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Sample records for isolation structure elucidation

  1. Isolation and Structure Elucidation of Pentahydroxyscirpene, a Trichothecene Fusarium Mycotoxin

    PubMed Central

    2013-01-01

    Pentahydroxyscirpene, a novel trichothecene-type compound, was isolated from Fusarium-inoculated rice. The structure of pentahydroxyscirpene was elucidated by 1D and 2D NMR spectroscopy and X-ray single-crystal diffraction. The conformation in solution was determined by NOESY experiments supported by quantum chemical calculations. In vitro toxicity tests showed that pentahydroxyscirpene inhibits protein synthesis as do other trichothecenes. PMID:24367932

  2. Isolation and structural elucidation of biotransformation products from acarbose.

    PubMed

    Boberg, M; Kurz, J; Ploschke, H J; Schmitt, P; Scholl, H; Schüller, M; Wünsche, C

    1990-05-01

    Following oral administration the a-glucosidase inhibitor acarbose (O-4,6-dideoxy-4-[[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl) -2-cyclohexen-1-yl]amino]-a-D-glucopyranosyl-(1----4)-O-a-D-glu copyranosyl-(1----4)-D-glucopyranose, Bay g 5421) is degraded by digestive enzymes and/or intestinal microorganism. The effect of anaerobic intestinal bacteria can be studied in an in vitro model which involves the incubation of acarbose with human or animal intestinal flora. Acarbose and nine biotransformation products can be isolated from the incubation mixture. These products were identified by nuclear magnetic resonance and mass spectrometry as so-called component 2 (loss of the terminal glucose), component 1 (loss of both glucose rings), hexose homologues of acarbose and component 2, methyl homologues of acarbose, butyric acid ester of component 2, basic disaccharide (loss of the cyclitol ring of component 2), delta-aminovaleric acid and gamma-aminobutyric acid. Following oral administration of [14C]-acarbose to healthy volunteers, 35% of the radioactivity was excreted in the form of at least 13 metabolites in the urine. Three of the metabolites were isolated by Craig countercurrent distribution and ion-pair HPLC and characterized by virtue of their nuclear magnetic resonance and mass spectra as derivatives of 4-methylpyrogallol. Two were shown to be monomethylether-monosulphates while the third was a monosulphate-monoglucuronide. The synthesis of ten reference substances and the comparison of HPLC and UV data clearly indicated that the majority of the non-isolated metabolites were also 4-methylpyrogallol derivatives. The peculiarities of the nuclear magnetic resonance and mass spectra of this type of compound are discussed.

  3. Nature's Anti-Alzheimer's Drug: Isolation and Structure Elucidation of Galantamine from "Leucojum Aestivum"

    ERIC Educational Resources Information Center

    Halpin, Catherine M.; Reilly, Ciara; Walsh, John J.

    2010-01-01

    The discovery that galantamine penetrates the blood-brain barrier has led to its clinical use in the treatment of choline-deficiency conditions in the brain, such as Alzheimer's disease. This experiment involves the isolation and structure elucidation of galantamine from "Leucojum aestivum". Isolation of the alkaloid constituents in "L. aestivum"…

  4. Nature's Migraine Treatment: Isolation and Structure Elucidation of Parthenolide from "Tanacetum parthenium"

    ERIC Educational Resources Information Center

    Walsh, Emma L.; Ashe, Siobhan; Walsh, John J.

    2012-01-01

    The purpose of this experiment is to provide students with the essential skills and knowledge required to perform the extraction, isolation, and structural elucidation of parthenolide from "Tanacetum parthenium" or feverfew. Students are introduced to a background of the traditional medicinal uses of parthenolide, while more modern applications of…

  5. Isolation and structural elucidation of chondrosterins F-H from the marine fungus Chondrostereum sp.

    PubMed

    Li, Hou-Jin; Chen, Ting; Xie, Ying-Lu; Chen, Wen-Dan; Zhu, Xiao-Feng; Lan, Wen-Jian

    2013-02-01

    The marine fungus Chondrostereum sp. was collected from a soft coral of the species Sarcophyton tortuosum from the South China Sea. Three new compounds, chondrosterins F-H (1, 4 and 5), together with three known compounds, incarnal (2), arthrosporone (3), and (2E)-decene-4,6,8-triyn-1-ol (6), were isolated. Their structures were elucidated primarily based on NMR and MS data. Incarnal (2) exhibited potent cytotoxic activity against various cancer cell lines.

  6. Isolation, structural elucidation, and neuroprotective effects of iridoids from Valeriana jatamansi.

    PubMed

    Xu, Jing; Li, Yushan; Guo, Yuanqiang; Guo, Ping; Yamakuni, Tohru; Ohizumi, Yasushi

    2012-01-01

    Two new iridoids, jatadoids A (1) and B (2), and two known compounds (3 and 4) were isolated from Valeriana jatamansi. Their structures were elucidated on the basis of extensive spectroscopic analyses (IR, ESI-MS, HR-ESI-MS, 1D and 2D NMR). Compound 1 possessed an isovaleroxy group at the C-3 position that has previously been unreported in the class of iridoids. Four compounds were evaluated and compounds 1 and 3 showed moderate neuroprotective effects against MPP+-induced neuronal cell death in human dopaminergic neuroblastoma SH-SY5Y cells.

  7. Isolation, structure elucidation and DFT study on two novel oligosaccharides from yak milk

    NASA Astrophysics Data System (ADS)

    Singh, Meenakshi; Kumar, Alok; Srivastava, Gaurav; Deepak, Desh; Singh, M. P. V. V.

    2016-08-01

    Two novel oligosaccharides were isolated from yak milk. The milk was processed by the method of Kobata and Ginsberg involving deproteination, centrifugation and lyophilization followed by gel filtrate chromatography acetylation and silica gel column chromatography of derivatized oligosaccharides while their homogeneity was confirmed by HPLC. The structures of these isolated oligosaccharides were elucidated by chemical transformation, chemical degradation, 1H, 13C NMR, 2D NMR (COSY, TOCSY and HSQC) and mass spectrometry. The geometry of compound A (Bosiose) and B (Bovisose) have been optimized at B3LYP method and 6-311 + G(d,p) basis set. The difference between the energies of A and B is 1.269 a.u. or 796.309 kcal/mol.

  8. Meroparamycin production by newly isolated Streptomyces sp. strain MAR01: taxonomy, fermentation, purification and structural elucidation.

    PubMed

    El-Naggar, Moustafa Y; El-Assar, Samy A; Abdul-Gawad, Sahar M

    2006-08-01

    Twelve actinomycete strains were isolated from Egyptian soil. The isolated actinomycete strains were then screened with regard to their potential to generate antibiotics. The most potent of the producer strains was selected and identified. The cultural and physiological characteristics of the strain identified the strain as a member of the genus Streptomyces. The nucleotide sequence of the 16S rRNA gene (1.5 kb) of the most potent strain evidenced a 99% similarity with Streptomyces spp. and S. aureofaciens 16S rRNA genes, and the isolated strain was ultimately identified as Streptomyces sp. MAR01. The extraction of the fermentation broth of this strain resulted in the isolation of one major compound, which was active in vitro against gram-positive, gram-negative representatives and Candida albicans. The chemical structure of this bioactive compound was elucidated based on the spectroscopic data obtained from the application of MS, IR, UV, 1H NMR, 13C NMR, and elemental analysis techniques. Via comparison to the reference data in the relevant literature and in the database search, this antibiotic, which had a molecular formula of C19H29NO2 and a molecular weight of 303.44, was determined to differ from those produced by this genus as well as the available known antibiotics. Therefore, this antibiotic was designated Meroparamycin. PMID:16953179

  9. Isolation, Characterization, Crystal Structure Elucidation, and Anticancer Study of Dimethyl Cardamonin, Isolated from Syzygium campanulatum Korth

    PubMed Central

    Aisha, Abdalrahim F. A.; Al-Suede, Fouad Saleih Resq; Hamil, Mohammad Shahrul Ridzuan; Laghari, Madeeha; Abdul Majid, Amin Malik Shah

    2014-01-01

    Syzygium campanulatum Korth is an equatorial, evergreen, aboriginal shrub of Malaysia. Conventionally it has been used as a stomachic. However, in the currently conducted study dimethyl cardamonin or 2′,4′-dihydroxy-6′-methoxy-3′,5′-dimethylchalcone (DMC) was isolated from S. campanulatum Korth, leaf extract. The structural characterization of DMC was carried out by making use of various techniques including UV, IR, NMR spectral followed by LC-MS, and X-ray crystallographic techniques. For determining the purity of compound, highly effective techniques including TLC, HPLC, and melting point were used. The cytotoxicity of DMC and three different extracts of S. campanulatum was evaluated against human colon cancer cell line (HT-29) by three different assays. DMC and ethanolic extract revealed potent and dose-dependent cytotoxic activity on the cancer cell line with IC50 12.6 and 90.1 µg/mL, respectively. Quite astonishingly to our knowledge, this is the very first report on S. campanulatum as being a rich source (3.5%) of DMC, X-ray crystallography, and anticancer activity on human colon cancer cells. PMID:25530783

  10. Isolation and Structure Elucidation of GM4-Type Gangliosides from the Okinawan Starfish Protoreaster nodosus

    PubMed Central

    Pan, Ke; Tanaka, Chiaki; Inagaki, Masanori; Higuchi, Ryuichi; Miyamoto, Tomofumi

    2012-01-01

    Three new ganglioside molecular species, termed PNG-1, PNG-2A, and PNG-2B were isolated from pyloric caeca of the starfish Protoreaster nodosus. Their structures were elucidated using a combination of spectroscopic and chemical methods, and characterized as 1-O-[8-O-methyl-N-acetyl-α-neuraminosyl-(2→3)-β-galactopyranosyl]-ceramide for PNG-1, 1-O-[β-galactofuranosyl-(1→3)-α-galactopyranosyl-(1→4)-8-O-methyl-N-acetyl-α-neuraminosyl-(2→3)-β-galactopyranosyl]-ceramide for PNG-2A, and 1-O-[β-galactofuranosyl-(1→3)-α-galactopyranosyl-(1→9)-N-acetyl-α-neuraminosyl-(2→3)-β-galactopyranosyl]-ceramide for PNG-2B. PNG-2A and PNG-2B represent the first GM4 elongation products in nature. PMID:23203271

  11. Isolation and structure elucidation of linolipins C and D, complex oxylipins from flax leaves.

    PubMed

    Chechetkin, Ivan R; Blufard, Alexander S; Khairutdinov, Bulat I; Mukhitova, Fakhima K; Gorina, Svetlana S; Yarin, Andrey Y; Antsygina, Larisa L; Grechkin, Alexander N

    2013-12-01

    Two complex oxylipins (linolipins C and D) were isolated from the leaves of flax plants inoculated with phytopathogenic bacteria Pectobacterium atrosepticum. Their structures were elucidated based on UV, MS and NMR spectroscopic data. Both oxylipins were identified as digalactosyldiacylglycerol (DGDG) molecular species. Linolipin C contains one residue of divinyl ether (ω5Z)-etherolenic acid and one α-linolenate residue at sn-1 and sn-2 positions, respectively. Linolipin D possesses two (ω5Z)-etherolenic acid residues at both sn-1 and sn-2 positions. The rapid formation (2-30min) of linolipins C and D alongside with linolipins A and B occurred in the flax leaves upon their damage by freezing-thawing.

  12. Isolation and structural elucidation of novel antimicrobial compounds from maggots of Chrysomyis megacephala Fabricius.

    PubMed

    Gao, Jiayu; Li, Wenyuan; Niu, Lanlan; Cao, Ranran; Yin, Weiping

    2015-02-01

    The excretions/secretions from the maggot of Chrysomyis megacephala Fabricius are traditionally used to treat serious infections in China. In this study, bioassay-guided fractionation led to the isolation of three novel antibacterial compounds (1-3), including important fluorinated compounds (3 and 5), together with other nine known compounds from 70% methanol extract of C. megacephala. The structures of the new compounds were elucidated by NMR spectroscopic analysis and high-resolution mass spectroscopy. The antibacterial activities of the isolated compounds were evaluated using agar disc diffusion method. New compounds 1 and 2 exhibited moderate activity against Bacillus subtilis with a minimum inhibitory concentration (MIC) of 250 μg mL(- 1). The most active compounds 3 and 5 displayed a broad spectrum of antimicrobial activity with an MIC of 125 μg mL(- 1) against G(+) and G(- ) bacteria. The structure of the above-mentioned novel compounds and their antimicrobial activities are herein reported for the first time from the natural product of insects.

  13. [Isolation and structural elucidation of secondary metabolites from marine Streptomyces sp. SCSIO 1934].

    PubMed

    Niu, Siwen; Li, Sumei; Tian, Xinpeng; Hu, Tao; Ju, Jianhua; Ynag, Xiaohong; Zhang, Si; Zhang, Changsheng

    2011-07-01

    Marine Actinobacteria are emerging as new resources for bioactive natural products with promise in novel drug discovery. In recent years, the richness and diversity of marine Actinobacteria from the South China Sea and their ability in producing bioactive products have been investigated. The objective of this work is to isolate and identify bioactive secondary metabolites from a marine actinobacterium SCSIO 1934 derived from sediments of South China Sea. The strain was identified as a Streptomyces spieces by analyzing its 16S rDNA sequence. Streptomyces sp. SCSIO 1934 was fermented under optimized conditions and seven bioactive secondary metabolites were isolated and purified by chromatographic methods including colum chromatography over silica gel and Sephadex LH-20. Their structures were elucidated as 17-O-demethylgeldanamycin (1), lebstatin (2), 17-O-demethyllebstatin (3), nigericin (4), nigericin sodium salt (5), abierixin (6), respectively, by detailed NMR spectroscopic data (1H, 13C, COSY, HSQC and HMBC). This work provided a new marine actinobacterium Streptomyces sp. SCSIO 1934, capable of producing diverse bioactive natural products.

  14. Separation by thin-layer chromatography and structure elucidation of bilirubin conjugates isolated from dog bile.

    PubMed Central

    Heirwegh, K P; Fevery, J; Michiels, R; van Hees, G P; Compernolle, F

    1975-01-01

    1. A system for separation of bile pigments by t.l.c. and for their structure elucidation is presented. Separated bile pigments are characterized by t.l.c. of derived dipyrrolic azopigments. 2. At the tetrapyrrolic stage hydrolysis in strongly alkaline medium followed by t.l.c. demonstrates the presence of bilirubin-IIIalpha, -IXalpha and -XIIIalpha and allows assessment of their relative amounts. 3. Most structural information is derived from analysis of dipyrrolic azopigments. Such derivatives, obtained by treatment of separated bile pigments with diazotized ethyl anthranilate, were separated and purified by t.l.c. Micro methods showed (a) the nature of the dipyrrolic aglycone, (b) the nature of the bonds connecting aglycone to a conjugating group, (c) the ratio of vinyl/isovinyl isomers present in the aglycone and, (d) the nature of the conjugating groups (by suitable derivative formation and t.l.c. with reference to known compounds). 4. In bile of normal dogs at least 20 tetrapyrrolic, diazo-positive bile pigments could be recognized. Except for two pigments the tetrapyrrolic nucleus corresponded predominantly to bilirubin-IXalpha. All conjugated pigments had their conjugating groups connected in ester linkage to the tetrapyrrolic aglycone, Apart from bilirubin-IXalpha, monoconjugates and homogeneous and mixed diconjugates of bilirubin were demonstrated; conjugating groups of major importance were xylose, glucose and glucuronic acid. 5. Bilirubin isomer determination on native bile and isolated bile pigments, and dipyrrole-exchange assays with [14C8]bilirubin indicated (a) that the conjugates pre-exist in bile, and (b) that no significant dipyrrole exchange occurs during isolation of the pigments. PMID:1156357

  15. Isolation and structure elucidation of the major individual polyphenols in carob fibre.

    PubMed

    Owen, R W; Haubner, R; Hull, W E; Erben, G; Spiegelhalder, B; Bartsch, H; Haber, B

    2003-12-01

    Although it is already known that carob fibre contains several classes of polyphenolic substances, a comprehensive analysis of these has not been conducted to date. Therefore, the major polyphenolic compounds were extracted with organic solvents, and, following fractionation by normal-phase column chromatography on silicic acid, their structures were elucidated by liquid-chromatography electrospray-ionisation mass spectrometry (LC-ESI), nano-electrospray-ionisation mass spectrometry (ESI-MS), and gas-chromatography mass spectrometry (GC-MS). In addition, complete 1H and 13C NMR assignments were obtained for the isolated gallotannins 1,6-di-, 1,2,6-tri- and 1,2,3,6-tetra-O-galloyl-beta-D-glucose. Carob fibre was found to contain a rich variety of phenolic antioxidants. A total of 24 polyphenol compounds were identified with a yield of 3.94 g/kg (dry weight). The profile was dominated by gallic acid in various forms: free gallic acid (42% of polyphenols by weight), gallotannins (29%), and methyl gallate (1%), while simple phenols, mainly cinnamic acid, made up about 2% of the total. Flavonoids represented 26% of the polyphenols, and the major components were identified as the glycosides myricetin- and quercetin-3-O-alpha-L-rhamnoside (ca. 9% and 10%, respectively). These data indicate that carob fibre is rich in both amount and variety of phenolic antioxidant substances, and its inclusion in the diet may have chemopreventive properties.

  16. A major inducer of anticarcinogenic protective enzymes from broccoli: isolation and elucidation of structure.

    PubMed Central

    Zhang, Y; Talalay, P; Cho, C G; Posner, G H

    1992-01-01

    Consumption of vegetables, especially crucifers, reduces the risk of developing cancer. Although the mechanisms of this protection are unclear, feeding of vegetables induces enzymes of xenobiotic metabolism and thereby accelerates the metabolic disposal of xenobiotics. Induction of phase II detoxication enzymes, such as quinone reductase [NAD(P)H:(quinone-acceptor) oxidoreductase, EC 1.6.99.2] and glutathione S-transferases (EC 2.5.1.18) in rodent tissues affords protection against carcinogens and other toxic electrophiles. To determine whether enzyme induction is responsible for the protective properties of vegetables in humans requires isolation of enzyme inducers from these sources. By monitoring quinone reductase induction in cultured murine hepatoma cells as the biological assay, we have isolated and identified (-)-1-isothiocyanato-(4R)-(methylsulfinyl)butane [CH3-SO-(CH2)4-NCS, sulforaphane] as a major and very potent phase II enzyme inducer in SAGA broccoli (Brassica oleracea italica). Sulforaphane is a monofunctional inducer, like other anticarcinogenic isothiocyanates, and induces phase II enzymes selectively without the induction of aryl hydrocarbon receptor-dependent cytochromes P-450 (phase I enzymes). To elucidate the structural features responsible for the high inducer potency of sulforaphane, we synthesized racemic sulforaphane and analogues differing in the oxidation state of sulfur and the number of methylene groups: CH3-SOm-(CH2)n-NCS, where m = 0, 1, or 2 and n = 3, 4, or 5, and measured their inducer potencies in murine hepatoma cells. Sulforaphane is the most potent inducer, and the presence of oxygen on sulfur enhances potency. Sulforaphane and its sulfide and sulfone analogues induced both quinone reductase and glutathione transferase activities in several mouse tissues. The induction of detoxication enzymes by sulforaphane may be a significant component of the anticarcinogenic action of broccoli. Images PMID:1549603

  17. Nature's Cholesterol-Lowering Drug: Isolation and Structure Elucidation of Lovastatin from Red Yeast Rice-Containing Dietary Supplements

    ERIC Educational Resources Information Center

    Nazri, Maisarah Mohd; Samat, Farah D.; Kavanagh, Pierce V.; Walsh, John J.

    2012-01-01

    Red yeast rice, produced by fermenting the fungus, "Monascus purpureus", on rice ("Oryza sativa" L. gramineae), is commonly used as a dietary supplement. It contains lovastatin, a member of the statin family of compounds, and is licensed for use as a cholesterol-lowering agent. This experiment involves the isolation and structure elucidation of…

  18. Isolation and structure elucidation of phenolic antioxidants from Tamarind (Tamarindus indica L.) seeds and pericarp.

    PubMed

    Sudjaroen, Y; Haubner, R; Würtele, G; Hull, W E; Erben, G; Spiegelhalder, B; Changbumrung, S; Bartsch, H; Owen, R W

    2005-11-01

    Although it is already known that Tamarind (Tamarindus indica L.) seeds contain phenolic substances, the individual components of the seeds have not been fully identified and quantitated, and in the case of Tamarind pericarp not reported. Therefore, major polyphenolic compounds were extracted using organic solvents and the metabolites were isolated by semi-preparative high performance liquid chromatography. Their structures were elucidated by liquid chromatography-electrospray-ionisation-mass spectrometry (LC-ESI-MS), nano-electrospray-ionisation mass spectrometry (ESI-MS), and where possible by gas chromatography-mass spectrometry (GC-MS) and 1H and 13C NMR. Quantitative analysis of polyphenolic compounds in Tamarind seeds and pericarp was conducted by analytical high performance liquid chromatography (HPLC), calculated against standard curves of authentic compounds. The yields of total phenolic compounds after Soxhlet extraction with methanol were 6.54 and 2.82 g/kg (dry weight) in the seeds and pericarp respectively. The profile (%) of polyphenolics in Tamarind pericarp was dominated by proanthcyanidins (73.4) in various forms (+)-catechin (2.0), procyanidin B2 (8.2), (-)-epicatechin (9.4), procyanidin trimer (11.3), procyanidin tetramer (22.2), procyanidin pentamer (11.6), procyanidin hexamer (12.8) along with taxifolin (7.4), apigenin (2.0), eriodictyol (6.9), luteolin (5.0) and naringenin (1.4) of total phenols, respectively. The content of Tamarind seeds comprised only procyanidins, represented (%) mainly by oligomeric procyanidin tetramer (30.2), procyanidin hexamer (23.8), procyanidin trimer (18.1), procyanidin pentamer (17.6) with lower amounts of procyanidin B2 (5.5) and (-)-epicatechin (4.8). Extraction of Tamarind pericarp and seeds using acetone:methanol:acetic acid gave only procyanidin oligomers, but in much higher yield and variety. The antioxidant capacities of the Soxhlet methanolic extracts were determined, and indicates that Tamarind may be an

  19. Isolation and structure elucidation of phenolic antioxidants from Tamarind (Tamarindus indica L.) seeds and pericarp.

    PubMed

    Sudjaroen, Y; Haubner, R; Würtele, G; Hull, W E; Erben, G; Spiegelhalder, B; Changbumrung, S; Bartsch, H; Owen, R W

    2005-11-01

    Although it is already known that Tamarind (Tamarindus indica L.) seeds contain phenolic substances, the individual components of the seeds have not been fully identified and quantitated, and in the case of Tamarind pericarp not reported. Therefore, major polyphenolic compounds were extracted using organic solvents and the metabolites were isolated by semi-preparative high performance liquid chromatography. Their structures were elucidated by liquid chromatography-electrospray-ionisation-mass spectrometry (LC-ESI-MS), nano-electrospray-ionisation mass spectrometry (ESI-MS), and where possible by gas chromatography-mass spectrometry (GC-MS) and 1H and 13C NMR. Quantitative analysis of polyphenolic compounds in Tamarind seeds and pericarp was conducted by analytical high performance liquid chromatography (HPLC), calculated against standard curves of authentic compounds. The yields of total phenolic compounds after Soxhlet extraction with methanol were 6.54 and 2.82 g/kg (dry weight) in the seeds and pericarp respectively. The profile (%) of polyphenolics in Tamarind pericarp was dominated by proanthcyanidins (73.4) in various forms (+)-catechin (2.0), procyanidin B2 (8.2), (-)-epicatechin (9.4), procyanidin trimer (11.3), procyanidin tetramer (22.2), procyanidin pentamer (11.6), procyanidin hexamer (12.8) along with taxifolin (7.4), apigenin (2.0), eriodictyol (6.9), luteolin (5.0) and naringenin (1.4) of total phenols, respectively. The content of Tamarind seeds comprised only procyanidins, represented (%) mainly by oligomeric procyanidin tetramer (30.2), procyanidin hexamer (23.8), procyanidin trimer (18.1), procyanidin pentamer (17.6) with lower amounts of procyanidin B2 (5.5) and (-)-epicatechin (4.8). Extraction of Tamarind pericarp and seeds using acetone:methanol:acetic acid gave only procyanidin oligomers, but in much higher yield and variety. The antioxidant capacities of the Soxhlet methanolic extracts were determined, and indicates that Tamarind may be an

  20. Isolation and structure elucidation of a new antifungal and antibacterial antibiotic produced by Streptomyces sp. 201.

    PubMed

    Bordoloi, G N; Kumari, B; Guha, A; Bordoloi, M; Yadav, R N; Roy, M K; Bora, T C

    2001-08-01

    An antibacterial and antifungal antibiotic was isolated from the culture filtrate of Streptomyces sp. 201, and its structure was determined as 2-methyl-heptyl isonicotinate by extensive use of NMR spectroscopy. The compound exhibited marked antimicrobial activity against Bacillus subtilis, Shigella sp., Klebsiella sp., E. coli, Proteus mirabilis, and the pathogenic fungi, Fusarium moniliforme, F. semitectum, F. oxysporum, F. solani and Rhizoctonia solani.

  1. Isolation and structure elucidation of vicenistatin M, and importance of the vicenisamine aminosugar for exerting cytotoxicity of vicenistatin.

    PubMed

    Matsushima, Y; Nakayama, T; Fujita, M; Bhandari, R; Eguchi, T; Shindo, K; Kakinuma, K

    2001-03-01

    A new analogue of vicenistatin was isolated from the producing strain Streptomyces sp. HC-34. A characteristic of the elucidated structure involved the existence of a neutral sugar mycarose instead of an aminosugar vicenisamine of vicenistatin. The absolute stereochemistry of the new analogue (named as vicenistatin M) was determined by the synthesis of D-mycarose and of vicenistatin M itself. Biological testing of vicenistatin M suggested the importance of vicenisamine for exerting the cytotoxicity of vicenistatin. PMID:11372778

  2. Isolation and structure elucidation of anhydroluteins from cooked sorrel (Rumex rugosus Campd.).

    PubMed

    Molnár, Péter; Osz, Erzsébet; Zsila, Ferenc; Deli, József

    2005-07-01

    Anhydrolutein I (= (all-E,3R,6'R)-3',4'-didehydro-beta,gamma-caroten-3-ol; 2) and anhydrolutein II (= (all-E, 3R,6'S)-2',3'-didehydro-beta,epsilon-caroten-3-ol; 3) have been isolated and characterized from the extract of steam-cooked sorrel. The presence of these compounds in cooked vegetable is postulated to be due to acid-catalyzed dehydration of lutein (1; Scheme). The structures of the isolated anhydroluteins were established by UV/VIS, CD, and 1H-NMR spectroscopy, and mass spectrometry.

  3. Isolation and structure elucidation of azoricasterol, a new sterol of the deepwater sponge Macandrewia azorica

    NASA Astrophysics Data System (ADS)

    Gross, Harald; Reitner, Joachim; König, Gabriele M.

    2004-09-01

    Chemical investigation of the deepwater sponge Macandrewia azorica, collected from the flanks of the Gettysburg and Ormonde Sea Mount, North Atlantic, from a depth of 600 m, has led to the isolation of a new sterol with an unusual side chain (1), along with S-methylergothioneine (2). The structures of compounds 1 and 2 were established by employing spectroscopic techniques (NMR, MS, UV, IR and polarimetry). This is the first report of metabolites of a sponge belonging to the genus Macandrewia.

  4. Isolation and structural elucidation of a new cyclohexenone compound from Lasiodiplodia theobromae.

    PubMed

    Kitaoka, Naoki; Nabeta, Kensuke; Matsuura, Hideyuki

    2009-08-01

    A new cyclohexenone compound was isolated as a mixture of enantiomers from a culture filtrate of Lasiodiplodia theobromae. The relative structure was determined to be 4,5-dihydroxy-3-methyl-cyclohex-2-enone on the basis of MS, (1)H-NMR, and (13)C-NMR spectroscopic analyses, including 2D-NMR experiments. Resolution of the enantiomers was conducted by a coupling reaction with (S)-MTPA-Cl followed by HPLC separation. PMID:19661717

  5. Structure Elucidation and in Vitro Toxicity of New Azaspiracids Isolated from the Marine Dinoflagellate Azadinium poporum

    PubMed Central

    Krock, Bernd; Tillmann, Urban; Potvin, Éric; Jeong, Hae Jin; Drebing, Wolfgang; Kilcoyne, Jane; Al-Jorani, Ahmed; Twiner, Michael J.; Göthel, Qun; Köck, Matthias

    2015-01-01

    Two strains of Azadinium poporum, one from the Korean West coast and the other from the North Sea, were mass cultured for isolation of new azaspiracids. Approximately 0.9 mg of pure AZA-36 (1) and 1.3 mg of pure AZA-37 (2) were isolated from the Korean (870 L) and North Sea (120 L) strains, respectively. The structures were determined to be 3-hydroxy-8-methyl-39-demethyl-azaspiracid-1 (1) and 3-hydroxy-7,8-dihydro-39-demethyl-azaspiracid-1 (2) by 1H- and 13C-NMR. Using the Jurkat T lymphocyte cell toxicity assay, (1) and (2) were found to be 6- and 3-fold less toxic than AZA-1, respectively. PMID:26528990

  6. Computer-Assisted Structure Elucidation of Black Chokeberry (Aronia melanocarpa) Fruit Juice Isolates with a New Fused Pentacyclic Flavonoid Skeleton

    PubMed Central

    Naman, C. Benjamin; Li, Jie; Moser, Arvin; Hendrycks, Jeffery M.; Benatrehina, P. Annécie; Chai, Heebyung; Yuan, Chunhua; Keller, William J.; Kinghorn, A. Douglas

    2015-01-01

    Melanodiol 4″-O-protocatechuate (1) and melanodiol (2) represent novel flavonoid derivatives isolated from a botanical dietary supplement ingredient, dried black chokeberry (Aronia melanocarpa) fruit juice. These non-crystalline compounds possess an unprecedented fused pentacyclic core with two contiguous hemiketals. Due to having significant hydrogen deficiency indices, their structures were determined using computer-assisted structure elucidation software. The in vitro hydroxyl radical-scavenging and quinone reductase-inducing activity of each compound are reported, and a plausible biogenetic scheme is proposed PMID:26030740

  7. Computer-Assisted Structure Elucidation of Black Chokeberry (Aronia melanocarpa) Fruit Juice Isolates with a New Fused Pentacyclic Flavonoid Skeleton.

    PubMed

    Naman, C Benjamin; Li, Jie; Moser, Arvin; Hendrycks, Jeffery M; Benatrehina, P Annécie; Chai, Heebyung; Yuan, Chunhua; Keller, William J; Kinghorn, A Douglas

    2015-06-19

    Melanodiol 4″-O-protocatechuate (1) and melanodiol (2) represent novel flavonoid derivatives isolated from a botanical dietary supplement ingredient, dried black chokeberry (Aronia melanocarpa) fruit juice. These noncrystalline compounds possess an unprecedented fused pentacyclic core with two contiguous hemiketals. Due to having significant hydrogen deficiency indices, their structures were determined using computer-assisted structure elucidation software. The in vitro hydroxyl radical-scavenging and quinone reductase-inducing activity of each compound are reported, and a plausible biogenetic scheme is proposed.

  8. Aurantimycins, new depsipeptide antibiotics from Streptomyces aurantiacus IMET 43917. Production, isolation, structure elucidation, and biological activity.

    PubMed

    Gräfe, U; Schlegel, R; Ritzau, M; Ihn, W; Dornberger, K; Stengel, C; Fleck, W F; Gutsche, W; Härtl, A; Paulus, E F

    1995-02-01

    Aurantimycins A (1), B (2) and C (3) were isolated from the mycelium of Streptomyces aurantiacus JA 4570 as new representatives of the azinothricin group of hexadepsipeptide antibiotics. Their structures were settled by X-ray diffraction analysis of crystalline aurantimycin A (1), high field homo- and heteronuclear 2D NMR experiments, high-resolution mass spectrometry and amino acid analysis. Aurantimycins are characterized by a new side chain containing fourteen carbon atoms. They display strong activity against Gram-positive bacteria and cytotoxic effects against L-929 mouse fibroblast cells.

  9. Sulfated phenolic compounds from Limonium caspium: Isolation, structural elucidation, and biological evaluation

    PubMed Central

    Gadetskaya, Anastassiya V.; Tarawneh, Amer H.; Zhusupova, Galiya E.; Gemejiyeva, Nadezhda G.; Cantrell, Charles L.; Cutler, Stephen J.; Ross, Samir A.

    2016-01-01

    Three new compounds, (2S,3S)-5-methyldihydromyricetin (1), (2S,3S)-5-methyldihydromyricetin-3′-O-sulfate (2) and β-D-glucopyranoside, 3-methyl, but-3-en-1-yl 4-O-α-L-rhamnopyranosyl (3) have been isolated from the Limonium caspium, together with dihydromyricetin (4), dihydromyricetin-3′-O-sulfate (5), myricetin-3′-O-sulfate (6), 5-methylmyricetin (7), myricetin (8), myricetin-3-O-β-glucoside (9), as well as phloridzin (10), and tyramine (11). Compounds 5 and 6 were isolated for the first time as acids. This is the first report of all these compounds from this plant. Their structures were established by extensive NMR studies (1H NMR, 13C NMR, DEPT, 1H–1H COSY, HSQC, HMBC) as well as HRESIMS. All isolated compounds were evaluated for their antibacterial, antifungal, antimalarial and antileishmanial activities. Compounds 7, 8 and 9 exhibited good antifungal activity against Candida glabrata with IC50 values of 6.79, 15.37 and 8.53 μg/mL, respectively. Compound 8 displayed significant antimalarial activity against resistant and sensitive strains of Plasmodium falciparum with IC50 values of 1.82 and 1.51 μg/mL, respectively. Compounds 1, 4, 6, 8 and 9 showed excellent activity against Trypanosoma brucei with IC50 values of 6.93, 9.65, 8.52, 7.67 and 6.31 μg/mL, respectively. To date, this is the first report on the phytochemical and biological activity of secondary metabolites from L. caspium. PMID:26025854

  10. Rhizomes of Eremostachys laciniata: Isolation and Structure Elucidation of Chemical Constituents and a Clinical Trial on Inflammatory Diseases

    PubMed Central

    Delazar, Abbas; Sarker, Satyajit D.; Nahar, Lutfun; Jalali, Shahriar Barzegar; Modaresi, Masoud; Hamedeyazdan, Sanaz; Babaei, Hossein; Javadzadeh, Yousef; Asnaashari, Solmaz; Bamdad Moghadam, Sadeighe

    2013-01-01

    Purpose: The purpose of this study was the isolation and structure elucidation of chemical compounds from the rhizomes of Eremostachys laciniata (L) Bunge (EL), an Iranian traditional medicinal herb with a thick root and pale purple or white flowers as well as the clinical studies on the therapeutic efficacy and safety of topical application of the EL extract in the management of some inflammatory conditions, e.g., arthritis, rheumatoid arthritis and septic arthritis (Riter’s syndrome). Methods: The structures of the isolated compounds were elucidated unequivocally on the basis of one and two dimensional NMR, UV and HR-FABMS spectroscopic data analyses. A single-blinded randomized clinical trial was carried out with the extract of the rhizomes of E. laciniata (EL) to determine the efficacy and safety of the traditional uses of EL compared to that of piroxicam in treatment of inflammatory diseases, e.g., osteoarthritis, rheumatoid arthritis and Reiter’s syndrome. Results: Eleven iridoid glycosides, two phenylethanoids and two phytosterols were isolated and identified for the first time from the rhizomes of EL. After 14 days of treatment with the EL and piroxicam ointments, all groups showed significant improvements compared to the control groups. EL (5%) ointment induced better initial therapeutic response than piroxicam (5%) onitment. Conclusion: This clinical trial established that EL was suitable for topical applications as a safe and effective complementary therapy for inflammatory diseases. PMID:24312865

  11. Isolation, structure elucidation and cytotoxic evaluation of endiandrin B from the Australian rainforest plant Endiandra anthropophagorum.

    PubMed

    Davis, Rohan A; Barnes, Emma C; Longden, James; Avery, Vicky M; Healy, Peter C

    2009-02-01

    Chemical investigations of the DCM extract from the roots of Endiandra anthropophagorum resulted in the isolation of a new cyclobutane lignan endiandrin B (1), together with the known natural products, endiandrin A (2), and (-)-dihydroguaiaretic acid (3). The structure of 1 was determined by extensive spectroscopic analyses, and confirmed by single crystal X-ray crystallography. Methylation of 1 using diazomethane afforded the previously reported natural product, cinbalansan (4). All compounds were evaluated for their cytotoxicity towards human lung carcinoma cells (A549) using high-content screening. (-)-Dihydroguaiaretic acid (3) was found to be the most potent cytotoxin against the A549 lung carcinoma cell line, with an IC(50) value of 7.49 microM.

  12. Isolation, Structure Elucidation and Total Synthesis of Lajollamide A from the Marine Fungus Asteromyces cruciatus

    PubMed Central

    Gulder, Tobias A. M.; Hong, Hanna; Correa, Jhonny; Egereva, Ekaterina; Wiese, Jutta; Imhoff, Johannes F.; Gross, Harald

    2012-01-01

    The marine-derived filamentous fungus Asteromyces cruciatus 763, obtained off the coast of La Jolla, San Diego, USA, yielded the new pentapeptide lajollamide A (1), along with the known compounds regiolone (2), hyalodendrin (3), gliovictin (4), 1N-norgliovicitin (5), and bis-N-norgliovictin (6). The planar structure of lajollamide A (1) was determined by Nuclear Magnetic Resonance (NMR) spectroscopy in combination with mass spectrometry. The absolute configuration of lajollamide A (1) was unambiguously solved by total synthesis which provided three additional diastereomers of 1 and also revealed that an unexpected acid-mediated partial racemization (2:1) of the L-leucine and L-N-Me-leucine residues occurred during the chemical degradation process. The biological activities of the isolated metabolites, in particular their antimicrobial properties, were investigated in a series of assay systems. PMID:23342379

  13. Antineoplastic Agents. 570. Isolation and Structure Elucidation of Bacillistatins 1 and 2 from a Marine Bacillus silvestris†, ‡

    PubMed Central

    Pettit, George R.; Knight, John C.; Herald, Delbert L.; Pettit, Robin K.; Hogan, Fiona; Mukku, Venugopal J. R. V.; Hamblin, John S.; Dodson, Michael J.; Chapuis, Jean-Charles

    2009-01-01

    Two new cyclodepsipeptides designated bacillistatins 1 (1) and 2 (2) have been isolated from cultures of a sample of Bacillus silvestris that was obtained from a Pacific Ocean (southern Chile) crab. Each 12-unit cyclodepsipeptide strongly inhibited growth of a human cancer cell line panel, with GI50s of 10−4–10−5 μg/mL, and each compound was active against antibiotic-resistant Streptococcus pneumoniae. The structures were elucidated by a combination of X-ray diffraction and mass and 2D NMR spectroscopic analyses, together with chemical degradation. PMID:19226154

  14. Isolation and structural elucidation of antioxidant peptides from oyster (Saccostrea cucullata) protein hydrolysate.

    PubMed

    Umayaparvathi, S; Meenakshi, S; Vimalraj, V; Arumugam, M; Balasubramanian, T

    2014-01-01

    Protein derived from the oyster (Saccostrea cucullata) was hydrolyzed using protease from Bacillus cereus SU12 for isolation of antioxidant peptides. The oyster hydrolysate exhibited a strong antioxidant potential in DPPH (85.7±0.37%) followed by Hydrogen peroxide radical scavenging activity (81.6±0.3%), Hydroxyl radical-scavenging activity (79.32±0.6%), Reducing power assay (2.63±0.2 OD at 700nm). Due to the high antioxidant potential, hydrolysate was fractionated in Sephadex G-25 gel filtration chromatography. The active peptide fraction was further purified by UPLC-MS. Totally 7 antioxidant peptides were collected. Among 7 peptides (SCAP 1-7), 3 peptides (SCAP 1, 3 and 7) had highest scavenging ability on DPPH radicals. The amino acid sequence and molecular mass of purified antioxidant peptides (SCAP1, SCAP3 and SCAP7) were determined by Q-TOF ESI mass spectroscopy and structures of the peptides were Leu-Ala-Asn-Ala-Lys (MW=515.29Da), Pro-Ser-Leu-Val-Gly-Arg-Pro-Pro-Val-Gly-Lys-Leu-Thr-Leu (MW=1432.89Da) and Val-Lys-Val-Leu-Leu-Glu-His-Pro-Val-Leu (MW=1145.75Da), respectively. The unique amino acid composition and sequence in the peptides might play an important role in expression of their antioxidant activity. The results of this study suggest that oyster protein hydrolysate is good source of natural antioxidants.

  15. Acylated anthocyanins from sprouts of Raphanus sativus cv. Sango: isolation, structure elucidation and antioxidant activity.

    PubMed

    Matera, Riccardo; Gabbanini, Simone; Berretti, Serena; Amorati, Riccardo; De Nicola, Gina Rosalinda; Iori, Renato; Valgimigli, Luca

    2015-01-01

    Little is known on structure-activity relationships of antioxidant anthocyanins. Raphanus sativus cv Sango sprouts are among the richest sources (270 mg/100 g fresh weight). We isolated from sprouts' juice 9 acylated anthocyanins, including 4 new compounds. All comprise a cyanidin core bearing 3-4 glucose units, multiply acylated with malonic and phenolic acids (ferulic and sinapic). All compounds were equally effective in inhibiting the autoxidation of linoleic acid in aqueous micelles, with rate constant for trapping peroxyl radicals kinh=(3.8 ± 0.7) × 10(4)M(-1)s(-1) at 37 °C. In acetonitrile solution kinh varied with acylation: (0.9-2.1) × 10(5)M(-1)s(-1) at 30 °C. Each molecule trapped a number n of peroxyl radicals ranging from 4 to 7. Anthocyanins bearing sinapic acid were more effective than those bearing the ferulic moiety. Under identical settings, deacylated cyanin, ferulic and sinapic acids had kinh of 0.4 × 10(5), 0.3 × 10(5) and 1.6 × 10(5)M(-1)s(-1) respectively, with n ranging 2-3. Results show the major role of acylation on antioxidant performance.

  16. Nature's Sedative: Isolation and Structural Elucidation of Valtrate from Centranthus Ruber

    ERIC Educational Resources Information Center

    Doyle, Andrea M.; Reilly, Joe; Murphy, Niamh; Kavanagh, Pierce V.; O'Brien, John E.; Walsh, Martin S.; Walsh, John J.

    2004-01-01

    A member of a related genus of the valerianaceae, Centranthus ruber, is used, that yields a higher percentage valtrate than other related species such as "Valeriana officinalis," there by making easier isolation in pure form.

  17. Amitorines A and B, Nitrogenous Diterpene Metabolites of Theonella swinhoei: Isolation, Structure Elucidation, and Asymmetric Synthesis.

    PubMed

    Ota, Koichiro; Hamamoto, Yukiko; Eda, Wakiko; Tamura, Kenta; Sawada, Akiyoshi; Hoshino, Ayako; Mitome, Hidemichi; Kamaike, Kazuo; Miyaoka, Hiroaki

    2016-04-22

    Two new nitrogenous prenylbisabolanes never before found in Lithistid sponges have been isolated from Theonella swinhoei. These new diterpenes, named amitorine A (1) and amitorine B (2), containing a prenylbisabolane skeleton have been characterized by spectroscopic analyses, and the relative and absolute configurations of 1 and 2 were determined by asymmetric synthesis of both diastereomers via the common bicyclic lactone 6 intermediate.

  18. Isolation and Structure Elucidation of the Terpene "[beta]"-Thujone from Cedar Leaf Oil

    ERIC Educational Resources Information Center

    French, Larry G.

    2011-01-01

    Western red cedar leaf affords an essential oil characterized by high thujone content. Students in an advanced organic chemistry lab course isolate a single thujone diastereoisomer from commercially available cedar leaf oil. Treatment of crude oil, containing roughly 70% thujone, predominately as [alpha]-thujone (6.5:1), with ethanolic sodium…

  19. Amitorines A and B, Nitrogenous Diterpene Metabolites of Theonella swinhoei: Isolation, Structure Elucidation, and Asymmetric Synthesis.

    PubMed

    Ota, Koichiro; Hamamoto, Yukiko; Eda, Wakiko; Tamura, Kenta; Sawada, Akiyoshi; Hoshino, Ayako; Mitome, Hidemichi; Kamaike, Kazuo; Miyaoka, Hiroaki

    2016-04-22

    Two new nitrogenous prenylbisabolanes never before found in Lithistid sponges have been isolated from Theonella swinhoei. These new diterpenes, named amitorine A (1) and amitorine B (2), containing a prenylbisabolane skeleton have been characterized by spectroscopic analyses, and the relative and absolute configurations of 1 and 2 were determined by asymmetric synthesis of both diastereomers via the common bicyclic lactone 6 intermediate. PMID:27007992

  20. Isolation and Structural Elucidation of an Unknown Impurity in Prasugrel by Semi-Preparative Liquid Chromatography.

    PubMed

    Liu, Chao; Yu, Zhangxin; Wang, Fujun; Zhong, Xing; Jiang, Li; Zhang, Feifei; Tang, Yinxia; Yan, Zhaohua; Zeng, Su; Pu, Tong

    2015-08-01

    A brand-new impurity was detected by RP-HPLC in the prasugrel. The impurity was named as Impurity X. Impurity X was isolated by using semi-preparative HPLC followed by characterization using nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry. The functional mechanism of Impurity X was speculated. Impurity X could be controlled in the manufacture process of the prasugrel active pharmaceutical ingredient effectively. PMID:25644811

  1. Isolation, structural elucidation, and biological evaluation of a 5-hydroxymethyl-2-furfural derivative, asfural, from enzyme-treated asparagus extract.

    PubMed

    Ito, Tomohiro; Sato, Atsuya; Ono, Tomoko; Goto, Kazunori; Maeda, Takahiro; Takanari, Jun; Nishioka, Hiroshi; Komatsu, Kenichi; Matsuura, Hideyuki

    2013-09-25

    A novel 5-hydroxymethyl-2-furfural (HMF; 1) derivative, which is named asfural (compound 2), was isolated from enzyme-treated asparagus extract (ETAS) along with HMF (1) as a heat shock protein 70 (HSP70) inducible compound. The structure of compound 2 was elucidated on the basis of its spectroscopic data from HREIMS and NMR, whereas the absolute configuration was determined using chiral HPLC analysis, compared to two synthesized compounds, (S)- and (R)-asfural. As a result, compound 2 derived from ETAS was assigned as (S)-(2-formylfuran-5-yl)methyl 5-oxopyrrolidine-2-carboxylate. When compound 2, synthesized (S)- and (R)-asfural, and HMF (1) were evaluated in terms of HSP70 mRNA expression-enhancing activity in HL-60 cells, compound 2 and (S)-asfural significantly increased the expression level in a concentration-dependent manner. HMF (1) also showed significant activity at 0.25 mg/mL.

  2. Constituents of Azadirachta indica: isolation and structure elucidation of a new antibacterial tetranortriterpenoid, mahmoodin, and a new protolimonoid, naheedin.

    PubMed

    Siddiqui, S; Faizi, S; Siddiqui, B S; Ghiasuddin

    1992-03-01

    Mahmoodin [1], a new limonoid, has been isolated from Azadirachta indica (neem) oil, along with seven known tetranortriterpenoids, azadirone, epoxyazadiradione, nimbin, gedunin, azadiradione, deacetylnimbin, and 17-hydroxyazadiradione. A new protolimonoid, naheedin [3], has been obtained from the neem fruits along with azadirachtol. Their structures have been elucidated through chemical and spectral analyses including 2D nmr studies. The absolute configuration of 1 was established by comparison of its cd spectrum with those of the known tetranortriterpenoids. Mahmoodin showed significant antibacterial activity against various Gram-positive and Gram-negative organisms. Four hydrocarbons, icosane, docosane, 2-methyltricosane, and docosene, have also been identified by gc-ms of the EtOH extract of the fruit coats. Only docosane has earlier been reported from neem, while the remaining three are unreported from this plant. PMID:1593280

  3. Antimutagenic Compounds of White Shrimp (Litopenaeus vannamei): Isolation and Structural Elucidation.

    PubMed

    López-Saiz, Carmen-María; Hernández, Javier; Cinco-Moroyoqui, Francisco-Javier; Velázquez, Carlos; Ocaño-Higuera, Víctor-Manuel; Plascencia-Jatomea, Maribel; Robles-Sánchez, Maribel; Machi-Lara, Lorena; Burgos-Hernández, Armando

    2016-01-01

    According to the World Health Organization, cancer is the main cause of mortality worldwide; thus, the search of chemopreventive compounds to prevent the disease has become a priority. White shrimp (Litopenaeus vannamei) has been reported as a source of compounds with chemopreventive activities. In this study, shrimp lipids were extracted and then fractionated in order to isolate those compounds responsible for the antimutagenic activity. The antimutagenic activity was assessed by the inhibition of the mutagenic effect of aflatoxin B1 on TA98 and TA100 Salmonella tester strains using the Ames test. Methanolic fraction was responsible for the highest antimutagenic activity (95.6 and 95.9% for TA98 and TA100, resp.) and was further separated into fifteen different subfractions (M1-M15). Fraction M8 exerted the highest inhibition of AFB1 mutation (96.5 and 101.6% for TA98 and TA100, resp.) and, after further fractionation, four subfractions M8a, M8b, M8c, and M8d were obtained. Data from (1)H and (13)C NMR, and mass spectrometry analysis of fraction M8a (the one with the highest antimutagenic activity), suggest that the compound responsible for its antimutagenicity is an apocarotenoid.

  4. Antimutagenic Compounds of White Shrimp (Litopenaeus vannamei): Isolation and Structural Elucidation

    PubMed Central

    López-Saiz, Carmen-María; Hernández, Javier; Cinco-Moroyoqui, Francisco-Javier; Velázquez, Carlos; Ocaño-Higuera, Víctor-Manuel; Plascencia-Jatomea, Maribel; Robles-Sánchez, Maribel; Machi-Lara, Lorena; Burgos-Hernández, Armando

    2016-01-01

    According to the World Health Organization, cancer is the main cause of mortality worldwide; thus, the search of chemopreventive compounds to prevent the disease has become a priority. White shrimp (Litopenaeus vannamei) has been reported as a source of compounds with chemopreventive activities. In this study, shrimp lipids were extracted and then fractionated in order to isolate those compounds responsible for the antimutagenic activity. The antimutagenic activity was assessed by the inhibition of the mutagenic effect of aflatoxin B1 on TA98 and TA100 Salmonella tester strains using the Ames test. Methanolic fraction was responsible for the highest antimutagenic activity (95.6 and 95.9% for TA98 and TA100, resp.) and was further separated into fifteen different subfractions (M1–M15). Fraction M8 exerted the highest inhibition of AFB1 mutation (96.5 and 101.6% for TA98 and TA100, resp.) and, after further fractionation, four subfractions M8a, M8b, M8c, and M8d were obtained. Data from 1H and 13C NMR, and mass spectrometry analysis of fraction M8a (the one with the highest antimutagenic activity), suggest that the compound responsible for its antimutagenicity is an apocarotenoid. PMID:27006678

  5. Antimutagenic Compounds of White Shrimp (Litopenaeus vannamei): Isolation and Structural Elucidation.

    PubMed

    López-Saiz, Carmen-María; Hernández, Javier; Cinco-Moroyoqui, Francisco-Javier; Velázquez, Carlos; Ocaño-Higuera, Víctor-Manuel; Plascencia-Jatomea, Maribel; Robles-Sánchez, Maribel; Machi-Lara, Lorena; Burgos-Hernández, Armando

    2016-01-01

    According to the World Health Organization, cancer is the main cause of mortality worldwide; thus, the search of chemopreventive compounds to prevent the disease has become a priority. White shrimp (Litopenaeus vannamei) has been reported as a source of compounds with chemopreventive activities. In this study, shrimp lipids were extracted and then fractionated in order to isolate those compounds responsible for the antimutagenic activity. The antimutagenic activity was assessed by the inhibition of the mutagenic effect of aflatoxin B1 on TA98 and TA100 Salmonella tester strains using the Ames test. Methanolic fraction was responsible for the highest antimutagenic activity (95.6 and 95.9% for TA98 and TA100, resp.) and was further separated into fifteen different subfractions (M1-M15). Fraction M8 exerted the highest inhibition of AFB1 mutation (96.5 and 101.6% for TA98 and TA100, resp.) and, after further fractionation, four subfractions M8a, M8b, M8c, and M8d were obtained. Data from (1)H and (13)C NMR, and mass spectrometry analysis of fraction M8a (the one with the highest antimutagenic activity), suggest that the compound responsible for its antimutagenicity is an apocarotenoid. PMID:27006678

  6. Isolation and Structural Elucidation of Antiproliferative Compounds of Lipidic Fractions from White Shrimp Muscle (Litopenaeus vannamei)

    PubMed Central

    López-Saiz, Carmen-María; Velázquez, Carlos; Hernández, Javier; Cinco-Moroyoqui, Francisco-Javier; Plascencia-Jatomea, Maribel; Robles-Sánchez, Maribel; Machi-Lara, Lorena; Burgos-Hernández, Armando

    2014-01-01

    Shrimp is one of the most popular seafood items worldwide, and has been reported as a source of chemopreventive compounds. In this study, shrimp lipids were separated by solvent partition and further fractionated by semi-preparative RP-HPLC and finally by open column chromatography in order to obtain isolated antiproliferative compounds. Antiproliferative activity was assessed by inhibition of M12.C3.F6 murine cell growth using the MTT (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide) assay. The methanolic fraction showed the highest antiproliferative activity; this fraction was separated into 15 different sub-fractions (M1–M15). Fractions M8, M9, M10, M12, and M13 were antiproliferative at 100 µg/mL and they were further tested at lower concentrations. Fractions M12 and M13 exerted the highest growth inhibition with an IC50 of 19.5 ± 8.6 and 34.9 ± 7.3 µg/mL, respectively. Fraction M12 was further fractionated in three sub-fractions M12a, M12b, and M12c. Fraction M12a was identified as di-ethyl-hexyl-phthalate, fraction M12b as a triglyceride substituted by at least two fatty acids (predominantly oleic acid accompanied with eicosapentaenoic acid) and fraction M12c as another triglyceride substituted with eicosapentaenoic acid and saturated fatty acids. Bioactive triglyceride contained in M12c exerted the highest antiproliferative activity with an IC50 of 11.33 ± 5.6 µg/mL. Biological activity in shrimp had been previously attributed to astaxanthin; this study demonstrated that polyunsaturated fatty acids are the main compounds responsible for antiproliferative activity. PMID:25526568

  7. Isolation and structural elucidation of antiproliferative compounds of lipidic fractions from white shrimp muscle (Litopenaeus vannamei).

    PubMed

    López-Saiz, Carmen-María; Velázquez, Carlos; Hernández, Javier; Cinco-Moroyoqui, Francisco-Javier; Plascencia-Jatomea, Maribel; Robles-Sánchez, Maribel; Machi-Lara, Lorena; Burgos-Hernández, Armando

    2014-01-01

    Shrimp is one of the most popular seafood items worldwide, and has been reported as a source of chemopreventive compounds. In this study, shrimp lipids were separated by solvent partition and further fractionated by semi-preparative RP-HPLC and finally by open column chromatography in order to obtain isolated antiproliferative compounds. Antiproliferative activity was assessed by inhibition of M12.C3.F6 murine cell growth using the MTT (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide) assay. The methanolic fraction showed the highest antiproliferative activity; this fraction was separated into 15 different sub-fractions (M1-M15). Fractions M8, M9, M10, M12, and M13 were antiproliferative at 100 µg/mL and they were further tested at lower concentrations. Fractions M12 and M13 exerted the highest growth inhibition with an IC50 of 19.5 ± 8.6 and 34.9 ± 7.3 µg/mL, respectively. Fraction M12 was further fractionated in three sub-fractions M12a, M12b, and M12c. Fraction M12a was identified as di-ethyl-hexyl-phthalate, fraction M12b as a triglyceride substituted by at least two fatty acids (predominantly oleic acid accompanied with eicosapentaenoic acid) and fraction M12c as another triglyceride substituted with eicosapentaenoic acid and saturated fatty acids. Bioactive triglyceride contained in M12c exerted the highest antiproliferative activity with an IC50 of 11.33 ± 5.6 µg/mL. Biological activity in shrimp had been previously attributed to astaxanthin; this study demonstrated that polyunsaturated fatty acids are the main compounds responsible for antiproliferative activity. PMID:25526568

  8. Isolation and structural elucidation of a new tadalafil analogue in health supplements: bisprenortadalafil.

    PubMed

    Lee, Ji Hyun; Park, Han Na; Ganganna, Bogonda; Jeong, Ji Hye; Park, Sung-Kwan; Lee, Jongkook; Baek, Sun Young

    2016-06-01

    A new tadalafil analogue was found, along with nortadalafil, using HPLC-DAD during the inspection of a health product sold without official approval. The analogue was separated using a semi-preparative HPLC system and its structure was determined by a combination of mass spectrometry and NMR spectroscopy. The compound was identified as a tadalafil analogue in which the N-methyl group of tadalafil was replaced with a tadalafil precursor moiety. Nuclear Overhauser effect spectroscopy experiments suggested a cis-relationship between the substituents on a piperidine ring in the tadalafil moiety. PMID:27167568

  9. Isolation and structure elucidation of pectic polysaccharide from rose hip fruits (Rosa canina L.).

    PubMed

    Ognyanov, Manol; Remoroza, Connie; Schols, Henk A; Georgiev, Yordan; Kratchanova, Maria; Kratchanov, Christo

    2016-10-20

    A pectic polysaccharide from rose hip (RH) fruits has been obtained by extraction with 1% aqueous citric acid. It was found that the polysaccharide fraction mainly consisted of galacturonic acid (45.5%) next to galactose (5.5%) and arabinose (4.7%). RH pectin is having a relatively high degree of methylesterification (62%) and acetylation (10%) and consists of different molecular weight populations in the range of 10-100kDa. Enzymatic fingerprinting was performed using a combination of pectin lyase (PL) and endo-polygalacturonase. Detailed information about the structure and level of galacturonic acid oligomers released was obtained using LC-HILIC-MS/ELSD and HPAEC. Predominantly, unsaturated and methyl-esterified oligomers (DP 3-5) were released indicating that high proportions of methylesterified 'PL degradable' areas were present within the pectin. The data revealed that homogalacturonan is the main building block of the extracted pectin and consists of long methylesterified/acetylated GalA sequences interspersed with small blocks of non-methyl-esterified GalA units. PMID:27474627

  10. Isolation and structure elucidation of pectic polysaccharide from rose hip fruits (Rosa canina L.).

    PubMed

    Ognyanov, Manol; Remoroza, Connie; Schols, Henk A; Georgiev, Yordan; Kratchanova, Maria; Kratchanov, Christo

    2016-10-20

    A pectic polysaccharide from rose hip (RH) fruits has been obtained by extraction with 1% aqueous citric acid. It was found that the polysaccharide fraction mainly consisted of galacturonic acid (45.5%) next to galactose (5.5%) and arabinose (4.7%). RH pectin is having a relatively high degree of methylesterification (62%) and acetylation (10%) and consists of different molecular weight populations in the range of 10-100kDa. Enzymatic fingerprinting was performed using a combination of pectin lyase (PL) and endo-polygalacturonase. Detailed information about the structure and level of galacturonic acid oligomers released was obtained using LC-HILIC-MS/ELSD and HPAEC. Predominantly, unsaturated and methyl-esterified oligomers (DP 3-5) were released indicating that high proportions of methylesterified 'PL degradable' areas were present within the pectin. The data revealed that homogalacturonan is the main building block of the extracted pectin and consists of long methylesterified/acetylated GalA sequences interspersed with small blocks of non-methyl-esterified GalA units.

  11. Isolation and structure elucidation of avocado seed (Persea americana) lipid derivatives that inhibit Clostridium sporogenes endospore germination.

    PubMed

    Rodríguez-Sánchez, Dariana Graciela; Pacheco, Adriana; García-Cruz, María Isabel; Gutiérrez-Uribe, Janet Alejandra; Benavides-Lozano, Jorge Alejandro; Hernández-Brenes, Carmen

    2013-07-31

    Avocado fruit extracts are known to exhibit antimicrobial properties. However, the effects on bacterial endospores and the identity of antimicrobial compounds have not been fully elucidated. In this study, avocado seed extracts were tested against Clostridium sporogenes vegetative cells and active endospores. Bioassay-guided purification of a crude extract based on inhibitory properties linked antimicrobial action to six lipid derivatives from the family of acetogenin compounds. Two new structures and four compounds known to exist in nature were identified as responsible for the activity. Structurally, most potent molecules shared features of an acetyl moiety and a trans-enone group. All extracts produced inhibition zones on vegetative cells and active endospores. Minimum inhibitory concentrations (MIC) of isolated molecules ranged from 7.8 to 15.6 μg/mL, and bactericidal effects were observed for an enriched fraction at 19.5 μg/mL. Identified molecules showed potential as natural alternatives to additives and antibiotics used by the food and pharmaceutical industries to inhibit Gram-positive spore-forming bacteria. PMID:23829335

  12. Isolation and structure elucidation of avocado seed (Persea americana) lipid derivatives that inhibit Clostridium sporogenes endospore germination.

    PubMed

    Rodríguez-Sánchez, Dariana Graciela; Pacheco, Adriana; García-Cruz, María Isabel; Gutiérrez-Uribe, Janet Alejandra; Benavides-Lozano, Jorge Alejandro; Hernández-Brenes, Carmen

    2013-07-31

    Avocado fruit extracts are known to exhibit antimicrobial properties. However, the effects on bacterial endospores and the identity of antimicrobial compounds have not been fully elucidated. In this study, avocado seed extracts were tested against Clostridium sporogenes vegetative cells and active endospores. Bioassay-guided purification of a crude extract based on inhibitory properties linked antimicrobial action to six lipid derivatives from the family of acetogenin compounds. Two new structures and four compounds known to exist in nature were identified as responsible for the activity. Structurally, most potent molecules shared features of an acetyl moiety and a trans-enone group. All extracts produced inhibition zones on vegetative cells and active endospores. Minimum inhibitory concentrations (MIC) of isolated molecules ranged from 7.8 to 15.6 μg/mL, and bactericidal effects were observed for an enriched fraction at 19.5 μg/mL. Identified molecules showed potential as natural alternatives to additives and antibiotics used by the food and pharmaceutical industries to inhibit Gram-positive spore-forming bacteria.

  13. Isolation and Structure Elucidation of Fujikurins A-D: Products of the PKS19 Gene Cluster in Fusarium fujikuroi.

    PubMed

    von Bargen, Katharina Walburga; Niehaus, Eva-Maria; Krug, Isabel; Bergander, Klaus; Würthwein, Ernst-Ulrich; Tudzynski, Bettina; Humpf, Hans-Ulrich

    2015-08-28

    Fusarium fujikuroi is a member of the Gibberella fujikuroi species complex and well known for the production of gibberellins and mycotoxins including fusarins and fusaric acid. A recent genome sequencing study revealed that the fungus has the genetic potential to produce many more secondary metabolites than have been reported. This paper describes the structure elucidation of the products of the cryptic and silent PKS19 gene cluster that were recently identified (fujikurins A-D). We present the complete NMR data for the structure elucidation of the main compound fujikurin D, which shows tautomeric 1,3-diketo elements. The different tautomeric structures could be confirmed using quantum chemical calculations. Additionally, the structures of the minor compounds fujikurins A-C were elucidated by high-resolution mass spectrometric fragmentation experiments. It emerged that fujikurin A was identical to the bioactive compound CR377 of the taxonomically unclassified Fusarium strain CR377, while fujikurins B-D have not been reported from other fungi.

  14. Lipohexin, a new inhibitor of prolyl endopeptidase from Moeszia lindtneri (HKI-0054) and Paecilomyces sp. (HKI-0055; HKI-0096). I. Screening, isolation and structure elucidation.

    PubMed

    Heinze, S; Ritzau, M; Ihn, W; Hülsmann, H; Schlegel, B; Dornberger, K; Fleck, W F; Zerlin, M; Christner, C; Gräfe, U; Küllertz, G; Fischer, G

    1997-05-01

    Lipohexin was isolated as a novel lipohexapeptide (I) (C39H68N6O9) from three fungal strains, Moeszia lindtneri HKI-0054, Paecilomyces sp. HKI-0055 and Paecilomyces sp. HKI-0096. The structure was elucidated by detailed mass spectrometric and NMR experiments. The proline-containing peptide displays moderate antibacterial activity against Bacillus subtilis ATCC 6633 and inhibits competitively the prolyl endopeptidase from human placenta.

  15. Isolation and structure elucidation of tetrameric procyanidins from unripe apples (Malus pumila cv. Fuji) by NMR spectroscopy.

    PubMed

    Nakashima, Shohei; Oda, Chihiro; Masuda, Susumu; Tagashira, Motoyuki; Kanda, Tomomasa

    2012-11-01

    Procyanidins are plant secondary metabolites widely consumed and known to have various physiological functions, but their bioavailability and mechanism of action are still unclear especially for larger oligomers. One of the reasons is scarce information about the detailed structure of oligomeric procyanidins. As for apple, structures of procyanidin components larger than trimers are scarcely known. In this study, 11 tetrameric procyanidins including two known compounds were isolated from unripe apples (Malus pumila cv. Fuji) and identified by NMR spectroscopic analysis and phloroglucinol degradation. As a result, the detailed structural diversity of tetrameric procyanidins in apple was established.

  16. Isolation, structure elucidation and enzyme inhibition studies of a new hydroxy ester and other compounds from Berberis jaeschkeana Schneid stem.

    PubMed

    Alamzeb, Muhammad; Khan, M Rafiullah; Mamoon-Ur-Rashid; Ali, Saqib; Khan, Ashfaq Ahmad

    2015-01-01

    Bioassay-guided isolation and fractionation of Berberis jaeschkeana Schneid var. jaeschkeana stem resulted in the isolation and characterisation of a new long chain hydroxy ester named as berberinol (1) along with six known compounds (2-7). All the structures were established from 1D and 2D spectroscopic data. Crude extract, sub-fractions and all the isolated compounds were evaluated for their anti-fungal and urease enzyme inhibition properties. All of the sub-fractions and compounds showed good anti-fungal and urease enzyme inhibition properties. Minimum inhibitory concentrations (MICs) were calculated for all active samples in case of urease enzyme inhibition. MICs values were found to be in the range of 39.03-49.78 μg/mL for urease enzyme inhibition.

  17. Crystal Structure Elucidation and Anticancer Studies of (-)-Pseudosemiglabrin: A Flavanone Isolated from the Aerial Parts of Tephrosia apollinea

    PubMed Central

    Ahmed Hassan, Loiy Elsir; Khadeer Ahamed, Mohamed B.; Abdul Majid, Aman Shah; Iqbal, Muhammad Adnan; Al Suede, Fouad Saleih R.; Haque, Rosenani A.; Ismail, Zhari; Ein, Oon Chern; Majid, Amin Malik Shah Abdul

    2014-01-01

    Tephrosia apollinea is a perennial shrublet widely distributed in Africa and is known to have medicinal properties. The current study describes the bio-assay (cytotoxicity) guided isolation of (-)-pseudosemiglabrin from the aerial parts of T. apollinea. The structural and stereochemical features have been described using spectral and x-ray crystallographic techniques. The cytotoxicity of isolated compound was evaluated against nine cancer cell lines. In addition, human fibroblast was used as a model cell line for normal cells. The results showed that (-)-pseudosemiglabrin exhibited dose-dependent antiproliferative effect on most of the tested cancer cell lines. Selectively, the compound showed significant inhibitory effect on the proliferation of leukemia, prostate and breast cancer cell lines. Further studies revealed that, the compound exhibited proapoptotic phenomenon of cytotoxicity. Interestingly, the compound did not display toxicity against the normal human fibroblast. It can be concluded that (-)-pseudosemiglabrin is worthy for further investigation as a potential chemotherapeutic agent. PMID:24608571

  18. Isolation and structure elucidation of new nitrile and mustard oil glycosides from Moringa oleifera and their effect on blood pressure.

    PubMed

    Faizi, S; Siddiqui, B S; Saleem, R; Siddiqui, S; Aftab, K; Gilani, A H

    1994-09-01

    Bioassay-guided analysis of an EtOH extract of Moringa oleifera leaves showing hypotensive activity led to the isolation of two nitrile glycosides, niazirin [1] and niazirinin [2], and three mustard oil glycosides, 4-[(4'-O-acetyl-alpha-L-rhamnosyloxy)benzyl]isothiocyanate [4], niaziminin A, and niaziminin B. Glycoside 2 is a new compound. Niaziminins A and B have previously been obtained from the left extract as a mixture, while compound 4 is new from this source. Structural determination was accomplished by means of spectroscopic methods including appropriate 2D nmr experiments and chemical reactions. This is the first report of the isolation of nitriles, an isothiocyanate, and thiocarbamates from the same plant species. Isothiocyanate 4 and the thiocarbamate glycosides niaziminin A and B showed hypotensive activity while nitrile glycosides 1 and 2 were found to be inactive in this regard. PMID:7798960

  19. [Anthracycline antibiotics from genetically modified streptomycetes. The isolation, spectroscopic structural elucidation and biologic effects of beta-rhodomycin I].

    PubMed

    Ihn, W; Schlegel, B; Fleck, W F; Tresselt, D; Gutsche, W; Sedmera, P; Vokoun, J

    1984-03-01

    By mutagenic treatment and selection procedures the mutant ZIMET 43678 was obtained from a population of the interspecific recombinant Streptomyces violaceus subsp. iremyceticus ZIMET 43615, which showed a changed spectrum of secondary metabolites. The main component isolated from the fermentation broth was a pure anthracycline evidenced by TLC. By means of acid hydrolysis, identification of the degradation products and also by spectroscopic UV/VIS-, IR-, MS-, 1H/13C-NMR- and CD-investigations with intact anthracycline the structure 7-(alpha-L- rhodosaminyl )-beta- rhodomycinon with the absolute configuration 7S, 9R , 10R was found. The anthracycline called beta- rhodomycin -1 (1) exhibits antimicrobial and cytostatic activity in vitro and is also effective on tumour cells in tumour bearing animals. PMID:6427794

  20. Isolation of Montecristin, a Key Metabolite in Biogenesis of Acetogenins from Annona muricata and Its Structure Elucidation by Using Tandem Mass Spectrometry.

    PubMed

    Gleye, C.; Laurens, A.; Hocquemiller, R.; Cavé, A.; Laprévote, O.; Serani, L.

    1997-02-01

    During the course of our continuing search for acetogenins from Annonaceae, a new metabolite, montecristin, possibly involved in the biogenesis of acetogenins, was isolated from the roots of Annona muricata. Its structure was elucidated on the basis of UV, IR, (1)H and (13)C NMR, and mass spectrometry. The identification of the main stuctural features of montecristin (1) was obtained from the NMR spectra whereas their locations on the alkyl chain were evidenced by using mass spectrometry. The attribution of each carbon and location of substituents on the alkyl chain of this fatty acid gamma-lactone was evidenced by using tandem mass spectrometry (MS/MS) and high-energy collisional activation of [M + Li](+) lithium complexes. Finally, the structure determination of montecristin was strengthened by epoxidation and transformation leading to a known adjacent bis-tetrahydrofuran acetogenin.

  1. Nature's Chiral Catalyst and Anti-Malarial Agent: Isolation and Structure Elucidation of Cinchonine and Quinine from "Cinchona calisaya"

    ERIC Educational Resources Information Center

    Carroll, Anne-Marie; Kavanagh, David J.; McGovern, Fiona P.; Reilly, Joe W.; Walsh, John J.

    2012-01-01

    Nature is a well-recognized source of compounds of interest, but access is often an issue. One pertinent example is the cinchona alkaloids from the bark of "Cinchona calisaya." In this experiment, students at the third-year undergraduate level undertake the selective isolation and characterization of two of the four main alkaloids present in the…

  2. Structural elucidation of gemifloxacin mesylate degradation product.

    PubMed

    Paim, Clésio Soldateli; Führ, Fernanda; Martins, Magda Targa; Gnoatto, Simone; Bajerski, Lisiane; Garcia, Cássia Virginia; Steppe, Martin; Schapoval, Elfrides Eva Scherman

    2016-03-01

    Gemifloxacin mesylate (GFM), chemically (R,S)-7-[(4Z)-3-(aminomethyl)-4-(methoxyimino)-1-pyrrolidinyl]-1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-1,8-naphthyridine-3-carboxylic acid methanesulfonate, is a synthetic broad-spectrum antibacterial agent. Although many papers have been published in the literature describing the stability of fluorquinolones, little is known about the degradation products of GFM. Forced degradation studies of GFM were performed using radiation (UV-A), acid (1 mol L(-1) HCl) and alkaline conditions (0.2 mol L(-1) NaOH). The main degradation product, formed under alkaline conditions, was isolated using semi-preparative LC and structurally elucidated by nuclear magnetic resonance (proton - (1) H; carbon - (13) C; correlate spectroscopy - COSY; heteronuclear single quantum coherence - HSQC; heteronuclear multiple-bond correlation - HMBC; spectroscopy - infrared, atomic emission and mass spectrometry techniques). The degradation product isolated was characterized as sodium 7-amino-1-pyrrolidinyl-1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-1,8-naphthyridine-3-carboxylate, which was formed by loss of the 3-(aminomethyl)-4-(methoxyimino)-1-pyrrolidinyl ring and formation of the sodium carboxylate. The structural characterization of the degradation product was very important to understand the degradation mechanism of the GFM under alkaline conditions. In addition, the results highlight the importance of appropriate protection against hydrolysis and UV radiation during the drug-development process, storage, handling and quality control.

  3. Structural elucidation of rabeprazole sodium photodegradation products.

    PubMed

    Garcia, Cássia V; Nudelman, Norma S; Steppe, Martin; Schapoval, Elfrides E S

    2008-01-01

    Rabeprazole sodium is a proton pump inhibitor, used in acid-related disorders, like peptic ulcers and gastroesophageal reflux. It is known to be an acid-labile drug, however, few data about its stability under other factors are available. The aim of this work was to study the photodegradation of rabeprazole, to determine its kinetics and to elucidate the structures of the main degradation products. UVC-254 nm and metal-halide lamps were used. The analysis of the samples was carried out by HPLC. When the drug was in methanol solution, one main degradation product was formed; the degradation rate followed zero-order kinetics. The (1)H and (13)C NMR spectroscopic determinations revealed the product was the benzimidazolone. Another isolated product was identified as benzimidazole. The latter was confirmed against an authentic sample. A third photodegradation product was identified as the [4-(3-methoxy-propoxy)-3-methyl-pyridin-2-yl]methanol, by (1)H and (13)C NMR of the reaction mixture in chloroform-d. When powdered commercial tablets were exposed to UVC irradiation, they showed the same degradation products along with other unidentified, which appeared as traces; the degradation rate was slower than in solution. The intact tablets were stable after 50 days of exposition to the same light source. PMID:17945453

  4. The automation of natural product structure elucidation.

    PubMed

    Steinbeck, C

    2001-05-01

    The last two or three years have seen exciting developments in the field of computer-assisted structure elucidation (CASE) with a number of programs becoming commercially or freely available. This was the conditio sine qua non for CASE to be widely applied in the daily work of bench chemists and spectroscopists. A number of promising applications have been published in the area of structure generators, deterministic and stochastic CASE tools and property predictions, including the automatic distinction between natural products and artificial compounds, as well as the determination of 3-D structure from a connection table based on IR spectroscopy. Advancements in coupling techniques between chromatographic and spectroscopic methods demonstrate progress towards a fully automated structure elucidation or identification process starting at the earliest steps of obtaining crude extracts.

  5. Using Genomics for Natural Product Structure Elucidation.

    PubMed

    Tietz, Jonathan I; Mitchell, Douglas A

    2016-01-01

    Natural products (NPs) are the most historically bountiful source of chemical matter for drug development-especially for anti-infectives. With insights gleaned from genome mining, interest in natural product discovery has been reinvigorated. An essential stage in NP discovery is structural elucidation, which sheds light not only on the chemical composition of a molecule but also its novelty, properties, and derivatization potential. The history of structure elucidation is replete with techniquebased revolutions: combustion analysis, crystallography, UV, IR, MS, and NMR have each provided game-changing advances; the latest such advance is genomics. All natural products have a genetic basis, and the ability to obtain and interpret genomic information for structure elucidation is increasingly available at low cost to non-specialists. In this review, we describe the value of genomics as a structural elucidation technique, especially from the perspective of the natural product chemist approaching an unknown metabolite. Herein we first introduce the databases and programs of interest to the natural products chemist, with an emphasis on those currently most suited for general usability. We describe strategies for linking observed natural product-linked phenotypes to their corresponding gene clusters. We then discuss techniques for extracting structural information from genes, illustrated with numerous case examples. We also provide an analysis of the biases and limitations of the field with recommendations for future development. Our overview is not only aimed at biologically-oriented researchers already at ease with bioinformatic techniques, but also, in particular, at natural product, organic, and/or medicinal chemists not previously familiar with genomic techniques.

  6. A novel isoquinoline alkaloid, DD-carboxypeptidase inhibitor, with antibacterial activity isolated from Streptomyces sp. 8812. Part II: Physicochemical properties and structure elucidation.

    PubMed

    Solecka, Jolanta; Sitkowski, Jerzy; Bocian, Wojciech; Bednarek, Elzbieta; Kawecki, Robert; Kozerski, Lech

    2009-10-01

    A novel antimicrobial agent labeled JS-1, being a member of isoquinoline alkaloids, of molecular formula C10H9NO4 was isolated from the culture broth of Streptomyces sp. 8812. In this study, we present the structure based on physicochemical and spectroscopic NMR investigations and on quantum chemical structure modeling. The structure of a molecule suggests the biosynthetic path starting from 3'-hydroxy tyrosine. The synthesis was undertaken and it resulted in NMR data that fully agree with the presented analysis. PMID:19713991

  7. Dorrigocins: novel antifungal antibiotics that change the morphology of ras-transformed NIH/3T3 cells to that of normal cells. II. Isolation and elucidation of structures.

    PubMed

    Hochlowski, J E; Whittern, D N; Hill, P; McAlpine, J B

    1994-08-01

    Two novel antifungal antibiotics, named dorrigocin A and B have been isolated from the fermentation broth and mycelium of Streptomyces platensis subsp. rosaceus. These closely related compounds were separated from one another by countercurrent chromatography on an Ito coil planet centrifuge. The structures of the dorrigocins were determined by NMR and IR spectroscopy and mass spectrometry. Each is a putative propionate-acetate derived straight chain fatty acid terminating in cycloheximide. The dorrigocins differ from one another only in their oxidation pattern.

  8. Structure Elucidation of Nigricanoside A Through Enantioselective Total Synthesis

    PubMed Central

    Chen, Jie; Koswatta, Panduka; DeBergh, J. Robb; Fu, Peng; Pan, Ende; MacMillan, John B.; Ready, Joseph M.

    2016-01-01

    Nigricanoside A was isolated from green alga, and its dimethyl ester was found to display potent cytotoxicity. Its scarcity prevented a full structure elucidation, leaving total synthesis as the only means to determine its relative and absolute stereochemistry and to explore its biological activity. Here we assign the stereochemistry of the natural product through enantioselective total synthesis and provide initial studies of its cytotoxicity. PMID:26877863

  9. The isolation, total synthesis and structure elucidation of chlorofusin, a natural product inhibitor of the p53-MDM2 protein-protein interaction

    PubMed Central

    Clark, Ryan C.; Lee, Sang Yeul; Searcey, Mark; Boger, Dale L.

    2009-01-01

    Inhibitors of key protein-protein interactions are emerging as exciting therapeutic targets for the treatment of cancer. One such interaction between MDM2 (HDM2) and p53, that silences the tumour suppression activities of p53, was found to be inhibited by the recently isolated natural product chlorofusin. Synthetic studies on this complex natural product summarized herein have served to reassign its chromophore relative stereochemistry, assign its absolute stereochemistry, and provided access to a series of key analogues and partial structures for biological evaluation. PMID:19642417

  10. Isolation, Characterization, Crystal Structure Elucidation of Two Flavanones and Simultaneous RP-HPLC Determination of Five Major Compounds from Syzygium campanulatum Korth.

    PubMed

    Memon, Abdul Hakeem; Ismail, Zhari; Al-Suede, Fouad Saleih Resq; Aisha, Abdalrahim F A; Hamil, Mohammad Shahrul Ridzuan; Saeed, Mohammed Ali Ahmed; Laghari, Madeeha; Majid, Amin Malik Shah Abdul

    2015-08-04

    Two flavanones named (2S)-7-Hydroxy-5-methoxy-6,8-dimethyl flavanone (1), (S)-5,7-dihydroxy-6,8-dimethyl-flavanone (2), along with known chalcone, namely, (E)-2',4'- dihydroxy-6'-methoxy-3',5'-dimethylchalcone (3) and two triterpenoids, namely, betulinic and ursolic acids (4 and 5), were isolated from the leaves of Syzygium campanulatum Korth (Myrtaceae). The structures of compounds (1 and 2) were determined on the basis of UV-visible, FTIR, NMR spectroscopies and LC-EIMS analytical techniques. Furthermore, new, simple, precise, selective, accurate, highly sensitive, efficient and reproducible RP-HPLC method was developed and validated for the quantitative analysis of the compounds (1-5) from S. campanulatum plants of five different age. RP-HPLC method was validated in terms of specificity, linearity (r2 ≤ 0.999), precision (2.0% RSD), and recoveries (94.4%-105%). The LOD and LOQ of these compounds ranged from 0.13-0.38 and 0.10-2.23 μg·mL-1, OPEN ACCESS respectively. Anti-proliferative activity of isolated flavanones (1 and 2) and standardized extract of S. campanulatum was evaluated on human colon cancer (HCT 116) cell line. Compounds (1 and 2) and extract revealed potent and dose-dependent activity with IC50 67.6, 132.9 and 93.4 μg·mL-1, respectively. To the best of our knowledge, this is the first study on isolation, characterization, X-ray crystallographic analysis of compounds (1 and 2) and simultaneous RP-HPLC determination of five major compounds (1-5) from different age of S. campanulatum plants.

  11. Oleanane glycosides from Astragalus tauricolus: isolation and structural elucidation based on a preliminary liquid chromatography-electrospray ionization tandem mass spectrometry profiling.

    PubMed

    Gülcemal, Derya; Masullo, Milena; Napolitano, Assunta; Karayıldırım, Tamer; Bedir, Erdal; Alankuş-Çalışkan, Ozgen; Piacente, Sonia

    2013-02-01

    As a part of our ongoing research for bioactive compounds from Turkish Astragalus species, the investigation of Astragalus tauricolus has been carried out. An approach based on HPLC-ESIMS(n) experiments has been used to profile the triterpene glycosides occurring in the butanol extract of the whole plant. On the basis of the results of the online screening by HPLC-ESIMS(n), 22 oleanane-type triterpene glycosides, including ten compounds never reported before, were isolated, and their structures were established by the extensive use of 1D and 2D-NMR experiments along with ESIMS and HRMS analysis. Noteworthy, cycloartane-type triterpene glycosides, the main constituents of Astragalus spp., were not found. This peculiar feature characterizes a very limited group of Astragalus spp. The antiproliferative activity of the isolated compounds 1-12, 15, 17-19 was evaluated against a small panel of cancer cell lines. Only compound 11 showed an IC(50) of 22 μM against human leukemia cell line (U937). The other tested compounds, in a range of concentrations between 1 and 50 μM, did not cause any significant reduction of the cell number.

  12. Structure Elucidation, Relative LC-MS Response and In Vitro Toxicity of Azaspiracids 7-10 Isolated from Mussels (Mytilus edulis).

    PubMed

    Kilcoyne, Jane; Twiner, Michael J; McCarron, Pearse; Crain, Sheila; Giddings, Sabrina D; Foley, Barry; Rise, Frode; Hess, Philipp; Wilkins, Alistair L; Miles, Christopher O

    2015-05-27

    Azaspiracids (AZAs) are marine biotoxins produced by dinoflagellates that can accumulate in shellfish, which if consumed can lead to poisoning events. AZA7-10, 7-10, were isolated from shellfish and their structures, previously proposed on the basis of only LC-MS/MS data, were confirmed by NMR spectroscopy. Purified AZA4-6, 4-6, and 7-10 were accurately quantitated by qNMR and used to assay cytotoxicity with Jurkat T lymphocyte cells for the first time. LC-MS(MS) molar response studies performed using isocratic and gradient elution in both selected ion monitoring and selected reaction monitoring modes showed that responses for the analogues ranged from 0.3 to 1.2 relative to AZA1, 1. All AZA analogues tested were cytotoxic to Jurkat T lymphocyte cells in a time- and concentration-dependent manner; however, there were distinct differences in their EC50 values, with the potencies for each analogue being: AZA6 > AZA8 > AZA1 > AZA4 ≈ AZA9 > AZA5 ≈ AZA10. This data contributes to the understanding of the structure-activity relationships of AZAs. PMID:25909151

  13. New Isolated-Pentagon-Rule and Skeletally Transformed Isomers of C100 Fullerene Identified by Structure Elucidation of their Chloro Derivatives.

    PubMed

    Wang, Song; Yang, Shangfeng; Kemnitz, Erhard; Troyanov, Sergey I

    2016-03-01

    High-temperature chlorination of C100 fullerene followed by X-ray structure determination of the chloro derivatives enabled the identification of three isomers of C100 from the fullerene soot, specifically numbers 18, 425, and 417, which obey the isolated pentagon rule (IPR). Among them, isomers C1-C100 (425) and C2-C100 (18) afforded C1-C100 (425)Cl22 and C2-C100 (18)Cl28/30 compounds, respectively, which retain their IPR cage connectivities. In contrast, isomer C2v -C100 (417) gives Cs -C100 (417)Cl28 which undergoes a skeletal transformation by the loss of a C2  fragment, resulting in the formation of a nonclassical (NC) C1-C98 (NC)Cl26 with a heptagon in the carbon cage. Most probably, two nonclassical C1-C100 (NC)Cl18/22 chloro derivatives originate from the IPR isomer C1-C100 (382), although both C1-C100 (344) and even nonclassical C1-C100 (NC) can be also considered as the starting isomers. PMID:26848074

  14. Ultrahigh-performance liquid chromatography-ion trap mass spectrometry characterization of the steroidal saponins of Dioscorea panthaica Prain et Burkill and its application for accelerating the isolation and structural elucidation of steroidal saponins.

    PubMed

    Wang, Weihao; Zhao, Ye; Jing, Wenguang; Zhang, Jun; Xiao, Hui; Zha, Qin; Liu, An

    2015-03-01

    Dioscorea panthaica is a traditional Chinese medicinal herb used in the treatment of various physiological conditions, including cardiovascular disease, gastropathy and hypertension. Steroidal saponins (SS) are the main active ingredients of this herb and have effects on myocardial ischemia and cancer. The phytochemical evaluation of SS is both time-consuming and laborious, and the isolation and structural determination steps can be especially demanding. For this reason, the development of new methods to accelerate the processes involved in the identification, isolation and structural elucidation of SS is highly desirable. In this study, a new ultrahigh performance liquid chromatography-ion trap mass spectrometry (UHPLC-IT/MS(n)) method has been developed for the identification of the SS in D. panthaica Prain et Burkill. Notably, the current method can distinguish between spirostanol and furostanol-type compounds based on the fragmentation patterns observed by electrospray ionization-ion trap mass spectrometry (ESI-IT/MS(n)) analysis. UHPLC-IT/MS(n) was used to conduct a detailed investigation of the number, structural class and order of the sugar moieties in the sugar chains of the SS present in D. panthaica. The established fragmentation features were used to analyze the compounds found in the 65% ethanol fraction of the water extracts of D. panthaica. Twenty-three SS were identified, including 11 potential new compounds and six groups of isomers. Two of these newly identified SS were selected as representative examples, and their chemical structures were confirmed by (1)H and (13)C NMR analyses. This newly developed UHPLC-IT/MS(n) method therefore allowed for the efficient identification, isolation and structural determination of the SS in D. panthaica.

  15. Ultrahigh-performance liquid chromatography-ion trap mass spectrometry characterization of the steroidal saponins of Dioscorea panthaica Prain et Burkill and its application for accelerating the isolation and structural elucidation of steroidal saponins.

    PubMed

    Wang, Weihao; Zhao, Ye; Jing, Wenguang; Zhang, Jun; Xiao, Hui; Zha, Qin; Liu, An

    2015-03-01

    Dioscorea panthaica is a traditional Chinese medicinal herb used in the treatment of various physiological conditions, including cardiovascular disease, gastropathy and hypertension. Steroidal saponins (SS) are the main active ingredients of this herb and have effects on myocardial ischemia and cancer. The phytochemical evaluation of SS is both time-consuming and laborious, and the isolation and structural determination steps can be especially demanding. For this reason, the development of new methods to accelerate the processes involved in the identification, isolation and structural elucidation of SS is highly desirable. In this study, a new ultrahigh performance liquid chromatography-ion trap mass spectrometry (UHPLC-IT/MS(n)) method has been developed for the identification of the SS in D. panthaica Prain et Burkill. Notably, the current method can distinguish between spirostanol and furostanol-type compounds based on the fragmentation patterns observed by electrospray ionization-ion trap mass spectrometry (ESI-IT/MS(n)) analysis. UHPLC-IT/MS(n) was used to conduct a detailed investigation of the number, structural class and order of the sugar moieties in the sugar chains of the SS present in D. panthaica. The established fragmentation features were used to analyze the compounds found in the 65% ethanol fraction of the water extracts of D. panthaica. Twenty-three SS were identified, including 11 potential new compounds and six groups of isomers. Two of these newly identified SS were selected as representative examples, and their chemical structures were confirmed by (1)H and (13)C NMR analyses. This newly developed UHPLC-IT/MS(n) method therefore allowed for the efficient identification, isolation and structural determination of the SS in D. panthaica. PMID:25575790

  16. Epimers of azaspiracids: Isolation, structural elucidation, relative LC-MS response, and in vitro toxicity of 37-epi-azaspiracid-1.

    PubMed

    Kilcoyne, Jane; McCarron, Pearse; Twiner, Michael J; Nulty, Ciara; Crain, Sheila; Quilliam, Michael A; Rise, Frode; Wilkins, Alistair L; Miles, Christopher O

    2014-04-21

    Since azaspiracid-1 (AZA1) was identified in 1998, the number of AZA analogues has increased to over 30. The development of an LC-MS method using a neutral mobile phase led to the discovery of isomers of AZA1, AZA2, and AZA3, present at ~2-16% of the parent analogues in phytoplankton and shellfish samples. Under acidic mobile phase conditions, isomers and their parents are not separated. Stability studies showed that these isomers were spontaneous epimerization products whose formation is accelerated with the application of heat. The AZA1 isomer was isolated from contaminated shellfish and identified as 37-epi-AZA1 by nuclear magnetic resonance (NMR) spectroscopy and chemical analyses. Similar analysis indicated that the isomers of AZA2 and AZA3 corresponded to 37-epi-AZA2 and 37-epi-AZA3, respectively. The 37-epimers were found to exist in equilibrium with the parent compounds in solution. 37-epi-AZA1 was quantitated by NMR, and relative molar response studies were performed to determine the potential differences in LC-MS response of AZA1 and 37-epi-AZA1. Toxicological effects were determined using Jurkat T lymphocyte cells as an in vitro cell model. Cytotoxicity experiments employing a metabolically based dye (i.e., MTS) indicated that 37-epi-AZA1 elicited a lethal response that was both concentration- and time-dependent, with EC50 values in the subnanomolar range. On the basis of EC50 comparisons, 37-epi-AZA1 was 5.1-fold more potent than AZA1. This data suggests that the presence of these epimers in seafood products should be considered in the analysis of AZAs for regulatory purposes.

  17. Isolation and Structural Elucidation of Brevibacillin, an Antimicrobial Lipopeptide from Brevibacillus laterosporus That Combats Drug-Resistant Gram-Positive Bacteria

    PubMed Central

    Yang, Xu; Yuan, Chunhua; Zhang, Liwen

    2016-01-01

    A new environmental bacterial strain exhibited strong antimicrobial characteristics against methicillin-resistant Staphylococcus aureus, vancomycin-resistant strains of Enterococcus faecalis and Lactobacillus plantarum, and other Gram-positive bacteria. The producer strain, designated OSY-I1, was determined to be Brevibacillus laterosporus via morphological, biochemical, and genetic analyses. The antimicrobial agent was extracted from cells of OSY-I1 with isopropanol, purified by high-performance liquid chromatography, and structurally analyzed using mass spectrometry (MS) and nuclear magnetic resonance (NMR). The MS and NMR results, taken together, uncovered a linear lipopeptide consisting of 13 amino acids and an N-terminal C6 fatty acid (FA) chain, 2-hydroxy-3-methylpentanoic acid. The lipopeptide (FA-Dhb-Leu-Orn-Ile-Ile-Val-Lys-Val-Val-Lys-Tyr-Leu-valinol, where Dhb is α,β-didehydrobutyric acid and valinol is 2-amino-3-methyl-1-butanol) has a molecular mass of 1,583.0794 Da and contains three modified amino acid residues: α,β-didehydrobutyric acid, ornithine, and valinol. The compound, designated brevibacillin, was determined to be a member of a cationic lipopeptide antibiotic family. In addition to its potency against drug-resistant bacteria, brevibacillin also exhibited low MICs (1 to 8 μg/ml) against selected foodborne pathogenic and spoilage bacteria, such as Listeria monocytogenes, Bacillus cereus, and Alicyclobacillus acidoterrestris. Purified brevibacillin showed no sign of degradation when it was held at 80°C for 60 min, and it retained at least 50% of its antimicrobial activity when it was held for 22 h under acidic or alkaline conditions. On the basis of these findings, brevibacillin is a potent antimicrobial lipopeptide which is potentially useful to combat drug-resistant bacterial pathogens and foodborne pathogenic and spoilage bacteria. PMID:26921428

  18. Isolation and Structural Elucidation of Brevibacillin, an Antimicrobial Lipopeptide from Brevibacillus laterosporus That Combats Drug-Resistant Gram-Positive Bacteria.

    PubMed

    Yang, Xu; Huang, En; Yuan, Chunhua; Zhang, Liwen; Yousef, Ahmed E

    2016-05-01

    A new environmental bacterial strain exhibited strong antimicrobial characteristics against methicillin-resistant Staphylococcus aureus, vancomycin-resistant strains of Enterococcus faecalis and Lactobacillus plantarum, and other Gram-positive bacteria. The producer strain, designated OSY-I1, was determined to be Brevibacillus laterosporusvia morphological, biochemical, and genetic analyses. The antimicrobial agent was extracted from cells of OSY-I1 with isopropanol, purified by high-performance liquid chromatography, and structurally analyzed using mass spectrometry (MS) and nuclear magnetic resonance (NMR). The MS and NMR results, taken together, uncovered a linear lipopeptide consisting of 13 amino acids and an N-terminal C6 fatty acid (FA) chain, 2-hydroxy-3-methylpentanoic acid. The lipopeptide (FA-Dhb-Leu-Orn-Ile-Ile-Val-Lys-Val-Val-Lys-Tyr-Leu-valinol, where Dhb is α,β-didehydrobutyric acid and valinol is 2-amino-3-methyl-1-butanol) has a molecular mass of 1,583.0794 Da and contains three modified amino acid residues: α,β-didehydrobutyric acid, ornithine, and valinol. The compound, designated brevibacillin, was determined to be a member of a cationic lipopeptide antibiotic family. In addition to its potency against drug-resistant bacteria, brevibacillin also exhibited low MICs (1 to 8 μg/ml) against selected foodborne pathogenic and spoilage bacteria, such as Listeria monocytogenes,Bacillus cereus, and Alicyclobacillus acidoterrestris Purified brevibacillin showed no sign of degradation when it was held at 80 °C for 60 min, and it retained at least 50% of its antimicrobial activity when it was held for 22 h under acidic or alkaline conditions. On the basis of these findings, brevibacillin is a potent antimicrobial lipopeptide which is potentially useful to combat drug-resistant bacterial pathogens and foodborne pathogenic and spoilage bacteria. PMID:26921428

  19. Transcription initiation complex structures elucidate DNA opening.

    PubMed

    Plaschka, C; Hantsche, M; Dienemann, C; Burzinski, C; Plitzko, J; Cramer, P

    2016-05-19

    Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.

  20. NMR spectroscopy: structure elucidation of cycloelatanene A: a natural product case study.

    PubMed

    Urban, Sylvia; Dias, Daniel Anthony

    2013-01-01

    The structure elucidation of new secondary metabolites derived from marine and terrestrial sources is frequently a challenging task. The hurdles include the ability to isolate stable secondary metabolites of sufficient purity that are often present in <0.5 % of the dry weight of the sample. This usually involves a minimum of several chromatographic purification steps. The second issue is the stability of the compound isolated. It must always be assumed when dealing with the isolation of natural products that the compound may rapidly degrade during and/or after the isolation, due to sensitivity to light, air oxidation, and/or temperature. In this way, precautions need to be taken, as much as possible to avoid any such chemical inter-conversions and/or degradations. Immediately after purification, the next step is to rapidly acquire all analytical spectroscopic data in order to complete the characterization of the isolated secondary metabolite(s), prior to any possible decomposition. The final hurdle in this multiple step process, especially in the acquisition of the NMR spectroscopic and other analytical data (mass spectra, infrared and ultra-violet spectra, optical rotation, etc.), is to assemble the structural moieties/units in an effort to complete the structure elucidation. Often ambiguity with the elucidation of the final structure remains when structural fragments identified are difficult to piece together on the basis of the HMBC NMR correlations or when the relative configuration cannot be unequivocally identified on the basis of NOE NMR enhancements observed. Herein, we describe the methodology used to carry out the structure elucidation of a new C16 chamigrene, cycloelatanene A (5) which was isolated from the southern Australian marine alga Laurencia elata (Rhodomelaceae). The general approach and principles used in the structure determination of this compound can be applied to the structure elucidation of other small molecular weight compounds derived

  1. Elucidating the stop bands of structurally colored systems through recursion

    NASA Astrophysics Data System (ADS)

    Amir, Ariel; Vukusic, Peter

    2013-04-01

    Interference is the source of some of the spectacular colors of animals and plants in nature. In some of these systems, the physical structure consists of an ordered array of layers with alternating high and low refractive indices. This periodicity leads to an optical band structure that is analogous to the electronic band structure encountered in semiconductor physics: specific bands of wavelengths (the stop bands) are perfectly reflected. Here, we present a minimal model for optical band structure in a periodic multilayer structure and solve it using recursion relations. The stop bands emerge in the limit of an infinite number of layers by finding the fixed point of the recursion. We compare to experimental data for various beetles, whose optical structure resembles the proposed model. Thus, using only the phenomenon of interference and the idea of recursion, we are able to elucidate the concept of band structure in the context of the experimentally observed high reflectance and iridescent appearance of structurally colored beetles.

  2. Toward structural elucidation of the gamma-secretase complex

    SciTech Connect

    Li, H.; Wolfe, M. S.; Selkoe, D. J.

    2009-03-11

    {gamma}-Secretase is an intramembrane protease complex that mediates the Notch signaling pathway and the production of amyloid {beta}-proteins. As such, this enzyme has emerged as an important target for development of novel therapeutics for Alzheimer disease and cancer. Great progress has been made in the identification and characterization of the membrane complex and its biological functions. One major challenge now is to illuminate the structure of this fascinating and important protease at atomic resolution. Here, we review recent progress on biochemical and biophysical probing of the structure of the four-component complex and discuss obstacles and potential pathways toward elucidating its detailed structure.

  3. Structure elucidation and antioxidant activity of the phenolic compounds from Rhynchosia suaveolens.

    PubMed

    Rammohan, Aluru; Gunasekar, Duvvuru; Reddy, Netala Vasudeva; Vijaya, Tartte; Devillee, Alexandre; Bodo, Bernard

    2015-04-01

    A new benzophenone, 2-hydroxy-3,4-dimethoxybenzophenone (1), together with a known C-glycosylxanthone, mangiferin (2) and two known C-glycosylflavones, isovitexin (3) and isoorientin (4), were isolated from the flowers of Rhynchosia suaveolens DC. (Fabaceae). The structure of the new compound (1) and the known compounds (2-4) were elucidated by extensive 1D and 2D NMR spectral studies. The plant extracts, as well as the isolated compounds, were evaluated for their total phenolic content (TPC), total flavonoid content (TFC) and DPPH radical scavenging activity. Among the isolated compounds, mangiferin (2) and isoorientin (4) showed significant radical scavenging activity comparable with that of ascorbic acid.

  4. Advances in structure elucidation of small molecules using mass spectrometry

    PubMed Central

    Fiehn, Oliver

    2010-01-01

    The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. Electronic supplementary material The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users. PMID:21289855

  5. X-ray structure of dopamine transporter elucidates antidepressant mechanism.

    PubMed

    Penmatsa, Aravind; Wang, Kevin H; Gouaux, Eric

    2013-11-01

    Antidepressants targeting Na(+)/Cl(-)-coupled neurotransmitter uptake define a key therapeutic strategy to treat clinical depression and neuropathic pain. However, identifying the molecular interactions that underlie the pharmacological activity of these transport inhibitors, and thus the mechanism by which the inhibitors lead to increased synaptic neurotransmitter levels, has proven elusive. Here we present the crystal structure of the Drosophila melanogaster dopamine transporter at 3.0 Å resolution bound to the tricyclic antidepressant nortriptyline. The transporter is locked in an outward-open conformation with nortriptyline wedged between transmembrane helices 1, 3, 6 and 8, blocking the transporter from binding substrate and from isomerizing to an inward-facing conformation. Although the overall structure of the dopamine transporter is similar to that of its prokaryotic relative LeuT, there are multiple distinctions, including a kink in transmembrane helix 12 halfway across the membrane bilayer, a latch-like carboxy-terminal helix that caps the cytoplasmic gate, and a cholesterol molecule wedged within a groove formed by transmembrane helices 1a, 5 and 7. Taken together, the dopamine transporter structure reveals the molecular basis for antidepressant action on sodium-coupled neurotransmitter symporters and elucidates critical elements of eukaryotic transporter structure and modulation by lipids, thus expanding our understanding of the mechanism and regulation of neurotransmitter uptake at chemical synapses.

  6. X-ray structure of dopamine transporter elucidates antidepressant mechanism.

    PubMed

    Penmatsa, Aravind; Wang, Kevin H; Gouaux, Eric

    2013-11-01

    Antidepressants targeting Na(+)/Cl(-)-coupled neurotransmitter uptake define a key therapeutic strategy to treat clinical depression and neuropathic pain. However, identifying the molecular interactions that underlie the pharmacological activity of these transport inhibitors, and thus the mechanism by which the inhibitors lead to increased synaptic neurotransmitter levels, has proven elusive. Here we present the crystal structure of the Drosophila melanogaster dopamine transporter at 3.0 Å resolution bound to the tricyclic antidepressant nortriptyline. The transporter is locked in an outward-open conformation with nortriptyline wedged between transmembrane helices 1, 3, 6 and 8, blocking the transporter from binding substrate and from isomerizing to an inward-facing conformation. Although the overall structure of the dopamine transporter is similar to that of its prokaryotic relative LeuT, there are multiple distinctions, including a kink in transmembrane helix 12 halfway across the membrane bilayer, a latch-like carboxy-terminal helix that caps the cytoplasmic gate, and a cholesterol molecule wedged within a groove formed by transmembrane helices 1a, 5 and 7. Taken together, the dopamine transporter structure reveals the molecular basis for antidepressant action on sodium-coupled neurotransmitter symporters and elucidates critical elements of eukaryotic transporter structure and modulation by lipids, thus expanding our understanding of the mechanism and regulation of neurotransmitter uptake at chemical synapses. PMID:24037379

  7. Synthesis and structural elucidation of a novel polymorph of alcaftadine

    NASA Astrophysics Data System (ADS)

    Pansuriya, Pramod B.; Maguire, Glenn E. M.; Friedrich, Holger B.

    2015-05-01

    In this study, we have synthesized and elucidated the structure of the H1 histamine antagonist, 2-(1-methylpiperidin-4-ylidene)-4,7-diazatricyclo[8.4.0.0(3,7)]tetradeca-1(14),3,5,10,12-pentaene-6-carbaldehyde in the solution and solid-state. We have also studied the thermal dilapidation of the compound. Solution structure analysis was achieved by employing NMR spectroscopy including 2D experiments NOESY, HSQC and HMBC, while solid state investigations were undertaken using SXRD, PXRD, TGA, DSC, and IR spectroscopy. For the first time the single crystal structure of alcaftadine has now been solved. Crystallographic data are as follows: monoclinic, Cc, a = 11.5694(6) Å, b = 14.5864(6) Å, c = 10.2688(4) Å, α = 90°, β = 111.793(3)°, γ = 90°, V = 1609.07(13) Å3, Z = 4. The Hirshfeld surface analyses also have been performed using the crystal structure.

  8. Elucidation of operon structures across closely related bacterial genomes.

    PubMed

    Zhou, Chuan; Ma, Qin; Li, Guojun

    2014-01-01

    About half of the protein-coding genes in prokaryotic genomes are organized into operons to facilitate co-regulation during transcription. With the evolution of genomes, operon structures are undergoing changes which could coordinate diverse gene expression patterns in response to various stimuli during the life cycle of a bacterial cell. Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes. In the constructed graph, each node represents one orthologous gene group (OGG) and a pair of nodes will be connected if any two genes, from the corresponding two OGGs respectively, are located in the same operon as immediate neighbors in any of the considered genomes. Through identifying the connected components in the above graph, we found that genes in a connected component are likely to be functionally related and these identified components tend to form treelike topology, such as paths and stars, corresponding to different biological mechanisms in transcriptional regulation as follows. Specifically, (i) a path-structure component integrates genes encoding a protein complex, such as ribosome; and (ii) a star-structure component not only groups related genes together, but also reflects the key functional roles of the central node of this component, such as the ABC transporter with a transporter permease and substrate-binding proteins surrounding it. Most interestingly, the genes from organisms with highly diverse living environments, i.e., biomass degraders and animal pathogens of clostridia in our study, can be clearly classified into different topological groups on some connected components.

  9. Elucidation of operon structures across closely related bacterial genomes.

    PubMed

    Zhou, Chuan; Ma, Qin; Li, Guojun

    2014-01-01

    About half of the protein-coding genes in prokaryotic genomes are organized into operons to facilitate co-regulation during transcription. With the evolution of genomes, operon structures are undergoing changes which could coordinate diverse gene expression patterns in response to various stimuli during the life cycle of a bacterial cell. Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes. In the constructed graph, each node represents one orthologous gene group (OGG) and a pair of nodes will be connected if any two genes, from the corresponding two OGGs respectively, are located in the same operon as immediate neighbors in any of the considered genomes. Through identifying the connected components in the above graph, we found that genes in a connected component are likely to be functionally related and these identified components tend to form treelike topology, such as paths and stars, corresponding to different biological mechanisms in transcriptional regulation as follows. Specifically, (i) a path-structure component integrates genes encoding a protein complex, such as ribosome; and (ii) a star-structure component not only groups related genes together, but also reflects the key functional roles of the central node of this component, such as the ABC transporter with a transporter permease and substrate-binding proteins surrounding it. Most interestingly, the genes from organisms with highly diverse living environments, i.e., biomass degraders and animal pathogens of clostridia in our study, can be clearly classified into different topological groups on some connected components. PMID:24959722

  10. Computer-assisted methods for molecular structure elucidation: realizing a spectroscopist's dream

    PubMed Central

    2009-01-01

    Background This article coincides with the 40 year anniversary of the first published works devoted to the creation of algorithms for computer-aided structure elucidation (CASE). The general principles on which CASE methods are based will be reviewed and the present state of the art in this field will be described using, as an example, the expert system Structure Elucidator. Results The developers of CASE systems have been forced to overcome many obstacles hindering the development of a software application capable of drastically reducing the time and effort required to determine the structures of newly isolated organic compounds. Large complex molecules of up to 100 or more skeletal atoms with topological peculiarity can be quickly identified using the expert system Structure Elucidator based on spectral data. Logical analysis of 2D NMR data frequently allows for the detection of the presence of COSY and HMBC correlations of "nonstandard" length. Fuzzy structure generation provides a possibility to obtain the correct solution even in those cases when an unknown number of nonstandard correlations of unknown length are present in the spectra. The relative stereochemistry of big rigid molecules containing many stereocenters can be determined using the StrucEluc system and NOESY/ROESY 2D NMR data for this purpose. Conclusion The StrucEluc system continues to be developed in order to expand the general applicability, provide improved workflows, usability of the system and increased reliability of the results. It is expected that expert systems similar to that described in this paper will receive increasing acceptance in the next decade and will ultimately be integrated directly to analytical instruments for the purpose of organic analysis. Work in this direction is in progress. In spite of the fact that many difficulties have already been overcome to deliver on the spectroscopist's dream of "fully automated structure elucidation" there is still work to do. Nevertheless

  11. Identification and structural elucidation of ozonation transformation products of estrone

    PubMed Central

    2013-01-01

    Background Quantitative methods for the analysis of contaminants of emerging concern (CECs) are abundant in the scientific literature. However, there are few reports on systematic methods of identification and structural identification of transformation products. For this reason, a new method based on high-resolution mass spectrometry and differential analysis was developed in order to facilitate and accelerate the process of identification and structural elucidation of transformation products CECs. This method was applied to the study of ozonation transformation products (OTPs) of the natural hormone estrone (E1). Results A control compare trend experiment consisting in the comparison of a control sample to several samples having been exposed to decreasing concentrations of O3(aq) indicated that 593 peaks could be associated with OTPs. After applying various filters to remove background noise, sample contaminants and signal spikes, this data set was reduced to 16 candidate peaks. By inspection of the shape of these peaks, only two compounds OTP-276 (m/z 275.12930) and OTP-318 (m/z 317.14008) were considered as good candidates for further study. Multi-stage tandem mass spectrometry (MSn) experiments of SPE extracts of the ozonated samples of E1 and of a deuterium-labeled analogue (E1-d4) showed that OTP-276 and OTP-318 had carboxylic acid and hydroxyl functional groups, as previously reported for OTPs of other hormones. Structures for these two compounds were proposed based on their MSn spectra. Conclusion These results indicate that the method proposed is a systematic and rapid approach to study transformation products of CECs. PMID:23618537

  12. Pyripyropenes, novel ACAT inhibitors produced by Aspergillus fumigatus. IV. Structure elucidation of pyripyropenes M to R.

    PubMed

    Tomoda, H; Tabata, N; Yang, D J; Namatame, I; Tanaka, H; Omura, S; Kaneko, T

    1996-03-01

    Six new pyripyropenes, M to R, were isolated from the ethyl acetate extracts of the jar fermentation broth of Aspergillus fumigatus FO-1289-2501. Structural elucidation indicated that all the pyripyropenes have the same pyridino-alpha-pyrone sesquiterpene core as pyripyropenes A to L. Among them pyripyropene M showed the most potent inhibition against acyl-CoA : cholesterol acyltransferase activity with an IC50 value of 3.80 microM in rat liver microsomes, but pyripyropenes N to R showed moderate inhibitory activity (IC50 11.0 approximately 78.0 microM). PMID:8626247

  13. Pyripyropenes, Novel ACAT inhibitors produced by Aspergillus fumigatus. III. Structure elucidation of pyripyropenes E to L.

    PubMed

    Tomoda, H; Tabata, N; Yang, D J; Takayanagi, H; Nishida, H; Omura, S; Kaneko, T

    1995-06-01

    Eight new pyripyropenes, E to L, were isolated from the culture broth of Aspergillus fumigatus FO-1289-2501 selected as a higher producer by NTG mutation. Structural elucidation indicated that all the pyripyropenes have the same pyridino-alpha-pyrone sesquiterpene core as pyripyropenes A to D. Among them, pyripyropene L showed the most potent inhibition against acyl-CoA: cholesterol acyltransferase (ACAT) activity with an IC50 value of 0.27 microM in rat liver microsomes. PMID:7622436

  14. Separation and structural elucidation of a new tadalafil analogue diethylaminopretadalafil included as an adulterant in a dietary supplement.

    PubMed

    Zhang, Gaofei; Yu, Yue; Wu, Xiaoou; Li, Jun

    2014-06-01

    A new tadalafil analogue was detected and isolated from a dietary supplement, the structure was elucidated by means of nuclear magnetic resonance (NMR) and mass spectroscopy. The compound was determined to be diethylaminopretadalafil, which might be derived from a precursor in the synthesis of tadalafil. PMID:24631840

  15. Structure elucidation of three diphenyl ether derivatives from the mangrove endophytic fungus SBE-14 from the South China Sea.

    PubMed

    Liu, Fan; Li, Qing; Yang, Hong; Cai, Xiao-Ling; Xia, Xue-Kui; Chen, Sheng-Ping; Li, Meng-Feng; She, Zhi-Gang; Lin, Yong-Cheng

    2009-05-01

    Two new natural products, tenelate A (1) and B (2), together with the known compound, tenellic acid C (3), were isolated from the mangrove endophytic fungus Talaromyces sp. (SBE-14), from the South China Sea. Their structures were elucidated by spectroscopic methods, mainly 1D and 2D NMR techniques.

  16. Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques

    NASA Astrophysics Data System (ADS)

    Topcu, Gulacti; Ulubelen, Ayhan

    2007-05-01

    In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.

  17. Structural elucidation of humulone autoxidation products and analysis of their occurrence in stored hops.

    PubMed

    Taniguchi, Yoshimasa; Taniguchi, Harumi; Matsukura, Yasuko; Kawachi, Yasuji; Shindo, Kazutoshi

    2014-06-27

    The transformation of α-acids [in hops (Humulus lupulus L.)] to iso-α-acids (in beer) during the brewing process is well known, but the occurrence and structure of the oxidized α-acids during hop storage are not well documented. Because an understanding of these oxidized compounds is essential to optimize the effects of oxidized hops on the quality of beer, we investigated the autoxidation products of humulone (a representative congener of α-acids) using a simplified autoxidation model. Among the oxidation products, tricyclooxyisohumulones A (1) and B (2), tricycloperoxyisohumulone A (3), deisopropyltricycloisohumulone (4), and the hemiacetal 5 of tricycloperoxyhumulone A (5') were isolated, and their structures were elucidated for the first time. The occurrence of compounds 1-4 in stored hops was verified using LC/MS/MS analysis. We also monitored the levels of compounds 1-4 during hop storage using LC/MS/MS analysis. PMID:24875004

  18. Structure Elucidation and Immunomodulatory Activity of A Beta Glucan from the Fruiting Bodies of Ganoderma sinense

    PubMed Central

    Yue, Rui-Qi; Dong, Cai-Xia; Chan, Chung-Lap; Ko, Chun-Hay; Cheung, Wing-Shing; Luo, Ke-Wang; Dai, Hui; Wong, Chun-Kwok; Leung, Ping-Chung; Han, Quan-Bin

    2014-01-01

    A polysaccharide named GSP-2 with a molecular size of 32 kDa was isolated from the fruiting bodies of Ganoderma sinense. Its structure was well elucidated, by a combined utilization of chemical and spectroscopic techniques, to be a β-glucan with a backbone of (1→4)– and (1→6)–Glcp, bearing terminal- and (1→3)–Glcp side-chains at O-3 position of (1→6)–Glcp. Immunological assay exhibited that GSP-2 significantly induced the proliferation of BALB/c mice splenocytes with target on only B cells, and enhanced the production of several cytokines in human peripheral blood mononuclear cells and derived dendritic cells. Besides, the fluorescent labeled GSP-2 was phagocytosed by the RAW 264.7 cells and induced the nitric oxide secretion from the cells. PMID:25014571

  19. Protein structure elucidation from minimal NMR data: the CLOUDS approach.

    PubMed

    Grishaev, Alexander; Llinás, Miguel

    2005-01-01

    In this chapter we review automated methods of protein NMR data analysis and expand on the assignment-independent CLOUDS approach. As presented, given a set of reliable NOEs it is feasible to derive a spatial H-atom distribution that provides a low-resolution image of the protein structure. In order to generate such a list of unambiguous NOEs, a probabilistic assessment of the NOE identities (in terms of frequency-labeled H-atom sources) was developed on the basis of Bayesian inference. The methodology, encompassing programs SPI and BACUS, provides a list of "clean" NOEs that does not hinge on prior knowledge of sequence-specific resonance assignments or a preliminary structural model. As such, the combined SPI/BACUS approach, intrinsically adaptable to include 13C- and/or 15N-edited experiments, affords a useful tool for the analysis of NMR data irrespective of whether the adopted structure calculation protocol is assignment-dependent.

  20. Optimization techniques in molecular structure and function elucidation.

    PubMed

    Sahinidis, Nikolaos V

    2009-12-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly via combinatorial optimization algorithms that are applied to discrete approximations. The main purpose of the paper is to offer an introduction and motivate further systems approaches to these problems. PMID:20160866

  1. Structure elucidation and DNA binding specificity of natural compounds from Cassia siamea leaves: A biophysical approach.

    PubMed

    Parveen, Mehtab; Ahmad, Faheem; Malla, Ali Mohammed; Khan, Mohd Sohrab; Rehman, Sayeed Ur; Tabish, Mohammad; Silva, Manuela Ramos; Silva, P S Pereira

    2016-06-01

    A novel isoflavone, 5,6,7-trimethoxy-3-(3',4',5'-trimethoxyphenyl)-4H-chromen-4-one (1) along with a known pyranocoumarin, Seselin (2) have been isolated from the ethanolic extract of the leaves of Cassia siamea (Family: Fabaceae). Compound 1 has been reported for the first time from any natural source and has not been synthesized so far. Their structures were elucidated on the basis of chemical and physical evidences viz. elemental analysis, UV, FT-IR, (1)H-NMR, (13)C-NMR and mass spectral analysis. Structure of compound (1) was further authenticated by single-crystal X-ray analysis and density functional theory (DFT) calculations. A multi-technique approach employing UV-Visible spectroscopy, fluorescence, KI quenching studies, competitive displacement assay, circular dichroism and viscosity studies have been utilized to probe the extent of interaction and possible binding modes of isolated compounds (1-2) with calf thymus DNA (CT-DNA). Both the compounds were found to interact with DNA via non-intercalative binding mode with moderate proficiencies. Groove binding was the major interaction mode in the case of compound 2 while compound 1 probably interacts with DNA through electrostatic interactions. These studies provide deeper insight in understanding of DNA-drug (natural products) interaction which could be helpful to improve their bioavailability for therapeutic purposes. PMID:27085054

  2. Atomic structure of anthrax protective antigen pore elucidates toxin translocation.

    PubMed

    Jiang, Jiansen; Pentelute, Bradley L; Collier, R John; Zhou, Z Hong

    2015-05-28

    Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (Φ)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed.

  3. Atomic structure of anthrax PA pore elucidates toxin translocation

    PubMed Central

    Jiang, Jiansen; Pentelute, Bradley L.; Collier, R. John; Zhou, Z. Hong

    2015-01-01

    Summary Anthrax toxin, comprising protective antigen (PA), lethal factor (LF) and edema factor (EF), is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in human and animals. PA forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes LF and EF into the cytosol of target cells1. PA is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. Based on biochemical and electrophysiological results, researchers have proposed that a Φ-clamp composed of Phe427 residues of PA catalyzes protein translocation via a charge-state dependent Brownian ratchet2–9. Although atomic structures of PA prepores are available10–14, how PA senses low pH, converts to active pore and translocates LF and EF are not well defined without an atomic model of the PA pore. Here, by cryo electron microscopy (cryoEM) with direct electron counting, we have determined the PA pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low-pH is sensed and the membrane-spanning channel is formed. PMID:25778700

  4. Compositional analysis and structural elucidation of glycosaminoglycans in chicken eggs

    PubMed Central

    Liu, Zhangguo; Zhang, Fuming; Li, Lingyun; Li, Guoyun; He, Wenqing; Linhardt, Robert J.

    2014-01-01

    Glycosaminoglycans (GAGs) have numerous applications in the fields of pharmaceuticals, cosmetics, nutraceuticals, and foods. GAGs are also critically important in the developmental biology of all multicellular animals. GAGs were isolated from chicken egg components including yolk, thick egg white, thin egg white, membrane, calcified shell matrix supernatant, and shell matrix deposit. Disaccharide compositional analysis was performed using ultra high-performance liquid chromatography-mass spectrometry. The results of these analyses showed that all four families of GAGs were detected in all egg components. Keratan sulfate was found in egg whites (thick and thin) and shell matrix (calcified shell matrix supernatant and deposit) with high level. Chondroitin sulfates were much more plentiful in both shell matrix components and membrane. Hyaluronan was plentiful in both shell matrix components and membrane, but were only present in a trace of quantities in the yolk. Heparan sulfate was plentiful in the shell matrix deposit but was present in a trace of quantities in the egg content components (yolk, thick and thin egg whites). Most of the chondroitin and heparan sulfate disaccharides were present in the GAGs found in chicken eggs with the exception of chondroitin and heparan sulfate 2,6-disulfated disaccharides. Both CS and HS in the shell matrix deposit contained the most diverse chondroitin and heparan sulfate disaccharide compositions. Eggs might provide a potential new source of GAGs. PMID:25218438

  5. Fatty Acid Biosynthesis Revisited: Structure Elucidation and Metabolic Engineering

    PubMed Central

    Beld, Joris; Lee, D. John

    2014-01-01

    Fatty acids are primary metabolites synthesized by complex, elegant, and essential biosynthetic machinery. Fatty acid synthases resemble an iterative assembly line, with an acyl carrier protein conveying the growing fatty acid to necessary enzymatic domains for modification. Each catalytic domain is a unique enzyme spanning a wide range of folds and structures. Although they harbor the same enzymatic activities, two different types of fatty acid synthase architectures are observed in nature. During recent years, strained petroleum supplies have driven interest in engineering organisms to either produce more fatty acids or specific high value products. Such efforts require a fundamental understanding of the enzymatic activities and regulation of fatty acid synthases. Despite more than one hundred years of research, we continue to learn new lessons about fatty acid synthases’ many intricate structural and regulatory elements. In this review, we summarize each enzymatic domain and discuss efforts to engineer fatty acid synthases, providing some clues to important challenges and opportunities in the field. PMID:25360565

  6. Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering.

    PubMed

    Beld, Joris; Lee, D John; Burkart, Michael D

    2015-01-01

    Fatty acids are primary metabolites synthesized by complex, elegant, and essential biosynthetic machinery. Fatty acid synthases resemble an iterative assembly line, with an acyl carrier protein conveying the growing fatty acid to necessary enzymatic domains for modification. Each catalytic domain is a unique enzyme spanning a wide range of folds and structures. Although they harbor the same enzymatic activities, two different types of fatty acid synthase architectures are observed in nature. During recent years, strained petroleum supplies have driven interest in engineering organisms to either produce more fatty acids or specific high value products. Such efforts require a fundamental understanding of the enzymatic activities and regulation of fatty acid synthases. Despite more than one hundred years of research, we continue to learn new lessons about fatty acid synthases' many intricate structural and regulatory elements. In this review, we summarize each enzymatic domain and discuss efforts to engineer fatty acid synthases, providing some clues to important challenges and opportunities in the field. PMID:25360565

  7. Collision-Induced Dissociation Mass Spectrometry: A Powerful Tool for Natural Product Structure Elucidation.

    PubMed

    Johnson, Andrew R; Carlson, Erin E

    2015-11-01

    Mass spectrometry is a powerful tool in natural product structure elucidation, but our ability to directly correlate fragmentation spectra to these structures lags far behind similar efforts in peptide sequencing and proteomics. Often, manual data interpretation is required and our knowledge of the expected fragmentation patterns for many scaffolds is limited, further complicating analysis. Here, we summarize advances in natural product structure elucidation based upon the application of collision induced dissociation fragmentation mechanisms.

  8. Towards a structural elucidation of the alternative oxidase in plants.

    PubMed

    Albury, Mary S; Elliott, Catherine; Moore, Anthony L

    2009-12-01

    In addition to the conventional cytochrome c oxidase, mitochondria of all plants studied to date contain a second cyanide-resistant terminal oxidase or alternative oxidase (AOX). The AOX is located in the inner mitochondrial membrane and branches from the cytochrome pathway at the level of the quinone pool. It is non-protonmotive and couples the oxidation of ubiquinone to the reduction of oxygen to water. For many years, the AOX was considered to be confined to plants, fungi and a small number of protists. Recently, it has become apparent that the AOX occurs in wide range of organisms including prokaryotes and a moderate number of animal species. In this paper, we provide an overview of general features and current knowledge available about the AOX with emphasis on structure, the active site and quinone-binding site. Characterisation of the AOX has advanced considerably over recent years with information emerging about the role of the protein, regulatory regions and functional sites. The large number of sequences available is now enabling us to obtain a clearer picture of evolutionary origins and diversity.

  9. Structural elucidation of two photolytic degradation products of tetrabenazine.

    PubMed

    Bourezg, Zouaoui; Cartiser, Nathalie; Ettouati, Laurent; Guillon, Jean; Lacoudre, Aline; Pinaud, Noël; Le Borgne, Marc; Fessi, Hatem

    2014-03-01

    During solution formulation study of tetrabenazine (TBZ), a dopamine depleting agent, used in chorea associated with Huntington's disease and symptomatic treatment of hyperkinetic movement disorder it was observed a strong discoloration upon storage. We investigated this physico-chemical behavior by implementing forced degradation studies. It was observed yellowing only under Suntest(®) light exposure of TBZ solution. LC-MS (liquid chromatography coupled to mass spectrometer detection) analysis of light exposed TBZ samples allowed us to propose 1,11b-dedihydrotetrabenazine (DTBZ) and 1,3,4,11b-detetrahydrotetrabenazine (TTBZ) as the main TBZ impurities. Synthesis and complete structural determination of DTBZ and TTBZ·HCl by NMR and X-ray crystallography were carried out. They were identical in LC-MS with polar impurities found in light exposed TBZ samples. However, even if these TBZ degradation products are correlated with discoloration of TBZ solution there is no evidence they are directly responsible of it. PMID:24457996

  10. Structure elucidation and chromatographic identification of anthraquinone components of cochineal (Dactylopius coccus) detected in historical objects.

    PubMed

    Stathopoulou, Konstantina; Valianou, Lemonia; Skaltsounis, Alexios-Leandros; Karapanagiotis, Ioannis; Magiatis, Prokopios

    2013-12-01

    Cochineal is one of the most well known organic red dyes. Dactylopius coccus Costa (Dactylopiidae) is a scale insect that is used as the source of the dye known as Mexican cochineal. Although cochineal is today a natural food colorant (E120) and although it has been used in art objects (textiles and paintings) for centuries, its exact chemical consistency is not well clarified except for carminic acid which is the major component and kermesic and flavokermesic acids. Several minor components (typically less than 5% of the colouring material) remained unknown or partially studied, although their presence has been reported in numerous analytical works related to art objects. Chemical investigation of the methanol extract of the dried insects, after subsequent HPLC chromatographic separations, led to the isolation and structure elucidation of six new anthraquinones, along with the known compounds carminic acid, kermesic acid and flavokermesic acid. The new compounds formerly described as DCII and DCIII, were found to be the 2-C-glucoside of flavokermesic acid and 4-aminocarminic acid, respectively, while DCIV and DCVII were found to be the α/β C-glucofuranosides of kermesic acid, and were studied as a mixture due to equilibrium. In addition, 3-O-glucoside of flavokermesic acid (DCOFK), and 3,4-dideoxycarminic acid (DDCA) were identified. The structures of the new compounds were elucidated on the basis of their NMR and MS data. Finally, the new compounds were detected in silk dyed with cochineal, lake pigment and, furthermore, in historical objects of the cultural heritage (icon and textile) using LC-DAD and LC-MS. PMID:24267092

  11. Are deterministic expert systems for computer-assisted structure elucidation obsolete?

    PubMed

    Elyashberg, Mikhail E; Blinov, Kirill A; Williams, Antony J; Molodtsov, Sergey G; Martin, Gary E

    2006-01-01

    Expert systems for spectroscopic molecular structure elucidation have been developed since the mid-1960s. Algorithms associated with the structure generation process within these systems are deterministic; that is, they are based on graph theory and combinatorial analysis. A series of expert systems utilizing 2D NMR spectra have been described in the literature and are capable of determining the molecular structures of large organic molecules including complex natural products. Recently, an opinion was expressed in the literature that these systems would fail when elucidating structures containing more than 30 heavy atoms. A suggestion was put forward that stochastic algorithms for structure generation would be necessary to overcome this shortcoming. In this article, we describe a comprehensive investigation of the capabilities of the deterministic expert system Structure Elucidator. The results of performing the structure elucidation of 250 complex natural products with this program were studied and generalized. The conclusion is that 2D NMR deterministic expert systems are certainly capable of elucidating large structures (up to about 100 heavy atoms) and can deal with the complexities associated with both poor and contradictory spectral data.

  12. Structure elucidation of two novel yak milk oligosaccharides and their DFT studies

    NASA Astrophysics Data System (ADS)

    Singh, Ashish Kumar; Ranjan, Ashok Kr.; Srivastava, Gaurav; Deepak, Desh

    2016-03-01

    Milk is a primary dynamic biological fluid responsible for development of neonates. Besides the other regular constituents it have oligosaccharides in it which are responsible for antitumor, anticancer, antigenic and immunostimulant activities. In our endeavor to find biologically active novel oligosaccharides, yak milk was taken, which is a rich source of oligosaccharide and its milk is used as antihypertensive, antioxidative and heart strengthening agent in folk medicine. For this purpose yak milk was processed by method of Kobata and Ginsburg followed by gel filtration HPLC and CC which resulted in the isolation of two novel milk oligosaccharides namely (I) Grunniose and (II) Vakose. The structure of purified milk oligosaccharides were elucidated with the help of chemical degradation, chemical transformation, spectroscopic techniques like NMR (1H, 13C and 2D-NMR), structure reporter group theory and mass spectrometry. The optimized geometry of compound Grunniose and Vakose, at B3LYP method and 6-311 + G basis set on Gaussian 09 program, show that the compound Grunniose is lower in energy as compared to compound Vakose.

  13. Structure elucidation of two novel yak milk oligosaccharides and their DFT studies

    NASA Astrophysics Data System (ADS)

    Singh, Ashish Kumar; Ranjan, Ashok Kr.; Srivastava, Gaurav; Deepak, Desh

    2016-03-01

    Milk is a primary dynamic biological fluid responsible for development of neonates. Besides the other regular constituents it have oligosaccharides in it which are responsible for antitumor, anticancer, antigenic and immunostimulant activities. In our endeavor to find biologically active novel oligosaccharides, yak milk was taken, which is a rich source of oligosaccharide and its milk is used as antihypertensive, antioxidative and heart strengthening agent in folk medicine. For this purpose yak milk was processed by method of Kobata and Ginsburg followed by gel filtration HPLC and CC which resulted in the isolation of two novel milk oligosaccharides namely (I) Grunniose and (II) Vakose. The structure of purified milk oligosaccharides were elucidated with the help of chemical degradation, chemical transformation, spectroscopic techniques like NMR (1H, 13C and 2D-NMR), structure reporter group theory and mass spectrometry. The optimized geometry of compound Grunniose and Vakose, at B3LYP method and 6-311 + G basis set on Gaussian 09 program, show that the compound Grunniose is lower in energy as compared to compound Vakose.

  14. Structural elucidation of XR586, a peptaibol-like antibiotic from Acremonium persicinum.

    PubMed Central

    Sharman, G J; Try, A C; Williams, D H; Ainsworth, A M; Beneyto, R; Gibson, T M; McNicholas, C; Renno, D V; Robinson, N; Wood, K A; Wrigley, S K

    1996-01-01

    A novel peptide, XR586, has been isolated from fermentations of Acremonium persicinum (Xenova culture collection number X21488). The structure of XR586 has been elucidated by means of NMR spectroscopy, electrospray and fast-atom bombardment MS, derivatization and enzymic digestion. It has been shown to be helical by CD measurements. XR586 shows many structural and conformational features in common with peptaibols, particularly the zervamicins. Peptaibol antibiotics are peptides, typically of 15-20 residues, containing a large proportion of alpha-aminoisobutyric acid (Aib) residues. These peptides adopt a helical conformation in solution and display anti-bacterial and toxic properties due to their ability to form pores in membranes. However, while XR586 contains several Aib residues, it lacks a terminal phenylalaninol and terminates in the sequence Phe-Gly. The lack of reduction of the penultimate residue at the C-terminus may indicate that this step is normally at the end of the biosynthetic pathway of peptaibols and occurs with cleavage of Gly. The 1H chemical shift assignments of XR586 are reported in Supplementary Publication SUP 50179 (3 pages), which has been deposited at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1996) 313, 9 ("Deposition of data'). PMID:9003355

  15. Structural elucidation of XR586, a peptaibol-like antibiotic from Acremonium persicinum.

    PubMed

    Sharman, G J; Try, A C; Williams, D H; Ainsworth, A M; Beneyto, R; Gibson, T M; McNicholas, C; Renno, D V; Robinson, N; Wood, K A; Wrigley, S K

    1996-12-15

    A novel peptide, XR586, has been isolated from fermentations of Acremonium persicinum (Xenova culture collection number X21488). The structure of XR586 has been elucidated by means of NMR spectroscopy, electrospray and fast-atom bombardment MS, derivatization and enzymic digestion. It has been shown to be helical by CD measurements. XR586 shows many structural and conformational features in common with peptaibols, particularly the zervamicins. Peptaibol antibiotics are peptides, typically of 15-20 residues, containing a large proportion of alpha-aminoisobutyric acid (Aib) residues. These peptides adopt a helical conformation in solution and display anti-bacterial and toxic properties due to their ability to form pores in membranes. However, while XR586 contains several Aib residues, it lacks a terminal phenylalaninol and terminates in the sequence Phe-Gly. The lack of reduction of the penultimate residue at the C-terminus may indicate that this step is normally at the end of the biosynthetic pathway of peptaibols and occurs with cleavage of Gly. The 1H chemical shift assignments of XR586 are reported in Supplementary Publication SUP 50179 (3 pages), which has been deposited at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1996) 313, 9 ("Deposition of data'). PMID:9003355

  16. An Exercise on Structure Elucidation Based on a Tricky Aldol Reaction

    ERIC Educational Resources Information Center

    Sierra, Manuel Gonzalez; Pellegrinet, Silvina C.; Colombo, Maria I.; Ruveda, Edmundo A.

    2008-01-01

    An exercise on structure elucidation for advanced undergraduate students is described. To determine the structure of an unknown product, students are required to use spectra together with an organic chemistry mechanism. This exercise exemplifies the procedure commonly used in research, thus helping students develop problem-solving skills. In…

  17. Consensus structure elucidation combining GC/EI-MS, structure generation, and calculated properties.

    PubMed

    Schymanski, Emma L; Gallampois, Christine M J; Krauss, Martin; Meringer, Markus; Neumann, Steffen; Schulze, Tobias; Wolf, Sebastian; Brack, Werner

    2012-04-01

    This article explores consensus structure elucidation on the basis of GC/EI-MS, structure generation, and calculated properties for unknown compounds. Candidate structures were generated using the molecular formula and substructure information obtained from GC/EI-MS spectra. Calculated properties were then used to score candidates according to a consensus approach, rather than filtering or exclusion. Two mass spectral match calculations (MOLGEN-MS and MetFrag), retention behavior (Lee retention index/boiling point correlation, NIST Kovat's retention index), octanol-water partitioning behavior (log K(ow)), and finally steric energy calculations were used to select candidates. A simple consensus scoring function was developed and tested on two unknown spectra detected in a mutagenic subfraction of a water sample from the Elbe River using GC/EI-MS. The top candidates proposed using the consensus scoring technique were purchased and confirmed analytically using GC/EI-MS and LC/MS/MS. Although the compounds identified were not responsible for the sample mutagenicity, the structure-generation-based identification for GC/EI-MS using calculated properties and consensus scoring was demonstrated to be applicable to real-world unknowns and suggests that the development of a similar strategy for multidimensional high-resolution MS could improve the outcomes of environmental and metabolomics studies. PMID:22414024

  18. Structural elucidation and NMR assignments of four aromatic lactones from a mangrove endophytic fungus (No. GX4-1B).

    PubMed

    Huang, Hongbo; Li, Qing; Feng, Xiaojun; Chen, Bin; Wang, Jun; Liu, Lan; She, Zhigang; Lin, Yongcheng

    2010-06-01

    Two new aromatic lactones, 6-hydroxy-4-hydroxymethyl-8-methoxy-3- methylisocoumarin (1) and 1,10-dihydroxy-8-methyl-dibenz[b, e]oxepin-6,11-dione (2), together with two known compounds, 1,10-dihydroxy-dibenz[b, e]oxepin-6,11-dione (3) and 3-hydroxymethyl-6,8-dimethoxycoumarin (4), were isolated from a mangrove endophytic fungus (No. GX4-1B) collected from the South China Sea. Their structures were elucidated and the data of (1)H and (13)C NMR were assigned completely by HREIMS, 1D and 2D NMR experiments including HMQC, HMBC and NOESY.

  19. Chemical synthesis and structure elucidation of bovine {kappa}-casein (1-44)

    SciTech Connect

    Bansal, Paramjit S.; Grieve, Paul A.; Marschke, Ronald J.; Daly, Norelle L.; McGhie, Emily; Craik, David J.; Alewood, Paul F. . E-mail: p.alewood@imb.uq.edu.au

    2006-02-24

    The caseins ({alpha}{sub s1}, {alpha}{sub s2}, {beta}, and {kappa}) are phosphoproteins present in bovine milk that have been studied for over a century and whose structures remain obscure. Here we describe the chemical synthesis and structure elucidation of the N-terminal segment (1-44) of bovine {kappa}-casein, the protein which maintains the micellar structure of the caseins. {kappa}-Casein (1-44) was synthesised by highly optimised Boc solid-phase peptide chemistry and characterised by mass spectrometry. Structure elucidation was carried out by circular dichroism and nuclear magnetic resonance spectroscopy. CD analysis demonstrated that the segment was ill defined in aqueous medium but in 30% trifluoroethanol it exhibited considerable helical structure. Further, NMR analysis showed the presence of a helical segment containing 26 residues which extends from Pro{sup 8} to Arg{sup 34}. This is First report which demonstrates extensive secondary structure within the casein class of proteins.

  20. Anti-inflammatory effects and structure elucidation of two new compounds from Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge) Hsiao

    NASA Astrophysics Data System (ADS)

    Wang, Qing-Hu; Han, Na-Ren-Chao-Ke-Tu; Dai, Na-Yin-Tai; Wang, Xiu-Lan; Ao, Wu-Li-Ji

    2014-09-01

    Phytochemical study of the ethanol extract of Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge) Hsiao resulted to the isolation of two new compounds, 1-hydroxy-5-methylolbenzol-2-O-β-D-glucoside (1) and (3R, 4R)-4,7-hydroxy-2‧,3‧-dimethoxyisoflavane-4‧-O-β-D-glucoside (2). The structure of the isolated compounds were elucidated on the basis of the spectroscopic methods including UV, IR, ESI-MS, 1D NMR and 2D NMR techniques, and by comparison with those reported in the literature. The new compounds were investigated for its effect against inflammation induced by egg-albumin and carrageenan in rats.

  1. Structure elucidation of degradation products of Z-ligustilide by UPLC-QTOF-MS and NMR spectroscopy.

    PubMed

    Zuo, Ai-Hua; Cheng, Meng-Chun; Zhuo, Rong-Jie; Wang, Li; Xiao, Hong-Bin

    2013-06-01

    Z-Ligustilide, a major phthalide isolated from a widely used traditional Chinese medicine Ligusticum chuanxiong, possesses various pharmacological activities including neuroprotective, anti-inflammatory, antiproliferative and vasorelaxing effects. However, it is unstable and inclined to degrade in natural conditions, which limits its study and application greatly. In this study, degradation behavior of Z-ligustilide and its degradation products stored at room temperature under direct sunlight were investigated and structure elucidated by HPLC-UV, UPLC-QTOF-MS and NMR. Z-ligustilide degradation and total five degradation products were generated and detected. Two degradation products were unequivocally identified as senkyunolide I and senkyunolide H by comparison with reference compounds. Another two degradation products were further isolated by semi-preparative HPLC and structure elucidated as (E)-6, 7-trans-dihydroxyligustilide and (Z)-6, 7-epoxyligustilide by 1H and 13C NMR, respectively. The degradation pathways of Z-ligustilide were finally proposed. Oxidation, hydrolysis and isomerization are the major degradation reactions. PMID:23984528

  2. Thermodynamic Properties of Asphaltenes: A Predictive Approach Based On Computer Assisted Structure Elucidation and Atomistic Simulations

    SciTech Connect

    Diallo, Mamadou S.; Cagin, Tahir; Faulon, Jean Loup; Goddard, William A.

    2000-08-01

    The authors describe a new methodology for predicting the thermodynamic properties of petroleum geomacromolecules (asphaltenes and resins). This methodology combines computer assisted structure elucidation (CASE) with atomistic simulations (molecular mechanics and molecular dynamics and statistical mechanics). They use quantitative and qualitative structural data as input to a CASE program (SIGNATURE) to generate a sample of ten asphaltene model structures for a Saudi crude oil (Arab Berri). MM calculations and MD simulations are used to estimate selected volumetric and thermal properties of the model structures.

  3. Lepadiformine: a case study of the value of total synthesis in natural product structure elucidation.

    PubMed

    Weinreb, Steven M

    2003-01-01

    Since the emergence of routine X-ray crystallography and high-field FT NMR in the mid-twentieth century, the importance of total synthesis in structure elucidation has become underappreciated by most organic chemists. However, the limitations and fallibility of spectral methodology has recently been highlighted by the mischaracterization of a number of complex natural products, the correct structures of which were all ultimately assigned by total synthesis. This account describes how total synthesis was not only instrumental in disproving the erroneously assigned structure of the marine alkaloid, lepadiformine, but also was also pivotal in establishing the correct structure and absolute configuration.

  4. Haplofungins, new inositol phosphorylceramide synthase inhibitors, from Lauriomyces bellulus SANK 26899 II. Structure elucidation.

    PubMed

    Ohnuki, Takashi; Yano, Tatsuya; Takatsu, Toshio

    2009-10-01

    Eight new inositol phosphorylceramide synthase inhibitors: haplofungin A, B, C, D, E, F, G and H, were discovered in a culture broth of the fungus Lauriomyces bellulus SANK 26899. The planar structures for these haplofungins were elucidated by various spectroscopic analyses and a GC/MS analysis of their degradation products. All eight compounds were found to comprise an arabinonic acid moiety linked through an ester bond to a modified long alkyl chain.

  5. A comprehensive review of the structure elucidation and biological activity of triterpenoids from Ganoderma spp.

    PubMed

    Xia, Qing; Zhang, Huazheng; Sun, Xuefei; Zhao, Haijuan; Wu, Lingfang; Zhu, Dan; Yang, Guanghui; Shao, Yanyan; Zhang, Xiaoxue; Mao, Xin; Zhang, Lanzhen; She, Gaimei

    2014-10-30

    Ganoderma triterpenes (GTs) are the major secondary metabolites of Ganoderma lucidum, a traditional Chinese medicine, popularly used for complementary cancer therapy. GTs are lanostane-tetracyclic triterpenes. They have been reported to possess anti-tumor, anti-inflammation, antioxidant, antimicrobial and blood fat reducing effects. To date, 316 GTs have been found and their similar chemical structures have proved difficult to elucidate. This paper compiles 316 naturally occurring triterpenes from Ganoderma based on the literature published through January 2013 along with their structures, physiological activities and 13C-NMR spectral data.

  6. New improvements in automatic structure elucidation using the LSD (Logic for Structure Determination) and the SISTEMAT expert systems.

    PubMed

    Plainchont, Bertrand; Nuzillard, Jean-Marc; Rodrigues, Gilberto V; Ferreira, Marcelo J P; Scotti, Marcus T; Emerenciano, Vicente P

    2010-05-01

    This article describes the integration of the LSD (Logic for Structure Determination) and SISTEMAT expert systems that were both designed for the computer-assisted structure elucidation of small organic molecules. A first step has been achieved towards the linking of the SISTEMAT database with the LSD structure generator. The skeletal descriptions found by the SISTEMAT programs are now easily transferred to LSD as substructural constraints. Examples of the synergy between these expert systems are given for recently reported natural products.

  7. Elucidation of fluoranthene degradative characteristics in a newly isolated Achromobacter xylosoxidans DN002.

    PubMed

    Ma, Yan-Ling; Lu, Wei; Wan, Li-Li; Luo, Na

    2015-02-01

    Strain DN002 isolated from petroleum-contaminated soil was identified as Achromobacter xylosoxidans based on morphological and biochemical properties and 16S rRNA phylogeny, and investigated for its potential to utilize numerous polycyclic aromatic hydrocarbons (PAHs) such as fluoranthene and pyrene as sole carbon and energy resource. Biodegradation studies showed that 500 mg(·)l(-1)fluranthene was degraded to 35.6 ± 0.3 mg(·)l(-1) by DN002 after 14 days incubation. During fluoranthene biodegradation, catechol 2,3 dioxygenase (C23O) activity was augmented 1.5 times more than catechol 1,2 dioxygenase (C12O), which indicated that C23O played a major role in fluoranthene degradation by DN002. Protein profiles were examined by sodium dodecyl sulfate polyacrylamide gel electrophoresis and two-dimensional electrophoresis then analyzed by mass spectrometry induced by fluoranthene; a molecular mass range of 18 ∼ 66 kDa proteins were found upregulated compared with the uninduced control sample, including multiple isoenzymes of β-oxidation and dehydrogenases as well as dioxygenases. Besides, some new proteins, i.e., dihydrolipoamide succinyltransferase and aldehyde dehydrogenase family proteins and isocitrate lyase were also synthesized.

  8. Structural elucidation of sulfaquinoxaline metabolism products and their occurrence in biological samples using high-resolution Orbitrap mass spectrometry.

    PubMed

    Hoff, Rodrigo Barcellos; Meneghini, Leonardo; Pizzolato, Tânia Mara; Peralba, Maria do Carmo Ruaro; Díaz-Cruz, M Silvia; Barceló, Damià

    2014-06-01

    Four previously unreported metabolism products of sulfaquinoxaline (SQX), a widely used veterinary medicine, were isolated and analyzed using liquid chromatography coupled to high-resolution Orbitrap mass spectrometry. Metabolites were structurally elucidated, and a fragmentation pathway was proposed. The combination of high-resolution MS(2) spectra, linear ion trap MS(2), in-source collision-induced dissociation (CID) fragmentation, and photolysis were used to analyze SQX and its metabolites. All metabolism products identified showed a similar fragmentation pattern to that of the original drug. Differential product ions were produced at m/z 162 and 253 which contain the radical moiety with more 16 Da units than sulfaquinoxaline. This occurs by a hydroxyl attachment to the quinoxaline moiety. With the exception of two low-intensity compounds, all the mass errors were below 5.0 ppm. The distribution of these metabolites in some animal species are also presented and discussed. PMID:24796379

  9. New anthracycline antibiotics produced by interspecific recombinants of streptomycetes. III. Isolation and structure of iremycin.

    PubMed

    Ihn, W; Schlegel, B; Fleck, W F; Sedmera, P

    1980-12-01

    The structure of the anthracycline antibiotic iremycin isolated from Streptomyces violaceus subspecies iremyceticus has been elucidated as 10-(alpha-L-rhodosaminyl)-gamma-rhodomycinone (I) on the basis of spectroscopic analyses and chemical reactions. PMID:7251489

  10. Tannin structural elucidation and quantitative ³¹P NMR analysis. 1. Model compounds.

    PubMed

    Melone, Federica; Saladino, Raffaele; Lange, Heiko; Crestini, Claudia

    2013-10-01

    Tannins and flavonoids are secondary metabolites of plants that display a wide array of biological activities. This peculiarity is related to the inhibition of extracellular enzymes that occurs through the complexation of peptides by tannins. Not only the nature of these interactions, but more fundamentally also the structure of these heterogeneous polyphenolic molecules are not completely clear. This first paper describes the development of a new analytical method for the structural characterization of tannins on the basis of tannin model compounds employing an in situ labeling of all labile H groups (aliphatic OH, phenolic OH, and carboxylic acids) with a phosphorus reagent. The ³¹P NMR analysis of ³¹P-labeled samples allowed the unprecedented quantitative and qualitative structural characterization of hydrolyzable tannins, proanthocyanidins, and catechin tannin model compounds, forming the foundations for the quantitative structural elucidation of a variety of actual tannin samples described in part 2 of this series. PMID:24059814

  11. Structure elucidation of three triterpene glycosides from the trunk of Argania spinosa.

    PubMed

    Oulad-Ali, A; Kirchner, V; Lobstein, A; Weniger, B; Anton, R; Guillaume, D; Charrouf, Z

    1996-02-01

    The structures of three novel saponins from Argania spinosa, named arganines G, H, and J, have been elucidated by MS and NMR techniques as 3-O-beta-D-apiofuranosyl- (1-->4)-beta-D-glucopyranosyl-28-O-beta-D-glucopyranosylbayogenin (1), 3-O-beta-D-apiofuranosyl-(1-->4)-beta-D-glucopyranosyl-28-O-alpha- L- arabinopyranosylbayogenin (2), and 3-O-beta-D-apiofuranosyl-(1-->4)-beta-D-glucopyranosyl-28-O- [beta-D-apiofuranosyl-(1-->3)-beta-D-xylopyranosyl-(1-->4)-alpha-L - rhamnopyranosyl-(1-->2)-alpha-L-arabinopyranosyl]bayogenin (3), respectively. PMID:8991953

  12. Structure elucidation of three triterpene glycosides from the trunk of Argania spinosa.

    PubMed

    Oulad-Ali, A; Kirchner, V; Lobstein, A; Weniger, B; Anton, R; Guillaume, D; Charrouf, Z

    1996-02-01

    The structures of three novel saponins from Argania spinosa, named arganines G, H, and J, have been elucidated by MS and NMR techniques as 3-O-beta-D-apiofuranosyl- (1-->4)-beta-D-glucopyranosyl-28-O-beta-D-glucopyranosylbayogenin (1), 3-O-beta-D-apiofuranosyl-(1-->4)-beta-D-glucopyranosyl-28-O-alpha- L- arabinopyranosylbayogenin (2), and 3-O-beta-D-apiofuranosyl-(1-->4)-beta-D-glucopyranosyl-28-O- [beta-D-apiofuranosyl-(1-->3)-beta-D-xylopyranosyl-(1-->4)-alpha-L - rhamnopyranosyl-(1-->2)-alpha-L-arabinopyranosyl]bayogenin (3), respectively.

  13. New tricyclic and tetracyclic pyranocoumarins with an unprecedented C-4 substituent. Structure elucidation of tamanolide, tamanolide D and tamanolide P from Calophyllum inophyllum of French Polynesia.

    PubMed

    Leu, T; Raharivelomanana, P; Soulet, S; Bianchini, J P; Herbette, G; Faure, R

    2009-11-01

    Three new pyranocoumarin derivatives, tamanolide (1), tamanolide D (2) and tamanolide P (3), were isolated from the almond seeds of Calophyllum inophyllum L. (Clusiaceae) grown in French Polynesia. These compounds, having an unprecedented C-4 isobutyl substituent, have been characterized as a new class of pyranocoumarins called tamanolides. Their structures were elucidated on the basis of 1D and 2D NMR techniques (COSY, NOESY, HSQC and HMBC) in association with MS (HR-ESI-MS) data analysis. PMID:19603395

  14. New dithiolopyrrolone antibiotics from Saccharothrix sp. SA 233. II. Physicochemical properties and structure elucidation.

    PubMed

    Lamari, Lynda; Zitouni, Abdelghani; Dob, Tahar; Sabaou, Nasserdine; Lebrihi, Ahmed; Germain, Pierre; Seguin, Elisabeth; Tillequin, François

    2002-08-01

    Three new natural dithiopyrrolone antibiotics, 3-methyl-2-butenoylpyrrothine (1), tigloylpyrrothine (2), and n-butyropyrrothine (3) were isolated along with the known isobutyropyrrothine (4) and thiolutin (5) from the fermentation broth of Saccharothrix sp. SA 233. The structures of the novel compounds were established on the basis on their spectral data.

  15. Advances in ion trap mass spectrometry: Photodissociation as a tool for structural elucidation

    SciTech Connect

    Stephenson, J.L. Jr.; Booth, M.M.; Eyler, J.R.; Yost, R.A.

    1995-12-01

    Photo-induced dissociation (PID) is the next most frequently used method (after collisional activation) for activation of Polyatomic ions in tandem mass spectrometry. The range of internal energies present after the photon absorption process are much narrower than those obtained with collisional energy transfer. Therefore, the usefulness of PID for the study of ion structures is greatly enhanced. The long storage times and instrumental configuration of the ion trap mass spectrometer are ideally suited for photodissociation experiments. This presentation will focus on both the fundamental and analytical applications of CO{sub 2} lasers in conjunction with ion trap mass spectrometry. The first portion of this talk will examine the fundamental issues of wavelength dependence, chemical kinetics, photoabsorption cross section, and collisional effects on photodissociation efficiency. The second half of this presentation will look at novel instrumentation for electrospray/ion trap mass spectrometry, with the concurrent development of photodissociation as a tool for structural elucidation of organic compounds and antibiotics.

  16. Structure elucidation of anti-methicillin resistant Staphylococcus aureus (MRSA) flavonoids from balsam poplar buds.

    PubMed

    Simard, François; Gauthier, Charles; Legault, Jean; Lavoie, Serge; Mshvildadze, Vakhtang; Pichette, André

    2016-09-15

    There is nowadays an urgent need for developing novel generations of antibiotic agents due to the increased resistance of pathogenic bacteria. As a rich reservoir of structurally diverse compounds, plant species hold promise in this regard. Within this framework, we isolated a unique series of antibacterial flavonoids, named balsacones N-U, featuring multiple cinnamyl chains on the flavan skeleton. The structures of these compounds, isolated as racemates, were determined using extensive 1D and 2D NMR analysis in tandem with HRMS. Balsacones N-U along with previously isolated balsacones A-M were evaluated for their antibacterial activity against clinical isolates of methicillin resistant Staphylococcus aureus (MRSA). Several of the tested balsacones were potent anti-MRSA agents showing MIC values in the low micromolar range. Structure-activity relationships study highlighted some important parameters involved in the antibacterial activity of balsacones such as the presence of cinnamyl and cinnamoyl chains at the C-3 and C-8 positions of the flavan skeleton, respectively. These results suggest that balsacones could represent a potential novel class of naturally occurring anti-MRSA agents.

  17. Structure elucidation of anti-methicillin resistant Staphylococcus aureus (MRSA) flavonoids from balsam poplar buds.

    PubMed

    Simard, François; Gauthier, Charles; Legault, Jean; Lavoie, Serge; Mshvildadze, Vakhtang; Pichette, André

    2016-09-15

    There is nowadays an urgent need for developing novel generations of antibiotic agents due to the increased resistance of pathogenic bacteria. As a rich reservoir of structurally diverse compounds, plant species hold promise in this regard. Within this framework, we isolated a unique series of antibacterial flavonoids, named balsacones N-U, featuring multiple cinnamyl chains on the flavan skeleton. The structures of these compounds, isolated as racemates, were determined using extensive 1D and 2D NMR analysis in tandem with HRMS. Balsacones N-U along with previously isolated balsacones A-M were evaluated for their antibacterial activity against clinical isolates of methicillin resistant Staphylococcus aureus (MRSA). Several of the tested balsacones were potent anti-MRSA agents showing MIC values in the low micromolar range. Structure-activity relationships study highlighted some important parameters involved in the antibacterial activity of balsacones such as the presence of cinnamyl and cinnamoyl chains at the C-3 and C-8 positions of the flavan skeleton, respectively. These results suggest that balsacones could represent a potential novel class of naturally occurring anti-MRSA agents. PMID:27436809

  18. Bridging the gap between modules in isolation and as part of networks: A systems framework for elucidating interaction and regulation of signalling modules

    NASA Astrophysics Data System (ADS)

    Menon, Govind; Krishnan, J.

    2016-07-01

    While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules. We systematically examine the interaction of these modules by analyzing (a) sequential interaction without shared components, (b) sequential interaction with shared components, and (c) oblique interactions. Our studies reveal that the behaviour of a module in isolation may be substantially different from that in a network, and explicitly demonstrate how the behaviour of a given module, the characteristics of the ambient network, and the possibility of shared components can result in new effects. Our global approach illuminates different aspects of the structure and functioning of modules, revealing the importance of dynamical characteristics as well as biochemical features; this provides a methodological platform for investigating the complexity of natural modules shaped by evolution, elucidating the effects of ambient networks on a module in multiple cellular contexts, and highlighting the capabilities and constraints for engineering robust synthetic modules. Overall, such a systems framework provides a platform for bridging the gap between non-linear information processing modules, in isolation and as parts of networks, and a basis for understanding new aspects of natural and engineered cellular networks.

  19. Bridging the gap between modules in isolation and as part of networks: A systems framework for elucidating interaction and regulation of signalling modules.

    PubMed

    Menon, Govind; Krishnan, J

    2016-07-21

    While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules. We systematically examine the interaction of these modules by analyzing (a) sequential interaction without shared components, (b) sequential interaction with shared components, and (c) oblique interactions. Our studies reveal that the behaviour of a module in isolation may be substantially different from that in a network, and explicitly demonstrate how the behaviour of a given module, the characteristics of the ambient network, and the possibility of shared components can result in new effects. Our global approach illuminates different aspects of the structure and functioning of modules, revealing the importance of dynamical characteristics as well as biochemical features; this provides a methodological platform for investigating the complexity of natural modules shaped by evolution, elucidating the effects of ambient networks on a module in multiple cellular contexts, and highlighting the capabilities and constraints for engineering robust synthetic modules. Overall, such a systems framework provides a platform for bridging the gap between non-linear information processing modules, in isolation and as parts of networks, and a basis for understanding new aspects of natural and engineered cellular networks.

  20. Bridging the gap between modules in isolation and as part of networks: A systems framework for elucidating interaction and regulation of signalling modules.

    PubMed

    Menon, Govind; Krishnan, J

    2016-07-21

    While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules. We systematically examine the interaction of these modules by analyzing (a) sequential interaction without shared components, (b) sequential interaction with shared components, and (c) oblique interactions. Our studies reveal that the behaviour of a module in isolation may be substantially different from that in a network, and explicitly demonstrate how the behaviour of a given module, the characteristics of the ambient network, and the possibility of shared components can result in new effects. Our global approach illuminates different aspects of the structure and functioning of modules, revealing the importance of dynamical characteristics as well as biochemical features; this provides a methodological platform for investigating the complexity of natural modules shaped by evolution, elucidating the effects of ambient networks on a module in multiple cellular contexts, and highlighting the capabilities and constraints for engineering robust synthetic modules. Overall, such a systems framework provides a platform for bridging the gap between non-linear information processing modules, in isolation and as parts of networks, and a basis for understanding new aspects of natural and engineered cellular networks. PMID:27448907

  1. Absolute structural elucidation of natural products--a focus on quantum-mechanical calculations of solid-state CD spectra.

    PubMed

    Pescitelli, Gennaro; Kurtán, Tibor; Flörke, Ulrich; Krohn, Karsten

    2009-01-01

    In this review article we examine state-of-the-art techniques for the structural elucidation of organic compounds isolated from natural sources. In particular, we focus on the determination of absolute configuration (AC), perhaps the most challenging but inevitable step in the whole process, especially when newly isolated compounds are screened for biological activity. Among the many methods employed for AC assignment that we review, special attention is paid to electronic circular dichroism (CD) and to the modern tools available for quantum-mechanics CD predictions, including TDDFT. In this context, we stress that conformational flexibility often poses a limit to practical CD calculations of solution CD spectra. Many crystalline natural products suitable for X-ray analysis do not contain heavy atoms for a confidential AC assignment by resonant scattering. However, their CD spectra can be recorded in the solid state, for example with the KCl pellet technique, and analyzed possibly by nonempirical means to provide stereochemical information. In particular, solid-state CD spectra can be compared with those calculated with TDDFT or other high-level methods, using the X-ray geometry as input. The solid-state CD/TDDFT approach, described in detail, represents a quick and reliable tool for AC assignment of natural products.

  2. Comprehensive Secondary Structure Elucidation of Four Genera of the Family Pospiviroidae

    PubMed Central

    Giguère, Tamara; Raj Adkar-Purushothama, Charith; Perreault, Jean-Pierre

    2014-01-01

    Viroids are small, circular, single stranded RNA molecules that infect plants. Since they are non-coding, their structures play a critical role in their life cycles. To date, little effort has been spend on elucidating viroid structures in solution due to both the experimental difficulties and the time-consuming nature of the methodologies implicated. Recently, the technique of high-throughput selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) was adapted for the probing of the members of family Avsunviroidae, all of whom replicate in the chloroplast and demonstrate ribozyme activity. In the present work, twelve viroid species belonging to four different genera of the family Pospiviroidae, whose members are characterized by the presence of a central conserved region (CCR) and who replicate in nucleus of the host, were probed. Given that the structures of five distinct viroid species from the family Pospiviroidae have been previously reported, an overview of the different structural characteristics for all genera and the beginning of a manual classification of the different viroids based on their structural features are presented here. PMID:24897295

  3. Elucidation of the molecular structures of components of the phycobilisome: reconstructing a giant.

    PubMed

    Adir, Noam

    2005-01-01

    The molecular architectures of photosynthetic complexes are rapidly becoming available through the power of X-ray crystallography. These complexes are comprised of antenna complexes, which absorb and transfer energy into photochemical reaction centers. Most reaction centers, found in both oxygenic and non-oxygenic species, are connected to transmembrane chlorophyll containing antennas, and the crystal structures of these antennas contain information on the structure of the entire complex as well as clear indications on their modes of functional association. In cyanobacteria and red alga, most of the Photosystem II associated light harvesting is performed by an enormous (3-7 MDa) membrane attached complex called the phycobilisome (PBS). While the crystal structures of many isolated components of different PBSs have been determined, the structure of the entire complex as well as its manner of association with Photosystem II can only be suggested. In this review, the structural information obtained on the isolated components will be described. The structural information obtained from the components provides the basis for the modeled reconstruction of this giant complex.

  4. Structure-based elucidation of the regulatory mechanism for aminopeptidase activity.

    PubMed

    Ta, Hai Minh; Bae, Sangsu; Han, Seungsu; Song, Jihyuck; Ahn, Tae Kyu; Hohng, Sungchul; Lee, Sangho; Kim, Kyeong Kyu

    2013-09-01

    The specificity of proteases for the residues in and length of substrates is key to understanding their regulatory mechanism, but little is known about length selectivity. Crystal structure analyses of the bacterial aminopeptidase PepS, combined with functional and single-molecule FRET assays, have elucidated a molecular basis for length selectivity. PepS exists in open and closed conformations. Substrates can access the binding hole in the open conformation, but catalytic competency is only achieved in the closed conformation by formation of the S1 binding pocket and proximal movement of Glu343, a general base, to the cleavage site. Hence, peptides longer than the depth of the binding hole block the transition from the open to the closed conformation, and thus length selection is a prerequisite for catalytic activation. A triple-sieve interlock mechanism is proposed featuring the coupling of length selectivity with residue specificity and active-site positioning.

  5. Elucidation of Peptide-Directed Palladium Surface Structure for Biologically Tunable Nanocatalysts

    SciTech Connect

    Bedford, Nicholas M.; Ramezani-Dakhel, Hadi; Slocik, Joseph M.; Briggs, Beverly D.; Ren, Yang; Frenkel, Anatoly I.; Petkov, Valeri; Heinz, Hendrik; Naik, Rajesh R.; Knecht, Mark R.

    2015-05-01

    Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information available to correlate peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach is introduced to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, which was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then eluddated by identification of the catalytic active sites at the atomic level and quantitative prediction of relative reaction rates. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through rational tailoring of peptide sequences

  6. Identification tree based on fragmentation rules for structure elucidation of organophosphorus esters by electrospray mass spectrometry.

    PubMed

    Schwarzenberg, Adrián; Ichou, Farid; Cole, Richard B; Machuron-Mandard, Xavier; Junot, Christophe; Lesage, Denis; Tabet, Jean-Claude

    2013-05-01

    Organophosphorus compounds have played important roles as pesticides, chemical warfare agents and extractors of radioactive material. Structural elucidation of phosphonates poses a particular challenge because their initial forms can be hydrolyzed, thus, degradation products may predominate in samples acquired in the field. The analysis of non-volatile organophosphorus compounds and their degradation products is possible using electrospray tandem mass spectrometry ESI-MS/MS. Here, we present a generic strategy that allows the unambiguous identification of substituents for two families of organophosphorus compounds: the phosphonates and phosphates. General fragmentation rules were deduced based on the study of decomposition pathways of 55 organophosphorus esters, including examples found in the literature. Multistage MS (MS(n)) experiments at high resolution in a hybrid mass spectrometer provide accurate mass measurements, whereas collision-induced dissociation experiments in a triple quadrupole give access to small fragment ions. The creation of a specific nomenclature for each possible structure of organophosphorus compound, depending on the alkyl side chain linked to the oxygen, was achieved by applying these fragmentation rules. This led to the creation of an 'identification tree' based upon the unique consecutive decomposition pathways uncovered for each individual compound. Hence, seven structural motifs were created that orient an unequivocal identification using the 'identification tree'. Despite the similar structures of the ensemble of phosphate and phosphonate esters, distinct identifications based upon characteristic neutral losses and diagnostic fragment ions were possible in all cases. PMID:23674282

  7. Cell division factors from crown gall tumors: a strategy for structural elucidation

    SciTech Connect

    Manning, K.S.

    1985-01-01

    Mitogenic compounds present in extracts of Vinca rosea crown gall tumor tissue were investigated. An isolation procedure, consisting of solvent partitions and reverse phase chromatography, has yielded a group of isomeric compounds which show activity in the tobacco pith bioassay. Initial characterizations revealed an unsaturated base, a sugar residue, a ..beta..-linked glucose, an allylic alcohol, and two methyl groups. A two part strategy of mass spectrometry (MS) in combination with proton nuclear magnetic resonance (/sup 1/H NMR) was envisioned. The aglycone structure would be determined by MS and the regiochemical relationships among the structural units would be defined by /sup 1/H NMR data. The utility of this approach was demonstrated by the structure assignment of a specific inhibitor of ..beta..-D-glucuronidase, 2(S)-carboxy-3(R),4(R),5(S)-trihydroxypiperidine. The relative stereochemistry of the hydroxyls was revealed by /sup 1/H NMR and the absolute configuration was deduced by a comparison of Cotton effects with a model compound. The use of /sup 1/H NMR to establish regiochemical relationships was investigated. Terpenes containing quaternary carbons and methyl groups were excellent models for the regiochemical problems presented by the mitogenic factors. This /sup 1/H NMR spectroscopy has been applied to the cell division factor structure problem. These data, with information from two dimensional nOe experiments, have defined some of the regio-relationships among the structural units present in the isolated factors.

  8. Towards theory driven structure elucidation of complex natural products: mandelalides and coibamide A.

    PubMed

    Snyder, Kevin M; Sikorska, Justyna; Ye, Tao; Fang, Lijing; Su, Wu; Carter, Rich G; McPhail, Kerry L; Cheong, Paul H-Y

    2016-06-28

    The effectiveness of computational tools in determining relative configurations of complex molecules is investigated, using natural products mandelalides A-D and coibamide A, towards a generalized recipe for the scientific community at large. Ultimately, continuing efforts in this vein will accelerate and strengthen relative structure elucidation of complex molecules, such as natural products. Molecular mechanics conformational search, quantum mechanical NMR chemical shift predictions, and DP4 analyses led to confirmation of the revised structures of mandelalides A-D and coibamide A. All chiral centers in the northern hemisphere of mandelalides A-D are inverted with respect to the originally proposed structures, in agreement with recent total syntheses of mandelalide A by Ye, Fürstner & Carter. In the case of coibamide A, it was found that Fang & Su's revision, in which both the macrocycle [MeAla(11)] and the side chain [HIV(2)] residues are inverted from l to d, was consistent with the authentic natural product and computations. PMID:27152741

  9. Developing new isotope-coded mass spectrometry-cleavable cross-linkers for elucidating protein structures.

    PubMed

    Yu, Clinton; Kandur, Wynne; Kao, Athit; Rychnovsky, Scott; Huang, Lan

    2014-02-18

    Structural characterization of protein complexes is essential for the understanding of their function and regulation. However, it remains challenging due to limitations in existing tools. With recent technological improvements, cross-linking mass spectrometry (XL-MS) has become a powerful strategy to define protein-protein interactions and elucidate structural topologies of protein complexes. To further advance XL-MS studies, we present here the development of new isotope-coded MS-cleavable homobifunctional cross-linkers: d0- and d10-labeled dimethyl disuccinimidyl sulfoxide (DMDSSO). Detailed characterization of DMDSSO cross-linked peptides further demonstrates that sulfoxide-containing MS-cleavable cross-linkers offer robust and predictable MS2 fragmentation of cross-linked peptides, permitting subsequent MS3 analysis for simplified, unambiguous identification. Concurrent usage of these reagents provides a characteristic doublet pattern of DMDSSO cross-linked peptides, thus aiding in the confidence of cross-link identification by MS(n) analysis. More importantly, the unique isotopic profile permits quantitative analysis of cross-linked peptides and therefore expands the capability of XL-MS strategies to analyze both static and dynamic protein interactions. Together, our work has established a new XL-MS workflow for future studies toward the understanding of structural dynamics of protein complexes.

  10. Structure-Specific Ribonucleases for MS-Based Elucidation of Higher-Order RNA Structure

    NASA Astrophysics Data System (ADS)

    Scalabrin, Matteo; Siu, Yik; Asare-Okai, Papa Nii; Fabris, Daniele

    2014-07-01

    Supported by high-throughput sequencing technologies, structure-specific nucleases are experiencing a renaissance as biochemical probes for genome-wide mapping of nucleic acid structure. This report explores the benefits and pitfalls of the application of Mung bean (Mb) and V1 nuclease, which attack specifically single- and double-stranded regions of nucleic acids, as possible structural probes to be employed in combination with MS detection. Both enzymes were found capable of operating in ammonium-based solutions that are preferred for high-resolution analysis by direct infusion electrospray ionization (ESI). Sequence analysis by tandem mass spectrometry (MS/MS) was performed to confirm mapping assignments and to resolve possible ambiguities arising from the concomitant formation of isobaric products with identical base composition and different sequences. The observed products grouped together into ladder-type series that facilitated their assignment to unique regions of the substrate, but revealed also a certain level of uncertainty in identifying the boundaries between paired and unpaired regions. Various experimental factors that are known to stabilize nucleic acid structure, such as higher ionic strength, presence of Mg(II), etc., increased the accuracy of cleavage information, but did not completely eliminate deviations from expected results. These observations suggest extreme caution in interpreting the results afforded by these types of reagents. Regardless of the analytical platform of choice, the results highlighted the need to repeat probing experiments under the most diverse possible conditions to recognize potential artifacts and to increase the level of confidence in the observed structural information.

  11. Discovery and structural elucidation of the illegal azo dye Basic Red 46 in sumac spice.

    PubMed

    Ruf, J; Walter, P; Kandler, H; Kaufmann, A

    2012-01-01

    An unknown red dye was discovered in a sumac spice sample during routine analysis for Sudan dyes. LC-DAD and LC-MS/MS did not reveal the identity of the red substance. Nevertheless, using LC-high-resolution MS and isotope ratio comparisons the structure was identified as Basic Red 46. The identity of the dye was further confirmed by comparison with a commercial hair-staining product and two textile dye formulations containing Basic Red 46. Analogous to the Sudan dyes, Basic Red 46 is an azo dye. However, some of the sample clean-up methodology utilised for the analysis of Sudan dyes in food prevents its successful detection. In contrast to the Sudan dyes, Basic Red 46 is a cation. Its cationic properties make it bind strongly to gel permeation columns and silica solid-phase extraction cartridges and prevent elution with standard eluents. This is the first report of Basic Red 46 in food. The structure elucidation of this compound as well as the disadvantages of analytical methods focusing on a narrow group of targeted analytes are discussed. PMID:22455543

  12. Structural Elucidation of Novel Saponins in the Sea Cucumber Holothuria lessoni

    PubMed Central

    Bahrami, Yadollah; Zhang, Wei; Chataway, Tim; Franco, Chris

    2014-01-01

    Sea cucumbers are prolific producers of a wide range of bioactive compounds. This study aimed to purify and characterize one class of compound, the saponins, from the viscera of the Australian sea cucumber Holothuria lessoni. The saponins were obtained by ethanolic extraction of the viscera and enriched by a liquid-liquid partition process and adsorption column chromatography. A high performance centrifugal partition chromatography (HPCPC) was applied to the saponin-enriched mixture to obtain saponins with high purity. The resultant purified saponins were profiled using MALDI-MS/MS and ESI-MS/MS which revealed the structure of isomeric saponins to contain multiple aglycones and/or sugar residues. We have elucidated the structure of five novel saponins, Holothurins D/E and Holothurinosides X/Y/Z, along with seven reported triterpene glycosides, including sulfated and non-sulfated saponins containing a range of aglycones and sugar moieties, from the viscera of H. lessoni. The abundance of novel compounds from this species holds promise for biotechnological applications. PMID:25110919

  13. Synergic application of spectroscopic and theoretical methods to the chlorogenic acid structure elucidation

    NASA Astrophysics Data System (ADS)

    Marković, Svetlana; Tošović, Jelena; Dimitrić Marković, Jasmina M.

    2016-07-01

    Although chlorogenic acid (5-O-caffeoylquinic acid, 5CQA) is a dietary polyphenol known for its pharmacological and nutritional properties, its structural features have not been completely elucidated. This is the first study whose aim is to contribute to clarification of the 5CQA structure by comparing the experimental and simulated IR, Raman, 1H NMR, 13C NMR, and UV spectra. For this purpose, a comprehensive conformational analysis of 5CQA was performed to reveal its most stable conformations in the gas-state and solution (DMSO and methanol). The lowest-energy conformers were used to predict the spectra at two levels of theory: B3LYP-D3/and M06-2X/6-311+G(d,p) in combination with the CPCM solvation model. Both methods provide very good agreement between all experimental and simulated spectra, thus indicating correct arrangement of the atoms in the 5CQA molecule. The quinic moiety is characterized with directed hydrogen bonds, where the carboxylic hydrogen is not oriented towards the carbonyl oxygen of the carboxylic group, but towards the oxygen of the proximate hydroxyl group. In the gas-state the lowest-energy conformers are characterized with the O4sbnd H4 ⋯ O9‧ hydrogen bond, whereas in the solvated state the structures with the O4sbnd H4 ⋯ O10‧ hydrogen bond prevail. Knowing the fine structural details, i.e. the proper conformation of 5CQA, provides a solid base for all further investigations related to this compound.

  14. Structural elucidation of olive pomace fed sea bass (Dicentrarchus labrax) polar lipids with cardioprotective activities.

    PubMed

    Nasopoulou, Constantina; Smith, Terry; Detopoulou, Maria; Tsikrika, Constantina; Papaharisis, Leonidas; Barkas, Dimitris; Zabetakis, Ioannis

    2014-02-15

    The purpose of this study was to structurally characterise the polar lipids of sea bass (Dicentrarchus labrax), fed with an experimental diet containing olive pomace (OP), that exhibit cardioprotective activities. OP has been added to conventional fish oil (FO) feed at 4% and this was the OP diet, having been supplemented as finishing diet to fish. Sea bass was aquacultured using either FO or OP diet. At the end of the dietary experiment, lipids in both samples of fish muscle were quantified and HPLC fractionated. The in vitro cardioprotective properties of the polar lipid fractions, using washed rabbit's platelets, have been assessed and the two most biologically active fractions were further analysed by mass spectrometry. The gas-chromatrograpy-mass spectrometric data shows that these two fractions contain low levels of myristic (14:0), oleic (18:1 cis ω-9) and linoleic acids (18:2 ω-6), but high levels of palmitic (16:0) and stearic acids (18:0) as well as eicosadienoic acid (20:2 ω-6). The first fraction (MS1) also contained significant levels of arachidonic acid (20:4 ω-6) and the omega-3 fatty acids: eicosapentaenoic acid (22:5) and docosahexaenoic acid (22:6). Electrospray-mass spectrometry elucidated that the lipid composition of the two fractions contained various diacyl-glycerophospholipids species, where the majority of them have either 18:0 or 18:1 fatty acids in the sn-1 position and either 22:6 or 20:2 fatty acids in the sn-2 position for MS1 and MS2, respectively. Our research focuses on the structure/function relationship of fish muscle polar lipids and cardiovascular diseases and structural data are given for polar lipid HPLC fractions with strong cardioprotective properties. PMID:24128590

  15. Structural elucidation of olive pomace fed sea bass (Dicentrarchus labrax) polar lipids with cardioprotective activities.

    PubMed

    Nasopoulou, Constantina; Smith, Terry; Detopoulou, Maria; Tsikrika, Constantina; Papaharisis, Leonidas; Barkas, Dimitris; Zabetakis, Ioannis

    2014-02-15

    The purpose of this study was to structurally characterise the polar lipids of sea bass (Dicentrarchus labrax), fed with an experimental diet containing olive pomace (OP), that exhibit cardioprotective activities. OP has been added to conventional fish oil (FO) feed at 4% and this was the OP diet, having been supplemented as finishing diet to fish. Sea bass was aquacultured using either FO or OP diet. At the end of the dietary experiment, lipids in both samples of fish muscle were quantified and HPLC fractionated. The in vitro cardioprotective properties of the polar lipid fractions, using washed rabbit's platelets, have been assessed and the two most biologically active fractions were further analysed by mass spectrometry. The gas-chromatrograpy-mass spectrometric data shows that these two fractions contain low levels of myristic (14:0), oleic (18:1 cis ω-9) and linoleic acids (18:2 ω-6), but high levels of palmitic (16:0) and stearic acids (18:0) as well as eicosadienoic acid (20:2 ω-6). The first fraction (MS1) also contained significant levels of arachidonic acid (20:4 ω-6) and the omega-3 fatty acids: eicosapentaenoic acid (22:5) and docosahexaenoic acid (22:6). Electrospray-mass spectrometry elucidated that the lipid composition of the two fractions contained various diacyl-glycerophospholipids species, where the majority of them have either 18:0 or 18:1 fatty acids in the sn-1 position and either 22:6 or 20:2 fatty acids in the sn-2 position for MS1 and MS2, respectively. Our research focuses on the structure/function relationship of fish muscle polar lipids and cardiovascular diseases and structural data are given for polar lipid HPLC fractions with strong cardioprotective properties.

  16. Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software.

    PubMed

    Tsugawa, Hiroshi; Kind, Tobias; Nakabayashi, Ryo; Yukihira, Daichi; Tanaka, Wataru; Cajka, Tomas; Saito, Kazuki; Fiehn, Oliver; Arita, Masanori

    2016-08-16

    Compound identification from accurate mass MS/MS spectra is a bottleneck for untargeted metabolomics. In this study, we propose nine rules of hydrogen rearrangement (HR) during bond cleavages in low-energy collision-induced dissociation (CID). These rules are based on the classic even-electron rule and cover heteroatoms and multistage fragmentation. We evaluated our HR rules by the statistics of MassBank MS/MS spectra in addition to enthalpy calculations, yielding three levels of computational MS/MS annotation: "resolved" (regular HR behavior following HR rules), "semiresolved" (irregular HR behavior), and "formula-assigned" (lacking structure assignment). With this nomenclature, 78.4% of a total of 18506 MS/MS fragment ions in the MassBank database and 84.8% of a total of 36370 MS/MS fragment ions in the GNPS database were (semi-) resolved by predicted bond cleavages. We also introduce the MS-FINDER software for structure elucidation. Molecular formulas of precursor ions are determined from accurate mass, isotope ratio, and product ion information. All isomer structures of the predicted formula are retrieved from metabolome databases, and MS/MS fragmentations are predicted in silico. The structures are ranked by a combined weighting score considering bond dissociation energies, mass accuracies, fragment linkages, and, most importantly, nine HR rules. The program was validated by its ability to correctly calculate molecular formulas with 98.0% accuracy for 5063 MassBank MS/MS records and to yield the correct structural isomer with 82.1% accuracy within the top-3 candidates. In a test with 936 manually identified spectra from an untargeted HILIC-QTOF MS data set of human plasma, formulas were correctly predicted in 90.4% of the cases, and the correct isomer structure was retrieved at 80.4% probability within the top-3 candidates, including for compounds that were absent in mass spectral libraries. The MS-FINDER software is freely available at http

  17. Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software.

    PubMed

    Tsugawa, Hiroshi; Kind, Tobias; Nakabayashi, Ryo; Yukihira, Daichi; Tanaka, Wataru; Cajka, Tomas; Saito, Kazuki; Fiehn, Oliver; Arita, Masanori

    2016-08-16

    Compound identification from accurate mass MS/MS spectra is a bottleneck for untargeted metabolomics. In this study, we propose nine rules of hydrogen rearrangement (HR) during bond cleavages in low-energy collision-induced dissociation (CID). These rules are based on the classic even-electron rule and cover heteroatoms and multistage fragmentation. We evaluated our HR rules by the statistics of MassBank MS/MS spectra in addition to enthalpy calculations, yielding three levels of computational MS/MS annotation: "resolved" (regular HR behavior following HR rules), "semiresolved" (irregular HR behavior), and "formula-assigned" (lacking structure assignment). With this nomenclature, 78.4% of a total of 18506 MS/MS fragment ions in the MassBank database and 84.8% of a total of 36370 MS/MS fragment ions in the GNPS database were (semi-) resolved by predicted bond cleavages. We also introduce the MS-FINDER software for structure elucidation. Molecular formulas of precursor ions are determined from accurate mass, isotope ratio, and product ion information. All isomer structures of the predicted formula are retrieved from metabolome databases, and MS/MS fragmentations are predicted in silico. The structures are ranked by a combined weighting score considering bond dissociation energies, mass accuracies, fragment linkages, and, most importantly, nine HR rules. The program was validated by its ability to correctly calculate molecular formulas with 98.0% accuracy for 5063 MassBank MS/MS records and to yield the correct structural isomer with 82.1% accuracy within the top-3 candidates. In a test with 936 manually identified spectra from an untargeted HILIC-QTOF MS data set of human plasma, formulas were correctly predicted in 90.4% of the cases, and the correct isomer structure was retrieved at 80.4% probability within the top-3 candidates, including for compounds that were absent in mass spectral libraries. The MS-FINDER software is freely available at http://prime.psc.riken.jp/ .

  18. Structure elucidation, proliferation effect on macrophage and its mechanism of a new heteropolysaccharide from Lactarius deliciosus Gray.

    PubMed

    Hou, Yiling; Liu, Lu; Ding, Xiang; Zhao, Daqun; Hou, Wanru

    2016-11-01

    A new heteropolysaccharide was isolated from the fruiting bodies of Lactarius deliciosus Gray which had a molecular weight of 16kDa and was mainly composed of the galactose and glucose. Structural elucidation results indicated that Lactarius deliciosus Gray polysaccharide (LDG-B) had a backbone of (1,6)-linked d-galactose and (1, 2, 6)-linked d-galactose which branches were mainly composed of 4-linked d-glucose and 6-linked d-galactose residue. Cell cycle test results showed that LDG-B could promote the proliferation of B cells and macrophage cells by affecting G0/G1 phase, S phases and G2/M phases. The analysis of transcriptomes sequence of macrophages showed a total of 1839 genes were identified as DEGs, and approximately 708 genes were up-regulated, whereas 1131 genes were down-regulated in LDG-B group. KEGG pathway enrichment analysis showed that the MAPK, JAK-STAT and NF-κB signaling pathways are significantly enriched for DEGs in LDG-B group. Analysis of transcriptome resources enabled us to examine gene expression profiles, verify differential gene expression, and select candidate signaling pathways as the mechanisms of the immunomodulatory activity of LDG-B. PMID:27516315

  19. Structural elucidation of a pectin from flowers of Lonicera japonica and its antipancreatic cancer activity.

    PubMed

    Lin, Liyan; Wang, Peipei; Du, Zhenyun; Wang, Wucheng; Cong, Qifei; Zheng, Changping; Jin, Can; Ding, Kan; Shao, Chenghao

    2016-07-01

    To investigate polysaccharide structure from Lonicera japonica, and study its effects on behavior of pancreatic cells, a homogenous polysaccharide, LJ-02-1, was extracted and purified from flowers of L. japonica by DEAE-cellulose and Sephacryl S-200HR column. The molecular weight was estimated to be 54kDa. Monosaccharide composition was determined to be rhamnose, galacturonic acid, galactose and arabinose in the molar ratio of 10.77:7.88:15.45:65.89 by analyzing the PMP derivatives of the monosaccharides from 2M trifluoracetic acid hydrolysis via HPLC. Based on methylation analysis, partial acid hydrolysis, and NMR spectra, the polysaccharide was elucidated to be a rhamnogalacturonan backbone and substituted partly at C-4 of rhamnose. The branches were determined to be T- and 1,4,6-linked β-d-Galp, T- and 1,5-linked α-l-Araf. The polysaccharide might inhibit BxPC-3 and PANC-1 pancreatic cancer cells growth at the concentration of 1mg/mL with inhibitory ratio of 66.7% and 52.1%, respectively. PMID:27000440

  20. Structural elucidation of the interaction between neurodegenerative disease-related tau protein with model lipid membranes

    NASA Astrophysics Data System (ADS)

    Jones, Emmalee M.

    A protein's sequence of amino acids determines how it folds. That folded structure is linked to protein function, and misfolding to dysfunction. Protein misfolding and aggregation into beta-sheet rich fibrillar aggregates is connected with over 20 neurodegenerative diseases, including Alzheimer's disease (AD). AD is characterized in part by misfolding, aggregation and deposition of the microtubule associated tau protein into neurofibrillary tangles (NFTs). However, two questions remain: What is tau's fibrillization mechanism, and what is tau's cytotoxicity mechanism? Tau is prone to heterogeneous interactions, including with lipid membranes. Lipids have been found in NFTs, anionic lipid vesicles induced aggregation of the microtubule binding domain of tau, and other protein aggregates induced ion permeability in cells. This evidence prompted our investigation of tau's interaction with model lipid membranes to elucidate the structural perturbations those interactions induced in tau protein and in the membrane. We show that although tau is highly charged and soluble, it is highly surface active and preferentially interacts with anionic membranes. To resolve molecular-scale structural details of tau and model membranes, we utilized X-ray and neutron scattering techniques. X-ray reflectivity indicated tau aggregated at air/water and anionic lipid membrane interfaces and penetrated into membranes. More significantly, membrane interfaces induced tau protein to partially adopt a more compact conformation with density similar to folded protein and ordered structure characteristic of beta-sheet formation. This suggests possible membrane-based mechanisms of tau aggregation. Membrane morphological changes were seen using fluorescence microscopy, and X-ray scattering techniques showed tau completely disrupts anionic membranes, suggesting an aggregate-based cytotoxicity mechanism. Further investigation of protein constructs and a "hyperphosphorylation" disease mimic helped

  1. Adxanthromycins A and B, new inhibitors of ICAM-1/LFA-1 mediated cell adhesion molecule from Streptomyces sp. NA-148. II. Physico-chemical properties and structure elucidation.

    PubMed

    Takahashi, S; Nakano, T; Koiwa, T; Noshita, T; Funayama, S; Koshino, H; Nakagawa, A

    2000-02-01

    Adxanthromycins A and B are new inhibitors of ICAM-1/LFA-1 mediated cell adhesion molecule isolated from the fermentation broth of Streptomyces sp. NA-148. The molecular formula of adxanthromycins A and B were determined as C42H40O17 and C48H50O22, respectively by FAB-MS and NMR spectral analyses, and the structures of both compounds were elucidated to be a dimeric anthrone peroxide skeleton containing alpha-D-galactose by various NMR spectral analyses and chemical degradation. PMID:10805577

  2. Secondary structure of double-stranded DNA under stretching: Elucidation of the stretched form

    SciTech Connect

    Maaloum, M.; Muller, P.; Beker, A-F.

    2011-03-15

    Almost two decades ago, measurements of force versus extension on isolated double-stranded DNA molecules revealed a force plateau. This unusual stretching phenomenon in DNA suggests that the long molecules may be extended from the usual B form into a new conformation. Different models have been proposed to describe the nature of DNA in its stretched form, S-DNA. Using atomic force microscopy combined with a molecular combing method, we identified the structure of {lambda}-phage DNA for different stretching values. We provide strong evidence for the existence of a first-order transition between B form and S form. Beyond a certain extension of the natural length, DNA molecules adopt a new double-helix conformation characterized by a diameter of 1.2 nm and a helical pitch of18 nm.

  3. Elucidating the Effect of Biomolecule Structure on Calcium Carbonate Crystal Formation

    NASA Astrophysics Data System (ADS)

    Kulbok, K. E.; Duckworth, O.

    2011-12-01

    Anthropogenic emissions of carbon dioxide have lead to a steady increase in atmospheric concentration. This greenhouse gas has been identified as a key driver of climate change and also has lead to increased acidification of marine and terrestrial waters. Calcium carbonate precipitation at the Earth's surface is an integral linkage in the global carbon cycle, especially in regards to regulating atmospheric carbon dioxide. As concern for the effect of increasing atmospheric CO2 levels grows, the need to understand calcium carbonate systems escalates concurrently. Calcium carbonate phases are the most abundant group of biominerals; therefore, elucidating the mechanism of biomineralization is critical to understanding CaCO3 precipitation and may aid in the development of novel carbon sequestration strategies. The ubiquity of microorganisms leads to an extensive number of biomolecules present in the Earth's systems, and thus an extensive range of possible effects on CaCO3 formation. Carboxylic acids are very common biomolecules and have a relatively simple structure, thus making them an ideal family of model compounds. This study examines the kinetics, thermodynamics, phase, and morphology of calcium carbonate crystals precipitated in the presence of carboxylate-containing biomolecules, including citric acid, succinic acid, and aspartic acid. The experiments utilize a unique (NH4)2CO3 gas-diffusion reactor, which allows in-situ measurements of chemical conditions during the precipitation and growth of crystals. Continuous monitoring of the in-situ conditions of pCO2, pH, [Ca2+], and optical absorbance provides data on the supersaturation at which nucleation occurs and the kinetics of mineral growth. The use of scanning electron microscopy and X-ray diffraction provides information on the morphology and mineralogy of precipitates. The combination of these data sets will provide an in-depth view of the ideal concentration of calcium ions required for solution saturation

  4. pH-Controlled Oxidation of an Aromatic Ketone: Structural Elucidation of the Products of Two Green Chemical Reactions

    ERIC Educational Resources Information Center

    Ballard, C. Eric

    2010-01-01

    A laboratory experiment emphasizing the structural elucidation of organic compounds has been developed as a discovery exercise. The "unknown" compounds are the products of the pH-controlled oxidation of 4'-methoxyacetophenone with bleach. The chemoselectivity of this reaction is highly dependent on the pH of the reaction media: under basic…

  5. Isolation and chemical structure of aklanonic acid, an early intermediate in the biosynthesis of anthracyclines.

    PubMed

    Eckardt, K; Tresselt, D; Schumann, G; Ihn, W; Wagner, C

    1985-08-01

    The fermentation, isolation and structure elucidation of aklanonic acid are described. The compound was isolated from fermentations of Streptomyces strain ZIMET 43,717. Aklanonic acid is a yellow-orange crystalline substance, melting at 203-204 degrees C (dec), having the molecular formula C21H16O8, and possessing UV maxima at 258, 282 (sh) and 438 nm (CHCl3). In dimethyl sulfoxide or pyridine aklanonic acid is unstable and a new compound (aklanone) is formed as a conversion product. The elucidation of the structures has shown that aklanonic acid and aklanone are derivatives of 1,8-dihydroxyanthraquinone. PMID:3862658

  6. Structure elucidation, anticancer and antioxidant activities of a novel polysaccharide from Gomphus clavatus Gray.

    PubMed

    Ding, Xiang; Hou, Yiling; Zhu, Yuanxiu; Wang, Panpan; Fu, Lei; Zhu, Hongqing; Zhang, Nan; Qin, Hang; Qu, Wei; Wang, Fang; Hou, Wanru

    2015-06-01

    A novel heteropolysaccharide from the fruiting bodies of Gomphus clavatus Gray was isolated through Sephadex G-200 and DEAE-cellulose columns. The Gomphus clavatus Gray polysaccharide (GCG-1) was mainly composed of β-D-glucosepyranose (β-D-Glu) and α-D-galactopyranose (α-D-Gal) in a ratio of 3:2 and had a molecular weight of ~50,000 Da. The structure of GCG-1 was investigated by a combination of total hydrolysis, gas chromatography-mass spectrometry, methylation analysis, nuclear magnetic resonance spectroscopy and infrared spectra. The results indicated that GCG-1 had a backbone of (1 → 4)-β-D-glucosepyranose residues with branches at O-6 and the branches consisted of two with (1 → 3)-α-D-galactopyranose residue. Antioxidation test in vitro showed that it possessed strong free radical scavenging activity, which may be comparable to vitamin C and butylated hydroxytoluene. GCG-1 also induced the apoptosis of HepG-2 cells and affected the mRNA expression of various housekeeping genes in the HepG-2 cells. The results indicated that Gomphus clavatus Gray may be an ideal sources for antioxidant and anticancer agents.

  7. Structural elucidation and biological studies of a novel exopolysaccaride from Klebsiella pneumoniae PB12.

    PubMed

    Mandal, Amit K; Sen, Ipsita K; Maity, Prasenjit; Chattopadhyay, Sourav; Chakraborty, Ranadhir; Roy, Somenath; Islam, Syed S

    2015-08-01

    An exopolysaccharide (KNPS) of an average molecular weight ∼1.8×10(5) Da was isolated from the culture medium of Klebsiella pneumoniae PB12. Structural characterization of KNPS was carried out using sugar and methylation analysis, Smith degradation and 1D/2D NMR experiments. Sugar analysis showed that the KNPS composed of arabinose, galactose, 3-O-methyl-galctose and glucose in a molar ratio of nearly 4:3:1:1. The proposed repeating unit of the KNPS has a backbone chain consisting of two (1→6)-galactopyranosyl residues, two (1→5)-arabinofuranosyl residues, one (1→6)-glucopyranosyl residue and one (1→3)-arabinopyranosyl residue, out of which one (1→6)-galactopyranosyl residue was branched at O-2 position with a (1→2)-linked-galactopyranosyl residue terminated with non reducing arabinofuranosyl residue and one (1→5)-arabinofuranosyl residue branched at O-3 position with non reducing end 3-O-Me-galactopyranosyl residue. KNPS was found non-toxic toward human lymphocyte up to the dosage of 100 μg/ml. KNPS enhanced malondialdehyde (MDA), reactive oxygen species (ROS), and have the potential to alter the ratio of oxidized glutathione (GSSG) and reduced glutathione (GSH) levels in the cellular system.

  8. Structural elucidation and biological studies of a novel exopolysaccaride from Klebsiella pneumoniae PB12.

    PubMed

    Mandal, Amit K; Sen, Ipsita K; Maity, Prasenjit; Chattopadhyay, Sourav; Chakraborty, Ranadhir; Roy, Somenath; Islam, Syed S

    2015-08-01

    An exopolysaccharide (KNPS) of an average molecular weight ∼1.8×10(5) Da was isolated from the culture medium of Klebsiella pneumoniae PB12. Structural characterization of KNPS was carried out using sugar and methylation analysis, Smith degradation and 1D/2D NMR experiments. Sugar analysis showed that the KNPS composed of arabinose, galactose, 3-O-methyl-galctose and glucose in a molar ratio of nearly 4:3:1:1. The proposed repeating unit of the KNPS has a backbone chain consisting of two (1→6)-galactopyranosyl residues, two (1→5)-arabinofuranosyl residues, one (1→6)-glucopyranosyl residue and one (1→3)-arabinopyranosyl residue, out of which one (1→6)-galactopyranosyl residue was branched at O-2 position with a (1→2)-linked-galactopyranosyl residue terminated with non reducing arabinofuranosyl residue and one (1→5)-arabinofuranosyl residue branched at O-3 position with non reducing end 3-O-Me-galactopyranosyl residue. KNPS was found non-toxic toward human lymphocyte up to the dosage of 100 μg/ml. KNPS enhanced malondialdehyde (MDA), reactive oxygen species (ROS), and have the potential to alter the ratio of oxidized glutathione (GSSG) and reduced glutathione (GSH) levels in the cellular system. PMID:25999015

  9. Heteroglycan of an edible mushroom Termitomyces clypeatus: structure elucidation and antioxidant properties.

    PubMed

    Pattanayak, Manabendra; Samanta, Surajit; Maity, Prasenjit; Sen, Ipsita K; Nandi, Ashis K; Manna, Dilip K; Mitra, Payel; Acharya, Krishnendu; Islam, Syed S

    2015-09-01

    A water-soluble heteroglycan (PS) of an average molecular weight ∼1.98 ×10(5) Da was isolated from the aqueous extract of an edible mushroom Termitomyces clypeatus (R. Heim). The structure of the polysaccharide (PS) was established using total hydrolysis, methylation analysis, Smith degradation, and 1D/2D NMR experiments. Total hydrolysis indicated the presence of d-glucose, d-galactose, d-mannose, and l-fucose in a molar ratio of 4.10:1.95:1.0:0.95, respectively. The chemical and NMR analysis indicated the presence of a repeating unit with a backbone consisting of one each of the residues (1→3)-α-d-galactopyranosyl, (1→3)-α-d-mannopyranosyl, (1→3)-α-d-glucopyranosyl, (1→3)-β-d-glucopyranosyl, (1→6)-β-d-glucopyranosyl, and (1→6)-α-d-galactopyranosyl, respectively. The (1→3)-α-d-mannopyranosyl residue was found branched at O-2 with terminal α-l-fucopyranosyl moiety and (1→3)-β-d-glucopyranosyl residue was branched at O-6 with terminal α-d-glucopyranosyl residue. The PS exhibited antioxidant properties.

  10. Seismic Behaviour of Vertical Mass Isolated Structures

    SciTech Connect

    Nekooei, M.; Ziyaeifar, M.

    2008-07-08

    In this paper, the seismic behaviour of vertical mass isolated structures against the earthquake is studied. These structures are assumed to be consisted of two subsystems. Mass subsystem possesses low lateral stiffness but carries the major part of mass of the system. Stiffness subsystem, however, controls the deformation of the mass subsystem and attributes with much higher stiffness. The isolator layer is, therefore, located in between the mass and the stiffness subsystems and assumed to be a viscous damper layer. The analytical model used for this investigation is a dual mass-spring model which is an extended form of the three element Maxwell model. In this study, the ability of mass isolation techniques in reducing earthquake effects on buildings with two approaches, parametric and numerical approaches, is shown. In the parametric approach, by definition an isolation factor for structure and determination the dynamic characteristics of system, the relative optimum value of the isolator damping coefficient is obtained. The results provide an insight on role of relative stiffness and mass ratio of the two subsystems. Finally, in the numerical approach, the spectral responses of these structures due to the earthquake are investigated. The results show a noticeable decrease in earthquake input force to vertical mass isolated structures in comparison with non-isolated structures.

  11. Membrane structure in isolated and intact myelins.

    PubMed Central

    Inouye, H; Karthigasan, J; Kirschner, D A

    1989-01-01

    The biochemical composition of myelin and the topology of its constituent lipids and proteins are typically studied using membranes that have been isolated from whole, intact tissue using procedures involving hypotonic shock and sucrose density gradient centrifugation. To what extent, however, are the structure and intermembrane interactions of isolated myelin similar to those of intact myelin? We have previously reported that intact and isolated myelins do not always show identical myelin periods, indicating a difference in membrane-membrane interactions. The present study addresses the possibility that this is due to altered membrane structure. Because x-ray scattering from isolated myelin sometimes consists of overlapping Bragg reflections or is continuous, we developed nonlinear least squares procedures for analyzing the total intensity distribution after film scaling, background subtraction, and Lorentz correction. We calculated electron density profiles of isolated myelin for comparison with membrane profiles from intact myelin. The change in the width of the extracellular space and the relative invariance of the cytoplasmic space as a function of pH and ionic strength that we previously found for intact nerve was largely paralleled by isolated myelin. There were two exceptions: isolated CNS myelin was resistant to swelling under all conditions, and isolated PNS myelin in hypotonic saline showed indefinite swelling at the extracellular apposition. However, electron density profiles of isolated myelins, calculated to 30 A resolution, did not show any major change in structure compared with intact myelin that could account for the differences in interactions. PMID:2752082

  12. Structural investigation of the lipopolysaccharide O-chain isolated from Burkholderia fungorum strain DSM 17061.

    PubMed

    De Felice, Antonia; Di Lorenzo, Flaviana; Scherlach, Kirstin; Ross, Claudia; Silipo, Alba; Hertweck, Christian; Molinaro, Antonio

    2016-10-01

    Gram-negative bacteria exhibit lipopolysaccharides (LPSs) on their outer membrane surface. LPS is considered one of the most potent bacterial virulence factors. Here we report the elucidation of the LPS O-chain structure isolated from Burkholderia fungorum, a bacterium isolated from the white-rot fungus Phanerochaete chrysosporium that can act as a pathogen for plants and domesticated animals. The structure was determined by the employment of detailed chemical and NMR spectroscopy analyses as the following.

  13. Microfabricated structures with electrical isolation and interconnections

    NASA Technical Reports Server (NTRS)

    Clark, William A. (Inventor); Juneau, Thor N. (Inventor); Roessig, Allen W. (Inventor); Lemkin, Mark A. (Inventor)

    2001-01-01

    The invention is directed to a microfabricated device. The device includes a substrate that is etched to define mechanical structures at least some of which are anchored laterally to the remainder of the substrate. Electrical isolation at points where mechanical structures are attached to the substrate is provided by filled isolation trenches. Filled trenches may also be used to electrically isolate structure elements from each other at points where mechanical attachment of structure elements is desired. The performance of microelectromechanical devices is improved by 1) having a high-aspect-ratio between vertical and lateral dimensions of the mechanical elements, 2) integrating electronics on the same substrate as the mechanical elements, 3) good electrical isolation among mechanical elements and circuits except where electrical interconnection is desired.

  14. Chemical structure elucidation from ¹³C NMR chemical shifts: efficient data processing using bipartite matching and maximal clique algorithms.

    PubMed

    Koichi, Shungo; Arisaka, Masaki; Koshino, Hiroyuki; Aoki, Atsushi; Iwata, Satoru; Uno, Takeaki; Satoh, Hiroko

    2014-04-28

    Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct structure if all of the fragments are included in the database. Even if not all of the fragments are in the database, the elucidator proposes relevant substructures that can help chemists to identify the actual chemical structures. The elucidator, called the CAST/CNMR Structure Elucidator, plays a complementary role to the CAST/CNMR Chemical Shift Predictor, and together these two functions can be used to analyze the structures of organic compounds.

  15. Large-scale isolation of flavonolignans from Silybum marianum extract affords new minor constituents and preliminary structure-activity relationships.

    PubMed

    Sy-Cordero, Arlene; Graf, Tyler N; Nakanishi, Yuka; Wani, Mansukh C; Agarwal, Rajesh; Kroll, David J; Oberlies, Nicholas H

    2010-04-01

    The gram-scale isolation of the major flavonolignan diastereoisomers from milk thistle ( Silybum marianum) extract provided an entree into the isolation of two related analogues that are present in extremely minute quantities. The isolation and structure elucidation of these two new compounds, which we have termed isosilybin C and isosilybin D due to their structural similarities to isosilybin A and isosilybin B, respectively, afforded a preliminary analysis of structure-activity relationships toward prostate cancer growth, survival, and apoptotic endpoints.

  16. Elucidation and Structural Analysis of Conserved Pools for Genome-Scale Metabolic Reconstructions

    PubMed Central

    Nikolaev, Evgeni V.; Burgard, Anthony P.; Maranas, Costas D.

    2005-01-01

    In this article, we introduce metabolite concentration coupling analysis (MCCA) to study conservation relationships for metabolite concentrations in genome-scale metabolic networks. The analysis allows the global identification of subsets of metabolites whose concentrations are always coupled within common conserved pools. Also, the minimal conserved pool identification (MCPI) procedure is developed for elucidating conserved pools for targeted metabolites without computing the entire basis conservation relationships. The approaches are demonstrated on genome-scale metabolic reconstructions of Helicobacter pylori, Escherichia coli, and Saccharomyces cerevisiae. Despite significant differences in the size and complexity of the examined organism's models, we find that the concentrations of nearly all metabolites are coupled within a relatively small number of subsets. These correspond to the overall exchange of carbon molecules into and out of the networks, interconversion of energy and redox cofactors, and the transfer of nitrogen, sulfur, phosphate, coenzyme A, and acyl carrier protein moieties among metabolites. The presence of large conserved pools can be viewed as global biophysical barriers protecting cellular systems from stresses, maintaining coordinated interconversions between key metabolites, and providing an additional mode of global metabolic regulation. The developed approaches thus provide novel and versatile tools for elucidating coupling relationships between metabolite concentrations with implications in biotechnological and medical applications. PMID:15489308

  17. Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations.

    PubMed

    Toukach, Filip V; Ananikov, Valentine P

    2013-11-01

    All living systems are comprised of four fundamental classes of macromolecules--nucleic acids, proteins, lipids, and carbohydrates (glycans). Glycans play a unique role of joining three principal hierarchical levels of the living world: (1) the molecular level (pathogenic agents and vaccine recognition by the immune system, metabolic pathways involving saccharides that provide cells with energy, and energy accumulation via photosynthesis); (2) the nanoscale level (cell membrane mechanics, structural support of biomolecules, and the glycosylation of macromolecules); (3) the microscale and macroscale levels (polymeric materials, such as cellulose, starch, glycogen, and biomass). NMR spectroscopy is the most powerful research approach for getting insight into the solution structure and function of carbohydrates at all hierarchical levels, from monosaccharides to oligo- and polysaccharides. Recent progress in computational procedures has opened up novel opportunities to reveal the structural information available in the NMR spectra of saccharides and to advance our understanding of the corresponding biochemical processes. The ability to predict the molecular geometry and NMR parameters is crucial for the elucidation of carbohydrate structures. In the present paper, we review the major NMR spectrum simulation techniques with regard to chemical shifts, coupling constants, relaxation rates and nuclear Overhauser effect prediction applied to the three levels of glycomics. Outstanding development in the related fields of genomics and proteomics has clearly shown that it is the advancement of research tools (automated spectrum analysis, structure elucidation, synthesis, sequencing and amplification) that drives the large challenges in modern science. Combining NMR spectroscopy and the computational analysis of structural information encoded in the NMR spectra reveals a way to the automated elucidation of the structure of carbohydrates.

  18. Isolation and structure determination of a lignan from the bark of Salix alba.

    PubMed

    Du, Qizhen; Jerz, Gerold; Shen, Lianqing; Xiu, Lili; Winterhalter, Peter

    2007-05-01

    A lignan, sisymbrifolin (1) found in the fruits of Solanum sisymbriflolium has been isolated from the bark extract of Salix alba (Salicaceae). Its structure was elucidated by its direct spectrum data of ESI-MS and one- and two-dimensional NMR spectroscopy for the first time.

  19. Elucidation of the chemical structure and determination of the production conditions for a bioactive Maillard reaction product, [5-(5,6-dihydro-4H-pyridin-3-ylidenemethyl)furan-2-yl]methanol, isolated from a glucose-lysine heated mixture.

    PubMed

    Chen, Xiu-Min; Chen, Gang; Chen, Hongwen; Zhang, Yilin; Kitts, David D

    2015-02-18

    We previously isolated a bioactive molecule, named F3-A, from an aqueous glucose (Glc) and lysine (Lys) Maillard reaction (MR) model system. Herein, F3-A was verified as [5-(5,6-dihydro-4H-pyridin-3-ylidenemethyl)furan-2-yl]methanol (5) and was subsequently synthesized for confirmation of bioactivity. Using Taguchi and factorial designs, we determined that the conditions which best increased the yield of F3-A were at pH 6 with a sugar:amino acid ratio of 2:1 and heating time of 12 h at 100 °C. The MR mixtures containing glucose produced highest yield, compared to fructose, lactose, and sucrose. Both the F3-A recovered from Glc-Lys MR mixture and the synthesized product exhibited significant (P < 0.05), dose dependent, nitric oxide (NO) inhibitory activity in Caco-2 cells that was comparable to aminoguanidine (AG) and pyrrolidine dithiocarbamate (PDTC), respectively. Finally, an additional inhibitory effect of F3-A was determined when coincubated with AG in cytokine-induced Caco-2 cells. This bioactivity points to a potential role in preventing intestinal inflammation.

  20. Elucidation of structure-function relationships in plant major light-harvesting complex (LHC II) by nonlinear spectroscopy.

    PubMed

    Lokstein, Heiko; Betke, Alexander; Krikunova, Maria; Teuchner, Klaus; Voigt, Bernd

    2012-03-01

    Conventional linear and time-resolved spectroscopic techniques are often not appropriate to elucidate specific pigment-pigment interactions in light-harvesting pigment-protein complexes (LHCs). Nonlinear (laser-) spectroscopic techniques, including nonlinear polarization spectroscopy in the frequency domain (NLPF) as well as step-wise (resonant) and simultaneous (non-resonant) two-photon excitation spectroscopies may be advantageous in this regard. Nonlinear spectroscopies have been used to elucidate substructure(s) of very complex spectra, including analyses of strong excitonic couplings between chlorophylls and of interactions between (bacterio)chlorophylls and "optically dark" states of carotenoids in LHCs, including the major antenna complex of higher plants, LHC II. This article shortly reviews our previous study and outlines perspectives regarding the application of selected nonlinear laser-spectroscopic techniques to disentangle structure-function relationships in LHCs and other pigment-protein complexes.

  1. Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment

    PubMed Central

    Henson, Michael W.; Santo Domingo, Jorge W.; Kourtev, Peter S.; Jensen, Roderick V.; Dunn, James A.

    2015-01-01

    Hexavalent chromium [Cr(VI)] is a soluble carcinogen that has caused widespread contamination of soil and water in many industrial nations. Bacteria have the potential to aid remediation as certain strains can catalyze the reduction of Cr(VI) to insoluble and less toxic Cr(III). Here, we examine Cr(VI) reducing Microbacterium spp. (Cr-K1W, Cr-K20, Cr-K29, and Cr-K32) isolated from contaminated sediment (Seymore, Indiana) and show varying chromate responses despite the isolates’ phylogenetic similarity (i.e., identical 16S rRNA gene sequences). Detailed analysis identified differences based on genomic metabolic potential, growth and general metabolic capabilities, and capacity to resist and reduce Cr(VI). Taken together, the discrepancies between the isolates demonstrate the complexity inter-strain variation can have on microbial physiology and related biogeochemical processes. PMID:26587353

  2. Bioactive Structure of Membrane Lipids and Natural Products Elucidated by a Chemistry-Based Approach.

    PubMed

    Murata, Michio; Sugiyama, Shigeru; Matsuoka, Shigeru; Matsumori, Nobuaki

    2015-08-01

    Determining the bioactive structure of membrane lipids is a new concept, which aims to examine the functions of lipids with respect to their three-dimensional structures. As lipids are dynamic by nature, their "structure" does not refer solely to a static picture but also to the local and global motions of the lipid molecules. We consider that interactions with lipids, which are completely defined by their structures, are controlled by the chemical, functional, and conformational matching between lipids and between lipid and protein. In this review, we describe recent advances in understanding the bioactive structures of membrane lipids bound to proteins and related molecules, including some of our recent results. By examining recent works on lipid-raft-related molecules, lipid-protein interactions, and membrane-active natural products, we discuss current perspectives on membrane structural biology.

  3. Fragmentation follows structure: top-down mass spectrometry elucidates the topology of engineered cystine-knot miniproteins.

    PubMed

    Reinwarth, Michael; Avrutina, Olga; Fabritz, Sebastian; Kolmar, Harald

    2014-01-01

    Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS(3) spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin's folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before. PMID:25303319

  4. Fragmentation follows structure: top-down mass spectrometry elucidates the topology of engineered cystine-knot miniproteins.

    PubMed

    Reinwarth, Michael; Avrutina, Olga; Fabritz, Sebastian; Kolmar, Harald

    2014-01-01

    Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS(3) spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin's folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before.

  5. Fragmentation Follows Structure: Top-Down Mass Spectrometry Elucidates the Topology of Engineered Cystine-Knot Miniproteins

    PubMed Central

    Reinwarth, Michael; Avrutina, Olga; Fabritz, Sebastian; Kolmar, Harald

    2014-01-01

    Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS3 spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin’s folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before. PMID:25303319

  6. Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry.

    PubMed

    Reading, Eamonn; Munoz-Muriedas, Jordi; Roberts, Andrew D; Dear, Gordon J; Robinson, Carol V; Beaumont, Claire

    2016-02-16

    Ion mobility-mass spectrometry (IM-MS) in combination with molecular modeling offers the potential for small molecule structural isomer identification by measurement of their gas phase collision cross sections (CCSs). Successful application of this approach to drug metabolite identification would facilitate resource reduction, including animal usage, and may benefit other areas of pharmaceutical structural characterization including impurity profiling and degradation chemistry. However, the conformational behavior of drug molecules and their metabolites in the gas phase is poorly understood. Here the gas phase conformational space of drug and drug-like molecules has been investigated as well as the influence of protonation and adduct formation on the conformations of drug metabolite structural isomers. The use of CCSs, measured from IM-MS and molecular modeling information, for the structural identification of drug metabolites has also been critically assessed. Detection of structural isomers of drug metabolites using IM-MS is demonstrated and, in addition, a molecular modeling approach has been developed offering rapid conformational searching and energy assessment of candidate structures which agree with experimental CCSs. Here it is illustrated that isomers must possess markedly dissimilar CCS values for structural differentiation, the existence and extent of CCS differences being ionization state and molecule dependent. The results present that IM-MS and molecular modeling can inform on the identity of drug metabolites and highlight the limitations of this approach in differentiating structural isomers. PMID:26752623

  7. Elucidation of the Covalent and Tertiary Structures of Biologically Active Ts3 Toxin.

    PubMed

    Dang, Bobo; Kubota, Tomoya; Mandal, Kalyaneswar; Correa, Ana M; Bezanilla, Francisco; Kent, Stephen B H

    2016-07-18

    Ts3 is an alpha scorpion toxin from the venom of the Brazilian scorpion Tityus serrulatus. Ts3 binds to the domain IV voltage sensor of voltage-gated sodium channels (Nav ) and slows down their fast inactivation. The covalent structure of the Ts3 toxin is uncertain, and the structure of the folded protein molecule is unknown. Herein, we report the total chemical synthesis of four candidate Ts3 toxin protein molecules and the results of structure-activity studies that enabled us to establish the covalent structure of biologically active Ts3 toxin. We also report the synthesis of the mirror image form of the Ts3 protein molecule, and the use of racemic protein crystallography to determine the folded (tertiary) structure of biologically active Ts3 toxin by X-ray diffraction. PMID:27244051

  8. Using FT-IR Spectroscopy to Elucidate the Structures of Ablative Polymers

    NASA Technical Reports Server (NTRS)

    Fan, Wendy

    2011-01-01

    The composition and structure of an ablative polymer has a multifaceted influence on its thermal, mechanical and ablative properties. Understanding the molecular level information is critical to the optimization of material performance because it helps to establish correlations with the macroscopic properties of the material, the so-called structure-property relationship. Moreover, accurate information of molecular structures is also essential to predict the thermal decomposition pathways as well as to identify decomposition species that are fundamentally important to modeling work. In this presentation, I will describe the use of infrared transmission spectroscopy (FT-IR) as a convenient tool to aid the discovery and development of thermal protection system materials.

  9. Vestitol Isolated from Brazilian Red Propolis Inhibits Neutrophils Migration in the Inflammatory Process: Elucidation of the Mechanism of Action.

    PubMed

    Franchin, Marcelo; Cólon, David F; Castanheira, Fernanda V S; da Cunha, Marcos G; Bueno-Silva, Bruno; Alencar, Severino M; Cunha, Thiago M; Rosalen, Pedro L

    2016-04-22

    Vestitol is an isoflavonoid isolated from Brazilian red propolis with potential anti-inflammatory activity. This study investigated the mechanism of action of vestitol on the modulation of neutrophil migration in the inflammatory process. Pre-treatment with vestitol at 1, 3, or 10 mg/kg reduced LPS- or mBSA-induced neutrophil migration and the release of CXCL1/KC and CXCL2/MIP-2 in vivo. Likewise, pre-treatment with vestitol at 1, 3, or 10 μM reduced the levels of CXCL1/KC and CXCL2/MIP-2 in macrophage supernatants in vitro. Moreover, the administration of vestitol (10 mg/kg) reduced leukocyte rolling and adherence in the mesenteric microcirculation of mice. The pre-treatment with vestitol (10 mg/kg) in iNOS(-/-) mice did not block its activity concerning neutrophil migration. With regard to the activity of vestitol on neutrophils isolated from the bone marrow of mice, there was a reduction on the chemotaxis of CXCL2/MIP-2 or LTB4-induced neutrophils and on calcium influx after pre-treatment with the compound at 3 or 10 μM. There was no change in CXCR2 expression by neutrophils treated with vestitol at 10 μM. These findings demonstrate that vestitol is a promising novel anti-inflammatory agent. PMID:26938776

  10. Vestitol Isolated from Brazilian Red Propolis Inhibits Neutrophils Migration in the Inflammatory Process: Elucidation of the Mechanism of Action.

    PubMed

    Franchin, Marcelo; Cólon, David F; Castanheira, Fernanda V S; da Cunha, Marcos G; Bueno-Silva, Bruno; Alencar, Severino M; Cunha, Thiago M; Rosalen, Pedro L

    2016-04-22

    Vestitol is an isoflavonoid isolated from Brazilian red propolis with potential anti-inflammatory activity. This study investigated the mechanism of action of vestitol on the modulation of neutrophil migration in the inflammatory process. Pre-treatment with vestitol at 1, 3, or 10 mg/kg reduced LPS- or mBSA-induced neutrophil migration and the release of CXCL1/KC and CXCL2/MIP-2 in vivo. Likewise, pre-treatment with vestitol at 1, 3, or 10 μM reduced the levels of CXCL1/KC and CXCL2/MIP-2 in macrophage supernatants in vitro. Moreover, the administration of vestitol (10 mg/kg) reduced leukocyte rolling and adherence in the mesenteric microcirculation of mice. The pre-treatment with vestitol (10 mg/kg) in iNOS(-/-) mice did not block its activity concerning neutrophil migration. With regard to the activity of vestitol on neutrophils isolated from the bone marrow of mice, there was a reduction on the chemotaxis of CXCL2/MIP-2 or LTB4-induced neutrophils and on calcium influx after pre-treatment with the compound at 3 or 10 μM. There was no change in CXCR2 expression by neutrophils treated with vestitol at 10 μM. These findings demonstrate that vestitol is a promising novel anti-inflammatory agent.

  11. Elucidating the Structure of Sugars: MW Spectroscopy Combined with Ultrafast UV Laser Vaporization

    NASA Astrophysics Data System (ADS)

    Cocinero, Emilio J.; Ecija, Patricia; Basterretxea, Francisco J.; Fernandez, Jose A.; Castano, Fernando; Lesarri, Alberto; Grabow, Jens-Uwe; Cimas, Alvaro

    2013-06-01

    Carbohydrates are one of the most versatile biochemicalbuilding blocks, widely acting in energetic, structural or recognition processes. Even the small monosaccharides display unique structural and conformational freedom and may coexist in many open-chain or cyclic forms. We recently initiated the investigation of a series of monosaccharides using a combination of ultrafast laser vaporization and microwave spectroscopy in supersonic jet expansions. We present several structural studies on carbohydrates of aldoses and ketoses of five and six carbon sugars vaporized by UV ultrafast laser vaporization and stabilized in a jet expansion. The experimental evidence confirms that sugars exhibits a α-/β-pyranose conformation (6-membered ring), sharply contrasting with the furanose form (5-membered ring) found in the nature (as component of RNA, sucrose). In addition, thanks to the use of enriched samples, we have experimentally determined the substitution and effective structures. Finally, the structure of several monosaccharides was compared and common structural patterns of their conformational landscape will be showed. E. J. Cocinero, A. Lesarri, P. écija, F. J. Basterretxea, J. U. Grabow, J. A. Fernández and F. Castaño Angew. Chem. Int. Ed. 51, 3119-3124, 2012. E. J. Cocinero, A. Lesarri, P. écija, Á. Cimas, B. G. Davis, F. J. Basterretxea, J. A. Fernández and F. Castaño J. Am. Chem. Soc. 135, 2845-2852, 2013.

  12. Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms

    SciTech Connect

    Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J.

    2012-05-09

    Obtaining single crystals for X-ray diffraction remains a major bottleneck in structural biology; when existing crystal growth methods fail to yield suitable crystals, often the target rather than the crystallization approach is reconsidered. Here we demonstrate that polymer-induced heteronucleation, a powerful technique that has been used for small molecule crystallization form discovery, can be applied to protein crystallization by optimizing the heteronucleant composition and crystallization formats for crystallizing a wide range of protein targets. Applying these advances to two benchmark proteins resulted in dramatically increased crystal size, enabling structure determination, for a half century old form of bovine liver catalase (BLC) that had previously only been characterized by electron microscopy, and the discovery of two new forms of concanavalin A (conA) from the Jack bean and accompanying structural elucidation of one of these forms.

  13. Elucidating the Structure of Chiral Molecules by using Amplified Vibrational Circular Dichroism: From Theory to Experimental Realization.

    PubMed

    Domingos, Sérgio R; Hartl, František; Buma, Wybren Jan; Woutersen, Sander

    2015-11-16

    Recent experimental observations of enhanced vibrational circular dichroism (VCD) in molecular systems with low-lying electronically excited states suggest interesting new applications of VCD spectroscopy. The theory describing VCD enhancement through vibronic coupling schemes was derived by Nafie in 1983, but only recently experimental evidence of VCD amplification has demonstrated the extent to which this effect can be exploited as a structure elucidation tool to probe local structure. In this Concept paper, we give an overview of the physics behind vibrational circular dichroism, in particular the equations governing the VCD amplification effect, and review the latest experimental developments with a prospective view on the application of amplified VCD to locally probe biomolecular structure.

  14. Structural elucidation of rapid solution-mediated phase transitions in pharmaceutical solids using in situ synchrotron SAXS/WAXS.

    PubMed

    Boetker, Johan; Rades, Thomas; Rantanen, Jukka; Hawley, Adrian; Boyd, Ben J

    2012-09-01

    In situ elucidation of kinetics of solution-mediated phase transformations using direct structural determination has been achieved using synchrotron SAXS/WAXS radiation. Using theophylline as a model drug with known phase transformation from anhydrate to monohydrate form in aqueous conditions within a few minutes, the kinetics of the structural transition were resolved at the second scale, and the results achieved agreed well with those determined using indirect approaches such as Raman spectroscopy. The recrystallization of the monohydrate in situ (due to its lower solubility) from dissolved anhydrate solution (higher solubility) is demonstrated directly, highlighting a major issue for such compounds in application. The technique has the additional benefit of having the potential to identify intermediate structures which are not readily achievable with in situ spectroscopic techniques, as well as being amenable to high throughput approaches. PMID:22871088

  15. Structural elucidation of rapid solution-mediated phase transitions in pharmaceutical solids using in situ synchrotron SAXS/WAXS.

    PubMed

    Boetker, Johan; Rades, Thomas; Rantanen, Jukka; Hawley, Adrian; Boyd, Ben J

    2012-09-01

    In situ elucidation of kinetics of solution-mediated phase transformations using direct structural determination has been achieved using synchrotron SAXS/WAXS radiation. Using theophylline as a model drug with known phase transformation from anhydrate to monohydrate form in aqueous conditions within a few minutes, the kinetics of the structural transition were resolved at the second scale, and the results achieved agreed well with those determined using indirect approaches such as Raman spectroscopy. The recrystallization of the monohydrate in situ (due to its lower solubility) from dissolved anhydrate solution (higher solubility) is demonstrated directly, highlighting a major issue for such compounds in application. The technique has the additional benefit of having the potential to identify intermediate structures which are not readily achievable with in situ spectroscopic techniques, as well as being amenable to high throughput approaches.

  16. Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography

    PubMed Central

    Mandal, Pradeep K.; Collie, Gavin W.; Srivastava, Suresh C.; Kauffmann, Brice; Huc, Ivan

    2016-01-01

    It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods—that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence ‘TATAAT’. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65–2.3 Å), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence. PMID:27137886

  17. Expression, crystallization and structure elucidation of γ-terpinene synthase from Thymus vulgaris.

    PubMed

    Rudolph, Kristin; Parthier, Christoph; Egerer-Sieber, Claudia; Geiger, Daniel; Muller, Yves A; Kreis, Wolfgang; Müller-Uri, Frieder

    2016-01-01

    The biosynthesis of γ-terpinene, a precursor of the phenolic isomers thymol and carvacrol found in the essential oil from Thymus sp., is attributed to the activitiy of γ-terpinene synthase (TPS). Purified γ-terpinene synthase from T. vulgaris (TvTPS), the Thymus species that is the most widely spread and of the greatest economical importance, is able to catalyze the enzymatic conversion of geranyl diphosphate (GPP) to γ-terpinene. The crystal structure of recombinantly expressed and purified TvTPS is reported at 1.65 Å resolution, confirming the dimeric structure of the enzyme. The putative active site of TvTPS is deduced from its pronounced structural similarity to enzymes from other species of the Lamiaceae family involved in terpenoid biosynthesis: to (+)-bornyl diphosphate synthase and 1,8-cineole synthase from Salvia sp. and to (4S)-limonene synthase from Mentha spicata. PMID:26750479

  18. Mechanism driven structural elucidation of forced degradation products from hydrocortisone in solution.

    PubMed

    Zhang, Fa; Zhou, Jay; Shi, Yiqun; Tavlarakis, Panagiotis; Karaisz, Kenneth

    2016-09-01

    Hydrocortisone degradation products 1, 2, 3, and 4 along with hemiacetal derivatives 5, 6, 7, and 8 were observed through stressed hydrocortisone in solution. Their structures were identified based on HPLC-UV, HPLC-MS, and HPLC-HRMS (high resolution/high accuracy mass spectrometry) analyses as well as reaction mechanistic investigation and synthesis for structural confirmation. 1 and 2 are a pair of E/Z isomers and they were generated through acid catalyzed tautomerization/dehydration of hydrocortisone. Incorporation of water to 1 and 2 resulted in the formation of 3. We also discovered new degradation product 4 which was converted from 3 by oxidation. The degradation products were synthesized by stressing hydrocortisone under the optimized conditions and their structures were characterized by NMR ((1)H/(13)C, COSY, HMBC, HSQC, NOESY) and HRMS analyses. The degradation pathway of hydrocortisone is postulated.

  19. Mechanism driven structural elucidation of forced degradation products from hydrocortisone in solution.

    PubMed

    Zhang, Fa; Zhou, Jay; Shi, Yiqun; Tavlarakis, Panagiotis; Karaisz, Kenneth

    2016-09-01

    Hydrocortisone degradation products 1, 2, 3, and 4 along with hemiacetal derivatives 5, 6, 7, and 8 were observed through stressed hydrocortisone in solution. Their structures were identified based on HPLC-UV, HPLC-MS, and HPLC-HRMS (high resolution/high accuracy mass spectrometry) analyses as well as reaction mechanistic investigation and synthesis for structural confirmation. 1 and 2 are a pair of E/Z isomers and they were generated through acid catalyzed tautomerization/dehydration of hydrocortisone. Incorporation of water to 1 and 2 resulted in the formation of 3. We also discovered new degradation product 4 which was converted from 3 by oxidation. The degradation products were synthesized by stressing hydrocortisone under the optimized conditions and their structures were characterized by NMR ((1)H/(13)C, COSY, HMBC, HSQC, NOESY) and HRMS analyses. The degradation pathway of hydrocortisone is postulated. PMID:27328360

  20. Structural elucidation of sorghum lignins from an integrated biorefinery process based on hydrothermal and alkaline treatments.

    PubMed

    Sun, Shao-Long; Wen, Jia-Long; Ma, Ming-Guo; Sun, Run-Cang

    2014-08-13

    An integrated process based on hydrothermal pretreatment (HTP) (i.e., 110-230 °C, 0.5-2.0 h) and alkaline post-treatment (2% NaOH at 90 °C for 2.0 h) has been performed for the production of xylooligosaccharide, lignin, and digestible substrate from sweet sorghum stems. The yield, purity, dissociation mechanisms, structural features, and structural transformations of alkali lignins obtained from the integrated process were investigated. It was found that the HTP process facilitated the subsequent alkaline delignification, releasing lignin with the highest yield (79.3%) and purity from the HTP residue obtained at 190 °C for 0.5 h. All of the results indicated that the cleavage of the β-O-4 linkages and degradation of β-β and β-5 linkages occurred under the harsh HTP conditions. Depolymerization and condensation reactions simultaneously occurred at higher temperatures (≥ 170 °C). Moreover, the thermostability of lignin was positively related to its molecular weight, but was also affected by the inherent structures, such as β-O-4 linkages and condensed units. These findings will enhance the understanding of structural transformations of the lignins during the integrated process and maximize the potential utilizations of the lignins in a current biorefinery process.

  1. Synthesis, structural elucidation and carbon dioxide adsorption on Zn (II) hexacyanoferrate (II) Prussian blue analogue

    NASA Astrophysics Data System (ADS)

    Roque-Malherbe, R.; Lugo, F.; Polanco, R.

    2016-11-01

    In the course of the last years hexacyanoferrates have been widely studied; even though, the adsorption properties of Zn (II) hexacyanoferrate(II) (labelled here Zn-HII) have not been thoroughly considered. In addition, soft porous crystals, i.e., adsorbents that display structural flexibility have been, as well, extensively studied, however this property has not been reported for Zn (II) hexacyanoferrate(II). In this regard, the key questions addressed here were the synthesis and structural characterization of Zn-HII together with the investigation of their low (up to 1 bar) and high pressure (up to 30 bar) adsorption properties, to found if these materials show structural flexibility. Then, to attain the anticipated goals, structural characterizations were made with: X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDAX), diffuse reflectance infrared Fourier transform spectrometry (DRIFTS) and thermo-gravimetric analysis (TGA), simultaneously, with the investigation of the adsorption of carbon dioxide. As a result of the research process we concluded that the Zn-HII displayed Fm barm space group framework. Besides, the carbon dioxide adsorption investigation demonstrated the presence of the framework expansion effect together with an extremely high adsorption heat, properties that could be useful for the use of Zn(II) hexacyanoferrate(II) as an excellent adsorbent.

  2. Using Jigsaw-Style Spectroscopy Problem-Solving to Elucidate Molecular Structure through Online Cooperative Learning

    ERIC Educational Resources Information Center

    Winschel, Grace A.; Everett, Renata K.; Coppola, Brian P.; Shultz, Ginger V.

    2015-01-01

    Cooperative learning was employed as an instructional approach to facilitate student development of spectroscopy problem solving skills. An interactive online environment was used as a framework to structure weekly discussions around spectroscopy problems outside of class. Weekly discussions consisted of modified jigsaw-style problem solving…

  3. High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence.

    PubMed

    Heggelund, Julie Elisabeth; Burschowsky, Daniel; Bjørnestad, Victoria Ariel; Hodnik, Vesna; Anderluh, Gregor; Krengel, Ute

    2016-04-01

    Cholera is the prime example of blood-group-dependent diseases, with individuals of blood group O experiencing the most severe symptoms. The cholera toxin is the main suspect to cause this relationship. We report the high-resolution crystal structures (1.1-1.6 Å) of the native cholera toxin B-pentamer for both classical and El Tor biotypes, in complexes with relevant blood group determinants and a fragment of its primary receptor, the GM1 ganglioside. The blood group A determinant binds in the opposite orientation compared to previously published structures of the cholera toxin, whereas the blood group H determinant, characteristic of blood group O, binds in both orientations. H-determinants bind with higher affinity than A-determinants, as shown by surface plasmon resonance. Together, these findings suggest why blood group O is a risk factor for severe cholera.

  4. High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence

    PubMed Central

    Heggelund, Julie Elisabeth; Burschowsky, Daniel; Bjørnestad, Victoria Ariel; Hodnik, Vesna; Anderluh, Gregor; Krengel, Ute

    2016-01-01

    Cholera is the prime example of blood-group-dependent diseases, with individuals of blood group O experiencing the most severe symptoms. The cholera toxin is the main suspect to cause this relationship. We report the high-resolution crystal structures (1.1–1.6 Å) of the native cholera toxin B-pentamer for both classical and El Tor biotypes, in complexes with relevant blood group determinants and a fragment of its primary receptor, the GM1 ganglioside. The blood group A determinant binds in the opposite orientation compared to previously published structures of the cholera toxin, whereas the blood group H determinant, characteristic of blood group O, binds in both orientations. H-determinants bind with higher affinity than A-determinants, as shown by surface plasmon resonance. Together, these findings suggest why blood group O is a risk factor for severe cholera. PMID:27082955

  5. Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein

    PubMed Central

    Bokori-Brown, Monika; Martin, Thomas G.; Naylor, Claire E.; Basak, Ajit K.; Titball, Richard W.; Savva, Christos G.

    2016-01-01

    Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel. PMID:27048994

  6. Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein.

    PubMed

    Bokori-Brown, Monika; Martin, Thomas G; Naylor, Claire E; Basak, Ajit K; Titball, Richard W; Savva, Christos G

    2016-01-01

    Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel. PMID:27048994

  7. Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein

    NASA Astrophysics Data System (ADS)

    Bokori-Brown, Monika; Martin, Thomas G.; Naylor, Claire E.; Basak, Ajit K.; Titball, Richard W.; Savva, Christos G.

    2016-04-01

    Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel.

  8. Structure elucidation of fucoidan composed of a novel tetrafucose repeating unit from sea cucumber Thelenota ananas.

    PubMed

    Yu, Long; Xue, Changhu; Chang, Yaoguang; Xu, Xiaoqi; Ge, Lei; Liu, Guanchen; Wang, Yanchao

    2014-03-01

    Thelenota ananas is one of the most popular edible sea cucumber species consumed in China and some Southeast Asian countries. In this study, the delicate structure of fucoidan from T. ananas (Ta-FUC) was clarified. Oligosaccharides and low molecular weight polysaccharides of Ta-FUC were prepared by enzymatic degradation. Their structures, which retained primary structural features of Ta-FUC, were investigated using tandem mass spectrometry and nuclear magnetic resonance. As a result, Ta-FUC was found to be composed of a novel tetrafucose repeating unit [→3-α-L-Fucp-1→3-α-L-Fucp-1→3-α-L-Fucp2,4(OSO3(-))-1→3-α-L-Fucp2(OSO3(-))-1→]. Meanwhile, it was proven to possess a significant inhibitory effect on superoxide radicals with an IC50 of 17.46±0.14μg/ml. This effect was related to its sulphation pattern.

  9. Membrane transporters studied by EPR spectroscopy: structure determination and elucidation of functional dynamics.

    PubMed

    Mullen, Anna; Hall, Jenny; Diegel, Janika; Hassan, Isa; Fey, Adam; MacMillan, Fraser

    2016-06-15

    During their mechanistic cycles membrane transporters often undergo extensive conformational changes, sampling a range of orientations, in order to complete their function. Such membrane transporters present somewhat of a challenge to conventional structural studies; indeed, crystallization of membrane-associated proteins sometimes require conditions that vary vastly from their native environments. Moreover, this technique currently only allows for visualization of single selected conformations during any one experiment. EPR spectroscopy is a magnetic resonance technique that offers a unique opportunity to study structural, environmental and dynamic properties of such proteins in their native membrane environments, as well as readily sampling their substrate-binding-induced dynamic conformational changes especially through complementary computational analyses. Here we present a review of recent studies that utilize a variety of EPR techniques in order to investigate both the structure and dynamics of a range of membrane transporters and associated proteins, focusing on both primary (ABC-type transporters) and secondary active transporters which were key interest areas of the late Professor Stephen Baldwin to whom this review is dedicated. PMID:27284059

  10. Elucidation of the EP defect in Diamond-Blackfan anemia by characterization and prospective isolation of human EPs.

    PubMed

    Iskander, Deena; Psaila, Bethan; Gerrard, Gareth; Chaidos, Aristeidis; En Foong, Hui; Harrington, Yvonne; Karnik, Leena C; Roberts, Irene; de la Fuente, Josu; Karadimitris, Anastasios

    2015-04-16

    Diamond-Blackfan anemia (DBA) is a disorder characterized by a selective defect in erythropoiesis. Delineation of the precise defect is hampered by a lack of markers that define cells giving rise to erythroid burst- and erythroid colony-forming unit (BFU-E and CFU-E) colonies, the clonogenic assays that quantify early and late erythroid progenitor (EEP and LEP) potential, respectively. By combining flow cytometry, cell-sorting, and single-cell clonogenic assays, we identified Lin(-)CD34(+)CD38(+)CD45RA(-)CD123(-)CD71(+)CD41a(-)CD105(-)CD36(-) bone marrow cells as EEP giving rise to BFU-E, and Lin(-)CD34(+/-)CD38(+)CD45RA(-)CD123(-)CD71(+)CD41a(-)CD105(+)CD36(+) cells as LEP giving rise to CFU-E, in a hierarchical fashion. We then applied these definitions to DBA and identified that, compared with controls, frequency, and clonogenicity of DBA, EEP and LEP are significantly decreased in transfusion-dependent but restored in corticosteroid-responsive patients. Thus, both quantitative and qualitative defects in erythroid progenitor (EP) contribute to defective erythropoiesis in DBA. Prospective isolation of defined EPs will facilitate more incisive study of normal and aberrant erythropoiesis. PMID:25755292

  11. Elucidation of the EP defect in Diamond-Blackfan anemia by characterization and prospective isolation of human EPs.

    PubMed

    Iskander, Deena; Psaila, Bethan; Gerrard, Gareth; Chaidos, Aristeidis; En Foong, Hui; Harrington, Yvonne; Karnik, Leena C; Roberts, Irene; de la Fuente, Josu; Karadimitris, Anastasios

    2015-04-16

    Diamond-Blackfan anemia (DBA) is a disorder characterized by a selective defect in erythropoiesis. Delineation of the precise defect is hampered by a lack of markers that define cells giving rise to erythroid burst- and erythroid colony-forming unit (BFU-E and CFU-E) colonies, the clonogenic assays that quantify early and late erythroid progenitor (EEP and LEP) potential, respectively. By combining flow cytometry, cell-sorting, and single-cell clonogenic assays, we identified Lin(-)CD34(+)CD38(+)CD45RA(-)CD123(-)CD71(+)CD41a(-)CD105(-)CD36(-) bone marrow cells as EEP giving rise to BFU-E, and Lin(-)CD34(+/-)CD38(+)CD45RA(-)CD123(-)CD71(+)CD41a(-)CD105(+)CD36(+) cells as LEP giving rise to CFU-E, in a hierarchical fashion. We then applied these definitions to DBA and identified that, compared with controls, frequency, and clonogenicity of DBA, EEP and LEP are significantly decreased in transfusion-dependent but restored in corticosteroid-responsive patients. Thus, both quantitative and qualitative defects in erythroid progenitor (EP) contribute to defective erythropoiesis in DBA. Prospective isolation of defined EPs will facilitate more incisive study of normal and aberrant erythropoiesis.

  12. Elucidating the pH-Dependent Structural Transition of T7 Bacteriophage Endolysin.

    PubMed

    Sharma, Meenakshi; Kumar, Dinesh; Poluri, Krishna Mohan

    2016-08-23

    Bacteriophages are the most abundant and diverse biological entities on earth. Bacteriophage endolysins are unique peptidoglycan hydrolases and have huge potential as effective enzybiotics in various infectious models. T7 bacteriophage endolysin (T7L), also known as N-acetylmuramoyl-l-alanine amidase or T7 lysozyme, is a 17 kDa protein that lyses a range of Gram-negative bacteria by hydrolyzing the amide bond between N-acetylmuramoyl residues and the l-alanine of the peptidoglycan layer. Although the activity profiles of several of the T7 family members have been known for many years, the molecular basis for their pH-dependent differential activity is not clear. In this study, we explored the pH-induced structural, stability, and activity characteristics of T7L by applying a variety of biophysical techniques and protein nuclear magnetic resonance (NMR) spectroscopy. Our studies established a reversible structural transition of T7L below pH 6 and the formation of a partially denatured conformation at pH 3. This low-pH conformation is thermally stable and exposed its hydrophobic pockets. Further, NMR relaxation measurements and structural analysis unraveled that T7L is highly dynamic in its native state and a network of His residues are responsible for the observed pH-dependent conformational dynamics and transitions. As bacteriophage chimeric and engineered endolysins are being developed as novel therapeutics against multiple drug resistance pathogens, we believe that our results are of great help in designing these entities as broadband antimicrobial and/or antibacterial agents.

  13. Tackling the stacking disorder of melon--structure elucidation in a semicrystalline material.

    PubMed

    Seyfarth, Lena; Seyfarth, Jan; Lotsch, Bettina V; Schnick, Wolfgang; Senker, Jürgen

    2010-03-01

    In this work we tackle the stacking disorder of melon, a layered carbon imide amide polymer with the ideal composition (C(6)N(7)(NH)(NH(2))). Although its existence has been postulated since 1834 the structure of individual melon layers could only recently be solved via electron diffraction and high-resolution (15)N solid-state NMR spectroscopy. With only weak van der Waals interactions between neighboring layers its long range stacking order is poorly defined preventing an efficient use of diffraction techniques. We, therefore, rely on a combination of solid-state NMR experiments and force field calculations. The key information is obtained based on heteronuclear ((1)H-(13)C) and homonuclear ((1)H-(1)H) second moments M(2) acquired from (1)H-(13)C cross polarization experiments. To allow for an interpretation of the polarization transfer rates the resonances in the (13)C MAS spectra have to be assigned and the hydrogen atoms have to be located. The assignment was performed using a two-dimensional (15)N-(13)C iDCP experiment. For the determination of the position of the hydrogen atoms NH and HH distances were measured via(1)H-(15)N Lee-Goldburg CP and (1)H-(1)H double-quantum build-up curves, respectively. Furthermore, the homogeneity of the material under examination was investigated exploiting (15)N spin-diffusion. Based on force field methods 256 structure models with varying lateral arrangements between neighboring layers were created. For each model the M(2) were calculated allowing them to be ranked by comparing calculated and measured M(2) as well as via their force field energies. This allows the creation of markedly structured hypersurfaces with two distinctly favored shift vectors for the displacement of neighboring layers. PMID:20165772

  14. Elucidating the pH-Dependent Structural Transition of T7 Bacteriophage Endolysin.

    PubMed

    Sharma, Meenakshi; Kumar, Dinesh; Poluri, Krishna Mohan

    2016-08-23

    Bacteriophages are the most abundant and diverse biological entities on earth. Bacteriophage endolysins are unique peptidoglycan hydrolases and have huge potential as effective enzybiotics in various infectious models. T7 bacteriophage endolysin (T7L), also known as N-acetylmuramoyl-l-alanine amidase or T7 lysozyme, is a 17 kDa protein that lyses a range of Gram-negative bacteria by hydrolyzing the amide bond between N-acetylmuramoyl residues and the l-alanine of the peptidoglycan layer. Although the activity profiles of several of the T7 family members have been known for many years, the molecular basis for their pH-dependent differential activity is not clear. In this study, we explored the pH-induced structural, stability, and activity characteristics of T7L by applying a variety of biophysical techniques and protein nuclear magnetic resonance (NMR) spectroscopy. Our studies established a reversible structural transition of T7L below pH 6 and the formation of a partially denatured conformation at pH 3. This low-pH conformation is thermally stable and exposed its hydrophobic pockets. Further, NMR relaxation measurements and structural analysis unraveled that T7L is highly dynamic in its native state and a network of His residues are responsible for the observed pH-dependent conformational dynamics and transitions. As bacteriophage chimeric and engineered endolysins are being developed as novel therapeutics against multiple drug resistance pathogens, we believe that our results are of great help in designing these entities as broadband antimicrobial and/or antibacterial agents. PMID:27513288

  15. Tannin structural elucidation and quantitative ³¹P NMR analysis. 2. Hydrolyzable tannins and proanthocyanidins.

    PubMed

    Melone, Federica; Saladino, Raffaele; Lange, Heiko; Crestini, Claudia

    2013-10-01

    An unprecedented analytical method that allows simultaneous structural and quantitative characterization of all functional groups present in tannins is reported. In situ labeling of all labile H groups (aliphatic and phenolic hydroxyls and carboxylic acids) with a phosphorus-containing reagent (Cl-TMDP) followed by quantitative ³¹P NMR acquisition constitutes a novel fast and reliable analytical tool for the analysis of tannins and proanthocyanidins with significant implications for the fields of food and feed analyses, tannery, and the development of natural polyphenolics containing products. PMID:23998855

  16. The substituted-cysteine accessibility method (SCAM) to elucidate membrane protein structure.

    PubMed

    Liapakis, G; Simpson, M M; Javitch, J A

    2001-05-01

    The substituted-cysteine accessibility method (SCAM) provides an approach to identifying the residues in the membrane-spanning segments that line a channel, transporter, or binding-site crevice. SCAM can also be used to determine differences in the structures of the membrane-spanning segments in different functional states of the proteins, to map electrostatic potential in the membrane-spanning domains, and to size a channel or binding-site crevice. The protocol in this unit describes the use of SCAM to map the binding-site crevice of a G-protein coupled receptor (GPCR) which binds ligand within the transmembrane portion of the receptor.

  17. Chemical profiling of the major components in natural waxes to elucidate their role in liquid oil structuring.

    PubMed

    Doan, Chi Diem; To, Chak Ming; De Vrieze, Mike; Lynen, Frederic; Danthine, Sabine; Brown, Allison; Dewettinck, Koen; Patel, Ashok R

    2017-01-01

    Elucidating the composition of waxes is of utmost importance to explain their behavior in liquid oil structuring. The chemical components (hydrocarbons - HCs, free fatty acids - FFAs, free fatty alcohols - FALs and wax esters - WEs) of natural waxes were analyzed using HPLC-ELSD and GC-MS followed by evaluation of their oil structuring properties. The gel strength, including the average storage modulus and oscillation yield stress, displayed a negative correlation with FALs and a positive correlation with HCs, FFAs and WEs. The components dictating the gel strength are HCs, FFAs and WEs in a descending order of importance. The consistency of the oleogels increased with the increasing amount of FFAs and HCs and the decreasing amount of WEs and FALs. The presence of more WEs results in a strong but brittle gel with a high initial flow yield stress. We believe these results might be useful in selecting the right waxes to combine in certain fat-based food products. PMID:27507530

  18. Chemical profiling of the major components in natural waxes to elucidate their role in liquid oil structuring.

    PubMed

    Doan, Chi Diem; To, Chak Ming; De Vrieze, Mike; Lynen, Frederic; Danthine, Sabine; Brown, Allison; Dewettinck, Koen; Patel, Ashok R

    2017-01-01

    Elucidating the composition of waxes is of utmost importance to explain their behavior in liquid oil structuring. The chemical components (hydrocarbons - HCs, free fatty acids - FFAs, free fatty alcohols - FALs and wax esters - WEs) of natural waxes were analyzed using HPLC-ELSD and GC-MS followed by evaluation of their oil structuring properties. The gel strength, including the average storage modulus and oscillation yield stress, displayed a negative correlation with FALs and a positive correlation with HCs, FFAs and WEs. The components dictating the gel strength are HCs, FFAs and WEs in a descending order of importance. The consistency of the oleogels increased with the increasing amount of FFAs and HCs and the decreasing amount of WEs and FALs. The presence of more WEs results in a strong but brittle gel with a high initial flow yield stress. We believe these results might be useful in selecting the right waxes to combine in certain fat-based food products.

  19. Top-Down Strategies for the Structural Elucidation of Intact Gram-negative Bacterial Endotoxins

    PubMed Central

    O’Brien, John P.; Needham, Brittany D.; Brown, Dusty B.; Trent, M. Stephen

    2014-01-01

    Re-modelling of lipopolysaccharides, which are the primary constituent of the outer cell membrane of Gram-negative bacteria, modulates pathogenesis and resistance to microbials. Reported herein is the characterization of intact Gram-negative bacterial lipooligosaccharides (LOS) via a new strategy utilizing online liquid chromatography (LC) coupled with ultraviolet photodissociation (UVPD) mass spectrometry. Compared to collision-based MS/MS methods, UVPD and UVPD/HCD promoted a greater array of cleavages within both the glycan and lipid moieties, including C-C, C-N, C-O cleavages in the acyl chains as well as glycosidic and cross-ring cleavages, thus providing the most far-reaching structural characterization of LOS. This LC-MS/MS strategy affords a robust analytical method to structurally characterize complex mixtures of bacterial endotoxins that maintains the integrity of the core oligosaccharide and lipid A domains of LOS, providing direct feedback about the cell envelope architectures and LOS modification strategies involved in resistance host innate immune defense. PMID:25386333

  20. Synthesis and Structural Elucidation of Triazolylmolybdenum(VI) Oxide Hybrids and Their Behavior as Oxidation Catalysts.

    PubMed

    Lysenko, Andrey B; Senchyk, Ganna A; Domasevitch, Konstantin V; Hauser, Jürg; Fuhrmann, Daniel; Kobalz, Merten; Krautscheid, Harald; Neves, Patrícia; Valente, Anabela A; Gonçalves, Isabel S

    2015-09-01

    A large family of bifunctional 1,2,4-triazole molecular tectons (tr) has been explored for engineering molybdenum(VI) oxide hybrid solids. Specifically, tr ligands bearing auxiliary basic or acidic groups were of the type amine, pyrazole, 1H-tetrazole, and 1,2,4-triazole. The organically templated molybdenum(VI) oxide solids with the general compositions [MoO3(tr)], [Mo2O6(tr)], and [Mo2O6(tr)(H2O)2] were prepared under mild hydrothermal conditions or by refluxing in water. Their crystal structures consist of zigzag chains, ribbons, or helixes of alternating cis-{MoO4N2} or {MoO5N} polyhedra stapled by short [N-N]-tr bridges that for bitriazole ligands convert the motifs into 2D or 3D frameworks. The high thermal (235-350 °C) and chemical stability observed for the materials makes them promising for catalytic applications. The molybdenum(VI) oxide hybrids were successfully explored as versatile oxidation catalysts with tert-butyl hydroperoxide (TBHP) or aqueous H2O2 as an oxygen source, at 70 °C. Catalytic performances were influenced by the different acidic-basic properties and steric hindrances of coordinating organic ligands as well as the structural dimensionality of the hybrid. PMID:26280712

  1. ELUCIDATION OF HUMAN CHOLINE KINASE CRYSTAL STRUCTURES IN COMPLEX WITH THE PRODUCTS ADP OR PHOSPHOCHOLINE

    PubMed Central

    Malito, Enrico; Sekulic, Nikolina; Too, Wei Cun See; Konrad, Manfred; Lavie, Arnon

    2006-01-01

    Summary Choline kinase, responsible for the phosphorylation of choline to phosphocholine as the first step of the CDP-choline pathway for the biosynthesis of phosphatidylcholine, has been recognized as a new target for anticancer therapy. Crystal structures of human choline kinase in its apo, ADP- and phosphocholine-bound complexes, respectively, reveal the molecular details of the substrate binding sites. ATP binds in a cavity where residues from both the N- and C-terminal lobes contribute to form a cleft, while the choline-binding site constitutes a deep hydrophobic groove in the C-terminal domain with a rim composed of negatively charged residues. Upon binding of choline, the enzyme undergoes conformational changes independently affecting the N-terminal domain and the ATP-binding loop. From this structural analysis and comparison with other kinases, and from mutagenesis data on the homologous C. elegans choline kinase, a model of the ternary ADP·Phosphocholine complex was built that reveals the molecular basis for the phosphoryl transfer activity of this enzyme. PMID:17007874

  2. Elucidation of human choline kinase crystal structures in complex with the products ADP or phosphocholine.

    PubMed

    Malito, Enrico; Sekulic, Nikolina; Too, Wei Cun See; Konrad, Manfred; Lavie, Arnon

    2006-11-24

    Choline kinase, responsible for the phosphorylation of choline to phosphocholine as the first step of the CDP-choline pathway for the biosynthesis of phosphatidylcholine, has been recognized as a new target for anticancer therapy. Crystal structures of human choline kinase in its apo, ADP and phosphocholine-bound complexes, respectively, reveal the molecular details of the substrate binding sites. ATP binds in a cavity where residues from both the N and C-terminal lobes contribute to form a cleft, while the choline-binding site constitutes a deep hydrophobic groove in the C-terminal domain with a rim composed of negatively charged residues. Upon binding of choline, the enzyme undergoes conformational changes independently affecting the N-terminal domain and the ATP-binding loop. From this structural analysis and comparison with other kinases, and from mutagenesis data on the homologous Caenorhabditis elegans choline kinase, a model of the ternary ADP.phosphocholine complex was built that reveals the molecular basis for the phosphoryl transfer activity of this enzyme.

  3. Structural elucidation of a novel mechanism for the bacteriophage-based inhibition of the RNA degradosome.

    PubMed

    Van den Bossche, An; Hardwick, Steven W; Ceyssens, Pieter-Jan; Hendrix, Hanne; Voet, Marleen; Dendooven, Tom; Bandyra, Katarzyna J; De Maeyer, Marc; Aertsen, Abram; Noben, Jean-Paul; Luisi, Ben F; Lavigne, Rob

    2016-01-01

    In all domains of life, the catalysed degradation of RNA facilitates rapid adaptation to changing environmental conditions, while destruction of foreign RNA is an important mechanism to prevent host infection. We have identified a virus-encoded protein termed gp37/Dip, which directly binds and inhibits the RNA degradation machinery of its bacterial host. Encoded by giant phage фKZ, this protein associates with two RNA binding sites of the RNase E component of the Pseudomonas aeruginosa RNA degradosome, occluding them from substrates and resulting in effective inhibition of RNA degradation and processing. The 2.2 Å crystal structure reveals that this novel homo-dimeric protein has no identifiable structural homologues. Our biochemical data indicate that acidic patches on the convex outer surface bind RNase E. Through the activity of Dip, фKZ has evolved a unique mechanism to down regulate a key metabolic process of its host to allow accumulation of viral RNA in infected cells. PMID:27447594

  4. Structural elucidation of a novel mechanism for the bacteriophage-based inhibition of the RNA degradosome

    PubMed Central

    Van den Bossche, An; Hardwick, Steven W; Ceyssens, Pieter-Jan; Hendrix, Hanne; Voet, Marleen; Dendooven, Tom; Bandyra, Katarzyna J; De Maeyer, Marc; Aertsen, Abram; Noben, Jean-Paul

    2016-01-01

    In all domains of life, the catalysed degradation of RNA facilitates rapid adaptation to changing environmental conditions, while destruction of foreign RNA is an important mechanism to prevent host infection. We have identified a virus-encoded protein termed gp37/Dip, which directly binds and inhibits the RNA degradation machinery of its bacterial host. Encoded by giant phage фKZ, this protein associates with two RNA binding sites of the RNase E component of the Pseudomonas aeruginosa RNA degradosome, occluding them from substrates and resulting in effective inhibition of RNA degradation and processing. The 2.2 Å crystal structure reveals that this novel homo-dimeric protein has no identifiable structural homologues. Our biochemical data indicate that acidic patches on the convex outer surface bind RNase E. Through the activity of Dip, фKZ has evolved a unique mechanism to down regulate a key metabolic process of its host to allow accumulation of viral RNA in infected cells. DOI: http://dx.doi.org/10.7554/eLife.16413.001 PMID:27447594

  5. Structure elucidation of a major fucopyranose-rich heteropolysaccharide (STP-II) from Sargassum thunbergii.

    PubMed

    Luo, Dianhui; Yuan, Xiumei; Zeng, Yawei; Nie, Kaiying; Li, Zhiming; Wang, Zhaojing

    2016-06-01

    A crude polysaccharide was extracted from the edible algae S. thunbergii. DEAE-Sepharose CL-6B column chromatography was used to separate and purify a major polysaccharide STP-II (63.75%) from the crude polysaccharide. STP-II was found to be a homogeneous polysaccharide with a single peak by high-performance size-exclusion chromatography with a Sugar KS-804 column, have a molecular weight of 550 kD, and consist mainly of fucose, xylose, galactose, glucose and glucuronic acid. The structural assignment of STP-II was carried out using Fourier transform infrared spectroscopy analysis, periodate oxidation-smith degradation, partial hydrolysis with acid, methylation analysis and nuclear magnetic resonance studies, and the repeating unit of STP-II was thus determined. The result indicated that (1→3)-linked-fucose, (1→3)-linked-xylose and (1→3)-linked-galactose formed the major components of the main-chain structure, and the branch ratios were 17.5%. The branching and terminal residues were (1→2)-linked-glucuronic acid, (1→4)-linked-glucose, (1→)-linked-xylose and (1→)-linked-4-O-acetyl-glucose, respectively. PMID:27083337

  6. X-ray Crystal Structures Elucidate the Nucleotidyl Transfer Reaction of Transcript Initiation Using Two Nucleotides

    SciTech Connect

    M Gleghorn; E Davydova; R Basu; L Rothman-Denes; K Murakami

    2011-12-31

    We have determined the X-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage N4 RNA polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit RNA polymerase. As observed during T7 RNA polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the O helix, but only the correct base pairing between the +2 substrate and DNA base is able to complete the O-helix conformational transition. Substrate binding also facilitates catalytic metal binding that leads to alignment of the reactive groups of substrates for the nucleotidyl transfer reaction. Although all nucleic acid polymerases use two divalent metals for catalysis, they differ in the requirements and the timing of binding of each metal. In the case of bacteriophage RNA polymerase, we propose that catalytic metal binding is the last step before the nucleotidyl transfer reaction.

  7. Preparation and structural elucidation of (-)-tetrahydroberberine-(+)-2,3-di( p-toluyl) tartaric acid complex

    NASA Astrophysics Data System (ADS)

    Gao, Jin-Ming; Liu, Wei-Tao; Li, Man-Lin; Liu, Han-Wei; Zhang, Xing-Chang; Li, Zong-Xiao

    2008-12-01

    A new (2:1) complex of (-)-13a S-tetrahydroberberine [(-)-13a S-THB] with (+)-2,3-di( p-toluyl) tartaric acid (DTTA), i.e. 5,8,13,13a-tetrahydro-9,10-dimethoxy-2,3-methylenedioxy- 6H dibenzo[a,g] quinolizine·2,3-di( p-toluyl) tartaric acid [2C 20H 20NO 4·C 20H 18O 8], as well as its optical active component (-)-THB, has been obtained from the resolution process of (±)-THB in methanol. The structures of this complex and an enantiomer (-)-13a S-THB have been characterized by CD, IR and NMR spectroscopy as well as by X-ray single crystal diffraction.

  8. In vivo deuteration of a native bacterial biopolymer for structural elucidation using SANS

    NASA Astrophysics Data System (ADS)

    Holden, P. J.; Russell, R. A.; Stone, D. J. M.; Garvey, C. J.; Foster, L. J. R.

    2004-07-01

    In order to facilitate future structural studies, biodeuteration of bacterial polyhydroxyalkanoates (PHAs) was investigated. We report here the in vivo deuteration of poly 3-hydroxyoctanoate (PHO) produced by its native host, the bacterium Pseudomonas oleovorans. Bacterial biomass was produced in bioreactor studies by growth on hydrogenated substrates and PHO was subsequently produced intracellularly (10-20% w/w) during batch fed growth on deuterated octanoic acid under oxygen limitation. GC-MS analyses of the PHO demonstrated that 13 of the 15 hydrogen atoms had been replaced with deuterium (except in position 3), the remaining two hydrogen presumably being derived from water. A SANS contrast variation study was conducted on whole cells and the results indicate the potential to discriminate inclusion bodies formed from deuterated precursor from an otherwise hydrogenated background.

  9. Structural Elucidation and Antioxidant Activities of Proanthocyanidins from Chinese Bayberry (Myrica rubra Sieb. et Zucc.) Leaves

    PubMed Central

    Fu, Yu; Qiao, Liping; Cao, Yuming; Zhou, Xiaozhou; Liu, Yu; Ye, Xingqian

    2014-01-01

    Proanthocyanidins in Chinese bayberry leaves (PCBLs) were qualitatively analyzed. NMR data suggest that PCBLs are mostly composed of (epi)gallocatechin gallate units. Matrix-assisted laser desorption time-of-flight MS data indicate 95 possible prodelphinidin structures, ranging from dimers to tridecamers. Preparative normal-phase HPLC and further analysis by reverse-phase HPLC together with electrospray ionization MS enabled detection of 20 compounds, including seven newly identified compounds in Chinese bayberry leaves. The antioxidant capacity of PCBLs was evaluated by (1,1-diphenyl-2-picryl-hydrazyl), ferric-reducing antioxidant power, and oxygen radical absorption capacity assays. The EC50 of DPPH radical scavenging activities (as 50% decrease in the initial DPPH concentration) were 7.60 µg. The FRAP and ORAC values were 8859.33±978.39 and 12991.61±1553.34 µmol Trolox equivalents per gram, respectively. The results indicate the high antioxidant potency of PCBLs. PMID:24805126

  10. Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure.

    PubMed

    Ye, Xiaoduan; O'Neil, Patrick K; Foster, Adrienne N; Gajda, Michal J; Kosinski, Jan; Kurowski, Michal A; Bujnicki, Janusz M; Friedman, Alan M; Bailey-Kellogg, Chris

    2004-12-01

    Emerging high-throughput techniques for the characterization of protein and protein-complex structures yield noisy data with sparse information content, placing a significant burden on computation to properly interpret the experimental data. One such technique uses cross-linking (chemical or by cysteine oxidation) to confirm or select among proposed structural models (e.g., from fold recognition, ab initio prediction, or docking) by testing the consistency between cross-linking data and model geometry. This paper develops a probabilistic framework for analyzing the information content in cross-linking experiments, accounting for anticipated experimental error. This framework supports a mechanism for planning experiments to optimize the information gained. We evaluate potential experiment plans using explicit trade-offs among key properties of practical importance: discriminability, coverage, balance, ambiguity, and cost. We devise a greedy algorithm that considers those properties and, from a large number of combinatorial possibilities, rapidly selects sets of experiments expected to discriminate pairs of models efficiently. In an application to residue-specific chemical cross-linking, we demonstrate the ability of our approach to plan experiments effectively involving combinations of cross-linkers and introduced mutations. We also describe an experiment plan for the bacteriophage lambda Tfa chaperone protein in which we plan dicysteine mutants for discriminating threading models by disulfide formation. Preliminary results from a subset of the planned experiments are consistent and demonstrate the practicality of planning. Our methods provide the experimenter with a valuable tool (available from the authors) for understanding and optimizing cross-linking experiments. PMID:15557270

  11. Crystal Structure of Human Thymine DNA Glycosylase Bound to DNA Elucidates Sequence-Specific Mismatch Recognition

    SciTech Connect

    Maiti, A.; Morgan, M.T.; Pozharski, E.; Drohat, A.C.

    2009-05-19

    Cytosine methylation at CpG dinucleotides produces m{sup 5}CpG, an epigenetic modification that is important for transcriptional regulation and genomic stability in vertebrate cells. However, m{sup 5}C deamination yields mutagenic G{center_dot}T mispairs, which are implicated in genetic disease, cancer, and aging. Human thymine DNA glycosylase (hTDG) removes T from G{center_dot}T mispairs, producing an abasic (or AP) site, and follow-on base excision repair proteins restore the G{center_dot}C pair. hTDG is inactive against normal A{center_dot}T pairs, and is most effective for G{center_dot}T mispairs and other damage located in a CpG context. The molecular basis of these important catalytic properties has remained unknown. Here, we report a crystal structure of hTDG (catalytic domain, hTDG{sup cat}) in complex with abasic DNA, at 2.8 {angstrom} resolution. Surprisingly, the enzyme crystallized in a 2:1 complex with DNA, one subunit bound at the abasic site, as anticipated, and the other at an undamaged (nonspecific) site. Isothermal titration calorimetry and electrophoretic mobility-shift experiments indicate that hTDG and hTDG{sup cat} can bind abasic DNA with 1:1 or 2:1 stoichiometry. Kinetics experiments show that the 1:1 complex is sufficient for full catalytic (base excision) activity, suggesting that the 2:1 complex, if adopted in vivo, might be important for some other activity of hTDG, perhaps binding interactions with other proteins. Our structure reveals interactions that promote the stringent specificity for guanine versus adenine as the pairing partner of the target base and interactions that likely confer CpG sequence specificity. We find striking differences between hTDG and its prokaryotic ortholog (MUG), despite the relatively high (32%) sequence identity.

  12. Structural elucidation and genomic scrutiny of the C60-C100 mycolic acids of Segniliparus rotundus.

    PubMed

    Lanéelle, Marie-Antoinette; Eynard, Nathalie; Spina, Lucie; Lemassu, Anne; Laval, Françoise; Huc, Emilie; Etienne, Gilles; Marrakchi, Hedia; Daffé, Mamadou

    2013-01-01

    Mycolic acids, very long-chain α-alkyl, β-hydroxylated fatty acids, occur in the members of the order Corynebacteriales where their chain lengths (C(26)-C(88)) and structural features (oxygen functions, cis or trans double bonds, cyclopropane rings and methyl branches) are genus- and species-specific. The molecular composition and structures of the mycolic acids of two species belonging to the genus Segniliparus were determined by a combination of modern analytical chemical techniques, which include MS and NMR. They consist of mono-ethylenic C(62-)C(64) (α'), di-ethylenic C(77)-C(79) (α) and extremely long-chain mycolic acids (α(+)) ranging from 92 to 98 carbon atoms and containing three unsaturations, cis and/or trans double bonds and/or cyclopropanes. The double bonds in each class of mycolic acids were positioned by oxidative cleavage and exhibit locations similar to those of α- and α'-mycolic acids of mycobacteria. For the ultralong chain α-mycolic acids, the three double bonds were located at equally spaced carbon intervals (C(13)-C(16)), with the methyl branches adjacent to the proximal and distal trans double bonds. Examination of the Segniliparus rotundus genome compared with those of other members of the Corynebacteriales indicated two obvious differences in genes encoding the elongation fatty acid (FAS-II) enzymes involved in the biosynthesis of mycolic acids: the organization of 3-ketoacyl-ACP synthases (KasA and KasB) and (3R)-hydroxyacyl-ACP dehydratases (HadAB/BC), on one hand, and the presence of two copies of the hadB gene encoding the catalytic domain of the latter enzyme type, on the other. This observation is discussed in light of the most recent data accumulated on the biosynthesis of this hallmark of Corynebacteriales. PMID:23154972

  13. Elucidating the structure of cyclotides by partial acid hydrolysis and LC-MS/MS analysis.

    PubMed

    Sze, Siu Kwan; Wang, Wei; Meng, Wei; Yuan, Randong; Guo, Tiannan; Zhu, Yi; Tam, James P

    2009-02-01

    We describe here a rapid method to determine the cyclic structure and disulfide linkages of highly stable cyclotides via a combination of flash partial acid hydrolysis, LC-MS/MS, and computational tools. Briefly, a mixture of closely related cyclotides, kalata B1 and varv A purified from Viola yedoensis was partially hydrolyzed in 2 M HCl for 5 min by microwave-assisted hydrolysis or for 30 min in an autoclave oven (121 degrees C and 15 psi). The partially hydrolyzed peptide mixture was then subjected to LC-MS/MS analysis, with the disulfide linked-peptides fragmented by collision activated dissociation (CAD). A computer program written in-house (available for download at http://proteomics.sbs.ntu.edu.sg/cyclotide_SS ) was used for interpreting LC-MS/MS spectra and assigning the disulfide bonds. Time-point analysis of single-disulfide fragments revealed that nonrandom acid catalyzed fragmentation mostly occurred at the turns which are solvent-exposed and often contain side chain functionalized amino acids such as Asx/Glx and Ser/Thr. In particular, the most susceptible bond for acid hydrolysis in kalata B1 and varv A was found to be the highly conserved N25-G26 which is also the head-to-tail ligation site of the linear precursor proteins, indicating that formation of the three disulfide bonds might precede cyclic structure closure by N25-G26 ligation. This observation is consistent with the recent report that the N25-G26 bond formation is the last step in the cyclotide biosynthetic pathway. The process demonstrated here can potentially be a high throughput method that is generally applicable to determine disulfide bonds of other relatively low-abundance cyclotides.

  14. Characteristic conformation of Mosher's amide elucidated using the cambridge structural database.

    PubMed

    Ichikawa, Akio; Ono, Hiroshi; Mikata, Yuji

    2015-07-16

    Conformations of the crystalline 3,3,3-trifluoro-2-methoxy-2-phenylpropanamide derivatives (MTPA amides) deposited in the Cambridge Structural Database (CSD) were examined statistically as Racid-enantiomers. The majority of dihedral angles (48/58, ca. 83%) of the amide carbonyl groups and the trifluoromethyl groups ranged from -30° to 0° with an average angle θ1 of -13°. The other conformational properties were also clarified: (1) one of the fluorine atoms was antiperiplanar (ap) to the amide carbonyl group, forming a staggered conformation; (2) the MTPA amides prepared from primary amines showed a Z form in amide moieties; (3) in the case of the MTPA amide prepared from a primary amine possessing secondary alkyl groups (i.e., Mosher-type MTPA amide), the dihedral angles between the methine groups and the carbonyl groups were syn and indicative of a moderate conformational flexibility; (4) the phenyl plane was inclined from the O-Cchiral bond of the methoxy moiety with an average dihedral angle θ2 of +21°; (5) the methyl group of the methoxy moiety was ap to the ipso-carbon atom of the phenyl group.

  15. Structural elucidation and physicochemical properties of mononuclear Uranyl(VI) complexes incorporating dianionic units

    PubMed Central

    Azam, Mohammad; Velmurugan, Gunasekaran; Wabaidur, Saikh Mohammad; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Al-Resayes, Saud I.; Al-Othman, Zeid A.; Venuvanalingam, Ponnambalam

    2016-01-01

    Two derivatives of organouranyl mononuclear complexes [UO2(L)THF] (1) and [UO2(L)Alc] (2), where L = (2,2′-(1E,1′E)-(2,2-dimethylpropane-1,3-dyl)bis(azanylylidene, THF = Tetrahydrofuran, Alc = Alcohol), have been prepared. These complexes have been determined by elemental analyses, single crystal X-ray crystallography and various spectroscopic studies. Moreover, the structure of these complexes have also been studied by DFT and time dependent DFT measurements showing that both the complexes have distorted pentagonal bipyramidal environment around uranyl ion. TD-DFT results indicate that the complex 1 displays an intense band at 458.7 nm which is mainly associated to the uranyl centered LMCT, where complex 2 shows a band at 461.8 nm that have significant LMCT character. The bonding has been further analyzed by EDA and NBO. The photocatalytic activity of complexes 1 and 2 for the degradation of rhodamine-B (RhB) and methylene blue (MB) under the irradiation of 500W Xe lamp has been explored, and found more efficient in presence of complex 1 than complex 2 for both dyes. In addition, dye adsorption and photoluminescence properties have also been discussed for both complexes. PMID:27595801

  16. Structural elucidation and physicochemical properties of mononuclear Uranyl(VI) complexes incorporating dianionic units.

    PubMed

    Azam, Mohammad; Velmurugan, Gunasekaran; Wabaidur, Saikh Mohammad; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Al-Resayes, Saud I; Al-Othman, Zeid A; Venuvanalingam, Ponnambalam

    2016-01-01

    Two derivatives of organouranyl mononuclear complexes [UO2(L)THF] (1) and [UO2(L)Alc] (2), where L = (2,2'-(1E,1'E)-(2,2-dimethylpropane-1,3-dyl)bis(azanylylidene, THF = Tetrahydrofuran, Alc = Alcohol), have been prepared. These complexes have been determined by elemental analyses, single crystal X-ray crystallography and various spectroscopic studies. Moreover, the structure of these complexes have also been studied by DFT and time dependent DFT measurements showing that both the complexes have distorted pentagonal bipyramidal environment around uranyl ion. TD-DFT results indicate that the complex 1 displays an intense band at 458.7 nm which is mainly associated to the uranyl centered LMCT, where complex 2 shows a band at 461.8 nm that have significant LMCT character. The bonding has been further analyzed by EDA and NBO. The photocatalytic activity of complexes 1 and 2 for the degradation of rhodamine-B (RhB) and methylene blue (MB) under the irradiation of 500W Xe lamp has been explored, and found more efficient in presence of complex 1 than complex 2 for both dyes. In addition, dye adsorption and photoluminescence properties have also been discussed for both complexes. PMID:27595801

  17. Facile synthesis, structural elucidation and spectral analysis of pyrrole 4-imidazole derivatives

    NASA Astrophysics Data System (ADS)

    Singh, R. N.; Rawat, Poonam; Baboo, Vikas

    2015-12-01

    In this work pyrrole 4-imidazole derivatives (3A-3D): benzimidazoles and pyrrole 4-imidazoline have been synthesized by condensation, cyclization and oxidation of ethyl 4-formyl-3,5-dimethyl-1H-pyrrole carboxylate and phenylene diamine derivatives/ethylene diamine. The structure of these biheterocyclic compounds have been derived by elemental and spectroscopic - IR, UV, MS, 1H and 13C NMR analysis as well as theoretical study. The static first hyperpolarizability, β0 values for pyrrole 4-imidazole derivatives, (3A-3D) have been calculated as 10.901 × 10-31, 19.607 × 10-31, 40.323 × 10-31, 5.686 × 10-31 esu, respectively. The gradual increase in β0 value of synthesized pyrrole-benzimidazole derivatives from 3A to 3C is due to addition of acceptors -Cl atom in 3B to -NO2 group in 3C on benzimidazole side. The experimental absorption spectra found to be in UV region and the high β0 values show that the synthesized pyrrole-imidazoles are suitable as non-linear optical (NLO) materials.

  18. Structural elucidation and physicochemical properties of mononuclear Uranyl(VI) complexes incorporating dianionic units.

    PubMed

    Azam, Mohammad; Velmurugan, Gunasekaran; Wabaidur, Saikh Mohammad; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Al-Resayes, Saud I; Al-Othman, Zeid A; Venuvanalingam, Ponnambalam

    2016-09-06

    Two derivatives of organouranyl mononuclear complexes [UO2(L)THF] (1) and [UO2(L)Alc] (2), where L = (2,2'-(1E,1'E)-(2,2-dimethylpropane-1,3-dyl)bis(azanylylidene, THF = Tetrahydrofuran, Alc = Alcohol), have been prepared. These complexes have been determined by elemental analyses, single crystal X-ray crystallography and various spectroscopic studies. Moreover, the structure of these complexes have also been studied by DFT and time dependent DFT measurements showing that both the complexes have distorted pentagonal bipyramidal environment around uranyl ion. TD-DFT results indicate that the complex 1 displays an intense band at 458.7 nm which is mainly associated to the uranyl centered LMCT, where complex 2 shows a band at 461.8 nm that have significant LMCT character. The bonding has been further analyzed by EDA and NBO. The photocatalytic activity of complexes 1 and 2 for the degradation of rhodamine-B (RhB) and methylene blue (MB) under the irradiation of 500W Xe lamp has been explored, and found more efficient in presence of complex 1 than complex 2 for both dyes. In addition, dye adsorption and photoluminescence properties have also been discussed for both complexes.

  19. Elucidating the structural chemistry of glycosaminoglycan recognition by protein C inhibitor.

    PubMed Central

    Kuhn, L A; Griffin, J H; Fisher, C L; Greengard, J S; Bouma, B N; España, F; Tainer, J A

    1990-01-01

    Glycosaminoglycans (GAGs) including heparin accelerate the inhibition of serine proteases by serine protease inhibitors (serpins), an essential process in regulating blood coagulation. to analyze the molecular basis for GAG recognition by the plasma serpin protein C inhibitor (PCI; also known as plasminogen activator inhibitor 3), we have constructed a complete, energy-minimized, three-dimensional model of PCI by using the structure of homologous alpha 1-antitrypsin as a template. Sequence analysis, hydrogen-bonding environment, and shape complementarity suggested that the N-terminal residues of PCI, which are not homologous to those of alpha 1-antitrypsin, form an amphipathic alpha-helix, here designated A+ since it precedes the alpha 1-antitrypsin A helix. Electrostatic calculations revealed a single, highly positive surface region arising from both the A+ and H helices, suggesting that this two-helix motif is required for GAG binding by PCI. The dominant role of electrostatic interactions in PCI-heparin binding was confirmed by the strong ionic strength dependence of heparin stimulation. The involvement of the A+ helix in heparin binding was verified by demonstrating that an anti-PCI antibody that specifically binds the A+ peptide blocks heparin binding. Images PMID:2172989

  20. Structural elucidation and physicochemical properties of mononuclear Uranyl(VI) complexes incorporating dianionic units

    NASA Astrophysics Data System (ADS)

    Azam, Mohammad; Velmurugan, Gunasekaran; Wabaidur, Saikh Mohammad; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Al-Resayes, Saud I.; Al-Othman, Zeid A.; Venuvanalingam, Ponnambalam

    2016-09-01

    Two derivatives of organouranyl mononuclear complexes [UO2(L)THF] (1) and [UO2(L)Alc] (2), where L = (2,2‧-(1E,1‧E)-(2,2-dimethylpropane-1,3-dyl)bis(azanylylidene, THF = Tetrahydrofuran, Alc = Alcohol), have been prepared. These complexes have been determined by elemental analyses, single crystal X-ray crystallography and various spectroscopic studies. Moreover, the structure of these complexes have also been studied by DFT and time dependent DFT measurements showing that both the complexes have distorted pentagonal bipyramidal environment around uranyl ion. TD-DFT results indicate that the complex 1 displays an intense band at 458.7 nm which is mainly associated to the uranyl centered LMCT, where complex 2 shows a band at 461.8 nm that have significant LMCT character. The bonding has been further analyzed by EDA and NBO. The photocatalytic activity of complexes 1 and 2 for the degradation of rhodamine-B (RhB) and methylene blue (MB) under the irradiation of 500W Xe lamp has been explored, and found more efficient in presence of complex 1 than complex 2 for both dyes. In addition, dye adsorption and photoluminescence properties have also been discussed for both complexes.

  1. Structural elucidation of Argonne premium coals: Molecular weights, heteroatom distributions and linkages between clusters

    SciTech Connect

    Winans, R.E.,; Kim, Y.; Hunt, J.E.; McBeth, R.L.

    1995-12-31

    The objective of this study is to create a statistically accurate picture of important structural features for a group of coals representing a broad rank range. Mass spectrometric techniques are used to study coals, coal extracts and chemically modified coals and extracts. Laser desorption mass spectrometry is used to determine molecular weight distributions. Desorption chemical ionization high resolution mass spectrometry provides detailed molecular information on compound classes of molecules is obtained using tandem mass spectrometry. These results are correlated with other direct studies on these samples such as solid NMR, XPS and X-ray absorption spectroscopy. From the complex sets of data, several general trends are emerging especially for heteroatom containing species. From a statistical point of view, heteroatoms must play important roles in the reactivity of all coals. Direct characterization of sulfur containing species in the Argonne coals has been reported from XANES analysis. Indirect methods used include: TG-FTIR and HRMS which rely on thermal desorption and pyrolysis to vaporize the samples. Both XANES and XPS data on nitrogen has been reported, but at this time, the XPS information is probably more reliable. Results from HRMS are discussed in this paper. Most other information on nitrogen is limited to analysis of liquefaction products. However, nitrogen can be important in influencing characteristics of coal liquids and as a source of NO{sub x}`s in coal combustion.

  2. Characteristic conformation of Mosher's amide elucidated using the cambridge structural database.

    PubMed

    Ichikawa, Akio; Ono, Hiroshi; Mikata, Yuji

    2015-01-01

    Conformations of the crystalline 3,3,3-trifluoro-2-methoxy-2-phenylpropanamide derivatives (MTPA amides) deposited in the Cambridge Structural Database (CSD) were examined statistically as Racid-enantiomers. The majority of dihedral angles (48/58, ca. 83%) of the amide carbonyl groups and the trifluoromethyl groups ranged from -30° to 0° with an average angle θ1 of -13°. The other conformational properties were also clarified: (1) one of the fluorine atoms was antiperiplanar (ap) to the amide carbonyl group, forming a staggered conformation; (2) the MTPA amides prepared from primary amines showed a Z form in amide moieties; (3) in the case of the MTPA amide prepared from a primary amine possessing secondary alkyl groups (i.e., Mosher-type MTPA amide), the dihedral angles between the methine groups and the carbonyl groups were syn and indicative of a moderate conformational flexibility; (4) the phenyl plane was inclined from the O-Cchiral bond of the methoxy moiety with an average dihedral angle θ2 of +21°; (5) the methyl group of the methoxy moiety was ap to the ipso-carbon atom of the phenyl group. PMID:26193245

  3. Design, structural and spectroscopic elucidation, and the in vitro biological activities of new diorganotin dithiocarbamates.

    PubMed

    Ferreira, Isabella P; de Lima, Geraldo M; Paniago, Eucler B; Rocha, Willian R; Takahashi, Jacqueline A; Pinheiro, Carlos B; Ardisson, José D

    2012-12-01

    The reaction of 2,2-dimethoxy-N-methylethyllamine or 2-methyl-1,3-dioxolane with CS(2) in alkaline media produced two novel dithiocarbamate salts. Subsequent reactions with organotin halides yielded six new complexes: [SnMe(2){S(2)CNR(R(1))(2)}(2)] (1), [Sn(n-Bu)(2){S(2)CNR(R(1))(2)}(2)] (2), [SnPh(2){S(2)CNR(R(1))(2)}(2)] (3), [SnMe(2){S(2)CNR(R(2))(2)}(2)] (4), [Sn(n-Bu)(2){S(2)CNR(R(2))(2)}(2)] (5), [SnPh(2){S(2)CNR(R(2))(2)}(2)] (6), where R = methyl, R(1) = CH(2)CH(OMe)(2), and R(2) = 2-methyl-1,3-dioxolane. All compounds were identified in terms of infrared, (1)H and (13)C NMR, and the complexes were also characterized using (119)Sn NMR, (119)Sn Mössbauer and X-ray crystallography. The biological activity of all derivatives has been screened in terms of IC(90) and IC(50) against Aspergillus flavus, Aspergillus niger, Aspergillus parasiticus, Penicillium citrinum, Curvularia senegalensis, Staphylococcus aureus, Listeria monocytogenes, Bacillus cereus, Streptococcus sanguinis, Escherichia coli, Citrobacter freundii, Salmonella typhimurium, and Pseudomonas aeruginosa and the results correlated well with a performed study of structure-activity relationship (SAR). Complexes (3), (5) and (6) displayed the best IC(90) and IC(50) in the presence of the fungi, greater than that of miconazole, used as control drug. PMID:23159807

  4. Structural and Functional Elucidation of Peptide Ts11 Shows Evidence of a Novel Subfamily of Scorpion Venom Toxins

    PubMed Central

    Cremonez, Caroline M.; Maiti, Mohitosh; Peigneur, Steve; Cassoli, Juliana Silva; Dutra, Alexandre A. A.; Waelkens, Etienne; Lescrinier, Eveline; Herdewijn, Piet; de Lima, Maria Elena; Pimenta, Adriano M. C.; Arantes, Eliane C.; Tytgat, Jan

    2016-01-01

    To date, several families of peptide toxins specifically interacting with ion channels in scorpion venom have been described. One of these families comprise peptide toxins (called KTxs), known to modulate potassium channels. Thus far, 202 KTxs have been reported, belonging to several subfamilies of KTxs (called α, β, γ, κ, δ, and λ-KTxs). Here we report on a previously described orphan toxin from Tityus serrulatus venom, named Ts11. We carried out an in-depth structure-function analysis combining 3D structure elucidation of Ts11 and electrophysiological characterization of the toxin. The Ts11 structure is highlighted by an Inhibitor Cystine Knot (ICK) type scaffold, completely devoid of the classical secondary structure elements (α-helix and/or β-strand). This has, to the best of our knowledge, never been described before for scorpion toxins and therefore represents a novel, 6th type of structural fold for these scorpion peptides. On the basis of their preferred interaction with voltage-gated K channels, as compared to all the other targets tested, it can be postulated that Ts11 is the first member of a new subfamily, designated as ε-KTx. PMID:27706049

  5. Asparagine-linked oligosaccharides on lutropin, follitropin, and thyrotropin: structural elucidation of the sulfated and sialylated oligosaccharides on bovine, ovine, and human pituitary glycoprotein hormones

    SciTech Connect

    Green, E.D.; Baenziger, J.U.

    1988-01-05

    The authors have elucidated the structures of the anionic asparagine-linked oligosaccharides present on the glycoprotein hormones lutropin (luteinizing hormone), follitropin (follicle-stimulating hormone), and thyrotropin (thyroid-stimulating hormone). Purified hormones, isolated from bovine, ovine, and human pituitaries, were digested with N-glycanase, and the released oligosaccharides were reduced with NaB(/sup 3/H)/sub 4/. The /sup 3/H-labeled oligosaccharides from each hormone were then fractionated by anion-exchange high performance liquid chromatography (HPLC) into populations differing in the number of sulfate and/or sialic acid moieties. The sulfated, sialylated, and sulfated/sialylated structures, which together comprised 67-90% of the asparagine-linked oligosaccharides on the pituitary glycoprotein hormones, were highly heterogeneous and displayed hormone- as well as animal species-specific features. A previously uncharacterized dibranched oligosaccharide, bearing one residue each of sulfate and sialic acid, was found on all of the hormones except bovine lutropin. In this study, they describe the purification and detailed structural characterizations of the sulfated, sialylated, and sulfated/sialylated oligosaccharides found on lutropin, follitropin, and thyrotropin from several animal species.

  6. Choosing the best pulse sequences, acquisition parameters, postacquisition processing strategies, and probes for natural product structure elucidation by NMR spectroscopy.

    PubMed

    Reynolds, William F; Enríquez, Raúl G

    2002-02-01

    The relative merits of different pairs of two-dimensional NMR pulse sequences (COSY-90 vs COSY-45, NOESY vs T-ROESY, HSQC vs HMQC, HMBC vs CIGAR, etc.) are compared and recommendations are made for the preferred choice of sequences for natural product structure elucidation. Similar comparisons are made between different selective 1D sequences and the corresponding 2D sequences. Many users of 2D NMR use longer than necessary relaxation delays and neglect to use forward linear prediction processing. It is shown that using shorter relaxation delays in combination with forward linear prediction allows one to get better resolved spectra in less time. The relative merits of different probes and likely future probe developments are also discussed.

  7. Structure elucidation of the capsular polysaccharide of Acinetobacter baumannii AB5075 having the KL25 capsule biosynthesis locus.

    PubMed

    Senchenkova, Sof'ya N; Shashkov, Alexander S; Popova, Anastasiya V; Shneider, Mikhail M; Arbatsky, Nikolay P; Miroshnikov, Konstantin A; Volozhantsev, Nikolay V; Knirel, Yuriy A

    2015-05-18

    Capsular polysaccharide was isolated by the phenol-water extraction of Acinetobacter baumannii AB5075 and studied by 1D and 2D (1)H and (13)C NMR spectroscopy. The following structure of the linear trisaccharide repeating unit was established: → 3)-β-D-ManpNAcA-(1 → 4)-β-D-ManpNAcA-(1 → 3)-α-D-QuipNAc4NR-(1 → where R indicates (S)-3-hydroxybutanoyl or acetyl in the ratio ∼ 2.5:1. The genes in the polysaccharide biosynthesis locus designated KL25 are appropriate to the established CPS structure.

  8. Structural elucidation of a 3-O-methyl-D-galactose-containing neutral polysaccharide from the fruiting bodies of Phellinus igniarius.

    PubMed

    Yang, Yan; Zhang, Jingsong; Liu, Yanfang; Tang, Qingjiu; Zhao, Zigao; Xia, Wenshui

    2007-06-11

    PIP60-1, a novel heteropolysaccharide isolated from fruiting bodies of the medicinal fungus, Phellinus igniarius, has a molecular weight of 1.71 x 10(4)Da and is composed of L-fucose, D-glucose, D-mannose, D-galactose and 3-O-Me-D-galactose in a ratio of 1:1:1:2:1. A structural investigation of PIP60-1 carried out using sugar and methylation analyses, combined with (1)H and (13)C NMR spectroscopy, including COSY, TOCSY, NOESY, HSQC and HMBC experiments, established the repeating unit of the polysaccharide as the following: [structure: see text] PMID:17359952

  9. Structural elucidation of estrus urinary lipocalin protein (EULP) and evaluating binding affinity with pheromones using molecular docking and fluorescence study

    PubMed Central

    Rajesh, Durairaj; Muthukumar, Subramanian; Saibaba, Ganesan; Siva, Durairaj; Akbarsha, Mohammad Abdulkader; Gulyás, Balázs; Padmanabhan, Parasuraman; Archunan, Govindaraju

    2016-01-01

    Transportation of pheromones bound with carrier proteins belonging to lipocalin superfamily is known to prolong chemo-signal communication between individuals belonging to the same species. Members of lipocalin family (MLF) proteins have three structurally conserved motifs for delivery of hydrophobic molecules to the specific recognizer. However, computational analyses are critically required to validate and emphasize the sequence and structural annotation of MLF. This study focused to elucidate the evolution, structural documentation, stability and binding efficiency of estrus urinary lipocalin protein (EULP) with endogenous pheromones adopting in-silico and fluorescence study. The results revealed that: (i) EULP perhaps originated from fatty acid binding protein (FABP) revealed in evolutionary analysis; (ii) Dynamic simulation study shows that EULP is highly stable at below 0.45 Å of root mean square deviation (RMSD); (iii) Docking evaluation shows that EULP has higher binding energy with farnesol and 2-iso-butyl-3-methoxypyrazine (IBMP) than 2-naphthol; and (iv) Competitive binding and quenching assay revealed that purified EULP has good binding interaction with farnesol. Both, In-silico and experimental studies showed that EULP is an efficient binding partner to pheromones. The present study provides impetus to create a point mutation for increasing longevity of EULP to develop pheromone trap for rodent pest management. PMID:27782155

  10. Building a replisome solution structure by elucidation of protein-protein interactions in the bacteriophage T4 DNA polymerase holoenzyme.

    PubMed

    Alley, S C; Trakselis, M A; Mayer, M U; Ishmael, F T; Jones, A D; Benkovic, S J

    2001-10-19

    Assembly of DNA replication systems requires the coordinated actions of many proteins. The multiprotein complexes formed as intermediates on the pathway to the final DNA polymerase holoenzyme have been shown to have distinct structures relative to the ground-state structures of the individual proteins. By using a variety of solution-phase techniques, we have elucidated additional information about the solution structure of the bacteriophage T4 holoenzyme. Photocross-linking and mass spectrometry were used to demonstrate interactions between I107C of the sliding clamp and the DNA polymerase. Fluorescence resonance energy transfer, analytical ultracentrifugation, and isothermal titration calorimetry measurements were used to demonstrate that the C terminus of the DNA polymerase can interact at two distinct locations on the sliding clamp. Both of these binding modes may be used during holoenzyme assembly, but only one of these binding modes is found in the final holoenzyme. Present and previous solution interaction data were used to build a model of the holoenzyme that is consistent with these data.

  11. Structural elucidation of the hormonal inhibition mechanism of the bile acid cholate on human carbonic anhydrase II

    SciTech Connect

    Boone, Christopher D.; Tu, Chingkuang; McKenna, Robert

    2014-06-01

    The structure of human carbonic anhydrase II in complex with cholate has been determined to 1.54 Å resolution. Elucidation of the novel inhibition mechanism of cholate will aid in the development of a nonsulfur-containing, isoform-specific therapeutic agent. The carbonic anhydrases (CAs) are a family of mostly zinc metalloenzymes that catalyze the reversible hydration/dehydration of CO{sub 2} into bicarbonate and a proton. Human isoform CA II (HCA II) is abundant in the surface epithelial cells of the gastric mucosa, where it serves an important role in cytoprotection through bicarbonate secretion. Physiological inhibition of HCA II via the bile acids contributes to mucosal injury in ulcerogenic conditions. This study details the weak biophysical interactions associated with the binding of a primary bile acid, cholate, to HCA II. The X-ray crystallographic structure determined to 1.54 Å resolution revealed that cholate does not make any direct hydrogen-bond interactions with HCA II, but instead reconfigures the well ordered water network within the active site to promote indirect binding to the enzyme. Structural knowledge of the binding interactions of this nonsulfur-containing inhibitor with HCA II could provide the template design for high-affinity, isoform-specific therapeutic agents for a variety of diseases/pathological states, including cancer, glaucoma, epilepsy and osteoporosis.

  12. Active isolation of vibrations with adaptive structures

    NASA Technical Reports Server (NTRS)

    Guigou, C.; Fuller, C. R.; Wagstaff, P. R.

    1991-01-01

    Vibration transmission in structures is controlled by means of a technique which employs distributed arrays of piezoelectric transducers bonded to the supporting structure. Distributed PVDF piezoelectric strips are employed as error sensors, and a two-channel feedforward adaptive LMS algorithm is used for minimizing error signals and thereby controlling the structure. A harmonic force input excites a thick plate, and a receiving plate is configured with three pairs of piezoelectric actuators. Modal analyses are performed to determine the resonant frequencies of the system, and a scanning laser vibrometer is used to study the shape of the response of the receiving plate during excitation with and without the control algorithm. Efficient active isolation of the vibrations is achieved with modal suppression, and good control is noted in the on-resonance cases in which increased numbers of PVDF sensors and piezoelectric actuators are employed.

  13. Structure elucidation of two new xanthone derivatives from the marine fungus Penicillium sp. (ZZF 32#) from the South China Sea.

    PubMed

    Shao, Changlun; Wang, Changyun; Wei, Meiyan; Gu, Yucheng; Xia, Xuekui; She, Zhigang; Lin, Yongcheng

    2008-11-01

    Two new xanthones, 8-(methoxycarbonyl)-1-hydroxy-9-oxo-9H-xanthene-3-carboxylic acid (1) and dimethyl 8-methoxy-9-oxo-9H-xanthene-1,6-dicarboxylate (2) and one known xanthone methyl 8-hydroxy-6-methyl-9-oxo-9H-xanthene-1-carboxylate (3) were isolated from the culture broth of the mangrove fungus Penicillium sp. (ZZF 32#) collected from the South China Sea. Their structures were established by comprehensive analysis of one-dimensional (1D) and two-dimensional (2D) NMR data. The structure of compound 3 was confirmed by X-ray crystallography, which led to the suggestion that janthinone (4) might have the same structure as 3. Compounds 1-3 were inactive against KB or KBv200 cells during cytotoxicity evaluations.

  14. Dose-dependent targeted knockout methodology combined with deep structure elucidation strategies for Chinese licorice chemical profiling.

    PubMed

    Jiang, Zhenzuo; Wang, Yuefei; Zhu, Yan; Zhang, Lei; Chai, Xin; Jiang, Miaomiao; Shan, Lihua

    2015-11-10

    One of the limitations with regards to the chemical profiling of Chinese herbs is that low-level compounds are masked by high-level structures. Here, we established a novel methodology based on a dose-dependent targeted knockout (DDTK) technique combined with deep structure elucidation strategies to allow the chemical profiling of Chinese licorice. We employed ultra-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UPLC-Q/TOF MS) incorporated with the DDTK technique to identify the compounds in different concentration samples and found that the compounds at the high- or medium-level were detected readily in the sample at a low concentration; subsequently, minor or trace-level constituents were identified in the sample at a high concentration by rejecting high-level constituents detected in the sample at a low concentration based on a heart-cutting technique during analysis. In this study, among the 232 compounds detected, 27 compounds were unequivocally identified and 165 compounds, including 29 new compounds and two new natural products, were tentatively characterized. The novel methodology established in this work paves the way the further identification of compounds from complicated mixtures, especially traditional Chinese medicines.

  15. Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D

    PubMed Central

    Fabris, Daniele; Yu, Eizadora T.

    2010-01-01

    Chemical probing represents a very versatile alternative for studying the structure and dynamics of substrates that are intractable by established high-resolution techniques. The implementation of MS-based strategies for the characterization of probing products has not only extended the range of applicability to virtually all types of biopolymers, but has also paved the way for the introduction of new reagents that would not have been viable with traditional analytical platforms. As the availability of probing data is steadily increasing on the wings of the development of dedicated interpretation aids, powerful computational approaches have been explored to enable the effective utilization of such information to generate valid molecular models. This combination of factors has contributed to making the possibility of obtaining actual 3D structures by MS-based technologies (MS3D) a reality. Although approaches for achieving structure determination of unknown substrates or assessing the dynamics of known structures may share similar reagents and development trajectories, they clearly involve distinctive experimental strategies, analytical concerns, and interpretation paradigms. This Perspective offers a commentary on methods aimed at obtaining distance constraints for the modeling of full-fledged structures, while highlighting common elements, salient distinctions, and complementary capabilities exhibited by methods employed in dynamics studies. We discuss critical factors to be addressed for completing effective structural determinations and expose possible pitfalls of chemical methods. We survey programs developed for facilitating the interpretation of experimental data and discuss possible computational strategies for translating sparse spatial constraints into all-atom models. Examples are provided to illustrate how the concerted application of very diverse probing techniques can lead to the solution of actual biological substrates. PMID:20648672

  16. Relationships between functional genes in Lactobacillus delbrueckii ssp. bulgaricus isolates and phenotypic characteristics associated with fermentation time and flavor production in yogurt elucidated using multilocus sequence typing.

    PubMed

    Liu, Wenjun; Yu, Jie; Sun, Zhihong; Song, Yuqin; Wang, Xueni; Wang, Hongmei; Wuren, Tuoya; Zha, Musu; Menghe, Bilige; Heping, Zhang

    2016-01-01

    Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is well known for its worldwide application in yogurt production. Flavor production and acid producing are considered as the most important characteristics for starter culture screening. To our knowledge this is the first study applying functional gene sequence multilocus sequence typing technology to predict the fermentation and flavor-producing characteristics of yogurt-producing bacteria. In the present study, phenotypic characteristics of 35 L. bulgaricus strains were quantified during the fermentation of milk to yogurt and during its subsequent storage; these included fermentation time, acidification rate, pH, titratable acidity, and flavor characteristics (acetaldehyde concentration). Furthermore, multilocus sequence typing analysis of 7 functional genes associated with fermentation time, acid production, and flavor formation was done to elucidate the phylogeny and genetic evolution of the same L. bulgaricus isolates. The results showed that strains significantly differed in fermentation time, acidification rate, and acetaldehyde production. Combining functional gene sequence analysis with phenotypic characteristics demonstrated that groups of strains established using genotype data were consistent with groups identified based on their phenotypic traits. This study has established an efficient and rapid molecular genotyping method to identify strains with good fermentation traits; this has the potential to replace time-consuming conventional methods based on direct measurement of phenotypic traits. PMID:26547656

  17. Relationships between functional genes in Lactobacillus delbrueckii ssp. bulgaricus isolates and phenotypic characteristics associated with fermentation time and flavor production in yogurt elucidated using multilocus sequence typing.

    PubMed

    Liu, Wenjun; Yu, Jie; Sun, Zhihong; Song, Yuqin; Wang, Xueni; Wang, Hongmei; Wuren, Tuoya; Zha, Musu; Menghe, Bilige; Heping, Zhang

    2016-01-01

    Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is well known for its worldwide application in yogurt production. Flavor production and acid producing are considered as the most important characteristics for starter culture screening. To our knowledge this is the first study applying functional gene sequence multilocus sequence typing technology to predict the fermentation and flavor-producing characteristics of yogurt-producing bacteria. In the present study, phenotypic characteristics of 35 L. bulgaricus strains were quantified during the fermentation of milk to yogurt and during its subsequent storage; these included fermentation time, acidification rate, pH, titratable acidity, and flavor characteristics (acetaldehyde concentration). Furthermore, multilocus sequence typing analysis of 7 functional genes associated with fermentation time, acid production, and flavor formation was done to elucidate the phylogeny and genetic evolution of the same L. bulgaricus isolates. The results showed that strains significantly differed in fermentation time, acidification rate, and acetaldehyde production. Combining functional gene sequence analysis with phenotypic characteristics demonstrated that groups of strains established using genotype data were consistent with groups identified based on their phenotypic traits. This study has established an efficient and rapid molecular genotyping method to identify strains with good fermentation traits; this has the potential to replace time-consuming conventional methods based on direct measurement of phenotypic traits.

  18. Elucidating structural characteristics of biomass using solution-state 2 D NMR with a mixture of deuterated dimethylsulfoxide and hexamethylphosphoramide

    DOE PAGES

    Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun; Li, Mi

    2016-04-26

    In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO-d6) and hexamethylphosphoramide (HMPA-d18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO-d6/HMPA-d18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass, facilitating a facile sample preparation and involvingmore » with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.« less

  19. Structural elucidation of SrtA enzyme in Enterococcus faecalis: an emphasis on screening of potential inhibitors against the biofilm formation.

    PubMed

    Selvaraj, Chandrabose; Sivakamavalli, Jeyachandran; Vaseeharan, Baskaralingam; Singh, Poonam; Singh, Sanjeev Kumar

    2014-07-01

    Enterococcus faecalis is a pathogenic Gram-positive bacterium, which mainly infects humans through urinary tract infections. SrtA is an essential enzyme for survival of E. faecalis, and inhibition of this particular enzyme will reduce the virulence of biofilm formation. It is proved to be associated with the microbial surface protein embedded signal transduction mechanism and promising as a suitable anti-microbial drug target for E. faecalis. The present work gives an inclusive description of SrtA isolated from E. faecalis through computational and experimental methodologies. For exploring the mechanism of SrtA and to screen potential leads against E. faecalis, we have generated three-dimensional models through homology modeling. The 3D model showed conformational stability over time, confirming the quality of the starting 3D model. Large scale 100 ns molecular dynamics simulations show the intramolecular changes occurring in SrtA, and multiple conformations of structure based screening elucidate potential leads against this pathogen. Experimental results showed that the screened compounds are active showing anti-microbial and anti-biofilm activity, as SrtA is known to play an important role in E. faecalis biofilm formation. Experimental results also suggest that SrtA specific screened compounds have better anti-biofilm activity than the available inhibitors. Therefore, we believe that development of these compounds would be an impetus to design the novel chief SrtA inhibitors against E. faecalis.

  20. Structural elucidation of SrtA enzyme in Enterococcus faecalis: an emphasis on screening of potential inhibitors against the biofilm formation.

    PubMed

    Selvaraj, Chandrabose; Sivakamavalli, Jeyachandran; Vaseeharan, Baskaralingam; Singh, Poonam; Singh, Sanjeev Kumar

    2014-07-01

    Enterococcus faecalis is a pathogenic Gram-positive bacterium, which mainly infects humans through urinary tract infections. SrtA is an essential enzyme for survival of E. faecalis, and inhibition of this particular enzyme will reduce the virulence of biofilm formation. It is proved to be associated with the microbial surface protein embedded signal transduction mechanism and promising as a suitable anti-microbial drug target for E. faecalis. The present work gives an inclusive description of SrtA isolated from E. faecalis through computational and experimental methodologies. For exploring the mechanism of SrtA and to screen potential leads against E. faecalis, we have generated three-dimensional models through homology modeling. The 3D model showed conformational stability over time, confirming the quality of the starting 3D model. Large scale 100 ns molecular dynamics simulations show the intramolecular changes occurring in SrtA, and multiple conformations of structure based screening elucidate potential leads against this pathogen. Experimental results showed that the screened compounds are active showing anti-microbial and anti-biofilm activity, as SrtA is known to play an important role in E. faecalis biofilm formation. Experimental results also suggest that SrtA specific screened compounds have better anti-biofilm activity than the available inhibitors. Therefore, we believe that development of these compounds would be an impetus to design the novel chief SrtA inhibitors against E. faecalis. PMID:24718729

  1. Structure elucidation and HPLC-MS/MS determination of a potential biomarker for estradiol administration in cattle.

    PubMed

    Regal, Patricia; Seijas, Julio A; Cepeda, Alberto; Fente, Cristina

    2013-11-01

    Administration of hormonal compounds as growth promoters in livestock farming was banned by Council Directive 96/22/EC. However, this kind of substances is sometimes reported within the framework of European monitoring residue plans. Various analytical methods have been previously developed to screen for their misuse, and they are now especially efficient for monitoring the illegal administration of synthetic and semisynthetic hormones. Nevertheless, proving an exogenous administration of hormones from natural origin (i.e., estradiol-17β or progesterone) still remains a challenge for European authorities. These target compounds are indeed always present in the animal matrix, and the establishment of reference thresholds appears very difficult because of the extreme variability existing among animals. In 2011, a metabolomics study was performed on serum samples obtained from cows treated with estradiol-17β (or its ester estradiol benzoate) and from control animals using a high-performance liquid chromatography (HPLC)-LTQ-Orbitrap system. After appropriate data processing and multivariate statistical analysis (orthogonal partial least squares discriminant analysis), it was possible to highlight one potential biomarker candidate of estradiol treatments in bovine animals. Now, this biomarker has been structurally elucidated as a dipeptide, and its usefulness has been tested through a targeted HPLC-MS/MS method. Its presence in the previous samples has been confirmed and also in additional samples from estradiol-treated animals.

  2. Adenine photodimerization in deoxyadenylate sequences: elucidation of the mechanism through structural studies of a major d(ApA) photoproduct.

    PubMed Central

    Kumar, S; Joshi, P C; Sharma, N D; Bose, S N; Jeremy, R; Davies, H; Takeda, N; McCloskey, J A

    1991-01-01

    The mechanism of the photodimerization of adjacent adenine bases on the same strand of DNA has been elucidated by determining the structure of one of the two major photoproducts that are formed by UV irradiation of the deoxydinucleoside monophosphate d(ApA). The photoproduct, denoted d(ApA)*, corresponds to a species of adenine photodimer first described by Pörschke (Pörschke, D. (1973) J.Am.Chem.Soc. 95, 8440-8446). From a detailed examination of its chemical and spectroscopic properties, including comparisons with the model compound N-cyano-N1-(1-methylimidazol-5-yl)formamidine, it is deduced that d(ApA)* contains a deoxyadenosine unit covalently linked through its C(8) position to C(4) of an imidazole N(1) deoxyribonucleoside moiety bearing an N-cyanoformamidino substituent at C(5). On treatment with acid, d(ApA)* is degraded with high specificity to 8-(5-amino-imidazol-4-yl)adenine whose identity has been confirmed by independent chemical synthesis. It is concluded that the primary event in adenine photodimerization entails photoaddition of the N(7)-C(8) double bond of the 5'-adenine across the C(6) and C(5) positions of the 3'-adenine. The azetidine species thus generated acts as a common precursor to both types of d(ApA) photoproduct which are formed from it by competing modes of azetidine ring fission. PMID:2057348

  3. Identification and structural elucidation of four cannabimimetic compounds (RCS-4, AM-2201, JWH-203 and JWH-210) in seized products.

    PubMed

    Denooz, Raphael; Vanheugen, Jean-Claude; Frederich, Michel; de Tullio, Pascal; Charlier, Corinne

    2013-03-01

    Since 2008, herbal mixtures with synthetic cannabinoid compounds have been sold as incense throughout the world. Although these new drugs are labeled as not for human consumption, these products are smoked for their cannabis-like effects. This study reports the structural and spectral elucidation of four cannabimimetic compounds seized in Belgium: (4-methoxyphenyl)-1-(pentyl-1H-indol-3-yl)methanone (RCS-4), 1-(5-fluoropentyl)-3-(1-naphtoyl)indole (AM-2201), 2-(2-chlorophenyl)-1-(1-pentylindol-3-yl)ethanone (JWH-203) and 4-ethylnaphthalen-1-yl-(1-pentylindol-3-yl)methanone (JWH-210). Laboratory investigations were conducted by liquid chromatography (LC)-ultraviolet spectroscopy, high-resolution accurate mass detection and nuclear magnetic resonance (NMR) analysis. This combined analytical approach allowed the detection of illicit compounds for which reference materials were not available. To facilitate identification and to complete existing databases, ultraviolet spectra and NMR data of all seized products are presented. Additionally, LC-quadrupole time-of-flight data were recorded to provide absolute identification.

  4. Structure elucidation and in vitro cytotoxicity of ochratoxin α amide, a new degradation product of ochratoxin A.

    PubMed

    Bittner, Andrea; Cramer, Benedikt; Harrer, Henning; Humpf, Hans-Ulrich

    2015-05-01

    The mycotoxin ochratoxin A is a secondary metabolite occurring in a wide range of commodities. During the exposure of ochratoxin A to white and blue light, a cleavage between the carbon atom C-14 and the nitrogen atom was described. As a reaction product, the new compound ochratoxin α amide has been proposed based on mass spectrometry (MS) experiments. In the following study, we observed that this compound is also formed at high temperatures such as used for example during coffee roasting and therefore represents a further thermal ochratoxin A degradation product. To confirm the structure of ochratoxin α amide, the compound was prepared in large scale and complete structure elucidation via nuclear magnetic resonance (NMR) and MS was performed. Additionally, first studies on the toxicity of ochratoxin α amide were performed using immortalized human kidney epithelial (IHKE) cells, a cell line known to be sensitive against ochratoxin A with an IC50 value of 0.5 μM. Using this system, ochratoxin α amide revealed no cytotoxicity up to concentrations of 50 μM. Thus, these results propose that the thermal degradation of ochratoxin A to ochratoxin α amide might be a detoxification process. Finally, we present a sample preparation and a HPLC-tandem mass spectrometry (HPLC-MS/MS) method for the analysis of ochratoxin α amide in extrudates and checked its formation during the extrusion of artificially contaminated wheat grits at 150 and 180 °C, whereas no ochratoxin α amide was detectable under these conditions. PMID:25566949

  5. Structure of constituents isolated from the flower buds of Cananga odorata and their inhibitory effects on aldose reductase.

    PubMed

    Matsumoto, Takahiro; Nakamura, Seikou; Fujimoto, Katsuyoshi; Ohta, Tomoe; Ogawa, Keiko; Yoshikawa, Masayuki; Matsuda, Hisashi

    2014-10-01

    Three new terpenoid derivatives, canangaterpenes IV-VI, were isolated from the flower buds of Cananga odorata, cultivated in Thailand, together with eight known flavonoids. The chemical structures of the new compounds were elucidated on the basis of chemical and physicochemical evidence. The inhibitory effects of the isolated compounds on aldose reductase were also investigated. Several terpenoid derivatives and flavonoids were shown to inhibit aldose reductase. PMID:24816646

  6. 3-Ishwarone, a rare ishwarane sesquiterpene from Peperomia scandens Ruiz & Pavon: structural elucidation through a joint experimental and theoretical study.

    PubMed

    Junior, Fernando M dos S; Velozo, Leosvaldo S M; de Carvalho, Erika M; Marques, André M; Borges, Ricardo M; Trindade, Ana Paula F; dos Santos, Maria Isabel S; de Albuquerque, Ana Carolina F; Costa, Fabio L P; Kaplan, Maria Auxiliadora C; de Amorim, Mauro B

    2013-01-01

    3-Ishwarone, (1), a sesquiterpene with a rare ishwarane skeleton, was isolated from Peperomia scandens Ruiz & Pavon (Piperaceae). Its structure was unambiguously determined by 1D- and 2D-NMR and infrared analyses, as well as by comparative theoretical studies which involved calculations of 13C-NMR chemical shifts, using the Density Functional Theory (DFT) with the mPW1PW91 hybrid functional and Pople's 6-31G(d) basis set, and of vibrational frequencies, using the B3LYP hybrid functional and triple ζ Dunning's correlation consistent basis set (cc-pVTZ), of (1) and three of its possible diastereomers, compounds 2-4. PMID:24184821

  7. Structure elucidation of Sch 20562, a glucosidic cyclic dehydropeptide lactone--the major component of W-10 antifungal antibiotic.

    PubMed

    Afonso, A; Hon, F; Brambilla, R

    1999-04-01

    A novel bacterium designated as Aeromonas sp. W-10 produces the antibiotic W-10 complex which comprises of two major and several minor components. The two major components from this complex, Sch 20562 (1) and Sch 20561 (1a), are of biological interest in view of their potent antifungal activity. The chemical degradation studies utilized for the assignment of structure 1 for Sch 20562 are described here. Some of the noteworthy diversity of structural features in this glucosidic cyclic dehydrononapeptide lactone 1 are: an N-terminal (D)-beta-hydroxymyristyl unit, three D-amino acid units, two (E)-alpha-aminocrotonyl units, and an O-alpha-D-glucosyl-N-methyl-L-allo-threonine unit. The structure determination of 1 utilized the selective cleavage of the dehydropeptide units by ozonolysis to form fragments that were sequenced by mass spectrometry. The stereochemistry of the amino acid units were assigned by isolation of the free amino acids from the hydrolysates of the fragments. The stereochemistry of the alpha-aminocrotonyl units and the glucosidic linkage were assigned by nmr spectroscopy and molecular rotation data.

  8. Porphyrins from Messel oil shale (Eocene, Germany): Structure elucidation, geochemical and biological significance, and distribution as a function of depth

    NASA Astrophysics Data System (ADS)

    Ocampo, Rubén; Bauder, Claude; Callot, Henry J.; Albrecht, Pierre

    1992-02-01

    The extraction and isolation procedures of twenty nickel porphyrins (seven alkylporphyrins, thirteen carboxylic acids) from lacustrine Messel shale (Eocene, Germany), as well as the unequivocal structural assignments (obtained using 200 and 400 MHz nuclear magnetic resonance (NMR), nuclear Overhauser effect, mass spectrometry and total or partial synthesis of six reference compounds) are described. Ten porphyrins could be specifically correlated with biological precursors: algal chlorophyll c (4), bacteriochlorophylls d (3) and heme (3), while the remaining ones may arise from several chlorophylls. The structures of these fossil pigments mostly confirm the classical "Treibs scheme," including the origin of some porphyrins from nonchlorophyll sources. They also show that, even in a very immature sediment, deep modifications occur, including, in particular, extensive degradation of chlorophyll E ring. The composition of the porphyrin fractions of Messel oil shale was also studied as a function of depth. A porphyrin acids/alkylporphyrins ratio varying from 0.35 to 24.8 demonstrated that the apparent homogeneity of the shale is not reflected on the molecular scale. This was confirmed when the abundance of the twenty individual porphyrins of known structure was measured along the core. Significant correlations between individual porphyrins were found: fossils of bacteriochlorophylls d, homolog pairs of porphyrins (3-H/3-ethyl), etc.

  9. Anti- and pro-lipase activity of selected medicinal, herbal and aquatic plants, and structure elucidation of an anti-lipase compound.

    PubMed

    Ado, Muhammad Abubakar; Abas, Faridah; Mohammed, Abdulkarim Sabo; Ghazali, Hasanah M

    2013-01-01

    Plants that help in slowing down the digestion of triacylglycerols (TAGs) in the pancreas and small intestine of humans play an important role in the reduction of obesity. On the other hand, there may be plants or plant parts that stimulate intestinal lipolytic activity, thus contributing to greater TAG assimilation. The aim of this study was to evaluate the aqueous methanolic extracts of ninety eight (98) medicinal, herbal and aquatic plant materials from Malaysia for their effect on porcine pancreatic lipase (PPL) activity and to identify the structure of an anti-lipase compound from one of the sources. The degree of inhibition was also quantified as relative to orlistat activity against PPL (orlistat equivalents). Results revealed that while 19.4% of the extracts were found to have anti-lipase activity ≥80%, 12% were actually found to promote PPL activity. Twenty two percent (22.4%) exhibited moderate inhibition (41%-80%) and 2% were neutral toward PPL activity. The ripe fruit of Averrhoa carambola and the leaves of Archidendron jiringa (Jack) I.C Nielsen L. (jering), Cynometra cauliflora (nam-nam) and Aleurites moluccana (L.) Willd (candle nut/buah keras) had the highest (100%) anti-lipase activity and are equivalent to 0.11 µg orlistat/mL. Plants that stimulated lipase activity included Pimpinella anisum L. (aniseed/jintan manis), activating the enzyme by 186.5%. Kaempferol 3-O-rhamnoside was isolated from the ethyl acetate fraction of C. cauliflora leaves and found to be an active lipase inhibitor. The structure was elucidated using 1H-NMR, 13C-NMR and 2D-NMR analyses. PMID:24287996

  10. Anti- and pro-lipase activity of selected medicinal, herbal and aquatic plants, and structure elucidation of an anti-lipase compound.

    PubMed

    Ado, Muhammad Abubakar; Abas, Faridah; Mohammed, Abdulkarim Sabo; Ghazali, Hasanah M

    2013-11-26

    Plants that help in slowing down the digestion of triacylglycerols (TAGs) in the pancreas and small intestine of humans play an important role in the reduction of obesity. On the other hand, there may be plants or plant parts that stimulate intestinal lipolytic activity, thus contributing to greater TAG assimilation. The aim of this study was to evaluate the aqueous methanolic extracts of ninety eight (98) medicinal, herbal and aquatic plant materials from Malaysia for their effect on porcine pancreatic lipase (PPL) activity and to identify the structure of an anti-lipase compound from one of the sources. The degree of inhibition was also quantified as relative to orlistat activity against PPL (orlistat equivalents). Results revealed that while 19.4% of the extracts were found to have anti-lipase activity ≥80%, 12% were actually found to promote PPL activity. Twenty two percent (22.4%) exhibited moderate inhibition (41%-80%) and 2% were neutral toward PPL activity. The ripe fruit of Averrhoa carambola and the leaves of Archidendron jiringa (Jack) I.C Nielsen L. (jering), Cynometra cauliflora (nam-nam) and Aleurites moluccana (L.) Willd (candle nut/buah keras) had the highest (100%) anti-lipase activity and are equivalent to 0.11 µg orlistat/mL. Plants that stimulated lipase activity included Pimpinella anisum L. (aniseed/jintan manis), activating the enzyme by 186.5%. Kaempferol 3-O-rhamnoside was isolated from the ethyl acetate fraction of C. cauliflora leaves and found to be an active lipase inhibitor. The structure was elucidated using 1H-NMR, 13C-NMR and 2D-NMR analyses.

  11. 3-D structural modeling of humic acids through experimental characterization, computer assisted structure elucidation and atomistic simulations 1. Chelsea soil humic acid.

    SciTech Connect

    Gassman, Paul; Hatcher, Patrick G.; Faulon, Jean-Loup Michel; Simpson, Andre; Goddard, William A., III; Diallo, Mamadou S.; Johnson, James H. Jr.

    2003-07-01

    This paper describes an integrated experimental and computational framework for developing 3-D structural models for humic acids (HAs). This approach combines experimental characterization, computer assisted structure elucidation (CASE), and atomistic simulations to generate all 3-D structural models or a representative sample of these models consistent with the analytical data and bulk thermodynamic/structural properties of HAs. To illustrate this methodology, structural data derived from elemental analysis, diffuse reflectance FT-IR spectroscopy, 1-D/2-D {sup 1}H and {sup 13}C solution NMR spectroscopy, and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QqTOF MS) are employed as input to the CASE program SIGNATURE to generate all 3-D structural models for Chelsea soil humic acid (HA). These models are subsequently used as starting 3-D structures to carry out constant temperature-constant pressure molecular dynamics simulations to estimate their bulk densities and Hildebrand solubility parameters. Surprisingly, only a few model isomers are found to exhibit molecular compositions and bulk thermodynamic properties consistent with the experimental data. The simulated {sup 13}C NMR spectrum of an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA.

  12. Structural elucidation of degradation products of a benzopyridooxathiazepine under stress conditions using electrospray orbitrap mass spectrometry - study of degradation kinetic.

    PubMed

    Lecoeur, Marie; Vérones, Valérie; Vaccher, Claude; Bonte, Jean-Paul; Lebegue, Nicolas; Goossens, Jean-François

    2012-04-11

    1-(4-Methoxyphenylethyl)-11H-benzo[f]-1,2-dihydro-pyrido[3,2,c][1,2,5]oxathiazepine 5,5 dioxide (BZN) is a cytotoxic derivative with very promising in vitro activity. Regulatory authority for registration of pharmaceuticals for human use requires to evaluate the stability of active compound under various stress conditions. Forced degradation of BZN was investigated under hydrolytic (0.1M NaOH, 0.1M HCl, neutral), oxidative (3.3% H(2)O(2)), photolytic (visible light) and thermal (25 °C, 70 °C) settings. Relevant degradation took place under thermal acidic (0.1M HCl, 70 °C) and oxidative (3.3% H(2)O(2)) conditions. Liquid chromatography-mass spectrometry (LC-MS) analyses revealed the presence of ten degradation products whose structures were characterized by electrospray ionization-orbitrap mass spectrometry. The full scan accurate mass analysis of degradation products was confirmed or refuted using three tools furnished by the MS software: (1) predictive chemical formula and corresponding mass error; (2) double bond equivalent (DBE) calculation; and (3) accurate mass product ion spectra of degradation products. The structural elucidation showed that the tricycle moiety was unstable under thermal acidic and oxidative conditions since four degradation products possess an opened oxathiazepine ring. Then, a simple and fast HPLC-UV method was developed and validated for the determination of the degradation kinetic of BZN under acidic and oxidative conditions. The method was linear in the 5-100 μg mL(-1) concentration range with a good precision (RSD=2.2% and 2.7% for the repeatability and the intermediate precision, respectively) and a bias which never exceeded 1.6%, whatever the quality control level. With regards to the BZN concentration, a first-order degradation process was determined, with t(1/2)=703 h and 1140 h, under oxidative and acidic conditions, respectively.

  13. Elucidating the electronic structure of supported gold nanoparticles and its relevance to catalysis by means of hard X-ray photoelectron spectroscopy

    NASA Astrophysics Data System (ADS)

    Reinecke, Benjamin N.; Kuhl, Kendra P.; Ogasawara, Hirohito; Li, Lin; Voss, Johannes; Abild-Pedersen, Frank; Nilsson, Anders; Jaramillo, Thomas F.

    2016-08-01

    We report on the electronic structure of Au (gold) nanoparticles supported onto TiO2 with a goal of elucidating the most important effects that contribute to their high catalytic activity. We synthesize and characterize with high resolution transmission electron microscopy (HRTEM) 3.4, 5.3, and 9.5 nm diameter TiO2-supported Au nanoparticles with nearly spherical shape and measure their valence band using Au 5d subshell sensitive hard X-ray photoelectron spectroscopy (HAXPES) conducted at Spring-8. Based on density functional theory (DFT) calculations of various Au surface structures, we interpret the observed changes in the Au 5d valence band structure as a function of size in terms of an increasing percentage of Au atoms at corners/edges for decreasing particle size. This work elucidates how Au coordination number impacts the electronic structure of Au nanoparticles, ultimately giving rise to their well-known catalytic activity.

  14. Structural Elucidation of a Novel Polysaccharide from Pseudostellaria heterophylla and Stimulating Glucose Uptake in Cells and Distributing in Rats by Oral.

    PubMed

    Chen, Jinlong; Pang, Wensheng; Shi, Wentao; Yang, Bin; Kan, Yongjun; He, Zhaodong; Hu, Juan

    2016-01-01

    The semi-refined polysaccharide of Pseudostellaria heterophylla is a complex polysaccharide that exhibits significantly hypoglycemic activities. A novel homogeneous polysaccharide, named as H-1-2, was isolated from the semi-refined polysaccharide. The mean molecular weight of H-1-2 was 1.4 × 10⁴ Da and it was only composed of d-glucose monosaccharide. Structure elucidation indicated that H-1-2 contains pyranride, and has the characteristics of the α-iso-head configuration, a non-reducing end (T-), 4-, 1,6-, and 1,4,6-connection, in all four ways to connect glucose. H-1-2 was a type of glucan, where chemical combination exists in the main chain between 1→4 linked glucose, and contains a small amount of 1,6-linked glucose, which was in the branched chain. In vitro HepG2, 3T3-L1, and L6 cells were used to assess cellular glucose consumption and cellular glucose uptake by glucose oxidase, and the transport of 2-NBDG fluorescence probe results showed that H-1-2 could clearly increase glucose uptake and utilization in muscle and adipose cells, which is beneficial to screen for in the discovery of anti-diabetes lead compounds. H-1-2 was labeled with radioisotopes ((99m)Tc-pertechnetate). (99m)Tc-labeled-H-1-2 was performed by SPECT/CT analysis images after oral administration in rats. At 4 h post ingestion, about 50% of the radioactivity was observed in the intestine. No significant radioactivity was found in the heart, liver, and kidney, conjecturing that absorption of (99m)Tc-labeled H-1-2 might, via intestinal mucosa, be absorbed into systemic circulation. This problem, as to whether the polysaccharide is absorbed orally, will need further examination. PMID:27649122

  15. Technical decision making with higher order structure data: utilization of differential scanning calorimetry to elucidate critical protein structural changes resulting from oxidation.

    PubMed

    Arthur, Kelly K; Dinh, Nikita; Gabrielson, John P

    2015-04-01

    Differential scanning calorimetry (DSC) is a useful tool for monitoring thermal stability of the molecular conformation of proteins. Here, we present an example of the sensitivity of DSC to changes in stability arising from a common chemical degradation pathway, oxidation. This Note is part of a series of industry case studies demonstrating the application of higher order structure data for technical decision making. For this study, six protein products from three structural classes were evaluated at multiple levels of oxidation. For each protein, the melting temperature (Tm ) decreased linearly as a function of oxidation; however, differences in the rate of change in Tm , as well as differences in domain Tm stability were observed across and within structural classes. For one protein, analysis of the impact of oxidation on protein function was also performed. For this protein, DSC was shown to be a leading indicator of decreased antigen binding suggesting a subtle conformation change may be underway that can be detected using DSC prior to any observable impact on product potency. Detectable changes in oxidized methionine by mass spectrometry (MS) occurred at oxidation levels below those with a detectable conformational or functional impact. Therefore, by using MS, DSC, and relative potency methods in concert, the intricate relationship between a primary structural modification, changes in conformational stability, and functional impact can be elucidated.

  16. 3-D Structural Modeling of Humic Acids through Experimental Characterization, Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Chelsea Soil Humic Acid

    SciTech Connect

    Diallo, Mamadou S.; Simpson, Andre; Gassman, Paul L.; Faulon, Jean Loup; Johnson, Jr., James H.; Goddard, III, William A.; Hatcher, Patrick G.

    2003-05-01

    This paper describes an integrated experimental and computational framework for developing 3-D structural models for humic acids (HAs). This approach combines experimental characterization, computer assisted structure elucidation (CASE), and atomistic simulations to generate all 3-D structural models or a representative sample of these models consistent with the analytical data and bulk thermodynamic/structural properties of HAs. To illustrate this methodology, structural data derived from elemental analysis, diffuse reflectance FT-IR spectroscopy, 1-D/2-D | 1H and 13C solution NMR spectroscopy, and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QqTOF MS) are employed as input to the CASE program SIGNATURE to generate all 3-D structural models for Chelsea soil humic acid (HA). These models are subsequently used as starting 3-D structures to carry out constant temperature-constant pressure molecular dynamics simulations to estimate their bulk densities and Hildebrand solubility parameters. Surprisingly, only a few model isomers are found to exhibit molecular compositions and bulk thermodynamic properties consistent with the experimental data. The simulated 13C NMR spectrum of * Corresponding author phone: (626)395-2730; fax: (626)585-0918; e-mail: diallo@wag.caltech.edu and mdiallo@howard.edu. Present address: Materials and Process Simulation Center,BeckmanInstitute 139-74, California Institute of Technology, Pasadena, CA 91125. † California Institute of Technology. ‡ Howard University. § University of Toronto. Pacific Northwest National Laboratory. ^ Sandia National Laboratories. # The Ohio State University. ã xxxx American Chemical Society PAGE EST: 11 10.1021/es0259638 CCC: $25.00 Published on Web 00/00/0000 an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA.

  17. Mutational analysis of structural elements in a class-I cyclic di-GMP riboswitch to elucidate its regulatory mechanism.

    PubMed

    Inuzuka, Saki; Nishimura, Kei-Ichiro; Kakizawa, Hitoshi; Fujita, Yuki; Furuta, Hiroyuki; Matsumura, Shigeyoshi; Ikawa, Yoshiya

    2016-09-01

    The Vc2 riboswitch possesses an aptamer domain belonging to the class-I c-di-GMP riboswitch family. This domain has been analysed and the molecular mechanism by which it recognizes the c-di-GMP ligand has been elucidated. On the other hand, the regulatory mechanism of the full-length Vc2 riboswitch to control its downstream open reading frame (ORF) remains largely unknown. In this study, we performed in vivo reporter assays and in vitro biochemical analyses of the full-length riboswitch and its aptamer domain. We evaluated the results of in vivo and in vitro analyses to elucidate the regulatory mechanism of the Vc2 riboswitch. The present results suggest that recognition of c-di-GMP ligand by the Vc2 riboswitch aptamer domain downregulates expression of its downstream ORF primarily at the translational level.

  18. Elucidation of the structure-property relationship of p-type organic semiconductors through rapid library construction via a one-pot, Suzuki-Miyaura coupling reaction.

    PubMed

    Fuse, Shinichiro; Matsumura, Keisuke; Wakamiya, Atsushi; Masui, Hisashi; Tanaka, Hiroshi; Yoshikawa, Susumu; Takahashi, Takashi

    2014-09-01

    The elucidation of the structure-property relationship is an important issue in the development of organic electronics. Combinatorial synthesis and the evaluation of systematically modified compounds is a powerful tool in the work of elucidating structure-property relationships. In this manuscript, D-π-A structure, 32 p-type organic semiconductors were rapidly synthesized via a one-pot, Suzuki-Miyaura coupling with subsequent Knoevenagel condensation. Evaluation of the solubility and photovoltaic properties of the prepared compounds revealed that the measured solubility was strongly correlated with the solubility parameter (SP), as reported by Fedors. In addition, the SPs were correlated with the Jsc of thin-film organic solar cells prepared using synthesized compounds. Among the evaluated photovoltaic properties of the solar cells, Jsc and Voc had strong correlations with the photoconversion efficiency (PCE).

  19. Determination of the chemical structures of tandyukisins B-D, isolated from a marine sponge-derived fungus.

    PubMed

    Yamada, Takeshi; Umebayashi, Yoshihide; Kawashima, Maiko; Sugiura, Yuma; Kikuchi, Takashi; Tanaka, Reiko

    2015-05-01

    Tandyukisins B-D (1-3), novel decalin derivatives, have been isolated from a strain of Trichoderma harzianum OUPS-111D-4 originally derived from the marine sponge Halichondria okadai, and their structures have been elucidated on the basis of spectroscopic analyses using 1D and 2D NMR techniques. In addition, their chemical structures were established by chemical transformation. They exhibited weak cytotoxicity, but selective growth inhibition on panel screening using 39 human cancer cell lines. PMID:26006715

  20. Structural elucidation and protective role of a polysaccharide from Sargassum fusiforme on ameliorating learning and memory deficiencies in mice.

    PubMed

    Hu, Pei; Li, Zhixiong; Chen, Mingcang; Sun, Zhaolin; Ling, Yun; Jiang, Jian; Huang, Chenggang

    2016-03-30

    A fucoidan, Sargassum fusiforme polysaccharide 65 (SFPS65) A, was isolated from a brown alga (S. fusiforme). SFPS65A had an estimated molecular weight of 90kDa and showed αD(20) -74.3288 (c 0.05, H2O). SFPS65A is composed of fucose, galactose, xylose, glucose, glucuronic acid, and mannose in the ratio of 19.23:9.58:6.64:1:6.52:2.57. The structural features of SFPS65A were investigated using composition analysis, methylation analysis, infrared spectrum, nuclear magnetic resonance spectroscopy, and electrospray ionization quadruple time-of-flight tandem mass spectroscopy. Results showed that SFPS65A has a main chain composed of →3)-β-l-Fucp-(1→3,4)-β-l-Fucp-(1→3,4)-β-l-Fucp-(1→ and connected with →3,4)-α-d-GlcAp-(1→, →4)-β-d-Xylp-(1→, →4)-α-d-Galp-(1→, →3,6)-α-d-Manp-(1→ alternately. The branches at O-3 of the fucosyl residue and O-3 of the hexosyl residues may include sulfate, →4)-β-l-Fucp-(1→, β-d-Xylp-(1→, and β-d-Xylp-(1→. SFPS65A exhibited an activity on Alzheimer's disease in vivo in the pharmacological experiments by increasing the cognitive abilities of scopolamine-, ethanol-, and sodium nitrite-treated mice against memory deficits. PMID:26794958

  1. Elucidation of the Structure and Reaction Mechanism of Sorghum Hydroxycinnamoyltransferase and Its Structural Relationship to Other Coenzyme A-Dependent Transferases and Synthases1[C][W

    PubMed Central

    Walker, Alexander M.; Hayes, Robert P.; Youn, Buhyun; Vermerris, Wilfred; Sattler, Scott E.; Kang, ChulHee

    2013-01-01

    Hydroxycinnamoyltransferase (HCT) from sorghum (Sorghum bicolor) participates in an early step of the phenylpropanoid pathway, exchanging coenzyme A (CoA) esterified to p-coumaric acid with shikimic or quinic acid as intermediates in the biosynthesis of the monolignols coniferyl alcohol and sinapyl alcohol. In order to elucidate the mode of action of this enzyme, we have determined the crystal structures of SbHCT in its apo-form and ternary complex with shikimate and p-coumaroyl-CoA, which was converted to its product during crystal soaking. The structure revealed the roles of threonine-36, serine-38, tyrosine-40, histidine-162, arginine-371, and threonine-384 in catalysis and specificity. Based on the exact chemistry of p-coumaroyl-CoA and shikimic acid in the active site and an analysis of kinetic and thermodynamic data of the wild type and mutants, we propose a role for histidine-162 and threonine-36 in the catalytic mechanism of HCT. Considering the calorimetric data, substrate binding of SbHCT should occur sequentially, with p-coumaroyl-CoA binding prior to the acyl acceptor molecule. While some HCTs can use both shikimate and quinate as an acyl acceptor, SbHCT displays low activity toward quinate. Comparison of the structure of sorghum HCT with the HCT involved in chlorogenic acid synthesis in coffee (Coffea canephora) revealed many shared features. Taken together, these observations explain how CoA-dependent transferases with similar structural features can participate in different biochemical pathways across species. PMID:23624856

  2. The potential utility of predicted one bond carbon-proton coupling constants in the structure elucidation of small organic molecules by NMR spectroscopy.

    PubMed

    Venkata, Chandrasekhar; Forster, Mark J; Howe, Peter W A; Steinbeck, Christoph

    2014-01-01

    NMR spectroscopy is the most popular technique used for structure elucidation of small organic molecules in solution, but incorrect structures are regularly reported. One-bond proton-carbon J-couplings provide additional information about chemical structure because they are determined by different features of molecular structure than are proton and carbon chemical shifts. However, these couplings are not routinely used to validate proposed structures because few software tools exist to predict them. This study assesses the accuracy of Density Functional Theory for predicting them using 396 published experimental observations from a diverse range of small organic molecules. With the B3LYP functional and the TZVP basis set, Density Functional Theory calculations using the open-source software package NWChem can predict one-bond CH J-couplings with good accuracy for most classes of small organic molecule. The root-mean-square deviation after correction is 1.5 Hz for most sp3 CH pairs and 1.9 Hz for sp2 pairs; larger errors are observed for sp3 pairs with multiple electronegative substituents and for sp pairs. These results suggest that prediction of one-bond CH J-couplings by Density Functional Theory is sufficiently accurate for structure validation. This will be of particular use in strained ring systems and heterocycles which have characteristic couplings and which pose challenges for structure elucidation.

  3. The Potential Utility of Predicted One Bond Carbon-Proton Coupling Constants in the Structure Elucidation of Small Organic Molecules by NMR Spectroscopy

    PubMed Central

    Venkata, Chandrasekhar; Forster, Mark J.; Howe, Peter W. A.; Steinbeck, Christoph

    2014-01-01

    NMR spectroscopy is the most popular technique used for structure elucidation of small organic molecules in solution, but incorrect structures are regularly reported. One-bond proton-carbon J-couplings provide additional information about chemical structure because they are determined by different features of molecular structure than are proton and carbon chemical shifts. However, these couplings are not routinely used to validate proposed structures because few software tools exist to predict them. This study assesses the accuracy of Density Functional Theory for predicting them using 396 published experimental observations from a diverse range of small organic molecules. With the B3LYP functional and the TZVP basis set, Density Functional Theory calculations using the open-source software package NWChem can predict one-bond CH J-couplings with good accuracy for most classes of small organic molecule. The root-mean-square deviation after correction is 1.5 Hz for most sp3 CH pairs and 1.9 Hz for sp2 pairs; larger errors are observed for sp3 pairs with multiple electronegative substituents and for sp pairs. These results suggest that prediction of one-bond CH J-couplings by Density Functional Theory is sufficiently accurate for structure validation. This will be of particular use in strained ring systems and heterocycles which have characteristic couplings and which pose challenges for structure elucidation. PMID:25365289

  4. Isolation and structure determination of obyanamide, a novel cytotoxic cyclic depsipeptide from the marine cyanobacterium Lyngbya confervoides.

    PubMed

    Williams, Philip G; Yoshida, Wesley Y; Moore, Richard E; Paul, Valerie J

    2002-01-01

    Obyanamide (1) was isolated from a variety of the marine cyanobacterium Lyngbya confervoides collected in Saipan, Commonwealth of the Northern Mariana Islands. Gross structure elucidation of this novel cyclic depsipeptide relied on extensive application of 2D NMR techniques. The absolute stereochemistry was deduced by chiral chromatography of the hydrolysis products and comparison with authentic and synthetic standards. Obyanamide (1) was cytotoxic against KB cells with an IC(50) of 0.58 microg/mL.

  5. Irmpd Action Spectroscopy and Computational Approaches to Elucidate Gas-Phase Structures and Energetics of 2'-DEOXYCYTIDINE and Cytidine Sodium Complexes

    NASA Astrophysics Data System (ADS)

    Zhu, Yanlong; Hamlow, Lucas; He, Chenchen; Gao, Juehan; Oomens, Jos; Rodgers, M. T.

    2016-06-01

    The local structures of DNA and RNA are influenced by protonation, deprotonation and noncovalent interactions with cations. In order to determine the effects of Na+ cationization on the gas-phase structures of 2'-deoxycytidine, [dCyd+Na]+, and cytidine, [Cyd+Na]+, infrared multiple photon dissociation (IRMPD) action spectra of these sodium cationized nucleosides are measured over the range extending from 500 to 1850 wn using the FELIX free electron laser. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of these complexes. Geometry optimizations, frequency analyses, and IR spectra of these species are determined at the B3LYP/6-311+G(d,p) level of theory. Single-point energies are calculated at the B3LYP/6-311+G(2d,2p) level of theory to determine the relative stabilities of these conformations. Comparison of the measure IRMPD action spectra and computed linear IR spectra enable the conformations accessed in the experiments to be elucidated. For both cytosine nucleosides, tridentate binding of the Na+ cation to the O2, O4' and O5' atoms of the nucleobase and sugar is observed. Present results for the sodium cationized nucleosides are compared to results for the analogous protonated forms of these nucleosides to elucidate the effects of multiple chelating interactions with the sodium cation vs. hydrogen bonding interactions in the protonated systems on the structures and stabilities of these nucleosides.

  6. Assignment of the sup 1 H NMR spectrum and secondary structure elucidation of the single-stranded DNA binding protein encoded by the filamentous bacteriophage IKe

    SciTech Connect

    van Duynhoven, J.P.M.; Folkers, P.J.M.; Prinse, C.W.J.M.; Harmsen, B.J.M.; Konings, R.N.H.; Hilbers, C.W. )

    1992-02-04

    By means of 2D NMR techniques, all backbone resonances in the {sup 1}H NMR spectrum of the single-stranded DNA binding protein encoded by gene V of the filamentous phage IKe have been assigned sequence specifically. In addition, a major part of the side chain resonances could be assigned as well. Analysis of NOESY data permitted the elucidation of the secondary structure of IKe gene V protein. The major part of the secondary structure is present as an antiparallel {beta}-sheet, i.e., as two {beta}-loops which partly combine into a triple-stranded {beta}-sheet structure, one {beta}-loop and one triple-stranded {beta}-sheet structure. It is shown that a high degree of homology exists with the single-stranded DNA binding protein encoded by gene V of the distantly related filamentous phase M13.

  7. Wire rope isolators for vibration isolation of equipment and structures - A review

    NASA Astrophysics Data System (ADS)

    Balaji, P. S.; Rahman, M. E.; Moussa, Leblouba; Lau, H. H.

    2015-04-01

    Vibrations and shocks are studied using various techniques and analyzed to predict their detrimental effect on the equipment and structures. In cases, where the effects of vibration become unacceptable, it may cause structural damage and affect the operation of the equipment. Hence, adding a discrete system to isolate the vibration from source becomes necessary. The Wire Rope Isolator (WRI) can be used to effectively isolate the system from disturbing vibrations. The WRI is a type of passive isolator that exhibits nonlinear behavior. It consists of stranded wire rope held between two metal retainer bars and the metal wire rope is made up of individual wire strands that are in frictional contact with each other, hence, it is a kind of friction-type isolator. This paper compiles the research work on wire rope isolators. This paper presents the research work under two categories, namely monotonic and cyclic loading behaviors of WRI. The review also discusses the different terminologies associated with vibration isolation system and highlights the comparison between various isolation systems.

  8. Elucidation of Antimicrobial Susceptibility Profiles and Genotyping of Salmonella enterica Isolates from Clinical Cases of Salmonellosis in New Mexico in 2008.

    PubMed

    Smith, Kenneth P; George, Jeffy; Cadle, Kathleen M; Kumar, Sanath; Aragon, Steven J; Hernandez, Ricardo L; Jones, Suzanna E; Floyd, Jody L; Varela, Manuel F

    2010-06-01

    In this study, we investigated the antimicrobial susceptibility profiles and the distribution of some well known genetic determinants of virulence in clinical isolates of Salmonella enterica from New Mexico. The minimum inhibitory concentrations (MICs) for various antimicrobials were determined by using the E-test strip method according to CLSI guidelines. Virulence genotyping was performed by polymerase chain reaction (PCR) using primers specific for known virulence genes of Salmonella enterica. Of 15 isolates belonging to 11 different serovars analyzed, one isolate of Salmonella Typhimurium was resistant to multiple drugs namely ampicillin, amoxicillin / clavulanic acid, chloramphenicol and tetracycline, that also harbored class 1 intergron, bla(TEM) encoding genes for β-lactamase, chloramphenicol acetyl transferase (cat1), plus floR, tet(C) and tet(G). This strain was phage typed as DT104. PCR analysis revealed the presence of invA, hilA, stn, agfA and spvR virulence genes in all the isolates tested. The plasmid-borne pefA gene was absent in 11 isolates, while 5 isolates lacked sopE. One isolate belonging to serogroup E4 (Salmonella Sombre) was devoid of multiple virulence genes pefA, iroB, shdA and sopE. These results demonstrate that clinical Salmonella serotypes from New Mexico used here are predominantly sensitive to multiple antimicrobial agents, but vary in their virulence genotypes. Information on antimicrobial sensitivity and virulence genotypes will help in understanding the evolution and spread of epidemic strains of Salmonella enterica in the region of study.

  9. Short Communication: Elucidation of bacterial community structure on thin-spined porcupine (Chaetomys subspinosus) spines by denaturing.

    PubMed

    Bezerra, R A; Giné, G A F; Marques, E L S; Abreu-Tarazi, M F; Rezende, R P; Gaiotto, F A

    2015-01-01

    Thin-spined porcupines (Chaetomys subspinosus) are threatened with extinction and are categorized as vulnerable. This is because of alteration to and loss of their habitat and possible hunting activities in their distribution area. Their spines constitute one of their defense mechanisms, which can be fomites for pathogens to humans. However, little is known about such pathogens. The present study aimed to detect bacteria on spines of C. subspinosus, from the Una Biological Reserve, South of Bahia, northeastern Brazil, by analyzing metagenomic DNA, isolating bacterial culture, using the denaturing gradient gel electrophoresis (DGGE) technique, and sequencing. Six anatomical points were selected for withdrawing spine samples from an individual C. subspinosus. At all sample points, bacteria were detected by bacteriological culture and/or DGGE and sequencing of excised bands. When all samples were combined, standard PCR-DGGE analysis of bacteria present in the spines identified 15 distinct bands, thereby revealing a distinct bacterial community. The main pathogens identified through sequencing were Bacillus cereus, B. thuringiensis, B. anthracis, and B. pumilus. The present study demonstrated the isolation and identification of non-pathogenic and pathogenic bacteria on the spines of C. subspinosus.

  10. Structural elucidation of oxygenated storage lipids in cucumber cotyledons. Implication of lipid body lipoxygenase in lipid mobilization during germination.

    PubMed

    Feussner, I; Balkenhohl, T J; Porzel, A; Kühn, H; Wasternack, C

    1997-08-22

    At early stages of germination, a special lipoxygenase is expressed in cotyledons of cucumber and several other plants. This enzyme is localized at the lipid storage organelles and oxygenates their storage triacylglycerols. We have isolated this lipid body lipoxygenase from cucumber seedlings and found that it is capable of oxygenating in vitro di- and trilinolein to the corresponding mono-, di-, and trihydroperoxy derivatives. To investigate the in vivo activity of this enzyme during germination, lipid bodies were isolated from cucumber seedlings at different stages of germination, and the triacylglycerols were analyzed for oxygenated derivatives by a combination of high pressure liquid chromatography, gas chromatography/mass spectrometry, and nuclear magnetic resonance spectroscopy. We identified as major oxygenation products triacylglycerols that contained one, two, or three 13S-hydroperoxy-9(Z),11(E)-octadecadienoic acid residues. During germination, the amount of oxygenated lipids increased strongly, reaching a maximum after 72 h and declining afterward. The highly specific pattern of hydroperoxy lipids formed suggested the involvement of the lipid body lipoxygenase in their biosynthesis. These data suggest that this lipoxygenase may play an important role during the germination process of cucumber and other plants and support our previous hypothesis that the specific oxygenation of the storage lipids may initiate their mobilization as a carbon and energy source for the growing seedling. PMID:9261186

  11. Short Communication: Elucidation of bacterial community structure on thin-spined porcupine (Chaetomys subspinosus) spines by denaturing.

    PubMed

    Bezerra, R A; Giné, G A F; Marques, E L S; Abreu-Tarazi, M F; Rezende, R P; Gaiotto, F A

    2015-01-01

    Thin-spined porcupines (Chaetomys subspinosus) are threatened with extinction and are categorized as vulnerable. This is because of alteration to and loss of their habitat and possible hunting activities in their distribution area. Their spines constitute one of their defense mechanisms, which can be fomites for pathogens to humans. However, little is known about such pathogens. The present study aimed to detect bacteria on spines of C. subspinosus, from the Una Biological Reserve, South of Bahia, northeastern Brazil, by analyzing metagenomic DNA, isolating bacterial culture, using the denaturing gradient gel electrophoresis (DGGE) technique, and sequencing. Six anatomical points were selected for withdrawing spine samples from an individual C. subspinosus. At all sample points, bacteria were detected by bacteriological culture and/or DGGE and sequencing of excised bands. When all samples were combined, standard PCR-DGGE analysis of bacteria present in the spines identified 15 distinct bands, thereby revealing a distinct bacterial community. The main pathogens identified through sequencing were Bacillus cereus, B. thuringiensis, B. anthracis, and B. pumilus. The present study demonstrated the isolation and identification of non-pathogenic and pathogenic bacteria on the spines of C. subspinosus. PMID:26436511

  12. Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

    PubMed

    Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda

    2016-04-01

    Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions. PMID:27050261

  13. Sympatric species distribution, genetic diversity and population structure of Haemonchus isolates from domestic ruminants in Pakistan.

    PubMed

    Hussain, Tanveer; Periasamy, Kathiravan; Nadeem, Asif; Babar, Masroor Ellahi; Pichler, Rudolf; Diallo, Adama

    2014-12-15

    Haemonchus species are major gastro-intestinal parasites affecting ruminants across the world. The present study aimed to assess the sympatric species distribution, genetic diversity, population structure and frequency of β-tubulin isotype 1 alleles associated with benzimidazole resistance. Internal transcribed spacer 2 (ITS2) sequences revealed three sympatric species of Haemonchus, H. contortus, H. placei and H. longistipes with 12 distinct genotypes circulating among ruminant hosts in Pakistan. High genetic variability was observed in Pakistani Haemonchus isolates at nicotine amide dehydrogenase subunit 4 (ND4) and cytochrome oxidase subunit 1 (COI) gene loci. Intra-population diversity parameters were higher in H. contortus isolates than H. placei. Phylogenetic analysis of ND4 and COI sequences did not reveal clustering of haplotypes originating from a particular host indicating high rate of gene flow among Haemonchus parasites infecting sheep, goat and cattle in Pakistan. ND4 and COI haplotypes from Pakistan were compared to sequences of Haemonchus isolates from 11 countries to elucidate the population structure. Multidimensional scaling (MDS) plot of pairwise FST derived from 531 ND4 haplotypes revealed clustering together of H. contortus from Pakistan, China, Malaysia and Italy while the isolates from Yemen and United States were found to be genetically distinct. With respect to H. placei, isolates from Pakistan were found to be genetically differentiated from isolates of other countries. The tests for selective neutrality revealed negative D statistics and did not reveal significant deviations in Pakistani Haemonchus populations while significant deviation (P < 0.05) was observed in Brazilian and Chinese H. contortus populations. Median Joining (MJ) network of ND4 haplotypes revealed Yemenese H. contortus being closer to H. placei cluster. β-tubulin isotype 1 genotyping revealed 7.86% frequency of Y allele associated with benzimidazole resistance at F200Y

  14. Sympatric species distribution, genetic diversity and population structure of Haemonchus isolates from domestic ruminants in Pakistan.

    PubMed

    Hussain, Tanveer; Periasamy, Kathiravan; Nadeem, Asif; Babar, Masroor Ellahi; Pichler, Rudolf; Diallo, Adama

    2014-12-15

    Haemonchus species are major gastro-intestinal parasites affecting ruminants across the world. The present study aimed to assess the sympatric species distribution, genetic diversity, population structure and frequency of β-tubulin isotype 1 alleles associated with benzimidazole resistance. Internal transcribed spacer 2 (ITS2) sequences revealed three sympatric species of Haemonchus, H. contortus, H. placei and H. longistipes with 12 distinct genotypes circulating among ruminant hosts in Pakistan. High genetic variability was observed in Pakistani Haemonchus isolates at nicotine amide dehydrogenase subunit 4 (ND4) and cytochrome oxidase subunit 1 (COI) gene loci. Intra-population diversity parameters were higher in H. contortus isolates than H. placei. Phylogenetic analysis of ND4 and COI sequences did not reveal clustering of haplotypes originating from a particular host indicating high rate of gene flow among Haemonchus parasites infecting sheep, goat and cattle in Pakistan. ND4 and COI haplotypes from Pakistan were compared to sequences of Haemonchus isolates from 11 countries to elucidate the population structure. Multidimensional scaling (MDS) plot of pairwise FST derived from 531 ND4 haplotypes revealed clustering together of H. contortus from Pakistan, China, Malaysia and Italy while the isolates from Yemen and United States were found to be genetically distinct. With respect to H. placei, isolates from Pakistan were found to be genetically differentiated from isolates of other countries. The tests for selective neutrality revealed negative D statistics and did not reveal significant deviations in Pakistani Haemonchus populations while significant deviation (P < 0.05) was observed in Brazilian and Chinese H. contortus populations. Median Joining (MJ) network of ND4 haplotypes revealed Yemenese H. contortus being closer to H. placei cluster. β-tubulin isotype 1 genotyping revealed 7.86% frequency of Y allele associated with benzimidazole resistance at F200Y

  15. Detection of low-level PTFE contamination: An application of solid-state NMR to structure elucidation in the pharmaceutical industry.

    PubMed

    Pham, Tran N; Day, Caroline J; Edwards, Andrew J; Wood, Helen R; Lynch, Ian R; Watson, Simon A; Bretonnet, Anne-Sophie Z; Vogt, Frederick G

    2011-01-25

    We report a novel use of solid-state ¹⁹F nuclear magnetic resonance to detect and quantify polytetrafluoroethylene contamination from laboratory equipment, which due to low quantity (up to 1% w/w) and insolubility remained undetected by standard analytical techniques. Solid-state ¹⁹F NMR is shown to be highly sensitive to such fluoropolymers (detection limit 0.02% w/w), and is demonstrated as a useful analytical tool for structure elucidation of unknown solid materials.

  16. Combined (Super 31)P and (Super 1)H NMR Experiments in the Structural Elucidation of Polynuclear Thiolate Complexes

    ERIC Educational Resources Information Center

    Cerrada, Elena; Laguna, Mariano

    2005-01-01

    A facile synthesis of two gold(I) complexes with 1,2-benzenedithiolate ligand and two different bidentate phosphines are described. A detailed sequence of NMR experiments is suggested to determine the structure of the compounds.

  17. Structural elucidation of the DFG-Asp in and DFG-Asp out states of TAM kinases and insight into the selectivity of their inhibitors.

    PubMed

    Messoussi, Abdellah; Peyronnet, Lucile; Feneyrolles, Clémence; Chevé, Gwénaël; Bougrin, Khalid; Yasri, Aziz

    2014-10-10

    Structural elucidation of the active (DFG-Asp in) and inactive (DFG-Asp out) states of the TAM family of receptor tyrosine kinases is required for future development of TAM inhibitors as drugs. Herein we report a computational study on each of the three TAM members Tyro-3, Axl and Mer. DFG-Asp in and DFG-Asp out homology models of each one were built based on the X-ray structure of c-Met kinase, an enzyme with a closely related sequence. Structural validation and in silico screening enabled identification of critical amino acids for ligand binding within the active site of each DFG-Asp in and DFG-Asp out model. The position and nature of amino acids that differ among Tyro-3, Axl and Mer, and the potential role of these residues in the design of selective TAM ligands, are discussed.

  18. Molecular Mechanism for Conformational Dynamics of Ras·GTP Elucidated from In-Situ Structural Transition in Crystal

    PubMed Central

    Matsumoto, Shigeyuki; Miyano, Nao; Baba, Seiki; Liao, Jingling; Kawamura, Takashi; Tsuda, Chiemi; Takeda, Azusa; Yamamoto, Masaki; Kumasaka, Takashi; Kataoka, Tohru; Shima, Fumi

    2016-01-01

    Ras•GTP adopts two interconverting conformational states, state 1 and state 2, corresponding to inactive and active forms, respectively. However, analysis of the mechanism for state transition was hampered by the lack of the structural information on wild-type Ras state 1 despite its fundamental nature conserved in the Ras superfamily. Here we solve two new crystal structures of wild-type H-Ras, corresponding to state 1 and state 2. The state 2 structure seems to represent an intermediate of state transition and, intriguingly, the state 1 crystal is successfully derived from this state 2 crystal by regulating the surrounding humidity. Structural comparison enables us to infer the molecular mechanism for state transition, during which a wide range of hydrogen-bonding networks across Switch I, Switch II and the α3-helix interdependently undergo gross rearrangements, where fluctuation of Tyr32, translocation of Gln61, loss of the functional water molecules and positional shift of GTP play major roles. The NMR-based hydrogen/deuterium exchange experiments also support this transition mechanism. Moreover, the unveiled structural features together with the results of the biochemical study provide a new insight into the physiological role of state 1 as a stable pool of Ras•GTP in the GDP/GTP cycle of Ras. PMID:27180801

  19. Structural elucidation of the NADP(H) phosphatase activity of staphylococcal dual-specific IMPase/NADP(H) phosphatase.

    PubMed

    Bhattacharyya, Sudipta; Dutta, Anirudha; Dutta, Debajyoti; Ghosh, Ananta Kumar; Das, Amit Kumar

    2016-02-01

    NADP(H)/NAD(H) homeostasis has long been identified to play a pivotal role in the mitigation of reactive oxygen stress (ROS) in the intracellular milieu and is therefore critical for the progression and pathogenesis of many diseases. NAD(H) kinases and NADP(H) phosphatases are two key players in this pathway. Despite structural evidence demonstrating the existence and mode of action of NAD(H) kinases, the specific annotation and the mode of action of NADP(H) phosphatases remains obscure. Here, structural evidence supporting the alternative role of inositol monophosphatase (IMPase) as an NADP(H) phosphatase is reported. Crystal structures of staphylococcal dual-specific IMPase/NADP(H) phosphatase (SaIMPase-I) in complex with the substrates D-myo-inositol-1-phosphate and NADP(+) have been solved. The structure of the SaIMPase-I-Ca(2+)-NADP(+) ternary complex reveals the catalytic mode of action of NADP(H) phosphatase. Moreover, structures of SaIMPase-I-Ca(2+)-substrate complexes have reinforced the earlier proposal that the length of the active-site-distant helix α4 and its preceding loop are the predisposing factors for the promiscuous substrate specificity of SaIMPase-I. Altogether, the evidence presented suggests that IMPase-family enzymes with a shorter α4 helix could be potential candidates for previously unreported NADP(H) phosphatase activity.

  20. Elucidating the domain structure of the cobalt oxide water splitting catalyst by X-ray pair distribution function analysis.

    PubMed

    Du, Pingwu; Kokhan, Oleksandr; Chapman, Karena W; Chupas, Peter J; Tiede, David M

    2012-07-11

    Pair distribution function (PDF) analysis was applied for structural characterization of the cobalt oxide water-splitting catalyst films using high energy X-ray scattering. The catalyst was found to be composed of domains consistent with a cobalt dioxide lattice sheet structure, possibly containing a Co(4)O(4) cubane-type "defect". The analysis identifies the film to consist of domains composed of 13-14 cobalt atoms with distorted coordination geometries that can be modeled by alteration in terminal oxygen atom positions at the domain edge. Phosphate is seen as a disordered component in the films. This work establishes an approach that can be applied to study the structure of in situ cobalt oxide water-splitting film under functional catalytic conditions.

  1. Structure elucidation of Sch 20561, a cyclic dehydropeptide lactone--a major component of W-10 antifungal antibiotic.

    PubMed

    Afonso, A; Hon, F; Brambilla, R; Puar, M S

    1999-04-01

    Antibiotic W-10 is a fermentation complex produced by the bacterium Aeromonas sp. W-10. The cyclic dehydropeptide lactones Sch 20562 (1) and Sch 20561 (2) are the major components of this fermentation complex and are of biological interest in view of their unique structural features and potent antifungal activity. The chemical degradation studies that were utilized in the assignment of structure 2 for Sch 20561 are described here. The structure determination of 2 made use of the ozonolytic cleavage of the dehydropeptide units to form fragments that were sequenced by mass spectrometry. The cyclic dehydropeptide lactone Sch 20561 (2) was found to be the aglycone of Sch 20562 (1) and these two natural products were correlated by a chemical transformation involving the deglucosidation of 1 to form 2.

  2. [Elucidating the structure of two cyclotides of Viola tianshanica maxim by MALDI TOF/TOF MS analysis].

    PubMed

    Xiang, Bin; Du, Guo-Hua; Wang, Xu-Chen; Zhang, Shu-Xiang; Qin, Xian-Yun; Kong, Jian-Qiang; Cheng, Ke-Di; Li, Yong-Ji; Wang, Wei

    2010-11-01

    The cyclotides are a family of cyclic "mini" proteins that occur in Violaceae, Rubiaceae and Cucurbitaceae plant families and contain a head-to-tail cyclic backbone and a cystine knot arranged by three disulfide bonds. To study the natural cyclotides of V tianshanica, dried herb was extracted with 50% ethanol, and the concentrated aqueous extract was subjected to a solvent-solvent partitioning between water and hexane, ethyl acetate and n-butanol, separately. The n-butanol extract containing cyclotides was subjected to column chromatography over Sephadex LH-20, eluted with 30% methanol. The subfractions were directly reduced by DTT and analyzed by reverse-phase HPLC. The peaks with different retention times were shown on the profile of RP-HPLC and collected. The cyclotides were speculated based on masses range from 3 000 to 3 500 Da. The purified cyclotides were reduced with DTT, alkylated with iodoacetamide, and then were cleaved with endoproteinase Glu-C, endoproteinase Lys-C and Trypsin, separately. The digested peptides were purified on RP-HPLC and analyzed on MALDI TOF/TOF analyzer. A new cyclotide, cycloviolacin T1 and a reported cyclotide varv E were systemically determined using MALDI TOF/TOF system. So the method for the isolation and characterization of cyclotides was quickly built up in succession.

  3. Mitochondrial Structure and Function Are Disrupted by Standard Isolation Methods

    PubMed Central

    Picard, Martin; Taivassalo, Tanja; Ritchie, Darmyn; Wright, Kathryn J.; Thomas, Melissa M.; Romestaing, Caroline; Hepple, Russell T.

    2011-01-01

    Mitochondria regulate critical components of cellular function via ATP production, reactive oxygen species production, Ca2+ handling and apoptotic signaling. Two classical methods exist to study mitochondrial function of skeletal muscles: isolated mitochondria and permeabilized myofibers. Whereas mitochondrial isolation removes a portion of the mitochondria from their cellular environment, myofiber permeabilization preserves mitochondrial morphology and functional interactions with other intracellular components. Despite this, isolated mitochondria remain the most commonly used method to infer in vivo mitochondrial function. In this study, we directly compared measures of several key aspects of mitochondrial function in both isolated mitochondria and permeabilized myofibers of rat gastrocnemius muscle. Here we show that mitochondrial isolation i) induced fragmented organelle morphology; ii) dramatically sensitized the permeability transition pore sensitivity to a Ca2+ challenge; iii) differentially altered mitochondrial respiration depending upon the respiratory conditions; and iv) dramatically increased H2O2 production. These alterations are qualitatively similar to the changes in mitochondrial structure and function observed in vivo after cellular stress-induced mitochondrial fragmentation, but are generally of much greater magnitude. Furthermore, mitochondrial isolation markedly altered electron transport chain protein stoichiometry. Collectively, our results demonstrate that isolated mitochondria possess functional characteristics that differ fundamentally from those of intact mitochondria in permeabilized myofibers. Our work and that of others underscores the importance of studying mitochondrial function in tissue preparations where mitochondrial structure is preserved and all mitochondria are represented. PMID:21512578

  4. Crystallographic elucidation of purely structural, thermal and light-induced spin transitions in an iron(II) binuclear complex.

    PubMed

    Kaiba, A; Shepherd, H J; Fedaoui, D; Rosa, P; Goeta, A E; Rebbani, N; Létard, J F; Guionneau, P

    2010-03-21

    The intricate phase diagram of the binuclear iron(II) spin-crossover complex [{Fe(3-bpp)(NCS)(2)}(2)(4,4'-bypiridine)].2CH(3)OH where 3-bpp is 2,6-bis(pyrazol-3-yl)pyridine has been investigated by variable temperature single crystal X-ray diffraction including a study into the effect of photo-irradiation. This sample is known to exhibit an incomplete spin transition at low temperature. At room temperature, in phase I, iron ions are all crystallographically equivalent, adopting the high spin state (HS). X-Ray structural investigation has revealed two phase transitions in the range (300-30 K). The first transition (T approximately 161 K) leading to phase II is of a purely structural nature and corresponds to a break in symmetry as a result of a twist of the two rings of 4,4'-bipyridine; the two iron sites of the binuclear unit becoming crystallographically independent but remaining all HS. The second structural transition corresponds to the spin crossover, one of the two Fe(II) ions of the binuclear complex being in the low spin state (LS) in phase III. The crystal structure shows an ordered HS-LS crystal packing where HS and LS sites are clearly identified and not randomly distributed in the metal ion sites as often observed. Moreover, light irradiation of single crystals in phase III at 30 K, leading to phase III*, induces a light-induced spin-state trapping (LIESST) effect corresponding to the full conversion of all the iron sites to HS. The crystal packing in phase III* is closer to that of phase III than to those observed in the other HS phases, I and II. This reveals an unusual differentiation between the thermal and light-induced HS states. A deeper analysis of the structural properties first demonstrates the key role of the bipyridine bridge in the peculiar preliminary pure structural transition shown by the title compound. Elsewhere, it also shows that the molecular packing is strongly dependent on the nature of the external perturbation contrary to the

  5. Elucidation of molecular structures at buried polymer interfaces and biological interfaces using sum frequency generation vibrational spectroscopy

    PubMed Central

    Zhang, Chi; Myers, John; Chen, Zhan

    2013-01-01

    Sum frequency generation (SFG) vibrational spectroscopy has been developed into an important technique to study surfaces and interfaces. It can probe buried interfaces in situ and provide molecular level structural information such as the presence of various chemical moieties, quantitative molecular functional group orientation, and time dependent kinetics or dynamics at such interfaces. This paper focuses on these three most important advantages of SFG and reviews some of the recent progress in SFG studies on interfaces related to polymer materials and biomolecules. The results discussed here demonstrate that SFG can provide important molecular structural information of buried interfaces in situ and in real time, which is difficult to obtain by other surface sensitive analytical techniques. PMID:23710244

  6. Nano-Structural Elucidation in Carbon Black Loaded NR Vulcanizate by 3D-TEM and In Situ WAXD Measurements

    SciTech Connect

    Ikeda,Y.; Kato, A.; Shimanuki, J.; Kohjiya, S.; Tosaka, M.; Poompradub, S.; Toki, S.; Hsiao, B.

    2007-01-01

    Three dimensional (3D) visualization of nanometer structure of carbon black dispersion in rubbery matrix has successfully been studied and reported in this paper. Use of 3D-TEM, which is computerized tomography combined with transmission electron microscopy (TEM), enabled us to reconstruct 3D images of carbon black aggregates in natural rubber (NR) matrix. The TEM measurements were conducted by a bright-field method on thin samples without any electron staining. The sample was subject to uni-axial tilting (+65 degree to -65 degree with 2 degree increment) in the sample chamber, and 66 TEM images were taken on each sample. These TEM images were used for computerized tomography to reconstruct the 3D image. This technique is designated as 3D-TEM. The nano-structural features observed by 3D-TEM were in conformity with the electron-conductivity results, and the percolation behavior was recognized. These results were further supplemented by in situ wide-angle X-ray diffraction (WAXD), i.e., simultaneous WAXD and tensile measurements on the sample to observe the strain-induced crystallization in NR vulcanizate. Upon tensile elongation, the crystallization was clearly observed in WAXD in the presence of carbon black, and it contributed to the tensile properties. In order to understand the performances of filled NR vulcanizates, it surely is necessary to know the structural states of the mixed nano-filler and the crystallites produced upon elongation.

  7. Adsorption and Reaction of Acetaldehyde on Shape-Controlled CeO2 Nanocrystals: Elucidation of Structure-function Relationships

    SciTech Connect

    Mann, Amanda K; Wu, Zili; Calaza, Florencia; Overbury, Steven {Steve} H

    2014-01-01

    CeO2 cubes with {100} facets, octahedra with {111} facets, and wires with highly defective structures were utilized to probe the structure-dependent reactivity of acetaldehyde. Using temperature-programmed desorption (TPD), temperature-programmed surface reactions (TPSR), and in situ infrared spectroscopy it was found that acetaldehyde desorbs unreacted or undergoes reduction, coupling, or C-C bond scission reactions depending on the surface structure of CeO2. Room temperature FTIR indicates that acetaldehyde binds primarily as 1-acetaldehyde on the octahedra, in a variety of conformations on the cubes, including coupling products and acetate and enolate species, and primarily as coupling products on the wires. The percent consumption of acetaldehyde follows the order of wires > cubes > octahedra. All the nanoshapes produce the coupling product crotonaldehyde; however, the selectivity to produce ethanol follows the order wires cubes >> octahedra. The selectivity and other differences can be attributed to the variation in the basicity of the surfaces, defects densities, coordination numbers of surface atoms, and the reducibility of the nanoshapes.

  8. AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments.

    PubMed

    Dao, Phuong; Hoinka, Jan; Takahashi, Mayumi; Zhou, Jiehua; Ho, Michelle; Wang, Yijie; Costa, Fabrizio; Rossi, John J; Backofen, Rolf; Burnett, John; Przytycka, Teresa M

    2016-07-01

    Aptamers, short RNA or DNA molecules that bind distinct targets with high affinity and specificity, can be identified using high-throughput systematic evolution of ligands by exponential enrichment (HT-SELEX), but scalable analytic tools for understanding sequence-function relationships from diverse HT-SELEX data are not available. Here we present AptaTRACE, a computational approach that leverages the experimental design of the HT-SELEX protocol, RNA secondary structure, and the potential presence of many secondary motifs to identify sequence-structure motifs that show a signature of selection. We apply AptaTRACE to identify nine motifs in C-C chemokine receptor type 7 targeted by aptamers in an in vitro cell-SELEX experiment. We experimentally validate two aptamers whose binding required both sequence and structural features. AptaTRACE can identify low-abundance motifs, and we show through simulations that, because of this, it could lower HT-SELEX cost and time by reducing the number of selection cycles required. PMID:27467247

  9. Isolation and structural elucidation of two secondary metabolites from the filamentous fungus Penicillium ochrochloron with antimicrobial activity.

    PubMed

    Rančić, Ana; Soković, Marina; Karioti, Anastasia; Vukojević, Jelena; Skaltsa, Helen

    2006-07-01

    In this investigation, the extracts of filamentous fungi exhibited inhibitory effect on the growth of Gram positive and Gram negative bacteria, as well as against the yeast Candida albicans. Penicillium ochrochloron has been proven as the most active fungus against all tested microorganisms. Further bio-guided chemical analysis of P. ochrochloron afforded two components with antimicrobial activity identified as (-) 2, 3, 4-trihydroxybutanamide and (-) erythritol.

  10. Structural, Spectroscopic, And Theoretical Elucidation of a Redox-Active Pincer-Type Ancillary Applied in Catalysis

    SciTech Connect

    Adhikari, D.; Mossin, S.; Basuli, F.; Huffman, J.C.; Szilagyi, R.K.; Meyer, K.; Mindiola, D.J.

    2009-05-11

    Pincer-type ligands are believed to be very robust scaffolds that can support multifarious functionalities as well as highly reactive metal motifs applied in organometallic chemistry, especially in the realm of catalysis. In this paper, we describe the redox and, therefore, noninnocent behavior of a PNP (PNP{sup -} = N[2-P(CHMe{sub 2}){sub 2}-4-methylphenyl]{sub 2}) pincer ancillary bound to nickel. A combination of structural, spectroscopic, and theoretical techniques suggests that this type of framework can house an electron hole when coordinated to Ni(II).

  11. Elucidating the native sources of an invasive tree species, Acacia pycnantha, reveals unexpected native range diversity and structure

    PubMed Central

    Ndlovu, Joice; Richardson, David M.; Wilson, John R. U.; O'Leary, Martin; Le Roux, Johannes J.

    2013-01-01

    Background and Aims Understanding the introduction history of invasive plant species is important for their management and identifying effective host-specific biological control agents. However, uncertain taxonomy, intra- and interspecific hybridization, and cryptic speciation may obscure introduction histories, making it difficult to identify native regions to explore for host-specific agents. The overall aim of this study was to identify the native source populations of Acacia pycnantha, a tree native to south-eastern Australia and invasive in South Africa, Western Australia and Portugal. Using a phylogeographical approach also allowed an exploration of the historical processes that have shaped the genetic structure of A. pycnantha in its native range. Methods Nuclear (nDNA) and plastid DNA sequence data were used in network and tree-building analyses to reconstruct phylogeographical relationships between native and invasive A. pycnantha populations. In addition, mismatch distributions, relative rates and Bayesian analyses were used to infer recent demographic processes and timing of events in Australia that led to population structure and diversification. Key Results The plastid network indicated that Australian populations of A. pycnantha are geographically structured into two informally recognized lineages, the wetland and dryland forms, whereas the nuclear phylogeny showed little geographical structure between these two forms. Moreover, the dryland form of A. pycnantha showed close genetic similarity to the wetland form based on nDNA sequence data. Hybrid zones may explain these findings, supported here by incongruent phylogenetic placement of some of these taxa between nuclear and plastid genealogies. Conclusions It is hypothesized that habitat fragmentation due to cycles of aridity inter-dispersed with periods of abundant rainfall during the Pleistocene (approx. 100 kya) probably gave rise to native dryland and wetland forms of A. pycnantha. Although the

  12. Structure Elucidation of Poly-Faldaprevir: Polymer Backbone Solved Using Solid-State and Solution Nuclear Magnetic Resonance Spectroscopy.

    PubMed

    Gonnella, Nina C; Busacca, Carl A; Zhang, Li; Saha, Anjan; Wu, Jiang-Ping; Li, Guisheng; Davis, Mark; Offerdahl, Thomas; Jones, Paul-James; Herfurth, Lars; Reddig, Tim; Wagner, Klaus; Niemann, Michael; Werthmann, Ulrike; Grupe, Julia; Roos, Helmut; Reckzügel, Gaby; Ding, Andreas

    2016-06-01

    A large-scale synthesis of the hepatitis C virus drug Faldaprevir revealed precipitation of an unknown insoluble solid from methanol solutions of the drug substance. The unknown impurity was determined to be a polymer of Faldaprevir based on analytical methods that included size exclusion chromatography in combination with electrospray ionization mass spectrometry, solution nuclear magnetic resonance (NMR), matrix-assisted laser desorption ionization-time of flight, ultracentrifugation, elemental analysis, and sodium quantitation by atom absorption spectroscopy. Structure elucidation of the polymeric backbone was achieved using solid-state NMR cross-polarization/magic angle spinning (CP/MAS), cross polarization-polarization inversion, and heteronuclear correlation (HETCOR) experiments. The polymerization was found to occur at the vinyl cyclopropane via a likely free radical initiation mechanism. Full proton and carbon chemical shift assignments of the polymer were obtained using solution NMR spectroscopy. The polymer structure was corroborated with chemical synthesis of the polymer and solution NMR analysis. PMID:27238486

  13. Structure elucidation of cyclic pyoverdins and examination of rearrangement reactions in MS/MS experiments by determination of exact product ion masses.

    PubMed

    Schäfer, Mathias; Fuchs, Regine; Budzikiewicz, Herbert; Springer, Andreas; Meyer, Jean-Marie; Linscheid, Michael

    2006-09-01

    Structure elucidation of naturally occurring linear and cyclic peptidic compounds can be complicated by rearrangement reactions induced upon collision activation (CA) when parts of the molecule migrate, suggesting incorrect substitution patterns. Such complex rearrangements are examined and discussed for two iron complexing compounds produced by the bacterial genus Pseudomonas (so-called pyoverdins). Various MS2- and MS3-product ion experiments were performed using a quadrupole-ion trap (QIT) at low resolution and a FT-ICR at high resolution allowing accurate mass determinations. The results of the multidimensional study confirm the proposed processes. On the basis of the series of tandem-MS experiments the structure of a new pyoverdin from a P. fluorescens strain [PVD(D47)] is deduced. PMID:16888716

  14. Cobalt-Catalyzed [2π + 2π] Cycloadditions of Alkenes: Scope, Mechanism, and Elucidation of Electronic Structure of Catalytic Intermediates.

    PubMed

    Schmidt, Valerie A; Hoyt, Jordan M; Margulieux, Grant W; Chirik, Paul J

    2015-06-24

    Aryl-substituted bis(imino)pyridine cobalt dinitrogen compounds, ((R)PDI)CoN2, are effective precatalysts for the intramolecular [2π + 2π] cycloaddition of α,ω-dienes to yield the corresponding bicyclo[3.2.0]heptane derivatives. The reactions proceed under mild thermal conditions with unactivated alkenes, tolerating both amine and ether functional groups. The overall second order rate law for the reaction, first order with respect to both the cobalt precatalyst and the substrate, in combination with electron paramagnetic resonance (EPR) spectroscopic studies established the catalyst resting state as dependent on the identity of the precatalyst and diene substrate. Planar S = ½ κ(3)-bis(imino)pyridine cobalt alkene and tetrahedral κ(2)-bis(imino)pyridine cobalt diene complexes were observed by EPR spectroscopy and in the latter case structurally characterized. The hemilabile chelate facilitates conversion of a principally ligand-based singly occupied molecular orbital (SOMO) in the cobalt dinitrogen and alkene compounds to a metal-based SOMO in the diene intermediates, promoting C-C bond-forming oxidative cyclization. Structure-activity relationships on bis(imino)pyridine substitution were also established with 2,4,6-tricyclopentyl-substituted aryl groups, resulting in optimized catalytic [2π + 2π] cycloaddition. The cyclopentyl groups provide a sufficiently open metal coordination sphere that encourages substrate coordination while remaining large enough to promote a challenging, turnover-limiting C(sp(3))-C(sp(3)) reductive elimination. PMID:26030841

  15. Cobalt-Catalyzed [2π + 2π] Cycloadditions of Alkenes: Scope, Mechanism, and Elucidation of Electronic Structure of Catalytic Intermediates.

    PubMed

    Schmidt, Valerie A; Hoyt, Jordan M; Margulieux, Grant W; Chirik, Paul J

    2015-06-24

    Aryl-substituted bis(imino)pyridine cobalt dinitrogen compounds, ((R)PDI)CoN2, are effective precatalysts for the intramolecular [2π + 2π] cycloaddition of α,ω-dienes to yield the corresponding bicyclo[3.2.0]heptane derivatives. The reactions proceed under mild thermal conditions with unactivated alkenes, tolerating both amine and ether functional groups. The overall second order rate law for the reaction, first order with respect to both the cobalt precatalyst and the substrate, in combination with electron paramagnetic resonance (EPR) spectroscopic studies established the catalyst resting state as dependent on the identity of the precatalyst and diene substrate. Planar S = ½ κ(3)-bis(imino)pyridine cobalt alkene and tetrahedral κ(2)-bis(imino)pyridine cobalt diene complexes were observed by EPR spectroscopy and in the latter case structurally characterized. The hemilabile chelate facilitates conversion of a principally ligand-based singly occupied molecular orbital (SOMO) in the cobalt dinitrogen and alkene compounds to a metal-based SOMO in the diene intermediates, promoting C-C bond-forming oxidative cyclization. Structure-activity relationships on bis(imino)pyridine substitution were also established with 2,4,6-tricyclopentyl-substituted aryl groups, resulting in optimized catalytic [2π + 2π] cycloaddition. The cyclopentyl groups provide a sufficiently open metal coordination sphere that encourages substrate coordination while remaining large enough to promote a challenging, turnover-limiting C(sp(3))-C(sp(3)) reductive elimination.

  16. Templated Atom-Precise Galvanic Synthesis and Structure Elucidation of a [Ag24Au(SR)18](-) Nanocluster.

    PubMed

    Bootharaju, Megalamane S; Joshi, Chakra P; Parida, Manas R; Mohammed, Omar F; Bakr, Osman M

    2016-01-18

    Synthesis of atom-precise alloy nanoclusters with uniform composition is challenging when the alloying atoms are similar in size (for example, Ag and Au). A galvanic exchange strategy has been devised to produce a compositionally uniform [Ag24Au(SR)18](-) cluster (SR: thiolate) using a pure [Ag25(SR)18](-) cluster as a template. Conversely, the direct synthesis of Ag24Au cluster leads to a mixture of [Ag(25-x)Au(x)(SR)18](-), x=1-8. Mass spectrometry and crystallography of [Ag24Au(SR)18](-) reveal the presence of the Au heteroatom at the Ag25 center, forming Ag24Au. The successful exchange of the central Ag of Ag25 with Au causes perturbations in the Ag25 crystal structure, which are reflected in the absorption, luminescence, and ambient stability of the particle. These properties are compared with those of Ag25 and Ag24Pd clusters with same ligand and structural framework, providing new insights into the modulation of cluster properties with dopants at the single-atom level.

  17. Metal Interactions at the Biochar-Water Interface: Energetics and Structure-Sorption Relationships Elucidated by Flow Adsorption Microcalorimetry

    SciTech Connect

    Harvey, Omar R.; Herbert, Bruce; Rhue, Roy D.; Kuo, Li-Jung

    2011-06-01

    Interest in biochars and their role in the biogeochemical cycling of metals have increased in recent years. However, a systematic understanding of the mechanisms involved in biochar-metal interactions and conditions under which a given mechanism is predominant is still needed. We used flow adsorption micro-calorimetry to study structure-sorption relationships between twelve plant-derived biochars and two metals of different ionization potential (Ip). Biochar structure influenced the amount of K+ (Ip = 419 kJ mol-1) or Cd(II) (Ip = 868 kJ mol-17 ) sorption but had no effect on the mechanism of sorption. Irrespective of the biochar, K+ sorption was exothermic, surface-controlled and occurred via an ion-exchange mechanism on negatively- charged sites with molar heats of adsorption (_Hads) of -4 kJ mol-1 on wood versus -8 kJ mol-1 on grass biochars. In contrast, Cd(II) sorption was endothermic and favored surface complexation on uncharged biochar surfaces with _Hads of around +17 kJ mol-1. Cadmium sorption transitioned from surface- to diffusion-controlled on biochars formed at ≥ 350 oC and _Hads for Cd(II) sorption was the same on grass and wood biochars. We concluded that, in general, metals with lower Ip favor electrostatic interactions with biochars, while metals of higher Ip favor more covalent-like interactions.

  18. 3D NMR spectroscopy for resonance assignment and structure elucidation of proteins under MAS: novel pulse schemes and sensitivity considerations.

    PubMed

    Heise, Henrike; Seidel, Karsten; Etzkorn, Manuel; Becker, Stefan; Baldus, Marc

    2005-03-01

    Two types of 3D MAS NMR experiments are introduced, which combine standard (NC,CC) transfer schemes with (1H,1H) mixing to simultaneously detect connectivities and structural constraints of uniformly 15N,13C-labeled proteins with high spectral resolution. The homonuclear CCHHC and CCC experiments are recorded with one double-quantum evolution dimension in order to avoid a cubic diagonal in the spectrum. Depending on the second transfer step, spin systems or proton-proton contacts can be determined with reduced spectral overlap. The heteronuclear NHHCC experiment encodes NH-HC proton-proton interactions, which are indicative for the backbone conformation of the protein. The third dimension facilitates the identification of the amino acid spin system. Experimental results on U-[15N,13C]valine and U-[15N,13C]ubiquitin demonstrate their usefulness for resonance assignments and for the determination of structural constraints. Furthermore, we give a detailed analysis of alternative multidimensional sampling schemes and their effect on sensitivity and resolution. PMID:15705514

  19. Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity

    PubMed Central

    Long, Feng; Fong, Rachel H.; Austin, Stephen K.; Chen, Zhenguo; Klose, Thomas; Fokine, Andrei; Liu, Yue; Porta, Jason; Sapparapu, Gopal; Akahata, Wataru; Doranz, Benjamin J.; Crowe, James E.; Diamond, Michael S.; Rossmann, Michael G.

    2015-01-01

    Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. Here, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain’s β-ribbon connector of the viral glycoprotein E2. The footprints of these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. This finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes. PMID:26504196

  20. Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity.

    PubMed

    Long, Feng; Fong, Rachel H; Austin, Stephen K; Chen, Zhenguo; Klose, Thomas; Fokine, Andrei; Liu, Yue; Porta, Jason; Sapparapu, Gopal; Akahata, Wataru; Doranz, Benjamin J; Crowe, James E; Diamond, Michael S; Rossmann, Michael G

    2015-11-10

    Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. Here, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain's β-ribbon connector of the viral glycoprotein E2. The footprints of these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. This finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes. PMID:26504196

  1. Mass-spectrometric structure elucidation of dog bile azopigments as the acyl glycosides of glucopyranose and xylopyranose

    PubMed Central

    Compernolle, F.; Van Hees, G. P.; Fevery, J.; Heirwegh, K. P. M.

    1971-01-01

    1. The structures of the α2- and α3-azopigments, prepared by diazotization of dog bile with ethyl anthranilate, were shown by mass spectrometry and g.l.c. to correspond to azobilirubin β-d-xylopyranoside and azobilirubin β-d-glucopyranoside respectively. 2. Both azopigments consist of a mixture of two methyl vinyl isomers having structures (IIIa) and (IIIb) for the α2-azopigment and structures (IVa) and (IVb) for the α3-azopigment. Separation of methyl vinyl isomers was obtained by t.l.c. or column chromatography performed on the acetylated azopigments. Hydrolysis of the less polar acetates derived from components (IIIa) and (IVa) gave rise to the azopigment (Ia), whereas hydrolysis of the more polar acetates derived from components (IIIb) and (IVb) gave rise to the azopigment acid (Ib). The positions of methyl and vinyl substituents in compounds (Ia) and (Ib) were assigned on the basis of their n.m.r. spectra. 3. Molecular ions in the mass spectra of the trimethylsilyl and acetyl derivatives of the azopigments indicated the presence of a pentose and a hexose conjugating sugar. 4. The ester functions linking the sugars to the propionic acid side chain of azobilirubin were demonstrated by ammonolysis and identification of the amide of azobilirubin as the aglycone derivative. 5. The sugar moieties were shown to occur as xylopyranose (α2) and glucopyranose (α3), bound at C-1, by application of a sequence of reactions performed on a micro-scale. The sugar hydroxyl groups were acetylated and the 1-acyl aglycone removed selectively by treatment with hydrogen bromide in acetic acid. Hydrolysis of the 1-bromo sugar acetates followed by acetylation afforded the α- and β-xylopyranose tetra-acetates and α- and β-glucopyranose penta-acetates, identified by a combination of g.l.c. and mass spectrometry. 6. The validity of this degradation scheme was confirmed (a) by g.l.c.–mass spectrometry identification of the α- and β-1-propionyl derivatives of glucopyranose

  2. The elucidation of the structure of Thermotoga maritima peptidoglycan reveals two novel types of cross-link.

    PubMed

    Boniface, Audrey; Parquet, Claudine; Arthur, Michel; Mengin-Lecreulx, Dominique; Blanot, Didier

    2009-08-14

    Thermotoga maritima is a Gram-negative, hyperthermophilic bacterium whose peptidoglycan contains comparable amounts of L- and D-lysine. We have determined the fine structure of this cell-wall polymer. The muropeptides resulting from the digestion of peptidoglycan by mutanolysin were separated by high-performance liquid chromatography and identified by amino acid analysis after acid hydrolysis, dinitrophenylation, enzymatic determination of the configuration of the chiral amino acids, and mass spectrometry. The high-performance liquid chromatography profile contained four main peaks, two monomers, and two dimers, plus a few minor peaks corresponding to anhydro forms. The first monomer was the d-lysine-containing disaccharide-tripeptide in which the D-Glu-D-Lys bond had the unusual gamma-->epsilon arrangement (GlcNAc-MurNAc-L-Ala-gamma-D-Glu-epsilon-D-Lys). The second monomer was the conventional disaccharide-tetrapeptide (GlcNAc-MurNAc-L-Ala-gamma-D-Glu-L-Lys-D-Ala). The first dimer contained a disaccharide-L-Ala as the acyl donor cross-linked to the alpha-amine of D-Lys in a tripeptide acceptor stem with the sequence of the first monomer. In the second dimer, donor and acceptor stems with the sequences of the second and first monomers, respectively, were connected by a D-Ala4-alpha-D-Lys3 cross-link. The cross-linking index was 10 with an average chain length of 30 disaccharide units. The structure of the peptidoglycan of T. maritima revealed for the first time the key role of D-Lys in peptidoglycan synthesis, both as a surrogate of L-Lys or meso-diaminopimelic acid at the third position of peptide stems and in the formation of novel cross-links of the L-Ala1(alpha-->alpha)D-Lys3 and D-Ala4(alpha-->alpha)D-Lys3 types.

  3. 3-Dimensional atomic scale structure of the ionic liquid-graphite interface elucidated by AM-AFM and quantum chemical simulations.

    PubMed

    Page, Alister J; Elbourne, Aaron; Stefanovic, Ryan; Addicoat, Matthew A; Warr, Gregory G; Voïtchovsky, Kislon; Atkin, Rob

    2014-07-21

    In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)-bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL-solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level structure immersed in a viscous liquid and (d) it has been demonstrated that the IL structure at solid surfaces is a consequence of both thermodynamic and kinetic effects. The lateral structure of the PAN-graphite interface is highly ordered and consists of remarkably well-defined domains of a rhomboidal superstructure composed of propylammonium cations preferentially aligned along two of the three directions in the underlying graphite lattice. The nanostructure is primarily determined by the cation. Van der Waals interactions between the propylammonium chains and the surface mean that the cation is enriched in the surface layer, and is much less mobile than the anion. The presence of a heterogeneous lateral structure at an ionic liquid-solid interface has wide ranging ramifications for ionic liquid applications, including lubrication, capacitive charge storage and electrodeposition.

  4. Novel transglutaminase-like peptidase and C2 domains elucidate the structure, biogenesis and evolution of the ciliary compartment.

    PubMed

    Zhang, Dapeng; Aravind, L

    2012-10-15

    C2 domains aid in the proper reconstruction of the Y-shaped linkers, which are key structures in the transitional zone of cilia, by allowing precise prediction of the multiple membrane-contacting and protein-protein interaction sites in these structures. These findings help decipher key events in the evolutionary separation of the ciliary and nuclear compartments in course of the emergence of the eukaryotic cell.

  5. Structure elucidation at the nanomole scale. 1. Trisoxazole macrolides and thiazole-containing cyclic peptides from the nudibranch Hexabranchus sanguineus.

    PubMed

    Dalisay, Doralyn S; Rogers, Evan W; Edison, Arthur S; Molinski, Tadeusz F

    2009-04-01

    A single specimen of Hexabranchus sanguineus, a nudibranch from the Indo-Pacific that is known to sequester kabiramides B and C and other trisoxazole macrolides, yielded new kabiramide analogues, 9-desmethylkbiramide B and 33-methyltetrahydrohalichondramide, and two new unexpected thiazole-containing cyclic peptides in submicromolar amounts. The structures of these cyclic peptides were determined by analyses of 1D and 2D NMR spectra recorded with a state-of-the-art 1 mm (1)H NMR high-temperature superconducting microcryoprobe, together with mass spectra. In addition to two proline residues, each peptide contains a thiazole- or oxazole-modified amino acid residue, together with conventional amino acid residues. All of the amino acid residues were l, as determined by Marfey's analysis of the acid hydrolysates of the peptides. This is the first report of cyclic thiazole peptides from H. sanguineus. Since thiazole-oxazole-modified peptides are typically associated with cyanobacteria and tunicates, the finding may imply a dietary component of the H. sanguineus that was previously overlooked. PMID:19254038

  6. Elucidation of Structural Elements for Selectivity across Monoamine Transporters: Novel 2-[(Diphenylmethyl)sulfinyl]acetamide (Modafinil) Analogues

    PubMed Central

    2015-01-01

    2-[(Diphenylmethyl)sulfinyl]acetamide (modafinil, (±)-1) is a unique dopamine uptake inhibitor that binds the dopamine transporter (DAT) differently than cocaine and may have potential for the treatment of psychostimulant abuse. To further investigate structural requirements for this divergent binding mode, novel thio- and sulfinylacetamide and ethanamine analogues of (±)-1 were synthesized wherein (1) the diphenyl rings were substituted with methyl, trifluoromethyl, and halogen substituents and (2) substituents were added to the terminal amide/amine nitrogen. Halogen substitution of the diphenyl rings of (±)-1 gave several amide analogues with improved binding affinity for DAT and robust selectivity over the serotonin transporter (SERT), whereas affinity improved at SERT over DAT for the p-halo-substituted amine analogues. Molecular docking studies, using a subset of analogues with DAT and SERT homology models, and functional data obtained with DAT (A480T) and SERT (T497A) mutants defined a role for TM10 in the substrate/inhibitor S1 binding sites of DAT and SERT. PMID:24494745

  7. Antimicrobial efficacy of phenanthrenequinone based Schiff base complexes incorporating methionine amino acid: Structural elucidation and in vitro bio assay

    NASA Astrophysics Data System (ADS)

    Arun, Thesingu Rajan; Raman, Natarajan

    2014-06-01

    This work focuses the synthesis and characterization of few novel mixed ligand Schiff base metal complexes and their biological activities. For deriving the structural aspects, spectral techniques such as FT-IR, UV-Vis., 1H NMR, Raman, EPR and the physicochemical characterizations including elemental analysis, molar conductance and magnetic susceptibility method have been involved. All the complexes adopt square planar geometry. DNA binding ability of these complexes has been explored using diverse techniques viz. UV-Vis. absorption, fluorescence spectroscopy, viscometry and cyclic voltammetry. These studies prove that CT-DNA binding of the complexes follows the intercalation mode. Comparative DNA oxidative cleavage ability of the complexes has been done under ultraviolet photo radiation on pUC19 DNA. In addition, the biocidal action of the complexes has been investigated against few pathogenic bacteria and fungi by disc diffusion method. Importantly, the amylase inhibition activity of Cu(II) complex has been explored. The amylase inhibition property has been found to be increased upon increasing the complex concentration.

  8. Structure elucidation of a pungent compound in black cardamom: Amomum tsao-ko Crevost et Lemarié (Zingiberaceae).

    PubMed

    Starkenmann, Christian; Mayenzet, Fabienne; Brauchli, Robert; Wunsche, Laurent; Vial, Christian

    2007-12-26

    Natural plant extracts containing taste modifier compounds will gain more commercial interest in the future. Black cardamom, Amomum tsao-ko Crevost et Lemarié, used as a spice in Asia, produces a nice refreshing effect in the mouth. Therefore, an ethyl acetate extract was prepared, and constituents were separated by liquid chromatography. Guided by the tasting of each fraction (LC tasting), a new pungent compound was discovered, (+/-)-trans-2,3,3a,7a-tetrahydro-1H-indene-4-carbaldehyde. To confirm this new structure, a synthesis was performed starting from cyclopentene-1-carbaldehyde. The Wittig conditions were determined to control the stereochemistry of the ring fusion to prepare (+/-)-trans-(2,3,3a,7a-tetrahydro-1 H-inden-4-yl) methanol and (+/-)-cis-(2,3,3a,7a-tetrahydro-1H-inden-4-yl) methanol. After oxidation, (+/-)-trans-2,3,3a,7a-tetrahydro-1H-indene-4-carbaldehyde and (+/-)-cis-2,3,3a,7a-tetrahydro-1H-indene-4-carbaldehyde were tasted in water and only the trans-2,3,3a,7a-tetrahydro-1H-indene-4-carbaldehyde, present in black cardamom, produced a trigeminal effect in the mouth.

  9. Structure elucidation of the thermal degradation products of the nucleotide cofactors NADH and NADPH by nano-ESI-FTICR-MS and HPLC-MS.

    PubMed

    Hofmann, Diana; Wirtz, Astrid; Santiago-Schübel, Beatrix; Disko, Ulrich; Pohl, Martina

    2010-12-01

    Redox cofactors like NADH and NADPH are essential for the catalytic activity of several oxidoreductases. Here, we describe a comparative study of the thermal degradation products of both cofactors in the dry and liquid states. The degradation products were first separated, detected, and quantified by high-performance liquid chromatography (HPLC). Subsequently, selected main fractions were investigated by nanoelectrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry (MS). Additionally, HPLC-MS was used to elucidate the structure of all degradation products. From these data, degradation pathways for both the liquid and the solid states were elucidated. Thermal degradation in water is significantly faster compared to degradation in the solid state. Hydrolysis and oxidative ring opening of the reduced nicotinamide adenine dinucleotide (phosphate) were shown to be the main reaction paths. Surprisingly, no significant differences were observed between the degradation of both cofactors in solution and in the solid state. Our results demonstrate that the stability of both cofactors is not limiting at moderate temperatures if they are used in the dry state (e.g., solid/gas catalysis). Significant degradation of dry cofactors was only observed under conditions, which are usually not appropriate for biocatalysis (>95 °C). Besides, the situation is completely different in solution where degradation is already observed at moderate temperatures.

  10. Structure elucidation and anti-tumor activities of water-soluble oligosaccharides from Lactarius deliciosus (L. ex Fr.) Gray

    PubMed Central

    Ding, Xiang; Hou, Yiling; Hou, Wanru; Zhu, Yuanxiu; Fu, Lei; Zhu, Hongqing

    2015-01-01

    Background: Oligosaccharides are composed of a variable number of monosaccharide units and very important in the biologically diverse of biological systems. Materials and Methods: Crude water-soluble oligosaccharide was extracted from the fruiting bodies with water and then successively purified by DEAE–cellulose 52 and Sephadex G-100 column chromatography, yielding one major oligosaccharides fractions: LES-A. Structural features of Lactarius deliciosus (L. ex Fr.) Gray oligosaccharide (LDGO-A) were investigated by a combination of monosaccharide component analysis by thin layer chromatography, infrared spectra, nuclear magnetic resonance spectroscopy, scanning electron microscopy, and high-performance gel permeation chromatography analysis. Result: The results indicated that LDGO-A was composed of D-glucose and D-xylose, and the average molecular sizes was approximately 945 Da. The anti-tumor activity of LDGO-A was evaluated in vivo. The inhibitory rate in mice treated with 40 mg/kg LDGO-A can reach 40.02%, being the highest in the three doses, which may be comparable to mannatide. Histology of immune organs shows that the tissues arranged more regular and firmer, but the tumor tissue arranged looser in LDGO-A group than those in the control group. Meanwhile, there is no obvious damage to other organs, such as heart. The anti-tumor activity of the LDGO-A was usually believed to be a consequence of the stimulation of the cell-mediated immune response because it can significantly promote the lymphocyte and macrophage cells in the dose range of 100–400 μg/mL in vitro. LDGO-A also effected the expression of some housekeeping genes mRNA in S180 tumor. Conclusion: Accordingly, the LDGO-A might serve as an effective healthcare food and source of natural anti-tumor compounds. PMID:26600715

  11. Carbohydrates of influenza virus. Structural elucidation of the individual glycans of the FPV hemagglutinin by two-dimensional 1H n.m.r. and methylation analysis.

    PubMed Central

    Keil, W; Geyer, R; Dabrowski, J; Dabrowski, U; Niemann, H; Stirm, S; Klenk, H D

    1985-01-01

    The structures of the oligosaccharides of the hemagglutinin of fowl plague virus [influenza A/FPV/Rostock/34 (H7N1)] have been elucidated by one- and two-dimensional 1H n.m.r. spectroscopy at 500 MHz and by microscale methylation analysis. N-Glycosidic oligosaccharides of the oligomannosidic (OM) and of the N-acetyllactosaminic type have been found, the latter type comprising biantennary structures, without (A) or with (E) bisecting N-acetylglucosamine, and triantennary (C) structures. Analysis of the tryptic and thermolytic glycopeptides of the hemagglutinin allowed the allocation of these oligosaccharides to the individual glycosylation sites. Each attachment site contained a unique set of oligosaccharides. Asn12 contains predominantly structures C and E which are highly fucosylated. Asn28 contains OM and A structures that lack fucose and sulfate. Asn123 shows A that has incomplete antennae but is highly fucosylated and sulfated. Asn149 has fucosylated A and E. Asn231 shows fucosylated A and E with incomplete antennae. Asn406 has OM oligosaccharides. Asn478 has A and E with little fucose. Localization of the oligosaccharides on the three-dimensional structure of the hemagglutinin revealed that the oligomannosidic glycans are attached to glycosylation sites at which the enzymes responsible for carbohydrate processing do not have proper access. These observations demonstrate that an important structural determinant for the oligosaccharide side chains is the structure of the glycoprotein itself. In addition, evidence was obtained that the rate of glycoprotein synthesis also has an influence on carbohydrate structure. Images Fig. 10. PMID:4054103

  12. Two dimensional laser induced fluorescence spectroscopy: A powerful technique for elucidating rovibronic structure in electronic transitions of polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Gascooke, Jason R.; Alexander, Ula N.; Lawrance, Warren D.

    2011-05-01

    We demonstrate the power of high resolution, two dimensional laser induced fluorescence (2D-LIF) spectroscopy for observing rovibronic transitions of polyatomic molecules. The technique involves scanning a tunable laser over absorption features in the electronic spectrum while monitoring a segment, in our case 100 cm-1 wide, of the dispersed fluorescence spectrum. 2D-LIF images separate features that overlap in the usual laser induced fluorescence spectrum. The technique is illustrated by application to the S1-S0 transition in fluorobenzene. Images of room temperature samples show that overlap of rotational contours by sequence band structure is minimized with 2D-LIF allowing a much larger range of rotational transitions to be observed and high precision rotational constants to be extracted. A significant advantage of 2D-LIF imaging is that the rotational contours separate into their constituent branches and these can be targeted to determine the three rotational constants individually. The rotational constants determined are an order of magnitude more precise than those extracted from the analysis of the rotational contour and we find the previously determined values to be in error by as much as 5% [G. H. Kirby, Mol. Phys. 19, 289 (1970), 10.1080/00268977000101291]. Comparison with earlier ab initio calculations of the S0 and S1 geometries [I. Pugliesi, N. M. Tonge, and M. C. R. Cockett, J. Chem. Phys. 129, 104303 (2008), 10.1063/1.2970092] reveals that the CCSD/6-311G** and RI-CC2/def2-TZVPP levels of theory predict the rotational constants, and hence geometries, with comparable accuracy. Two ground state Fermi resonances were identified by the distinctive patterns that such resonances produce in the images. 2D-LIF imaging is demonstrated to be a sensitive method capable of detecting weak spectral features, particularly those that are otherwise hidden beneath stronger bands. The sensitivity is demonstrated by observation of the three isotopomers of fluorobenzene

  13. On the use of X-ray absorption spectroscopy to elucidate the structure of lutetium adenosine mono- and triphosphate complexes.

    PubMed

    Mostapha, S; Berthon, C; Fontaine-Vive, F; Gaysinski, M; Guérin, L; Guillaumont, D; Massi, L; Monfardini, I; Solari, P L; Thomas, O P; Charbonnel, M C; Den Auwer, C

    2014-02-01

    chemical calculations has been implemented in order to assess the lutetium coordination arrangement for the two nucleotides. In all the complexes described in the article, the lutetium cation is coordinated by the phosphate groups of the nucleotide plus additional putative water molecules with various tridimensional arrangements. With AMP 1:2 and ATP 1:1 solid-state compounds, polynuclear complexes are assumed to be obtained. In contrast, with ATP 1:2 soluble compound, the Lu coordination sphere is saturated by two ATP ligands, and this favors the formation of a mononuclear complex. In order to further interpret the EXAFS data obtained at the Lu LIII edge, model structures have been calculated for the 1:1 and 1:2 ATP complexes. They are discussed and compared to the EXAFS best fit metrical parameters.

  14. The reaction of azoles with 17-chloro-16-formylandrosta-5,16-dien-3β-yl-acetate: synthesis and structural elucidation of novel 16-azolylmethylene-17-oxoandrostanes.

    PubMed

    Moreira, Vânia M; Salvador, Jorge A R; Beja, Ana Matos; Paixão, José A

    2011-05-01

    The synthesis and structural elucidation, by 1D and 2D NMR and X-ray diffraction techniques, of novel E/Z 16-azolylmethylene-17-oxoandrostanes 2-9 prepared from the Vilsmeier-Hack reaction product 17-chloro-16-formylandrosta-5,16-dien-3β-yl acetate 1 is reported. The reaction proceeds with pyrrole and pyrrole-alike nitrogen heterocycles such as 7-azaindole, indole, and 3-methylindole, in DMF, at 80°C, in the presence of K(2)CO(3), and allowed the attachment of privileged heterocyclic moieties, through the nitrogen atom to the steroid core at C16 via a methine carbon bridge, which is unprecedented in the literature and of potential synthetic and biological interest. Considerations on the possible reaction mechanism are included. All the synthesized compounds are new and are currently being tested for biological activities.

  15. Structural elucidation of biologically active neomycin N-octyl derivatives in a regioisomeric mixture by means of liquid chromatography/ion trap time-of-flight mass spectrometry.

    PubMed

    Giera, Martin; de Vlieger, Jon S B; Lingeman, Henk; Irth, Hubertus; Niessen, Wilfried M A

    2010-05-30

    Structural elucidation of six regioisomers of mono-N-octyl derivatized neomycin is achieved using MS(n) (up to n = 4) on an ion trap time-of-flight (IT-TOF) instrument equipped with electrospray ionization. The mixture of six derivatized neomycin analogues was generated by reductive amination in a shotgun synthetic approach. In parallel to the liquid chromatography/mass spectrometry (LC/MS) detection, the antibacterial activity of the neomycin regioisomers was tested by post-column addition of buffer and bacterial inocula, subsequent microfractionation of the resulting mixture, incubation, and finally a chemiluminescence-based bioactivity measurement based on the production of bacterial ATP. The MS-based high-resolution screening approach described can be applied in medicinal chemistry to help in designing and producing new antibiotic substances, which is particularly challenging due to the high functionality of most antibiotic substances, therefore requiring advanced (hyphenated) separation and detection techniques for compound mixtures.

  16. Proteogenomic elucidation of the initial steps in the benzene degradation pathway of a novel halophile, Arhodomonas sp. strain Rozel, isolated from a hypersaline environment.

    PubMed

    Dalvi, Sonal; Azetsu, Sei; Patrauchan, Marianna A; Aktas, Deniz F; Fathepure, Babu Z

    2012-10-01

    Lately, there has been a special interest in understanding the role of halophilic and halotolerant organisms for their ability to degrade hydrocarbons. The focus of this study was to investigate the genes and enzymes involved in the initial steps of the benzene degradation pathway in halophiles. The extremely halophilic bacteria Arhodomonas sp. strain Seminole and Arhodomonas sp. strain Rozel, which degrade benzene and toluene as the sole carbon source at high salinity (0.5 to 4 M NaCl), were isolated from enrichments developed from contaminated hypersaline environments. To obtain insights into the physiology of this novel group of organisms, a draft genome sequence of the Seminole strain was obtained. A cluster of 13 genes predicted to be functional in the hydrocarbon degradation pathway was identified from the sequence. Two-dimensional (2D) gel electrophoresis and liquid chromatography-mass spectrometry were used to corroborate the role of the predicted open reading frames (ORFs). ORFs 1080 and 1082 were identified as components of a multicomponent phenol hydroxylase complex, and ORF 1086 was identified as catechol 2,3-dioxygenase (2,3-CAT). Based on this analysis, it was hypothesized that benzene is converted to phenol and then to catechol by phenol hydroxylase components. The resulting catechol undergoes ring cleavage via the meta pathway by 2,3-CAT to form 2-hydroxymuconic semialdehyde, which enters the tricarboxylic acid cycle. To substantiate these findings, the Rozel strain was grown on deuterated benzene, and gas chromatography-mass spectrometry detected deuterated phenol as the initial intermediate of benzene degradation. These studies establish the initial steps of the benzene degradation pathway in halophiles.

  17. ION COMPOSITION ELUCIDATION (ICE)

    EPA Science Inventory



    Ion Composition Elucidation (ICE) utilizes selected ion recording with a double focusing mass spectrometer to simultaneously determine exact masses and relative isotopic abundances from mass peak profiles. These can be determined more accurately and at higher sensitivity ...

  18. Isolation, structural assignment, and total synthesis of barmumycin.

    PubMed

    Lorente, Adriana; Pla, Daniel; Cañedo, Librada M; Albericio, Fernando; Alvarez, Mercedes

    2010-12-17

    Barmumycin was isolated from an extract of the marine actinomycete Streptomyces sp. BOSC-022A and found to be cytotoxic against various human tumor cell lines. On the basis of preliminary one- and two-dimensional (1)H and (13)C NMR spectra, the natural compound was initially assigned the structure of macrolactone-type compound 1, which was later prepared by two different routes. However, major spectroscopic differences between isolated barmumycin and 1 led to revision of the proposed structure as E-16. On the basis of the synthesis of this new compound, and subsequent spectroscopic comparison of it to an authentic sample of barmumycin, the structure of the natural compound was indeed confirmed as that of E-16.

  19. [Isolation and structure identification of chemical constituents from the skin of Bufo bufo gargarizans].

    PubMed

    Dai, Li-Ping; Gao, Hui-Min; Wang, Zhi-Min; Wang, Wei-Hao

    2007-08-01

    The skin of Bufo bufo gargarizans, originated from Bufo bufo gargarizans Cantor (Bufonidae), is widely used in traditional Chinese medicine for the treatment of hepatoma, lung cancer and etc. The preparation of the aqueous components has significant therapeutic effect against the digestive tract cancer. The water-soluble chemical constituents in the skin of Bufo bufo gargarizans were then investigated to make clear the active compounds. Six compounds were isolated and purified by recrystallization and column chromatography on silica gel and ODS, their structures were elucidated as 4-amido-3-hydroxymethyl-cyclooctylamidezotetra-alpha-furanone (I), bufogargarizanine C (II), bufothionine (III), dehydrobufotenine hydrobromide (IV), suberic acid (V) and succinic acid (VI) on the basis of physicochemical properties and spectral data (UV, IR, 1H NMR, 13C NMR and MS). Of the above compounds, compounds I and II are new compounds and named bufogargarizanine B and C, respectively. PMID:17944235

  20. An insilico approach to structural elucidation of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Arabidopsis thaliana: hints for herbicide design.

    PubMed

    Bhattacharya, Sushmita; Kumar, Pravindra

    2012-01-01

    3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS), the first enzyme of the shikimate pathway, is responsible for the synthesis of aromatic amino acids in microorganisms and plants. The pathway has been of increasing interest in the recent past as the enzymes are being targeted for antimicrobial drug and herbicide design. In the present work the three dimensional structure of the type II DAHPS present in Arabidopsis thaliana (At-DAHPS) is described and compared with type I DAHPS. The structure shows that the enzyme belongs to the (β/α)(8) TIM barrel family and that most of the active site residues are conserved in the type I DAHPS enzymes. Although the overall structures of the type I and type II enzymes are similar, there are differences in the extra barrel elements which may explain the different modes of enzyme regulation. At the N-terminus of At-DAHPS, there are three non-core helices, α0a (Ala72-Lys83), α0b (Ala94-Ala106) and α0c (Ala113-Val128), but no β(0), in contrast to the microbial type II DAHPS. Also, the (I/L)GAR motif in the type I DAHPS is substituted with xGxR in the case of type II DAHPS. Also, a motif NK(/I)PGR(/K) is present in the sequences of type II DAHPS including At-DAHPS. The elucidation of the active site architecture of At-DAHPS may provide a structural framework useful for the design of specific inhibitors towards herbicide development. PMID:22000723

  1. Solution Structures of the Prototypical 18 kDa Translocator Protein Ligand, PK 11195, Elucidated with 1H/13C NMR Spectroscopy and Quantum Chemistry

    PubMed Central

    2012-01-01

    Eighteen kilodalton translocator protein (TSPO) is an important target for drug discovery and for clinical molecular imaging of brain and peripheral inflammatory processes. PK 11195 [1a; 1-(2-chlorophenyl)-N-methyl-(1-methylpropyl)-3-isoquinoline carboxamide] is the major prototypical high-affinity ligand for TSPO. Elucidation of the solution structure of 1a is of interest for understanding small-molecule ligand interactions with the lipophilic binding site of TSPO. Dynamic 1H/13C NMR spectroscopy of 1a revealed four quite stable but interconverting rotamers, due to amide bond and 2-chlorophenyl group rotation. These rotamers have been neglected in previous descriptions of the structure of 1a and of the binding of 1a to TSPO. Here, we used quantum chemistry at the level of B3LYP/6-311+G(2d,p) to calculate 13C and 1H chemical shifts for the rotamers of 1a and for the very weak TSPO ligand, N-desmethyl-PK 11195 (1b). These data, plus experimental NMR data, were then used to characterize the structures of rotamers of 1a and 1b in organic solution. Energy barriers for both the amide bond and 2′-chlorophenyl group rotation of 1a were determined from dynamic 1H NMR to be similar (ca.17 to 18 kcal/mol), and they compared well with those calculated at the level of B3LYP/6-31G*. Furthermore, the computed barrier for Z to E rotation is considerably lower in 1a(18.7 kcal/mol) than in 1b (25.4 kcal/mol). NMR (NOE) unequivocally demonstrated that the E rotamer of 1a is the more stable in solution by about 0.4 kcal/mol. These detailed structural findings will aid future TSPO ligand design and support the notion that TSPO prefers to bind ligands as amide E-rotamers. PMID:22860199

  2. Synthesis, spectroscopic and structural elucidation of 1-butyl-4-[2-(3,5-dimethoxy-4-hydroxyphenyl)ethenyl)]pyridinium chloride tetrahydrate

    NASA Astrophysics Data System (ADS)

    Koleva, B. B.; Kolev, T.; Lamshöft, M.; Mayer-Figge, H.; Sheldrick, W. S.; Spiteller, M.

    2009-12-01

    The novel chloride salt of 1-butyl-4-[2-(4-hydroxyphenyl)ethenyl)]pyridine ( 1), has been synthesized as the tetrahydrate and its structure and properties elucidated in detail spectroscopically, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid-state IR-spectroscopy, UV-spectroscopy and mass spectrometry. Quantum chemical calculations were performed with a view to supporting and explaining the experimental structural and spectroscopic data. The compound ( 1) crystallizes in triclinic P1¯ space group and its unit cell contains two independent 1-butyl-4-[2-(3,5-dimethoxy4-hydroxyphenyl)ethenyl)]pyridinium] cations, differing with respect to the butyl chain torsion angle for which values of 80.0(9)° and 173.6(3)° are observed. The cations and anions are joined into infinite layers, formed by two different dimers and including solvent molecules. Hydrogen bonds OH⋯OH 2 (2.814 Å), HOH⋯O(CH 3) (2.960 Å), OH⋯Cl (2.967 Å), HOH⋯Cl - (3.034, 3.188, 3.161 and 3.062 Å) and HOH⋯OH 2 (2.772 Å) are observed. For first time in the literature, we are reporting the crystal structure of the dye with the syring-fragment in the molecule. The spectroscopic properties of the novel compound are compared and with those of the corresponding quinoide form ( 2). Both the forms ( 1) and ( 2) are characterized by 21 and 140 nm solvatochromic effects depending of the type of the solvent. The UV-spectroscopic data in solution confirm the formation of classical H-aggregates in polar protic solvent mixture.

  3. Structural Revisions of a Class of Natural Products: Scaffolds of Aglycon Analogues of Fusicoccins and Cotylenins Isolated from Fungi.

    PubMed

    Tang, Ying; Xue, Yongbo; Du, Guang; Wang, Jianping; Liu, Junjun; Sun, Bin; Li, Xiao-Nian; Yao, Guangmin; Luo, Zengwei; Zhang, Yonghui

    2016-03-14

    The reisolation and structural revision of brassicicene D is described, and inspired us to reassign the core skeletons of brassicicenes C-H, J and K, ranging from dicyclopenta[a,d]cyclooctane to tricyclo[9.2.1.0(3,7)]tetradecane using quantum-chemical predictions and experimental validation strategies. Three novel, highly modified fusicoccanes, brassicicenes L-N, were also isolated from the fungus Alternaria brassicicola, and their structures were unequivocally established by spectroscopic data, ECD calculations, and crystallography. The reassigned structures represent the first class of bridgehead double-bond-containing natural products with a bicyclo[6.2.1]undecane carbon skeleton. Furthermore, their stabilities were first predicted with olefin strain energy calculations. Collectively, these findings extend our view of the application of computational predictions and biosynthetic logic-based structure elucidation to address problems related to the structure and stability of natural products. PMID:26916098

  4. Stability-indicating liquid chromatographic method for determination of saxagliptin and structure elucidation of the major degradation products using LC-MS.

    PubMed

    Abdel-Ghany, Maha F; Abdel-Aziz, Omar; Ayad, Miriam F; Tadros, Mariam M

    2015-04-01

    A new, simple, selective, reproducible and sensitive stability-indicating liquid chromatographic method was developed and subsequently validated for the determination of saxagliptin (SXG). SXG was subjected to oxidation, thermal, acid hydrolysis, alkali hydrolysis and photodegradation according to ICH guidelines. The major degradation products were separated from the pure drug and the proposed structures' elucidation was performed, using an LC-MS technique. Isocratic chromatographic elution was achieved on a Symmetry(®) C18 column (150 × 4.6 mm, 5 µm), using a mobile phase of potassium dihydrogen phosphate buffer (pH 4.6)-acetonitrile-methanol (40 : 30 : 30, v/v/v) at a flow rate of 1 mL min(-1) with UV detection at 208 nm. Linearity, accuracy and precision were found to be acceptable over the concentration range of 25-400 µg mL(-1). All the results were statistically compared with the reference method, using one-way analysis of variance. The developed method was validated and proved to be specific and accurate for quality control of SXG in pharmaceutical dosage form.

  5. Structural Elucidation and Toxicity Assessment of Degraded Products of Aflatoxin B1 and B2 by Aqueous Extracts of Trachyspermum ammi

    PubMed Central

    Iram, Wajiha; Anjum, Tehmina; Iqbal, Mazhar; Ghaffar, Abdul; Abbas, Mateen

    2016-01-01

    In this study aqueous extract of seeds and leaves of Trachyspermum ammi were evaluated for their ability to detoxify aflatoxin B1 and B2 (AFB1; 100 μg L−1 and AFB2; 50 μg L−1) by in vitro and in vivo assays. Results indicated that T. ammi seeds extract was found to be significant (P < 0.05) in degrading AFB1 and AFB2 i.e., 92.8 and 91.9% respectively. However, T. ammi leaves extract proved to be less efficient in degrading these aflatoxins, under optimized conditions i.e., pH 8, temperature 30°C and incubation period of 72 h. The structural elucidation of degraded toxin products by LCMS/MS analysis showed that eight degraded products of AFB1 and AFB2 were formed. MS/MS spectra showed that most of the products were formed by the removal of double bond in the terminal furan ring and modification of lactone group indicating less toxicity as compared to parent compounds. Brine shrimps bioassay further confirmed the low toxicity of degraded products, showing that T. ammi seeds extract can be used as an effective tool for the detoxification of aflatoxins. PMID:27064492

  6. Structural elucidation and magnetic behavior evaluation of rare earth (La, Nd, Gd, Tb, Dy) doped BaCoNi-X hexagonal nano-sized ferrites

    NASA Astrophysics Data System (ADS)

    Majeed, Abdul; Khan, Muhammad Azhar; Raheem, Faseeh ur; Hussain, Altaf; Iqbal, F.; Murtaza, Ghulam; Akhtar, Majid Niaz; Shakir, Imran; Warsi, Muhammad Farooq

    2016-06-01

    Rare-earth (RE=La3+, Nd3+, Gd3+, Tb3+, Dy3+) doped Ba2NiCoRExFe28-xO46 (x=0.25) hexagonal ferrites were synthesized for the first time via micro-emulsion route, which is a fast chemistry route for obtaining nano-sized ferrite powders. These nanomaterials were investigated by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), as well as vibrating sample magnetometer (VSM). The XRD analysis exhibited that all the samples crystallized into single X-type hexagonal phase. The crystalline size calculated by Scherrer's formula was found in the range 7-19 nm. The variations in lattice parameters elucidated the incorporation of rare-earth cations in these nanomaterials. FTIR absorption spectra of these X-type ferrites were investigated in the wave number range 500-2400 cm-1. Each spectrum exhibited absorption bands in the low wave number range, thereby confirming the X-type hexagonal structure. The enhancement in the coercivity was observed with the doping of rare-earth cations. The saturation magnetization was lowered owing to the redistribution of rare-earth cations on the octahedral site (3bVI). The higher values of coercivity (664-926 Oe) of these nanomaterials suggest their use in longitudinal recording media.

  7. Structure elucidation of an artifact discharging from rubber-based vial closures by means of gas chromatography/tandem mass spectrometry.

    PubMed

    Kapp, Thomas; Vetter, Walter

    2006-12-01

    The use of vial closures equipped with butyl rubber septa may lead to sample contamination by rubber additives discharging from the septum material. In this study, the structure elucidation of an artifact causing intense signals in gas chromatography/electron capture negative ion mass spectrometry (GC/ECNI-MS) and gas chromatographic analyses with electron capture detection is described. Tentative identification of the leached compound was achieved by employing tandem mass spectrometric techniques both in electron capture negative ion and in electron ionization modes. The artifact could thus be characterized as 2-benzothiazolyl-N,N-dimethyl dithiocarbamate, which is a known vulcanization accelerator for rubber. It is conceivable that the identified compound or related substances are also used in other applications. Therefore, two food-related matrixes were investigated for a possible migration of this compound into foods. During these analyses, the tentatively identified rubber additive was detected in an aqueous extract of a rubber seal ring for canning jars. GC/ECNI-MS provided better sensitivity and selectivity than GC/EI-MS for the determination of the rubber additive and other mercaptobenzothiazole-derived substances. PMID:17134153

  8. Application of LC-MS(n) in conjunction with mechanism-based stress studies in the elucidation of drug impurity structure: rapid identification of a process impurity in betamethasone 17-valerate drug substance.

    PubMed

    Li, Min; Lin, Mingxiang; Rustum, Abu

    2008-12-15

    Through a case study, the use of LC-MS(n) technique in conjunction with a mechanism-based stress study is shown to be a very effective way in the rapid elucidation of unknown drug impurities. In this case, the drug substance sample was first analyzed using LC-MS(n) through which the unknown species was found to be a valeryl-containing, isomeric impurity of the active pharmaceutical ingredient (API), betamethasone 17-valerate, based on its molecular ion and major fragments. Since a substantial knowledge regarding a large number of isomeric impurities of betamethasone has been accumulated in the literature as well as in our laboratory, a hydrolytic stress study (forced degradation) of the isolated unknown species was then designed and carried out accordingly in order to remove the valeryl group from the unknown species. During the stress study, a betamethasone isomer was generated as expected. However, a new unknown species isomeric to betamethasone 17-valerate was also formed unexpectedly. By comparing the UV spectra and more importantly MS(n) fragmentation patterns of the two newly formed species with those of betamethasone, dexamethasone, betamethasone 17-valerate, and betamethasone 21-valerate, these two unknown species generated in the stress study were identified as dexamethasone and dexamethasone 21-valerate, respectively. Based on the plausible reaction mechanism of the forced degradation, the original impurity present in betamethasone 17-valerate drug substance was then identified as dexamethasone 17-valerate; the structure assignment was later confirmed by various 1D and 2D NMR experiments. The efficient conversion from dexamethasone 17-valerate to dexamethasone 21-valerate was also observed during a 2D NMR acquisition of the isolated dexamethasone 17-valerate sample.

  9. Harnessing the Unique Structural Properties of Isolated α-Helices*

    PubMed Central

    Swanson, Carter J.; Sivaramakrishnan, Sivaraj

    2014-01-01

    The α-helix is a ubiquitous secondary structural element that is almost exclusively observed in proteins when stabilized by tertiary or quaternary interactions. However, beginning with the unexpected observations of α-helix formation in the isolated C-peptide in ribonuclease A, there is growing evidence that a significant percentage (0.2%) of all proteins contain isolated stable single α-helical domains (SAH). These SAH domains provide unique structural features essential for normal protein function. A subset of SAH domains contain a characteristic ER/K motif, composed of a repeating sequence of ∼4 consecutive glutamic acids followed by ∼4 consecutive basic arginine or lysine (R/K) residues. The ER/K α-helix, also termed the ER/K linker, has been extensively characterized in the context of the myosin family of molecular motors and is emerging as a versatile structural element for protein and cellular engineering applications. Here, we review the structure and function of SAH domains, as well as the tools to identify them in natural proteins. We conclude with a discussion of recent studies that have successfully used the modular ER/K linker for engineering chimeric myosin proteins with altered mechanical properties, as well as synthetic polypeptides that can be used to monitor and systematically modulate protein interactions within cells. PMID:25059657

  10. Systematic Structural Elucidation for the Protonated Form of Rare Earth Bis(porphyrinato) Double-Decker Complexes: Direct Structural Evidence of the Location of the Attached Proton.

    PubMed

    Yamashita, Ken-Ichi; Sakata, Naoya; Ogawa, Takuji

    2016-09-01

    Direct structural evidence of the presence and location of the attached proton in the protonated form of rare earth bis(porphyrinato) double-decker complexes is obtained from an X-ray diffraction study of single crystals for a series of protonated forms of bis(tetraphenylporphyrinato) complexes [M(III)(tpp)(tppH)] (M = Tb, Y, Sm, Nd, and La). When CHCl3 is used as a solvent for crystallization of the complexes, their nondisordered molecular structures are obtained and the attached proton is identified on one of the eight nitrogen atoms. Use of other solvents affords another type of crystal, in which the position of the proton is disordered and thus the molecular structure is averaged. La complex also affords the disordered average structure even when CHCl3 is used for crystallization. A variable-temperature diffraction study for the Tb complex reveals that the dynamics of the proton in the nondisordered crystal is restricted. PMID:27541189

  11. Systematic Structural Elucidation for the Protonated Form of Rare Earth Bis(porphyrinato) Double-Decker Complexes: Direct Structural Evidence of the Location of the Attached Proton.

    PubMed

    Yamashita, Ken-Ichi; Sakata, Naoya; Ogawa, Takuji

    2016-09-01

    Direct structural evidence of the presence and location of the attached proton in the protonated form of rare earth bis(porphyrinato) double-decker complexes is obtained from an X-ray diffraction study of single crystals for a series of protonated forms of bis(tetraphenylporphyrinato) complexes [M(III)(tpp)(tppH)] (M = Tb, Y, Sm, Nd, and La). When CHCl3 is used as a solvent for crystallization of the complexes, their nondisordered molecular structures are obtained and the attached proton is identified on one of the eight nitrogen atoms. Use of other solvents affords another type of crystal, in which the position of the proton is disordered and thus the molecular structure is averaged. La complex also affords the disordered average structure even when CHCl3 is used for crystallization. A variable-temperature diffraction study for the Tb complex reveals that the dynamics of the proton in the nondisordered crystal is restricted.

  12. Elucidating the band structure and free charge carrier dynamics of pure and impurities doped CH3NH3PbI(3-x)Cl(x) perovskite thin films.

    PubMed

    Zhang, Zhen-Yu; Chen, Xin; Wang, Hai-Yu; Xu, Ming; Gao, Bing-Rong; Chen, Qi-Dai; Sun, Hong-Bo

    2015-11-28

    CH3NH3PbI3-xClx perovskite material has been commonly used as the free charge generator and reservoir in highly efficient perovskite-based solid-state solar photovoltaic devices. However, many of the underlying fundamental photophysical mechanisms in this material such as the perovskite transition band structure as well as the dependent relationship between the carrier properties and lattice properties still lack sufficient understanding. Here, we elucidated the fundamental band structure of the pure CH3NH3PbI3-xClx pervoskite lattice, and then reported about the dependent relationship between the free charge carrier characteristic and the different CH3NH3PbI3-xClx pervoskite lattice thin films utilizing femtosecond time-resolved pump-probe technologies. The data demonstrated that the pure perovskite crystal band structure should only have one conduction and one valence band rather than dual valences, and the pure perovskite lattice could trigger more free charge carriers with a slower recombination rate under an identical pump intensity compared with the impurities doped perovskite crystal. We also investigated the perovskite film performance when exposed to moisture and water, the corresponding results gave us a dip in the optimization of the performance of perovskite based devices, and so as a priority this material should be isolated from moisture (water). This work may propose a deeper perspective on the comprehension for this material and it is useful for future optimization of applications in photovoltaic and light emission devices. PMID:26497219

  13. Oligosaccharides in goat milk: structure, health effects and isolation.

    PubMed

    Kiskini, A; Difilippo, E

    2013-11-03

    Oligosaccharides have been widely recognized for their prebiotic and anti-infective properties. Among the different types of mammalian milk, the one of humans is the richest source of naturally derived oligosaccharides. However, their use as a basis for functional foods is hampered, due to their structural complexity, which in turn makes their re-synthesis extremely difficult. Thus, oligosaccharides from other sources have to be used. In this sense, goat milk constitutes a very appealing candidate, as it contains the highest amount of oligosaccharides among domestic animals, while goat milk oligosaccharides show significant similarities to human milk oligosaccharides from a structural point of view. Studies on goat milk oligosaccharides are scant, and more data is required in order to provide solid clinical evidence of their beneficial effects on humans. The aim of this review is to collect and present the main research findings on goat milk oligosaccharides structure, health effects and isolation.

  14. Optical investigation of functional structures in isolated perfused pig heart

    NASA Astrophysics Data System (ADS)

    Rauh, Robert; Boehnert, Markus; Mahlke, Christine; Kessler, Manfred D.

    2000-11-01

    Light scattering in tissue of mammals and humans is affected by subcellular structures. Since these structures correlate well with the status of cells and tissue, light scattering seems to be ideal for monitoring of functional tissue state. By use of EMPHO SSK Oxyscan we investigated functional parameters in a novel kind of isolated perfused pig heart model. In this perfusion model we use organs obtained by the local slaughterhouse that are reanimated at our institute by application of a heart-lung machine. By creating 3D-images of tissue scattering we found an interesting relation between anatomical structures of myocardium and the 3D-images. Additionally, we detected coherence between backscattered light intensity and functional tissue status. Furthermore, we got a sight into the redox state of cytochrome aa3, b and c by creating difference spectra. We believe that this new kind of tissue imaging method will give us the opportunity to get new insights into myocardial function.

  15. Bioassay-Guided Isolation and Structural Modification of the Anti-TB Resorcinols from Ardisia gigantifolia.

    PubMed

    Guan, Yi-Fu; Song, Xun; Qiu, Ming-Hua; Luo, Shi-Hong; Wang, Bao-Jie; Van Hung, Nguyen; Cuong, Nguyen M; Soejarto, Djaja Doel; Fong, Harry H S; Franzblau, Scott G; Li, Sheng-Hong; He, Zhen-Dan; Zhang, Hong-Jie

    2016-08-01

    Tuberculosis (TB) is a highly contagious disease mainly caused by Mycobacterium tuberculosis H37 RV . Antitubercular (anti-TB) bioassay-guided isolation of the CHCl3 extract of the leaves and stems of the medicinal plant Ardisia gigantifolia led to the isolation of two anti-TB 5-alkylresorcinols, 5-(8Z-heptadecenyl) resorcinol (1) and 5-(8Z-pentadecenyl) resorcinol (2). We further synthesized 15 derivatives based on these two natural products. These compounds (natural and synthetic) were evaluated for their anti-TB activity against Mycobacterium tuberculosis H37 RV . Resorcinols 1 and 2 exhibited anti-TB activity with MIC values at 34.4 and 79.2 μm in MABA assay, respectively, and 91.7 and 168.3 μm in LORA assay, respectively. Among these derivatives, compound 8 was found to show improved anti-TB activity than its synthetic precursor (2) with MIC values at 42.0 μm in MABA assay and 100.2 μm in LORA assay. The active compounds should be regarded as new hits for further study as a novel class of anti-TB agents. The distinct structure-activity correlations of the parent compound were elucidated based on these derivatives.

  16. Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition

    PubMed Central

    Choi, Sung-Jin; Ban, Changill

    2016-01-01

    Structural elements are key elements for understanding single-stranded nucleic acid folding. Although various RNA structural elements have been documented, structural elements of single-stranded DNA (ssDNA) have rarely been reported. Herein, we determined a crystal structure of PvLDH in complex with a DNA aptamer called pL1. This aptamer folds into a hairpin-bulge contact by adopting three novel structural elements, viz, DNA T-loop-like motif, base–phosphate zipper, and DNA G·G metal ion zipper. Moreover, the pL1:PvLDH complex shows unique properties compared with other protein:nucleic acid complexes. Generally, extensive intermolecular hydrogen bonds occur between unpaired nucleotides and proteins for specific recognitions. Although most protein-interacting nucleotides of pL1 are unpaired nucleotides, pL1 recognizes PvLDH by predominant shape complementarity with many bridging water molecules owing to the combination of three novel structural elements making protein-binding unpaired nucleotides stable. Moreover, the additional set of Plasmodium LDH residues which were shown to form extensive hydrogen bonds with unpaired nucleotides of 2008s does not participate in the recognition of pL1. Superimposition of the pL1:PvLDH complex with hLDH reveals steric clashes between pL1 and hLDH in contrast with no steric clashes between 2008s and hLDH. Therefore, specific protein recognition mode of pL1 is totally different from that of 2008s. PMID:27725738

  17. Synthesis, spectroscopic, thermal and structural elucidation of 5-amino-2-methoxypyridine ester amide of squaric acid ethyl ester: A new material with an infinite pseudo-layered structure and manifested NLO application

    NASA Astrophysics Data System (ADS)

    Kolev, Tsonko; Koleva, Bojidarka B.; Spassov, Tony; Cherneva, Emilya; Spiteller, Michael; Mayer-Figge, Heike; Sheldrick, William S.

    2008-03-01

    The novel squaric acid derivative, 5-amino-2-methoxypyridin ester amide of squaric acid ethyl ester with second order NLO application in solution and in the bulk has been synthesized and is structure and properties elucidated in detail spectroscopic, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid state IR-spectroscopy, UV-spectroscopy, and TGA, DSC, DTA, MS and SHG methods. Quantum chemical calculations were used for obtain in the electronic structure, vibrational data and NLO properties. At room temperature the studied compound crystallizes in the noncentrosymmetric space group Cc and exhibits a pseudo-layer structure (solid phase 1) with molecules linked by NH⋯O dbnd C intermolecular hydrogen bonds with length of 2.955 Å and NH⋯O angle of 153.41°, respectively. At 200 °C a phase transition is observed, with the solid phase 2 exhibiting new intermolecular NH⋯N interactions, as elucidated by IR-spectroscopy and thermal analysis. The obtained large powder SHG efficiency of 609 times urea proves the NLO application of studied compound in the bulk.

  18. Isolation and structural analysis of ajugose from Vigna mungo L.

    PubMed

    Kotiguda, Girigowda; Peterbauer, Thomas; Mulimani, Veerappa H

    2006-09-01

    The hexasaccharide ajugose, alpha-D-galactopyranosyl-(1-->6)-alpha-D-galactopyranosyl-(1-->6)-O-alpha-D-galactopyranosyl-(1-->6)-alpha-D-galactopyranosyl-(1-->6)-alpha-D-glucopyranosyl-(1<-->2)-beta-D-fructofuranoside, generally uncommon in legumes, was detected in the seeds of Vigna mungo L. by TLC and paper chromatography. Ajugose was then isolated by silica gel chromatography and its structure was established by acid and enzymatic hydrolysis, fast atom bombardment mass spectrometry and both one- and two-dimensional 1H and 13C NMR techniques.

  19. Elucidation of a masked repeating structure of the O-specific polysaccharide of the halotolerant soil bacteria Azospirillum halopraeferens Au4

    PubMed Central

    Fedonenko, Yuliya P; Shashkov, Alexander S; Arbatsky, Nikolay P; Zdorovenko, Evelina L; Konnova, Svetlana A; Ignatov, Vladimir V; Knirel, Yuriy A

    2016-01-01

    Summary An O-specific polysaccharide was obtained by mild acid hydrolysis of the lipopolysaccharide isolated by the phenol–water extraction from the halotolerant soil bacteria Azospirillum halopraeferens type strain Au4. The polysaccharide was studied by sugar and methylation analyses, selective cleavages by Smith degradation and solvolysis with trifluoroacetic acid, one- and two-dimensional 1H and 13C NMR spectroscopy. The following masked repeating structure of the O-specific polysaccharide was established: →3)-α-L-Rhap2Me-(1→3)-[β-D-Glcp-(1→4)]-α-D-Fucp-(1→2)-β-D-Xylp-(1→, where non-stoichiometric substituents, an O-methyl group (~45%) and a side-chain glucose residue (~65%), are shown in italics. PMID:27340454

  20. First attempts at an elucidation of the interface structure resulting from the interaction between methacrylonitrile and a platinum anode: an experimental and theoretical (ab initio) study

    NASA Astrophysics Data System (ADS)

    Bureau, Christophe; Deniau, Guy; Valin, Françoise; Guittet, Marie-Joseph; Lécayon, Gérard; Delhalle, Joseph

    1996-06-01

    The aim of the present paper is to contribute to the elucidation of the molecular structures obtained on a platinum surface as this surface is submitted to an anodic potential (with respect to a silver reference electrode) when dipped into pure 2-methyl 2-propenenitrile (methacrylonitrile). Modified surfaces are examined using X- and UV-photoelectron spectroscopies (UPS and XPS). The results evidence the formation of an ultra-thin (20-40 Å) grafted oligomer film, which is not classical polymethacrylonitrile (PMAN), as obtained through a radical or anionic mechanism: spectral characteristics argue in the sense of a cationic polymerization of methacrylonitrile through its nitrile groups, as evidenced by a lowering of the gap as well as by the UPS and XPS (N 1s region) spectra. Molecular models of the reactants and reaction intermediates are proposed for the cationic polymerization of methacrylonitrile, and show that this polymerization is about as feasible as that of acetonitrile, at least on kinetic control grounds. Two different mechanisms are nonetheless possible, leading either to a quasi conjugated poly-imine type -(N  C) n-, or to a poly-cumulene type -(N  C  C) n- network. Theoretical consierations on reactants properties lead us to select the poly-imine way as the most plausible. Along with literature data concerning chemisorbed nitriles on platinum surfaces, a molecular model of the final state of the poly-imine reaction is then designed, comprising a three atom cluster to render the grafting site, and a dimer to render the grafted structure. A full geometry optimization is performed on the organic moiety at the Hartree-Fock (ab initio) level of theory, and a rough evaluation of the spectral footprint of the interface bond in the N 1s region is performed on the basis of Koopmans theorem with calibration on the bulk polymer peak. A preliminary 2.7 eV downward shift is predicted for N 1s interface nitrogens with respect to the polymer peak, which can

  1. Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes

    PubMed Central

    Obi, Chioma C.; Adebusoye, Sunday A.; Ugoji, Esther O.; Ilori, Mathew O.; Amund, Olukayode O.; Hickey, William J.

    2016-01-01

    Estuarine sediments are significant repositories of anthropogenic contaminants, and thus knowledge of the impacts of pollution upon microbial communities in these environments is important to understand potential effects on estuaries as a whole. The Lagos lagoon (Nigeria) is one of Africa’s largest estuarine ecosystems, and is impacted by hydrocarbon pollutants and other industrial and municipal wastes. The goal of this study was to elucidate microbial community structure in Lagos lagoon sediments to identify groups that may be adversely affected by pollution, and those that may serve as degraders of environmental contaminants, especially polycyclic aromatic hydrocarbons (PAHs). Sediment samples were collected from sites that ranged in types and levels of anthropogenic impacts. The sediments were characterized for a range of physicochemical properties, and microbial community structure was determined by Illumina sequencing of the 16S rRNA genes. Microbial diversity (species richness and evenness) in the Apapa and Eledu sediments was reduced compared to that of the Ofin site, and communities of both of the former two were dominated by a single operational taxonomic unit (OTU) assigned to the family Helicobacteraceae (Epsilonproteobacteria). In the Ofin community, Epsilonproteobacteria were minor constituents, while the major groups were Cyanobacteria, Bacteroidetes, and Firmicutes, which were all minor in the Apapa and Eledu sediments. Sediment oxygen demand (SOD), a broad indicator of contamination, was identified by multivariate analyses as strongly correlated with variation in alpha diversity. Environmental variables that explained beta diversity patterns included SOD, as well as levels of naphthalene, acenaphthylene, cobalt, cadmium, total organic matter, or nitrate. Of 582 OTU identified, abundance of 167 was significantly correlated (false discovery rate q≤ 0.05) to environmental variables. The largest group of OTU correlated with PAH levels were PAH

  2. Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes.

    PubMed

    Obi, Chioma C; Adebusoye, Sunday A; Ugoji, Esther O; Ilori, Mathew O; Amund, Olukayode O; Hickey, William J

    2016-01-01

    Estuarine sediments are significant repositories of anthropogenic contaminants, and thus knowledge of the impacts of pollution upon microbial communities in these environments is important to understand potential effects on estuaries as a whole. The Lagos lagoon (Nigeria) is one of Africa's largest estuarine ecosystems, and is impacted by hydrocarbon pollutants and other industrial and municipal wastes. The goal of this study was to elucidate microbial community structure in Lagos lagoon sediments to identify groups that may be adversely affected by pollution, and those that may serve as degraders of environmental contaminants, especially polycyclic aromatic hydrocarbons (PAHs). Sediment samples were collected from sites that ranged in types and levels of anthropogenic impacts. The sediments were characterized for a range of physicochemical properties, and microbial community structure was determined by Illumina sequencing of the 16S rRNA genes. Microbial diversity (species richness and evenness) in the Apapa and Eledu sediments was reduced compared to that of the Ofin site, and communities of both of the former two were dominated by a single operational taxonomic unit (OTU) assigned to the family Helicobacteraceae (Epsilonproteobacteria). In the Ofin community, Epsilonproteobacteria were minor constituents, while the major groups were Cyanobacteria, Bacteroidetes, and Firmicutes, which were all minor in the Apapa and Eledu sediments. Sediment oxygen demand (SOD), a broad indicator of contamination, was identified by multivariate analyses as strongly correlated with variation in alpha diversity. Environmental variables that explained beta diversity patterns included SOD, as well as levels of naphthalene, acenaphthylene, cobalt, cadmium, total organic matter, or nitrate. Of 582 OTU identified, abundance of 167 was significantly correlated (false discovery rate q≤ 0.05) to environmental variables. The largest group of OTU correlated with PAH levels were PAH

  3. Post-translational heterocyclic backbone modifications in the 43-peptide antibiotic microcin B17. Structure elucidation and NMR study of a 13C,15N-labelled gyrase inhibitor.

    PubMed

    Bayer, A; Freund, S; Jung, G

    1995-12-01

    Microcin B17 (McB17), the first known gyrase inhibitor of peptidic nature, is produced by ribosomal synthesis and post-translational modification of the 69-residue precursor protein by an Escherichia coli strain. To elucidate the chemical structure of the mature 43-residue peptide antibiotic, fermentation and purification protocols were established and optimized which allowed the isolation and purification of substantial amounts of highly pure McB17 (non-labelled, 15N-labelled and 13C/15N-labelled peptide. By ultraviolet-absorption spectroscopy. HPLC-electrospray mass spectrometry and GC-mass spectrometry, amino acid analysis, protein sequencing, and, in particular, multidimensional NMR, we could demonstrate and unequivocally prove that the enzymic modification of the precursor backbone at Gly-Cys and Gly-Ser segments leads to the formation of 2-aminomethylthiazole-4-carboxylic acid and 2-aminomethyloxazole-4-carboxylic acid, respectively. In addition, two bicyclic modifications 2-(2-aminomethyloxazolyl)thiazole-4-carboxylic acid and 2-(2-aminomethylthiazolyl)oxazole-4-carboxylic acid were found that consist of directly linked thiazole and oxazole rings derived from one Gly-Ser-Cys and one Gly-Cys-Ser segment. Analogous to the thiazole and oxazole rings found in antitumor peptides of microbial and marine origin, these heteroaromatic ring systems of McB17 presumably play an important role in its gyrase-inhibiting activity, e.g. interacting with the DNA to trap the covalent protein-DNA intermediate of the breakage-reunion reaction of the gyrase.

  4. Isolation and structural characterization of a polysaccharide FCAP1 from the fruit of Cornus officinalis.

    PubMed

    Yang, Liyan; Wang, Zhongfu; Huang, Linjuan

    2010-09-01

    A water-soluble polysaccharide, FCAP1, was isolated from an alkaline extract from the fruits of Cornus officinalis. Its molecular weight was 34.5kDa. Monosaccharide composition analysis revealed that it was composed of fucose, arabinose, xylose, mannose, glucose, and galactose in a molar ratio of 0.29:0.19:1.74:1:3.30:1.10. On the basis of partial acid hydrolysis and methylation analysis, FCAP1 was shown to be a highly branched polysaccharide with a backbone of beta-(1-->4)-linked-glucose partially substituted at the O-6 position with xylopyranose residues. The branches were composed of (1-->3)-linked-Ara, (1-->4)-linked-Man, (1-->4,6)-linked-Man, (1-->4)-linked-Glc, and (1-->2)-linked-Gal. Arabinose, fucose, and galactose were located at the terminal of the branches. The structure was further elucidated by a specific enzymatic degradation with an endo-beta-(1-->4)-glucanase and MALDI-TOF-MS analysis. Oligosaccharides generated from FCAP1 indicated that FCAP1 contained XXXG-type and XXG-type xyloglucan fragments.

  5. Isolation and structural characterization of a new tadalafil analog (2-hydroxyethylnortadalafil) found in a dietary supplement.

    PubMed

    Kern, Sara E; Nickum, Elisa A; Flurer, Rick A; Toomey, Valerie M; Litzau, Jonathan J

    2015-01-25

    A screen for known PDE-5 inhibitors in a dietary supplement product marketed for "enhanced sexual performance" detected a compound that structurally resembled tadalafil. The compound was isolated from the supplement matrix using high-performance liquid chromatography with ultraviolet detection (HPLC-UV) and a fraction collector, and was further characterized using nuclear magnetic resonance (NMR), liquid chromatography-mass spectrometry (LC-MS), as well as high-resolution accurate mass mass spectrometry (HRAM-MS). The analog had an accurate mass of m/z 420.15614 (error is 1.77235ppm) for the protonated species [M+H](+), corresponding to a molecular formula of C23H22N3O5. Mass spectral fragmentation data suggested that the modification occurred in place of the CH3 located on the pyrazinopyridoindole-1,4-dione of tadalafil. NMR was utilized to further elucidate the configuration of the substitution. The analysis indicated that the moiety is a CH2CH2OH, hydroxyethyl group. The new analog has been named 2-hydroxyethylnortadalafil. PMID:25462127

  6. Isolation, structural characterization and neurotrophic activity of a polysaccharide from Phellinus ribis.

    PubMed

    Liu, Yuhong; Liu, Chunhui; Jiang, Haiqiang; Zhou, Honglei; Li, Pingli; Wang, Fengshan

    2015-01-01

    A new polysaccharide named PRG was isolated from the fruiting bodies of Phellinus ribis by hot water extraction, ethanol precipitation, anion-exchange and gel-filtration chromatography. PRG was homogeneous, with a molecular weight of 5.16 × 10(3)Da, as determined by high-performance size-exclusion chromatography-multiangle laser light scattering analysis. Its structural characteristics were investigated and elucidated by methylation analysis, partial acid hydrolysis, gas-liquid chromatography mass spectrometry, Fourier transform infrared and nuclear magnetic resonance spectroscopy. Based on obtained data, PRG was found to be a β-d-glucan containing a (1 → 3)-linked backbone, with a branch of two (1 → 6)-linked and one terminal glucoses substituting at the C-6 position every three residues, along the main chain. PRG exhibited neurotrophic activity, which significantly promoted the neurite outgrowth of the nerve growth factor-stimulated PC12 cells, suggesting that it might be a potential candidate for the treatment of neurodegenerative diseases.

  7. Preparative isolation and structural characterization of sucrose ester isomers from oriental tobacco.

    PubMed

    Jia, Chunxiao; Wang, Yingying; Zhu, Yonghua; Xu, Chunping; Mao, Duobin

    2013-05-01

    To date, the structures of the sucrose tetraester (STE) isomers, a main kind of sucrose esters (SEs) in Solanum, have not been conclusively assigned. In this study, three groups of STE isomers with the molecular weight 650, 664 and 678 (designated as STE I, STE II and STE III, respectively) have been isolated and purified from the oriental tobacco-Komotini Basma using a semi-preparative RP-HPLC method. The full characterization of the isomers in the three groups of STE were investigated for the first time by MS (HRMS, MS(2)) and NMR ((1)H, (13)C, HSQC) spectroscopy combined with alkaline hydrolysis and STE derivation experiments. The STE III (a single compound) was confirmed as a known sucrose tetraester. Furthermore, the STE II was found to contain three isomers and the structures were first unambiguously established as 6-O-acetyl (2,3 or 2,4 or 3,4)-di-O-3-methylvaleryl-(4 or 3 or 2)-O-2-methylbutyryl-α-d-glucopyranosyl-β-d-fructofuranoside. Finally, the STE I was discovered to contain seven isomers and the structures were elucidated as 6-O-acetyl (2 or 3 or 4)-O-3-methylvaleryl-(3,4 or 2,4 or 2,3)-di-O-2-methylbutyryl-α-d-glucopyranosyl-β-d-fructofuranoside, 6-O-acetyl (2 or 3 or 4)-O-3-methylvaleryl-(3,4 or 2,4 or 2,3)-di-O-isovaleryl-α-d-glucopyranosyl-β-d-fructofuranoside and 6-O-acetyl (2,3 or 2,4 or 3,4)-di-O-3-methylvaleryl-(4 or 3 or 2)-O-isobutyryl-α-d-glucopyranosyl-β-d-fructofuranoside (one of the 3 isomers). PMID:23542308

  8. Structure of turbulent wedges created by isolated surface roughness

    NASA Astrophysics Data System (ADS)

    Kuester, Matthew S.; White, Edward B.

    2016-04-01

    Isolated surface roughness in a laminar boundary layer can create a wedge of turbulence that spreads laterally into the surrounding laminar flow. Some recent studies have identified high- and low-speed streaks along the exterior of turbulent wedges. In this experiment, developing turbulent wedges are measured to observe the creation of these streaks. Naphthalene shear stress surface visualization and hotwire measurements are utilized to investigate the details of turbulent wedges created by cylinders in a laminar flat-plate boundary layer. Both the surface visualization and the hotwire measurements show high- and low-speed streaks in the wake of the cylinder that devolve into a turbulent wedge. The turbulent wedge spreading is associated with the emergence of these high- and low-speed streaks along the outside of the wedge. As the wedge evolves in the streamwise direction, these streaks persist inside of the core of the wedge, while new, lower amplitude streaks form along the outside of the wedge. Adding asymmetry to the cylinder moved the virtual origin closer to the roughness and increased the vortex shedding frequency, while adding small-scale roughness features did not strongly affect turbulent wedge development. Intermittency calculations additionally show the origin of the turbulent core inside of the wedge. The structure and spacing of the high-speed streaks along the extremities of the turbulent wedge give insight into the spreading angle of the turbulent wedge.

  9. Nonlinear dynamic analysis of multi-base seismically isolated structures with uplift potential I: formulation

    NASA Astrophysics Data System (ADS)

    Tsopelas, Panos C.; Roussis, Panayiotis C.; Constantinou, Michael C.

    2009-09-01

    The complexity of modern seismically isolated structures requires the analysis of the structural system and the isolation system in its entirety and the ability to capture potential discontinuous phenomena such as isolator uplift and their effects on the superstructures and the isolation hardware. In this paper, an analytical model is developed and a computational algorithm is formulated to analyze complex seismically isolated superstructures even when undergoing highly-nonlinear phenomena such as uplift. The computational model has the capability of modeling various types of isolation devices with strong nonlinearities, analyzing multiple superstructures (up to five separate superstructures) on multiple bases (up to five bases), and capturing the effects of lateral loads on bearing axial forces, including bearing uplift. The model developed herein has been utilized to form the software platform 3D-BASIS-ME-MB, which provides the practicing engineering community with a versatile tool for analysis and design of complex structures with modern isolation systems.

  10. Structural confirmation of novel oligosaccharides isolated from sugar beet molasses.

    PubMed

    Abe, Tatsuya; Kikuchi, Hiroto; Aritsuka, Tsutomu; Takata, Yusuke; Fukushi, Eri; Fukushi, Yukiharu; Kawabata, Jun; Ueno, Keiji; Onodera, Shuichi; Shiomi, Norio

    2016-07-01

    Eleven oligosaccharides were isolated from sugar beet molasses using carbon-Celite column chromatography and HPLC. The constituent sugars and linkage positions were determined using methylation analysis, MALDI-TOF-MS, and NMR measurements. The configurations of isolated oligosaccharides were confirmed based on detailed NMR analysis. Based on our results, three of the 11 oligosaccharides were novel. PMID:26920296

  11. Population structure and genetic diversity within California Citrus tristeza virus (CTV) isolates.

    PubMed

    Kong, P; Rubio, L; Polek, M; Falk, B W

    2000-10-01

    The Closterovirus, Citrus tristeza virus (CTV) is an aphid-borne RNA virus that is the causal agent of important worldwide economic losses in citrus. Biological and molecular variation has been observed for many CTV isolates. In this work we detected and analyzed sequence variants (haplotypes) within individual CTV isolates. We studied the population structure of five California CTV isolates by single strand conformation polymorphism (SSCP) analysis of four CTV genomic regions. Also, we estimated the genetic diversity within and between isolates by analysis of haplotype nucleotide sequences. Most CTV isolates were composed of a population of genetically related variants (haplotypes), one being predominant. However in one case, we found a high nucleotide divergence between haplotypes of the same isolate. Comparison of these haplotypes with those from other isolates suggests that some CTV isolates could have arisen as result of a mixed infection of two divergent isolates. PMID:11129629

  12. Scopariusicides, Novel Unsymmetrical Cyclobutanes: Structural Elucidation and Concise Synthesis by a Combination of Intermolecular [2 + 2] Cycloaddition and C-H Functionalization.

    PubMed

    Zhou, Min; Li, Xing-Ren; Tang, Jian-Wei; Liu, Yang; Li, Xiao-Nian; Wu, Bin; Qin, Hong-Bo; Du, Xue; Li, Li-Mei; Wang, Wei-Guang; Pu, Jian-Xin; Sun, Han-Dong

    2015-12-18

    Scopariusicides A (1) and B (2), two novel immunosuppressive unsymmetrical cyclobutane derivatives, were isolated from the aerial parts of Isodon scoparius. Moreover, based on the results of phytochemical investigation, a concise stereocontrolled synthesis of scopariusicide A and its analogues with enhanced biological activities was efficiently achieved using the main diterpenoid (3) isolated from this plant as a readily available starting material. A crossed intermolecular [2 + 2] photocycloaddition and a Pd-catalyzed sp(3) C-H bond β-arylation were used synergistically to access the highly congested unsymmetrical cyclobutane core with four contiguous stereocenters. PMID:26617269

  13. A novel polysaccharide isolated from mulberry fruits (Murus alba L.) and its selenide derivative: structural characterization and biological activities.

    PubMed

    Chen, Chun; Zhang, Bin; Fu, Xiong; Liu, Rui Hai

    2016-06-15

    A novel polysaccharide (MFP3P) was isolated from Murus alba L. through the hot water extraction method followed by chromatographic purification. The chemical structure of MFP3P was elucidated by acid hydrolysis, Smith degradation and methylation analysis, along with FT-IR, GC-MS, (1)H and (13)C NMR spectroscopy. Its morphological properties were further characterized by SEM and AFM. The selenide of the polysaccharide (MFP3P-Se) was obtained by the Na2SeO3/BaCl2 method. The antioxidant properties showed that MFP3P-Se exhibited higher peroxy radical-scavenging capacity than MFP3P in vitro. Moreover, MFP3P-Se had more significant hypoglycemic effects than MFP3P through promoting pancreatic cell proliferation and increasing glucose metabolism and insulin secretion. PMID:27241036

  14. Structural and biological characterization of one antibacterial acylpolyamine isolated from the hemocytes of the spider Acanthocurria gomesiana

    SciTech Connect

    Pereira, Lourivaldo S.; Silva, Pedro I.; Miranda, M. Teresa M.; Almeida, Igor C.; Naoki, Hideo; Konno, Katsuhiro; Daffre, Sirlei . E-mail: sidaffre@icb.usp.br

    2007-01-26

    We have isolated a 417 Da antibacterial molecule, named mygalin, from the hemocytes of the spider Acanthoscurria gomesiana. The structure of mygalin was elucidated by tandem mass spectrometry (MS/MS) and by two spectroscopic techniques, nuclear magnetic resonance (NMR) and ultraviolet (UV) spectroscopy. Mygalin was identified as bis-acylpolyamine N1,N8-bis(2,5-dihydroxybenzoyl)spermidine, in which the primary amino groups of the spermidine are acylated with the carboxyl group of the 2,5-dihydroxybenzoic acid. Mygalin was active against Escherichia coli at 85 {mu}M, being this activity inhibited completely by catalase. Therefore, the antibacterial activity of mygalin was attributed to its production of hydrogen peroxide (H{sub 2}O{sub 2}). The putative mechanisms of formation of H{sub 2}O{sub 2} from mygalin are discussed. To our knowledge this is the first report of one bis-acylpolyamine with antibacterial activity purified from animal source.

  15. X-ray absorption spectroscopy elucidates the impact of structural disorder on electron mobility in amorphous zinc-tin-oxide thin films

    SciTech Connect

    Siah, Sin Cheng E-mail: buonassisi@mit.edu; Lee, Yun Seog; Buonassisi, Tonio E-mail: buonassisi@mit.edu; Lee, Sang Woon; Gordon, Roy G.; Heo, Jaeyeong; Shibata, Tomohiro; Segre, Carlo U.

    2014-06-16

    We investigate the correlation between the atomic structures of amorphous zinc-tin-oxide (a-ZTO) thin films grown by atomic layer deposition (ALD) and their electronic transport properties. We perform synchrotron-based X-ray absorption spectroscopy at the K-edges of Zn and Sn with varying [Zn]/[Sn] compositions in a-ZTO thin films. In extended X-ray absorption fine structure (EXAFS) measurements, signal attenuation from higher-order shells confirms the amorphous structure of a-ZTO thin films. Both quantitative EXAFS modeling and X-ray absorption near edge spectroscopy (XANES) reveal that structural disorder around Zn atoms increases with increasing [Sn]. Field- and Hall-effect mobilities are observed to decrease with increasing structural disorder around Zn atoms, suggesting that the degradation in electron mobility may be correlated with structural changes.

  16. Semi-active control of isolated and damaged structures using online damage detection

    NASA Astrophysics Data System (ADS)

    Amini, Fereidoun; Mohajeri, Seyed Ahmad; Javanbakht, Majd

    2015-10-01

    The idea of using semi-active or active control devices within a base isolation system has been developed recently, since applying this system to building structures has some shortcomings such as the creation of large displacements at the base level and the system's lack of adaptability to different seismic excitations. In this study, an integrated structural health monitoring and semi-active control scheme is proposed to enhance the seismic behavior of damaged isolated structures. The nonlinear behavior of an isolated structure is limited to the isolator level and the superstructure is assumed to remain linear. Then, using an online damage detection algorithm based on identified system Markov parameters and a semi-active fuzzy controller, the damage in the base isolator is mitigated and the seismic response of the structure is reduced. In addition, a magnetorheological damper is utilized as a well-studied semi-active actuator in the control system. The effectiveness of the proposed control system is evaluated through the numerical study of a six-degrees-of-freedom model of base-isolated buildings excited by various near-fault and far-field earthquake records. The results of the simulation show that the integrated algorithm is substantially effective in improving the dynamic behavior of isolated structures and reducing the damage in the isolator.

  17. Development of adaptive seismic isolators for ultimate seismic protection of civil structures

    NASA Astrophysics Data System (ADS)

    Li, Jianchun; Li, Yancheng; Li, Weihua; Samali, Bijan

    2013-04-01

    Base isolation is the most popular seismic protection technique for civil engineering structures. However, research has revealed that the traditional base isolation system due to its passive nature is vulnerable to two kinds of earthquakes, i.e. the near-fault and far-fault earthquakes. A great deal of effort has been dedicated to improve the performance of the traditional base isolation system for these two types of earthquakes. This paper presents a recent research breakthrough on the development of a novel adaptive seismic isolation system as the quest for ultimate protection for civil structures, utilizing the field-dependent property of the magnetorheological elastomer (MRE). A novel adaptive seismic isolator was developed as the key element to form smart seismic isolation system. The novel isolator contains unique laminated structure of steel and MR elastomer layers, which enable its large-scale civil engineering applications, and a solenoid to provide sufficient and uniform magnetic field for energizing the field-dependent property of MR elastomers. With the controllable shear modulus/damping of the MR elastomer, the developed adaptive seismic isolator possesses a controllable lateral stiffness while maintaining adequate vertical loading capacity. In this paper, a comprehensive review on the development of the adaptive seismic isolator is present including designs, analysis and testing of two prototypical adaptive seismic isolators utilizing two different MRE materials. Experimental results show that the first prototypical MRE seismic isolator can provide stiffness increase up to 37.49%, while the second prototypical MRE seismic isolator provides amazing increase of lateral stiffness up to1630%. Such range of increase of the controllable stiffness of the seismic isolator makes it highly practical for developing new adaptive base isolation system utilizing either semi-active or smart passive controls.

  18. Luminescence from electroformed metal-isolator-metal-structures

    NASA Astrophysics Data System (ADS)

    Bischoff, Manfred

    The electroluminescence from metal-isolator-metal diodes is measured with a photon counter. From the time dependance of the electron temperature and density it appears that the electrons are not heated in the conduction band of the separating isolator or in vaccuum between the electrodes but in a highly degenerated semiconductor. The experimental results show that the grid temperature of the semiconductor filament material in case of a voltage pulse adds up to 1,500 K. The temperature of the hot electrons drops from 3,000 to 2,000 K. The charge carrier density and the recombination rate also increase.

  19. Structural and functional effects of social isolation on the hippocampus of rats with traumatic brain injury.

    PubMed

    Khodaie, Babak; Lotfinia, Ahmad Ali; Ahmadi, Milad; Lotfinia, Mahmoud; Jafarian, Maryam; Karimzadeh, Fariba; Coulon, Philippe; Gorji, Ali

    2015-02-01

    Social isolation has significant long-term psychological and physiological consequences. Both social isolation and traumatic brain injury (TBI) alter normal brain function and structure. However, the influence of social isolation on recovery from TBI is unclear. This study aims to evaluate if social isolation exacerbates the anatomical and functional deficits after TBI in young rats. Juvenile male rats were divided into four groups; sham operated control with social contacts, sham control with social isolation, TBI with social contacts, and TBI with social isolation. During four weeks after brain injury in juvenile rats, we evaluated the animal behaviors by T-maze and open-field tests, recorded brain activity with electrocorticograms and assessed structural changes by histological procedures in the hippocampal dentate gyrus, CA1, and CA3 areas. Our findings revealed significant memory impairments and hyperactivity conditions in rats with TBI and social isolation compared to the other groups. Histological assessments showed an increase of the mean number of dark neurons, apoptotic cells, and caspase-3 positive cells in all tested areas of the hippocampus in TBI rats with and without social isolation compared to sham rats. Furthermore, social isolation significantly increased the number of dark cells, apoptotic neurons, and caspase-3 positive cells in the hippocampal CA3 region in rats with TBI. This study indicates the harmful effect of social isolation on anatomical and functional deficits induced by TBI in juvenile rats. Prevention of social isolation may improve the outcome of TBI.

  20. Pyripyropenes, novel inhibitors of acyl-CoA:cholesterol acyltransferase produced by Aspergillus fumigatus. II. Structure elucidation of pyripyropenes A, B, C and D.

    PubMed

    Kim, Y K; Tomoda, H; Nishida, H; Sunazuka, T; Obata, R; Omura, S

    1994-02-01

    The structures of pyripyropenes A, B, C and D, novel acyl-CoA:cholesterol acyltransferase (ACAT) inhibitors, were determined mainly by spectroscopic studies including various NMR measurements. Pyripyropenes have a common structure which consists of pyridine, alpha-pyrone and sesquiterpene moieties. One of the three O-acetyl residues in the sesquiterpene moiety of pyripyropene A is replaced with an O-propionyl residue in pyripyropenes B, C and D. PMID:8150710

  1. Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C.

    PubMed

    Chattopadhyay, Debasish; Swingle, Mark R; Salter, Edward A; Wood, Eric; D'Arcy, Brandon; Zivanov, Catherine; Abney, Kevin; Musiyenko, Alla; Rusin, Scott F; Kettenbach, Arminja; Yet, Larry; Schroeder, Chad E; Golden, Jennifer E; Dunham, Wade H; Gingras, Anne-Claude; Banerjee, Surajit; Forbes, David; Wierzbicki, Andrzej; Honkanen, Richard E

    2016-06-01

    Cantharidin is a natural toxin and an active constituent in a traditional Chinese medicine used to treat tumors. Cantharidin acts as a semi-selective inhibitor of PPP-family ser/thr protein phosphatases. Despite sharing a common catalytic mechanism and marked structural similarity with PP1C, PP2AC and PP5C, human PP4C was found to be insensitive to the inhibitory activity of cantharidin. To explore the molecular basis for this selectivity, we synthesized and tested novel C5/C6-derivatives designed from quantum-based modeling of the interactions revealed in the co-crystal structures of PP5C in complex with cantharidin. Structure-activity relationship studies and analysis of high-resolution (1.25Å) PP5C-inhibitor co-crystal structures reveal close contacts between the inhibitor bridgehead oxygen and both a catalytic metal ion and a non-catalytic phenylalanine residue, the latter of which is substituted by tryptophan in PP4C. Quantum chemistry calculations predicted that steric clashes with the bulkier tryptophan side chain in PP4C would force all cantharidin-based inhibitors into an unfavorable binding mode, disrupting the strong coordination of active site metal ions observed in the PP5C co-crystal structures, thereby rendering PP4C insensitive to the inhibitors. This prediction was confirmed by inhibition studies employing native human PP4C. Mutation of PP5C (F446W) and PP1C (F257W), to mimic the PP4C active site, resulted in markedly suppressed sensitivity to cantharidin. These observations provide insight into the structural basis for the natural selectivity of cantharidin and provide an avenue for PP4C deselection. The novel crystal structures also provide insight into interactions that provide increased selectivity of the C5/C6 modifications for PP5C versus other PPP-family phosphatases.

  2. Structural Elucidation of the Cell-Penetrating Penetratin Peptide in Model Membranes at the Atomic Level: Probing Hydrophobic Interactions in the Blood-Brain Barrier.

    PubMed

    Bera, Swapna; Kar, Rajiv K; Mondal, Susanta; Pahan, Kalipada; Bhunia, Anirban

    2016-09-01

    Cell-penetrating peptides (CPPs) have shown promise in nonpermeable therapeutic drug delivery, because of their ability to transport a variety of cargo molecules across the cell membranes and their noncytotoxicity. Drosophila antennapedia homeodomain-derived CPP penetratin (RQIKIWFQNRRMKWKK), being rich in positively charged residues, has been increasingly used as a potential drug carrier for various purposes. Penetratin can breach the tight endothelial network known as the blood-brain barrier (BBB), permitting treatment of several neurodegenerative maladies, including Alzheimer's disease, Parkinson's disease, and Huntington's disease. However, a detailed structural understanding of penetratin and its mechanism of action is lacking. This study defines structural features of the penetratin-derived peptide, DK17 (DRQIKIWFQNRRMKWKK), in several model membranes and describes a membrane-induced conformational transition of the DK17 peptide in these environments. A series of biophysical experiments, including high-resolution nuclear magnetic resonance spectroscopy, provides the three-dimensional structure of DK17 in different membranes mimicking the BBB or total brain lipid extract. Molecular dynamics simulations support the experimental results showing preferential binding of DK17 to particular lipids at atomic resolution. The peptide conserves the structure of the subdomain spanning residues Ile6-Arg11, despite considerable conformational variation in different membrane models. In vivo data suggest that the wild type, not a mutated sequence, enters the central nervous system. Together, these data highlight important structural and functional attributes of DK17 that could be utilized in drug delivery for neurodegenerative disorders.

  3. Engine isolation for structural-borne interior noise reduction in a general aviation aircraft

    NASA Technical Reports Server (NTRS)

    Unruh, J. F.; Scheidt, D. C.

    1981-01-01

    Engine vibration isolation for structural-borne interior noise reduction is investigated. A laboratory based test procedure to simulate engine induced structure-borne noise transmission, the testing of a range of candidate isolators for relative performance data, and the development of an analytical model of the transmission phenomena for isolator design evaluation are addressed. The isolator relative performance test data show that the elastomeric isolators do not appear to operate as single degree of freedom systems with respect to noise isolation. Noise isolation beyond 150 Hz levels off and begins to decrease somewhat above 600 Hz. Coupled analytical and empirical models were used to study the structure-borne noise transmission phenomena. Correlation of predicted results with measured data show that (1) the modeling procedures are reasonably accurate for isolator design evaluation, (2) the frequency dependent properties of the isolators must be included in the model if reasonably accurate noise prediction beyond 150 Hz is desired. The experimental and analytical studies were carried out in the frequency range from 10 Hz to 1000 Hz.

  4. Synthesis and structure elucidation of a series of pyranochromene chalcones and flavanones using 1D and 2D NMR spectroscopy and X-ray crystallography.

    PubMed

    Pawar, Sunayna S; Koorbanally, Neil A

    2014-06-01

    A series of novel pyranochromene chalcones and corresponding flavanones were synthesized. This is the first report on the confirmation of the absolute configuration of chromene-based flavanones using X-ray crystallography. These compounds were characterized by 2D NMR spectroscopy, and their assignments are reported herein. The 3D structure of the chalcone 3b and flavanone 4g was determined by X-ray crystallography, and the structure of the flavanone was confirmed to be in the S configuration at C-2.

  5. Population Structure of Blueberry Mosaic Associated Virus: Evidence of Genetic Exchange in Geographically Distinct Isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The population structure of blueberry mosaic associated virus (BlMaV), a putative member of the family Ophioviridae, was examined using 59 isolates collected from North America and Slovenia. The studied isolates displayed low genetic diversity in the movement and nucleoprotein regions and low ratios...

  6. Elucidating a Key Anti-HIV-1 and Cancer-Associated Axis: The Structure of CCL5 (Rantes) in Complex with CCR5

    NASA Astrophysics Data System (ADS)

    Tamamis, Phanourios; Floudas, Christodoulos A.

    2014-06-01

    CCL5 (RANTES) is an inflammatory chemokine which binds to chemokine receptor CCR5 and induces signaling. The CCL5:CCR5 associated chemotactic signaling is of critical biological importance and is a potential HIV-1 therapeutic axis. Several studies provided growing evidence for the expression of CCL5 and CCR5 in non-hematological malignancies. Therefore, the delineation of the CCL5:CCR5 complex structure can pave the way for novel CCR5-targeted drugs. We employed a computational protocol which is primarily based on free energy calculations and molecular dynamics simulations, and report, what is to our knowledge, the first computationally derived CCL5:CCR5 complex structure which is in excellent agreement with experimental findings and clarifies the functional role of CCL5 and CCR5 residues which are associated with binding and signaling. A wealth of polar and non-polar interactions contributes to the tight CCL5:CCR5 binding. The structure of an HIV-1 gp120 V3 loop in complex with CCR5 has recently been derived through a similar computational protocol. A comparison between the CCL5 : CCR5 and the HIV-1 gp120 V3 loop : CCR5 complex structures depicts that both the chemokine and the virus primarily interact with the same CCR5 residues. The present work provides insights into the blocking mechanism of HIV-1 by CCL5.

  7. Seismic Performance of a Base Isolated Structure by Shake Table Tests

    SciTech Connect

    Yenidogan, Cem; Uckan, Eren

    2008-07-08

    A 1/4 scaled model structure has been tested on a shake table to investigate the effectiveness of a passive-hybrid isolation system for a three-storey mass concentric steel structure. The isolation system consists of two high damping rubber bearings (HDRB) and four flat sliding bearings (PTFE), which are located below the central and corner columns, respectively. To maintain dynamic similitude, each earthquake record was compressed in time by a factor of two. Measurements were taken at structural points and at the bearings. Two different type of HDRB's were tested. A numerical model for the structure was developed and calibrated by the data from the experimental studies. The effectiveness of the hybrid isolation system is verified by comparing the results obtained from both isolated and fixed base models.

  8. Structural design of active seismic isolation floor with a charging function

    NASA Astrophysics Data System (ADS)

    Nakakoji, Hayato; Miura, Nanako

    2016-04-01

    This study shows an optimum structure of a seismic isolation floor against horizontal ground motions. Although a seismic isolation floor is effective with vibration reduction, the response of the floor becomes larger when excited by long-period ground motions. It is shown that caster equipment move and suffer damage in a seismic isolation structure by an experiment. Moreover, the permissible displacement of the floor is limited. Therefore, the focus is on an active seismic isolation. About active control, the system cannot operate without power supply. To solve these problems an energy regeneration is considered in our previous study. These studies only analyze simple model and did not choose the suitable structure for active control and energy regeneration. This research propose a new structure which has regenerated energy exceeds the energy required for the active control by numerical simulation.

  9. Structural elucidation of specific noncovalent association of folic acid with native cyclodextrins using an ion mobility mass spectrometry and theoretical approach.

    PubMed

    Zimnicka, Magdalena; Troć, Anna; Ceborska, Magdalena; Jakubczak, Michał; Koliński, Michał; Danikiewicz, Witold

    2014-05-01

    The combination of ion mobility mass spectrometry studies and theoretical calculations including docking studies permitted a detailed structural description of noncovalent complexes of folic acid (FA) and native cyclodextrins (α-CD, β-CD, and γ-CD). The mode of noncovalent association depended on the cavity size of the cyclodextrin. The structure of FA/α-CD represented the exclusion complex in which the aminobenzoic moiety and the aromatic pteridine ring of folic acid remain outside the cyclodextrin cavity, while the glutamate residue is anchored in the interior of the α-cyclodextrin. A rotaxane-type structure was proposed for the FA/β-CD complex with the aminobenzoic part of FA being trapped in the central cavity of β-CD. The glutamate residue and the aromatic pteridine ring interact with the primary and secondary rim hydroxyl residues, respectively, enhancing complex stability. Two possible structures of FA/γ-CD were suggested, the first one being analogous to the FA/β-CD complex and the second one being more stable-in which the aromatic pteridine ring penetrates into the CD cavity while the glutamate residue with the aminobenzoic part of FA is exposed to the cone exterior of CD at its wider edge. Further insight into the association behavior of the folic acid toward cyclodextrins evaluated by thermodynamic calculations indicates that the process is highly exothermic. The complex stability increased in the order FA/α-CD < FA/β-CD < FA/γ-CD. This order is consistent with the previously determined relative gas-phase stability established based on the dissociation efficiency curves of the FA/CD complexes.

  10. Chain-Folding Structures of a Semi-crystalline Polymer in Bulk and Single Crystals Elucidated by 13C-13C Double Quantum NMR

    NASA Astrophysics Data System (ADS)

    Hong, You-Lee; Miyoshi, Toshikazu

    2014-03-01

    Semi-crystalline polymers are crystallized as folded chains in thin lamellae of ca. 5-20 nm from random coils in the melt and solution states. However, understanding of detailed chain-folding structure and crystallization mechanism are still challenging issue due to various experimental limitations. We recently developed a new strategy using 13C-13C double-quantum (DQ) NMR with selectively 13C isotope labeled isotactic poly(1-butene) form I to investigate chain-trajectory in solution and melt grown crystals at various Tcs. This new method can determine the re-entrance sites, the successive folding number (n) , and the fractions (F) of chain-folding in a wide Tc range. In melt grown crystals at Tc = 95 °C, a comparison of experimental and simulated DQ efficiency determined that the polymer chains alternatively change chain-folding directions and the stems tightly pack via intramolecular interactions, and the fraction (F) of adjacent re-entry structure ranges from 70% at n = 4 to 100% at mixed structures of n = 1 and 2. Furthermore, DQ efficiency is independent of Tc in bulk crystals. This means chain-folding do not change in a wide Tcs. DMR-1105829.

  11. A structure-differential binding method for elucidating the interactions between flavonoids and cytochrome-c by ESI-MS and molecular docking.

    PubMed

    Wang, Xian; Liu, Yingzhi; Wang, Haidong

    2013-11-15

    The study of noncovalent interactions between pharmaceutical molecules and proteins is essential for understanding molecular mechanisms of protein function, and provides foundations for de novo therapeutic agent design. Electrospray ionization mass spectrometry (ESI-MS) has nowadays become a popular tool for analyzing the noncovalent protein complexes, however it usually has difficulty in determining the interaction sites and binding mechanisms. In this work, a new structure-differential binding (SDB) method, combined with ESI-MS and molecular docking (MD) techniques (SDB-ESIMS-MD), was developed and applied to a study of the binding interactions in noncovalent protein-small drug molecule complexes for the characterization of binding sites and binding modes. Using this developed method, protein complexes of flavonoid and flavonoid glycoside ligands and cytochrome-c (Cyt-c) were studied in detail. ESI-MS was used to determine the relative binding affinities and dissociation constants of flavonoid-Cyt-c complexes, and to measure the changes in the stability of the protein complexes with the structural modifications of the ligands for identifying effective binding functional groups. Molecular docking simulations complemented ESI-MS experiments by providing the protein-ligand interaction profile of each complex and displaying the binding mode for each interaction. This SDB-ESIMS-MD method can be applied to a broad range of protein-drug interactions and used to guide further research in the study of structure-binding relationship between drug molecules and targeted biomacromolecules.

  12. The metazoan parasite communities of the Argentinean sandperch Pseudopercis semifasciata (Pisces: Perciformes) and their use to elucidate the stock structure of the host.

    PubMed

    Timi, J T; Lanfranchi, A L

    2009-09-01

    The use of parasites as biological tags allowed the identification of 3 stocks of Argentinean sandperch, Pseudopercis semifasciata (Cuvier), in the Argentine Sea. A total of 100 specimens caught in 3 zones: Villa Gesell (37 degrees 15'S, 57 degrees 23'W; n=20), Miramar (38 degrees 03'S, 57 degrees 30'W-38 degrees 44'S, 58 degrees 44'W; n=30) and Península Valdes (42 degrees 00'-42 degrees 45'S; n=50), were examined and 28 parasite species were found, 15 of them being new host records. Both univariate and multivariate analyses identified discrete stocks in each zone. The observed differences were not related to the host size or sex. Each locality was characterized by its own indicator species. Villa Gesell was typified by unidentified cestode plerocercoids, Corynosoma cetaceum and Hysterothylacium sp., Miramar by Heterosentis sp. and Pseudoterranova sp. and Península Valdes by A. simplex s.l. Fishes from both northern localities shared gnathiid pranizae, Corynosoma australe and Grillotia sp. as indicators, whereas Miramar and Península Valdes shared only Trifur tortuosus. The most distant localities showed no indicator species in common. Discriminant analyses of parasite assemblages agreed with populational comparisons in identifying the same set of biological tags, whereas some differences in the identity of indicator species were obtained by similarity analysis. However, the 3 approaches were congruent in identifying Grillotia sp., C. australe and C. cetaceum as indicators of northern localities, and A. simplex s.l. as related to Patagonian waters. Differences among zones could be enhanced by the sedentary habits, limited dispersal and high site fidelity of P. semifasciata, and their spawning in rocky outcrops, which are isolated environments. PMID:19627631

  13. Follow-up of natural products isolation.

    PubMed

    Cannell, Richard J P; Sarker, Satyajit D; Nahar, Lutfun

    2012-01-01

    Follow-up of natural products isolation refers to re-isolation of compound(s) of interest in larger amounts for further pharmacological testing, conclusive structure elucidation, structure modifications to synthesize analogs for structure-activity relationships (SAR) studies, preformulation and formulation studies or clinical trials. In addition to conventional synthetic chemistry approaches, several other methodologies can be applied for following-up natural products isolation. This chapter outlines, with specific examples, various strategies and methods involved in follow-up of natural products isolation. PMID:22367909

  14. Structural elucidation of b-(Y,Sc){sub 2}Si{sub 2}O{sub 7} : combined use of {sub 89}Y MAS NMR and powder diffraction.

    SciTech Connect

    Allix, M.; Alba, M. D.; Florian, P.; Fernandez-Carrion, A. J.; Suchomel, M. R.; Escudero, A.; Suard, E.; Becerro, A. I.

    2011-08-01

    Although the structures of pure Sc{sub 2}Si{sub 2}O{sub 7} and {beta}-Y{sub 2}Si{sub 2}O{sub 7} have been described in the literature using the C2/m space group, {sup 29}Si magic angle spinning (MAS) NMR measurements of the intermediate members of the Sc{sub 2}Si{sub 2}O{sub 7}-{beta}-Y{sub 2}Si{sub 2}O{sub 7} system indicate a lowering of the symmetry to the C2 space group. Indeed, these compositions exhibit a unique Si crystallographic site and an Si-O-Si angle lower than 180{sup o}, incompatible with the C2/m space group. C2 is the only possible alternative. Space group Cm can be discarded with regard to its two different Si sites per unit cell. Moreover, {sup 89}Y MAS NMR data have revealed the existence of two different Y sites in the structure of the intermediate members of the Sc{sub 2}Si{sub 2}O{sub 7}-{beta}-Y{sub 2}Si{sub 2}O{sub 7} system, confirming the lowering of the symmetry to the C2 space group. The viability of the C2 model has therefore been tested and confirmed by refinement of synchrotron and neutron powder diffraction data for the different members of the system. The structural evolutions across the Sc{sub 2}Si{sub 2}O{sub 7}-{beta}-Y{sub 2}Si{sub 2}O{sub 7} system are discussed.

  15. Structural and Functional Elucidation of the Mechanism Promoting Error-prone Synthesis by Human DNA Polymerase [kappa] Opposite the 7,8-Dihydro-8-oxo-2'-deoxyguanosine Adduct

    SciTech Connect

    Irimia, Adriana; Eoff, Robert L.; Guengerich, F.Peter; Egli, Martin

    2009-09-25

    Human polymerase kappa (hPol {kappa}) is one of four eukaryotic Y-class DNA polymerases and may be an important element in the cellular response to polycyclic aromatic hydrocarbons such as benzo[a]pyrene, which can lead to reactive oxygenated metabolite-mediated oxidative stress. Here, we present a detailed analysis of the activity and specificity of hPol {kappa} bypass opposite the major oxidative adduct 7,8-dihydro-8-oxo-2{prime}-deoxyguanosine (8-oxoG). Unlike its archaeal homolog Dpo4, hPol {kappa} bypasses this lesion in an error-prone fashion by inserting mainly dATP. Analysis of transient-state kinetics shows diminished 'bursts' for dATP:8-oxoG and dCTP:8-oxoG incorporation, indicative of non-productive complex formation, but dATP:8-oxoG insertion events that do occur are 2-fold more efficient than dCTP:G insertion events. Crystal structures of ternary hPol {kappa} complexes with adducted template-primer DNA reveal non-productive (dGTP and dATP) alignments of incoming nucleotide and 8-oxoG. Structural limitations placed upon the hPol {kappa} by interactions between the N-clasp and finger domains combined with stabilization of the syn-oriented template 8-oxoG through the side chain of Met-135 both appear to contribute to error-prone bypass. Mutating Leu-508 in the little finger domain of hPol {kappa} to lysine modulates the insertion opposite 8-oxoG toward more accurate bypass, similar to previous findings with Dpo4. Our structural and activity data provide insight into important mechanistic aspects of error-prone bypass of 8-oxoG by hPol {kappa} compared with accurate and efficient bypass of the lesion by Dpo4 and polymerase {eta}.

  16. Application of Molecular Techniques to Elucidate the Influence of Cellulosic Waste on the Bacterial Community Structure at a Simulated Low-Level-Radioactive-Waste Site

    SciTech Connect

    Erin K. Field; Seth D'Imperio; Amber R. Miller; Michael R. VanEngelen; Robin Gerlach; Brady D. Lee; William A. Apel; Brent M. Peyton

    2010-05-01

    Low-level radioactive waste sites, including those at various U.S. Department of Energy (DOE) sites, frequently contain cellulosic waste in the form of paper towels, cardboard boxes, or wood contaminated with heavy metals and radionuclides such as chromium and uranium. To understand how the soil microbial community is influenced by the presence of cellulosic waste products, multiple soil samples were obtained from a non-radioactive model low-level waste test pit at the Idaho National Laboratory. Samples were analyzed using 16S rDNA clone libraries and 16S rRNA gene microarray (PhyloChip) analyses. Both the clone library and PhyloChip results revealed changes in the bacterial community structure with depth. In all samples, the PhyloChip detected significantly more unique Operational Taxonomic Units (OTUs), and therefore more relative diversity, than the clone libraries. Calculated diversity indices suggest that diversity is lowest in the Fill (F) and Fill Waste (FW) layers and greater in the Wood Waste (WW) and Waste Clay (WC) layers. Principal coordinates analysis and lineage specific analysis determined that Bacteroidetes and Actinobacteria phyla account for most of the significant differences observed between the layers. The decreased diversity in the FW layer and increased members of families containing known cellulose degrading microorganisms suggests the FW layer is an enrichment environment for cellulose degradation. Overall, these results suggest that the presence of the cellulosic material significantly influences the bacterial community structure in a stratified soil system.

  17. Multisite constrained model of trans-4-(N,N-dimethylamino)-4'-nitrostilbene for structural elucidation of radiative and nonradiative excited states.

    PubMed

    Lin, Cheng-Kai; Wang, Yu-Fu; Cheng, Yuan-Chung; Yang, Jye-Shane

    2013-04-18

    A constrained model compound of trans-4-(N,N-dimethylamino)-4'-nitrostilbene (DNS), namely, compound DNS-B3 that is limited to torsions about the phenyl-nitro C-N bond and the central C═C bond, was prepared to investigate the structural nature of the radiative and nonradiative states of electronically excited DNS. The great similarities in solvent-dependent electronic spectra, fluorescence decay times, and quantum yields for fluorescence (Φf) and trans → cis photoisomerization (Φtc) between DNS and DNS-B3 indicate that the fluorescence is from a planar charge-transfer state and torsion of the nitro group is sufficient to account for the nonradiative decay of DNS. This conclusion is supported by TDDFT calculations on DNS-B3 in dichloromethane. The structure at the conical intersection for internal conversion is associated with not only a twisting but also a pyramidalization of the nitro group. The mechanism of the NO2 torsion is discussed in terms of the effects of solvent polarity, the substituents, and the volume demand. The differences and analogies of the NO2- vs amino-twisted intramolecular charge-transfer (TICT) state of trans-aminostilbenes are also discussed.

  18. Use of Protein Cross-Linking and Radiolytic Labeling To Elucidate the Structure of PsbO within Higher-Plant Photosystem II.

    PubMed

    Mummadisetti, Manjula P; Frankel, Laurie K; Bellamy, Henry D; Sallans, Larry; Goettert, Jost S; Brylinski, Michal; Bricker, Terry M

    2016-06-14

    We have used protein cross-linking with the zero-length cross-linker 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide, and radiolytic footprinting coupled with high-resolution tandem mass spectrometry, to examine the structure of higher-plant PsbO when it is bound to Photosystem II. Twenty intramolecular cross-linked residue pairs were identified. On the basis of this cross-linking data, spinach PsbO was modeled using the Thermosynechococcus vulcanus PsbO structure as a template, with the cross-linking distance constraints incorporated using the MODELLER program. Our model of higher-plant PsbO identifies several differences between the spinach and cyanobacterial proteins. The N-terminal region is particularly interesting, as this region has been suggested to be important for oxygen evolution and for the specific binding of PsbO to Photosystem II. Additionally, using radiolytic mapping, we have identified regions on spinach PsbO that are shielded from the bulk solvent. These domains may represent regions on PsbO that interact with other components, as yet unidentified, of the photosystem. PMID:27203407

  19. Application of molecular techniques to elucidate the influence of cellulosic waste on the bacterial community structure at a simulated low-level-radioactive-waste site.

    PubMed

    Field, Erin K; D'Imperio, Seth; Miller, Amber R; VanEngelen, Michael R; Gerlach, Robin; Lee, Brady D; Apel, William A; Peyton, Brent M

    2010-05-01

    Low-level-radioactive-waste (low-level-waste) sites, including those at various U.S. Department of Energy sites, frequently contain cellulosic waste in the form of paper towels, cardboard boxes, or wood contaminated with heavy metals and radionuclides such as chromium and uranium. To understand how the soil microbial community is influenced by the presence of cellulosic waste products, multiple soil samples were obtained from a nonradioactive model low-level-waste test pit at the Idaho National Laboratory. Samples were analyzed using 16S rRNA gene clone libraries and 16S rRNA gene microarray (PhyloChip) analyses. Both methods revealed changes in the bacterial community structure with depth. In all samples, the PhyloChip detected significantly more operational taxonomic units, and therefore relative diversity, than the clone libraries. Diversity indices suggest that diversity is lowest in the fill and fill-waste interface (FW) layers and greater in the wood waste and waste-clay interface layers. Principal-coordinate analysis and lineage-specific analysis determined that the Bacteroidetes and Actinobacteria phyla account for most of the significant differences observed between the layers. The decreased diversity in the FW layer and increased members of families containing known cellulose-degrading microorganisms suggest that the FW layer is an enrichment environment for these organisms. These results suggest that the presence of the cellulosic material significantly influences the bacterial community structure in a stratified soil system. PMID:20305022

  20. Application of Molecular Techniques To Elucidate the Influence of Cellulosic Waste on the Bacterial Community Structure at a Simulated Low-Level-Radioactive-Waste Site▿ †

    PubMed Central

    Field, Erin K.; D'Imperio, Seth; Miller, Amber R.; VanEngelen, Michael R.; Gerlach, Robin; Lee, Brady D.; Apel, William A.; Peyton, Brent M.

    2010-01-01

    Low-level-radioactive-waste (low-level-waste) sites, including those at various U.S. Department of Energy sites, frequently contain cellulosic waste in the form of paper towels, cardboard boxes, or wood contaminated with heavy metals and radionuclides such as chromium and uranium. To understand how the soil microbial community is influenced by the presence of cellulosic waste products, multiple soil samples were obtained from a nonradioactive model low-level-waste test pit at the Idaho National Laboratory. Samples were analyzed using 16S rRNA gene clone libraries and 16S rRNA gene microarray (PhyloChip) analyses. Both methods revealed changes in the bacterial community structure with depth. In all samples, the PhyloChip detected significantly more operational taxonomic units, and therefore relative diversity, than the clone libraries. Diversity indices suggest that diversity is lowest in the fill and fill-waste interface (FW) layers and greater in the wood waste and waste-clay interface layers. Principal-coordinate analysis and lineage-specific analysis determined that the Bacteroidetes and Actinobacteria phyla account for most of the significant differences observed between the layers. The decreased diversity in the FW layer and increased members of families containing known cellulose-degrading microorganisms suggest that the FW layer is an enrichment environment for these organisms. These results suggest that the presence of the cellulosic material significantly influences the bacterial community structure in a stratified soil system. PMID:20305022

  1. Structural elucidation, density functional calculations and contribution of intermolecular interactions in cholest-4-en-3-one crystals: Insights from X-ray and Hirshfeld surface analysis

    NASA Astrophysics Data System (ADS)

    Khanam, Hena; Mashrai, Ashraf; Siddiqui, Nazish; Ahmad, Musheer; Alam, Mohammad Jane; Ahmad, Shabbir; Shamsuzzaman

    2015-03-01

    The foremost objective of the present work is systematic analysis of intermolecular interactions in crystal structure of cholest-4-en-3-one (2) molecule. It is accomplished by Hirshfeld surface analysis and fingerprint plot. Hirshfeld surface analysis has been used to visualize the fidelity of the crystal structure. This method permitted for the identification of individual types of intermolecular contacts and their impact on the complete packing. Molecules are linked by a combination of Cdbnd O---H, Csbnd H---H, and C---H contacts, which have clear signatures in the fingerprint plots. The theoretical study was attempted to predict the optimized geometry and computed spectra by the Density Functional Theory (DFT) using the B3LYP function with the 6-311++G(d,p) basis set. Atomic charges, MEP mapping, HOMO-LUMO, various thermodynamic and molecular properties have been reported. In addition thermal stability, optical, morphological, and microstructral properties of the title compound (2) have also been explored.

  2. On-line nano-HPLC/ESI QTOF MS and tandem MS for separation, detection, and structural elucidation of human erythrocytes neutral glycosphingolipid mixture.

    PubMed

    Kirsch, Stephan; Zarei, Mostafa; Cindrić, Mario; Müthing, Johannes; Bindila, Laura; Peter-Katalinić, Jasna

    2008-06-15

    A superior approach involving nano-high-performance liquid chromatography (nano-HPLC) in on-line conjunction to electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QTOF MS) and tandem MS for screening and structural characterization of complex mixtures of neutral glycosphingolipids (GSLs) is here described. Neutral GSLs purified from human erythrocytes were efficiently separated according to the differences in carbohydrate chain length by an optimized nano-HPLC protocol and flow-through detected by ESI QTOF MS at the low femtomole level. Additionally, GSL species were accurately distinguished from the accompanying lipids in the mixture, thus permitting the determination of detailed structural characteristics by data-dependent analysis for identification of GSL constitution within single experiments. An alternative nano-HPLC/ESI QTOF MS approach was designed for dissection of unsaturation/saturation degree of the ceramide moieties defining the hydrophobic portion of GSLs and subsequent localization by nano-HPLC/ESI QTOF MS/MS of the -CH=CH- within the ceramide regions. The method is fast, highly sensitive, and high-throughput amenable and is highlighted as a new and valuable analytical dimension in glycolipidomics.

  3. The Network Modification (NeMo) Tool: Elucidating the Effect of White Matter Integrity Changes on Cortical and Subcortical Structural Connectivity

    PubMed Central

    Maruta, Jun; Relkin, Norman; Raj, Ashish

    2013-01-01

    Abstract Accurate prediction of brain dysfunction caused by disease or injury requires the quantification of resultant neural connectivity changes compared with the normal state. There are many methods with which to assess anatomical changes in structural or diffusion magnetic resonance imaging, but most overlook the topology of white matter (WM) connections that make up the healthy brain network. Here, a new neuroimaging software pipeline called the Network Modification (NeMo) Tool is presented that associates alterations in WM integrity with expected changes in neural connectivity between gray matter regions. The NeMo Tool uses a large reference set of healthy tractograms to assess implied network changes arising from a particular pattern of WM alteration on a region- and network-wise level. In this way, WM integrity changes can be extrapolated to the cortices and deep brain nuclei, enabling assessment of functional and cognitive alterations. Unlike current techniques that assess network dysfunction, the NeMo tool does not require tractography in pathological brains for which the algorithms may be unreliable or diffusion data are unavailable. The versatility of the NeMo Tool is demonstrated by applying it to data from patients with Alzheimer's disease, fronto-temporal dementia, normal pressure hydrocephalus, and mild traumatic brain injury. This tool fills a gap in the quantitative neuroimaging field by enabling an investigation of morphological and functional implications of changes in structural WM integrity. PMID:23855491

  4. Elucidating the structural basis of diphenyl ether derivatives as highly potent enoyl-ACP reductase inhibitors through molecular dynamics simulations and 3D-QSAR study.

    PubMed

    Kamsri, Pharit; Punkvang, Auradee; Saparpakorn, Patchareenart; Hannongbua, Supa; Irle, Stephan; Pungpo, Pornpan

    2014-07-01

    Diphenyl ether derivatives are good candidates for anti-tuberculosis agents that display a promising potency for inhibition of InhA, an essential enoyl-acyl carrier protein (ACP) reductase involved in fatty acid biosynthesis pathways in Mycobacterium tuberculosis. In this work, key structural features for the inhibition were identified by 3D-QSAR CoMSIA models, constructed based on available experimental binding properties of diphenyl ether inhibitors, and a set of four representative compounds was subjected to MD simulations of inhibitor-InhA complexes for the calculation of binding free energies. The results show that bulky groups are required for the R1 substituent on the phenyl A ring of the inhibitors to favor a hydrophobic pocket formed by residues Phe149, Met155, Pro156, Ala157, Tyr158, Pro193, Met199, Val203, Leu207, Ile215, and Leu218. Small substituents with a hydrophilic property are required at the R3 and R4 positions of the inhibitor phenyl B rings to form hydrogen bonds with the backbones of Gly96 and Met98, respectively. For the R2 substituent, small substituents with simultaneous hydrophilic or hydrophobic properties are required to favor the interaction with the pyrophosphate moiety of NAD(+) and the methyl side chain of Ala198, respectively. The reported data provide structural guidance for the design of new and potent diphenyl ether-based inhibitors with high inhibitory activities against M. tuberculosis InhA. PMID:24935113

  5. How to produce a chemical defense: structural elucidation and anatomical distribution of aplysioviolin and phycoerythrobilin in the sea hare Aplysia californica.

    PubMed

    Kamio, Michiya; Nguyen, Linh; Yaldiz, Seymanur; Derby, Charles D

    2010-05-01

    We previously used bioassay-guided fractionation to identify phycoerythrobilin (1) and its monomethyl ester, aplysioviolin (2), as components in the ink secretion of a marine gastropod, the sea hare Aplysia californica, that act as chemical deterrents against predatory blue crabs. This was the first report of 1 as a natural product. Compound 2 was previously reported as a natural product from three species of Aplysia (A. fasciata, A. dactylomela, and A. parvula), but the reported structure and composition of stereoisomers of 2 are different among these species. Sea hares are thought to produce 2 from phycoerythrin, a photosynthetic pigment in their red-algal diet composed of a phycobiliprotein covalently linked to the chromophore 1, by cleavage of the covalent bond and methylation of 1, but neither the sequence nor the anatomical location of the cleavage and methylation is known. In this study, we clarify the structure of 1 and 2 in ink secretion of A. californica, and describe the distribution of 1 and 2 in the tissues of sea hares. We conclude that cleavage of the covalent bond in phycoerythrin occurs first, forming 1 in the digestive gland, followed by methylation of 1 to yield 2 in the ink gland.

  6. Elucidating the structural basis of diphenyl ether derivatives as highly potent enoyl-ACP reductase inhibitors through molecular dynamics simulations and 3D-QSAR study.

    PubMed

    Kamsri, Pharit; Punkvang, Auradee; Saparpakorn, Patchareenart; Hannongbua, Supa; Irle, Stephan; Pungpo, Pornpan

    2014-07-01

    Diphenyl ether derivatives are good candidates for anti-tuberculosis agents that display a promising potency for inhibition of InhA, an essential enoyl-acyl carrier protein (ACP) reductase involved in fatty acid biosynthesis pathways in Mycobacterium tuberculosis. In this work, key structural features for the inhibition were identified by 3D-QSAR CoMSIA models, constructed based on available experimental binding properties of diphenyl ether inhibitors, and a set of four representative compounds was subjected to MD simulations of inhibitor-InhA complexes for the calculation of binding free energies. The results show that bulky groups are required for the R1 substituent on the phenyl A ring of the inhibitors to favor a hydrophobic pocket formed by residues Phe149, Met155, Pro156, Ala157, Tyr158, Pro193, Met199, Val203, Leu207, Ile215, and Leu218. Small substituents with a hydrophilic property are required at the R3 and R4 positions of the inhibitor phenyl B rings to form hydrogen bonds with the backbones of Gly96 and Met98, respectively. For the R2 substituent, small substituents with simultaneous hydrophilic or hydrophobic properties are required to favor the interaction with the pyrophosphate moiety of NAD(+) and the methyl side chain of Ala198, respectively. The reported data provide structural guidance for the design of new and potent diphenyl ether-based inhibitors with high inhibitory activities against M. tuberculosis InhA.

  7. Evaluation of structural issues related to isolation of the 100-KE/100-KW discharge chute

    SciTech Connect

    Winkel, B.V.; Hyde, L.L.

    1995-03-10

    The issue of excessive post-seismic leakage in the discharge chute of the K East and K West fuel storage basins was resolved by designing isolation barriers to maintain basin water levels if the discharge chute should drain. This report addresses the structural issues associated with isolation of the discharge chute. The report demonstrates the structural adequacy of the components associated with chute isolation for normal and seismic loading. Associated issues, such as hardware drop accidents and seismic slosh heights are also addressed.

  8. A 6DOF passive vibration isolator using X-shape supporting structures

    NASA Astrophysics Data System (ADS)

    Wu, Zhijing; Jing, Xingjian; Sun, Bo; Li, Fengming

    2016-10-01

    A novel 6 degree of freedom (6-DOF) passive vibration isolator is studied theoretically and validated with experiments. Based on the Stewart platform configuration, the 6-DOF isolator is constructed by 6 X-shape structures as legs, which can realize very good and tunable vibration isolation performance in all 6 directions with a passive manner. The mechanic model is established for static analysis of the working range, static stiffness and loading capacity. Thereafter, the equation of motion of the isolator is derived with the Hamilton principle. The equivalent stiffness and the displacement transmissibility in the six decoupled DOFs direction are then discussed with experimental results for validation. The results reveal that (a) by designing the structure parameters, the system can possess flexible stiffness such as negative, quasi-zero and positive stiffness, (b) due to the combination of the Stewart platform and the X-shape structure, the system can have very good vibration isolation performance in all the 6 directions and in a passive manner, and (c) compared with the simplified linear-stiffness legs, the nonlinearity of the X-shape structures enhance the passive isolator to have much better vibration isolation performance.

  9. Hydrolyzable tannins of tamaricaceous plants. V. Structures of monomeric-trimeric tannins and cytotoxicity of macrocyclic-type tannins isolated from Tamarix nilotica (1).

    PubMed

    Orabi, Mohamed A A; Taniguchi, Shoko; Sakagami, Hiroshi; Yoshimura, Morio; Yoshida, Takashi; Hatano, Tsutomu

    2013-05-24

    Three new ellagitannin monomers, nilotinins M5-M7 (1-3), a dimer, nilotinin D10 (4), and a trimer, nilotinin T1 (5), together with three known dimers, hirtellin D (7) and tamarixinins B (8) and C (9), and a trimer, hirtellin T2 (6), were isolated from Tamarix nilotica dried leaves. The structures of the tannins were elucidated by intensive spectroscopic methods and chemical conversions into known tannins. The new trimer (5) is a unique macrocyclic type whose monomeric units are linked together by an isodehydrodigalloyl and two dehydrodigalloyl moieties. Additionally, dimeric and trimeric macrocyclic-type tannins isolated from T. nilotica in this study were assessed for possible cytotoxic activity against four human tumor cell lines. Tumor-selective cytotoxicities of the tested compounds were higher than those of synthetic and natural potent cytotoxic compounds, including polyphenols, and comparable with those of 5-fluorouracil and melphalan. PMID:23675651

  10. Coupling multistripe laser triangulation with hyperspectral imaging VisNIR spectroscopy to elucidate the feedbacks between soil structure, hydrology, and organic matter

    NASA Astrophysics Data System (ADS)

    Hirmas, Daniel; Steffens, Markus; Sullivan, Pamela; Zhang, Chi; Giménez, Daniel

    2016-04-01

    Recent advances in three-dimensional (3-D) laser scanning techniques and reflectance spectroscopy provide the high-resolution quantitative measures needed to unravel the feedbacks mechanism between soil structure, hydrology, and organic matter at the pedon scale. Multistripe laser triangulation (MLT) can be used to quantify the shape, size, orientation, abundance, and spatial distribution of soil peds and associated macropore networks, while imaging visible light near infrared spectroscopy (imVisIR) can be used to examine the spatial distribution, quality and quantity of total, labile, and non-labile organic matter (SOM), iron, and manganese oxides at high spatial resolutions. In this work, we sought to investigate the potential for coupling these two disparate sensors (MLT and imVisIR) to examine relationships between soil structure, soil hydrology, and SOM. Soils were sampled from four landscape positions (summit, backslope, footslope, and toeslope) along an oak-hickory forest catena at the University of Kansas Field Station (KUFS) Fitch Natural History Reserve in conjunction with the installation of a National Ecological Observatory Network (NEON) site. Soil pits were excavated at each position to 1 m, described in detail by US Department of Agriculture-Natural Resource Conservation (USDA-NRCS) soil scientists, and sampled by morphological horizon for standard chemical and physical soil analyses. In addition, samples were taken from each horizon for root density and size determination, cores sampled to estimate water content, pore-size distribution, and hydraulic conductivity via low field nuclear magnetic resonance (NMR), and clods taken for water retention determination. Two intact soil monoliths per pit, carefully carved from the excavation walls at two depths (0-40 and 30-70 cm), were sampled in custom steel trays that were 15 cm wide by 40 cm long with a lip around the edge approximately 2 cm deep. The monoliths were prepared and dried at 40° C for 12

  11. Structure elucidation of β-cyclodextrin–xylazine complex by a combination of quantitative 1H–1H ROESY and molecular dynamics studies

    PubMed Central

    Fatma, Kehkeshan; Dhokale, Snehal

    2013-01-01

    Summary The complexation of xylazine with β-cyclodextrin was studied in aqueous medium. 1H NMR titrations confirmed the formation of a 1:1 inclusion complex. A ROESY spectrum was recorded with long mixing time which contained TOCSY artifacts. It only confirmed the presence of xylazine aromatic ring in the β-cyclodextrin cavity. No information regarding the mode of penetration, from the wide or narrow side, could be obtained. We calculated the peak intensity ratio from the inter-proton distances for the most stable conformations obtained by molecular dynamics studies in vacuum. The results show that highly accurate structural information can be deduced efficiently by the combined use of quantitative ROESY and molecular dynamics analysis. On the other hand, a ROESY spectrum with no spin diffusion can only compliment an averaged ensemble conformation obtained by molecular dynamics which is generally considered ambiguous. PMID:24204401

  12. The structure elucidation of mequindox and 1,4-bisdesoxymequindox: NMR analyses, FT-IR spectra, DFT calculations and thermochemical studies

    NASA Astrophysics Data System (ADS)

    Zhang, Jiaheng; He, Xin; Gao, Haixiang

    2011-10-01

    In the current work, we report a combined experimental and theoretical study on the molecular conformation, vibrational spectra, and nuclear magnetic resonance (NMR) spectra of mequindox (MEQ) and 1,4-bisdesoxymequindox (1,4-BDM). The geometric structure and vibrational frequencies of MEQ and 1,4-BDM have been calculated by density functional theory employing the B3LYP functional and 6-311++G(d,p) basis set. The 1H and 13C NMR chemical shifts have been calculated by gauge-including atomic orbital method with B3LYP 6-311++G(2df,2pd) approach. The calculation results have been applied to simulate the infrared and NMR spectra of the compounds. The theoretical results agree well with the observed spectra. The bond dissociation enthalpy of MEQ and the heat of formation of MEQ and 1,4-BDM have also been computed.

  13. The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches.

    PubMed

    Yu, Eizadora T; Hawkins, Arie; Kuntz, Irwin D; Rahn, Larry A; Rothfuss, Andrew; Sale, Kenneth; Young, Malin M; Yang, Christine L; Pancerella, Carmen M; Fabris, Daniele

    2008-11-01

    Modern biomedical research is evolving with the rapid growth of diverse data types, biophysical characterization methods, computational tools and extensive collaboration among researchers spanning various communities and having complementary backgrounds and expertise. Collaborating researchers are increasingly dependent on shared data and tools made available by other investigators with common interests, thus forming communities that transcend the traditional boundaries of the single research laboratory or institution. Barriers, however, remain to the formation of these virtual communities, usually due to the steep learning curve associated with becoming familiar with new tools, or with the difficulties associated with transferring data between tools. Recognizing the need for shared reference data and analysis tools, we are developing an integrated knowledge environment that supports productive interactions among researchers. Here we report on our current collaborative environment, which focuses on bringing together structural biologists working in the area of mass spectrometric based methods for the analysis of tertiary and quaternary macromolecular structures (MS3D) called the Collaboratory for MS3D (C-MS3D). C-MS3D is a Web-portal designed to provide collaborators with a shared work environment that integrates data storage and management with data analysis tools. Files are stored and archived along with pertinent meta data in such a way as to allow file handling to be tracked (data provenance) and data files to be searched using keywords and modification dates. While at this time the portal is designed around a specific application, the shared work environment is a general approach to building collaborative work groups. The goal of this is to not only provide a common data sharing and archiving system, but also to assist in the building of new collaborations and to spur the development of new tools and technologies. PMID:18817429

  14. Structural elucidation and location of Mn(II) ion in Tetraaquabis(hydrogen maleato)cadium(II): Single crystal EPR studies

    NASA Astrophysics Data System (ADS)

    Ramachitra, Somasundaram; Hema, Ramesh; Muthuausteria, Premkumar; Parthipan, Krishnan

    2014-01-01

    Electron paramagnetic resonance study of Mn2+ ion-doped Tetraaquabis(hydrogen maleato)cadmium(II) single crystal was carried out at X-band frequency to ascertain its structural properties. EPR spectrum exhibits group of five fine structure transitions each splits into six hyperfine components. The spin Hamiltonian parameters calculated from the crystal rotations are: gxx = 2.109, gyy = 2.029, gzz = 2.008, Axx = -9.51 mT, Ayy = -8.30 mT, Azz = -8.09 mT, Dxx = 20.29 mT, Dyy = 4.11 mT, Dzz = -24.40 mT, E = 8.09 mT and it indicates Mn2+ ion has orthorhombic symmetry. The direction cosines of spin Hamiltonian parameters (g, A and D) are suggesting that Mn2+ ion has entered the lattice interstitially and its exact location has been established with the help of position of atoms in the host lattice. Covalency of Mn-ligand bonds are evaluated using Matumura's plot is 7.3%. FT-IR and powder XRD data confirm the formation of host lattice. Optical absorption study suggests distortion around incorporated ion. The observed bands are assigned as transitions from the 6A1g(S) ground state to various excited quartet levels of Mn2+ ion in distorted octahedral crystalline field. The theoretical band positions are estimated using energy expressions and good agreement is observed with the experimental values. The best fit values of the crystal field (Dq) and Racah inter electronic repulsion parameters were evaluated from the observed band positions.

  15. Structure of the HCMV UL16-MICB complex elucidates select binding of a viral immunoevasin to diverse NKG2D ligands.

    PubMed

    Müller, Steffen; Zocher, Georg; Steinle, Alexander; Stehle, Thilo

    2010-01-01

    The activating immunoreceptor NKG2D promotes elimination of infected or malignant cells by cytotoxic lymphocytes through engagement of stress-induced MHC class I-related ligands. The human cytomegalovirus (HCMV)-encoded immunoevasin UL16 subverts NKG2D-mediated immune responses by retaining a select group of diverse NKG2D ligands inside the cell. We report here the crystal structure of UL16 in complex with the NKG2D ligand MICB at 1.8 A resolution, revealing the molecular basis for the promiscuous, but highly selective, binding of UL16 to unrelated NKG2D ligands. The immunoglobulin-like UL16 protein utilizes a three-stranded beta-sheet to engage the alpha-helical surface of the MHC class I-like MICB platform domain. Intriguingly, residues at the center of this beta-sheet mimic a central binding motif employed by the structurally unrelated C-type lectin-like NKG2D to facilitate engagement of diverse NKG2D ligands. Using surface plasmon resonance, we find that UL16 binds MICB, ULBP1, and ULBP2 with similar affinities that lie in the nanomolar range (12-66 nM). The ability of UL16 to bind its ligands depends critically on the presence of a glutamine (MICB) or closely related glutamate (ULBP1 and ULBP2) at position 169. An arginine residue at this position however, as found for example in MICA or ULBP3, would cause steric clashes with UL16 residues. The inability of UL16 to bind MICA and ULBP3 can therefore be attributed to single substitutions at key NKG2D ligand locations. This indicates that selective pressure exerted by viral immunoevasins such as UL16 contributed to the diversification of NKG2D ligands.

  16. Elucidation of the Nature of Structural Heterogeneity During Alkali Leaching of Non-activated and Mechanically Activated Boehmite ( γ-AlOOH)

    NASA Astrophysics Data System (ADS)

    Kumar, Rakesh; Alex, Thomas C.

    2015-08-01

    Crystal joints and faces in non-activated boehmite and, state of agglomeration of particles, degree of amorphization, microcrystallite dimension and, strain in mechanically activated boehmite are indicators of structural heterogeneity which influences reactivity of the solid phase. The focus of this paper is on understanding the manifestation of the heterogeneity during alkali leaching of a boehmite (specific surface area—263 m2/g), without and with mechanical activation using planetary milling up to 240 minutes. A two-prong strategy is used for this purpose which involved analysis of the kinetics of leaching by a model-free approach using `isoconversional method' and, in parallel, characterization of the reacting solid after different durations of leaching. Unlike model-fitting methods, the kinetic analysis revealed sample-dependent variation of apparent activation energy with fraction leached. Changes observed in the morphology of samples (by SEM), particle size distribution (by laser diffraction), and crystalline nature (by powder X-ray diffraction) are used to explain activation energy changes and propose mechanisms of leaching. The effect of mechanical activation on rate constant is assessed and it has been found that up to ~23-fold increase in rate is possible depending on the activation time, leaching temperature, and fraction leached. Further, based on binary correlations between activation energy at different fractions leached and initial characteristics of the samples, it is found that the leaching is predominantly influenced by structural changes during milling, namely, degree of amorphization, microcrystallite dimension, and strain, vis-à-vis specific surface area. Significantly, the paper highlights limitation of model-fitting methods used by most researchers to analyze the kinetics of leaching, especially for mechanically activated minerals.

  17. Structure of the HCMV UL16-MICB complex elucidates select binding of a viral immunoevasin to diverse NKG2D ligands.

    PubMed

    Müller, Steffen; Zocher, Georg; Steinle, Alexander; Stehle, Thilo

    2010-01-01

    The activating immunoreceptor NKG2D promotes elimination of infected or malignant cells by cytotoxic lymphocytes through engagement of stress-induced MHC class I-related ligands. The human cytomegalovirus (HCMV)-encoded immunoevasin UL16 subverts NKG2D-mediated immune responses by retaining a select group of diverse NKG2D ligands inside the cell. We report here the crystal structure of UL16 in complex with the NKG2D ligand MICB at 1.8 A resolution, revealing the molecular basis for the promiscuous, but highly selective, binding of UL16 to unrelated NKG2D ligands. The immunoglobulin-like UL16 protein utilizes a three-stranded beta-sheet to engage the alpha-helical surface of the MHC class I-like MICB platform domain. Intriguingly, residues at the center of this beta-sheet mimic a central binding motif employed by the structurally unrelated C-type lectin-like NKG2D to facilitate engagement of diverse NKG2D ligands. Using surface plasmon resonance, we find that UL16 binds MICB, ULBP1, and ULBP2 with similar affinities that lie in the nanomolar range (12-66 nM). The ability of UL16 to bind its ligands depends critically on the presence of a glutamine (MICB) or closely related glutamate (ULBP1 and ULBP2) at position 169. An arginine residue at this position however, as found for example in MICA or ULBP3, would cause steric clashes with UL16 residues. The inability of UL16 to bind MICA and ULBP3 can therefore be attributed to single substitutions at key NKG2D ligand locations. This indicates that selective pressure exerted by viral immunoevasins such as UL16 contributed to the diversification of NKG2D ligands. PMID:20090832

  18. Crystal structure of a bioactive sesquiterpene isolated from Artemisia reticulata.

    PubMed

    Bauri, A K; Foro, Sabine; Do, Nhu Quynh Nguyen

    2016-04-01

    The title compound, C15H24O2 {systematic name: 1-[6-hy-droxy-7-(propan-2-yl)-4-methyl-idene-2,3,3a,4,5,6,7,7a-octa-hydro-1H-inden-1-yl]ethanone} was iso-la-ted from A. reticulata by column chromatography over silica gel by gradient solvent elution. The mol-ecule comprises a bi-cyclo-[4.3.0]nonane ring bearing acet-oxy, hy-droxy and isopropyl substituents, and an exocyclic double bond on the cyclo-hexane ring. In the bicyclic skeleton, the cyclo-hexane ring adopts a chair conformation ring and the cyclo-pentane ring is in an envelope conformation. In the crystal, mol-ecules are linked by O-H⋯O hydrogen bonds, forming chains along [010]. These chains are cross-linked by C-H⋯O hydrogen bonds. PMID:27375864

  19. Food web structure and seasonality of slope megafauna in the NW Mediterranean elucidated by stable isotopes: Relationship with available food sources

    NASA Astrophysics Data System (ADS)

    Papiol, V.; Cartes, J. E.; Fanelli, E.; Rumolo, P.

    2013-03-01

    The food-web structure and seasonality of the dominant taxa of benthopelagic megafauna (fishes and decapods) on the middle slope of the Catalan Sea (Balearic Basin, NW Mediterranean) were investigated using the carbon and nitrogen stable isotope ratios of 29 species. Macrofauna (infauna, suprabenthos and zooplankton) were also analysed as potential prey. Samples were collected on a seasonal basis from 600 to 1000 m depth between February 2007 and February 2008. The fishes and decapods were classified into feeding groups based on the literature: benthic feeders (including suprabenthos) and zooplankton feeders, the latter further separated into migratory and non-migratory species. Decapods exhibited depleted δ15N and enriched δ13C compared to fishes. Annual mean δ13C of fishes ranged from - 19.15‰ (Arctozenus risso) to - 16.65‰ (Phycis blennoides) and of δ15N from 7.27‰ (Lampanyctus crocodilus) to 11.31‰ (Nezumia aequalis). Annual mean values of δ13C of decapods were from - 18.94‰ (Sergestes arcticus) to - 14.78‰ (Pontophilus norvegicus), and of δ15N from 6.36‰ (Sergia robusta) to 9.72‰ (Paromola cuvieri). Stable isotopes distinguished well amongst the 3 feeding guilds established a priori, pointing to high levels of resource partitioning in deep-sea communities. The trophic structure of the community was a function of the position of predators along the benthic-pelagic gradient, with benthic feeders isotopically enriched relative to pelagic feeders. This difference allowed the identification of two food webs based on pelagic versus benthic consumption. Prey and predator sizes were also important in structuring the community. The most generalised seasonal pattern was δ13C depletion from winter to spring and summer, especially amongst migratory macroplankton feeders. This suggests greater consumption of pelagic prey, likely related with increases in pelagic production or with ontogenic migrations of organisms from mid-water to the Benthic

  20. Synthesis, structure elucidation, biological screening, molecular modeling and DNA binding of some Cu(II) chelates incorporating imines derived from amino acids

    NASA Astrophysics Data System (ADS)

    Abdel-Rahman, Laila H.; Abu-Dief, Ahmed M.; Ismael, Mohammed; Mohamed, Mounir A. A.; Hashem, Nahla Ali

    2016-01-01

    Three tridentate Schiff bases amino acids were prepared by direct condensation of 3-methoxysalicylaldehyde (MS) or 4-diethylaminosalicylaldehyde (DS) with α-amino acid ligands [L-phenylalanine (P), L-histidine (H) and DL-tryptophan (T)]. The prepared Schiff bases amino acids were investigated by melting points, elemental analysis, 1HNMR and 13CNMR, IR, UV-Vis spectra, conductivity and magnetic measurements analyses. Subsequently, copper was introduced and Cu(II) complexes formed. These complexes were analyzed by thermal and elemental analyses and further investigated by FT-IR and UV/Vis spectroscopies. The experimental results indicating that all Cu(II) complexes contain hydrated water molecules (except DSPCu complex) and don't contain coordinated water molecules. The kinetic and thermal parameters were extracted from the thermal data using Coast and Redfern method. The molar conductance values of the Schiff base amino acid ligands and their Cu(II) complexes were relatively low, showing that these compounds have non-electrolytic nature. Magnetic susceptibility measurements showed the diamagnetic nature of the Schiff base amino acid ligands and paramagnetic nature of their complexes. Additionally, a spectrophotometric method was determined to extract their stability constants. It was found that the complexes possess 1:2 (M:L) stoichiometry. The results suggested that 3-methoxysalicylaldehyde and 4-diethylaminosalicylaldehyde amino acid Schiff bases behave as monobasic tridentate ONO ligands and coordinate Cu(II) ions in octahedral geometry according to the general formula [Cu(HL)2]·nH2O. To further understanding the structural and electronic properties of these complexes, Density Functional Theory (DFT) calculations were employed and provided a satisfactory description. The optimized structures of MST Schiff base ligand and its complex were calculated using DFT. The antimicrobial activity of the Schiff base ligands and their complexes were screened against some

  1. Synthesis, structure elucidation and redox properties of 99Tc complexes of lacunary Wells Dawson polyoxometalates: insights into molecular 99Tc - metal oxide interactions

    SciTech Connect

    McGregor, Donna; Burton-Pye, Benjamin P.; Howell, Robertha C.; Mbomekalle, Israel M.; Lukens Jr, Wayne W.; Bian, Fang; Mausolf, Edward; Poineau, Frederic; Czerwinski, Kenneth R; Francesconi, Lynn C.

    2011-01-10

    The isotope 99Tc (beta max: 250 keV, half-life: 2 x 105 year) is an abundant product of uranium-235 fission in nuclear reactors and is present throughout the radioactive waste stored in underground tanks at Hanford and Savannah River. Understanding and controlling the extensive redox chemistry of 99Tc is important to identify tunable strategies to separate 99Tc from spent fuel and from waste tanks and once separated, to identify and develop an appropriately stable waste-form for 99Tc. Polyoxometalates (POMs), nanometer sized models for metal oxide solid-state materials, are used in this study to provide a molecular level understanding of the speciation and redox chemistry of incorporated 99Tc. In this study, 99Tc complexes of the (alpha 2-P2W17O61)10- and (alpha 1-P2W17O61)10- isomers were prepared. Ethylene glycol was used as a"transfer ligand" to minimize the formation of TcO2 cdot xH2O. The solution structures, formulations, and purity of TcVO(alpha 1/alpha 2-P2W17O61)7- were determined by multinuclear NMR. X-ray Absorption Spectroscopy of the complexes are in agreement with the formulation and structures determined from 31P and 183W NMR. Preliminary electrochemistry results are consistent with the EXAFS results, showing a facile reduction of the TcVO(alpha 1-P2W17O61)7- species compared to the TcVO(alpha 2-P2W17O61)7- analog. The alpha1- defect is unique in that a basic oxygen atom is positioned toward the alpha1- site and the TcVO center appears to form a dative metal-metal bond with a framework W site. These attributes may lead to the assistance of protonation events that facilitate reduction. Electrochemistry comparison shows that the ReV analogs are about 200 mV more difficult to reduce in accordance with periodic trends.

  2. Synthesis, structure elucidation, and redox properties of 99Tc complexes of lacunary Wells-Dawson polyoxometalates: insights into molecular 99Tc-metal oxide interactions.

    PubMed

    McGregor, Donna; Burton-Pye, Benjamin P; Howell, Robertha C; Mbomekalle, Israel M; Lukens, Wayne W; Bian, Fang; Mausolf, Edward; Poineau, Frederic; Czerwinski, Kenneth R; Francesconi, Lynn C

    2011-03-01

    The isotope (99)Tc (β(max), 293.7; half-life, 2.1 × 10(5) years) is an abundant product of uranium-235 fission in nuclear reactors and is present throughout the radioactive waste stored in underground tanks at the Hanford and Savannah River sites. Understanding and controlling the extensive redox chemistry of (99)Tc is important in identifying tunable strategies to separate (99)Tc from spent fuel and from waste tanks and, once separated, to identify and develop an appropriately stable waste form for (99)Tc. Polyoxometalates (POMs), nanometer-sized models for metal oxide solid-state materials, are used in this study to provide a molecular level understanding of the speciation and redox chemistry of incorporated (99)Tc. In this study, (99)Tc complexes of the (α(2)-P(2)W(17)O(61))(10-) and (α(1)-P(2)W(17)O(61))(10-) isomers were prepared. Ethylene glycol was used as a "transfer ligand" to minimize the formation of TcO(2)·xH(2)O. The solution structures, formulations, and purity of Tc(V)O(α(1)/α(2)-P(2)W(17)O(61))(7-) were determined by multinuclear NMR. X-ray absorption spectroscopy of the complexes is in agreement with the formulation and structures determined from (31)P and (183)W NMR. Preliminary electrochemistry results are consistent with the EXAFS results, showing a facile reduction of the Tc(V)O(α(1)-P(2)W(17)O(61))(7-) species compared to the Tc(V)O(α(2)-P(2)W(17)O(61))(7-) analog. The α(1) defect is unique in that a basic oxygen atom is positioned toward the α(1) site, and the Tc(V)O center appears to form a dative metal-metal bond with a framework W site. These attributes may lead to the assistance of protonation events that facilitate reduction. Electrochemistry comparison shows that the Re(V) analogs are about 200 mV more difficult to reduce in accordance with periodic trends.

  3. Bio-sensitive activities of coordination compounds containing 1,10-phenanthroline as co-ligand: Synthesis, structural elucidation and DNA binding properties of metal(II) complexes

    NASA Astrophysics Data System (ADS)

    Raman, Natarajan; Mahalakshmi, Rajkumar; Mitu, Liviu

    2014-10-01

    Present work reports the DNA binding and cleavage characteristics of a series of mixed-ligand complexes having the composition [M(L)(phen)2]Cl2 (where M = Cu(II), Ni(II), Co(II) and Zn(II) and phen as co-ligand) in detail. Their structural features and other properties have been deduced from their elemental analyses, magnetic susceptibility and molar conductivity as well as from IR, UV-Vis, 1H NMR and EPR spectral studies. The UV-Vis, magnetic susceptibility and EPR spectral data of metal complexes suggest an octahedral geometry. The binding properties of these complexes with calf thymus DNA (CT-DNA) have been explored using electronic absorption spectroscopy, viscosity measurement, cyclic voltammetry and differential pulse voltammetry. The DNA-binding constants for Cu(II), Ni(II), Co(II), and Zn(II) complexes are 6.14 × 105 M-1, 1.8 × 105 M-1, 6.7 × 104 M-1 and 2.5 × 104 M-1 respectively. Detailed analysis reveals that these complexes interact with DNA through intercalation binding. Nuclease activity has also been investigated by gel electrophoresis. Moreover, the synthesized Schiff base and its mixed-ligand complexes have been screened for antibacterial and antifungal activities. The data reveal that the complexes exhibit higher activity than the parent ligand.

  4. Design, structural and spectroscopic elucidation of new nitroaromatic carboxylic acids and semicarbazones for the in vitro screening of anti-leishmanial activity

    NASA Astrophysics Data System (ADS)

    Dias, L. C.; de Lima, G. M.; Pinheiro, C. B.; Rodrigues, B. L.; Donnici, C. L.; Fujiwara, R. T.; Bartholomeu, D. C.; Ferreira, R. A.; Ferreira, S. R.; Mendes, T. A. O.; da Silva, J. G.; Alves, M. R. A.

    2015-01-01

    In this paper we report the synthesis and characterization of four new nitroaromatic compounds, 2-{6-nitrobenzo[1,3]dioxol-5-(methyleneamino)}benzoic acid (1), 2-{[5-(2-nitrophenyl)furan-2-yl]methylene-amino}benzoic acid (2), 2-{(6-nitrobenzo[1,3]dioxol-5-yl)methylene}hydrazinecarboxamide (3) and 2-{[5-(2-nitrophenyl)furan-2-yl]methylene}hydrazinecarboxamide (4). Compounds (1)-(4) have been authenticated by infrared and NMR spectroscopy, and the structure of (1), (2) and (4) have been determined by X-ray diffraction. In addition, the in vitro ability of compounds (1)-(4) to inhibit the growth of Leishmania infantum has been evaluated. Comparisons of the redox potential of the compounds and leishmanicidal activity indicate that the presence of the electroactive nitro group is important for the biological activity. The inhibition activity of compound (3) is comparable to that of the reference drug, SbCl3. Considering the important side effects and the low efficiency of SbCl3 in the case of resistance, compound (3) deserves further attention as a promising anti-leishmanicidal drug for veterinary use.

  5. Structure Elucidation at the Nanomole-Scale. 1. Trisoxazole Macrolides and Thiazole-containing Cyclic Peptides from the Nudibranch Hexabranchus sanguineus

    PubMed Central

    Dalisay, Doralyn S.; Rogers, Evan W.; Edison, Arthur S.; Molinski, Tadeusz F.

    2009-01-01

    A single specimen of Hexabranchus sanguineus, a nudibranch from the Indo-Pacific that is known to sequester kabiramides B, C and other trisoxazole macrolides, yielded new kabiramide analogs – 9-desmethylkabiramide B and 33-methyltetrahydrohalichondramide – and two new unexpected thiazole-containing cyclic peptides in sub-micromole amounts. The structures of these cyclic peptides were determined by analyses of 1D and 2D NMR spectra recorded with a state-of-the-art 1-mm 1H NMR high-temperature superconducting micro-cryoprobe, together with mass spectra. In addition to two proline residues, each peptide contains a thiazole- or oxazole-modified amino acid residue, together with conventional amino acid residues. All of the amino acid residues were L- as determined by Marfey’s analysis of the acid hydrolysates of the peptides. This is the first report of cyclic thiazole peptides from H. sanguineus. Since thiazole-oxazole modified peptides are typically associated with cyanobacteria and tunicates, the finding may imply a dietary component of the H. sanguineus that was previously overlooked. PMID:19254038

  6. Crystallographic analysis of human hemoglobin elucidates the structural basis of the potent and dual antisickling activity of pyridyl derivatives of vanillin

    SciTech Connect

    Abdulmalik, Osheiza; Ghatge, Mohini S.; Musayev, Faik N.; Parikh, Apurvasena; Chen, Qiukan; Yang, Jisheng; Nnamani, Ijeoma; Danso-Danquah, Richmond; Eseonu, Dorothy N.; Asakura, Toshio; Abraham, Donald J.; Venitz, Jurgen; Safo, Martin K.

    2011-11-01

    Pyridyl derivatives of vanillin increase the fraction of the more soluble oxygenated sickle hemoglobin and/or directly increase the solubility of deoxygenated sickle hemoglobin. Crystallographic analysis reveals the structural basis of the potent and dual antisickling activity of these derivatives. Vanillin has previously been studied clinically as an antisickling agent to treat sickle-cell disease. In vitro investigations with pyridyl derivatives of vanillin, including INN-312 and INN-298, showed as much as a 90-fold increase in antisickling activity compared with vanillin. The compounds preferentially bind to and modify sickle hemoglobin (Hb S) to increase the affinity of Hb for oxygen. INN-312 also led to a considerable increase in the solubility of deoxygenated Hb S under completely deoxygenated conditions. Crystallographic studies of normal human Hb with INN-312 and INN-298 showed that the compounds form Schiff-base adducts with the N-terminus of the α-subunits to constrain the liganded (or relaxed-state) Hb conformation relative to the unliganded (or tense-state) Hb conformation. Interestingly, while INN-298 binds and directs its meta-positioned pyridine-methoxy moiety (relative to the aldehyde moiety) further down the central water cavity of the protein, that of INN-312, which is ortho to the aldehyde, extends towards the surface of the protein. These studies suggest that these compounds may act to prevent sickling of SS cells by increasing the fraction of the soluble high-affinity Hb S and/or by stereospecific inhibition of deoxygenated Hb S polymerization.

  7. High accuracy NMR chemical shift corrected for bulk magnetization as a tool for structural elucidation of dilutable microemulsions. Part 1 - Proof of concept.

    PubMed

    Hoffman, Roy E; Darmon, Eliezer; Aserin, Abraham; Garti, Nissim

    2016-02-01

    In microemulsions, changes in droplet size and shape and possible transformations occur under various conditions. They are difficult to characterize by most analytical tools because of their nano-sized structure and dynamic nature. Several methods are usually combined to obtain reliable information, guiding the scientist in understanding their physical behavior. We felt that there is a need for a technique that complements those in use today in order to provide more information on the microemulsion behavior, mainly as a function of dilution with water. The improvement of NMR chemical shift measurements independent of bulk magnetization effects makes it possible to study the very weak intermolecular chemical shift effects. In the present study, we used NMR high resolution magic angle spinning to measure the chemical shift very accurately, free of bulk magnetization effects. The chemical shift of microemulsion components is measured as a function of the water content in order to validate the method in an interesting and promising, U-type dilutable microemulsion, which had been previously studied by a variety of techniques. Phase transition points of the microemulsion (O/W, bicontinuous, W/O) and changes in droplet shape were successfully detected using high-accuracy chemical shift measurements. We analyzed the results and found them to be compatible with the previous studies, paving the way for high-accuracy chemical shifts to be used for the study of other microemulsion systems. We detected two transition points along the water dilution line of the concentrate (reverse micelles) corresponding to the transition from swollen W/O nano-droplets to bicontinuous to the O/W droplets along with the changes in the droplets' sizes and shapes. The method seems to be in excellent agreement with other previously studied techniques and shows the advantage of this easy and valid technique.

  8. Prediction Models of Retention Indices for Increased Confidence in Structural Elucidation during Complex Matrix Analysis: Application to Gas Chromatography Coupled with High-Resolution Mass Spectrometry.

    PubMed

    Dossin, Eric; Martin, Elyette; Diana, Pierrick; Castellon, Antonio; Monge, Aurelien; Pospisil, Pavel; Bentley, Mark; Guy, Philippe A

    2016-08-01

    Monitoring of volatile and semivolatile compounds was performed using gas chromatography (GC) coupled to high-resolution electron ionization mass spectrometry, using both headspace and liquid injection modes. A total of 560 reference compounds, including 8 odd n-alkanes, were analyzed and experimental linear retention indices (LRI) were determined. These reference compounds were randomly split into training (n = 401) and test (n = 151) sets. LRI for all 552 reference compounds were also calculated based upon computational Quantitative Structure-Property Relationship (QSPR) models, using two independent approaches RapidMiner (coupled to Dragon) and ACD/ChromGenius software. Correlation coefficients for experimental versus predicted LRI values calculated for both training and test set compounds were calculated at 0.966 and 0.949 for RapidMiner and at 0.977 and 0.976 for ACD/ChromGenius, respectively. In addition, the cross-validation correlation was calculated at 0.96 from RapidMiner and the residual standard error value obtained from ACD/ChromGenius was 53.635. These models were then used to predict LRI values for several thousand compounds reported present in tobacco and tobacco-related fractions, plus a range of specific flavor compounds. It was demonstrated that using the mean of the LRI values predicted by RapidMiner and ACD/ChromGenius, in combination with accurate mass data, could enhance the confidence level for compound identification from the analysis of complex matrixes, particularly when the two predicted LRI values for a compound were in close agreement. Application of this LRI modeling approach to matrixes with unknown composition has already enabled the confirmation of 23 postulated compounds, demonstrating its ability to facilitate compound identification in an analytical workflow. The goal is to reduce the list of putative candidates to a reasonable relevant number that can be obtained and measured for confirmation. PMID:27403731

  9. Liquid chromatography/quadrupole time-of-flight mass spectrometry in combination with online hydrogen/deuterium exchange technique for structural elucidation of phase I metabolites of iso-phenylcyclopentylamine in rat bile.

    PubMed

    Liu, Xiaoxue; Wang, Suilou; Ding, Li; Chen, Xiaoping; Shen, Wenbin; Dong, Xin; Yun, Changhong; Lin, Hongda

    2014-10-01

    MS/MS experiment and accurate mass measurement are powerful tools in metabolite identification. However, sometimes these data do not provide enough information to assign an unambiguous structure to a metabolite. In combination with MS techniques, hydrogen/deuterium (H/D) exchange can provide additional information for structural elucidation by determination of the number of exchangeable hydrogen atoms in a structure. In this study, the principal phase I metabolites of iso-phenylcyclopentylamine in rat bile were identified by high-performance liquid chromatography with electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-Q-TOF-MS). Since N-oxidation may occur because of the existence of the primary amino group in the structure, it was difficult to differentiate the hydroxylated metabolites from N-oxides by ESI-Q-TOF-MS alone. Therefore, online H/D exchange technique was applied to solve this problem. Finally, 25 phase I metabolites were detected and structurally described, in which 11 were confirmed to be N-oxides. This study demonstrated the effectiveness of high-resolution mass spectrometry in combination with an online H/D exchange technique in rapid identification of drug metabolites, especially in discriminating hydroxylated metabolites from N-oxides.

  10. Purification, structural elucidation and bioactivity of tryptophan containing diketopiperazines, from Comamonas testosteroni associated with a rhabditid entomopathogenic nematode against major human-pathogenic bacteria.

    PubMed

    Kumar, S Nishanth; Mohandas, C; Nambisan, Bala

    2014-03-01

    The cell free culture filtrate of a Comamonas testosteroni associated with an Entomopathogenic nematode (EPN), Rhabditis (Oscheius) sp. exhibited promising antimicrobial activity. The ethyl acetate extract of the bacterial culture filtrate was purified by silica gel column chromatography to obtain five diketopiperazines or cyclic dipeptides (DKP 1-5). The structure and absolute stereochemistry of the compounds were determined based on extensive spectroscopic analyses (HR-MS, (1)HNMR, (13)CNMR, (1)H-(1)H COSY, (1)H-(13)C HMBC) and Marfey's method. Based on the spectral data the compounds were identified as Cyclo-(L-Trp-L-Pro) (1), Cyclo-(L-Trp-L-Tyr) (2), Cyclo-(L-Trp-L-Ile) (3), Cyclo-(L-Trp-L-Leu) (4) and Cyclo-(L-Trp-L-Phe) (5), respectively. Three diketopiperazines (DKP 2, 3 and 5) were active against all the ten bacteria tested. The highest activity of 0.5μg/ml by Cyclo-(L-Trp-L-Phe) was recorded against Vibrio cholerae followed by Salmonella typhi (1 μg/ml) a human pathogen responsible for life threatening diseases like profuse watery diarrhea and typhoid or enteric fever. The activity of this compound against V. cholerae and S. typhi is more effective than ciprofloxacin and ampicillin, the standard antibiotics. Cyclo-(L-Trp-L-Phe) recorded significant antibacterial activity against all the test bacteria when compared to other compounds. Five diketopiperazines were active against all the test fungi and are more effective than bavistin the standard fungicide. Diketopiperazines recorded no cytotoxicity to FS normal fibroblast and VERO cells (African green monkey kidney) except DKP 3 and 4. To our best knowledge this is the first report of antimicrobial activity of the tryptophan containing diketopiperazines against the human pathogenic microbes. The production of cyclic dipeptides by C. testosteroni is also reported here for the first time. We conclude that the C. testosteroni is promising sources of natural bioactive secondary metabolites against human

  11. Population structure and acquisition of the vanB resistance determinant in German clinical isolates of Enterococcus faecium ST192

    PubMed Central

    Bender, Jennifer K.; Kalmbach, Alexander; Fleige, Carola; Klare, Ingo; Fuchs, Stephan; Werner, Guido

    2016-01-01

    In the context of the global action plan to reduce the dissemination of antibiotic resistances it is of utmost importance to understand the population structure of resistant endemic bacterial lineages and to elucidate how bacteria acquire certain resistance determinants. Vancomycin resistant enterococci represent one such example of a prominent nosocomial pathogen on which nation-wide population analyses on prevalent lineages are scarce and data on how the bacteria acquire resistance, especially of the vanB genotype, are still under debate. With respect to Germany, an increased prevalence of VRE was noted in recent years. Here, invasive infections caused by sequence type ST192 VRE are often associated with the vanB-type resistance determinant. Hence, we analyzed 49 vanB-positive and vanB-negative E. faecium isolates by means of whole genome sequencing. Our studies revealed a distinct population structure and that spread of the Tn1549-vanB-type resistance involves exchange of large chromosomal fragments between vanB-positive and vanB-negative enterococci rather than independent acquisition events. In vitro filter-mating experiments support the hypothesis and suggest the presence of certain target sequences as a limiting factor for dissemination of the vanB element. Thus, the present study provides a better understanding of how enterococci emerge into successful multidrug-resistant nosocomial pathogens. PMID:26902259

  12. Isolation, antimicrobial activities, and primary structures of hamster neutrophil defensins.

    PubMed Central

    Mak, P; Wójcik, K; Thogersen, I B; Dubin, A

    1996-01-01

    Hamster (Mesocricetus auratus) neutrophil granules contain at least four microbicidal peptides belonging to the defensin family. These compounds were purified from granule acid extracts by reverse-phase chromatography and termed HaNP-1 to -4 (hamster neutrophil peptide). HaNP-1 and HaNP-3 revealed the most bactericidal activity, with a 50% inhibitory concentration of 0.3 to 0.8 microg/ml for Staphylococcus aureus and Streptococcus pyogenes strains. The HaNP-4 was always isolated in concentrations exceeding about 10 times the concentrations of other hamster peptides, but its antibacterial activity as well as that of HaNP-2 was relatively lower, probably as a result of conserved Arg residue substitutions. Other microorganisms were also tested, and generally, hamster defensins exhibited less potency against gram-negative bacteria. The amino acid sequence of hamster defensins showed a high percentage of identity to the sequence of mouse enteric defensins, reaching about 60% identical residues in the case of HaNP-3 and cryptdin 3. PMID:8890190

  13. Isolation and X-ray structures of labile benzoic- and acetic-acidium carbocations.

    PubMed

    Lindeman, S V; Neretin, I S; Davlieva, M G; Kochi, J K

    2005-04-15

    New carbocationic salts (via O-protonation of substituted benzoic acids) are prepared for the first time by controlled hydration of the corresponding benzoylium salts and isolated in pure crystalline form. Precise X-ray structural analyses reveal the rather unexpected (electronic) structure of the carboxylic-acidium functionality. PMID:15822990

  14. Mounting Systems for Structural Members, Fastening Assemblies Thereof, and Vibration Isolation Systems Including the Same

    NASA Technical Reports Server (NTRS)

    Young, Ken (Inventor); Hindle, Timothy (Inventor); Barber, Tim Daniel (Inventor)

    2016-01-01

    Mounting systems for structural members, fastening assemblies thereof, and vibration isolation systems including the same are provided. Mounting systems comprise a pair of mounting brackets, each clamped against a fastening assembly forming a mounting assembly. Fastening assemblies comprise a spherical rod end comprising a spherical member having a through opening and an integrally threaded shaft, first and second seating members on opposite sides of the spherical member and each having a through opening that is substantially coaxial with the spherical member through opening, and a partially threaded fastener that threadably engages each mounting bracket forming the mounting assembly. Structural members have axial end portions, each releasably coupled to a mounting bracket by the integrally threaded shaft. Axial end portions are threaded in opposite directions for permitting structural member rotation to adjust a length thereof to a substantially zero strain position. Structural members may be vibration isolator struts in vibration isolation systems.

  15. Isolation, Characterization, and Aggregation of a Structured Bacterial Matrix Precursor*

    PubMed Central

    Chai, Liraz; Romero, Diego; Kayatekin, Can; Akabayov, Barak; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

    2013-01-01

    Biofilms are surface-associated groups of microbial cells that are embedded in an extracellular matrix (ECM). The ECM is a network of biopolymers, mainly polysaccharides, proteins, and nucleic acids. ECM proteins serve a variety of structural roles and often form amyloid-like fibers. Despite the extensive study of the formation of amyloid fibers from their constituent subunits in humans, much less is known about the assembly of bacterial functional amyloid-like precursors into fibers. Using dynamic light scattering, atomic force microscopy, circular dichroism, and infrared spectroscopy, we show that our unique purification method of a Bacillus subtilis major matrix protein component results in stable oligomers that retain their native α-helical structure. The stability of these oligomers enabled us to control the external conditions that triggered their aggregation. In particular, we show that stretched fibers are formed on a hydrophobic surface, whereas plaque-like aggregates are formed in solution under acidic pH conditions. TasA is also shown to change conformation upon aggregation and gain some β-sheet structure. Our studies of the aggregation of a bacterial matrix protein from its subunits shed new light on assembly processes of the ECM within bacterial biofilms. PMID:23632024

  16. Mashed potatoes enriched with soy protein isolate and inulin: chemical, rheological and structural basis.

    PubMed

    Alvarez, M D; Olivares, M D; Blanch, M; Canet, W

    2013-10-01

    Soy protein isolate is typical vegetable protein with health-enhancing activities. Inulin, a prebiotic no digestible carbohydrate, has functional properties. A mashed potato serving of 200 g with added soy protein isolate and/or inulin concentrations of 15-60 g/kg provides from 3 to 12 g of soy protein isolate and/or inulin, respectively. Currently, no information is available about the possible texture-modifying effect of this non-ionizable polar carbohydrate in different soy-based food systems. In this study, the effect of the addition of soy protein isolate and inulin blends at different soy protein isolate: inulin ratios on the degree of inulin polymerization and the rheological and structural properties of fresh mashed and frozen/thawed mashed potatoes were evaluated. The inulin chemical structure remained intact throughout the various treatments, and soy protein isolate did not affect inulin composition being a protein compatible with this fructan. Small-strain rheology showed that both ingredients behaved like soft fillers. In the frozen/thawed mashed potatoes samples, addition of 30 : 30 and 15 : 60 blend ratios significantly increased elasticity (G' value) compared with 0 : 0 control, consequently reducing the freeze/thaw stability conferred by the cryoprotectants. Inulin crystallites caused a significant strengthening effect on soy protein isolate gel. Micrographs revealed that soy protein isolate supports the inulin structure by building up a second fine-stranded network. Thereby, possibility of using soy protein isolate and inulin in combination with mashed potatoes to provide a highly nutritious and healthy product is promising.

  17. Composition, structure and functional properties of protein concentrates and isolates produced from walnut (Juglans regia L.).

    PubMed

    Mao, Xiaoying; Hua, Yufei

    2012-01-01

    In this study, composition, structure and the functional properties of protein concentrate (WPC) and protein isolate (WPI) produced from defatted walnut flour (DFWF) were investigated. The results showed that the composition and structure of walnut protein concentrate (WPC) and walnut protein isolate (WPI) were significantly different. The molecular weight distribution of WPI was uniform and the protein composition of DFWF and WPC was complex with the protein aggregation. H(0) of WPC was significantly higher (p < 0.05) than those of DFWF and WPI, whilst WPI had a higher H(0) compared to DFWF. The secondary structure of WPI was similar to WPC. WPI showed big flaky plate like structures; whereas WPC appeared as a small flaky and more compact structure. The most functional properties of WPI were better than WPC. In comparing most functional properties of WPI and WPC with soybean protein concentrate and isolate, WPI and WPC showed higher fat absorption capacity (FAC). Emulsifying properties and foam properties of WPC and WPI in alkaline pH were comparable with that of soybean protein concentrate and isolate. Walnut protein concentrates and isolates can be considered as potential functional food ingredients.

  18. Isolation of eight microsatellite markers from Moina macrocopa for assessing cryptic genetic structure in the wild.

    PubMed

    Tatsuta, Haruki; Yao, Izumi; Tanaka, Yoshinari

    2009-05-01

    We isolated eight polymorphic microsatellite loci from the zooplankton Moina macrocopa (Straus), which is sensitive to pollutants such as insecticides and heavy metals. The isolated loci were polymorphic, with three to seven alleles among 23 individuals. Expected heterozygosities ranged from 0.167 to 0.787. These loci can be used to examine cryptic genetic structure and to infer the connectivity among metapopulations. PMID:21564785

  19. Arbutin: Isolation, X-ray structure and computional studies

    NASA Astrophysics Data System (ADS)

    Nycz, Jacek E.; Malecki, Grzegorz; Morag, Monika; Nowak, Gerard; Ponikiewski, Lukasz; Kusz, Joachim; Switlicka, Anna

    2010-09-01

    Arbutin, an active component originated from Serratula quinquefolia for skin-whitening use and treating skin related allergic inflammation, was characterized by microanalysis, FTIR, UV-Vis, multinuclear NMR spectroscopy, and single crystal X-ray diffraction method. The geometries of the studied compound were optimized in singlet states using the density functional theory (DFT) method with B3LYP functional. Electronic spectra were calculated by TDDFT method. In general, the predicted bond lengths and angles are in a good agreement with the values based on the X-ray crystal structure data.

  20. Isolation and structural characterization of chondroitin sulfate from bony fishes.

    PubMed

    Maccari, Francesca; Galeotti, Fabio; Volpi, Nicola

    2015-09-20

    Chondroitin sulfate (CS) was purified from the bones of common fishes, monkfish, cod, spiny dogfish, salmon and tuna, and characterized in an effort to find alternative sources and new peculiar structures of this complex biomacromolecule utilized in the pharmaceutical and nutraceutical industry. Quantitative analyses yielded a CS content ranging from 0.011% for cod up to 0.34% for monkfish. The disaccharide pattern showed the presence of nonsulfated disaccharide, monosulfated species ΔDi6s and ΔDi4s, and disulfated disaccharides in different percentages. The disulfated species ΔDi2,6dis was present in all CS extracts in a range of 1.3-10.5%. The presence of these disulfated disaccharides may be a useful marker for the marine origin of CS. The newly identified sources would certainly enable the production of CS with unique disaccharide composition and properties.

  1. Structure analysis and laxative effects of oligosaccharides isolated from bananas.

    PubMed

    Wang, Juan; Huang, Hui Hua; Cheng, Yan Feng; Yang, Gong Ming

    2012-10-01

    Banana oligosaccharides (BOS) were extracted with water, and then separated and purified using column chromatography. Gel penetration chromatography was used to determine the molecular weights. Thin layer chromatogram and capillary electrophoresis were employed to analyze the monosaccharide composition. The indican bond and structure of the BOS molecule were determined using Fourier transform infrared spectroscopy and nuclear magnetic resonance. Results showed that BOS were probably composed of eight β-D-pyran glucose units linked with 1→6 indican bonds. The laxative effects of BOS were investigated in mice using the method described in "Handbook of Technical Standards for Testing and Assessment of Health Food in China." The length of the small intestine over which a carbon suspension solution advanced in mice treated with low-, middle-, and high-dose BOS was significantly greater than that in the model group, suggesting that BOS are effective in accelerating the movement of the small intestine.

  2. Structure and Interactions of Isolated Biomolecular Building Blocks.

    NASA Astrophysics Data System (ADS)

    de Vries, Mattanjah

    2006-03-01

    We investigate biomolecular building blocks and their clusters with each other and with water on a single molecular level. The motivation is the need to distinguish between intrinsic molecular properties and those that result from the biological environment. This is achieved by a combination of laser desorption and jet cooling, applied to aromatic amino acids, small peptides containing those, nucleobases and nucleosides. This approach is coupled with a number of laser spectroscopic techniques, including resonant multi-photon ionization, spectral hole burning and infra-red ion-dip spectroscopy. We will discuss examples illustrating how information can be obtained on spatial structure of individual biomolecules, including peptide conformations and details of DNA base-pairing.

  3. A new alkaloid isolated from Abies webbiana leaf

    PubMed Central

    Ghosh, Ashoke K.; Sen, Debanjan; Bhattacharya, Sanjib

    2010-01-01

    A new alkaloid namely 1-(4’-methoxyphenyl)-aziridine was isolated from the leaf of Abies webbiana Lindl. (Pinaceae), grown in Sikkim Himalayan region of India. Its chemical structure was elucidated on the basis of elemental and spectral analyses. This is the first experimental report of the isolation of any alkaloid from A. webbiana. PMID:21808564

  4. Recent Research and Application on Seismic Isolation, Energy Dissipation and Control for Structures in China

    SciTech Connect

    Zhou Fulin; Tan Ping; Cui Jie; Xian Qiaoling; Wei Lushun; Huang Dongyang

    2008-07-08

    This paper briefly introduces the recent research, testing analysis, design and application on seismic isolation, energy dissipation, tuned mass damper and active control for buildings and bridges in mainland China. Paper introduces some typical researches, testing and analysis, including the mechanical tests for bearings and control devices, and the shaking table tests for structural models with different control systems. Paper also introduces the Chinese design codes for structures with seismic isolation and energy dissipation. Paper describes the recent application status and typical examples, especially introduces the largest isolation buildings group in the world, and the using passive and semi active control for structures. Also the paper makes discussion some problems existed on passive and active control technique now and the tendency of development on seismic control in future.

  5. Isolation, Purification, and Structural Identification of an Antifungal Compound from a Trichoderma Strain.

    PubMed

    Li, Chong-Wei; Song, Rui-Qing; Yang, Li-Bin; Deng, Xun

    2015-08-01

    Trichoderma strain T-33 has been demonstrated to have inhibitory effect on the fungus species Cytospora chrysosperma. Here, an active antifungal compound was obtained from Trichoderma strain T-33 extract via combined separation technologies, including organic solvent extraction, liquid chromatography, and thin-layer chromatography. The purified compound was further characterized by advanced analytical technologies to elucidate its chemical structure. Results indicated that the active antifungal compound in Trichoderma strain T-33 extract is 2,5- cyclohexadiene-1,4-dione-2,6-bis (1,1-dimethylethyl). PMID:25876599

  6. Isolation, Purification, and Structural Identification of an Antifungal Compound from a Trichoderma Strain.

    PubMed

    Li, Chong-Wei; Song, Rui-Qing; Yang, Li-Bin; Deng, Xun

    2015-08-01

    Trichoderma strain T-33 has been demonstrated to have inhibitory effect on the fungus species Cytospora chrysosperma. Here, an active antifungal compound was obtained from Trichoderma strain T-33 extract via combined separation technologies, including organic solvent extraction, liquid chromatography, and thin-layer chromatography. The purified compound was further characterized by advanced analytical technologies to elucidate its chemical structure. Results indicated that the active antifungal compound in Trichoderma strain T-33 extract is 2,5- cyclohexadiene-1,4-dione-2,6-bis (1,1-dimethylethyl).

  7. Isolated magnetic field structures in Mercury's magnetosheath as possible analogues for terrestrial magnetosheath plasmoids and jets

    NASA Astrophysics Data System (ADS)

    Karlsson, Tomas; Liljeblad, Elisabet; Kullen, Anita; Raines, Jim M.; Slavin, James A.; Sundberg, Torbjörn

    2016-09-01

    We have investigated MESSENGER magnetic field data from the Mercury magnetosheath and near solar wind, to identify isolated magnetic field structures (defined as clear, isolated changes in the field magnitude). Their properties are studied in order to determine if they may be considered as analogues to plasmoids and jets known to exist in Earth's magnetosheath. Both isolated decreases of the magnetic field absolute value ('negative magnetic field structures') and increases ('positive structures') are found in the magnetosheath, whereas only negative structures are found in the solar wind. The similar properties of the solar wind and magnetosheath negative magnetic field structures suggests that they are analogous to diamagnetic plasmoids found in Earth's magnetosheath and near solar wind. The latter have earlier been identified with solar wind magnetic holes. Positive magnetic field structures are only found in the magnetosheath, concentrated to a region relatively close to the magnetopause. Their proximity to the magnetopause, their scale sizes, and the association of a majority of the structures with bipolar magnetic field signatures identify them as flux transfer events (which generally are associated with a decrease of plasma density in the magnetosheath). The positive magnetic field structures are therefore not likely to be analogous to terrestrial paramagnetic plasmoids but possibly to a sub-population of magnetosheath jets. At Earth, a majority of magnetosheath jets are associated with the quasi-parallel bow shock. We discuss some consequences of the findings of the present investigation pertaining to the different nature of the quasi-parallel bow shock at Mercury and Earth.

  8. Structure Elucidation of the Diagnostic Product Ion at m/z 97 Derived from Androst-4-en-3-One-Based Steroids by ESI-CID and IRMPD Spectroscopy

    NASA Astrophysics Data System (ADS)

    Thevis, Mario; Beuck, Simon; Höppner, Sebastian; Thomas, Andreas; Held, Joseph; Schäfer, Mathias; Oomens, Jos; Schänzer, Wilhelm

    2012-03-01

    Structure elucidation of steroids by mass spectrometry has been of great importance to various analytical arenas and numerous studies were conducted to provide evidence for the composition and origin of (tandem) mass spectrometry-derived product ions used to characterize and identify steroidal substances. The common product ion at m/z 97 generated from androst-4-ene-3-one analogs has been subject of various studies, including stable isotope-labeling and (high resolution/high accuracy) tandem mass spectrometry, but its gas-phase structure has never been confirmed. Using high resolution/high accuracy mass spectrometry and low resolution tandem mass spectrometry, density functional theory (DFT) calculation, and infrared multiple photon dissociation (IRMPD) spectroscopy employing a free electron laser, the structure of m/z 97 derived from testosterone was assigned to protonated 3-methyl-2-cyclopenten-1-one. This ion was identified in a set of six cyclic C6H9O+ isomers as computed at the B3LYP/6-311++G(2d,2p) level of theory (protonated 3-methyl-2-cyclopenten-1-one, 2-methyl-2-cyclopenten-1-one and 2-cyclohexen-1-one). Product ions of m/z 97 obtained from MS2 and MS3 experiments of protonated 3-methyl-2-cyclopenten-1-one, 2-methyl-2-cyclopenten-1-one, 2-cyclohexen-1-one, and testosterone corroborated the suggested gas-phase ion structure, which was eventually substantiated by IRMPD spectroscopy yielding a spectrum that convincingly matched the predicted counterpart. Finally, the dissociation pathway of the protonated molecule of testosterone to m/z 97 was revisited and an alternative pathway was suggested that considers the exclusion of C-10 along with the inclusion of C-5, which was experimentally demonstrated with stable isotope labeling.

  9. Charge‐Induced Unzipping of Isolated Proteins to a Defined Secondary Structure

    PubMed Central

    González Flórez, Ana Isabel; Mucha, Eike; Ahn, Doo‐Sik; Gewinner, Sandy; Schöllkopf, Wieland; Pagel, Kevin

    2016-01-01

    Abstract Here we present a combined experimental and theoretical study on the secondary structure of isolated proteins as a function of charge state. In infrared spectra of the proteins ubiquitin and cytochrome c, amide I (C=O stretch) and amide II (N–H bend) bands can be found at positions that are typical for condensed‐phase proteins. For high charge states a new band appears, substantially red‐shifted from the amide II band observed at lower charge states. The observations are interpreted in terms of Coulomb‐driven transitions in secondary structures from mostly helical to extended C5‐type hydrogen‐bonded structures. Support for this interpretation comes from simple energy considerations as well as from quantum chemical calculations on model peptides. This transition in secondary structure is most likely universal for isolated proteins that occur in mass spectrometric experiments. PMID:26847383

  10. Structure Elucidation of the Metabolites of 2', 3', 5'-Tri-O-Acetyl-N6-(3-Hydroxyphenyl) Adenosine in Rat Urine by HPLC-DAD, ESI-MS and Off-Line Microprobe NMR

    PubMed Central

    Miao, Zhaoxia; Qu, Kai; Liu, Xia; Zhang, Peicheng; Qin, Hailin; Zhu, Haibo; Wang, Yinghong

    2015-01-01

    2', 3', 5'-tri-O-acetyl-N6-(3-hydroxyphenyl) adenosine (also known as WS070117) is a new adenosine analog that displays anti-hyperlipidemic activity both in vitro and in vivo experiments as shown in many preliminary studies. Due to its new structure, little is known about the metabolism of WS070117. Hence, the in vivo metabolites of WS070117 in rat urine following oral administration were investigated. Identification of the metabolites was conducted using the combination of high-performance liquid chromatography (HPLC) coupled with diode array detector (DAD), ion trap electrospray ionization-mass spectrometry (ESI-MS), and off-line microprobe nuclear magnetic resonance (NMR) measurements. Seven metabolites were obtained as pure compounds at the sub-milligram to milligram levels. Results of structure elucidation unambiguously revealed that the phase I metabolite, N6-(3-hydroxyphenyl) adenosine (M8), was a hydrolysate of WS070117 by hydrolysis on the three ester groups. N6-(3-hydr-oxyphenyl) adenine (M7), also one of the phase I metabolites, was the derivative of M8 by the loss of ribofuranose. In addition to two phase I metabolites, there were five phase II metabolites of WS070117 found in rat urine. 8-hydroxy-N6-(3-hydroxy-phenyl) adenosine (M6) was the product of M7 by hydrolysis at position 8. The other four were elucidated to be N6-(3-O-β-D-glucuronyphenyl) adenine (M2), N8-hydroxy-N6-(3-O-sulfophenyl) adenine (M3), N6-(3-O-β-D-glucuronyphenyl) adenosine (M4), and N6-(3-O- sulfophenyl) adenosine (M5). Phase II metabolic pathways were proven to consist of hydroxylation, glucuronidation and sulfation. This study provides new and valuable information on the metabolism of WS070117, and also demonstrates the HPLC/MS/off-line microprobe NMR approach as a robust means for rapid identification of metabolites. PMID:26029929

  11. Hydramycin, a new antitumor antibiotic. Taxonomy, isolation, physico-chemical properties, structure and biological activity.

    PubMed

    Hanada, M; Kaneta, K; Nishiyama, Y; Hoshino, Y; Konishi, M; Oki, T

    1991-08-01

    A new antitumor antibiotic hydramycin was isolated from the fermentation broth of Streptomyces violaceus P950-4 (ATCC 53807). It showed potent antibacterial and cytotoxic activity and increased the survival time of mice inoculated with P388 leukemia. A new structure related to the pluramycin group antibiotics was assigned by its spectroscopic experiments. PMID:1833366

  12. On inertia nonlinearity in irregular-plan isolated structures under seismic excitations

    NASA Astrophysics Data System (ADS)

    Amin Afshar, Majid; Aghaei Pour, Sepehr

    2016-02-01

    The influence of nonlinear inertia as a function of acceleration, velocity, and displacement is investigated for an asymmetric isolated structure. Six degrees of freedom (6-DOFs) are defined to illustrate translational and rotational displacements of the superstructure and base isolation. Motion equations of such DOFs are derived using the Lagrangian formalism. Two coordinate systems of the reference are defined, one fixed on the building base (global coordinate) and the other at the torsional isolation level (local coordinate). The motion governing equations in the conventional approach is formulated on a linear form in the global coordinate system, whereas in the novel approach, the local coordinate system leads to a nonlinear form of dynamic equations. The difference between two linear and nonlinear models is appeared because of the existence of nonlinear inertia terms just in the nonlinear one. Afterwards, three particular types of isolated structures are employed with the peculiar ratio of torsional-lateral coupled frequency on symmetric frequency. Numerical analysis is applied to investigate the performance of two structural models by exerting harmonic excitations and earthquakes. The results are obtained while analyzing time history and frequency content and show that the coupling effects of nonlinear inertia lead to differences in the responses of linear and nonlinear models of such structures; also, some nonlinear phenomena such as energy transfer between modes, saturation, rigid displacement, and super-harmonic created due to geometrical (inertial) nonlinearities are studied.

  13. Improved isolation protocol to detect high molecular weight polysaccharide structures of Campylobacter jejuni.

    PubMed

    Kovács, Judit K; Felső, Péter; Emődy, Levente; Schneider, György; Kocsis, Béla

    2014-12-01

    Simple detection of high molecular weight, LPS-like structures of Campylobacter jejuni is still an unsolved problem. A phenol-free extraction method for the detection of HMW polysaccharide was developed without the need for Western blot. This method provides a reliable technique for large-scale screening and comparative characterization study of different isolates.

  14. Effect of structural flexibility on the design of vibration-isolating mounts for aircraft engines

    NASA Technical Reports Server (NTRS)

    Phillips, W. H.

    1984-01-01

    Previous analyses of the design of vibration-isolating mounts for a rear-mounted engine to decouple linear and rotational oscillations are extended to take into account flexibility of the engine-mount structure. Equations and curves are presented to allow the design of mount systems and to illustrate the results for a range of design conditions.

  15. Structure of complex cell wall polysaccharides isolated from Trichoderma and Hypocrea species.

    PubMed

    Prieto, A; Leal, J A; Poveda, A; Jiménez-Barbero, J; Gómez-Miranda, B; Domenech, J; Ahrazem, O; Bernabé, M

    1997-11-28

    The structure of fungal polysaccharides isolated from the cell wall of Trichoderma reesei, T. koningii, and Hypocrea psychrophila, have been investigated by means of chemical analyses and 1D and 2D NMR spectroscopy. The polysaccharides have an irregular structure, idealized as follows: [formula: see text] The proportions of the different side chains vary from a species to another, being n above some three times larger in H. psychrophila than in T. reesei or T. koningii. PMID:9468630

  16. Structure of complex cell wall polysaccharides isolated from Trichoderma and Hypocrea species.

    PubMed

    Prieto, A; Leal, J A; Poveda, A; Jiménez-Barbero, J; Gómez-Miranda, B; Domenech, J; Ahrazem, O; Bernabé, M

    1997-11-28

    The structure of fungal polysaccharides isolated from the cell wall of Trichoderma reesei, T. koningii, and Hypocrea psychrophila, have been investigated by means of chemical analyses and 1D and 2D NMR spectroscopy. The polysaccharides have an irregular structure, idealized as follows: [formula: see text] The proportions of the different side chains vary from a species to another, being n above some three times larger in H. psychrophila than in T. reesei or T. koningii.

  17. Ravynic acid, an antibiotic polyeneyne tetramic acid from Penicillium sp. elucidated through synthesis.

    PubMed

    Myrtle, J D; Beekman, A M; Barrow, R A

    2016-09-21

    A new antibiotic natural product, ravynic acid, has been isolated from a Penicillium sp. of fungus, collected from Ravensbourne National Park. The 3-acylpolyenyne tetramic acid structure was definitively elucidated via synthesis. Highlights of the synthetic method include the heat induced formation of the 3-acylphosphorane tetramic acid and a selective Wittig cross-coupling to efficiently prepare the natural compounds carbon skeleton. The natural compound was shown to inhibit the growth of Staphylococcus aureus down to concentrations of 2.5 µg mL(-1). PMID:27519121

  18. Structural and functional interactions between extraradical mycelia of ectomycorrhizal Pisolithus isolates.

    PubMed

    Wu, Bingyun; Maruyama, Haruka; Teramoto, Munemasa; Hogetsu, Taizo

    2012-06-01

    Extraradical mycelia from different ectomycorrhizal (ECM) roots coexist and interact under the forest floor. We investigated structural connections of conspecific mycelia and translocation of carbon and phosphorus between the same or different genets. Paired ECM Pinus thunbergii seedlings colonized by the same or different Pisolithus isolates were grown side by side in a rhizobox as their mycelia contacted each other. (14)CO(2) or (33)P-phosphoric acid was fed to leaves or a spot on the mycelium in one of the paired seedlings. Time-course distributions of (14)C and (33)P were visualized using a digital autoradiographic technique with imaging plates. Hyphal connections were observed between mycelia of the same Pisolithus isolate near the contact site, but hyphae did not connect between different isolates. (14)C and (33)P were translocated between mycelia of the same isolate. In (33)P-fed mycelia, accumulation of (33)P from the feeding spot toward the host ECM roots was observed. No (14)C and (33)P translocation occurred between mycelia of different isolates. These results provide direct evidence that contact and hyphal connection between mycelia of the same ECM isolate can cause nutrient translocation. The ecological significance of contact between extraradical mycelia is discussed.

  19. [Characteristics of microbial community structure during isolation of electrical active bacteria].

    PubMed

    Wang, Min; Zhao, Yang- Guo; Lu, Shan-Shan

    2014-10-01

    To investigate the effect of selective culturing on microorganisms and functional role of electrical active bacteria in biofilm, some exoelectrogens were isolated from microbial fuel cell (MFC) anodic biofilm using Hungate roll-tube technique with iron oxide as indicator. At the same time, the dynamics of the microbial community structure was monitored during the pure culture isolation. The results show that maximum voltages of MFCs feeding with lactic acid, acetic acid and steroid wastewater are 0.57, 0.60 and 0.40 V respectively. The dominant bacteria isolated from seed sludge and anodic films feeding with acetate and lactate belong to phylum Proteobacteria; while steroid wastewater contains relative high diversity of bacteria, i. e. Proteobacteria, Firmicutes and Bacteroidetes. After enriching and culturing, two bacteria were consequently obtained, which shared the highest similarity with Enterobacter ludwigii and Citrobacter freundii respectively. When inoculated in MFC with lactic acid as the substrate, they produced maximum voltage of 0.10 and 0.17 V individually. This study shows that electrical active bacteria can be isolated from the MFC anodic biofilm using anaerobic gradient dilution culture techniques with iron oxide as indicator. Microbial community structure presents markedly shifting during the bacteria isolation owing to its selectivity.

  20. Elucidating the structure-property relationships of donor-π-acceptor dyes for dye-sensitized solar cells (DSSCs) through rapid library synthesis by a one-pot procedure.

    PubMed

    Fuse, Shinichiro; Sugiyama, Sakae; Maitani, Masato M; Wada, Yuji; Ogomi, Yuhei; Hayase, Shuzi; Katoh, Ryuzi; Kaiho, Tatsuo; Takahashi, Takashi

    2014-08-18

    The creation of organic dyes with excellent high power conversion efficiency (PCE) is important for the further improvement of dye-sensitized solar cells. We wish to describe the rapid synthesis of a 112-membered donor-π-acceptor dye library by a one-pot procedure, evaluation of PCEs, and elucidation of structure-property relationships. No obvious correlations between ε, and the η were observed, whereas the HOMO and LUMO levels of the dyes were critical for η. The dyes with a more positive E(HOMO), and with an E(LUMO)<-0.80 V, exerted higher PCEs. The proper driving forces were crucial for a high J(sc), and it was the most important parameter for a high η. The above criteria of E(HOMO) and E(LUMO) should be useful for creating high PCE dyes; nevertheless, that was not sufficient for identifying the best combination of donor, π, and acceptor blocks. Combinatorial synthesis and evaluation was important for identifying the best dye.

  1. Spectral, structural elucidation and coordination abilities of Co(II) and Mn(II) coordination entities of 2,6,11,15-tetraoxa-9,17-diaza-1,7,10,16-(1,2)-tetrabenzenacyclooctadecaphan-8,17-diene.

    PubMed

    Rajiv, Kumar; Rajni, Johar

    2011-09-01

    Designing tactics were tailored and followed by synthetic and formulation methodologies to prepare 2,6,11,15-tetraoxa-9,17-diaza-1,7,10,16-(1,2)-tetrabenzenacyclooctadecaphan-8,17-diene. Spectral techniques (MS, infrared, 1H NMR, 13C NMR, electronic and EPR), physiochemical measurements (elemental analysis, molar conductance and magnetic susceptibility), electrochemistry (cyclic voltammetry) and classical mechanics (molecular modeling) were employed for structural elucidation of Co(II) and Mn(II) coordination entities having N2O4 chromophore. Comparative spectral analysis revealed legating nature of N2O4 donor macrocycle and confirmed host/guest connectivity between ligand and metal(s). Mass spectrometry (MS) determined 1:1 stoichiometry in CEs. Further electrochemical study confirmed change in oxidation and reduction patterns of CEs. Inhibiting potential (antifungal screened against Aspergillus flavus) showed enhanced antimicrobial properties of CEs as compared to ligand. Molecular modeling was employed to find out different molecular features along with their stabilization energies.

  2. Comparison of lipopolysaccharide structures of Bordetella pertussis clinical isolates from pre- and post-vaccine era.

    PubMed

    Albitar-Nehme, Sami; Basheer, Soorej M; Njamkepo, Elisabeth; Brisson, Jean-Robert; Guiso, Nicole; Caroff, Martine

    2013-08-30

    Endotoxins are lipopolysaccharides (LPS), and major constituents of the outer membrane of Gram-negative bacteria. Bordetella pertussis LPS were the only major antigens, of this agent of whooping-cough, that were not yet analyzed on isolates from the pre- and post-vaccination era. We compared here the LPS structures of four clinical isolates with that of the vaccine strain BP 1414. All physico-chemical analyses, including SDS-PAGE, TLC, and different MALDI mass spectrometry approaches were convergent. They helped demonstrating that, on the contrary to some other B. pertussis major antigens, no modification occurred in the dodecasaccharide core structure, as well as in the whole LPS molecules. These results are rendering these major antigens good potential vaccine components. Molecular modeling of this conserved LPS structure also confirmed the conclusions of previous experiments leading to the production of anti-LPS monoclonal antibodies and defining the main epitopes of these major antigens.

  3. Finite element prediction of seismic response modification of monumental structures utilizing base isolation

    NASA Astrophysics Data System (ADS)

    Spanos, Konstantinos; Anifantis, Nikolaos; Kakavas, Panayiotis

    2015-05-01

    The analysis of the mechanical behavior of ancient structures is an essential engineering task concerning the preservation of architectural heritage. As many monuments of classical antiquity are located in regions of earthquake activity, the safety assessment of these structures, as well as the selection of possible restoration interventions, requires numerical models capable of correctly representing their seismic response. The work presented herein was part of a research project in which a better understanding of the dynamics of classical column-architrave structures was sought by means of numerical techniques. In this paper, the seismic behavior of ancient monumental structures with multi-drum classical columns is investigated. In particular, the column-architrave classical structure under strong ground excitations was represented by a finite element method. This approach simulates the individual rock blocks as distinct rigid blocks interconnected with slidelines and incorporates seismic isolation dampers under the basement of the structure. Sliding and rocking motions of individual stone blocks and drums are modeled utilizing non-linear frictional contact conditions. The seismic isolation is modeled through the application of pad bearings under the basement of the structure. These pads are interpreted by appropriate rubber and steel layers. Time domain analyses were performed, considering the geometric and material non-linear behavior at the joints and the characteristics of pad bearings. The deformation and failure modes of drum columns subject to seismic excitations of various types and intensities were analyzed. The adverse influence of drum imperfections on structural safety was also examined.

  4. Analysis of population structure among Korean and Japanese Legionella pneumophila isolates using hsp60 sequences.

    PubMed

    Park, Chan Geun; Kim, Byoung Jun; Kim, Hee-Youn; Yun, Yeo-Jun; Ko, Kwan Soo; Miyamoto, Hiroshi; Kim, Bum-Joon; Kook, Yoon-Hoh

    2012-08-01

    The population structure of Korean (150 strains) and Japanese (92 strains) Legionella pneumophila isolates along with 18 reference strains were investigated using hsp60 sequence (1647 bp) analysis. Twelve clonal subgroups (hsP-I to hsP-X and hsF-I and hsF-II) were designated on the hsp60 tree, inferred from representative sequences using the neighbor-joining method. Some of the isolates showed unique subgroups depending on the source of isolates, including hsP-I, hsF-I, and hsF-II from cooling tower water, and subgroups hsP-VIII and hsP-X from circulating hot water bath. These subgroups may be useful for epidemiological studies to chase or specify sources of infection in Korea and Japan. PMID:22672106

  5. The population structure of Escherichia coli isolated from subtropical and temperate soils

    USGS Publications Warehouse

    Byappanahalli, Muruleedhara N.; Yan, Tao; Hamilton, Matthew J.; Ishii, Satoshi; Fujioka, Roger S.; Whitman, Richard L.; Sadowsky, Michael J.

    2012-01-01

    While genotypically-distinct naturalized Escherichia coli strains have been shown to occur in riparian soils of Lake Michigan and Lake Superior watersheds, comparative analyses of E. coli populations in diverse soils across a range of geographic and climatic conditions have not been investigated. The main objectives of this study were to: (a) examine the population structure and genetic relatedness of E. coli isolates collected from different soil types on a tropical island (Hawaii), and (b) determine if E. coli populations from Hawaii and temperate soils (Indiana, Minnesota) shared similar genotypes that may be reflective of biome-related soil conditions. DNA fingerprint and multivariate statistical analyses were used to examine the population structure and genotypic characteristics of the E. coli isolates. About 33% (98 of 293) of the E. coli from different soil types and locations on the island of Oahu, Hawaii, had unique DNA fingerprints, indicating that these bacteria were relatively diverse; the Shannon diversity index for the population was 4.03. Nearly 60% (171 of 293) of the E. coli isolates from Hawaii clustered into two major groups and the rest, with two or more isolates, fell into one of 22 smaller groups, or individual lineages. Multivariate analysis of variance of 89, 21, and 106 unique E. coli DNA fingerprints for Hawaii, Indiana, and Minnesota soils, respectively, showed that isolates formed tight cohesive groups, clustering mainly by location. However, there were several instances of clonal isolates being shared between geographically different locations. Thus, while nearly identical E. coli strains were shared between disparate climatologically- and geographically-distinct locations, a vast majority of the soil E. coli strains were genotypically diverse and were likely derived from separate lineages. This supports the hypothesis that these bacteria are not unique and multiple genotypes can readily adapt to become part of the soil autochthonous

  6. Characterization of structures in biofilms formed by a Pseudomonas fluorescens isolated from soil

    PubMed Central

    2009-01-01

    Background Microbial biofilms represent an incompletely understood, but fundamental mode of bacterial growth. These sessile communities typically consist of stratified, morphologically-distinct layers of extracellular material, where numerous metabolic processes occur simultaneously in close proximity. Limited reports on environmental isolates have revealed highly ordered, three-dimensional organization of the extracellular matrix, which may hold important implications for biofilm physiology in vivo. Results A Pseudomonas spp. isolated from a natural soil environment produced flocculent, nonmucoidal biofilms in vitro with unique structural features. These mature biofilms were made up of numerous viable bacteria, even after extended culture, and contained up to 50% of proteins and accumulated 3% (by dry weight) calcium, suggesting an important role for the divalent metal in biofilm formation. Ultrastructurally, the mature biofilms contained structural motifs consisting of dense, fibrillary clusters, nanofibers, and ordered, honeycomb-like chambers enveloped in thin sheets. Conclusion Mature biofilms contained living bacteria and were structurally, chemically, and physiologically heterogeneous. The principal architectural elements observed by electron microscopy may represent useful morphological clues for identifying bacterial biofilms in vivo. The complexity and reproducibility of the structural motifs observed in bacterial biofilms appear to be the result of organized assembly, suggesting that this environmental isolate may possess ecological advantages in its natural habitat. PMID:19460161

  7. Active pneumatic vibration isolation system using negative stiffness structures for a vehicle seat

    NASA Astrophysics Data System (ADS)

    Danh, Le Thanh; Ahn, Kyoung Kwan

    2014-02-01

    In this paper, an active pneumatic vibration isolation system using negative stiffness structures (NSS) for a vehicle seat in low excitation frequencies is proposed, which is named as an active system with NSS. Here, the negative stiffness structures (NSS) are used to minimize the vibratory attraction of a vehicle seat. Owing to the time-varying and nonlinear behavior of the proposed system, it is not easy to build an accurate dynamic for model-based controller design. Thus, an adaptive intelligent backstepping controller (AIBC) is designed to manage the system operation for high-isolation effectiveness. In addition, an auxiliary control effort is also introduced to eliminate the effect of the unpredictable perturbations. Moreover, a radial basis function neural network (RBFNN) model is utilized to estimate the optimal gain of the auxiliary control effort. Final control input and the adaptive law for updating coefficients of the approximate series can be obtained step by step using a suitable Lyapunov function. Afterward, the isolation performance of the proposed system is assessed experimentally. In addition, the effectiveness of the designed controller for the proposed system is also compared with that of the traditional backstepping controller (BC). The experimental results show that the isolation effectiveness of the proposed system is better than that of the active system without NSS. Furthermore, the undesirable chattering phenomenon in control effort is quite reduced by the estimation mechanism. Finally, some concluding remarks are given at the end of the paper.

  8. Isolation, properties, and structural features of divalent cation ionophores derived from beef heart mitochondria.

    PubMed

    Blondin, G A

    1975-12-30

    The notion of small molecular weight ion carriers in biological systems is herein documented by a description of the isolation and ionophoretic properties of a family of oxyoctadecadienoate congeners derived from beef-heart mitochondria. Although certain members of this family of compounds have been shown to possess unique ionophoretic properties, one should not lose sight of the fact that the compounds that we have described represented only a portion of the total picture. Other chemically unrelated, yet structurally unknown species have been isolated from beef-heart mitochondria, and compounds similar in both chromatographic and spectroscopic properties to the oxyoctadecadienoate family, as well as other unique structures, have been isolated in our laboratory from sarcoplasmic reticulum and chloroplasts. The important points to be derived from these findings are that there is an apparent abundance of natural ionophores and we should no longer concern should address ourselves to the more relevant task of digging them out and ourselves with the question "are there ionophores in biological systems?" but describing their chemical and physical properties. In view of the apparent abundance of natural ionophores, this is an enormous task, especially when one considers that it only represents half of the problem. The isolation and description of the ionophoroprotein or channel-forming complexes share equally in the overall significance and level of understanding attributable to this area of inquiry and it would appear that many fruitful collaborative ventures are, or should be, on the horizon.

  9. Susceptibility of whey protein isolate to oxidation and changes in physicochemical, structural, and digestibility characteristics.

    PubMed

    Feng, Xianchao; Li, Chenyi; Ullah, Niamat; Cao, Jiqianrui; Lan, Yongli; Ge, Wupeng; Hackman, Robert M; Li, Zhixi; Chen, Lin

    2015-11-01

    Oxidation is an important factor for denaturing of whey protein isolate (WPI) during food processing. We studied the effects of chemical oxidation on physicochemical and structural changes along with in vitro digestibility of WPI in this work. Evaluation of physicochemical changes showed that carbonyl level and dityrosine content increased, whereas total and free thiol group levels decreased for oxidized WPI samples. For the structural changes, protein aggregation was measured by surface hydrophobicity, turbidity, and particle diameter, which was increased for oxidized WPI samples. The increase of the secondary structure β-sheets and antiparallel β-sheet also supported the aggregation of oxidized WPI. A direct quantitative relationship between physicochemical and structural changes and protein digestibility indicated that oxidation-related damage restricts the susceptibility of WPI to proteases. In conclusion, WPI had high susceptibility to oxidative stress, and both physicochemical and structural changes caused by severe oxidative stress could decrease the rate of in vitro digestibility of WPI.

  10. Low-resolution molecular structures of isolated functional units from arthropodan and molluscan hemocyanin.

    PubMed Central

    Grossmann, J G; Ali, S A; Abbasi, A; Zaidi, Z H; Stoeva, S; Voelter, W; Hasnain, S S

    2000-01-01

    Synchrotron x-ray scattering measurements were performed on dilute solutions of the purified hemocyanin subunit (Bsin1) from scorpion (Buthus sindicus) and the N-terminal functional unit (Rta) from a marine snail (Rapana thomasiana). The model-independent approach based on spherical harmonics was applied to calculate the molecular envelopes directly from the scattering profiles. Their molecular shapes in solution could be restored at 2-nm resolution. We show that these units represent stable, globular building blocks of the two hemocyanin families and emphasize their conformational differences on a subunit level. Because no crystallographic or electron microscopy data are available for isolated functional units, this study provides for the first time structural information for isolated, monomeric functional subunits from both hemocyanin families. This has been made possible through the use of low protein concentrations (< or = 1 mg/ml). The observed structural differences may offer advantages in building very different overall molecular architectures of hemocyanin by the two phyla. PMID:10653810

  11. Design and Nuclear Magnetic Resonance (NMR) Structure Determination of the Second Extracellular Immunoglobulin Tyrosine Kinase A (TrkAIg2) Domain Construct for Binding Site Elucidation in Drug Discovery

    PubMed Central

    2014-01-01

    The tyrosine kinase A (TrkA) receptor is a validated therapeutic intervention point for a wide range of conditions. TrkA activation by nerve growth factor (NGF) binding the second extracellular immunoglobulin (TrkAIg2) domain triggers intracellular signaling cascades. In the periphery, this promotes the pain phenotype and, in the brain, cell survival or differentiation. Reproducible structural information and detailed validation of protein–ligand interactions aid drug discovery. However, the isolated TrkAIg2 domain crystallizes as a β-strand-swapped dimer in the absence of NGF, occluding the binding surface. Here we report the design and structural validation by nuclear magnetic resonance spectroscopy of the first stable, biologically active construct of the TrkAIg2 domain for binding site confirmation. Our structure closely mimics the wild-type fold of TrkAIg2 in complex with NGF (1WWW.pdb), and the 1H–15N correlation spectra confirm that both NGF and a competing small molecule interact at the known binding interface in solution. PMID:25454499

  12. Isolation of an Isocoumarin and an Isobenzofuran Derivatives from a Fungicolous Isolate of Acremonium crotocinigenum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    6,8-dimethoxy-4,5-dimethyl-3-methyleneisochroman-1-one (1) and 5,7-dimethoxy-3,4-dimethyl-3-hydroxy-isobenzofuranone (2), have been isolated from an organic extract of the fungicolous fungus Acremonium crotocinigenum (NRRL 40192). The structures of these compounds were elucidated on the basis of NM...

  13. Structure and synthesis of a unique isonitrile lipid isolated from the marine mollusk Actinocyclus papillatus.

    PubMed

    Manzo, Emiliano; Carbone, Marianna; Mollo, Ernesto; Irace, Carlo; Di Pascale, Antonio; Li, Yan; Ciavatta, Maria Letizia; Cimino, Guido; Guo, Yue-Wei; Gavagnin, Margherita

    2011-04-15

    The first chemical study of an Actinocyclidae nudibranch, Actinocyclus papillatus, resulted in the isolation of (-)-actisonitrile (1), a lipid based on a 1,3-propanediol ether skeleton. The structure was established by spectroscopic methods, whereas the absolute configuration of the chiral center was determined by comparing the optical properties of natural actisonitrile with those of (+)- and (-)-synthetic enantiomers, opportunely prepared. Both (-)- and (+)-actisonitrile were tested in preliminary in vitro cytotoxicity bioassays on tumor and nontumor mammalian cells. PMID:21405058

  14. Isolation and Structure of Cancer Cell Growth Inhibitory Tetracyclic Triterpenoids from the Zimbabwean Monadenium lugardae.

    PubMed

    Pettit, George R; Ye, Qinghua; Herald, Delbert L; Knight, John C; Hogan, Fiona; Melody, Noeleen; Mukku, Venugopal J R V; Doubek, Dennis L; Chapuis, Jean-Charles

    2016-06-24

    The Zimbabwean medicinal plant Monadenium lugardae was evaluated as a potential source of new anticancer constituents. Four new tetracyclic triterpene (1-4) were isolated, accompanied by four previously known triterpenes (5-8). Against a panel of human tumor cell lines, lugardstatins 1 (1) and 2 (2) had good cancer cell growth inhibitory activity. All of the triterpene structures (1-8) were established by 1D and 2D NMR spectrometric and HR mass spectrometric analysis. PMID:27214528

  15. Isolation and structure determination of blepharismin, a conjugation initiating gamone in the ciliate blepharisma.

    PubMed

    Kubota, T; Tokoroyama, T; Tsukuda, Y; Koyama, H; Miyake, A

    1973-01-26

    One of the gamones (gamone II) which are effective for the induction of conjugation in Blepharisma intermedium has been isolated in a crystalline form and designated as blepharismin. From the result of chemical and spectroscopic investigations, in which x-ray crystallographic analysis was used as a definitive tool, blepharismin has been found to have the structure of calcium 3-(2'-formylamino-5'-hydroxybenzoyl)lactate.

  16. Spectral analysis, structural elucidation and evaluation of chemical reactivity of synthesized ethyl-4-[(2-cyano-acetyl)-hydrazonomethyl]-3,5-dimethyl-1H-pyrrole-2-carboxylate through experimental studies and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Rawat, P.; Singh, R. N.

    2014-09-01

    This paper describes the synthesis, spectral analysis, structural elucidation and chemical reactivity of pyrrole hydrazide-hydrazone: ethyl-4-[(2-cyano-acetyl)-hydrazonomethyl]-3,5-dimethyl-1H-pyrrole-2-carboxylate (ECAHDPC). The 1H, 13C NMR isotropic chemical shifts and electronic absorption spectra have been calculated by GIAO and TD-DFT methods, respectively, and corroborate well with experimental data. The NH proton of the hydrazide-hydrazones (lbond2 Cdbnd NNHCO) frame appears as singlet at δ = 11.69 ppm due to delocalization of nitrogen lone pair with carbonyl group and its proton involvement in intramolecular H-bonding. The calculated wavenumbers of dimer are in good agreement with the experimental results and confirm that the stable conformer forms dimer by hydrogen bonding interactions between pyrrolic NH and carbonyl Cdbnd O group of ester giving red shift and resonance assisted hydrogen bonding. The binding energy of intermolecular interaction is found to be 10.19 kcal/mol after basis set superposition error correction. QTAIM calculations confirm the existence of intermolecular conventional hydrogen bond (Nsbnd H⋯O), intra and intermolecular non-conventional hydrogen bond (Csbnd H⋯O) and intramolecular interaction (C⋯N). The NBO analysis has been performed to evaluate charge transfer and delocalization of electron density. The static first hyperpolarizability (β0) of monomer has been found to be 6.59 × 10-30 esu. The maximum value of reactivity descriptors (fk+, sk+, ωk+) at C(9) indicate that this site is more susceptible to nucleophilic attack, favoring for the formation of heterocyclic compounds.

  17. Structural degradation of Thar lignite using MW1 fungal isolate: optimization studies

    USGS Publications Warehouse

    Haider, Rizwan; Ghauri, Muhammad A.; Jones, Elizabeth J.; Orem, William H.; SanFilipo, John R.

    2015-01-01

    Biological degradation of low-rank coals, particularly degradation mediated by fungi, can play an important role in helping us to utilize neglected lignite resources for both fuel and non-fuel applications. Fungal degradation of low-rank coals has already been investigated for the extraction of soil-conditioning agents and the substrates, which could be subjected to subsequent processing for the generation of alternative fuel options, like methane. However, to achieve an efficient degradation process, the fungal isolates must originate from an appropriate coal environment and the degradation process must be optimized. With this in mind, a representative sample from the Thar coalfield (the largest lignite resource of Pakistan) was treated with a fungal strain, MW1, which was previously isolated from a drilled core coal sample. The treatment caused the liberation of organic fractions from the structural matrix of coal. Fungal degradation was optimized, and it showed significant release of organics, with 0.1% glucose concentration and 1% coal loading ratio after an incubation time of 7 days. Analytical investigations revealed the release of complex organic moieties, pertaining to polyaromatic hydrocarbons, and it also helped in predicting structural units present within structure of coal. Such isolates, with enhanced degradation capabilities, can definitely help in exploiting the chemical-feedstock-status of coal.

  18. Structure activity characterization of Bordetella petrii lipid A, from environment to human isolates.

    PubMed

    Basheer, Soorej M; Bouchez, Valerie; Novikov, Alexey; Augusto, Luis A; Guiso, Nicole; Caroff, Martine

    2016-01-01

    Bordetella petrii, a facultative anaerobic species, is the only known member of the Bordetella genus with environmental origin. However it was also recently isolated from humans. The structures of the B. petrii lipid A moieties of the endotoxins were characterized here for the first time for an environmental strain and compared to that of human isolates. Characterization was achieved using chemical analyses, gas chromatography-mass spectrometry, and Matrix Assisted Laser Desorption Ionisation mass spectrometry. The analyses revealed that the different lipid A structures contain a common bisphosphorylated β-(1→6)-linked d-glucosamine disaccharide with hydroxytetradecanoic acid in amide as well at the C-3' in ester linkages. Similar to Bordetella pertussis and Bordetella bronchiseptica lipids A, the hydroxytetradecanoic acid at the C-2' position was substituted by tetradecanoic acid. Unlike B. pertussis, the hydroxytetradecanoic acid at the C-2 position was substituted with either 12:0 or 14:0 and/or their 2-OH forms. Depending on the environmental or human origin the structures differed in the length and degree of fatty acid acylation and impacted the IL-6 and TNF-α inflammatory responses tested. In one isolate we showed the presence at the C-3 position of the short-chain 10:0(3-OH), which according to our previous analyses is more characteristic of the human pathogens in the genus like B. pertussis and Bordetella parapertussis. PMID:26164553

  19. Structure activity characterization of Bordetella petrii lipid A, from environment to human isolates.

    PubMed

    Basheer, Soorej M; Bouchez, Valerie; Novikov, Alexey; Augusto, Luis A; Guiso, Nicole; Caroff, Martine

    2016-01-01

    Bordetella petrii, a facultative anaerobic species, is the only known member of the Bordetella genus with environmental origin. However it was also recently isolated from humans. The structures of the B. petrii lipid A moieties of the endotoxins were characterized here for the first time for an environmental strain and compared to that of human isolates. Characterization was achieved using chemical analyses, gas chromatography-mass spectrometry, and Matrix Assisted Laser Desorption Ionisation mass spectrometry. The analyses revealed that the different lipid A structures contain a common bisphosphorylated β-(1→6)-linked d-glucosamine disaccharide with hydroxytetradecanoic acid in amide as well at the C-3' in ester linkages. Similar to Bordetella pertussis and Bordetella bronchiseptica lipids A, the hydroxytetradecanoic acid at the C-2' position was substituted by tetradecanoic acid. Unlike B. pertussis, the hydroxytetradecanoic acid at the C-2 position was substituted with either 12:0 or 14:0 and/or their 2-OH forms. Depending on the environmental or human origin the structures differed in the length and degree of fatty acid acylation and impacted the IL-6 and TNF-α inflammatory responses tested. In one isolate we showed the presence at the C-3 position of the short-chain 10:0(3-OH), which according to our previous analyses is more characteristic of the human pathogens in the genus like B. pertussis and Bordetella parapertussis.

  20. Solution structure of the isolated histone H2A-H2B heterodimer.

    PubMed

    Moriwaki, Yoshihito; Yamane, Tsutomu; Ohtomo, Hideaki; Ikeguchi, Mitsunori; Kurita, Jun-Ichi; Sato, Masahiko; Nagadoi, Aritaka; Shimojo, Hideaki; Nishimura, Yoshifumi

    2016-01-01

    During chromatin-regulated processes, the histone H2A-H2B heterodimer functions dynamically in and out of the nucleosome. Although detailed crystal structures of nucleosomes have been established, that of the isolated full-length H2A-H2B heterodimer has remained elusive. Here, we have determined the solution structure of human H2A-H2B by NMR coupled with CS-Rosetta. H2A and H2B each contain a histone fold, comprising four α-helices and two β-strands (α1-β1-α2-β2-α3-αC), together with the long disordered N- and C-terminal H2A tails and the long N-terminal H2B tail. The N-terminal αN helix, C-terminal β3 strand, and 310 helix of H2A observed in the H2A-H2B nucleosome structure are disordered in isolated H2A-H2B. In addition, the H2A α1 and H2B αC helices are not well fixed in the heterodimer, and the H2A and H2B tails are not completely random coils. Comparison of hydrogen-deuterium exchange, fast hydrogen exchange, and {(1)H}-(15)N hetero-nuclear NOE data with the CS-Rosetta structure indicates that there is some conformation in the H2A 310 helical and H2B Lys11 regions, while the repression domain of H2B (residues 27-34) exhibits an extended string-like structure. This first structure of the isolated H2A-H2B heterodimer provides insight into its dynamic functions in chromatin. PMID:27181506

  1. Solution structure of the isolated histone H2A-H2B heterodimer

    PubMed Central

    Moriwaki, Yoshihito; Yamane, Tsutomu; Ohtomo, Hideaki; Ikeguchi, Mitsunori; Kurita, Jun-ichi; Sato, Masahiko; Nagadoi, Aritaka; Shimojo, Hideaki; Nishimura, Yoshifumi

    2016-01-01

    During chromatin-regulated processes, the histone H2A-H2B heterodimer functions dynamically in and out of the nucleosome. Although detailed crystal structures of nucleosomes have been established, that of the isolated full-length H2A-H2B heterodimer has remained elusive. Here, we have determined the solution structure of human H2A-H2B by NMR coupled with CS-Rosetta. H2A and H2B each contain a histone fold, comprising four α-helices and two β-strands (α1–β1–α2–β2–α3–αC), together with the long disordered N- and C-terminal H2A tails and the long N-terminal H2B tail. The N-terminal αN helix, C-terminal β3 strand, and 310 helix of H2A observed in the H2A-H2B nucleosome structure are disordered in isolated H2A-H2B. In addition, the H2A α1 and H2B αC helices are not well fixed in the heterodimer, and the H2A and H2B tails are not completely random coils. Comparison of hydrogen-deuterium exchange, fast hydrogen exchange, and {1H}-15N hetero-nuclear NOE data with the CS-Rosetta structure indicates that there is some conformation in the H2A 310 helical and H2B Lys11 regions, while the repression domain of H2B (residues 27–34) exhibits an extended string-like structure. This first structure of the isolated H2A-H2B heterodimer provides insight into its dynamic functions in chromatin. PMID:27181506

  2. Glycolonitrile oligomerization: structure of isolated oxazolines, potential heterocycles on the early earth

    NASA Technical Reports Server (NTRS)

    Arrhenius, G.; Baldridge, K. K.; Richards-Gross, S.; Siegel, J. S.; Bada, J. L. (Principal Investigator)

    1997-01-01

    A study of glycolonitrile polymerization has led to the isolation and characterization of two 2,5-dihydro-4-aminooxazoles, 4 and 5. Previous reports have misassigned these structures as s-triazines or pyrimidines. X-ray diffraction analysis of crystals of 4 and an acetylated oxazole derivative of 5 (6) confirm the proposed structures. Ab initio computations are used to assess the relative thermodynamic stability of three trimer isomers (an s-triazine, an aminohydroxypyrimidine, and an aminooxazoline), and the results indicate that 4 is a novel kinetic product. Mechanistic considerations rationalize kinetic oxazole formation over the more customary triazine or pyrimidine trimers.

  3. Isolation and structural characterization of a mainly ligand-based dimetallic radical.

    PubMed

    Li, Shuyu; Wang, Xingyong; Zhang, Zaichao; Zhao, Yue; Wang, Xinping

    2015-12-14

    A radical cation of ruthenium was isolated and structurally characterized. The EPR spectrum and theoretical calculations indicate that the spin density mainly resides on ligands. The X-ray structure shows that the change in metal-metal bond lengths is negligible upon one-electron oxidation. sp(3) C-H bond activation was observed during the reaction of the parent molecule with the trityl cation, which possibly occurs via an oxidative EC mechanism: a thermodynamically favorable electron-transfer to give the radical cation intermediate, followed by the hydrogen atom abstraction to afford a cationic tetramethylfulvene complex with formation of a metal-carbon bond.

  4. Roles of soil-structure interaction and damping in base-isolated structures built on numerous soil layers overlying a half-space

    NASA Astrophysics Data System (ADS)

    Tsai, C. S.; Hsueh, C. I.; Su, H. C.

    2016-06-01

    This study examines the roles of soil-structure interaction (SSI), higher modes, and damping in a base-isolated structure built on multiple layers of soil overlying a half space. Closed-form solutions for the entire system, including a superstructure, seismic isolator, and numerous soil layers overlying a half-space, were obtained. The formulations obtained in this study simply in terms of well-known frequencies and mechanical impedance ratios can explicitly interpret the dynamic behavior of a base-isolated structure interacting with multiple soil layers overlying a half-space. The key factors influencing the performance of the isolation system are the damping ratio of the isolator and the ratio of the natural frequency of the fixed-base structure to that of the isolated structure by assuming that the superstructure moves as a rigid body. This study reveals that higher damping in the base isolator is unfavorable to higher mode responses that usually dominate the responses of the superstructure and that the damping mechanism plays an important role in transmitting energy in addition to absorbing energy. It is also concluded that it is possible to design a soft soil layer as an isolation system for isolating vibration energy.

  5. Nonlinear dynamic analysis of multi-base seismically isolated structures with uplift potential II: verification examples

    NASA Astrophysics Data System (ADS)

    Roussis, Panayiotis C.; Tsopelas, Panos C.; Constantinou, Michael C.

    2010-03-01

    The work presented in this paper serves as numerical verification of the analytical model developed in the companion paper for nonlinear dynamic analysis of multi-base seismically isolated structures. To this end, two numerical examples have been analyzed using the computational algorithm incorporated into program 3D-BASIS-ME-MB, developed on the basis of the newly-formulated analytical model. The first example concerns a seven-story model structure that was tested on the earthquake simulator at the University at Buffalo and was also used as a verification example for program SAP2000. The second example concerns a two-tower, multi-story structure with a split-level seismic-isolation system. For purposes of verification, key results produced by 3D-BASIS-ME-MB are compared to experimental results, or results obtained from other structural/finite element programs. In both examples, the analyzed structure is excited under conditions of bearing uplift, thus yielding a case of much interest in verifying the capabilities of the developed analysis tool.

  6. Contribution of spoligotyping to the characterization of the population structure of Mycobacterium tuberculosis isolates in Portugal.

    PubMed

    David, Suzana; Ribeiro, Diana Raposo; Antunes, Abílio; Portugal, Clara; Sancho, Luísa; de Sousa, José Germano

    2007-09-01

    Tuberculosis is a major health problem in Portugal. To begin characterizing the population structure of Mycobacterium tuberculosis, spoligotyping was used for the systematic typing, through consecutive sampling, of patient isolates from the Amadora-Sintra area of Greater Lisbon. Distribution amongst major spoligotype families, including the Latin American Mediterranean (LAM), T, Haarlem and Beijing, was compared to that of the international spoligotype database SpolDB4 and to the European countries of traditional Portuguese immigration represented in SpolDB4. Spoligotypes from 665 isolates were analyzed and 97 shared international types (SITs) identified. In SpolDB4 Portugal is represented by part of the spoligotypes from this study explaining the reduced number of unidentified patterns. The importance of the LAM family, and especially of LAM1 and LAM9 sub-families that alone represented 38% of all the isolates in this study as compared to 8% relative to the European sub group, led us to believe that at least in this respect the population structure was closer to that of Africa and South America than to Europe. Spoligotypes characteristic of Portugal or Portuguese related settings were identified. These included SIT244 a T1 sub-family predominant in Portugal and Bangladesh, SIT64 a LAM 6 sub-family common to Portugal and Brazil, and SIT1106 a LAM 9 sub-family. These studies were the first in Portugal stressing the importance of monitoring the population structure of M. tuberculosis isolates, an important step towards gaining an understanding of tuberculosis and the dynamics of this disease.

  7. Structural characterization of heparan sulfate proteoglycan subclasses isolated from bovine aortic endothelial cell cultures

    SciTech Connect

    Kinsella, M.G.; Wight, T.N.

    1988-03-22

    Labeled heparan sulfate proteoglycans (HSPG) were isolated from wounded and confluent cultures of bovine aortic endothelial cells by nondegradative extraction with 4 M guanidine hydrochloride and detergent. HSPG were separated from more highly charged chondroitin or dermatan sulfate proteoglycans by ion-exchange chromatography, and subclasses of different hydrodynamic size were isolated by gel filtration. Three major subclasses of HSPG were characterized structurally with respect to the presence and relative size of protein core, the presence and amount of nonsulfated oligosaccharide, and size and structure of heparan sulfate (HS) chains. The largest (600-800-kDa) HSPG subclass (I), isolated from cell layers and media of confluent cultures, bears 38-kDa HS chains on an apparently heterogeneous class of relatively large glycoprotein cores. HSPG II (150-200 kDa), isolated from cell layer or media, has 22-kDa HS chains and smaller core glycoproteins (less than 50 kDa). HSPG III, the subclass of smallest hydrodynamic size, has 13-kDa HS chains and a glycopeptide core of less than 15 kDa. All subclasses bear varying proportions of non-sulfated oligosaccharides of similar sizes. Comparisons of HS chain structure indicated that the different subclasses have similar proportions (49-55%) of N-sulfate, with both O-sulfate and highly N-sulfated blocks of disaccharide distributed similarly along HS chains. In addition, HS chains from subclasses II and III contain sequences that are insensitive to periodate oxidation or heparitinase digestion, suggesting that they contain increased proportions of iduronate.

  8. New complete structure of Hafnia alvei clinical isolate strain PCM 2670 semi-rough lipopolysaccharide.

    PubMed

    Bobko, Ewelina; Tyras, Michal; Jachymek, Wojciech

    2013-06-01

    Hafnia alvei strain PCM 2670 is a clinical isolate from a patient with chronic reproductive tract infection. The novel structure of the semi-rough lipopolysaccharide was established with the use of NMR spectroscopy and mass spectrometry as well as immunochemical techniques. According to the mass spectrometry data, heptose in the oligosaccharide is partially substituted by glycine. H. alvei PCM 2670 core structure encompasses the common core of H. alvei which is modified with two additional galactose units. [structure: see text]. The 6-substituted galactose is the O-antigen repeating unit substitution residue. The repeating unit consists of five monosaccharide residues and has the following structure: →2)-β-Galp-(1→6)-α-Glcp-(1→6)-αGlcpNAc3OAc-(1→4)-α-GalpA-(1→3)-β-GlcpNAc6OAc-(1→6)-core. PMID:23643833

  9. Vibration control of platform structures with magnetorheological elastomer isolators based on an improved SAVS law

    NASA Astrophysics Data System (ADS)

    Xu, Zhao-Dong; Suo, Si; Lu, Yong

    2016-06-01

    This paper presents a study on the vibration control of platform structures with magnetorheological elastomer (MRE) isolators. Firstly, a novel MRE isolator design is put forward based on the mechanical properties of MREs, and subsequently a single-degree-of-freedom (SDOF) dynamic model and a multiple-degree-of-freedom (MDOF) dynamic model for platform systems incorporating such isolators are developed. In order to overcome the shortcomings of the conventional on–off control law, an improved semi-active variable stiffness (SAVS) control law is proposed. The proposed SAVS scheme makes full use of the continuously variable stiffness of MREs, and it takes into account the influence of the sampling interval such that the field-dependent restoring force is made to do negative work during the whole sampling interval as far as possible. The results of numerical simulations demonstrate that the improved SAVS control law can achieve better vibration-control effectiveness than the on–off control law. The comparative results are discussed through examining the mechanisms of these two control laws in light of the power spectral density and the energy input. For an MDOF platform a simplified approach is proposed to combine the local response signals with an equivalent SDOF representation to generate the control parameters for individual isolators, and the effectiveness of such a scheme is also verified through numerical simulation.

  10. The phylogenetic structure of plant-pollinator networks increases with habitat size and isolation.

    PubMed

    Aizen, Marcelo A; Gleiser, Gabriela; Sabatino, Malena; Gilarranz, Luis J; Bascompte, Jordi; Verdú, Miguel

    2016-01-01

    Similarity among species in traits related to ecological interactions is frequently associated with common ancestry. Thus, closely related species usually interact with ecologically similar partners, which can be reinforced by diverse co-evolutionary processes. The effect of habitat fragmentation on the phylogenetic signal in interspecific interactions and correspondence between plant and animal phylogenies is, however, unknown. Here, we address to what extent phylogenetic signal and co-phylogenetic congruence of plant-animal interactions depend on habitat size and isolation by analysing the phylogenetic structure of 12 pollination webs from isolated Pampean hills. Phylogenetic signal in interspecific interactions differed among webs, being stronger for flower-visiting insects than plants. Phylogenetic signal and overall co-phylogenetic congruence increased independently with hill size and isolation. We propose that habitat fragmentation would erode the phylogenetic structure of interaction webs. A decrease in phylogenetic signal and co-phylogenetic correspondence in plant-pollinator interactions could be associated with less reliable mutualism and erratic co-evolutionary change.

  11. Qualitative Fault Isolation of Hybrid Systems: A Structural Model Decomposition-Based Approach

    NASA Technical Reports Server (NTRS)

    Bregon, Anibal; Daigle, Matthew; Roychoudhury, Indranil

    2016-01-01

    Quick and robust fault diagnosis is critical to ensuring safe operation of complex engineering systems. A large number of techniques are available to provide fault diagnosis in systems with continuous dynamics. However, many systems in aerospace and industrial environments are best represented as hybrid systems that consist of discrete behavioral modes, each with its own continuous dynamics. These hybrid dynamics make the on-line fault diagnosis task computationally more complex due to the large number of possible system modes and the existence of autonomous mode transitions. This paper presents a qualitative fault isolation framework for hybrid systems based on structural model decomposition. The fault isolation is performed by analyzing the qualitative information of the residual deviations. However, in hybrid systems this process becomes complex due to possible existence of observation delays, which can cause observed deviations to be inconsistent with the expected deviations for the current mode in the system. The great advantage of structural model decomposition is that (i) it allows to design residuals that respond to only a subset of the faults, and (ii) every time a mode change occurs, only a subset of the residuals will need to be reconfigured, thus reducing the complexity of the reasoning process for isolation purposes. To demonstrate and test the validity of our approach, we use an electric circuit simulation as the case study.

  12. Zebrafish cardiac muscle thick filaments: isolation technique and three-dimensional structure.

    PubMed

    González-Solá, Maryví; Al-Khayat, Hind A; Behra, Martine; Kensler, Robert W

    2014-04-15

    To understand how mutations in thick filament proteins such as cardiac myosin binding protein-C or titin, cause familial hypertrophic cardiomyopathies, it is important to determine the structure of the cardiac thick filament. Techniques for the genetic manipulation of the zebrafish are well established and it has become a major model for the study of the cardiovascular system. Our goal is to develop zebrafish as an alternative system to the mammalian heart model for the study of the structure of the cardiac thick filaments and the proteins that form it. We have successfully isolated thick filaments from zebrafish cardiac muscle, using a procedure similar to those for mammalian heart, and analyzed their structure by negative-staining and electron microscopy. The isolated filaments appear well ordered with the characteristic 42.9 nm quasi-helical repeat of the myosin heads expected from x-ray diffraction. We have performed single particle image analysis on the collected electron microscopy images for the C-zone region of these filaments and obtained a three-dimensional reconstruction at 3.5 nm resolution. This reconstruction reveals structure similar to the mammalian thick filament, and demonstrates that zebrafish may provide a useful model for the study of the changes in the cardiac thick filament associated with disease processes.

  13. Zebrafish Cardiac Muscle Thick Filaments: Isolation Technique and Three-Dimensional Structure

    PubMed Central

    González-Solá, Maryví; AL-Khayat, Hind A.; Behra, Martine; Kensler, Robert W.

    2014-01-01

    To understand how mutations in thick filament proteins such as cardiac myosin binding protein-C or titin, cause familial hypertrophic cardiomyopathies, it is important to determine the structure of the cardiac thick filament. Techniques for the genetic manipulation of the zebrafish are well established and it has become a major model for the study of the cardiovascular system. Our goal is to develop zebrafish as an alternative system to the mammalian heart model for the study of the structure of the cardiac thick filaments and the proteins that form it. We have successfully isolated thick filaments from zebrafish cardiac muscle, using a procedure similar to those for mammalian heart, and analyzed their structure by negative-staining and electron microscopy. The isolated filaments appear well ordered with the characteristic 42.9 nm quasi-helical repeat of the myosin heads expected from x-ray diffraction. We have performed single particle image analysis on the collected electron microscopy images for the C-zone region of these filaments and obtained a three-dimensional reconstruction at 3.5 nm resolution. This reconstruction reveals structure similar to the mammalian thick filament, and demonstrates that zebrafish may provide a useful model for the study of the changes in the cardiac thick filament associated with disease processes. PMID:24739166

  14. Tuning upconversion through a sensitizer/activator-isolated NaYF4 core/shell structure

    NASA Astrophysics Data System (ADS)

    Ye, Shuai; Chen, Guanying; Shao, Wei; Qu, Junle; Prasad, Paras N.

    2015-02-01

    The ability to tune the emission color of upconversion nanoparticles (UCNPs) will greatly enhance the scope of their applications, ranging from infrared solar cells to volumetric multiplexed bioimaging. Conventional methods to tune upconversion are to vary the type and/or the concentration of doped rare-earth ions in these nanoparticle formulations. Here, we introduce a different approach to vary the emission colors of the frequently used sensitizer/activator pairs of Yb3+/RE3+ (RE = Ho, Er, Tm) via utilization of a sensitizer/activator-isolated NaYF4 core-shell structure. We show that the typical green, yellow, and blue luminescent colors from Yb3+/Ho3+-, Yb3+/Er3+-, and Yb3+/Tm3+-co-doped NaYF4 UCNPs can be converted into the quasi-white, green, and pink blue, when corresponding core-shell structures of NaYF4:Yb3+ @NaYF4:Ho3+, NaYF4:Yb3+ @NaYF4:Er3+ and NaYF4:Yb3+ @NaYF4:Tm3+ are built. Time-resolved spectra indicate that decay lifetimes of the emission bands from the sensitizer/activator-isolated core-shell structure significantly vary from that of the sensitizer/activator-codoped NaYF4 UCNPs, verifying the strain-induced modulation of emission channels in the core-shell structure. These sensitizer-activator-isolated core-shell UCNPs have implications for a range of biophotonic or photonic applications.The ability to tune the emission color of upconversion nanoparticles (UCNPs) will greatly enhance the scope of their applications, ranging from infrared solar cells to volumetric multiplexed bioimaging. Conventional methods to tune upconversion are to vary the type and/or the concentration of doped rare-earth ions in these nanoparticle formulations. Here, we introduce a different approach to vary the emission colors of the frequently used sensitizer/activator pairs of Yb3+/RE3+ (RE = Ho, Er, Tm) via utilization of a sensitizer/activator-isolated NaYF4 core-shell structure. We show that the typical green, yellow, and blue luminescent colors from Yb3+/Ho3+-, Yb3+/Er

  15. Population genetic structure of Theileria parva field isolates from indigenous cattle populations of Uganda.

    PubMed

    Muwanika, Vincent; Kabi, Fredrick; Masembe, Charles

    2016-03-01

    Theileria parva causes East Coast Fever (ECF) a protozoan infection which manifests as a non-symptomatic syndrome among endemically stable indigenous cattle populations. Knowledge of the current genetic diversity and population structure of T. parva is critical for predicting pathogen evolutionary trends to inform development of effective control strategies. In this study the population genetic structure of 78 field isolates of T. parva from indigenous cattle (Ankole, n=41 and East African shorthorn Zebu (EASZ), n=37) sampled from the different agro ecological zones (AEZs) of Uganda was investigated. A total of eight mini- and micro-satellite markers encompassing the four chromosomes of T. parva were used to genotype the study field isolates. The genetic diversity of the surveyed T. parva populations was observed to range from 0.643±0.55 to 0.663±0.41 among the Central and Western AEZs respectively. The overall Wright's F index showed significant genetic variation between the surveyed T. parva populations based on the different AEZs and indigenous cattle breeds (FST=0.133, p<0.01) and (FST=0.101, p<0.01) respectively. Significant pairwise population genetic differentiations (p<0.05) were observed with FST values ranging from 0.048 to 0.173 between the eastern and northern, eastern and western populations respectively. The principal component analysis (PCA) showed a high level of genetic and geographic sub-structuring among populations. Linkage disequilibrium was observed when populations from all the study AEZs were treated as a single population and when analysed separately. On the overall, the significant genetic diversity and geographic sub-structuring exhibited among the study T. parva isolates has critical implications for ECF control. PMID:26613662

  16. Tuning upconversion through a sensitizer/activator-isolated NaYF₄ core/shell structure.

    PubMed

    Ye, Shuai; Chen, Guanying; Shao, Wei; Qu, Junle; Prasad, Paras N

    2015-03-01

    The ability to tune the emission color of upconversion nanoparticles (UCNPs) will greatly enhance the scope of their applications, ranging from infrared solar cells to volumetric multiplexed bioimaging. Conventional methods to tune upconversion are to vary the type and/or the concentration of doped rare-earth ions in these nanoparticle formulations. Here, we introduce a different approach to vary the emission colors of the frequently used sensitizer/activator pairs of Yb(3+)/RE(3+) (RE = Ho, Er, Tm) via utilization of a sensitizer/activator-isolated NaYF4 core-shell structure. We show that the typical green, yellow, and blue luminescent colors from Yb(3+)/Ho(3+)-, Yb(3+)/Er(3+)-, and Yb(3+)/Tm(3+)-co-doped NaYF4 UCNPs can be converted into the quasi-white, green, and pink blue, when corresponding core-shell structures of NaYF4:Yb(3+) @NaYF4:Ho(3+), NaYF4:Yb(3+) @NaYF4:Er(3+) and NaYF4:Yb(3+) @NaYF4:Tm(3+) are built. Time-resolved spectra indicate that decay lifetimes of the emission bands from the sensitizer/activator-isolated core-shell structure significantly vary from that of the sensitizer/activator-codoped NaYF4 UCNPs, verifying the strain-induced modulation of emission channels in the core-shell structure. These sensitizer-activator-isolated core-shell UCNPs have implications for a range of biophotonic or photonic applications.

  17. Isolation and structure of whiskey polyphenols produced by oxidation of oak wood ellagitannins.

    PubMed

    Fujieda, Miho; Tanaka, Takashi; Suwa, Yoshihide; Koshimizu, Seiichi; Kouno, Isao

    2008-08-27

    Three new phenolic compounds named whiskey tannins A and B and carboxyl ellagic acid were isolated from commercial Japanese whiskey, along with gallic acid, ellagic acid, brevifolin carboxylic acid, three galloyl glucoses, a galloyl ester of phenolic glucoside, 2,3-(S)-hexahydroxydiphenoylglucose, and castacrenin B. Whiskey tannins A and B were oxidation products of a major oak wood ellagitannin, castalagin, in which the pyrogallol ring at the glucose C-1 position of castalagin was oxidized to a cyclopentenone moiety. These tannins originated from ellagitannins contained in the oak wood used for barrel production; however, the original oak wood ellagitannins were not detected in the whiskey. To examine whether the whiskey tannins were produced during the charring process of barrel production, pyrolysis products of castalagin were investigated. Dehydrocastalagin and a new phenolcarboxylic acid trislactone having an isocoumarin structure were isolated, along with castacrenin F and ellagic acid. However, whiskey tannins were not detected in the products.

  18. Isolation and structure of whiskey polyphenols produced by oxidation of oak wood ellagitannins.

    PubMed

    Fujieda, Miho; Tanaka, Takashi; Suwa, Yoshihide; Koshimizu, Seiichi; Kouno, Isao

    2008-08-27

    Three new phenolic compounds named whiskey tannins A and B and carboxyl ellagic acid were isolated from commercial Japanese whiskey, along with gallic acid, ellagic acid, brevifolin carboxylic acid, three galloyl glucoses, a galloyl ester of phenolic glucoside, 2,3-(S)-hexahydroxydiphenoylglucose, and castacrenin B. Whiskey tannins A and B were oxidation products of a major oak wood ellagitannin, castalagin, in which the pyrogallol ring at the glucose C-1 position of castalagin was oxidized to a cyclopentenone moiety. These tannins originated from ellagitannins contained in the oak wood used for barrel production; however, the original oak wood ellagitannins were not detected in the whiskey. To examine whether the whiskey tannins were produced during the charring process of barrel production, pyrolysis products of castalagin were investigated. Dehydrocastalagin and a new phenolcarboxylic acid trislactone having an isocoumarin structure were isolated, along with castacrenin F and ellagic acid. However, whiskey tannins were not detected in the products. PMID:18672883

  19. Vibration isolation and reduction by spring-stiffness control based on theory of variable structure systems

    SciTech Connect

    Yamaguchi, H.; Shioya, S.; Oda, M.

    1995-12-31

    By controlling spring stiffness, vibration reduction and isolation for the mass-spring system are achieved in this paper. The control algorithm of the spring stiffness is based on the variable structure systems (VSS) theory. The stiffness-controllable spring is achieved by using two straight bars that are hinged to the mass in a line perpendicular to the direction of mass motion and are applied axial force. Since the axial force causes restoring force equivalent to the spring, the stiffness is controlled by the axial force. In the numerical simulations and experiments, the settling time of the impulse response and the displacement transmissibility are investigated. The results show that the proposed method is effective in suppressing shock motion and isolating vibration transmitted from the floor.

  20. Xylarenones C-E from an endophytic fungus isolated from Alibertia macrophylla.

    PubMed

    de Oliveira, Camila Martins; Silva, Geraldo Humberto; Regasini, Luis Octávio; Flausino, Otávio; López, Silvia Noelí; Abissi, Bárbara Marcondes; Berlinck, Roberto Gomes de Souza; Sette, Lara Durães; Bonugli-Santos, Rafaella Costa; Rodrigues, André; Bolzani, Vanderlan da Silva; Araujo, Angela Regina

    2011-06-24

    Xylarenones C-E (2-4), three new eremophilane sesquiterpenes, have been isolated from solid substrate cultures of a Camarops-like endophytic fungus isolated from Alibertia macrophylla. The structures were elucidated by analysis of spectroscopic data. Compounds were evaluated in subtilisin and pepsin protease assays, and compound 2 showed potent inhibitory activity against both proteases.