. Toward Sustainable Amino Acid Production.

    PubMed

    Usuda, Yoshihiro; Hara, Yoshihiko; Kojima, Hiroyuki

    2016-11-22

    Because the global amino acid production industry has been growing steadily and is expected to grow even more in the future, efficient production by fermentation is of great importance from economic and sustainability viewpoints. Many systems biology technologies, such as genome breeding, omics analysis, metabolic flux analysis, and metabolic simulation, have been employed for the improvement of amino acid-producing strains of bacteria. Synthetic biological approaches have recently been applied to strain development. It is also important to use sustainable carbon sources, such as glycerol or pyrolytic sugars from cellulosic biomass, instead of conventional carbon sources, such as glucose or sucrose, which can be used as food. Furthermore, reduction of sub-raw substrates has been shown to lead to reduction of environmental burdens and cost. Recently, a new fermentation system for glutamate production under acidic pH was developed to decrease the amount of one sub-raw material, ammonium, for maintenance of culture pH. At the same time, the utilization of fermentation coproducts, such as cells, ammonium sulfate, and fermentation broth, is a useful approach to decrease waste. In this chapter, further perspectives for future amino acid fermentation from one-carbon compounds are described.

  10. Strong positive selection and habitat-specific amino acid substitution patterns in MHC from an estuarine fish under intense pollution stress.

    PubMed

    Cohen, Sarah

    2002-11-01

    Population-level studies using the major histocompatibility complex (Mhc) have linked specific alleles with specific diseases, but data requirements are high and the power to detect disease association is low. A novel use of Mhc population surveys involves mapping allelic substitutions onto the inferred structural molecular model to show functional differentiation related to local selective pressures. In the estuarine fish Fundulus heteroclitus, populations experiencing strong differences in antigenic challenges show significant differences in amino acid substitution patterns that are reflected as variation in the structural location of changes between populations. Fish from a population genetically adapted to severe chemical pollution also show novel patterns of DNA substitution at a highly variable Mhc class II B locus including strong signals of positive selection at inferred antigen-binding sites and population-specific signatures of amino acid substitution. Heavily parasitized fish from an extreme PCB-contaminated (U.S. Environmental Protection Agency Superfund) site show enhanced population-specific substitutions in the a-helix portion of the inferred antigen-binding region. In contrast, fish from an unpolluted site show a significantly different pattern focused on the first strand of the B-pleated sheet. Whether Mhc population profile differences represent the direct effects of chemical toxicants or indirect parasite-mediated selection, the result is a composite habitat-specific signature of strong selection and evolution affecting the genetic repertoire of the major histocompatibility complex.

  11. Nonprotein Amino Acids in the Murchison Meteorite

    PubMed Central

    Kvenvolden, Keith A.; Lawless, James G.; Ponnamperuma, Cyril

    1971-01-01

    Twelve nonprotein amino acids appear to be present in the Murchison meteorite. The identity of eight of them has been conclusively established as N-methylglycine, β-alanine, 2-methylalanine, α-amino-n-butyric acid, β-amino-n-butyric acid, γ-amino-n-butyric acid, isovaline, and pipecolic acid. Tentative evidence is presented for the presence of N-methylalanine, N-ethylglycine, β-aminoisobutyric acid, and norvaline. These amino acids appear to be extraterrestrial in origin and may provide new evidence for the hypothesis of chemical evolution. PMID:16591908

  12. Worldwide differences in the incidence of type I diabetes are associated with amino acid variation at position 57 of the HLA-DQ. beta. chain

    SciTech Connect

    Dorman, J.S.; LaPorte, R.E.; Trucco, M. ); Stone, R.A. )

    1990-10-01

    The presence of an amino acid other than aspartic acid at position 57 of the HLA-DQ {beta} chain (non-Asp-57) is highly associated with susceptibility to insulin-dependent diabetes mellitus (IDDM), whereas an aspartic acid at this position (Asp-57) appears to confer resistance to the disease. The authors hypothesize that the 30-fold difference in IDDM incidence across racial groups and countries is related to variability in the frequency of these alleles. Diabetic and nondiabetic individuals were evaluated in five populations, including those at low, moderate, and high risk. HLA-DQ {beta} genotype distributions among the IDDM case groups were markedly different as were those among nondiabetic controls. Non-Asp-57 alleles were significantly associated with IDDM in all areas; population-specific odds ratios for non-Asp-57 homozygotes relative to Asp-57 homozygotes ranged from 14 to 111. Relative risk information from the case-control study and population incidence data were combined to estimate genotype-specific incidence rates for the Allegheny county, PA, Caucasians. These rates were used to predict the overall incidence rates in the remaining populations, which were within the 95% confidence intervals of the actual rates established from incidence registries. These results are consistent with the hypothesis that population variation in the distribution of non-Asp-57 alleles may explain much of the geographic variation in IDDM incidence.

  13. Unnatural reactive amino acid genetic code additions

    DOEpatents

    Deiters, Alexander; Cropp, T. Ashton; Chin, Jason W.; Anderson, J. Christopher; Schultz, Peter G.

    2014-08-26

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  14. Amino acid analyses of Apollo 14 samples.

    NASA Technical Reports Server (NTRS)

    Gehrke, C. W.; Zumwalt, R. W.; Kuo, K.; Aue, W. A.; Stalling, D. L.; Kvenvolden, K. A.; Ponnamperuma, C.

    1972-01-01

    Detection limits were between 300 pg and 1 ng for different amino acids, in an analysis by gas-liquid chromatography of water extracts from Apollo 14 lunar fines in which amino acids were converted to their N-trifluoro-acetyl-n-butyl esters. Initial analyses of water and HCl extracts of sample 14240 and 14298 samples showed no amino acids above background levels.

  15. Amino acids as antioxidants for frying oil

    USDA-ARS?s Scientific Manuscript database

    Amino acids, proteins and hydrolysates of proteins have been known to protect edible oils from oxidation. While amino acids and related materials have high potential as antioxidants for frying oil, effectiveness of each amino acid and mechanisms of their activities are not well understood yet. Propo...

  16. Unnatural reactive amino acid genetic code additions

    SciTech Connect

    Deiters, Alexander; Cropp, Ashton T; Chin, Jason W; Anderson, Christopher J; Schultz, Peter G

    2013-05-21

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  17. Unnatural reactive amino acid genetic code additions

    SciTech Connect

    Deiters, Alexander; Cropp, T Ashton; Chin, Jason W; Anderson, J Christopher; Schultz, Peter G

    2011-02-15

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  18. Unnatural reactive amino acid genetic code additions

    SciTech Connect

    Deiters, Alexander; Cropp, T Ashton; Chin, Jason W; Anderson, J Christopher; Schultz, Peter G

    2011-08-09

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNAsyn-thetases, pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  19. Amino acid analyses of Apollo 14 samples.

    NASA Technical Reports Server (NTRS)

    Gehrke, C. W.; Zumwalt, R. W.; Kuo, K.; Aue, W. A.; Stalling, D. L.; Kvenvolden, K. A.; Ponnamperuma, C.

    1972-01-01

    Detection limits were between 300 pg and 1 ng for different amino acids, in an analysis by gas-liquid chromatography of water extracts from Apollo 14 lunar fines in which amino acids were converted to their N-trifluoro-acetyl-n-butyl esters. Initial analyses of water and HCl extracts of sample 14240 and 14298 samples showed no amino acids above background levels.

  20. Amino acids of the Murchison meteorite. I - Six carbon acyclic primary alpha-amino alkanoic acids

    NASA Technical Reports Server (NTRS)

    Cronin, J. R.; Gandy, W. E.; Pizzarello, S.

    1981-01-01

    Six of the seven chain isomers of six-carbon acyclic primary alpha-amino alkanoic acids (leucine isomers) have been either identified or confirmed in hot-water extracts of the Murchison meteorite using combined gas chromatography-mass spectrometry (GC-MS) and ion exchange chromatography. 2-Amino-2-ethylbutyric acid, 2-amino-2,3-dimethylbutyric acid, pseudoleucine, and 2-methylnorvaline were positively identified by GC-MS. These amino acids have not been previously reported to occur in natural materials and may be uniquely meteoritic in origin. The presence of leucine and isoleucine (including the diastereoisomer, alloisoleucine) was confirmed. Peaks corresponding to norleucine were seen by ion-exchange and gas chromatography but characteristic mass spectra were not obtained. The alpha-branched chain isomers in this series are quantitatively the most significant. These results are compared with literature data on amino acid synthesis by electrical discharge and Fischer-Tropsch-type catalysis. Neither model system produces an amino acid suite that is completely comparable to that found in the Murchison meteorite.

  1. Role of positively charged amino acids in the M2D transmembrane helix of Ktr/Trk/HKT type cation transporters.

    PubMed

    Kato, Naoki; Akai, Masaro; Zulkifli, Lalu; Matsuda, Nobuyuki; Kato, Yasuhiro; Goshima, Shinobu; Hazama, Akihiro; Yamagami, Mutsumi; Guy, H Robert; Uozumi, Nobuyuki

    2007-01-01

    Studies suggest that Ktr/Trk/HKT-type transporters have evolved from multiple gene fusions of simple K(+) channels of the KcsA type into proteins that span the membrane at least eight times. Several positively charged residues are present in the eighth transmembrane segment, M2(D), in the transporters but not K(+) channels. Some models of ion transporters require a barrier to prevent free diffusion of ions down their electrochemical gradient, and it is possible that the positively charged residues within the transporter pore may prevent transporters from being channels. Here we studied the functional role of these positive residues in three Ktr/Trk/HKT-type transporters (Synechocystis KtrB-mediated K(+) uniporter, Arabidopsis AtHKT1-mediated Na(+) uniporter and wheat TaHKT1-mediated K(+)/Na(+) symporter) by examining K(+) uptake rates in E. coli, electrophysiological measurements in oocytes and growth rates of E. coli and yeast. The conserved Arg near the middle of the M2(D) segment was essential for the K(+) transport activity of KtrB and plant HKTs. Combined replacement of several positive residues in TaHKT1 showed that the positive residue at the beginning of the M2(D), which is conserved in many K(+) channels, also contributed to cation transport activity. This positive residue and the conserved Arg both face towards the ion conducting pore side. We introduced an atomic-scale homology model for predicting amino acid interactions. Based on the experimental results and the model, we propose that a salt bridge(s) exists between positive residues in the M2(D) and conserved negative residues in the pore region to reduce electrostatic repulsion against cation permeation caused by the positive residue(s). This salt bridge may help stabilize the transporter configuration, and may also prevent the conformational change that occurs in channels.

  2. Available amino acid score for evaluating protein quality of foods.

    PubMed

    Sarwar, G

    1984-01-01

    Amino acid scores corrected for true digestibility of individual amino acids (as determined by rat balance method) were termed "available amino acid scores" in the present investigation. Available amino acid scores were calculated for 7 protein sources and their 10 supplementary or complementary mixtures which have been tested in collaborative amino acid and rat growth assays for evaluating protein quality. The available amino acid scores were as follows: casein + methionine (100); egg white (100); rapeseed protein concentrate, RPC (94); casein (93); beef (89); soya assay protein, SAP (62); pea flour (61); whole wheat flour, WW (38); SAP + methionine (88); pea flour + methionine (72); WW + lysine (67); WW + casein (84); WW + egg white (79); WW + RPC (65); WW + beef (77); WW + SAP (70); and WW + pea flour (75). These scores were similar to the collaborative relative NPR values; the differences were less than 10 units (2-9 units) in most cases. The positive correlation (r = 0.92) between available amino acid scores and relative net protein ratio (RNPR, a rat growth method) values was highly significant (P less than 0.01) and the origin of the regression line (y = 0.92x + 1.88) was not significantly different from zero. Amino acid bioavailability has previously been a problem, preventing widespread acceptance of amino acid score. Available amino acid score solves this problem.

  3. Amino Acid Properties Conserved in Molecular Evolution

    PubMed Central

    Rudnicki, Witold R.; Mroczek, Teresa; Cudek, Paweł

    2014-01-01

    That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts – one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications. PMID:24967708

  4. Amino acid contents of infant foods.

    PubMed

    Bosch, Lourdes; Alegría, Amparo; Farré, Rosaura

    2006-01-01

    The protein quality of three milk-cereal-based infant foods (paps) was evaluated by determining their amino acid contents and calculating the amino acid score. Proteins were subjected to acid hydrolysis, prior to which cysteine and methionine were oxidized with performic acid. Amino acids were determined by reverse-phase high-performance liquid chromatography with fluorescence detection with a prior derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate. Tryptophan was determined by reverse-phase high-performance liquid chromatography with ultraviolet detection after basic hydrolysis. Glutamic acid, proline and leucine were the most abundant amino acids, whereas tryptophan and cysteine had the lowest contents. Tryptophan was the limiting amino acid in the analyzed infant foods. A pap serving (250 ml) contributes significantly to fulfillment of the recommended dietary allowances of essential and semi-essential amino acids for infants (7-12 months old) and young children (1-3 years old).

  5. The amino acid sequence of wood duck lysozyme.

    PubMed

    Araki, T; Torikata, T

    1999-01-01

    The amino acid sequence of wood duck (Aix sponsa) lysozyme was analyzed. Carboxymethylated lysozyme was digested with trypsin and the resulting peptides were sequenced. The established amino acid sequence had the highest similarity to duck III lysozyme with four amino acid substitutions, and had eighteen amino acid substitutions from chicken lysozyme. The valine at position 75 was newly detected in chicken-type lysozymes. In the active site, Tyr34 and Glu57 were found at subsites F and D, respectively, when compared with chicken lysozyme.

  6. The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA

    PubMed Central

    Law, Michael J.; Linde, Michael E.; Chambers, Eric J.; Oubridge, Chris; Katsamba, Phinikoula S.; Nilsson, Lennart; Haworth, Ian S.; Laird-Offringa, Ite A.

    2006-01-01

    Previous kinetic investigations of the N-terminal RNA recognition motif (RRM) domain of spliceosomal protein U1A, interacting with its RNA target U1 hairpin II, provided experimental evidence for a ‘lure and lock’ model of binding in which electrostatic interactions first guide the RNA to the protein, and close range interactions then lock the two molecules together. To further investigate the ‘lure’ step, here we examined the electrostatic roles of two sets of positively charged amino acids in U1A that do not make hydrogen bonds to the RNA: Lys20, Lys22 and Lys23 close to the RNA-binding site, and Arg7, Lys60 and Arg70, located on ‘top’ of the RRM domain, away from the RNA. Surface plasmon resonance-based kinetic studies, supplemented with salt dependence experiments and molecular dynamics simulation, indicate that Lys20 predominantly plays a role in association, while nearby residues Lys22 and Lys23 appear to be at least as important for complex stability. In contrast, kinetic analyses of residues away from the RNA indicate that they have a minimal effect on association and stability. Thus, well-positioned positively charged residues can be important for both initial complex formation and complex maintenance, illustrating the multiple roles of electrostatic interactions in protein–RNA complexes. PMID:16407334

  7. The DNA invertase Gin of phage Mu: formation of a covalent complex with DNA via a phosphoserine at amino acid position 9.

    PubMed Central

    Klippel, A; Mertens, G; Patschinsky, T; Kahmann, R

    1988-01-01

    The DNA invertase Gin encoded by bacteriophage Mu catalyses efficient site-specific recombination between inverted repeat sequences (IR) in vivo and in vitro in the presence of the host factor FIS and the recombinational enhancer. We demonstrate that Gin alone is able to introduce single strand breaks into duplex DNA fragments which contain the IR sequence. Strand cleavage is site-specific and can occur on either strand within the IR. Cleaved molecules contain Gin covalently attached to DNA. The covalent complex is formed through linkage of Gin to the 5' DNA phosphate at the site of the break via a phosphoserine. Extensive site-directed mutational analysis showed that all mutants altered at serine position 9 were completely recombination deficient in vivo and in vitro. The mutant proteins bind to DNA but lack topoisomerase activity and are unable to introduce nicks. This holds true even for a conservative amino acid substitution at position 9. We conclude that serine at position 9 is part of the catalytic domain of Gin. The intriguing finding that the DNA invertase Gin has the same catalytic center as the DNA resolvases that promote deletions without recombinational enhancer and host factor FIS is discussed. Images PMID:3042382

  8. Positive selection of Kranz and non-Kranz C4 phosphoenolpyruvate carboxylase amino acids in Suaedoideae (Chenopodiaceae).

    PubMed

    Rosnow, Josh J; Edwards, Gerald E; Roalson, Eric H

    2014-07-01

    In subfamily Suaedoideae, four independent gains of C4 photosynthesis are proposed, which includes two parallel origins of Kranz anatomy (sections Salsina and Schoberia) and two independent origins of single-cell C4 anatomy (Bienertia and Suaeda aralocaspica). Additional phylogenetic support for this hypothesis was generated from sequence data of the C-terminal portion of the phosphoenolpyruvate carboxylase (PEPC) gene used in C4 photosynthesis (ppc-1) in combination with previous sequence data. ppc-1 sequence was generated for 20 species in Suaedoideae and two outgroup Salsola species that included all types of C4 anatomies as well as two types of C3 anatomies. A branch-site test for positively selected codons was performed using the software package PAML. From labelling of the four branches where C4 is hypothesized to have developed (foreground branches), residue 733 (maize numbering) was identified to be under positive selection with a posterior probability >0.99 and residue 868 at the >0.95 interval using Bayes empirical Bayes (BEB). When labelling all the branches within C4 clades, the branch-site test identified 13 codons to be under selection with a posterior probability >0.95 by BEB; this is discussed considering current information on functional residues. The signature C4 substitution of an alanine for a serine at position 780 in the C-terminal end (which is considered a major determinant of affinity for PEP) was only found in four of the C4 species sampled, while eight of the C4 species and all the C3 species have an alanine residue; indicating that this substitution is not a requirement for C4 function.

  9. Positive selection of Kranz and non-Kranz C4 phosphoenolpyruvate carboxylase amino acids in Suaedoideae (Chenopodiaceae)

    PubMed Central

    Rosnow, Josh J.; Edwards, Gerald E.; Roalson, Eric H.

    2014-01-01

    In subfamily Suaedoideae, four independent gains of C4 photosynthesis are proposed, which includes two parallel origins of Kranz anatomy (sections Salsina and Schoberia) and two independent origins of single-cell C4 anatomy (Bienertia and Suaeda aralocaspica). Additional phylogenetic support for this hypothesis was generated from sequence data of the C-terminal portion of the phosphoenolpyruvate carboxylase (PEPC) gene used in C4 photosynthesis (ppc-1) in combination with previous sequence data. ppc-1 sequence was generated for 20 species in Suaedoideae and two outgroup Salsola species that included all types of C4 anatomies as well as two types of C3 anatomies. A branch-site test for positively selected codons was performed using the software package PAML. From labelling of the four branches where C4 is hypothesized to have developed (foreground branches), residue 733 (maize numbering) was identified to be under positive selection with a posterior probability >0.99 and residue 868 at the >0.95 interval using Bayes empirical Bayes (BEB). When labelling all the branches within C4 clades, the branch-site test identified 13 codons to be under selection with a posterior probability >0.95 by BEB; this is discussed considering current information on functional residues. The signature C4 substitution of an alanine for a serine at position 780 in the C-terminal end (which is considered a major determinant of affinity for PEP) was only found in four of the C4 species sampled, while eight of the C4 species and all the C3 species have an alanine residue; indicating that this substitution is not a requirement for C4 function. PMID:24600021

  10. Sugar amino acids in designing new molecules.

    PubMed

    Chakraborty, Tushar Kanti; Srinivasu, Pothukanuri; Tapadar, Subhasish; Mohan, Bajjuri Krishna

    2005-03-01

    Emulating the basic principles followed by nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks and using them to create 'nature-like' and yet unnatural organic molecules. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl termini provide an excellent opportunity to organic chemists to create structural diversities akin to Nature's molecular arsenal. This article describes some of our works on various sugar amino acids and many other related building blocks, like furan amino acids, pyrrole amino acids etc. used in wide-ranging peptidomimetic studies.

  11. Branched-Chain Amino Acids.

    PubMed

    Yamamoto, Keisuke; Tsuchisaka, Atsunari; Yukawa, Hideaki

    Branched-chain amino acids (BCAAs), viz., L-isoleucine, L-leucine, and L-valine, are essential amino acids that cannot be synthesized in higher organisms and are important nutrition for humans as well as livestock. They are also valued as synthetic intermediates for pharmaceuticals. Therefore, the demand for BCAAs in the feed and pharmaceutical industries is increasing continuously. Traditional industrial fermentative production of BCAAs was performed using microorganisms isolated by random mutagenesis. A collection of these classical strains was also scientifically useful to clarify the details of the BCAA biosynthetic pathways, which are tightly regulated by feedback inhibition and transcriptional attenuation. Based on this understanding of the metabolism of BCAAs, it is now possible for us to pursue strains with higher BCAA productivity using rational design and advanced molecular biology techniques. Additionally, systems biology approaches using augmented omics information help us to optimize carbon flux toward BCAA production. Here, we describe the biosynthetic pathways of BCAAs and their regulation and then overview the microorganisms developed for BCAA production. Other chemicals, including isobutanol, i.e., a second-generation biofuel, can be synthesized by branching the BCAA biosynthetic pathways, which are also outlined.

  12. Improving Escherichia coli FucO for Furfural Tolerance by Saturation Mutagenesis of Individual Amino Acid Positions

    PubMed Central

    Zheng, Huabao; Wang, Xuan; Yomano, Lorraine P.; Geddes, Ryan D.; Shanmugam, Keelnatham T.

    2013-01-01

    Furfural is an inhibitory side product formed during the depolymerization of hemicellulose with mineral acids. In Escherichia coli, furfural tolerance can be increased by expressing the native fucO gene (encoding lactaldehyde oxidoreductase). This enzyme also catalyzes the NADH-dependent reduction of furfural to the less toxic alcohol. Saturation mutagenesis was combined with growth-based selection to isolate a mutated form of fucO that confers increased furfural tolerance. The mutation responsible, L7F, is located within the interfacial region of FucO homodimers, replacing the most abundant codon for leucine with the most abundant codon for phenylalanine. Plasmid expression of the mutant gene increased FucO activity by more than 10-fold compared to the wild-type fucO gene and doubled the rate of furfural metabolism during fermentation. No inclusion bodies were evident with either the native or the mutated gene. mRNA abundance for the wild-type and mutant fucO genes differed by less than 2-fold. The Km (furfural) for the mutant enzyme was 3-fold lower than that for the native enzyme, increasing efficiency at low substrate concentrations. The L7F mutation is located near the FucO N terminus, within the ribosomal binding region associated with translational initiation. Free-energy calculations for mRNA folding in this region (nucleotides −7 to +37) were weak for the native gene (−4.1 kcal mol−1) but weaker still for the fucO mutant (−1.0 to −0.1 kcal mol−1). The beneficial L7F mutation in FucO is proposed to increase furfural tolerance by improving gene expression and increasing enzyme effectiveness at low substrate levels. PMID:23475621

  13. Improving Escherichia coli FucO for furfural tolerance by saturation mutagenesis of individual amino acid positions.

    PubMed

    Zheng, Huabao; Wang, Xuan; Yomano, Lorraine P; Geddes, Ryan D; Shanmugam, Keelnatham T; Ingram, Lonnie O

    2013-05-01

    Furfural is an inhibitory side product formed during the depolymerization of hemicellulose with mineral acids. In Escherichia coli, furfural tolerance can be increased by expressing the native fucO gene (encoding lactaldehyde oxidoreductase). This enzyme also catalyzes the NADH-dependent reduction of furfural to the less toxic alcohol. Saturation mutagenesis was combined with growth-based selection to isolate a mutated form of fucO that confers increased furfural tolerance. The mutation responsible, L7F, is located within the interfacial region of FucO homodimers, replacing the most abundant codon for leucine with the most abundant codon for phenylalanine. Plasmid expression of the mutant gene increased FucO activity by more than 10-fold compared to the wild-type fucO gene and doubled the rate of furfural metabolism during fermentation. No inclusion bodies were evident with either the native or the mutated gene. mRNA abundance for the wild-type and mutant fucO genes differed by less than 2-fold. The Km (furfural) for the mutant enzyme was 3-fold lower than that for the native enzyme, increasing efficiency at low substrate concentrations. The L7F mutation is located near the FucO N terminus, within the ribosomal binding region associated with translational initiation. Free-energy calculations for mRNA folding in this region (nucleotides -7 to +37) were weak for the native gene (-4.1 kcal mol(-1)) but weaker still for the fucO mutant (-1.0 to -0.1 kcal mol(-1)). The beneficial L7F mutation in FucO is proposed to increase furfural tolerance by improving gene expression and increasing enzyme effectiveness at low substrate levels.

  14. Predicting protein submitochondrial locations by incorporating the positional-specific physicochemical properties into Chou's general pseudo-amino acid compositions.

    PubMed

    Jiao, Ya-Sen; Du, Pu-Feng

    2017-03-07

    Predicting protein submitochondrial locations has been studied for about ten years. A dozen of methods were developed in this regard. Although a mitochondrion has four submitochondrial compartments, all existing studies considered only three of them. The mitochondrial intermembrane space proteins were always excluded in these studies. However, there are over 50 mitochondrial intermembrane space proteins in the recent release of UniProt database. We think it is time to incorporate these proteins in predicting protein submitochondrial locations. We proposed the functional domain enrichment score, which can be used as an enhancement to our positional-specific physicochemical properties method. We constructed a high-quality working dataset from the UniProt database. This dataset contains proteins from all four submitochondrial locations. Proteins with multiple submitochondrial locations are also included. Our method achieved over 70% prediction accuracy for proteins with single location on this dataset. On the M3-317 benchmarking dataset, our method achieved comparable prediction performance to other state-of-the-art methods. Our results indicate that the intermembrane space proteins can be incorporated in predicting protein submitochondrial locations. By evaluating our method with the proteins that have multiple submitochondrial locations, we conclude that our method is capable of predicting multiple submitochondrial locations. This is the first report of ab initio methods that can identify intermembrane space proteins. This is also the first attempt to incorporate proteins with multiple submitochondrial locations. The benchmarking dataset can be obtained by emails to the corresponding author. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Amino and fatty acids in carbonaceous meteorites

    NASA Technical Reports Server (NTRS)

    Kvenvolden, K. A.

    1974-01-01

    Analyses of two carbonaceous meteorites have provided much of the latest evidence which seems to support Oparin's theory on the origin of life. The meteorites involved are the Murray meteorite, which fell in 1950, and the Murchison meteorite, which fell in 1969. The amino acids in the two meteorites are similar in composition. Eight of the twenty amino acids found belong to amino acids present in proteins. A number of monocarboxylic and dicarboxylic fatty acids were also found in the meteorites.

  16. Amino and fatty acids in carbonaceous meteorites

    NASA Technical Reports Server (NTRS)

    Kvenvolden, K. A.

    1974-01-01

    Analyses of two carbonaceous meteorites have provided much of the latest evidence which seems to support Oparin's theory on the origin of life. The meteorites involved are the Murray meteorite, which fell in 1950, and the Murchison meteorite, which fell in 1969. The amino acids in the two meteorites are similar in composition. Eight of the twenty amino acids found belong to amino acids present in proteins. A number of monocarboxylic and dicarboxylic fatty acids were also found in the meteorites.

  17. THE AMINO ACID COMPOSITION OF CRYSTALLINE PEPSIN

    PubMed Central

    Blumenfeld, Olga O.; Perlmann, Gertrude E.

    1959-01-01

    The amino acid composition of twice recrystallized pepsin (Worthington Biochemical Corporation) has been determined chromatographically on columns of Amberlite IR 120 resin. The results of the analyses obtained on four different preparations indicate a close agreement in their amino acid composition. Pepsin is unique in that it has a great predominance of acidic amino acids over basic ones. Moreover, all the preparations contain a small and constant amount of hydroxyproline, corresponding to about 0.1 residue per molecule. PMID:13620885

  18. Oxidation of methionine 216 in sheep and elk prion protein is highly dependent upon the amino acid at position 218 but is not important for prion propagation.

    PubMed

    Silva, Christopher J; Dynin, Irina; Erickson, Melissa L; Requena, Jesús R; Balachandran, Aru; Hui, Colleen; Onisko, Bruce C; Carter, John Mark

    2013-03-26

    We employed a sensitive mass spectrometry-based method to deconstruct, confirm, and quantitate the prions present in elk naturally infected with chronic wasting disease and sheep naturally infected with scrapie. We used this approach to study the oxidation of a methionine at position 216 (Met216), because this oxidation (MetSO216) has been implicated in prion formation. Three polymorphisms (Ile218, Val218, and Thr218) of sheep recombinant prion protein were prepared. Our analysis showed the novel result that the proportion of MetSO216 was highly dependent upon the amino acid residue at position 218 (I > V > T), indicating that Ile218 in sheep and elk prion protein (PrP) renders the Met216 intrinsically more susceptible to oxidation than the Val218 or Thr218 analogue. We were able to quantitate the prions in the attomole range. The presence of prions was verified by the detection of two confirmatory peptides: GENFTETDIK (sheep and elk) and ESQAYYQR (sheep) or ESEAYYQR (elk). This approach required much smaller amounts of tissue (600 μg) than traditional methods of detection (enzyme-linked immunosorbent assay, Western blot, and immunohistochemical analysis) (60 mg). In sheep and elk, a normal cellular prion protein containing MetSO216 is not actively recruited and converted to prions, although we observed that this Met216 is intrinsically more susceptible to oxidation.

  19. Positively charged amino acids at the SNAP-25 C terminus determine fusion rates, fusion pore properties, and energetics of tight SNARE complex zippering.

    PubMed

    Fang, Qinghua; Zhao, Ying; Herbst, Adam Drew; Kim, Brian N; Lindau, Manfred

    2015-02-18

    SNAP-25 is a Q-SNARE protein mediating exocytosis of neurosecretory vesicles including chromaffin granules. Previous results with a SNAP-25 construct lacking the nine C terminal residues (SNAP-25Δ9) showed changed fusion pore properties (Fang et al., 2008), suggesting a model for fusion pore mechanics that couple C terminal zipping of the SNARE complex to the opening of the fusion pore. The deleted fragment contains the positively charged residues R198 and K201, adjacent to layers 7 and 8 of the SNARE complex. To determine how fusion pore conductance and dynamics depend on these residues, single exocytotic events in bovine chromaffin cells expressing R198Q, R198E, K201Q, or K201E mutants were investigated by carbon fiber amperometry and cell-attached patch capacitance measurements. Coarse grain molecular dynamics simulations revealed spontaneous transitions between a loose and tightly zippered state at the SNARE complex C terminus. The SNAP-25 K201Q mutant showed no changes compared with SNAP-25 wild-type. However, K201E, R198Q, and R198E displayed reduced release frequencies, slower release kinetics, and prolonged fusion pore duration that were correlated with reduced probability to engage in the tightly zippered state. The results show that the positively charged amino acids at the SNAP-25 C terminus promote tight SNARE complex zippering and are required for high release frequency and rapid release in individual fusion events.

  20. Amino-acid contamination of aqueous hydrochloric acid.

    NASA Technical Reports Server (NTRS)

    Wolman, Y.; Miller, S. L.

    1971-01-01

    Considerable amino-acid contamination in commercially available analytical grade hydrochloric acid (37% HCl) was found. One bottle contained 8,300 nmol of amino-acids per liter. A bottle from another supplier contained 6,700 nmol per liter. The contaminants were mostly protein amino-acids and several unknowns. Data on the volatility of the amino-acids during HCl distillation were also obtained.

  1. Amino-acid contamination of aqueous hydrochloric acid.

    NASA Technical Reports Server (NTRS)

    Wolman, Y.; Miller, S. L.

    1971-01-01

    Considerable amino-acid contamination in commercially available analytical grade hydrochloric acid (37% HCl) was found. One bottle contained 8,300 nmol of amino-acids per liter. A bottle from another supplier contained 6,700 nmol per liter. The contaminants were mostly protein amino-acids and several unknowns. Data on the volatility of the amino-acids during HCl distillation were also obtained.

  2. Positive net movements of amino acids in the hindlimb after overnight food deprivation contribute to sustaining the elevated anabolism of neonatal pigs

    USDA-ARS?s Scientific Manuscript database

    During the neonatal period, high protein breakdown rate is a metabolic process inherent to elevated rates of protein accretion in skeletal muscle. To determine the relationship between hindlimb net movements of essential and nonessential amino acids in the regulation of hindlimb protein breakdown du...

  3. Amino Acid Contents of Meteorite Mineral Separates

    NASA Technical Reports Server (NTRS)

    Berger, E. L.; Burton, A. S; Locke, D.

    2017-01-01

    Indigenous amino acids have been found indigenous all 8 carbonaceous chondrite groups. However, the abundances, structural, enantiomeric and isotopic compositions of amino acids differ significantly among meteorites of different groups and petrologic types. This suggests that parent-body conditions (thermal or aqueous alteration), mineralogy, and the preservation of amino acids are linked. Previously, elucidating specific relationships between amino acids and mineralogy was not possible because the samples analyzed for amino acids were much larger than the scale at which petrologic heterogeneity is observed (sub mm-scale differences corresponding to sub-mg samples). Recent advances in amino acid measurements and application of techniques such as high resolution X-ray diffraction (HR-XRD) and scanning electron microscopy (SEM) with energy dispersive spectroscopy (EDS) for mineralogical characterizations allow us to perform coordinated analyses on the scale at which mineral heterogeneity is observed.

  4. Amino Acid Auxotrophy as Immunological Control Nodes

    PubMed Central

    Murray, Peter J.

    2016-01-01

    Summary Cells of the immune system are auxotrophs for most amino acids, including non-essential ones. Arginine and tryptophan are used within the regulatory immune networks to control proliferation and function through pathways that deplete the amino acid, or create regulatory molecules such as nitric oxide or kynurenines. Strategies to harness amino acid auxotrophy to block cancerous lymphocyte growth have been attempted for decades, with limited success. How immune cells integrate information about external essential amino acids supplies and transfer signals to growth and activation pathways remains unclear, but has potential for pathway discovery. Emerging insights may lead to strategies to both degrade amino acids and to block the immunoregulatory pathways controlled by amino acids. PMID:26784254

  5. Indigenous amino acids in primitive CR meteorites

    NASA Astrophysics Data System (ADS)

    Martins, Z.; Alexander, C. M. O. D.; Orzechowska, G. E.; Fogel, M. L.; Ehrenfreund, P.

    CR chondrites are among the most primitive meteorites. In this paper, we report the first measurements of amino acids in Antarctic CR meteorites. Three CRs, Elephant Moraine (EET) 92042, Graves Nunataks (GRA) 95229, and Grosvenor Mountains (GRO) 95577, were analyzed for their amino acid content using high-performance liquid chromatography with UV fluorescence detection (HPLC-FD) and gas chromatography-mass spectrometry (GC-MS). Our data show that EET 92042 and GRA 95229 are the most amino acid-rich chondrites ever analyzed, with total amino acid concentrations ranging from 180 ppm to 249 ppm. The most abundant amino acids present in the EET 92042 and GRA 95229 meteorites are the α-amino acids glycine, isovaline, α-aminoisobutyric acid (α-AIB), and alanine, with δ13C values ranging from +31.6‰ to +50.5‰. The carbon isotope results together with racemic enantiomeric ratios determined for most amino acids strongly indicate an extraterrestrial origin for these compounds. Compared to Elephant Moraine (EET) 92042 and GRA 95229, the more aqueously altered GRO 95577 is depleted in amino acids. In both CRs and CMs, the absolute amino acid abundances appear to be related to the degree of aqueous alteration in their parent bodies. In addition, the relative abundances of α-AIB and β-alanine in the Antarctic CRs also appear to depend on the degree of aqueous alteration.

  6. Study on the thermal reactions of [60]fullerene with amino acids and amino acid esters.

    PubMed

    Zhu, San-E; Cheng, Xin; Li, Yu-Jin; Mai, Cheng-Kang; Huang, Yong-Shun; Wang, Guan-Wu; Peng, Ru-Fang; Jin, Bo; Chu, Shi-Jin

    2012-11-21

    Thermal reactions of [60]fullerene with a series of amino acids and amino acid esters under aerobic and dark conditions have been investigated. Fulleropyrrolidines can be obtained from these reactions although an aldehyde is not added purposely. Possible reaction mechanisms involving uncommon C-N bond cleavages have been proposed to generate aldehydes, which then react with amino acids and amino acid esters to provide azomethine ylides, followed by 1,3-dipolar cycloaddition to [60]fullerene affording fulleropyrrolidines. Control experiments support our proposed mechanisms, and elucidate the innate nature of C-N bond cleavages of amino acids and amino acid esters.

  7. Amino acids in the Tagish Lake Meteorite

    NASA Technical Reports Server (NTRS)

    Kminek, G.; Botta, O.; Glavin, D. P.; Bada, J. L.

    2002-01-01

    High-performance liquid chromatography (HPLC) based amino acid analysis of a Tagish Lake meteorite sample recovered 3 months after the meteorite fell to Earth have revealed that the amino acid composition of Tagish Lake is strikingly different from that of the CM and CI carbonaceous chondrites. We found that the Tagish Lake meteorite contains only trace levels of amino acids (total abundance = 880 ppb), which is much lower than the total abundance of amino acids in the CI Orgueil (4100 ppb) and the CM Murchison (16 900 ppb). Because most of the same amino acids found in the Tagish Lake meteorite are also present in the Tagish Lake ice melt water, we conclude that the amino acids detected in the meteorite are terrestrial contamination. We found that the exposure of a sample of Murchison to cold water lead to a substantial reduction over a period of several weeks in the amount of amino acids that are not strongly bound to the meteorite matrix. However, strongly bound amino acids that are extracted by direct HCl hydrolysis are not affected by the leaching process. Thus even if there had been leaching of amino acids from our Tagish Lake meteorite sample during its 3 month residence in Tagish Lake ice and melt water, a Murchison type abundance of endogenous amino acids in the meteorite would have still been readily detectable. The low amino acid content of Tagish Lake indicates that this meteorite originated fiom a different type of parent body than the CM and CI chondrites. The parent body was apparently devoid of the reagents such as aldehyldes/ketones, HCN and ammonia needed for the effective abiotic synthesis of amino acids. Based on reflectance spectral measurements, Tagish Lake has been associated with P- or D-type asteroids. If the Tagish Lake meteorite was indeed derived fiom these types of parent bodies, our understanding of these primitive asteroids needs to be reevaluated with respect to their potential inventory of biologically important organic compounds.

  8. Amino acids in the Tagish Lake Meteorite

    NASA Technical Reports Server (NTRS)

    Kminek, G.; Botta, O.; Glavin, D. P.; Bada, J. L.

    2002-01-01

    High-performance liquid chromatography (HPLC) based amino acid analysis of a Tagish Lake meteorite sample recovered 3 months after the meteorite fell to Earth have revealed that the amino acid composition of Tagish Lake is strikingly different from that of the CM and CI carbonaceous chondrites. We found that the Tagish Lake meteorite contains only trace levels of amino acids (total abundance = 880 ppb), which is much lower than the total abundance of amino acids in the CI Orgueil (4100 ppb) and the CM Murchison (16 900 ppb). Because most of the same amino acids found in the Tagish Lake meteorite are also present in the Tagish Lake ice melt water, we conclude that the amino acids detected in the meteorite are terrestrial contamination. We found that the exposure of a sample of Murchison to cold water lead to a substantial reduction over a period of several weeks in the amount of amino acids that are not strongly bound to the meteorite matrix. However, strongly bound amino acids that are extracted by direct HCl hydrolysis are not affected by the leaching process. Thus even if there had been leaching of amino acids from our Tagish Lake meteorite sample during its 3 month residence in Tagish Lake ice and melt water, a Murchison type abundance of endogenous amino acids in the meteorite would have still been readily detectable. The low amino acid content of Tagish Lake indicates that this meteorite originated fiom a different type of parent body than the CM and CI chondrites. The parent body was apparently devoid of the reagents such as aldehyldes/ketones, HCN and ammonia needed for the effective abiotic synthesis of amino acids. Based on reflectance spectral measurements, Tagish Lake has been associated with P- or D-type asteroids. If the Tagish Lake meteorite was indeed derived fiom these types of parent bodies, our understanding of these primitive asteroids needs to be reevaluated with respect to their potential inventory of biologically important organic compounds.

  9. Amino acids precursors in lunar finds

    NASA Technical Reports Server (NTRS)

    Fox, S. W.; Harada, K.; Hare, P. E.; Hinsch, G.; Mueller, G.

    1975-01-01

    The consistent pattern is discussed of amino acids found in lunar dust from Apollo missions. The evidence indicates that compounds yielding amino acids were implanted into the surface of the moon by the solar wind, and the kind and amounts of amino acids found on the moon are closely similar to those found in meteorites. It is concluded that there is a common cosmochemical pattern for the moom and meteorites, and this offers evidence of a common course of cosmochemical reactions for carbon.

  10. α-Amino Acid-Isosteric α-Amino Tetrazoles

    PubMed Central

    Zhao, Ting; Kurpiewska, Katarzyna; Kalinowska-Tłuścik, Justyna; Herdtweck, Eberhardt

    2016-01-01

    The synthesis of all 20 common natural proteinogenic and 4 otherα-amino acid-isosteric α-amino tetrazoles has been accomplished, whereby the carboxyl group is replaced by the isosteric 5-tetrazolyl group. The short process involves the use of the key Ugi tetrazole reaction followed by deprotection chemistries. The tetrazole group is bioisosteric to the carboxylic acid and is widely used in medicinal chemistry and drug design. Surprisingly, several of the common α-amino acid-isosteric α-amino tetrazoles are unknown up to now. Therefore a rapid synthetic access to this compound class and non-natural derivatives is of high interest to advance the field. PMID:26817531

  11. Amino acid composition of some Mexican foods.

    PubMed

    Morales de León, Josefina; Camacho, M Elena; Bourges, Héctor

    2005-06-01

    Knowledge of the amino acid composition of foods is essential to calculate their chemical score, which is used to predict protein quality of foods and diets. Though amino acid composition of many foods is reasonably well established, better knowledge is needed on native foods consumed in different regions and countries. This paper presents the amino acid composition of different presentations of raw and processed foods produced and consumed in Mexico. The amino acid composition was determined using Beckman amino acid analyzers (models 116 and 6300). Tryptophan was determined using the Spies and Chambers method. Of the different foods analyzed, some comments are made on native or basic foods in Mexico: Spirulin, where lysine is the limiting amino acid, with a chemical score of 67%, is a good source of tryptophan (1.16g/16 gN); amaranth contains high levels of sulphur amino acids (4.09 to 5.34 g/16gN), with a protein content of 15 g/100g; and pulque, a Pre-Hispanic beverage that contains high levels of tryptophan (2.58 g/16 gN) and sulphur amino acids (2.72 g/16 gN). Finally, insects are good sources of sulphur amino acids and lysine.

  12. Relationship between amino acid usage and amino acid evolution in primates.

    PubMed

    Liu, Haoxuan; Xie, Zhengqing; Tan, Shengjun; Zhang, Xiaohui; Yang, Sihai

    2015-02-25

    Amino acid usage varies from species to species. A previous study has found a universal trend in amino acid gain and loss in many taxa and a one-way model of amino acid evolution in which the number of new amino acids increases as the number of old amino acids decreases was proposed. Later studies showed that this pattern of amino acid gain and loss is likely to be compatible with the neutral theory. The present work aimed to further study this problem by investigating the evolutionary patterns of amino acids in 8 primates (the nucleotide and protein alignments are available online http://gattaca.nju.edu.cn/pub_data.html). First, the number of amino acids gained and lost was calculated and the evolution trend of each amino acid was inferred. These values were found to be closely related to the usage of each amino acid. Then we analyzed the mutational trend of amino acid substitution in human using SNPs, this trend is highly correlated with fixation trend only with greater variance. Finally, the trends in the evolution of 20 amino acids were evaluated in human on different time scales, and the increasing rate of 5 significantly increasing amino acids was found to decrease as a function of time elapsed since divergence, and the dS/dN ratio also found to increase as a function of time elapsed since divergence. These results suggested that the observed amino acid substitution pattern is influenced by mutation and purifying selection. In conclusion, the present study shows that usage of amino acids is an important factor capable of influencing the observed pattern of amino acid evolution, and also presented evidences suggesting that the observed universal trend of amino acid gain and loss is compatible with neutral evolution. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Effect of domoic acid on brain amino acid levels.

    PubMed

    Durán, R; Arufe, M C; Arias, B; Alfonso, M

    1995-03-01

    The administration of Domoic Acid (Dom) in a 0.2 mg/kg i.p. dose induces changes in the levels of amino acids of neurochemical interest (Asp, Glu, Gly, Tau, Ala, GABA) in different rat brain regions (hypothalamus, hippocampus, amygdala, striatum, cortex and midbrain). The most affected amino acid is the GABA, the main inhibitory amino acid neurotransmitter, whereas glutamate, the main excitatory amino acid, is not affected. The rat brain regions that seem to be the main target of the Dom action belong to the limbic system (hippocampus, amygdala). The possible implication of the amino acids in the actions of Dom is also discussed.

  14. Transposition of three amino acids transforms the human metabotropic glutamate receptor (mGluR)-3-positive allosteric modulation site to mGluR2, and additional characterization of the mGluR2-positive allosteric modulation site.

    PubMed

    Rowe, Blake A; Schaffhauser, Hervé; Morales, Sylvia; Lubbers, Laura S; Bonnefous, Celine; Kamenecka, Theodore M; McQuiston, Jeffrey; Daggett, Lorrie P

    2008-07-01

    Glutamate is a major neurotransmitter in the central nervous system, and abnormal glutamate neurotransmission has been implicated in many neurological disorders, including schizophrenia, Alzheimer's disease, Parkinson's disease, addiction, anxiety, depression, epilepsy, and pain. Metabotropic glutamate receptors (mGluRs) activate intracellular signaling cascades in a G protein-dependent manner, which offer the opportunity for developing drugs that regulate glutamate neurotransmission in a functionally selective manner. In the present study, we further characterize the human mGluR2 (hmGluR2) potentiator binding site by showing that the substitution of the three amino acids found to be required for hmGluR2 potentiation, specifically Ser(688), Gly(689), and Asn(735), with the homologous hmGluR3 amino acids, inactivates the positive allosteric modulator activity of several structurally unique mGluR2 potentiators. Based on the characterization of the hmGluR2 potentiator binding site, we developed a novel scintillation proximity assay that was able to discriminate between compounds that were hmGluR2-specific potentiators, and those that were active on both hmGluR2 and hmGluR3. In addition, we substituted Ser(688), Gly(689), and Asn(735) into hmGluR3 and created an active hmGluR2 allosteric modulation site on the hmGluR3 receptor.

  15. Suppressive effect of oral administration of branched-chain amino acid granules on oxidative stress and inflammation in HCV-positive patients with liver cirrhosis.

    PubMed

    Ohno, Tomoyoshi; Tanaka, Yasuhito; Sugauchi, Fuminaka; Orito, Etsuro; Hasegawa, Izumi; Nukaya, Haruhiko; Kato, Atsunaga; Matunaga, Seijiro; Endo, Masayuki; Tanaka, Yoshito; Sakakibara, Kenji; Mizokami, Masashi

    2008-07-01

    In chronic hepatitis C virus (HCV) infection, it is thought that both chronic persistent inflammation and oxidative stress contribute to the development of hepatocellular carcinoma (HCC), and it has been reported that long-term oral supplementation with branched-chain amino acid (BCAA) granules could inhibit liver carcinogenesis. However, the extent of the involvement of these factors remains obscure. To clarify the involvement of inflammation and oxidative stress in the inhibition of liver carcinogenesis, we evaluated the effect of oral administration of BCAA granules on oxidative stress and inflammation in HCV-positive patients with liver cirrhosis. Twenty-seven patients were enrolled in the study: 18 of the patients were treated with BCAA granules (administered group) and nine were observed without BCAA granules (non-administered group). In the non-administered group, the production of oxidative stress, as indicated by urine 8-hydroxydeoxyguanosine (8-OHdG) and 15-F2t-Isoprostane (8-IsoPs), significantly increased with time, while in the administered group the levels of ferritin and 8-OHdG decreased significantly. Comparison of the two groups demonstrated that highly sensitive CRP, ferritin, 8-OHdG and 8-IsoPs were significantly reduced by taking BCAA granules. The time-course analysis showed that ferritin and highly sensitive CRP seemed to decrease first, followed by a decrease of 8-OHdG and 8-IsoPs. These findings indicated that the administration of BCAA granules influenced microinflammation and the metabolism of iron in HCV-positive patients with liver cirrhosis, and subsequently seemed to reduce the production of oxidative stress, possibly leading to a decrease in the occurrence of HCC.

  16. Research for amino acids in lunar samples.

    NASA Technical Reports Server (NTRS)

    Gehrke, C. W.; Zumwalt, R. W.; Kuo, K.; Rash, J. J.; Aue , W. A.; Stalling, D. L.; Kvenvolden, K. A.; Ponnamperuma, C.

    1972-01-01

    The study was primarily directed toward the examination of Apollo 14 lunar fines for indigenous amino acids or materials which could be converted to amino acids on hydrolysis with 6 N hydrochloric acid. Initial experiments were conducted to confirm the integrity of the derivatization reactions and reagents, and to optimize the gas-liquid chromatographic (GLC) instrumental and chromatographic system for the separation and flame ionization detection of the amino acid derivatives. In studies on the recovery of amino acids added to lunar fines, low recoveries were obtained when 10 ng of each amino acid were added to 50 mg of virgin fines, but the subsequent addition of 50 ng of each to the previously extracted sample resulted in much higher recoveries.

  17. Research for amino acids in lunar samples.

    NASA Technical Reports Server (NTRS)

    Gehrke, C. W.; Zumwalt, R. W.; Kuo, K.; Rash, J. J.; Aue , W. A.; Stalling, D. L.; Kvenvolden, K. A.; Ponnamperuma, C.

    1972-01-01

    The study was primarily directed toward the examination of Apollo 14 lunar fines for indigenous amino acids or materials which could be converted to amino acids on hydrolysis with 6 N hydrochloric acid. Initial experiments were conducted to confirm the integrity of the derivatization reactions and reagents, and to optimize the gas-liquid chromatographic (GLC) instrumental and chromatographic system for the separation and flame ionization detection of the amino acid derivatives. In studies on the recovery of amino acids added to lunar fines, low recoveries were obtained when 10 ng of each amino acid were added to 50 mg of virgin fines, but the subsequent addition of 50 ng of each to the previously extracted sample resulted in much higher recoveries.

  18. Adsorption of amino acids by fullerenes and fullerene nanowhiskers

    NASA Astrophysics Data System (ADS)

    Hashizume, Hideo; Hirata, Chika; Fujii, Kazuko; Miyazawa, Kun'ichi

    2015-12-01

    We have investigated the adsorption of some amino acids and an oligopeptide by fullerene (C60) and fullerene nanowhiskers (FNWs). C60 and FNWs hardly adsorbed amino acids. Most of the amino acids used have a hydrophobic side chain. Ala and Val, with an alkyl chain, were not adsorbed by the C60 or FNWs. Trp, Phe and Pro, with a cyclic structure, were not adsorbed by them either. The aromatic group of C60 did not interact with the side chain. The carboxyl or amino group, with the frame structure of an amino acid, has a positive or negative charge in solution. It is likely that the C60 and FNWs would not prefer the charged carboxyl or amino group. Tri-Ala was adsorbed slightly by the C60 and FNWs. The carboxyl or amino group is not close to the center of the methyl group of Tri-Ala. One of the methyl groups in Tri-Ala would interact with the aromatic structure of the C60 and FNWs. We compared our results with the theoretical interaction of 20 bio-amino acids with C60. The theoretical simulations showed the bonding distance between C60 and an amino acid and the dissociation energy. The dissociation energy was shown to increase in the order, Val < Phe < Pro < Asp < Ala < Trp < Tyr < Arg < Leu. However, the simulation was not consistent with our experimental results. The adsorption of albumin (a protein) by C60 showed the effect on the side chains of Try and Trp. The structure of albumin was changed a little by C60. In our study Try and Tyr were hardly adsorbed by C60 and FNWs. These amino acids did not show a different adsorption behavior compared with other amino acids. The adsorptive behavior of mono-amino acids might be different from that of polypeptides.

  19. Adsorption of amino acids by fullerenes and fullerene nanowhiskers.

    PubMed

    Hashizume, Hideo; Hirata, Chika; Fujii, Kazuko; Miyazawa, Kun'ichi

    2015-12-01

    We have investigated the adsorption of some amino acids and an oligopeptide by fullerene (C60) and fullerene nanowhiskers (FNWs). C60 and FNWs hardly adsorbed amino acids. Most of the amino acids used have a hydrophobic side chain. Ala and Val, with an alkyl chain, were not adsorbed by the C60 or FNWs. Trp, Phe and Pro, with a cyclic structure, were not adsorbed by them either. The aromatic group of C60 did not interact with the side chain. The carboxyl or amino group, with the frame structure of an amino acid, has a positive or negative charge in solution. It is likely that the C60 and FNWs would not prefer the charged carboxyl or amino group. Tri-Ala was adsorbed slightly by the C60 and FNWs. The carboxyl or amino group is not close to the center of the methyl group of Tri-Ala. One of the methyl groups in Tri-Ala would interact with the aromatic structure of the C60 and FNWs. We compared our results with the theoretical interaction of 20 bio-amino acids with C60. The theoretical simulations showed the bonding distance between C60 and an amino acid and the dissociation energy. The dissociation energy was shown to increase in the order, Val < Phe < Pro < Asp < Ala < Trp < Tyr < Arg < Leu. However, the simulation was not consistent with our experimental results. The adsorption of albumin (a protein) by C60 showed the effect on the side chains of Try and Trp. The structure of albumin was changed a little by C60. In our study Try and Tyr were hardly adsorbed by C60 and FNWs. These amino acids did not show a different adsorption behavior compared with other amino acids. The adsorptive behavior of mono-amino acids might be different from that of polypeptides.

  20. Fmoc/Trt-amino acids: comparison to Fmoc/tBu-amino acids in peptide synthesis.

    PubMed

    Barlos, K; Gatos, D; Koutsogianni, S

    1998-03-01

    Model peptides containing the nucleophilic amino acids Trp and Met have been synthesized with the application of Fmoc/Trt- and Fmoc/tBu-amino acids, for comparison. The deprotection of the peptides synthesized using Fmoc/Trt-amino acids in all cases leads to crude peptides of higher purity than that of the same peptides synthesized using Fmoc/tBu-amino acids.

  1. Amino acid regulation of gene expression.

    PubMed Central

    Fafournoux, P; Bruhat, A; Jousse, C

    2000-01-01

    The impact of nutrients on gene expression in mammals has become an important area of research. Nevertheless, the current understanding of the amino acid-dependent control of gene expression is limited. Because amino acids have multiple and important functions, their homoeostasis has to be finely maintained. However, amino-acidaemia can be affected by certain nutritional conditions or various forms of stress. It follows that mammals have to adjust several of their physiological functions involved in the adaptation to amino acid availability by regulating the expression of numerous genes. The aim of the present review is to examine the role of amino acids in regulating mammalian gene expression and protein turnover. It has been reported that some genes involved in the control of growth or amino acid metabolism are regulated by amino acid availability. For instance, limitation of several amino acids greatly increases the expression of the genes encoding insulin-like growth factor binding protein-1, CHOP (C/EBP homologous protein, where C/EBP is CCAAT/enhancer binding protein) and asparagine synthetase. Elevated mRNA levels result from both an increase in the rate of transcription and an increase in mRNA stability. Several observations suggest that the amino acid regulation of gene expression observed in mammalian cells and the general control process described in yeast share common features. Moreover, amino acid response elements have been characterized in the promoters of the CHOP and asparagine synthetase genes. Taken together, the results discussed in the present review demonstrate that amino acids, by themselves, can, in concert with hormones, play an important role in the control of gene expression. PMID:10998343

  2. The Apollo Program and Amino Acids

    ERIC Educational Resources Information Center

    Fox, Sidney W.

    1973-01-01

    Discusses the determination of hydrolyzable amino acid precursors and a group of six amino acids in the returned lunar samples of the Apollo programs. Indicates that molecular evolution is arrested at the precursor stage on the Moon because of lack of water. (CC)

  3. 6th Amino Acid Assessment Workshop

    USDA-ARS?s Scientific Manuscript database

    The focus of the 6th workshop is on lysine, arginine, and related amino acids. Functions, metabolic pathways, clinical uses, and upper tolerance intakes are emphasized in the articles that follow. Lysine is arguably the most deficient amino acid in the food supply of countries where poverty exists, ...

  4. The Apollo Program and Amino Acids

    ERIC Educational Resources Information Center

    Fox, Sidney W.

    1973-01-01

    Discusses the determination of hydrolyzable amino acid precursors and a group of six amino acids in the returned lunar samples of the Apollo programs. Indicates that molecular evolution is arrested at the precursor stage on the Moon because of lack of water. (CC)

  5. Human Protein and Amino Acid Requirements.

    PubMed

    Hoffer, L John

    2016-05-01

    Human protein and amino acid nutrition encompasses a wide, complex, frequently misunderstood, and often contentious area of clinical research and practice. This tutorial explains the basic biochemical and physiologic principles that underlie our current understanding of protein and amino acid nutrition. The following topics are discussed: (1) the identity, measurement, and essentiality of nutritional proteins; (2) the definition and determination of minimum requirements; (3) nutrition adaptation; (4) obligatory nitrogen excretion and the minimum protein requirement; (5) minimum versus optimum protein intakes; (6) metabolic responses to surfeit and deficient protein intakes; (7) body composition and protein requirements; (8) labile protein; (9) N balance; (10) the principles of protein and amino acid turnover, including an analysis of the controversial indicator amino acid oxidation technique; (11) general guidelines for evaluating protein turnover articles; (12) amino acid turnover versus clearance; (13) the protein content of hydrated amino acid solutions; (14) protein requirements in special situations, including protein-catabolic critical illness; (15) amino acid supplements and additives, including monosodium glutamate and glutamine; and (16) a perspective on the future of protein and amino acid nutrition research. In addition to providing practical information, this tutorial aims to demonstrate the importance of rigorous physiologic reasoning, stimulate intellectual curiosity, and encourage fresh ideas in this dynamic area of human nutrition. In general, references are provided only for topics that are not well covered in modern textbooks. © 2016 American Society for Parenteral and Enteral Nutrition.

  6. A common periodic table of codons and amino acids.

    PubMed

    Biro, J C; Benyó, B; Sansom, C; Szlávecz, A; Fördös, G; Micsik, T; Benyó, Z

    2003-06-27

    A periodic table of codons has been designed where the codons are in regular locations. The table has four fields (16 places in each) one with each of the four nucleotides (A, U, G, C) in the central codon position. Thus, AAA (lysine), UUU (phenylalanine), GGG (glycine), and CCC (proline) were placed into the corners of the fields as the main codons (and amino acids) of the fields. They were connected to each other by six axes. The resulting nucleic acid periodic table showed perfect axial symmetry for codons. The corresponding amino acid table also displaced periodicity regarding the biochemical properties (charge and hydropathy) of the 20 amino acids and the position of the stop signals. The table emphasizes the importance of the central nucleotide in the codons and predicts that purines control the charge while pyrimidines determine the polarity of the amino acids. This prediction was experimentally tested.

  7. Protein biosynthesis with conformationally restricted amino acids

    SciTech Connect

    Mendel, D. Lawrence Berkeley Lab., CA ); Ellman, J.; Schultz, P.G. )

    1993-05-19

    The incorporation of conformationally constrained amino acids into peptides is a powerful approach for generating structurally defined peptides as conformational probes and bioactive agents. The ability to site-specifically introduce constrained amino acids into large polypeptide chains would provide a similar opportunity to probe the flexibility, conformation, folding and stability of proteins. To this end, we have examined the competence of the Escherichia coli protein biosynthetic machinery to incorporate a number of these unnatural amino acids into the 164 residue protein T4 lysozyme (T4L). Results clearly demonstrate that the protein biosynthetic machinery can accommodate a wide variety of conformationally constrained amino acids. The expansion of structural motifs that can be biosynthetically incorporated into proteins to include a large number of conformationally constrained amino acids significantly increases the power of mutagenesis methods as probes of protein structure and function and provides additional insights into the steric requirements of the translational machinery. 13 refs., 2 figs.

  8. Amino acid chemoreceptors of Bacillus subtilis.

    PubMed Central

    Ordal, G W; Villani, D P; Gibson, K J

    1977-01-01

    Specificities of chemoreceptors for the 20 common amino acids, toward which Bacillus subtilis shows chemotaxis, were assessed by competition ("jamming") experiments using a modification of the traditional capillary assay, called the "sensitivity capillary assay." Many amino acids were sensed by at least two chemoreceptors. All the highest affinity chemoreceptors for the amino acids were distinct, except glutamate and aspartate, which may share one chemoreceptor, and tyrosine, for which the data could not be collected due to low solubility. The data suggest the hypothesis that each amino acid-chemoreceptor complex binds to a different signaler (from each amino acid-chemoreceptor complex binds to a different signaler (from which signals travel to the flagella to modify behavior appropriately), and that many of the signalers can also bind other attractant-chemoreceptor complexes as antagonists (no signals to flagella). PMID:401491

  9. Differential distribution of amino acids in plants.

    PubMed

    Kumar, Vinod; Sharma, Anket; Kaur, Ravdeep; Thukral, Ashwani Kumar; Bhardwaj, Renu; Ahmad, Parvaiz

    2017-05-01

    Plants are a rich source of amino acids and their individual abundance in plants is of great significance especially in terms of food. Therefore, it is of utmost necessity to create a database of the relative amino acid contents in plants as reported in literature. Since in most of the cases complete analysis of profiles of amino acids in plants was not reported, the units used and the methods applied and the plant parts used were different, amino acid contents were converted into relative units with respect to lysine for statistical analysis. The most abundant amino acids in plants are glutamic acid and aspartic acid. Pearson's correlation analysis among different amino acids showed that there were no negative correlations between the amino acids. Cluster analysis (CA) applied to relative amino acid contents of different families. Alismataceae, Cyperaceae, Capparaceae and Cactaceae families had close proximity with each other on the basis of their relative amino acid contents. First three components of principal component analysis (PCA) explained 79.5% of the total variance. Factor analysis (FA) explained four main underlying factors for amino acid analysis. Factor-1 accounted for 29.4% of the total variance and had maximum loadings on glycine, isoleucine, leucine, threonine and valine. Factor-2 explained 25.8% of the total variance and had maximum loadings on alanine, aspartic acid, serine and tyrosine. 14.2% of the total variance was explained by factor-3 and had maximum loadings on arginine and histidine. Factor-4 accounted 8.3% of the total variance and had maximum loading on the proline amino acid. The relative content of different amino acids presented in this paper is alanine (1.4), arginine (1.8), asparagine (0.7), aspartic acid (2.4), cysteine (0.5), glutamic acid (2.8), glutamine (0.6), glycine (1.0), histidine (0.5), isoleucine (0.9), leucine (1.7), lysine (1.0), methionine (0.4), phenylalanine (0.9), proline (1.1), serine (1.0), threonine (1

  10. Amino acids in the Martian meteorite Nakhla.

    PubMed

    Glavin, D P; Bada, J L; Brinton, K L; McDonald, G D

    1999-08-03

    A suite of protein and nonprotein amino acids were detected with high-performance liquid chromatography in the water- and acid-soluble components of an interior fragment of the Martian meteorite Nakhla, which fell in Egypt in 1911. Aspartic and glutamic acids, glycine, alanine, beta-alanine, and gamma-amino-n-butyric acid (gamma-ABA) were the most abundant amino acids detected and were found primarily in the 6 M HCl-hydrolyzed, hot water extract. The concentrations ranged from 20 to 330 parts per billion of bulk meteorite. The amino acid distribution in Nakhla, including the D/L ratios (values range from <0.1 to 0.5), is similar to what is found in bacterially degraded organic matter. The amino acids in Nakhla appear to be derived from terrestrial organic matter that infiltrated the meteorite soon after its fall to Earth, although it is possible that some of the amino acids are endogenous to the meteorite. The rapid amino acid contamination of Martian meteorites after direct exposure to the terrestrial environment has important implications for Mars sample-return missions and the curation of the samples from the time of their delivery to Earth.

  11. Amino acids in the Martian meteorite Nakhla

    PubMed Central

    Glavin, Daniel P.; Bada, Jeffrey L.; Brinton, Karen L. F.; McDonald, Gene D.

    1999-01-01

    A suite of protein and nonprotein amino acids were detected with high-performance liquid chromatography in the water- and acid-soluble components of an interior fragment of the Martian meteorite Nakhla, which fell in Egypt in 1911. Aspartic and glutamic acids, glycine, alanine, β-alanine, and γ-amino-n-butyric acid (γ-ABA) were the most abundant amino acids detected and were found primarily in the 6 M HCl-hydrolyzed, hot water extract. The concentrations ranged from 20 to 330 parts per billion of bulk meteorite. The amino acid distribution in Nakhla, including the d/l ratios (values range from <0.1 to 0.5), is similar to what is found in bacterially degraded organic matter. The amino acids in Nakhla appear to be derived from terrestrial organic matter that infiltrated the meteorite soon after its fall to Earth, although it is possible that some of the amino acids are endogenous to the meteorite. The rapid amino acid contamination of Martian meteorites after direct exposure to the terrestrial environment has important implications for Mars sample-return missions and the curation of the samples from the time of their delivery to Earth. PMID:10430856

  12. Amino acids in the Martian meteorite Nakhla

    NASA Technical Reports Server (NTRS)

    Glavin, D. P.; Bada, J. L.; Brinton, K. L.; McDonald, G. D.

    1999-01-01

    A suite of protein and nonprotein amino acids were detected with high-performance liquid chromatography in the water- and acid-soluble components of an interior fragment of the Martian meteorite Nakhla, which fell in Egypt in 1911. Aspartic and glutamic acids, glycine, alanine, beta-alanine, and gamma-amino-n-butyric acid (gamma-ABA) were the most abundant amino acids detected and were found primarily in the 6 M HCl-hydrolyzed, hot water extract. The concentrations ranged from 20 to 330 parts per billion of bulk meteorite. The amino acid distribution in Nakhla, including the D/L ratios (values range from <0.1 to 0.5), is similar to what is found in bacterially degraded organic matter. The amino acids in Nakhla appear to be derived from terrestrial organic matter that infiltrated the meteorite soon after its fall to Earth, although it is possible that some of the amino acids are endogenous to the meteorite. The rapid amino acid contamination of Martian meteorites after direct exposure to the terrestrial environment has important implications for Mars sample-return missions and the curation of the samples from the time of their delivery to Earth.

  13. Amino Acids in the Martian Meteorite Nakhla

    NASA Astrophysics Data System (ADS)

    Glavin, Daniel P.; Bada, Jeffrey L.; Brinton, Karen L. F.; McDonald, Gene D.

    1999-08-01

    A suite of protein and nonprotein amino acids were detected with high-performance liquid chromatography in the water- and acid-soluble components of an interior fragment of the Martian meteorite Nakhla, which fell in Egypt in 1911. Aspartic and glutamic acids, glycine, alanine, β -alanine, and γ -amino-n-butyric acid (γ -ABA) were the most abundant amino acids detected and were found primarily in the 6 M HCl-hydrolyzed, hot water extract. The concentrations ranged from 20 to 330 parts per billion of bulk meteorite. The amino acid distribution in Nakhla, including the D/L ratios (values range from <0.1 to 0.5), is similar to what is found in bacterially degraded organic matter. The amino acids in Nakhla appear to be derived from terrestrial organic matter that infiltrated the meteorite soon after its fall to Earth, although it is possible that some of the amino acids are endogenous to the meteorite. The rapid amino acid contamination of Martian meteorites after direct exposure to the terrestrial environment has important implications for Mars sample-return missions and the curation of the samples from the time of their delivery to Earth.

  14. Exogenous amino acids as fuel in shock.

    PubMed

    Daniel, A M; Kapadia, B; MacLean, L D

    1982-01-01

    It has been suggested that in shock branched-chain amino acids are preferentially oxidized resulting in continued proteolysis and stimulated gluconeogenesis. To determine if exogenous amino acids could be used as fuel in shock, dogs rendered hypotensive by controlled cardiac tamponade and normotensive controls were infused with amino acid mixtures and individual amino acids. When Nephramine, a mixture rich in branched-chain amino acids, was infused, plasma alpha-amino nitrogen levels rose but urea output did not increase in either the control state or in shock, suggesting that these amino acids were not rapidly deaminated to serve as fuels. Travasol, which in addition contained large amounts of alanine and glycine, tripled urea output in the controls and doubled it in shock. The limit of urea production was reached in both groups at 35 mumoles urea/minute/kg. In the Travasol-infused animals plasma alpha-amino nitrogen levels were maintained in normotension but rose sharply in shock. When glycine alone was infused into five dogs in shock urea production rate was 30.6 + 2.1 mumoles/minute/kg; with alanine the same value was 22.5 + 2.2 mumoles/minute/kg. In both cases plasma alpha-amino nitrogen levels were high, suggesting that transport of these amino acids into the cell was slow in shock. In four dogs in shock glycine-14C was added to the glycine infusate as a tracer. At radioactive equilibrium 28% of the label infused appeared in CO2; another 22% appeared in glucose. It is concluded that of all the amino acids tested only glycine and alanine are deaminated rapidly enough to serve as exogenous fuels in shock.

  15. Positive alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor modulators have different impact on synaptic transmission in the thalamus and hippocampus.

    PubMed

    Xia, Yan-Fang; Kessler, Markus; Arai, Amy C

    2005-04-01

    Earlier studies showed that positive modulators of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors enhance synaptic responses and facilitate synaptic plasticity. Those studies focused mainly on hippocampal functions. However, AMPA receptors have regionally distinct subunit compositions and thus potencies and efficacies of modulators may vary across the brain. The present study compared the effects of CX546 [1-(1,4-benzodioxan-6-ylcarbonyl) piperidine], a benzamide-type modulator, on synaptic transmission in neurons of the reticular thalamic nucleus (RTN), which regulates the firing mode of relay cells in other thalamic nuclei, and on hippocampal CA1 pyramidal cells. CX546 greatly prolonged synaptic responses in CA1 pyramidal cells, but at the same concentration it had only weak modulatory effects in RTN neurons. Effects on miniature excitatory postsynaptic currents (EPSCs) were similar to those on EPSCs in both regions, suggesting that variations in neuronal morphology and transmitter release kinetics do not account for the differences. Relay cells in the ventrobasal thalamus also exhibited weak modulatory effects that were comparable with those in RTN neurons. Regionally different effects on response duration were also observed with CX516 [BDP-12, 1-(quinoxalin-6-ylcarbonyl)piperidine], a second benzamide drug. In contrast, 100 microM cyclothiazide produced comparable synaptic enhancements in hippocampus and RTN. The regional selectivity of benzamide drugs (ampakines) may be explained, at least in part, by a lower potency at thalamic AMPA receptors, perhaps due to the prevalence of the subunits GluR3 and 4. Although regional preferences of the ampakines were modest in their extent, they may be sufficient to be of relevance when considering future therapeutic applications of such compounds.

  16. Gemini surfactants from natural amino acids.

    PubMed

    Pérez, Lourdes; Pinazo, Aurora; Pons, Ramon; Infante, Mrosa

    2014-03-01

    In this review, we report the most important contributions in the structure, synthesis, physicochemical (surface adsorption, aggregation and phase behaviour) and biological properties (toxicity, antimicrobial activity and biodegradation) of Gemini natural amino acid-based surfactants, and some potential applications, with an emphasis on the use of these surfactants as non-viral delivery system agents. Gemini surfactants derived from basic (Arg, Lys), neutral (Ser, Ala, Sar), acid (Asp) and sulphur containing amino acids (Cys) as polar head groups, and Geminis with amino acids/peptides in the spacer chain are reviewed.

  17. An overview on D-amino acids.

    PubMed

    Genchi, Giuseppe

    2017-07-05

    More than half a century ago researchers thought that D-amino acids had a minor function compared to L-enantiomers in biological processes. Many evidences have shown that D-amino acids are present in high concentration in microorganisms, plants, mammals and humans and fulfil specific biological functions. In the brain of mammals, D-serine (D-Ser) acts as a co-agonist of the N-methyl-D-aspartate (NMDA)-type glutamate receptors, responsible for learning, memory and behaviour. D-Ser metabolism is relevant for disorders associated with an altered function of the NMDA receptor, such as schizophrenia, ischemia, epilepsy and neurodegenerative disorders. On the other hand, D-aspartate (D-Asp) is one of the major regulators of adult neurogenesis and plays an important role in the development of endocrine function. D-Asp is present in the neuroendocrine and endocrine tissues and testes, and regulates the synthesis and secretion of hormones and spermatogenesis. Also food proteins contain D-amino acids that are naturally originated or processing-induced under conditions such as high temperatures, acid and alkali treatments and fermentation processes. The presence of D-amino acids in dairy products denotes thermal and alkaline treatments and microbial contamination. Two enzymes are involved in the metabolism of D-amino acids: amino acid racemase in the synthesis and D-amino acid oxidase in the degradation.

  18. Amino acid analogs for tumor imaging

    DOEpatents

    Goodman, M.M.; Shoup, T.

    1998-09-15

    The invention provides novel amino acid compounds of use in detecting and evaluating brain and body tumors. These compounds combine the advantageous properties of 1-amino-cycloalkyl-1-carboxylic acids, namely, their rapid uptake and prolonged retention in tumors with the properties of halogen substituents, including certain useful halogen isotopes including fluorine-18, iodine-123, iodine-125, iodine-131, bromine-75, bromine-76, bromine-77 and bromine-82. In one aspect, the invention features amino acid compounds that have a high specificity for target sites when administered to a subject in vivo. Preferred amino acid compounds show a target to non-target ratio of at least 5:1, are stable in vivo and substantially localized to target within 1 hour after administration. An especially preferred amino acid compound is [{sup 18}F]-1-amino-3-fluorocyclobutane-1-carboxylic acid (FACBC). In another aspect, the invention features pharmaceutical compositions comprised of an {alpha}-amino acid moiety attached to either a four, five, or a six member carbon-chain ring. In addition, the invention features analogs of {alpha}-aminoisobutyric acid.

  19. Amino acid analogs for tumor imaging

    DOEpatents

    Goodman, Mark M.; Shoup, Timothy

    1998-09-15

    The invention provides novel amino acid compounds of use in detecting and evaluating brain and body tumors. These compounds combine the advantageous properties of 1-amino-cycloalkyl-1-carboxylic acids, namely, their rapid uptake and prolonged retention in tumors with the properties of halogen substituents, including certain useful halogen isotopes including fluorine-18, iodine-123, iodine-125, iodine-131, bromine-75, bromine-76, bromine-77 and bromine-82. In one aspect, the invention features amino acid compounds that have a high specificity for target sites when administered to a subject in vivo. Preferred amino acid compounds show a target to non-target ratio of at least 5:1, are stable in vivo and substantially localized to target within 1 hour after administration. An especially preferred amino acid compound is ›.sup.18 F!-1-amino-3-fluorocyclobutane-1-carboxylic acid (FACBC). In another aspect, the invention features pharmaceutical compositions comprised of an .alpha.-amino acid moiety attached to either a four, five, or a six member carbon-chain ring. In addition, the invention features analogs of .alpha.-aminoisobutyric acid.

  20. Amino acid analogs for tumor imaging

    DOEpatents

    Goodman, Mark M.; Shoup, Timothy

    1998-10-06

    The invention provides novel amino acid compounds of use in detecting and evaluating brain and body tumors. These compounds combine the advantageous properties of 1-amino-cycloalkyl-1-carboxylic acids, namely, their rapid uptake and prolonged retention in tumors with the properties of halogen substituents, including certain useful halogen isotopes including fluorine-18, iodine-123, iodine-125, iodine-131, bromine-75, bromine-76, bromine-77 and bromine-82. In one aspect, the invention features amino acid compounds that have a high specificity for target sites when administered to a subject in vivo. Preferred amino acid compounds show a target to non-target ratio of at least 5:1, are stable in vivo and substantially localized to target within 1 hour after administration. An especially preferred amino acid compound is ›.sup.18 F!-1-amino-3-fluorocyclobutane-1-carboxylic acid (FACBC). In another aspect, the invention features pharmaceutical compositions comprised of an .alpha.-amino acid moiety attached to either a four, five, or a six member carbon-chain ring. In addition, the invention features analogs of .alpha.-aminoisobutyric acid.

  1. Amino acid analogs for tumor imaging

    DOEpatents

    Goodman, M.M.; Shoup, T.

    1998-10-06

    The invention provides novel amino acid compounds of use in detecting and evaluating brain and body tumors. These compounds combine the advantageous properties of 1-amino-cycloalkyl-1-carboxylic acids, namely, their rapid uptake and prolonged retention in tumors with the properties of halogen substituents, including certain useful halogen isotopes including fluorine-18, iodine-123, iodine-125, iodine-131, bromine-75, bromine-76, bromine-77 and bromine-82. In one aspect, the invention features amino acid compounds that have a high specificity for target sites when administered to a subject in vivo. Preferred amino acid compounds show a target to non-target ratio of at least 5:1, are stable in vivo and substantially localized to target within 1 hour after administration. An especially preferred amino acid compound is [{sup 18}F]-1-amino-3-fluorocyclobutane-1-carboxylic acid (FACBC). In another aspect, the invention features pharmaceutical compositions comprised of an {alpha}-amino acid moiety attached to either a four, five, or a six member carbon-chain ring. In addition, the invention features analogs of {alpha}-aminoisobutyric acid.

  2. A Novel Method for Presenting the Amino Acids in an Introductory Biochemistry Course.

    ERIC Educational Resources Information Center

    Kuehl, LeRoy

    1978-01-01

    Introduces an approach to teaching amino acids that employs the use of a poem containing information on the structure and properties of amino acids, and of slides illustrating the poem. Student response to the method was positive. (MA)

  3. A Novel Method for Presenting the Amino Acids in an Introductory Biochemistry Course.

    ERIC Educational Resources Information Center

    Kuehl, LeRoy

    1978-01-01

    Introduces an approach to teaching amino acids that employs the use of a poem containing information on the structure and properties of amino acids, and of slides illustrating the poem. Student response to the method was positive. (MA)

  4. Amino acid transporters: roles in amino acid sensing and signalling in animal cells.

    PubMed Central

    Hyde, Russell; Taylor, Peter M; Hundal, Harinder S

    2003-01-01

    Amino acid availability regulates cellular physiology by modulating gene expression and signal transduction pathways. However, although the signalling intermediates between nutrient availability and altered gene expression have become increasingly well documented, how eukaryotic cells sense the presence of either a nutritionally rich or deprived medium is still uncertain. From recent studies it appears that the intracellular amino acid pool size is particularly important in regulating translational effectors, thus, regulated transport of amino acids across the plasma membrane represents a means by which the cellular response to amino acids could be controlled. Furthermore, evidence from studies with transportable amino acid analogues has demonstrated that flux through amino acid transporters may act as an initiator of nutritional signalling. This evidence, coupled with the substrate selectivity and sensitivity to nutrient availability classically associated with amino acid transporters, plus the recent discovery of transporter-associated signalling proteins, demonstrates a potential role for nutrient transporters as initiators of cellular nutrient signalling. Here, we review the evidence supporting the idea that distinct amino acid "receptors" function to detect and transmit certain nutrient stimuli in higher eukaryotes. In particular, we focus on the role that amino acid transporters may play in the sensing of amino acid levels, both directly as initiators of nutrient signalling and indirectly as regulators of external amino acid access to intracellular receptor/signalling mechanisms. PMID:12879880

  5. Extending enzyme molecular recognition with an expanded amino acid alphabet

    PubMed Central

    Windle, Claire L.; Simmons, Katie J.; Ault, James R.; Trinh, Chi H.; Nelson, Adam

    2017-01-01

    Natural enzymes are constructed from the 20 proteogenic amino acids, which may then require posttranslational modification or the recruitment of coenzymes or metal ions to achieve catalytic function. Here, we demonstrate that expansion of the alphabet of amino acids can also enable the properties of enzymes to be extended. A chemical mutagenesis strategy allowed a wide range of noncanonical amino acids to be systematically incorporated throughout an active site to alter enzymic substrate specificity. Specifically, 13 different noncanonical side chains were incorporated at 12 different positions within the active site of N-acetylneuraminic acid lyase (NAL), and the resulting chemically modified enzymes were screened for activity with a range of aldehyde substrates. A modified enzyme containing a 2,3-dihydroxypropyl cysteine at position 190 was identified that had significantly increased activity for the aldol reaction of erythrose with pyruvate compared with the wild-type enzyme. Kinetic investigation of a saturation library of the canonical amino acids at the same position showed that this increased activity was not achievable with any of the 20 proteogenic amino acids. Structural and modeling studies revealed that the unique shape and functionality of the noncanonical side chain enabled the active site to be remodeled to enable more efficient stabilization of the transition state of the reaction. The ability to exploit an expanded amino acid alphabet can thus heighten the ambitions of protein engineers wishing to develop enzymes with new catalytic properties. PMID:28196894

  6. Extending enzyme molecular recognition with an expanded amino acid alphabet.

    PubMed

    Windle, Claire L; Simmons, Katie J; Ault, James R; Trinh, Chi H; Nelson, Adam; Pearson, Arwen R; Berry, Alan

    2017-03-07

    Natural enzymes are constructed from the 20 proteogenic amino acids, which may then require posttranslational modification or the recruitment of coenzymes or metal ions to achieve catalytic function. Here, we demonstrate that expansion of the alphabet of amino acids can also enable the properties of enzymes to be extended. A chemical mutagenesis strategy allowed a wide range of noncanonical amino acids to be systematically incorporated throughout an active site to alter enzymic substrate specificity. Specifically, 13 different noncanonical side chains were incorporated at 12 different positions within the active site of N-acetylneuraminic acid lyase (NAL), and the resulting chemically modified enzymes were screened for activity with a range of aldehyde substrates. A modified enzyme containing a 2,3-dihydroxypropyl cysteine at position 190 was identified that had significantly increased activity for the aldol reaction of erythrose with pyruvate compared with the wild-type enzyme. Kinetic investigation of a saturation library of the canonical amino acids at the same position showed that this increased activity was not achievable with any of the 20 proteogenic amino acids. Structural and modeling studies revealed that the unique shape and functionality of the noncanonical side chain enabled the active site to be remodeled to enable more efficient stabilization of the transition state of the reaction. The ability to exploit an expanded amino acid alphabet can thus heighten the ambitions of protein engineers wishing to develop enzymes with new catalytic properties.

  7. Modification of fetal plasma amino acid composition by placental amino acid exchangers in vitro

    PubMed Central

    Cleal, Jane K; Brownbill, Paul; Godfrey, Keith M; Jackson, John M; Jackson, Alan A; Sibley, Colin P; Hanson, Mark A; Lewis, Rohan M

    2007-01-01

    Fetal growth is dependent on both the quantity and relative composition of amino acids delivered to the fetal circulation, and impaired placental amino acid supply is associated with restricted fetal growth. Amino acid exchangers can alter the composition, but not the quantity, of amino acids in the intra- and extracellular amino acid pools. In the placenta, exchangers may be important determinants of the amino acid composition in the fetal circulation. This study investigates the substrate specificity of exchange between the placenta and the feto-placental circulation. Maternal–fetal transfer of radiolabelled amino acids and creatinine were measured in the isolated perfused human placental cotyledon. Transfer of l-[14C]serine or l-[14C]leucine, and [3H]glycine, were measured in the absence of amino acids in the fetal circulation (transfer by non-exchange mechanisms) and following 10–20 μmol boluses of unlabelled amino acids into the fetal circulation to provide substrates for exchange (transfer by exchange and non-exchange mechanisms). The ability of fetal arterial boluses of l-alanine and l-leucine to stimulate release of amino acids from the placenta was also determined using HPLC in order to demonstrate the overall pattern of amino acid release. Experiments with radiolabelled amino acids demonstrated increased maternal–fetal transfer of l-serine and l-leucine, but not glycine, following boluses of specific amino acids into the fetal circulation. l-[14C]Leucine, but not l-[14C]serine or [3H]glycine, was transferred from the maternal to the fetal circulation by non-exchange mechanisms also (P < 0.01). HPLC analysis demonstrated that fetal amino acid boluses stimulated increased transport of a range of different amino acids by 4–7 μmol l−1 (P < 0.05). Amino acid exchange provides a mechanism to supply the fetus with amino acids that it requires for fetal growth. This study demonstrates that these transporters have the capacity to exchange micromolar

  8. Amino Acid Stability in the Early Oceans

    NASA Technical Reports Server (NTRS)

    Parker, E. T.; Brinton, K. L.; Burton, A. S.; Glavin, D. P.; Dworkin, J. P.; Bada, J. L.

    2015-01-01

    It is likely that a variety of amino acids existed in the early oceans of the Earth at the time of the origin and early evolution of life. "Primordial soup", hydrothermal vent, and meteorite based processes could have contributed to such an inventory. Several "protein" amino acids were likely present, however, based on prebiotic synthesis experiments and carbonaceous meteorite studies, non-protein amino acids, which are rare on Earth today, were likely the most abundant. An important uncertainty is the length of time these amino acids could have persisted before their destruction by abiotic and biotic processes. Prior to life, amino acid concentrations in the oceans were likely regulated by circulation through hydro-thermal vents. Today, the entire ocean circulates through vent systems every 10(exp 7) years. On the early Earth, this value was likely smaller due to higher heat flow and thus marine amino acid life-time would have been shorter. After life, amino acids in the oceans could have been assimilated by primitive organisms.

  9. Enantiomer-specific selection of amino acids

    PubMed Central

    Ren, Xueying; Tellez, Luis A; de Araujo, Ivan E

    2013-01-01

    Dietary intake of L-amino acids impacts on several physiological functions, including the control of gastrointestinal motility, pancreatic secretion, and appetite. However, the biological mechanisms regulating behavioral predilections for certain amino acid types remain poorly understood. We tested the hypothesis that, in mice, the potency with which a given glucogenic amino acid increases glucose utilization reflects its rewarding properties. We have found that: 1. During long-, but not short-, term preference tests, L-alanine and L-serine were preferred over their D-enantiomer counterparts, while no such effect was observed for L-threonine vs. D-threonine; 2. These behavioral patterns were closely associated with the ability of L-amino acids to promote increases in respiratory exchange ratios such that those, and only those, L-amino acids able to promote increases in respiratory exchange ratios were preferred over their D-isomers; 3. These behavioral preferences were independent of gustatory influences, since taste-deficient Trpm5 knockout mice displayed ingestive responses very similar to those of their wild-type counterparts. We conclude that the ability to promote increases in respiratory exchange ratios enhances the reward value of nutritionally relevant amino acids, and suggest a mechanistic link between substrate utilization and amino acid preferences. PMID:24072505

  10. Amino Acid Detection in Cometary Matter?

    NASA Astrophysics Data System (ADS)

    Meierhenrich, U. J.; Munoz Caro, G. M.; Thiemann, W.; Goesmann, F.; Rosenbauer, H.

    2003-04-01

    The recent identification of amino acid structures in interstellar ice analogues [1, 2] strongly supports the assumption that amino acids are abundant in cometary matter too. Cometary matter is assumed to be built up of aggregates of interstellar dust particles. Amino acids are the molecular building blocks of proteins in living organisms. These results amplified the scientific interest in the ESA cometary mission Rosetta. The Rosetta Lander includes the Cosac experiment dedicated to the identification of chiral organic molecules in cometary matter itshape in situ \\upshape by multi column gas chromatography coupled with a reflectron time-of-flight mass spectrometer. However, the envisaged itshape in situ \\upshape amino acid analysis on the cometary surface requires special technical emphasis of the COSAC instrumentation. The context in which the amino acid identification in cometary matter is of interest will be outlined and the analytical solutions that make amino acids accessible to the COSAC instrument will be presented. A succesful identification of amino acid structures in cometary matter would help to understand the beginnings of the biomolecular evolution and the origin of the biomolecular asymmetry. [1] G.M. Muñoz Caro, U.J. Meierhenrich, W.A. Schutte, B. Barbier, A. Arcones Sergovia, H. Rosenbauer, W.H.-P. Thiemann, A. Brack, J.M. Greenberg: itshape Nature \\upshape 416 (2002), 403-406. [2] M.P. Bernstein, J.P. Dworkin, S.A. Sandford, G.W. Cooper, L.J. Allamandola: itshape Nature \\upshape 416 (2002), 401-403.

  11. Distribution of Amino Acids in Lunar Regolith

    NASA Technical Reports Server (NTRS)

    Elsila, J. E.; Callahan, M. P.; Glavin, D. P.; Dworkin, J. P.; Noble, S. K.; Gibson, E. K., Jr.

    2014-01-01

    One of the most eagerly studied questions upon initial return of lunar samples was whether significant amounts of organic compounds, including amino acids, were present. Analyses during the 1970s produced only tentative and inconclusive identifications of indigenous amino acids. Those analyses were hampered by analytical difficulties including relative insensitivity to certain compounds, the inability to separate chiral enantiomers, and the lack of compound-specific isotopic measurements, which made it impossible to determine whether the detected amino acids were indigenous to the lunar samples or the results of contamination. Numerous advances have been made in instrumentation and methodology for amino acid characterization in extraterrestrial samples in the intervening years, yet the origin of amino acids in lunar regolith samples has been revisited only once for a single lunar sample, (3) and remains unclear. Here, we present initial data from the analyses of amino acid abundances in 12 lunar regolith samples. We discuss these abundances in the context of four potential amino acid sources: (1) terrestrial biological contamination; (2) contamination from lunar module (LM) exhaust; (3) derivation from solar windimplanted precursors; and (4) exogenous delivery from meteorites.

  12. Amino Acid Degradation after Meteoritic Impact Simulation

    NASA Technical Reports Server (NTRS)

    Bertrand, M.; Westall, F.; vanderGaast, S.; Vilas, F.; Hoerz, F.; Barnes, G.; Chabin, A.; Brack, A.

    2008-01-01

    Amino acids are among the most important prebiotic molecules as it is from these precursors that the building blocks of life were formed [1]. Although organic molecules were among the components of the planetesimals making up the terrestrial planets, large amounts of primitive organic precursor molecules are believed to be exogenous in origin and to have been imported to the Earth via micrometeorites, carbonaceous meteorites and comets, especially during the early stages of the formation of the Solar System [1,2]. Our study concerns the hypothesis that prebiotic organic matter, present on Earth, was synthesized in the interstellar environment, and then imported to Earth by meteorites or micrometeorites. We are particularly concerned with the formation and fate of amino acids. We have already shown that amino acid synthesis is possible inside cometary grains under interstellar environment conditions [3]. We are now interested in the effects of space conditions and meteoritic impact on these amino acids [4-6]. Most of the extraterrestrial organic molecules known today have been identified in carbonaceous chondrite meteorites [7]. One of the components of these meteorites is a clay with a composition close to that of saponite, used in our experiments. Two American teams have studied the effects of impact on various amino acids [8,9]. [8] investigated amino acids in saturated solution in water with pressure ranges between 5.1 and 21 GPa and temperature ranges between 412 and 870 K. [9] studied amino acids in solid form associated with and without minerals (Murchison and Allende meteorite extracts) and pressure ranges between 3 and 30 GPa. In these two experiments, the amino acids survived up to 15 GPa. At higher pressure, the quantity of preserved amino acids decreases quickly. Some secondary products such as dipeptides and diketopiperazins were identified in the [8] experiment.

  13. Amino acid analysis for pharmacopoeial purposes.

    PubMed

    Wahl, Oliver; Holzgrabe, Ulrike

    2016-07-01

    The impurity profile of amino acids depends strongly on the production process. Since there are many different production methods (e.g. fermentation, protein hydrolysis or chemical synthesis) universal, state of the art methods are required to determine the impurity profile of amino acids produced by all relevant competitors. At the moment TLC tests provided by the Ph. Eur. are being replaced by a very specific amino acid analysis procedure possibly missing out on currently unknown process related impurities. Production methods and possible impurities as well as separation and detection methods suitable for said impurities are subject to this review. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. ANTIGENICITY OF POLYPEPTIDES (POLY ALPHA AMINO ACIDS)

    PubMed Central

    Pinchuck, Paul; Maurer, Paul H.

    1965-01-01

    The response of mice to synthetic linear polypeptides of known composition but random sequence has been studied. Neither Swiss mice nor a number of inbred strains could respond to copolymers of only 2 amino acids (G60L40, G60A40, G90T10). Upon introduction of as little as 4 mole per cent of a third amino acid, good immune responses were obtained, regardless of the nature of the third amino acid. The level of the immune response to a series of glu-lys-ala polymers increased with increasing alanine content of the polymer. PMID:5849232

  15. Amino acids in healthy aging skeletal muscle.

    PubMed

    Riddle, Emily S; Stipanuk, Martha H; Thalacker-Mercer, Anna E

    2016-01-01

    Life expectancy in the U.S. and globally continues to increase. Despite increased life expectancy quality of life is not enhanced, and older adults often experience chronic age-related disease and functional disability, including frailty. Additionally, changes in body composition such as the involuntary loss of skeletal muscle mass (i.e. sarcopenia) and subsequent increases in adipose tissue can augment disease and disability in this population. Furthermore, increased oxidative stress and decreased antioxidant concentrations may also lead to metabolic dysfunction in older adults. Specific amino acids, including leucine, cysteine and its derivative taurine, and arginine can play various roles in healthy aging, especially in regards to skeletal muscle health. Leucine and arginine play important roles in muscle protein synthesis and cell growth while cysteine and arginine play important roles in quenching oxidative stress. Evidence suggests that supplemental doses of each of these amino acids may improve the aging phenotype. However, additional research is required to establish the doses required to achieve positive outcomes in humans.

  16. Kinetic Trapping of Metastable Amino Acid Polymorphs

    NASA Astrophysics Data System (ADS)

    Simpson, Garth

    2014-06-01

    Second harmonic generation (SHG) microscopy was integrated with synchrotron X-ray diffraction (XRD) to test the Ostwald Rule of Stages, in which is hypothesized that crystals dynamically transition through metastable polymorphs before settling on the most thermodynamically favored form. The presence or absence of metastable forms has historically been challenging to probe due to the stochastic randomness of crystal nucleation coupled with the relatively short time-frame over which the metastable forms may survive. In this work, inkjet printing of a racemic amino acid solutions results in rapid solvent evaporation, placing crystallization under kinetic rather than thermodynamic control. SHG microscopy is used to rapidly and selectively identify the positions of metastable crystal forms. Coupling this measurement with synchrotron XRD allows diffraction analysis to be performed on individual inkjet printed dots of only a few pg of total material, prepared from single 1 pL droplets. In studies of amino acids, we have shown that the homochiral crystals emerge when printed, while those same solutions exclusively generate the racemic co-crystals upon slow solvent evaporation.

  17. Regulation of the plasma amino acid profile by leucine via the system L amino acid transporter.

    PubMed

    Zhen, Hongmin; Nakamura, Koichi; Kitaura, Yasuyuki; Kadota, Yoshihiro; Ishikawa, Takuya; Kondo, Yusuke; Xu, Minjun; Shimomura, Yoshiharu

    2015-01-01

    Plasma concentrations of amino acids reflect the intracellular amino acid pool in mammals. However, the regulatory mechanism requires clarification. In this study, we examined the effect of leucine administration on plasma amino acid profiles in mice with and without the treatment of 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (BCH) or rapamycin as an inhibitor of system L or mammalian target of rapamycin complex 1, respectively. The elevation of plasma leucine concentration after leucine administration was associated with a significant decrease in the plasma concentrations of isoleucine, valine, methionine, phenylalanine, and tyrosine; BCH treatment almost completely blocked the leucine-induced decrease in plasma amino acid concentrations. Rapamycin treatment had much less effects on the actions of leucine than BCH treatment. These results suggest that leucine regulates the plasma concentrations of branched-chain amino acids, methionine, phenylalanine, and tyrosine, and that system L amino acid transporters are involved in the leucine action.

  18. Amino acid odorants stimulate microvillar sensory neurons.

    PubMed

    Lipschitz, David L; Michel, William C

    2002-03-01

    The olfactory epithelium (OE) of zebrafish is populated with ciliated and microvillar olfactory sensory neurons (OSNs). Whether distinct classes of odorants specifically activate either of these unique populations of OSNs is unknown. Previously we demonstrated that zebrafish OSNs could be labeled in an activity-dependent fashion by amino acid but not bile acid odorants. To determine which sensory neuron type was stimulated by amino acid odorants, we labeled OSNs using the ion channel permeant probe agmatine (AGB) and analyzed its distribution with conventional light- and electron-microscope immunocytochemical techniques. Approximately 7% of the sensory epithelium was labeled by AGB exposure alone. Following stimulation with one of the eight amino acids tested, the proportion of labeled epithelium increased from 9% for histidine to 19% for alanine; amino acid stimulated increases in labeling of 2-12% over control labeling. Only histidine failed to stimulate a significant increase in the proportion of labeled OSNs compared to control preparations. Most amino acid sensitive OSNs were located superficially in the epithelium and immuno-electron microscopy demonstrated that the labeled OSNs were predominantly microvillar. Large numbers of nanogold particles (20-60 per 1.5 microm(2)) were associated with microvillar olfactory sensory neurons (MSNs), while few such particles (<15 per 1.5 microm(2)) were observed over ciliated olfactory sensory neurons (CSNs), supporting cells (SCs) and areas without tissue, such as the lumen above the OE. Collectively, these findings indicate that microvillar sensory neurons are capable of detecting amino acid odorants.

  19. Discovery and History of Amino Acid Fermentation.

    PubMed

    Hashimoto, Shin-Ichi

    2016-12-02

    There has been a strong demand in Japan and East Asia for L-glutamic acid as a seasoning since monosodium glutamate was found to present umami taste in 1907. The discovery of glutamate fermentation by Corynebacterium glutamicum in 1956 enabled abundant and low-cost production of the amino acid, creating a large market. The discovery also prompted researchers to develop fermentative production processes for other L-amino acids, such as lysine. Currently, the amino acid fermentation industry is so huge that more than 5 million metric tons of amino acids are manufactured annually all over the world, and this number continues to grow. Research on amino acid fermentation fostered the notion and skills of metabolic engineering which has been applied for the production of other compounds from renewable resources. The discovery of glutamate fermentation has had revolutionary impacts on both the industry and science. In this chapter, the history and development of glutamate fermentation, including the very early stage of fermentation of other amino acids, are reviewed.

  20. Genetics Home Reference: aromatic l-amino acid decarboxylase deficiency

    MedlinePlus

    ... aromatic l-amino acid decarboxylase deficiency aromatic l-amino acid decarboxylase deficiency Printable PDF Open All Close All ... view the expand/collapse boxes. Description Aromatic l-amino acid decarboxylase (AADC) deficiency is an inherited disorder that ...

  1. Amino Acid Biosynthesis Pathways in Diatoms

    PubMed Central

    Bromke, Mariusz A.

    2013-01-01

    Amino acids are not only building blocks for proteins but serve as precursors for the synthesis of many metabolites with multiple functions in growth and other biological processes of a living organism. The biosynthesis of amino acids is tightly connected with central carbon, nitrogen and sulfur metabolism. Recent publication of genome sequences for two diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum created an opportunity for extensive studies on the structure of these metabolic pathways. Based on sequence homology found in the analyzed diatomal genes, the biosynthesis of amino acids in diatoms seems to be similar to higher plants. However, one of the most striking differences between the pathways in plants and in diatomas is that the latter possess and utilize the urea cycle. It serves as an important anaplerotic pathway for carbon fixation into amino acids and other N-containing compounds, which are essential for diatom growth and contribute to their high productivity. PMID:24957993

  2. Enantioenrichment in sublimed amino acid mixtures.

    PubMed

    Viedma, Cristóbal; Ortiz, José E; de Torres, Trinidad; Cintas, Pedro

    2012-04-14

    A real amplification of an initial enantiomeric excess can be detected when two amino acids are sublimed at high temperature, even if one of the components is a racemic compound that does not convert into a conglomerate by sublimation.

  3. Amino acid interaction preferences in proteins

    PubMed Central

    Nath Jha, Anupam; Vishveshwara, Saraswathi; Banavar, Jayanth R

    2010-01-01

    Understanding the key factors that influence the interaction preferences of amino acids in the folding of proteins have remained a challenge. Here we present a knowledge-based approach for determining the effective interactions between amino acids based on amino acid type, their secondary structure, and the contact based environment that they find themselves in the native state structure as measured by their number of neighbors. We find that the optimal information is approximately encoded in a 60 × 60 matrix describing the 20 types of amino acids in three distinct secondary structures (helix, beta strand, and loop). We carry out a clustering scheme to understand the similarity between these interactions and to elucidate a nonredundant set. We demonstrate that the inferred energy parameters can be used for assessing the fit of a given sequence into a putative native state structure. PMID:20073083

  4. Production of amino acids by yogurt bacteria.

    PubMed

    Beshkova, D M; Simova, E D; Frengova, G I; Simov, Z I; Adilov, E F

    1998-01-01

    The dynamics of free amino acid production by the selected strains Streptococcus thermophilus 13a and Lactobacillus bulgaricus 2-11 were studied in pure and mixed cultivations during yogurt starter culture manufacture. L. bulgaricus 2-11 showed the highest activity for producing free amino acids with high individual concentrations over the first hour of growth (50% of the total amount). By the end of milk's full coagulation (4.5 h), 70% of the total amount of amino acids was released. S. thermophilus 13a showed poor proteolytic properties and consumed up to 70% of the free amino acids produced by L. bulgaricus 2-11 in the process of coagulation of milk with the mixed culture.

  5. Molecular cloning of mouse amino acid transport system B0, a neutral amino acid transporter related to Hartnup disorder.

    PubMed

    Bröer, Angelika; Klingel, Karin; Kowalczuk, Sonja; Rasko, John E J; Cavanaugh, Juleen; Bröer, Stefan

    2004-06-04

    Resorption of amino acids in kidney and intestine is mediated by transporters, which prefer groups of amino acids with similar physico-chemical properties. It is generally assumed that most neutral amino acids are transported across the apical membrane of epithelial cells by system B(0). Here we have characterized a novel member of the Na(+)-dependent neurotransmitter transporter family (B(0)AT1) isolated from mouse kidney, which shows all properties of system B(0). Flux experiments showed that the transporter is Na(+)-dependent, electrogenic, and actively transports most neutral amino acids but not anionic or cationic amino acids. Superfusion of mB(0)AT1-expressing oocytes with neutral amino acids generated inward currents, which were proportional to the fluxes observed with labeled amino acids. In situ hybridization showed strong expression in intestinal microvilli and in the proximal tubule of the kidney. Expression of mouse B(0)AT1 was restricted to kidney, intestine, and skin. It is generally assumed that mutations of the system B(0) transporter underlie autosomal recessive Hartnup disorder. In support of this notion mB(0)AT1 is located on mouse chromosome 13 in a region syntenic to human chromosome 5p15, the locus of Hartnup disorder. Thus, the human homologue of this transporter is an excellent functional and positional candidate for Hartnup disorder.

  6. Genetically encoded fluorescent coumarin amino acids

    DOEpatents

    Wang, Jiangyun [San Diego, CA; Xie, Jianming [San Diego, CA; Schultz, Peter G [La Jolla, CA

    2012-06-05

    The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetases that can incorporate the coumarin unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine into proteins produced in eubacterial host cells such as E. coli. The invention provides, for example but not limited to, novel orthogonal synthetases, methods for identifying and making the novel synthetases, methods for producing proteins containing the unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine and related translation systems.

  7. Genetically encoded fluorescent coumarin amino acids

    DOEpatents

    Wang, Jiangyun; Xie, Jianming; Schultz, Peter G.

    2010-10-05

    The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetases that can incorporate the coumarin unnatural amino acid L-(7-hydroxycoumarin-4-yl) ethylglycine into proteins produced in eubacterial host cells such as E. coli. The invention provides, for example but not limited to, novel orthogonal synthetases, methods for identifying and making the novel synthetases, methods for producing proteins containing the unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine and related translation systems.

  8. Nonprotein Amino Acids from Spark Discharges and Their Comparison with the Murchison Meteorite Amino Acids

    PubMed Central

    Wolman, Yecheskel; Haverland, William J.; Miller, Stanley L.

    1972-01-01

    All the nonprotein amino acids found in the Murchison meteorite are products of the action of electric discharge on a mixture of methane, nitrogen, and water with traces of ammonia. These amino acids include α-amino-n-butyric acid, α-aminoisobutyric acid, norvaline, isovaline, pipecolic acid, β-alanine, β-amino-n-butyric acid, β-aminoisobutyric acid, γ-aminobutyric acid, sarcosine, N-ethylglycine, and N-methylalanine. In addition, norleucine, alloisoleucine, N-propylglycine, N-isopropylglycine, N-methyl-β-alanine, N-ethyl-β-alanine α,β-diaminopropionic acid, isoserine, α,γ-diaminobutyric acid, and α-hydroxy-γ-aminobutyric acid are produced by the electric discharge, but have not been found in the meteorite. PMID:16591973

  9. Amino Acid Analyses of Acid Hydrolysates in Desert Varnish

    NASA Technical Reports Server (NTRS)

    Perry, Randall S.; Staley, James T.; Dworkin, Jason P.; Engel, Mike

    2001-01-01

    There has long been a debate as to whether rock varnish deposits are microbially mediated or are deposited by inorganic processes. Varnished rocks are found throughout the world primarily in arid and semi-arid regions. The varnish coats are typically up to 200 microns thick and are composed of clays and alternating layers enriched in manganese and iron oxides. The individual layers range in thickness from 1 micron to greater than 10 microns and may continue laterally for more than a 100 microns. Overlapping botryoidal structures are visible in thin section and scanning electron micrographs. The coatings also include small amounts of organic mater and detrital grains. Amino-acid hydrolysates offer a means of assessing the organic composition of rock varnish collected from the Sonoran Desert, near Phoenix, AZ. Chromatographic analyses of hydrolysates from powdered samples of rock varnish suggest that the interior of rock varnish is relatively enriched in amino acids and specifically in d-alanine and glutamic acid. Peptidoglycan (murein) is the main structural component of gram-positive bacterial cell walls. The d-enantiomer of alanine and glutamic acid are specific to peptidoglycan and are consequently an indicator for the presence of bacteria. D-alanine is also found in teichoic acid which is only found in gram-positive bacteria. Several researchers have cultured bacteria from the surface of rock varnish and most have been gram-positive, suggesting that gram-positive bacteria are intimately associated with varnish coatings and may play a role in the formation of varnish coatings.

  10. Amino Acid Analyses of Acid Hydrolysates in Desert Varnish

    NASA Technical Reports Server (NTRS)

    Perry, Randall S.; Staley, James T.; Dworkin, Jason P.; Engel, Mike

    2001-01-01

    There has long been a debate as to whether rock varnish deposits are microbially mediated or are deposited by inorganic processes. Varnished rocks are found throughout the world primarily in arid and semi-arid regions. The varnish coats are typically up to 200 microns thick and are composed of clays and alternating layers enriched in manganese and iron oxides. The individual layers range in thickness from 1 micron to greater than 10 microns and may continue laterally for more than a 100 microns. Overlapping botryoidal structures are visible in thin section and scanning electron micrographs. The coatings also include small amounts of organic mater and detrital grains. Amino-acid hydrolysates offer a means of assessing the organic composition of rock varnish collected from the Sonoran Desert, near Phoenix, AZ. Chromatographic analyses of hydrolysates from powdered samples of rock varnish suggest that the interior of rock varnish is relatively enriched in amino acids and specifically in d-alanine and glutamic acid. Peptidoglycan (murein) is the main structural component of gram-positive bacterial cell walls. The d-enantiomer of alanine and glutamic acid are specific to peptidoglycan and are consequently an indicator for the presence of bacteria. D-alanine is also found in teichoic acid which is only found in gram-positive bacteria. Several researchers have cultured bacteria from the surface of rock varnish and most have been gram-positive, suggesting that gram-positive bacteria are intimately associated with varnish coatings and may play a role in the formation of varnish coatings.

  11. Intermolecular Vibrations of Hydrophobic Amino Acids

    NASA Astrophysics Data System (ADS)

    Williams, Michael Roy Casselman

    ). While most peaks were indeed observed to blueshift as the sample was cooled, the temperature dependence of the peak position and intensity varied significantly for different modes: while some peaks were hardly affected by the decreasing temperature, others sharpened and/or blueshifted appreciably. Theoretical modeling of intermolecular vibrations in hydrophobic amino acids is challenging because the van der Waals dispersion interactions between the molecules are not accounted for in standard density functional theory (DFT). However, recent advances in theory have made it possible to incorporate these non-local electron correlation forces within the framework of DFT. In addition to carrying out these calculations, methods for comparing results from different theoretical models were devised and evaluated. Perhaps most significantly, a new approach was developed to allow for concise description and easy comparison of vibrational modes that involve complicated mixtures of inter- and intramolecular displacements.

  12. Evaluation of amino acids as turfgrass nematicides.

    PubMed

    Zhang, Yun; Luc, John E; Crow, William T

    2010-12-01

    Laboratory experiments revealed that DL-methionine, sodium methionate, potassium methionate, and methionine hydroxyl analog at rates of 224 and 448 kg amino acid/ha reduced the number of Belonolaimus longicaudatus mixed life-stages and Meloidogyne incognita J2 in soil, whereas L-threonine and lysine were not effective in reducing the number of either nematode. Futhermore, greenhouse experiments demonstrated that DL-methionine, sodium methionate, potassium methionate, and methionine hydroxyl analog were equally effective against B. longicaudatus at rates of 112, 224, and 448 kg amino acid/ha, and the highest rate (448 kg amino acid/ha) of all amino acids was more effective in reducing the number of B. longicaudatus than the lower rate. However, phytotoxicity was observed on creeping bentgrass (Agrostis palustris) treated with 448 kg amino acid/ha of methionine hydroxyl analog and DL methionine. In addition, in one of two field experiments on bermudagrass (Cynodon dactylon × C. transvaalensis) turf percentage green cover was increased and the number of B. longicaudatus was reduced by 224 kg amino acid/ha of DL-methionine and potassium methionate compared to untreated controls in one of two trials.

  13. Free amino acids in spider hemolymph.

    PubMed

    Tillinghast, Edward K; Townley, Mark A

    2008-11-01

    We examined the free amino acid composition of hemolymph from representatives of five spider families with an interest in knowing if the amino acid profile in the hemolymph of orb-web-building spiders reflects the high demands for small organic compounds in the sticky droplets of their webs. In nearly all analyses, on both orb and non-orb builders, glutamine was the most abundant free amino acid. Glycine, taurine, proline, histidine, and alanine also tended to be well-represented in orb and non-orb builders. While indications of taxon-specific differences in amino acid composition were observed, it was not apparent that two presumptive precursors (glutamine, taurine) of orb web sticky droplet compounds were uniquely enriched in araneids (orb builders). However, total amino acid concentrations were invariably highest in the araneids and especially so in overwintering juveniles, even as several of the essential amino acids declined during this winter diapause. Comparing the data from this study with those from earlier studies revealed a number of discrepancies. The possible origins of these differences are discussed.

  14. Amino acid composition and amino acid-metabolic network in supragingival plaque.

    PubMed

    Washio, Jumpei; Ogawa, Tamaki; Suzuki, Keisuke; Tsukiboshi, Yosuke; Watanabe, Motohiro; Takahashi, Nobuhiro

    2016-01-01

    Dental plaque metabolizes both carbohydrates and amino acids. The former can be degraded to acids mainly, while the latter can be degraded to various metabolites, including ammonia, acids and amines, and associated with acid-neutralization, oral malodor and tissue inflammation. However, amino acid metabolism in dental plaque is still unclear. This study aimed to elucidate what kinds of amino acids are available as metabolic substrates and how the amino acids are metabolized in supragingival plaque, by a metabolome analysis. Amino acids and the related metabolites in supragingival plaque were extracted and quantified comprehensively by CE-TOFMS. Plaque samples were also incubated with amino acids, and the amounts of ammonia and amino acid-related metabolites were measured. The concentration of glutamate was the highest in supragingival plaque, while the ammonia-production was the highest from glutamine. The obtained metabolome profile revealed that amino acids are degraded through various metabolic pathways, including deamination, decarboxylation and transamination and that these metabolic systems may link each other, as well as with carbohydrate metabolic pathways in dental plaque ecosystem. Moreover, glutamine and glutamate might be the main source of ammonia production, as well as arginine, and contribute to pH-homeostasis and counteraction to acid-induced demineralization in supragingival plaque.

  15. Abc Amino Acids: Design, Synthesis, and Properties of New Photoelastic Amino Acids

    SciTech Connect

    Standaert, Robert F; Park, Dr Seung Bum

    2006-01-01

    Photoisomerizable amino acids provide a direct avenue to the experimental manipulation of bioactive polypeptides, potentially allowing real-time, remote control of biological systems and enabling useful applications in nanobiotechnology. Herein, we report a new class of photoisomerizable amino acids intended to cause pronounced expansion and contraction in the polypeptide backbone, i.e., to be photoelastic. These compounds, termed Abc amino acids, employ a photoisomerizable azobiphenyl chromophore to control the relative disposition of aminomethyl and carboxyl substituents. Molecular modeling of nine Abc isomers led to the identification of one with particularly attractive properties, including the ability to induce contractions up to 13A in the backbone upon transa?cis photoisomerization. This isomer, designated mpAbc, has substituents at meta and para positions on the inner (azo-linked) and outer rings, respectively. An efficient synthesis of Fmoc-protected mpAbc was executed in which the biaryl components were formed via Suzuki couplings and the azo linkage was formed via amine/nitroso condensation; protected forms of three other Abc isomers were prepared similarly. A decapeptide incorporating mpAbc was synthesized by conventional solid-phase methods and displayed characteristic azobenzene photochemical behavior with optimal conversion to the cis isomer at 360 nm and a thermal cisa?trans half life of 100 min. at 80 AoC.

  16. Evidence of Selection for Low Cognate Amino Acid Bias in Amino Acid Biosynthetic Enzymes

    PubMed Central

    Alves, Rui; Savageau, Michael A.

    2006-01-01

    Summary If the enzymes responsible for biosynthesis of a given amino acid are repressed and the cognate amino acid pool suddenly depleted, then derepression of these enzymes and replenishment of the pool would be problematic, if the enzymes were largely composed of the cognate amino acid. In the proverbial ‘Catch 22’, cells would lack the necessary enzymes to make the amino acid, and they would lack the necessary amino acid to make the needed enzymes. Based on this scenario, we hypothesize that evolution would lead to the selection of amino acid biosynthetic enzymes that have a relatively low content of their cognate amino acid. We call this the ‘cognate bias hypothesis’. Here we test several implications of this hypothesis directly using data from the proteome of Escherichia coli. Several lines of evidence show that low cognate bias is evident in 15 of the 20 amino acid biosynthetic pathways. Comparison with closely related Salmonella typhimurium shows similar results. Comparison with more distantly related Bacillus subtilis shows general similarities as well as significant differences in the detailed profiles of cognate bias. Thus, selection for low cognate bias plays a significant role in shaping the amino acid composition for a large class of cellular proteins. PMID:15853887

  17. Mutations at positions 547-553 of rat glucocorticoid receptors reveal that hsp90 binding requires the presence, but not defined composition, of a seven-amino acid sequence at the amino terminus of the ligand binding domain.

    PubMed

    Kaul, Sunil; Murphy, Patrick J M; Chen, Jun; Brown, Lloyd; Pratt, William B; Simons, S Stoney

    2002-09-27

    Glucocorticoid receptors (GRs) must heterocomplex with hsp90 to have an open steroid binding cleft that can be accessed by steroid. We reported that a seven-amino acid sequence (547-553 of rat GR) overlapping the amino-terminal end of the ligand binding domain is required for hsp90 binding to GR. We have now conducted saturation mutagenesis of this sequence, which appears to be part of the surface where the ligand binding cleft merges with the surface of the ligand binding domain. No single point mutation causes significant changes in any of a variety of biochemical and biological properties in addition to hsp90 binding. A triple mutation (P548A/T549A/V551A) increases by >100-fold the steroid concentration required for half-maximal induction without affecting the level of maximal induction or coactivator response. Interestingly, this triple mutant displays reduced binding of steroid and hsp90 in whole cells, but it possesses wild type affinity for steroid and normal hsp90 binding capacity under cell-free conditions. This phenotype of a dramatic shift in the dose response for transactivation would be expected from an increase in the rate of disassembly of the triple mutant GR.hsp90 heterocomplex in the cell. Mutation of the entire seven-amino acid region to CAAAAAC maintains the presence of a critical alpha-helical structure and heterocomplex formation with hsp90 but eliminates steroid binding and transcriptional activation, thus disconnecting hsp90 binding from opening of the ligand binding cleft and steroid binding.

  18. Amino Acid Transport into Cultured Tobacco Cells

    PubMed Central

    Harrington, H. Michael; Henke, Randolph R.

    1981-01-01

    Lysine transport into suspension-cultured Wisconsin-38 tobacco cells was observed. Uptake was linear (up to 90 minutes) with respect to time and amount of tissue only after 4 to 6 hours preincubation in calcium-containing medium. The observed cellular accumulation of lysine was against a concentration gradient and not due to exchange diffusion. Transport was stimulated by low pH and characterized by a biphasic uptake isotherm with two Km values for lysine. System I (Km ≃ 5 × 10−6 molar; Vmax ≃ 180 nanomoles per gram fresh weight per hour) and system II (Km ≃ 10−4 molar; Vmax ≃ 1900 nanomoles per gram fresh weight per hour) were inhibited by N-ethylmaleimide and a variety of respiratory inhibitors. This inhibition was not due to increased efflux. In antagonism experiments, system I was inhibited most effectively by basic amino acids, followed by the sulfur amino acids. System I was only slightly inhibited by the neutral and aromatic amino acids and was not inhibited by the acidic amino acids aspartic and glutamic acids. Transport by system II was inhibited by all of the tested amino acids (including aspartic and glutamic acids) and analogs; however, this system was not inhibited by d-arginine. Neither system was strongly inhibited by d-lysine or the lysine analog S-2-aminoethyl-l-cysteine. Arginine was shown to be a competitive inhibitor of both systems with values for Ki similar to the respective Km values. These studies suggest the presence of at least two amino acid permeases in W-38 tobacco cells. PMID:16661678

  19. Amino acids in modern and fossil woods

    NASA Technical Reports Server (NTRS)

    Lee, C.; Bada, J. L.; Peterson, E.

    1976-01-01

    The amino acid composition and the extent of racemization in several modern and fossil woods are reported. The method of analysis is described, and data are presented on the total amino acid concentration, the amino acid ratios, and the enantiomeric ratios in each sample. It is found that the amino acid concentration per gram of dry wood decreases with age of the sample, that the extent of racemization increases with increasing age, and that the amounts of aspartic acid, threonine, and serine decrease relative to valine with increasing age. The relative racemization rates of amino acids in wood, bone, and aqueous solution are compared, and it is shown that racemization in wood is much slower than in bone or aqueous solution. Racemization results for woods from the Kalambo Falls area of Zambia are used to calculate a minimum age of 110,000 years for the transition between the Sangoan and Acheulian industries at that site. This result is shown to be consistent with numerous radiometric dates for older Acheulian sites in Africa and to compare well with geologically inferred dates for the beginning of the Eemian and the end of the Acheulian industry in southern Africa.

  20. Amino acids in modern and fossil woods

    NASA Technical Reports Server (NTRS)

    Lee, C.; Bada, J. L.; Peterson, E.

    1976-01-01

    The amino acid composition and the extent of racemization in several modern and fossil woods are reported. The method of analysis is described, and data are presented on the total amino acid concentration, the amino acid ratios, and the enantiomeric ratios in each sample. It is found that the amino acid concentration per gram of dry wood decreases with age of the sample, that the extent of racemization increases with increasing age, and that the amounts of aspartic acid, threonine, and serine decrease relative to valine with increasing age. The relative racemization rates of amino acids in wood, bone, and aqueous solution are compared, and it is shown that racemization in wood is much slower than in bone or aqueous solution. Racemization results for woods from the Kalambo Falls area of Zambia are used to calculate a minimum age of 110,000 years for the transition between the Sangoan and Acheulian industries at that site. This result is shown to be consistent with numerous radiometric dates for older Acheulian sites in Africa and to compare well with geologically inferred dates for the beginning of the Eemian and the end of the Acheulian industry in southern Africa.

  1. Amino acid survival in large cometary impacts

    NASA Astrophysics Data System (ADS)

    Pierazzo, E.; Chyba, C. F.

    1999-11-01

    A significant fraction of the Earth's prebiotic volatile inventory may have been delivered by asteroidal and cometary impacts during the period of heavy bombardment. The realization that comets are particularly rich in organic material seemed to strengthen this suggestion. Previous modeling studies, however, indicated that most organics would be entirely destroyed in large comet and asteroid impacts. The availability of new kinetic parameters for the thermal degradation of amino acids in the solid phase made it possible to readdress this question. We present the results of new high-resolution hydrocode simulations of asteroid and comet impact coupled with recent experimental data for amino acid pyrolysis in the solid phase. Differences due to impact velocity as well as projectile material have been investigated. Effects of angle of impacts were also addressed. The results suggest that some amino acids would survive the shock heating of large (kilometer-radius) cometary impacts. At the time of the origins of life on Earth, the steady-state oceanic concentration of certain amino acids (like aspartic and glutamic acid) delivered by comets could have equaled or substantially exceeded that due to Miller-Urey synthesis in a carbon dioxide-rich atmosphere. Furthermore, in the unlikely case of a grazing impact (impact angle around 5 degrees from the horizontal) an amount of some amino acids comparable to that due to the background steady-state production or delivery would be delivered to the early Earth.

  2. Amino acids derived from Titan tholins

    NASA Technical Reports Server (NTRS)

    Khare, B. N.; Sagan, C.; Ogino, H.; Nagy, B.; Er, C.; Schram, K. H.; Arakawa, E. T.

    1986-01-01

    An organic heteropolymer (Titan tholin) was produced by continuous dc discharge through a 0.9 N2/0.1 CH4 gas mixture at 0.2 mbar pressure, roughly simulating the cloudtop atmosphere of Titan. Treatment of this tholin with 6N HCl yielded 16 amino acids by gas chromatography after derivatization of N-trifluroacetyl isopropyl esters on two different capillary columns. Identifications were confirmed by GC/MS. Glycine, aspartic acid, and alpha- and beta-alanine were produced in greatest abundance; the total yield of amino acids was approximately 10(-2), approximately equal to the yield of urea. The presence of "nonbiological" amino acids, the absence of serine, and the fact that the amino acids are racemic within experimental error together indicate that these molecules are not due to microbial or other contamination, but are derived from the tholin. In addition to the HCN, HC2CN, and (CN)2 found by Voyager, nitriles and aminonitriles should be sought in the Titanian atmosphere and, eventually, amino acids on the surface. These results suggest that episodes of liquid water in the past or future of Titan might lead to major further steps in prebiological organic chemistry on that body.

  3. Trifluoroselenomethionine: A new unnatural amino acid

    USDA-ARS?s Scientific Manuscript database

    Trifluoroselenomethionine (TFSeM), a novel non-natural amino acid, was synthesized in seven steps from N-(tert-butoxycarbonyl)-L-aspartic acid tert-butyl ester. TFSeM shows enhanced methioninase-induced cytotoxicity toward human colon cancer derived HCT- 116 cells compared to selenomethionine (SeM)....

  4. [Dependence of metabolic fecal amino acids on the amino acid content of the feed. 1. Metabolic fecal amino acids of rats fed with maize].

    PubMed

    Krawielitzki, K; Schadereit, R; Völker, T; Reichel, K

    1981-07-01

    The amount of metabolic fecal amino acids (MFAA) in dependence on the amino acid intake was determined for graded maize rations with 15N-labelled rats and the quota of labelled endogenous amino acids in faeces was calculated according to the isotope dilution method. The excretion of amino acids and MFAA in faeces are described as functions of the amino acid intake for 17 amino acids and regressively calculated. For all 17 amino acids investigated, there was a more or less steep increase of MFAA according to an increasing amino acid intake. In contrast to MFAA in N-free feeding, MFAA in feeding with pure maize (16.5% crude protein) increase to the 2- to 4.5-fold value. The thesis of the constancy of the excretion of MFAA can consequently be no longer maintained. The true digestibility according to the conventional method is, on an average of all amino acids, 7.3 units below the one ascertained according to the 15N-isotope method. For the limiting amino acids lysine and threonine the difference is biggest (23 resp. 17 units). Tryptophane as first limiting amino acid could not be determined. The true digestibility of nearly all amino acids ascertained for maize according to the isotope method is above 90%. For the limiting amino acids the expenditure resp. the loss of endogenous amino acids is biggest.

  5. Analysis of amino acids by miniaturised isotachophoresis.

    PubMed

    Prest, Jeff E; Baldock, Sara J; Fielden, Peter R; Goddard, Nicholas J; Brown, Bernard J Treves

    2004-10-08

    A method allowing the miniaturised isotachophoretic analysis of amino acids has been developed. To overcome the problems of carbonate contamination which occur when performing separations at alkaline pH levels glycolate was used as the leading ion. Addition of magnesium to the leading electrolyte as a counter species was found to improve the separations. The method has been used on a poly(methyl methacrylate) microdevice with integrated on-column conductivity detectors. The behaviour of a range of common amino acids was investigated and successful separations of up to seven amino acids were made. Good linearity was observed with calibration curves for aspartic acid and phenylalanine over the range 0.063-1.0 mM. Limits of detection for these two species were calculated to be 0.060 and 0.018 mM, respectively.

  6. Amino acid intake during lactation and amino acids of plasma and human milk.

    PubMed

    Ramirez, I; DeSantiago, S; Tovar, A R; Torres, N

    2001-01-01

    The aim of this study was to determine the free amino acid pool in plasma and milk in marginally nourished lactating women. Twenty-eight rural women (age, 23.9+/-5y; weight 50.2+/-4.9 kg; height, 148.2+/-4.8 cm) were studied under metabolic balance conditions. Subjects were divided into 6 groups (5-6 women in each), representing rural mothers postweaning and in the 15, 3rd, and 6th months of lactation; nonpregnant, nonlactating controls were from rural and urban areas. Amino acid analyses of diet and of plasma and milk samples were performed using a Beckman 6300 amino acid analyzer. Lysine intakes were lower than the recommended intake for lactating women (RDA). Plasma amino acid profiles differed between the lactating and weaned groups: aspartate and isoleucine increased at the 6th month (P < 0.05), while valine declined over weaning time (P < 0.05). In milk, valine and proline decreased at the 6th month (P < 0.05), while serine rose at the 3rd month. Free amino acid pools were 1- to 15-fold higher in plasma than in milk for branched-chain amino acids and basic, aromatic, and neutral amino acids. In mammary tissue these amino acids can be channeled to tissue and milk protein synthesis or to catabolic pathways. Glutamate was 40-fold higher in milk with respect to plasma content. This was the predominant amino acid in the free amino acid pool in milk. These results suggest selective amino acid transport in mammary tissue during lactation.

  7. Amino acids in the Yamato carbonaceous chrondrite from Antarctica

    NASA Technical Reports Server (NTRS)

    Shimoyama, A.; Ponnamperuma, C.; Yanai, K.

    1979-01-01

    Evidence for the presence of amino acids of extraterrestrial origin in the Antarctic Yamato carbonaceous chrondrite is presented. Hydrolyzed and nonhydrolyzed water-extracted amino acid samples from exterior, middle and interior portions of the meteorite were analyzed by an amino acid analyzer and by gas chromatography of N-TFA-isopropyl amino acid derivatives. Nine protein and six nonprotein amino acids were detected in the meteorite at abundances between 34 and less than one nmole/g, with equal amounts in interior and exterior portions. Nearly equal abundances of the D and L enantiomers of alanine, aspartic acid and glutamic acid were found, indicating the abiotic, therefore extraterrestrial, origin of the amino acids. The Antarctic environment and the uniformity of protein amino acid abundances are discussed as evidence against the racemization of terrestrially acquired amino acids, and similarities between Yamato amino acid compositions and the amino acid compositions of the Murchison and Murray type II carbonaceous chrondrites are indicated.

  8. Computational protein design quantifies structural constraints on amino acid covariation.

    PubMed

    Ollikainen, Noah; Kortemme, Tanja

    2013-01-01

    Amino acid covariation, where the identities of amino acids at different sequence positions are correlated, is a hallmark of naturally occurring proteins. This covariation can arise from multiple factors, including selective pressures for maintaining protein structure, requirements imposed by a specific function, or from phylogenetic sampling bias. Here we employed flexible backbone computational protein design to quantify the extent to which protein structure has constrained amino acid covariation for 40 diverse protein domains. We find significant similarities between the amino acid covariation in alignments of natural protein sequences and sequences optimized for their structures by computational protein design methods. These results indicate that the structural constraints imposed by protein architecture play a dominant role in shaping amino acid covariation and that computational protein design methods can capture these effects. We also find that the similarity between natural and designed covariation is sensitive to the magnitude and mechanism of backbone flexibility used in computational protein design. Our results thus highlight the necessity of including backbone flexibility to correctly model precise details of correlated amino acid changes and give insights into the pressures underlying these correlations.

  9. Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation

    PubMed Central

    Ollikainen, Noah; Kortemme, Tanja

    2013-01-01

    Amino acid covariation, where the identities of amino acids at different sequence positions are correlated, is a hallmark of naturally occurring proteins. This covariation can arise from multiple factors, including selective pressures for maintaining protein structure, requirements imposed by a specific function, or from phylogenetic sampling bias. Here we employed flexible backbone computational protein design to quantify the extent to which protein structure has constrained amino acid covariation for 40 diverse protein domains. We find significant similarities between the amino acid covariation in alignments of natural protein sequences and sequences optimized for their structures by computational protein design methods. These results indicate that the structural constraints imposed by protein architecture play a dominant role in shaping amino acid covariation and that computational protein design methods can capture these effects. We also find that the similarity between natural and designed covariation is sensitive to the magnitude and mechanism of backbone flexibility used in computational protein design. Our results thus highlight the necessity of including backbone flexibility to correctly model precise details of correlated amino acid changes and give insights into the pressures underlying these correlations. PMID:24244128

  10. Detection of non-protein amino acids in the presence of protein amino acids. II.

    NASA Technical Reports Server (NTRS)

    Shapshak, P.; Okaji, M.

    1972-01-01

    Studies conducted with the JEOL 5AH amino acid analyzer are described. This instrument makes possible the programming of the chromatographic process. Data are presented showing the separations of seventeen non-protein amino acids in the presence of eighteen protein amino acids. It is pointed out that distinct separations could be obtained in the case of a number of chemically similar compounds, such as ornithine and lysine, N-amidino alanine and arginine, and iminodiacetic acid and S-carboxymethyl cysteine and aspartic acid.

  11. Biodegradable polymers derived from amino acids.

    PubMed

    Khan, Wahid; Muthupandian, Saravanan; Farah, Shady; Kumar, Neeraj; Domb, Abraham J

    2011-12-08

    In the past three decades, the use of polymeric materials has increased dramatically for biomedical applications. Many α-amino acids derived biodegradable polymers have also been intensely developed with the main goal to obtain bio-mimicking functional biomaterials. Polymers derived from α-amino acids may offer many advantages, as these polymers: (a) can be modified further to introduce new functions such as imaging, molecular targeting and drugs can be conjugated chemically to these polymers, (b) can improve on better biological properties like cell migration, adhesion and biodegradability, (c) can improve on mechanical and thermal properties and (d) their degradation products are expected to be non-toxic and readily metabolized/excreted from the body. This manuscript focuses on biodegradable polymers derived from natural amino acids, their synthesis, biocompatibility and biomedical applications. It is observed that polymers derived from α-amino acids constitute a promising family of biodegradable materials. These provide innovative multifunctional polymers possessing amino acid side groups with biological activity and with innumerous potential applications.

  12. Distinguishing Proteins From Arbitrary Amino Acid Sequences

    PubMed Central

    Yau, Stephen S.-T.; Mao, Wei-Guang; Benson, Max; He, Rong Lucy

    2015-01-01

    What kinds of amino acid sequences could possibly be protein sequences? From all existing databases that we can find, known proteins are only a small fraction of all possible combinations of amino acids. Beginning with Sanger's first detailed determination of a protein sequence in 1952, previous studies have focused on describing the structure of existing protein sequences in order to construct the protein universe. No one, however, has developed a criteria for determining whether an arbitrary amino acid sequence can be a protein. Here we show that when the collection of arbitrary amino acid sequences is viewed in an appropriate geometric context, the protein sequences cluster together. This leads to a new computational test, described here, that has proved to be remarkably accurate at determining whether an arbitrary amino acid sequence can be a protein. Even more, if the results of this test indicate that the sequence can be a protein, and it is indeed a protein sequence, then its identity as a protein sequence is uniquely defined. We anticipate our computational test will be useful for those who are attempting to complete the job of discovering all proteins, or constructing the protein universe. PMID:25609314

  13. Amino acid pools in cultured muscle cells.

    PubMed

    Low, R B; Stirewalt, W S; Rittling, S R; Woodworth, R C

    1984-01-01

    Compartmentalization of cellular amino acid pools occurs in cultures of cardiac and skeletal muscle cells, but the factors involved in this are not clear. We have further defined this problem by analyzing the intracellular free leucine and the transfer-RNA-(tRNA)-bound leucine pool in cultures of skeletal and cardiac muscle incubated with 3H-leucine in the presence and absence of serum and amino acids. Withdrawal of nitrogen substrates caused substantial changes in leucine pool relationships--in particular, a change in the degree to which intracellular free leucine and tRNA-leucine were derived from the culture medium. In separate experiments, the validity of our tRNA measurements was confirmed by measurements of the specific activity of newly synthesized ferritin after iron induction. We discuss the implications of these findings with regard to factors involved in the control of amino acid flux through the cell, as well as with regard to design of experiments using isotopic amino acids to measure rates of amino acid utilization.

  14. Amino acid uptake in rust fungi

    PubMed Central

    Struck, Christine

    2015-01-01

    The plant pathogenic rust fungi colonize leaf tissue and feed off their host plants without killing them. Certain economically important species of different genera such as Melampsora, Phakopsora, Puccinia, or Uromyces are extensively studied for resolving the mechanisms of the obligate biotrophy. As obligate parasites rust fungi only can complete their life cycle on living hosts where they grow through the leaf tissue by developing an extended network of intercellular hyphae from which intracellular haustoria are differentiated. Haustoria are involved in key functions of the obligate biotrophic lifestyle: suppressing host defense responses and acquiring nutrients. This review provides a survey of rust fungi nitrogen nutrition with special emphasis on amino acid uptake. A variety of sequences of amino acid transporter genes of rust fungi have been published; however, transport activity of only three in planta highly up-regulated amino acid permeases have been characterized. Functional and immunohistochemical investigations have shown the specificity and localization of these transporters. Sequence data of various genome projects allowed identification of numerous rust amino acid transporter genes. An in silico analysis reveals that these genes can be classified into different transporter families. In addition, genetic and molecular data of amino acid transporters have provided new insights in the corresponding metabolic pathways. PMID:25699068

  15. Amino acid uptake in rust fungi.

    PubMed

    Struck, Christine

    2015-01-01

    The plant pathogenic rust fungi colonize leaf tissue and feed off their host plants without killing them. Certain economically important species of different genera such as Melampsora, Phakopsora, Puccinia, or Uromyces are extensively studied for resolving the mechanisms of the obligate biotrophy. As obligate parasites rust fungi only can complete their life cycle on living hosts where they grow through the leaf tissue by developing an extended network of intercellular hyphae from which intracellular haustoria are differentiated. Haustoria are involved in key functions of the obligate biotrophic lifestyle: suppressing host defense responses and acquiring nutrients. This review provides a survey of rust fungi nitrogen nutrition with special emphasis on amino acid uptake. A variety of sequences of amino acid transporter genes of rust fungi have been published; however, transport activity of only three in planta highly up-regulated amino acid permeases have been characterized. Functional and immunohistochemical investigations have shown the specificity and localization of these transporters. Sequence data of various genome projects allowed identification of numerous rust amino acid transporter genes. An in silico analysis reveals that these genes can be classified into different transporter families. In addition, genetic and molecular data of amino acid transporters have provided new insights in the corresponding metabolic pathways.

  16. Amino Acids Profiles in Biological Media

    SciTech Connect

    Iordache, A.; Horj, E.; Morar, S.; Cozar, O.; Culea, M.; Ani, A. R.; Mesaros, C.

    2010-08-04

    An accurate analytical method was developed to determine amino acids in some biological specimens by GC/MS technique. Stable isotopes provide useful tools for a variety of studies, offering ideal internal standards in quantitative information. Isotopic dilution gas chromatography--mass spectrometry (ID-GC/MS) is the techniques used for quantitative analysis of compounds labeled with stable isotopes. A Trace DSQ Thermo Finnigan quadrupole mass spectrometer coupled with a Trace GC was used. Amino acids were separated on a Rtx-5 MS capillary column, 30 mx0.25 mm, 0.25 {mu}m film thickness, using a temperature program from 50 deg. C, 1 min, 6 deg. C/min at 100 deg. C, 4 deg. C/min at 200 deg. C, 20 deg. C/min at 300 deg. C, (3 min). The transfer line temperature was 250 deg. C, the injector temperature 200 deg. C and ion source temperature 250 deg. C; splitter: 10:1. Electron energy was 70 eV and emission current, 100 {mu}A. The amino acids were purified on a Dowex 50W-W8 exchange resin and were derivatized in a procedure following two steps to obtain trifluoroacetyl butyl esters. The identification of amino acids was obtained by using NIST library but also by using amino acid standards.

  17. Regulation of renal amino acid transporters during metabolic acidosis.

    PubMed

    Moret, Caroline; Dave, Mital H; Schulz, Nicole; Jiang, Jean X; Verrey, Francois; Wagner, Carsten A

    2007-02-01

    The kidney plays a major role in acid-base homeostasis by adapting the excretion of acid equivalents to dietary intake and metabolism. Urinary acid excretion is mediated by the secretion of protons and titratable acids, particularly ammonia. NH(3) is synthesized in proximal tubule cells from glutamine taken up via specific amino acid transporters. We tested whether kidney amino acid transporters are regulated in mice in which metabolic acidosis was induced with NH(4)Cl. Blood gas and urine analysis confirmed metabolic acidosis. Real-time RT-PCR was performed to quantify the mRNAs of 16 amino acid transporters. The mRNA of phosphoenolpyruvate carboxykinase (PEPCK) was quantified as positive control for the regulation and that of GAPDH, as internal standard. In acidosis, the mRNA of kidney system N amino acid transporter SNAT3 (SLC38A3/SN1) showed a strong induction similar to that of PEPCK, whereas all other tested mRNAs encoding glutamine or glutamate transporters were unchanged or reduced in abundance. At the protein level, Western blotting and immunohistochemistry demonstrated an increased abundance of SNAT3 and reduced expression of the basolateral cationic amino acid/neutral amino acid exchanger subunit y(+)-LAT1 (SLC7A7). SNAT3 was localized to the basolateral membrane of the late proximal tubule S3 segment in control animals, whereas its expression was extended to the earlier S2 segment of the proximal tubule during acidosis. Our results suggest that the selective regulation of SNAT3 and y(+)LAT1 expression may serve a major role in the renal adaptation to acid secretion and thus for systemic acid-base balance.

  18. Amino acid "little Big Bang": representing amino acid substitution matrices as dot products of Euclidian vectors.

    PubMed

    Zimmermann, Karel; Gibrat, Jean-François

    2010-01-04

    Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This paper deals with the problem of finding a representation that provides a comprehensive description of amino acid intrinsic properties consistent with the substitution matrices. We present a Euclidian vector representation of the amino acids, obtained by the singular value decomposition of the substitution matrices. The substitution matrix entries correspond to the dot product of amino acid vectors. We apply this vector encoding to the study of the relative importance of various amino acid physicochemical properties upon the substitution matrices. We also characterize and compare the PAM and BLOSUM series substitution matrices. This vector encoding introduces a Euclidian metric in the amino acid space, consistent with substitution matrices. Such a numerical description of the amino acid is useful when intrinsic properties of amino acids are necessary, for instance, building sequence profiles or finding consensus sequences, using machine learning algorithms such as Support Vector Machine and Neural Networks algorithms.

  19. Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors

    PubMed Central

    2010-01-01

    Background Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This paper deals with the problem of finding a representation that provides a comprehensive description of amino acid intrinsic properties consistent with the substitution matrices. Results We present a Euclidian vector representation of the amino acids, obtained by the singular value decomposition of the substitution matrices. The substitution matrix entries correspond to the dot product of amino acid vectors. We apply this vector encoding to the study of the relative importance of various amino acid physicochemical properties upon the substitution matrices. We also characterize and compare the PAM and BLOSUM series substitution matrices. Conclusions This vector encoding introduces a Euclidian metric in the amino acid space, consistent with substitution matrices. Such a numerical description of the amino acid is useful when intrinsic properties of amino acids are necessary, for instance, building sequence profiles or finding consensus sequences, using machine learning algorithms such as Support Vector Machine and Neural Networks algorithms. PMID:20047649

  20. Implications of amino acid substitutions in GyrA at position 83 in terms of oxolinic acid resistance in field isolates of Burkholderia glumae, a causal agent of bacterial seedling rot and grain rot of rice.

    PubMed

    Maeda, Yukiko; Kiba, Akinori; Ohnishi, Kouhei; Hikichi, Yasufumi

    2004-09-01

    Oxolinic acid (OA), a quinolone, inhibits the activity of DNA gyrase composed of GyrA and GyrB and shows antibacterial activity against Burkholderia glumae. Since B. glumae causes bacterial seedling rot and grain rot of rice, both of which are devastating diseases, the emergence of OA-resistant bacteria has important implications on rice cultivation in Japan. Based on the MIC of OA, 35 B. glumae field isolates isolated from rice seedlings grown from OA-treated seeds in Japan were divided into sensitive isolates (OSs; 0.5 microg/ml), moderately resistant isolates (MRs; 50 microg/ml), and highly resistant isolates (HRs; > or =100 microg/ml). Recombination with gyrA of an OS, Pg-10, led MRs and HRs to become OA susceptible, suggesting that gyrA mutations are involved in the OA resistance of field isolates. The amino acid at position 83 in the GyrA of all OSs was Ser, but in all MRs and HRs it was Arg and Ile, respectively. Ser83Arg and Ser83Ile substitutions in the GyrA of an OS, Pg-10, resulted in moderate and high OA resistance, respectively. Moreover, Arg83Ser and Ile83Ser substitutions in the GyrA of MRs and HRs, respectively, resulted in susceptibility to OA. These results suggest that Ser83Arg and Ser83Ile substitutions in GyrA are commonly responsible for resistance to OA in B. glumae field isolates.

  1. The metabolism of "surplus" amino acids.

    PubMed

    Bender, David A

    2012-08-01

    For an adult in N balance, apart from small amounts of amino acids required for the synthesis of neurotransmitters, hormones, etc, an amount of amino acids almost equal to that absorbed from the diet can be considered to be "surplus" in that it will be catabolized. The higher diet-induced thermogenesis from protein than from carbohydrate or fat has generally been assumed to be due to increased protein synthesis, which is ATP expensive. To this must be added the ATP cost of protein catabolism through the ubiquitin-proteasome pathway. Amino acid catabolism will add to thermogenesis. Deamination results in net ATP formation except when serine and threonine deaminases are used, but there is the energy cost of synthesizing glutamine in extra-hepatic tissues. The synthesis of urea has a net cost of only 1·5 × ATP when the ATP yield from fumarate metabolism is offset against the ATP cost of the urea cycle, but this offset is thermogenic. In fasting and on a low carbohydrate diet as much of the amino acid carbon as possible will be used for gluconeogenesis - an ATP-expensive, and hence thermogenic, process. Complete oxidation of most amino acid carbon skeletons also involves a number of thermogenic steps in which ATP (or GTP) or reduced coenzymes are utilized. There are no such thermogenic steps in the metabolism of pyruvate, acetyl CoA or acetoacetate, but for amino acids that are metabolized by way of the citric acid cycle intermediates there is thermogenesis ranging from 1 up to 7 × ATP equivalent per mol.

  2. Economic aspects of amino acids production.

    PubMed

    Mueller, Udo; Huebner, Susanna

    2003-01-01

    Amino acids represent basic elements of proteins, which as a main source of nutrition themselves serve as a major reserve for maintaining essential functions of humans as well as animals. Taking the recent state of scientific knowledge into account, the industrial sector of amino acids is a priori "suitable" to a specific kind of an ecologically sound way of production, which is based on biotechnology. The following article may point out characteristics of this particular industrial sector and illustrates the applicability of the latest economic methods, founded on development of the discipline of bionics in order to describe economic aspects of amino acids markets. The several biochemical and technological fields of application of amino acids lead to specific market structures in high developed and permanently evolving systems. The Harvard tradition of industrial economics explains how market structures mould the behaviour of the participants and influences market results beyond that. A global increase in intensity of competition confirms the notion that the supply-side is characterised by asymmetric information in contrast to Kantzenbachs concept of "narrow oligopoly" with symmetrical shared knowledge about market information. Departing from this point, certain strategies of companies in this market form shall be derived. The importance of Research and Development increases rapidly and leads to innovative manufacturing methods which replace more polluting manufacturing processes like acid hydrolysis. In addition to these modifications within the production processes the article deals furthermore with the pricing based on product life cycle concept and introduces specific applications of tools like activity based costing and target costing to the field of amino acid production. The authors come to the conclusion that based on a good transferability of latest findings in bionics and ecological compatibility competitors in amino acids manufacturing are well advised

  3. Exogenous amino acids stimulate net muscle protein synthesis in the elderly.

    PubMed Central

    Volpi, E; Ferrando, A A; Yeckel, C W; Tipton, K D; Wolfe, R R

    1998-01-01

    We have investigated the response of amino acid transport and protein synthesis in healthy elderly individuals (age 71+/-2 yr) to the stimulatory effect of increased amino acid availability. Muscle protein synthesis and breakdown, and amino acid transport were measured in the postabsorptive state and during the intravenous infusion of an amino acid mixture. Muscle-free amino acid kinetics were calculated by means of a three compartment model using data obtained by femoral arterio-venous catheterization and muscle biopsies from the vastus lateralis during the infusion of stable isotope tracers of amino acids. In addition, muscle protein fractional synthetic rate (FSR) was measured. Peripheral amino acid infusion significantly increased amino acid delivery to the leg, amino acid transport, and muscle protein synthesis when measured either with the three compartment model (P < 0.05) or with the traditional precursor-product approach (FSR increased from 0. 0474+/-0.0054 to 0.0940+/-0.0143%/h, P < 0.05). Because protein breakdown did not change during amino acid infusion, a positive net balance of amino acids across the muscle was achieved. We conclude that, although muscle mass is decreased in the elderly, muscle protein anabolism can nonetheless be stimulated by increased amino acid availability. We thus hypothesize that muscle mass could be better maintained with an increased intake of protein or amino acids. PMID:9576765

  4. Amino acid composition and chemical evaluation of protein quality of cereals as affected by insect infestation.

    PubMed

    Jood, S; Kapoor, A C; Singh, R

    1995-09-01

    A significant decrease in essential amino acids of wheat, maize and sorghum was observed due to grain infestation caused by mixed populations of Trogoderma granarium Everts and Rhizopertha dominica Fabricius (50:50). Non-essential amino acids were also adversely affected. Among the essential amino acids, maximum reduction was found in methionine, isoleucine and lysine in infested wheat, maize and sorghum grains, respectively. Lysine, with lowest chemical score in uninfested and infested grains of three cereals, is the first limiting amino acid. Insect infestation caused significant (p < 0.05) reduction in the chemical score of all the essential amino acids, yet did not change the position of first and second limiting amino acids in wheat and sorghum. However, in case of maize, isoleucine became the second limiting amino acid. Infested grains also showed substantial reduction in essential amino acid index, calculated biological value and requirement index.

  5. Amino acid composition of human milk is not unique.

    PubMed

    Davis, T A; Nguyen, H V; Garcia-Bravo, R; Fiorotto, M L; Jackson, E M; Lewis, D S; Lee, D R; Reeds, P J

    1994-07-01

    To determine whether the amino acid pattern of human milk is unique, we compared the amino acid pattern of human milk with the amino acid patterns of the milks of great apes (chimpanzee and gorilla), lower primates (baboon and rhesus monkey) and nonprimates (cow, goat, sheep, llama, pig, horse, elephant, cat and rat). Amino acid pattern was defined as the relative proportion of each amino acid (protein-bound plus free) (in mg) to the total amino acids (in g). Total amino acid concentration was lower in primate milk than in nonprimate milk. There were commonalities in the overall amino acid pattern of the milks of all species sampled; the most abundant amino acids were glutamate (plus glutamine, 20%), proline (10%) and leucine (10%). Essential amino acids were 40%, branched-chain amino acids 20%, and sulfur amino acids 4% of the total amino acids. The amino acid pattern of human milk was more similar to those of great apes than to those of lower primates. For example, cystine was higher and methionine was lower in primate milks than in nonprimate milks, and in great ape and human milks than in lower primate milks. Because the milk amino acid patterns of the human and elephant, both slow-growing species, were dissimilar, the amino acid pattern of human milk seems unrelated to growth rate.

  6. A new classification of HLA-DRB1 alleles based on acid-base properties of the amino acids located at positions 13, 70 and 71: impact on ACPA status or structural progression, and meta-analysis on 1235 patients with rheumatoid from two cohorts (ESPOIR and EAC cohort).

    PubMed

    Ruyssen-Witrand, Adeline; van Steenbergen, Hanna W; van Heemst, Jurgen; Gourraud, Pierre-Antoine; Nigon, Delphine; Lukas, Cédric; Miceli-Richard, Corinne; Jamard, Bénédicte; Cambon-Thomsen, Anne; Cantagrel, Alain; Dieudé, Philippe; van der Helm-van Mil, Annette H M; Constantin, Arnaud

    2015-01-01

    To group HLA-DRB1 alleles based on acid-base properties of amino acids at positions 13, 70 and 71 and analyse their association with the presence of anticitrullinated peptide antibodies (ACPA) and structural progression in 2 cohorts of early rheumatoid arthritis (RA). Patients with RA (N=612) from ESPOIR cohort and from EAC cohort (n=624) were genotyped for HLA-DRB1 alleles. The alleles containing the RAA sequence at positions 72-74 were classified into 3 groups according to the amino acid at positions 13, 70 and 71: BB encoding basic amino acids at positions 13, 70 and 71; A encoding acidic amino acids at positions 70 and 71; and BN encoding either neutral amino acids at position 13 and basic amino acids at positions 70 and 71, or basic amino acid at position 13 and neutral amino acids at positions 70 and 71. The associations between the different alleles and (1) the ACPA presence, and (2) the structural progression were assessed by χ(2) test; a meta-analysis was performed on the 2 cohorts using the Mantel-Haenszel method. After meta-analysis, BB alleles were significantly associated with ACPA presence (OR (95% CI) 4.08 (3.14 to 5.31)) and structural progression (OR (95% CI) 2.33 (1.76 to 3.09)). The alleles protected significantly against ACPA presence (OR (95% CI) 0.37 (0.28 to 0.50)) and structural progression (OR (95% CI) 0.34 (0.23 to 0.50)). This acid-base classification allowed to separate another group BN with an intermediate risk of ACPA production (OR (95% CI) 1.14 (0.91 to 1.44)) and structural progression (OR (95% CI) 1.01 (0.77 to 1.33)). This new classification permitted to make a hierarchy of HLA-DRB1 alleles in terms of association with ACPA presence or structural progression in early RA.

  7. L-amino acid oxidases with specificity for basic L-amino acids in cyanobacteria.

    PubMed

    Gau, Achim E; Heindl, Achim; Nodop, Anke; Kahmann, Uwe; Pistorius, Elfriede K

    2007-01-01

    The two closely related fresh water cyanobacteria Synechococcus elongatus PCC 6301 and Synechococcus elongatus PCC 7942 have previously been shown to constitutively express a FAD-containing L-amino acid oxidase with high specificity for basic L-amino acids (L-arginine being the best substrate). In this paper we show that such an enzyme is also present in the fresh water cyanobacterium Synechococcus cedrorum PCC 6908. In addition, an improved evaluation of the nucleotide/amino acid sequence of the L-amino acid oxidase of Synechococcus elongatus PCC 6301 (encoded by the aoxA gene) with respect to the FAD-binding site and a translocation pathway signal sequence will be given. Moreover, the genome sequences of 24 cyanobacteria will be evaluated for the occurrence of an aoxA-similar gene. In the evaluated cyanobacteria 15 genes encoding an L-amino acid oxidase-similar protein will be found.

  8. Glutamate: a truly functional amino acid.

    PubMed

    Brosnan, John T; Brosnan, Margaret E

    2013-09-01

    Glutamate is one of the most abundant of the amino acids. In addition to its role in protein structure, it plays critical roles in nutrition, metabolism and signaling. Post-translational carboxylation of glutamyl residues increases their affinity for calcium and plays a major role in hemostasis. Glutamate is of fundamental importance to amino acid metabolism, yet the great bulk of dietary glutamate is catabolyzed within the intestine. It is necessary for the synthesis of key molecules, such as glutathione and the polyglutamated folate cofactors. It plays a major role in signaling. Within the central nervous system, glutamate is the major excitatory neurotransmitter and its product, GABA, the major inhibitory neurotransmitter. Glutamate interaction with specific taste cells in the tongue is a major component of umami taste. The finding of glutamate receptors throughout the gastrointestinal tract has opened up a new vista in glutamate function. Glutamate is truly a functional amino acid.

  9. Cometary Amino Acids from the STARDUST Mission

    NASA Technical Reports Server (NTRS)

    Cook, Jamie Elsila

    2009-01-01

    NASA's Stardust spacecraft returned samples from comet 81 P/WiId 2 to Earth in January 2006. Examinations of the organic compounds in cometary samples can reveal information about the prebiotic organic inventory present on the early Earth and within the early Solar System, which may have contributed to the origin of life. Preliminary studies of Stardust material revealed the presence of a suite of organic compounds including several amines and amino acids, but the origin of these compounds (cometary vs. terrestrial contamination) could not be identified. We have recently measured the carbon isotopic ratios of these amino acids to determine their origin, leading to the first detection of a cometary amino acid.

  10. Cometary Amino Acids from the STARDUST Mission

    NASA Technical Reports Server (NTRS)

    Cook, Jamie Elsila

    2009-01-01

    NASA's Stardust spacecraft returned samples from comet 81 P/WiId 2 to Earth in January 2006. Examinations of the organic compounds in cometary samples can reveal information about the prebiotic organic inventory present on the early Earth and within the early Solar System, which may have contributed to the origin of life. Preliminary studies of Stardust material revealed the presence of a suite of organic compounds including several amines and amino acids, but the origin of these compounds (cometary vs. terrestrial contamination) could not be identified. We have recently measured the carbon isotopic ratios of these amino acids to determine their origin, leading to the first detection of a cometary amino acid.

  11. Inhibited muscle amino acid uptake in sepsis.

    PubMed Central

    Hasselgren, P O; James, J H; Fischer, J E

    1986-01-01

    Amino acid uptake in vivo was determined in soleus (SOL) muscle, diaphragm, heart, and liver following intravenous injection of [3H]-alpha-amino-isobutyric acid ([3H]-AIB) in rats made septic by cecal ligation and puncture (CLP) and in sham-operated controls. Muscle amino acid transport was also measured in vitro by determining uptake of [3H]-AIB in incubated extensor digitorum longus (EDL) and SOL muscles. Results were expressed as distribution ratio between [3H]-AIB in intracellular and extracellular fluid. AIB uptake in vivo was reduced by 90% in SOL and cardiac muscle and by 45% in diaphragm 16 hours after CLP. In contrast, AIB uptake by liver was almost four times higher in septic than in control animals. AIB uptake in vitro was reduced by 18% in EDL 8 hours after CLP but was not significantly altered in SOL at the same time point. Sixteen hours after CLP, AIB uptake was significantly reduced in both muscles, i.e., by 17% in EDL and by 65% in SOL. When muscles from untreated rats were incubated in the presence of plasma from septic animals (16 hours CLP) or from animals injected with endotoxin (2 mg/kg body weight), AIB uptake was reduced. Addition of endotoxin in vitro (2-200 micrograms/ml) to incubated muscles did not affect AIB uptake. The results suggest that sepsis leads to marked impairment of amino acid transport system A in muscle and that this impairment is mediated by a circulating factor that is not endotoxin. Reduced uptake of amino acids by skeletal muscle during sepsis may divert amino acids to the liver for increased gluconeogenesis and protein synthesis. PMID:3963895

  12. Microbial degradation of poly(amino acid)s.

    PubMed

    Obst, Martin; Steinbüchel, Alexander

    2004-01-01

    Natural poly(amino acid)s are a group of poly(ionic) molecules (ionomers) with various biological functions and putative technical applications and play, therefore, an important role both in nature and in human life. Because of their biocompatibility and their synthesis from renewable resources, poly(amino acid)s may be employed for many different purposes covering a broad spectrum of medical, pharmaceutical, and personal care applications as well as the domains of agriculture and of environmental applications. Biodegradability is one important advantage of naturally occurring poly(amino acid)s over many synthetic polymers. The intention of this review is to give an overview about the enzyme systems catalyzing the initial steps in poly(amino acid) degradation. The focus is on the naturally occurring poly(amino acid)s cyanophycin, poly(epsilon-L-lysine) and poly(gamma-glutamic acid); but biodegradation of structurally related synthetic polyamides such as poly(aspartic acid) and nylons, which are known from various technical applications, is also included.

  13. Amino acid nutrition of fishes: requirements and supplementation of diets

    USGS Publications Warehouse

    Ketola, H.G.

    1982-01-01

    The purpose of this paper is: (1) to make a concise review of the published dietary requirements of fishes for amino acids, (2) to describe recent findings at the Tunison Laboratory concerning amino acid nutrition of trout, (3) to review specific signs of deficiency of amino acids, and (4) to discuss use of the fish egg amino acid pattern as a guideline to formulating new feeds or studying amino acid requirements of fishes for which there is limited information on their quantitative requirements.

  14. Substrate specificity of the human UDP-glucuronosyltransferase UGT2B4 and UGT2B7. Identification of a critical aromatic amino acid residue at position 33.

    PubMed

    Barre, Lydia; Fournel-Gigleux, Sylvie; Finel, Moshe; Netter, Patrick; Magdalou, Jacques; Ouzzine, Mohamed

    2007-03-01

    The human UDP-glucuronosyltransferase (UGT) isoforms UGT2B4 and UGT2B7 play a major role in the detoxification of bile acids, steroids and phenols. These two isoforms present distinct but overlapping substrate specificity, sharing common substrates such as the bile acid hyodeoxycholic acid (HDCA) and catechol-estrogens. Here, we show that in UGT2B4, substitution of phenylalanine 33 by leucine suppressed the activity towards HDCA, and impaired the glucuronidation of several substrates, including 4-hydroxyestrone and 17-epiestriol. On the other hand, the substrate specificity of the mutant UGT2B4F33Y, in which phenylalanine was replaced by tyrosine, as found at position 33 of UGT2B7, was similar to wild-type UGT2B4. In the case of UGT2B7, replacement of tyrosine 33 by leucine strongly reduced the activity towards all the tested substrates, with the exception of 17-epiestriol. In contrast, mutation of tyrosine 33 by phenylalanine exhibited similar or even somewhat higher activities than wild-type UGT2B7. Hence, the results strongly indicated that the presence of an aromatic residue at position 33 is important for the activity and substrate specificity of both UGT2B4 and UGT2B7.

  15. Amino acid homeostasis and signalling in mammalian cells and organisms

    PubMed Central

    Bröer, Angelika

    2017-01-01

    Cells have a constant turnover of proteins that recycle most amino acids over time. Net loss is mainly due to amino acid oxidation. Homeostasis is achieved through exchange of essential amino acids with non-essential amino acids and the transfer of amino groups from oxidised amino acids to amino acid biosynthesis. This homeostatic condition is maintained through an active mTORC1 complex. Under amino acid depletion, mTORC1 is inactivated. This increases the breakdown of cellular proteins through autophagy and reduces protein biosynthesis. The general control non-derepressable 2/ATF4 pathway may be activated in addition, resulting in transcription of genes involved in amino acid transport and biosynthesis of non-essential amino acids. Metabolism is autoregulated to minimise oxidation of amino acids. Systemic amino acid levels are also tightly regulated. Food intake briefly increases plasma amino acid levels, which stimulates insulin release and mTOR-dependent protein synthesis in muscle. Excess amino acids are oxidised, resulting in increased urea production. Short-term fasting does not result in depletion of plasma amino acids due to reduced protein synthesis and the onset of autophagy. Owing to the fact that half of all amino acids are essential, reduction in protein synthesis and amino acid oxidation are the only two measures to reduce amino acid demand. Long-term malnutrition causes depletion of plasma amino acids. The CNS appears to generate a protein-specific response upon amino acid depletion, resulting in avoidance of an inadequate diet. High protein levels, in contrast, contribute together with other nutrients to a reduction in food intake. PMID:28546457

  16. A Single-Amino-Acid Substitution at Position 225 in HA Alters the Transmissibility of Eurasian Avian-like H1N1 Swine Influenza Virus in Guinea Pigs.

    PubMed

    Wang, Zeng; Yang, Huanliang; Chen, Yan; Tao, Shiyu; Liu, Liling; Kong, Huihui; Ma, Shujie; Meng, Fei; Suzuki, Yasuo; Qiao, Chuanling; Chen, Hualan

    2017-08-16

    Efficient transmission from human to human is the prerequisite for an influenza virus to cause a pandemic; however, the molecular determinants of influenza virus transmission are still largely unknown. In this study, we explored the molecular basis for transmission of Eurasian avian-like H1N1 (EAH1N1) swine influenza viruses by comparing two viruses that are genetically similar but differ in their transmissibility in guinea pigs: the A/swine/Guangxi/18/2011 virus (GX/18) is highly transmissible by respiratory droplet in guinea pigs, whereas the A/swine/Heilongjiang/27/2012 virus (HLJ/27) does not transmit in this animal model. We used reverse genetics to generate a series of reassortants and mutants in the GX/18 background and tested their transmissibility in guinea pigs. We found that a single amino acid substitution of glycine (G) for glutamic acid (E) at position 225 (E225G) in the HA1 protein completely abolished the respiratory droplet transmission of GX/18, whereas the substitution of E for G at the same position (G225E) in HA1 enabled HLJ/27 to transmit in guinea pigs. We investigated the underlying mechanism and found that viruses bearing 225E in HA1 replicated more rapidly than viruses bearing 225G due to differences in assembly and budding efficiency. Our study indicates that the amino acid 225E in HA1 plays a key role in EAH1N1 swine influenza virus transmission and provides important information for evaluating the pandemic potential of field influenza strains.IMPORTANCE Efficient transmission among humans is a prerequisite for a novel influenza virus to cause a human pandemic. Transmissibility of influenza viruses is a polygenic trait, and understanding the genetic determinants for transmissibility will provide useful insights for evaluating the pandemic potential of influenza viruses in the field. Several amino acids in the hemagglutinin (HA) protein of influenza viruses have been shown to be important for transmissibility, usually by increasing virus

  17. Polymerization of amino acids containing nucleotide bases

    NASA Technical Reports Server (NTRS)

    Ben Cheikh, Azzouz; Orgel, Leslie E.

    1990-01-01

    The nucleoamino acids 1-(3'-amino,3'-carboxypropyl)uracil (3) and 9-(3'-amino,3'-carboxypropyl)adenine (4) have been prepared as (L)-en-antiomers and as racemic mixtures. When 3 or 4 is suspended in water and treated with N,N'-carbon-yldiimidazole, peptides are formed in good yield. The products formed from the (L)-enantiomers are hydrolyzed to the monomeric amino acids by pronase. Attempts to improve the efficiency of these oligomerizations by including a polyuridylate template in the reaction mixture were not successful. Similarly, oligomers derived from the (L)-enantiomer of 3 did not act as templates to facilitate the oligomerization of 4.

  18. Porcine proinsulin: characterization and amino acid sequence.

    PubMed

    Chance, R E; Ellis, R M; Bromer, W W

    1968-07-12

    Proinsulin in nearly homogeneous form has been isolated from a preparation of porcine insulin. A molecular weight close to 9100 was calculated from the amino acid composition and from sedimentation-equilibrium studies. Through the action of trypsin this single-chain protein is transformed to desalanine insulin by cleavage of a polypeptide chain connecting the carboxy-terminus of the B chain to the amino-terminus of the A chain of insulin. The amino acid sequence of this connecting peptide was found to be Arg-Arg-Glu-Ala-Gln-Asn-Pro-Gln-Ala-Gly-Ala-Val-Glu-Leu-Gly-Gly-Gly-Leu-Gly-Gly-Leu-Gln-Ala-Leu-Ala-Leu-Glu-Gly-Pro-Pro-Gln-Lys-Arg.

  19. Polymerization of amino acids containing nucleotide bases

    NASA Technical Reports Server (NTRS)

    Ben Cheikh, Azzouz; Orgel, Leslie E.

    1990-01-01

    The nucleoamino acids 1-(3'-amino,3'-carboxypropyl)uracil (3) and 9-(3'-amino,3'-carboxypropyl)adenine (4) have been prepared as (L)-en-antiomers and as racemic mixtures. When 3 or 4 is suspended in water and treated with N,N'-carbon-yldiimidazole, peptides are formed in good yield. The products formed from the (L)-enantiomers are hydrolyzed to the monomeric amino acids by pronase. Attempts to improve the efficiency of these oligomerizations by including a polyuridylate template in the reaction mixture were not successful. Similarly, oligomers derived from the (L)-enantiomer of 3 did not act as templates to facilitate the oligomerization of 4.

  20. Functional characterization of Caenorhabditis elegans heteromeric amino acid transporters.

    PubMed

    Veljkovic, Emilija; Stasiuk, Susan; Skelly, Patrick J; Shoemaker, Charles B; Verrey, François

    2004-02-27

    Mammalian heteromeric amino acid transporters (HATs) are composed of a multi-transmembrane spanning catalytic protein covalently associated with a type II glycoprotein (e.g. 4F2hc, rBAT) through a disulfide bond. Caenorhabditis elegans has nine genes encoding close homologues of the HAT catalytic proteins. Three of these genes (designated AAT-1 to AAT-3) have a much higher degree of similarity to the mammalian homologues than the other six, including the presence of a cysteine residue at the position known to form a disulfide bridge to the glycoprotein partner in mammalian HATs. C. elegans also has two genes encoding homologues of the heteromeric amino acid transporter type II glycoprotein subunits (designated ATG-1 and ATG-2). Both ATG, and/or AAT-1, -2, -3 proteins were expressed in Xenopus oocytes and tested for amino acid transport function. This screen revealed that AAT-1 and AAT-3 facilitate amino acid transport when expressed together with ATG-2 but not with ATG-1 or the mammalian type II glycoproteins 4F2hc and rBAT. AAT-1 and AAT-3 covalently bind to both C. elegans ATG glycoproteins, but only the pairs with ATG-2 traffic to the oocyte surface. Both of these functional, surface-expressed C. elegans HATs transport most neutral amino acids and display the highest transport rate for l-Ala and l-Ser (apparent K(m) 100 microm range). Similar to their mammalian counterparts, the C. elegans HATs function as (near) obligatory amino acid exchangers. Taken together, this study demonstrates that the heteromeric structure and the amino acid exchange function of HATs have been conserved throughout the evolution of nematodes to mammals.

  1. Monoclonal antibodies recognizing single amino acid substitutions in hemoglobin

    SciTech Connect

    Stanker, L.H.; Branscomb, E.; Vanderlaan, M.; Jensen, R.H.

    1986-06-01

    Four monoclonal antibodies (mAb) to non-human primate hemoglobin referred to as Cap-4, Cap-5, Rh-2, and Rh-4, and two mAb to human hemoglobin, referred to as H-1 and H-3 were isolated and were partially characterized. Binding studies with these mAb on a panel of hemoglobins and isolated ..cap alpha.. and ..beta.. globin chains revealed a unique reactivity pattern for each mAb. Amino acid sequence analysis of the antigens used to generate the binding data suggests that the specific recognition of certain hemoglobin antigens by each mAb is controlled by the presence of a particular amino acid at a specific position within the epitope. The use of synthetic peptides as antigens confirmed this observation for five of the mAb. No synthetic peptides were tested with the sixth mAb, Rh-2. The amino acids required for binding of mAb Cap-4, Cap-5, Rh-4, and Rh-2 to hemoglobin are alanine at ..beta..5, threonine at ..beta..13, glutamine at ..beta..125, and leucine at ..cap alpha..68. The non-human primate hemoglobin antibodies require a specific amino acid that is not present in human hemoglobin. The amino acid required for binding of Cap-4, Cap-5, and Rh-4 could arise by a single base change in the ..beta.. globin gene, whereas the amino acid required for Rh-2 binding could only occur if two base changes occurred. Thus these mAb are candidate probes for a somatic cell mutation assay on the basis of the detection of peripheral blood red cells that possess single amino acid substituted hemoglobin as a result of single base substitutions in the globin genes of precursor cells.

  2. NH2-Terminal Amino Acid Distribution and Amino Acid Composition of Streptococcus faecalis R Soluble and Ribosomal Proteins

    PubMed Central

    Samuel, Charles E.; Murray, Cheryl L.; Rabinowitz, Jesse C.

    1973-01-01

    The NH2-terminal amino acid distribution of Streptococcus faecalis R soluble and ribosomal proteins isolated from cells at different stages of growth on either folate-sufficient or folate-deficient medium was determined by the dinitrophenyl method. The NH2-terminal residues do not follow the random distribution observed for the total amino acid composition of S. faecalis soluble and ribosomal proteins. Methionine and alanine occur most frequently; serine, threonine, aspartic and glutamic acids, and glycine are also present at the NH2-terminal position of S. faecalis R proteins. The absence of folic acid yields cells that are incapable of formylating methionyl-transfer ribonucelic acid tRNAfMet, but does not affect either the qualitative or quantitative NH2-terminal distribution of total soluble or total ribosomal proteins compared to cells grown with folate. A small quantitative difference was observed in the frequency of distribution of certain amino acids at the NH2-termini between log and stationary phase soluble proteins. The amino acid residues found at the NH2-terminal position of S. faecalis proteins are qualitatively similar to those reported for several other organisms. PMID:4200842

  3. Intestinal metabolism of sulfur amino acids

    USDA-ARS?s Scientific Manuscript database

    The gastrointestinal tract (GIT) is a metabolically significant site of sulfur amino acid (SAA) metabolism in the body and metabolizes approx. 20% of the dietary methionine intake that is mainly transmethylated to homocysteine and transsulfurated to cysteine. The GIT accounts for approx. 25% of the ...

  4. Amino Acid Formation on Interstellar Dust Particles

    NASA Astrophysics Data System (ADS)

    Meierhenrich, U. J.; Munoz Caro, G. M.; Barbier, B.; Brack, A.; Thiemann, W.; Goesmann, F.; Rosenbauer, H.

    2003-04-01

    In the dense interstellar medium dust particles accrete ice layers of known molecular composition. In the diffuse interstellar medium these ice layers are subjected to energetic UV-irradiation. Here, photoreactions form complex organic molecules. The interstellar processes were recently successfully simulated in two laboratories. At NASA Ames Research Center three amino acids were detected in interstellar ice analogues [1], contemporaneously, our European team reported on the identification of 16 amino acids therein [2]. Amino acids are the molecular building blocks of proteins in living organisms. The identification of amino acids on the simulated icy surface of interstellar dust particles strongly supports the assumption that the precursor molecules of life were delivered from interstellar and interplanetary space via (micro-) meteorites and/or comets to the earyl Earth. The results shall be verified by the COSAC experiment onboard the ESA cometary mission Rosetta [3]. [1] M.P. Bernstein, J.P. Dworkin, S.A. Sandford, G.W. Cooper, L.J. Allamandola: itshape Nature \\upshape 416 (2002), 401-403. [2] G.M. Muñoz Caro, U.J. Meierhenrich, W.A. Schutte, B. Barbier, A. Arcones Sergovia, H. Rosenbauer, W.H.-P. Thiemann, A. Brack, J.M. Greenberg: itshape Nature \\upshape 416 (2002), 403-406. [3] U. Meierhenrich, W.H.-P. Thiemann, H. Rosenbauer: itshape Chirality \\upshape 11 (1999), 575-582.

  5. Manganese alters rat brain amino acids levels

    PubMed Central

    Santos, Dinamene; Batoreu, M. Camila; Almeida, Isabel; Ramos, Ruben; Sidoryk-Wegrzynowicz, M.; Aschner, Michael; Marreilha dos Santos, A.P.

    2012-01-01

    Manganese (Mn) is an essential element and it acts as a cofactor for a number of enzymatic reactions, including those involved in amino acid, lipid, protein and carbohydrate metabolism. Excessive exposure to Mn can lead to poisoning, characterized by psychiatric disturbances and an extrapyramidal disorder. Mn-induced neuronal degeneration is associated with alterations in amino acids metabolism. In the present study, we analyzed whole rat brain amino acid content subsequent to 4 or 8 intraperitoneal (ip) injections, with 25 mg MnCl2/kg/day, at 48-hour (h) intervals. We noted a significant increase in glycine brain levels after 4 or 8 Mn injections (p<0.05 and p<0.01, respectively) and arginine also after 4 or 8 injections (p<0.001). Significant increases were also noted in brain proline (p<0.01), cysteine (p<0.05), phenylalanine (p<0.01) and tyrosine (p<0.01) levels after 8 Mn injections vs. the control group. These findings suggest that Mn-induced alterations in amino acid levels secondary to Mn affect the neurochemical milieu. PMID:22971893

  6. Biological activity of silylated amino acid containing substance P analogues.

    PubMed

    Cavelier, F; Marchand, D; Martinez, J; Sagan, S

    2004-03-01

    The need to replace natural amino acids in peptides with nonproteinogenic counterparts to obtain new medicinal agents has stimulated a great deal of innovation on synthetic methods. Here, we report the incorporation of non-natural silylated amino acids in substance P (SP), the binding affinity for the two hNK-1 binding sites and, the potency to stimulate phospholipase C (PLC) and adenylate cyclase of the resulting peptide. We also assess the improvement of their stability towards enzyme degradation. Altogether, we found that replacing glycine with silaproline (Sip) in position 9 of SP leads to a potent analogue exhibiting an increased resistance to angiotensin-converting enzyme hydrolysis.

  7. Human splanchnic amino-acid metabolism.

    PubMed

    Neis, Evelien P J G; Sabrkhany, S; Hundscheid, I; Schellekens, D; Lenaerts, K; Olde Damink, S W; Blaak, E E; Dejong, C H C; Rensen, Sander S

    2017-01-01

    Plasma levels of several amino acids are correlated with metabolic dysregulation in obesity and type 2 diabetes. To increase our understanding of human amino-acid metabolism, we aimed to determine splanchnic interorgan amino-acid handling. Twenty patients planned to undergo a pylorus preserving pancreatico-duodenectomy were included in this study. Blood was sampled from the portal vein, hepatic vein, superior mesenteric vein, inferior mesenteric vein, splenic vein, renal vein, and the radial artery during surgery. The difference between arterial and venous concentrations of 21 amino acids was determined using liquid chromatography as a measure of amino-acid metabolism across a given organ. Whereas glutamine was significantly taken up by the small intestine (121.0 ± 23.8 µmol/L; P < 0.0001), citrulline was released (-36.1 ± 4.6 µmol/L; P < 0.0001). This, however, was not seen for the colon. Interestingly, the liver showed a small, but a significant uptake of citrulline from the circulation (4.8 ± 1.6 µmol/L; P = 0.0138) next to many other amino acids. The kidneys showed a marked release of serine and alanine into the circulation (-58.0 ± 4.4 µmol/L and -61.8 ± 5.2 µmol/L, P < 0.0001), and a smaller, but statistically significant release of tyrosine (-12.0 ± 1.3 µmol/L, P < 0.0001). The spleen only released taurine (-9.6 ± 3.3 µmol/L; P = 0.0078). Simultaneous blood sampling in different veins provides unique qualitative and quantitative information on integrative amino-acid physiology, and reveals that the well-known intestinal glutamine-citrulline pathway appears to be functional in the small intestine but not in the colon.

  8. Hydrophobicity and Aromaticity Are Primary Factors Shaping Variation in Amino Acid Usage of Chicken Proteome

    PubMed Central

    Chai, Xuewen; Nie, Qinghua; Zhang, Xiquan

    2014-01-01

    Amino acids are utilized with different frequencies both among species and among genes within the same genome. Up to date, no study on the amino acid usage pattern of chicken has been performed. In the present study, we carried out a systematic examination of the amino acid usage in the chicken proteome. Our data indicated that the relative amino acid usage is positively correlated with the tRNA gene copy number. GC contents, including GC1, GC2, GC3, GC content of CDS and GC content of the introns, were correlated with the most of the amino acid usage, especially for GC rich and GC poor amino acids, however, multiple linear regression analyses indicated that only approximately 10–40% variation of amino acid usage can be explained by GC content for GC rich and GC poor amino acids. For other intermediate GC content amino acids, only approximately 10% variation can be explained. Correspondence analyses demonstrated that the main factors responsible for the variation of amino acid usage in chicken are hydrophobicity, aromaticity and genomic GC content. Gene expression level also influenced the amino acid usage significantly. We argued that the amino acid usage of chicken proteome likely reflects a balance or near balance between the action of selection, mutation, and genetic drift. PMID:25329059

  9. Brain amino acid metabolism and ketosis.

    PubMed

    Yudkoff, M; Daikhin, Y; Nissim, I; Lazarow, A; Nissim, I

    2001-10-15

    The relationship between ketosis and brain amino acid metabolism was studied in mice that consumed a ketogenic diet (>90% of calories as lipid). After 3 days on the diet the blood concentration of 3-OH-butyrate was approximately 5 mmol/l (control = 0.06-0.1 mmol/l). In forebrain and cerebellum the concentration of 3-OH-butyrate was approximately 10-fold higher than control. Brain [citrate] and [lactate] were greater in the ketotic animals. The concentration of whole brain free coenzyme A was lower in ketotic mice. Brain [aspartate] was reduced in forebrain and cerebellum, but [glutamate] and [glutamine] were unchanged. When [(15)N]leucine was administered to follow N metabolism, this labeled amino acid accumulated to a greater extent in the blood and brain of ketotic mice. Total brain aspartate ((14)N + (15)N) was reduced in the ketotic group. The [(15)N]aspartate/[(15)N]glutamate ratio was lower in ketotic animals, consistent with a shift in the equilibrium of the aspartate aminotransferase reaction away from aspartate. Label in [(15)N]GABA and total [(15)N]GABA was increased in ketotic animals. When the ketotic animals were injected with glucose, there was a partial blunting of ketoacidemia within 40 min as well as an increase of brain [aspartate], which was similar to control. When [U-(13)C(6)]glucose was injected, the (13)C label appeared rapidly in brain lactate and in amino acids. Label in brain [U-(13)C(3)]lactate was greater in the ketotic group. The ratio of brain (13)C-amino acid/(13)C-lactate, which reflects the fraction of amino acid carbon that is derived from glucose, was much lower in ketosis, indicating that another carbon source, i.e., ketone bodies, were precursor to aspartate, glutamate, glutamine and GABA.

  10. D-Amino Acids in Living Higher Organisms

    NASA Astrophysics Data System (ADS)

    Fujii, Noriko

    2002-04-01

    The homochirality of biological amino acids (L-amino acids) and of the RNA/DNA backbone (D-ribose) might have become established before the origin of life. It has been considered that D-amino acids and L-sugars were eliminated on the primitive Earth. Therefore, the presence and function of D-amino acids in living organisms have not been studied except for D-amino acids in the cell walls of microorganisms. However, D-amino acids were recently found in various living higher organisms in the form of free amino acids, peptides, and proteins. Free D-aspartate and D-serine are present and may have important physiological functions in mammals. D-amino acids in peptides are well known as opioid peptides and neuropeptides. In protein, D-aspartate residues increase during aging. This review deals with recent advances in the study of D-amino acids in higher organisms.

  11. Present Global Situation of Amino Acids in Industry.

    PubMed

    Tonouchi, Naoto; Ito, Hisao

    2016-11-11

    At present, amino acids are widely produced and utilized industrially. Initially, monosodium glutamate (MSG) was produced by extraction from a gluten hydrolysate. The amino acid industry started using the residual of the lysate. The discovery of the functions of amino acids has led to the expansion of their field of use. In addition to seasoning and other food use, amino acids are used in many fields such as animal nutrients, pharmaceuticals, and cosmetics. On the other hand, the invention of the glutamate fermentation process, followed by the development of fermentation methods for many other amino acids, is no less important. The supply of these amino acids at a low price is very essential for their industrial use. Most amino acids are now produced by fermentation. The consumption of many amino acids such as MSG or feed-use amino acids is still rapidly increasing.

  12. Implications of Amino Acid Substitutions in GyrA at Position 83 in Terms of Oxolinic Acid Resistance in Field Isolates of Burkholderia glumae, a Causal Agent of Bacterial Seedling Rot and Grain Rot of Rice

    PubMed Central

    Maeda, Yukiko; Kiba, Akinori; Ohnishi, Kouhei; Hikichi, Yasufumi

    2004-01-01

    Oxolinic acid (OA), a quinolone, inhibits the activity of DNA gyrase composed of GyrA and GyrB and shows antibacterial activity against Burkholderia glumae. Since B. glumae causes bacterial seedling rot and grain rot of rice, both of which are devastating diseases, the emergence of OA-resistant bacteria has important implications on rice cultivation in Japan. Based on the MIC of OA, 35 B. glumae field isolates isolated from rice seedlings grown from OA-treated seeds in Japan were divided into sensitive isolates (OSs; 0.5 μg/ml), moderately resistant isolates (MRs; 50 μg/ml), and highly resistant isolates (HRs; ≥100 μg/ml). Recombination with gyrA of an OS, Pg-10, led MRs and HRs to become OA susceptible, suggesting that gyrA mutations are involved in the OA resistance of field isolates. The amino acid at position 83 in the GyrA of all OSs was Ser, but in all MRs and HRs it was Arg and Ile, respectively. Ser83Arg and Ser83Ile substitutions in the GyrA of an OS, Pg-10, resulted in moderate and high OA resistance, respectively. Moreover, Arg83Ser and Ile83Ser substitutions in the GyrA of MRs and HRs, respectively, resulted in susceptibility to OA. These results suggest that Ser83Arg and Ser83Ile substitutions in GyrA are commonly responsible for resistance to OA in B. glumae field isolates. PMID:15345450

  13. Biosynthesis of natural products containing β-amino acids.

    PubMed

    Kudo, Fumitaka; Miyanaga, Akimasa; Eguchi, Tadashi

    2014-08-01

    Covering: up to January, 2014. We focus here on β-amino acids as components of complex natural products because the presence of β-amino acids produces structural diversity in natural products and provides characteristic architectures beyond those of ordinary α-L-amino acids, thus generating significant and unique biological functions in nature. In this review, we first survey the known bioactive β-amino acid-containing natural products including nonribosomal peptides, macrolactam polyketides, and nucleoside-β-amino acid hybrids. Next, the biosynthetic enzymes that form β-amino acids from α-amino acids and the de novo synthesis of β-amino acids are summarized. Then, the mechanisms of β-amino acid incorporation into natural products are reviewed. Because it is anticipated that the rational swapping of the β-amino acid moieties with various side chains and stereochemistries by biosynthetic engineering should lead to the creation of novel architectures and bioactive compounds, the accumulation of knowledge regarding β-amino acid-containing natural product biosynthetic machinery could have a significant impact in this field. In addition, genome mining of characteristic β-amino acid biosynthetic genes and unique β-amino acid incorporation machinery could lead to the discovery of new β-amino acid-containing natural products.

  14. 40 CFR 721.10126 - Alkyl amino substituted triazine amino substituted benezenesulfonic acid reaction product with...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... substituted triazine amino substituted benezenesulfonic acid reaction product with naphthalenesulfonato azo... substituted triazine amino substituted benezenesulfonic acid reaction product with naphthalenesulfonato azo... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Alkyl amino substituted triazine amino...

  15. 40 CFR 721.10126 - Alkyl amino substituted triazine amino substituted benezenesulfonic acid reaction product with...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... substituted triazine amino substituted benezenesulfonic acid reaction product with naphthalenesulfonato azo... substituted triazine amino substituted benezenesulfonic acid reaction product with naphthalenesulfonato azo... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Alkyl amino substituted triazine amino...

  16. 40 CFR 721.10126 - Alkyl amino substituted triazine amino substituted benezenesulfonic acid reaction product with...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... substituted triazine amino substituted benezenesulfonic acid reaction product with naphthalenesulfonato azo... substituted triazine amino substituted benezenesulfonic acid reaction product with naphthalenesulfonato azo... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Alkyl amino substituted triazine amino...

  17. 40 CFR 721.10126 - Alkyl amino substituted triazine amino substituted benezenesulfonic acid reaction product with...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... substituted triazine amino substituted benezenesulfonic acid reaction product with naphthalenesulfonato azo... substituted triazine amino substituted benezenesulfonic acid reaction product with naphthalenesulfonato azo... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Alkyl amino substituted triazine amino...

  18. 40 CFR 721.10126 - Alkyl amino substituted triazine amino substituted benezenesulfonic acid reaction product with...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... substituted triazine amino substituted benezenesulfonic acid reaction product with naphthalenesulfonato azo... substituted triazine amino substituted benezenesulfonic acid reaction product with naphthalenesulfonato azo... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Alkyl amino substituted triazine amino...

  19. Electronic coupling through natural amino acids

    SciTech Connect

    Berstis, Laura; Beckham, Gregg T. E-mail: gregg.beckham@nrel.gov; Crowley, Michael F. E-mail: gregg.beckham@nrel.gov

    2015-12-14

    Myriad scientific domains concern themselves with biological electron transfer (ET) events that span across vast scales of rate and efficiency through a remarkably fine-tuned integration of amino acid (AA) sequences, electronic structure, dynamics, and environment interactions. Within this intricate scheme, many questions persist as to how proteins modulate electron-tunneling properties. To help elucidate these principles, we develop a model set of peptides representing the common α-helix and β-strand motifs including all natural AAs within implicit protein-environment solvation. Using an effective Hamiltonian strategy with density functional theory, we characterize the electronic coupling through these peptides, furthermore considering side-chain dynamics. For both motifs, predictions consistently show that backbone-mediated electronic coupling is distinctly sensitive to AA type (aliphatic, polar, aromatic, negatively charged and positively charged), and to side-chain orientation. The unique properties of these residues may be employed to design activated, deactivated, or switch-like superexchange pathways. Electronic structure calculations and Green’s function analyses indicate that localized shifts in the electron density along the peptide play a role in modulating these pathways, and further substantiate the experimentally observed behavior of proline residues as superbridges. The distinct sensitivities of tunneling pathways to sequence and conformation revealed in this electronic coupling database help improve our fundamental understanding of the broad diversity of ET reactivity and provide guiding principles for peptide design.

  20. Electronic coupling through natural amino acids

    NASA Astrophysics Data System (ADS)

    Berstis, Laura; Beckham, Gregg T.; Crowley, Michael F.

    2015-12-01

    Myriad scientific domains concern themselves with biological electron transfer (ET) events that span across vast scales of rate and efficiency through a remarkably fine-tuned integration of amino acid (AA) sequences, electronic structure, dynamics, and environment interactions. Within this intricate scheme, many questions persist as to how proteins modulate electron-tunneling properties. To help elucidate these principles, we develop a model set of peptides representing the common α-helix and β-strand motifs including all natural AAs within implicit protein-environment solvation. Using an effective Hamiltonian strategy with density functional theory, we characterize the electronic coupling through these peptides, furthermore considering side-chain dynamics. For both motifs, predictions consistently show that backbone-mediated electronic coupling is distinctly sensitive to AA type (aliphatic, polar, aromatic, negatively charged and positively charged), and to side-chain orientation. The unique properties of these residues may be employed to design activated, deactivated, or switch-like superexchange pathways. Electronic structure calculations and Green's function analyses indicate that localized shifts in the electron density along the peptide play a role in modulating these pathways, and further substantiate the experimentally observed behavior of proline residues as superbridges. The distinct sensitivities of tunneling pathways to sequence and conformation revealed in this electronic coupling database help improve our fundamental understanding of the broad diversity of ET reactivity and provide guiding principles for peptide design.

  1. Amino acid addition to Vibrio cholerae LPS establishes a link between surface remodeling in gram-positive and gram-negative bacteria.

    PubMed

    Hankins, Jessica V; Madsen, James A; Giles, David K; Brodbelt, Jennifer S; Trent, M Stephen

    2012-05-29

    Historically, the O1 El Tor and classical biotypes of Vibrio cholerae have been differentiated by their resistance to the antimicrobial peptide polymyxin B. However, the molecular mechanisms associated with this phenotypic distinction have remained a mystery for 50 y. Both gram-negative and gram-positive bacteria modify their cell wall components with amine-containing substituents to reduce the net negative charge of the bacterial surface, thereby promoting cationic antimicrobial peptide resistance. In the present study, we demonstrate that V. cholerae modify the lipid A anchor of LPS with glycine and diglycine residues. This previously uncharacterized lipid A modification confers polymyxin resistance in V. cholerae El Tor, requiring three V. cholerae proteins: Vc1577 (AlmG), Vc1578 (AlmF), and Vc1579 (AlmE). Interestingly, the protein machinery required for glycine addition is reminiscent of the gram-positive system responsible for D-alanylation of teichoic acids. Such machinery was not thought to be used by gram-negative organisms. V. cholerae O1 El Tor mutants lacking genes involved in transferring glycine to LPS showed a 100-fold increase in sensitivity to polymyxin B. This work reveals a unique lipid A modification and demonstrates a charge-based remodeling strategy shared between gram-positive and gram-negative organisms.

  2. Identification of essential amino acids in the Streptococcus mutans glucosyltransferases.

    PubMed Central

    Tsumori, H; Minami, T; Kuramitsu, H K

    1997-01-01

    A comparison of the amino acid sequences of the glucosyltransferases (GTFs) of mutans streptococci with those from the alpha-amylase family of enzymes revealed a number of conserved amino acid positions which have been implicated as essential in catalysis. Utilizing a site-directed mutagenesis approach with the GTF-I enzyme of Streptococcus mutans GS-5, we identified three of these conserved amino acid positions, Asp413, Trp491, and His561, as being important in enzymatic activity. Mutagenesis of Asp413 to Thr resulted in a GTF which expressed only about 12% of the wild-type activity. In contrast, mutagenesis of Asp411 did not inhibit enzyme activity. In addition, the D413T mutant was less stable than was the parental enzyme when expressed in Escherichia coli. Moreover, conversion of Trp491 or His561 to either Gly or Ala resulted in enzymes devoid of GTF activity, indicating the essential nature of these two amino acids for activity. Furthermore, mutagenesis of the four Tyr residues present at positions 169 to 172 which are part of a subdomain with homology to the direct repeating sequences present in the glucan-binding domain of the GTFs had little overall effect on enzymatic activity, although the glucan products appeared to be less adhesive. These results are discussed relative to the mechanisms of catalysis proposed for the GTFs and related enzymes. PMID:9171379

  3. 'Trophic' and 'source' amino acids in trophic estimation: a likely metabolic explanation.

    PubMed

    O'Connell, T C

    2017-06-01

    Amino acid nitrogen isotopic analysis is a relatively new method for estimating trophic position. It uses the isotopic difference between an individual's 'trophic' and 'source' amino acids to determine its trophic position. So far, there is no accepted explanation for the mechanism by which the isotopic signals in 'trophic' and 'source' amino acids arise. Yet without a metabolic understanding, the utility of nitrogen isotopic analyses as a method for probing trophic relations, at either bulk tissue or amino acid level, is limited. I draw on isotopic tracer studies of protein metabolism, together with a consideration of amino acid metabolic pathways, to suggest that the 'trophic'/'source' groupings have a fundamental metabolic origin, to do with the cycling of amino-nitrogen between amino acids. 'Trophic' amino acids are those whose amino-nitrogens are interchangeable, part of a metabolic amino-nitrogen pool, and 'source' amino acids are those whose amino-nitrogens are not interchangeable with the metabolic pool. Nitrogen isotopic values of 'trophic' amino acids will reflect an averaged isotopic signal of all such dietary amino acids, offset by the integrated effect of isotopic fractionation from nitrogen cycling, and modulated by metabolic and physiological effects. Isotopic values of 'source' amino acids will be more closely linked to those of equivalent dietary amino acids, but also modulated by metabolism and physiology. The complexity of nitrogen cycling suggests that a single identifiable value for 'trophic discrimination factors' is unlikely to exist. Greater consideration of physiology and metabolism should help in better understanding observed patterns in nitrogen isotopic values.

  4. [Secretion of endogenous amino acids in the gastrointestinal tract and amino acid resorption in the swine].

    PubMed

    Zebrowska, T; Simon, O; Münchmeyer, R; Bergner, H

    1976-02-01

    A trial was performed with 2 fistula pigs (each with 2 fistulas, one located about 30 cm below the pyloric orifice and the other at the end of the small intestine). Animal A received a casein diet containing 14% crude protein for a period of 2 weeks before the tracer amino acid was administered. Animal B received the same diet for a period of 10 days and was then fed a diet (at the same protein level) containing gluten as sole protein source. The two tracer amino acids, 14C-U-L-leucine and 3H-4,5-(N)-L-lysine, were injected intravenously. The passage rates for dry matter, organic matter and N measured at the beginning of the small intestine were higher than the rate of intake. The rate of passage of amino acids was also found to be increased relative to the rate of intake. In general, this increase involved the non-essential amino acids to a much larger extent. A considerable proportion of the amino acids passing into the large intestine is not excreted with the faeces but is probably converted in catabolic processes. It is for this reason that any values for the efficiency of amino acid absorption calculated on the basis of data on the faecal excretion of amino acids will not provide conclusive evidence for the availability of dietary amino acids in processes of the intermediate metabolism. The rate of secretion of 3H and 14C radioactivity into the digesta of the small intestine was found to increase rapidly within 1-2 hrs after administration of the tracer amino acids. The 14C radioactivity detected was found to be almost exclusively derived from 14C leucine while only about 60% of the 3H activity found in the digesta of fistula I were shown to be bound to lysine. Labelled lysine and leucine (of endogenic origin) are absorbed into the small intestine at a slower rate (i.e. endogenic proteins are less efficiently digested) than the non-radioactive amino acids (of exogenic origin) so that a process of concentration of endogenic amino acids is observed towards the

  5. Evolution from amino acids - Lunar occurrence of their precursors.

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1972-01-01

    Review of the present state of experimentally based concepts of organic evolution from amino acids. Earlier studies of the synthesis of amino acid precursors from meteoritic material, lunar dust, and terrestrial lava are briefly summarized, and laboratory experiments in which polymers of amino acids were obtained either by direct heating of dry amino acids or by heating aqueous solutions of mixtures of amino acids are described. In particular, a process is described by which alpha-amino acids were made to react to form linear chains of proteinoids. It is concluded that a proteinoid microsystem was a common ancestor of all life on earth.

  6. Criteria for distinguishing biogenic and abiogenic amino acids - Preliminary considerations.

    NASA Technical Reports Server (NTRS)

    Kvenvolden, K. A.

    1973-01-01

    Criteria to determine the mode of origin of amino acids can be established by consideration of their structure, enantiometric distribution, composition, and relative abundance. A population of dominantly protein amino acids with one enantiomeric configuration most likely had a biological origin. Biological amino acids do racemize, however, so the absence of optical activity would not rule out the possibility that the amino acids in a racemic mixture were originally synthesized biologically. For racemic amino acids, therefore, structure, composition and relative abundance become important in ascertaining the origin of these compounds. Abiotically synthesized amino acids have a population composed of both protein and nonprotein structures present as racemic mixtures.

  7. Permeability of membranes to amino acids and modified amino acids: mechanisms involved in translocation

    NASA Technical Reports Server (NTRS)

    Chakrabarti, A. C.; Deamer, D. W. (Principal Investigator); Miller, S. L. (Principal Investigator)

    1994-01-01

    The amino acid permeability of membranes is of interest because they are one of the key solutes involved in cell function. Membrane permeability coefficients (P) for amino acid classes, including neutral, polar, hydrophobic, and charged species, have been measured and compared using a variety of techniques. Decreasing lipid chain length increased permeability slightly (5-fold), while variations in pH had only minor effects on the permeability coefficients of the amino acids tested in liposomes. Increasing the membrane surface charge increased the permeability of amino acids of the opposite charge, while increasing the cholesterol content decreased membrane permeability. The permeability coefficients for most amino acids tested were surprisingly similar to those previously measured for monovalent cations such as sodium and potassium (approximately 10(-12)-10(-13) cm s-1). This observation suggests that the permeation rates for the neutral, polar and charged amino acids are controlled by bilayer fluctuations and transient defects, rather than partition coefficients and Born energy barriers. Hydrophobic amino acids were 10(2) more permeable than the hydrophilic forms, reflecting their increased partition coefficient values. External pH had dramatic effects on the permeation rates for the modified amino acid lysine methyl ester in response to transmembrane pH gradients. It was established that lysine methyl ester and other modified short peptides permeate rapidly (P = 10(-2) cm s-1) as neutral (deprotonated) molecules. It was also shown that charge distributions dramatically alter permeation rates for modified di-peptides. These results may relate to the movement of peptides through membranes during protein translocation and to the origin of cellular membrane transport on the early Earth.

  8. [Amino acid composition of polynucleotide-peptide complexes isolated from algae].

    PubMed

    Pusheva, M A; Khoreva, M A

    1977-01-01

    The amino acid composition of the peptide moiety of sulphur containing polynucleotide-peptide complexes (S-PNPC) was studied with four species of green algae and two species of blue-green algae. S-PNPC contained almost all amino acids which were usually encountered in acid hydrolysates of proteins, and also unidentified ninhydrin-positive compounds. The amino acid composition of the peptide moiety of S-PNPC was rather similar in the case of different algae, and was characterized by the prevailence of acid amino acids.

  9. Some of the amino acid chemistry going on in the Laboratory of Amino Acids, Peptides and Proteins.

    PubMed

    Bouifraden, S; Drouot, C; el Hadrami, M; Guenoun, F; Lecointe, L; Mai, N; Paris, M; Pothion, C; Sadoune, M; Sauvagnat, B; Amblard, M; Aubagnac, J L; Calmes, M; Chevallet, P; Daunis, J; Enjalbal, C; Fehrentz, J A; Lamaty, F; Lavergne, J P; Lazaro, R; Rolland, V; Roumestant, M L; Viallefont, P; Vidal, Y; Martinez, J

    1999-01-01

    Some of the chemistry of amino acids going on in our laboratory (Laboratoire des Amino acides Peptides et Protéines) is described as well as some mass spectrometry methodology for their characterization particularly on solid supports. Several aspects are presented including: (i) the stereoselective synthesis of natural and unnatural amino acids using 2-hydroxypinan-3-one as chiral auxiliary; (ii) the stereoselective synthesis of natural and unnatural amino acids by deracemization of alpha-amino acids via their ketene derivatives; (iii) the synthesis of alpha-aryl-alpha-amino acids via reaction of organometallics with a glycine cation; (iv) the diastereoselective synthesis of glycosyl-alpha-amino acids; (v) the synthesis of beta-amino acids using alpha-aminopyrrolidinopiperazinediones as chiral templates; (vi) the reactivity of urethane-N-protected N-carboxyanhydrides. To characterize natural and non natural amino acids through their immonium ions by mass spectrometry, some methodology is also described.

  10. Amino acids regulate the intracellular trafficking of the general amino acid permease of Saccharomycescerevisiae.

    PubMed

    Chen, Esther J; Kaiser, Chris A

    2002-11-12

    The delivery to the plasma membrane of the general amino acid permease, Gap1p, of Saccharomyces cerevisiae is regulated by the quality of the nitrogen source in the growth medium. In an effort to define how different nitrogen sources control Gap1p sorting, we find that mutations in GDH1 and GLN1 that decrease the flux through the glutamate and glutamine synthesis pathways result in increased Gap1p sorting to the plasma membrane. Conversely, deletion of MKS1, which increases glutamate and glutamine synthesis, decreases Gap1p sorting to the plasma membrane. Glutamate and glutamine are not unusual in their ability to regulate Gap1p sorting, because the addition of all natural amino acids and many amino acid analogs to the growth medium results in increased Gap1p sorting to the vacuole. Importantly, amino acids have the capacity to signal Gap1p sorting to the vacuole regardless of whether they can be used as a source of nitrogen. Finally, we show that rapamycin does not affect Gap1p sorting, indicating that Gap1p sorting is not directly influenced by the TOR pathway. Together, these data show that amino acids are a signal for sorting Gap1p to the vacuole and imply that the nitrogen-regulated Gap1p sorting machinery responds to amino acid-like compounds rather than to the overall nutritional status associated with growth on a particular nitrogen source.

  11. Roles of phytochemicals in amino acid nutrition.

    PubMed

    Kong, Xiangfeng; Wu, Guoyao; Yin, Yinlong

    2011-01-01

    Chinese herbal medicine (CHM) is often used as dietary supplements to maintain good health in animals and humans. Here, we review the current knowledge about effects of CHM (including ultra-fine Chinese herbal powder, Acanthopanax senticosus extracts, Astragalus polysaccharide, and glycyrrhetinic acid) as dietary additives on physiological and biochemical parameters in pigs, chickens and rodents. Additionally, we propose possible mechanisms for the beneficial effects of CHM on the animals. These mechanisms include (a) increased digestion and absorption of dietary amino acids; (b) altered catabolism of amino acids in the small intestine and other tissues; (c) enhanced synthesis of functional amino acids (e.g., arginine, glutamine and proline) and polyamines; and (d) improved metabolic control of nutrient utilization through cell signaling. Notably, some phytochemicals and glucocorticoids share similarities in structure and physiological actions. New research findings provide a scientific and clinical basis for the use of CHM to improve well-being in livestock species and poultry, while enhancing the efficiency of protein accretion. Results obtained from animal studies also have important implications for human nutrition and health.

  12. Nonconventional techniques for separation of biosynthetic amino acids.

    PubMed

    Kloetzer, Lenuţa; Poştaru, Mădălina; Cheptea, Corina; Caşcaval, D; Galaction, Anca-Irina

    2014-01-01

    Amino acids can be obtained by biosynthesis, by protein hydrolysis or by extraction from natural sources. The most efficient methods are the first two, but the separation of amino acids from fermentation broths or protein hydrolysates is rather difficult. Amino acids dissociate in aqueous solutions, forming characteristic ionic species depending on the solution pH-value. These properties make amino acids to be hydrophilic at any pH-value. This paper presents a review of the separation studies of some amino acids by nonconventional methods, namely individual or selective reactive extraction. Separation of some amino acids from their mixture obtained either by fermentation or protein hydrolysis by reactive extraction with different extractants indicated the possibility of the amino acids selective separation as a function of the pH-value of aqueous solution correlated with the acidic or basic character of each amino acid.

  13. Fatty acid-amino acid conjugates diversification in Lepidopteran caterpillars

    USDA-ARS?s Scientific Manuscript database

    Fatty acid amino acid conjugates (FACs) have been found in Noctuid as well as Sphingid caterpillar oral secretions and especially volicitin [N-(17-hydroxylinolenoyl)-L-Glutamine] and its biochemical precursor, N-linolenoyl-L-glutamine, are known elicitors of induced volatile emissions in corn plants...

  14. The amino acid sequence of iguana (Iguana iguana) pancreatic ribonuclease.

    PubMed

    Zhao, W; Beintema, J J; Hofsteenge, J

    1994-01-15

    The pyrimidine-specific ribonuclease superfamily constitutes a group of homologous proteins so far found only in higher vertebrates. Four separate families are found in mammals, which have resulted from gene duplications in mammalian ancestors. To learn more about the evolutionary history of this superfamily, the primary structure and other characteristics of the pancreatic enzyme from iguana (Iguana iguana), a herbivorous lizard species belonging to the reptiles, have been determined. The polypeptide chain consists of 119 amino acid residues. The positions of insertions and deletions in the sequence are identical to those in the enzyme from snapping turtle. However, the two enzymes differ at 54% of the amino acid positions. Iguana ribonuclease contains no carbohydrate, although the enzyme possesses three recognition sites for carbohydrate attachment, and has a high number of acidic residues in a localized part of the sequence.

  15. AMINO ACID CROSS RESISTANCE IN AGROBACTERIUM TUMEFACIENS

    PubMed Central

    Beardsley, Robert E.

    1962-01-01

    Beardsley, Robert E. (Manhattan College, New York, N. Y.). Amino acid cross resistance in Agrobacterium tumefaciens. J. Bacteriol. 84:1237–1240. 1962.—Resistant clones selected on medium supplemented with glycine were also resistant to d-methionine, d-valine, dl-norleucine, and dl-serine. Cross resistance was similarly exhibited by clones selected on d-methionine, d-valine, or dl-norleucine. Two types of resistant organisms were observed. One produced colonies containing normal rods on selection medium. The other produced translucent colonies containing L forms. Both grew as typical rods in unsupplemented medium. Some resistant clones did not produce a temperate phage carried by the parental strain, but these retained immunity to homologous phage. The toxicity of d-methionine and d-valine for nonresistant bacteria is not reversed by the l isomers. The lethal effects of toxic amino acids are additive. PMID:13969951

  16. Ionic liquid crystals derived from amino acids.

    PubMed

    Mansueto, Markus; Frey, Wolfgang; Laschat, Sabine

    2013-11-18

    Novel chiral amino acid derived ionic liquid crystals with amine and amide moieties as spacers between the imidazolium head group and the alkyl chain were synthesised. The key step in the synthesis utilised the relatively uncommon SO3 leaving group in a microwave-assisted reaction. The mesomorphic properties of the mesogens were determined by differential scanning calorimetry (DSC), polarising optical microscopy (POM) and X-ray diffraction. All liquid crystalline salts exhibit a smectic A mesophase geometry with strongly interdigitated bilayer structures. An increase of the steric bulk of the stereogenic centre hindered the formation of mesophases. In case of phenylalanine-derived derivatives a mesomorphic behaviour was observed for shorter alkyl chains as compared to other amino acid derivatives indicating an additional stabilising effect by the phenyl moiety.

  17. Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability.

    PubMed

    Hu, Xiao-Pan; Yang, Yi; Ma, Bin-Guang

    2015-06-09

    Protein translation is a central step in gene expression and affected by many factors such as codon usage bias, mRNA folding energy and tRNA abundance. Despite intensive previous studies, how metabolic amino acid supply correlates with protein translation efficiency remains unknown. In this work, we estimated the amino acid flux from metabolic network for each protein in Escherichia coli and Saccharomyces cerevisiae by using Flux Balance Analysis. Integrated with the mRNA expression level, protein abundance and ribosome profiling data, we provided a detailed description of the role of amino acid supply in protein translation. Our results showed that amino acid supply positively correlates with translation efficiency and ribosome density. Moreover, with the rank-based regression model, we found that metabolic amino acid supply facilitates ribosome utilization. Based on the fact that the ribosome density change of well-amino-acid-supplied genes is smaller than poorly-amino-acid-supply genes under amino acid starvation, we reached the conclusion that amino acid supply may buffer ribosome density change against amino acid starvation and benefit maintaining a relatively stable translation environment. Our work provided new insights into the connection between metabolic amino acid supply and protein translation process by revealing a new regulation strategy that is dependent on resource availability.

  18. Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability

    PubMed Central

    Hu, Xiao-Pan; Yang, Yi; Ma, Bin-Guang

    2015-01-01

    Protein translation is a central step in gene expression and affected by many factors such as codon usage bias, mRNA folding energy and tRNA abundance. Despite intensive previous studies, how metabolic amino acid supply correlates with protein translation efficiency remains unknown. In this work, we estimated the amino acid flux from metabolic network for each protein in Escherichia coli and Saccharomyces cerevisiae by using Flux Balance Analysis. Integrated with the mRNA expression level, protein abundance and ribosome profiling data, we provided a detailed description of the role of amino acid supply in protein translation. Our results showed that amino acid supply positively correlates with translation efficiency and ribosome density. Moreover, with the rank-based regression model, we found that metabolic amino acid supply facilitates ribosome utilization. Based on the fact that the ribosome density change of well-amino-acid-supplied genes is smaller than poorly-amino-acid-supply genes under amino acid starvation, we reached the conclusion that amino acid supply may buffer ribosome density change against amino acid starvation and benefit maintaining a relatively stable translation environment. Our work provided new insights into the connection between metabolic amino acid supply and protein translation process by revealing a new regulation strategy that is dependent on resource availability. PMID:26056817

  19. 40 CFR 721.1705 - Benzoic acid, 3-amino-, diazotized, coupled with 6-amino-4-hydroxy-2-naphthalenesulfonic acid...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Benzoic acid, 3-amino-, diazotized, coupled with 6-amino-4-hydroxy-2-naphthalenesulfonic acid, diazotized, (3-aminophenyl)phosphonic acid and... Significant New Uses for Specific Chemical Substances § 721.1705 Benzoic acid, 3-amino-, diazotized, coupled...

  20. 40 CFR 721.1705 - Benzoic acid, 3-amino-, diazotized, coupled with 6-amino-4-hydroxy-2-naphthalenesulfonic acid...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Benzoic acid, 3-amino-, diazotized, coupled with 6-amino-4-hydroxy-2-naphthalenesulfonic acid, diazotized, (3-aminophenyl)phosphonic acid and... Significant New Uses for Specific Chemical Substances § 721.1705 Benzoic acid, 3-amino-, diazotized, coupled...

  1. 40 CFR 721.1705 - Benzoic acid, 3-amino-, diazotized, coupled with 6-amino-4-hydroxy-2-naphthalenesulfonic acid...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Benzoic acid, 3-amino-, diazotized, coupled with 6-amino-4-hydroxy-2-naphthalenesulfonic acid, diazotized, (3-aminophenyl)phosphonic acid and... Significant New Uses for Specific Chemical Substances § 721.1705 Benzoic acid, 3-amino-, diazotized, coupled...

  2. 40 CFR 721.1705 - Benzoic acid, 3-amino-, diazotized, coupled with 6-amino-4-hydroxy-2-naphthalenesulfonic acid...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Benzoic acid, 3-amino-, diazotized, coupled with 6-amino-4-hydroxy-2-naphthalenesulfonic acid, diazotized, (3-aminophenyl)phosphonic acid and... Significant New Uses for Specific Chemical Substances § 721.1705 Benzoic acid, 3-amino-, diazotized, coupled...

  3. 40 CFR 721.1705 - Benzoic acid, 3-amino-, diazotized, coupled with 6-amino-4-hydroxy-2-naphthalenesulfonic acid...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Benzoic acid, 3-amino-, diazotized, coupled with 6-amino-4-hydroxy-2-naphthalenesulfonic acid, diazotized, (3-aminophenyl)phosphonic acid and... Significant New Uses for Specific Chemical Substances § 721.1705 Benzoic acid, 3-amino-, diazotized, coupled...

  4. Alterations of amino Acid level in depressed rat brain.

    PubMed

    Yang, Pei; Li, Xuechun; Ni, Jian; Tian, Jingchen; Jing, Fu; Qu, Changhai; Lin, Longfei; Zhang, Hui

    2014-10-01

    Amino-acid neurotransmitter system dysfunction plays a major role in the pathophysiology of depression. Several studies have demonstrated the potential of amino acids as a source of neuro-specific biomarkers could be used in future diagnosis of depression. Only partial amino acids such as glycine and asparagine were determined from certain parts of rats' brain included hippocampi and cerebral cortex in previous studies. However, according to systematic biology, amino acids in different area of brain are interacted and interrelated. Hence, the determination of 34 amino acids through entire rats' brain was conducted in this study in order to demonstrate more possibilities for biomarkers of depression by discovering other potential amino acids in more areas of rats' brain. As a result, 4 amino acids (L-aspartic acid, L-glutamine, taurine and γ-amino-n-butyric acid) among 34 were typically identified as potentially primary biomarkers of depression by data statistics. Meanwhile, an antidepressant called Fluoxetine was employed to verify other potential amino acids which were not identified by data statistics. Eventually, we found L-α-amino-adipic acid could also become a new potentially secondary biomarker of depression after drug validation. In conclusion, we suggested that L-aspartic acid, L-glutamine, taurine, γ-amino-n-butyric acid and L-α-amino-adipic acid might become potential biomarkers for future diagnosis of depression and development of antidepressant.

  5. Rotational Study of Natural Amino Acid Glutamine

    NASA Astrophysics Data System (ADS)

    Varela, Marcelino; Cabezas, Carlos; Alonso, José L.

    2014-06-01

    Recent improvements in laser ablation molecular beam Fourier transform microwave spectroscopy (LA-MB-FTMW) have allowed the investigation of glutamine (COOH-CH(NH2)-CH2-CH2-CONH2), a natural amino acid with a long polar side chain. One dominant structure has been detected in the rotational spectrum. The nuclear quadrupole hyperfine structure of two 14N nuclei has been totally resolved allowing the conclusive identification of the observed species.

  6. Amino acid analyses of R and CK chondrites

    NASA Astrophysics Data System (ADS)

    Burton, Aaron S.; McLain, Hannah; Glavin, Daniel P.; Elsila, Jamie E.; Davidson, Jemma; Miller, Kelly E.; Andronikov, Alexander V.; Lauretta, Dante; Dworkin, Jason P.

    2015-03-01

    Exogenous delivery of amino acids and other organic molecules to planetary surfaces may have played an important role in the origins of life on Earth and other solar system bodies. Previous studies have revealed the presence of indigenous amino acids in a wide range of carbon-rich meteorites, with the abundances and structural distributions differing significantly depending on parent body mineralogy and alteration conditions. Here we report on the amino acid abundances of seven type 3-6 CK chondrites and two Rumuruti (R) chondrites. Amino acid measurements were made on hot water extracts from these meteorites by ultrahigh-performance liquid chromatography with fluorescence detection and time-of-flight mass spectrometry. Of the nine meteorites analyzed, four were depleted in amino acids, and one had experienced significant amino acid contamination by terrestrial biology. The remaining four, comprised of two R and two CK chondrites, contained low levels of amino acids that were predominantly the straight chain, amino-terminal (n-ω-amino) acids β-alanine, and γ-amino-n-butyric acid. This amino acid distribution is similar to what we reported previously for thermally altered ureilites and CV and CO chondrites, and these n-ω-amino acids appear to be indigenous to the meteorites and not the result of terrestrial contamination. The amino acids may have been formed by Fischer-Tropsch-type reactions, although this hypothesis needs further testing.

  7. Alimentary proteins, amino acids and cholesterolemia.

    PubMed

    Blachier, François; Lancha, Antonio H; Boutry, Claire; Tomé, Daniel

    2010-01-01

    Numerous data from both epidemiological and experimental origins indicate that some alimentary proteins and amino acids in supplements can modify the blood LDL cholesterol, HDL cholesterol and total cholesterol. After an initial approval of the health claim for soy protein consumption for the prevention of coronary heart disease, more recently it has been concluded from an overall analysis of literature that isolated soy protein with isoflavones only slightly decrease LDL and total cholesterol. Other plant extracts and also some proteins from animal origin have been reported to exert a lowering effect on blood cholesterol when compared with a reference protein (often casein). The underlying mechanisms are still little understood. Individual amino acids and mixture of amino acids have also been tested (mostly in animal studies) for their effects on cholesterol parameters and on cholesterol metabolism. Methionine, lysine, cystine, leucine, aspartate and glutamate have been tested individually and in combination in different models of either normo or hypercholesterolemic animals and found to be able to modify blood cholesterol and/or LDL cholesterol and/or HDL cholesterol. It is however not known if these results are relevant to human nutrition.

  8. Allied Health Chemistry Laboratory: Amino Acids, Insulin, Proteins, and Skin

    ERIC Educational Resources Information Center

    Dever, David F.

    1975-01-01

    Presents a laboratory experiment specifically designed for allied health students. The students construct molecular models of amino acids, extract amino acids from their skin with hot water, and chromatographically analyze the skin extract and hydrolyzed insulin. (MLH)

  9. Allied Health Chemistry Laboratory: Amino Acids, Insulin, Proteins, and Skin

    ERIC Educational Resources Information Center

    Dever, David F.

    1975-01-01

    Presents a laboratory experiment specifically designed for allied health students. The students construct molecular models of amino acids, extract amino acids from their skin with hot water, and chromatographically analyze the skin extract and hydrolyzed insulin. (MLH)

  10. Control of the Position of Oxygen Delivery in Soybean Lipoxygenase-1 by Amino Acid Side Chains within a Gas Migration Channel.

    PubMed

    Collazo, Lara; Klinman, Judith P

    2016-04-22

    Understanding gas migration pathways is critical to unraveling structure-function relationships in enzymes that process gaseous substrates such as O2, H2, and N2 This work investigates the role of a defined pathway for O2 in regulating the peroxidation of linoleic acid by soybean lipoxygenase 1. Computational and mutagenesis studies provide strong support for a dominant delivery channel that shuttles molecular oxygen to a specific region of the active site, thereby ensuring the regio- and stereospecificity of product. Analysis of reaction kinetics and product distribution in channel mutants also reveals a plasticity to the gas migration pathway. The findings show that a single site mutation (I553W) limits oxygen accessibility to the active site, greatly increasing the fraction of substrate that reacts with oxygen free in solution. They also show how a neighboring site mutation (L496W) can result in a redirection of oxygen toward an alternate position of the substrate, changing the regio- and stereospecificity of peroxidation. The present data indicate that modest changes in a protein scaffold may modulate the access of small gaseous molecules to enzyme-bound substrates.

  11. [Novel L-amino acid ligases catalyzing oligopeptide synthesis].

    PubMed

    Kino, Kuniki

    2010-11-01

    L-Amino acid ligase (EC 6.3.2.28) is a microbial enzyme catalyzing formation of an alpha-peptide bond from unprotected L-amino acids in an ATP-dependent manner. The YwfE protein from Bacillus subtilis 168 was the first reported L-amino acid ligase, and it synthesizes various dipeptides. Thereafter, several L-amino acid ligases were newly obtained by in silico analysis using the ATP-grasp motif. But these L-amino acid ligases synthesize only dipeptide and no longer peptide. A novel L-amino acid ligase capable of catalyzing oligopeptide synthesis is required to increase the variety of peptides. We have previously found a new member of L-amino acid ligase, RizA, from B. subtilis NBRC3134, a microorganism that produces the peptide-antibiotic rhizocticin. We newly found that a gene at approximately 9 kbp upstream of rizA encoded a novel L-amino acid ligase RizB. Recombinant RizB synthesized homo-oligomers of branched-chain amino acids consisting of 2 to 5 amino acids, and also synthesized various heteropeptides. RizB is the first reported L-amino acid ligase that catalyzes oligopeptide synthesis. In addition, we obtained L-amino acid ligases showing oligopeptide synthesis activities by in silico analysis using BLAST, which is a set of similarity search programs. These L-amino acid ligases showed low similarity in amino acid sequence, but commonly used branched-chain amino acids, such as RizB, as substrates. Furthermore, the spr0969 protein of Streptococcus pneumoniae synthesized longer peptides than those synthesized by RizB, and the BAD_1200 protein of Bifidobacteria adolescentis showed higher activity toward aromatic amino acids than toward branched-chain ones.

  12. 40 CFR 721.2584 - Dodecanoic acid, 12-amino-.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Dodecanoic acid, 12-amino-. 721.2584... Substances § 721.2584 Dodecanoic acid, 12-amino-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as dodecanoic acid, 12-amino- (PMN P-98-0823; CAS No. 693...

  13. 40 CFR 721.1643 - Benzenesulfonic acid, amino substituted phenylazo-.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Benzenesulfonic acid, amino... Specific Chemical Substances § 721.1643 Benzenesulfonic acid, amino substituted phenylazo-. (a) Chemical... as a benzenesulfonic acid, amino substituted phenylazo- (PMN P-95-86) is subject to reporting under...

  14. 40 CFR 721.2584 - Dodecanoic acid, 12-amino-.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Dodecanoic acid, 12-amino-. 721.2584... Substances § 721.2584 Dodecanoic acid, 12-amino-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as dodecanoic acid, 12-amino- (PMN P-98-0823; CAS No. 693...

  15. 40 CFR 721.1643 - Benzenesulfonic acid, amino substituted phenylazo-.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Benzenesulfonic acid, amino... Specific Chemical Substances § 721.1643 Benzenesulfonic acid, amino substituted phenylazo-. (a) Chemical... as a benzenesulfonic acid, amino substituted phenylazo- (PMN P-95-86) is subject to reporting under...

  16. 40 CFR 721.2584 - Dodecanoic acid, 12-amino-.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Dodecanoic acid, 12-amino-. 721.2584... Substances § 721.2584 Dodecanoic acid, 12-amino-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as dodecanoic acid, 12-amino- (PMN P-98-0823; CAS No. 693...

  17. 40 CFR 721.1643 - Benzenesulfonic acid, amino substituted phenylazo-.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Benzenesulfonic acid, amino... Specific Chemical Substances § 721.1643 Benzenesulfonic acid, amino substituted phenylazo-. (a) Chemical... as a benzenesulfonic acid, amino substituted phenylazo- (PMN P-95-86) is subject to reporting under...

  18. 40 CFR 721.2584 - Dodecanoic acid, 12-amino-.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Dodecanoic acid, 12-amino-. 721.2584... Substances § 721.2584 Dodecanoic acid, 12-amino-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as dodecanoic acid, 12-amino- (PMN P-98-0823; CAS No. 693...

  19. 40 CFR 721.1643 - Benzenesulfonic acid, amino substituted phenylazo-.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Benzenesulfonic acid, amino... Specific Chemical Substances § 721.1643 Benzenesulfonic acid, amino substituted phenylazo-. (a) Chemical... as a benzenesulfonic acid, amino substituted phenylazo- (PMN P-95-86) is subject to reporting under...

  20. 40 CFR 721.2584 - Dodecanoic acid, 12-amino-.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Dodecanoic acid, 12-amino-. 721.2584... Substances § 721.2584 Dodecanoic acid, 12-amino-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as dodecanoic acid, 12-amino- (PMN P-98-0823; CAS No. 693...

  1. 40 CFR 721.1643 - Benzenesulfonic acid, amino substituted phenylazo-.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Benzenesulfonic acid, amino... Specific Chemical Substances § 721.1643 Benzenesulfonic acid, amino substituted phenylazo-. (a) Chemical... as a benzenesulfonic acid, amino substituted phenylazo- (PMN P-95-86) is subject to reporting under...

  2. Origin, Microbiology, Nutrition, and Pharmacology of D-Amino Acids

    USDA-ARS?s Scientific Manuscript database

    Exposure of food proteins to certain processing conditions induces two major chemical changes: racemization of all L-amino acids (LAA) to D-amino acids (DAA) and concurrent formation of crosslinked amino acids such as lysinoalanine (LAL). The diet contains both processing-induced and naturally-form...

  3. GCN2 whets the appetite for amino acids.

    PubMed

    Dever, Thomas E; Hinnebusch, Alan G

    2005-04-15

    In response to amino acid starvation, the kinase GCN2 in yeast activates amino acid biosynthesis. Two recent studies (Maurin et al., 2005; Hao et al., 2005) reveal that GCN2 in the brain of mice restricts intake of diets lacking essential amino acids.

  4. Soil amino acid composition across a boreal forest successional sequence

    Treesearch

    Nancy R. Werdin-Pfisterer; Knut Kielland; Richard D. Boone

    2009-01-01

    Soil amino acids are important sources of organic nitrogen for plant nutrition, yet few studies have examined which amino acids are most prevalent in the soil. In this study, we examined the composition, concentration, and seasonal patterns of soil amino acids across a primary successional sequence encompassing a natural gradient of plant productivity and soil...

  5. Nutritional and medicinal aspects of D-amino acids

    USDA-ARS?s Scientific Manuscript database

    This paper describes a method for determining the nutritional value of D-amino acids, D-peptides, and amino acid derivatives using a growth assay in mice fed a synthetic all-amino acid diet. A large number of experiments were carried out in which a molar equivalent of the test compound replaced a nu...

  6. Amino acid auxotrophy as a system of immunological control nodes.

    PubMed

    Murray, Peter J

    2016-02-01

    Cells of the immune system are auxotrophs for most amino acids, including several nonessential ones. Arginine and tryptophan are used within the regulatory immune networks to control proliferation and function through pathways that actively deplete the amino acid from the microenvironment or that create regulatory molecules such as nitric oxide or kynurenines. How immune cells integrate information about essential amino acid supplies and then transfer these signals to growth and activation pathways remains unclear but has potential for pathway discovery about amino sensing. In applied research, strategies to harness amino acid auxotrophy so as to block cancerous lymphocyte growth have been attempted for decades with limited success. Emerging insights about amino acid metabolism may lead to new strategies in clinical medicine whereby both amino acid auxotrophy and the immunoregulatory pathways controlled by amino acids can be manipulated.

  7. Computational model of abiogenic amino acid condensation to obtain a polar amino acid profile.

    PubMed

    Polanco, Carlos; Buhse, Thomas; Samaniego, José Lino; Castañón González, Jorge Alberto; Arias Estrada, Miguel

    2014-01-01

    In accordance with the second law of thermodynamics, the Universe as a whole tends to higher entropy. However, the sequence of far-from-equilibrium events that led to the emergence of life on Earth could have imposed order and complexity during the course of chemical reactions in the so-called primordial soup of life. Hence, we may expect to find characteristic profiles or biases in the prebiotic product mixtures, as for instance among the first amino acids. Seeking to shed light on this hypothesis, we have designed a high performance computer program that simulates the spontaneous formation of the amino acid monomers in closed environments. The program was designed in reference to a prebiotic scenario proposed by Sydney W. Fox. The amino acid abundances and their polarities as the two principal biases were also taken into consideration. We regarded the computational model as exhaustive since 200,000 amino acid dimers were formed by simulation, subsequently expressed in a vector and compared with the corresponding amino acid dimers that were experimentally obtained by Fox. We found a very high similarity between the experimental results and our simulations.

  8. Effect of amino acid intake on brush-border membrane uptake of sulfur amino acids.

    PubMed

    Chesney, R W; Gusowski, N; Padilla, M; Lippincott, S

    1986-07-01

    Alterations in the intake of sulfur amino acids (SAA) changes the rat renal brush-border membrane uptake of the beta-amino acid, taurine. A low-SAA diet enhances and a high-taurine diet reduces uptake (Chesney et al., Kidney Int. 24: 588-594, 1983). Neither the low-SAA diet nor the high-taurine diet alters the time course or concentration-dependent accumulation of the sulfur amino acids methionine and cystine or of inorganic sulfate. By contrast the uptake of beta-alanine, another beta-amino acid that competes with taurine, is greater in animals on the low-SAA diet. The high-taurine diet does not change beta-alanine uptake. The plasma levels of taurine are altered by dietary change, but not the values for methionine and cystine. This study indicates that renal adaptation is expressed for beta-alanine, a nonsulfur-containing beta-amino acid. By contrast, methionine, cystine, and sulfate, which participate in a variety of synthetic and conjugative processes, are not conserved by the renal brush-border surface following ingestion of either a low-methionine and -cystine diet or high-taurine diet.

  9. Analysis of Saccharides by the Addition of Amino Acids

    NASA Astrophysics Data System (ADS)

    Ozdemir, Abdil; Lin, Jung-Lee; Gillig, Kent J.; Gulfen, Mustafa; Chen, Chung-Hsuan

    2016-06-01

    In this work, we present the detection sensitivity improvement of electrospray ionization (ESI) mass spectrometry of neutral saccharides in a positive ion mode by the addition of various amino acids. Saccharides of a broad molecular weight range were chosen as the model compounds in the present study. Saccharides provide strong noncovalent interactions with amino acids, and the complex formation enhances the signal intensity and simplifies the mass spectra of saccharides. Polysaccharides provide a polymer-like ESI spectrum with a basic subunit difference between multiply charged chains. The protonated spectra of saccharides are not well identified because of different charge state distributions produced by the same molecules. Depending on the solvent used and other ions or molecules present in the solution, noncovalent interactions with saccharides may occur. These interactions are affected by the addition of amino acids. Amino acids with polar side groups show a strong tendency to interact with saccharides. In particular, serine shows a high tendency to interact with saccharides and significantly improves the detection sensitivity of saccharide compounds.

  10. The Synthesis and Evaluation of Arctigenin Amino Acid Ester Derivatives.

    PubMed

    Cai, En-Bo; Yang, Li-Min; Jia, Cai-Xia; Zhang, Wei-Yuan; Zhao, Yan; Li, Wei; Song, Xing-Zhuo; Zheng, Man-Ling

    2016-10-01

    The use of arctigenin (ARG), a traditional medicine with many pharmacological activities, has been restricted due to its poor solubility in water. Five amino acid derivatives of ARG have been synthesized using glycine, o-alanine, valine, leucine, and isoleucine, which have t-butyloxy carbonyl (BOC) as a protective group. In this study, we examined the effects of removing these protective groups. The results showed that the amino acid derivatives have better solubility and nitrite-clearing ability than ARG. Among the compounds tested, the amino acid derivatives without protective group were the best. Based on these results, ARG and its two amino acid derivatives without protective group (ARG8, ARG10) were selected to evaluate their anti-tumor activity in vivo at a dosage of 40 mg/kg. The results indicated that ARG8 and ARG10 both exhibit more anti-tumor activity than ARG in H22 tumor-bearing mice. The tumor inhibition rates of ARG8 and ARG10 were 69.27 and 43.58%, which was much higher than ARG. Furthermore, the mice treated with these compounds exhibited less damage to the liver, kidney and immune organs compared with the positive group. Furthermore, ARG8 and ARG10 improved the serum cytokine levels significantly compared to ARG. In brief, this study provides a method to improve the water solubility of drugs, and we also provide a reference basis for new drug development.

  11. The amino acid sequence of monal pheasant lysozyme and its activity.

    PubMed

    Araki, T; Matsumoto, T; Torikata, T

    1998-10-01

    The amino acid sequence of monal pheasant lysozyme and its activity were analyzed. Carboxymethylated lysozyme was digested with trypsin and the resulting peptides were sequenced. The established amino acid sequence had one amino acid substitution at position 102 (Arg to Gly) comparing with Indian peafowl lysozyme and four amino acid substitutions at positions 3 (Phe to Tyr), 15 (His to Leu), 41 (Gln to His), and 121 (Gln to His) with chicken lysozyme. Analysis of the time-courses of reaction using N-acetylglucosamine pentamer as a substrate showed a difference of binding free energy change (-0.4 kcal/mol) at subsites A between monal pheasant and Indian peafowl lysozyme. This was assumed to be caused by the amino acid substitution at subsite A with loss of a positive charge at position 102 (Arg102 to Gly).

  12. Amino acid compositional shifts during streptophyte transitions to terrestrial habitats.

    PubMed

    Jobson, Richard W; Qiu, Yin-Long

    2011-02-01

    Across the streptophyte lineage, which includes charophycean algae and embryophytic plants, there have been at least four independent transitions to the terrestrial habitat. One of these involved the evolution of embryophytes (bryophytes and tracheophytes) from a charophycean ancestor, while others involved the earliest branching lineages, containing the monotypic genera Mesostigma and Chlorokybus, and within the Klebsormidiales and Zygnematales lineages. To overcome heat, water stress, and increased exposure to ultraviolet radiation, which must have accompanied these transitions, adaptive mechanisms would have been required. During periods of dehydration and/or desiccation, proteomes struggle to maintain adequate cytoplasmic solute concentrations. The increased usage of charged amino acids (DEHKR) may be one way of maintaining protein hydration, while increased use of aromatic residues (FHWY) protects proteins and nucleic acids by absorbing damaging UV, with both groups of residues thought to be important for the stabilization of protein structures. To test these hypotheses we examined amino acid sequences of orthologous proteins representing both mitochondrion- and plastid-encoded proteomes across streptophytic lineages. We compared relative differences within categories of amino acid residues and found consistent patterns of amino acid compositional fluxuation in extra-membranous regions that correspond with episodes of terrestrialization: positive change in usage frequency for residues with charged side-chains, and aromatic residues of the light-capturing chloroplast proteomes. We also found a general decrease in the usage frequency of hydrophobic, aliphatic, and small residues. These results suggest that amino acid compositional shifts in extra-membrane regions of plastid and mitochondrial proteins may represent biochemical adaptations that allowed green plants to colonize the land.

  13. Intestinal absorption of amino acids and peptides in Hartnup disorder.

    PubMed

    Leonard, J V; Marrs, T C; Addison, J M; Burston, D; Clegg, K M; Lloyd, J K; Matthews, D M; Seakins, J W

    1976-04-01

    Absorption of free and peptide-bound amino acids was investigated in a girl with Hartnup disorder aged 26 months. Plasma levels of amino acids were followed after oral administration of (1) an amino acid mixture simulating casein and (2) an equivalent dose of a partial enzymic hydrolysate of casein containing oligopeptides in addition to free amino acids. The results suggested that many neutral amino acids were poorly absorbed when given in the free form, but much more readily absorbed when given as peptides. Unexpectedly, the results also suggested that glutamic acid was poorly absorbed when given in the free form. The results obtained with threonine could not be interpreted. There was an increased renal clearance of many neutral amino acids, including glycine, but clearance of proline was not increased. Most amino acids with an increased renal clearance also appeared to be poorly absorbed when given by mouth in the free form.

  14. Neighbor Preferences of Amino Acids and Context-Dependent Effects of Amino Acid Substitutions in Human, Mouse, and Dog

    PubMed Central

    Fu, Mingchuan; Huang, Zhuoran; Mao, Yuanhui; Tao, Shiheng

    2014-01-01

    Amino acids show apparent propensities toward their neighbors. In addition to preferences of amino acids for their neighborhood context, amino acid substitutions are also considered to be context-dependent. However, context-dependence patterns of amino acid substitutions still remain poorly understood. Using relative entropy, we investigated the neighbor preferences of 20 amino acids and the context-dependent effects of amino acid substitutions with protein sequences in human, mouse, and dog. For 20 amino acids, the highest relative entropy was mostly observed at the nearest adjacent site of either N- or C-terminus except C and G. C showed the highest relative entropy at the third flanking site and periodic pattern was detected at G flanking sites. Furthermore, neighbor preference patterns of amino acids varied greatly in different secondary structures. We then comprehensively investigated the context-dependent effects of amino acid substitutions. Our results showed that nearly half of 380 substitution types were evidently context dependent, and the context-dependent patterns relied on protein secondary structures. Among 20 amino acids, P elicited the greatest effect on amino acid substitutions. The underlying mechanisms of context-dependent effects of amino acid substitutions were possibly mutation bias at a DNA level and natural selection. Our findings may improve secondary structure prediction algorithms and protein design; moreover, this study provided useful information to develop empirical models of protein evolution that consider dependence between residues. PMID:25210846

  15. [Genetic code: codon bases--the symbols of amino acid synthesis and catabolism pathways].

    PubMed

    Konyshev, V A

    1983-01-01

    The correlations between genetic codes of amino acids and pathways of synthesis and catabolism of carbon backbone of amino acids are considered. Codes of amino acids which are synthesized from oxoacids of glycolysis, the Krebs cycle and glyoxalic cycle via transamination without any additional chemical reactions, are initiated with guanine (alanine, glutamic and aspartic acids, glycine). Codons of amino acids which are formed on the branches of glycolysis at the level of compounds with three carbon atoms, begin with uracil (phenylalanine, serine, leucine, tyrosine, cysteine, tryptophan). Codes of amino acids formed from aspartate begin with adenine (methionine, isoleucine, threonine, asparagine, lysine, serine), while those of the amino acids formed from the compounds with five carbon atoms (glutamic acid and phosphoribosyl pyrophosphate) begin with cytosine (arginine, proline, glutamine, histidine). The second letter of codons is linked to catabolic pathways of amino acids: most of amino acids entering glycolysis and the Krebs cycle through even-numbered carbon compounds, have adenine and uracil at the second position of codes (A-U type); most of amino acids entering the glycolysis and the Krebs cycle via odd-numbered carbon compounds, have codons with guanine and cytidine at the second position (G-C type). The usage of purine and pyrimidine as the third letter of weak codones in most of amino acids is linked to the enthropy of amino acid formation. A hypothesis claiming that the linear genetic code was assembled from the purine and pyrimidine derivatives which have acted as participants of primitive control of amino acid synthesis and catabolism, is suggested.

  16. Synthesis of new kojic acid based unnatural α-amino acid derivatives.

    PubMed

    Balakrishna, C; Payili, Nagaraju; Yennam, Satyanarayana; Devi, P Uma; Behera, Manoranjan

    2015-11-01

    An efficient method for the preparation of kojic acid based α-amino acid derivatives by alkylation of glycinate schiff base with bromokojic acids have been described. Using this method, mono as well as di alkylated kojic acid-amino acid conjugates have been prepared. This is the first synthesis of C-linked kojic acid-amino acid conjugate where kojic acid is directly linked to amino acid through a C-C bond.

  17. [Impairments of placental amino acid metabolism in fetal growth restriction].

    PubMed

    Pogorelova, T N; Gunko, V O; Avrutskaya, V V; Kaushanskaya, L V; Durnitsyna, O A

    2017-05-01

    The content of the amino acids in the placenta during physiological pregnancy and fetal growth restriction (FGR) has been investigated my means of the method of ion-exchange chromatography. It has been found that in FGR the placental amino acid pool is characterized by a decreased content of arginine, proline, alanine, serine, cysteine, methionine, tryptophan, leucine, threonine, tyrosine, phenylalanine, glutamine and an increased content of dicarboxylic amino acids, lysine, histidine and glycine. These changes are accompanied by altered activity of some enzymes of amino acid metabolism, and the degree of these changes correlates with the level of corresponding amino acids.

  18. [Bound amino acids in local strains of Trichomonas vaginalis].

    PubMed

    Tsvetkova, A; Osinovski, E; Vasilevska, M

    1990-01-01

    Amino acid composition of water-soluble and water-insoluble proteins of 8 strains of Tr. vaginalis is studied. 17 amino acids are found in both protein hydrolyzates. Despite the complete coincidence of their qualitative compositions there are reliable differences in the quantitative contents of some amino acids. Differences in the contents of main amino acids of water-soluble proteins of different strains reflect the belonging of the latter to different sero-groups. No reliable differences in the quantitative contents of amino acids of both water-soluble and water-insoluble proteins in strains belonging to one sero-group are recognised.

  19. Amino acids from the late Precambrian Thule group, Greenland.

    PubMed

    Akiyama, M; Shimoyama, A; Ponnamperuma, C

    1982-06-01

    Amino acids were recovered at concentration level of 10-9 M/g from the interior of chert and dolomite of the Late Precambrian Thule Group. Examination of the stability of amino acids in chert under dry-heating conditions suggests that these amino acids have been preserved with a predominance of L-enantiomers in the precambrian chert. Enantiomer analysis of amino acids in dolomite showed a thermal effect resulting from a late precambrian igneous intrusion. This evidence indicates that the amino acids isolated from the Thule samples were chemical fossils and not recent contaminants.

  20. Free Amino-acid Concentrations in Fetal Fluids

    PubMed Central

    Cockburn, F.; Robins, S. P.; Forfar, J. O.

    1970-01-01

    The pattern of free amino-acid concentrations in maternal venous plasma, fetal umbilical arterial plasma, fetal urine, and amniotic fluid at 15 to 20 weeks' gestation has been determined. Free amino-acid concentrations were greater in fetal plasma than in maternal plasma, amniotic fluid, or fetal urine. The ratios of amino-acid concentrations in fetal umbilical arterial plasma and urine indicate that the fetal kidney can effectively conserve amino-acids, possibly reaching an adult level of competence in this respect. There was little correlation between amino-acid concentrations in the fluids analysed with the exception of that between amniotic fluid and fetal urine. PMID:5472758

  1. Influence of different amino substituents in position 1 and 4 on spectroscopic and acid base properties of 9,10-anthraquinone moiety

    NASA Astrophysics Data System (ADS)

    Wcisło, Anna; Niedziałkowski, Paweł; Wnuk, Elżbieta; Zarzeczańska, Dorota; Ossowski, Tadeusz

    2013-05-01

    A series of novel 1-amino and 1,4-diamino-9,10-anthraquinones, substituted with different alkyl groups, were synthesized as the result of alkylation with amino substituents. All the obtained aminoanthraquinone derivatives were characterized by NMR, IR spectroscopy and mass spectrometry. The spectroscopic properties of these compounds were determined by using UV-Vis spectroscopy in acetonitrile, and in the mixture of acetonitrile and methanol at different pH ranges. The effects of various substituents present in the newly developed anthraquinone derivatives and their ability to form hydrogen bonds between the carbonyl oxygen atom of anthraquinone moiety and nitrogen atom of N-H group in 1-aminoanthraquinone (1-AAQ) and 1,4-diaminoanthraquinone (1,4-DAAQ) were studied. Additionally, the effects of hydrogen bond formation between O-H group in hydroxyethylamino substituent and the carbonyl oxygen atom of anthraquinone were investigated. The spectroscopic behavior of the studied derivatives strongly depended on the solvent-solute interactions and the nature of solvent. The values of pKa for the new anthraquinones were determined by the combined potentiometric and spectrophotometric titration methods.

  2. Influence of different amino substituents in position 1 and 4 on spectroscopic and acid base properties of 9,10-anthraquinone moiety.

    PubMed

    Wcisło, Anna; Niedziałkowski, Paweł; Wnuk, Elżbieta; Zarzeczańska, Dorota; Ossowski, Tadeusz

    2013-05-01

    A series of novel 1-amino and 1,4-diamino-9,10-anthraquinones, substituted with different alkyl groups, were synthesized as the result of alkylation with amino substituents. All the obtained aminoanthraquinone derivatives were characterized by NMR, IR spectroscopy and mass spectrometry. The spectroscopic properties of these compounds were determined by using UV-Vis spectroscopy in acetonitrile, and in the mixture of acetonitrile and methanol at different pH ranges. The effects of various substituents present in the newly developed anthraquinone derivatives and their ability to form hydrogen bonds between the carbonyl oxygen atom of anthraquinone moiety and nitrogen atom of N-H group in 1-aminoanthraquinone (1-AAQ) and 1,4-diaminoanthraquinone (1,4-DAAQ) were studied. Additionally, the effects of hydrogen bond formation between O-H group in hydroxyethylamino substituent and the carbonyl oxygen atom of anthraquinone were investigated. The spectroscopic behavior of the studied derivatives strongly depended on the solvent-solute interactions and the nature of solvent. The values of pKa for the new anthraquinones were determined by the combined potentiometric and spectrophotometric titration methods.

  3. GC constituents and relative codon expressed amino acid composition in cyanobacterial phycobiliproteins.

    PubMed

    Kannaujiya, Vinod K; Rastogi, Rajesh P; Sinha, Rajeshwar P

    2014-08-10

    The genomic as well as structural relationship of phycobiliproteins (PBPs) in different cyanobacterial species are determined by nucleotides as well as amino acid composition. The genomic GC constituents influence the amino acid variability and codon usage of particular subunit of PBPs. We have analyzed 11 cyanobacterial species to explore the variation of amino acids and causal relationship between GC constituents and codon usage. The study at the first, second and third levels of GC content showed relatively more amino acid variability on the levels of G3+C3 position in comparison to the first and second positions. The amino acid encoded GC rich level including G rich and C rich or both correlate the codon variability and amino acid availability. The fluctuation in amino acids such as Arg, Ala, His, Asp, Gly, Leu and Glu in α and β subunits was observed at G1C1 position; however, fluctuation in other amino acids such as Ser, Thr, Cys and Trp was observed at G2C2 position. The coding selection pressure of amino acids such as Ala, Thr, Tyr, Asp, Gly, Ile, Leu, Asn, and Ser in α and β subunits of PBPs was more elaborated at G3C3 position. In this study, we observed that each subunit of PBPs is codon specific for particular amino acid. These results suggest that genomic constraint linked with GC constituents selects the codon for particular amino acids and furthermore, the codon level study may be a novel approach to explore many problems associated with genomics and proteomics of cyanobacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Inferring Selection on Amino Acid Preference in Protein Domains

    PubMed Central

    Durbin, Richard

    2009-01-01

    Models that explicitly account for the effect of selection on new mutations have been proposed to account for “codon bias” or the excess of “preferred” codons that results from selection for translational efficiency and/or accuracy. In principle, such models can be applied to any mutation that results in a preferred allele, but in most cases, the fitness effect of a specific mutation cannot be predicted. Here we show that it is possible to assign preferred and unpreferred states to amino acid changing mutations that occur in protein domains. We propose that mutations that lead to more common amino acids (at a given position in a domain) can be considered “preferred alleles” just as are synonymous mutations leading to codons for more abundant tRNAs. We use genome-scale polymorphism data to show that alleles for preferred amino acids in protein domains occur at higher frequencies in the population, as has been shown for preferred codons. We show that this effect is quantitative, such that there is a correlation between the shift in frequency of preferred alleles and the predicted fitness effect. As expected, we also observe a reduction in the numbers of polymorphisms and substitutions at more important positions in domains, consistent with stronger selection at those positions. We examine the derived allele frequency distribution and polymorphism to divergence ratios of preferred and unpreferred differences and find evidence for both negative and positive selections acting to maintain protein domains in the human population. Finally, we analyze a model for selection on amino acid preferences in protein domains and find that it is consistent with the quantitative effects that we observe. PMID:19095755

  5. Evolution of the genetic code by incorporation of amino acids that improved or changed protein function.

    PubMed

    Francis, Brian R

    2013-10-01

    Fifty years have passed since the genetic code was deciphered, but how the genetic code came into being has not been satisfactorily addressed. It is now widely accepted that the earliest genetic code did not encode all 20 amino acids found in the universal genetic code as some amino acids have complex biosynthetic pathways and likely were not available from the environment. Therefore, the genetic code evolved as pathways for synthesis of new amino acids became available. One hypothesis proposes that early in the evolution of the genetic code four amino acids-valine, alanine, aspartic acid, and glycine-were coded by GNC codons (N = any base) with the remaining codons being nonsense codons. The other sixteen amino acids were subsequently added to the genetic code by changing nonsense codons into sense codons for these amino acids. Improvement in protein function is presumed to be the driving force behind the evolution of the code, but how improved function was achieved by adding amino acids has not been examined. Based on an analysis of amino acid function in proteins, an evolutionary mechanism for expansion of the genetic code is described in which individual coded amino acids were replaced by new amino acids that used nonsense codons differing by one base change from the sense codons previously used. The improved or altered protein function afforded by the changes in amino acid function provided the selective advantage underlying the expansion of the genetic code. Analysis of amino acid properties and functions explains why amino acids are found in their respective positions in the genetic code.

  6. ABRF ESRG 2005 Study: Identification of Seven Modified Amino Acids by Edman Sequencing

    PubMed Central

    Brune, D.; Denslow, N.D.; Kobayashi, R.; Lane, W.S.; Leone, J.W.; Madden, B.J.; Neveu, J. M.; Pohl, J.

    2006-01-01

    Identification of modified amino acids can be a challenging part for Edman degradation sequence analysis, largely because they are not included among the commonly used phenylthiohydantion amino acid standards. Yet many can have unique retention times and can be assigned by an experienced researcher or through the use of a guide showing their typical chromatography characteristics. The Edman Sequencing Research Group (ESRG) 2005 study is a continuation of the 2004 study, in which the participating laboratories were provided a synthetic peptide and asked to identify the modified amino acids present in the sequence. The study sample provided an opportunity to sequence a peptide containing a variety of modified amino acids and note their retention times relative to the common amino acids. It also allowed the ESRG to compile the chromatographic properties and intensities from multiple instruments and tabulate an average elution position for these modified amino acids on commonly used instruments. Participating laboratories were given 2000 pmoles of a synthetic peptide, 18 amino acids long, containing the following modified amino acids: dimethyl- and trimethyl-lysine, 3-methyl-histidine, N-carbamyl-lysine, cystine, N-methyl-alanine, and isoaspartic acid. The modified amino acids were interspersed with standard amino acids to help in the assessment of initial and repetitive yields. In addition to filling in an assignment sheet, which included retention times and peak areas, participants were asked to provide specific details about the parameters used for the sequencing run. References for some of the modified amino acid elution characteristics were provided and the participants had the option of viewing a list of the modified amino acids present in the peptide at the ESRG Web site. The ABRF ESRG 2005 sample is the seventeenth in a series of studies designed to aid laboratories in evaluating their abilities to obtain and interpret amino acid sequence data. PMID:17122064

  7. Protein and Amino Acid Requirements during Pregnancy.

    PubMed

    Elango, Rajavel; Ball, Ronald O

    2016-07-01

    Protein forms an essential component of a healthy diet in humans to support both growth and maintenance. During pregnancy, an exceptional stage of life defined by rapid growth and development, adequate dietary protein is crucial to ensure a healthy outcome. Protein deposition in maternal and fetal tissues increases throughout pregnancy, with most occurring during the third trimester. Dietary protein intake recommendations are based on factorial estimates because the traditional method of determining protein requirements, nitrogen balance, is invasive and undesirable during pregnancy. The current Estimated Average Requirement and RDA recommendations of 0.88 and 1.1 g · kg(-1) · d(-1), respectively, are for all stages of pregnancy. The single recommendation does not take into account the changing needs during different stages of pregnancy. Recently, with the use of the minimally invasive indicator amino acid oxidation method, we defined the requirements to be, on average, 1.2 and 1.52 g · kg(-1) · d(-1) during early (∼16 wk) and late (∼36 wk) stages of pregnancy, respectively. Although the requirements are substantially higher than current recommendations, our values are ∼14-18% of total energy and fit within the Acceptable Macronutrient Distribution Range. Using swine as an animal model we showed that the requirements for several indispensable amino acids increase dramatically during late gestation compared with early gestation. Additional studies should be conducted during pregnancy to confirm the newly determined protein requirements and to determine the indispensable amino acid requirements during pregnancy in humans. © 2016 American Society for Nutrition.

  8. Stimulation of nonselective amino acid export by glutamine dumper proteins.

    PubMed

    Pratelli, Réjane; Voll, Lars M; Horst, Robin J; Frommer, Wolf B; Pilot, Guillaume

    2010-02-01

    Phloem and xylem transport of amino acids involves two steps: export from one cell type to the apoplasm, and subsequent import into adjacent cells. High-affinity import is mediated by proton/amino acid cotransporters, while the mechanism of export remains unclear. Enhanced expression of the plant-specific type I membrane protein Glutamine Dumper1 (GDU1) has previously been shown to induce the secretion of glutamine from hydathodes and increased amino acid content in leaf apoplasm and xylem sap. In this work, tolerance to low concentrations of amino acids and transport analyses using radiolabeled amino acids demonstrate that net amino acid uptake is reduced in the glutamine-secreting GDU1 overexpressor gdu1-1D. The net uptake rate of phenylalanine decreased over time, and amino acid net efflux was increased in gdu1-1D compared with the wild type, indicating increased amino acid export from cells. Independence of the export from proton gradients and ATP suggests that overexpression of GDU1 affects a passive export system. Each of the seven Arabidopsis (Arabidopsis thaliana) GDU genes led to similar phenotypes, including increased efflux of a wide spectrum of amino acids. Differences in expression profiles and functional properties suggested that the GDU genes fulfill different roles in roots, vasculature, and reproductive organs. Taken together, the GDUs appear to stimulate amino acid export by activating nonselective amino acid facilitators.

  9. Organic geochemistry of amino acids: Precambrian to recent

    SciTech Connect

    Engel, M.H.; Macko, S.A.

    1985-01-01

    Since the discovery of amino acids in fossils (Abelson, 1954), considerable effort has been made to elucidate the origin and distribution of amino acids in geologic materials. Racemization and decomposition reactions of amino acids and peptides derived via the natural hydrolysis of protein constituents of organisms have been extensively studied. While the ubiquity of amino acids presents a challenge for discerning their indigeneity in geologic samples, careful analyses have resulted in successful applications of amino acid racemization and decomposition reactions for investigations of geochronologic, paleoclimatic, stratigraphic, diagenetic and chemotaxonomic problems for Quaternary age samples. An investigation of amino acids in sediments from Baffin Island fjords indicates that their distribution may also provide data with respect to the relative contributions of marine and terrigenous organic matter to recent sediments. While the absence of unstable amino acids and the presence of racemic amino acids in a sample may preclude very recent contamination, the possibility of retardation of amino acid racemization rates subsequent to geopolymer formation must also be considered. Studies of amino acids in Paleozoic, Mesozoic and early Cenozoic age samples are limited. Precambrian samples, however, have received much attention, given the potential (however slight) for isolating compounds representative of the earliest living systems. A future approach for elucidating the origin(s) of amino acids in ancient samples may be analyses of their individual stable isotopic compositions.

  10. Dissolved amino acids in oceanic basaltic basement fluids

    NASA Astrophysics Data System (ADS)

    Lin, Huei-Ting; Amend, Jan P.; LaRowe, Douglas E.; Bingham, Jon-Paul; Cowen, James P.

    2015-09-01

    The oceanic basaltic basement contains the largest aquifer on Earth and potentially plays an important role in the global carbon cycle as a net sink for dissolved organic carbon (DOC). However, few details of the organic matter cycling in the subsurface are known because great water depths and thick sediments typically hinder direct access to this environment. In an effort to examine the role of water-rock-microorganism interaction on organic matter cycling in the oceanic basaltic crust, basement fluid samples collected from three borehole observatories installed on the eastern flank of the Juan de Fuca Ridge were analyzed for dissolved amino acids. Our data show that dissolved free amino acids (1-13 nM) and dissolved hydrolyzable amino acids (43-89 nM) are present in the basement. The amino acid concentrations in the ridge-flank basement fluids are at the low end of all submarine hydrothermal fluids reported in the literature and are similar to those in deep seawater. Amino acids in recharging deep seawater, in situ amino acid production, and diffusional input from overlying sediments are potential sources of amino acids in the basement fluids. Thermodynamic modeling shows that amino acid synthesis in the basement can be sustained by energy supplied from inorganic substrates via chemolithotrophic metabolisms. Furthermore, an analysis of amino acid concentrations and compositions in basement fluids support the notion that heterotrophic activity is ongoing. Similarly, the enrichment of acidic amino acids and depletion of hydrophobic ones relative to sedimentary particulate organic matter suggests that surface sorption and desorption also alters amino acids in the basaltic basement. In summary, although the oceanic basement aquifer is a net sink for deep seawater DOC, similar amino acid concentrations in basement aquifer and deep seawater suggest that DOC is preferentially removed in the basement over dissolved amino acids. Our data also suggest that organic carbon

  11. Synthesis of alpha-amino acids

    DOEpatents

    Davis, Jr., Jefferson W.

    1983-01-01

    A method for synthesizing alpha amino acids proceeding through novel intermediates of the formulas: R.sub.1 R.sub.2 C(OSOCl)CN, R.sub.1 R.sub.2 C(Cl)CN and [R.sub.1 R.sub.2 C(CN)O].sub.2 SO wherein R.sub.1 and R.sub.2 are each selected from hydrogen monovalent substituted and unsubstituted hydrocarbon radicals of 1 to 12 carbon atoms. The use of these intermediates allows the synthesis steps to be exothermic and results in an overall synthesis method which is faster than the synthesis methods of the prior art.

  12. Synthesis of alpha-amino acids

    DOEpatents

    Davis, Jr., Jefferson W.

    1983-01-01

    A method for synthesizing alpha amino acids proceding through novel intermediates of the formulas: R.sub.1 R.sub.2 C(OSOCl)CN, R.sub.1 R.sub.2 C(Cl)CN and [R.sub.1 R.sub.2 C(CN)O].sub.2 SO wherein R.sub.1 and R.sub.2 are each selected from hydrogen monovalent substituted and unsubstituted hydrocarbon radicals of 1 to 10 carbon atoms. The use of these intermediates allows the synthesis steps to be exothermic and results in an overall synthesis method which is faster than the snythesis methods of the prior art.

  13. Synthesis of alpha-amino acids

    DOEpatents

    Davis, Jr., Jefferson W.

    1983-01-01

    A method for synthesizing alpha amino acids proceding through novel intermediates of the formulas: R.sub.1 R.sub.2 C(OSOCl)CN, R.sub.1 R.sub.2 C(Cl)CN and [R.sub.1 R.sub.2 C(CN)O].sub.2 SO wherein R.sub.1 and R.sub.2 are each selected from hydrogen monovalent substituted and unsubstituted hydrocarbon radicals of 1 to 12 carbon atoms. The use of these intermediates allows the synthesis steps to be exothermic and results in an overall synthesis method which is faster than the synthesis methods of the prior art.

  14. Characterization of amino acids using Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Jenkins, Amanda L.; Larsen, Richard A.; Williams, Timothy B.

    2005-05-01

    A key process in the development of new drugs is elucidation of the interaction between the drug molecule and the target protein. Such knowledge then makes it possible to make systematic structural modifications of the drug molecule to optimize the interaction. Many analytical techniques can be applied to proteins in solution such as circular dichroism, ultraviolet, and fluorescence spectroscopy but these all have limitations. In this paper, we investigate the feasibility of using relatively simple, visible light Raman spectroscopic methods to investigate amino acids and related biopolymers.

  15. Food safety and amino acid balance in processed cassava "Cossettes".

    PubMed

    Diasolua Ngudi, Delphin; Kuo, Yu Haey; Lambein, Fernand

    2002-05-08

    Processed cassava (Manihot esculenta Crantz) roots provide more than 60% of the daily energy intake for the population of the Democratic Republic of Congo. Insufficiently processed cassava roots in a diet deficient in sulfur amino acid have been reported to cause the irreversible paralytic disease konzo, afflicting thousands of women and children in the remote rural areas of Bandundu Province. "Cossettes" (processed cassava roots) purchased in several markets of Kinshasa were analyzed for their content of cyanogens, free amino acids, and total protein amino acids. Residual cyanogen levels were below the safe limit recommended by the codex FAO/WHO for cassava flour (10 mg kg(-1)). The amino acid score was evaluated. Lysine and leucine were the limiting amino acids. Methionine content was very low and contributed about 13% of the total sulfur amino acids. Dietary requirements for sulfur amino acids need to be adjusted for the loss caused by cyanogen detoxification.

  16. Extraterrestrial Amino Acids in the Almahata Sitta Meteorite

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Aubrey, Andrew D.; Callahan, Michael P.; Dworkin, Jason P.; Elsila, Jamie E.; Parker, Eric T.; Bada, Jeffrey L.

    2010-01-01

    Amino acid analysis of a meteorite fragment of asteroid 2008 TC3 called Almahata Sitta was carried out using reverse-phase liquid chromatography coupled with UV fluorescence detection and time-of-flight mass spectrometry (LC-FD/ToF-MS) as part of a sample analysis consortium. LC-FD/ToF-MS analyses of hot-water extracts from the meteorite revealed a complex distribution of two- to seven-carbon aliphatic amino acids and one- to three-carbon amines with abundances ranging from 0.5 to 149 parts-per-billion (ppb). The enantiomeric ratios of the amino acids alanine, R-amino-n-butyric acid (beta-ABA), 2-amino-2-methylbutanoic acid (isovaline), and 2-aminopentanoic acid (norvaline) in the meteorite were racemic (D/L approximately 1), indicating that these amino acids are indigenous to the meteorite and not terrestrial contaminants. Several other non-protein amino acids were also identified in the meteorite above background levels including alpha-aminoisobutyric acid (alpha-AIB), 4-amino-2- methylbutanoic acid, 4-amino-3-methylbutanoic acid, and 3-, 4-, and 5-aminopentanoic acid. The total abundances of isovaline and alpha-AIB in Almahata Sitta are 1000 times lower than the abundances of these amino acids found in the CM carbonaceous chondrite Murchison. The extremely low abundances and unusual distribution of five carbon amino acids in Almahata Sitta compared to Cl, CM, and CR carbonaceous chondrites may reflect extensive thermal alteration of amino acids on the parent asteroid by partial melting during formation or subsequent impact shock heating. It is also possible that amino acids were synthesized by catalytic reactions on the parent body after asteroid 2008 TC3 cooled to lower temperatures.

  17. Extraterrestrial amino acids in the Almahata Sitta meteorite

    NASA Astrophysics Data System (ADS)

    Glavin, Daniel P.; Aubrey, Andrew D.; Callahan, Michael P.; Dworkin, Jason P.; Elsila, Jamie E.; Parker, Eric T.; Bada, Jeffrey L.; Jenniskens, Peter; Shaddad, Muawia H.

    2010-10-01

    Amino acid analysis of a meteorite fragment of asteroid 2008 TC3 called Almahata Sitta was carried out using reverse-phase liquid chromatography coupled with UV fluorescence detection and time-of-flight mass spectrometry (LC-FD/ToF-MS) as part of a sample analysis consortium. LC-FD/ToF-MS analyses of hot-water extracts from the meteorite revealed a complex distribution of two- to seven-carbon aliphatic amino acids and one- to three-carbon amines with abundances ranging from 0.5 to 149 parts-per-billion (ppb). The enantiomeric ratios of the amino acids alanine, β-amino-n-butyric acid, 2-amino-2-methylbutanoic acid (isovaline), and 2-aminopentanoic acid (norvaline) in the meteorite were racemic (D/L ˜ 1), indicating that these amino acids are indigenous to the meteorite and not terrestrial contaminants. Several other nonprotein amino acids were also identified in the meteorite above background levels including α-aminoisobutyric acid (α-AIB), 4-amino-2-methylbutanoic acid, 4-amino-3-methylbutanoic acid, and 3-, 4-, and 5-aminopentanoic acid. The total abundances of isovaline and α-AIB in Almahata Sitta are approximately 1000 times lower than the abundances of these amino acids found in the CM carbonaceous chondrite Murchison. The extremely low abundances and unusual distribution of five-carbon amino acids in Almahata Sitta compared to CI, CM, and CR carbonaceous chondrites may reflect extensive thermal alteration of amino acids on the parent asteroid by partial melting during formation or subsequent impact shock heating. It is also possible that amino acids were synthesized by catalytic reactions on the parent body after asteroid 2008 TC3 cooled to lower temperatures, or introduced as a contaminant from unrelated meteorite clasts and chemically altered by α-decarboxylation.

  18. The amino acid sequence of chymopapain from Carica papaya.

    PubMed Central

    Watson, D C; Yaguchi, M; Lynn, K R

    1990-01-01

    Chymopapain is a polypeptide of 218 amino acid residues. It has considerable structural similarity with papain and papaya proteinase omega, including conservation of the catalytic site and of the disulphide bonding. Chymopapain is like papaya proteinase omega in carrying four extra residues between papain positions 168 and 169, but differs from both papaya proteinases in the composition of its S2 subsite, as well as in having a second thiol group, Cys-117. Some evidence for the amino acid sequence of chymopapain has been deposited as Supplementary Publication SUP 50153 (12 pages) at the British Library Document Supply Centre, Boston Spa., Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained on the terms indicated in Biochem. J. (1990) 265, 5. The information comprises Supplement Tables 1-4, which contain, in order, amino acid compositions of peptides from tryptic, peptic, CNBr and mild acid cleavages, Supplement Fig. 1, showing re-fractionation of selected peaks from Fig. 2 of the main paper. Supplement Fig. 2, showing cation-exchange chromatography of the earliest-eluted peak of Fig. 3 of the main paper, Supplement Fig. 3, showing reverse-phase h.p.l.c. of the later-eluted peak from Fig. 3 of the main paper, and Supplement Fig. 4, showing the separation of peptides after mild acid hydrolysis of CNBr-cleavage fragment CB3. PMID:2106878

  19. Amino acid sequence of porcine spleen cathepsin D.

    PubMed Central

    Shewale, J G; Tang, J

    1984-01-01

    The amino acid sequence of porcine spleen cathepsin D heavy chain has been determined and, hence, the complete structure of this enzyme is now known. The sequence of heavy chain was constructed by aligning the structures of peptides generated by cyanogen bromide, trypsin, and endo-proteinase Lys C cleavages. The structure of the light chain has been published previously. The cathepsin D molecule contains 339 amino acid residues in two polypeptide chains: a 97-residue light chain and a 242-residue heavy chain, with a combined Mr of 36,779 (without carbohydrate). There are two carbohydrate units linked to asparagine residues 70 and 192. The disulfide bond arrangement in cathepsin D is probably similar to that of pepsin, because the positions of six half-cystine residues are conserved. The active site aspartyl residues, corresponding to aspartic acid-32 and -215 of pepsin, are located at residues 33 and 224 in the cathepsin D molecule. The amino acid sequence around these aspartyl residues is strongly conserved. Cathepsin D shows a strong homology with other acid proteases. When the sequence of cathepsin D, renin, and pepsin are aligned, 32.7% of the residues are identical. The homology is observed throughout the length of the molecules, indicating that three-dimensional structures of all three molecules are similar. PMID:6587385

  20. Evolutionary systems biology of amino acid biosynthetic cost in yeast.

    PubMed

    Barton, Michael D; Delneri, Daniela; Oliver, Stephen G; Rattray, Magnus; Bergman, Casey M

    2010-08-17

    Every protein has a biosynthetic cost to the cell based on the synthesis of its constituent amino acids. In order to optimise growth and reproduction, natural selection is expected, where possible, to favour the use of proteins whose constituents are cheaper to produce, as reduced biosynthetic cost may confer a fitness advantage to the organism. Quantifying the cost of amino acid biosynthesis presents challenges, since energetic requirements may change across different cellular and environmental conditions. We developed a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models and investigated the effects of the cost of amino acid synthesis on Saccharomyces cerevisiae gene expression and protein evolution. First, we used our two new and six previously reported measures of amino acid cost in conjunction with codon usage bias, tRNA gene number and atomic composition to identify which of these factors best predict transcript and protein levels. Second, we compared amino acid cost with rates of amino acid substitution across four species in the genus Saccharomyces. Regardless of which cost measure is used, amino acid biosynthetic cost is weakly associated with transcript and protein levels. In contrast, we find that biosynthetic cost and amino acid substitution rates show a negative correlation, but for only a subset of cost measures. In the economy of the yeast cell, we find that the cost of amino acid synthesis plays a limited role in shaping transcript and protein expression levels compared to that of translational optimisation. Biosynthetic cost does, however, appear to affect rates of amino acid evolution in Saccharomyces, suggesting that expensive amino acids may only be used when they have specific structural or functional roles in protein sequences. However, as there appears to be no single currency to compute the cost of amino acid synthesis across all cellular and environmental conditions, we conclude that

  1. Evolutionary Systems Biology of Amino Acid Biosynthetic Cost in Yeast

    PubMed Central

    Barton, Michael D.; Delneri, Daniela; Oliver, Stephen G.; Rattray, Magnus; Bergman, Casey M.

    2010-01-01

    Every protein has a biosynthetic cost to the cell based on the synthesis of its constituent amino acids. In order to optimise growth and reproduction, natural selection is expected, where possible, to favour the use of proteins whose constituents are cheaper to produce, as reduced biosynthetic cost may confer a fitness advantage to the organism. Quantifying the cost of amino acid biosynthesis presents challenges, since energetic requirements may change across different cellular and environmental conditions. We developed a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models and investigated the effects of the cost of amino acid synthesis on Saccharomyces cerevisiae gene expression and protein evolution. First, we used our two new and six previously reported measures of amino acid cost in conjunction with codon usage bias, tRNA gene number and atomic composition to identify which of these factors best predict transcript and protein levels. Second, we compared amino acid cost with rates of amino acid substitution across four species in the genus Saccharomyces. Regardless of which cost measure is used, amino acid biosynthetic cost is weakly associated with transcript and protein levels. In contrast, we find that biosynthetic cost and amino acid substitution rates show a negative correlation, but for only a subset of cost measures. In the economy of the yeast cell, we find that the cost of amino acid synthesis plays a limited role in shaping transcript and protein expression levels compared to that of translational optimisation. Biosynthetic cost does, however, appear to affect rates of amino acid evolution in Saccharomyces, suggesting that expensive amino acids may only be used when they have specific structural or functional roles in protein sequences. However, as there appears to be no single currency to compute the cost of amino acid synthesis across all cellular and environmental conditions, we conclude that

  2. Formation of Amino Acid Thioesters for Prebiotic Peptide Synthesis: Catalysis By Amino Acid Products

    NASA Technical Reports Server (NTRS)

    Weber, Arthur L.; DeVincenzi, Donald L. (Technical Monitor)

    1999-01-01

    The origin of life can be described as a series of events in which a prebiotic chemical process came increasingly under the control of its catalytic products. In our search for this prebiotic process that yielded catalytic takeover products (such as polypeptides), we have been investigating a reaction system that generates peptide-forming amino acid thioesters from formaldehyde, glycolaldehyde, and ammonia in the presence of thiols. As shown below, this model process begins by aldol condensation of formaldehyde and glycolaldehyde to give trioses and releases. These sugars then undergo beta-dehydration yielding their respective alpha-ketoaldehydes. Addition of ammonia to the alpha-ketoaldehydes yields imines which can either: (a) rearrange in the presence of thesis to give amino acid thioesters or (be react with another molecule of aldehyde to give imidazoles. This 'one-pot' reaction system operates under mild aqueous conditions, and like modem amino acid biosynthesis, uses sugar intermediates which are converted to products by energy-yielding redox reactions. Recently, we discovered that amino acids, such as the alanine reaction product, catalyze the first and second steps of the process. In the presence of ammonia the process also generates other synthetically useful products, like the important biochemical -- pyruvic acid.

  3. Formation of Amino Acid Thioesters for Prebiotic Peptide Synthesis: Catalysis By Amino Acid Products

    NASA Technical Reports Server (NTRS)

    Weber, Arthur L.; DeVincenzi, Donald L. (Technical Monitor)

    1999-01-01

    The origin of life can be described as a series of events in which a prebiotic chemical process came increasingly under the control of its catalytic products. In our search for this prebiotic process that yielded catalytic takeover products (such as polypeptides), we have been investigating a reaction system that generates peptide-forming amino acid thioesters from formaldehyde, glycolaldehyde, and ammonia in the presence of thiols. As shown below, this model process begins by aldol condensation of formaldehyde and glycolaldehyde to give trioses and releases. These sugars then undergo beta-dehydration yielding their respective alpha-ketoaldehydes. Addition of ammonia to the alpha-ketoaldehydes yields imines which can either: (a) rearrange in the presence of thesis to give amino acid thioesters or (be react with another molecule of aldehyde to give imidazoles. This 'one-pot' reaction system operates under mild aqueous conditions, and like modem amino acid biosynthesis, uses sugar intermediates which are converted to products by energy-yielding redox reactions. Recently, we discovered that amino acids, such as the alanine reaction product, catalyze the first and second steps of the process. In the presence of ammonia the process also generates other synthetically useful products, like the important biochemical -- pyruvic acid.

  4. Accumulated analyses of amino acid precursors in returned lunar samples

    NASA Technical Reports Server (NTRS)

    Fox, S. W.; Harada, K.; Hare, P. E.

    1973-01-01

    Six amino acids (glycine, alanine, aspartic acid, glutamic acid, serine, and threonine) obtained by hydrolysis of extracts have been quantitatively determined in ten collections of fines from five Apollo missions. Although the amounts found, 7-45 ng/g, are small, the lunar amino acid/carbon ratios are comparable to those of the carbonaceous chondrites, Murchison and Murray, as analyzed by the same procedures. Since both the ratios of amino acid to carbon, and the four or five most common types of proteinous amino acid found, are comparable for the two extraterrestrial sources despite different cosmophysical histories of the moon and meteorites, common cosmochemical processes are suggested.

  5. Beneficial Effects of the Amino Acid Glycine.

    PubMed

    Pérez-Torres, Israel; Zuniga-Munoz, Alejandra María; Guarner-Lans, Veronica

    2017-01-01

    Glycine is the smallest non-essential, neutral and metabolically inert amino acid, with a carbon atom bound to two hydrogen atoms, and to an amino and a carboxyl group. This amino acid is an essential substrate for the synthesis of several biologically important biomolecules and compounds. It participates in the synthesis of proteins, of the tripeptide glutathione and in detoxification reactions. It has a broad spectrum of anti-inflammatory, cytoprotective and immunomodulatory properties. To exert its actions, glycine binds to different receptors. The GlyR anion channel is the most studied receptor for glycine. However, there are GlyR-independent mechanisms for glycine cytoprotection and other possible binding molecules of glycine are the NMDA receptor and receptors GlyT1 and GlyT2. Although, in humans, the normal serum level of glycine is approximately 300 μM, increasing glycine intake can lead to blood levels of more than 900 μM that increase its benefic actions without having harmful side effects. The herbal pesticide glyphosate might disrupt glycine homeostasis. Many in vitro studies involving different cell types have demonstrated beneficial effects of the addition of glycine. Glycine also improved conditions of isolated perfused or stored organs. In vivo studies in experimental animals have also tested glycine as a protector molecule and some studies on the beneficial effects of glycine after its clinical application have been done. Although at high-doses, glycine may cause toxic effects, further studies are needed to investigate the safe range of usage of this aminoacid and to test the diverse routes of administration.

  6. Conformational properties of oxazoline-amino acids

    NASA Astrophysics Data System (ADS)

    Staś, Monika; Broda, Małgorzata A.; Siodłak, Dawid

    2016-04-01

    Oxazoline-amino acids (Xaa-Ozn) occur in natural peptides of potentially important bioactivity. The conformations of the model compounds: Ac-(S)-Ala-Ozn(4R-Me), Ac-(S)-Ala-Ozn(4S-Me), and (gauche+, gauche-, anti) Ac-(S)-Val-Ozn(4R-Me) were studied at meta-hybrid M06-2X/6-311++G(d,p) method including solvent effect. Boc-L-Ala-L-Ozn-4-COOMe and Boc-L-Val-L-Ozn-4-COOMe were synthesized and studied by FT-IR and NMR-NOE methods. The conformations in crystal state were gathered from the Cambridge Structural Data Base. The main conformational feature of the oxazoline amino acids is the conformation β2 (ϕ,ψ ∼ -161°, -6°), which predominates in weakly polar environment and still is accessible in polar surrounding. The changes of the conformational preferences towards the conformations αR (ϕ,ψ ∼ -70°, -15°) and then β (ϕ,ψ ∼ -57°, -155°) are observed with increase of the environment polarity.

  7. Amphipathic helices from aromatic amino acid oligomers.

    PubMed

    Gillies, Elizabeth R; Dolain, Christel; Léger, Jean-Michel; Huc, Ivan

    2006-10-13

    Synthetic helical foldamers are of significant interest for mimicking the conformations of naturally occurring molecules while at the same time introducing new structures and properties. In particular, oligoamides of aromatic amino acids are attractive targets, as their folding is highly predictable and stable. Here the design and synthesis of new amphipathic helical oligoamides based on quinoline-derived amino acids having either hydrophobic or cationic side chains are described. Their structures were characterized in the solid state by single-crystal X-ray diffraction and in solution by NMR. Results of these studies suggest that an oligomer as short as a pentamer folds into a stable helical conformation in protic solvents, including MeOH and H(2)O. The introduction of polar proteinogenic side chains to these foldamers, as described here for the first time, promises to provide possibilities for the biological applications of these molecules. In particular, amphipathic helices are versatile targets to explore due to their importance in a variety of biological processes, and the unique structure and properties of the quinoline-derived oligoamides may allow new structure-activity relationships to be developed.

  8. Formation and transformation of amino acids and amino acid precursors by high-velocity impacts

    NASA Astrophysics Data System (ADS)

    Kaneko, T.; Kobayashi, K.; Yamori, A.

    A wide variety of organic compounds have been found in extraterrestrial bodies such as comets and carbonaceous chondrites. It is plausible that these extraterrestrial bodies carried organic compounds such as amino acids or their precursors to the early Earth. It is claimed, however, that these extraterrestrial organics were destroyed during impacts to the Earth. We therefore examined possible transformation of amino acids and their precursors during high-velocity impacts by using a rail gun "HYPAC" in ISAS. Starting materials used in the impact experiments were (i) aqueous solution of glycine (10 mM or 1.0 M), and (ii) a mixture of ammonia, methanol and water. The target materials were sealed in stainless steel capsules, and shocked by impact with a polycarbonate projectile accelerated with "HYPAC" to the velocities of 2.5 - 7.0 km/s. A part of the products was acid-hydrolyzed. Both hydrolyzed an unhydrolyzed products were analyzed by mass spectrometry, high performance liquid chromatography and capillary electrophoresis and chromatography. When an aqueous solution containing ammonia, methanol and water was shocked by impact at the velocity of 6.4 km/s, a number of amino acids (e.g., serine and glycine) were detected after hydrolysis. The present results suggest that amino acid precursors could be formed during cometary impacts. When glycine solution was used as a starting material, about 40 % of glycine was recovered even after 6 km/s impact. Methylamine and ammonia, which are known as pyrolytic products of glycine, were detected, besides them, diketopiperazine and an unidentified product whose molecular weight was 134, were detected, while no glycine peptides were identified in them. It was shown that the impact processes resulted in the formation of amino acid condensates. Thermal stability of glycine precursor is comparable with glycine. The present results suggest that organic material could survive and/or formed during an impact process. Most of organic

  9. Inadequacy of prebiotic synthesis as origin of proteinous amino acids.

    PubMed

    Wong, J T; Bronskill, P M

    1979-07-18

    The production of some nonproteinous, and lack of production of other proteinous, amino acids in model prebiotic synthesis, along with the instability of glutamine and asparagine, suggest that not all of the 20 present day proteinous amino acids gained entry into proteins directly from the primordial soup. Instead, a process of active co-evolution of the genetic code and its constituent amino acids would have to precede the final selection of these proteinous amono acids.

  10. Prebiotic Synthesis of Hydrophobic and Protein Amino Acids

    PubMed Central

    Ring, David; Wolman, Yecheskel; Friedmann, Nadav; Miller, Stanley L.

    1972-01-01

    The formation of amino acids by the action of electric discharges on a mixture of methane, nitrogen, and water with traces of ammonia was studied in detail. The presence of glycine, alanine, α-amino-n-butyric acid, α-aminoisobutyric acid, valine, norvaline, isovaline, leucine, isoleucine, alloisoleucine, norleucine, proline, aspartic acid, glutamic acid, serine, threonine, allothreonine, α-hydroxy-γ-aminobutyric acid, and α,γ-diaminobutyric acid was confirmed by ion-exchange chromatography and gas chromatography-mass spectrometry. All of the primary α-amino acids found in the Murchison Meteorite have been synthesized by this electric discharge experiment. PMID:4501592

  11. Amino Acid Transport in Mycobacterium smegmatis

    PubMed Central

    Yabu, Kunihiko

    1970-01-01

    The transport of d-alanine, d-glutamic acid, and d-valine in Mycobacterium smegmatis was compared quantitatively with that of their l-isomers. It appeared that the uptake of d-alanine was mediated by an active process displaying saturation kinetics characteristic of enzyme function, whereas the uptake of d-glutamic acid was accomplished by a passive process showing diffusion kinetics. Both processes were involved in the uptake of l-alanine, l-glutamic acid, d-valine, and l-valine. d-Valine competed with l-valine for entry into the cell through a single active process. d-Alanine and l-alanine also utilized the same active process, but the d-isomer could not enter the cell through the passive process. The passive process exhibited characteristics of diffusion, but was sensitive to sulfhydryl-blocking reagents and showed competition among structurally related amino acids. These last findings suggested that the passive process is a facilitated diffusion. PMID:5437732

  12. ANTIGENICITY OF POLYPEPTIDES (POLY ALPHA AMINO ACIDS)

    PubMed Central

    Maurer, Paul H.; Gerulat, Bernard F.; Pinchuck, Paul

    1964-01-01

    A new group of synthetic random polymers of α-L-amino acids has been studied for immunogenicity. With the glutamic acid and alanine copolymers, those consisting of almost equimolar amounts of the two (G60A40 and G40A60) were effective antigens in rabbits whereas those with higher glutamic acid contents (G75A25, G90A10) were poor antigens. The substitution of alanine by valine or leucine (G75V25 and G80Leu20) produced copolymers which were poor antigens in rabbits but effective in guinea pigs. L70A30, although capable of "non-specifically" precipitating serum proteins, was shown not to be antigenic in either rabbits or guinea pigs. The introduction of alanine into glutamic acid and lysine polymers (GLA series) enhanced the immunogenicity of the terpolymers, i.e., GLA30 > GLA20 > GLA10 > GL. The mechanism by which this may be accomplished is discussed as possibly being related to the reduction of the interactions between glutamyl and lysyl residues which allows the carboxyl groups to act as strong immunogenic determinants. PMID:14176288

  13. [Amino acid exchange in paeci lomycosis-complicated echinococcosis].

    PubMed

    Streliaeva, A V; Akhmedov, Iu M; Gasparian, É R; Lazareva, N B; Samylina, I A; Chebyshev, N V; Polzikov, V V; Prokina, E S; Kurilov, D V; Zuev, S S; Shcheglova, T A; Gabchenko, A K; Sadykov, V M

    2011-01-01

    The authors have detected atypical paecilomycosis-associated myocarditis with impaired amino acid exchange and pain syndrome for the first time. At first, pain occurs in the chest and radiates into the axilla, to the left arm to the finger tips, by paralyzing the arm. In some patients, pain manifests itself in both arms with radiation to the belly, by accompanying by fainting. The skin is wet, cold; the pulse is frequent and of poor volume and difficult-to-count. Heart pain spreads into the armpit and down the arm, by making the fingers numb. Attempts to use current analgesics (movalis, sirdalud, nimesil, morphine) in combination with fungicides (diflucan, mycosist, orungal) have failed to yield positive results. The homeopathic drug Latrodectus mactans, prepared from caracurt venom, in combination with the authors' designed diet and other homeopathic agents have relieved pain syndrome and normalized amino acid exchange, which offered possibilities for successful surgical treatment for echinococcosis with later recovery.

  14. A reexamination of amino acids in lunar soil

    NASA Astrophysics Data System (ADS)

    Brinton, K. L. F.; Bada, J. L.; Arnold, J. R.

    1993-03-01

    Amino acids in lunar soils provide an important indicator of the level of prebiotic organic compounds on the moon. The results provide insight into the chemistry of amino acid precursors, and furthermore, given the flux of carbonaceous material to the moon, we can evaluate the survival of organics upon impact. The amino acid contents of both hydrolyzed and unhydrolyzed hot-water extracts of Apollo 17 lunar soil were determined using ophthaldialdehyde/N-acetyl cysteine (OPA/NAC) derivatization followed by HPLC analysis. Previous studies of lunar amino acids were inconclusive, as the technique used (derivatization with ninhydrin followed by HPLC analysis) was unable to discriminate between cosmogenic amino acids and terrestrial contaminants. Cosmogenic amino acids are racemic, and many of the amino acids found in carbonaceous meteorites such as Murchison, i.e., alpha-amino-i-butyric acid (aib), are extremely rare on Earth. The ninhydrin method does not distinguish amino acid enantiomers, nor does it detect alpha-alkyl amino acids such as aib, whereas the OPA/NAC technique does both.

  15. Relative Amino Acid Composition Signatures of Organisms and Environments

    PubMed Central

    Moura, Alexandra; Savageau, Michael A.; Alves, Rui

    2013-01-01

    Background Identifying organism-environment interactions at the molecular level is crucial to understanding how organisms adapt to and change the chemical and molecular landscape of their habitats. In this work we investigated whether relative amino acid compositions could be used as a molecular signature of an environment and whether such a signature could also be observed at the level of the cellular amino acid composition of the microorganisms that inhabit that environment. Methodologies/Principal Findings To address these questions we collected and analyzed environmental amino acid determinations from the literature, and estimated from complete genomic sequences the global relative amino acid abundances of organisms that are cognate to the different types of environment. Environmental relative amino acid abundances clustered into broad groups (ocean waters, host-associated environments, grass land environments, sandy soils and sediments, and forest soils), indicating the presence of amino acid signatures specific for each environment. These signatures correlate to those found in organisms. Nevertheless, relative amino acid abundance of organisms was more influenced by GC content than habitat or phylogeny. Conclusions Our results suggest that relative amino acid composition can be used as a signature of an environment. In addition, we observed that the relative amino acid composition of organisms is not highly determined by environment, reinforcing previous studies that find GC content to be the major factor correlating to amino acid composition in living organisms. PMID:24204807

  16. A reexamination of amino acids in lunar soil

    NASA Technical Reports Server (NTRS)

    Brinton, K. L. F.; Bada, J. L.; Arnold, J. R.

    1993-01-01

    Amino acids in lunar soils provide an important indicator of the level of prebiotic organic compounds on the moon. The results provide insight into the chemistry of amino acid precursors, and furthermore, given the flux of carbonaceous material to the moon, we can evaluate the survival of organics upon impact. The amino acid contents of both hydrolyzed and unhydrolyzed hot-water extracts of Apollo 17 lunar soil were determined using ophthaldialdehyde/N-acetyl cysteine (OPA/NAC) derivatization followed by HPLC analysis. Previous studies of lunar amino acids were inconclusive, as the technique used (derivatization with ninhydrin followed by HPLC analysis) was unable to discriminate between cosmogenic amino acids and terrestrial contaminants. Cosmogenic amino acids are racemic, and many of the amino acids found in carbonaceous meteorites such as Murchison, i.e., alpha-amino-i-butyric acid (aib), are extremely rare on Earth. The ninhydrin method does not distinguish amino acid enantiomers, nor does it detect alpha-alkyl amino acids such as aib, whereas the OPA/NAC technique does both.

  17. A reexamination of amino acids in lunar soil

    NASA Technical Reports Server (NTRS)

    Brinton, K. L. F.; Bada, J. L.; Arnold, J. R.

    1993-01-01

    Amino acids in lunar soils provide an important indicator of the level of prebiotic organic compounds on the moon. The results provide insight into the chemistry of amino acid precursors, and furthermore, given the flux of carbonaceous material to the moon, we can evaluate the survival of organics upon impact. The amino acid contents of both hydrolyzed and unhydrolyzed hot-water extracts of Apollo 17 lunar soil were determined using ophthaldialdehyde/N-acetyl cysteine (OPA/NAC) derivatization followed by HPLC analysis. Previous studies of lunar amino acids were inconclusive, as the technique used (derivatization with ninhydrin followed by HPLC analysis) was unable to discriminate between cosmogenic amino acids and terrestrial contaminants. Cosmogenic amino acids are racemic, and many of the amino acids found in carbonaceous meteorites such as Murchison, i.e., alpha-amino-i-butyric acid (aib), are extremely rare on Earth. The ninhydrin method does not distinguish amino acid enantiomers, nor does it detect alpha-alkyl amino acids such as aib, whereas the OPA/NAC technique does both.

  18. Limiting amino acids in bengal gram (Cicer arietinum) as determined from blood amino acid levels and amino acid supplementation studies in the rat.

    PubMed

    Khader, V; Rao, S V

    1982-01-01

    The limiting amino acids of Bengal gram (Cicer arietinum) were determined from plasma amino acid score and ratio and growth response of weanling rats to supplements of amino acids. The results indicated that methionine, threonine and tryptophan are the most limiting amino acids. Protein efficiency ratio of raw and cooked Bengal gram fed at a dietary level of 10% protein increased from 2.7 to 3.7 and 2.4 to 3.4, respectively, on supplementing the diets with methionine, threonine and tryptophan. Plasma levels of lysine, methionine, threonine and tryptophan were similar in rats fed raw or cooked Bengal gram, indicating that the trypsin or other inhibitors that may be present in the raw gram do not affect the biological availability of these amino acids.

  19. Fatty acid production from amino acids and alpha-keto acids by Brevibacterium linens BL2.

    PubMed

    Ganesan, Balasubramanian; Seefeldt, Kimberly; Weimer, Bart C

    2004-11-01

    Low concentrations of branched-chain fatty acids, such as isobutyric and isovaleric acids, develop during the ripening of hard cheeses and contribute to the beneficial flavor profile. Catabolism of amino acids, such as branched-chain amino acids, by bacteria via aminotransferase reactions and alpha-keto acids is one mechanism to generate these flavorful compounds; however, metabolism of alpha-keto acids to flavor-associated compounds is controversial. The objective of this study was to determine the ability of Brevibacterium linens BL2 to produce fatty acids from amino acids and alpha-keto acids and determine the occurrence of the likely genes in the draft genome sequence. BL2 catabolized amino acids to fatty acids only under carbohydrate starvation conditions. The primary fatty acid end products from leucine were isovaleric acid, acetic acid, and propionic acid. In contrast, logarithmic-phase cells of BL2 produced fatty acids from alpha-keto acids only. BL2 also converted alpha-keto acids to branched-chain fatty acids after carbohydrate starvation was achieved. At least 100 genes are potentially involved in five different metabolic pathways. The genome of B. linens ATCC 9174 contained these genes for production and degradation of fatty acids. These data indicate that brevibacteria have the ability to produce fatty acids from amino and alpha-keto acids and that carbon metabolism is important in regulating this event.

  20. Transfer of Asymmetry between Proteinogenic Amino Acids under Harsh Conditions

    NASA Astrophysics Data System (ADS)

    Tarasevych, Arkadii V.; Vives, Thomas; Snytnikov, Valeriy N.; Guillemin, Jean-Claude

    2017-03-01

    The heating above 400 °C of serine, cysteine, selenocysteine and threonine leads to a complete decomposition of the amino acids and to the formation in low yields of alanine for the three formers and of 2-aminobutyric acid for the latter. At higher temperature, this amino acid is observed only when sublimable α-alkyl-α-amino acids are present, and with an enantiomeric excess dependent on several parameters. Enantiopure or enantioenriched Ser, Cys, Sel or Thr is not able to transmit its enantiomeric excess to the amino acid formed during its decomposition. The presence during the sublimation-decomposition of enantioenriched valine or isoleucine leads to the enantioenrichment of all sublimable amino acids independently of the presence of many decomposition products coming from the unstable derivative. All these studies give information on a potentially prebiotic key-reaction of abiotic transformations between α-amino acids and their evolution to homochirality.

  1. Transfer of Asymmetry between Proteinogenic Amino Acids under Harsh Conditions

    NASA Astrophysics Data System (ADS)

    Tarasevych, Arkadii V.; Vives, Thomas; Snytnikov, Valeriy N.; Guillemin, Jean-Claude

    2017-09-01

    The heating above 400 °C of serine, cysteine, selenocysteine and threonine leads to a complete decomposition of the amino acids and to the formation in low yields of alanine for the three formers and of 2-aminobutyric acid for the latter. At higher temperature, this amino acid is observed only when sublimable α-alkyl-α-amino acids are present, and with an enantiomeric excess dependent on several parameters. Enantiopure or enantioenriched Ser, Cys, Sel or Thr is not able to transmit its enantiomeric excess to the amino acid formed during its decomposition. The presence during the sublimation-decomposition of enantioenriched valine or isoleucine leads to the enantioenrichment of all sublimable amino acids independently of the presence of many decomposition products coming from the unstable derivative. All these studies give information on a potentially prebiotic key-reaction of abiotic transformations between α-amino acids and their evolution to homochirality.

  2. Transfer of Asymmetry between Proteinogenic Amino Acids under Harsh Conditions.

    PubMed

    Tarasevych, Arkadii V; Vives, Thomas; Snytnikov, Valeriy N; Guillemin, Jean-Claude

    2017-03-31

    The heating above 400 °C of serine, cysteine, selenocysteine and threonine leads to a complete decomposition of the amino acids and to the formation in low yields of alanine for the three formers and of 2-aminobutyric acid for the latter. At higher temperature, this amino acid is observed only when sublimable α-alkyl-α-amino acids are present, and with an enantiomeric excess dependent on several parameters. Enantiopure or enantioenriched Ser, Cys, Sel or Thr is not able to transmit its enantiomeric excess to the amino acid formed during its decomposition. The presence during the sublimation-decomposition of enantioenriched valine or isoleucine leads to the enantioenrichment of all sublimable amino acids independently of the presence of many decomposition products coming from the unstable derivative. All these studies give information on a potentially prebiotic key-reaction of abiotic transformations between α-amino acids and their evolution to homochirality.

  3. [Amino acid level in pastry with low caloric value].

    PubMed

    Barkhatov, V Iu; Vyskubova, N K; Felipas, T B; Pshemurzova, R M; Kamenetskaia, E V

    1988-01-01

    The effect of fruit paste additives on amino acid composition of farinaceous and decorative confectionery semifinished products was studied to decrease their fuel value. It was found that a partial replacement of sugar and fat for apple and quince pastes in apple biscuit and apple shortbread semiproducts led to an increase in the content of essential and sulfur-containing amino acids. Cream prepared from egg albumin and quince paste had reduced content of amino acids (except for glutamic acid) due to the diminished content of egg albumin, however, the balance of amino acid composition was improved.

  4. Single Amino Acid Substitutions at Specific Positions of the Heptad Repeat Sequence of Piscidin-1 Yielded Novel Analogs That Show Low Cytotoxicity and In Vitro and In Vivo Antiendotoxin Activity

    PubMed Central

    Kumar, Amit; Tripathi, Amit Kumar; Kathuria, Manoj; Shree, Sonal; Tripathi, Jitendra Kumar; Purshottam, R. K.; Ramachandran, Ravishankar; Mitra, Kalyan

    2016-01-01

    Piscidin-1 possesses significant antimicrobial and cytotoxic activities. To recognize the primary amino acid sequence(s) in piscidin-1 that could be important for its biological activity, a long heptad repeat sequence located in the region from amino acids 2 to 19 was identified. To comprehend the possible role of this motif, six analogs of piscidin-1 were designed by selectively replacing a single isoleucine residue at a d (5th) position or at an a (9th or 16th) position with either an alanine or a valine residue. Two more analogs, namely, I5F,F6A-piscidin-1 and V12I-piscidin-1, were designed for investigating the effect of interchanging an alanine residue at a d position with an adjacent phenylalanine residue and replacing a valine residue with an isoleucine residue at another d position of the heptad repeat of piscidin-1, respectively. Single alanine-substituted analogs exhibited significantly reduced cytotoxicity against mammalian cells compared with that of piscidin-1 but appreciably retained the antibacterial and antiendotoxin activities of piscidin-1. All the single valine-substituted piscidin-1 analogs and I5F,F6A-piscidin-1 showed cytotoxicity greater than that of the corresponding alanine-substituted analogs, antibacterial activity marginally greater than or similar to that of the corresponding alanine-substituted analogs, and also antiendotoxin activity superior to that of the corresponding alanine-substituted analogs. Interestingly, among these peptides, V12I-piscidin-1 showed the highest cytotoxicity and antibacterial and antiendotoxin activities. Lipopolysaccharide (12 mg/kg of body weight)-treated mice, further treated with I16A-piscidin-1, the piscidin-1 analog with the highest therapeutic index, at a single dose of 1 or 2 mg/kg of body weight, showed 80 and 100% survival, respectively. Structural and functional characterization of these peptides revealed the basis of their biological activity and demonstrated that nontoxic piscidin-1 analogs with

  5. Snorkeling preferences foster an amino acid composition bias in transmembrane helices.

    PubMed

    Chamberlain, Aaron K; Lee, Yohan; Kim, Sanguk; Bowie, James U

    2004-05-28

    By analyzing transmembrane (TM) helices in known structures, we find that some polar amino acids are more frequent at the N terminus than at the C terminus. We propose the asymmetry occurs because most polar amino acids are better able to snorkel their polar atoms away from the membrane core at the N terminus than at the C terminus. Two findings lead us to this proposition: (1) side-chain conformations are influenced strongly by the N or C-terminal position of the amino acid in the bilayer, and (2) the favored snorkeling direction of an amino acid correlates well with its N to C-terminal composition bias. Our results suggest that TM helix predictions should incorporate an N to C-terminal composition bias, that rotamer preferences of TM side-chains are position-dependent, and that the ability to snorkel influences the evolutionary selection of amino acids for the helix N and C termini.

  6. [Accumulation of amino acid substitutions promotes irreversible structural changes in the hemagglutinin of human influenza AH3 virus during evolution].

    PubMed

    Nakajima, Katsuhisa; Nobusawa, Eri; Nakajima, Setsuko

    2006-06-01

    During protein evolution the amino acid substitutions accumulate with time. However, the effect of accumulation of the amino acid substitutions to structural changes has not been estimated well. We will propose that the discordance of amino acid substitution on the HA protein of influenza A virus is useful for the assessment of structural changes during evolution. Discordance value can be obtained from the experimental data of tolerance or intolerance by introducing site directed mutagenesis at the homologous positions of two HA proteins holding the same amino acid residues. The value of discordance correlated to the number of amino acid differences among proteins. In the H3HA discordance rate was calculated to be 0.45% per one amino acid change. Furthermore, discordance of amino acid substitutions suggests that tolerable amino acid substitutions in different order have a probability of promoting irreversible divergence of the HA protein to different subtypes.

  7. Cooperation between Lactococcus lactis and nonstarter lactobacilli in the formation of cheese aroma from amino acids.

    PubMed

    Kieronczyk, Agnieszka; Skeie, Siv; Langsrud, Thor; Yvon, Mireille

    2003-02-01

    In Gouda and Cheddar type cheeses the amino acid conversion to aroma compounds, which is a major process for aroma formation, is essentially due to lactic acid bacteria (LAB). In order to evaluate the respective role of starter and nonstarter LAB and their interactions in cheese flavor formation, we compared the catabolism of phenylalanine, leucine, and methionine by single strains and strain mixtures of Lactococcus lactis subsp. cremoris NCDO763 and three mesophilic lactobacilli. Amino acid catabolism was studied in vitro at pH 5.5, by using radiolabeled amino acids as tracers. In the presence of alpha-ketoglutarate, which is essential for amino acid transamination, the lactobacillus strains degraded less amino acids than L. lactis subsp. cremoris NCDO763, and produced mainly nonaromatic metabolites. L. lactis subsp. cremoris NCDO763 produced mainly the carboxylic acids, which are important compounds for cheese aroma. However, in the reaction mixture containing glutamate, only two lactobacillus strains degraded amino acids significantly. This was due to their glutamate dehydrogenase (GDH) activity, which produced alpha-ketoglutarate from glutamate. The combination of each of the GDH-positive lactobacilli with L. lactis subsp. cremoris NCDO763 had a beneficial effect on the aroma formation. Lactobacilli initiated the conversion of amino acids by transforming them mainly to keto and hydroxy acids, which subsequently were converted to carboxylic acids by the Lactococcus strain. Therefore, we think that such cooperation between starter L. lactis and GDH-positive lactobacilli can stimulate flavor development in cheese.

  8. Cooperation between Lactococcus lactis and Nonstarter Lactobacilli in the Formation of Cheese Aroma from Amino Acids

    PubMed Central

    Kieronczyk, Agnieszka; Skeie, Siv; Langsrud, Thor; Yvon, Mireille

    2003-01-01

    In Gouda and Cheddar type cheeses the amino acid conversion to aroma compounds, which is a major process for aroma formation, is essentially due to lactic acid bacteria (LAB). In order to evaluate the respective role of starter and nonstarter LAB and their interactions in cheese flavor formation, we compared the catabolism of phenylalanine, leucine, and methionine by single strains and strain mixtures of Lactococcus lactis subsp. cremoris NCDO763 and three mesophilic lactobacilli. Amino acid catabolism was studied in vitro at pH 5.5, by using radiolabeled amino acids as tracers. In the presence of α-ketoglutarate, which is essential for amino acid transamination, the lactobacillus strains degraded less amino acids than L. lactis subsp. cremoris NCDO763, and produced mainly nonaromatic metabolites. L. lactis subsp. cremoris NCDO763 produced mainly the carboxylic acids, which are important compounds for cheese aroma. However, in the reaction mixture containing glutamate, only two lactobacillus strains degraded amino acids significantly. This was due to their glutamate dehydrogenase (GDH) activity, which produced α-ketoglutarate from glutamate. The combination of each of the GDH-positive lactobacilli with L. lactis subsp. cremoris NCDO763 had a beneficial effect on the aroma formation. Lactobacilli initiated the conversion of amino acids by transforming them mainly to keto and hydroxy acids, which subsequently were converted to carboxylic acids by the Lactococcus strain. Therefore, we think that such cooperation between starter L. lactis and GDH-positive lactobacilli can stimulate flavor development in cheese. PMID:12570989

  9. Catalytic hydrogenation of amino acids to amino alcohols with complete retention of configuration.

    PubMed

    Tamura, Masazumi; Tamura, Riku; Takeda, Yasuyuki; Nakagawa, Yoshinao; Tomishige, Keiichi

    2014-06-25

    Rh-MoOx/SiO2 is an effective heterogeneous catalyst for selective hydrogenation of amino acids to amino alcohols in a water solvent. MoOx modification of Rh drastically enhanced the activity and improved the selectivity and ee. Various amino alcohols were obtained in high yields (90-94%) with complete retention of configuration.

  10. A new classification of HLA-DRB1 alleles based on acid–base properties of the amino acids located at positions 13, 70 and 71: impact on ACPA status or structural progression, and meta-analysis on 1235 patients with rheumatoid from two cohorts (ESPOIR and EAC cohort)

    PubMed Central

    Ruyssen-Witrand, Adeline; van Steenbergen, Hanna W; van Heemst, Jurgen; Gourraud, Pierre-Antoine; Nigon, Delphine; Lukas, Cédric; Miceli-Richard, Corinne; Jamard, Bénédicte; Cambon-Thomsen, Anne; Cantagrel, Alain; Dieudé, Philippe; van der Helm-van Mil, Annette H M; Constantin, Arnaud

    2015-01-01

    Objective To group HLA-DRB1 alleles based on acid–base properties of amino acids at positions 13, 70 and 71 and analyse their association with the presence of anticitrullinated peptide antibodies (ACPA) and structural progression in 2 cohorts of early rheumatoid arthritis (RA). Methods Patients with RA (N=612) from ESPOIR cohort and from EAC cohort (n=624) were genotyped for HLA-DRB1 alleles. The alleles containing the RAA sequence at positions 72–74 were classified into 3 groups according to the amino acid at positions 13, 70 and 71: BB encoding basic amino acids at positions 13, 70 and 71; A encoding acidic amino acids at positions 70 and 71; and BN encoding either neutral amino acids at position 13 and basic amino acids at positions 70 and 71, or basic amino acid at position 13 and neutral amino acids at positions 70 and 71. The associations between the different alleles and (1) the ACPA presence, and (2) the structural progression were assessed by χ2 test; a meta-analysis was performed on the 2 cohorts using the Mantel-Haenszel method. Results After meta-analysis, BB alleles were significantly associated with ACPA presence (OR (95% CI) 4.08 (3.14 to 5.31)) and structural progression (OR (95% CI) 2.33 (1.76 to 3.09)). The alleles protected significantly against ACPA presence (OR (95% CI) 0.37 (0.28 to 0.50)) and structural progression (OR (95% CI) 0.34 (0.23 to 0.50)). This acid–base classification allowed to separate another group BN with an intermediate risk of ACPA production (OR (95% CI) 1.14 (0.91 to 1.44)) and structural progression (OR (95% CI) 1.01 (0.77 to 1.33)). Conclusions This new classification permitted to make a hierarchy of HLA-DRB1 alleles in terms of association with ACPA presence or structural progression in early RA. PMID:26629363

  11. Unprecedented concentrations of indigenous amino acids in primitive CR meteorites

    NASA Astrophysics Data System (ADS)

    Ehrenfreund, Pascale; Martins, Zita; Alexander, Conel; Orzechowska, Grazyna; Fogel, Marylin

    CR meteorites are among the most primitive meteorites. We have performed pioneering work determining the compositional characteristics of amino acids in this type of carbonaceous chondrites. We report the first measurements of amino acids in Antarctic CR meteorites, two of which show the highest amino acid concentrations ever found in a chondrite. We have analyzed the amino acid content of the Antarctic CRs EET92042, GRA95229 and GRO95577 using high performance liquid chromatography with UV fluorescence detection (HPLC-FD) and gas chromatography-mass spectrometry (GC-MS). Additionally, compound-specific carbon isotopic measurements for most of the individual amino acids from the EET92042 and GRA95229 meteorites were achieved by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). Our data show that EET92042 and GRA95229 are the most amino acid-rich chondrites ever analyzed, with total amino acid concentrations of 180 and 249 parts-per-million (ppm), respectively. GRO95577, however, is depleted in amino acids (<1 ppm). The most abundant amino acids present in the EET92042 and GRA95229 meteorites are the α-amino acids glycine, isovaline, α-aminoisobutyric acid (α-AIB), and alanine, with δ 13 C values ranging from +31.6% to +50.5%. The highly enriched carbon isotope results together with racemic enantiomeric ratios determined for most amino acids indicate that primitive organic matter was preserved in these meteorites. In addition, the relative abundances of α-AIB and β-alanine amongst Antarctic CR meteorites appear to correspond to the degree of aqueous alteration on their respective parent body. Investigating the abundances and isotopic composition of amino acids in primitive chondrites helps to understand the role of meteorites as a source of extraterrestrial prebiotic organic compounds to the early Earth.

  12. Extraterrestrial Amino Acids in the Almahata Sitta Meteorite

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Aubrey, Andrew D.; Callahan, Michael P.; Dworkin, Jason P.; Elsila, Jamie E.; Parker, Eric T.; Bada, Jeffrey L.

    2009-01-01

    Amino acid analysis of a meteorite fragment of asteroid 2008 TC(sub 3) called Almahata Sitta was carried out using reverse-phase high-perfo rmance liquid chromatography coupled with UV fluorescence detection a nd time-of-flight mass spectrometry (HPLC-FD/ToF-MS) as part of a sam ple analysis consortium. HPLC analyses of hot-water extracts from the meteorite revealed a complex distribution of two- to six-carbon aliph atic amino acids and one- to three carbon amines with abundances rang ing from 0.5 to 149 parts-per-billion (ppb). The enantiomeric ratios of the amino acids alanine, Beta-amino-n-butyric acid (Beta-ABA), 2-amino-2- methylbutanoic acid (isovaline), and 2-aminopentanoic acid (no rvaline) in the meteorite were racemic (D/L approximately 1), indicat ing that these amino acids are indigenous to the meteorite and not te rrestrial contaminants. Several other non-protein amino acids were also identified in the meteorite above background levels including alpha -aminoisobutyric acid (alpha-AIB), 4-amino-2- methybutanoic acid, 4-a mino-3-methylbutanoic acid, and 3-, 4-, and 5-aminopentanoic acid. Th e total abundances of isovaline and AlB in Almahata Sitta are approximately 1000 times lower than the abundances of these amino acids found in the CM carbonaceous meteorite Murchison. The extremely love abund ances and unusual distribution of five carbon amino acids in Almahata Sitta compared to Cl, CM, and CR carbonaceous meteorites and may be due to extensive thermal alteration of amino acids on the parent aster oid by partial melting during formation or impact shock heating.

  13. Relationship of maternal amino acids and proteins to fetal growth and mental development.

    PubMed

    Moghissi, K S; Churchill, J A; Kurrie, D

    1975-10-15

    The relationship of maternal amino acids, proteins, and certain other factors to fetal development (weight and cranial volume at birth and mental and motor scores at 8 months of age) was investigated in 129 gravidas. Maternal prepregnancy weight was significantly related to birth weight and cranial volume in the newborn. Among amino acids, glycine, lysine, and total amino acids were positively correlated with birth weight, whereas valine and threonine showed a negative correlation. Cranial volume at birth was significantly related to the level of glycine and alpha1 globulin. Other protein and amino acids which contributed to cranial volume included threonine, histidine, glutamic acid, and beta globulin, negatively correlated, whereas glutamine was positively correlated. Alpha1 globulin (negatively) and glycine (positively) made significant contributions to motor development. For mental development, alpha 1 globulin and histidine showed a negative correlation, whereas isoleucine was positively correlated. Findings indicated that the concentrations of certain maternal amino acids and proteins in the third trimester of pregnancy correlated significantly with fetal growth and development. This study suggests: (1) specific proteins or amino acids may be responsible for different developmental measures; (2) injudicious dietary restrictions in pregnancy should be avoided; (3) the determination of alpha1 globulin and a few amino acids such as glycine, lysine, and histidine in late pregancy may be used as predictors of fetal growth and development.

  14. Nectar amino acids enhance reproduction in male butterflies.

    PubMed

    Cahenzli, Fabian; Erhardt, Andreas

    2013-01-01

    After over 30 years of research, it was recently shown that nectar amino acids increase female butterfly fecundity. However, little attention has been paid to the effect of nectar amino acids on male butterfly reproduction. Here, we show that larval food conditions (nitrogen-rich vs. nitrogen-poor host plants) and adult diet quality (nectar with or without amino acids) affected the amount of consumed nectar in Coenonympha pamphilus males. Furthermore, amino acids in the nectar diet of males increased progeny's larval hatching mass, irrespective of paternal larval reserves. Our study takes the whole reproductive cycle of male butterflies into account, and also considers the role of females in passing male nutrients to offspring, as males' realized reproduction was examined indirectly via nuptial gifts, by female performance. With this comprehensive approach, we demonstrate for the first time that nectar amino acids can improve male butterfly reproduction, supporting the old postulate that nectar amino acids generally enhance butterfly fitness.

  15. Transport of Aromatic Amino Acids by Pseudomonas aeruginosa

    PubMed Central

    Kay, W. W.; Gronlund, Audrey F.

    1971-01-01

    Kinetic studies of the transport of aromatic amino acids by Pseudomonas aeruginosa revealed the existence of two high-affinity transport systems which recognized the three aromatic amino acids. From competition data and studies on the exchange of preformed aromatic amino acid pools, the first transport system was found to be functional with phenylalanine, tyrosine, and tryptophan (in order of decreasing activity), whereas the second system was active with tryptophan, phenylalanine, and tyrosine. The two systems also transported a number of aromatic amino acid analogues but not other amino acids. Mutants defective in each of the two and in both transport systems were isolated and described. When the amino acids were added at low external concentrations to cells growing logarithmically in glucose minimal medium, the tryptophan pool very quickly became saturated. Under identical conditions, phenylalanine and tyrosine each accumulated in the intracellular pool of P. aeruginosa at a concentration which was 10 times greater than that of tryptophan. PMID:4994029

  16. Distribution and Origin of Amino Acids in Lunar Regolith Samples

    NASA Technical Reports Server (NTRS)

    Elsila, J. E.; Callahan, M. P.; Glavin, D. P.; Dworkin, J. P.; McLain, H. L.; Noble, S. K.; Gibson, E. K., Jr.

    2015-01-01

    The existence of organic compounds on the lunar surface has been a question of interest from the Apollo era to the present. Investigations of amino acids immediately after collection of lunar samples yielded inconclusive identifications, in part due to analytical limitations including insensitivity to certain compounds, an inability to separate enantiomers, and lack of compound-specific isotopic measurements. It was not possible to determine if the detected amino acids were indigenous to the lunar samples or the result of terrestrial contamination. Recently, we presented initial data from the analysis of amino acid abundances in 12 lunar regolith samples and discussed those results in the context of four potential amino acid sources [5]. Here, we expand on our previous work, focusing on amino acid abundances and distributions in seven regolith samples and presenting the first compound-specific carbon isotopic ratios measured for amino acids in a lunar sample.

  17. Modulatory Effects of Dietary Amino Acids on Neurodegenerative Diseases.

    PubMed

    Rajagopal, Senthilkumar; Sangam, Supraj Raja; Singh, Shubham; Joginapally, Venkateswara Rao

    2016-01-01

    Proteins are playing a vital role in maintaining the cellular integrity and function, as well as for brain cells. Protein intake and supplementation of individual amino acids can affect the brain functioning and mental health, and many of the neurotransmitters in the brain are made from amino acids. The amino acid supplementation has been found to reduce symptoms, as they are converted into neurotransmitters which in turn extenuate the mental disorders. The biosynthesis of amino acids in the brain is regulated by the concentration of amino acids in plasma. The brain diseases such as depression, bipolar disorder, schizophrenia, obsessive-compulsive disorder (OCD), and Alzheimer's (AD), Parkinson's (PD), and Huntington's diseases (HD) are the most common mental disorders that are currently widespread in numerous countries. The intricate biochemical and molecular machinery contributing to the neurological disorders is still unknown, and in this chapter, we revealed the involvement of dietary amino acids on neurological diseases.

  18. Surface Propensity of Atmospherically Relevant Amino Acids Studied by XPS.

    PubMed

    Mocellin, Alexandra; Gomes, Anderson Herbert de Abreu; Araújo, Oscar Cardoso; de Brito, Arnaldo Naves; Bjorneholm, Olle

    2017-03-30

    Amino acids constitute an important fraction of the water-soluble organic nitrogen (WSON) compounds in aerosols and are involved in many processes in the atmosphere. In this work, we applied XPS to study aqueous solutions of four amino acids: glycine, alanine, valine and methionine, in their zwitterionic forms. We found that amino acids with hydrophilic side chains and smaller size, GLY and ALA, tend to stay in the bulk of the liquid, while the hydrophobic and bigger amino acids, VAL and MET, are found to concentrate more on the surface. We found experimental evidences that the amino acids have preferential orientation relative to the surface, with the hydrophobic side chain being closer to the surface than the hydrophilic carboxylate group. The observed amino acid surface propensity has implications in atmospheric science as the surface interaction play a central role in cloud droplet formation, and they should be considered in climate models.

  19. Amino acids as chiral selectors in enantioresolution by liquid chromatography.

    PubMed

    Bhushan, Ravi; Dixit, Shuchi

    2012-08-01

    Amino acids are unique in terms of their structural features and multidimensional uses. With their simple structures and the ready availability of both enantiomers, amino acids not only serve as a chiral pool for synthesis but also provide an inexpensive pool for resolution studies. There has been no attempt to review the application of amino acids as chiral selectors for chromatographic enantioresolution of pharmaceuticals and other compounds. The present paper deals with application of l-amino acids and complexes of l-amino acids with a metal ion, particularly Cu(II), as an impregnating reagent in thin-layer chromatography or as a chiral ligand exchange reagent or a chiral mobile phase additive in both thin-layer chromatography and high-performance liquid chromatography. Enantiomeric resolution of β-blockers, nonsteroidal anti-inflammatories, amino acids (and their derivatives) and certain other compounds is discussed.

  20. Geochemistry of amino acids in shells of the clam Saxidomus

    USGS Publications Warehouse

    Kvenvolden, K.A.; Blunt, D.J.; McMenamin, M.A.; Straham, S.E.

    1980-01-01

    Concentrations of amino acids and their corresponding d l enantiomeric ratios have been measured in shells of the bivalve mollusk Saxidomus from eleven localities, ranging in age from modern to probably more than 500,000 yr, along the Pacific coast of North America. Natural logarithms of amino acid concentrations correlate well with d l ratios, and the relationship provides a possible guide to the selection of fossils for use in amino acid dating. The relative order of the extents of racemization of amino acids at any given time appears to change with increasing sample age. Application of the amino acid dating method to shells from Whidbey Island, Washington, yields an age of about 80,000 yr, in contrast to the previously determined radiocarbon age of 36,000 yr which was measured on some shell carbonate and considered a minimum age. The amino acid age is compatible with the geologic record in the area. ?? 1980.

  1. Stereoselective synthesis of stable-isotope-labeled amino acids

    SciTech Connect

    Unkefer, C.J.; Martinez, R.A.; Silks, L.A. III; Lodwig, S.N.

    1994-12-01

    For magnetic resonance and vibrational spectroscopies to reach their full potential, they must be used in combination with sophisticated site-specific stable isotope labeling of biological macromolecules. Labeled amino acids are required for the study of the structure and function of enzymes and proteins. Because there are 20 common amino acids, each with its own distinguishing chemistry, they remain a synthetic challenge. The Oppolzer chiral auxiliary provides a general tool with which to approach the synthesis of labeled amino acids. By using the Oppolzer auxiliary, amino acids can be constructed from several small molecules, which is ideal for stable isotope labeling. In addition to directing the stereochemistry at the {alpha}-carbon, the camphorsultam can be used for stereo-specific isotope labeling at prochiral centers in amino acids. By using the camphorsultam auxiliary we have the potential to synthesize virtually any isotopomer of all of the common amino acids.

  2. Twenty natural amino acids identification by a photochromic sensor chip.

    PubMed

    Qin, Meng; Li, Fengyu; Huang, Yu; Ran, Wei; Han, Dong; Song, Yanlin

    2015-01-20

    All 20 natural amino acids identification shows crucial importance in biochemistry and clinical application while it is still a challenge due to highly similarity in molecular configuration of the amino acids. Low efficiency, complicated sensing molecules and environment hindered the successful identification. Here, we developed a facile sensor chip composed of one photochromic molecule with metal ions spotted to form spirooxazine-metallic complexes, and successfully recognized all the 20 natural amino acids as well as their mixtures. The sensor chip gives distinct fluorescent fingerprint pattern of each amino acid, based on multistate of spirooxazine under different light stimulations and discriminated interaction between various metal ions and amino acids. The sensor chip demonstrates powerful capability of amino acids identification, which promotes sensing of biomolecules.

  3. Recombinant thiopeptides containing noncanonical amino acids

    PubMed Central

    Luo, Xiaozhou; Zambaldo, Claudio; Liu, Tao; Zhang, Yuhan; Xuan, Weimin; Wang, Chen; Reed, Sean A.; Yang, Peng-Yu; Wang, Rongsheng E.; Javahishvili, Tsotne; Schultz, Peter G.; Young, Travis S.

    2016-01-01

    Thiopeptides are a subclass of ribosomally synthesized and posttranslationally modified peptides (RiPPs) with complex molecular architectures and an array of biological activities, including potent antimicrobial activity. Here we report the generation of thiopeptides containing noncanonical amino acids (ncAAs) by introducing orthogonal amber suppressor aminoacyl-tRNA synthetase/tRNA pairs into a thiocillin producer strain of Bacillus cereus. We demonstrate that thiopeptide variants containing ncAAs with bioorthogonal chemical reactivity can be further postbiosynthetically modified with biophysical probes, including fluorophores and photo-cross-linkers. This work allows the site-specific incorporation of ncAAs into thiopeptides to increase their structural diversity and probe their biological activity; similar approaches can likely be applied to other classes of RiPPs. PMID:26976568

  4. Amino Acid Sensing in Skeletal Muscle.

    PubMed

    Moro, Tatiana; Ebert, Scott M; Adams, Christopher M; Rasmussen, Blake B

    2016-11-01

    Aging impairs skeletal muscle protein synthesis, leading to muscle weakness and atrophy. However, the underlying molecular mechanisms remain poorly understood. Here, we review evidence that mammalian/mechanistic target of rapamycin complex 1 (mTORC1)-mediated and activating transcription factor 4 (ATF4)-mediated amino acid (AA) sensing pathways, triggered by impaired AA delivery to aged skeletal muscle, may play important roles in skeletal muscle aging. Interventions that alleviate age-related impairments in muscle protein synthesis, strength, and/or muscle mass appear to do so by reversing age-related changes in skeletal muscle AA delivery, mTORC1 activity, and/or ATF4 activity. An improved understanding of the mechanisms and roles of AA sensing pathways in skeletal muscle may lead to evidence-based strategies to attenuate sarcopenia.

  5. Synthesis of alpha-amino acids

    DOEpatents

    Davis, J.W. Jr.

    1983-01-25

    A method is described for synthesizing alpha amino acids proceeding through novel intermediates of the formulas: R[sub 1]R[sub 2]C(OSOCl)CN, R[sub 1]R[sub 2]C(Cl)CN and [R[sub 1]R[sub 2]C(CN)O][sub 2]SO wherein R[sub 1] and R[sub 2] are each selected from hydrogen monovalent substituted and unsubstituted hydrocarbon radicals of 1 to 10 carbon atoms. The use of these intermediates allows the synthesis steps to be exothermic and results in an overall synthesis method which is faster than the synthesis methods of the prior art. No Drawings

  6. Survival of Amino Acids in Micrometeorites During Atmospheric Entry

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Bada, Jeffrey L.

    2003-01-01

    The delivery of amino acids by micrometeorites to the early Earth during the period of heavy bombardment could have been a significant source of the Earth's prebiotic amino acid inventory provided that these organic compounds survived atmospheric entry heating. To investigate the sublimation of amino acids from a micrometeorite analog at elevated temperature, grains from the CM-type carbonaceous chondrite Murchison were heated to 550 C inside a glass sublimation apparatus (SA) under reduced pressure. The sublimed residue that had collected on the cold finger of the SA after heating was analyzed for amino acids by HPLC. We found that when the temperature of the meteorite reached approx. 150 C, a large fraction of the amino acid glycine had vaporized from the meteorite, recondensed onto the end of the SA cold finger, and survived as the rest of the grains heated to 550 C. alpha-Aminoisobutryic acid and isovaline, which are two of the most abundant non-protein amino acids in Murchison, did not sublime from the meteorite and were completely destroyed during the heating experiment. Our experimental results suggest that sublimation of glycine present in micrometeorite grains may provide a way for this amino acid to survive atmospheric entry heating at temperatures less than 550 C; all other amino acids apparently are destroyed. Key Words: Amino acids-Exogenous delivery-Micrometeorites-Sublimation.

  7. Preference for and learning of amino acids in larval Drosophila

    PubMed Central

    Kudow, Nana; Miura, Daisuke; Schleyer, Michael; Toshima, Naoko; Gerber, Bertram

    2017-01-01

    ABSTRACT Relative to other nutrients, less is known about how animals sense amino acids and how behaviour is organized accordingly. This is a significant gap in our knowledge because amino acids are required for protein synthesis − and hence for life as we know it. Choosing Drosophila larvae as a case study, we provide the first systematic analysis of both the preference behaviour for, and the learning of, all 20 canonical amino acids in Drosophila. We report that preference for individual amino acids differs according to the kind of amino acid, both in first-instar and in third-instar larvae. Our data suggest that this preference profile changes across larval instars, and that starvation during the third instar also alters this profile. Only aspartic acid turns out to be robustly attractive across all our experiments. The essentiality of amino acids does not appear to be a determinant of preference. Interestingly, although amino acids thus differ in their innate attractiveness, we find that all amino acids are equally rewarding. Similar discrepancies between innate attractiveness and reinforcing effect have previously been reported for other tastants, including sugars, bitter substances and salt. The present analyses will facilitate the ongoing search for the receptors, sensory neurons, and internal, homeostatic amino acid sensors in Drosophila. PMID:28193602

  8. Preference for and learning of amino acids in larval Drosophila.

    PubMed

    Kudow, Nana; Miura, Daisuke; Schleyer, Michael; Toshima, Naoko; Gerber, Bertram; Tanimura, Teiichi

    2017-03-15

    Relative to other nutrients, less is known about how animals sense amino acids and how behaviour is organized accordingly. This is a significant gap in our knowledge because amino acids are required for protein synthesis - and hence for life as we know it. Choosing Drosophila larvae as a case study, we provide the first systematic analysis of both the preference behaviour for, and the learning of, all 20 canonical amino acids in Drosophila We report that preference for individual amino acids differs according to the kind of amino acid, both in first-instar and in third-instar larvae. Our data suggest that this preference profile changes across larval instars, and that starvation during the third instar also alters this profile. Only aspartic acid turns out to be robustly attractive across all our experiments. The essentiality of amino acids does not appear to be a determinant of preference. Interestingly, although amino acids thus differ in their innate attractiveness, we find that all amino acids are equally rewarding. Similar discrepancies between innate attractiveness and reinforcing effect have previously been reported for other tastants, including sugars, bitter substances and salt. The present analyses will facilitate the ongoing search for the receptors, sensory neurons, and internal, homeostatic amino acid sensors in Drosophila. © 2017. Published by The Company of Biologists Ltd.

  9. Diversity of amino acids in a typical chernozem of Moldova

    NASA Astrophysics Data System (ADS)

    Frunze, N. I.

    2014-12-01

    The content and composition of the amino acids in typical chernozems were studied. The objects of the study included a reference soil under an old fallow and three variants under fodder crop rotations: not fertilized, with mineral fertilizers, and with organic fertilizers. The contents of 18 amino acids were determined in these soils. The amino acids were extracted by the method of acid hydrolysis and identified by the method of ion-exchange chromatography. The total content of most of the amino acids was maximal in the reference soil; it was much lower in the cultivated soils and decreased in the following sequence: organic background > mineral background > no fertilization. The diversity of amino acids was evaluated quantitatively using different parameters applied in ecology for estimating various aspects of the species composition of communities (Simpson, Margalef, Menhinick, and Shannon's indices). The diversity and contribution of different amino acids to the total pool of amino acids also varied significantly in the studied variants. The maximum diversity of amino acids and maximum evenness of their relative abundance indices were typical of the reference chernozem; these parameters were lower in the cultivated soils. It was concluded that the changes in the structure of the amino acids under the impact of agricultural loads are similar to those that are usually observed under stress conditions.

  10. Survival of Amino Acids in Micrometeorites During Atmospheric Entry

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Bada, Jeffrey L.

    2003-01-01

    The delivery of amino acids by micrometeorites to the early Earth during the period of heavy bombardment could have been a significant source of the Earth's prebiotic amino acid inventory provided that these organic compounds survived atmospheric entry heating. To investigate the sublimation of amino acids from a micrometeorite analog at elevated temperature, grains from the CM-type carbonaceous chondrite Murchison were heated to 550 C inside a glass sublimation apparatus (SA) under reduced pressure. The sublimed residue that had collected on the cold finger of the SA after heating was analyzed for amino acids by HPLC. We found that when the temperature of the meteorite reached approx. 150 C, a large fraction of the amino acid glycine had vaporized from the meteorite, recondensed onto the end of the SA cold finger, and survived as the rest of the grains heated to 550 C. alpha-Aminoisobutryic acid and isovaline, which are two of the most abundant non-protein amino acids in Murchison, did not sublime from the meteorite and were completely destroyed during the heating experiment. Our experimental results suggest that sublimation of glycine present in micrometeorite grains may provide a way for this amino acid to survive atmospheric entry heating at temperatures less than 550 C; all other amino acids apparently are destroyed. Key Words: Amino acids-Exogenous delivery-Micrometeorites-Sublimation.

  11. Chemoenzymatic synthesis of surfactants from carbohydrates, amino acids, and fatty acids.

    PubMed

    Bellahouel, S; Rolland, V; Roumestant, M L; Viallefont, P; Martinez, J

    2001-02-01

    The chemoenzymatic synthesis of new surfactants is reported; they were prepared from unprotected carbohydrates, amino acids, and fatty acids. This study pointed out the factors that govern the possibility to enzymatically bind the carbohydrate to the amino acid.

  12. The Origin of Amino Acids in Lunar Regolith Samples

    NASA Technical Reports Server (NTRS)

    Cook, Jamie E.; Callahan, Michael P.; Dworkin, Jason P.; Glavin, Daniel P.; McLain, Hannah L.; Noble, Sarah K.; Gibson, Everett K., Jr.

    2016-01-01

    We analyzed the amino acid content of seven lunar regolith samples returned by the Apollo 16 and Apollo 17 missions and stored under NASA curation since collection using ultrahigh-performance liquid chromatography with fluorescence detection and time-of-flight mass spectrometry. Consistent with results from initial analyses shortly after collection in the 1970s, we observed amino acids at low concentrations in all of the curated samples, ranging from 0.2 parts-per-billion (ppb) to 42.7 ppb in hot-water extracts and 14.5 ppb to 651.1 ppb in 6M HCl acid-vapor-hydrolyzed, hot-water extracts. Amino acids identified in the Apollo soil extracts include glycine, D- and L-alanine, D- and L-aspartic acid, D- and L-glutamic acid, D- and L-serine, L-threonine, and L-valine, all of which had previously been detected in lunar samples, as well as several compounds not previously identified in lunar regoliths: -aminoisobutyric acid (AIB), D-and L-amino-n-butyric acid (-ABA), DL-amino-n-butyric acid, -amino-n-butyric acid, -alanine, and -amino-n-caproic acid. We observed an excess of the L enantiomer in most of the detected proteinogenic amino acids, but racemic alanine and racemic -ABA were present in some samples.

  13. Trophic spectra under the lens of amino acid isotopic analysis

    USDA-ARS?s Scientific Manuscript database

    Recent advances in compound specific isotopic ratio analysis (CSIRA) have allowed researchers to measure trophic fractionation of 15N in specific amino acids, namely glutamic acid and phenylalanine. These amino acids have proven useful in food web studies because of the wide and consistent disparity...

  14. The Origin of Amino Acids in Lunar Regolith Samples

    NASA Technical Reports Server (NTRS)

    Cook, Jamie E.; Callahan, Michael P.; Dworkin, Jason P.; Glavin, Daniel P.; McLain, Hannah L.; Noble, Sarah K.; Gibson, Everett K., Jr.

    2016-01-01

    We analyzed the amino acid content of seven lunar regolith samples returned by the Apollo 16 and Apollo 17 missions and stored under NASA curation since collection using ultrahigh-performance liquid chromatography with fluorescence detection and time-of-flight mass spectrometry. Consistent with results from initial analyses shortly after collection in the 1970s, we observed amino acids at low concentrations in all of the curated samples, ranging from 0.2 parts-per-billion (ppb) to 42.7 ppb in hot-water extracts and 14.5 ppb to 651.1 ppb in 6M HCl acid-vapor-hydrolyzed, hot-water extracts. Amino acids identified in the Apollo soil extracts include glycine, D- and L-alanine, D- and L-aspartic acid, D- and L-glutamic acid, D- and L-serine, L-threonine, and L-valine, all of which had previously been detected in lunar samples, as well as several compounds not previously identified in lunar regoliths: -aminoisobutyric acid (AIB), D-and L-amino-n-butyric acid (-ABA), DL-amino-n-butyric acid, -amino-n-butyric acid, -alanine, and -amino-n-caproic acid. We observed an excess of the L enantiomer in most of the detected proteinogenic amino acids, but racemic alanine and racemic -ABA were present in some samples.

  15. Understanding and identifying amino acid repeats

    PubMed Central

    Nijveen, Harm

    2014-01-01

    Amino acid repeats (AARs) are abundant in protein sequences. They have particular roles in protein function and evolution. Simple repeat patterns generated by DNA slippage tend to introduce length variations and point mutations in repeat regions. Loss of normal and gain of abnormal function owing to their variable length are potential risks leading to diseases. Repeats with complex patterns mostly refer to the functional domain repeats, such as the well-known leucine-rich repeat and WD repeat, which are frequently involved in protein–protein interaction. They are mainly derived from internal gene duplication events and stabilized by ‘gate-keeper’ residues, which play crucial roles in preventing inter-domain aggregation. AARs are widely distributed in different proteomes across a variety of taxonomic ranges, and especially abundant in eukaryotic proteins. However, their specific evolutionary and functional scenarios are still poorly understood. Identifying AARs in protein sequences is the first step for the further investigation of their biological function and evolutionary mechanism. In principle, this is an NP-hard problem, as most of the repeat fragments are shaped by a series of sophisticated evolutionary events and become latent periodical patterns. It is not possible to define a uniform criterion for detecting and verifying various repeat patterns. Instead, different algorithms based on different strategies have been developed to cope with different repeat patterns. In this review, we attempt to describe the amino acid repeat-detection algorithms currently available and compare their strategies based on an in-depth analysis of the biological significance of protein repeats. PMID:23418055

  16. Interactions between homopolymeric amino acids (HPAAs).

    PubMed

    Oma, Yoko; Kino, Yoshihiro; Toriumi, Kazuya; Sasagawa, Noboru; Ishiura, Shoichi

    2007-10-01

    Many human proteins contain consecutive amino acid repeats, known as homopolymeric amino acid (HPAA) tracts. Some inherited diseases are caused by proteins in which HPAAs are expanded to an excessive length. To this day, nine polyglutamine-related diseases and nine polyalanine-related diseases have been reported, including Huntington's disease and oculopharyngeal muscular dystrophy. In this study, potential HPAA-HPAA interactions were examined by yeast two-hybrid assays using HPAAs of approximately 30 residues in length. The results indicate that hydrophobic HPAAs interact with themselves and with other hydrophobic HPAAs. Previously, we reported that hydrophobic HPAAs formed large aggregates in COS-7 cells. Here, those HPAAs were shown to have significant interactions with each other, suggesting that hydrophobicity plays an important role in aggregation. Among the observed HPAA-HPAA interactions, the Ala28-Ala29 interaction was notable because polyalanine tracts of these lengths have been established to be pathogenic in several polyalanine-related diseases. By testing several constructs of different lengths, we clarified that polyalanine self-interacts at longer lengths (>23 residues) but not at shorter lengths (six to approximately 23 residues) in a yeast two-hybrid assay and a GST pulldown assay. This self-interaction was found to be SDS sensitive in SDS-PAGE and native-PAGE assays. Moreover, the intracellular localization of these long polyalanine tracts was also observed to be disturbed. Our results suggest that long tracts of polyalanine acquire SDS-sensitive self-association properties, which may be a prerequisite event for their abnormal folding. The misfolding of these tracts is thought to be a common molecular aspect underlying the pathogenesis of polyalanine-related diseases.

  17. Interactions between homopolymeric amino acids (HPAAs)

    PubMed Central

    Oma, Yoko; Kino, Yoshihiro; Toriumi, Kazuya; Sasagawa, Noboru; Ishiura, Shoichi

    2007-01-01

    Many human proteins contain consecutive amino acid repeats, known as homopolymeric amino acid (HPAA) tracts. Some inherited diseases are caused by proteins in which HPAAs are expanded to an excessive length. To this day, nine polyglutamine-related diseases and nine polyalanine-related diseases have been reported, including Huntington's disease and oculopharyngeal muscular dystrophy. In this study, potential HPAA–HPAA interactions were examined by yeast two-hybrid assays using HPAAs of ∼30 residues in length. The results indicate that hydrophobic HPAAs interact with themselves and with other hydrophobic HPAAs. Previously, we reported that hydrophobic HPAAs formed large aggregates in COS-7 cells. Here, those HPAAs were shown to have significant interactions with each other, suggesting that hydrophobicity plays an important role in aggregation. Among the observed HPAA–HPAA interactions, the Ala28–Ala29 interaction was notable because polyalanine tracts of these lengths have been established to be pathogenic in several polyalanine-related diseases. By testing several constructs of different lengths, we clarified that polyalanine self-interacts at longer lengths (>23 residues) but not at shorter lengths (six to ∼23 residues) in a yeast two-hybrid assay and a GST pulldown assay. This self-interaction was found to be SDS sensitive in SDS-PAGE and native-PAGE assays. Moreover, the intracellular localization of these long polyalanine tracts was also observed to be disturbed. Our results suggest that long tracts of polyalanine acquire SDS-sensitive self-association properties, which may be a prerequisite event for their abnormal folding. The misfolding of these tracts is thought to be a common molecular aspect underlying the pathogenesis of polyalanine-related diseases. PMID:17766374

  18. Amino acids of the Murchison meteorite. II - Five carbon acyclic primary beta-, gamma-, and delta-amino alkanoic acids

    NASA Technical Reports Server (NTRS)

    Cronin, J. R.; Pizzarello, S.; Yuen, G. U.

    1985-01-01

    The five-carbon acyclic primary beta, gamma, and delta amino alkanoic acids of the Murchison meteorite are studied using gas chromatography-mass spectrometry and ion exchange chromatography. The chromatograms reveal that alpha is the most abundant monoamino alkanoic acid followed by gamma and beta, and an exponential increase in the amount of amino acid is observed as the carbon number increases in the homologous series. The influence of frictional heating, spontaneous thermal decomposition, and radiation of the synthesis of amino acids is examined. The data obtained support an amino acid synthesis process involving random combination of single-carbon precursors.

  19. A molecular biological approach to reducing dietary amino acid needs.

    PubMed

    Rees, W D; Flint, H J; Fuller, M F

    1990-07-01

    Rapid developments in transgenic animal technology make it possible to consider introducing new metabolic capabilities into animals, using genes from other species. Lysine and threonine are both essential amino acids in mammals, and are commonly the first and second limiting amino acids, respectively, for protein accretion in pigs and poultry fed cereal based diets. Here we consider the potential for transgenic animals with microbial biosynthetic pathways for these amino acids.

  20. The number of positively charged amino acids in the basic domain of Tat is critical for trans-activation and complex formation with TAR RNA.

    PubMed Central

    Delling, U; Roy, S; Sumner-Smith, M; Barnett, R; Reid, L; Rosen, C A; Sonenberg, N

    1991-01-01

    The basic domain of Tat is required for trans-activation of viral gene expression. We have performed scanning peptide studies to demonstrate that only this domain is capable of binding to the TAR RNA stem-loop. Strikingly, the basic domain of the other human immunodeficiency virus trans-acting factor, Rev, but no other region, is also capable of binding to TAR. Peptide derivatives of Tat do not require the highly conserved glutamine residue at position 54 for TAR binding, since it may be substituted or deleted. In addition, the two lysine residues may be replaced by arginines. Analysis of binding and trans-activation demonstrated that homopolymers of arginine can completely substitute for the basic domain. Such homopolymers have high affinity for wild-type TAR RNA and lower affinity for mutant TAR. Homopolymers of six to nine arginines substituting for the basic domain of Tat enable full trans-activation in vivo. Homopolymers of at least seven arginines are required for detectable in vitro complex formation, although approximately 30% trans-activation is achieved with a mutant Tat containing only five arginines. Images PMID:2068104

  1. Enhancing offspring quality or quantity? Different ways for using nectar amino acids in female butterflies.

    PubMed

    Cahenzli, Fabian; Erhardt, Andreas

    2012-08-01

    Butterfly-pollinated flowers offer nectar with higher amino acid concentrations than most flowers pollinated by other animals, and female butterflies of some species prefer to consume amino acid-rich nectar. However, for over 30 years, there has been an ongoing discussion about whether nectar amino acids benefit butterfly fitness. A clear positive effect was only shown for the nectar-feeding Araschnia levana, and females of the fruit-feeding Bicyclus anynana also increased offspring quality when they were fed amino acids as adults. Thus, severe doubts remain about the general significance of these single positive results. We therefore tested a further species from a phylogenetically different butterfly subfamily, the small heath (Coenonympha pamphilus L., Satyrinae), taking into account feeding conditions over the whole life cycle of this species. C. pamphilus females receiving nectar amino acids as adults, irrespective of larval food quality, produced heavier larvae and also increased the hatching success of their eggs over the oviposition period. Furthermore, females raised under nitrogen-poor larval conditions tended to use nectar amino acids to increase the number of eggs laid. Thus, C. pamphilus females used nectar amino acids primarily to increase their offspring quality, and secondly tended to increase offspring quantity, if larval resources were scarce, showing a resource allocation pattern differing from both B. anynana and A. levana. Our study supports the old postulate that nectar amino acids generally enhance butterfly fitness.

  2. Is the intravenous supplementation of amino acid to cancer patients adequate? A critical appraisal of literature.

    PubMed

    Bozzetti, Federico; Bozzetti, Valentina

    2013-02-01

    International guidelines are quite vague regarding the optimal doses of amino acid to administer to cancer patients and standard practice appears not to be supported by specific investigations. The purpose of this study is to determine from the literature whether there are some correlates among amino acid infusions and nutritional-metabolic or clinical outcomes. Through the help of PubMed (www.ncbi.nlm.nih.gov) and the use of a personal database we analysed papers reporting details of infused amino acid and metabolic-nutritional or clinical effects. Five short-term metabolic studies using isotopes showed that infusion of about 2 g amino acid/kg/day (including high doses of branched chain amino acid) positively affects protein metabolism of severely malnourished cancer patients. In eight studies in less malnourished patients receiving longer periods of parenteral nutrition, to allow the administration of oncologic therapy or to compensate for a decline in oral alimentation, the intravenous addition of 1.5 g amino acid/kg/day to the oral diet achieved positive results. These findings are concordant with recent metabolic results achieved in cancer patients receiving amino acid orally. We think that a higher quantity of parenteral amino acids than that usually administered might be useful to cancer patients and further studies on this issue are warranted. Copyright © 2012 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

  3. Reactivity of consecutive basic amino acid residues in peptides.

    PubMed

    Bayle-Lacoste, M; De Tinguy-Moreaud, E; Geoffre, S; Neuzil, E

    1987-03-01

    Different tetrapeptides of general formula L-Ala-X-X-Gly, possessing a basic doublet in the second and third position (X = Arg or Lys), have been synthesized as free or N-acetylated molecules. The chemical reactivity of the arginine guanidino group and of the lysine epsilon-amino group were studied using respectively the Sakaguchi and the ortho-diacetylbenzene reactions, in the tetrapeptides as well as in related molecules. In both cases, the colour yield is markedly influenced by the length of the polypeptide chain and by the relative positions of the arginine and lysine residues, suggesting the occurrence of intramolecular bonds within the tetrapeptide molecule. Tryptic hydrolysis of the tetrapeptides was followed by evaluating the amino acids or peptides which appear to be specific for the different possible cleavages at the arginyl or at the lysyl bonds. The susceptibility to trypsin of the carboxylic group of the second basic amino acid decreases progressively in the order Lys-Arg greater than Arg-Arg much greater than Lys-Lys greater than Arg-Lys, which shows a fair correlation with the intra-cellular cleavage of the bonds observed during the processing of preproteins of of the precursors of several physiologically active peptides.

  4. Amino acid sequence of bovine heart coupling factor 6.

    PubMed Central

    Fang, J K; Jacobs, J W; Kanner, B I; Racker, E; Bradshaw, R A

    1984-01-01

    The amino acid sequence of bovine heart mitochondrial coupling factor 6 (F6) has been determined by automated Edman degradation of the whole protein and derived peptides. Preparations based on heat precipitation and ethanol extraction showed allotypic variation at three positions while material further purified by HPLC yielded only one sequence that also differed by a Phe-Thr replacement at residue 62. The mature protein contains 76 amino acids with a calculated molecular weight of 9006 and a pI of approximately equal to 5, in good agreement with experimentally measured values. The charged amino acids are mainly clustered at the termini and in one section in the middle; these three polar segments are separated by two segments relatively rich in nonpolar residues. Chou-Fasman analysis suggests three stretches of alpha-helix coinciding (or within) the high-charge-density sequences with a single beta-turn at the first polar-nonpolar junction. Comparison of the F6 sequence with those of other proteins did not reveal any homologous structures. PMID:6149548

  5. Interactions between amino-acid-defined MHC class II variants and smoking for seropositive rheumatoid arthritis

    PubMed Central

    Kim, Kwangwoo; Jiang, Xia; Cui, Jing; Lu, Bing; Costenbader, Karen H.; Sparks, Jeffrey A.; Bang, So-Young; Lee, Hye-soon; Okada, Yukinori; Raychaudhuri, Soumya; Alfredsson, Lars; Bae, Sang-Cheol; Klareskog, Lars; Karlson, Elizabeth W.

    2015-01-01

    Objective This study aimed to refine the interaction between cigarette smoking and human leukocyte antigen (HLA) polymorphisms in seropositive rheumatoid arthritis (RA), in the context of a recent amino-acid based HLA model for RA susceptibility. Methods We imputed HLA amino acids and classical alleles from case-control Immunochip array data of 3,588 Swedish Epidemiological Investigation of Rheumatoid Arthritis (EIRA; case/control=1654/1934), 589 Nurses’ Health Study (NHS; 229/360) and 2,125 Korean (1390/735) subjects. We examined interaction effects between heavy smoking (>10 pack-years) and genetic risk score (GRS) from RA-associated amino-acid positions (11, 13, 71 and 74 in HLA-DRβ1; 9 in HLA-B; and 9 in HLA-DPβ1) and from HLA-DRβ1 four-amino-acid haplotypes with an attributable proportion due to interaction (AP) using the additive interaction model. Results Heavy smoking and all investigated HLA amino-acid positions and haplotypes were associated with RA susceptibility in all three populations. In the interaction analysis, we found a significant deviation from the expected additive joint effect between heavy smoking and the HLA-DRβ1 amino-acid haplotype in all three studies (0.416≤AP≤0.796). We further identified the key interacting variants as being located at amino-acid positions 11 and 13 of HLA-DRβ1 but not the other RA-risk amino-acid positions in all populations. At the positions 11 and 13, there were similar patterns between RA-risk effects and interaction effects of residues. Conclusion Our findings of significant gene-environment interaction effects implicate that a physical interaction between citrullinated auto-antigens produced by smoking and HLA-DR molecules is characterized by the HLA-DRβ1 four-amino-acid haplotype, primarily by the positions 11 and 13. PMID:26098791

  6. [Detection of amino acids based on terahertz spectroscopy].

    PubMed

    Tang, Zhong-feng; Lin, Hai-tao; Chen, Xiao-wei; Zhang, Zeng-fang

    2009-09-01

    Terahertz (THz) is the frequency region ranging from 0.1 to 2.0 THz, which lies in the far-infrared region. Compared to Fourier transform infrared spectra (FTIR), terahertz time-domain spectra (THz-TDS) has low energy, high signal-to-noise ratio (SNR) and is non-ionizing radiation. Low-frequency vibrational modes of some amino acids, such as torsional and collective vibrational modes and hydrogen-bond modes, exist in the THz region. Amino acids are important organic compounds and are the fundamental components of proteins. Amino acids can exist with a highly ordered crystal structure linked by hydrogen intermolecular bonds in the solid phase. The absorption spectra of amino acids in the THz region show marked differences while mid-infrared absorption spectra usually show very little difference. Up to now, absorption spectra of twenty kinds of amino acids have been studied by many researchers using THz technique; the quantitative analysis of amino acids by THZ-TDS is also included. Investigation of THz spectra of amino acids are of fundamental interests, and will lead to further understanding of low-frequency vibrations of protein/DNA and relevant biological reactions and activities. In the present paper, the latest progress in absorption spectra of amino acids determined by THz spectroscopy is reviewed and a database is built. Some brief remarks on future developments in and prospects for THz application in amino acids are also provided.

  7. Amino acids in the cultivation of mammalian cells.

    PubMed

    Salazar, Andrew; Keusgen, Michael; von Hagen, Jörg

    2016-05-01

    Amino acids are crucial for the cultivation of mammalian cells. This importance of amino acids was realized soon after the development of the first cell lines, and a solution of a mixture of amino acids has been supplied to cultured cells ever since. The importance of amino acids is further pronounced in chemically defined mammalian cell culture media, making the consideration of their biological and chemical properties necessary. Amino acids concentrations have been traditionally adjusted to their cellular consumption rates. However, since changes in the metabolic equilibrium of amino acids can be caused by changes in extracellular concentrations, metabolomics in conjunction with flux balance analysis is being used in the development of culture media. The study of amino acid transporters is also gaining importance since they control the intracellular concentrations of these molecules and are influenced by conditions in cell culture media. A better understanding of the solubility, stability, dissolution kinetics, and interactions of these molecules is needed for an exploitation of these properties in the development of dry powdered chemically defined media for mammalian cells. Due to the complexity of these mixtures however, this has proven to be challenging. Studying amino acids in mammalian cell culture media will help provide a better understanding of how mammalian cells in culture interact with their environment. It would also provide insight into the chemical behavior of these molecules in solutions of complex mixtures, which is important in the understanding of the contribution of individual amino acids to protein structure.

  8. Recent advances in microchip electrophoresis for amino acid analysis.

    PubMed

    Ou, Gaozhi; Feng, Xiaojun; Du, Wei; Liu, Xin; Liu, Bi-Feng

    2013-10-01

    With the maturation of microfluidic technologies, microchip electrophoresis has been widely employed for amino acid analysis owing to its advantages of low sample consumption, reduced analysis time, high throughput, and potential for integration and automation. In this article, we review the recent progress in amino acid analysis using microchip electrophoresis during the period from 2007 to 2012. Innovations in microchip materials, surface modification, sample introduction, microchip electrophoresis, and detection methods are documented, as well as nascent applications of amino acid analysis in single-cell analysis, microdialysis sampling, food analysis, and extraterrestrial exploration. Without doubt, more applications of microchip electrophoresis in amino acid analysis may be expected soon.

  9. Amino acid metabolism and protein synthesis in malarial parasites*

    PubMed Central

    Sherman, I. W.

    1977-01-01

    Malaria-infected red cells and free parasites have limited capabilities for the biosynthesis of amino acids. Therefore, the principal amino acid sources for parasite protein synthesis are the plasma free amino acids and host cell haemoglobin. Infected cells and plasmodia incorporate exogenously supplied amino acids into protein. However, the hypothesis that amino acid utilization (from an external source) is related to availability of that amino acid in haemoglobin is without universal support: it is true for isoleucine and for Plasmodium knowlesi and P. falciparum, but not for methionine, cysteine, and other amino acids, and it does not apply to P. lophurae. More by default than by direct evidence, haemoglobin is believed to be the main amino acid reservoir available to the intraerythrocytic plasmodium. Haemoglobin, ingested via the cytostome, is held in food vacuoles where auto-oxidation takes place. As a consequence, haem is released and accumulates in the vacuole as particulate haemozoin (= malaria pigment). Current evidence favours the view that haemozoin is mainly haematin. Acid and alkaline proteases (identified in crude extracts from mammalian and avian malarias) are presumably secreted directly into the food vacuole. They then digest the denatured globin and the resulting amino acids are incorporated into parasite protein. Cell-free protein synthesizing systems have been developed using P. knowlesi and P. lophurae ribosomes. In the main these systems are typically eukaryotic. Studies of amino acid metabolism are exceedingly limited. Arginine, lysine, methionine, and proline are incorporated into protein, whereas glutamic acid is metabolized via an NADP-specific glutamic dehydrogenase. Glutamate oxidation generates NADPH and auxiliary energy (in the form of α-ketoglutarate). The role of red cell glutathione in the economy of the parasite remains obscure. Important goals for future research should be: quantitative assessment of the relative importance of

  10. Complete amino acid sequence of three reptile lysozymes.

    PubMed

    Ponkham, Pornpimol; Daduang, Sakda; Kitimasak, Wachira; Krittanai, Chartchai; Chokchaichamnankit, Daranee; Srisomsap, Chantragan; Svasti, Jisnuson; Kawamura, Shunsuke; Araki, Tomohiro; Thammasirirak, Sompong

    2010-01-01

    To study the structure and function of reptile lysozymes, we have reported their purification, and in this study we have established the amino acid sequence of three egg white lysozymes in soft-shelled turtle eggs (SSTL A and SSTL B from Trionyx sinensis, ASTL from Amyda cartilaginea) by using the rapid peptide mapping method. The established amino acid sequence of SSTL A, SSTL B, and ASTL showed substitutions of 43, 42, and 44 residues respectively when compared with the HEWL (hen egg white lysozyme) sequence. In these reptile lysozymes, SSTL A had one substitution compared with SSTL B (Gly126Asp) and had an N-terminal extra Gly and 11 substitutions compared with ASTL. SSTL B had an N-terminal extra Gly and 10 residues different from ASTL. The sequence of SSTL B was identical to soft-shelled turtle lysozyme from STL (Trionyx sinensis japonicus). The Ile residue at position 93 of ASTL is the first report in all C-type lysozymes. Furthermore, amino acid substitutions (Phe34His, Arg45Tyr, Thr47Arg, and Arg114Tyr) were also found at subsites E and F when compared with HEWL. The time course using N-acetylglucosamine pentamer as a substrate exhibited a reduction of the rate constant of glycosidic cleavage and increase of binding free energy for subsites E and F, which proved the contribution for amino acids mentioned above for substrate binding at subsites E and F. Interestingly, the variable binding free energy values occurred on ASTL, may be contributed from substitutions at outside of subsites E and F.

  11. An amino acid code for β-sheet packing structure.

    PubMed

    Joo, Hyun; Tsai, Jerry

    2014-09-01

    To understand the relationship between protein sequence and structure, this work extends the knob-socket model in an investigation of β-sheet packing. Over a comprehensive set of β-sheet folds, the contacts between residues were used to identify packing cliques: sets of residues that all contact each other. These packing cliques were then classified based on size and contact order. From this analysis, the two types of four-residue packing cliques necessary to describe β-sheet packing were characterized. Both occur between two adjacent hydrogen bonded β-strands. First, defining the secondary structure packing within β-sheets, the combined socket or XY:HG pocket consists of four residues i, i+2 on one strand and j, j+2 on the other. Second, characterizing the tertiary packing between β-sheets, the knob-socket XY:H+B consists of a three-residue XY:H socket (i, i+2 on one strand and j on the other) packed against a knob B residue (residue k distant in sequence). Depending on the packing depth of the knob B residue, two types of knob-sockets are found: side-chain and main-chain sockets. The amino acid composition of the pockets and knob-sockets reveal the sequence specificity of β-sheet packing. For β-sheet formation, the XY:HG pocket clearly shows sequence specificity of amino acids. For tertiary packing, the XY:H+B side-chain and main-chain sockets exhibit distinct amino acid preferences at each position. These relationships define an amino acid code for β-sheet structure and provide an intuitive topological mapping of β-sheet packing.

  12. The rules of variation: Amino acid exchange according to the rotating circular genetic code

    PubMed Central

    Castro-Chavez, Fernando

    2011-01-01

    General guidelines for the molecular basis of functional variation are presented while focused on the rotating circular genetic code and allowable exchanges that make it resistant to genetic diseases under normal conditions. The rules of variation, bioinformatics aids for preventive medicine, are: (1) same position in the four quadrants for hydrophobic codons, (2) same or contiguous position in two quadrants for synonymous or related codons, and (3) same quadrant for equivalent codons. To preserve protein function, amino acid exchange according to the first rule takes into account the positional homology of essential hydrophobic amino acids with every codon with a central uracil in the four quadrants, the second rule includes codons for identical, acidic, or their amidic amino acids present in two quadrants, and the third rule, the smaller, aromatic, stop codons, and basic amino acids, each in proximity within a 90 degree angle. I also define codifying genes and palindromati, CTCGTGCCGAATTCGGCACGAG. PMID:20371250

  13. Amino Acid Transporters and Release of Hydrophobic Amino Acids in the Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120.

    PubMed

    Pernil, Rafael; Picossi, Silvia; Herrero, Antonia; Flores, Enrique; Mariscal, Vicente

    2015-04-23

    Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that can use inorganic compounds such as nitrate or ammonium as nitrogen sources. In the absence of combined nitrogen, it can fix N2 in differentiated cells called heterocysts. Anabaena also shows substantial activities of amino acid uptake, and three ABC-type transporters for amino acids have been previously characterized. Seven new loci encoding predicted amino acid transporters were identified in the Anabaena genomic sequence and inactivated. Two of them were involved in amino acid uptake. Locus alr2535-alr2541 encodes the elements of a hydrophobic amino acid ABC-type transporter that is mainly involved in the uptake of glycine. ORF all0342 encodes a putative transporter from the dicarboxylate/amino acid:cation symporter (DAACS) family whose inactivation resulted in an increased uptake of a broad range of amino acids. An assay to study amino acid release from Anabaena filaments to the external medium was set up. Net release of the alanine analogue α-aminoisobutyric acid (AIB) was observed when transport system N-I (a hydrophobic amino acid ABC-type transporter) was engaged in the uptake of a specific substrate. The rate of AIB release was directly proportional to the intracellular AIB concentration, suggesting leakage from the cells by diffusion.

  14. Amino Acid Transporters and Release of Hydrophobic Amino Acids in the Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120

    PubMed Central

    Pernil, Rafael; Picossi, Silvia; Herrero, Antonia; Flores, Enrique; Mariscal, Vicente

    2015-01-01

    Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that can use inorganic compounds such as nitrate or ammonium as nitrogen sources. In the absence of combined nitrogen, it can fix N2 in differentiated cells called heterocysts. Anabaena also shows substantial activities of amino acid uptake, and three ABC-type transporters for amino acids have been previously characterized. Seven new loci encoding predicted amino acid transporters were identified in the Anabaena genomic sequence and inactivated. Two of them were involved in amino acid uptake. Locus alr2535-alr2541 encodes the elements of a hydrophobic amino acid ABC-type transporter that is mainly involved in the uptake of glycine. ORF all0342 encodes a putative transporter from the dicarboxylate/amino acid:cation symporter (DAACS) family whose inactivation resulted in an increased uptake of a broad range of amino acids. An assay to study amino acid release from Anabaena filaments to the external medium was set up. Net release of the alanine analogue α-aminoisobutyric acid (AIB) was observed when transport system N-I (a hydrophobic amino acid ABC-type transporter) was engaged in the uptake of a specific substrate. The rate of AIB release was directly proportional to the intracellular AIB concentration, suggesting leakage from the cells by diffusion. PMID:25915115

  15. Amino acid fermentation at the origin of the genetic code

    PubMed Central

    2012-01-01

    There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments

  16. Receptor-level interrelationships of amino acids and the adequate amino acid type hormones in Tetrahymena: a receptor evolution model.

    PubMed

    Csaba, G; Darvas, Z

    1986-01-01

    Histidine stimulates the phagocytosis of Tetrahymena to the same extent as histamine, and also stimulates its division, which histamine does not. Tyrosine and diiodotyrosine equally stimulate the growth of the Tetrahymena. Both amino acids inhibit the characteristic influence of the adequate amino acid hormone when added to Tetrahymena culture 72 h in advance of it. Primary interaction with diiodotyrosine and tyrosine notably increases the cellular growth rate. Histamine has a similar, although less notable effect than histidine. In the light of these experimental observations there is reason to postulate that the receptors of the amino acid hormones have developed from amino acid receptors.

  17. Preferential Treatment: Interaction Between Amino Acids and Minerals

    NASA Astrophysics Data System (ADS)

    Crapster-Pregont, E. J.; Cleaves, H. J.; Hazen, R. M.

    2008-12-01

    Amino acids are the building blocks of proteins and are important for some models of the origin of life. Polymerization of amino acids from dilute solution is unlikely without a scaffold or catalyst. The surfaces of early Earth minerals are the most likely candidates for this role. The surface adsorption behavior of 12 amino acids (L-alanine, L-serine, L-aspartic acid, L-proline, L- phenylalanine, L-valine, L-arginine, d-amino valeric acid, glycine, L-lysine, L-isoleucine, and B-alanine) on 21 minerals (quartz, calcite, enstatite, illite, olivine, pyrrhotite, pyrite, alkali basalt, albite, analcime, chlorite, barite, hydroxyl apatite, hematite, magnetite, aluminum hydroxide, kaolin, silica gel, corundum, rutile, and montmorillonite) was determined via batch adsorption experiments. Absorption was determined for concentrations between 10-4M and 10-6M in the presence of 0.1M NaCl, and between pH values of 3 and 9 at 25 degrees C. The equilibrated solutions were centrifuged, filtered, derivatized using a fluorescent amino group tag (dansyl-chloride) and analyzed by HPLC. Adsorption was standardized using BET surface area measurements for each mineral to give the number of mols of each amino acid adsorbed per square meter for each mineral. The results indicate an enormous difference in the adsorption of amino acids between minerals, along with major differences in the adsorption of individual amino acids on the same mineral surface. There is also a change in the absorbance of amino acids as the pH changes. Many previous studies of amino acid concentration and catalysis by minerals have used clay minerals because of their high surface areas, however, this data suggests that the surfaces of minerals such as calcite, quartz and pyrite have even higher affinities for amino acids. The results suggest mineral surfaces that could be optimal locations for the polymerization of molecules linked to the origin of life.

  18. Amino Acid Availability Modulates Vacuolar H+-ATPase Assembly*

    PubMed Central

    Stransky, Laura A.; Forgac, Michael

    2015-01-01

    The vacuolar H+-ATPase (V-ATPase) is an ATP-dependent proton pump composed of a peripheral ATPase domain (V1) and a membrane-integral proton-translocating domain (V0) and is involved in many normal and disease processes. An important mechanism of regulating V-ATPase activity is reversible assembly of the V1 and V0 domains. Increased assembly in mammalian cells occurs under various conditions and has been shown to involve PI3K. The V-ATPase is necessary for amino acid-induced activation of mechanistic target of rapamycin complex 1 (mTORC1), which is important in controlling cell growth in response to nutrient availability and growth signals. The V-ATPase undergoes amino acid-dependent interactions with the Ragulator complex, which is involved in recruitment of mTORC1 to the lysosomal membrane during amino acid sensing. We hypothesized that changes in the V-ATPase/Ragulator interaction might involve amino acid-dependent changes in V-ATPase assembly. To test this, we measured V-ATPase assembly by cell fractionation in HEK293T cells treated with and without amino acids. V-ATPase assembly increases upon amino acid starvation, and this effect is reversed upon readdition of amino acids. Lysosomes from amino acid-starved cells possess greater V-ATPase-dependent proton transport, indicating that assembled pumps are catalytically active. Amino acid-dependent changes in both V-ATPase assembly and activity are independent of PI3K and mTORC1 activity, indicating the involvement of signaling pathways distinct from those implicated previously in controlling assembly. By contrast, lysosomal neutralization blocks the amino acid-dependent change in assembly and reactivation of mTORC1 after amino acid starvation. These results identify an important new stimulus for controlling V-ATPase assembly. PMID:26378229

  19. Amino acids regulate transgene expression in MDCK cells.

    PubMed

    Torrente, Marta; Guetg, Adriano; Sass, Jörn Oliver; Arps, Lisa; Ruckstuhl, Lisa; Camargo, Simone M R; Verrey, François

    2014-01-01

    Gene expression and cell growth rely on the intracellular concentration of amino acids, which in metazoans depends on extracellular amino acid availability and transmembrane transport. To investigate the impact of extracellular amino acid concentrations on the expression of a concentrative amino acid transporter, we overexpressed the main kidney proximal tubule luminal neutral amino acid transporter B0AT1-collectrin (SLC6A19-TMEM27) in MDCK cell epithelia. Exogenously expressed proteins co-localized at the luminal membrane and mediated neutral amino acid uptake. However, the transgenes were lost over few cell culture passages. In contrast, the expression of a control transgene remained stable. To test whether this loss was due to inappropriately high amino acid uptake, freshly transduced MDCK cell lines were cultivated either with physiological amounts of amino acids or with the high concentration found in standard cell culture media. Expression of exogenous transporters was unaffected by physiological amino acid concentration in the media. Interestingly, mycoplasma infection resulted in a significant increase in transgene expression and correlated with the rapid metabolism of L-arginine. However, L-arginine metabolites were shown to play no role in transgene expression. In contrast, activation of the GCN2 pathway revealed by an increase in eIF2α phosphorylation may trigger transgene derepression. Taken together, high extracellular amino acid concentration provided by cell culture media appears to inhibit the constitutive expression of concentrative amino acid transporters whereas L-arginine depletion by mycoplasma induces the expression of transgenes possibly via stimulation of the GCN2 pathway.

  20. Amino Acids Regulate Transgene Expression in MDCK Cells

    PubMed Central

    Torrente, Marta; Guetg, Adriano; Sass, Jörn Oliver; Arps, Lisa; Ruckstuhl, Lisa; Camargo, Simone M. R.; Verrey, François

    2014-01-01

    Gene expression and cell growth rely on the intracellular concentration of amino acids, which in metazoans depends on extracellular amino acid availability and transmembrane transport. To investigate the impact of extracellular amino acid concentrations on the expression of a concentrative amino acid transporter, we overexpressed the main kidney proximal tubule luminal neutral amino acid transporter B0AT1-collectrin (SLC6A19-TMEM27) in MDCK cell epithelia. Exogenously expressed proteins co-localized at the luminal membrane and mediated neutral amino acid uptake. However, the transgenes were lost over few cell culture passages. In contrast, the expression of a control transgene remained stable. To test whether this loss was due to inappropriately high amino acid uptake, freshly transduced MDCK cell lines were cultivated either with physiological amounts of amino acids or with the high concentration found in standard cell culture media. Expression of exogenous transporters was unaffected by physiological amino acid concentration in the media. Interestingly, mycoplasma infection resulted in a significant increase in transgene expression and correlated with the rapid metabolism of L-arginine. However, L-arginine metabolites were shown to play no role in transgene expression. In contrast, activation of the GCN2 pathway revealed by an increase in eIF2α phosphorylation may trigger transgene derepression. Taken together, high extracellular amino acid concentration provided by cell culture media appears to inhibit the constitutive expression of concentrative amino acid transporters whereas L-arginine depletion by mycoplasma induces the expression of transgenes possibly via stimulation of the GCN2 pathway. PMID:24797296

  1. Utilization of acidic α-amino acids as acyl donors: an effective stereo-controllable synthesis of aryl-keto α-amino acids and their derivatives.

    PubMed

    Wang, Lei; Murai, Yuta; Yoshida, Takuma; Okamoto, Masashi; Tachrim, Zetryana Puteri; Hashidoko, Yasuyuki; Hashimoto, Makoto

    2014-05-16

    Aryl-keto-containing α-amino acids are of great importance in organic chemistry and biochemistry. They are valuable intermediates for the construction of hydroxyl α-amino acids, nonproteinogenic α-amino acids, as well as other biofunctional components. Friedel-Crafts acylation is an effective method to prepare aryl-keto derivatives. In this review, we summarize the preparation of aryl-keto containing α-amino acids by Friedel-Crafts acylation using acidic α-amino acids as acyl-donors and Lewis acids or Brönsted acids as catalysts.

  2. Synthesis of gold nanoparticles using various amino acids.

    PubMed

    Maruyama, Tatsuo; Fujimoto, Yuhei; Maekawa, Tetsuya

    2015-06-01

    Gold nanoparticles (4-7nm) were synthesized from tetraauric acid using various amino acids as reducing and capping agents. The gold nanoparticles were produced from the incubation of a AuCl4(-) solution with an amino acid at 80°C for 20min. Among the twenty amino acids tested, several amino acids produced gold nanoparticles. The color of the nanoparticle solutions varied with the amino acids used for the reduction. We adopted l-histidine as a reducing agent and investigated the effects of the synthesis conditions on the gold nanoparticles. The His and AuCl4(-) concentrations affected the size of the gold nanoparticles and their aggregates. The pH of the reaction solution also affected the reaction yields and the shape of the gold nanoparticles.

  3. Polysulfone affinity membranes for the treatment of amino acid mixtures.

    PubMed

    Rodemann, K; Staude, E

    1995-06-20

    Affinity membranes for the treatment of solutions containing amino acids were obtained via lithiating polysulfone that was subsequently converted with glycidylether. From this polymer asymmetric ultrafiltration membranes were cast. The membranes were reacted with iminodiacetic acid yielding membranes fitted out with bidentate chelates. The same reaction path was applied to commercially available symmetric microfiltration membranes. The chelate-bearing membranes were complexed with Cu, Ni, and Zn ions. For the experiments with amino acids only the Cu-complexed membranes were used. The complexation constants for histidine and tryptophan for six different membranes were determined. Because of the affinity of these two amino acids for the complexed Cu ions, they could easily be separated from solutions containing amino acids such as alanine, glycine, and valine. Also, concentrating very dilute amino acid solutions was carried out successfully.

  4. Free amino acids in botanicals and botanical preparations.

    PubMed

    Carratù, B; Boniglia, C; Giammarioli, S; Mosca, M; Sanzini, E

    2008-06-01

    Numerous studies were carried out about aminoacidic composition of vegetable proteins, but information about the free amino acid pool and the role of these substances is very incomplete. The aim of this paper was to contribute to the scarce knowledge concerning the composition of free amino acids in botanicals and botanical preparations widely used as food, in dietary supplements, and in pharmaceutical products. This work studied the composition of free amino acids, identified the major components of 19 species of plants, and evaluated the influence of different types of extraction on the amino acid profile. Amino acids were determined using an automatic precolumn derivatization with fluorenylmethyl-chloroformate and reversed-phase liquid chromatography with fluorescence and ultraviolet detection. The amounts of total free amino acids varied widely between plants, from approximately 12 g in 100 g of Echinacea pallida extract to less than 60 mg in the same amount of Coleus forskohlii, Garcinia cambogia, and Glycine max. In 13 plants arginine, asparagine, glutamine, proline, and gamma-aminobutyric acid were the free amino acids found in preponderant quantities. The levels of free amino acids above the quantification limit in 36 assayed samples of botanicals, extracts, and supplements are shown.

  5. Selective amino acid substitutions convert the creatine transporter to a gamma-aminobutyric acid transporter.

    PubMed

    Dodd, Joanna R; Christie, David L

    2007-05-25

    The creatine transporter (CRT) is a member of a large family of sodium-dependent neurotransmitter and amino acid transporters. The CRT is closely related to the gamma-aminobutyric acid (GABA) transporter, GAT-1, yet GABA is not an effective substrate for the CRT. The high resolution structure of a prokaryotic homologue, LeuT has revealed precise details of the substrate binding site for leucine (Yamashita, A., Singh, S. K., Kawate, T., Jin, Y., and Gouaux, E. (2005) Nature 437, 215-223). We have now designed mutations based on sequence comparisons of the CRT with GABA transporters and the LeuT structural template in an attempt to alter the substrate specificity of the CRT. Combinations of two or three amino acid substitutions at four selected positions resulted in the loss of creatine transport activity and gain of a specific GABA transport function. GABA transport by the "gain of function" mutants was sensitive to nipecotic acid, a competitive inhibitor of GABA transporters. Our results show LeuT to be a good structural model to identify amino acid residues involved in the substrate and inhibitor selectivity of eukaryotic sodium-dependent neurotransmitter and amino acid transporters. However, modification of the binding site alone appears to be insufficient for efficient substrate translocation. Additional residues must mediate the conformational changes required for the diffusion of substrate from the binding site to the cytoplasm.

  6. Gas-phase acidities of aspartic acid, glutamic acid, and their amino acid amides

    NASA Astrophysics Data System (ADS)

    Li, Zhong; Matus, Myrna H.; Velazquez, Hector Adam; Dixon, David A.; Cassady, Carolyn J.

    2007-09-01

    Gas-phase acidities (GA or [Delta]Gacid) for the two most acidic common amino acids, aspartic acid and glutamic acid, have been determined for the first time. Because of the amide linkage's importance in peptides and as an aid in studying side chain versus main chain deprotonation, aspartic acid amide and glutamic acid amide were also studied. Experimental GA values were measured by proton transfer reactions in an electrospray ionization/Fourier transform ion cyclotron resonance mass spectrometer. Calculated GAs were obtained by density functional and molecular orbital theory approaches. The best agreement with experiment was found at the G3MP2 level; the MP2/CBS and B3LYP/aug-cc-pVDZ results are 3-4 kcal/mol more acidic than the G3MP2 results. Experiment shows that aspartic acid is more acidic than glutamic acid by ca. 3 kcal/mol whereas the G3MP2 results show a smaller acidity difference of 0.2 kcal/mol. Similarly, aspartic acid amide is experimentally observed to be ca. 2 kcal/mol more acidic than glutamic acid amide whereas the G3MP2 results show a correspondingly smaller energy difference of 0.7 kcal/mol. The computational results clearly show that the anions are all ring-like structures with strong hydrogen bonds between the OH or NH2 groups and the CO2- group from which the proton is removed. The two amino acids are main-chain deprotonated. In addition, use of the COSMO model for the prediction of the free energy differences in aqueous solution gave values in excellent agreement with the most recent experimental values for pKa. Glutamic acid is predicted to be more acidic than aspartic acid in aqueous solution due to differential solvation effects.

  7. [The relatioship between decomposition of amino acid chloramines and their structures].

    PubMed

    Roshchupkin, D I; Murina, M A; Petrova, A O; Sergienko, V I

    2009-01-01

    Rate constants of the decomposition of monoamine alpha-amino acid chloramine derivatives were determined by a spectrophotometeric method. Several amino acid chloramines with elevated stability have been found. These included n-chloroglycine, n-chlorovaline, n-chlorothreonine, and n-chloroisoleucine. Their molecular structures are characterized by some characteristic feature at the beta-position. In the case of glycine chloramine, carbon atom at this position is absent, and the chloramine derivatives of three other amino acids possess branched chains. Partial atomic charges of the electrostatic potential (Wang-Ford) for chloramines of alpha-amino acids were computed using the semiempirical quantum-mechanical method AM1. The chloramines with elevated stability have high positive sums of charges of three carbon atoms that are atoms at alpha- and beta-positions and a carboxyl group atom. High partial charge also was obtained for one carbon atom at the beta-position. These computational values may be employed for prediction of the stability of designed amino acid chloramines. One of the important predictions is that the highest atomic charges and stabilities are characteristics of the amino acid chloramines, in which all hydrogen atoms at the beta-position are replaced by carbon-hydrogen chains or hydroxyl groups.

  8. Thermal copoly/amino acids/ as inhibitors of glyoxalase I

    NASA Technical Reports Server (NTRS)

    Fox, S. W.; Syren, R. M.; Windsor, C. R.

    1979-01-01

    A number of copoly(alpha-amino acids) have been prepared thermally; some have been found to function as inhibitors of glyoxalase I, an enzyme which occupies a central position in Szent-Gyorgyi's theory of tumour genesis. These polymers are also of interest in the search for synthetic peptides having carcinostatic activity, since many natural peptides are active. The way in which the inhibitory activity varies with composition of the synthetic polymers has been investigated. Various properties (hydrophobicity, molecular weight, UV absorption, kinetic type) have been examined in a search for correlates of inhibitory activity.

  9. Terrestrial evolution of polymerization of amino acids - Heat to ATP

    NASA Technical Reports Server (NTRS)

    Fox, S. W.; Nakashima, T.

    1981-01-01

    Sets of amino acids containing sufficient trifunctional monomer are thermally polymerized at temperatures such as 65 deg; the amino acids order themselves. Various polymers have diverse catalytic activities. The polymers aggregate, in aqueous solution, to cell-like structures having those activities plus emergent properties, e.g. proliferatability. Polyamino acids containing sufficient lysine catalyze conversion of free amino acids, by ATP, to small peptides and a high molecular weight fraction. The lysine-rich proteinoid is active in solution, within suspensions of cell-like particles, or in other particles composed of lysine-rich proteinoid and homopolyribonucleotide. Selectivities are observed. An archaic polyamino acid prelude to coded protein synthesis is indicated.

  10. Polymerization of beta-amino acids in aqueous solution

    NASA Technical Reports Server (NTRS)

    Liu, R.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    1998-01-01

    We have compared carbonyl diimidazole (CDI) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDAC) as activating agents for the oligomerization of negatively-charged alpha- and beta-amino acids in homogeneous aqueous solution. alpha-Amino acids can be oligomerized efficiently using CDI, but not by EDAC. beta-Amino acids can be oligomerized efficiently using EDAC, but not by CDI. Aspartic acid, an alpha- and beta-dicarboxylic acid is oligomerized efficiently by both reagents. These results are explained in terms of the mechanisms of the reactions, and their relevance to prebiotic chemistry is discussed.

  11. The Path of Carbon in Photosynthesis II. Amino Acids

    DOE R&D Accomplishments Database

    Stepka, W.; Benson, A. A.; Calvin, M.

    1948-05-25

    The radioactive amino acid's synthesized from C{sup 14}O{sub 2} by green algae both in the light and in the dark after CO{sub 2}-free preillumination have been separated and identified using paper chromatography and radioautography. The radioactive amino acids identified were aspartic acid, alanine and smaller amounts of 3- and 4-carbon amino acids. This finding as well as the total absence of radioactive glutamic acid substantiates the mechanism for reduction of CO{sub 2} previously postulated by members of this laboratory.

  12. Polymerization of beta-amino acids in aqueous solution

    NASA Technical Reports Server (NTRS)

    Liu, R.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    1998-01-01

    We have compared carbonyl diimidazole (CDI) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDAC) as activating agents for the oligomerization of negatively-charged alpha- and beta-amino acids in homogeneous aqueous solution. alpha-Amino acids can be oligomerized efficiently using CDI, but not by EDAC. beta-Amino acids can be oligomerized efficiently using EDAC, but not by CDI. Aspartic acid, an alpha- and beta-dicarboxylic acid is oligomerized efficiently by both reagents. These results are explained in terms of the mechanisms of the reactions, and their relevance to prebiotic chemistry is discussed.

  13. Amino Acid Racemization and the Preservation of Ancient DNA

    NASA Technical Reports Server (NTRS)

    Poinar, Hendrik N.; Hoss, Matthias

    1996-01-01

    The extent of racemization of aspartic acid, alanine, and leucine provides criteria for assessing whether ancient tissue samples contain endogenous DNA. In samples in which the D/L ratio of aspartic acid exceeds 0.08, ancient DNA sequences could not be retrieved. Paleontological finds from which DNA sequences purportedly millions of years old have been reported show extensive racemization, and the amino acids present are mainly contaminates. An exception is the amino acids in some insects preserved in amber.

  14. Amino Acids in Nectar Enhance Longevity of Female Culex quinquefasciatus

    DTIC Science & Technology

    2010-01-01

    and that some insects show a preference for carbohydrate sources containing amino acids (Alm et al., 1990; Mevi-Schutz and Erhardt, 2003b), has led...to an increased interest in the role that they play in insect life histories (Baker and Baker, 1973). Some insects rely on nectar as a primary source ...2003a; Hill and Pierce, 1989). Certain flowers contain high levels of amino acids, and have been studied as potentially important sources for amino

  15. Boron containing amino acid compounds and methods for their use

    DOEpatents

    Glass, John D.; Coderre, Jeffrey A.

    2000-01-01

    The present invention provides new boron containing amino acid compounds and methods for making these compounds by contacting melphalan or another nitrogen mustard derivative and sodium borocaptate. The present invention also provides a method of treating a mammal having a tumor by administering to the mammal a therapeutically effective amount of the new boron containing amino acid compounds.

  16. BAT1, a bidirectional amino acid transporter in Arabidopsis.

    PubMed

    Dündar, Ekrem; Bush, Daniel R

    2009-04-01

    The Arabidopsis thaliana At2g01170 gene is annotated as a putative gamma amino butyric acid (GABA) permease based on its sequence similarity to a yeast GABA transporting gene (UGA4). A cDNA of At2g01170 was expressed in yeast and analyzed for amino acid transport activity. Both direct measurement of amino acid transport and yeast growth experiments demonstrated that the At2g01170 encoded-protein exhibits transport activity for alanine, arginine, glutamate and lysine, but not for GABA or proline. Significantly, unlike other amino acid transporters described in plants to date, At2g01170 displayed both export and import activity. Based on that observation, it was named bidirectional amino acid transporter 1 (BAT1). Sequence comparisons show BAT1 is not a member of any previously defined amino acid transporter family. It does share, however, several conserved protein domains found in a variety of prokaryotic and eukaryotic amino acid transporters, suggesting membership in an ancient family of transporters. BAT1 is a single copy gene in the Arabidopsis genome, and its mRNA is ubiquitously expressed in all organs. A transposon--GUS gene-trap insert in the BAT1 gene displays GUS localization in the vascular tissues (Dundar in Ann Appl Biol, 2009) suggesting BAT1 may function in amino acid export from the phloem into sink tissues.

  17. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    Schultz, Peter G [La Jolla, CA; Wang, Lei [San Diego, CA

    2008-10-07

    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 keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  18. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    Schultz, Peter G [La Jolla, CA; Wang, Lei [San Diego, CA

    2011-03-22

    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 keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  19. Production of amino acids using auxotrophic mutants of methylotrophic bacillus

    DOEpatents

    Hanson, Richard S.; Flickinger, Michael C.; Schendel, Frederick J.; Guettler, Michael V.

    2001-07-17

    A method of producing amino acids by culturing an amino acid auxotroph of a biologically pure strain of a type I methylotrophic bacterium of the genus Bacillus which exhibits sustained growth at 50.degree. C. using methanol as a carbon and energy source and requiring vitamin B.sub.12 and biotin is provided.

  20. Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

    NASA Astrophysics Data System (ADS)

    Ilardo, Melissa; Meringer, Markus; Freeland, Stephen; Rasulev, Bakhtiyor; Cleaves, H. James, II

    2015-03-01

    Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or ``chemistry space.'' Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set.

  1. Site specific incorporation of keto amino acids into proteins

    SciTech Connect

    Schultz, Peter G; Wang, Lei

    2012-02-14

    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 keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  2. Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

    PubMed Central

    Ilardo, Melissa; Meringer, Markus; Freeland, Stephen; Rasulev, Bakhtiyor; Cleaves II, H. James

    2015-01-01

    Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or “chemistry space.” Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set. PMID:25802223

  3. Site specific incorporation of keto amino acids into proteins

    SciTech Connect

    Schultz, Peter G; Wang, Lei

    2011-12-06

    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 keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  4. Meteoritic Amino Acids: Diversity in Compositions Reflects Parent Body Histories

    NASA Technical Reports Server (NTRS)

    Elsila, Jamie E.; Aponte, Jose C.; Blackmond, Donna G.; Burton, Aaron S.; Dworkin, Jason P.; Glavin, Daniel P.

    2016-01-01

    The analysis of amino acids in meteorites dates back over 50 years; however, it is only in recent years that research has expanded beyond investigations of a narrow set of meteorite groups (exemplied by the Murchison meteorite) into meteorites of other types and classes. These new studies have shown a wide diversity in the abundance and distribution of amino acids across carbonaceous chondrite groups, highlighting the role of parent body processes and composition in the creation, preservation, or alteration of amino acids. Although most chiral amino acids are racemic in meteorites, the enantiomeric distribution of some amino acids, particularly of the nonprotein amino acid isovaline, has also been shown to vary both within certain meteorites and across carbonaceous meteorite groups. Large -enantiomeric excesses of some extraterrestrial protein amino acids (up to 60) have also been observed in rare cases and point to nonbiological enantiomeric enrichment processes prior to the emergence of life. In this Outlook, we review these recent meteoritic analyses, focusing on variations in abundance, structural distributions, and enantiomeric distributions of amino acids and discussing possible explanations for these observations and the potential for future work.

  5. Parenteral sulfur amino acid requirements in septic infants

    USDA-ARS?s Scientific Manuscript database

    To investigate parenteral methionine requirements of critically ill, septic infants, we conducted an investigation involving 12 infants (age 2+/-1 years; weight 13+/-2kg) using the intravenous indicator amino acid oxidation and balance technique. They received a balanced parenteral amino acid formul...

  6. Amino acid determination in some edible Mexican insects.

    PubMed

    Ladrón de Guevara, O; Padilla, P; García, L; Pino, J M; Ramos-Elorduy, J

    1995-06-01

    The amino acid contents of edible insects from different provinces of Mexico and reference proteins were analysed by reversed-phase high-performance liquid chromatography and ion exchange chromatography. The insect amino acid contents were higher than the adult requirements indicated by the WHO/FAO pattern.

  7. Site-selective covalent reactions on proteinogenic amino acids.

    PubMed

    So, Wing Ho; Zhang, Yu; Kang, Wei; Wong, Clarence T T; Sun, Hongyan; Xia, Jiang

    2017-07-05

    To achieve precise control of the signaling events or to achieve unmistakable synthesis of biomolecules, nature has evolved organic reactions involving proteinogenic amino acids with unparalleled site selectivity. For example, dedicated enzymes accurately dictate the site of post-translational modifications in signaling proteins, and ribosomes precisely link the C-terminal carboxylic acid of one unprotected amino acid with the N-terminal amino group of the other amino acid through spatially confined proximity. For many years, chemists have been striving to achieve site selectivity on biomolecules by mimicking nature. Driven by the development of chemoselective protein conjugation reactions, enzymology and protein-protein interactions, the past decade has witnessed a boom in site-selective protein conjugation reactions. (In this review, a site-selective protein conjugation reaction is defined as an organic reaction that targets a single amino acid instead of a kind of amino acids in a protein or a proteome under physiological conditions, for example, a single cysteine residue among all of the cysteines.) In this review, we summarize the recent advancements of bioconjugation reactions that demonstrate this feature of precise site selectivity, focusing on the reactions of the proteinogenic amino acids (excluding those at non-coded or non-proteinogenic amino acids that are introduced to proteins through genetic manipulations). Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Natural toxins that affect plant amino acid metabolism

    USDA-ARS?s Scientific Manuscript database

    A diverse range of natural compounds interfere with the synthesis and other aspects of amino acid metabolism. Some are amino acid analogues, but most are not. This review covers a number of specific natural phytotoxic compounds by molecular target site. Inhibition of glutamine synthetase is of part...

  9. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    Schultz, Peter G.; Wang, Lei

    2009-04-28

    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 keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  10. Interactive Hangman Teaches Amino Acid Structures and Abbreviations

    ERIC Educational Resources Information Center

    Pennington, Britney O.; Sears, Duane; Clegg, Dennis O.

    2014-01-01

    We developed an interactive exercise to teach students how to draw the structures of the 20 standard amino acids and to identify the one-letter abbreviations by modifying the familiar game of "Hangman." Amino acid structures were used to represent single letters throughout the game. To provide additional practice in identifying…

  11. Deaminative and decarboxylative catalytic alkylation of amino acids with ketones.

    PubMed

    Kalutharage, Nishantha; Yi, Chae S

    2013-12-16

    It cuts two ways: The cationic [Ru-H] complex catalyzes selective coupling of α- and β-amino acids with ketones to form α-alkylated ketone products. The reaction involves CC and CN bond cleavage which result in regio- and stereoselective alkylation using amino acids. A broad substrate scope and high functional-group tolerance is demonstrated.

  12. Interactive Hangman Teaches Amino Acid Structures and Abbreviations

    ERIC Educational Resources Information Center

    Pennington, Britney O.; Sears, Duane; Clegg, Dennis O.

    2014-01-01

    We developed an interactive exercise to teach students how to draw the structures of the 20 standard amino acids and to identify the one-letter abbreviations by modifying the familiar game of "Hangman." Amino acid structures were used to represent single letters throughout the game. To provide additional practice in identifying…

  13. Boron containing amino acid compounds and methods for their use

    SciTech Connect

    Glass, J.D.; Coderre, J.A.

    2000-01-25

    The present invention provides new boron containing amino acid compounds and methods for making these compounds by contacting melphalan or another nitrogen mustard derivative and sodium borocaptate. The present invention also provides a method of treating a mammal having a tumor by administering to the mammal a therapeutically effective amount of the new boron containing amino acid compounds.

  14. Parenteral amino acid intakes in critically ill children

    USDA-ARS?s Scientific Manuscript database

    Parenteral amino acid formulas used in parenteral nutrition have a variable composition. To determine the amino acid intake of parenterally fed, critically ill children, and compare it with recommended dietary allowances (RDA) established by the Institute of Medicine (IOM), we retrospectively review...

  15. Meteoritic Amino Acids: Diversity in Compositions Reflects Parent Body Histories

    PubMed Central

    2016-01-01

    The analysis of amino acids in meteorites dates back over 50 years; however, it is only in recent years that research has expanded beyond investigations of a narrow set of meteorite groups (exemplified by the Murchison meteorite) into meteorites of other types and classes. These new studies have shown a wide diversity in the abundance and distribution of amino acids across carbonaceous chondrite groups, highlighting the role of parent body processes and composition in the creation, preservation, or alteration of amino acids. Although most chiral amino acids are racemic in meteorites, the enantiomeric distribution of some amino acids, particularly of the nonprotein amino acid isovaline, has also been shown to vary both within certain meteorites and across carbonaceous meteorite groups. Large l-enantiomeric excesses of some extraterrestrial protein amino acids (up to ∼60%) have also been observed in rare cases and point to nonbiological enantiomeric enrichment processes prior to the emergence of life. In this Outlook, we review these recent meteoritic analyses, focusing on variations in abundance, structural distributions, and enantiomeric distributions of amino acids and discussing possible explanations for these observations and the potential for future work. PMID:27413780

  16. Amino acids in a carbonaceous chondrite from Antarctica

    NASA Technical Reports Server (NTRS)

    Kotra, R. K.; Shimoyama, A.; Ponnamperuma, C.; Hare, P. E.

    1979-01-01

    A carbonaceous chondrite from the Antarctic, referred to as the Allan Hills meteorite 77306, appears to be free from terrestrial organic contamination. The presence of both protein and non-protein amino acids and an equal abundance of D- and L-enantiomers of amino acids, is testimony to the extraterrestrial nature of these compounds.

  17. Amino Acid Carbamates As Prodrugs Of Resveratrol.

    PubMed

    Mattarei, Andrea; Azzolini, Michele; La Spina, Martina; Zoratti, Mario; Paradisi, Cristina; Biasutto, Lucia

    2015-10-14

    Resveratrol (3, 5, 4'-trihydroxy-trans-stilbene), a plant polyphenol, has important drug-like properties, but its pharmacological exploitation in vivo is hindered by its rapid transformation via phase II conjugative metabolism. One approach to bypass this problem relies on prodrugs. We report here the synthesis, characterization, stability and in vivo pharmacokinetic behaviour of prodrugs of resveratrol in which the OH groups are engaged in an N-monosubstituted carbamate ester (-OC(O)NHR) linkage with a natural amino acid (Leu, Ile, Phe, Thr) to prevent conjugation and modulate the physicochemical properties of the molecule. We also report a convenient, high-yield protocol to obtain derivatives of this type. The new carbamate ester derivatives are stable at pH 1, while they undergo slow hydrolysis at physiological pH and hydrolyse with kinetics suitable for use in prodrugs in whole blood. After administration to rats by oral gavage the isoleucine-containing prodrug was significantly absorbed, and was present in the bloodstream as non-metabolized unaltered or partially deprotected species, demonstrating effective shielding from first-pass metabolism. We conclude that prodrugs based on the N-monosubstituted carbamate ester bond have the appropriate stability profile for the systemic delivery of phenolic compounds.

  18. Marine Planktonic Archaea Take Up Amino Acids

    PubMed Central

    Ouverney, Cleber C.; Fuhrman, Jed A.

    2000-01-01

    Archaea are traditionally thought of as “extremophiles,” but recent studies have shown that marine planktonic Archaea make up a surprisingly large percentage of ocean midwater microbial communities, up to 60% of the total prokaryotes. However, the basic physiology and contribution of Archaea to community microbial activity remain unknown. We have studied Archaea from 200-m depths of the northwest Mediterranean Sea and the Pacific Ocean near California, measuring the archaeal activity under simulated natural conditions (8 to 17°C, dark and anaerobic) by means of a method called substrate tracking autoradiography fluorescence in situ hybridization (STARFISH) that simultaneously detects specific cell types by 16S rRNA probe binding and activity by microautoradiography. In the 200-m-deep Mediterranean and Pacific samples, cells binding the archaeal probes made up about 43 and 14% of the total countable cells, respectively. Our results showed that the Archaea are active in the uptake of dissolved amino acids from natural concentrations (nanomolar) with about 60% of the individuals in the archaeal communities showing measurable uptake. Bacteria showed a similar proportion of active cells. We concluded that a portion of these Archaea is heterotrophic and also appears to coexist successfully with Bacteria in the same water. PMID:11055931

  19. Amino acids: metabolism, functions, and nutrition.

    PubMed

    Wu, Guoyao

    2009-05-01

    Recent years have witnessed the discovery that amino acids (AA) are not only cell signaling molecules but are also regulators of gene expression and the protein phosphorylation cascade. Additionally, AA are key precursors for syntheses of hormones and low-molecular weight nitrogenous substances with each having enormous biological importance. Physiological concentrations of AA and their metabolites (e.g., nitric oxide, polyamines, glutathione, taurine, thyroid hormones, and serotonin) are required for the functions. However, elevated levels of AA and their products (e.g., ammonia, homocysteine, and asymmetric dimethylarginine) are pathogenic factors for neurological disorders, oxidative stress, and cardiovascular disease. Thus, an optimal balance among AA in the diet and circulation is crucial for whole body homeostasis. There is growing recognition that besides their role as building blocks of proteins and polypeptides, some AA regulate key metabolic pathways that are necessary for maintenance, growth, reproduction, and immunity. They are called functional AA, which include arginine, cysteine, glutamine, leucine, proline, and tryptophan. Dietary supplementation with one or a mixture of these AA may be beneficial for (1) ameliorating health problems at various stages of the life cycle (e.g., fetal growth restriction, neonatal morbidity and mortality, weaning-associated intestinal dysfunction and wasting syndrome, obesity, diabetes, cardiovascular disease, the metabolic syndrome, and infertility); (2) optimizing efficiency of metabolic transformations to enhance muscle growth, milk production, egg and meat quality and athletic performance, while preventing excess fat deposition and reducing adiposity. Thus, AA have important functions in both nutrition and health.

  20. The tangled bank of amino acids

    PubMed Central

    Pollock, David D.

    2016-01-01

    Abstract The use of amino acid substitution matrices to model protein evolution has yielded important insights into both the evolutionary process and the properties of specific protein families. In order to make these models tractable, standard substitution matrices represent the average results of the evolutionary process rather than the underlying molecular biophysics and population genetics, treating proteins as a set of independently evolving sites rather than as an integrated biomolecular entity. With advances in computing and the increasing availability of sequence data, we now have an opportunity to move beyond current substitution matrices to more interpretable mechanistic models with greater fidelity to the evolutionary process of mutation and selection and the holistic nature of the selective constraints. As part of this endeavour, we consider how epistatic interactions induce spatial and temporal rate heterogeneity, and demonstrate how these generally ignored factors can reconcile standard substitution rate matrices and the underlying biology, allowing us to better understand the meaning of these substitution rates. Using computational simulations of protein evolution, we can demonstrate the importance of both spatial and temporal heterogeneity in modelling protein evolution. PMID:27028523

  1. How Do Haloarchaea Synthesize Aromatic Amino Acids?

    PubMed Central

    Gulko, Miriam Kolog; Dyall-Smith, Mike; Gonzalez, Orland; Oesterhelt, Dieter

    2014-01-01

    Genomic analysis of H. salinarum indicated that the de novo pathway for aromatic amino acid (AroAA) biosynthesis does not follow the classical pathway but begins from non-classical precursors, as is the case for M. jannaschii. The first two steps in the pathway were predicted to be carried out by genes OE1472F and OE1475F, while the 3rd step follows the canonical pathway involving gene OE1477R. The functions of these genes and their products were tested by biochemical and genetic methods. In this study, we provide evidence that supports the role of proteins OE1472F and OE1475F catalyzing consecutive enzymatic reactions leading to the production of 3-dehydroquinate (DHQ), after which AroAA production proceeds via the canonical pathway starting with the formation of DHS (dehydroshikimate), catalyzed by the product of ORF OE1477R. Nutritional requirements and AroAA uptake studies of the mutants gave results that were consistent with the proposed roles of these ORFs in AroAA biosynthesis. DNA microarray data indicated that the 13 genes of the canonical pathway appear to be utilised for AroAA biosynthesis in H. salinarum, as they are differentially expressed when cells are grown in medium lacking AroAA. PMID:25216252

  2. Amino acid composition predicts prion activity.

    PubMed

    Afsar Minhas, Fayyaz Ul Amir; Ross, Eric D; Ben-Hur, Asa

    2017-04-10

    Many prion-forming proteins contain glutamine/asparagine (Q/N) rich domains, and there are conflicting opinions as to the role of primary sequence in their conversion to the prion form: is this phenomenon driven primarily by amino acid composition, or, as a recent computational analysis suggested, dependent on the presence of short sequence elements with high amyloid-forming potential. The argument for the importance of short sequence elements hinged on the relatively-high accuracy obtained using a method that utilizes a collection of length-six sequence elements with known amyloid-forming potential. We weigh in on this question and demonstrate that when those sequence elements are permuted, even higher accuracy is obtained; we also propose a novel multiple-instance machine learning method that uses sequence composition alone, and achieves better accuracy than all existing prion prediction approaches. While we expect there to be elements of primary sequence that affect the process, our experiments suggest that sequence composition alone is sufficient for predicting protein sequences that are likely to form prions. A web-server for the proposed method is available at http://faculty.pieas.edu.pk/fayyaz/prank.html, and the code for reproducing our experiments is available at http://doi.org/10.5281/zenodo.167136.

  3. Amino Acid Carbamates As Prodrugs Of Resveratrol

    PubMed Central

    Mattarei, Andrea; Azzolini, Michele; La Spina, Martina; Zoratti, Mario; Paradisi, Cristina; Biasutto, Lucia

    2015-01-01

    Resveratrol (3, 5, 4′-trihydroxy-trans-stilbene), a plant polyphenol, has important drug-like properties, but its pharmacological exploitation in vivo is hindered by its rapid transformation via phase II conjugative metabolism. One approach to bypass this problem relies on prodrugs. We report here the synthesis, characterization, stability and in vivo pharmacokinetic behaviour of prodrugs of resveratrol in which the OH groups are engaged in an N-monosubstituted carbamate ester (-OC(O)NHR) linkage with a natural amino acid (Leu, Ile, Phe, Thr) to prevent conjugation and modulate the physicochemical properties of the molecule. We also report a convenient, high-yield protocol to obtain derivatives of this type. The new carbamate ester derivatives are stable at pH 1, while they undergo slow hydrolysis at physiological pH and hydrolyse with kinetics suitable for use in prodrugs in whole blood. After administration to rats by oral gavage the isoleucine-containing prodrug was significantly absorbed, and was present in the bloodstream as non-metabolized unaltered or partially deprotected species, demonstrating effective shielding from first-pass metabolism. We conclude that prodrugs based on the N-monosubstituted carbamate ester bond have the appropriate stability profile for the systemic delivery of phenolic compounds. PMID:26463125

  4. Evolutionary patterns of amino acid substitutions in 12 Drosophila genomes

    PubMed Central

    2010-01-01

    Background Harnessing vast amounts of genomic data in phylogenetic context stemming from massive sequencing of multiple closely related genomes requires new tools and approaches. We present a tool for the genome-wide analysis of frequencies and patterns of amino acid substitutions in multiple alignments of genes’ coding regions, and a database of amino acid substitutions in the phylogeny of 12 Drosophila genomes. We illustrate the use of these resources to address three types of evolutionary genomics questions: about fluxes in amino acid composition in proteins, about asymmetries in amino acid substitutions and about patterns of molecular evolution in duplicated genes. Results We demonstrate that amino acid composition of Drosophila proteins underwent a significant shift over the last 70 million years encompassed by the studied phylogeny, with less common amino acids (Cys, Met, His) increasing in frequency and more common ones (Ala, Leu, Glu) becoming less frequent. These fluxes are strongly correlated with polarity of source and destination amino acids, resulting in overall systematic decrease of mean polarity of amino acids found in Drosophila proteins. Frequency and radicality of amino acid substitutions are higher in paralogs than in orthologous single-copy genes and are higher in gene families with paralogs than in gene families without surviving duplications. Rate and radicality of substitutions, as expected, are negatively correlated with overall level and uniformity of gene expression. However, these correlations are not observed for substitutions occurring in duplicated genes, indicating a different selective constraint on the evolution of paralogous sequences. Clades resulting from duplications show a marked asymmetry in rate and radicality of amino acid substitutions, possibly a signal of widespread neofunctionalization. These patterns differ among protein families of different functionality, with genes coding for RNA-binding proteins differing from

  5. Interaction of metal ions and amino acids - Possible mechanisms for the adsorption of amino acids on homoionic smectite clays

    NASA Technical Reports Server (NTRS)

    Gupta, A.; Loew, G. H.; Lawless, J.

    1983-01-01

    A semiempirical molecular orbital method is used to characterize the binding of amino acids to hexahydrated Cu(2+) and Ni(2+), a process presumed to occur when they are adsorbed in the interlamellar space of homoionic smectite clays. Five alpha-amino acids, beta-alanine, and gamma-aminobutyric acid were used to investigate the metal ion and amino acid specificity in binding. It was assumed that the alpha, beta, and gamma-amino acids would bind as bidentate anionic ligands, forming either 1:1 or 1:2 six-coordinated five, six, and seven-membered-ring chelate complexes, respectively. Energies of complex formation, optimized geometries, and electron and spin distribution were determined; and steric constraints of binding of the amino acids to the ion-exchanged cations in the interlamellar spacing of a clay were examined. Results indicate that hexahydrated Cu(2+) forms more stable complexes than hexahydrated Ni(2+) with all the amino acids studied. However, among these amino acids, complex formation does not favor the adsorption of the biological subset. Calculated energetics of complex formation and steric constraints are shown to predict that 1:1 rather than 1:2 metal-amino acid complexes are generally favored in the clay.

  6. Interaction of metal ions and amino acids - Possible mechanisms for the adsorption of amino acids on homoionic smectite clays

    NASA Technical Reports Server (NTRS)

    Gupta, A.; Loew, G. H.; Lawless, J.

    1983-01-01

    A semiempirical molecular orbital method is used to characterize the binding of amino acids to hexahydrated Cu(2+) and Ni(2+), a process presumed to occur when they are adsorbed in the interlamellar space of homoionic smectite clays. Five alpha-amino acids, beta-alanine, and gamma-aminobutyric acid were used to investigate the metal ion and amino acid specificity in binding. It was assumed that the alpha, beta, and gamma-amino acids would bind as bidentate anionic ligands, forming either 1:1 or 1:2 six-coordinated five, six, and seven-membered-ring chelate complexes, respectively. Energies of complex formation, optimized geometries, and electron and spin distribution were determined; and steric constraints of binding of the amino acids to the ion-exchanged cations in the interlamellar spacing of a clay were examined. Results indicate that hexahydrated Cu(2+) forms more stable complexes than hexahydrated Ni(2+) with all the amino acids studied. However, among these amino acids, complex formation does not favor the adsorption of the biological subset. Calculated energetics of complex formation and steric constraints are shown to predict that 1:1 rather than 1:2 metal-amino acid complexes are generally favored in the clay.

  7. Concentration variations of amino acids in mammalian fossils: effects of diagenesis and the implications for amino acid racemization analysis

    SciTech Connect

    Blackwell, B.; Rutter, N.W.

    1985-01-01

    Detailed amino acid analysis of bones, teeth, and antler from several mammal species have shown that concentrations of several amino acids can be related to three factors: type of material analyzed, diagenetic alteration of the material, and relative age of the fossil. Concentrations of several amino acids are significantly different in enamel compared to those of dentine or cement. This can be used to check that no contamination of one material by another has occurred, which is critical for using the data for amino acid dating, since all three materials have different racemization rates for some acids. With increased in growth of secondary minerals, generally reduced amino acid concentrations are observed. Interacid ratios and concentrations vary significantly the norms expected for the type of material with increasing degrees of alteration. These effects can be linked to abnormal racemization ratios observed in the same samples. Therefore, abnormal concentrations and/or interacid ratios can be used to detect samples in which the D/L amino acid ratios otherwise appear normal, thereby insuring better accuracy of amino acid racemization analysis. For unaltered fossils, with increasing sample age regardless the type of material, some amino acids steadily degrade, while others actually increase in concentration initially due to their generation as by-products of decay. Preliminary studies indicate that this progressive alteration can used to complement racemization data for determining relative stratigraphic sequences.

  8. Supernovae, Neutrinos and the Chirality of Amino Acids

    PubMed Central

    Boyd, Richard N.; Kajino, Toshitaka; Onaka, Takashi

    2011-01-01

    A mechanism for creating an enantioenrichment in the amino acids, the building blocks of the proteins, that involves global selection of one handedness by interactions between the amino acids and neutrinos from core-collapse supernovae is defined. The chiral selection involves the dependence of the interaction cross sections on the orientations of the spins of the neutrinos and the 14N nuclei in the amino acids, or in precursor molecules, which in turn couple to the molecular chirality. It also requires an asymmetric distribution of neutrinos emitted from the supernova. The subsequent chemical evolution and galactic mixing would ultimately populate the Galaxy with the selected species. The resulting amino acids could either be the source thereof on Earth, or could have triggered the chirality that was ultimately achieved for Earth’s proteinaceous amino acids. PMID:21747686

  9. Supernovae, neutrinos and the chirality of amino acids.

    PubMed

    Boyd, Richard N; Kajino, Toshitaka; Onaka, Takashi

    2011-01-01

    A mechanism for creating an enantioenrichment in the amino acids, the building blocks of the proteins, that involves global selection of one handedness by interactions between the amino acids and neutrinos from core-collapse supernovae is defined. The chiral selection involves the dependence of the interaction cross sections on the orientations of the spins of the neutrinos and the (14)N nuclei in the amino acids, or in precursor molecules, which in turn couple to the molecular chirality. It also requires an asymmetric distribution of neutrinos emitted from the supernova. The subsequent chemical evolution and galactic mixing would ultimately populate the Galaxy with the selected species. The resulting amino acids could either be the source thereof on Earth, or could have triggered the chirality that was ultimately achieved for Earth's proteinaceous amino acids.

  10. Essential role for collectrin in renal amino acid transport.

    PubMed

    Danilczyk, Ursula; Sarao, Renu; Remy, Christine; Benabbas, Chahira; Stange, Gerti; Richter, Andreas; Arya, Sudha; Pospisilik, J Andrew; Singer, Dustin; Camargo, Simone M R; Makrides, Victoria; Ramadan, Tamara; Verrey, Francois; Wagner, Carsten A; Penninger, Josef M

    2006-12-21

    Angiotensin -converting enzyme 2 (ACE2) is a regulator of the renin angiotensin system involved in acute lung failure, cardiovascular functions and severe acute respiratory syndrome (SARS) infections in mammals. A gene encoding a homologue to ACE2, termed collectrin (Tmem27), has been identified in immediate proximity to the ace2 locus. The in vivo function of collectrin was unclear. Here we report that targeted disruption of collectrin in mice results in a severe defect in renal amino acid uptake owing to downregulation of apical amino acid transporters in the kidney. Collectrin associates with multiple apical transporters and defines a novel group of renal amino acid transporters. Expression of collectrin in Xenopus oocytes and Madin-Darby canine kidney (MDCK) cells enhances amino acid transport by the transporter B(0)AT1. These data identify collectrin as a key regulator of renal amino acid uptake.

  11. Stardust, Supernovae and the Chirality of the Amino Acids

    SciTech Connect

    Boyd, R N; Kajino, T; Onaka, T

    2011-03-09

    A mechanism for creating enantiomerism in the amino acids, the building blocks of the proteins, that involves global selection of one chirality by interactions between the amino acids and neutrinos from core-collapse supernovae is described. The selection involves the dependence of the interaction cross sections on the orientations of the spins of the neutrinos and the 14N nuclei in the amino acids, or in precursor molecules, which in turn couple to the molecular chirality. The subsequent chemical evolution and galactic mixing would ultimately populate the Galaxy with the selected species. The resulting amino acids could either be the source thereof on Earth, or could have triggered the chirality that was ultimately achieved for Earth's amino acids.

  12. Amino Acids Are an Ineffective Fertilizer for Dunaliella spp. Growth

    PubMed Central

    Murphree, Colin A.; Dums, Jacob T.; Jain, Siddharth K.; Zhao, Chengsong; Young, Danielle Y.; Khoshnoodi, Nicole; Tikunov, Andrey; Macdonald, Jeffrey; Pilot, Guillaume; Sederoff, Heike

    2017-01-01

    Autotrophic microalgae are a promising bioproducts platform. However, the fundamental requirements these organisms have for nitrogen fertilizer severely limit the impact and scale of their cultivation. As an alternative to inorganic fertilizers, we investigated the possibility of using amino acids from deconstructed biomass as a nitrogen source in the genus Dunaliella. We found that only four amino acids (glutamine, histidine, cysteine, and tryptophan) rescue Dunaliella spp. growth in nitrogen depleted media, and that supplementation of these amino acids altered the metabolic profile of Dunaliella cells. Our investigations revealed that histidine is transported across the cell membrane, and that glutamine and cysteine are not transported. Rather, glutamine, cysteine, and tryptophan are degraded in solution by a set of oxidative chemical reactions, releasing ammonium that in turn supports growth. Utilization of biomass-derived amino acids is therefore not a suitable option unless additional amino acid nitrogen uptake is enabled through genetic modifications of these algae. PMID:28603530

  13. Transport of Amino Acids to the Maize Root 1

    PubMed Central

    Oaks, Ann

    1966-01-01

    When 5-mm maize root tips were excised and placed in an inorganic salts solution for 6 hours, there was a loss of alcohol-insoluble nitrogen. The levels of threonine, proline, valine, isoleucine, leucine, tyrosine, phenylalanine, and lysine in the alcohol soluble fraction were severely reduced, whereas those of glutamate, aspartate, ornithine, and alanine were scarcely affected. There was a 4-fold increase in the level of γ-aminobutyrate. Those amino acids whose synthesis appeared to be deficient in excised root tips also showed poor incorporation of acetate carbon. In addition, the results show that asparagine and the amino acids of the neutral and basic fraction were preferentially transported to the root tip region. The results therefore suggest that the synthesis of certain amino acids in the root tip region is restricted, and that this requirement for amino acids in the growing region could regulate the flow of amino acids to the root tip. PMID:16656225

  14. Peptide and amino acid separation with nanofiltration membranes

    SciTech Connect

    Tsuru, Toshinori; Shutou, Takatoshi; Nakao, Shin-Ichi; Kimura, Shoji )

    1994-05-01

    Several nanofiltration membranes [UTC-20, 60 (Toray Industries), NF-40 (Film-Tech Corporation), Desal-5, G-20 (Desalination Systems), and NTR-7450 (Nitto Electric Industrial Co.)] were applied to separate amino acids and peptides on the basis of charge interaction with the membranes since most of them contain charged functional groups. Nanofiltration membranes having a molecular weight cutoff (MWCO) below 300 (UTC-20, 60, NF-40 and Desal-5) were not suitable for separation of amino acids. On the other hand, separation of amino acids and peptides with nanofiltration membranes having a MWCO around 2000-3000 (NTR-7450 and G-20) was satisfactory based on a charge effect mechanism; charged amino acids and peptides were rejected while neutral amino acids and peptides permeated through the membranes. Separation of peptides having different isoelectric points with nanofiltration membranes was possible by adjusting the pH. 15 refs., 11 figs., 4 tabs.

  15. Crystallization of jarosite in the presence of amino acids

    NASA Astrophysics Data System (ADS)

    Crabbe, Harrison; Fernandez, Natalya; Jones, Franca

    2015-04-01

    Jarosite was formed in the presence of five amino acids at two pHs, namely 1.75 and 2.9, to determine what impact amino acids have on its formation. It was found that at the lower pH glycine was the most potent in terms of morphological and yield impacts. XRD analysis showed that incorporation of the amino acid occurs at this low pH for glycine and proline. Dynamic light scattering studies showed that glycine impacts significantly on the jarosite nucleation rate while proline and alanine do not. At the higher pH all of the amino acids had much less impact on morphology or yield. At pH 3 the solids were found to be a 3-phase system consisting of goethite, schwertmannite and jarosite. In this case, alanine appeared to stabilise the presence of schwertmannite more than the other amino acids.

  16. Uptake and release of amino acids in the fetal-placental unit in human pregnancies.

    PubMed

    Holm, Maia Blomhoff; Bastani, Nasser Ezzatkhah; Holme, Ane Moe; Zucknick, Manuela; Jansson, Thomas; Refsum, Helga; Mørkrid, Lars; Blomhoff, Rune; Henriksen, Tore; Michelsen, Trond Melbye

    2017-01-01

    The current concepts of human fetal-placental amino acid exchange and metabolism are mainly based on animal-, in vitro- and ex vivo models. We aimed to determine and assess the paired relationships between concentrations and arteriovenous differences of 19 amino acids on the maternal and fetal sides of the human placenta in a large study sample. This cross-sectional in vivo study included 179 healthy women with uncomplicated term pregnancies. During planned cesarean section, we sampled blood from incoming and outgoing vessels on the maternal (radial artery and uterine vein) and fetal (umbilical vein and artery) sides of the placenta. Amino acid concentrations were measured by liquid chromatography-tandem mass spectrometry. We calculated paired arteriovenous differences and performed Wilcoxon signed-rank tests and Spearman's correlations. In the umbilical circulation, we observed a positive venoarterial difference (fetal uptake) for 14 amino acids and a negative venoarterial difference (fetal release) for glutamic acid (p<0.001). In the maternal circulation, we observed a positive arteriovenous difference (uteroplacental uptake) for leucine (p = 0.005), isoleucine (p = 0.01), glutamic acid (p<0.001) and arginine (p = 0.04) and a negative arteriovenous difference (uteroplacental release) for tyrosine (p = 0.002), glycine (p = 0.01) and glutamine (p = 0.02). The concentrations in the maternal artery and umbilical vein were correlated for all amino acids except tryptophan, but we observed no correlations between the uteroplacental uptake and the fetal uptake or the umbilical vein concentration. Two amino acids showed a correlation between the maternal artery concentration and the fetal uptake. Our human in vivo study expands the current insight into fetal-placental amino acid exchange, and discloses some differences from what has been previously described in animals. Our findings are consistent with the concept that the fetal supply of amino acids in the human is the

  17. Amino acid contribution to protein solubility: Asp, Glu, and Ser contribute more favorably than the other hydrophilic amino acids in RNase Sa

    PubMed Central

    Trevino, Saul R.; Scholtz, J. Martin; Pace, C. Nick

    2009-01-01

    SUMMARY Poor protein solubility is a common problem in high resolution structural studies, formulation of protein pharmaceuticals, and biochemical characterization of proteins. One popular strategy to improve protein solubility is to use site-directed mutagenesis to make hydrophobic to hydrophilic mutations on the protein surface. However, a systematic investigation of the relative contributions of all twenty amino acids to protein solubility has not been done. Here, twenty variants at the completely solvent-exposed position 76 of Ribonuclease (RNase) Sa are made to compare the contributions of each amino acid. Stability measurements were also made for these variants, which occur at the i+1 position of a type II β-turn. Solubility measurements in ammonium sulfate solutions were made at high positive net charge, low net charge, and high negative net charge. Surprisingly, there was a wide range of contributions to protein solubility even among the hydrophilic amino acids. The results suggest that aspartic acid, glutamic acid, and serine contribute significantly more favorably than the other hydrophilic amino acids especially at high net charge. Therefore, to increase protein solubility, asparagine, glutamine, or threonine should be replaced with aspartic acid, glutamic acid or serine. PMID:17174328

  18. Codes in the codons: construction of a codon/amino acid periodic table and a study of the nature of specific nucleic acid-protein interactions.

    PubMed

    Benyo, B; Biro, J C; Benyo, Z

    2004-01-01

    The theory of "codon-amino acid coevolution" was first proposed by Woese in 1967. It suggests that there is a stereochemical matching - that is, affinity - between amino acids and certain of the base triplet sequences that code for those amino acids. We have constructed a common periodic table of codons and amino acids, where the nucleic acid table showed perfect axial symmetry for codons and the corresponding amino acid table also displayed periodicity regarding the biochemical properties (charge and hydrophobicity) of the 20 amino acids and the position of the stop signals. The table indicates that the middle (2/sup nd/) amino acid in the codon has a prominent role in determining some of the structural features of the amino acids. The possibility that physical contact between codons and amino acids might exist was tested on restriction enzymes. Many recognition site-like sequences were found in the coding sequences of these enzymes and as many as 73 examples of codon-amino acid co-location were observed in the 7 known 3D structures (December 2003) of endonuclease-nucleic acid complexes. These results indicate that the smallest possible units of specific nucleic acid-protein interaction are indeed the stereochemically compatible codons and amino acids.

  19. Soil Bacteria Take Up D-Amino Acids, Protect Plants

    NASA Astrophysics Data System (ADS)

    Sun, H. J.; Zhang, G.

    2011-12-01

    Recently, many groups reported D-amino acid uptake by plant roots, raising the question of whether soil D-amino acids represent a source of nitrogen or a source of toxicity. The discussion needs to be placed in the context of competition with rhizosphere bacteria. To provide this context, we followed the concentrations of D- and L-enantiomers of alanine, glutamic acid, aspartic acid, and leucine after they were added to soils in the laboratory. In all cases, the uptake of L-enantiomer began immediately and proceeded rapidly until exhausted. In contrast, the uptake of D-enantiomer required induction: an initial period of inactivity followed by rapid consumption comparable in rate to L-enantiomer. The induced nature of the D activity was confirmed by the addition of rifampicin, an mRNA synthesis inhibitor. Preventing the synthesis of new enzymes abolished soil flora's ability to consume D-amino acids, but not L-amino acids. These results suggest that inducible special racemase enzymes, which can convert D-amino acids back to their native L-forms, are widespread among soil microorganisms. This finding does not rule out the possibility that some plants may out-compete microorganisms and be able to access D-amino acids. It does suggest, however, that rhizosphere bacteria can shield plants from the toxic effect of D-amino acids.

  20. Metabolic effects of intraoperative amino acid infusion in mongrel dogs.

    PubMed

    Jin, Lin; Ge, Shengjin; Wang, Hongshan; Gao, Xiaodong; Jin, Jianjun; Xue, Zhanggang

    2012-01-01

    Intraoperative amino acid infusion can attenuate the decrease in core temperature, but the metabolic effects are uncertain. Thirty-six healthy mongrel dogs undergoing ileectomy under general anesthesia were infused intraoperatively with normal saline or 18 compound amino acids at 6, 12, and 24 kJ·kg⁻¹·h⁻¹ (NS, 6-, 12-, and 24-kJ groups) and studied until 24 h after the operation. Blood glucose, plasma insulin, free fatty acids, and triglyceride concentrations were determined at 7 defined time points. Muscle aminograms, urinary urea, and 3-methylhistidine excretions were measured before and after the operation. Blood glucose and plasma insulin increased amino acid dose dependently during the operation and in the early period after the operation. Free fatty acids were significantly lower in the 12- and 24-kJ groups compared with the NS group at the end of the operation. The negative nitrogen balance was alleviated dose dependently in the amino acid groups on operation day. The urinary 3-methylhistidine decreased significantly during the first 24 h after the operation in the 24-kJ group, while it increased in the other groups with the largest increase in the NS group. Basic, branched-chain, and aromatic amino acids in the vastus lateralis muscle increased dose dependently at the end of the operation in the amino acid groups. Intraoperative amino acid infusion has the dose-dependent effects of increasing blood glucose, inhibiting fat mobilization and muscle protein breakdown.

  1. Wet, Carbonaceous Asteroids: Altering Minerals, Changing Amino Acids

    NASA Astrophysics Data System (ADS)

    Taylor, G. J.

    2011-04-01

    Many carbonaceous chondrites contain alteration products from water-rock interactions at low temperature and organic compounds. A fascinating fact known for decades is the presence in some of them of an assortment of organic compounds, including amino acids, sometimes called the building blocks of life. Murchison and other CM carbonaceous chondrites contain hundreds of amino acids. Early measurements indicated that the amino acids in carbonaceous chondrites had equal proportions of L- and D-structures, a situation called racemic. This was in sharp contrast to life on Earth, which heavily favors L- forms. However, beginning in 1997, John Cronin and Sandra Pizzarello (Arizona State University) found L- excesses in isovaline and several other amino acids in the Murchison carbonaceous chondrite. In 2009, Daniel Glavin and Jason Dworkin (Astrobiology Analytical Lab, Goddard Space Flight Center) reported the first independent confirmation of L-isovaline excesses in Murchison using a different analytical technique than employed by Cronin and Pizzarello. Inspired by this work, Daniel Glavin, Michael Callahan, Jason Dworkin, and Jamie Elsila (Astrobiology Analytical Lab, Goddard Space Flight Center), have done an extensive study of the abundance and symmetry of amino acids in carbonaceous chondrites that experienced a range of alteration by water in their parent asteroids. The results show that amino acids are more abundant in the less altered meteorites, implying that aqueous processing changes the mix of amino acids. They also confirmed the enrichment in L-structures of some amino acids, especially isovaline, confirming earlier work. The authors suggest that aqueously-altered planetesimals might have seeded the early Earth with nonracemic amino acids, perhaps explaining why life from microorganisms to people use only L- forms to make proteins. The initial imbalance caused by non-biologic processes in wet asteroids might have been amplified by life on Earth. Alternatively

  2. Genetics of Amino Acid Taste and Appetite123

    PubMed Central

    Bosak, Natalia P; Glendinning, John I; Inoue, Masashi; Li, Xia; Manita, Satoshi; McCaughey, Stuart A; Murata, Yuko; Beauchamp, Gary K

    2016-01-01

    The consumption of amino acids by animals is controlled by both oral and postoral mechanisms. We used a genetic approach to investigate these mechanisms. Our studies have shown that inbred mouse strains differ in voluntary amino