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Sample records for isolation structure elucidation

  1. Isolation and structural elucidation of cyclic tetrapeptides from Onychocola sclerotica.

    PubMed

    Pérez-Victoria, Ignacio; Martín, Jesús; González-Menéndez, Víctor; de Pedro, Nuria; El Aouad, Noureddine; Ortiz-López, Francisco Javier; Tormo, José Rubén; Platas, Gonzalo; Vicente, Francisca; Bills, Gerald F; Genilloud, Olga; Goetz, Michael A; Reyes, Fernando

    2012-06-22

    Three new cyclic tetrapeptides (1-3) have been isolated from the crude fermentation extract of Onychocola sclerotica. The planar structures of 1-3 were elucidated by detailed spectroscopic analyses using one- and two-dimensional NMR experiments and high-resolution mass spectrometry. The absolute configuration of the amino acid residues in each cyclotetrapeptide was established by Marfey's method. Compounds 1-3 displayed activity as cardiac calcium channel blockers (Cav1.2) but did not inhibit the hERG potassium channel and were not cytotoxic. These peptides are the first secondary metabolites ever reported from fungi of the order Arachnomycetales.

  2. Carotenoids from guava (Psidium guajava l.): isolation and structure elucidation.

    PubMed

    Mercadante, A Z; Steck, A; Pfander, H

    1999-01-01

    Sixteen carotenoids were isolated from the flesh of Brazilian red guavas (Psidium guajava L.). Their structures were established by means of UV-visible, 400 and 500 MHz (1)H NMR, 120 and 125 MHz (13)C NMR, mass, and circular dichroism spectra. The carotenoids were identified as phytofluene, (all-E)-, (9Z)-, (13Z)-, and (15Z)-beta-carotene, (all-E)-gamma-carotene, (all-E)-, (9Z)-, (13Z)-, and (15Z)-lycopene, (all-E,3R)-beta-cryptoxanthin, (all-E, 3R)-rubixanthin, (all-E,3S,5R,8S)-cryptoflavin, (all-E,3R,3'R, 6'R)-lutein, (all-E,3S,5R,6R,3'S,5'R,8'R)-, and (all-E,3S,5R,6R,3'S, 5'R,8'S)-neochrome. Thirteen of the carotenoids identified are reported as guava carotenoids for the first time.

  3. Compounds from Ageratum conyzoides: isolation, structural elucidation and insecticidal activity.

    PubMed

    Moreira, Márcio D; Picanço, Marcelo C; Barbosa, Luiz Cláudio A; Guedes, Raul Narciso C; Barros, Emerson C; Campos, Mateus R

    2007-06-01

    This work aimed at identifying plant compounds with insecticidal activity against Diaphania hyalinata (L.) (Lepidoptera: Pyralidae), Musca domestica (L.) (Diptera: Muscidae), Periplaneta americana (L.) (Blattodea: Blattidae) and Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae). The plant species used were: basil (Ocimum selloi Benth.), rue (Ruta graveolens L.), lion's ear (Leonotis nepetaefolia L.), Jimson weed (Datura stramonium L.), 'baleeira' herb (Cordia verbenaceae L.), mint (Mentha piperita L.), wild balsam apple (Mormodica charantia L.) and billy goat weed (Ageratum conyzoides L.). Firstly, the insecticidal activities of hexane and ethanol plant extracts were evaluated against adults of R. dominica. Among them, only the hexane extract of A. conyzoides showed insecticidal activity. The hexane extract of this plant species was therefore fractionated by silica gel column chromatography to isolate and purify its bioactive chemical constituents. Three compounds were identified using IR spectra, (1)H NMR, (13)C NMR, HMBC and NOE after gel chromatography: 5,6,7,8,3', 4', 5'-heptamethoxyflavone, 5,6,7,8,3'-pentamethoxy-4', 5'-methylenedioxyflavone and coumarin. The complete assignment of (13)C NMR to 5,6,7,8,3'-pentamethoxy-4', 5'-methylenedioxyflavone was successfully made for the first time. 5,6,7,8,3'-Pentamethoxy-4', 5'-methylenedioxyflavone did not show any insecticidal activity against the four insect species tested. 5,6,7,8,3', 4', 5'-Heptamethoxyflavone showed low activity against D. hyalinata and R. dominica and was not toxic to M. domestica or P. americana. In contrast, coumarin showed insecticidal activity against all four insect pest species tested, with the following order of susceptibility: R. dominica < P. americana < D. hyalinata < M. domestica after 24 h exposure. Copyright 2007 Society of Chemical Industry.

  4. 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"…

  5. 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"…

  6. Isolation and Structure Elucidation of Three New Dolastanes from the Brown Alga Dilophus spiralis

    PubMed Central

    Ioannou, Efstathia; Vagias, Constantinos; Roussis, Vassilios

    2013-01-01

    Three new dolastane diterpenes (1–3) and five previously reported perhydroazulenes were isolated from the organic extracts of the brown alga Dilophus spiralis. The structure elucidation and the assignment of the relative configurations of the isolated natural products were based on extensive analyses of their spectroscopic data, whereas the absolute configuration of metabolite 2 was determined through its chemical conversion to a previously isolated compound of known configuration. PMID:23549282

  7. 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…

  8. 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…

  9. Isolation and Structural Elucidation of Chondrosterins F–H from the Marine Fungus Chondrostereum sp

    PubMed Central

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

    2013-01-01

    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. PMID:23434797

  10. Isolation and structure elucidation of gymnemic acids, antisweet principles of Gymnema sylvestre.

    PubMed

    Liu, H M; Kiuchi, F; Tsuda, Y

    1992-06-01

    The structure of gymnemagenin (3 beta,16 beta,21 beta,22 alpha,23,28-hexahydroxy-olean-12-ene), the sapogenin of the antisweet principles of Gymnema sylvestre, was established by X-ray analysis of the 3 beta,23;21 beta,22 alpha-di-O-isopropylidene derivative. On the basis of this result, the structure of deacylgymnemic acid was elucidated as the 3-O-beta-glucuronide from the carbon-13 nuclear magnetic resonance spectra. Five antisweet principles, gymnemic acid-III, -IV, -V, -VIII, and -IX, were isolated in pure states from the hot water extract of leaves of Gymnema sylvestre. Of these, three (GA-III, -IV, and -V) were known, while two (GA-VIII and -IX) were new compounds. The structures of GA-VIII and -IX were elucidated as 3'-O-beta-D-arabino-2-hexulopyranosyl gymnemic acid-III and -IV, respectively.

  11. Isolation and structure elucidation of cytotoxic polyacetylenes and polyenes from Echinacea pallida.

    PubMed

    Pellati, Federica; Calò, Samuele; Benvenuti, Stefania; Adinolfi, Barbara; Nieri, Paola; Melegari, Michele

    2006-07-01

    Bioassay-guided fractionation of n-hexane extracts of Echinacea pallida (Asteraceae) roots led to the isolation and structure elucidation of two polyacetylenes (1, 3) and three polyenes (2, 4, 5). Two are known hydroxylated compounds, namely 8-hydroxy-pentadeca-(9E)-ene-11,13-diyn-2-one (1) and 8-hydroxy-pentadeca-(9E,13Z)-dien-11-yn-2-one (2). Two dicarbonylic constituents, namely pentadeca-(9E)-ene-11,13-diyne-2,8-dione (3) and pentadeca-(9E,13Z)-dien-11-yne-2,8-dione (4), were isolated and characterized for the first time. Furthermore, the structure elucidation of pentadeca-(8Z,13Z)-dien-11-yn-2-one (5) is described. The structure of the compounds isolated was determined on the basis of UV, IR, NMR (including 1D and 2D NMR experiments, such as 1H-1H gCOSY, gHSQC-DEPT, gHMBC, gNOESY) and MS spectroscopic data. The cytotoxic activity of the isolated constituents against MIA PaCa-2 human pancreatic adenocarcinoma cells was evaluated in the concentration range 1-100 microg/ml. Results show that the hydroxylated compounds (1, 2) have low cytotoxicity, while the more hydrophobic polyacetylenes (3) and polyenes (4, 5) displayed moderate activity.

  12. Plant antimutagenic agents, 4. Isolation and structure elucidation of maesol, an inactive constituent of Maesa spp.

    PubMed

    Wall, M E; Wani, M C; Gaetano, K; Manikumar, G; Taylor, H; McGivney, R

    1988-01-01

    Maesol, a novel dimeric phenol, was isolated from seeds of Maesa montana and Maesa indica. Maesol was shown to have the formula C28H42O4 with structure 1, a dimeric, symmetrical 1,12-bis(3,3'-dihydroxy-4,4'-dimethyl-5,5'-dimethoxyphenyl)dodecane. It is the first compound with such structure to be isolated from plant material. Structure elucidation was based largely on 1H- and 13C-nmr techniques and comparison with a known synthetic isomeric dimer 3. Although crude extracts showed strong inhibition of 2-aminoanthracene activity against Salmonella typhimurium (T-98), the pure compound was inactive when tested for inhibition of the mutagenic activity of several mutagens.

  13. Isolation, structure elucidation and biological activity of angucycline antibiotics from an epiphytic yew streptomycete.

    PubMed

    Maruna, Michal; Sturdikova, Maria; Liptaj, Tibor; Godany, Andrej; Muckova, Marta; Certik, Milan; Pronayova, Nadezda; Proksa, Bohumil

    2010-04-01

    In the course of study of epiphytic microorganisms occurring on the surface of roots of Taxus baccata L. a new strain Streptomyces sp. AC113 was isolated. According to 16S ribosomal DNA-based identification the new strain is 99% identical with Streptomyces flavidofuscus. This strain cultivated in an arginine glycerol medium produced three major metabolites identified as (-)-8-O -methyltetrangomycin (1), 8-O -methyltetrangulol (2) and 8-O -methyl-7-deoxo-7-hydroxytetrangomycin (3). The chemical structures of these angucyclines were elucidated by 1D and 2D NMR as well as by mass spectrometry. Isolated angucycline metabolites showed significant antimicrobial activity against Bacillus cereus and Listeria mocytogenes. Cytotoxic activities of compounds 1, 2 and 3 against four cell lines (B16, HT-29 and non - tumor V79, L929) were evaluated. Compound 3 was the most potent anticancer agents with IC(50) 0.054 microg/ml against cell line B16.

  14. 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.

  15. Methods for isolation, purification and structural elucidation of bioactive secondary metabolites from marine invertebrates.

    PubMed

    Ebada, Sherif S; Edrada, Ru Angelie; Lin, Wenhan; Proksch, Peter

    2008-01-01

    In the past few decades, marine natural products bioprospecting has yielded a considerable number of drug candidates. Two marine natural products have recently been admitted as new drugs: Prialt (also known as ziconotide) as a potent analgesic for severe chronic pain and Yondelis (known also as trabectedin or E-743) as antitumor agent for the treatment of advanced soft tissue sarcoma. In this protocol, methods for bioactivity-guided isolation, purification and identification of secondary metabolites from marine invertebrates such as sponges, tunicates, soft corals and crinoids are discussed. To achieve this goal, solvent extraction of usually freeze-dried sample of marine organisms is performed. Next, the extract obtained is fractionated by liquid-liquid partitioning followed by various chromatographic separation techniques including thin layer chromatography, vacuum liquid chromatography, column chromatography (CC) and preparative high-performance reversed-phase liquid chromatography. Isolation of bioactive secondary metabolites is usually monitored by bioactivity assays, e.g., antioxidant (2,2-diphenyl-1-picryl hydrazyl) and cytotoxicity (microculture tetrazolium) activities that ultimately yield the active principles. Special care should be taken when performing isolation procedures adapted to the physical and chemical characteristics of the compounds isolated, particularly their lipo- or hydrophilic characters. Examples of isolation of compounds of different polarities from extracts of various marine invertebrates will be presented in this protocol. Structure elucidation is achieved using recent spectroscopic techniques, especially 2D NMR and mass spectrometry analysis.

  16. 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

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

    PubMed

    Memon, Abdul Hakeem; Ismail, Zhari; Aisha, Abdalrahim F A; Al-Suede, Fouad Saleih Resq; Hamil, Mohammad Shahrul Ridzuan; Hashim, Suzana; Saeed, Mohammed Ali Ahmed; 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.

  18. 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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Isolation and structural elucidation of a new sildenafil analogue from a functional coffee.

    PubMed

    Li, Lin; Low, Min-Yong; Ge, Xiaowei; Bloodworth, Bosco C; Koh, Hwee-Ling

    2013-05-01

    A sildenafil analogue was detected in a functional coffee sample labelled to have male sexual performance enhancement effects. This analogue was isolated and purified by flash chromatography and preparative high-performance liquid chromatography. Its structure was elucidated using high-resolution mass spectrometry; electrospray ionization-tandem mass spectrometry; and nuclear magnetic resonance spectroscopy, ultraviolet spectroscopy, and infrared spectroscopy. Compared with sildenafil, instead of an N-methylpiperazinyl moiety, ring opening of the piperazine ring with the loss of a carbon atom resulted in a substituted benzenesulfonamide. The chemical name of this analogue is N-[2-(dimethylamino)ethyl]-4-ethoxy-3-(1-methyl-7-oxo-3-propyl-6,7-dihydro-1H-pyrazolo[4,3-d]pyrimidin-5-yl)benzenesulfonamide. It is named descarbonsildenafil because it has one less carbon atom when compared with sildenafil.

  20. Isolation and structural elucidation of two impurities from a diacerein bulk drug.

    PubMed

    Ashok, Chaudhari; Golak, Maikap; Adwait, Deo; Krishna, Vivek; Himani, Agrawal; Umesh, Peshawe; Amol, Gawande; Srinivas, Sompalli; Sharad, Mane; Deepali, Jadhav; Atul, Chaudhari

    2009-02-20

    Two impurities were found in the crude sample of diacerein. The level of these impurities 1.14% and 1.24% were detected by isocratic reverse-phase high performance liquid chromatography (HPLC). The molecular weights of the impurities were determined by liquid chromatography-mass spectroscopy (LC-MS) analysis. These impurities were isolated from crude sample of diacerein by reverse-phase preparative liquid chromatography. These impurities were characterized as 5-acetoxy-4-hydroxy-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid (Impurity-1) and 4-acetoxy-5-hydroxy-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid (Impurity-2) respectively. Structural elucidation of both the impurities were carried out by (1)H NMR, (13)C NMR, DEPT, 1D NOESY, MS and IR spectroscopy.

  1. 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

  2. Isolation and structure elucidation of new phthalide and phthalane derivatives, isolated as antimicrobial agents from Emericella sp. IFM57991.

    PubMed

    Saito, Tetsuya; Itabashi, Takeshi; Wakana, Daigo; Takeda, Hisashi; Yaguchi, Takashi; Kawai, Ken-ichi; Hosoe, Tomoo

    2016-02-01

    Three new phthalide derivatives, emefuranones A1, A2 and B (1-3); six new phthalane derivatives, emefuran A, B1, B2, C1, C2 and D (4-9); three new farnesylated phthalide derivatives, farnesylemefuranones A-C (10-12); xylarinol C (13); and emericelloxide (14), along with four known compounds (dustanin, sorbicillin, aspergillodiol and xylarinol A), were isolated from the culture extracts of Emericella sp. IFM57991. Structures of 1-14 were elucidated on the basis of spectroscopic analysis and chemical evidence. Compounds 4-7 and 13 showed moderate antibacterial activities against Bacillus subtilis.

  3. Isolation and Structural Elucidation of Euryjanicins B–D, Proline-Containing Cycloheptapeptides from the Caribbean Marine Sponge Prosuberites laughlini†

    PubMed Central

    Vera, Brunilda; Vicente, Jan; Rodríguez, Abimael D.

    2016-01-01

    Three new cyclic peptides, euryjanicins B (2), C (3), and D (4), have been isolated from the Puerto Rican marine sponge Prosuberites laughlini, and the structures were elucidated by chemical degradation, ESIMS/MS, and extensive 2D NMR methods. When tested against the National Cancer Institute 60 tumor cell line panel, all of the purified isolates displayed weak cytotoxicity. PMID:19743810

  4. Isolation and structural elucidation of cyclopentynafil and N-octylnortadalafil found in a dietary supplement.

    PubMed

    Hasegawa, Takashi; Takahashi, Kazunaga; Saijo, Masaaki; Ishii, Toshiyasu; Nagata, Tomoko; Kurihara, Masaaki; Haishima, Yuji; Goda, Yukihiro; Kawahara, Nobuo

    2009-02-01

    A new sildenafil analogue, cyclopentynafil (1) and a new tadalafil analogue, N-octylnortadalafil (2) were isolated from a dietary supplement illegally marketed for erectile dysfunction. The structures of the sildenafil and tadalafil analogues were elucidated by using HPLC-photodiode array (PDA), LC-MS, high-resolution MS, NMR and circular dichroism (CD). These compounds were determined to be 5-[2-ethoxy-5-(4-cyclopentylpiperazin-1-ylsulfonyl)phenyl]-1-methyl-3-propyl-1,6-dihydro-7H-pyrazolo[4,3-d]pyrimidin-7-one and (6R,12aR)-2-octyl-6-(1,3-benzodioxol-5-yl)-2,3,6,7,12,12a-hexahydropyrazino[1',2':1,6]pyrido[3,4-b]indole-1,4-dione, respectively. Recently, a large number of phosphodiesterase-5 (PDE-5) inhibitors, including their analogues, have been isolated from dietary supplements, while cyclopentynafil and N-octylnortadalafil are the first compounds reported to be new sildenafil and tadalafil analogues, respectively. Quantitative HPLC analysis showed that the contents of 1 and 2 in the product were about 130 mg/tablet (301 microg/mg) and about 27 mg/tablet (64.1 microg/mg), respectively.

  5. [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.

  6. Structure elucidation, DNA binding specificity and antiproliferative proficiency of isolated compounds from Garcinia nervosa.

    PubMed

    Parveen, Mehtab; Azaz, Shaista; Zafar, Atif; Ahmad, Faheem; Silva, Manuela Ramos; Silva, Pedro Sidonio Pereira

    2017-02-01

    Garcinia nervosa is an abundant source of bioactive phytochemicals. The present paper deals with the isolation of a novel isoflavone 5,7-dihydroxy-3-(3'-hydroxy-4',5'-dimethoxyphenyl)-6-methoxy-4H-chromen-4-one (1) along with a known compound DL-Allantoin (2) from the ethanolic extract of the leaves of Garcinia nervosa (Family: Guttiferae). 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. Single-crystal X-ray analysis was further used for the authentication of structure of both compounds (1 and 2). Interaction studies of compound (1) and (2) with ctDNA were studied by UV-Visible spectroscopy, fluorescence, KI quenching studies, competitive displacement assay and circular dichroism studies, which showed groove binding interaction (non-intercalation) of both the compounds 1 and 2 with ctDNA. However, compound 1 (K=3.9×10(4)M(-1)) shows higher binding affinity to the ctDNA than compound 2 (K=1.44×10(4)M(-1)). The molecular modeling results also illustrated that compound 1 strongly binds to groove of DNA by relative binding energy of docked structure -6.82kcal/mol. In addition the antiproliferative activity also showed high potential of compound 1 against MCF-7 and MDA-MB 231 cell line with IC50 value 8.44±3.5μM and 6.94±2.6μM, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. 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…

  8. 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…

  9. Isolation and structural elucidation of a novel rotenoid from the seeds of Clitoria fairchildiana.

    PubMed

    Mathias, Leda; Da Silva, Bernadete Pereira; Mors, Walter Baptist; Parente, José Paz

    2005-06-01

    The seeds of Clitoria fairchildiana provided a new rotenoid, 6-hydroxy-2,3,9-trimethoxy-[1]benzopyrano[3,4-b][1]benzopyran-12(6H)-one. The structural elucidation was performed using detailed analyses of H- and 13C-NMR spectra including 2DNMR spectroscopic techniques (1H-13CHETCOR) and by comparison with spectrometric data from the literature. The anti-inflammatory activity was investigated using a capillary permeability assay.

  10. Isolation and extraction of lucidin primeveroside from Rubia tinctorum L. and crystal structure elucidation.

    PubMed

    Henderson, Robert L; Rayner, Christopher M; Blackburn, Richard S

    2013-11-01

    Madder (Rubia tinctorum L.) has been used as a dye for over 2000 years with alizarin and purpurin the major natural dyes analysed from extractions undertaken. The use of ethanol as the solvent in the extraction process produced an extract that yielded four anthraquinone compounds lucidin primeveroside, ruberythric acid, alizarin and lucidin-ω-ethyl ether. Gravitational separation of the extract was used to record the first crystal structure of lucidin primeveroside, which is also the first ever known crystal structure of a glycoside containing anthraquinone moiety. The crystal structure along with (1)H and (13)C NMR helped elucidate and confirm the structure of this overlooked natural dye which has been shown to be a major compound in R. tinctorum L.

  11. Isolation and structure elucidation of radical scavengers from Thymus vulgaris leaves.

    PubMed

    Dapkevicius, Airidas; van Beek, Teris A; Lelyveld, Gerrit P; van Veldhuizen, Albertus; de Groot, Aede; Linssen, Jozef P H; Venskutonis, Rimantas

    2002-06-01

    2,2-Diphenyl-1-picrylhydrazyl radical (DPPH*) scavenging activity-guided fractionation of a leaf extract of Thymus vulgaris led to the isolation of the radical scavengers rosmarinic acid 1, eriodictyol, taxifolin, luteolin 7-glucuronide, p-cymene 2,3-diol, p-cymene 2,3-diol 6-6'-dimer, carvacrol, thymol, and a new compound, 2. The fractionation was considerably facilitated by using an on-line HPLC detector for radical scavenging activity. In this detector activity is monitored as the disappearance of the color of a postcolumn added stable radical after reacting with radical scavengers in a reaction coil. Compound 2, which consists of rosmarinic and caffeic acid moieties linked via a C-3'-C-8' ' ether bridge, was mainly elucidated by various NMR techniques and CD. Phenylpropanoid trimer 2 was a weaker and stronger radical scavenger than rosmarinic acid 1 in off-line TEAC and DPPH* assays, respectively.

  12. Isolation and structure elucidation of procyanidin oligomers from Saskatoon berries (Amelanchier alnifolia).

    PubMed

    Hellström, Jarkko; Sinkkonen, Jari; Karonen, Maarit; Mattila, Pirjo

    2007-01-10

    Proanthocyanidin oligomers with different degrees of polymerization were isolated from Saskatoon berries (Amelanchier alnifolia) by means of gel adsorption and normal-phase liquid chromatography. The proanthocyanidins were identified using electrospray ionization mass spectrometry, nuclear magnetic resonance spectroscopy, and thiolytic degradation coupled with reversed-phase liquid chromatography. The results established that Saskatoon berries contain proanthocyanidins from dimers through heptamers and higher polymers. Saskatoon proanthocyanidins are essentially of procyanidin type, consisting mainly of epicatechin units linked by B-type bonds. The simple procyanidin profile of Saskatoon berries allowed the procyanidins to be separated precisely according to their degrees of polymerization. In the future they can be used as standard compounds for qualitative and quantitative analysis of procyanidins as well as for elucidation of the biological activities of proanthocyanidins.

  13. Tauramamide, a lipopeptide antibiotic produced in culture by Brevibacillus laterosporus isolated from a marine habitat: structure elucidation and synthesis.

    PubMed

    Desjardine, Kelsey; Pereira, Alban; Wright, Helen; Matainaho, Teatulohi; Kelly, Michael; Andersen, Raymond J

    2007-12-01

    Tauramamide (1), a new lipopeptide antibiotic, is produced by cultures of the marine bacterial isolate Brevibacillus laterosporus PNG276 obtained from Papua New Guinea. Tauramamide was isolated as its methyl and ethyl esters 2 and 3, whose structures were elucidated by analysis of NMR, MS, and chemical degradation data. A total synthesis of tauramamide (1) and tauramamide ethyl ester (3) confirmed the structure proposed from spectroscopic analysis and provided the natural product for antimicrobial testing. Tauramamide (1) and ethyl ester 3 show potent and relatively selective inhibition of pathogenic Enterococcus sp.

  14. Isolation and structural elucidation of chemical constituents from the fruits of Morinda citrifolia Linn.

    PubMed

    Siddiqui, Bina S; Sattar, Fouzia A; Ahmad, Fayaz; Begum, Sabira

    2007-08-01

    The fruits of Morinda citrifolia, Linn. afforded a new constituent, morinaphthalenone (1), and three known constituents, scopoletin (2), 1, 3-dimethoxy-anthraquinone (3) and 1, 2-dihydroxy-anthraquinone (4). The structures of these isolated compounds were determined by spectroscopic methods, including 1D- and 2D-NMR (COSY-45, HMQC, HMBC) techniques, as well as by comparison with published values.

  15. Isolation, identification and structure elucidation of two novel process-related impurities of retigabine.

    PubMed

    Zhang, Dengfeng; Song, Xin; Su, Jiangtao

    2014-10-01

    Retigabine was the first neuronal potassium channel opener for the treatment of epilepsy. During the manufacture of retigabine, two unknown impurities were present in laboratory batches in the range of 0.05-0.1% based upon HPLC analysis. These unknown impurities were obtained from the enriched reaction mother liquor by column chromatography. The structure of these process-related impurities were elucidated using FT-IR, (1)H NMR, (13)C NMR, 2D NMR (HSQC, HMBC, NOESY) and MS spectral data. Based on the complete spectral analysis and knowledge of the synthetic route of retigabine, these two new impurities were designated as ethyl 4-fluorobenzyl(2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)carbamate (impurity-II) and diethyl 5-((ethoxycarbonyl)(4-fluorobenzyl)amino)-2-oxo-1H-benzo[d]imidazole-1,3(2H)-dicarboxylate (impurity-III). Impurity identification, structure elucidation and the formation of impurities were also discussed.

  16. 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.

  17. Structure elucidation and antioxidant activity of (-)-isosilandrin isolated from Silybum marianum L.

    PubMed

    Samu, Zsuzsanna; Nyiredy, Szabolcs; Baitz-Gács, Eszter; Varga, Zsuzsa; Kurtán, Tibor; Dinya, Zoltán; Antus, Sándor

    2004-11-01

    A regioisomer of the known flavanolignan (-)-silandrin (3a), named (-)-isosilandrin (8a), was isolated from the fruits of a white-flowered variant of Silybum marianum L. populated in Hungary. Its structure was established both by spectroscopic methods and total synthesis, and its absolute configuration was determined by means of circular dichroism. This compound showed stronger inhibitory activity on the superoxide anion (O2*-) release by human polymorphonuclear leukocytes (PMNL) than (+)-silybin (1a,b).

  18. Isolation and structure elucidation of a new prenylcoumarin from Murraya paniculata var. omphalocarpa (Rutaceae).

    PubMed

    Kinoshita, Takeshi; Shimada, Motoko

    2002-01-01

    A new C-8 prenylated 5,7-dimethoxycoumarin named omphamurrayin was isolated from the leaves of Murraya paniculata var. omphalocarpa, and its structure was established as 5,7-dimethoxy-8-(1-oxo-2-senecioyl-3-methyl-3-butenyl)-2H-1-benzopyran-2-one on the basis of the spectroscopic evidence. The taxonomic status of M. paniculata var. omphalocarpa is briefly discussed, along with its synonymity to M. paniculata from the chemosystematic viewpoint.

  19. Novel Isochroman Dimers from Stachybotrys sp. PH30583: Fermentation, Isolation, Structural Elucidation and Biological Activities.

    PubMed

    Li, Wei; Yang, Ya-Bin; Yang, Xue-Qiong; Xie, Hui-Ding; Shao, Zhi-Hui; Zhou, Hao; Miao, Cui-Ping; Zhao, Li-Xing; Ding, Zhong-Tao

    2017-05-01

    The rare anishidiol and five new isochromans, including three novel dimers with unprecedented skeletons, were isolated from Stachybotrys sp. PH30583. Their structures were determined by spectral analyses. The bioactivities of these compounds were also investigated. The dimers (6-10) inhibited acetylcholinesterase at 50 µM, but the monomers did not. To investigate the biogenesis of the novel dimers, a time-course investigation of metabolite production was undertaken. Georg Thieme Verlag KG Stuttgart · New York.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. Phytochemicals of apple peels: isolation, structure elucidation, and their antiproliferative and antioxidant activities.

    PubMed

    He, Xiangjiu; Liu, Rui Hai

    2008-11-12

    Bioactivity-guided fractionation of Red Delicious apple peels was used to determine the chemical identity of bioactive constituents, which showed potent antiproliferative and antioxidant activities. Twenty-nine compounds, including triterpenoids, flavonoids, organic acids and plant sterols, were isolated using gradient solvent fractionation, Diaion HP-20, silica gel, and ODS columns, and preparative HPLC. Their chemical structures were identified using HR-MS and 1D and 2D NMR. Antiproliferative activities of isolated pure compounds against HepG2 human liver cancer cells and MCF-7 human breast cancer cells were evaluated. On the basis of the yields of isolated flavonoids (compounds 18- 23), the major flavonoids in apple peels are quercetin-3-O-beta-D-glucopyranoside (compound 20, 82.6%), then quercetin-3-O-beta-D-galactopyranoside (compound 19, 17.1%), followed by trace amounts of quercetin (compound 18, 0.2%), (-)-catechin (compound 22), (-)-epicatechin (compound 23), and quercetin-3-O-alpha-L-arabinofuranoside (compound 21). Among the compounds isolated, quercetin (18) and quercetin-3-O-beta-D-glucopyranoside (20) showed potent antiproliferative activities against HepG2 and MCF-7 cells, with EC 50 values of 40.9 +/- 1.1 and 49.2 +/- 4.9 microM to HepG2 cells and 137.5 +/- 2.6 and 23.9 +/- 3.9 microM to MCF-7 cells, respectively. Six flavonoids (18-23) and three phenolic compounds (10, 11, and 14) showed potent antioxidant activities. Caffeic acid (10), quercetin (18), and quercetin-3-O-beta-D-arabinofuranoside (21) showed higher antioxidant activity, with EC 50 values of <10 microM. Most tested flavonoids and phenolic compounds had high antioxidant activity when compared to ascorbic acid and might be responsible for the antioxidant activities of apples. These results showed apple peel phytochemicals have potent antioxidant and antiproliferative activities.

  5. 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

  6. Eclipta prostrata L. phytochemicals: isolation, structure elucidation, and their antitumor activity.

    PubMed

    Liu, Qi-Mei; Zhao, Hai-Yan; Zhong, Xian-Ke; Jiang, Jian-Guo

    2012-11-01

    Eclipta prostrata L., (Asteraceae), is used in China for both food and medicine purposes. This research is concerned with the isolation and purification of phytochemical constituents from the aerial parts of E. prostrata, using gradient solvent fractionation, macroporous resin, silica gel, Sephadex LH-20 and ODS columns, and TLC analyses. Four fractions (water, 30% ethanol, 60% ethanol and 90% ethanol) were obtained. Four compounds, wedelolactone (I), eclalbasaponin I (II), luteolin (III) and luteolin-7-O-glucoside (IV) were purified and their structures were identified by the interpretation of spectroscopic analyses including MS, (1)H and (13)C NMR. Antitumor activities of extracts (total fraction), four fractions and the isolated compounds were assessed using hepatoma cell smmc-7721 as an in vitro assay system. The 30% ethanol fraction and eclalbasaponin I dose-dependently inhibited the proliferation of hepatoma cell smmc-7721 with IC(50) values of 74.2399 and 111.1703 μg/ml, respectively, more strongly compared with 5-fluorouracil positive control group with the IC(50) value of 195.3131 μg/ml. Antitumor activities of other fractions and compounds were lower than positive control. These results suggested that some specific compounds or extracts from E. prostrata are potential sources of natural anti-tumor materials and worthy of further study. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Isolation and structure elucidation of new radical oxidation products of 5-hydroxy steroids.

    PubMed

    Khripach, Vladimir A; Zhabinskii, Vladimir N; Kuchto, Anna I; Zhiburtovich, Yuliya Y; Lyakhov, Alexander S; Govorova, Alla A; Groen, Marinus B; van der Louw, Jaap; de Groot, Aede

    2006-06-01

    Three new products have been isolated from the lead-tetraacetate version of the hypoiodite oxidation of 3beta,17beta-diacetoxy-5-hydroxy-5 alpha-androstane. Along with the expected 1(10)-unsaturated 5,10-seco steroidal 5-ketones, the fragmentation reaction gave two epimeric C-4 iodides. Their structural assignment was based on X-ray data of one of them ((4R,10S)-4-iodo-3beta,17beta-diacetoxy-5,10-secoandrostan-5-one). The third new product was found to be the 5 beta,6 beta-epoxide resulting from the dehydration of the tertiary alcohol followed by epoxidation of the intermediate Delta(5)-olefin.

  8. 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

  9. Structural elucidation of an immunoenhancing heteroglycan isolated from Russula albonigra (Krombh.) Fr.

    PubMed

    Nandi, Ashis K; Samanta, Surajit; Sen, Ipsita K; Devi, K Sanjana P; Maiti, Tapas K; Acharya, Krishnendu; Islam, Syed S

    2013-05-15

    A water soluble heteroglycan (PS-II) of average molecular weight ∼1.45 × 10(5)Da was isolated from the aqueous extract of an ectomycorrhizal edible mushroom, Russula albonigra (Krombh.) Fr. Structural characterization of PS-II was carried out using acid hydrolysis, methylation analysis, periodate oxidation, and 1D/2D NMR studies. Structural analysis revealed that PS-II was composed of terminal 2-O-methyl-Fucp, terminal Manp, (1→2)-Fucp, (1→3)-Glcp, (1→3,4)-Glcp, (1→6)-Galp, and (1→2,6)-Galp residues in a relative proportion of approximately 1:1:1:1:1:1:1. The proposed repeating unit of the PS-II had a backbone consisting of two (1→3)-β-d-glucopyranosyl, two (1→6)-α-d-galactopyranosyl, and one (1→2)-α-l-fucopyranosyl residues, out of which one (1→3)-β-d-glucopyranosyl residue was branched at O-4 position with terminal 2-O-methyl-α-l-fucopyranosyl and one (1→6)-α-d-galactopyranosyl residue was branched at O-2 position with terminal α-d-mannopyranosyl residue. This PS-II showed in vitro macrophage activation by NO production as well as splenocytes and thymocytes proliferation.

  10. Isolation, structural elucidation and immunomodulatory activity of fructans from aged garlic extract.

    PubMed

    Chandrashekar, Puthanapura M; Prashanth, Keelara V Harish; Venkatesh, Yeldur P

    2011-02-01

    Traditionally, garlic (Allium sativum) is known to be a significant immune booster. Aged garlic extract (AGE) possesses superior immunomodulatory effects than raw garlic; these effects are attributed to the transformed organosulfur compounds. AGE is also known to contain fructans; the amount of fructans in AGE represents a small fraction (0.22%) of the total fructans in raw garlic. In order to evaluate the biological activity of fructans present in AGE, both high molecular weight (>3.5 kDa; HF) and low molecular weight (<3 kDa; LF) fructans were isolated. The structures of purified HF and LF from AGE determined by (1)H NMR and (13)C NMR spectroscopy revealed that both have (2→1) β-D-fructofuranosyl bonds linked to a terminal glucose at the non-reducing end and β-D-fructofuranosyl branching on its backbone. Biological activity of fructans was assessed by immunostimulatory activity using murine lymphocytes and peritoneal exudate cells (source of macrophages). Both HF and LF displayed mitogenic activity and activation of macrophages including phagocytosis. These activities were comparable to that of known polysaccharide immunomodulators such as zymosan and mannan. This study clearly demonstrates that garlic fructans also contribute to the immunomodulatory properties of AGE, and is the first such study on the biological effects of garlic fructans.

  11. 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.

  12. Structural elucidation and immunostimulatory activity of polysaccharide isolated by subcritical water extraction from Cordyceps militaris.

    PubMed

    Luo, Xiaoping; Duan, Yuqing; Yang, Wenya; Zhang, Haihui; Li, Changzheng; Zhang, Jixian

    2017-02-10

    Water-soluble polysaccharides were obtained from Cordyceps militaris (C. militaris) (CMP) by subcritical water extraction (SWE). Two polysaccharides fractions, CMP-W1 and CMP-S1, were isolated from CMP using DEAE-52 cellulose and Sephadex G-150 column chromatography. The structural characteristics of CMP-W1 and CMP-S1 were investigated. The results showed that the molecular weight of CMP-W1 and CMP-S1 are 3.66×105Da and 4.60×105Da, respectively, and both of them were heteropolysaccharides composed of d-mannose, d-glucose, d-galactose with the molar ratios of 2.84:1:1.29 and 2.05:1:1.09, respectively. FT-IR spectra analysis suggested that CMP-W1 and CMP-S1 belonged to pyranose form sugar and protein free. For immunostimulatory activity assay in vitro, CMP-W1 and CMP-S1 significantly promoted lymphatic spleen cell proliferation of mice. Therefore, the polysaccharides obtained from C. militaris by SWE can be used as potential natural immunostimulant in functional foods or medicine.

  13. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. 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.

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

    USDA-ARS?s Scientific Manuscript database

    Three new compounds, 5-methyldihydromyricetin (1), 5-methyldihydromyricetin-3'-O-sulfate (2) and ß-D-glucopyranoside, 3-methyl, but-3-en-1-yl 4-O-a-L-rhamnopyranosyl (3) have been isolated from the Limonium caspium, together with dihydromyricetin (4), dihydromyricetin-3'-O-sulfate (5), myricetin-3'-...

  16. 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…

  17. Isolation and structure elucidation of bioactive compounds from the roots of the Tunisian Ononis angustissima L.

    PubMed

    Ghribi, Lotfi; Waffo-Téguo, Pierre; Cluzet, Stéphanie; Marchal, Axel; Marques, Jessica; Mérillon, Jean-Michel; Ben Jannet, Hichem

    2015-09-15

    A phytochemical investigation of the roots of Ononis angustissima L. (Fabaceae) offered to the bio-guided isolation of new isoflavone 3-(4-(glucopyranosyloxy)-5-hydroxy-2-methoxyphenyl)-7-hydroxy-4H-chromen-4-one 1, together with nine known compounds, ononin 2, formononetin 3, (+)-puerol A-2'-O-β-D-glucose 4, (-)-puerol B-2'-O-β-D-glucopyranose ((-)-sophoraside A) 5, (+)-puerol A 6, (-)-trifolirhizin 7, (-)-trifolirhizin-6'-O-malonate 8, (-)-maackiain 9 and (-)-medicarpin 10. Compounds 2-10 were isolated and identified for the first time in Ononis angustissima. We investigated antioxidant capacities of isolated molecules and results showed that compound 6 exhibited the highest antioxidant activity with IC50 values of 19.53 μg/mL, 28.29 μg/mL and 38.53 μg/mL by DPPH radical, ABTS radical cation and reducing power assay, respectively, and an interesting IC50 (20.45 μg/mL) of 1 against DPPH. In addition, the neuroprotective activity of six isolated molecules (4-7, 9, 10) were evaluated. Following the exposure of PC12 cells to Aβ25-35, compounds 9 and 10 triggered a significant increase of cell viability and in a dose dependent manner.

  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. Suppressors of cancer cell proliferation from fig (Ficus carica) resin: isolation and structure elucidation.

    PubMed

    Rubnov, S; Kashman, Y; Rabinowitz, R; Schlesinger, M; Mechoulam, R

    2001-07-01

    A mixture of 6-O-acyl-beta-D-glucosyl-beta-sitosterols, the acyl moeity being primarily palmitoyl and linoleyl with minor amounts of stearyl and oleyl, has been isolated as a potent cytotoxic agent from fig (Ficuscarica) latex and soybeans. Identity was established by spectroscopic methods (NMR, MS) and confirmed by chemical synthesis. Both the natural and the synthetic compounds showed in vitro inhibitory effects on proliferation of various cancer cell lines.

  20. Isolation of a Paenibacillus sp. Strain and Structural Elucidation of Its Broad-Spectrum Lipopeptide Antibiotic

    PubMed Central

    Guo, Yaoqi; Huang, En; Yuan, Chunhua; Zhang, Liwen

    2012-01-01

    This research was initiated to search for novel antimicrobial compounds produced by food or environmental microorganisms. A new bacterial strain, designated OSY-SE, which produces a unique and potent antimicrobial agent was isolated from soil. The isolate was identified as a Paenibacillus sp. through cultural, biochemical, and genetic analyses. An antimicrobial compound was extracted from Paenibacillus OSY-SE with acetonitrile and purified using liquid chromatography. After analyses by mass spectrometry (MS) and nuclear magnetic resonance (NMR), the antimicrobial compound was determined to be a cyclic lipopeptide consisting of a C15 fatty acyl (FA) chain and 13 amino acids. The deduced sequence is FA-Orn-Val-Thr-Orn-Ser-Val-Lys-Ser-Ile-Pro-Val-Lys-Ile. The carboxyl-terminal Ile is connected to Thr by ester linkage. The new compound, designated paenibacterin, showed antagonistic activities against most Gram-positive and Gram-negative bacteria tested, including Listeria monocytogenes, methicillin-resistant Staphylococcus aureus, Escherichia coli O157:H7, and Salmonella enterica serovar Typhimurium. Paenibacterin is resistant to trypsin, lipase, α-glucosidase, and lysozyme. Its antimicrobial activity was lost after digestion by pronase and polymyxin acylase. Paenibacterin is readily soluble in water and fairly stable to exposure to heat and a wide range of pH values. The new isolate and its antimicrobial agent are being investigated for usefulness in food and medical applications. PMID:22367082

  1. Novel bioactive maloyl glucans from aloe vera gel: isolation, structure elucidation and in vitro bioassays.

    PubMed

    Esua, Macniell F; Rauwald, Johann-Wilhelm

    2006-02-27

    In this study, three novel maloyl glucans were isolated at temperatures below 15 degrees C from aloe vera gel (Aloe barbadensis Miller). These compounds were characterized using NMR spectroscopy, ESIMS, MALDITOF-MS and capillary electrophoresis. The compounds were characterized as 6-O-(1-L-maloyl)-alpha-,beta-D-Glcp (veracylglucan A), alpha-D-Glcp-(1-->4)-6-O-(1-L-maloyl)-alpha,-beta,-D-Glcp (veracylglucan B) and alpha-D-Glcp-(1-->4)-tetra-[6-O-(1-L-maloyl)-alpha-D-Glcp-(1-->4)]-6-O-(1-L-maloyl)-alpha,-beta-D-Glcp (veracylglucan C). These unusual malic acid acylated carbohydrates were then tested in vitro for effects on cell proliferation and gene expression of proinflammatory cytokines, IL-6, IL-8 and ICAM-1, using RT-PCR. Veracylglucan B demonstrated potent anti-inflammatory and anti-proliferative effects, while Veracylglucan C, on the other hand, exhibited significant cell proliferative and anti-inflammatory activities. Veracylglucan A could only be isolated in smaller quantities, and it proved to be very unstable. Thus no biological effects could be observed in this respect. The in vitro bioassays also indicated that Veracylglucan B and C are antagonistic and competitive in their effects on cell proliferation. The results of this work represent a major step forward in the research on aloe vera gel. This is the first time that two fully chemically characterized compounds are shown to be responsible for known biological activities of aloe vera gel.

  2. Isolation, Structure Elucidation, and (Bio)Synthesis of Haprolid, a Cell-Type-Specific Myxobacterial Cytotoxin.

    PubMed

    Steinmetz, Heinrich; Li, Jun; Fu, Chengzhang; Zaburannyi, Nestor; Kunze, Birgitte; Harmrolfs, Kirsten; Schmitt, Viktoria; Herrmann, Jennifer; Reichenbach, Hans; Höfle, Gerhard; Kalesse, Markus; Müller, Rolf

    2016-08-16

    Myxobacteria are well-established sources for novel natural products exhibiting intriguing bioactivities. We here report on haprolid (1) isolated from Byssovorax cruenta Har1. The compound exhibits an unprecedented macrolactone comprising four modified amino acids and a polyketide fragment. As configurational assignment proved difficult, a bioinformatic analysis of the biosynthetic gene cluster was chosen to predict the configuration of each stereocenter. In-depth analysis of the corresponding biosynthetic proteins established a hybrid polyketide synthase/nonribosomal peptide synthetase origin of haprolid and allowed for stereochemical assignments. A subsequent total synthesis yielded haprolid and corroborated all predictions made. Intriguingly, haprolid showed cytotoxicity against several cell lines in the nanomolar range whereas other cells were almost unaffected by treatment with the compound. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Structure Elucidation, Antimicrobial and Cytotoxic Activities of a Halimane Isolated from Vellozia kolbekii Alves (Velloziaceae).

    PubMed

    Silva, Carmelita G; Santos Júnior, Helvécio M; Barbosa, Jussara P; Costa, Gisela L; Rodrigues, Felipe A R; Oliveira, Denilson F; Costa-Lotufo, Letícia V; Alves, Ruy J V; Eleutherio, Elis C A; Rezende, Claudia M

    2015-12-01

    A new halimane diterpene was isolated from Vellozia kolbekii Alves (Velloziaceae) and identified as (5R,8R,9S,13R)-halim-1,10-ene-15,16-diol (1). It showed cytotoxicity against three human cancer cell lines, SF-295 (glioblastoma), MDA-MB-435 (melanoma), and HCT-8 (colon adenocarcinoma). In the mechanism of cytotoxic action, halimane 1 interferes in two major phases of the cell cycle: in S phase, in which DNA synthesis occurs and where it is very sensitive to damage, and G2M phase which is the phase of preparation for mitosis and mitosis itself, showing apoptosis-inducing properties. Antimicrobial activity towards Gram-positive and Gram-negative bacteria was studied and, against Bacillus cereus, B. subtilis, Escherichia coli, and Pseudomonas aeruginosa, a MIC value of 0.025 μM was observed for halimane 1, which is more active than the positive control chloramphenicol.

  4. 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.

  5. Characterization and structure elucidation of antibacterial compound of Streptomyces sp. ECR77 isolated from east coast of India.

    PubMed

    Thirumurugan, D; Vijayakumar, R

    2015-05-01

    Forty marine actinobacteria were isolated from the sediments of east coast (Bay of Bengal) region of Tamilnadu, India. Morphologically distinct colonies were primarily tested against fish pathogenic bacteria such as Vibrio cholerae, V. parahaemolyticus, V. alginolyticus, Pseudomonas fluorescens and Aeromonas hydrophila by cross-streak plate method. The secondary metabolites produced by the highly potential strain cultured on starch casein broth were extracted separately with various solvents such as alcohol, ethyl acetate, methanol, petroleum ether and chloroform. The antibacterial assay of the bioactive compounds was tested against the fish pathogenic bacteria by well diffusion method. Of the various solvents used, the ethyl acetate extract of the isolate had good antibacterial activity. The potential strain was identified as Streptomyces labedae by phenotypic, 16S rRNA gene sequence and phylogenetic analysis. Purification of the biologically active compounds by column chromatography led to isolation of 27 fractions. The biologically active fraction was re-chromatographed on a silica gel column to obtain a single active compound, namely N-isopentyltridecanamide. The structure of the compounds was elucidated on the basis of ultra violet, Fourier transform infrared and nuclear magnetic resonance spectra.

  6. 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

  7. 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.

  8. Electrochemical oxidation of xanthosine. Isolation and structure elucidation of a new dimeric xanthine nucleoside

    SciTech Connect

    Xinhua Ji; Subramanian, P.; van der Helm, D.; Dryhurst, G. )

    1990-02-16

    Electrochemical oxidation of xanthosine (2) at pH 2 at a pyrolytic graphite electrode generates an electrophilic radical cation intermediate. Nucleophilic attack by 2 on this radical results, ultimately, in formation of 3-(8-xanthosyl)xanthosine (7). Hydrolytic cleavage of one ribose residue from 7 in acidic solution leads to 3-(8-xanthosyl)xanthine (8). The structure of 8, a new dimeric xanthine nucleoside, has been established using spectral and X-ray diffraction methods.

  9. 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

  10. Isolation and structural elucidation of biologically active phospholipids from Scytonema julianum (cyanobacteria).

    PubMed Central

    Antonopoulou, Smaragdi; Oikonomou, Alexandra; Karantonis, Haralabos C; Fragopoulou, Elizabeth; Pantazidou, Adriani

    2002-01-01

    The role of platelet-activating factor (PAF) as a mediator appeared in rather primitive organisms like protozoans and was maintained in more evolved organisms. No reports exist for the presence of PAF or PAF analogues - or even compounds that exhibit PAF-like activity - in cyanobacteria, even though they belong to a a group of organisms at a low evolutionary level where the content of alkylacyl forms of ether lipids is expected to be high. In addition, cyanobacteria serve as a rich source of novel bioactive metabolites. In the present study the total lipids of a strain of Scytonema julianum, a filamentous cyanobacterium isolated from a Greek cave, were separated into neutral lipids and phospholipids, the latter being further fractionated by HPLC. Each phospholipid fraction was tested in vitro for its ability to inhibit PAF-, arachidonic acid- and ADP-induced washed-rabbit-platelet aggregation and/or to cause platelet aggregation. Two types of phospholipids causing platelet aggregation were detected and shown to be an acetylsphingomyelin and an acylacetylglycerol phosphoacetylated glycolipid. The existence of the sphingomyelin analogues is very important, since ceramides, cerebrosides and related lipids are intracellular second messengers. The identification of the phosphoglycoglycerolipid demonstrates a new type of lipid in cyanobacteria, namely one that exhibits a biological activity very similar to that of PAF. Its presence reinforces the concept that PAF is a member of a large family of lipid mediators, apparently having different physiological roles in prokaryotic and eukaryotic organisms. In addition, Scytonema julianum contains a phosphatidylcholine (C(16:0)/(18:2)), even though bacteria in general seldom contain choline-containing phosphoacylglycerols. PMID:12038967

  11. 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

    2014-12-17

    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.

  12. 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.

  13. Isolation, Structural Elucidation, and Synthesis of Lepteridine From Ma̅nuka (Leptospermum scoparium) Honey.

    PubMed

    Daniels, Benjamin J; Prijic, Gordana; Meidinger, Sarah; Loomes, Kerry M; Stephens, Jonathan M; Schlothauer, Ralf C; Furkert, Daniel P; Brimble, Margaret A

    2016-06-22

    Ma̅nuka honey, made from the nectar of Leptospermum scoparium, has garnered scientific and economical interest due to its nonperoxide antibacterial activity. Biomarkers for genuine ma̅nuka honey are increasingly in demand due to the presence of counterfeit ma̅nuka honey. This work reports the identification of a compound previously unreported in ma̅nuka honey by HPLC, and determination of the structure of the as 3,6,7-trimethyllumazine using NMR, MS, IR, and UV/vis spectroscopy. This assignment was confirmed by total synthesis. The natural product, renamed lepteridine, was only observed in ma̅nuka honeys and could potentially serve as a biomarker for genuine ma̅nuka honey.

  14. 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.

  15. Structure Elucidation of a Natural Product.

    ERIC Educational Resources Information Center

    Letcher, Roy M.

    1983-01-01

    Describes an experiment simulating a real-life structure elucidation problem through isolation, characterization, and chemical transformation of an "unknown," naturally occurring monoterpene, with extensive use being made of spectroscopy and aided by biogenetic considerations. Information given to students, procedures, results, and discussion of…

  16. Structure Elucidation of a Natural Product.

    ERIC Educational Resources Information Center

    Letcher, Roy M.

    1983-01-01

    Describes an experiment simulating a real-life structure elucidation problem through isolation, characterization, and chemical transformation of an "unknown," naturally occurring monoterpene, with extensive use being made of spectroscopy and aided by biogenetic considerations. Information given to students, procedures, results, and discussion of…

  17. 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. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. 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.

  19. Isolation and structure elucidation of unexpected in-process impurities during tetrazole ring formation of an investigational drug substance.

    PubMed

    Silva Elipe, Maria Victoria; Yoo, Chul; Xia, Fang; Simiens, Jason; Crossley, Kevin; Huckins, John R; Guo, Hong-Xun; Tedrow, Jason; Wong-Moon, Kirby

    2016-02-03

    During the formation of a tetrazole ring on an investigational drug, two in-process impurities were detected and analyzed by LC-MS, which suggested that both impurities were drug-related with the same mass-to-charge ratio. To understand and control their formation, both impurities were isolated from the mother liquor of the reaction using a multi-step isolation procedure to obtain a sufficient amount for high-resolution mass spectrometry (HRMS) and NMR structural analysis. HRMS suggested a protonated mass of 577.32 Da for both impurities; however, MS fragmentation patterns provided limited information on their structures. NMR analysis indicated the presence on an additional NH functional group in both isolates with similar spatial and bond correlations to one of the dimethylcarbamoyl moieties and the corresponding aromatic ring. A phenyldimethylcarbamoylamino moiety was supported by the NMR and HRMS data and could be explained based on the 'Schmidt-like' reaction mechanism, which was an unexpected reaction pathway. Because the reaction conditions were fixed because of safety concerns, the crystallization protocol was redesigned to reduce the levels of these impurities significantly. Copyright © 2016 John Wiley & Sons, Ltd.

  20. 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

  1. Crystal structure elucidation and anticancer studies of (-)-pseudosemiglabrin: a flavanone isolated from the aerial parts of Tephrosia apollinea.

    PubMed

    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.

  2. Isolation and structure elucidation of halymeniaol, a new antimalarial sterol derivative from the red alga Halymenia floresii.

    PubMed

    Meesala, Srinu; Gurung, Pratima; Karmodiya, Krishanpal; Subrayan, Parameswaran; Watve, Milind G

    2017-06-29

    A new mono-hydroxy acetylated sterol derivative: 12β-hydroxy-3β, 15α, 16β-triacetoxy-cholest-5-en-7-one (halymeniaol) (1), and cholesterol (2) were isolated from the marine red alga Halymenia floresii. The structure of the compound 1 (halymeniaol) was established from its spectral data, derived from HRMS/MS and 2D NMR. Compound 1 exhibited growth inhibitory activity against chloroquine-resistant Plasmodium falciparum 3D7 strain with an IC50 of 3.0 μM.

  3. PC-766B, a new macrolide antibiotic produced by Nocardia brasiliensis. II. Isolation, physico-chemical properties and structure elucidation.

    PubMed

    Kumagai, K; Fukui, A; Tanaka, S; Ikemoto, M; Moriguchi, K; Nabeshima, S

    1993-07-01

    A new macrolide antibiotic, PC-766B, was isolated from the cells of Nocardia brasiliensis SC-4710 by acetone extraction, and purified by gel filtration, silica gel chromatography, HPLC and TLC. The structure of PC-766B was determined by NMR spectral analysis to be a new class of the hygrolidin family antibiotics. PC-766B had a 16-membered macrocyclic lactone ring, a 6-membered hemiketal ring and a 2-deoxy-D-rhamnose moiety. DL-alpha-Tocopherol, known as an antioxidant agent, significantly improved the stability of PC-766B and prevented the decomposition of PC-766B during the storage of the antibiotic.

  4. Isolation and structure elucidation of secondary metabolites in Central and South American Calea species and their biochemical systematic implications

    SciTech Connect

    Ober, A.G.

    1984-01-01

    Fourteen species of the genus Calea (Family Compositae, Tribe Heliantheae) from Central and northern South America, including the type species for the genus, were investigated chemically to determine their secondary metabolites. The taxa studied were C. leptocephala Blake, C. megacephala Rob, and Greenm., and C. trichotoma B. Smith from Mexico, C. prunifolia Kunth (syn. C. pittieri) from Costa Rica, C. prunifolia Kunth from Panama, C. jamaicensis L. from Jamaica, and the Venezuelan species C. berteriana DC., C. divaricata Benthem, C. oliverii Rob. and Greenm., C. prunifolia Kunth, C. septuplinervia Hieron., C. solidaginea Kunth, and C. subcordata Kunth. The chemical investigation of these Calea species, undertaken as part of biochemical systematic study, has resulted in the isolation of 83 compounds, of which 38 are new natural products. The isolated compounds were represented by a dioxin derivative, 3 benzofuranes, 5 chromenes, 12 flavones, and 62 sesquiterpene lactones. The structures of the new compounds were established by chemical and spectroscopic methods. These methods included MS, IR, UV, and CD, /sup 1/H NMR, /sup 13/C NMR, and single crystal x-ray diffraction analysis.

  5. Isolation, structure elucidation, total synthesis, and evaluation of new natural and synthetic ceramides on human SK-MEL-1 melanoma cells.

    PubMed

    León, Francisco; Brouard, Ignacio; Rivera, Augusto; Torres, Fernando; Rubio, Sara; Quintana, José; Estévez, Francisco; Bermejo, Jaime

    2006-09-21

    Two new long-chain ceramides, trametenamides A (1) and B (2), were isolated from the methanolic extract of the fruiting body of the fungus Trametes menziesii. The structures were elucidated by spectroscopic analyses and chemical transformations, and the absolute stereochemistry of trametenamide B (2) was determined by stereoselective total synthesis of four possible diastereomers. The acetyl derivative of the natural ceramide (1a) and synthetic ceramides (24-27) showed cytotoxicity on the human melanoma cell line SK-MEL-1, which was caused by induction of apoptosis as determined by DNA fragmentation, poly(ADP-ribose) polymerase cleavage, and procaspase-9 and -8 processing.

  6. Isolation, structural elucidation, MS profiling, and evaluation of triglyceride accumulation inhibitory effects of benzophenone C-glucosides from leaves of Mangifera indica L.

    PubMed

    Zhang, Yi; Han, Lifeng; Ge, Dandan; Liu, Xuefeng; Liu, Erwei; Wu, Chunhua; Gao, Xiumei; Wang, Tao

    2013-02-27

    Seventy percent ethanol-water extract from the leaves of Mangifera indica L. (Anacardiaceae) was found to show an inhibitory effect on triglyceride (TG) accumulation in 3T3-L1 cells. From the active fraction, six new benzophenone C-glucosides, foliamangiferosides A(3) (1), A(4) (2), C(4) (3), C(5) (4), C(6) (5), and C(7) (6) together with 11 known benzophenone C-glucosides (7-17) were obtained. In this paper, isolation, structure elucidation (1-6), and MS fragment cleavage pathways of all 17 isolates were studied. 1-6 showed inhibitory effects on TG and free fatty acid accumulation in 3T3-L1 cells at 10 μM.

  7. Isolation, structure elucidation, and biomimetic total synthesis of versicolamide B and the isolation of antipodal (-)-stephacidin A and (+)-notoamide B from Aspergillus versicolor

    USDA-ARS?s Scientific Manuscript database

    A new prenylated indole alkaloid, versicolamide B, was isolated from cultures of Aspergillus versicolor NRRL 35600. The structure was assigned by 2D NMR data, and confirmed by a biomimetic total synthesis. Versicolamide B is the first member of the paraherquamide-stephacidin family of alkaloids fo...

  8. Isolation, structure elucidation and biological activity of metabolites from Sch-642305-producing endophytic fungus Phomopsis sp. CMU-LMA.

    PubMed

    Adelin, Emilie; Servy, Claudine; Cortial, Sylvie; Lévaique, Hélène; Martin, Marie-Thérèse; Retailleau, Pascal; Le Goff, Géraldine; Bussaban, Boonsom; Lumyong, Saisamorn; Ouazzani, Jamal

    2011-12-01

    Eight polyketide compounds were isolated from the cultivation broth of Phomopsis sp. CMU-LMA. We have recently described LMA-P1, a bicyclic 10-membered macrolide, obtained as a bioconversion derivative of Sch-642305, the major compound isolated in this study. Benquinol is the ethyl ester derivative of the 13-dihydroxytetradeca-2,4,8-trienoic acid produced by Valsa ambiens. This compound is concomitantly produced with the 6,13-dihydroxytetradeca-2,4,8-trienoic acid (DHTTA) previously isolated from Mycosphaerellarubella. The absolute configuration of the new compound, (2R,3R,4S,5R)-3-hydroxy-2,4-dimethyl-5-[(S,Z)-3-methylpentenyl]-tetrahydro-pyranone LMA-P2 was confirmed by X-ray crystallography. The δ-lactone 2,3-dihydroxytetradecan-5-olide (DHTO) was previously isolated from Seiridium unicorne. This compound may form through the cyclization of the methyl-2,3,5-trihydroxytridecanoate LMA-P3, a new linear polyketide isolated in this study. Benquoine, a new 14-membered lactone generated from the cyclization of benquinol, is proposed as the key precursor for the biosynthesis of Sch-642305. Antimicrobial activity and cancer cell viability inhibition by the new compounds were investigated. Benquoine exhibits antimicrobial activity against Gram positive bacteria, and cytotoxicity against HCT-116 cancer cell line.

  9. 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…

  10. 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…

  11. New cirramycin-family antibiotics F-1 and F-2. Selection of producer mutants, fermentation, isolation, structural elucidation and antibacterial activity.

    PubMed

    Sawada, Y; Tsuno, T; Miyaki, T; Naito, T; Oki, T

    1989-02-01

    Two new 16-membered macrolides, cirramycins F-1 and F-2, were isolated from the culture filtrate of a mutant strain B-1425 of Streptomyces cirratus JTB-3. The antibiotics were also produced by bio-transformation of cirramycin A1 using a blocked mutant strain A-0033. Structures of F-1 and F-2 have been elucidated by spectral interpretation and analysis of acid degradation products. Both involved isomeric modification of a neutral sugar; F-1 contained L-rhodinose, and F-2 L-amicetose. Based on spectral data, cirramycin F-1 and antibiotic A6888C were found to be identical. Cirramycins F-1 and F-2 are active against Gram-positive bacteria, but less active than cirramycin A1.

  12. Toward better annotation in plant metabolomics: isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses.

    PubMed

    Yang, Zhigang; Nakabayashi, Ryo; Okazaki, Yozo; Mori, Tetsuya; Takamatsu, Satoshi; Kitanaka, Susumu; Kikuchi, Jun; Saito, Kazuki

    2014-01-01

    Metabolomics plays an important role in phytochemical genomics and crop breeding; however, metabolite annotation is a significant bottleneck in metabolomic studies. In particular, in liquid chromatography-mass spectrometry (MS)-based metabolomics, which has become a routine technology for the profiling of plant-specialized metabolites, a substantial number of metabolites detected as MS peaks are still not assigned properly to a single metabolite. Oryza sativa (rice) is one of the most important staple crops in the world. In the present study, we isolated and elucidated the structures of specialized metabolites from rice by using MS/MS and NMR. Thirty-six compounds, including five new flavonoids and eight rare flavonolignan isomers, were isolated from the rice leaves. The MS/MS spectral data of the isolated compounds, with a detailed interpretation of MS fragmentation data, will facilitate metabolite annotation of the related phytochemicals by enriching the public mass spectral data depositories, including the plant-specific MS/MS-based database, ReSpect.

  13. 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. Copyright © 2015 John Wiley & Sons, Ltd.

  14. Application of comprehensive NMR-based analysis strategy in annotation, isolation and structure elucidation of low molecular weight metabolites of Ricinus communis seeds.

    PubMed

    Vučković, Ivan; Rapinoja, Marja-Leena; Vaismaa, Matti; Vanninen, Paula; Koskela, Harri

    2016-01-01

    Powder-like extract of Ricinus communis seeds contain a toxic protein, ricin, which has a history of military, criminal and terroristic use. As the detection of ricin in this "terrorist powder" is difficult and time-consuming, related low mass metabolites have been suggested to be useful for screening as biomarkers of ricin. To apply a comprehensive NMR-based analysis strategy for annotation, isolation and structure elucidation of low molecular weight plant metabolites of Ricinus communis seeds. The seed extract was prepared with a well-known acetone extraction approach. The common metabolites were annotated from seed extract dissolved in acidic solution using (1)H NMR spectroscopy with spectrum library comparison and standard addition, whereas unconfirmed metabolites were identified using multi-step off-line HPLC-DAD-NMR approach. In addition to the common plant metabolites, two previously unreported compounds, 1,3-digalactoinositol and ricinyl-alanine, were identified with support of MS analyses. The applied comprehensive NMR-based analysis strategy provided identification of the prominent low molecular weight metabolites with high confidence. Copyright © 2015 John Wiley & Sons, Ltd.

  15. Structural elucidation of rabeprazole sodium photodegradation products.

    PubMed

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

    2008-01-07

    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.

  16. 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.

  17. Structural elucidation of a cell wall fungal polysaccharide isolated from Ustilaginoidea virens, a pathogenic fungus of Oriza sativa and Zea mays.

    PubMed

    Leal, J A; Jiménez-Barbero, Jesús; Bernabé, Manuel; Prieto, Alicia

    2008-11-24

    The alkali-extractable water-soluble polysaccharides (F1SS) isolated from the outer cell wall of two strains of Ustilaginoidea virens have been studied by chemical and methylation analyses, and 1D and 2D (1)H and (13)C NMR spectroscopy. The structures of these polysaccharides are very similar, and can be described by the following idealized repeating unit: where n and m are approximately 1 and 2, respectively.

  18. 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

  19. 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.

  20. Isolation and structure elucidation of a highly haemolytic saponin from the Merck saponin extract using high-field gradient-enhanced NMR techniques.

    PubMed

    Delay, C; Gavin, J A; Aumelas, A; Bonnet, P A; Roumestand, C

    1997-07-11

    Saponins SAPO50 and SAPO30, of which SAPO50 is highly haemolytic, have been isolated from the commercial Merck Saponin. Their structures have been determined exclusively by high-field gradient-enhanced NMR methods. The 1H and 13C NMR spectra of these saponins in pyridine-deuterium oxide have been assigned by homonuclear and heteronuclear correlation experiments. Anomeric configurations were obtained by combined use of 1JCH, 3JH-1.H-2, and 1D-NOESY data. Sugar residues were identified by use of 3JHH values obtained from their subspectra recorded using an optimized 1D-zeta-TOCSY sequence. Linkage assignments were made using the ge-HMBC and 1D-NOESY spectra. This study shows that SAPO50 represents a hitherto undescribed saponin with the following structure: 3-O-beta-D-xylopyranosyl-(1-->3)-[beta-D-galactopyranosyl- (1-->2)]-beta-D-glucuronopyranosyl gypsogenin 28-O-(6-deoxy-beta-D-glucopyranosyl)-(1-->4)-[beta-D-xylopyranosyl-(1--> 3)- beta-D-xylopyranosyl-(1-->4)]-alpha-L-rhamnopyranosyl-(1-->2)-beta-D- fucopyranoside. SAPO30, however, corresponds to a saponin previously described [D. Frechet, B. Christ, B. Monegier du Sorbier, H. Fischer, and M. Vuilhorgne, Phytochemistry, 30 (1991) 927-931].

  1. Isolation and structural elucidation of 4-(beta-D-glucopyranosyldisulfanyl)butyl glucosinolate from leaves of rocket salad (Eruca sativa L.) and its antioxidative activity.

    PubMed

    Kim, Sun-Ju; Jin, Shigeki; Ishii, Gensho

    2004-12-01

    A structurally unique glucosinolate (GSL) was identified to be 4-(beta-D-glucopyranosyldisulfanyl)butyl GSL in rocket leaves. The positive-ion electrospray ionization mass spectrometry (ESI-MS) data indicated that the new GSL had a molecular weight of 521 (m/z 522, [M+H](+), as desulfo-GSL). The molecular formula of the substance was determined to be C(17)H(32)O(11)NS(3) (m/z 522.1143, [M+H](+)) based on its positive-ion high-resolution fast atom bombardment mass spectrometry (HR-FAB-MS) data. For the further confirmation, desulfated GSL of 4-(beta-D-glucopyranosyldisulfanyl)butyl GSL was prepared by commercial 1-thio-beta-D-glucose and dimeric 4-mercaptobutyl desulfo-GSL, which was also isolated from rocket leaves, and its chemical structure was then confirmed by MS data and nuclear magnetic resonance (NMR) spectroscopy. In addition, the antioxidative activity of 4-(beta-D-glucopyranosyldisulfanyl)butyl desulfo-GSL was measured by means of chemiluminescence (CL) for evaluating the functional properties. The antioxidative activity (2.089 unit/g) was relatively higher than that of dimeric 4-mercaptobutyl desulfo-GSL (1.227).

  2. Structural elucidation of inhomogeneous lignins from bamboo.

    PubMed

    Wen, Jia-Long; Sun, Shao-Long; Xue, Bai-Liang; Sun, Run-Cang

    2015-01-01

    A better understanding of the inhomogeneous molecular structure of lignin from bamboo is a prerequisite for promoting the "biorefinery" technologies of the bamboo feedstock. A mild and successive method for fractionating native lignin from bamboo species was proposed in the present study. The molecular structure and structural inhomogeneity of the isolated lignin polymers were comprehensively investigated by elemental analysis, carbohydrate analysis, state-of-the-art NMR and analytical pyrolysis techniques (quantitative (13)C NMR, (13)C-DEPT 135 NMR, 2D-HSQC NMR, (31)P NMR, and pyrolysis-GC-MS). The results showed that the proposed method is effective for extracting lignin from bamboo. NMR results showed that syringyl (S) was the predominant unit in bamboo lignin over guaiacyl (G) and p-hydroxyphenyl (H) units. In addition, the lignin was associated with p-coumarates and ferulates via ester and ether bonds, respectively. Moreover, various substructures, such as β-O-4, β-β, β-5, β-1, and α,β-diaryl ether linkages, were identified and quantified by NMR techniques. Based on the results obtained, a proposed schematic diagram of structural heterogeneity of the lignin polymers extracted from the bamboo is presented. In short, well-defined inhomogeneous structures of native lignin from bamboo will facilitate further applications of bamboo in current biorefineries.

  3. Aggregation arrestant pheromone of the German cockroach,Blattella germanica (L.) (Dictyoptera: Blattellidae): Isolation and structure elucidation of blattellastanoside-A and -B.

    PubMed

    Sakuma, M; Fukami, H

    1993-11-01

    The aggregation pheromone of the German cockroach,Blattella germanica, consists of attractant and arrestant, which can be detected by olfactometer and choice-chamber assay, respectively. Both were extracted from the frass-contaminated filter paper being used as a shelter. They were separated by solvent partition withn-butanol and water. The arrestant from then-butanol phase was purified by open column chromatography and then successive HPLC isolated two major arrestant components. Spectral evidence from SI-MS, HR-EI-MS, and NMR experiments with pulse techniques provided possible structures as 1-(6α-chloro-4β,5β-epoxy-5β-stigmast-3β-yl)-β-D-glucopyranoside and 1-(6α-chloro-5β-hydroxy-5β-stigmast-3β-yl)-β-D-glu-copyranoside, denoted as blattellastanoside-A and blattellastanoside-B, respectively. They represented arrestant activity as median effective doses (ED50) at 0.044 (A) and 3.2 (B) nmol on 1.0 cm(2) of Whatman No. 1 filter paper.

  4. 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.

  5. Isolation and structural elucidation by 2D NMR of planteose, a major oligosaccharide in the mucilage of chia (Salvia hispanica L.) seeds.

    PubMed

    Xing, Xiaohui; Hsieh, Yves S Y; Yap, Kuok; Ang, Main E; Lahnstein, Jelle; Tucker, Matthew R; Burton, Rachel A; Bulone, Vincent

    2017-11-01

    An oligosaccharide was isolated in high purity and excellent yield from the water-extractable mucilage of chia (Salvia hispanica L.) seeds using an optimized solid-phase extraction method. LC-MS analysis showed that the compound presents a molecular mass of 504Da and trifluoroacetic acid hydrolysis revealed that it consists of galactose, glucose and fructose. Glycosidic linkage analysis showed that the oligosaccharide contains two non-reducing ends corresponding to terminal glucopyranose and terminal galactopyranose, respectively. The oligosaccharide was identified as planteose by the complete assignment of a series of 2D NMR spectra (COSY, TOCSY, ROESY, HSQC, and HMBC). The significance of the presence of planteose in chia seeds is discussed in the context of nutrition and food applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Isolation and Structure Elucidation by LC-DAD-MS and LC-DAD-SPE-NMR of Cyclopeptide Alkaloids from the Roots of Ziziphus oxyphylla and Evaluation of Their Antiplasmodial Activity.

    PubMed

    Tuenter, Emmy; Ahmad, Rizwan; Foubert, Kenn; Amin, Adnan; Orfanoudaki, Maria; Cos, Paul; Maes, Louis; Apers, Sandra; Pieters, Luc; Exarchou, Vassiliki

    2016-11-23

    Nine cyclopeptide alkaloids (1-9), of which five (compounds 2, 3, 5, 8, and 9) are described herein for the first time, were isolated from roots of Ziziphus oxyphylla by means of conventional separation methods as well as semipreparative HPLC with DAD and ESIMS detection and LC-DAD-SPE-NMR. Structure elucidation was done by spectroscopic means. Nummularine-R (1), a previously known constituent from this species, was isolated along with its new derivatives O-desmethylnummularine-R (2) and O-desmethylnummularine-R N-oxide (3). In addition, the known compounds hemsine-A (4) and ramosine-A (6), as well as hemsine-A N-oxide (5), were isolated. Moreover, oxyphylline-C (7), a known constituent of Z. oxyphylla stems, was obtained, and two new compounds were identified, oxyphyllines-E (8) and -F (9). Just like oxyphylline-C, oxyphyllines-E and -F belong to the relatively rare class of neutral cyclopeptide alkaloids. The antiplasmodial activity and cytotoxicity of compounds 1, 2, 4, 6, and 9 were evaluated, and the most promising activity was found for O-desmethylnummularine-R (2), which exhibited an IC50 value of 3.2 ± 2.6 μM against Plasmodium falciparum K1, whereas an IC50 value of >64.0 μM was evident for its cytotoxicity against MRC-5 cells.

  7. Identification and structural elucidation of ergotryptamine, a new ergot alkaloid produced by genetically modified aspergillus nidulans and natural isolates of Epichloë species.

    PubMed

    Ryan, Katy L; Akhmedov, Novruz G; Panaccione, Daniel G

    2015-01-14

    Ergot alkaloid pathway reconstruction in Aspergillus nidulans is an approach used to better understand the biosynthesis of these mycotoxins. An engineered strain named A. nidulans WFC (expressing ergot alkaloid synthesis genes dmaW, easF, and easC) produced the established intermediate N-methyl-4-dimethylallyltryptophan, as well as an uncharacterized ergot alkaloid. We investigated the chemical structure of the new metabolite and its role in the ergot alkaloid pathway. Mass spectrometry, labeling, and NMR studies showed that the unknown ergot alkaloid, designated here as ergotryptamine, differed from N-methyl-4-dimethylallyltryptophan by the loss of the carboxyl group, addition of a hydroxyl group, and shift in position of a carbon–carbon double bond. Feeding studies with Aspergillus mutants did not show ergotryptamine turnover, suggesting it is a pathway byproduct as opposed to an authentic intermediate. Several Epichloë species also produced this metabolite, and further investigations revealed the equivalency of ergotryptamine with an Epichloë-derived ergot alkaloid provisionally described as 6,7-secolysergine.

  8. 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.

  9. 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

  10. Blind trials of computer-assisted structure elucidation software

    PubMed Central

    2012-01-01

    Background One of the largest challenges in chemistry today remains that of efficiently mining through vast amounts of data in order to elucidate the chemical structure for an unknown compound. The elucidated candidate compound must be fully consistent with the data and any other competing candidates efficiently eliminated without doubt by using additional data if necessary. It has become increasingly necessary to incorporate an in silico structure generation and verification tool to facilitate this elucidation process. An effective structure elucidation software technology aims to mimic the skills of a human in interpreting the complex nature of spectral data while producing a solution within a reasonable amount of time. This type of software is known as computer-assisted structure elucidation or CASE software. A systematic trial of the ACD/Structure Elucidator CASE software was conducted over an extended period of time by analysing a set of single and double-blind trials submitted by a global audience of scientists. The purpose of the blind trials was to reduce subjective bias. Double-blind trials comprised of data where the candidate compound was unknown to both the submitting scientist and the analyst. The level of expertise of the submitting scientist ranged from novice to expert structure elucidation specialists with experience in pharmaceutical, industrial, government and academic environments. Results Beginning in 2003, and for the following nine years, the algorithms and software technology contained within ACD/Structure Elucidator have been tested against 112 data sets; many of these were unique challenges. Of these challenges 9% were double-blind trials. The results of eighteen of the single-blind trials were investigated in detail and included problems of a diverse nature with many of the specific challenges associated with algorithmic structure elucidation such as deficiency in protons, structure symmetry, a large number of heteroatoms and poor quality

  11. 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.

  12. Structural elucidation and bioactivity of biflavonoids from the stems of Wikstroemia taiwanensis.

    PubMed

    Chen, Li-Yin; Chen, Ih-Sheng; Peng, Chien-Fang

    2012-01-01

    Three new biflavonoids, wikstaiwanones A-C (1-3), along with four known compounds (4-7) were isolated from the stems of Wikstroemia taiwanensis (Thymelaeaceae). Their structures were elucidated by spectroscopic analysis. Compounds 4 and 5 showed antitubercular activity against Mycobacterium tuberculosis with MIC values of 15 μg/mL, respectively.

  13. Structural Elucidation and Bioactivity of Biflavonoids from the Stems of Wikstroemia taiwanensis

    PubMed Central

    Chen, Li-Yin; Chen, Ih-Sheng; Peng, Chien-Fang

    2012-01-01

    Three new biflavonoids, wikstaiwanones A–C (1–3), along with four known compounds (4–7) were isolated from the stems of Wikstroemia taiwanensis (Thymelaeaceae). Their structures were elucidated by spectroscopic analysis. Compounds 4 and 5 showed antitubercular activity against Mycobacterium tuberculosis with MIC values of 15 μg/mL, respectively. PMID:22312302

  14. Structure elucidation and NMR assignments of two unusual monoterpene indole alkaloids from Psychotria stachyoides.

    PubMed

    Pimenta, Antonia Torres Avila; Braz-Filho, Raimundo; Delprete, Piero Giuseppe; de Souza, Elnatan Bezerra; Silveira, Edilberto Rocha; Lima, Mary Anne Sousa

    2010-09-01

    Two unusual monoterpene indole alkaloids, stachyoside (1) and nor-methyl-23-oxo-correantoside (2), have been isolated from the aerial parts of Psychotria stachyoides. The structural elucidation of both compounds was performed by the aid of HRESIMS, FT-IR, and 1D- and 2D-NMR techniques including COSY, HSQC, HMBC, and NOESY.

  15. Recent developments in automated structure elucidation of natural products.

    PubMed

    Steinbeck, Christoph

    2004-08-01

    Advancements in the field of Computer-Assisted Structure Elucidation (CASE) of Natural Products achieved in the past five years are discussed. This process starts with a dereplication procedure, supported by structure-spectrum databases. Both commercial and free products are available to support the procedure. A number of new programs,as well as advancements in existing ones, are presented. Finally, the option to validate the result by an independent procedure, a high quality ab initio quantum mechanical calculation, is discussed.

  16. 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.

  17. Toward structural elucidation of the γ-secretase complex

    PubMed Central

    Li, Huilin; Wolfe, Michael S.; Selkoe, Dennis J.

    2009-01-01

    γ-Secretase is an intramembrane protease complex that mediates the Notch signaling pathway and the production of amyloid β-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 barriers and potential pathways toward elucidating its detailed structure. PMID:19278647

  18. 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.

  19. Desktop NMR for structure elucidation and identification of strychnine adulteration.

    PubMed

    Singh, Kawarpal; Blümich, Bernhard

    2017-03-27

    Elucidating the structure of complex molecules is difficult at low magnetic fields due to the overlap of different peak multiplets and second-order coupling effects. This is even more challenging for rigid molecules with small chemical shift differences and with prochiral centers. Since low-field NMR spectroscopy is sometimes presumed as restricted to the analysis of only small and simple molecules, this paper aims at countering this misconception: it demonstrates the use of low-field NMR spectroscopy in chemical forensics for identifying strychnine and its counterions by exploring the chemical shift as a signature in different 1D (1)H and (13)C experiments. Hereby the applied methodologies combine various 1D and 2D experiments such as 1D (1)H, (13)C, DEPT, and 2D COSY, HETCOR, HSQC, HMBC and J-resolved spectroscopy to elucidate the molecular structure and skeleton of strychnine at 1 Tesla. Strychnine is exemplified here, because it is a basic precursor in the chemistry of natural products and is employed as a chemical weapon and as a doping agent in sports including the Olympics. In our study, the molecular structure of the compound could be identified either with a 1D experiment at high magnetic field or with HMBC and HSQC experiments at 1 T. In conclusion, low-field NMR spectroscopy enables the chemical elucidation of the strychnine structure through a simple click with a computer mouse. In situations where a high-field NMR spectrometer is unavailable, compact NMR spectrometers can nevertheless generate knowledge of the structure, important for identifying the different chemical reaction mechanisms associated with the molecule. Desktop NMR is a cost-effective viable option in chemical forensics. It can prove adulteration and identify the origin of different strychnine salts, in particular, the strychnine free base, strychnine hemisulphate and strychnine hydrochloride. The chemical shift signatures report the chemical structure of the molecules due to the impact

  20. [Pharmacokinetics of sodium 4-[alpha-hydroxy-5-(1-imidazolyl)-2-methylbenzyl]-3,5-dimethylbenzoate (Y-20811), a new thromboxane synthetase inhibitor. I. Isolation and structure elucidation of urinary metabolite in dog].

    PubMed

    Iwata, T; Tsuruda, M; Demizu, K; Isobe, M; Takamatsu, R; Yokobe, T

    1989-09-01

    The urinary metabolites of sodium 4-[alpha-hydroxy-5-(1-imidazolyl)-2-methylbenzyl]-3,5-dimethylbenzoat e (Y-20811) in dog were investigated. The main metabolite was isolated by high performance liquid chromatography and subsequent preparative thin layer chromatography. The structure of this metabolite was established as 4-[alpha-hydroxy-2-hydroxymethyl-5-(1-imidazolyl)benzyl]-3,5- dimethylbenzoic acid on the basis of spectral analyses and confirmed by its total synthesis.

  1. Natural dibenzoxazepinones from leaves of Carex distachya: Structural elucidation and radical scavenging activity.

    PubMed

    Fiorentino, Antonio; D'Abrosca, Brigida; Pacifico, Severina; Cefarelli, Giuseppe; Uzzo, Piera; Monaco, Pietro

    2007-02-01

    Two new dibenzoxazepinones have been isolated from the leaves of Carex distachya, an herbaceous plant growing in the Mediterranean area. The structures have been elucidated on the basis of their spectroscopic properties. Bidimensional NMR (DQ-COSY, TOCSY, NOESY, ROESY, HSQC, and HMBC) furnished important data useful for the characterization of the molecules. The compounds have been assayed, for the antioxidant activity, by measuring its capacity to scavenge the DPPH, the superoxide anion, and nitric oxide radicals.

  2. Structure elucidation and complete NMR spectral assignments of four new diterpenoids from Smallantus sonchifolius.

    PubMed

    Dou, De-Qiang; Tian, Fang; Qiu, Ying-Kun; Kang, Ting-Guo; Dong, Feng

    2008-08-01

    Four new diterpenoids, named smaditerpenic acid A-D, together with five known compounds, were isolated from the H(2)O extract of the leaves of Smallantus sonchifolius (yacon) cultivated in Liaoning, China and their structures were elucidated on the basis of one- and two-dimensional NMR (including (1)H, (13)C-NMR, (1)H-(1)H COSY, HSQC, TOCSY, HMBC, and ROESY), electrospray ionization mass spectrometry (ESI-MS), and chemical methods.

  3. 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

  4. Micropreparative isolation and NMR structure elucidation of metabolites of the drug candidate 1-isopropyl-4-(4-isopropylphenyl)-6-(prop-2-yn-1-yloxy) quinazolin-2(1H)-one from rat bile and urine.

    PubMed

    Blanz, Joachim; Délémonté, Thierry; Pearson, David; Luneau, Alexandre; Ritzau, Michael; Gertsch, Werner; Ramstein, Philippe; Dayer, Jérôme; Desrayaud, Sandrine; Braun, Elisabeth; Aichholz, Reiner

    2015-05-01

    LC-MS based drug metabolism studies are effective in the optimization stage of drug discovery for rapid partial structure identification of metabolites. However, these studies usually do not provide unambiguous structural characterization of all metabolites, due to the limitations of MS-based structure identification. LC-MS-SPE-NMR is a technique that allows complete structure identification, but is difficult to apply to complex in vivo samples (such as bile collected during in vivo drug metabolism studies) due to the presence, at high concentrations, of interfering endogenous components, and potentially also dosage excipient components (e.g. polyethylene glycols). Here, we describe the isolation and structure characterization of seven metabolites of the drug development candidate 1-isopropyl-4-(4-isopropylphenyl)-6-(prop-2-yn-1-yloxy) quinazolin-2(1H)-one from a routine metabolism study in a bile-duct cannulated rat by LC-MS-SPE. The metabolites were isolated from bile and urine by repeated automatic trapping of the chromatographic peak of each metabolite on separate Oasis HLB SPE columns. The micropreparative HPLC/MS was performed on an XBridge BEH130 C18 HPLC column using aqueous formic acid/acetonitrile/methanol as mobile phase for the gradient elution. Mass spectrometric detection was performed on a LTQ XL linear ion trap mass spectrometer using electrospray ionization. Desorption of each metabolite was performed after the separation sequence. NMR spectra ((1)H, (13)C, 2D ROESY, HSQC and HMBC were measured on a Bruker AVANCE III spectrometer (600 MHz proton frequency) equipped with a 1.7 mm (1)H{(13)C,(15)N} Bruker Biospin's TCI MicroCryoProbe™. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Structural elucidation of organic contaminants by chemical ionisation mass spectrometry

    NASA Astrophysics Data System (ADS)

    Moldovan, Zaharie

    2009-08-01

    The PI-CI mass spectra formation for a new family of aromatic amines, with general formula: R1-Ph-NH-Ph-R2 is discussed in correlation with the R1 and R2 structure. The compounds where isolated from some environmental samples by GC/MS technique. The characteristic ions are produced by rearrangement processes involving olefin and alkane neutral molecule elimination from [M+H]+ and sole olefin molecule elimination from [M+ C2H5]+.

  6. Structure elucidation of casbane diterpenes from Croton argyrophyllus.

    PubMed

    e Silva-Filho, Francisco Artur; Braz-Filho, Raimundo; Silveira, Edilberto Rocha; Lima, Mary Anne Sousa

    2011-06-01

    Two novel casbane diterpenes 1-hydroxy-(2E,6Z,12E)-casba-2,6,12-triene-4,5-dione (1) and 6E,12E-casba-1,3,6,12-tetraen-1,4-epoxy-5-one (2) were isolated from the ethanol extract of the stems of Croton argyrophyllus. Structural characterization including the relative stereochemistry of all compounds was established on the basis of spectroscopic methods, mainly 1D and 2D NMR, and HRESIMS.

  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 the structures of residual and dissolved pine kraft lignins using an HMQC NMR technique.

    PubMed

    Balakshin, Mikhail Yu; Capanema, Ewellyn A; Chen, Chen-Loung; Gracz, Hanna S

    2003-10-08

    Comparative studies on the structures of residual and dissolved lignins isolated from pine kraft pulp and pulping liquor have been undertaken using the (1)H-(13)C HMQC NMR technique, GPC, and sugar analysis to elucidate the reaction mechanisms in kraft pulping and the lignin reactivity. A modified procedure for the isolation of enzymatic residual lignins has resulted in an appreciable decrease in protein contaminants in the residual lignin preparations (N content < 0.2%). The very high dispersion of HMQC spectra allows identification of different lignin moieties, which signals appear overlapped in 1D (13)C NMR spectra. Elucidation of the role of condensation reactions indicates that an increase in the degree of lignin condensation during pulping results from accumulation of original condensed lignin moieties rather than from the formation of new alkyl-aryl structures. Among aryl-vinyl type moieties, only stilbene structures are accumulated in lignin in appreciable amounts. Benzyl ether lignin-carbohydrate bonds involving primary hydroxyl groups of carbohydrates have been detected in residual and dissolved lignin preparations. Structures of the alpha-hydroxyacid type have been postulated to be among the important lignin degradation products in kraft pulping. The effect of the isolation method on the lignin structure and differences between the residual and dissolved lignins are discussed.

  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.

  10. Elucidation of Operon Structures across Closely Related Bacterial Genomes

    PubMed Central

    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

  11. 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

  12. Structure elucidation and absolute stereochemistry of isomeric monoterpene chromane esters.

    PubMed

    Batista, João M; Batista, Andrea N L; Mota, Jonas S; Cass, Quezia B; Kato, Massuo J; Bolzani, Vanderlan S; Freedman, Teresa B; López, Silvia N; Furlan, Maysa; Nafie, Laurence A

    2011-04-15

    Six novel monoterpene chromane esters were isolated from the aerial parts of Peperomia obtusifolia (Piperaceae) using chiral chromatography. This is the first time that chiral chromane esters of this kind, ones with a tethered chiral terpene, have been isolated in nature. Due to their structural features, it is not currently possible to assess directly their absolute stereochemistry using any of the standard classical approaches, such as X-ray crystallography, NMR, optical rotation, or electronic circular dichroism (ECD). Herein we report the absolute configuration of these molecules, involving four chiral centers, using vibrational circular dichroism (VCD) and density functional theory (DFT) (B3LYP/6-31G*) calculations. This work further reinforces the capability of VCD to determine unambiguously the absolute configuration of structurally complex molecules in solution, without crystallization or derivatization, and demonstrates the sensitivity of VCD to specify the absolute configuration for just one among a number of chiral centers. We also demonstrate the sufficiency of using the so-called inexpensive basis set 6-31G* compared to the triple-ζ basis set TZVP for absolute configuration analysis of larger molecules using VCD. Overall, this work extends our knowledge of secondary metabolites in plants and provides a straightforward way to determine the absolute configuration of complex natural products involving a chiral parent moiety combined with a chiral terpene adduct.

  13. Phospholpid studies of marine organisms: 2.(1) Phospholipids, phospholipid-bound fatty acids and free sterols of the spongeAplysina fistularis (Pallas) formafulva (Pallas) (=Verongia thiona)(2). Isolation and structure elucidation of unprecedented branched fatty acids.

    PubMed

    Walkup, R D; Jamieson, G C; Ratcliff, M R; Djerassi, C

    1981-09-01

    The free sterols and phospholipids of the demospongeAplysina fistularis were isolated and analyzed. The free sterols consisted mainly of the unusual 26-methylated sterols aplysterol (53%) and 24(28)-dehydroaplysterol (7%) together with 7 commonly occurring sterods. The major phospholipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, phosphatidylserine and diphosphatidylglycerol. The major fatty acyl components of the phospholipids consisted of 85% C14-C20 acids, including the unprecedented 2,6,10-trimethyl-5-tetradecenoic acid and 11-methyloctadecanoic acid. The remaining 15% were C27-C30 demospongic acids, including 2 novel acids tentatively assigned the structures 5,9,23-octacosatrienoic acid and 5,9,23-nonacosatrienoic acid, and 3 novel acids proven to be 5,9,21-octacosatrienoic acid, Z,Z-20-methyl-5,9-hexacosadienoic acid and Z,Z-22-methyl-5,9-octacosadienoic acid. The biosyntheses of the novel demospongic acids are proposed to occur by chain elongation of monoenoic or branched precursors followed by desaturation. The large quantities of typically bacterial phospholipids and fatty acids found implied the presence of bacteria in the sponge, in agreement with microscopic studies. Analysis of the phospholipid-bound fatty acids in a sponge cell-enriched fraction indicated that the demospongic acids, including the 2 branched structures, were the major acids of the sponge cells. The presence inA. fistularis of demospongic acids containing membrane disordering groups-methyl branches or double bonds-on the ω7 carbon is proposed to be due to the need by the sponge for membranes possessing fluidity near the middle of the phospholipid bilayer. It is also proposed that the C26 methyl group of aplysterol causes disordering of the phospholipid bilayer in the same region, and thus also evolved in response to this need.

  14. 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.

  15. 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.

  16. Structural elucidation of polysaccharide containing 3-O-methyl galactose from fruiting bodies of Pleurotus citrinopileatus.

    PubMed

    He, Pengfei; Zhang, Anqiang; Zhou, Saijing; Zhang, Fuming; Linhardt, Robert J; Sun, Peilong

    2016-11-03

    A water-soluble polysaccharide containing 3-O-methyl galactose (PCP60W) was isolated from fruiting bodies of Pleurotus citrinopileatus and purified by anion-exchange and gel column chromatography. This polysaccharide has an average molecular weight of 2.74 × 10(4) Da and its structure was elucidated using monosaccharide composition and methylation analysis combined with one- and two-dimensional (COSY, TOCSY, NOESY, HMQC and HMBC) NMR spectroscopy. PCP60W was shown to be a linear partially 3-O-methylated α-galactopyranan comprised of 6-linked galactose, 6-linked 3-O-methyl galactose and 4-linked glucose in a ratio of 3.0:1.0:0.6. This work provides additional evidence for the view that 3-O-methyl galactose is common to the genus Pleurotus.

  17. 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

  18. Structural Elucidation of Chalcone Reductase and Implications for Deoxychalcone Biosynthesis

    PubMed Central

    Bomati, Erin K.; Austin, Michael B.; Bowman, Marianne E.; Dixon, Richard A.; Noel, Joseph P.

    2010-01-01

    4,2′,4′,6′-tetrahydroxychalcone (chalcone) and 4,2′,4′-trihydroxychalcone (deoxychalcone) serve as precursors of ecologically important flavonoids and isoflavonoids. Deoxychalcone formation depends on chalcone synthase and chalcone reductase; however, the identity of the chalcone reductase substrate out of the possible substrates formed during the multistep reaction catalyzed by chalcone synthase remains experimentally elusive. We report here the three-dimensional structure of alfalfa chalcone reductase bound to the NADP+ cofactor and propose the identity and binding mode of its substrate, namely the non-aromatized coumaryl-trione intermediate of the chalcone synthase-catalyzed cyclization of the fully extended coumaryl-tetraketide thioester intermediate. In the absence of a ternary complex, the quality of the refined NADP+-bound chalcone reductase structure serves as a template for computer-assisted docking to evaluate the likelihood of possible substrates. Interestingly, chalcone reductase adopts the three-dimensional structure of the aldo/keto reductase superfamily. The aldo/keto reductase fold is structurally distinct from all known ketoreductases of fatty acid biosynthesis, which instead belong to the short-chain dehydrogenase/reductase superfamily. The results presented here provide structural support for convergent functional evolution of these two ketoreductases that share similar roles in the biosynthesis of fatty acids/polyketides. In addition, the chalcone reductase structure represents the first protein structure of a member of the aldo/ketoreductase 4 family. Therefore, the chalcone reductase structure serves as a template for the homology modeling of other aldo/ketoreductase 4 family members, including the reductase involved in morphine biosynthesis, namely codeinone reductase. PMID:15970585

  19. Elucidation of kinematical and dynamical structure of the Galactic bulge

    NASA Astrophysics Data System (ADS)

    Yano, T.; Gouda, N.; Ueda, H.; Koyama, H.; Kan-ya, Y.; Taruya, A.

    2008-07-01

    Future space mission of astrometric satellite, GAIA and JASMINE (Japan Astrometry Satellite Mission for Infrared Exploration), will produce astrometric parameter, such as positions, parallaxes, and proper motions of stars in the Galactic bulge. Then kinematical information will be obtained in the future. Accordingly it is expected that our understanding of the dynamical structure will be greatly improved. Therefore it is important to make a method to construct a kinematical and dynamical structure of the Galactic bulge immediately.

  20. Structure elucidation of dimeric transmembrane domains of bitopic proteins

    PubMed Central

    Volynsky, Pavel E.; Pavlov, Konstantin V.; Efremov, Roman G.; Arseniev, Alexander S.

    2010-01-01

    The interaction between transmembrane helices is of great interest because it directly determines biological activity of a membrane protein. Either destroying or enhancing such interactions can result in many diseases related to dysfunction of different tissues in human body. One much studied form of membrane proteins known as bitopic protein is a dimer containing two membrane-spanning helices associating laterally. Establishing structure-function relationship as well as rational design of new types of drugs targeting membrane proteins requires precise structural information about this class of objects. At present time, to investigate spatial structure and internal dynamics of such transmembrane helical dimers, several strategies were developed based mainly on a combination of NMR spectroscopy, optical spectroscopy, protein engineering and molecular modeling. These approaches were successfully applied to homo- and heterodimeric transmembrane fragments of several bitopic proteins, which play important roles in normal and in pathological conditions of human organism. PMID:20421711

  1. 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.

  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. 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

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

    PubMed

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

    2014-11-01

    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 was 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.

  5. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Cytotoxic 1,3-Thiazole and 1,2,4-Thiadiazole Alkaloids from Penicillium oxalicum: Structural Elucidation and Total Synthesis.

    PubMed

    Yang, Zheng; Huang, Nianyu; Xu, Bang; Huang, Wenfeng; Xie, Tianpeng; Cheng, Fan; Zou, Kun

    2016-02-26

    Two new thiazole and thiadiazole alkaloids, penicilliumthiamine A and B (2 and 3), were isolated from the culture broth of Penicillium oxalicum, a fungus found in Acrida cinerea. Their structures were elucidated mainly by spectroscopic analysis, total synthesis and X-ray crystallographic analysis. Biological evaluations indicated that compound 1, 3a and 3 exhibit potent cytotoxicity against different cancer cell lines through inhibiting the phosphorylation of AKT/PKB (Ser 473), one of important cancer drugs target.

  7. Fatty acid biosynthesis revisited: Structure elucidation and metabolic engineering

    SciTech Connect

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

    2014-10-20

    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. Lastly, 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.

  8. 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.

  9. 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

  10. Using Machine Learning to Accelerate Complex Atomic Structure Elucidation

    NASA Astrophysics Data System (ADS)

    Brouwer, William; Calderin, Lazaro; Sofo, Jorge

    2012-02-01

    Workers in various scientific disciplines seek to develop chemical models for extended and molecular systems. The modeling process revolves around the gradual refinement of model assumptions, through comparison of experimental and computational results. Solid state Nuclear Magnetic Resonance (NMR) is one such experimental technique, providing great insight into chemical order over Angstrom length scales. However, interpretation of spectra for complex materials is difficult, often requiring intensive simulations. Similarly, working forward from the model in order to produce experimental quantities via ab initio is computationally demanding. The work involved in these two significant steps, compounded by the need to iterate back and forth, drastically slows the discovery process for new materials. There is thus great motivation for the derivation of structural models directly from complex experimental data, the subject of this work. Using solid state NMR experimental datasets, in conjunction with ab initio calculations of measurable NMR parameters, a network of machine learning kernels are trained to rapidly yield structural details, on the basis of input NMR spectra. Results for an environmentally relevant material will be presented, and directions for future work.

  11. Fatty acid biosynthesis revisited: Structure elucidation and metabolic engineering

    DOE PAGES

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

    2014-10-20

    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 understandingmore » 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. Lastly, 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.« less

  12. N-methylcodeinium iodide—Crystal structure and spectroscopic elucidation

    NASA Astrophysics Data System (ADS)

    Seidel, R. W.; Bakalska, B. R.; Kolev, T.; Vassilev, D.; Mayer-Figge, H.; Spiteller, M.; Sheldrick, W. S.; Koleva, B. B.

    2009-07-01

    The correlation between the structure and the spectroscopic properties of N-methylcodeinium iodide ( 1) has been studied, using the methods of single crystal X-ray diffraction, IR-LD spectroscopy of oriented samples as a suspension in nematic liquid crystals, UV-vis spectroscopy and 1H and 13C NMR spectroscopy. HPLC tandem mass spectrometry (HPLC ESI MS/MS) and thermal methods were also employed. Quantum chemical calculations have been performed with a view to obtaining the electronic structure and vibrational properties of the title compound. Compound ( 1) crystallizes in the space group P2 12 12 1 and its cations and anions are joined by moderate intermolecular OH…I - interaction of length 3.442 Å. The codeine molecule exhibits the classical T-shape for opiates. A dihedral angle value of 86.4(5)° between the A/B/C and D/E planes is obtained. Rings A and B are effectively coplanar with an interplanar angle of 3.6(3)°.

  13. N-methylcodeinium iodide--crystal structure and spectroscopic elucidation.

    PubMed

    Seidel, R W; Bakalska, B R; Kolev, T; Vassilev, D; Mayer-Figge, H; Spiteller, M; Sheldrick, W S; Koleva, B B

    2009-07-01

    The correlation between the structure and the spectroscopic properties of N-methylcodeinium iodide (1) has been studied, using the methods of single crystal X-ray diffraction, IR-LD spectroscopy of oriented samples as a suspension in nematic liquid crystals, UV-vis spectroscopy and 1H and 13C NMR spectroscopy. HPLC tandem mass spectrometry (HPLC ESI MS/MS) and thermal methods were also employed. Quantum chemical calculations have been performed with a view to obtaining the electronic structure and vibrational properties of the title compound. Compound (1) crystallizes in the space group P2(1)2(1)2(1) and its cations and anions are joined by moderate intermolecular OH...I- interaction of length 3.442A. The codeine molecule exhibits the classical T-shape for opiates. A dihedral angle value of 86.4(5) degrees between the A/B/C and D/E planes is obtained. Rings A and B are effectively coplanar with an interplanar angle of 3.6(3) degrees.

  14. Fluorescent monolayer protected gold nanoparticles - Preparation and structure elucidation

    NASA Astrophysics Data System (ADS)

    Angelova, P.; Kuchukova, N.; Dobrikov, G. M.; Timtcheva, I.; Kostova, K.; Petkova, I.; Vauthey, E.

    2011-05-01

    A novel N-substituted 4-methoxy-1,8-naphthalimide (NAFTA 8) especially designed for fluorescent labeling of gold nanoparticles has been synthesized. NAFTA 8 bears a long methylene chain at the imide N atom and has a terminal SH group, which enables its chemical binding to gold nanostructures. The longest wavelength absorption maximum of NAFTA 8 in chloroform is at 370 nm, the fluorescent maximum is at 430 nm and the fluorescent quantum yield is 0.95. The newly synthesized fluorophore is applied for functionalization of gold nanoparticles with diameter 1.5 ± 0.5 nm prepared through chemical reduction. The obtained Monolayer Protected Clusters are characterized by elemental analysis, TEM, XPS, FT-IR, absorption and fluorescence spectroscopy. The performed investigations provide evidence for the formation of chemical bond between the thiol ligand and the gold surface. They also show that the obtained metal/dielectric 3D structures are highly fluorescent.

  15. Structural elucidation of polysaccharide fractions from brown seaweed Sargassum pallidum.

    PubMed

    Ye, Hong; Zhou, Chunhong; Li, Wei; Hu, Bing; Wang, Xiaoqing; Zeng, Xiaoxiong

    2013-09-12

    The structural characteristics of two purified fractions of polysaccharides from Sargassum pallidum (SPS) were investigated in the present study. As results, the molecular weights of the two polysaccharide fractions, SPS-3-1 and SPS-3-2, were determined to be 5.87 and 7.25 kDa, respectively. SPS-3-1 was composed of glucose, mannose and galactose in a molar ratio of 11.18:1.00:0.96, while SPS-3-2 was composed of fucose, xylose, mannose, glucose and galactose in a molar ratio of 2.53:0.61:1.00:0.46:0.92. Both SPS-3-1 and SPS-3-2 exhibited the characteristics of polysaccharide in the frequency range of 4000-400 cm(-1) based on their Fourier-transform infrared spectra. Furthermore, the results of periodic acid oxidation, Smith degradation, methylation analysis and nuclear magnetic resonance spectroscopic analysis suggested that SPS-3-2 was composed of (1→4)-linked fucopyranosyl backbone and (1→3)-linked galactopyranosyl, (1→3)-linked mannopyranosyl, (1→2)-linked xylopyranosyl and (1→6)-linked glucopyranosyl branch chains.

  16. The fundamentals behind solving for unknown molecular structures using computer-assisted structure elucidation: a free software package at the undergraduate and graduate levels.

    PubMed

    Moser, Arvin; Pautler, Brent G

    2016-05-15

    The successful elucidation of an unknown compound's molecular structure often requires an analyst with profound knowledge and experience of advanced spectroscopic techniques, such as Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. The implementation of Computer-Assisted Structure Elucidation (CASE) software in solving for unknown structures, such as isolated natural products and/or reaction impurities, can serve both as elucidation and teaching tools. As such, the introduction of CASE software with 112 exercises to train students in conjunction with the traditional pen and paper approach will strengthen their overall understanding of solving unknowns and explore of various structural end points to determine the validity of the results quickly. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  17. A hundred years in the elucidation of the structures of natural products.

    PubMed

    Hanson, James R

    2017-03-01

    The development in the strategies for elucidating the structures of natural products from 1916 to 2016 are reviewed revealing the transition from chemical to spectroscopic methods and using examples drawn from the chemistry of terpenoids and steroids.

  18. Production and structure elucidation of di- and oligosaccharide lipids (biosurfactants) from Tsukamurella sp. nov.

    PubMed

    Vollbrecht, E; Heckmann, R; Wray, V; Nimtz, M; Lang, S

    1998-11-01

    The bacterium Tsukamurella sp. nov., isolated from soil, was found to produce novel glycolipids when grown on sunflower oil as the sole carbon source. The glycolipids were isolated by chromatography on silica columns and their structures elucidated using a combination of multidimensional NMR and MS techniques. The three main components are 2,3-di-O-acyl-alpha-D-glucopyranosyl-(1-1)-alpha-D-glucopyranose, 2,3-di-O-acyl-beta-D-glucopyranosyl-(1-2)-4,6-di-O-acyl-alpha-D- glucopyranosyl-(1-1)-alpha-D-glucopyranose and 2,3-di-O-acyl-beta-D-glucopyranosyl-(1-2)-beta-D-galactopyranosyl- (1-6)-4,6-di-O-acyl-alpha-D-glucopyranosyl-(1-1)-alpha-D- glucopyranosyl which are linked to fatty acids varying in chain length from C4 to C18. The glycolipids are mainly extracellular but are also found attached to the cell walls. During the cultivation the composition of the glycolipids changed from disaccharide- to tri- and tetrasaccharide lipids. The glycolipids show good surface-active behaviour and have antimicrobial properties.

  19. Production and structure elucidation of glycoglycerolipids from a marine sponge-associated microbacterium species.

    PubMed

    Wicke, C; Hüners, M; Wray, V; Nimtz, M; Bilitewski, U; Lang, S

    2000-05-01

    The bacterium Microbacterium sp., isolated from the sponge Halichondria panicea, produced four unusual cell-associated glycoglycerolipids and one diphosphatidylglycerol when grown on marine broth and on artificial seawater media. The lipids were isolated by chromatography on silica columns and their structures elucidated using a combination of multidimensional NMR and MS techniques. The main compound was 1-O-acyl-3-[alpha-glucopyranosyl-(1-3)-(6-O-acyl-alpha-mannopyranosyl )]glycerol (GGL.2) with 14-methyl-hexadecanoic acid and 12-methyl-tetradecanoic acid positioned at C-6 of the mannose unit and at the glycerol moiety. Glycolipid production was correlated with growth and reached a maximum value of 200 mg/L when grown on artificial seawater medium with 20 g/L glucose. The main compound decreased the surface tension of water down to 33 mN/m and the interfacial tension of the water/n-hexadecane system down to 5 mN/m. In addition to this good surface-active behavior, the main glycoglycerolipid showed antitumor activities.

  20. Isolation and purification of a new kalimantacin/batumin-related polyketide antibiotic and elucidation of its biosynthesis gene cluster.

    PubMed

    Mattheus, Wesley; Gao, Ling-Jie; Herdewijn, Piet; Landuyt, Bart; Verhaegen, Jan; Masschelein, Joleen; Volckaert, Guido; Lavigne, Rob

    2010-02-26

    Kal/bat, a polyketide, isolated to high purity (>95%) is characterized by strong and selective antibacterial activity against Staphylococcus species (minimum inhibitory concentration, 0.05 microg/mL), and no resistance was observed in strains already resistant to commonly used antibiotics. The kal/bat biosynthesis gene cluster was determined to a 62 kb genomic region of Pseudomonas fluorescens BCCM_ID9359. The kal/bat gene cluster consists of 16 open reading frames (ORF), encoding a hybrid PKS-NRPS system, extended with trans-acting tailoring functions. A full model for kal/bat biosynthesis is postulated and experimentally tested by gene inactivation, structural confirmation (using NMR spectroscopy), and complementation. The structural and microbiological study of biosynthetic kal/bat analogs revealed the importance of the carbamoyl group and 17-keto group for antibacterial activity. The mechanism of self-resistance lies within the production of an inactive intermediate, which is activated in a one-step enzymatic oxidation upon export. The genetic basis and biochemical elucidation of the biosynthesis pathway of this antibiotic will facilitate rational engineering for the design of novel structures with improved activities. This makes it a promising new therapeutic option to cope with multidrug-resistant clinical infections. Copyright 2010 Elsevier Ltd. All rights reserved.

  1. 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.

  2. Preparation and structural elucidation of a glucomannogalactan from marine fungus Penicillium commune.

    PubMed

    Chen, Yanli; Mao, Wenjun; Wang, Junfeng; Zhu, Weiming; Zhao, Chunqi; Li, Na; Wang, Chunyan; Yan, Mengxia; Guo, Tao; Liu, Xue

    2013-09-12

    The coral-associated fungus Penicillium commune produces an extracellular polysaccharide, FP2-1, when grown in potato dextrose-agar medium. FP2-1 was isolated from the fermented broth using anion-exchange and size-exclusion chromatography, and its structure was elucidated by chemical and spectroscopic analyses, including detailed nuclear magnetic resonance spectroscopy. The results showed that FP2-1 was a glucomannogalactan with a molar ratio of galactose, mannose and glucose of 3.9:1.9:1.0. Structure of FP2-1 may be represented, at an average, as a backbone of (1→2)-linked α-mannopyranose with the every second residue substituted at position 6 by a pentasaccharide branch. The branches consist of four (1→6)-linked β-galactofuranose residues with terminal α-glucopyranose residue attached to the last galactofuranose residue at position 2. FP2-1 was a novel galactofuranose-containing extracellular polysaccharide differing from previously described extracellular polysaccharides. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Annotation and structural elucidation of bovine milk oligosaccharides and determination of novel fucosylated structures

    PubMed Central

    Aldredge, Danielle L; Geronimo, Maria R; Hua, Serenus; Nwosu, Charles C; Lebrilla, Carlito B; Barile, Daniela

    2013-01-01

    Bovine milk oligosaccharides (BMOs) are recognized by the dairy and food industries, as well as by infant formula manufacturers, as novel, high-potential bioactive food ingredients. Recent studies revealed that bovine milk contains complex oligosaccharides structurally related to those previously thought to be present in only human milk. These BMOs are microbiotic modulators involved in important biological activities, including preventing pathogen binding to the intestinal epithelium and serving as nutrients for a selected class of beneficial bacteria. Only a small number of BMO structures are fully elucidated. To better understand the potential of BMOs as a class of biotherapeutics, their detailed structure analysis is needed. This study initiated the development of a structure library of BMOs and a comprehensive evaluation of structure-related specificity. The bovine milk glycome was profiled by high-performance mass spectrometry and advanced separation techniques to obtain a comprehensive catalog of BMOs, including several novel, lower abundant neutral and fucosylated oligosaccharides that are often overlooked during analysis. Structures were identified using isomer-specific tandem mass spectroscopy and targeted exoglycosidase digestions to produce a BMO library detailing retention time, accurate mass and structure to allow their rapid identification in future studies. PMID:23436288

  4. Annotation and structural elucidation of bovine milk oligosaccharides and determination of novel fucosylated structures.

    PubMed

    Aldredge, Danielle L; Geronimo, Maria R; Hua, Serenus; Nwosu, Charles C; Lebrilla, Carlito B; Barile, Daniela

    2013-06-01

    Bovine milk oligosaccharides (BMOs) are recognized by the dairy and food industries, as well as by infant formula manufacturers, as novel, high-potential bioactive food ingredients. Recent studies revealed that bovine milk contains complex oligosaccharides structurally related to those previously thought to be present in only human milk. These BMOs are microbiotic modulators involved in important biological activities, including preventing pathogen binding to the intestinal epithelium and serving as nutrients for a selected class of beneficial bacteria. Only a small number of BMO structures are fully elucidated. To better understand the potential of BMOs as a class of biotherapeutics, their detailed structure analysis is needed. This study initiated the development of a structure library of BMOs and a comprehensive evaluation of structure-related specificity. The bovine milk glycome was profiled by high-performance mass spectrometry and advanced separation techniques to obtain a comprehensive catalog of BMOs, including several novel, lower abundant neutral and fucosylated oligosaccharides that are often overlooked during analysis. Structures were identified using isomer-specific tandem mass spectroscopy and targeted exoglycosidase digestions to produce a BMO library detailing retention time, accurate mass and structure to allow their rapid identification in future studies.

  5. Methods for the comprehensive structural elucidation of constitution and stereochemistry of lipopeptides.

    PubMed

    Gerhardt, Heike; Sievers-Engler, Adrian; Jahanshah, Ghazaleh; Pataj, Zoltán; Ianni, Federica; Gross, Harald; Lindner, Wolfgang; Lämmerhofer, Michael

    2016-01-08

    A panel of methods of general suitability for complete structural elucidation of the stereochemistry of cyclopeptides, depsipeptides and lipopeptides is presented and described in detail. The suitability of the proposed methods was exemplified on the lipopeptide poaeamide from Pseudomonas poae. Amino acid configurations have been assigned by direct LC enantiomer separation with Chiralpak ZWIX(+) and were confirmed by GC enantiomer separation on Chirasil L-Val. 3-Hydroxydecanoic acid absolute configuration was analyzed on Chiralpak ZWIX(+) and confirmed by injection on ZWIX(-) which showed opposite elution order. Plenty of d-amino acids have been found in this lipopeptide. It contained in total 5 Leu residues of which one had d-configuration. The position of the d-Leu in the peptide sequence was determined by pepsin and chemical digestions in combination with isolation of diagnostic peptide-fragments and subsequent identification of absolute configurations of the Leu residues. This allowed pinpointing the position of the d-amino acid. The complementarity of the peptide retention profiles on Chiralpak ZWIX column as compared to both RPLC and HILIC suggests its great utility as an alternative peptide separation tool.

  6. Structural elucidation of the main water-soluble polysaccharide from Rubus anatolicus roots.

    PubMed

    Sahragard, Neda; Jahanbin, Kambiz

    2017-11-01

    An acidic heteropolysaccharide, RAPS-1, was isolated from the roots of Rubus anatolicus by water extraction (70°C) and purification using DEAE-cellulose A52 and Sephadex G-100 column chromatography. The total sugar content and specific optical rotation of RAPS-1 were 96.3% and +196°, respectively. RAPS-1 had a molecular weight of 7900Da, and was composed of glucose, galactose, and glucuronic acid with a relative molar ratio of 6.2: 1.0: 1.2. Structural features of RAPS-1 were elucidated by a combination of partial acid hydrolysis, periodate oxidation and Smith degradation, methylation, GC-MS, FTIR, and NMR ((13)C and (1)H) analysis. The results indicated that RAPS-1 had a backbone of →4)-α-d-Glcp-(1→ residues, with branches attached to O-6 by α-d-Galp-(1→ and by α-d-GlcAp-(1→. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. A new member of the fusaricidin family – structure elucidation and synthesis of fusaricidin E

    PubMed Central

    Reimann, Marcel; Sandjo, Louis P; Antelo, Luis; Thines, Eckhard; Siepe, Isabella

    2017-01-01

    Two hitherto unknown fusaricidins were obtained from fermentation broths of three Paenibacillus strains. After structure elucidation based on tandem mass spectrometry and NMR spectroscopy, fusaricidin E was synthesized to confirm the structure and the suggested stereochemistry. The synthesis was based on a new strategy which includes an efficient access to the 15-guanidino-3-hydroxypentadecanoyl (GHPD) side chain from erucamide. PMID:28781709

  8. A new member of the fusaricidin family - structure elucidation and synthesis of fusaricidin E.

    PubMed

    Reimann, Marcel; Sandjo, Louis P; Antelo, Luis; Thines, Eckhard; Siepe, Isabella; Opatz, Till

    2017-01-01

    Two hitherto unknown fusaricidins were obtained from fermentation broths of three Paenibacillus strains. After structure elucidation based on tandem mass spectrometry and NMR spectroscopy, fusaricidin E was synthesized to confirm the structure and the suggested stereochemistry. The synthesis was based on a new strategy which includes an efficient access to the 15-guanidino-3-hydroxypentadecanoyl (GHPD) side chain from erucamide.

  9. 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…

  10. New milbemycins from Streptomyces hygroscopicus subsp. aureolacrimosus: fermantation, isolation and strucutre elucidation.

    PubMed

    Nonaka, K; Tsukiyama, T; Okamoto, Y; Sato, K; Kumasaka, C; Yammoto, T; Maruyama, F; Yoshikawa, H

    2000-07-01

    Twelve new milbemycins have been isolated and characterized from some strains derived from Streptomyces hygroscopicus subsp. aureolacrimosus SANK 60286 and SANK 60526. The metabolites 1 approximately 4 and 9 approximately 11 were produced by strain RM28D-688 SANK 60797 as minor products. The metabolites 5 approximaetly 8 were obtained from a broth of strain 57-338 SANK 61796. Strain MK-1391 SANK 62896 was used for the production of metabolite 12. The new metabolites, eight alpha-class and four beta-class compounds, have new structural features. For example, milbemycins alpha26 and alpha27, have the 26-hydroxy moiety, and other derivatives (milbemycins alpha20 approximately 23) have different side chains at the C-26 position from those of milbemycins alpha11 and alpha14. In addition, 5-hydroxylmilbemycin beta7 (beta12), involved in the major biosynthetic pathway of 25-methyl and 25-ethyl milbemycins, was discovered.

  11. The structural elucidation and antimicrobial activities of two isoflavane glycosides 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

    2014-11-01

    Two isoflavane glycoside had been isolated from the EtOAc-soluble fraction of the roots of Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge) Hsiao. This is the first report on the structure elucidation of 2‧,5‧-dicarbonyl-3‧,4‧-dimethoxyisoflavanequinone-7-O-β-D-glucoside (1) based on spectroscopic methods including UV (Ultraviolet Spectrophotometry), IR (Infrared Absorption Spectroscopy), ESI-MS (Electrospray Ionization Mass Spectrometry), 1D NMR (Nuclear Magnetic Resonance Spectroscopy) and 2D NMR techniques. At the same time, antimicrobial activity of the two compounds was evaluated against various bacteria and fungi.

  12. Chemical synthesis and structure elucidation of bovine kappa-casein (1-44).

    PubMed

    Bansal, Paramjit S; Grieve, Paul A; Marschke, Ronald J; Daly, Norelle L; McGhie, Emily; Craik, David J; Alewood, Paul F

    2006-02-24

    The caseins (alphas1, alphas2, 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 Pro8 to Arg34. This is the first report which demonstrates extensive secondary structure within the casein class of proteins.

  13. 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.

  14. Structure Elucidation and Cytotoxic Evaluation of New Polyacetylenes from a Marine Sponge Petrosia sp.

    PubMed Central

    Juan, Yung-Shun; Lee, Chien-Chih; Tsao, Chia-Wei; Lu, Mei-Chin; El-Shazly, Mohamed; Shih, Huei-Chuan; Chen, Yu-Cheng; Wu, Yang-Chang; Su, Jui-Hsin

    2014-01-01

    The sponge Petrosia sp. yielded five polyacetylenic compounds (1–5), including two new polyacetylenes, petrosianynes A (1) and B (2). The structures of these compounds were elucidated by detailed spectroscopic analysis and by comparison with the physical and spectral data of related known analogues. Compounds 1–5 exhibited significant cytotoxic activity against a limited panel of cancer cell lines. PMID:25238415

  15. New beauvericins, potentiators of antifungal miconazole activity, Produced by Beauveria sp. FKI-1366. II. Structure elucidation.

    PubMed

    Fukuda, Takashi; Arai, Masayoshi; Tomoda, Hiroshi; Omura, Satoshi

    2004-02-01

    The structures of beauvericins D, E and F, novel potentiators of miconazole activity against Candida albicans produced by Beauveria sp. FKI 1366, were elucidated by various spectroscopic analyses including UV, NMR, and MS and degradation experiments. They have the common skeleton of the 18-membered cyclodepsipeptides.

  16. Biosynthesis of photodynamically active rubellins and structure elucidation of new anthraquinone derivatives produced by Ramularia collo-cygni.

    PubMed

    Miethbauer, Sebastian; Haase, Susann; Schmidtke, Kai-Uwe; Günther, Wolfgang; Heiser, Ingrid; Liebermann, Bernd

    2006-06-01

    Here we present the first isolation of the anthrachinone derivative rubellin A out of mycelium and culture filtrate of Ramularia collo-cygni. Furthermore, two compounds, rubellin E and 14-dehydro rubellin D were isolated and their structures elucidated. In comparison to the other rubellins, rubellin A shows increased photodynamic oxygen activation. By incorporating both [1-(13)C]-acetate and [2-(13)C]-acetate into the rubellins, we showed that such anthraquinone derivatives were biosynthesised via the polyketide pathway. The labelling pattern after being fed [U-(13)C(6)]-glucose proved the existence of fungal folding mode of the poly-beta-keto chain. The ability to produce rubellins is not limited to R. collo-cygni in the anamorph genus Ramularia.

  17. 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.

  18. 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.

  19. Structure elucidation and NMR assignments of an unusual triterpene saponin derivative from Ilex kudincha.

    PubMed

    Zuo, Wenjian; Wang, Qinghu; Li, Wen; Sha, Yi; Li, Xian; Wang, Jinhui

    2012-04-01

    One unusual triterpenoid derivative, ilekudinchoside E (1), was isolated from the leaves of Ilex kudincha. The structure was established by various spectroscopic techniques, including one- and two-dimensional NMR, HRTOFMS and CD spectra.

  20. X-ray crystallography and the elucidation of the structure of DNA.

    PubMed

    McGregor, Hugh C J; Gunderman, Richard B

    2011-06-01

    Since their discovery by Roentgen in 1895, x-rays have contributed to some of the most important advances in science. X-ray crystallography is an imaging technique that uses x-ray diffraction to evaluate the molecular structure of a crystalline solid. This article discusses the critical role played by x-ray crystallography in the elucidation of the structure of DNA. The story of DNA includes insights on molecular structure provided by x-rays and also lessons on scientific collaboration and innovation that can be applied to radiology today.

  1. Aqabamycins A-G: novel nitro maleimides from a marine Vibrio species: II. Structure elucidation.

    PubMed

    Fotso Fondja Yao, Clarisse Blandine; Al Zereini, Wael; Fotso, Serge; Anke, Heidrun; Laatsch, Hartmut

    2010-06-01

    The structures of secondary metabolites with antibacterial and cytotoxic activities produced by a marine Vibrio strain from the Red Sea were elucidated. Aqabamycin A (1a) and seven further nitro-substituted maleimide derivates named aqabamycins B-G (1b-f and 2) were obtained together with 12 known metabolites, 3-nitro-1H-indazole (3), indazole-3-carbaldehyde (4), 3-nitro-4-hydroxycinnamic acid, 4-hydroxycinnamic acid, 3-nitro-4-hydroxybenzaldehyde, phenyl-2-bis-indolylmethane (5a), turbomycin B (5b), vibrindole A (6), phenylacetic acid, 3-hydroxybenzoic acid, benzoic acid and 1,4-dithiane (7). Some of the known metabolites (for example, 3, 4 and 7) are described in this study for the first time as natural products. Their structures were elucidated based on 1D and 2D NMR, MS spectra and by comparison with synthetic material.

  2. Characterization of Cell Wall Proteins in Saccharomyces cerevisiae Clinical Isolates Elucidates Hsp150p in Virulence

    PubMed Central

    Hsu, Pang-Hung; Chiang, Pei-Chi; Liu, Chia-Hsun; Chang, Ya-Wen

    2015-01-01

    The budding yeast Saccharomyces cerevisiae has recently been described as an emerging opportunistic fungal pathogen. Fungal cell wall mannoproteins have been demonstrated to be involved in adhesion to inert surfaces and might be engaged in virulence. In this study, we observed four clinical isolates of S. cerevisiae with relatively hydrophobic cell surfaces. Yeast cell wall subproteome was evaluated quantitatively by liquid chromatography/tandem mass spectrometry. We identified totally 25 cell wall proteins (CWPs) from log-phase cells, within which 15 CWPs were quantified. The abundance of Scw10p, Pst1p, and Hsp150p/Pir2p were at least 2 folds higher in the clinical isolates than in S288c lab strain. Hsp150p is one of the members in Pir family conserved in pathogenic fungi Candida glabrata and Candida albicans. Overexpression of Hsp150p in lab strain increased cell wall integrity and potentially enhanced the virulence of yeast. Altogether, these results demonstrated that quantitative cell wall subproteome was analyzed in clinical isolates of S. cerevisiae, and several CWPs, especially Hsp150p, were found to be expressed at higher levels which presumably contribute to strain virulence and fungal pathogenicity. PMID:26270963

  3. Characterization of Cell Wall Proteins in Saccharomyces cerevisiae Clinical Isolates Elucidates Hsp150p in Virulence.

    PubMed

    Hsu, Pang-Hung; Chiang, Pei-Chi; Liu, Chia-Hsun; Chang, Ya-Wen

    2015-01-01

    The budding yeast Saccharomyces cerevisiae has recently been described as an emerging opportunistic fungal pathogen. Fungal cell wall mannoproteins have been demonstrated to be involved in adhesion to inert surfaces and might be engaged in virulence. In this study, we observed four clinical isolates of S. cerevisiae with relatively hydrophobic cell surfaces. Yeast cell wall subproteome was evaluated quantitatively by liquid chromatography/tandem mass spectrometry. We identified totally 25 cell wall proteins (CWPs) from log-phase cells, within which 15 CWPs were quantified. The abundance of Scw10p, Pst1p, and Hsp150p/Pir2p were at least 2 folds higher in the clinical isolates than in S288c lab strain. Hsp150p is one of the members in Pir family conserved in pathogenic fungi Candida glabrata and Candida albicans. Overexpression of Hsp150p in lab strain increased cell wall integrity and potentially enhanced the virulence of yeast. Altogether, these results demonstrated that quantitative cell wall subproteome was analyzed in clinical isolates of S. cerevisiae, and several CWPs, especially Hsp150p, were found to be expressed at higher levels which presumably contribute to strain virulence and fungal pathogenicity.

  4. Elucidation of peptide-directed palladium surface structure for biologically tunable nanocatalysts.

    PubMed

    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, Marc R

    2015-05-26

    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 elucidated 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.

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

    PubMed

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

    2013-10-02

    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.

  6. Structural Elucidation of a Small Molecule Inhibitor of Protein Disulfide Isomerase

    PubMed Central

    2015-01-01

    Compound libraries provide a starting point for multiple biological investigations, but the structural integrity of compounds is rarely assessed experimentally until a late stage in the research process. Here, we describe the discovery of a neuroprotective small molecule that was originally incorrectly annotated with a chemical structure. We elucidated the correct structure of the active compound using analytical chemistry, revealing it to be the natural product securinine. We show that securinine is protective in a cell model of Huntington disease and identify the binding site of securinine to its target, protein disulfide isomerase using NMR chemical shift perturbation studies. We show that securinine displays favorable pharmaceutical properties, making it a promising compound for in vivo studies in neurodegenerative disease models. In addition to finding this unexpected activity of securinine, this study provides a systematic roadmap to those who encounter compounds with incorrect structural annotation in the course of screening campaigns. PMID:26500720

  7. Genius: a genetic algorithm for automated structure elucidation from 13C NMR spectra.

    PubMed

    Meiler, Jens; Will, Martin

    2002-03-06

    The automated structure elucidation of organic molecules from experimentally obtained properties is extended by an entirely new approach. A genetic algorithm is implemented that uses molecular constitution structures as individuals. With this approach, the structure of organic molecules can be optimized to meet experimental criteria, if in addition a fast and accurate method for the prediction of the used physical or chemical features is available. This is demonstrated using 13C NMR spectrum as readily obtainable information. By means of artificial neural networks a fast and accurate method for calculating the 13C NMR spectrum of the generated structures exists. The method is implemented and tested successfully for organic molecules with up to 18 non-hydrogen atoms.

  8. 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.

  9. 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.

  10. Computer-Assisted 3D Structure Elucidation of Natural Products using Residual Dipolar Couplings.

    PubMed

    Troche-Pesqueira, Eduardo; Anklin, Clemens; Gil, Roberto R; Navarro-Vázquez, Armando

    2017-03-20

    An enhanced computer-assisted procedure for the determination of the relative configuration of natural products, which starts from the molecular formula and uses a combination of conventional 1D and 2D NMR spectra, and residual dipolar couplings (RDCs), is reported. Having already the data acquired (1D/2D NMR and RDCs), the procedure begins with the determination of the molecular constitution using standard computer-assisted structure elucidation (CASE) and is followed by fully automated determination of relative configuration through RDC analysis. In the case of moderately flexible molecules the simplest data-explaining conformational model is selected by the use of the Akaike information criterion.

  11. 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.

  12. Elucidation of the structure of the oligosaccharide from wild type Moraxella bovis Epp63 lipooligosaccharide.

    PubMed

    De Castro, Cristina; Grice, I Darren; Daal, Terese-Marie; Peak, Ian R; Molinaro, Antonio; Wilson, Jennifer C

    2014-03-31

    Moraxella bovis is a Gram-negative microorganism that causes Infectious Bovine Keratoconjunctivitis (IBK), colloquially known as 'Pink eye' in cattle worldwide. Lipopolysaccharides/lipooligosaccharides are the predominant glycans on the surface of Gram-negative microorganisms. Structural elucidation of the oligosaccharide structure of the rough phenotype of Moraxella bovis strain Epp63 was determined using GC-MS, methylation analysis, and NMR spectroscopy. The oligosaccharide is a branched structure that comprises 10 sugars in addition to KDO. The unusual features of this oligosaccharide include the fact that the oligosaccharide is devoid of heptose. The KDO residue is directly attached to a (→4,6)-branched glucose and additionally contains a terminal open chain acetal-linked N-acetylgalactosamine, (1S)-GalaNAc residue →4,6-linked to a sub-terminal galactose residue.

  13. Development of an analytical method for the unambiguous structure elucidation of cyclic peptides with special appliance for hepatotoxic desmethylated microcystins.

    PubMed

    Krüger, Thomas; Christian, Bernd; Luckas, Bernd

    2009-09-01

    The periodical occurrence of harmful algal blooms (HABs) in freshwater lakes requires the determination of potential cyanobacterial toxins, especially microcystins (MCs). On demand of an adequate risk assessment, the high diversity of these hepatotoxic cyclic heptapeptides implicates the need of an unambiguous detection of their specific structural variants. Therefore, LC-MS and LC-MS/MS methods are the approaches of choice for determination of MCs. In contrast, even tandem mass spectromic fragmentation patterns are not even sufficient in any kind of structural determination requirements, whereas NMR methods require very high amounts of MCs. In this study, we present a novel method for chromatographic separation of desmethylated microcystins (dm-MCs). Based on the isolation of the specific structural variants using semi-preparative HPLC, a method was developed for the structure elucidation of cyclic peptides with special appliance for the determination of dm-MCs via analysis of the specific amino acid composition after peptide hydrolysis followed by stereospecific detection of the amino acids and resulting keto acids. On the basis of this method it is demonstrated that dm-MC-RR with the structure [Dha(7)]MC-RR represented the major compound in the microcystin pattern of Microcystis aeruginosa bloom events in 2005 and 2006 in Lake Senftenberg, Germany.

  14. Complete structure elucidation of shishididemniols, complex lipids with tyramine-derived tether and two serinol units, from a marine tunicate of the family Didemnidae.

    PubMed

    Kobayashi, Hirotsugu; Ohashi, Jun'ichiro; Fujita, Tsuyoshi; Iwashita, Takashi; Nakao, Yoichi; Matsunaga, Shigeki; Fusetani, Nobuhiro

    2007-02-16

    Two new serinolipid derivatives, shishididemniols A (1) and B (2), were isolated as antibacterial constituents of a tunicate of the family Didemnidae. The structure of 1 was elucidated by interpretation of spectral data and the application of the modified Mosher method to 1 and its suitable degradation products. Compound 2 was the chlorohydrin of 1. Compounds 1 and 2 exhibited antibacterial activity against fish pathogenic bacterium Vibrio anguillarum.

  15. Structure elucidation and phytotoxicity of C13 nor-isoprenoids from Cestrum parqui.

    PubMed

    D'Abrosca, Brigida; DellaGreca, Marina; Fiorentino, Antonio; Monaco, Pietro; Oriano, Palma; Temussi, Fabio

    2004-02-01

    Twelve C(13) nor-isoprenoids have been isolated from the leaves of Cestrum parqui (Solanaceae). The structure (2R,6R,9R)-2,9-dihydroxy-4-megastigmen-3-one has been assigned to the new compound. All the structures have been determined by spectroscopic means and chemical correlations. The compounds showed phytotoxic effect on the germination and growth of Lactuca sativa L.

  16. Mitochondria: isolation, structure and function.

    PubMed

    Picard, Martin; Taivassalo, Tanja; Gouspillou, Gilles; Hepple, Russell T

    2011-09-15

    Mitochondria are complex organelles constantly undergoing processes of fusion and fission, processes that not only modulate their morphology, but also their function. Yet the assessment of mitochondrial function in skeletal muscle often involves mechanical isolation of the mitochondria, a process which disrupts their normally heterogeneous branching structure and yields relatively homogeneous spherical organelles. Alternatively, methods have been used where the sarcolemma is permeabilized and mitochondrial morphology is preserved, but both methods face the downside that they remove potential influences of the intracellular milieu on mitochondrial function. Importantly, recent evidence shows that the fragmented mitochondrial morphology resulting from routine mitochondrial isolation procedures used with skeletal muscle alters key indices of function in a manner qualitatively similar to mitochondria undergoing fission in vivo. Although these results warrant caution when interpreting data obtained with mitochondria isolated from skeletal muscle, they also suggest that isolated mitochondrial preparations might present a useful way of interrogating the stress resistance of mitochondria. More importantly, these new findings underscore the empirical value of studying mitochondrial function in minimally disruptive experimental preparations. In this review, we briefly discuss several considerations and hypotheses emerging from this work.

  17. Mitochondria: isolation, structure and function

    PubMed Central

    Picard, Martin; Taivassalo, Tanja; Gouspillou, Gilles; Hepple, Russell T

    2011-01-01

    Abstract Mitochondria are complex organelles constantly undergoing processes of fusion and fission, processes that not only modulate their morphology, but also their function. Yet the assessment of mitochondrial function in skeletal muscle often involves mechanical isolation of the mitochondria, a process which disrupts their normally heterogeneous branching structure and yields relatively homogeneous spherical organelles. Alternatively, methods have been used where the sarcolemma is permeabilized and mitochondrial morphology is preserved, but both methods face the downside that they remove potential influences of the intracellular milieu on mitochondrial function. Importantly, recent evidence shows that the fragmented mitochondrial morphology resulting from routine mitochondrial isolation procedures used with skeletal muscle alters key indices of function in a manner qualitatively similar to mitochondria undergoing fission in vivo. Although these results warrant caution when interpreting data obtained with mitochondria isolated from skeletal muscle, they also suggest that isolated mitochondrial preparations might present a useful way of interrogating the stress resistance of mitochondria. More importantly, these new findings underscore the empirical value of studying mitochondrial function in minimally disruptive experimental preparations. In this review, we briefly discuss several considerations and hypotheses emerging from this work. PMID:21708903

  18. Streamlined structure elucidation of an unknown compound in a pigment formulation.

    PubMed

    Yüce, Imanuel; Morlock, Gertrud E

    2016-10-21

    A fast and reliable quality control is important for ink manufacturers to ensure a constant production grade of mixtures and chemical formulations, and unknown components attract their attention. Structure elucidating techniques seem time-consuming in combination with column-based methods, but especially the low solubility of pigment formulations is challenging the analysis. In contrast, layer chromatography is more tolerant with regard to pigment particles. One PLC plate for NMR and FTIR analyses and one HPTLC plate for recording of high resolution mass spectra, MS/MS spectra and for gathering information on polarity and spectral properties were needed to characterize a structure, exemplarily shown for an unknown component in pigment Red 57:1 to be 3-hydroxy-2-naphtoic acid. A preparative layer chromatography (PLC) workflow was developed that used an Automated Multiple Development 2 (AMD 2) system. The 0.5-mm PLC plate could still be operated in the AMD 2 system and allowed a smooth switch from the analytical to the preparative gradient separation. Through automated gradient development and the resulting focusing of bands, the sharpness of the PLC bands was improved. For NMR, the necessary high load of the target compound on the PLC plate was achieved via a selective solvent extraction that discriminated the polar sample matrix and thus increased the application volume of the extract that could maximally be applied without overloading. By doing so, the yield for NMR analysis was improved by a factor of 9. The effectivity gain through a simple, but thoroughly chosen extraction solvent is often overlooked, and for educational purpose, it was clearly illustrated and demonstrated by an extended solvent screening. Thus, PLC using an automated gradient development after a selective extraction was proven to be a new powerful combination for structural elucidation by NMR.

  19. Natural bromophenols from the marine red alga Polysiphonia urceolata (Rhodomelaceae): structural elucidation and DPPH radical-scavenging activity.

    PubMed

    Li, Ke; Li, Xiao-Ming; Ji, Nai-Yun; Wang, Bin-Gui

    2007-11-01

    Three new natural occurring bromophenols, 3-(3-bromo-4,5-dihydroxyphenyl)-2-(3,5-dibromo-4-hydroxyphenyl)propionic acid (1), (E)-4-(3-bromo-4,5-dihydroxyphenyl)-but-3-en-2-one (2), and (3,5-dibromo-4-hydroxyphenyl) acetic acid butyl ester (3), together with one known bromophenol, 1,2-bis(3-bromo-4,5-dihydroxyphenyl)ethane (4), were isolated and identified from the marine red alga Polysiphonia urceolata. The structures of these compounds were elucidated by extensive analysis of 1D and 2D NMR and IR spectra and MS data. Each of the isolated compounds was evaluated for scavenging alpha, alpha-diphenyl-beta-picrylhydrazyl (DPPH) radical activity and all of them exhibited significant activity with IC(50) values ranging from 9.67 to 21.90 microM, compared to the positive control, a well-known antioxidant butylated hydroxytoluene (BHT), with IC(50) 83.84 microM.

  20. 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. (c) 2009 Wiley-Liss, Inc.

  1. 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.

  2. 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.

  3. Structure elucidation of an immunostimulatory arabinoxylan-type polysaccharide prepared from young barley leaves (Hordeum vulgare L.).

    PubMed

    Kim, Hoon; Hong, Hee-Do; Shin, Kwang-Soon

    2017-02-10

    We recently isolated an immunostimulating polysaccharide (BLE-P-I), which possesses a large proportion of arabinoxylan, from young barley leaves. In the present study, to elucidate the structural details of BLE-P-I, it was fractionated into enzyme-resistant fraction (BLE-P-I-X1) and arabinoxylan-rich oligosaccharide fraction (BLE-P-I-X2) after endo-xylanase hydrolysis. Commercial wheat arabinoxylan was also fractionated into WAX-XI and WAX-X2 after the same treatment. BLE-P-I-X2 consisted of arabinose and xylose, including 11 types of neutral glycosidic linkages, whereas WAX-X2 had less, with 6 types of linkages. Mass spectrometric results indicated that WAX-X2 was composed of a xylan backbone bearing only arabinose. In contrast, BLE-P-I-X2 consisted of a xylan backbone with acetate, arabinose, galactose, glucuronic acid, and 4-O-methylglucuronic acid, resembling structural characteristics as glucuronoarabinoxylan. Macrophage-stimulatory activity showed that BLE-P-I-X2 has a role in the expression of the activity. These results indicate that the structural complexity of arabinoxylan seems to be responsible for the immunomodulatory activity in barley leaf. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Structural elucidation of supramolecular alpha-cyclodextrin dimer/aliphatic monofunctional molecules complexes.

    PubMed

    Barrientos, L; Lang, E; Zapata-Torres, G; Celis-Barros, C; Orellana, C; Jara, P; Yutronic, N

    2013-05-01

    The structural elucidation of 2α-cyclodextrin/1-octanethiol, 2α-cyclodextrin/1-octylamine and 2α-cyclodextrin/1-nonanoic acid inclusion complexes by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling has been achieved. The detailed spatial configurations are proposed for the three inclusion complexes based on 2D NMR method. ROESY experiments confirm the inclusion of guest molecules inside the α-cyclodextrin (α-CD) cavity. On the other hand, the host-guest ratio observed was 2:1 for three complexes. The detailed spatial configuration proposed based on 2D NMR methods were further interpreted using molecular modeling studies. The theoretical calculations are in good agreement with the experimental data.

  5. Structure elucidation of metabolite x17299 by interpretation of mass spectrometric data.

    PubMed

    Zhang, Qibo; Ford, Lisa A; Evans, Anne M; Toal, Douglas R

    2017-01-01

    A major bottleneck in metabolomic studies is metabolite identification from accurate mass spectrometric data. Metabolite x17299 was identified in plasma as an unknown in a metabolomic study using a compound-centric approach where the associated ion features of the compound were used to determine the true molecular mass. The aim of this work is to elucidate the chemical structure of x17299, a new compound by de novo interpretation of mass spectrometric data. An Orbitrap Elite mass spectrometer was used for acquisition of mass spectra up to MS(4) at high resolution. Synthetic standards of N,N,N-trimethyl-l-alanyl-l-proline betaine (l,l-TMAP), a diastereomer, and an enantiomer were chemically prepared. The planar structure of x17299 was successfully proposed by de novo mechanistic interpretation of mass spectrometric data without any laborious purification and nuclear magnetic resonance spectroscopic analysis. The proposed structure was verified by deuterium exchanged mass spectrometric analysis and confirmed by comparison to a synthetic standard. Relative configuration of x17299 was determined by direct chromatographic comparison to a pair of synthetic diastereomers. Absolute configuration was assigned after derivatization of x17299 with a chiral auxiliary group followed by its chromatographic comparison to a pair of synthetic standards. The chemical structure of metabolite x17299 was determined to be l,l-TMAP.

  6. 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

  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. Structural identification of imatinib cyanide adducts by mass spectrometry and elucidation of bioactivation pathway.

    PubMed

    Li, Austin C; Yu, Erya; Ring, Steven C; Chovan, James P

    2014-01-15

    Recent publications have reported that imatinib forms cyanide and methoxylamine adducts in vitro but without detail structural identification. The current work reports the identification of seven cyanide adducts that elucidate the bioactivation pathways and may provide hints for observed clinical adverse effects of the drug. Imatinib was incubated with human liver microsomal proteins in the presence of a NADPH-regeneration system and the trapping agents reduced GSH, potassium cyanide and methoxylamine. Samples were analyzed by high-performance liquid chromatography (HPLC) coupled with a LTQ-Orbitrap data collection system. Chemical structures were determined and/or postulated based on data-dependent high-resolution tandem mass spectrometric (MS(n)) exact mass measurements in both positive and negative scan modes, as well as in combination with hydrogen-deuterium exchange (HDX). GSH and methoxylamine conjugates were either not detected or were in insufficient quantities for characterization. However, seven cyanide conjugates were identified, indicating that the piperazine and p-toluidine partial structures in imatinib can become bioactivated and subsequently trapped by the nucleophile cyanide ion. The reactive intermediates were postulated as imine and imine-carbonyl conjugate (α,β-unsaturated) structures on the piperazine ring, and imine-methide on the p-toluidine partial structure. Chemical structures of seven cyanide adducts of imatinib have been identified or proposed based on high-resolution MS/MS data. Mechanisms for the formation of the conjugates were also proposed. The findings may help to understand the mechanism of hepatotoxicity of imatinib in humans. Copyright © 2013 John Wiley & Sons, Ltd.

  9. Structure elucidation of thioketone analogues of sildenafil detected as adulterants in herbal aphrodisiacs.

    PubMed

    Reepmeyer, John C; d'Avignon, D André

    2009-01-15

    Two analogues of sildenafil were detected in herbal dietary supplements marketed as aphrodisiacs. Both compounds were identified as thioketone analogues of sildenafil in which the carbonyl group in the pyrimidine ring of sildenafil was substituted with a thiocarbonyl group. The first compound was identified as thiosildenafil, a compound that has recently been reported as an adulterant in health supplements. The structure of the second compound was established using LC-MS, UV spectroscopy, ESI-MS(n), NMR and a hydrolytic process. A detailed study of the hydrolysis products of sildenafil, thiosildenafil, and the second unknown compound proved that the second compound, named thiomethisosildenafil, had a structure analogous to sildenafil in which the N-methylpiperazine moiety had been replaced with 2,6-dimethylpiperazine and the oxygen atom of the carbonyl group in the heterocyclic ring had been replaced with a sulfur atom. Under the hydrolytic reaction conditions employed in this study, thioketones hydrolyze to ketones (e.g., thiosildenafil-->sildenafil), making this a valuable technique for the structure elucidation of thiosildenafil analogues. Ten herbal dietary supplements, each as a capsule dosage form, were found to contain 8-151 mg of thiomethisosildenafil per capsule, and one herbal dietary supplement was found to contain 35 mg of thiosildenafil per capsule.

  10. Analytical characterization and structure elucidation of metabolites from Aspergillus ochraceus MP2 fungi

    PubMed Central

    Meenupriya, J; Thangaraj, M

    2011-01-01

    Objective To isolate and characterize the bioactive secondary metabolites from Aspergillus ochraceus (A. ochraceus) MP2 fungi. Methods The anti bacterial activity of marine sponge derived fungi A. ochraceus MP2 was thoroughly investigated against antagonistic human pathogens. The optimum inhibitory concentration of the fungi in the elite solvent was also determined. The promising extracts that showed good antimicrobial activity were subjected to further analytical separation to get individual distinct metabolites and the eluants were further identified by GC MS instrumental analysis. The molecular characterization of the elite fungal strains were done by isolating their genomic DNA and amplify the internal transcribed spacer (ITS) region of 5.8s rRNA using specific ITS primer. The novelty of the strain was proved by homology search tools and elite sequences was submitted to GENBANK. Results Three bioactive compounds were characterized to reveal their identity, chemical formula and structure. The first elutant was identified asα- Campholene aldehyde with chemical formula C10 H16 O and molecular weight 152 Da. The second elutant was identified as Lucenin-2 and chemical formula C27 H30 O16 and molecular weight 610 Da. The third elutant was identified as 6-Ethyloct- 3-yl- 2- ethylhexyl ester with Chemical formula C26 H42 O4 with molecular weight 418 Da. Conclusions The isolated compounds showed significant antimicrobial activity against potential human pathogens. Microbial secondary metabolites represent a large source of compounds endowed with ingenious structures and potent biological activities. PMID:23569796

  11. 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.

  12. On-line NMR detection of microgram quantities of heparin-derived oligosaccharides and their structure elucidation by microcoil NMR.

    PubMed

    Korir, Albert K; Larive, Cynthia K

    2007-08-01

    The isolation and purification of sufficient quantities of heparin-derived oligosaccharides for characterization by NMR is a tedious and time-consuming process. In addition, the structural complexity and microheterogeneity of heparin makes its characterization a challenging task. The improved mass-sensitivity of microcoil NMR probe technology makes this technique well suited for characterization of mass-limited heparin-derived oligosaccharides. Although microcoil probes have poorer concentration sensitivity than conventional NMR probes, this limitation can be overcome by coupling capillary isotachophoresis (cITP) with on-line microcoil NMR detection (cITP-NMR). Strategies to improve the sensitivity of on-line NMR detection through changes in probe design and in the cITP-NMR experimental protocol are discussed. These improvements in sensitivity allow acquisition of cITP-NMR survey spectra facilitating tentative identification of unknown oligosaccharides. Complete structure elucidation for microgram quantities of the purified material can be carried out through acquisition of 2D NMR spectra using a CapNMR microcoil probe.

  13. Biosynthetic considerations could assist the structure elucidation of host plant produced rhizosphere signalling compounds (strigolactones) for arbuscular mycorrhizal fungi and parasitic plants.

    PubMed

    Rani, Kumkum; Zwanenburg, Binne; Sugimoto, Yukihiro; Yoneyama, Koichi; Bouwmeester, Harro J

    2008-07-01

    Parasitic plants cause devastating losses to crop yields in several parts of the world. The root parasites, Striga and Orobanche species, use chemical signalling molecules that are exuded by the roots of plants in extremely low concentrations, and that can induce germination of the seeds of these parasites, to detect the vicinity of a suitable host. The majority of the so far identified germination stimulants belong to the strigolactones. It was recently discovered that this class of compounds can also induce hyphal branching in the symbiotic arbuscular mycorrhizal fungi, a process involved in root colonisation. The elucidation of the structure of new strigolactones is hindered by their low abundance and instability. In the present paper, we have used existing knowledge on the structure of strigolactones and combined it with recently obtained insight in the biosynthetic origin of these signalling compounds. This enabled us to postulate structures for strigolactones that have been isolated but for which so far the structure has not been elucidated, but also to propose structures of strigolactones that may be discovered in the future. Considering the strongly increased importance of the strigolactones, we expect that more groups will look for these compounds and also in systems so far not exploited. This could lead to the discovery of new strigolactones for which we expect the present biogenetic considerations will facilitate identification and structure elucidation.

  14. A Mathematical Model to Elucidate Brain Tumor Abrogation by Immunotherapy with T11 Target Structure

    PubMed Central

    Chaudhuri, Swapna

    2015-01-01

    T11 Target structure (T11TS), a membrane glycoprotein isolated from sheep erythrocytes, reverses the immune suppressed state of brain tumor induced animals by boosting the functional status of the immune cells. This study aims at aiding in the design of more efficacious brain tumor therapies with T11 target structure. We propose a mathematical model for brain tumor (glioma) and the immune system interactions, which aims in designing efficacious brain tumor therapy. The model encompasses considerations of the interactive dynamics of glioma cells, macrophages, cytotoxic T-lymphocytes (CD8+ T-cells), TGF-β, IFN-γ and the T11TS. The system undergoes sensitivity analysis, that determines which state variables are sensitive to the given parameters and the parameters are estimated from the published data. Computer simulations were used for model verification and validation, which highlight the importance of T11 target structure in brain tumor therapy. PMID:25955428

  15. 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

  16. 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.

  17. Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle

    NASA Astrophysics Data System (ADS)

    Yu, Jin; Da, Lin-Tai; Huang, Xuhui

    2015-02-01

    The RNA polymerase II elongation is central in eukaryotic transcription. Although multiple intermediates of the elongation complex have been identified, the dynamical mechanisms remain elusive or controversial. Here we build a structure-based kinetic model of a full elongation cycle of polymerase II, taking into account transition rates and conformational changes characterized from both single molecule experimental studies and computational simulations at atomistic scale. Our model suggests a force-dependent slow transition detected in the single molecule experiments corresponds to an essential conformational change of a trigger loop (TL) opening prior to the polymerase translocation. The analyses on mutant study of E1103G and on potential sequence effects of the translocation substantiate this proposal. Our model also investigates another slow transition detected in the transcription elongation cycle which is independent of mechanical force. If this force-independent slow transition happens as the TL gradually closes upon NTP binding, the analyses indicate that the binding affinity of NTP to the polymerase has to be sufficiently high. Otherwise, one infers that the slow transition happens pre-catalytically but after the TL closing. Accordingly, accurate determination of intrinsic properties of NTP binding is demanded for an improved characterization of the polymerase elongation. Overall, the study provides a working model of the polymerase II elongation under a generic Brownian ratchet mechanism, with most essential structural transition and functional kinetics elucidated.

  18. Elucidation of structure-to-property relationships of piezoresistive polymer-carbon nanotube nanocomposites

    NASA Astrophysics Data System (ADS)

    Fang, Weiqing; Leung, Siu N.

    2015-07-01

    Polymeric nanocomposites (PNC) filled with carbon nanotubes (CNTs) possess superior multifunctionality, including electrical, thermal, and mechanical properties, making them an emerging family of advanced and multifunctional materials. In recent years, flexible polymer/CNT nanocomposites are increasingly being considered as promising alternatives to conventional smart materials. Their piezoresistive behaviours have led to many potential applications in strain sensing. Despite extensive experimental and theoretical research, the underlying mechanisms for polymer/CNT nanocomposites' piezoresistive behaviours have yet been elucidated. This paper reports comprehensive investigations on the mechanisms and the structure-to-property relationships of these piezoresistive nanocomposites. Quantitative analyses revealed that piezoresistivity of polymer/CNT nanocomposites is predominantly governed by the three mechanisms related to the strain-induced morphological evolution of the CNT network embedded in the polymer matrix. Furthermore, both CNT content and CNT alignment are key structural parameters that affect the contribution of different mechanisms on PNCs' piezoresistivity and the sensitivity of flexible PNCs as strain sensors. For PNC filled with high content of randomly dispersed CNTs, the piezoresistivity was predominantly caused by the breakage of a complex conductive network into two or more simpler conductive paths. For PNC filled with low content of highly aligned CNTs, the piezoresistivity was mainly contributed by the complete disruption of originally interconnected CNTs in electrically conductive pathways.

  19. Characterization of a bioactive polysaccharide from Ganoderma atrum: Re-elucidation of the fine structure.

    PubMed

    Zhang, Hui; Nie, Shaoping; Cui, Steve W; Xu, Ming; Ding, Huihuang; Xie, Mingyong

    2017-02-20

    The fine structure in terms of backbone and branch chain features of a bioactive polysaccharide from Ganoderma atrum (PSG-1) was re-elucidated systematically using high performance anion-exchange chromatography (HPAEC), methylation and GLC-MS analysis, and 1D & 2D NMR spectroscopy. Monosaccharide composition analysis revealed that PSG-1-F0.2 fraction mainly consisted of glucose (73.8%) and glucuronic acid (15.3%), with small amount of mannose (5.7%) and galactose (5.2%). Based on methylation, multistep partial acid hydrolysis and NMR study, were proposed to substitute at the O-6 position of β-(1→3)-glucan. The small amount of mannose and galactose residues were considered to be from the other fraction in PSG which was very difficult to be separated from PSG-1-F0.2. This revised structure as an acidic β-(1→3, 1→6)-glucan is considered to be more accurate than the previous proposal of PSG-1.

  20. Production and structural elucidation of exopolysaccharide from endophytic Pestalotiopsis sp. BC55.

    PubMed

    Mahapatra, Subhadip; Banerjee, Debdulal

    2016-01-01

    There is a little information on exopolysaccharide production by endophytic fungi. In this investigation endophytic Pestalotiopsis sp. BC55 was used for optimization of exopolysaccharide production. One variable at a time method and response surface methodology were adopted to find out the best culture conditions and medium compositions for maximum exopolysaccharide production. The organism produced maximum exopolysaccharide (4.320 ± 0.022 g/l EPS) in 250 ml Erlenmeyer flask containing 75 ml potato dextrose broth supplemented with (g%/l) glucose, 7.66; urea, 0.29; CaCl2, 0.05 with medium pH 6.93; after 3.76 days of incubation at 24°C. Exopolysaccharide [EPS (EP-I)] produced by this organism have Mw ∼2×10(5)Da with a melting point range of 122-124°C. Structural elucidation of the EPS (PS-I) was carried out after a series of experiments. Result indicated the presence of only (1→3)-linked β-d-glucopyranosyl moiety. The structure of the repeating unit was established as - →3)-β-d-Glcp-(1→. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. 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.

  2. 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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Isoflavones from Maclura pomifera: structural elucidation and in silico evaluation of their interaction with PDE5.

    PubMed

    Ribaudo, Giovanni; Vendrame, Tiziano; Bova, Sergio

    2017-09-01

    While osajin and pomiferin are known for their anticancer, antibacterial and antidiabetic properties, scandenone and auriculasin have been proposed as anti-inflammatory and antinociceptive agents. Curiously, these two couples of molecules are, from a chemical point of view, structural isomers which can all be extracted from Maclura pomifera. Although previous works described, separately, the isolation in reasonable amounts of the sole osajin/pomiferin couple or of scandenone/auriculasin, we report the extraction and characterization using direct spectral and chromatographical comparison of the four compounds. 2D NMR allowed to unambiguously assign the correct structures to the isomers. The compounds were screened in silico against PDE5 and their interaction pattern with the protein was compared with that of icarisid II, a natural PDE5 inhibitor.

  4. Preparation of a Ammonia-Treated Lac Dye and Structure Elucidation of Its Main Component.

    PubMed

    Nishizaki, Yuzo; Ishizuki, Kyoko; Akiyama, Hiroshi; Tada, Atsuko; Sugimoto, Naoki; Sato, Kyoko

    2016-01-01

    Lac dye and cochineal extract contain laccaic acids and carminic acid as the main pigments, respectively. Both laccaic acids and carminic acid are anthraquinone derivatives. 4-Aminocarminic acid (acid-stable carmine), an illegal colorant, has been detected in several processed foods. 4-Aminocarminic acid is obtained by heating cochineal extract (carminic acid) in ammonia solution. We attempted to prepare ammonia-treated lac dye and to identify the structures of the main pigment components. Ammonia-treated lac dye showed acid stability similar to that of 4-aminocarminic acid. The structures of the main pigments in ammonia-treated lac dye were analyzed using LC/MS. One of the main pigments was isolated and identified as 4-aminolaccaic acid C using various NMR techniques, including 2D-INADEQUATE. These results indicated that ammonia-treatment of lac dye results in the generation of 4-aminolaccaic acids.

  5. 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.

  6. Structural Elucidation of Cisoid and Transoid Cyclization Pathways of a Sesquiterpene Synthase Using 2-Fluorofarnesyl Diphosphates

    PubMed Central

    2010-01-01

    Sesquiterpene skeletal complexity in nature originates from the enzyme-catalyzed ionization of (trans,trans)-farnesyl diphosphate (FPP) (1a) and subsequent cyclization along either 2,3-transoid or 2,3-cisoid farnesyl cation pathways. Tobacco 5-epi-aristolochene synthase (TEAS), a transoid synthase, produces cisoid products as a component of its minor product spectrum. To investigate the cryptic cisoid cyclization pathway in TEAS, we employed (cis,trans)-FPP (1b) as an alternative substrate. Strikingly, TEAS was catalytically robust in the enzymatic conversion of (cis,trans)-FPP (1b) to exclusively (≥99.5%) cisoid products. Further, crystallographic characterization of wild-type TEAS and a catalytically promiscuous mutant (M4 TEAS) with 2-fluoro analogues of both all-trans FPP (1a) and (cis,trans)-FPP (1b) revealed binding modes consistent with preorganization of the farnesyl chain. These results provide a structural glimpse into both cisoid and transoid cyclization pathways efficiently templated by a single enzyme active site, consistent with the recently elucidated stereochemistry of the cisoid products. Further, computational studies using density functional theory calculations reveal concerted, highly asynchronous cyclization pathways leading to the major cisoid cyclization products. The implications of these discoveries for expanded sesquiterpene diversity in nature are discussed. PMID:20175559

  7. Deglycosylation of glycoproteins with trifluoromethanesulphonic acid: elucidation of molecular structure and function.

    PubMed Central

    Edge, Albert S B

    2003-01-01

    The alteration of proteins by post-translational modifications, including phosphorylation, sulphation, processing by proteolysis, lipid attachment and glycosylation, gives rise to a broad range of molecules that can have an identical underlying protein core. An understanding of glycosylation of proteins is important in clarifying the nature of the numerous variants observed and in determining the biological roles of these modifications. Deglycosylation with TFMS (trifluoromethanesulphonic acid) [Edge, Faltynek, Hof, Reichert, and Weber, (1981) Anal. Biochem. 118, 131-137] has been used extensively to remove carbohydrate from glycoproteins, while leaving the protein backbone intact. Glycosylated proteins from animals, plants, fungi and bacteria have been deglycosylated with TFMS, and the most extensively studied types of carbohydrate chains in mammals, the N-linked, O-linked and glycosaminoglycan chains, are all removed by this procedure. The method is based on the finding that linkages between sugars are sensitive to cleavage by TFMS, whereas the peptide bond is stable and is not broken, even with prolonged deglycosylation. The relative susceptibility of individual sugars in glycosidic linkage varies with the substituents at C-2 and the occurrence of amido and acetyl groups, but even the most stable sugars are removed under conditions that are sufficiently mild to prevent scission of peptide bonds. The post-translational modifications of proteins have been shown to be required for diverse biological functions, and selective procedures to remove these modifications play an important role in the elucidation of protein structure and function. PMID:12974674

  8. Elucidation of structural and functional properties of albumin bound to gold nanoparticles.

    PubMed

    Mariam, Jessy; Sivakami, S; Dongre, P M

    2017-02-01

    Nanoparticle-albumin complexes are being designed for targeted drug delivery and imaging. However, the changes in the functional properties of albumin due to adsorption on nanoparticles remain elusive. Thus, the objective of this work was to elucidate the structural and functional properties of human and bovine serum albumin bound to negatively charged gold nanoparticles (GNPs). Fluorescence data demonstrated static quenching of albumin by GNP with the quenching of buried as well as surface tryptophan in BSA. The binding process was enthalpy and entropy-driven in HSA and BSA, respectively. At lower concentrations of GNP there was a higher affinity for tryptophan, whereas at higher concentrations both tryptophan and tyrosine participated in the interaction. Synchronous fluorescence spectra revealed that the microenvironment of tryptophan in HSA turned more hydrophilic upon exposure to GNP. The α-helical content of albumin was unaltered by GNP. Approximately 37 and 23% reduction in specific activity of HSA and BSA was observed due to GNP binding. In presence of warfarin and ibuprofen the binding constants of albumin-GNP complexes were altered. A very interesting observation not reported so far is the retained antioxidant activity of albumin in presence of GNP i.e. we believe that GNPs did not bind to the free sulfhydryl groups of albumin. However enhanced levels of copper binding were observed. We have also highlighted the differential response in albumin due to gold and silver nanoparticles which could be attributed to differences in the charge of the nanoparticle.

  9. Elucidating the structure and function of S100 proteins in membranes

    NASA Astrophysics Data System (ADS)

    Valenzuela, Stella M.; Berkahn, Mark; Martin, Donald K.; Huynh, Thuan; Yang, Zheng; Geczy, Carolyn L.

    2006-01-01

    S100 proteins are important Ca 2+-binding proteins involved in vital cellular functions including the modulation of cell growth, migration and differentiation, regulation of intracellular signal transduction/phosphorylation pathways, energy metabolism, cytoskeletal interactions and modulation of ion channels. Furthermore, they are implicated in oncogenesis and numerous other disease states. Three S100 proteins: S100A8, S100A9 and S100A12 are constitutively expressed in neutrophils and monocytes. At low levels of intracellular Ca 2+, S100A8 and S100A9 are located predominantly in the cytosol but when Ca 2+ concentrations are elevated as a consequence of activation, they translocate to membranes and complex with cytoskeletal components such as vimentin. The functions of S100A8 and S100A9 at the plasma membrane remain unclear. A possible role may be the regulation of ion channel proteins. The current study uses the techniques of Atomic Force Microscopy and production of artificial lipid membranes in the form of liposomes to investigate possible mechanisms for the insertion of these proteins into membranes in order to elucidate their structure and stoichiometry in the transmembrane state. We have successfully imaged the liposomes as a lipid bilayer, the S100A8/A9 protein complex in solution and the S100A8/A9 complex associating with lipid, using tapping-mode atomic force microscopy, in buffer.

  10. In vitro biological studies and structural elucidation of fluoro-substituted phenyl acrylic acids.

    PubMed

    Hussain, Mukhtiar; Hanif, Muhammad; Ali, Saqib; Butcher, Ray; Mirza, Tahira; Vanderveer, Don; Aziz-ur-Rehman

    2010-09-01

    Synthesis, characterization, and biological significance of different substituted phenyl acrylic acids have been studied. These acids are contributing a key role during synthesis of antimicrobial drugs. The acids were prepared by condensation of various substituted phenyl acetic acids and aldehydes. o-piperonal was prepared using 2,3-methylenedioxy benzaldehyde. These phenyl acrylic acids were characterized by using analytical techniques, for example, Fourier transform infrared spectroscopy, multinuclear NMR (1H, 13C NMR), and GC-MS. The structure of crystalline products was also elucidated by X-ray crystallography. Small intermolecular and intramolecular weaker interactions were also studied by these characterization techniques. The geometry of compounds in solid and solution state has been studied. The presence of weaker interactions in these molecules is also observed which may increase the hydrolysis and lipophilicity and ultimately improve the activity against different microbes. The effect of different groups attached to the main rings and the presence of smaller interaction have been studied. Their factors may enhance the activity of these compounds.

  11. Structure elucidation of aplidine metabolites formed in vitro by human liver microsomes using triple quadrupole mass spectrometry.

    PubMed

    Brandon, Esther F A; van Ooijen, Ronald D; Sparidans, Rolf W; Lázaro, Luis López; Heck, Albert J R; Beijnen, Jos H; Schellens, Jan H M

    2005-06-01

    The cyclic depsipeptide aplidine is a new anti-cancer drug of marine origin. Four metabolites of this compound were found after incubation with pooled human microsomes using gradient high-performance liquid chromatography with ultraviolet detection. After chromatographic isolation, the metabolites have been identified using nano-electrospray triple quadrupole mass spectrometry. A highly specific sodium-ion interaction with the cyclic structure opens the depsipeptide ring, and cleavage of the amino acid residues gives sequence information when activated by collision-induced dissociation in the second quadrupole. The aplidine molecule could undergo the following metabolic reactions: hydroxylation at the isopropyl group (metabolites apli-h 1 and apli-h 2); C-dealkylation at the N(Me)-leucine group (metabolite apli-da); hydroxylation at the isopropyl group and C-dealkylation at the N(Me)-leucine group (metabolite apli-da/h), and C-demethylation at the threonine group (metabolite apli-dm). The identification of these metabolites formed in vitro may greatly aid the elucidation of the metabolic pathways of aplidine in humans.

  12. Purification and partial elucidation of the structure of an antioxidant carbohydrate biopolymer from the probiotic bacterium Bacillus coagulans RK-02.

    PubMed

    Kodali, Vidya P; Perali, Ramu S; Sen, R

    2011-08-26

    An exopolysaccharide (EPS) was isolated from Bacillus coagulans RK-02 and purified by size exclusion chromatography. The purified, homogeneous EPS had an average molecular weight of ∼3 × 10⁴ Da by comparison with FITC-labeled dextran standards. In vivo evaluations showed that, like other reported polysaccharides, this EPS displayed significant antioxidant activity. FTIR spectroscopy analysis showed the presence of hydroxy, carboxy, and α-glycosidic linkages and a mannose residue. GC analysis indicated that the EPS was a heteropolymer composed of glucose, mannose, galactose, glucosamine, and fucose as monomeric constituent units. Partial elucidation of the structure of the carbohydrate biopolymer based on GC-MS and NMR analysis showed the presence of two unique sets of tetrasaccharide repeating units that have 1→3 and 1→6 glycosidic linkages. This is also the first report of a Gram-positive bacterial polysaccharide with both fucose as a sugar monomer and 1→3 and 1→6 glycosidic linkages in the molecular backbone.

  13. 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

  14. Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake.

    PubMed

    van der Hooft, Justin J J; de Vos, Ric C H; Mihaleva, Velitchka; Bino, Raoul J; Ridder, Lars; de Roo, Niels; Jacobs, Doris M; van Duynhoven, John P M; Vervoort, Jacques

    2012-08-21

    In dietary polyphenol exposure studies, annotation and identification of urinary metabolites present at low (micromolar) concentrations are major obstacles. To determine the biological activity of specific components, it is necessary to have the correct structures and the quantification of the polyphenol-derived conjugates present in the human body. We present a procedure for identification and quantification of metabolites and conjugates excreted in human urine after single bolus intake of black or green tea. A combination of a solid-phase extraction (SPE) preparation step and two high pressure liquid chromatography (HPLC)-based analytical platforms was used, namely, accurate mass fragmentation (HPLC-FTMS(n)) and mass-guided SPE-trapping of selected compounds for nuclear magnetic resonance spectroscopy (NMR) measurements (HPLC-TOFMS-SPE-NMR). HPLC-FTMS(n) analysis led to the annotation of 138 urinary metabolites, including 48 valerolactone and valeric acid conjugates. By combining the results from MS(n) fragmentation with the one-dimensional (1D)-(1)H NMR spectra of HPLC-TOFMS-SPE-trapped compounds, we elucidated the structures of 36 phenolic conjugates, including the glucuronides of 3',4'-di- and 3',4',5'-trihydroxyphenyl-γ-valerolactone, three urolithin glucuronides, and indole-3-acetic acid glucuronide. We also obtained 26 h-quantitative excretion profiles for specific valerolactone conjugates. The combination of the HPLC-FTMS(n) and HPLC-TOFMS-SPE-NMR platforms results in the efficient identification and quantification of less abundant phenolic conjugates down to nanomoles of trapped amounts of metabolite corresponding to micromolar metabolite concentrations in urine.

  15. New triterpenoids from the tubers of Corydalis ternata: structural elucidation and bioactivity evaluation.

    PubMed

    Kim, Ki Hyun; Lee, Il Kyun; Choi, Sang Un; Lee, Jei Hyun; Moon, Eunjung; Kim, Sun Yeou; Lee, Kang Ro

    2011-09-01

    Two new triterpene glycosides, coryternic acid 3-O-β-D-glucuronopyranoside (1) and coryternic acid 3-O-β-D-glucuronopyranoside-6'-O-methyl ester (2), were isolated from a MeOH extract of the tubers of Corydalis ternata. Acidic hydrolysis of 1 and 2 yielded a new triterpene as their aglycone, coryternic acid (3). The structures of these new compounds were determined through spectral analysis, including extensive 2D-NMR data. In this study we reported that triterpenoids were first isolated from the genus Corydalis. Compound 2 exhibited significant cytotoxicity against the A549, SK-OV-3, SK-MEL-2, and HCT-15 cell lines (IC50 = 15.16, 17.07, 13.32, and 11.95 µM, respectively) and significantly reduced NO production in lipopolysaccharide (LPS)-activated microglia/BV-2 cells with an IC50 value of 16.2 µM without cell toxicity. © Georg Thieme Verlag KG Stuttgart · New York.

  16. Structural elucidation and antioxidant activity a novel Se-polysaccharide from Se-enriched Grifola frondosa.

    PubMed

    Li, Qian; Wang, Wei; Zhu, Yun; Chen, Yao; Zhang, Weijie; Yu, Ping; Mao, Guanghua; Zhao, Ting; Feng, Weiwei; Yang, Liuqing; Wu, Xiangyang

    2017-04-01

    Se-GFP-22, a heteropolysaccharide, with a weight-average Mw of 4.13×10(6)Da, was purified from the crude Se-polysaccharide (Se-GFP) isolated from fruit bodies of Se-enriched Grifola frondosa. Selenium was accumulated efficiently in Grifola frondosa during cultivation with Na2SeO3. The structure was investigated through FT-IR, GC, GC-MS, NMR, HPSEC-MALL-RI, particle size, Conge-red test, CD, AFM and SEM. Se-GFP-22 was deduced as a backbone chain of 1,4-α-d-Glcp units with a branched point at C6 of both 1,3,6-β-d-Manp and 1,4,6-α-d-Galp units. A typical absorption for selenium ester was existed in Se-GFP-22. Se-GFP-22 adopted as a spherical conformation with random coils. A novel Se-polysaccharide of different monosaccharide constituents, molecular weight, linkage types and high content of selenium has been isolated from G. frondosa. The antioxidant effect of Se-GFP-22 was more potent than that of G. frondosa polysaccharide (GFP-22), which may be influenced by the co-effect of polysaccharide and Se, molecular weight, degree of branching and configuration. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. 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.

  18. Structure elucidation of phenolic compounds from red/white wine with antiatherogenic properties.

    PubMed

    Fragopoulou, Elizabeth; Antonopoulou, Smaragdi; Nomikos, Tzortzis; Demopoulos, Constantinos A

    2003-06-10

    The oxidative modification of low-density lipoproteins (LDL) is supposed to play a critical role in atherogenesis. During this oxidation a potent inflammatory phospholipid mediator named platelet activating factor (PAF) is produced, and it is believed to be the key for the initiation of the inflammation and therefore for the process of atherogenesis. From many studies, it is established that wine has beneficial effects on health, including protection against cardiovascular diseases. According to our point of view, the cardioprotective effect of wine may be attributed partly to the existence of PAF antagonists in red or white wine and partly to the existence of antioxidants that reduce the oxidation of LDL and therefore the production of PAF. In this study, wine compounds that antagonize PAF were isolated and purified via chromatographic procedures, and determined structurally using chemical, enzymatic and spectroscopic methods.

  19. Structure elucidation of new oleanane-type glycosides from three species of Acanthophyllum.

    PubMed

    Timité, Gaoussou; Mitaine-Offer, Anne-Claire; Miyamoto, Tomofumi; Ramezani, Mohammad; Rustaiyan, Abdolhossein; Mirjolet, Jean-François; Duchamp, Olivier; Lacaille-Dubois, Marie-Aleth

    2010-05-01

    From the roots of three species of Acanthophyllum (Caryophyllaceae), two new gypsogenic acid glycosides, 1 and 2, were isolated, 1 from A. sordidum and A. lilacinum, 2 from A. elatius and A. lilacinum, together with three known saponins, glandulosides B and C, and SAPO50. The structures of 1 and 2 were established mainly by 2D NMR techniques as 23-O-beta-D-galactopyranosylgypsogenic acid-28-O-beta-D-glucopyranosyl-(1-->3)-[beta-D-glucopyranosyl-(1-->6)]-beta-D-galactopyranoside (1) and gypsogenic acid-28-O-beta-D-glucopyranosyl-(1-->3)-[beta-D-glucopyranosyl-(1-->6)]-beta-D-galactopyranoside (2). The cytotoxicity of several of these saponins was evaluated against two human colon cancer cell lines (HT-29 and HCT 116). Copyright 2010 John Wiley & Sons, Ltd.

  20. Differentiation of volatile aromatic isomers and structural elucidation of volatile compounds in essential oils by combination of HPLC separation and crystalline sponge method.

    PubMed

    Gu, Xiao-Fei; Zhao, Yue; Li, Kan; Su, Meng-Xiang; Yan, Fang; Li, Bo; Du, Ying-Xiang; Di, Bin

    2016-11-25

    Structure elucidation of volatile aromatic isomers at trace level has long been considered as an elusive task, due to their structural similarities and similar polarities, even with the aid of many spectroscopic techniques such as mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy. Single-crystal X-ray diffraction (SCD) is recognized as one of the most powerful structural elucidation techniques. The recently developed crystalline sponge method overcomes the intrinsic limitation of SCD that the target molecules must be single crystals, being able to analyze non-crystalline and trace-amount compounds without any special treatment. In order to investigate whether the crystalline sponge method could be used for the structure elucidation of closely related isomers or other volatile and even oily compounds in complex mixtures at trace level, we combined HPLC separation with the crystalline sponge method for X-ray crystallographic analysis. In this paper, two pairs of volatile aromatic isomers including cis/trans isomers of asarone and positional isomers of carvacrol and thymol, as well as the main volatile component in essential oil extracted from Acorus Tatarinowii, were first isolated by HPLC and encapsulated into the crystalline sponge then elucidated by X-ray crystallographic analysis. Direct observation of these volatile compounds by X-ray crystallography was achieved using only microgram quantities without crystallization or derivatization. Unambiguous identification of these compounds was realized without reference standards. This strategy offers a promising platform capable of providing high-confidence detailed structural information of closely related isomers as well as other volatile and even oily compounds in complex mixtures in microgram quantities. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Levothyroxine sodium revisited: A wholistic structural elucidation approach of new impurities via HPLC-HRMS/MS, on-line H/D exchange, NMR spectroscopy and chemical synthesis.

    PubMed

    Ruggenthaler, M; Grass, J; Schuh, W; Huber, C G; Reischl, R J

    2017-02-20

    The structural elucidation of unknown pharmaceutical impurities plays an important role in the quality control of newly developed and well-established active pharmaceutical ingredients (APIs). The United States Pharmacopeia (USP) monograph for the API Levothyroxine Sodium, a synthetic thyroid hormone, features two high pressure liquid chromatography (HPLC) methods using UV-VIS absorption detection to determine organic impurities in the drug substance. The impurity profile of the first USP method ("Procedure 1") has already been extensively studied, however for the second method ("Procedure 2"), which exhibits a significantly different impurity profile, no wholistic structural elucidation of impurities has been performed yet. Applying minor modifications to the chromatographic parameters of USP "Procedure 2" and using various comprehensive structural elucidation methods such as high resolution tandem mass spectrometry with on-line hydrogen-deuterium (H/D) exchange or two-dimensional nuclear magnetic resonance spectroscopy (NMR) we gained new insights about the complex impurity profile of the synthetic thyroid hormone. This resulted in the characterization of 24 compounds previously unknown to literature and the introduction of two new classes of Levothyroxine Sodium impurities. Five novel compounds were unambiguously identified via isolation or synthesis of reference substances and subsequent NMR spectroscopic investigation. Additionally, Collision-Induced Dissociation (CID)-type fragmentation of identified major impurities as well as neutral loss fragmentation patterns of many characterized impurities were discussed.

  2. 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

  3. The efficient structure elucidation of minor components in heparin digests using microcoil NMR.

    PubMed

    Limtiaco, John F K; Beni, Szabolcs; Jones, Christopher J; Langeslay, Derek J; Larive, Cynthia K

    2011-10-18

    The structural complexity and microheterogeneity of the glycosaminoglycans heparin and heparan sulfate make their characterization a daunting task. The methodology described herein utilizes a combination of enzymatic digestion, size-exclusion chromatography, strong anion-exchange HPLC, reverse-phase ion-pair ultrahigh performance liquid chromatography-mass spectrometry, and microcoil NMR for the efficient sequencing of heparin-derived tetrasaccharides. The high mass sensitivity of microcoil NMR makes this technique well suited for the characterization of mass-limited samples removing a bottleneck in the analysis workflow and permitting structural characterization of minor components isolated from a heparin enzymatic digestion. Complete characterization of one tetrasulfonated, five pentasulfonated isomers and two hexasulfonated tetrasaccharide sequences is described. To our knowledge, two of the identified minor tetrasaccharides are unique, and have not been previously reported: IdoA(2S)-GlcNS(6S)-IdoA(2S)-GlcNS(6S) and ΔUA(2S)-GlcNS(6S)-IdoA-GlcNS(6S).

  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. 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…

  6. Structural characteristics of the molecular species of tetraacylglycerols in lesquerella (Physaria fendleri) oil elucidated by mass spectrometry

    USDA-ARS?s Scientific Manuscript database

    The structure and ratios of regioisomers of the molecular species of tetraacylglycerols affect their physical properties. They were elucidated by ESI mass spectrometry of the lithium adducts of tetraacylglycerols from the HPLC fractions of lesquerella oil. The contents of acyl and acylacyl chains at...

  7. Structure elucidation of hexabromocyclododecanes--a class of compounds with a complex stereochemistry.

    PubMed

    Heeb, Norbert V; Schweizer, W Bernd; Kohler, Martin; Gerecke, Andreas C

    2005-09-01

    Hexabromocyclododecanes (HBCDs) are high production volume chemicals (16700 t worldwide in 2001) used as flame-retardants for plastics and textiles. HBCDs exhibit typical properties of persistent organic pollutants (POPs). They are highly lipophilic and accumulate in biota. Increasing environmental concentrations of HBCDs, mostly reported as sum values, have been observed. As such, HBCDs have to be considered as potential emerging POPs, but their occurrence and environmental fate have not yet been addressed at the level of individual HBCD stereoisomers. Considering the six stereogenic centers of HBCDs, 16 stereoisomers, six diastereomeric pairs of enantiomers as well as four meso forms, can be deduced. Herein, we report spectroscopic and chromatographic data for eight out of 16 possible HBCD stereoisomers, which were isolated from a technical product. Six stereoisomers were identified as three pairs of enantiomers ((+/-) alpha-, beta-, and gamma-HBCDs), differing in optical rotation and chromatographic retention on a chiral phase. The crystal structures of these pairs of enantiomers were determined. Another two of these eight HBCD stereoisomers, not yet described in the literature, showed no optical rotation and are tentatively assigned as meso forms (delta- and epsilon-HBCD). The given spectroscopic and chromatographic information allows the unambiguous identification of eight HBCD stereoisomers and the occurrence, fate, and toxicology of these individual stereoisomers can now be studied.

  8. Structural elucidation and immunostimulating property of a novel polysaccharide extracted from an edible mushroom Lentinus fusipes.

    PubMed

    Manna, Dilip K; Maity, Prasenjit; Nandi, Ashis K; Pattanayak, Manabendra; Panda, Bibhash C; Mandal, Amit K; Tripathy, Satyajit; Acharya, Krishnendu; Sahoo, Atish K; Gupta, Nibha; Roy, Somnath; Islam, Syed S

    2017-02-10

    A water soluble heteroglycan (PS-II) with an average molecular weight∼60kDa was isolated from the hot aqueous extract of an edible mushroom Lentinus fusipes. The structural characterization of PS-II was carried out using total acid hydrolysis, methylation analyses, periodate oxidation, Smith degradation and 1D/2D NMR experiments. Total acid hydrolysis indicated the presence of D-galactose and D-glucose in a molar ratio of approximately 1:1. The chemical and NMR analyses revealed that the proposed repeating unit of the PS-II had a backbone chain consisting of three (1→6)-linked α-d-galactopyranosyl residue and two (1→6)-linked β-d-glucopyranosyl residues, one of the β-d-glucopyranosyl residue was branched at O-3 position with a terminal β-d-glucopyranosyl. The PS-II exhibited significant in vitro splenocyte and macrophage activations with optimum dose of 20μg/ml and 80μg/ml respectively. Flow cytometry study revealed the protective role of the PS-II against nicotine stimulated lymphocytes. Moreover, the ROS scavenging property of PS-II was also established using DPPH radical scavenging assay.

  9. Isolation and structural characterization of two new metabolites from monascus.

    PubMed

    Loret, Marie-Odile; Morel, Sandrine

    2010-02-10

    Two new pale yellow metabolites have been isolated from commercially available Chinese food additive Red Monascus Pigment and from Monascus ruber culture broth. They were isolated by successive TLC and semipreparative HPLC. Their structural characterization was elucidated by a variety of spectroscopic techniques (UV, IR, NMR) and mass spectrometry. These two new metabolites present numerous similarities with monascorubrin and rubropunctatin, differing in their structure only by the absence of the lactone ring. High-resolution mass spectrometry indicated the molecular formulas C(20)H(26)O(4) and C(22)H(30)O(4). The new compounds, named monarubrin and rubropunctin, contain a propenyl group on a pyrone ring, an alkyl side chain, but no gamma-lactone ring. The new metabolites have the property of producing strong blue fluorescence at 340 nm.

  10. Structural elucidation of dioxa-cage compounds from tetrahydroisobenzofuran-1(3H)-one: analysis of NMR data and GIAO chemical shifts calculations.

    PubMed

    da Costa Resende, Gabriela; Alvarenga, Elson Santiago

    2016-12-01

    The polycyclic compounds, especially the dioxa-cages, have attracted considerable attention in recent years. In our work, a series of 9β-substituted 3-oxo-4,11-dioxatetracyclo[5.2.1.1(5,8) .0(2,6) ]undecane compounds were unexpectedly isolated during bromination, chlorination and epoxidation reactions of the 3-hydroxy-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one. After careful analysis of the NMR data, the chemical shifts of the isolated and the expected products were predicted by theoretical calculations using density functional theory and gauge including atomic orbitals. The best correlation between calculated and experimental data was evaluated by comparing mean absolute errors and applying DP4 probability methodology. Results from both approaches indicated a correct structural elucidation. Copyright © 2016 John Wiley & Sons, Ltd.

  11. 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.

  12. Structure Elucidation of a Polysaccharide from Umbilicaria esculenta and Its Immunostimulatory Activity

    PubMed Central

    Zhang, Bi-Wei; Xu, Jin-Long; Zhang, Hua; Zhang, Qiang; Lu, Jie; Wang, Jun-Hui

    2016-01-01

    Umbilicaria esculenta has been used as a tonic food in China for several centuries owing to its pleasant flavor and health benefits. In this study, a water soluble polysaccharide, which we designated as UP2, with an average molecular weight of 3.33 × 105 Da, was isolated from U. esculenta cultivated in the Huangshan Mountain, by consecutive hot water extraction and anion-exchange chromatography. Gas chromatography analysis indicated that UP2 contained three kinds of monosaccharides, including mannose, glucose, and galactose at a molar ratio of 1.7:1.0:1.2. Linkage analysis of UP2 revealed the presence of (1 → 6)-linked glucosyl, (1 → 3,6)-linked glucosyl, t-linked galactosyl, (1 → 6)-linked galactosyl and (1 → 6)-linked mannosyl at a molar ratio of 0.7:4.6:4.1:2.2:9.1. Structural analysis determined that UP2 possessed a backbone consisting of (1 → 6)-linked β-D-glucopyranosyl and (1 → 6)-linked α-D-mannopyranosyl residues, which substituted at the O-3 position of (1 → 6)-linked β-D-glucopyranosyl residues by branches of (1 → 6)-linked α-D-galactopyranosyl and 1-linked β-D-galactopyranosyl residues. Immunostimulatory activity analysis showed that UP2 could stimulate the proliferation of RAW264.7 cells in a dose-dependent manner, and all the samples (20–500 μg/mL) were found to enhance nitric oxide production. The highest phagocytic activity of UP2 was observed at 200 μg/mL. Thus, UP2 may be a potential source of biological and pharmacological agents. PMID:27997616

  13. Synthesis, structure elucidation, and determination of polyhalogenated N-methylpyrroles (PMPs) in blue mussels.

    PubMed

    Hauler, Carolin; Vetter, Walter

    2017-09-23

    Polyhalogenated N-methylpyrroles (PMPs) are halogenated natural products (HNPs) recently detected in seagrass, blue mussels, and other marine organisms. In this study, we synthesized 2,3,4,5-tetrachloro-N-methylpyrrole (Cl4-MP), 2,3,4,5-tetrabrominated-N-methylpyrrole (Br4-MP, aka TBMP), and mixed tetrahalogenated (Cl and Br) N-methylpyrrole congeners. Use of one- and two-dimensional (1)H and (13)C NMR verified the structures of isolated/enriched 3,4-dibromo-2,5-dichloro-N-methylpyrrole (3,4-Br2-2,5-Cl2-MP), 2,3,4-tribromo-5-chloro-N-methylpyrrole (2,3,4-Br3-5-Cl-MP), and 3-bromo-2,4,5-trichloro-N-methylpyrrole (3-Br-2,4,5-Cl3-MP). GC/EI-MS and GC/ECNI-MS mass spectra of the five PMPs were studied with regard to fragmentation pattern and individual responses which were strongly affected by the presence (or absence) of Br in α-position(s). Quantitative solutions of the synthesized standards were used to determine the elution order of isomers and to quantify PMPs in selected blue mussel samples (Mytilus sp.) from the European Atlantic coast (Spain, France), the North Sea (the Netherlands, Germany) and Baltic Sea (Germany). PMPs were detected in all samples and the concentrations ranged between 0.6 and 52 μg/kg lipids with Br4-MP being the most abundant representative of this substance class.

  14. 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.

  15. 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.

  16. Structure-function elucidation of a new α-conotoxin, Lo1a, from Conus longurionis.

    PubMed

    Lebbe, Eline K M; Peigneur, Steve; Maiti, Mohitosh; Devi, Prabha; Ravichandran, Samuthirapandian; Lescrinier, Eveline; Ulens, Chris; Waelkens, Etienne; D'Souza, Lisette; Herdewijn, Piet; Tytgat, Jan

    2014-04-04

    α-Conotoxins are peptide toxins found in the venom of marine cone snails and potent antagonists of various subtypes of nicotinic acetylcholine receptors (nAChRs). nAChRs are cholinergic receptors forming ligand-gated ion channels in the plasma membranes of certain neurons and the neuromuscular junction. Because nAChRs have an important role in regulating transmitter release, cell excitability, and neuronal integration, nAChR dysfunctions have been implicated in a variety of severe pathologies such as epilepsy, myasthenic syndromes, schizophrenia, Parkinson disease, and Alzheimer disease. To expand the knowledge concerning cone snail toxins, we examined the venom of Conus longurionis. We isolated an 18-amino acid peptide named α-conotoxin Lo1a, which is active on nAChRs. To the best of our knowledge, this is the first characterization of a conotoxin from this species. The peptide was characterized by electrophysiological screening against several types of cloned nAChRs expressed in Xenopus laevis oocytes. The three-dimensional solution structure of the α-conotoxin Lo1a was determined by NMR spectroscopy. Lo1a, a member of the α4/7 family, blocks the response to acetylcholine in oocytes expressing α7 nAChRs with an IC50 of 3.24 ± 0.7 μM. Furthermore, Lo1a shows a high selectivity for neuronal versus muscle subtype nAChRs. Because Lo1a has an unusual C terminus, we designed two mutants, Lo1a-ΔD and Lo1a-RRR, to investigate the influence of the C-terminal residue. Lo1a-ΔD has a C-terminal Asp deletion, whereas in Lo1a-RRR, a triple-Arg tail replaces the Asp. They blocked the neuronal nAChR α7 with a lower IC50 value, but remarkably, both adopted affinity for the muscle subtype α1β1δε.

  17. Structure-Function Elucidation of a New α-Conotoxin, Lo1a, from Conus longurionis

    PubMed Central

    Lebbe, Eline K. M.; Peigneur, Steve; Maiti, Mohitosh; Devi, Prabha; Ravichandran, Samuthirapandian; Lescrinier, Eveline; Ulens, Chris; Waelkens, Etienne; D'Souza, Lisette; Herdewijn, Piet; Tytgat, Jan

    2014-01-01

    α-Conotoxins are peptide toxins found in the venom of marine cone snails and potent antagonists of various subtypes of nicotinic acetylcholine receptors (nAChRs). nAChRs are cholinergic receptors forming ligand-gated ion channels in the plasma membranes of certain neurons and the neuromuscular junction. Because nAChRs have an important role in regulating transmitter release, cell excitability, and neuronal integration, nAChR dysfunctions have been implicated in a variety of severe pathologies such as epilepsy, myasthenic syndromes, schizophrenia, Parkinson disease, and Alzheimer disease. To expand the knowledge concerning cone snail toxins, we examined the venom of Conus longurionis. We isolated an 18-amino acid peptide named α-conotoxin Lo1a, which is active on nAChRs. To the best of our knowledge, this is the first characterization of a conotoxin from this species. The peptide was characterized by electrophysiological screening against several types of cloned nAChRs expressed in Xenopus laevis oocytes. The three-dimensional solution structure of the α-conotoxin Lo1a was determined by NMR spectroscopy. Lo1a, a member of the α4/7 family, blocks the response to acetylcholine in oocytes expressing α7 nAChRs with an IC50 of 3.24 ± 0.7 μm. Furthermore, Lo1a shows a high selectivity for neuronal versus muscle subtype nAChRs. Because Lo1a has an unusual C terminus, we designed two mutants, Lo1a-ΔD and Lo1a-RRR, to investigate the influence of the C-terminal residue. Lo1a-ΔD has a C-terminal Asp deletion, whereas in Lo1a-RRR, a triple-Arg tail replaces the Asp. They blocked the neuronal nAChR α7 with a lower IC50 value, but remarkably, both adopted affinity for the muscle subtype α1β1δϵ. PMID:24567324

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

    PubMed

    Toukach, Filip V; Ananikov, Valentine P

    2013-11-07

    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.

  19. Application of a computer-assisted structure elucidation program for the structural determination of a new terpenoid aldehyde with an unusual skeleton.

    PubMed

    Li, Xing-Nuo; Ridge, Clark D; Mazzola, Eugene P; Sun, Jianghao; Gutierrez, Osvaldo; Moser, Arvin; DiMartino, Joseph C; MacDonald, Scott A; Chen, Pei

    2017-03-01

    The structure of a novel compound from Adansonia digitata has been elucidated, and its (1) H and (13) C NMR spectra have been assigned employing a variety of one-dimensional and two-dimensional NMR techniques without degradative chemistry. The Advanced Chemistry Development ACD/Structure Elucidator software was important for determining part of this structure that contained a fused bicyclic system with very few hydrogen atoms, which in turn, exhibited essentially no discriminating HMBC connectivities throughout that portion of the molecule. Copyright © 2016 John Wiley & Sons, Ltd.

  20. Plantazolicin A and B: structure elucidation of ribosomally synthesized thiazole/oxazole peptides from Bacillus amyloliquefaciens FZB42.

    PubMed

    Kalyon, Bahar; Helaly, Soleiman E; Scholz, Romy; Nachtigall, Jonny; Vater, Joachim; Borriss, Rainer; Süssmuth, Roderich D

    2011-06-17

    The structures of the ribosomally synthesized peptide antibiotics from Bacillus amyloliquefaciens FZB42, plantazolicin A and B, have been elucidated by high resolving ESI-MSMS, 2D (1)H-(13)C-correlated NMR spectroscopy as well as (1)H-(15)N-HMQC/(1)H-(15)N-HMBC NMR experiments. (15)N-labeling prior to the experiments facilitated the structure determination, unveiling a hitherto unusual number of thiazoles and oxazoles formed from a linear 14mer precursor peptide. This finding further extends the number of known secondary metabolites from B. amyloliquefaciens and represents a new type of secondary metabolites from the genus Bacillus.

  1. 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.

  2. Natural occurring 2-(2-phenylethyl) chromones, structure elucidation and biological activities.

    PubMed

    Ibrahim, Sabrin R M; Mohamed, Gamal A

    2015-01-01

    2-(2-Phenylethyl) chromone (PEC), an uncommon class of chromones, possesses a phenylethyl substituent at the C2 position. They have been isolated from a few plant species. They have promising biological activities such as neuro-protective, cytotoxic, acetylcholinesterase inhibitory, antibacterial and anti-inflammatory. This review focuses on the naturally occurring PEC derivatives, their sources, physical and spectral data, as well as biological activities.

  3. Structure of E. coli 16S RNA elucidated by psoralen crosslinking

    SciTech Connect

    Thompson, J.F.; Hearst, J.E.

    1983-04-01

    E. coli 16S RNA in solution was photoreacted with hydroxymethyltrimethylpsoralen and long wave ultraviolet light. Positions of crosslinks were determined to high resolution by partially digesting the RNA with T/sub 1/ RNase, separating the crosslinked fragments by two-dimensional gel electrophoresis, reversing the crosslink, and sequencing the separated fragments. This method yielded the locations of crosslinks to +/-15 nucleotides. Even finer placement has been made on the basis of our knowledge of psoralen reactivity. Thirteen unique crosslinks were mapped. Seven crosslinks confirmed regions of secondary structure which had been predicted in published phylogenetic models, three crosslinks discriminated between phylogenetic models, and three proved the existence of new structures. The new structures were all long-range interactions which appear to be in dynamic equilibrium with local secondary structure. Because this technique yields direct information about the secondary structure of large RNAs, it should prove invaluable in studying the structure of other RNAs of all sizes.

  4. Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models.

    PubMed

    Toyoda, Tetsuro; Shinozaki, Kazuo

    2005-08-01

    Tiling arrays of high-density oligonucleotide probes spanning the entire genome are powerful tools for the discovery of new genes. However, it is difficult to determine the structure of the spliced product of a structurally unknown gene from noisy array signals only. Here we introduce a statistical method that estimates the precise splicing points and the exon/intron structure of a structurally unknown gene by maximizing the odds or the ratio of posterior probabilities of the structure under the observation of array signal intensities and nucleic acid sequences. Our method more accurately predicted the gene structures than the simple threshold-based method, and more correctly estimated the expression values of structurally unknown genes than the window-based method. It was observed that the Markov model contributed to the precision of splice points, and that the statistical significance of expression (P-value) represented the reliability of the estimated gene structure and expression value well. We have implemented the method as a program ARTADE (ARabidopsis Tiling Array-based Detection of Exons) and applied it to the Arabidopsis thaliana whole-genome array data analysis. The database of the predicted results and the ARTADE program are available at http://omicspace.riken.jp/ARTADE/.

  5. 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.

  6. 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

  7. 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

  8. Elucidating protein secondary structure with circular dichroism and a neural network.

    PubMed

    Hall, Vincent; Nash, Anthony; Hines, Evor; Rodger, Alison

    2013-12-15

    Circular dichroism spectroscopy is a quick method for determining the average secondary structures of proteins, probing their interactions with their environment, and aiding drug discovery. This article describes the development of a self-organising map structure-fitting methodology named secondary structure neural network (SSNN) to aid this process and reduce the level of expertise required. SSNN uses a database of spectra from proteins with known X-ray structures; prediction of structures for new proteins is then possible. It has been designed as 3 units: SSNN1 takes spectra for known proteins, clusters them into a map, and SSNN2 creates a matching structure map. SSNN3 places unknown spectra on the map and gives them structure vectors. SSNN3 output illustrates the process and results obtained. We detail the strengths and weaknesses of SSNN and compare it with widely accepted structure fitting programs. Current input format is Δε per amino acid residue from 240 to 190 nm in 1 nm steps for the known and unknown proteins and a vector summarizing the secondary structure elements of the known proteins. The format is readily modified to include input data with, for example, extended wavelength ranges or different assignment of secondary structures. SSNN can be used either pretrained with a reference set from the CDPro web site (direct application of SSNN3, with the provided output from SSNN1 and SSNN2) or all three modules can be used as required. SSNN3 is available trained (with the reference set of the 48-spectra set used in this work complemented by five additional spectra) at http://www2.warwick.ac.uk/fac/sci/chemistry/research/arodger/arodgergroup/research_intro/instrumentation/ssnn/. Copyright © 2013 Wiley Periodicals, Inc.

  9. Elucidation of the Structure Formation of Polymer-Conjugated Proteins in Solution and Block Copolymer Templates

    NASA Astrophysics Data System (ADS)

    Ferebee, Rachel L.

    The broader technical objective of this work is to contribute to the development of enzyme-functionalized nanoporous membranes that can function as autonomous and target selective dynamic separators. The scientific objective of the research performed within this thesis is to elucidate the parameters that control the mixing of proteins in organic host materials and in block copolymers templates in particular. A "biomimetic" membrane system that uses enzymes to selectively neutralize targets and trigger a change in permeability of nanopores lined with a pH-responsive polymer has been fabricated and characterized. Mechanical and functional stability, as well as scalability, have been demonstrated for this system. Additional research has focused on the role of polymeric ligands on the solubility characteristics of the model protein, Bovine Serum Albumin (BSA). For this purpose BSA was conjugated with poly(ethylene glycol) (PEG) ligands of varied degree of polymerization and grafting density. Combined static and dynamic light scattering was used (in conjunction with MALDI-TOF) to determine the second virial coefficient in PBS solutions. At a given mass fraction PEG or average number of grafts, the solubility of BSA-PEG conjugates is found to increase with the degree of polymerization of conjugated PEG. This result informs the synthesis of protein-conjugate systems that are optimized for the fabrication of block copolymer blend materials with maximum protein loading. Blends of BSA-PEG conjugates and block copolymer (BCP) matrices were fabricated to evaluate the dispersion morphology and solubility limits in a model system. Electron microscopy was used to evaluate the changes in lamellar spacing with increased filling fraction of BSA-PEG conjugates.

  10. Prokaryotic Chaperonins as Experimental Models for Elucidating Structure-Function Abnormalities of Human Pathogenic Mutant Counterparts

    PubMed Central

    Conway de Macario, Everly; Robb, Frank T.; Macario, Alberto J. L.

    2017-01-01

    All archaea have a chaperonin of Group II (thermosome) in their cytoplasm and some have also a chaperonin of Group I (GroEL; Cpn60; Hsp60). Conversely, all bacteria have GroEL, some in various copies, but only a few have, in addition, a chaperonin (tentatively designated Group III chaperonin) very similar to that occurring in all archaea, i.e., the thermosome subunit, and in the cytosol of eukaryotic cells, named CCT. Thus, nature offers a range of prokaryotic organisms that are potentially useful as experimental models to study the human CCT and its abnormalities. This is important because many diseases, the chaperonopathies, have been identified in which abnormal chaperones, including mutant CCT, are determinant etiologic-pathogenic factors and, therefore, research is needed to elucidate their pathologic features at the molecular level. Such research should lead to the clarification of the molecular mechanisms underlying the pathologic lesions observed in the tissues and organs of patients with chaperonopathies. Information on these key issues is necessary to make progress in diagnosis and treatment. Some of the archaeal organisms as well as some of the bacterial models suitable for studying molecular aspects pertinent to human mutant chaperones are discussed here, focusing on CCT. Results obtained with the archaeon Pyrococcus furiosus model to investigate the impact of a pathogenic CCT5 mutation on molecular properties and chaperoning functions are reviewed. The pathogenic mutation examined weakens the ability of the chaperonin subunit to form stable hexadecamers and as a consequence, the chaperoning functions of the complex are impaired. The future prospect is to find means for stabilizing the hexadecamer, which should lead to a recovering of chaperone function and the improving of lesions and clinical condition. PMID:28119916

  11. 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.

  12. Experimental and theoretical calculation studies on the structure elucidation and absolute configuration of calyxins from Alpinia katsumadai.

    PubMed

    Wang, Xiao-Bing; Yang, Chang-Shui; Luo, Jian-Guang; Zhang, Chao; Luo, Jun; Yang, Ming-Hua; Kong, Ling-Yi

    2017-06-01

    Six novel calyxins, named calyxin T-W, ent-calyxin T and ent-calyxin U were isolated from the seeds of Alpinia katsumadai Hayata. Their relative configurations were elucidated by means of detailed UV, IR, NMR and MS spectroscopic data. Their absolute configurations were assigned by collaborative studies on single crystal X-ray diffraction analysis, Mosher's method, electronic circular dichroism (ECD), optical rotation and theoretical calculations. These compounds are Friedel-Cranft alkylation adducts composed of coexisted diarylheptanoids and flavanone from the seeds of Alpinia katsumadai. The antiproliferative activity of the six compounds against NCI-H460, HeLa, SMMC-7721 and HCT-116 cell lines was also reported, and most of them showed moderate to strong activities. Copyright © 2017. Published by Elsevier B.V.

  13. Polycyclic aromatic hydrocarbons in Australian coals. III. Structural elucidation by proton nuclear magnetic resonance spectroscopy

    SciTech Connect

    Chaffee, A.L.; Fookes, C.J.R.

    1988-01-01

    The molecular structures of a number of tetra- and pentacyclic aromatic hydrocarbons present in extracts of Victorian brown coal have been unambiguously established by /sup 1/H-NMR. The determined structures support the hypothesis that these polycyclic aromatic hydrocarbons (PAHs) are diagenetically derived from triterpenoid precursors based on the oleanane, ursane and lupane skeletons. The occurrence of diastereoisomerism in these PAHs has been revealed for the first time and the diastereomeric configurations of one pair of triaromatic compounds (XI and XII) defined.

  14. 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.

  15. The structure elucidation of a new bromophenol metabolite from Polysiphonia urceolata by experimental and DFT theoretical methods

    NASA Astrophysics Data System (ADS)

    Liu, Quan-Wen; Qiao, Qing-An; Zhang, Ting; Sun, Li-Xiang; Wang, Mei-Shan

    2009-07-01

    A new bromophenol metabolite was obtained from the red alga Polysiphonia urceolata. The structure and absolute stereochemistry of this bromophenol were elucidated to be (5S, 10S)-2,7-dibromo-3,8-dihydroxy-5,10-dimethoxyl-5,10-dihydro-chromeno[5,4,3-cde]chromene on the basis of spectroscopic techniques and DFT theoretical analysis. The NMR spectra have been successfully reproduced from the theoretical calculations by means of the GIAO method. This bromophenol metabolite from marine source is reported for the first time.

  16. Structure elucidation of alkaline earth impregnated MCM-41 type mesoporous materials obtained by direct synthesis: An experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Paz, Gizeuda L.; Silva, Francisco das Chagas M.; Araújo, Maciel M.; Lima, Francisco das Chagas A.; Luz, Geraldo E.

    2014-06-01

    In this work, MCM-41 were synthesized hydrothermally and functionalized with calcium and strontium salts by direct method, using the Si/M = 50 molar ratio, in order to elucidate the way as the alkaline earth is incorporated on MCM-41 molecular sieve. The materials were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, nitrogen adsorption-desorption and theoretical calculations by DFT method. Experimental results and computer simulations showed that the alkaline earths were incorporated on MCM-41 through a complex structure, which negatively influences on basic sites formation.

  17. Perspectives in the application of residual dipolar couplings in the structure elucidation of weakly aligned small molecules.

    PubMed

    Schmidts, Volker

    2017-01-01

    This perspective article aims to review the general methodology in the application of residual dipolar couplings (RDCs) in the structure elucidation of small molecules and give the author's view on challenges for future applications. Recent improvements in the availability of alignment media, new pulse sequences for the measurement of couplings and improvements in the analysis software have garnered widespread interest in the technique. However, further generalization is needed in order to make RDC analysis into a truly "routine" method. Copyright © 2016 John Wiley & Sons, Ltd.

  18. Elucidating Peptide and Protein Structure and Dynamics: UV Resonance Raman Spectroscopy

    PubMed Central

    Oladepo, Sulayman A.; Xiong, Kan; Hong, Zhenmin; Asher, Sanford A.

    2011-01-01

    UV resonance Raman spectroscopy (UVRR) is a powerful method that has the requisite selectivity and sensitivity to incisively monitor biomolecular structure and dynamics in solution. In this perspective, we highlight applications of UVRR for studying peptide and protein structure and the dynamics of protein and peptide folding. UVRR spectral monitors of protein secondary structure, such as the Amide III3 band and the Cα-H band frequencies and intensities can be used to determine Ramachandran Ψ angle distributions for peptide bonds. These incisive, quantitative glimpses into conformation can be combined with kinetic T-jump methodologies to monitor the dynamics of biomolecular conformational transitions. The resulting UVRR structural insight is impressive in that it allows differentiation of, for example, different α-helix-like states that enable differentiating π- and 310- states from pure α-helices. These approaches can be used to determine the Gibbs free energy landscape of individual peptide bonds along the most important protein (un)folding coordinate. Future work will find spectral monitors that probe peptide bond activation barriers that control protein (un)folding mechanisms. In addition, UVRR studies of sidechain vibrations will probe the role of side chains in determining protein secondary, tertiary and quaternary structures. PMID:21379371

  19. 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.

  20. Dioximate- and Bis(salicylaldiminate)-Bridged Titanium and Zirconium Alkoxides: Structure Elucidation by Mass Spectrometry

    PubMed Central

    Maurer, Christian; Pittenauer, Ernst; Puchberger, Michael; Allmaier, Günter; Schubert, Ulrich

    2013-01-01

    The treatment of titanium alkoxides with 1,5-pentanedioxime or 2,5-hexanedioxime resulted in the formation of complexes [{TiL(OR)2}2] in which the dioximate ligands (L) bridge a dimeric Ti2(μ2-OR)2 unit. The structures of the complexes were determined by single-crystal structure analysis, ESI mass spectrometry, and 1D and 2D solution NMR spectroscopy. In contrast, the treatment of titanium alkoxides with dioximes bearing cyclic linkers, such as cyclohexyl or aryl groups, resulted in insoluble polymeric compounds. The treatment of various bis(salicylaldiminates) with titanium and zirconium alkoxides resulted in compounds with the same composition [{TiL(OR)2}2], in which, however, two monomeric Ti(OR)2 units are bridged by the ligands L. The two structural possibilities can be distinguished by low-energy collision-induced dissociation owing to their different fragmentation patterns. PMID:23795338

  1. Astellifadiene: Structure Determination by NMR Spectroscopy and Crystalline Sponge Method, and Elucidation of its Biosynthesis.

    PubMed

    Matsuda, Yudai; Mitsuhashi, Takaaki; Lee, Shoukou; Hoshino, Manabu; Mori, Takahiro; Okada, Masahiro; Zhang, Huiping; Hayashi, Fumiaki; Fujita, Makoto; Abe, Ikuro

    2016-05-04

    Genome mining of a terpene synthase gene from Emericella variecolor NBRC 32302 and its functional expression in Aspergillus oryzae led to the production of the new sesterterpene hydrocarbon, astellifadiene (1), having a 6-8-6-5-fused ring system. The structure of 1 was initially investigated by extensive NMR analyses, and was further confirmed by the crystalline sponge method, which established the absolute structure of 1 and demonstrated the usefulness of the method in the structure determination of complex hydrocarbon natural products. Furthermore, the biosynthesis of 1 was proposed on the basis of isotope-incorporation experiments performed both in vivo and in vitro. The cyclization of GFPP involves a protonation-initiated second cyclization sequence, 1,2-alkyl migration, and 1,5-hydride shift to generate the novel scaffold of 1. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    PubMed

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

    2016-09-05

    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. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Elucidating the structure of merocyanine dyes with the ASEC-FEG method. Phenol blue in solution

    NASA Astrophysics Data System (ADS)

    Franco, Leandro R.; Brandão, Idney; Fonseca, Tertius L.; Georg, Herbert C.

    2016-11-01

    The electronic structure of phenol blue (PB) was investigated in several protic and aprotic solvents, in a wide range of dielectric constants, using atomistic simulations. We employed the sequential QM/MM and the free energy gradient methods to optimize the geometry of PB in each solvent at the MP2/aug-cc-pVTZ level. The ASEC mean field is used to include the ensemble average of the solute-solvent interaction into the molecular hamiltonian, both for the geometry optimization and for the calculations of the electronic properties. We found that the geometry of PB changes considerably, from a polyene-like structure in nonpolar solvents to a cyanine-like in water. Moreover, and quite interestingly, in protic solvents with higher dielectric constant than water, the structure of the molecule is less affected and lies in an intermediate state. The results illustrate the important role played by hydrogen bonds in the conformation of merocyanine dyes.

  4. 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.

  5. Elucidation of the Fe(III) Gallate Structure in Historical Iron Gall Ink.

    PubMed

    Ponce, Aldo; Brostoff, Lynn B; Gibbons, Sarah K; Zavalij, Peter; Viragh, Carol; Hooper, Joseph; Alnemrat, Sufian; Gaskell, Karen J; Eichhorn, Bryan

    2016-05-17

    Synthetic, structural, spectroscopic and aging studies conclusively show that the main colorant of historical iron gall ink (IGI) is an amorphous form of Fe(III) gallate·xH2O (x = ∼1.5-3.2). Comparisons between experimental samples and historical documents, including an 18th century hand-written manuscript by George Washington, by IR and Raman spectroscopy, XRD, X-ray photoelectron spectroscopy, and Mössbauer spectroscopy confirm the relationship between the model and authentic samples. These studies settle controversy in the cultural heritage field, where an alternative structure for Fe(III) gallate has been commonly cited.

  6. 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.

  7. 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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Structure elucidation of DNA interstrand cross-link by a combination of nuclease P1 digestion with mass spectrometry.

    PubMed

    Wang, Yuesong; Wang, Yinsheng

    2003-11-15

    DNA interstrand cross-link reagents are among the most powerful agents for cancer treatment. Here we report a combined nuclease P1 digestion/mass spectrometry method for the structure elucidation of duplex oligodeoxynucleotides (ODNs) containing an interstrand cross-link. Our results demonstrate that nuclease P1 digestion of a double-stranded ODN containing an interstrand cross-link (ICL) of 4,5',8-trimethylpsoralen or mitomycin C gives a tetranucleotide bearing the cross-linked nucleobase moiety. Product ion spectra of the deprotonated ions of the tetranucleotides provide information about the structure of the cross-link. Furthermore, product-ion spectra of tetranucleotides containing two orientation isomers of mitomycin C interstrand cross-link are distinctive. We believe that the method described in this paper can be generally applicable for investigating the structures of other DNA ICLs.

  9. 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.

  10. 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…

  11. Structures of benzylsuccinate synthase elucidate roles of accessory subunits in glycyl radical enzyme activation and activity

    PubMed Central

    Funk, Michael A.; Judd, Evan T.; Marsh, E. Neil G.; Elliott, Sean J.; Drennan, Catherine L.

    2014-01-01

    Anaerobic degradation of the environmental pollutant toluene is initiated by the glycyl radical enzyme benzylsuccinate synthase (BSS), which catalyzes the radical addition of toluene to fumarate, forming benzylsuccinate. We have determined crystal structures of the catalytic α-subunit of BSS with its accessory subunits β and γ, which both bind a [4Fe-4S] cluster and are essential for BSS activity in vivo. We find that BSSα has the common glycyl radical enzyme fold, a 10-stranded β/α-barrel that surrounds the glycyl radical cofactor and active site. Both accessory subunits β and γ display folds related to high potential iron–sulfur proteins but differ substantially from each other in how they interact with the α-subunit. BSSγ binds distally to the active site, burying a hydrophobic region of BSSα, whereas BSSβ binds to a hydrophilic surface of BSSα that is proximal to the active site. To further investigate the function of BSSβ, we determined the structure of a BSSαγ complex. Remarkably, we find that the barrel partially opens, allowing the C-terminal region of BSSα that houses the glycyl radical to shift within the barrel toward an exit pathway. The structural changes that we observe in the BSSαγ complex center around the crucial glycyl radical domain, thus suggesting a role for BSSβ in modulating the conformational dynamics required for enzyme activity. Accompanying proteolysis experiments support these structural observations. PMID:24982148

  12. 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…

  13. Resource stoichiometry elucidates the structure and function of arbuscular mycorrhizas across scales.

    PubMed

    Johnson, Nancy Collins

    2010-02-01

    Despite the fact that arbuscular mycorrhizal (AM) associations are among the most ancient, abundant and important symbioses in terrestrial ecosystems, there are currently few unifying theories that can be used to help understand the factors that control their structure and function. This review explores how a stoichiometric perspective facilitates integration of three complementary ecological and evolutionary models of mycorrhizal structure and function. AM symbiotic function should be governed by the relative availability of carbon, nitrogen and phosphorus (trade balance model) and allocation to plant and fungal structures should depend on the availabilities of these resources (functional equilibrium model). Moreover, in an evolutionary framework, communities of plants and AM fungi are predicted to adapt to each other and their local soil environment (co-adaptation model). Anthropogenic enrichment of essential resources in the environment is known to impact AM symbioses. A more predictive theory of AM structure and function will help us to better understand how these impacts may influence plant communities and ecosystem properties.

  14. 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 Fm3 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.

  15. Structural and Functional Elucidation of Yeast Lanosterol 14α-Demethylase in Complex with Agrochemical Antifungals

    PubMed Central

    Sagatova, Alia A.; Keniya, Mikhail V.; Negroni, Jacopo; Wilson, Rajni K.; Woods, Matthew A.; Monk, Brian C.

    2016-01-01

    Azole antifungals, known as demethylase inhibitors (DMIs), target sterol 14α-demethylase (CYP51) in the ergosterol biosynthetic pathway of fungal pathogens of both plants and humans. DMIs remain the treatment of choice in crop protection against a wide range of fungal phytopathogens that have the potential to reduce crop yields and threaten food security. We used a yeast membrane protein expression system to overexpress recombinant hexahistidine-tagged S. cerevisiae lanosterol 14α-demethylase and the Y140F or Y140H mutants of this enzyme as surrogates in order characterize interactions with DMIs. The whole-cell antifungal activity (MIC50 values) of both the R- and S-enantiomers of tebuconazole, prothioconazole (PTZ), prothioconazole-desthio, and oxo-prothioconazole (oxo-PTZ) as well as for fluquinconazole, prochloraz and a racemic mixture of difenoconazole were determined. In vitro binding studies with the affinity purified enzyme were used to show tight type II binding to the yeast enzyme for all compounds tested except PTZ and oxo-PTZ. High resolution X-ray crystal structures of ScErg11p6×His in complex with seven DMIs, including four enantiomers, reveal triazole-mediated coordination of all compounds and the specific orientation of compounds within the relatively hydrophobic binding site. Comparison with CYP51 structures from fungal pathogens including Candida albicans, Candida glabrata and Aspergillus fumigatus provides strong evidence for a highly conserved CYP51 structure including the drug binding site. The structures obtained using S. cerevisiae lanosterol 14α-demethylase in complex with these agrochemicals provide the basis for understanding the impact of mutations on azole susceptibility and a platform for the structure-directed design of the next-generation of DMIs. PMID:27907120

  16. Elucidating in Vivo Structural Dynamics in Integral Membrane Protein by Hydroxyl Radical Footprinting*

    PubMed Central

    Zhu, Yi; Guo, Tiannan; Park, Jung Eun; Li, Xin; Meng, Wei; Datta, Arnab; Bern, Marshall; Lim, Sai Kiang; Sze, Siu Kwan

    2009-01-01

    We describe here a novel footprinting technique to probe the in vivo structural dynamics of membrane protein. This method utilized in situ generation of hydroxyl radicals to oxidize and covalently modify biomolecules on living Escherichia coli cell surface. After enriching and purifying the membrane proteome, the modified amino acid residues of the protein were identified with tandem mass spectrometry to map the solvent-accessible surface of the protein that will form the footprint of in vivo structure of the protein. Of about 100 outer membrane proteins identified, we investigated the structure details of a typical β-barrel structure, the porin OmpF. We found that six modified tryptic peptides of OmpF were reproducibly detected with 19 amino acids modified under the physiological condition. The modified amino acid residues were widely distributed in the external loop area, β-strands, and periplasmic turning area, and all of them were validated as solvent-accessible according to the crystallography data. We further extended this method to study the dynamics of the voltage gating of OmpF in vivo using mimic changes of physiological circumstance either by pH or by ionic strength. Our data showed the voltage gating of porin OmpF in vivo for the first time and supported the proposed mechanism that the local electrostatic field changes in the eyelet region may alter the porin channels to switch. Thus, this novel method can be a potentially efficient method to study the structural dynamics of the membrane proteins of a living cell. PMID:19473960

  17. Structural elucidation and molecular characterization of Marinobacter sp. α-amylase.

    PubMed

    Kumar, Sumit; Khan, Rizwan Hasan; Khare, S K

    2016-01-01

    Halophiles have been perceived as potential source of novel enzymes in recent years. The interest emanates from their ability to catalyze efficiently under high salt and organic solvents. Marinobacter sp. EMB8 α-amylase was found to be active and stable in salt and organic solvents. A study was carried out using circular dichroism (CD), fluorescence spectroscopy, and bioinformatics analysis of similar protein sequence to ascertain molecular basis of salt and solvent adaptability of α-amylase. Structural changes recorded in the presence of varying amounts of NaCl exhibited an increase in negative ellipticity as a function of salt, confirming that salt stabilizes the protein and increases the secondary structure, making it catalytically functional. The data of intrinsic and extrinsic fluorescence (using 1-anilinonaphthalene 8-sulfonate [ANS] as probe) further confirmed the role of salt. The α-amylase was active in the presence of nonpolar solvents, namely, hexane and decane, but inactivated by ethanol. The decrease in the activity was correlated with the loss of tertiary structure in the presence of ethanol. Guanidine hydrochloride and pH denaturation indicated the molten globule state at pH 4.0. Partial N-terminal amino acid sequence of the purified α-amylase revealed the relatedness to Pseudoalteromonas sp. α-amylase. "FVHLFEW" was found as the N-terminal signature sequence. Bioinformatics analysis was done using M. algicola α-amylase protein having the same N-terminal signature sequence. The three-dimensional structure of Marinobacter α-amylase was deduced using the I-TASSER server, which reflected the enrichment of acidic amino acids on the surface, imparting the stability in the presence of salt. Our study clearly indicate that salt is necessary for maintaining the secondary and tertiary structure of halophilic protein, which is a necessary prerequisite for catalysis.

  18. Structural and Functional Elucidation of Yeast Lanosterol 14α-Demethylase in Complex with Agrochemical Antifungals.

    PubMed

    Tyndall, Joel D A; Sabherwal, Manya; Sagatova, Alia A; Keniya, Mikhail V; Negroni, Jacopo; Wilson, Rajni K; Woods, Matthew A; Tietjen, Klaus; Monk, Brian C

    2016-01-01

    Azole antifungals, known as demethylase inhibitors (DMIs), target sterol 14α-demethylase (CYP51) in the ergosterol biosynthetic pathway of fungal pathogens of both plants and humans. DMIs remain the treatment of choice in crop protection against a wide range of fungal phytopathogens that have the potential to reduce crop yields and threaten food security. We used a yeast membrane protein expression system to overexpress recombinant hexahistidine-tagged S. cerevisiae lanosterol 14α-demethylase and the Y140F or Y140H mutants of this enzyme as surrogates in order characterize interactions with DMIs. The whole-cell antifungal activity (MIC50 values) of both the R- and S-enantiomers of tebuconazole, prothioconazole (PTZ), prothioconazole-desthio, and oxo-prothioconazole (oxo-PTZ) as well as for fluquinconazole, prochloraz and a racemic mixture of difenoconazole were determined. In vitro binding studies with the affinity purified enzyme were used to show tight type II binding to the yeast enzyme for all compounds tested except PTZ and oxo-PTZ. High resolution X-ray crystal structures of ScErg11p6×His in complex with seven DMIs, including four enantiomers, reveal triazole-mediated coordination of all compounds and the specific orientation of compounds within the relatively hydrophobic binding site. Comparison with CYP51 structures from fungal pathogens including Candida albicans, Candida glabrata and Aspergillus fumigatus provides strong evidence for a highly conserved CYP51 structure including the drug binding site. The structures obtained using S. cerevisiae lanosterol 14α-demethylase in complex with these agrochemicals provide the basis for understanding the impact of mutations on azole susceptibility and a platform for the structure-directed design of the next-generation of DMIs.

  19. Structural elucidation of the lignins from stems and foliage of Arundo donax Linn.

    PubMed

    You, Ting-Ting; Mao, Jian-Zhen; Yuan, Tong-Qi; Wen, Jia-Long; Xu, Feng

    2013-06-05

    As one of the potential energy crops, Arundo donax Linn. is a renewable source for the production of biofuels and bioproducts. In the present study, milled wood lignin (MWL) and alkaline lignin (AL) from stems and foliage of A. donax were isolated and characterized by FT-IR spectroscopy, UV spectroscopy, GPC, ³¹P NMR, 2D HSQC NMR, and DFRC. The results indicated that both stem and foliage lignins were HGS type lignins. The semiquantitative HSQC spectra analysis demonstrated a predominance of β-O-4' aryl ether linkages (71-82%), followed by β-β', β-5', β-1', and α,β-diaryl ethers linkages in the lignins. Compared to stem lignins, foliage lignins had less β-O-4' alkyl-aryl ethers, lower weight-average molecular weight, less phenolic OH, more H units, and lower S/G ratio. Moreover, tricin was found to incorporate into the foliage lignins (higher content of condensed G units) in significant amounts and might be alkaline-stable.

  20. Structural elucidation of the Brucella melitensis M antigen by high-resolution NMR at 500 MHz.

    PubMed

    Bundle, D R; Cherwonogrodzky, J W; Perry, M B

    1987-12-29

    The Brucella M antigen from the species type strain Brucella melitensis 16M has been identified as a component of the cell wall lipopolysaccharide (LPS). O polysaccharide liberated from this LPS by mild acid hydrolysis exhibited M activity in serological tests and was shown to be a homopolymer of 4-formamido-4,6-dideoxy-alpha-D-mannopyranosyl residues arranged in an oligosaccharide repeating unit as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the native lipopolysaccharide. Structural analysis of the O polysaccharide by NMR methods was difficult due to apparent microheterogeneity of the repeating unit, which was in fact caused by the presence of rotational isomers of the N-formyl moiety. This problem was resolved by chemical modification of the polysaccharide to its amino and N-acetyl derivatives, the 500-MHz 1H and 125-MHz 13C NMR spectra of which could be analyzed in terms of a unique structure through application of pH-dependent beta-shifts and two-dimensional techniques that included COSY, relayed COSY, and NOESY experiments together with heteronuclear C/H shift correlation spectroscopy. On the basis of these experiments and supported by methylation and periodate oxidation data, the structure of the M polysaccharide was determined as a linear polymer of unbranched pentasaccharide repeating units consisting of four 1,2-linked and one 1,3-linked 4,6-dideoxy-4-formamido-alpha-D-mannopyranosyl residues. The marked structural similarity of the M antigen and the A antigen, which is known to be a 1,2-linked homopolysaccharide of 4,6-dideoxy-4-formamido-alpha-D-mannopyranosyl units, accounts for cross-serological reactions of the two and the long-standing confusion surrounding the nature of their antigenic determinants. Structural and serological considerations in conjuction with the sodium dodecyl sulfate banding pattern of Brucella A LPS suggest that its biosynthesis differs appreciably from that of the M antigen, which appears to be

  1. 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.

  2. 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

    2016-07-22

    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.

  3. Structure elucidation and gene cluster characterization of the O-antigen of Escherichia coli O80.

    PubMed

    Senchenkova, Sof'ya N; Guo, Xi; Filatov, Andrei V; Perepelov, Andrei V; Liu, Bin; Shashkov, Alexander S; Knirel, Yuriy A

    2016-09-02

    Mild alkaline degradation of the lipopolysaccharide of Escherichia coli O80 afforded a polysaccharide, which was studied by sugar analysis, selective cleavage of glycosidic linkages, and (1)H and (13)C NMR spectroscopy. Solvolysis of the polysaccharide with CF3CO2H cleaved the linkages of α-Fuc and β-linked GlcNAc and GalNAc residues to give two disaccharides. The following structure of the hexasaccharide repeating unit of the O-polysaccharide was established: The polysaccharide repeat also contains a minor O-acetyl group but its position was not determined. The O-antigen gene cluster of E. coli O80 between the conserved galF and gnd genes was analyzed and found to be consistent with the O-polysaccharide structure established.

  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. Structural elucidation of the Brucella melitensis M antigen by high-resolution NMR at 500 MHz

    SciTech Connect

    Bundle, D.R.; Cherwonogrodzky, J.W.; Perry, M.B.

    1987-12-29

    The Brucella M antigen from the species type strain Brucella melitensis 16M has been identified as a component of the cell wall lipopolysaccharide (LPS). O polysaccharide liberated from this LPS by mild acid hydrolysis exhibited M activity in serological tests and was shown to be a homopolymer of 4-formamido-4,6-dideoxy-..cap alpha..-D-mannopyranosyl residues arranged in an oligosaccharide repeating unit as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the native lipopolysaccharide. Structural analysis of the O polysaccharide by NMR methods was difficult due to apparent microheterogeneity of the repeating unit, which was in fact caused by the presence of rotational isomers of the N-formyl moiety. This problem was resolved by chemical modification of the polysaccharide to its amino and N-acetyl derivatives, the 500-MHz /sup 1/H and 125-MHz /sup 13/C NMR spectra of which could be analyzed in terms of a unique structure through application of pH-dependent ..beta..-shifts and two-dimensional techniques that included COSY, relayed COSY, and NOESY experiments together with heteronuclear C/H shift correlation spectroscopy. On the basis of these experiments and supported by methylation and periodate oxidation data, the structure of the M polysaccharide was determined as a linear polymer of unbranched pentasaccharide repeating units consisting of four 1,2-linked and one 1,3-lined 4,6-dideoxy-4-formamido-..cap alpha..-D-mannopyranosyl residues. The marked structural similarity of the M antigen and the A antigen, which is known to be a 1,2-linked homopolysaccharide of 4,6-dideoxy-4-formamido-..cap alpha..-D-mannopyranosyl units, accounts for cross-serological reactions of the two and the long-standing confusion surrounding the nature of their antigenic determinants.

  6. Elucidating features that drive the design of selective antifolates using crystal structures of human dihydrofolate reductase.

    PubMed

    Lamb, Kristen M; G-Dayanandan, Narendran; Wright, Dennis L; Anderson, Amy C

    2013-10-15

    The pursuit of antimicrobial drugs that target dihydrofolate reductase (DHFR) exploits differences in sequence and dynamics between the pathogenic and human enzymes. Here, we present five crystal structures of human DHFR bound to a new class of antimicrobial agents, the propargyl-linked antifolates (PLAs), with a range of potency (IC50 values of 0.045-1.07 μM) for human DHFR. These structures reveal that interactions between the ligands and Asn 64, Phe 31, and Phe 34 are important for increased affinity for human DHFR and that loop residues 58-64 undergo ligand-induced conformational changes. The utility of these structural studies was demonstrated through the design of three new ligands that reduce the number of contacts with Asn 64, Phe 31, and Phe 34. Synthesis and evaluation show that one of the designed inhibitors exhibits the lowest affinity for human DHFR of any of the PLAs (2.64 μM). Comparisons of structures of human and Staphylococcus aureus DHFR bound to the same PLA reveal a conformational change in the ligand that enhances interactions with residues Phe 92 (Val 115 in huDHFR) and Ile 50 (Ile 60 in huDHFR) in S. aureus DHFR, yielding selectivity. Likewise, comparisons of human and Candida glabrata DHFR bound to the same ligand show that hydrophobic interactions with residues Ile 121 and Phe 66 (Val 115 and Asn 64 in human DHFR) yield selective inhibitors. The identification of residue substitutions that are important for selectivity and the observation of active site flexibility will help guide antimicrobial antifolate development for the inhibition of pathogenic species.

  7. Well-defined azazirconacyclopropane complexes supported on silica structurally determined by 2D NMR comparative elucidation.

    PubMed

    El Eter, Mohamad; Hamzaoui, Bilel; Abou-Hamad, Edy; Pelletier, Jérémie D A; Basset, Jean-Marie

    2013-05-21

    Grafting of Zr(NMe2)4 on mesoporous silica SBA-15 afforded selectively well-defined surface species [triple bond, length as m-dash]SiOZr(NMe2)(η2NMeCH2). 2D solid-state NMR ((1)H-(13)C HETCOR, Multiple Quantum) experiments have shown a unique structural rearrangement occurring on the immobilised zirconium bis methylamido ligand.

  8. Elucidating cerium + H2O reactivity through electronic structure: A combined PES and DFT study

    NASA Astrophysics Data System (ADS)

    Topolski, J. E.; Kafader, J. O.; Ray, M.; Jarrold, C. C.

    2017-06-01

    The anion photoelectron (PE) spectra of CexOyHz- products formed in sequential reactions between cerium oxide and hydroxide reactions with water are presented and interpreted with supporting density functional theory calculations. The PE spectra of CexOyHz- (x = 2, 3) complexes formed in the sequence of reactions initiated with CexOx- + H2O, exhibit a prominent photodetachment transition indicating that the highest occupied molecular orbital in these species can be described as combinations of Ce 6s atomic orbitals. The electrons in these diffuse orbitals reliably have low binding energies in the range of 0.6-1 eV. The combination of poor orbital overlap and low binding energy is amenable to ionic Cesbnd OH bond formation in reactions with water, rather than Cedbnd O bond formation, which is observed in more reduced clusters that have occupied Ce 5d-based molecular orbitals. Spectral simulations based on computational results, which predict numerous close-lying spin states arising from the singly occupied 4f orbital on each Ce center, support specific structural assignments for the Ce2OyHz- cluster series. A range of Ce3OyHz- products also exhibit the characteristic Ce 6s-based MO photodetachment transition. Based on comparison with calculations that predict stable cerium hydride structures, we infer that the sequence of Ce3OyHz- + H2O reactions proceeds along a path of metastable structures.

  9. Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry.

    PubMed

    Zheng, Xueyun; Renslow, Ryan S; Makola, Mpho M; Webb, Ian K; Deng, Liulin; Thomas, Dennis G; Govind, Niranjan; Ibrahim, Yehia M; Kabanda, Mwadham M; Dubery, Ian A; Heyman, Heino M; Smith, Richard D; Madala, Ntakadzeni E; Baker, Erin S

    2017-04-06

    Due to the recently uncovered health benefits and anti-HIV activities of dicaffeoylquinic acids (diCQAs), understanding their structures and functions is of great interest for drug discovery efforts. DiCQAs are analytically challenging to identify and quantify since they commonly exist as a diverse mixture of positional and geometric (cis/trans) isomers. In this work, we utilized ion mobility spectrometry coupled with mass spectrometry to separate the various isomers before and after UV irradiation. The experimental collision cross sections were then compared with theoretical structures to differentiate and identify the diCQA isomers. Our analyses found that naturally the diCQAs existed predominantly as trans/trans isomers, but after 3 h of UV irradiation, cis/cis, cis/trans, trans/cis, and trans/trans isomers were all present in the mixture. This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies.

  10. Structural elucidation of a heteroglycan from the fruiting bodies of Agaricus blazei Murill.

    PubMed

    Liu, Jicheng; Zhang, Chunjing; Wang, Yajun; Yu, Haitao; Liu, Han; Wang, Liping; Yang, Xiuzhen; Liu, Zhecheng; Wen, Xianchun; Sun, Yongxu; Yu, Chunlei; Liu, Lei

    2011-11-01

    One water-soluble polysaccharide (ABP-W1) was purified from the fruiting bodies of Agaricus blazei by DEAE Sepharose Fast Flow and Sepharose 6 Fast Flow column chromatography. Its molecular weight was about 3.9×10(2) kDa as determined by high-performance size-exclusion chromatography (HPSEC). The structural feature of ABP-W1 was investigated by a combination of chemical and instrumental analysis, including partial hydrolysis with acid, periodate oxidation-Smith degradation, acetylation, methylation analysis and nuclear magnetic resonance spectroscopy (NMR (1)H, (13)C). The results revealed that ABP-W1 had a backbone consisting of (1→6)-linked-α-D-galactopyranosyl and (1→2,6)-linked-α-D-glucopyranosyl, which was branched with one single terminal (1→)-α-D-glucopyranosyl at the O-2 position of (1→2,6)-linked-α-D-glucopyranosyl along the main chain in the ratio of 1:1:1. The observation of the complex-formation between ABP-W1 and Congo Red indicated that ABP-W1 probably existed in a triple-strand helical conformation in water. Based on the data obtained, ABP-W1 was composed of a repeating unit with a structure as below: [structure: see text].

  11. Structure elucidation of a new isoflavone by exclusive use of ¹H NMR measurements.

    PubMed

    Ortega, Alfredo R; Toscano, Rubén A; Hernández-Barragán, Angelina; Alvarez-Cisneros, Celina; Joseph-Nathan, Pedro

    2015-10-01

    The leaves of Piscidia carthagenensis provided new 7,2',5'-trimethoxy-3',4'-methylenedioxyisoflavone (1), admixed with known 6,7-dimethoxy-3',4'-methylenedioxyisoflavone (2), and 5,4'-dihydroxy-7,2',5'-trimethoxyisoflavone (3), which were separated by extensive fractional solubillization. Selective irradiation of the H-5 "singlet" of 2 allowed distinction of the two methoxy group signals, whose chemical shift difference is only 0.004 ppm (1.2 Hz at 300 MHz). The (1)H and (13)C NMR data of 3 were assigned with the aid of HETCOR and gHMBC measurements. Although 1 looked inhomogeneous in the solid state, its solution structure followed from (1)H NMR measurements, where it looked homogeneous. To clarify the solid state aspect and confirm the structure of 1, two types of crystals were mechanically separated and subjected to single crystal X-ray diffraction measurements. This study revealed polymorphism because of the concomitant presence of orthorhombic and triclinic crystals, but showed no atropisomerism. The structure of 3 was also verified by X-ray diffraction crystallography.

  12. 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.

  13. 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

  14. Isolation and structural elucidation of acidic terpenoid phytoalexins in maize and their interactions with Aspergillus flavus

    USDA-ARS?s Scientific Manuscript database

    Plants use a variety of physical and chemical defenses in response to herbivory and pathogen attack. Infection of maize by the fungal pathogen Aspergillus flavus results in the accumulation of aflatoxins, which are among the most detrimental biogenic substances known to man. The majority of maize de...

  15. Elucidation of the effect of ionic liquid pretreatment on rice husk via structural analyses

    PubMed Central

    2012-01-01

    Background In the present study, three ionic liquids, namely 1-butyl-3-methylimidazolium chloride ([BMIM]Cl), 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc), and 1-ethyl-3-methylimidazolium diethyl phosphate ([EMIM]DEP), were used to partially dissolve rice husk, after which the cellulose were regenerated by the addition of water. The aim of the investigation is to examine the implications of the ionic liquid pretreatments on rice husk composition and structure. Results From the attenuated total reflectance Fourier transform-infrared (ATR FT-IR) spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM) results, the regenerated cellulose were more amorphous, less crystalline, and possessed higher structural disruption compared with untreated rice husk. The major component of regenerated cellulose from [BMIM]Cl and [EMIM]DEP pretreatments was cellulose-rich material, while cellulose regenerated from [EMIM]OAc was a matrix of cellulose and lignin. Cellulose regenerated from ionic pretreatments could be saccharified via enzymatic hydrolysis, and resulted in relatively high reducing sugars yields, whereas enzymatic hydrolysis of untreated rice husk did not yield reducing sugars. Rice husk residues generated from the ionic liquid pretreatments had similar chemical composition and amorphousity to that of untreated rice husk, but with varying extent of surface disruption and swelling. Conclusions The structural architecture of the regenerated cellulose and rice husk residues showed that they could be used for subsequent fermentation or derivation of cellulosic compounds. Therefore, ionic liquid pretreatment is an alternative in the pretreatment of lignocellulosic biomass in addition to the conventional chemical pretreatments. PMID:22958710

  16. Studies on azaspiracid biotoxins. II. Mass spectral behavior and structural elucidation of azaspiracid analogs.

    PubMed

    Brombacher, Stephan; Edmonds, Suzanne; Volmer, Dietrich A

    2002-01-01

    In this report, the mass spectral analysis of azaspiracid biotoxins is described. Specifically, the collision-induced dissociation (CID) behavior and differences between CID spectra obtained on a triple-quadrupole, a quadrupole time-of-flight, and an ion-trap mass spectrometer are addressed here. The CID spectra obtained on the triple-quadrupole mass spectrometer allowed the classification of the major product ions of the five investigated compounds (AZA 1-5) into five distinct fragment ion groups, according to the backbone cleavage positions. Although the identification of unknown azaspiracids was difficult based on CID alone, the spectra provided sufficient structural information to allow confirmation of known azaspiracids in marine samples. Furthermore, we were able to detect two new azaspiracid analogs (AZA 1b and 6) in our samples and provide a preliminary structural analysis. The proposed dissociation pathways under tandem mass spectrometry (MS/MS) conditions were confirmed by a comparison with accurate mass data from electrospray quadrupole time-of-flight MS/MS experiments. Regular sequential MS(n) analysis on an ion-trap mass spectrometer was more restricted in comparison to the triple-quadrupole mass spectrometer, because the azaspiracids underwent multiple [M + H - nH(2)O](+) (n = 1-6) losses from the precursor ion under CID. Thus, the structural information obtained from MS(n) experiments was somewhat limited. To overcome this limitation, we developed a wide-range excitation technique using a 180-u window that provided results comparable to the triple-quadrupole instrument. To demonstrate the potential of the method, we applied it to the analysis of degraded azaspiracids from mussel tissue extracts.

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

    PubMed

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

    2010-03-07

    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.

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

    PubMed

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

    2013-10-02

    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.

  19. Synthesis and structure elucidation of fluoro substituted guanidines as potential therapeutic agents

    NASA Astrophysics Data System (ADS)

    Ullah, Waseem; Imtiaz-ud-Din; Raheel, Ahmad; Badshah, Amin; Tahir, Muhammad Nawaz

    2017-09-01

    Six new fluoro -substituted guanidines (1-6) were synthesized and characterized by 1H and 13C NMR spectroscopy to ascertain the structures in solution (DMSO) besides the solid state information collected through FT IR and single crystal X-ray spectroscopy. The XRD data for (1-3) show that molecules are stabilized by strong intramolecular hydrogen bonding. The compounds were also preliminary bio-assayed for anti-microbial studies and show good to moderate activities. The anti-oxidant data revealed that o and p-substituted fluoro-guanidines enhances their DPPH scavenging ability significantly.

  20. Structural Elucidation and Molecular Docking of a Novel Antibiotic Compound from Cyanobacterium Nostoc sp. MGL001.

    PubMed

    Niveshika; Verma, Ekta; Mishra, Arun K; Singh, Angad K; Singh, Vinay K

    2016-01-01

    Cyanobacteria are rich source of array of bioactive compounds. The present study reports a novel antibacterial bioactive compound purified from cyanobacterium Nostoc sp. MGL001 using various chromatographic techniques viz. thin layer chromatography (TLC) and high performance liquid chromatography (HPLC). Further characterization was done using electrospray ionization mass spectroscopy (ESIMS) and nuclear magnetic resonance (NMR) and predicted structure of bioactive compound was 9-Ethyliminomethyl-12-(morpholin - 4 - ylmethoxy) -5, 8, 13, 16-tetraaza-hexacene - 2, 3 dicarboxylic acid (EMTAHDCA). Structure of EMTAHDCA clearly indicated that it is a novel compound that was not reported in literature or natural product database. The compound exhibited growth inhibiting effects mainly against the gram negative bacterial strains and produced maximum zone of inhibition at 150 μg/mL concentration. The compound was evaluated through in silico studies for its ability to bind 30S ribosomal fragment (PDB ID: 1YRJ, 1MWL, 1J7T, and 1LC4) and OmpF porin protein (4GCP, 4GCQ, and 4GCS) which are the common targets of various antibiotic drugs. Comparative molecular docking study revealed that EMTAHDCA has strong binding affinity for these selected targets in comparison to a number of most commonly used antibiotics. The ability of EMTAHDCA to bind the active sites on the proteins and 30S ribosomal fragments where the antibiotic drugs generally bind indicated that it is functionally similar to the commercially available drugs.

  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. 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

    2016-06-05

    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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Structural elucidation of the mechanistic basis of degeneracy in the primary humoral response.

    PubMed

    Khan, Tarique; Salunke, Dinakar M

    2012-02-15

    The mechanistic basis for efficient combating of the infinite range of foreign Ags by the limited repertoire of naive Abs expressed on primary B cell surfaces during their first encounter was addressed through elegantly designed crystallographic analyses. Resolution of the discrepancy arising from the limited number of possible germline Ab receptors on primary B cells for recognizing the unlimited pool of possible Ags has been attempted by invoking the degenerate recognition potential of the germline Abs. Structural analyses of germline mAb BBE6.12H3 in an Ag-free state, as well as bound to four different peptide Ags, established the correlation of its degenerate specificity with conformational versatility of the paratope. Six distinct paratope topologies observed for a single germline mAb provided a quantitative description of the primary Ag recognition repertoire at the tertiary structural level. Each of the four different peptide Ags was bound specifically to a distinct conformation of the paratope, which was also different from that of the Ag-free states of the same germline mAb. A minimal conserved motif in the pristine Ag-combining site essential for multispecificity and Ag binding-mediated change in the elbow angle of Fab was also discernible. It is proposed that the generation of a primary Ab repertoire involves large, yet finite, germline Ab clones, each capable of adopting discrete conformations, which in turn exhibit diverse binding modes.

  4. Structural Elucidation and Molecular Docking of a Novel Antibiotic Compound from Cyanobacterium Nostoc sp. MGL001

    PubMed Central

    Niveshika; Verma, Ekta; Mishra, Arun K.; Singh, Angad K.; Singh, Vinay K.

    2016-01-01

    Cyanobacteria are rich source of array of bioactive compounds. The present study reports a novel antibacterial bioactive compound purified from cyanobacterium Nostoc sp. MGL001 using various chromatographic techniques viz. thin layer chromatography (TLC) and high performance liquid chromatography (HPLC). Further characterization was done using electrospray ionization mass spectroscopy (ESIMS) and nuclear magnetic resonance (NMR) and predicted structure of bioactive compound was 9-Ethyliminomethyl-12-(morpholin - 4 - ylmethoxy) -5, 8, 13, 16–tetraaza–hexacene - 2, 3 dicarboxylic acid (EMTAHDCA). Structure of EMTAHDCA clearly indicated that it is a novel compound that was not reported in literature or natural product database. The compound exhibited growth inhibiting effects mainly against the gram negative bacterial strains and produced maximum zone of inhibition at 150 μg/mL concentration. The compound was evaluated through in silico studies for its ability to bind 30S ribosomal fragment (PDB ID: 1YRJ, 1MWL, 1J7T, and 1LC4) and OmpF porin protein (4GCP, 4GCQ, and 4GCS) which are the common targets of various antibiotic drugs. Comparative molecular docking study revealed that EMTAHDCA has strong binding affinity for these selected targets in comparison to a number of most commonly used antibiotics. The ability of EMTAHDCA to bind the active sites on the proteins and 30S ribosomal fragments where the antibiotic drugs generally bind indicated that it is functionally similar to the commercially available drugs. PMID:27965634

  5. 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

  6. Structural elucidation of 4-(cystein-S-yl)butyl glucosinolate from the leaves of Eruca sativa.

    PubMed

    Kim, Sun-Ju; Kawaharada, Chiami; Jin, Shigeki; Hashimoto, Makoto; Ishii, Gensho; Yamauchi, Hiroaki

    2007-01-01

    The structurally unique glucosinolate (GSL), 4-(cystein-S-yl)butyl GSL, was identified in the leaves of hydroponically-grown rocket salad (Eruca sativa Mill.). Its electrospray ionization mass spectrometry (ESI-MS)/MS spectrum indicated that this unusual GSL had a molecular weight of 414 as a desulfo (DS)-GSL, and a molecular formula of C(14)H(25)N(2)O(8)S(2) based on its negative ion matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) spectrum. For further confirmation, the 4-(cystein-S-yl)butyl DS-GSL was prepared with authentic L-Ser and purified dimeric 4-mercaptobutyl DS-GSL, and its chemical structure then confirmed by ESI-MS/MS data. It is named "glucorucolamine" as a trivial name from its ammonia sensitivity. This unique GSL was found to the greatest extent when rocket salad was grown in a 100% NH4+-N nutrient solution. Despite it clearly seems to reduce the detoxification of excess NH4+ in the leaves of rocket salad, present knowledge about the unique GSL is still far from being sufficient.

  7. Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach

    PubMed Central

    Valeyev, Najl V; Bates, Declan G; Heslop-Harrison, Pat; Postlethwaite, Ian; Kotov, Nikolay V

    2008-01-01

    Background Calmodulin is an important multifunctional molecule that regulates the activities of a large number of proteins in the cell. Calcium binding induces conformational transitions in calmodulin that make it specifically active to particular target proteins. The precise mechanisms underlying calcium binding to calmodulin are still, however, quite poorly understood. Results In this study, we adopt a structural systems biology approach and develop a mathematical model to investigate various types of cooperative calcium-calmodulin interactions. We compare the predictions of our analysis with physiological dose-response curves taken from the literature, in order to provide a quantitative comparison of the effects of different mechanisms of cooperativity on calcium-calmodulin interactions. The results of our analysis reduce the gap between current understanding of intracellular calmodulin function at the structural level and physiological calcium-dependent calmodulin target activation experiments. Conclusion Our model predicts that the specificity and selectivity of CaM target regulation is likely to be due to the following factors: variations in the target-specific Ca2+ dissociation and cooperatively effected dissociation constants, and variations in the number of Ca2+ ions required to bind CaM for target activation. PMID:18518982

  8. Structural elucidation of 2-fluorothiophenol from Fourier transform microwave spectra and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Sun, Wenhao; van Wijngaarden, Jennifer

    2017-09-01

    Pure rotational transitions corresponding to the ground vibrational state of 2-fluorothiophenol (2FTPh) were recorded via Fourier transform microwave (FTMW) spectroscopy in the range of 4-26 GHz. The observed transitions were assigned to two planar conformers in which the SH bond is directed toward (cis-2FTPh) or away from (trans-2FTPh) the fluorine substituent with the former predicted to lie 3.86 kJ/mol lower in energy from ab initio calculations (MP2/6-311++G(2d,2p)). The rotational constants determined from the spectral analysis were used to derive effective ground state (r0) structures of the lower energy cis-2FTPh conformer using spectra of the corresponding 13C and 34S isotopologues which were observed in natural abundance. Geometry optimization at the MP2/6-311++G(2d,2p) level provided the equilibrium (re) structure which is in close agreement with the experimentally-derived geometry. Comparison with results from natural bond orbital (NBO) calculations provide evidence of a weak intramolecular interaction between the lone pair on sulfur and the CF moiety in cis-2FTPh that is not found in trans-2FTPh or thiophenol (TPh). This interaction stabilizes the cis-2FTPh conformer by 2.18 kJ/mol.

  9. Design, synthesis, structural elucidation, pharmacological evaluation of metal complexes with pyrazoline derivatives.

    PubMed

    Muneera, M Sirajul; Joseph, J

    2016-10-01

    A bioactive pyrazoline derivatives have been synthesized by the base-catalyzed Claisen-Schmidt condensation of imidazole-2-carboxaldehyde with 1-acetyl-2-hydroxynaphthalene followed by cyclization with phenylhydrazine (L(1))/2,3-dimethylphenylhydrazine (L(2)) and 3-nitrophenylhydrazine (L(3)). The metal(II) complexes [Ni(II), Co(II), Cu(II) and Zn(II)] were formed by reacting the corresponding metal acetates with the ligands. All complexes were characterized by elemental analyses, electronic, IR, NMR, mass and ESR spectroscopic techniques. The synthesized metal complexes of pyrazoline compounds showed significant antibacterial activity against the organisms Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Proteus mirabilis and Salmonella typhii when compared with the standard antibiotic (Streptomycin). The ligands and their metal complexes were screened for antioxidant activity using DPPH radical scavenging and superoxide radical scavenging assay methods. All the complexes showed good free radical scavenging activity which is comparable to that of the standards. Among the metal complexes, the copper complex has showed higher activity. The results were indicated that 2-pyrazoline (structural core) and copper ion could be responsible for the potential candidate eliciting antioxidant activity. All compounds were evaluated for their in vitro antimycobacterial activity against Mycobacterium tuberculosis. The ligands and metal complexes were subjected to fluorescence properties and exhibited that the variable fluorescence emission behavior of complexes. It can be attributed to the combined effect of the substituents and naphthyl structural core present in the ligands.

  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. © 2015 by The American Society of Hematology.

  11. 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.

  12. 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.

  13. Elucidating the Structural Changes to Populus Lignin during Consolidated Bioprocessing with Clostridium thermocellum

    DOE PAGES

    Akinosho, Hannah O.; Yoo, Chang Geun; Dumitrache, Alexandru; ...

    2017-07-20

    During consolidated bioprocessing (CBP), Clostridium thermocellum hydrolyzes several plant cell wall components. Cellulose hydrolysis, specifically, liberates sugars for fermentation, which generates ethanol, acetate, hydrogen, and other products. While several studies indicate that C. thermocellum hydrolyzes carbohydrates in biomass, the structural changes to lignin during CBP remain unclear. In this paper, the whole plant cell walls of untreated and C. thermocellum-treated Populus trichocarpa were characterized using NMR and FTIR. The results suggest that C. thermocellum reduces the β-O-4 linkage content and increases the lignin S/G ratio. Finally, this investigation indicates that C. thermocellum not only modifies lignin in order to accessmore » cellulose but also leaves behind a suitable lignin substrate for value-added applications in the cellulosic ethanol production scheme.« less

  14. 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.

  15. Structure elucidation of new compounds from acidic treatment of the progestins gestodene and drospirenone.

    PubMed

    Colombo, Diego; Bombieri, Gabriella; Lenna, Roberto; Marchini, Nicoletta; Modica, Emilia; Scala, Antonio

    2006-08-01

    Gestodene acidic treatment afforded a single rearrangement product, namely 13-beta-ethyl-18,19-dinorpregna-4,14,16-trien-3,20-dione 3, which was originated through HCl-catalyzed Rupe rearrangement. Drospirenone acidic treatment yielded two epimeric lactones by addition of HCl to the 6beta,7beta-cyclopropane ring, namely 7beta-(chloromethyl)-15beta,16beta-methylene-3-oxo-17beta-pregn-4-ene-21,17-carbolactone 4 and 7beta-(chloromethyl)-15beta,16beta-methylene-3-oxo-17alpha-pregn-4-ene-21,17-carbolactone 5. The structure of the compounds was assessed by spectroscopic and crystallographic methods.

  16. 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.

  17. 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.

  18. Shape-Controlled Synthesis of Trimetallic Nanoclusters: Structure Elucidation and Properties Investigation.

    PubMed

    Kang, Xi; Xiong, Lin; Wang, Shuxin; Yu, Haizhu; Jin, Shan; Song, Yongbo; Chen, Tao; Zheng, Liwei; Pan, Chensong; Pei, Yong; Zhu, Manzhou

    2016-11-21

    The shape-controlled synthesis of metal nanoclusters (NCs) with precise atomic arrangement is crucial for tailoring the properties. In this work, we successfully control the shape of alloy NCs by altering the dopants in the alloying processes. The shape of the spherical [Pt1 Ag24 (SPhMe2 )18 ] NC is maintained when [Au(I) SR] is used as dopant. By contrast, the shape of Pt1 Ag24 is changed to be rodlike by alloying with [Au(I) (PPh3 )Br]. The structures of the trimetallic NCs were determined by X-ray crystallography and further confirmed by both DFT and far-IR measurements. The shape-preserved [Pt1 Au6.4 Ag17.6 (SPhMe2 )18 ] NC is in a tristratified arrangement-[Pt(center)@Au/Ag(shell)@Ag(exterior)]-and is indeed the first X-ray crystal structure of thiolated trimetallic NCs. On the other hand, the resulting rodlike NC ([Pt2 Au10 Ag13 (PPh3 )10 Br7 ]) exhibits a high quantum yield (QY=14.7 %), which is in striking contrast to the weakly luminescent Pt1 Ag24 (QY=0.1 %, about 150-fold enhancement). In addition, the thermal stabilities of both trimetallic products are remarkably improved. This study presents a controllable strategy for synthesis of alloy NCs with different shapes (by alloying heteroatom complexes coordinated by different ligands), and may stimulate future work for a deeper understanding of the morphology (shape)-property correlation in NCs.

  19. Structural elucidation of an asparagine-linked oligosaccharide from the hyperthermophilic archaeon, Archaeoglobus fulgidus.

    PubMed

    Fujinami, Daisuke; Nyirenda, James; Matsumoto, Shunsuke; Kohda, Daisuke

    2015-09-02

    The genome of the hyperthermophilic archaeon, Archaeoglobus fulgidus, contains three paralogous AglB genes that encode oligosaccharyltransferase (OST) proteins. The OST enzymes catalyze the transfer of an oligosaccharide chain from lipid-linked oligosaccharides (LLO) to asparagine residues in proteins. The detergent-solubilized membrane fractions prepared from cultured A. fulgidus cells contain both OST and LLO. The addition of a peptide containing the glycosylation sequon produced oligosaccharide chains attached to a structurally defined peptide. To facilitate the NMR analysis, the cells were grown in rich medium supplemented with (13)C-glucose, to label the LLOs metabolically. The MS analysis of the glycopeptide revealed that the glucose and galactose residues were nearly fully (13)C-labeled, but the mannose residues were fractionally labeled with about 20% efficiency. An immunodetection experiment revealed that the longest AglB paralog (AfAglB-L) was expressed in the membrane fractions under our cell culture conditions, while the other two shorter AglB paralogs (AfAglB-S1 and AfAglB-S2) were not. Thus, the oligosaccharide chain analyzed in this study was the product of AfAglB-L. The N-glycan consists of eight hexose residues, as follows: The α1,3-linked glucose is an optional residue branching from the distal mannose residue. The MS analysis of the minor HPLC peak of the in vitro oligosaccharyl transfer products also revealed an optional sulfate modification on the glucose residue directly linked to the Asn residue. The present data will be useful for structural and functional studies of the N-glycosylation system of A. fulgidus.

  20. 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

  1. 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.

  2. Structural elucidation of potential impurities in Azilsartan bulk drug by HPLC.

    PubMed

    Zhou, Wentao; Zhou, Yuxia; Sun, Lili; Zou, Qiaogen; Wei, Ping; Ouyang, Pingkai

    2014-01-01

    During the synthesis of Azilsartan (AZS), it was speculated that 15 potential impurities would arise. This study investigated the possible mechanism for the formation of 14 of them, and their structures were characterized and confirmed by IR, NMR, and MS techniques. In addition, an efficient chromatographic method was developed to separate and quantify these impurities, using an Inertsil ODS-3 column (250 x 4.6 mm, 5 pm) in gradient mode with a mixture of acetonitrile and the potassium dihydrogen orthophosphate buffer (10 mM, pH adjusted to 3.0 with phosphoric acid). The HPLC method was validated for specificity, precision, accuracy, and sensitivity. LOQ of impurities were in the range of 1.04-2.20 ng. Correlation coefficient values of linearity were >0.9996 for AZS and its impurities. The mean recoveries of all impurities in AZS were between 93.0 and 109.7%. Thus, the validated HPLC method is suitable for the separation and quantification of all potential impurities in AZS.

  3. Quantification and structural elucidation of potential impurities in agomelatine active pharmaceutical ingredient.

    PubMed

    Liu, Yaxuan; Chen, Lei; Ji, Yibing

    2013-01-01

    Seven impurities in agomelatine drug substance were determined by a newly developed RP-HPLC method. Structures of potential impurities were confirmed by NMR and IR analysis. Efficient chromatographic separation was achieved on Hypersil BDS C18 column (250 mm × 4.6 mm, 5 μm) in gradient mode by using a binary mixture of potassium dihydrogen phosphate (15 mM, pH adjusted to 3.0) and acetonitrile at a flow rate of 1.0 ml/min. A photodiode array detector set at 230 nm was used for detection. Forced degradation studies showed that the proposed method was specific, and agomelatine was found to be susceptible to acidic and alkaline conditions. The method was validated according to ICH guidelines with respect to specificity, sensitivity, precision, linearity, accuracy, robustness and system suitability. Detection limit of impurities was in the range of 0.0008-0.0047%. Regression analysis showed correlation coefficient value greater than 0.999 for agomelatine and its seven impurities. Accuracy of the method was established based on the recovery obtained between 94.4% and 106.7% for all impurities. The validation results demonstrated that the developed method was suitable for the quantitative determination of potential impurities in agomelatine. A possible mechanism for the formation of impurities was proposed.

  4. 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.

  5. Structure and dynamics of retinal in rhodopsin elucidated by deuterium solid state NMR

    NASA Astrophysics Data System (ADS)

    Salgado, Gilmar Fernandes De Jesus

    Rhodopsin is a seven transmembrane helix GPCR found which mediates dim light vision, in which the binding pocket is occupied by the ligand 11- cis-retinal. A site-directed 2H-labeling approach utilizing solid-state 2H NMR spectroscopy was used to investigate the structure and dynamics of retinal within its binding pocket in the dark state of rhodopsin, and as well the MetaI and MetaII. 11-cis-[5-C 2H3]-, 11-cis-[9-C 2H3]-, and 11-cis-[13-C2H 3]-retinal were used to regenerate bleached rhodopsin. Recombinant membranes comprising purified rhodopsin and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) were prepared (1:50 molar ratio). Solid-state 2H NMR spectra were obtained for the aligned rhodopsin/POPC recombinant membranes at temperatures below the order-disorder phase transition temperature of POPC. The solid-state NMR studies of aligned samples, give the orientations of the 2H nuclear coupling tensor relative to the membrane frame, which involve both the conformation and orientation of the bound retinal chromophore. Theoretical simulations of the experimental 2H NMR spectra employed a new lineshape treatment for a semi-random distribution due to static uniaxial disorder. The analysis gives the orientation of the 2H-labeled C-C2H3 methyl bond axes relative to the membrane plane as well as the extent of three-dimensional alignment disorder (mosaic spread). These results clearly demonstrate the applicability of site-directed 2H NMR methods for investigating conformational changes and dynamics of ligands bound to rhodopsin and other GPCRs in relation to their characteristic mechanisms of action.

  6. Structural elucidation of rat biliary metabolites of corynoxeine and their quantification using LC-MS(n).

    PubMed

    Wang, Wei; Li, Xinmei; Chen, Yaping; Hattori, Masao

    2014-09-01

    Corynoxeine (COR) is one of 4 bioactive oxindole alkaloids in Uncaria species. In this work two phase I metabolites, namely 11-hydroxycorynoxeine (M1) and 10-hydroxycorynoxeine (M2), and two phase II metabolites, namely 11-hydroxycorynoxeine 11-O-β-d-glucuronide (M3) and 10-hydroxycorynoxeine 10-O-β-d-glucuronide (M4), were detected in rat bile after oral dose of COR (0.105 mmol/kg), by optimized high-performance liquid chromatography-tandem mass spectrometry (LC-MS(n) ) with electrospray ionization in positive ion mode. Structures of M1-4 were determined by LC-MS(n) , nuclear magnetic resonance, circular dichroism and high-resolution MS spectra. COR and its metabolites in rat bile were quantified by LC-MS(n) . The LC-MS(n) quantification methods for COR and its metabolites yielded a linearity with coefficient of determination ≥0.995 from 5.0 × 10(-10) to 5.0 × 10(-7)  m. The recoveries of stability tests varied from 96.80 to 103.10%. Accuracy ranged from 91.00 to 105.20%. Relative standard deviation for intra-day and inter-day assay was <5.0%. After the oral dose 0.14% of COR was detected in rat bile from 0 to 8 h, in which in total 97.8% COR biotransformed into M1-4. M1 and M2 yielded 48.1 and 49.7%, which successively glucuronidated to M3 and M4 at 47.2 and 43.8%, respectively.

  7. Elucidation of structural and functional integration of a novel antimicrobial peptide from Antheraea mylitta.

    PubMed

    Dutta, Suhrid R; Gauri, Samiran S; Ghosh, Twisa; Halder, Suman K; DasMohapatra, Pradeep K; Mondal, Keshab C; Ghosh, Ananta K

    2017-03-03

    We report here the amino acid sequence of an antimicrobial peptide of Antheraea mylitta (peptide fraction II) effectively killed urinary tract associated MDR E. coli (Dutta et al., 2016), as Gly-Gly-Gly-Gly-Gly-Gly-His-Leu-Val-Ala. The physicochemical and biological properties of this peptide were evaluated by computational analysis and its isoelectric point, grand average of hydropathicity and Boman index values were found to be 6.74, 0.42 and -1.17kcal/mol, respectively. One valid model of peptide fraction II was constructed, that contains two antiparallel β sheets with a hairpin and appeared as 'U' shaped structure. The glycine rich composition (Gly1, Gly5, Gly6 and Ala10) facilitates mostly for its flexibility or dynamicity, and in its other wing, aggregation prone residues (Leu8, Val9, Ala10) triggered its auto-aggregations when contacted only with the microbial membrane. We employed simulation of peptide binding on the membrane, showed stable and deep insertion of peptide fraction II into the membrane through its hydrophobic tail (up to 3.3±1.46Å). Molecular docking study with Patchdock server revealed that this peptide could interact with the lipid aliphatic chain of 1-palmitoyl-2-oleoyl-phosphoethanolamine (POPE) bilayer and may linked to membrane distortion as we have reported earlier. Further, the studied peptide has been predicted not to exhibit any antigenicity and non-responsive to RBC membrane. These data for the first time provide new insights of an antimicrobial peptide from silkworm A. mylitta and it may serve as the template for the design of novel peptide antibiotics from this group of insect against MDR Gram-negative bacteria.

  8. Exocyclic Deoxyadenosine Adducts of 1,2,3,4-Diepoxybutane: Synthesis, Structural Elucidation, and Mechanistic Studies

    PubMed Central

    Seneviratne, Uthpala; Antsypovich, Sergey; Goggin, Melissa; Dorr, Danae Quirk; Guza, Rebecca; Moser, Adam; Thompson, Carrie; York, Darrin M.; Tretyakova, Natalia

    2009-01-01

    1,2,3,4-Diepoxybutane (DEB)1 is considered the ultimate carcinogenic metabolite of 1,3-butadiene, an important industrial chemical and environmental pollutant present in urban air. Although it preferentially modifies guanine within DNA, DEB induces a large number of A → T transversions, suggesting that it forms strongly mispairing lesions at adenine nucleobases. We now report the discovery of three potentially mispairing exocyclic adenine lesions of DEB: N6,N6-(2,3-dihydroxybutan-1,4-diyl)-2′-deoxyadenosine (compound 2), 1,N6-(2-hydroxy-3-hydroxymethylpropan-1,3-diyl)-2′-deoxyadenosine (compound 3), and 1,N6-(1-hydroxymethyl-2-hydroxypropan-1,3-diyl)-2′-deoxyadenosine (compound 4). The structures and stereochemistry of the novel DEB-dA adducts were determined by a combination of UV and NMR spectroscopy, tandem mass spectrometry, and independent synthesis. We found that synthetic N6-(2-hydroxy-3,4-epoxybut-1-yl)-2′-deoxyadenosine (compound 1) representing the product of N6-adenine alkylation by DEB spontaneously cyclizes to form 3 under aqueous conditions or 2 under anhydrous conditions in the presence of organic base. Compound 3 can be interconverted with 4 by a reversible unimolecular pericyclic reaction favoring 4 as a more thermodynamically stable product. Both 3 and 4 are present in double stranded DNA treated with DEB in vitro and in liver DNA of laboratory mice exposed to 1,3-butadiene by inhalation. We propose that in DNA under physiological conditions, DEB alkylates the N-1 position of adenine in DNA to form N1-(2-hydroxy-3,4-epoxybut-1-yl)-adenine adducts, which undergo an SN2-type intramolecular nucleophilic substitution and rearrangement to give 3 (minor) and 4 (major). Formation of exocyclic DEB-adenine lesions following exposure to 1,3-butadiene provides a possible mechanism of mutagenesis at the A:T base pairs. PMID:19883087

  9. A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments

    PubMed Central

    Deusch, Simon; Camarinha-Silva, Amélia; Conrad, Jürgen; Beifuss, Uwe; Rodehutscord, Markus; Seifert, Jana

    2017-01-01

    The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal's feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology, and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or grass hay, each supplemented with a concentrate mixture. Samples were fractionated into ruminal fluid, particle-associated rumen liquid, and solid matter. DNA, proteins and metabolites were analyzed subsequently. DNA extracts were used for Illumina sequencing of the 16S rRNA gene and the metabolomes of rumen fluids were determined by 500 MHz-NMR spectroscopy. Tryptic peptides derived from protein extracts were measured by LC-ESI-MS/MS and spectra were processed by a two-step database search for quantitative metaproteome characterization. Data are available via ProteomeXchange with the identifier PXD006070. Protein- and DNA-based datasets revealed significant differences between sample fractions and diets and affirmed similar trends concerning shifts in phylogenetic composition. Ribosomal genes and proteins belonging to the phylum of Proteobacteria, particularly Succinivibrionaceae, exhibited a higher abundance in corn silage-based samples while fiber-degraders of the Lachnospiraceae family emerged in great quantities throughout the solid phase fractions. The analysis of 8163 quantified bacterial proteins revealed the presence of 166 carbohydrate active enzymes in varying abundance. Cellulosome affiliated proteins were less expressed in the grass silage, glycoside hydrolases appeared in slightest numbers in the corn silage. Most expressed glycoside hydrolases belonged to families 57 and 2. Enzymes analogous to ABC transporters for amino acids and monosaccharides were more

  10. Saponins in alfalfa (Medicago sativa L.) root and their structural elucidation.

    PubMed

    Bialy, Z; Jurzysta, M; Oleszek, W; Piacente, S; Pizza, C

    1999-08-01

    Twenty-four saponins have been identified in alfalfa roots, including 13 medicagenic acids, 2 zanhic acids, 4 hederagenins, 1 soyasapogenol A, 2 soyasapogenol B's, 1 soyasapogenol E, and 1 bayogenin glycoside. Ten of the identified compounds, including 3-O-[beta-D-glucopyranosyl(1-->3)-beta-D-glucopyranosyl]-28-O-beta-D- glucopyranoside medicagenate, 3-O-[alpha-L-rhamnopyranosyl(1-->2)-beta-D-glucopyranosyl(1-->2)-beta -D-glucopyranoside] medicagenic acid, 3-O-[beta-D-glucopyranosyl(1-->2)-beta-D-glucopyranosyl(1-->2)-beta-D -glucopyranosyl]-28-beta- D-glucopyranoside medicagenate, 3-O-[beta-D-glucuronopyranosyl methyl ester]-28-O-[beta-D-xylopyranosyl(1-->4)-alpha-L-rhamnopyranosyl(1--> 2)-alpha-L-arabinopyranoside] medicagenate, 3-O-[alpha-L-rhamnopyranosyl(1-->2)-beta-D-galactopyranosyl(1-->2)-be ta-D-glucuronopyranosyl]-21-O-alpha-L-rhamnopyranoside soyasapogenol A, 3-O-[beta-D-glucopyranosyl(1-->2)-beta-D-glucopyranosyl(1-->2)glucopy ranosyl]-28-O-[beta-D-xylopyranosyl(1-->4)-alpha-L-rhamnopyranosyl (1- ->2)-alpha-L-arabinopyranoside] medicagenate, 3-O-[beta-D-glucopyranosyl(1-->2)-beta-D-glucopyranosyl(1-->2)glucopy ranosyl]-28-O-¿beta-D-xylopyranosyl(1-->4)-)-[beta-D-apiofurano syl-(1 -->3)]- alpha-L-rhamnopyranosyl(1-->2)-alpha-L-arabinopyranoside¿ medicagenate, 3-O-[beta-D-glucopyranosyl(1-->2)-beta-D-glucopyranosyl(1-->2)-beta-D -glucopyranosyl]-28-O-[beta-D-xylopyranosyl(1-->4)-alpha-L-rhamnopyra nosyl(1-->2)-alpha-L-arabinopyranoside] zanhic acid, 3-O-[beta-D-glucopyranosyl(1-->2)-beta-D-glucopyranosyl(1-->2)-beta-D -glucopyranosyl]-28-O-¿beta-D-xylopyranosyl(1-->4)-[beta-D-apiofurano side-(1-->3)]- alpha-L-rhamnopyranosyl(1-->2)-alpha-L-arabinopyranoside¿zanhic acid, and 3-O-[beta-D-galactopyranosyl(1-->2)-beta-D-glucuronopyranosyl]-28- O-b eta-D-glucopyranoside bayogenin, were not reported before, and their structures were established by spectral (FAB-MS and NMR) techniques. In addition, 3-O-[alpha-L-rhamnopyranosyl(1-->2)-beta

  11. Structural elucidation and identification of a new derivative of phenethylamine using quadrupole time-of-flight mass spectrometry.

    PubMed

    Sekuła, Karolina; Zuba, Dariusz

    2013-09-30

    In recent years, the phenomenon of uncontrolled distribution of new psychoactive substances that were marketed without prior toxicological studies has been observed. Because many designer drugs are related in chemical structure, the potential for misidentifying them is an important problem. It is therefore essential to develop an analytical procedure for unequivocal elucidation of the structures of these compounds. The issue has been discussed in the context of 25I-NBMD [2-(4-iodo-2,5-dimethoxyphenyl)-N-[(2,3-methylenedioxyphenyl)methyl]ethanamine], a psychoactive substance first discovered on the drug market in 2012. The substance was extracted from blotter papers with methanol. Separation was achieved via liquid chromatography. Analysis was conducted by electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-QTOFMS). Identification of the psychoactive component was supported by electron impact gas chromatography/mass spectrometry (GC/EI-MS). The high accuracy of the LC/ESI-QTOFMS method allowed the molecular mass of the investigated substance (M(exp) = 441.0438 Da; mass error, ∆m = 0.2 ppm) and the formulae of ions formed during fragmentation to be determined. The main ions were recorded at m/z = 135.0440, 290.9876 and 305.9981. Structures of the obtained ions were elucidated in the tandem mass spectrometry (MS/MS) experiments by comparing them to mass spectra of previously detected derivatives of phenethylamine. The performed study indicated the potential for using LC/QTOFMS method to identify new designer drugs. This technique can be used supplementary to standard GC/MS. Prior knowledge of the fragmentation mechanisms of phenethylamines allowed to predict the mass spectra of the novel substance--25I-NBMD. Copyright © 2013 John Wiley & Sons, Ltd.

  12. Investigating the Web Structure by Isolated Stars

    NASA Astrophysics Data System (ADS)

    Uno, Yushi; Ota, Yoshinobu; Uemichi, Akio

    The link structure of the Web is generally represented by the webgraph, and it is often used for web structure mining that mainly aims to find hidden communities on the Web. In this paper, we identify a common frequent substructure and give it a formal graph definition, which we call an isolated star (i-star), and propose an efficient enumeration algorithm of i-stars. We then investigate the structure of the Web by enumerating i-stars from real web data. As a result, we observed that most i-stars correspond to index structures in single domains, while some of them are verified to be candidates of communities, which implies the validity of i-stars as useful substructure for web structure mining and link spam detecting. We also observed that the distributions of i-star sizes show power-law, which is another new evidence of the scale-freeness of the webgraph.

  13. 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

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

    PubMed

    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

    2016-09-30

    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.

  15. 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.

  16. Application of fast atom bombardment combined with tandem mass spectrometry to the structural elucidation of O-demethylabierixin and related polyether antibiotics.

    PubMed

    Kim, Y H; Yoo, J S; Lee, C H; Goo, Y M; Kim, M S

    1996-08-01

    O-Demethylabierixin, a new polyether antibiotic, was isolated from a Streptomyces spp. Its structure elucidation was carried out with fast atom bombardment mass spectrometry (FAB-MS) and fast atom bombardment mass spectrometry-mass spectrometry (FAB-MS/MS) by comparing spectral patterns with those of structurally similar polyether compounds, nigericin and abierixin. The collision-induced dissociation (CID) of sodium-adduct and deprotonated molecular ions produced many cyclic ether rings-opened product ions via a series of the dissociative processes. Because of the negative charge of the carboxylate group at the end of the molecule, the charge-remote fragmentation pattern in the negative CID spectra of deprotonated molecular ions was very helpful for complete identification of product ions which are characteristic for cyclic ether structures. From this study, the new polyether antibiotic was identified to be O-demethylabierixin in which the methoxy group of six-membered ether ring in abierixin was replaced by the hydroxy group.

  17. Heparin sodium compliance to the new proposed USP monograph: elucidation of a minor structural modification responsible for a process dependent 2.10 ppm NMR signal.

    PubMed

    Mourier, Pierre A J; Guichard, Olivier Y; Herman, Fréderic; Viskov, Christian

    2011-01-25

    Heparin is a highly sulfated hetero polysaccharide mixture found and extracted from mammalian tissues. It has been widely used as an anticoagulant drug during the past decades. In the new proposed USP heparin monograph, the ¹H NMR acceptance criteria to prevent contamination by over sulfated chondroitin sulfate (OSCS), or other persulfated glycosaminoglycans, specifies that no unidentified signals greater than 4% of the mean of signal height of 1 and 2 should be present in the following ranges: 0.10-2.00, 2.10-3.20, and 5.70-8.00 ppm. However, those criteria do not take into account the impact of potential structural modifications generated by the heparin manufacturing processes. In fact, starting from pig mucosa, heparin purification involves oxidizing reagents such as sodium peroxide, potassium permanganate and peracetic acid. In the present work, we demonstrate that potassium permanganate treated heparins show a small but characteristic extra signal at 2.10 ppm. Controlled heparinase I depolymerisation is used to target and excise the oligosaccharide responsible for this extra signal from the polysaccharide backbone. By using orthogonal chromatographic techniques, the fingerprint oligosaccharide was isolated and its structure elucidated. Without the identification of this structural moiety, such purified heparins may have been considered as non-compliant drug substance and not suitable for pharmaceutical use. Copyright © 2010 Elsevier B.V. All rights reserved.

  18. Active vibration isolation using smart structures

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    Passive technologies for the isolation of structures from vibrating sources are often inadequate. Using active control inputs applied directly to the source or designing a structure integrating the transducers required for the control inputs and the response measurements are ways of dealing with the problem. Results are given which were obtained on an experimental set up simulating this kind of problem where the form and the position of the transducers could be varied. By measuring the response of the structure integrated over a particular area the effects of particular types of modes could be taken into account to deal with specific types of input or limit particular modes of response more efficiently. Results of using different modes of vibration excitation of the receiving structure with and without control are presented for particular input frequencies. The problems of optimizing the control system to deal with multiple frequency inputs are discussed.

  19. Structural elucidation and evaluation of multidrug-resistance modulatory capability of amarissinins A-C, diterpenes derived from Salvia amarissima.

    PubMed

    Bautista, Elihú; Fragoso-Serrano, Mabel; Ortiz-Pastrana, Naytzé; Toscano, Rubén A; Ortega, Alfredo

    2016-10-01

    Three new diterpenes (amarissinins A-C, 1-3) containing several oxygenated functionalities were isolated from the leaves and flowers of Salvia amarissima. The structures of these compounds were established through the analysis of their NMR spectroscopy and mass spectrometry data. The structures of compounds 1 and 2 were confirmed by single crystal X-ray diffraction. Compound 2 was identified as a C-10 epimer of dugesin F (5). The cytotoxic activity of these compounds against five human cancer cell lines was determined. Additionally, the capability to modulate the multidrug resistance (MDR) in the MCF-7 cancer cell line resistant to vinblastine was tested.

  20. 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

  1. 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.

  2. 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

    2016-10-04

    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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Mass spectrometry for the elucidation of the subtle molecular structure of biodegradable polymers and their degradation products.

    PubMed

    Kowalczuk, Marek; Adamus, Grażyna

    2016-01-01

    Contemporary reports by Polish authors on the application of mass spectrometric methods for the elucidation of the subtle molecular structure of biodegradable polymers and their degradation products will be presented. Special emphasis will be given to natural aliphatic (co)polyesters (PHA) and their synthetic analogues, formed through anionic ring-opening polymerization (ROP) of β-substituted β-lactones. Moreover, the application of MS techniques for the evaluation of the structure of biodegradable polymers obtained in ionic and coordination polymerization of cyclic ethers and esters as well as products of step-growth polymerization, in which bifunctional or multifunctional monomers react to form oligomers and eventually long chain polymers, will be discussed. Furthermore, the application of modern MS techniques for the assessment of polymer degradation products, frequently bearing characteristic end groups that can be revealed and differentiated by MS, will be discussed within the context of specific degradation pathways. Finally, recent Polish accomplishments in the area of mass spectrometry will be outlined.

  4. 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

  5. Structure elucidation of capsular polysaccharides from Streptococcus pneumoniae serotype 33C, 33D, and revised structure of serotype 33B.

    PubMed

    Lin, Fiona L; Vinogradov, Evgeny; Deng, Chenghua; Zeller, Sandra; Phelan, Lynn; Green, Bruce A; Jansen, Kathrin U; Pavliak, Viliam

    2014-01-13

    We report herein the previously unknown structures of the pneumococcal capsular polysaccharides serotype 33C and 33D, and a revised structure of serotype 33B. The syntenic pair 33B/33D has nearly identical polysaccharide repeat units with the exception of one sugar residue (→2-α-Glcp in 33B and →2-α-Galp in 33D). Serotype 33C is structurally more similar to 33B/33D than 33A/33F, in that it also possesses a backbone ribitol-phosphate group and a →3-β-GalpNAc residue, both of which are absent in the repeat units of 33A/33F. Serotype 33C is notably different from all other serogroup 33 polysaccharides, as there is no →3-β-Glcp residue and the location of the O-acetylation of the →5-β-Galf residue (O-6) differs from the other serogroup 33 polysaccharides (O-2). This completes the structural assignments of polysaccharides within serogroup 33 and provides a framework for understanding the recognition of epitopes by serogroup 33 typing sera based on observed cross-reactivities reported in the literature. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Frequency response characteristics and response spectra of base-isolated and un-isolated structures

    SciTech Connect

    Mok, G.C.; Namba, H.

    1995-07-06

    The transmissibility of seismic loads through a linear base-isolation system is analyzed using an impedance method. The results show that the system acts like a {open_quotes}low-pass{close_quotes} filter. It attenuates high-frequency loads but passes through low-frequency ones. The filtering effect depends on the vibration frequencies and damping of the isolated structure and the isolation system. This paper demonstrates the benefits and design principles of base isolation by comparing the transmissibilities and response spectra of isolated and un-isolated structures. Parameters of typical isolated buildings and ground motions of the 1994 Northridge earthquake are used for the demonstration.

  7. 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; ...

    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

  8. Heparin sodium compliance to USP monograph: structural elucidation of an atypical 2.18 ppm NMR signal.

    PubMed

    Mourier, Pierre A J; Guichard, Olivier Y; Herman, Fréderic; Viskov, Christian

    2012-01-01

    The ¹H nuclear magnetic resonance (NMR) acceptance criteria in the new heparin US Pharmacopeia (USP) monograph do not take into account potential structural modifications responsible for any extra signals observed in ¹H NMR spectra, some purified heparins may be non-compliant under the proposed new USP guidelines and incorrectly classified as unsuitable for pharmaceutical use. Heparins from the "ES" source, containing an extra signal at 2.18 ppm, were depolymerized under controlled conditions using heparinases I, II, and III. The oligosaccharides responsible for the 2.18 ppm signal were enriched using orthogonal chromatographic techniques. After multiple purification steps, we obtained an oligosaccharide mixture containing a highly enriched octasaccharide bearing the structural modification responsible for the extra signal. Following heparinase I depolymerization, a pure tetrasaccharide containing the fingerprint structural modification was isolated for full structural determination. Using 1D and 2D ¹H NMR spectroscopy, the structural moiety responsible for the extra signal at 2.18 ppm was identified as an acetyl group on the heparin backbone, most likely resulting from a very minor manufacturing process side reaction that esterifies the uronic acid at position 3. Such analytical peculiarity has always been present in this heparin source and it was used safety over the years.

  9. Structural elucidation, in vitro antioxidant and photoprotective capacities of a purified polyphenolic-enriched fraction from a saltmarsh plant.

    PubMed

    Surget, Gwladys; Stiger-Pouvreau, Valérie; Le Lann, Klervi; Kervarec, Nelly; Couteau, Céline; Coiffard, Laurence J M; Gaillard, Fanny; Cahier, Karine; Guérard, Fabienne; Poupart, Nathalie

    2015-02-01

    In temperate saltmarshes, halophytic plants have to daily protect their internal tissues against sunlight and UV rays. Consequently, they develop adaptive responses such as the synthesis of secondary metabolites, including polyphenols. The present study focused on the biological activities of fractions enriched in polyphenols from Salicornia ramosissima. Three different extracts were obtained by purification processes to concentrate polyphenols: a crude hydroalcoholic extract, and two purified fractions: an ethyl acetate fraction (EAF) and an aqueous fraction. Phenolic and flavonoid contents, antioxidant (DPPH radical-scavenging activity, reducing activity, β-carotene linoleic acid system and the ORAC method) and sunscreen properties (Sun Protection Factor and UVA-Protection Factor) were assessed by in vitro tests. The purification process was effective in increasing phenolic and flavonoid contents as well as antioxidant and sunscreen capacities of the EAF. The EAF appeared to be a broad spectrum UV absorber. The chemical structure of 10 EAF polyphenols was elucidated using 2D NMR and mass spectrometry spectra. Furthermore, a correlation was observed between phenolic composition and biological activity. These findings are encouraging for the future use of S. ramosissima as a potential source of antioxidant and photoprotectant molecules for industrial applications. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. 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.

  11. Biotransformation pathways of biocides and pharmaceuticals in freshwater crustaceans based on structure elucidation of metabolites using high resolution mass spectrometry.

    PubMed

    Jeon, Junho; Kurth, Denise; Hollender, Juliane

    2013-03-18

    So far, there is limited information on biotransformation mechanisms and products of polar contaminants in freshwater crustaceans. In the present study, metabolites of biocides and pharmaceuticals formed in Gammarus pulex and Daphnia magna were identified using liquid chromatography-high resolution mass spectrometry. Different confidence levels were assigned to the identification of metabolites without reference standards using a framework based on the background evidence used for structure elucidation. Twenty-five metabolites were tentatively identified for irgarol, terbutryn, tramadol, and venlafaxine in G. pulex (21 via oxidation and 4 via conjugation reactions) and 11 metabolites in D. magna (7 via oxidation and 4 via conjugation reactions), while no evidence of metabolites for clarithromycin and valsartan was found. Of the 360 metabolites predicted for the four parent compounds using pathway prediction systems and expert knowledge, 23 products were true positives, while 2 identified metabolites were unexpected products. Observed oxidative reactions included N- and O-demethylation, hydroxylation, and N-oxidation. Glutathione conjugation of selected biocides followed by subsequent reactions forming cysteine conjugates was described for the first time in freshwater invertebrates.

  12. Structure elucidation of a sodium salified anthraquinone from the seeds of Cassia obtusifolia by NMR technique assisted with acid-alkali titration.

    PubMed

    Zhang, Chen; Wang, Rufeng; Liu, Bin; Tu, Guangzhong

    2011-08-01

    A new sodium salt of anthraquinone named sodium emodin-1-O-β-gentiobioside, together with nine known compounds, viz. rubrofusarin-6-O-β-D-gentiobioside, chrysophanol-1-O-β-D-glucopyranosyl-(1-3)-β-D-glucopyranosyl-(1-6)-β-D-glucopyranoside, obtusifolin-2-O-β-D-glucopyranoside, aurantio-obtusin-6-O-β-D-glucopyranoside, physcion-8-O-β-D-glucopyranoside, 1-hydroxyl-2-acetyl-3,8-dimethoxy-6-O-β-D-apiofuranosyl-(1-2)-β-D-glucosylnaphthalene, toralactone-9-O-β-D-gentiobioside, aurantio-obtusin, rubrofusarin-6-O-β-D-apiofuranosyl-(1-6)-O-β-D-glucopyranoside, was isolated from the seeds of Cassia obtusifolia and its structure was elucidated by (1)H and (13)C NMR technique assisted with acid-alkali titration. The change of chemical shifts of sodium emodin-1-O-β-gentiobioside before and after acid-alkali titration was also characterized. Copyright © 2011 John Wiley & Sons, Ltd.

  13. Structural investigation and elucidation of new communesins from a marine-derived Penicillium expansum Link by liquid chromatography/electrospray ionization mass spectrometry.

    PubMed

    Kerzaon, Isabelle; Pouchus, Yves F; Monteau, Fabrice; Le Bizec, Bruno; Nourrisson, Marie-Renée; Biard, Jean-François; Grovel, Olivier

    2009-12-01

    Penicillium expansum is a ubiquitous species for which there are only few reports for chemical investigation in marine environments. Among the numerous secondary metabolites produced by this species, communesins represent a new class of cytotoxic and insecticidal indole alkaloids. In this study, we investigated a marine P. expansum strain exhibiting neuroactivity on a Diptera larvae bioassay. Bio-guided purification led to the isolation and the identification of communesin B as the main active compound by HRMS and 1H and 13C NMR. Liquid chromatography analyses with detection by electrospray ionization coupled with tandem mass spectrometry (LC/ESI-MS/MS) and high-resolution tandem mass spectrometry (LC/HRMS/MS) allowed the identification and characterization of four other known communesins (A, D, E and F) in the crude extract. A fragmentation model for dimethyl epoxide communesins was proposed after detailed interpretation of their MS/MS spectra. Further analyses of the extract using the modelled fragmentations led to the detection of seven new communesins found as minor compounds. Chemical structural elucidation of these new derivatives is discussed based on their fragmentation characteristics.

  14. 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.

  15. Accelerated X-ray structure elucidation of a 36 kDa muramidase/transglycosylase using wARP.

    PubMed

    Van Asselt, E J; Perrakis, A; Kalk, K H; Lamzin, V S; Dijkstra, B W

    1998-01-01

    The X-ray structure of the 36 kDa soluble lytic transglycosylase from Escherichia coli has been determined starting with the multiple isomorphous replacement method with inclusion of anomalous scattering at 2.7 A resolution. Subsequently, before any model building was carried out, phases were extended to 1.7 A resolution with the weighted automated refinement procedure wARP, which gave a dramatic improvement in the phases. The electron-density maps from wARP were of outstanding quality for both the main chain and the side chains of the protein, which allowed the time spent on the tracing, interpretation and building of the X-ray structure to be substantially shortened. The structure of the soluble lytic transglycosylase was refined at 1.7 A resolution with X-PLOR to a final crystallographic R factor of 18.9%. Analysis of the wARP procedure revealed that the use of the maximum-likelihood refinement in wARP gave much better phases than least-squares refinement, provided that the ratio of reflections to protein atom parameters was approximately 1.8 or higher. Furthermore, setting aside 5% of the data for an Rfree test set had a negative effect on the phase improvement. The mean WwARP, a weight determined at the end of the wARP procedure and based on the variance of structure factors from six individually refined wARP models, proved to be a better indicator than the Rfree factor to judge different phase improvement protocols. The elongated Slt35 structure has three domains named the alpha, beta and core domains. The alpha domain contains mainly alpha-helices, while the beta domain consists of a five-stranded antiparallel beta-sheet flanked by a short alpha-helix. Sandwiched between the alpha and beta domains is the core domain, which bears some resemblance to the fold of the catalytic domain of the previously elucidated 70 kDa soluble lytic transglycosylase from E. coli. The putative active site is at the bottom of a large deep groove in the core domain.

  16. 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.

  17. Phase-shifting structures for isolated features

    NASA Astrophysics Data System (ADS)

    Garofalo, Joseph G.; Kostelak, Robert L.; Yang, Tungsheng

    1991-07-01

    The technique for improving optical projection-system resolution by phase-shifting alternate apertures of a periodic grating was introduced in 1982. This halves the frequency content of the image passing through the optics and should therefore double the effective resolution of such patterns. Unfortunately, as feature separation increases, the efficacy of this method diminishes. Previous work applying a similar approach to isolated features involves introducing minute, non-printable, phase-shifted assist slots around the desired feature. The diffraction side-lobes of these slots constructively interfere with the center lobe of the primary aperture. The resolution enhancement afforded be this technique is limited by the printability of the assist slots. This restraint also dictates 1X-size reticle feature dimensions and the employment of high contrast imaging resists. A new approach entails significantly oversizing the desired feature and introducing a phase-shifting region around the periphery. This type of structure affords substantial focus-exposure improvements and may either be fabricated in a single-level, self-aligned scheme or by a two-level exposure with conventional e-beam tools since the phase-shifting regions are on the order of 1 micrometers (reticle dimensions). Extensive modeling of this structure for isolated contact holes and spaces explores the myriad of trade- offs involved in an optimum design. Mask-fabrication tolerances, such as phase-shift uniformity, are also investigated. It is shown that the focus-exposure window enlarges as the overall structure dimensions increase. The degree of enhancement must therefore by weighed against packing density restrictions. Also, the structure suffers, to some degree, from the effect of side-lobes. However, for a given side-lobe intensity, this technique yields enhancements superior to the assist-slot approach. As is typical of phase-shifted systems, performance is improved as the partial coherence ((sigma

  18. 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.

  19. 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.

  20. Adenophostins A and B: potent agonists of inositol-1,4,5-trisphosphate receptor produced by Penicillium brevicompactum. Structure elucidation.

    PubMed

    Takahashi, S; Kinoshita, T; Takahashi, M

    1994-01-01

    Adenophostins A (1, C16H26N5O18P3) and B (2, C18H28N5O19P3), potent agonists of inositol-1,4,5-triphosphate (InsP3) receptor, were isolated from the culture broths of Penicillium brevicompactum SANK 11991 and SANK 12177. Hydrolysis of 2 with aq NaOH gave 1. Oxidation of 2 with NaNO2 gave the hypoxanthine derivative (3). Treatment of 1 or 2 with alkaline phosphatase gave 4 and 5. Treatment of 4 with alpha-glucosidase gave adenosine. Thus, their structures were deduced to be adenosine nucleotides by NMR, MS and the enzymatic degradation. The inhibitory constants (Ki value) of 1, 2, 3 and InsP3 itself for binding to the InsP3 receptor were 0.18 nM, 0.18 nM, 0.29 nM and 15 nM, respectively.

  1. Structural elucidation, modification and characterization of seed gum from Cassia javahikai seeds: A non-traditional source of industrial gums.

    PubMed

    Singh, Vandana; Srivastava, Archana; Tiwari, Ashutosh

    2009-10-01

    A water-soluble seed gum was isolated from seed endosperm of Cassia javahikai. The acid-catalyzed fragmentation, methylation, selective enzymatic degradation and periodate oxidation suggested a heteropolymeric structure for the polysaccharide. The polysaccharide was shown to have a linear chain of beta(1-->4) linked d-mannopyranosyls units with side chains of alpha(1-->6) d-galactopyranosyl units. Grafting of polyacrylamide onto the gum was performed using K(2)S(2)O(8)/ascorbic acid redox system in presence of Ag(+) as catalyst at 35+/-2 degrees C. The viscosity of the gum solution increased on grafting and the grafted gum was observed to resist biodegradation for more than 256h. Thermogravimetric analysis revealed that grafted gum was more thermally stable than native gum.

  2. Active-Site Structure of the Thermophilic Foc-Subunit Ring in Membranes Elucidated by Solid-State NMR

    PubMed Central

    Kang, Su-Jin; Todokoro, Yasuto; Yumen, Ikuko; Shen, Bo; Iwasaki, Iku; Suzuki, Toshiharu; Miyagi, Atsushi; Yoshida, Masasuke; Fujiwara, Toshimichi; Akutsu, Hideo

    2014-01-01

    FoF1-ATP synthase uses the electrochemical potential across membranes or ATP hydrolysis to rotate the Foc-subunit ring. To elucidate the underlying mechanism, we carried out a structural analysis focused on the active site of the thermophilic c-subunit (TFoc) ring in membranes with a solid-state NMR method developed for this purpose. We used stereo-array isotope labeling (SAIL) with a cell-free system to highlight the target. TFoc oligomers were purified using a virtual ring His tag. The membrane-reconstituted TFoc oligomer was confirmed to be a ring indistinguishable from that expressed in E. coli on the basis of the H+-translocation activity and high-speed atomic force microscopic images. For the analysis of the active site, 2D 13C-13C correlation spectra of TFoc rings labeled with SAIL-Glu and -Asn were recorded. Complete signal assignment could be performed with the aid of the Cαi+1-Cαi correlation spectrum of specifically 13C,15N-labeled TFoc rings. The Cδ chemical shift of Glu-56, which is essential for H+ translocation, and related crosspeaks revealed that its carboxyl group is protonated in the membrane, forming the H+-locked conformation with Asn-23. The chemical shift of Asp-61 Cγ of the E. coli c ring indicated an involvement of a water molecule in the H+ locking, in contrast to the involvement of Asn-23 in the TFoc ring, suggesting two different means of proton storage in the c rings. PMID:24461014

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

    PubMed

    Diallo, Mamadou S; Simpson, Andre; Gassman, Paul; Faulon, Jean Loup; Johnson, James H; Goddard, 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 an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA.

  4. 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.

  5. 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.

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

    SciTech Connect

    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 involving 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.

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

    SciTech Connect

    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 involving 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.

  8. 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.

  9. Isolation and structure of hematoside-type ganglioside from the starfish Linckia laevigata.

    PubMed

    Inagaki, Masanori; Saito, Takeshi; Miyamoto, Tomofumi; Higuchi, Ryuichi

    2009-02-01

    A hematoside-type ganglioside, LLG-1 (1), has been obtained from the polar lipid fraction of the chloroform/methanol extract of the starfish Linckia laevigata. The structure of the ganglioside has been determined on the basis of chemical and spectroscopic evidence as 1-O-[N-glycolyl-alpha-D-neuraminosyl-(2-->3)-beta-D-galactopyranosyl-(1-->4)-beta-D-glucopyranosyl]-ceramide. The ceramide moiety was composed of heterogeneous 2-hydroxy fatty acid and phytosphingosine units. This is the first report on the isolation and structure elucidation of naked hematoside-type ganglioside from echinoderms.

  10. 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.

  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

    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.

  12. Isolation and structure determination of oxidative degradation products of atorvastatin.

    PubMed

    Kracun, Matjaz; Kocijan, Andrej; Bastarda, Andrej; Grahek, Rok; Plavec, Janez; Kocjan, Darko

    2009-12-05

    Methods were developed for the preparation and isolation of four oxidative degradation products of atorvastatin. ATV-FX1 was prepared in the alkaline acetonitrile solution of atorvastatin with the addition of hydrogen peroxide. The exposition of aqueous acetonitrile solution of atorvastatin to sunlight for several hours followed by the alkalization of the solution with potassium hydroxide to pH 8-9 gave ATV-FXA. By the acidification of the solution with phosphoric acid to pH 3 ATV-FXA1 and FXA2 were prepared. The isolation of oxidative degradation products was carried out on a reversed-phase chromatographic column Luna prep C18(2) 10 microm applying several separation steps. The liquid chromatography coupled with a mass spectrometer (LC-MS), high resolution MS (HR-MS), 1D and 2D NMR spectroscopy methods were applied for the structure elucidation. All degradants are due to the oxidation of the pyrrole ring. The most probable reaction mechanism is intermediate endoperoxide formation with subsequent rearrangement and nucleophilic attack by the 5-hydroxy group of the heptanoic fragment. ATV-FX1 is 4-[1b-(4-Fluoro-phenyl)-6-hydroxy-6-isopropyl-1a-phenyl-6a-phenylcarbamoyl-hexahydro-1,2-dioxa-5a-aza-cyclopropa[a]inden-3-yl]-3-(R)-hydroxy-butyric acid and has a molecular mass increased by two oxygen atoms with regard to atorvastatin. ATV-FXA is the regioisomeric compound, 4-[6-(4-Fluoro-phenyl)-6-hydroxy-1b-isopropyl-6a-phenyl-1a-phenylcarbamoyl-hexahydro-1,2-dioxa-5a-aza-cyclopropa[a]inden-3-yl]-3-(R)-hydroxy-butyric acid. Its descendants ATV-FXA1 and FXA2 appeared without the atorvastatin heptanoic fragment and are 3-(4-Fluoro-benzoyl)-2-isobutyryl-3-phenyl-oxirane-2-carboxylic acid phenylamide and 4-(4-Fluoro-phenyl)-2,4-dihydroxy-2-isopropyl-5-phenyl-3,6-dioxa-bicyclo[3.1.0]hexane-1-carboxylic acid phenylamide, respectively. Quantitative NMR spectroscopy was employed for the assay determination of isolated oxidative degradation products. The results obtained were used

  13. 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

    2014-09-08

    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).

  14. Rat α-Fetoprotein binding affinities of a large set of structurally diverse chemicals elucidated the relationships between structures and binding affinities.

    PubMed

    Hong, Huixiao; Branham, William S; Dial, Stacey L; Moland, Carrie L; Fang, Hong; Shen, Jie; Perkins, Roger; Sheehan, Daniel; Tong, Weida

    2012-11-19

    Endocrine disrupting chemicals interfere with the endocrine system in animals, including humans, to exert adverse effects. One of the mechanisms of endocrine disruption is through the binding of receptors such as the estrogen receptor (ER) in target cells. The concentration of any chemical in serum is important for its entry into the target cells to bind the receptors. α-Fetoprotein (AFP) is a major transport protein in rodent serum that can bind with estrogens and thus change a chemical's availability for entrance into the target cell. Sequestration of an estrogen in the serum can alter the chemical's potential for disrupting estrogen receptor-mediated responses. To better understand endocrine disruption, we developed a competitive binding assay using rat amniotic fluid, which contains very high levels of AFP, and measured the binding to the rat AFP for 125 structurally diverse chemicals, most of which are known to bind ER. Fifty-three chemicals were able to bind the rat AFP in the assay, while 72 chemicals were determined to be nonbinders. Observations from closely examining the relationship between the binding data and structures of the tested chemicals are rationally explained in a manner consistent with proposed binding regions of rat AFP in the literature. The data reported here represent the largest data set of structurally diverse chemicals tested for rat AFP binding. The data assist in elucidating binding interactions and mechanisms between chemicals and rat AFP and, in turn, assist in the evaluation of the endocrine disrupting potential of chemicals.

  15. Structural elucidation of novel phosphocholine-containing glycosylinositol-phosphoceramides in filamentous fungi and their induction of cell death of cultured rice cells.

    PubMed Central

    Aoki, Kazuhiro; Uchiyama, Ryosuke; Itonori, Saki; Sugita, Mutsumi; Che, Fang-Sik; Isogai, Akira; Hada, Noriyasu; Hada, Junko; Takeda, Tadahiro; Kumagai, Hidehiko; Yamamoto, Kenji

    2004-01-01

    Novel ZGLs (zwitterionic glycosphingolipids) have been found in and extracted from the mycelia of filamentous fungi ( Acremonium sp.) isolated from soil. Five ZGLs (ZGL1-ZGL5) were structurally elucidated by sugar compositional analysis, methylation analysis, periodate oxidation, matrix-assisted laser-desorption ionization-time-of-flight MS, (1)H-NMR spectroscopy and fast-atom bombardment MS. Their chemical structures were as follows: GlcN(alpha1-2)Ins1-P-1Cer (ZGL1), Man(alpha1-6)GlcN(alpha1-2)Ins1-P-1Cer (ZGL2), Man(alpha1-6)Man(alpha1-6)GlcN(alpha1-2)Ins1-P-1Cer (ZGL3), PC-->6Man(alpha1-6)GlcN(alpha1-2)Ins1- P -1Cer (ZGL4), and PC-->6Man(alpha1-6)Man(alpha1-6)GlcN(alpha1-2)Ins1-P-1Cer (ZGL5) (where Cer is ceramide and PC is phosphocholine). In addition, one acidic glycosphingolipid, which was the precursor of ZGLs, was also characterized as inositol-phosphoceramide. The core structure of the ZGLs, GlcN(alpha1-2)Ins1- P, is rather different from those found in other fungi, such as Man(alpha1-2)Ins1- P and Man(alpha1-6)Ins1- P. Interestingly, the terminal mannose residue of ZGL4 and ZGL5 was modified further with a PC group. The presence of PC-containing glycosylinositol-phosphoceramides has not been reported previously in any organism. The ceramide constituents of both ZGLs and acidic glycosphingolipid were essentially the same, and consisted of a 4-hydroxyoctadecasphinganine (phytosphingosine) as the sole sphingoid base and 2-hydroxytetracosanoic acid (>90%) as the major fatty acid. ZGLs were found to cause cell death in suspensions of cultured rice cells. The cell death-inducing activity of ZGLs is probably due to the characteristic glycan moiety of Man(alpha1-6)GlcN, and PC-containing ZGLs had high activity. This study is the first to demonstrate that fungal glycosylinositol-phosphoceramides induce cell death in cultured rice cells. PMID:14583095

  16. Structural elucidation of polysaccharide fractions from the brown alga Coccophora langsdorfii and in vitro investigation of their anticancer activity.

    PubMed

    Imbs, Tatiana I; Ermakova, Svetlana P; Malyarenko Vishchuk, Olesya S; Isakov, Vladimir V; Zvyagintseva, Tatiana N

    2016-01-01

    Laminaran, fucoidan, and alginate were isolated from the brown alga Coccophora langsdorfii collected in the Japan Sea. The structural characteristics of polysaccharides were investigated by NMR spectroscopy. The laminaran was determined as β-d-glucan, which consisted of 80% of 1,3- and 20% of 1,6-linked residues and was terminated with mannitol. The alginate was a guluronic acid-rich polysaccharide (M/G=0.85). Fucoidan, sulfated α-l-fucan, contained a linear backbone of alternating (1→3)- and (1→4)- linked α-l-fucopyranose residues with sulfate at C2 and C4 of (1→3)-α-l-fucopyranose residues. Anticancer activity of this fucoidan was investigated in comparison with activity of fucoidan having similar linear backbone from the brown alga Fucus evanescens. The fucoidan from C. langsdorfii significantly inhibited colony formation of SK-MEL-5 and SK-MEL-28 melanoma cells (the percentage of inhibition was 28 and 76, respectively) and weakly inhibited colony formation of breast adenocarcinoma cells MDA-MB-231 (the percentage of inhibition was about 5). Similar results were obtained for fucoidan from F. evanescens; the percentage of inhibition of colony formation of SK-MEL-5 and SK-MEL-28 melanoma cells was 54 and 56, respectively. The inhibition of colony formation of breast adenocarcinoma cells MDA-MB-231 was weak. We suppose that other sulfated and partially acetylated fucoidans consisting of (1→3)- and (1→4)-linked α-l-fucopyranose residues may suppress progression of melanoma cell colony formation similar to fucoidans of C. langsdorfii and F. evanescens. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. 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

    2015-05-21

    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.

  18. Structure elucidation of degradation products of the antibiotic amoxicillin with ion trap MS(n) and accurate mass determination by ESI TOF.

    PubMed

    Nägele, Edgar; Moritz, Ralf

    2005-10-01

    Today, it is necessary to identify relevant compounds appearing in discovery and development of new drug substances in the pharmaceutical industry. For that purpose, the measurement of accurate molecular mass and empirical formula calculation is very important for structure elucidation in addition to other available analytical methods. In this work, the identification and confirmation of degradation products in a finished dosage form of the antibiotic drug amoxicillin obtained under stress conditions will be demonstrated. Structure elucidation is performed utilizing liquid chromatography (LC) ion trap MS/MS and MS3 together with accurate mass measurement of the molecular ions and of the collision induced dissociation (CID) fragments by liquid chromatography electro spray ionization time-of-flight mass spectrometry (LC/ESI-TOF).

  19. Chemical Structure of Lipid A Isolated from Flavobacterium meningosepticum Lipopolysaccharide

    PubMed Central

    Kato, Hitomi; Haishima, Yuji; Iida, Takatoshi; Tanaka, Akira; Tanamoto, Ken-ichi

    1998-01-01

    The chemical structure of the lipid A of the lipopolysaccharide component isolated from Flavobacterium meningosepticum IFO 12535 was elucidated. Methylation and nuclear magnetic resonance analyses showed that two kinds of hydrophilic backbone exist in the free lipid A: a β (1→6)-linked 2-amino-2-deoxy-d-glucose, which is usually present in enterobacterial lipid A’s, and a 2-amino-6-O-(2,3-diamino-2,3-dideoxy-β-d-glucopyranosyl)-2-deoxy-d-glucose, in a molar ratio of 1.00:0.35. Both backbones were α-glycosidically phosphorylated in position 1, and the hydroxyl groups at positions 4, 4′, and 6′ were unsubstituted. Liquid secondary ion-mass spectrometry revealed a pseudomolecular ion at m/z 1673 [M-H]− as a major monophosphoryl lipid A component carrying five acyl groups. Fatty acid analysis showed that the lipid A contained 1 mol each of amide-linked (R)-3-OH iC17:0, ester-linked (R)-3-OH iC15:0, amide-linked (R)-3-O-(iC15:0)-iC17:0, and both amide- and ester-linked (R)-3-OH C16:0. Fatty acid distribution analyses using several mass spectrometry determinations demonstrated that the former two constituents were distributed on positions 2 and 3 of the reducing terminal unit of the backbones and that the latter two were attached to the 2′ and 3′ positions in the nonreducing terminal residue. PMID:9683486

  20. Structure elucidation of indole-indoline type alkaloids: a retrospective account from the point of view of current NMR and MS technology.

    PubMed

    Béni, Zoltán; Háda, Viktor; Dubrovay, Zsófia; Szántay, Csaba

    2012-10-01

    In this review our aim is to look back on how the structure elucidation of bisindoles, especially with focus placed on vinblastine and vincristine analogues, has evolved alongside with the development of MS and NMR over the last 60 years from the perspective of our present-day use of state-of-the-art MS and NMR instrumentation and on the basis of our own accumulated views and experience in the field.

  1. LC MS analysis in the e-beam and gamma radiolysis of metoprolol tartrate in aqueous solution: Structure elucidation and formation mechanism of radiolytic products

    NASA Astrophysics Data System (ADS)

    Slegers, Catherine; Maquille, Aubert; Deridder, Véronique; Sonveaux, Etienne; Habib Jiwan, Jean-Louis; Tilquin, Bernard

    2006-09-01

    E-beam and gamma products from the radiolysis of aqueous solutions of (±)-metoprolol tartrate, saturated in nitrogen, are analyzed by HPLC with on-line mass and UV detectors. The structures of 10 radiolytic products common to e-beam and gamma irradiations are elucidated by comparing their fragmentation pattern to that of (±)-metoprolol. Two of the radiolytic products are also metabolites. Different routes for the formation of the radiolytic products are proposed.

  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 two new constituents from the fruits of Morinda citrifolia Linn.

    PubMed

    Siddiqui, Bina S; Sattar, Fouzia A; Ahmad, Fayaz; Begum, Sabira

    2008-01-01

    Studies on the chemical constituents of the fruits of Morinda citrifolia Linn. have led to the isolation of two new compounds, morinaphthalene (=1,3,6,7-tetrahydroxy-2-hydroxymethyl-1,2,3,4-tetrahydronaphthalene, (1); and morindafurone (=5-hydroxy-1,10b-dihydro-6H-anthra [1,9-bc] furan-6-one, (2); as well as two known constituents, 1,8-dihydroxy-6-methoxy-3-methyl-9-anthrone (3) and 2,4-dimethoxy-9-anthrone (4). Their structures were elucidated by spectral analysis including 2D NMR techniques.

  5. Isolation and structure of ciguatoxin-4A, a new ciguatoxin precursor, from cultures of dinoflagellate Gambierdiscus toxicus and parrotfish Scarus gibbus.

    PubMed

    Satake, M; Ishibashi, Y; Legrand, A M; Yasumoto, T

    1996-12-01

    A new ciguatoxin congener, ciguatoxin-4A (CTX4A), was isolated from cultures of marine dinoflagellate Gambierdiscus toxicus, and its structure was elucidated to be 52-epiciguatoxin-4B on the basis of spectroscopic data. Chromatographic and spectral comparisons indicated that CTX4A was identical with a structurally unelucidated congener known as scaritoxin or SG1.

  6. Structural elucidation of some antimicrobial constituents from the leaf latex of Aloe trigonantha L.C. Leach.

    PubMed

    Megeressa, Mekdes; Bisrat, Daniel; Mazumder, Avijit; Asres, Kaleab

    2015-08-12

    The incidents of drug resistant microorganisms and the need of treatments for newly emerging pathogens are of great concern to the global community. Our ability to treat infectious diseases is dependent on the development of new pharmaceuticals, and one potential source being medicinal plants with traditional claims. The leaves of Aloe trigonantha L.C. Leach, an endemic Ethiopian plant, are locally used for the treatment of infectious and inflammatory diseases. This study explores the potential of the latex of this plant and compounds isolated thereof for their in vitro antibacterial and antifungal properties. Analytical RP-HPLC and silica gel preparative TLC were used for identification and isolation of active constituents, respectively. Characterization of the compounds was based on UV, IR, HR-ESIMS, (1)H and (13)C NMR, and 2D-NMR spectral assignments. Antimicrobial activity studies were carried out against 21 pathogenic bacterial and 4 fungal strains using the disk diffusion method. Minimum inhibitory concentrations (MICs) were determined by the broth dilution method. A C-glycosylated chromone identified as aloesin, and three C-glycosylated anthrones characterized as 8-O-methy-7-hydroxyaloin A/B, aloin A/B and aloin-6'-O-acetate A/B were isolated. The latex and isolated compounds exhibited in vitro antibacterial activity against the tested pathogens. In some cases the activity of the isolated compounds (MIC = 10 μg/mL) was comparable with that of the standard drug ciprofloxacin, particularly against some of the Gram-negative bacterial strains tested. However, their activity towards the fungal pathogens tested was relatively weaker showing maximum activity against Candida albicans with MIC value of 400 μg/mL. The present findings can be used for further research aimed at the development of new antibacterial agents, and may also justify the ethnomedicinal claim of the plant for the treatment of infectious diseases.

  7. Vibration isolation via a scissor-like structured platform

    NASA Astrophysics Data System (ADS)

    Sun, Xiuting; Jing, Xingjian; Xu, Jian; Cheng, Li

    2014-04-01

    More and more attentions are attracted to the analysis and design of nonlinear vibration control/isolation systems for better isolation performance. In this study, an isolation platform with n-layer scissor-like truss structure is investigated to explore novel design of passive/semi-active/active vibration control/isolation systems and to exploit potential nonlinear benefits in vibration suppression. Due to the special scissor-like structure, the dynamic response of the platform has inherent nonlinearities both in equivalent damping and stiffness characteristics (although only linear components are applied), and demonstrates good loading capacity and excellent equilibrium stability. With the mathematical modeling and analysis of the equivalent stiffness and damping of the system, it is shown that: (a) the structural nonlinearity in the system is very helpful in vibration isolation, (b) both equivalent stiffness and damping characteristics are nonlinear and could be designed/adjusted to a desired nonlinearity by tuning structural parameters, and (c) superior vibration isolation performances (e.g., quasi-zero stiffness characteristics etc.) can be achieved with different structural parameters. This scissor-like truss structure can potentially be employed in different engineering practices for much better vibration isolation or control.

  8. Organic-Silica Interactions in Saline: Elucidating the Structural Influence of Calcium in Low-Salinity Enhanced Oil Recovery.

    PubMed

    Desmond, J L; Juhl, K; Hassenkam, T; Stipp, S L S; Walsh, T R; Rodger, P M

    2017-09-08

    Enhanced oil recovery using low-salinity solutions to sweep sandstone reservoirs is a widely-practiced strategy. The mechanisms governing this remain unresolved. Here, we elucidate the role of Ca(2+) by combining chemical force microscopy (CFM) and molecular dynamics (MD) simulations. We probe the influence of electrolyte composition and concentration on the adsorption of a representative molecule, positively-charged alkylammonium, at the aqueous electrolyte/silica interface, for four electrolytes: NaCl, KCl, MgCl2, and CaCl2. CFM reveals stronger adhesion on silica in CaCl2 compared with the other electrolytes, and shows a concentration-dependent adhesion not observed for the other electrolytes. Using MD simulations, we model the electrolytes at a negatively-charged amorphous silica substrate and predict the adsorption of methylammonium. Our simulations reveal four classes of surface adsorption site, where the prevalence of these sites depends only on CaCl2 concentration. The sites relevant to strong adhesion feature the O(-) silica site and Ca(2+) in the presence of associated Cl(-), which gain prevalence at higher CaCl2 concentration. Our simulations also predict the adhesion force profile to be distinct for CaCl2 compared with the other electrolytes. Together, these analyses explain our experimental data. Our findings indicate in general how silica wettability may be manipulated by electrolyte concentration.

  9. Elucidating the multiple genetic lineages and population genetic structure of the brooding coral Seriatopora (Scleractinia: Pocilloporidae) in the Ryukyu Archipelago

    NASA Astrophysics Data System (ADS)

    Nakajima, Yuichi; Nishikawa, Akira; Iguchi, Akira; Nagata, Tomofumi; Uyeno, Daisuke; Sakai, Kazuhiko; Mitarai, Satoshi

    2017-06-01

    The elucidation of species diversity and connectivity is essential for conserving coral reef communities and for understanding the characteristics of coral populations. To assess the species diversity, intraspecific genetic diversity, and genetic differentiation among populations of the brooding coral Seriatopora spp., we conducted phylogenetic and population genetic analyses using a mitochondrial DNA control region and microsatellites at ten sites in the Ryukyu Archipelago, Japan. At least three genetic lineages of Seriatopora (Seriatopora-A, -B, and -C) were detected in our specimens. We collected colonies morphologically similar to Seriatopora hystrix, but these may have included multiple, genetically distinct species. Although sexual reproduction maintains the populations of all the genetic lineages, Seriatopora-A and Seriatopora-C had lower genetic diversity than Seriatopora-B. We detected significant genetic differentiation in Seriatopora-B among the three populations as follows: pairwise F ST = 0.064-0.116 (all P = 0.001), pairwise G''ST = 0.107-0.209 (all P = 0.001). Additionally, only one migrant from an unsampled population was genetically identified within Seriatopora-B. Because the peak of the settlement of Seriatopora larvae is within 1 d and almost all larvae are settled within 5 d of spawning, our observations may be related to low dispersal ability. Populations of Seriatopora in the Ryukyu Archipelago will probably not recover unless there is substantial new recruitment from distant populations.

  10. Elucidation of the elusive structure and formula of the active pharmaceutical ingredient bismuth subgallate by continuous rotation electron diffraction.

    PubMed

    Wang, Yunchen; Takki, Sofia; Cheung, Ocean; Xu, Hongyi; Wan, Wei; Öhrström, Lars; Inge, A Ken

    2017-07-04

    Bismuth subgallate has been used in wound and gastrointestinal therapy for over a century. The combination of continuous rotation electron diffraction and sample cooling finally revealed its structure as a coordination polymer. The structure provides insight regarding its formula, poor solubility, acid resistance and previously unreported gas sorption properties.

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

    DOE PAGES

    Reinecke, Benjamin N.; Kuhl, Kendra P.; Ogasawara, Hirohito; ...

    2015-12-31

    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 sizemore » in terms of an increasing percentage of Au atoms at corners/edges for decreasing particle size. Finally, this work elucidates how Au coordination number impacts the electronic structure of Au nanoparticles, ultimately giving rise to their well-known catalytic activity.« less

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

    SciTech Connect

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

    2015-12-31

    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. Finally, this work elucidates how Au coordination number impacts the electronic structure of Au nanoparticles, ultimately giving rise to their well-known catalytic activity.

  13. 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.

  14. 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

    2015-10-02

    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.

  15. Stability-indicating HPLC method development and structural elucidation of novel degradation products in posaconazole injection by LC-TOF/MS, LC-MS/MS and NMR.

    PubMed

    Yang, Yidi; Zhu, Xi; Zhang, Fei; Li, Wei; Wu, Ying; Ding, Li

    2016-06-05

    Stress testing was carried out under acidic, alkaline, oxidative, thermal and photolytic conditions to evaluate the intrinsic stability of posaconazole injection. A total of four degradation products were detected and the drug was found to be susceptible to oxidative and thermal degradations. Three unknown degradants formed under oxidative stress condition were isolated by preparative HPLC and unambiguously elucidated by LC-TOF/MS, LC-MS/MS, (1)H NMR, (13)C NMR and 2D NMR techniques. Based on the spectrometric and spectroscopic information, these novel degradation products were unequivocally assigned as the N-oxides of posaconazole. Probable mechanisms for the formation of the degradants were proposed. A new and selective HPLC method was developed and validated to separate, detect and quantify all the degradants in posaconazole injection.

  16. 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.

  17. Elucidation of Antimicrobial Susceptibility Profiles and Genotyping of Salmonella enterica Isolates from Clinical Cases of Salmonellosis in New Mexico in 2008

    PubMed Central

    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.

    2010-01-01

    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, blaTEM 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. PMID:20514366

  18. 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.

  19. 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. Copyright © 2010 Elsevier B.V. All rights reserved.

  20. Exploiting the Complementarity between Dereplication and Computer-Assisted Structure Elucidation for the Chemical Profiling of Natural Cosmetic Ingredients: Tephrosia purpurea as a Case Study.

    PubMed

    Hubert, Jane; Chollet, Sébastien; Purson, Sylvain; Reynaud, Romain; Harakat, Dominique; Martinez, Agathe; Nuzillard, Jean-Marc; Renault, Jean-Hugues

    2015-07-24

    The aqueous-ethanolic extract of Tephrosia purpurea seeds is currently exploited in the cosmetic industry as a natural ingredient of skin lotions. The aim of this study was to chemically characterize this ingredient by combining centrifugal partition extraction (CPE) as a fractionation tool with two complementary identification approaches involving dereplication and computer-assisted structure elucidation. Following two rapid fractionations of the crude extract (2 g), seven major compounds namely, caffeic acid, quercetin-3-O-rutinoside, ethyl galactoside, ciceritol, stachyose, saccharose, and citric acid, were unambiguously identified within the CPE-generated simplified mixtures by a recently developed (13)C NMR-based dereplication method. The structures of four additional compounds, patuletin-3-O-rutinoside, kaempferol-3-O-rutinoside, guaiacylglycerol 8-vanillic acid ether, and 2-methyl-2-glucopyranosyloxypropanoic acid, were automatically elucidated by using the Logic for Structure Determination program based on the interpretation of 2D NMR (HSQC, HMBC, and COSY) connectivity data. As more than 80% of the crude extract mass was characterized without need for tedious and labor-intensive multistep purification procedures, the identification tools involved in this work constitute a promising strategy for an efficient and time-saving chemical profiling of natural extracts.

  1. 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.

  2. Trapping and Structural Elucidation of a Very Advanced Intermediate in the Lesion-Extrusion Pathway of hOGG1

    SciTech Connect

    Lee, Seongmin; Radom, Christopher T.; Verdine, Gregory L.

    2008-07-28

    Here we present the first structure of a very advanced intermediate in the lesion-extrusion pathway of a DNA glycosylase, human 8-oxoguanine DNA glycosylase (hOGG1), and a substrate DNA containing a mutagenic lesion, 8-oxoguanine (oxoG). The structure was obtained by irradiation and flash-freezing of a disulfide-cross-linked (DXLed) complex of hOgg1 bound to DNA containing a novel photocaged derivative of oxoG. The X-ray structure reveals that, upon irradiation, the oxoG lesion has transited from the exosite to the active site pocket, but has not undergone cleavage by the enzyme. Furthermore, all but one of the specificity-determining interactions between the lesion and the enzyme are unformed in the flashed complex (FC), because active site functionality and elements of the DNA backbone are mispositioned. This structure thus provides a first glimpse into the structure of a very late-stage intermediate in the lesion-extrusion pathway -- the latest observed to date for any glycosylase -- in which the oxoG has undergone insertion into the enzyme active site following photodeprotection, but the enzyme and DNA have not yet completed the slower process of adjusting to the presence of the lesion in the active site.

  3. Constitutive Relations Analyses of Plastic Flow in Dual-Phase Steels to Elucidate Structure-Strength-Ductility Correlations

    NASA Astrophysics Data System (ADS)

    Saimoto, S.; Timokhina, I. B.; Pereloma, E. V.

    2017-07-01

    The structure-strength characterization is typically performed by correlating the structure with x-ray, electron, or atomic imaging devices to the bulk mechanical tensile parameters of yield stress and the plastic yielding response. The problem is that structure parameters embedded in the stress-strain data cannot be revealed without an analyzable constitutive relation. New functional slip-based constitutive formulation with precise digital fitting parameters can replicate the measured data with at least two loci. Thus, this study examines the possibility of identifying the mechanical response as a result of the various microstructure components. The key parameter, the mean slip distance, can be calibrated from the initial work-hardening slope at 0.2% strain from which all the fit parameters can be determined. In this process, a newly derived friction stress is defined to separate the yield phenomenon from the plastic strains beyond yield-point elongation. This methodology has been applied to dual-phase steel specimens that resulted in excellent predictive correlations with prior structure-strength characterization. Hence, the structure-strength-ductility changes resulting from processing conditions can be more precisely surmised from mechanical testing. Thus, a method to delineate the nanostructure evolution with deformation using mesoscopic mechanical parameters has been introduced.

  4. Elucidating the structure of surface acid sites on {gamma}-Al{sub 2}O{sub 3}.

    SciTech Connect

    Chupas, P. J.; Chapman, K. W.; Halder, G. J.

    2011-05-12

    Differential pair distribution function analysis was applied to resolve, with crystallographic detail, the structure of catalytic sites on the surface of nanoscale {gamma}-Al{sup 2}O{sub 3}. The structure was determined for a basic probe molecule, monomethylamine (MMA), bound at the minority Lewis acid sites. These active sites were found to be five-coordinate, forming distorted octahedra upon MMA binding. This approach could be applied to study the interaction of molecules at surfaces in dye-sensitized solar cells, nanoparticles, sensors, materials for waste remediation, and catalysts.

  5. 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.

  6. First Structural Glimpse of CCN3 and CCN5 Multifunctional Signaling Regulators Elucidated by Small Angle X-ray Scattering*

    PubMed Central

    Holbourn, Kenneth P.; Malfois, Marc; Acharya, K. Ravi

    2011-01-01

    The CCN (cyr61, ctgf, nov) proteins (CCN1–6) are an important family of matricellular regulatory factors involved in internal and external cell signaling. They are central to essential biological processes such as adhesion, proliferation, angiogenesis, tumorigenesis, wound healing, and modulation of the extracellular matrix. They possess a highly conserved modular structure with four distinct modules that interact with a wide range of regulatory proteins and ligands. However, at the structural level, little is known although their biological function(s) seems to require cooperation between individual modules. Here we present for the first time structural determinants of two of the CCN family members, CCN3 and CCN5 (expressed in Escherichia coli), using small angle x-ray scattering. The results provide a description of the overall molecular shape and possible general three-dimensional modular arrangement for CCN proteins. These data unequivocally provide insight of the nature of CCN protein(s) in solution and thus important insight into their structure-function relationships. PMID:21543320

  7. Recent Advances and Applications in Synchrotron X-Ray Protein Footprinting for Protein Structure and Dynamics Elucidation.

    PubMed

    Gupta, Sayan; Feng, Jun; Chance, Mark; Ralston, Corie

    2016-01-01

    Synchrotron X-ray Footprinting is a powerful in situ hydroxyl radical labeling method for analysis of protein structure, interactions, folding and conformation change in solution. In this method, water is ionized by high flux density broad band synchrotron X-rays to produce a steady-state concentration of hydroxyl radicals, which then react with solvent accessible side-chains. The resulting stable modification products are analyzed by liquid chromatography coupled to mass spectrometry. A comparative reactivity rate between known and unknown states of a protein provides local as well as global information on structural changes, which is then used to develop structural models for protein function and dynamics. In this review we describe the XF-MS method, its unique capabilities and its recent technical advances at the Advanced Light Source. We provide a comparison of other hydroxyl radical and mass spectrometry based methods with XFMS. We also discuss some of the latest developments in its usage for studying bound water, transmembrane proteins and photosynthetic protein components, and the synergy of the method with other synchrotron based structural biology methods.

  8. Isolation and structure determination of one new metabolite isolated from the red fermented rice of Monascus purpureus.

    PubMed

    Cheng, Ming-Jen; Chen, Jih-Jung; Wu, Ming-Der; Yang, Ping-Shin; Yuan, Gwo-Fang

    2010-06-01

    The n-BuOH-soluble portion of the 95% EtOH extract of red fermented rice fermented with the yellow mutant of the fungus Monascus purpureus BCRC 38113 (Monascaceae) led to the isolation of one new pyran-2-one derivative, namely peroxymonascuspyrone (1), along with nine known compounds, monasfluore A (2), monasfluore B (3), 3-epi-betulinic acid (4), 3-epi-betulinic acid acetate (5), alpha-tocospiro A (6), friedelan-3-one (7), alpha-cadinol (8), anticopalol (9), and spathulenol (10). Interestingly, this is the first report of a naturally occurring pyran-2-one skeleton isolated from Monascus sp. Their structures and relative configurations were elucidated by spectroscopic methods, including 1D- and 2D-NMR ((1)H,(1)H-COSY, HMQC, HMBC and NOESY), as well as low- and high-resolution mass spectrometric analyses. In addition, cytotoxicities against MCF-7, NCI-H460 and SF-268 cancer cell lines were measured in vitro; the results revealed that these metabolites have no cytotoxicity against the selected tumour cells.

  9. Elucidation of hydrocarbon structure in an enzyme-catalyzed benzo[a]pyrene-poly (G) covalent complex.

    PubMed Central

    Meehan, T; Straub, K; Calvin, M

    1976-01-01

    The carcinogen, benzo[a]pyrene, was covalently attached to poly (G) by liver microsomes from rats pretreated with 3-methylcholanthrene. The complex was hydrolyzed with enzymes or base and products were isolated by Sephadex chromatography. Absorbance and fluorescence spectra of the products fit that of red-shifted pyrene aromatic system and suggest that metabolism has occurred at the 7-, 8-, 9-, and 10-positions of the hydrocarbon. Benzanthracene or chrysene fluorescence were not observed in these preparations. Benzo[a]pyrene derivatives were synthesized and purified by high-pressure liquid chromatography. Dehydration of 7,8-dihydroxy-7,8,9,10-tetrahydrobenzo[a]pyrene resulted in the formation of small amounts of 7-oxo-7,8,9,10-tetrahydrobenzoa[a]pyrene. A 7-keto species was also observed after similar treatment of the hydrocarbon-poly(G) hydrolysis products. Evidence of dehydration at the 9,10-positions was not observed. The hydrocarbon covalently bound to poly(G) is, therefore, a derivative of 7,8-dihydroxy-7,8,9,10-tetrahydrobenzol[a]pyrene with nucleic acid substitution at C-10 or 9. PMID:1064016

  10. Studies toward the Unique Pederin Family Member Psymberin: Full Structure Elucidation, Two Alternative Total Syntheses, and Analogs

    PubMed Central

    Feng, Yu; Jiang, Xin; De Brabander, Jef K.

    2012-01-01

    Two synthetic approaches to psymberin have been accomplished. A highly convergent first generation synthesis led to the complete stereochemical assignment and demonstrated that psymberin and irciniastatin A are identical compounds. This synthesis featured a diastereoselective aldol coupling between the aryl fragment and a central tetrahydropyran core, and a novel one-pot procedure to convert an amide, via intermediacy of a sensitive methyl imidate, to the N-acyl aminal reminiscent of psymberin. The highlights of the second generation synthesis include an efficient iridium-catalyzed enantioselective bis-allylation of neopentyl glycol, and a stepwise Sonogashira coupling/cycloisomerization/reduction sequence to construct the dihydroisocoumarin unit. The two synthetic avenues were achieved in 17–18 steps (longest linear sequence, ~14–15 isolations) from 3 fragments prepared in 7–8 steps (1st generation) and 3–8 steps (2nd generation) each. This convergent approach allowed for the preparation of sufficient amounts of psymberin (~ 0.5 g) for follow-up biological studies. Meanwhile, our highly flexible strategy enabled the design and synthesis of multiple analogs, including a psymberin-pederin hybrid termed psympederin that proved crucial to a comprehensive understanding of the chemical biology of psymberin and related compounds that will be described in a subsequent manuscript. PMID:23004238

  11. Studies toward the unique pederin family member psymberin: full structure elucidation, two alternative total syntheses, and analogs.

    PubMed

    Feng, Yu; Jiang, Xin; De Brabander, Jef K

    2012-10-17

    Two synthetic approaches to psymberin have been accomplished. A highly convergent first generation synthesis led to the complete stereochemical assignment and demonstrated that psymberin and irciniastatin A are identical compounds. This synthesis featured a diastereoselective aldol coupling between the aryl fragment and a central tetrahydropyran core and a novel one-pot procedure to convert an amide, via intermediacy of a sensitive methyl imidate, to the N-acyl aminal reminiscent of psymberin. The highlights of the second generation synthesis include an efficient iridium-catalyzed enantioselective bisallylation of neopentyl glycol and a stepwise Sonogashira coupling/cycloisomerization/reduction sequence to construct the dihydroisocoumarin unit. The two synthetic avenues were achieved in 17-18 steps (longest linear sequence, ~14-15 isolations) from 3 fragments prepared in 7-8 (first generation) and 3-8 (second generation) steps each. This convergent approach allowed for the preparation of sufficient amounts of psymberin (~ 0.5 g) for follow-up biological studies. Meanwhile, our highly flexible strategy enabled the design and synthesis of multiple analogs, including a psymberin-pederin hybrid, termed psympederin, that proved crucial to a comprehensive understanding of the chemical biology of psymberin and related compounds that will be described in a subsequent manuscript.

  12. [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.

  13. FINE STRUCTURE AND PIGMENT CONVERSION IN ISOLATED ETIOLATED PROPLASTIDS

    PubMed Central

    Klein, Shimon; Poljakoff-Mayber, A.

    1961-01-01

    Proplastids containing a prolamellar body were isolated from leaves of etiolated bean plants. The isolation methods do not necessarily lead to destruction of their submicroscopic structure and most of the isolated proplastids show well preserved outer membranes, lamellar strands, and the prolamellar body. Morphological intactness of the proplastids varies; certain leaf fractions contain single prolamellar bodies as well as proplastids. Since pellets after centrifugation between 350 g and 1000 to 3000 g contain intact proplastids and, as was shown by quantitative experiments, the same fractions show photoconversion of protochlorophyll to chlorophyll, it is supposed that the isolated particles probably retain many of the properties which are characteristic of them in situ. Isolated proplastids may thus be a valuable tool in investigations on the development of the photosynthetic apparatus. PMID:14456780

  14. Elucidation of the structure of organic solutions in solvent extraction by combining molecular dynamics and X-ray scattering.

    PubMed

    Ferru, Geoffroy; Gomes Rodrigues, Donatien; Berthon, Laurence; Diat, Olivier; Bauduin, Pierre; Guilbaud, Philippe

    2014-05-19

    Knowledge of the supramolecular structure of the organic phase containing amphiphilic ligand molecules is mandatory for full comprehension of ionic separation during solvent extraction. Existing structural models are based on simple geometric aggregates, but no consensus exists on the interaction potentials. Herein, we show that molecular dynamics crossed with scattering techniques offers key insight into the complex fluid involving weak interactions without any long-range ordering. Two systems containing mono- or diamide extractants in heptane and contacted with an aqueous phase were selected as examples to demonstrate the advantages of coupling the two approaches for furthering fundamental studies on solvent extraction. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. 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

  16. Structural elucidation of a novel transglycosylated compound α-glucosyl rhoifolin and of α-glucosyl rutin by NMR spectroscopy.

    PubMed

    Aoki, Chisa; Takeuchi, Yoshihiro; Higashi, Kenjirou; Okamoto, Yuta; Nakanishi, Akihito; Tandia, Mahamadou; Uzawa, Jun; Ueda, Keisuke; Moribe, Kunikazu

    2017-04-18

    We report the full assignment of (1)H and (13)C NMR signals belonging to α-glucosyl rhoifolin (Rhf-G), a novel transglycosylated compound synthesized from a flavone glycoside, rhoifolin, as well as its chemical structure. Furthermore, we report the complete NMR signal assignment for another transglycosylated compound, α-glucosyl rutin (Rutin-G), as the signals corresponding to its sugar moieties had not been identified. Electrospray ionization-mass spectrometry along with multiple NMR methods revealed that Rhf-G possesses three sugar moieties in its chemical structure. The additional glucose was bound directly via a transglycosylation to rhoifolin at position 3a of the sugar moiety. Interestingly, intramolecular hydrogen bonds in the basic Rhf-G and Rutin-G skeletons were confirmed by HMBC experiments. These findings will be helpful for comprehensive NMR studies on transglycosylated compounds in food, cosmetic, and pharmaceutical fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Structural differences between Abeta(1-40) intermediate oligomers and fibrils elucidated by proteolytic fragmentation and hydrogen/deuterium exchange.

    PubMed

    Zhang, Aming; Qi, Wei; Good, Theresa A; Fernandez, Erik J

    2009-02-01

    The aggregation of amyloid-beta protein (Abeta) in vivo is a critical pathological event in Alzheimer's disease. Although more and more evidence shows that the intermediate oligomers are the primary neurotoxic species in Alzheimer's disease, the particular structural features responsible for the toxicity of these intermediates are poorly understood. We measured the peptide level solvent accessibility of multiple Abeta(1-40) aggregated states using hydrogen exchange detected by mass spectrometry. A gradual reduction in solvent accessibility, spreading from the C-terminal region to the N-terminal region was observed with ever more aggregated states of Abeta peptide. The observed hydrogen exchange protection begins with reporter peptides 20-34 and 35-40 in low molecular weight oligomers found in fresh samples and culminates with increasing solvent protection of reporter peptide 1-16 in long time aged fibrillar species. The more solvent exposed structure of intermediate oligomers in the N-termini relative to well-developed fibrils provides a novel explanation for the structure-dependent neurotoxicity of soluble oligomers reported previously.

  18. 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.

  19. 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.

  20. Metal interactions at the biochar-water interface: energetics and structure-sorption relationships elucidated by flow adsorption microcalorimetry.

    PubMed

    Harvey, Omar R; Herbert, Bruce E; Rhue, Roy D; Kuo, Li-Jung

    2011-07-01

    Plant-derived biochars exhibit large physicochemical heterogeneity due to variations in biomass chemistry and combustion conditions. However, the influence of biochar heterogeneity on biochar-metal interaction mechanisms has not been systematically described. We used flow adsorption microcalorimetry to study structure-sorption relationships between twelve plant-derived biochars and two metals (K(+) and Cd(2+)) of different Lewis acidity. Irrespective of the biochar structure, sorption of K(+) (a hard Lewis acid) occurred predominantly on deprotonated functional groups via ion exchange with molar heats of adsorption (ΔH(ads)) of -4 kJ mol(-1) to -8 kJ mol(-1). By comparison, although ion exchange could not be completely ruled out, our data pointed to Cd(2+) (a soft Lewis acid) sorption occurring predominantly via two distinct cation-π bonding mechanisms, each with ΔH(ads) of +17 kJ mol(-1). The first, evident in low charge-low carbonized biochars, suggested Cd(2+)-π bonding to soft ligands such as -C ═ O; while the second, evident in low charge-highly carbonized biochars, pointed to Cd(2+)-π bonding with electron-rich domains on aromatic structures. Quantitative contributions of these mechanisms to Cd(2+) sorption can exceed 3 times that expected for ion exchange and therefore could have significant implications for the biogeochemical cycling of metals in fire-impacted or biochar-amended systems.

  1. 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

  2. Effect of Glu12-His89 Interaction on Dynamic Structures in HIV-1 p17 Matrix Protein Elucidated by NMR

    PubMed Central

    Konagaya, Yuta; Miyakawa, Rina; Sato, Masumi; Matsugami, Akimasa; Watanabe, Satoru; Hayashi, Fumiaki; Kigawa, Takanori; Nishimura, Chiaki

    2016-01-01

    To test the existence of the salt bridge and stability of the HIV-1 p17 matrix protein, an E12A (mutated at helix 1) was established to abolish possible electrostatic interactions. The chemical shift perturbation from the comparison between wild type and E12A suggested the existence of an electrostatic interaction in wild type between E12 and H89 (located in helix 4). Unexpectedly, the studies using urea denaturation indicated that the E12A substitution slightly stabilized the protein. The dynamic structure of E12A was examined under physiological conditions by both amide proton exchange and relaxation studies. The quick exchange method of amide protons revealed that the residues with faster exchange were located at the mutated region, around A12, compared to those of the wild-type protein. In addition, some residues at the region of helix 4, including H89, exhibited faster exchange in the mutant. In contrast, the average values of the kinetic rate constants for amide proton exchange for residues located in all loop regions were slightly lower in E12A than in wild type. Furthermore, the analyses of the order parameter revealed that less flexible structures existed at each loop region in E12A. Interestingly, the structures of the regions including the alpha1-2 loop and helix 5 of E12A exhibited more significant conformational exchanges with the NMR time-scale than those of wild type. Under lower pH conditions, for further destabilization, the helix 1 and alpha2-3 loop in E12A became more fluctuating than at physiological pH. Because the E12A mutant lacks the activities for trimer formation on the basis of the analytical ultra-centrifuge studies on the sedimentation distribution of p17 (Fledderman et al. Biochemistry 49, 9551–9562, 2010), it is possible that the changes in the dynamic structures induced by the absence of the E12-H89 interaction in the p17 matrix protein contributes to a loss of virus assembly. PMID:27907055

  3. Evaluation of levels of antibiotic resistance in groundwater-derived E. coli isolates in the Midwest of Ireland and elucidation of potential predictors of resistance

    NASA Astrophysics Data System (ADS)

    O'Dwyer, Jean; Hynds, Paul; Pot, Matthieu; Adley, Catherine C.; Ryan, Michael P.

    2017-06-01

    Antibiotic-resistant (pathogenic and non-pathogenic) organisms and genes are now acknowledged as significant emerging aquatic contaminants with potentially adverse human and ecological health impacts, and thus require monitoring. This study is the first to investigate levels of resistance among Irish groundwater (private wells) samples; Escherichia coli isolates were examined against a panel of commonly prescribed human and veterinary therapeutic antibiotics, followed by determination of the causative factors of resistance. Overall, 42 confirmed E. coli isolates were recovered from a groundwater-sampling cohort. Resistance to the human panel of antibiotics was moderate; nine (21.4%) E. coli isolates demonstrated resistance to one or more human antibiotics. Conversely, extremely high levels of resistance to veterinary antibiotics were found, with all isolates presenting resistance to one or more veterinary antibiotics. Particularly high levels of resistance (93%) were found with respect to the aminoglycoside class of antibiotics. Results of statistical analysis indicate a significant association between the presence of human (multiple) antibiotic resistance ( p = 0.002-0.011) and both septic tank density and the presence of vulnerable sub-populations (<5 years). For the veterinary antibiotics, results point to a significant relationship ( p = <0.001) between livestock (cattle) density and the prevalence of multiple antibiotic resistant E. coli. Groundwater continues to be an important resource in Ireland, particularly in rural areas; thus, results of this preliminary study offer a valuable insight into the prevalence of antibiotic resistance in the hydrogeological environment and establish a need for further research with a larger geological diversity.

  4. Evaluation of levels of antibiotic resistance in groundwater-derived E. coli isolates in the Midwest of Ireland and elucidation of potential predictors of resistance

    NASA Astrophysics Data System (ADS)

    O'Dwyer, Jean; Hynds, Paul; Pot, Matthieu; Adley, Catherine C.; Ryan, Michael P.

    2017-02-01

    Antibiotic-resistant (pathogenic and non-pathogenic) organisms and genes are now acknowledged as significant emerging aquatic contaminants with potentially adverse human and ecological health impacts, and thus require monitoring. This study is the first to investigate levels of resistance among Irish groundwater (private wells) samples; Escherichia coli isolates were examined against a panel of commonly prescribed human and veterinary therapeutic antibiotics, followed by determination of the causative factors of resistance. Overall, 42 confirmed E. coli isolates were recovered from a groundwater-sampling cohort. Resistance to the human panel of antibiotics was moderate; nine (21.4%) E. coli isolates demonstrated resistance to one or more human antibiotics. Conversely, extremely high levels of resistance to veterinary antibiotics were found, with all isolates presenting resistance to one or more veterinary antibiotics. Particularly high levels of resistance (93%) were found with respect to the aminoglycoside class of antibiotics. Results of statistical analysis indicate a significant association between the presence of human (multiple) antibiotic resistance (p = 0.002-0.011) and both septic tank density and the presence of vulnerable sub-populations (<5 years). For the veterinary antibiotics, results point to a significant relationship (p = <0.001) between livestock (cattle) density and the prevalence of multiple antibiotic resistant E. coli. Groundwater continues to be an important resource in Ireland, particularly in rural areas; thus, results of this preliminary study offer a valuable insight into the prevalence of antibiotic resistance in the hydrogeological environment and establish a need for further research with a larger geological diversity.

  5. STRUCTURAL ELUCIDATION OF CRITICAL RESIDUES INVOLVED IN BINDING OF HUMAN MONOCLONAL ANTIBODIES TO HEPATITIS C VIRUS E2 ENVELOPE GLYCOPROTEIN

    PubMed Central

    Iacob, Roxana E.; Keck, Zhenyong; Olson, Oakley; Foung, Steven K.H.; Tomer, Kenneth B.

    2008-01-01

    Human monoclonal antibodies derived from B cells of HCV infected individuals provide information on the immune response to native HCV envelope proteins as they are recognized during infection. Monoclonal antibodies have been useful in the determination of the function and structure of specific immunogenic domains of proteins and should also be useful for the structure/function characterization of HCV E1 and E2 envelope glycoproteins. The HCV E2 envelope glycoprotein has at least three immunodistinctive conformation domains, designated A, B, and C. Conformational epitopes within domain B and C are neutralizing antibody targets on HCV pseudoparticles as well as from infectious cell culture virus. In this study, a combination of differential surface modification and mass spectrometric limited proteolysis followed by alanine mutagenesis was used to provide insight into potential conformational changes within the E2 protein upon antibody binding. The arginine guanidine groups in the E2 protein were modified with CHD in both the affinity bound and free states followed by mass spectrometric analysis, and the regions showing protection upon antibody binding were identified. This protection can arise by direct contact between the residues and the monoclonal antibody, or by antibody-induced conformational changes. Based on the mass spectrometric data, site-directed mutagenesis experiments were performed which clearly identified additional amino acids residues on E2 distant from the site of antibody interaction, whose change to alanine inhibited antibody recognition by inducing conformational changes within the E2 protein. PMID:18230369

  6. Molecular and supramolecular properties of nitroaromatic thiosemicarbazones: Synthesis, spectroscopy, X-ray structure elucidation and DFT calculations

    NASA Astrophysics Data System (ADS)

    Dias, L. C.; de Lima, G. M.; Pinheiro, C. B.; Nascimento, M. A. C.; Bitzer, R. S.

    2017-03-01

    The reactions of 6-nitropiperonal with H2Nsbnd NHsbnd C(S)sbnd NHR, R = Me, Et, Ph or H, afforded four nitroaromatic thiosemicarbazones 1-4, respectively. 1-4 were characterized by elemental analysis (CHN), FTIR, and 1H and 13C{1H} NMR spectroscopy. In addition, the crystal structures of 2 and 3 were determined by single-crystal X-ray diffraction. Our X-ray structural results have shown that the nitropiperonal and thiosemicarbazone moieties exhibit an almost coplanar arrangement for both 2 and 3. Moreover, they establish 2-D networks along the [111] base vector by means of classical and nonclassical hydrogen bonds. Electronic and spectroscopic properties of 1-4 were investigated at the DFT B3LYP/6-311G** level of calculation. The Cdbnd S group of 1-4 constitutes a nucleophilic region, whereas the NO2 group defines an electrophilic centre, as expected. Furthermore, a DFT vibrational analysis of 4 allowed a reliable assignment of the thiosemicarbazone-based vibrations. Also, a good agreement between theoretical and experimental 13C chemical shift values was obtained for 1-4.

  7. In situ analysis and structural elucidation of sainfoin (Onobrychis viciifolia) tannins for high-throughput germplasm screening.

    PubMed

    Gea, An; Stringano, Elisabetta; Brown, Ron H; Mueller-Harvey, Irene

    2011-01-26

    A rapid thiolytic degradation and cleanup procedure was developed for analyzing tannins directly in chlorophyll-containing sainfoin ( Onobrychis viciifolia ) plants. The technique proved suitable for complex tannin mixtures containing catechin, epicatechin, gallocatechin, and epigallocatechin flavan-3-ol units. The reaction time was standardized at 60 min to minimize the loss of structural information as a result of epimerization and degradation of terminal flavan-3-ol units. The results were evaluated by separate analysis of extractable and unextractable tannins, which accounted for 63.6-113.7% of the in situ plant tannins. It is of note that 70% aqueous acetone extracted tannins with a lower mean degree of polymerization (mDP) than was found for tannins analyzed in situ. Extractable tannins had between 4 and 29 lower mDP values. The method was validated by comparing results from individual and mixed sample sets. The tannin composition of different sainfoin accessions covered a range of mDP values from 16 to 83, procyanidin/prodelphinidin (PC/PD) ratios from 19.2/80.8 to 45.6/54.4, and cis/trans ratios from 74.1/25.9 to 88.0/12.0. This is the first high-throughput screening method that is suitable for analyzing condensed tannin contents and structural composition directly in green plant tissue.

  8. Adsorption of divalent heavy metal ions onto IDA-chelating resins: simulation of physicochemical structures and elucidation of interaction mechanisms.

    PubMed

    Ling, Panpan; Liu, Fuqiang; Li, Lanjuan; Jing, Xiaosheng; Yin, Baorui; Chen, Kaibo; Li, Aimin

    2010-04-15

    The adsorption performances, under static as well as dynamic conditions, for such metal ions as Cu(II), Pb(II) and Cd(II) toward chelating resins (IRC748 and NDC702) similarly containing iminodiacetic acid group but diverse pore structures, are systematically performed and deeply exploited. The physicochemical characteristics of both IDA-chelating resins are thoroughly explored by EA, FT-IR, SEM-EDX and PSD. Langmuir isotherm and pseudo-second-order equation could satisfactorily describe the batch experimental data, based on which the equilibrium and kinetic parameters are calculated and compared. The adsorption capacities follow the order of Cu(II)>Pb(II)>Cd(II), due to the complicated impacts of metal ion electronegativity as well as resin pore textures. In the contrast of single and binary adsorption performances, more reduction of Cd(II) than Cu(II) is expectably investigated with the coexistence of competitive ion since the less affinity and hence weak competition of the former onto solid-phase. Using aqueous solution of 15 wt% HCl, nearly 100% recovery of Cu(II) and Cd(II) from IDA-resins could be strictly achieved in the column-tests. Furthermore, a schematic illustration of possible pore structure has been proposed and simulated. Meanwhile, the interaction mechanisms are thereby deduced and evidently confirmed by FT-IR as well as SEM analysis.

  9. Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity

    SciTech Connect

    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.

    2015-10-26

    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. In this paper, 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. Finally, 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.

  10. Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity

    DOE PAGES

    Long, Feng; Fong, Rachel H.; Austin, Stephen K.; ...

    2015-10-26

    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. In this paper, 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 ofmore » 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. Finally, 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.« less

  11. Crystal structure of Staphylococcus aureus transglycosylase in complex with a lipid II analog and elucidation of peptidoglycan synthesis mechanism.

    PubMed

    Huang, Chia-Ying; Shih, Hao-Wei; Lin, Li-Ying; Tien, Yi-Wen; Cheng, Ting-Jen Rachel; Cheng, Wei-Chieh; Wong, Chi-Huey; Ma, Che

    2012-04-24

    Bacterial transpeptidase and transglycosylase on the surface are essential for cell wall synthesis, and many antibiotics have been developed to target the transpeptidase; however, the problem of antibiotic resistance has arisen and caused a major threat in bacterial infection. The transglycosylase has been considered to be another excellent target, but no antibiotics have been developed to target this enzyme. Here, we determined the crystal structure of the Staphylococcus aureus membrane-bound transglycosylase, monofunctional glycosyltransferase, in complex with a lipid II analog to 2.3 Å resolution. Our results showed that the lipid II-contacting residues are not only conserved in WT and drug-resistant bacteria but also significant in enzymatic activity. Mechanistically, we proposed that K140 and R148 in the donor site, instead of the previously proposed E156, are used to stabilize the pyrophosphate-leaving group of lipid II, and E100 in the acceptor site acts as general base for the 4-OH of GlcNAc to facilitate the transglycosylation reaction. This mechanism, further supported by mutagenesis study and the structure of monofunctional glycosyltransferase in complex with moenomycin in the donor site, provides a direction for antibacterial drugs design.

  12. 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.

  13. NanoSIMS 50 elucidation of the natural element composition in structures of cyanobacteria and their exposure to halogen compounds.

    PubMed

    Eybe, T; Audinot, J N; Bohn, T; Guignard, C; Migeon, H N; Hoffmann, L

    2008-11-01

    NanoSIMS (secondary ion mass spectrometry) is a powerful technique for mapping the elemental composition of a variety of small-scale samples (e.g. in Material Research, Cosmochemistry and Geology). However, its analytical features are making it also valuable to address biological questions. We demonstrate the ability of the NanoSIMS 50 to map elements at subcellular lateral resolution (approx. 50 nm) within cyanobacteria (Anabaena sp. and Cylindrospermum alatosporum) and its feasibility to investigate the uptake of bromine-containing substances (NaBr and deltamethrin). Elemental maps of O, N, P and S were obtained from semi-thin sections of different cell types (chemically fixed and resin-embedded heterocysts, akinetes and vegetative cells). NanoSIMS enabled the detection of various characteristic cell sub-structures and inclusions. A homogenous bromine distribution was detected following NaBr and deltamethrin exposure, at Br-concentrations of 0.05, 0.5 (NaBr) and 0.0025 mmol l(-1) (deltamethrin). NanoSIMS allowed study of the mapping of common elements in cyanobacterial cells and the uptake of NaBr and deltamethrin. These results highlight the potential usefulness of NanoSIMS analysis for tracking elements within cell structures at the nanoscale and the ability to detect marker elements of xenobiotic compounds within exposed organisms.

  14. 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.

  15. The structure of a biosynthetic intermediate of pyrroloquinoline quinone (PQQ) and elucidation of the final step of PQQ biosynthesis.

    PubMed

    Magnusson, Olafur T; Toyama, Hirohide; Saeki, Megumi; Schwarzenbacher, Robert; Klinman, Judith P

    2004-05-05

    Pyrroloquinoline quinone (PQQ) is a tricyclic o-quinone, which serves as a cofactor in several enzyme-catalyzed redox reactions in certain bacteria. PQQ is also important for human health, and its role as a vitamin in mammals has recently been suggested. Although much is known about the function of enzymes that use PQQ as cofactor, relatively little is known about the biosynthesis of this coenzyme. Six gene products in Klebsiella pneumoniae (PqqA-F) are involved in PQQ biosynthesis, and PqqC has been shown to catalyze the last step in the pathway. The chemical structure of the substrate for PqqC has remained elusive and has hampered our understanding of the nature of this reaction. In this report we describe the purification and structure of the substrate as deduced by a number of spectroscopic and chemical methods. The substrate is 3a-(2-amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline-7,9-dicarboxylic acid-a fully reduced derivative of PQQ, which has not undergone ring cyclization. These results show that PqqC catalyzes a novel reaction, which involves ring closure and an amazing eight-electron oxidation of the substrate.

  16. Cryo-EM structures of the mammalian endo-lysosomal TRPML1 channel elucidate the combined regulation mechanism.

    PubMed

    Zhang, Sensen; Li, Ningning; Zeng, Wenwen; Gao, Ning; Yang, Maojun

    2017-09-21

    TRPML1 channel is a non-selective group-2 transient receptor potential (TRP) channel with Ca(2+) permeability. Located mainly in late endosome and lysosome of all mammalian cell types, TRPML1 is indispensable in the processes of endocytosis, membrane trafficking, and lysosome biogenesis. Mutations of TRPML1 cause a severe lysosomal storage disorder called mucolipidosis type IV (MLIV). In the present study, we determined the cryo-electron microscopy (cryo-EM) structures of Mus musculus TRPML1 (mTRPML1) in lipid nanodiscs and Amphipols. Two distinct states of mTRPML1 in Amphipols are added to the closed state, on which could represent two different confirmations upon activation and regulation. The polycystin-mucolipin domain (PMD) may sense the luminal/extracellular stimuli and undergo a "move upward" motion during endocytosis, thus triggering the overall conformational change in TRPML1. Based on the structural comparisons, we propose TRPML1 is regulated by pH, Ca(2+), and phosphoinositides in a combined manner so as to accommodate the dynamic endocytosis process.

  17. Crystal structure of Staphylococcus aureus transglycosylase in complex with a lipid II analog and elucidation of peptidoglycan synthesis mechanism

    PubMed Central

    Huang, Chia-Ying; Shih, Hao-Wei; Lin, Li-Ying; Tien, Yi-Wen; Cheng, Ting-Jen Rachel; Cheng, Wei-Chieh; Wong, Chi-Huey; Ma, Che

    2012-01-01

    Bacterial transpeptidase and transglycosylase on the surface are essential for cell wall synthesis, and many antibiotics have been developed to target the transpeptidase; however, the problem of antibiotic resistance has arisen and caused a major threat in bacterial infection. The transglycosylase has been considered to be another excellent target, but no antibiotics have been developed to target this enzyme. Here, we determined the crystal structure of the Staphylococcus aureus membrane-bound transglycosylase, monofunctional glycosyltransferase, in complex with a lipid II analog to 2.3 Å resolution. Our results showed that the lipid II-contacting residues are not only conserved in WT and drug-resistant bacteria but also significant in enzymatic activity. Mechanistically, we proposed that K140 and R148 in the donor site, instead of the previously proposed E156, are used to stabilize the pyrophosphate-leaving group of lipid II, and E100 in the acceptor site acts as general base for the 4-OH of GlcNAc to facilitate the transglycosylation reaction. This mechanism, further supported by mutagenesis study and the structure of monofunctional glycosyltransferase in complex with moenomycin in the donor site, provides a direction for antibacterial drugs design. PMID:22493270

  18. 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.

  19. Isolation and structure elucidation of natural products of three soft corals and a sponge from the coast of Madagascar.

    PubMed

    Rahelivao, Marie Pascaline; Lübken, Tilo; Gruner, Margit; Kataeva, Olga; Ralambondrahety, Rahanira; Andriamanantoanina, Hanta; Checinski, Marek P; Bauer, Ingmar; Knölker, Hans-Joachim

    2017-03-22

    We investigated the three soft corals Sarcophyton stellatum, Capnella fungiformis and Lobophytum crassum and the sponge Pseudoceratina arabica, which have been collected at the coast of Madagascar. In addition to previously known marine natural products, S. stellatum provided the new (+)-enantiomer of the cembranoid (1E,3E,11E)-7,8-epoxycembra-1,3,11,15-tetraene (2). Capnella fungiformis afforded three new natural products, ethyl 5-[(1E,5Z)-2,6-dimethylocta-1,5,7-trienyl]furan-3-carboxylate (6), ethyl 5-[(1E,5E)-2,6-dimethylocta-1,5,7-trienyl]furan-3-carboxylate (7) and the diepoxyguaiane sesquiterpene oxyfungiformin (9a). The extracts of all three soft corals exhibited moderate activities against the malarial parasite Plasmodium falciparum. Extracts of the sponge Pseudoceratina arabica proved to be very active against a series of Gram-positive and Gram-negative bacteria.

  20. Structural determination of the K14 capsular polysaccharide from an ST25 Acinetobacter baumannii isolate, D46.

    PubMed

    Kenyon, Johanna J; Hall, Ruth M; De Castro, Cristina

    2015-11-19

    The structure of the capsular polysaccharide (CPS) recovered from D46, an extensively antibiotic resistant ST25 Acinetobacter baumannii clinical isolate, was elucidated. The structure was resolved on the basis of NMR spectroscopy and chemical analyses, and was found to contain a branched neutral pentasaccharide with a backbone composed of GalpNAc and Galp residues, all d configured, and a d-Glcp side group. The KL14 gene cluster found in the D46 genome includes genes for four glycosyltransferases but no modules for synthesis of complex sugars, and this is consistent with the structure of K14. The K14 structure and KL14 sequence clarify the relationship between the structure and K locus sequence for A. nosocomialis isolate LUH5541. The identity of the first sugar of the K14 repeat unit (K unit), and the functions of the four encoded glycosyltransferases and Wzy polymerase were predicted.

  1. Conceptual optimization of seismic isolated long span structures

    NASA Astrophysics Data System (ADS)

    Mojolic, Cristian; Petrina, Tudor

    2017-07-01

    This paper presents a conceptual optimization problem for seismic isolated structures with large span roofs. The research proposes that the isolation level should be placed at the top of the columns that support the roof structure. This solution was mainly adopted because of the architectural conception of the model. Three distinct passive isolation systems are proposed in order to reduce the seismic response of the structure. The first case implies the use of Friction Pendulum systems (FP) while the other ones use High Damping Rubber Bearing (HDRB) and Lead Rubber Bearing (LRB) in combination with low friction pot-bearing systems. Using seven sets of accelerograms, the values for the main seismic response parameters are extracted and the efficiency of the system is underlined.

  2. Structural elucidation of the impurities in Enzalutamide bulk drug and the development, validation of corresponding HPLC method.

    PubMed

    Ma, Xingling; Zhou, Wentao; Zou, Qiaogen; Ouyang, Pingkai

    2016-11-30

    As the first approved androgen receptor(AR) signalling inhibitor, Enzalutamide was approved by the US Food and Drug Administration as an anticancer drug used to treat castration-resistant prostate cancer in 2012. In this manuscript, six potential impurities of Enzalutamide including process impurities and degradation products were studied. The structures of six impurities obtained by synthesis were characterized and confirmed by IR, NMR and MS techniques. In addition, an efficient chromatographic method to separate and quantify these impurities was developed, which achieved on Inertsil ODS-3 column (250mm×4.6mm,5μm) in gradient mode with a mixture of acetonitrile and the ammonium acetate buffer (10mM, pH adjusted to 4.0 with glacial acetic acid). The method was validated with respect to specificity, precision, accuracy, and sensitivity and satisfactory result was achieved. The method was demonstrated to be applicable in routine quality control and stability evaluation of Enzalutamide.

  3. Elucidation of the electronic structure of molecules with the help of NMR spin-spin coupling constants: the FH molecule.

    PubMed

    Gräfenstein, Jürgen; Tuttle, Tell; Cremer, Dieter

    2005-03-17

    It is demonstrated how the one-bond NMR spin-spin coupling constant (SSCC) (1)J(FH) can be used as a source of information on the electronic structure of the FH molecule. For this purpose, the best possible agreement between measured and calculated SSCC is achieved by large basis set coupled perturbed density functional theory calculations. Then, the calculated value is dissected into its four Ramsey terms: Fermi contact, the paramagnetic spin-orbit term, the diamagnetic spin-orbit term, and the spin dipole term, which in turn are decomposed into orbital contributions and then described by their spin densities and orbital current densities. In this way, the SSCC gives detailed information about the electronegativity of F, the bond polarity, the bond polarizability, the volume and the polarizability of sigma and pi lone pair orbitals, the s- or p-character of the bond orbital, the nature of the LUMO, and the density distribution around F.

  4. Designer reagents for mass spectrometry-based proteomics: clickable cross-linkers for elucidation of protein structures and interactions.

    PubMed

    Sohn, Chang Ho; Agnew, Heather D; Lee, J Eugene; Sweredoski, Michael J; Graham, Robert L J; Smith, Geoffrey T; Hess, Sonja; Czerwieniec, Gregg; Loo, Joseph A; Heath, James R; Deshaies, Raymond J; Beauchamp, J L

    2012-03-20

    We present novel homobifunctional amine-reactive clickable cross-linkers (CXLs) for investigation of three-dimensional protein structures and protein-protein interactions (PPIs). CXLs afford consolidated advantages not previously available in a simple cross-linker, including (1) their small size and cationic nature at physiological pH, resulting in good water solubility and cell-permeability, (2) an alkyne group for bio-orthogonal conjugation to affinity tags via the click reaction for enrichment of cross-linked peptides, (3) a nucleophilic displacement reaction involving the 1,2,3-triazole ring formed in the click reaction, yielding a lock-mass reporter ion for only clicked peptides, and (4) higher charge states of cross-linked peptides in the gas-phase for augmented electron transfer dissociation (ETD) yields. Ubiquitin, a lysine-abundant protein, is used as a model system to demonstrate structural studies using CXLs. To validate the sensitivity of our approach, biotin-azide labeling and subsequent enrichment of cross-linked peptides are performed for cross-linked ubiquitin digests mixed with yeast cell lysates. Cross-linked peptides are detected and identified by collision induced dissociation (CID) and ETD with linear quadrupole ion trap (LTQ)-Fourier transform ion cyclotron resonance (FTICR) and LTQ-Orbitrap mass spectrometers. The application of CXLs to more complex systems (e.g., in vivo cross-linking) is illustrated by Western blot detection of Cul1 complexes including known binders, Cand1 and Skp2, in HEK 293 cells, confirming good water solubility and cell-permeability.

  5. 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.

  6. Crystal structures of protein phosphatase-1 bound to motuporin and dihydromicrocystin-LA: elucidation of the mechanism of enzyme inhibition by cyanobacterial toxins.

    PubMed

    Maynes, Jason T; Luu, Hue A; Cherney, Maia M; Andersen, Raymond J; Williams, David; Holmes, Charles F B; James, Michael N G

    2006-02-10

    The microcystins and nodularins are tumour promoting hepatotoxins that are responsible for global adverse human health effects and wildlife fatalities in countries where drinking water supplies contain cyanobacteria. The toxins function by inhibiting broad specificity Ser/Thr protein phosphatases in the host cells, thereby disrupting signal transduction pathways. A previous crystal structure of a microcystin bound to the catalytic subunit of protein phosphatase-1 (PP-1c) showed distinct changes in the active site region when compared with protein phosphatase-1 structures bound to other toxins. We have elucidated the crystal structures of the cyanotoxins, motuporin (nodularin-V) and dihydromicrocystin-LA bound to human protein phosphatase-1c (gamma isoform). The atomic structures of these complexes reveal the structural basis for inhibition of protein phosphatases by these toxins. Comparisons of the structures of the cyanobacterial toxin:phosphatase complexes explain the biochemical mechanism by which microcystins but not nodularins permanently modify their protein phosphatase targets by covalent addition to an active site cysteine residue.

  7. Seismic Response Analysis and Design of Structure with Base Isolation

    SciTech Connect

    Rosko, Peter

    2010-05-21

    The paper reports the study on seismic response and energy distribution of a multi-story civil structure. The nonlinear analysis used the 2003 Bam earthquake acceleration record as the excitation input to the structural model. The displacement response was analyzed in time domain and in frequency domain. The displacement and its derivatives result energy components. The energy distribution in each story provides useful information for the structural upgrade with help of added devices. The objective is the structural displacement response minimization. The application of the structural seismic response research is presented in base-isolation example.

  8. Active Narrow-Band Vibration Isolation of Large Engineering Structures

    NASA Technical Reports Server (NTRS)

    Rahman, Zahidul; Spanos, John

    1994-01-01

    We present a narrow-band tracking control method using a variant of the Least Mean Squares (LMS) algorithm to isolate slowly changing periodic disturbances from engineering structures. The advantage of the algorithm is that it has a simple architecture and is relatively easy to implement while it can isolate disturbances on the order of 40-50 dB over decades of frequency band. We also present the results of an experiment conducted on a flexible truss structure. The average disturbance rejection achieved is over 40 dB over the frequency band of 5 Hz to 50 Hz.

  9. Active Narrow-Band Vibration Isolation of Large Engineering Structures

    NASA Technical Reports Server (NTRS)

    Rahman, Zahidul; Spanos, John

    1994-01-01

    We present a narrow-band tracking control method using a variant of the Least Mean Squares (LMS) algorithm to isolate slowly changing periodic disturbances from engineering structures. The advantage of the algorithm is that it has a simple architecture and is relatively easy to implement while it can isolate disturbances on the order of 40-50 dB over decades of frequency band. We also present the results of an experiment conducted on a flexible truss structure. The average disturbance rejection achieved is over 40 dB over the frequency band of 5 Hz to 50 Hz.

  10. Impurity profiling of trandolapril under stress testing: Structure elucidation of by-products and development of degradation pathway.

    PubMed

    Dendeni, M; Cimetiere, N; Amrane, A; Hamida, N Ben

    2012-11-15

    Various regulatory authorities like International Conference on Harmonization (ICH), US Food and Drug Administration, Canadian Drug and Health Agency are emphasizing on the purity requirements and the identification of impurities in active pharmaceutical drugs. Qualification of the impurities is the process of acquiring and evaluating data that establishes biological safety of an individual impurity; thus, revealing the need and scope of impurity profiling of drugs in pharmaceutical research. As no stability-indicating method is available for identification of degradation products of trandolapril, a new angiotensin converting enzyme inhibitor (ACEI), under stress testing, the development of an accurate method is needed for quantification and qualification of degradation products. Ultra high performance liquid chromatography (UPLC) coupled to electrospray tandem mass spectrometry was used for the rapid and simultaneous analysis of trandolapril and its degradation products. Chromatographic separation was achieved in less than 4 min, with improved peak resolution and sensitivity. Thanks to this method, the kinetics of trandolapril degradation under various operating conditions and the characterization of the structure of the by-products formed during stress testing have been determined. Thereafter, a mechanism of trandolapril degradation in acid and neutral conditions, including all the identified products, was then proposed.

  11. Application of the independent molecule model to elucidate the dynamics of structure I methane hydrate: a second report.

    PubMed

    Yoshioki, Shuzo

    2008-06-01

    Two model systems of methane hydrate are constructed. One has a small cage surrounded by 12 large cages. The other has a large cage surrounded by four small cages and ten large cages. Three different H-bonding network patterns between waters are formed, and three random configurations of methane in each cage are chosen. A new method called the surface water fixed model is presented in which the energy minimum conformations for both model systems are preserved close to the X-ray crystallized structure. With normal mode analysis, we calculated frequencies of 2916.6 cm(-1) for a small cage at a centre, 2915.9 cm(-1) not at a centre, and 2911.7 cm(-1) for a large cage at a centre, and 2911.3 cm(-1) not at a centre. These frequencies are in moderate agreement with the corresponding Raman spectra, though not adequate. With our new method, however, it should be possible to improve agreement with the Raman spectra, if a model system vastly larger than the present model systems were constructed.

  12. Application of the independent molecule model to elucidate the dynamics of structure I methane hydrate: a third report.

    PubMed

    Yoshioki, Shuzo

    2009-01-01

    Two new model systems of methane hydrate, larger than the previous systems, are constructed. One consists of 63 small and large cages with a small cage at the centre. The other has 65 small and large cages with a large cage at the centre. Three different H-bonding network patterns between water are formed, and three random orientations of methane in each cage are chosen. Using the surface water fixed method, we obtained the energy minimum conformations, fitted to the X-ray crystallographic structure. With normal mode analysis, we calculated frequencies of 2915.1 cm(-1) for a small cage, and 2911.0 cm(-1) for a large cage. These frequencies are a little nearer to the Raman spectra than were previous model systems. Treating three force constants of anharmonic potential energy and the strength of H-bonding between methane and water as four parameters, we obtained frequencies of 2913.6 cm(-1) for a small cage, a little lower than the Raman, and 2906.6 cm(-1) for a large cage, a little higher than the Raman. The calculations thus almost reach the Raman spectra.

  13. 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

  14. Identification and structure elucidation of a novel antifungal compound produced by Pseudomonas aeruginosa PGPR2 against Macrophomina phaseolina.

    PubMed

    Illakkiam, Devaraj; Ponraj, Paramasivan; Shankar, Manoharan; Muthusubramanian, Shanmugam; Rajendhran, Jeyaprakash; Gunasekaran, Paramasamy

    2013-12-01

    Pseudomonas aeruginosa PGPR2 was found to protect mungbean plants from charcoal rot disease caused by Macrophomina phaseolina. Secondary metabolites from the culture supernatant of P. aeruginosa PGPR2 were extracted with ethyl acetate and the antifungal compound was purified by preparative HPLC using reverse phase chromatography. The purified compound showed antifungal activity against M. phaseolina and other phytopathogenic fungi (Fusarium sp., Rhizoctonia sp. Alternaria sp., and Aspergillus sp.). The structure of the purified compound was determined using (1)H, (13)C, 2D NMR spectra and liquid chromatography-mass spectrometry (LC-MS). Spectral data suggest that the antifungal compound is 3,4-dihydroxy-N-methyl-4-(4-oxochroman-2-yl)butanamide, with the chemical formula C14H17NO5 and a molecular mass of 279. Though chemically synthesized chromanone derivatives have been shown to have antifungal activity, we report for the first time, the microbial production of a chromanone derivative with antifungal activity. This ability of P. aeruginosa PGPR2 makes it a suitable strain for biocontrol.

  15. Genome-Directed Lead Discovery: Biosynthesis, Structure Elucidation, and Biological Evaluation of Two Families of Polyene Macrolactams against Trypanosoma brucei.

    PubMed

    Schulze, Christopher J; Donia, Mohamed S; Siqueira-Neto, Jair L; Ray, Debalina; Raskatov, Jevgenij A; Green, Richard E; McKerrow, James H; Fischbach, Michael A; Linington, Roger G

    2015-10-16

    Marine natural products are an important source of lead compounds against many pathogenic targets. Herein, we report the discovery of lobosamides A-C from a marine actinobacterium, Micromonospora sp., representing three new members of a small but growing family of bacterially produced polyene macrolactams. The lobosamides display growth inhibitory activity against the protozoan parasite Trypanosoma brucei (lobosamide A IC50 = 0.8 μM), the causative agent of human African trypanosomiasis (HAT). The biosynthetic gene cluster of the lobosamides was sequenced and suggests a conserved cluster organization among the 26-membered macrolactams. While determination of the relative and absolute configurations of many members of this family is lacking, the absolute configurations of the lobosamides were deduced using a combination of chemical modification, detailed spectroscopic analysis, and bioinformatics. We implemented a "molecules-to-genes-to-molecules" approach to determine the prevalence of similar clusters in other bacteria, which led to the discovery of two additional macrolactams, mirilactams A and B from Actinosynnema mirum. These additional analogs have allowed us to identify specific structure-activity relationships that contribute to the antitrypanosomal activity of this class. This approach illustrates the power of combining chemical analysis and genomics in the discovery and characterization of natural products as new lead compounds for neglected disease targets.

  16. Screening and structural elucidation of the zwitterionic cocrystal o-picolinic acid with p-nitro aniline

    NASA Astrophysics Data System (ADS)

    Mekala, R.; Jagdish, P.; Mathammal, R.; Sangeetha, K.

    2017-04-01

    The cocrystal was screened by solvent drop grinding method and the crystals were grown by slow evaporation method at ambient conditions. The cocrystal formation of o-picolinic acid with p-nitro aniline was initially analysed by powder X-ray diffraction. Further the structural properties of the grown crystal were confirmed by the single X-ray diffraction which indicates that the cocrystal were connected by the strong N+sbnd H-⋯O hydrogen bond interaction. The cell parameters of the grown crystal were a = 14.2144(5) Å, b = 5.7558(2) Å, c = 16.0539(6) Å. The functional groups were identified using Fourier transform infrared and Raman spectral analysis. The excitation and emission state of the sample was analysed by the UV-Visible and Fluorescence studies. The red emission was observed from the Fluorescence studies. NMR studies revealed the chemical shift of the cocrystal. Thermal stability and its melting behaviour were studied by TGA and DSC analytical techniques. Electrical behaviour was studied using the dielectric studies. The intermolecular charge transfer within the molecule were analysed using HOMO- LUMO plots.

  17. 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.

  18. 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.

  19. Isolation and structural characterization of anthocyanin-furfuryl pigments.

    PubMed

    Sousa, André; Mateus, Nuno; Silva, Artur Manuel Soares; Vivas, Nicolas; Nonier, Marie-Françoise; Pianet, Isabelle; de Freitas, Victor

    2010-05-12

    Condensation reactions of malvidin-3-glucoside with two representative oak wood furanic aldehydes (furfural and methylfurfural) were conducted in wine-like model solutions. Methylfurfural led to the formation of malvidin-3-glucoside-methylfurfural (603 m/z), whereas furfural led to the formation of malvidin-3-glucoside-furfural (589 m/z). The latter was structurally characterized by 1D and 2D NMR, allowing an elucidation of the formation mechanism of these anthocyanin-furanic aldehyde adducts in the absence of flavanols.

  20. Elucidating the role of surface passivating ligand structural parameters in hole wave function delocalization in semiconductor cluster molecules.

    PubMed

    Teunis, Meghan B; Nagaraju, Mulpuri; Dutta, Poulami; Pu, Jingzhi; Muhoberac, Barry B; Sardar, Rajesh; Agarwal, Mangilal

    2017-09-28

    This article describes the mechanisms underlying electronic interactions between surface passivating ligands and (CdSe)34 semiconductor cluster molecules (SCMs) that facilitate band-gap engineering through the delocalization of hole wave functions without altering their inorganic core. We show here both experimentally and through density functional theory calculations that the expansion of the hole wave function beyond the SCM boundary into the ligand monolayer depends not only on the pre-binding energetic alignment of interfacial orbitals between the SCM and surface passivating ligands but is also strongly influenced by definable ligand structural parameters such as the extent of their π-conjugation [π-delocalization energy; pyrene (Py), anthracene (Anth), naphthalene (Naph), and phenyl (Ph)], binding mode [dithiocarbamate (DTC, -NH-CS2(-)), carboxylate (-COO(-)), and amine (-NH2)], and binding head group [-SH, -SeH, and -TeH]. We observe an unprecedentedly large ∼650 meV red-shift in the lowest energy optical absorption band of (CdSe)34 SCMs upon passivating their surface with Py-DTC ligands and the trend is found to be Ph- < Naph- < Anth- < Py-DTC. This shift is reversible upon removal of Py-DTC by triethylphosphine gold(i) chloride treatment at room temperature. Furthermore, we performed temperature-dependent (80-300 K) photoluminescence lifetime measurements, which show longer lifetime at lower temperature, suggesting a strong influence of hole wave function delocalization rather than carrier trapping and/or phonon-mediated relaxation. Taken together, knowledge of how ligands electronically interact with the SCM surface is crucial to semiconductor nanomaterial research in general because it allows the tuning of electronic properties of nanomaterials for better charge separation and enhanced charge transfer, which in turn will increase optoelectronic device and photocatalytic efficiencies.

  1. Elucidation of the mechanism and end products of glutaraldehyde crosslinking reaction by X-ray structure analysis.

    PubMed

    Wine, Yariv; Cohen-Hadar, Noa; Freeman, Amihay; Frolow, Felix

    2007-10-15

    Glutaraldehyde has been used for several decades as an effective crosslinking agent for many applications including sample fixation for microscopy, enzyme and cell immobilization, and stabilization of protein crystals. Despite of its common use as a crosslinking agent, the mechanism and chemistry involved in glutaraldehyde crosslinking reaction is not yet fully understood. Here we describe feasibility study and results obtained from a new approach to investigate the process of protein crystals stabilization by glutaraldehyde crosslinking. It involves exposure of a model protein crystal (Lysozyme) to glutaraldehyde in alkaline or acidic pH for different incubation periods and reaction arrest by medium exchange with crystallization medium to remove unbound glutaraldehyde. The crystals were subsequently incubated in diluted buffer affecting dissolution of un-crosslinked crystals. Samples from the resulting solution were subjected to protein composition analysis by gel electrophoresis and mass spectroscopy while crosslinked, dissolution resistant crystals were subjected to high resolution X-ray structural analysis. Data from gel electrophoresis indicated that the crosslinking process starts at specific preferable crosslinking site by lysozyme dimer formation, for both acidic and alkaline pH values. These dimer formations were followed by trimer and tetramer formations leading eventually to dissolution resistant crystals. The crosslinking initiation site and the end products obtained from glutaraldehyde crosslinking in both pH ranges resulted from reactions between lysine residues of neighboring protein molecules and the polymeric form of glutaraldehyde. Reaction rate was much faster at alkaline pH. Different reaction end products, indicating different reaction mechanisms, were identified for crosslinking taking place under alkaline or acidic conditions.

  2. Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition.

    PubMed

    Davis, Katherine M; Schramma, Kelsey R; Hansen, William A; Bacik, John P; Khare, Sagar D; Seyedsayamdost, Mohammad R; Ando, Nozomi

    2017-09-26

    Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. Here, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine-tryptophan cross-link, which is installed by the radical S-adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the active site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon-carbon cross-link in the streptide family of natural products.

  3. 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

  4. Two dimensional laser induced fluorescence spectroscopy: a powerful technique for elucidating rovibronic structure in electronic transitions of polyatomic molecules.

    PubMed

    Gascooke, Jason R; Alexander, Ula N; Lawrance, Warren D

    2011-05-14

    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 S(1)-S(0) 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)]. Comparison with earlier ab initio calculations of the S(0) and S(1) geometries [I. Pugliesi, N. M. Tonge, and M. C. R. Cockett, J. Chem. Phys. 129, 104303 (2008)] 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-d(1) in natural abundance in

  5. 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.

  6. 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.

  7. Dynamics, energetics, and structure of microclusters: Elucidating the physical basis for catalysis and surface chemistry, reactions in condensed phases, and aerosol formation: Final technical report

    SciTech Connect

    Castleman, A.W. Jr.

    1988-01-01

    In order to provide a data base for understanding of the mechanisms of gas-to-particle conversion and the nature and potential importance of heterogeneous reactions on surfaces, in droplets, and within the aqueous phase surrounding aerosol particles, we undertook an investigation of the dynamics of formation, energetics, and structure of microclusters of both neutral and ionized systems. The major thrust of the work conducted under the DOE grant was directed to an investigation of the basic processes responsible for aerosol formation and the chemical behavior of aerosol particles. Particular attention was focused on determining the properties of molecular clusters as a means to provide information on the changes in the properties of matter as it evolves from gaseous to particulate components. This information is also important in elucidating the processes by which substances that enter the environment as gases become associated with condensed phases. 38 refs., 3 figs.

  8. Dhilirolides E-N, meroterpenoids produced in culture by the fungus Penicillium purpurogenum collected in Sri Lanka: structure elucidation, stable isotope feeding studies, and insecticidal activity.

    PubMed

    Centko, Ryan M; Williams, David E; Patrick, Brian O; Akhtar, Yasmin; Garcia Chavez, Miguel Angel; Wang, Yan Alexander; Isman, Murray B; de Silva, E Dilip; Andersen, Raymond J

    2014-04-18

    Extracts of laboratory cultures of the fungus Penicilium purpurogenum obtained from rotting fruit of the tree Averrhoa bilimbi growing in Sri Lanka have yielded 10 new meroterpenoids, dhilirolides E-N (5-14). The structures of the new dhilirolides have been elucidated by analysis of spectroscopic data and a single-crystal X-ray diffraction analysis of dhilirolide L (12). Dhilirolides A-N (1-14) represent the four unprecedented and rearranged dhilirane, isodhilirane, 14,15-dinordhilirane, and 23,24-dinorisodhilirane meroterpenoid carbon skeletons. Stable isotope feeding studies have confirmed the meroterpenoid biogenetic origin of the dhilirolides and provided support for a proposed genesis of the new carbon skeletons. Dhilirolide L (12) showed significant feeding inhibition and sublethal developmental disruption in the cabbage looper Trichoplusia ni, an important agricultural pest, at low concentrations.

  9. Inelastic neutron scattering studies of 132,134Xe: Elucidating structure in a transitional region and possible interferences for 0vββ searches

    NASA Astrophysics Data System (ADS)

    Peters, E. E.; Ross, T. J.; Crider, B. P.; Ashley, S. F.; Chakraborty, A.; Hennek, M. D.; Kumar, A.; Liu, S. H.; McEllistrem, M. T.; Prados-Estévez, F. M.; Thrasher, J. S.; Yates, S. W.

    2015-05-01

    Highly enriched (> 99.9%) 132Xe and 134Xe gases were converted to solid 132XeF2 and 134XeF2 and were used as scattering samples for inelastic neutron scattering measurements at the University of Kentucky Accelerator Laboratory (UKAL). Lifetimes of levels up to 3.5MeV in excitation energy in these xenon isotopes were measured using the Doppler-shift attenuation method, allowing the determination of reduced transition probabilities. Gamma rays corresponding to new transitions and levels have been observed. In particular, tentative new excited 0+ states and associated decays have been examined in an effort to elucidate the structure of these nuclei in a transitional region, and comparisons have been drawn with models which seek to describe such nuclei, e.g., the E(5) critical-point symmetry of the IBM. Newly identified potential interferences for neutrinoless double-beta decay searches involving 136Xe are also discussed.

  10. Rhodomyrtials A and B, Two Meroterpenoids with a Triketone-Sesquiterpene-Triketone Skeleton from Rhodomyrtus tomentosa: Structural Elucidation and Biomimetic Synthesis.

    PubMed

    Zhang, Ya-Long; Chen, Chen; Wang, Xiao-Bing; Wu, Lin; Yang, Ming-Hua; Luo, Jun; Zhang, Can; Sun, Hong-Bin; Luo, Jian-Guang; Kong, Ling-Yi

    2016-08-19

    Rhodomyrtials A and B (1 and 2), two unprecedented triketone-sesquiterpene-triketone adducts, along with five biogenetically related intermediates, rhodomentone A (3) and tomentodiones A-D (4-7), were isolated from the leaves of Rhodomyrtus tomentosa. Their structures and absolute configurations were determined by a combination of NMR spectroscopy, chemical conversion, and X-ray diffraction analysis. Compounds 1 and 2 were biomimetically synthesized via 5 and 4, respectively, rather than 3, revealing their key ordering of biosynthetic events and confirming their structural assignments. Compound 7 exhibited potent metastatic inhibitory activity against DLD-1 cells by suppressing the activation of matrix metalloproteinase (MMP)-2 and MMP-9.

  11. Louisianins A, B, C and D: non-steroidal growth inhibitors of testosterone-responsive SC 115 cells. II. Physico-chemical properties and structural elucidation.

    PubMed

    Takamatsu, S; Kim, Y P; Hayashi, M; Furuhata, K; Takayanagi, H; Komiyama, K; Woodruff, H B; Omura, S

    1995-10-01

    New non-steroidal growth inhibitors of testosterone-responsive SC 115 cells, louisianins A (MW: 189; C11H11NO2), B (MW: 191; C11H13NO2), C (MW: 173; C11H11NO) and D (MW: 173; C11H11NO) were isolated from the cultured broth of Streptomyces sp. WK-4028. Their structures were determined on the basis of spectroscopic data. The structure of louisianin A in particular was confirmed by X-ray crystallographic analysis. The four compounds commonly possess a unique pyrindine skeleton in the molecule.

  12. 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 Central

    Dalvi, Sonal; Azetsu, Sei; Patrauchan, Marianna A.; Aktas, Deniz F.

    2012-01-01

    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. PMID:22885747

  13. 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 ...

  14. Structure elucidation of chlorophyll catabolites (phyllobilins) by ESI-mass spectrometry-Pseudo-molecular ions and fragmentation analysis of a nonfluorescent chlorophyll catabolite (NCC).

    PubMed

    Müller, Thomas; Vergeiner, Stefan; Kräutler, Bernhard

    2014-05-15

    The hyphenation of high performance chromatography with modern mass spectrometric techniques providing high-resolution data as well as structural information from MS/MS experiments has become a versatile tool for rapid natural product identification and characterization. A recent application of this methodology concerned the investigation of the annually occurring degradation of green plant pigments. Since the first structural elucidation of a breakdown product in the early 1990s, a number of similarly structured, tetrapyrrolic catabolites have been discovered with the help of chromatographic, spectroscopic and spectrometric methods. A prerequisite for a satisfactory, manually operated or database supported analysis of mass spectrometric fragmentation patterns is a deeper knowledge of the underlying gas phase chemistry. Still, a thorough investigation of the common fragmentation behavior of these ubiquitous, naturally occurring chlorophyll breakdown products is lacking. This study closes the gap and gives a comprehensive overview of collision-induced fragmentation reactions of a tetrapyrrolic nonfluorescent chlorophyll catabolite, which is intended to serve as a model compound for the substance class of phyllobilins.

  15. Structural insights into dynamics of RecU-HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state.

    PubMed

    Khavnekar, Sagar; Dantu, Sarath Chandra; Sedelnikova, Svetlana; Ayora, Sylvia; Rafferty, John; Kale, Avinash

    2017-01-25

    Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essential N-terminal region (NTR) previously unseen in our DNA unbound structure. The flexible nature of the NTR in solution was confirmed using SAXS. Thermofluor studies performed to assess the stability of RecU in complex with the arms of an HJ indicate that it confers stability. Further, we performed molecular dynamics (MD) simulations of wild type and an NTR deletion variant of RecU, with and without HJ. The NTR is observed to be highly flexible in simulations of the unbound RecU, in agreement with SAXS observations. These simulations revealed domain dynamics of RecU and their role in the formation of complex with HJ. The MD simulations also elucidate key roles of the NTR, stalk region, and breathing motion of RecU in the formation of the reactive state.

  16. Structural insights into dynamics of RecU–HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state

    PubMed Central

    Khavnekar, Sagar; Dantu, Sarath Chandra; Sedelnikova, Svetlana; Ayora, Sylvia; Rafferty, John; Kale, Avinash

    2017-01-01

    Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essential N-terminal region (NTR) previously unseen in our DNA unbound structure. The flexible nature of the NTR in solution was confirmed using SAXS. Thermofluor studies performed to assess the stability of RecU in complex with the arms of an HJ indicate that it confers stability. Further, we performed molecular dynamics (MD) simulations of wild type and an NTR deletion variant of RecU, with and without HJ. The NTR is observed to be highly flexible in simulations of the unbound RecU, in agreement with SAXS observations. These simulations revealed domain dynamics of RecU and their role in the formation of complex with HJ. The MD simulations also elucidate key roles of the NTR, stalk region, and breathing motion of RecU in the formation of the reactive state. PMID:27903910

  17. Structured residual technique for malfunction isolation in interacting systems

    SciTech Connect

    Hardy, C.R.; Miller, D.W.; Hajek, B.K. )

    1992-01-01

    Researchers in the field of fault detection and isolation have presented schemes for diagnosing faults in systems in the presence of unknown input disturbances. These techniques, known collectively as input disturbance decoupling, can be used to isolate a particular system from other systems in a complex process plant. The ability to isolate the operation of a system from systems with which it interacts is desirable when diagnosing faults in complex plants. The diagnosis problem can then be broken down into a set of relatively simple diagnostic tasks and the results evaluated using a knowledge-based approach. One such approach, known as hierarchical classification, has been used for malfunction diagnosis in both nuclear power and chemical plants. Systems that strongly interact are common in nuclear power plants. For example, in the simplified boiling water reactor (BWR) pressure control system (PCS) model of Fig. 1, steam flow from the main steam lines collects in the steam header. The header acts as a source of steam to several plant systems besides the high-pressure turbine. Thus, a change in any one of these auxiliary systems will affect the operation of the PCS. These unmeasured influences complicate the problem of isolating the PCS from the remainder of the plant. The authors have used structured residuals as a disturbance decoupling technique to isolate interacting systems in a BWR model. In this paper, we provide a brief summary of the method and show an example of its application.

  18. Comparison of chitin structures isolated from seven Orthoptera species.

    PubMed

    Kaya, Murat; Erdogan, Sevil; Mol, Abbas; Baran, Talat

    2015-01-01

    Differences in the physichochemical properties of the chitin structure of the exoskeleton of seven species from four genera were investigated in this study. The same method was used to isolate the chitin structure of the seven species. The physicochemical properties of the isolated chitins were revealed by ESEM, FTIR, TGA and XRD analyses. The FTIR, TGA and XRD results from the chitin samples were similar. The surface morphologies of the chitins were investigated by ESEM and interesting results were noted. While the surface morphologies of the chitins isolated from two species within the same genus were quite different, the surface morphologies of chitins isolated from species belonging to different genera showed similarity. It was determined that the dry weight chitin contents of the grasshopper species varied between 5.3% and 8.9%. The results of molecular analysis showed that the chitins from seven Orthoptera species (between 5.2 and 6.8 kDa) have low molecular weights. Considering that these invasive and harmful species are killed with insecticides and go to waste in large amounts, this study suggests that they should be collected and evaluated as an alternative chitin source.

  19. Elucidating connectivity and metal-binding structures of unlabeled paramagnetic complexes by 13C and 1H solid-state NMR under fast magic angle spinning.

    PubMed

    Wickramasinghe, Nalinda P; Shaibat, Medhat A; Ishii, Yoshitaka

    2007-08-23

    Characterizing paramagnetic complexes in solids is an essential step toward understanding their molecular functions. However, methodologies to characterize chemical and electronic structures of paramagnetic systems at the molecular level have been notably limited, particularly for noncrystalline solids. We present an approach to obtain connectivities of chemical groups and metal-binding structures for unlabeled paramagnetic complexes by 13C and 1H high-resolution solid-state NMR (SSNMR) using very fast magic angle spinning (VFMAS, spinning speed >or=20 kHz). It is experimentally shown for unlabeled Cu(II)(Ala-Thr) that 2D 13C/1H correlation SSNMR under VFMAS provides the connectivity of chemical groups and assignments for the characterization of unlabeled paramagnetic systems in solids. We demonstrate that on the basis of the assignments provided by the VFMAS approach multiple 13C-metal distances can be simultaneously elucidated by a combination of measurements of 13C anisotropic hyperfine shifts and 13C T1 relaxation due to hyperfine interactions for this peptide-Cu(II) complex. It is also shown that an analysis of 1H anisotropic hyperfine shifts allows for the determination of electron-spin states in Fe(III)-chloroprotoporphyin-IX in solid states.

  20. Collision-induced dissociation of the A + 2 isotope ion facilitates glucosinolates structure elucidation by electrospray ionization-tandem mass spectrometry with a linear quadrupole ion trap.

    PubMed

    Cataldi, Tommaso R I; Lelario, Filomena; Orlando, Donatella; Bufo, Sabino A

    2010-07-01

    An approach is presented that can be of general applicability for structural elucidation of naturally occurring glucosinolates (GLSs) in crude plant extracts based on the fragmentation of isotopic A and A + 2 peaks. The most important fragmentation pathways were studied by tandem mass spectrometry (MS(n), n = 2, 3) using a linear quadrupole ion trap (LTQ) upon GLSs separation by optimized reversed-phase liquid chromatography (RPLC) and electrospray ionization (ESI) in negative ion mode. As the LTQ MS analyzer ensures high sensitivity and linearity, the fragmentation behavior under collision induced dissociation (CID) of the isotopic peaks A and A + 2 as precursor ions was carefully examined. All GLSs (R-C(7)H(11)O(9)NS(2)(-)) share a common structure with at least two sulfur atoms and significant isotopic abundance of (34)S. Thus, dissociation of the +2 Da isotopomeric ions results in several fragment ion doublets containing a combination of (32)S and (34)S. Accordingly, their relative abundances allow one to speed up the structural recognition of GLSs with great confidence, as it produces more structurally informative ions than conventional tandem MS performed on A ions. This approach has been validated on known GLSs bearing two, three, four, and six sulfur atoms by comparing expected and measured isotopic peak abundance ratios (I(A)/I(A)(+2)). Both group- and compound-specific fragments were observed; the predominant pathway of fragmentation of GLSs gives rise to species having the following m/z values, [M - SO(3) - H](-), [M - 196 - H](-), [M - 178 - H](-), and [M - 162 - H](-) after H rearrangement from the R- side chain. The present strategy was successfully applied to extracts of rocket salad leaves (Eruca sativa L.), which was sufficient for the chemical identification of a not already known 6-methylsulfonyl-3-oxohexyl-GLS, a long-chain-length aliphatic glucosinolate, which contains three sulfurs and exhibits a deprotonated molecular ion at m/z 494.1.