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Sample records for acid covalently bound

  1. On the biosynthesis of free and covalently bound PQQ. Glutamic acid decarboxylase from Escherichia coli is a pyridoxo-quinoprotein.

    PubMed

    van der Meer, R A; Groen, B W; Duine, J A

    1989-03-27

    Analysis of glutamic acid decarboxylase (GDC) (EC 4.1.1.15) from Escherichia coli ATCC 11246 revealed the presence of six pyridoxal phosphates (PLPs) as well as six covalently bound pyrroloquinoline quinones (PQQs) per hexameric enzyme molecule. This is the second example of a pyridoxo-quinoprotein, suggesting that other atypical pyridoxoproteins (PLP-containing enzymes) have similar cofactor composition. Since the organism did not produce free PQQ and its quinoprotein glucose dehydrogenase was present in the apo form, free PQQ is not used in the assemblage of GDC. Most probably, biosynthesis of covalently bound cofactor occurs in situ via a route which is different from that of free PQQ. Thus, organisms previously believed to be unable to synthesize (free) PQQ could in fact be able to produce quinoproteins with covalently bound cofactor. Implications for the role of PQQ in eukaryotic cells are discussed.

  2. Hydrogen-bond acidic functionalized carbon nanotubes (CNTs) with covalently-bound hexafluoroisopropanol groups

    SciTech Connect

    Fifield, Leonard S.; Grate, Jay W.

    2010-06-01

    Fluorinated hydrogen-bond acidic groups are directly attached to the backbone of single walled carbon nanotubes (SWCNTs) without the introduction of intermediate electron donating surface groups. Hexafluoroalcohol functional groups are exceptionally strong hydrogen bond acids, and are added to the nanotube surface using the aryl diazonium approach to create hydrogen-bond acidic carbon nanotube (CNT) surfaces. These groups can promote strong hydrogen-bonding interactions with matrix materials in composites or with molecular species to be concentrated and sensed. In the latter case, this newly developed material is expected to find useful application in chemical sensors and in CNT-based preconcentrator devices for the detection of pesticides, chemical warfare agents and explosives.

  3. Nutritional and clinical evaluation of a modified soy protein with covalently bound branched-chain amino acids in cirrhotic sprague-dawley rats.

    PubMed

    Rodríguez, M F; Wall, A; Kondrup, J; López-Cervantes, G; Calderón de la Barca, A M

    2003-01-01

    Several studies suggested that branched-chain amino acids (BCAA) improve plasma amino acid imbalance as well as protein metabolism in patients with cirrhosis. However, commercial formulas supplemented with free BCAA have their limitations. We evaluated a modified soy protein diet with covalently bound BCAA (diet M) by comparing it with diets based on casein (diet C) or Hepatic Aid II (diet H; commercial formula) as protein sources. After 3 weeks of bile duct obstruction, 24 Sprague-Dawley rats divided into three groups received diets with 9% (w/w) protein/amino acids for 7 days. Nutritional and clinical parameters were determined. Nitrogen balance and weight gain (g)/protein intake (g) with diet M (0.19 +/- 0.31 and 1.33 +/- 1.43 g, respectively) were significantly higher (p < 0.05) than with diet H (-0.34 +/- 0.20 and -0.34 +/- 1.11 g), but comparable to those with diet C (0.04 +/- 0.38 and 0.20 +/- 0.93 g). Animals on diet M had a significantly (p < 0.05) increased plasma BCAA:aromatic amino acid ratio (1.8 +/- 0.3) as compared with those on diets H (1.3 +/- 0.1) and C (0.8 +/- 0.0). There were no significant differences in organ weight or liver function among the groups. We conclude that the BCAA-modified protein is an attractive option in the nutritional support of patients having cirrhosis.

  4. A component of the mitochondrial outer membrane proteome of T. brucei probably contains covalent bound fatty acids.

    PubMed

    Albisetti, Anna; Wiese, Sebastian; Schneider, André; Niemann, Moritz

    2015-08-01

    A subclass of eukaryotic proteins is subject to modification with fatty acids, the most common of which are palmitic and myristic acid. Protein acylation allows association with cellular membranes in the absence of transmembrane domains. Here we examine POMP39, a protein previously described to be present in the outer mitochondrial membrane proteome (POMP) of the protozoan parasite Trypanosoma brucei. POMP39 lacks canonical transmembrane domains, but is likely both myristoylated and palmitoylated on its N-terminus. Interestingly, the protein is also dually localized on the surface of the mitochondrion as well as in the flagellum of both insect-stage and the bloodstream form of the parasites. Upon abolishing of global protein acylation or mutation of the myristoylation site, POMP39 relocates to the cytosol. RNAi-mediated ablation of the protein neither causes a growth phenotype in insect-stage nor bloodstream form trypanosomes.

  5. Fluoride-Mediated Capture of a Noncovalent Bound State of a Reversible Covalent Enzyme Inhibitor: X-ray Crystallographic Analysis of an Exceptionally Potent [alpha]-Ketoheterocycle Inhibitor of Fatty Acid Amide Hydrolase

    SciTech Connect

    Mileni, Mauro; Garfunkle, Joie; Ezzili, Cyrine; Cravatt, Benjamin F.; Stevens, Raymond C.; Boger, Dale L.

    2011-11-02

    Two cocrystal X-ray structures of the exceptionally potent {alpha}-ketoheterocycle inhibitor 1 (K{sub i} = 290 pM) bound to a humanized variant of rat fatty acid amide hydrolase (FAAH) are disclosed, representing noncovalently and covalently bound states of the same inhibitor with the enzyme. Key to securing the structure of the noncovalently bound state of the inhibitor was the inclusion of fluoride ion in the crystallization conditions that is proposed to bind the oxyanion hole precluding inhibitor covalent adduct formation with stabilization of the tetrahedral hemiketal. This permitted the opportunity to detect important noncovalent interactions stabilizing the binding of the inhibitor within the FAAH active site independent of the covalent reaction. Remarkably, noncovalently bound 1 in the presence of fluoride appears to capture the active site in the same 'in action' state with the three catalytic residues Ser241-Ser217-Lys142 occupying essentially identical positions observed in the covalently bound structure of 1, suggesting that this technique of introducing fluoride may have important applications in structural studies beyond inhibiting substrate or inhibitor oxyanion hole binding. Key insights to emerge from the studies include the observations that noncovalently bound 1 binds in its ketone (not gem diol) form, that the terminal phenyl group in the acyl side chain of the inhibitor serves as the key anchoring interaction overriding the intricate polar interactions in the cytosolic port, and that the role of the central activating heterocycle is dominated by its intrinsic electron-withdrawing properties. These two structures are also briefly compared with five X-ray structures of {alpha}-ketoheterocycle-based inhibitors bound to FAAH recently disclosed.

  6. Covalently Bound Nitroxyl Radicals in an Organic Framework.

    PubMed

    Hughes, Barbara K; Braunecker, Wade A; Bobela, David C; Nanayakkara, Sanjini U; Reid, Obadiah G; Johnson, Justin C

    2016-09-15

    A series of covalent organic framework (COF) structures is synthesized that possesses a tunable density of covalently bound nitroxyl radicals within the COF pores. The highest density of organic radicals produces an electron paramagnetic resonance (EPR) signal that suggests the majority of radicals strongly interact with other radicals, whereas for smaller loadings the EPR signals indicate the radicals are primarily isolated but with restricted motion. The dielectric loss as determined from microwave absorption of the framework structures compared with an amorphous control suggests that free motion of the radicals is inhibited when more than 25% of available sites are occupied. The ability to tune the mode of radical interactions and the subsequent effect on redox, electrical, and optical characteristics in a porous framework may lead to a class of structures with properties ideal for photoelectrochemistry or energy storage.

  7. Covalently Bound Nitroxyl Radicals in an Organic Framework.

    PubMed

    Hughes, Barbara K; Braunecker, Wade A; Bobela, David C; Nanayakkara, Sanjini U; Reid, Obadiah G; Johnson, Justin C

    2016-09-15

    A series of covalent organic framework (COF) structures is synthesized that possesses a tunable density of covalently bound nitroxyl radicals within the COF pores. The highest density of organic radicals produces an electron paramagnetic resonance (EPR) signal that suggests the majority of radicals strongly interact with other radicals, whereas for smaller loadings the EPR signals indicate the radicals are primarily isolated but with restricted motion. The dielectric loss as determined from microwave absorption of the framework structures compared with an amorphous control suggests that free motion of the radicals is inhibited when more than 25% of available sites are occupied. The ability to tune the mode of radical interactions and the subsequent effect on redox, electrical, and optical characteristics in a porous framework may lead to a class of structures with properties ideal for photoelectrochemistry or energy storage. PMID:27583443

  8. Antiviral effect of interferon covalently bound to sepharose.

    PubMed

    Ankel, H; Chany, C; Galliot, B; Chevalier, M J; Robert, M

    1973-08-01

    Interferon, covalently bound to Sepharose 4B activated by cyanogen bromide, induces the antiviral state in sensitive cells. The antiviral effect is neutralized by antiserum specific to interferon and is recovered thereafter when the antibody is detached from the interferon by treatment at low pH. Binding interferon to Sepharose increases the stability of the molecule. It is likely that the interferon molecule acts on the cell receptor without being detached from the beads. However, the data do not exclude the possibility of a small loss of interferon, or fragments of it, after contact with the cell.

  9. Spin Labeling ESR Investigation of Covalently Bound Residues in Soil

    NASA Astrophysics Data System (ADS)

    Aleksandrova, Olga; Steinhoff, Heinz-Juergen; Klasmeier, Joerg; Schulz, Marcus; Matthies, Michael

    2013-04-01

    Organic xenobiotic chemicals, such as pesticides, biocides and veterinary pharmaceuticals, interact with soil, which results in the simultaneous formations of metabolites, mineralization products, and bound or non-extractable residues (NER). Substances or metabolites with reactive functional groups, such as aniline or phenol, have a tendency to give a larger proportion of NER. Despite numerous studies on NER, the majority of their chemical structures is still unknown. Reversible sequestration and irreversible formation of NER were also observed for veterinary antibiotic pharmaceuticals, after their application to soil with and without manure. For this purpose, we hypothesized a key role of specific functional groups of soil contaminants, via which contaminants are covalently bound to soil constituents, and advance a method of spin labeling ESR investigation of reaction products using a membrane method. Spin labels (SL) represent chemically stable paramagnetic molecules used as molecular labels and molecular probes for testing the covalent binding, structural properties, and molecular mobility of different physical, chemical, and biological systems. In the case of covalent binding of SL, their ESR spectra become broadened. We used stable nitroxide radicals (NR) as SL. These radicals modeled organic chemical contaminants and differed only in one functional group. The paramagnetic SL 4-Amino Tempo (4-amino-2,2,6,6-tetramethyl-1-piperidinylox) differed from Tempo (2,2,6,6-Tetramethylpiperidinooxy) in a substituent at the para-position of the piperidine ring, whereas Aniline Tempo (1-Piperidinyloxy, 2,2,6,-tetramethyl, 6-Aniline) differed from Tempo in an Aniline substituting one CH3 functional group. Before experimental analysis, we tested temporal changes in the concentration of both NR incubated with soil and found that the life-times of them in soil exceeded 3 days. We contaminated and labeled soil samples with NR, adding to soil the aqueous solution, which already

  10. Comparative biochemical characterization of peroxidases (class III) tightly bound to the maize root cell walls and modulation of the enzyme properties as a result of covalent binding.

    PubMed

    Hadži-Tašković Šukalović, Vesna; Vuletić, Mirjana; Marković, Ksenija; Cvetić Antić, Tijana; Vučinić, Željko

    2015-01-01

    Comparative biochemical characterization of class III peroxidase activity tightly bound to the cell walls of maize roots was performed. Ionically bound proteins were solubilized from isolated walls by salt washing, and the remaining covalently bound peroxidases were released, either by enzymatic digestion or by a novel alkaline extraction procedure that released covalently bound alkali-resistant peroxidase enzyme. Solubilized fractions, as well as the salt-washed cell wall fragments containing covalently bound proteins, were analyzed for peroxidase activity. Peroxidative and oxidative activities indicated that peroxidase enzymes were predominately associated with walls by ionic interactions, and this fraction differs from the covalently bound one according to molecular weight, isozyme patterns, and biochemical parameters. The effect of covalent binding was evaluated by comparison of the catalytic properties of the enzyme bound to the salt-washed cell wall fragments with the corresponding solubilized and released enzyme. Higher thermal stability, improved resistance to KCN, increased susceptibility to H2O2, stimulated capacity of wall-bound enzyme to oxidize indole-3-acetic acid (IAA) as well as the difference in kinetic parameters between free and bound enzymes point to conformational changes due to covalent binding. Differences in biochemical properties of ionically and covalently bound peroxidases, as well as the modulation of the enzyme properties as a result of covalent binding to the walls, indicate that these two fractions of apoplastic peroxidases play different roles.

  11. Synthesis and characterization of covalently bound benzocaine graphite oxide derivative

    NASA Astrophysics Data System (ADS)

    Kabbani, Ahmad; Kabbani, Mohamad; Safadi, Khadija

    2015-09-01

    Graphite oxide (GO) derived materials include chemically functionalize or reduced graphene oxide (exfoliated from GO) sheets, assembled paper-like forms , and graphene-based composites GO consists of intact graphitic regions interspersed with sp3-hybridized carbons containing hydroxyl and epoxide functional groups on the top and bottom surfaces of each sheet and sp2-hybridized carbons containing carboxyl and carbonyl groups mostly at the sheet edges. Hence, GO is hydrophilic and readily disperses in water to form stable colloidal suspensions Due to the attached oxygen functional groups, GO was used to prepare different derivatives which result in some physical and chemical properties that are dramatically different from their bulk counterparts .The present work discusses the covalent cross linking of graphite oxide to benzocaine or ethyl ester of para-aminobenzoic acid,structure I,used in many over-the-counter ointment drug.Synthesis is done via diazotization of the amino group.The product is characterized via IR,Raman, X-ray photoelectron spectroscopy as well as electron microscopy.

  12. Detection of free and covalently bound microcystins in animal tissues by liquid chromatography-tandem mass spectrometry.

    PubMed

    Neffling, Milla-Riina; Lance, Emilie; Meriluoto, Jussi

    2010-03-01

    Microcystins are cyanobacterial hepatotoxins capable of accumulation into animal tissues. The toxins act by inhibiting specific protein phosphatases and both non-covalent and covalent interactions occur. The 2-methyl-3-methoxy-4-phenylbutyric acid (MMPB) method determines the total, i.e. the sum of free and protein-bound microcystin in tissues. The aim of the method development in this paper was to tackle the problems with the MMPB methodology: the rather laborious workflow and the loss of material during different steps of the method. In the optimised workflow the oxidation recovery was of acceptable level (29-40%), the extraction efficiency good (62-97%), but the signal suppression effect from the matrix remained severe in our system (16-37% signal left). The extraction efficiency for the determination of the free, extractable microcystins, was found to be good, 52-100%, depending on the sample and the toxin variant and concentration.

  13. Nucleic acid duplexes incorporating a dissociable covalent base pair

    NASA Technical Reports Server (NTRS)

    Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    1999-01-01

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

  14. Nucleic acid duplexes incorporating a dissociable covalent base pair.

    PubMed

    Gao, K; Orgel, L E

    1999-12-21

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure. PMID:10611299

  15. Bovine serum amine oxidase: a mammalian enzyme having covalently bound PQQ as prosthetic group.

    PubMed

    Lobenstein-Verbeek, C L; Jongejan, J A; Frank, J; Duine, J A

    1984-05-21

    In addition to the metal ion, copper-containing amine oxidases possess an organic prosthetic group, the nature of which has long been controversial. We show here that in the case of bovine plasma amine oxidase, this second prosthetic group is covalently bound pyrroloquinoline quinone ( PQQ ). Until now the coenzyme PQQ has been found in several bacterial dehydrogenases. Thus the finding reported here is the first example of a quinoprotein oxidoreductase discovered in a eukaryotic organism.

  16. Bottom-up synthesis of chiral covalent organic frameworks and their bound capillaries for chiral separation

    PubMed Central

    Qian, Hai-Long; Yang, Cheng-Xiong; Yan, Xiu-Ping

    2016-01-01

    Covalent organic frameworks (COFs) are a novel class of porous materials, and offer great potential for various applications. However, the applications of COFs in chiral separation and chiral catalysis are largely underexplored due to the very limited chiral COFs available and their challenging synthesis. Here we show a bottom-up strategy to construct chiral COFs and an in situ growth approach to fabricate chiral COF-bound capillary columns for chiral gas chromatography. We incorporate the chiral centres into one of the organic ligands for the synthesis of the chiral COFs. We subsequently in situ prepare the COF-bound capillary columns. The prepared chiral COFs and their bound capillary columns give high resolution for the separation of enantiomers with excellent repeatability and reproducibility. The proposed strategy provides a promising platform for the synthesis of chiral COFs and their chiral separation application. PMID:27401541

  17. Bottom-up synthesis of chiral covalent organic frameworks and their bound capillaries for chiral separation

    NASA Astrophysics Data System (ADS)

    Qian, Hai-Long; Yang, Cheng-Xiong; Yan, Xiu-Ping

    2016-07-01

    Covalent organic frameworks (COFs) are a novel class of porous materials, and offer great potential for various applications. However, the applications of COFs in chiral separation and chiral catalysis are largely underexplored due to the very limited chiral COFs available and their challenging synthesis. Here we show a bottom-up strategy to construct chiral COFs and an in situ growth approach to fabricate chiral COF-bound capillary columns for chiral gas chromatography. We incorporate the chiral centres into one of the organic ligands for the synthesis of the chiral COFs. We subsequently in situ prepare the COF-bound capillary columns. The prepared chiral COFs and their bound capillary columns give high resolution for the separation of enantiomers with excellent repeatability and reproducibility. The proposed strategy provides a promising platform for the synthesis of chiral COFs and their chiral separation application.

  18. Bottom-up synthesis of chiral covalent organic frameworks and their bound capillaries for chiral separation.

    PubMed

    Qian, Hai-Long; Yang, Cheng-Xiong; Yan, Xiu-Ping

    2016-07-12

    Covalent organic frameworks (COFs) are a novel class of porous materials, and offer great potential for various applications. However, the applications of COFs in chiral separation and chiral catalysis are largely underexplored due to the very limited chiral COFs available and their challenging synthesis. Here we show a bottom-up strategy to construct chiral COFs and an in situ growth approach to fabricate chiral COF-bound capillary columns for chiral gas chromatography. We incorporate the chiral centres into one of the organic ligands for the synthesis of the chiral COFs. We subsequently in situ prepare the COF-bound capillary columns. The prepared chiral COFs and their bound capillary columns give high resolution for the separation of enantiomers with excellent repeatability and reproducibility. The proposed strategy provides a promising platform for the synthesis of chiral COFs and their chiral separation application.

  19. Microbial bioavailability of covalently bound polymer coatings on model engineered nanomaterials.

    PubMed

    Kirschling, Teresa L; Golas, Patricia L; Unrine, Jason M; Matyjaszewski, Krzysztof; Gregory, Kelvin B; Lowry, Gregory V; Tilton, Robert D

    2011-06-15

    By controlling nanoparticle flocculation and deposition, polymer coatings strongly affect nanoparticle fate, transport, and subsequent biological impact in the environment. Biodegradation is a potential route to coating breakdown, but it is unknown whether surface-bound polymers are bioavailable. Here we demonstrate, for the first time, that polymer coatings covalently bound to nanomaterials are bioavailable. Model poly(ethylene oxide) (PEO) brush-coated nanoparticles (densely cross-linked bottle brush copolymers) with hydrophobic divinyl benzene cross-linked cores and hydrophilic PEO brush shells, having ~ 30 nm hydrodynamic radii, were synthesized to obtain a nanomaterial in which biodegradation was the only available coating breakdown mechanism. PEO-degrading enrichment cultures were supplied with either PEO homopolymer or PEO brush nanoparticles as the sole carbon source, and protein and CO₂ production were monitored as a measure of biological conversion. Protein production after 90 h corresponded to 14% and 8% of the total carbon available in the PEO homopolymer and PEO brush nanoparticle cultures, respectively, and CO₂ production corresponded to 37% and 3.8% of the carbon added to the respective system. These results indicate that the PEO in the brush is bioavailable. Brush biodegradation resulted in particle aggregation, pointing to the need to understand biologically mediated transformations of nanoparticle coatings in order to understand the fate and transport of nanoparticles in the environment. PMID:21609011

  20. Covalent and non-covalent curcumin loading in acid-responsive polymeric micellar nanocarriers

    NASA Astrophysics Data System (ADS)

    Gao, Min; Chen, Chao; Fan, Aiping; Zhang, Ju; Kong, Deling; Wang, Zheng; Zhao, Yanjun

    2015-07-01

    Poor aqueous solubility, potential degradation, rapid metabolism and elimination lead to low bioavailability of pleiotropic impotent curcumin. Herein, we report two types of acid-responsive polymeric micelles where curcumin was encapsulated via both covalent and non-covalent modes for enhanced loading capacity and on-demand release. Biodegradable methoxy poly(ethylene glycol)-poly(lactic acid) copolymer (mPEG-PLA) was conjugated with curcumin via a hydrazone linker, generating two conjugates differing in architecture (single-tail versus double-tail) and free curcumin was encapsulated therein. The two micelles exhibited similar hydrodynamic size at 95 ± 3 nm (single-tail) and 96 ± 3 nm (double-tail), but their loading capacities differed significantly at 15.0 ± 0.5% (w/w) (single-tail) and 4.8 ± 0.5% (w/w) (double-tail). Under acidic sink conditions (pH 5.0 and 6.0), curcumin displayed a faster release from the single-tail nanocarrier, which was correlated to a low IC50 of 14.7 ± 1.6 (μg mL-1) compared to the value of double-tail micelle (24.9 ± 1.3 μg mL-1) in HeLa cells. The confocal imaging and flow cytometry analysis demonstrated a superior capability of single-tail micelle for intracellular curcumin delivery, which was a consequence of the higher loading capacity and lower degree of mPEG surface coverage. In conclusion, the dual loading mode is an effective means to increase the drug content in the micellar nanocarriers whose delivery efficiency is highly dependent on its polymer-drug conjugate architecture. This strategy offers an alternative nanoplatform for intracellularly delivering impotent hydrophobic agents (i.e. curcumin) in an efficient stimuli-triggered way, which is valuable for the enhancement of curcumin’s efficacy in managing a diverse range of disorders.

  1. Surface modification of titanium substrate with a novel covalently-bound copolymer thin film for improving its platelet compatibility.

    PubMed

    Shen, Ching-Hsiung; Cho, Yu-Jen; Lin, Yi-Ching; Chien, Li-Chin; Lee, Tzer-Min; Chuang, Wen-Hsi; Lin, Jui-Che

    2015-02-01

    Despite of its widely uses in various clinical applications, the titanium-based material still faces different challenges, such as hemocompatibility and anti-biofouling characteristics required in various situations. The objective of this investigation was to develop a novel surface modification strategy for titanium-based material to improve the platelet compatibility that is important in rigorous blood-contacting cardiovascular applications. In this work, a series of copolymers, which composed of novel 6-acryloyloxy hexyl phosphonic acid (AcrHPA) and sulfobetaine methacrylate (SBMA) was synthesized. The phosphonic acid group in these copolymers can impart covalent binding to the titanium substrate while the zwitterionic sulfobetaine functionality is considered being able to reduce the platelet adhesion and activation on the modified titanium substrate. NMR analyses suggested that copolymerization reaction is likely not an ideal statistical reaction but to add the monomers in a random order. Studies have shown that the composition of the monomers affected the surface characteristics and platelet compatibility of these covalent-bound AcrHPA-SBMA copolymers on titanium substrate. Contact angle analysis has shown the addition of SBMA can increase surface hydrophilicity of the spun-coated copolymers. In addition, AFM analyses have revealed that the surface roughness of the spun-coated copolymer layer were varied with the ratio of AcrHPA and SBMA. The most platelet compatible surface was noted on the one modified by the highest amount of SBMA added (i.e. 70 mol%) in copolymerization. In summary, the surface modification scheme presented here would be of potential as well as manufacturing process applicable for future development in blood-contacting titanium-based biomedical devices. PMID:25631276

  2. Covalent and non-covalent binding in the ion/ion charge inversion of peptide cations with benzene-disulfonic acid anions.

    PubMed

    Stutzman, John R; Luongo, Carl A; McLuckey, Scott A

    2012-06-01

    Protonated angiotensin II and protonated leucine enkephalin-based peptides, which included YGGFL, YGGFLF, YGGFLH, YGGFLK and YGGFLR, were subjected to ion/ion reactions with the doubly deprotonated reagents 4-formyl-1,3-benzenedisulfonic acid (FBDSA) and 1,3-benzenedisulfonic acid (BDSA). The major product of the ion/ion reaction is a negatively charged complex of the peptide and reagent. Following dehydration of [M + FBDSA-H](-) via collisional-induced dissociation (CID), angiotensin II (DRVYIHPF) showed evidence for two product populations, one in which a covalent modification has taken place and one in which an electrostatic modification has occurred (i.e. no covalent bond formation). A series of studies with model systems confirmed that strong non-covalent binding of the FBDSA reagent can occur with subsequent ion trap CID resulting in dehydration unrelated to the adduct. Ion trap CID of the dehydration product can result in cleavage of amide bonds in competition with loss of the FBDSA adduct. This scenario is most likely for electrostatically bound complexes in which the peptide contains both an arginine residue and one or more carboxyl groups. Otherwise, loss of the reagent species from the complex, either as an anion or as a neutral species, is the dominant process for electrostatically bound complexes. The results reported here shed new light on the nature of non-covalent interactions in gas phase complexes of peptide ions that can be used in the rationale design of reagent ions for specific ion/ion reaction applications. PMID:22707160

  3. Mass spectrometric quantitation of covalently bound cell wall proteins in Saccharomyces cerevisiae

    PubMed Central

    Yin, Qing Yuan; de Groot, Piet W J; de Jong, Luitzen; Klis, Frans M; De Koster, Chris G

    2007-01-01

    The cell wall of yeast consists of an internal skeletal layer and an external layer of glycoproteins covalently linked to the stress-bearing polysaccharides. The cell wall protein (CWP) population consists of over 20 different proteins, and may vary in composition. We present two complementary methods for quantifying CWPs, based on isobaric tagging and tandem MS: (1) absolute quantitation of individual CWPs, allowing estimation of surface densities; and (2) relative quantitation of CWPs, allowing monitoring of the dynamics of the CWP population. For absolute quantitation, we selected a representative group of five proteins (Cwp1p, Crh1p, Scw4p, Gas1p, and Ecm33p), which had 67 × 103, 44 × 103, 38 × 103, 11 × 103 and 6.5 × 103 of wall-bound copies per cell, respectively. As Cwp1p is predominantly incorporated in the birth scar, this corresponds to a protein density of c. 22 × 103 copies μm−2. For relative quantitation, we compared wild-type cells to gas1Δ cells, in which the cell wall integrity pathway is constitutively activated. The levels of Crh1p, Crh2p, Ecm33p, Gas5p, Pst1p and Pir3p increased about three- to fivefold, whereas the level of Scw4p was significantly decreased. We propose that our methods are widely applicable to other fungi. PMID:17617218

  4. Evaluation of Antimicrobial Efficiency of New Polymers Comprised by Covalently Attached and/or Electrostatically Bound Bacteriostatic Species, Based on Quaternary Ammonium Compounds.

    PubMed

    Kougia, Efstathia; Tselepi, Maria; Vasilopoulos, Gavriil; Lainioti, Georgia Ch; Koromilas, Nikos D; Druvari, Denisa; Bokias, Georgios; Vantarakis, Apostolos; Kallitsis, Joannis K

    2015-01-01

    In the present work a detailed study of new bacteriostatic copolymers with quaternized ammonium groups introduced in the polymer chain through covalent attachment or electrostatic interaction, was performed. Different copolymers have been considered since beside the active species, the hydrophobic/hydrophilic nature of the co-monomer was also evaluated in the case of covalently attached bacteriostatic groups, aiming at achieving permanent antibacterial activity. Homopolymers with quaternized ammonium/phosphonium groups were also tested for comparison reasons. The antimicrobial activity of the synthesized polymers after 3 and 24 h of exposure at 4 and 22 °C was investigated on cultures of Gram-negative (P. aeruginosa, E. coli) and Gram-positive (S. aureus, E. faecalis) bacteria. It was found that the combination of the hydrophilic monomer acrylic acid (AA), at low contents, with the covalently attached bacteriostatic group vinyl benzyl dimethylhexadecylammonium chloride (VBCHAM) in the copolymer P(AA-co-VBCHAM88), resulted in a high bacteriostatic activity against P. aeruginosa and E. faecalis (6 log reduction in certain cases). Moreover, the combination of covalently attached VBCHAM units with electrostatically bound cetyltrimethylammonium 4-styrene sulfonate (SSAmC16) units in the P(SSAmC16-co-VBCHAMx) copolymers led to efficient antimicrobial materials, especially against Gram-positive bacteria, where a log reduction between 4.9 and 6.2 was verified. These materials remain remarkably efficient even when they are incorporated in polysulfone membranes.

  5. Detection and Time Course of Formation of Major Thiamin Diphosphate-Bound Covalent Intermediates Derived from a Chromophoric Substrate Analogue on Benzoylformate Decarboxylase

    SciTech Connect

    Chakraborty, Sumit; Nemeria, Natalia S.; Balakrishnan, Anand; Brandt, Gabriel S.; Kneen, Malea M.; Yep, Alejandra; McLeish, Michael J.; Kenyon, George L.; Petsko, Gregory A.; Ringe, Dagmar; Jordan, Frank

    2009-04-02

    The mechanism of the enzyme benzoylformate decarboxylase (BFDC), which carries out a typical thiamin diphosphate (ThDP)-dependent nonoxidative decarboxylation reaction, was studied with the chromophoric alternate substrate (E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid (3-PKB). Addition of 3-PKB resulted in the appearance of two transient intermediates formed consecutively, the first one to be formed a predecarboxylation ThDP-bound intermediate with {lambda}{sub max} at 477 nm, and the second one corresponding to the first postdecarboxylation intermediate the enamine with {lambda}{sub max} at 437 nm. The time course of formation/depletion of the PKB-ThDP covalent complex and of the enamine showed that decarboxylation was slower than formation of the PKB-ThDP covalent adduct. When the product of decarboxylation 3-(pyridin-3-yl)acrylaldehyde (PAA) was added to BFDC, again an absorbance with {lambda}{sub max} at 473 nm was formed, corresponding to the tetrahedral adduct of PAA with ThDP. Addition of well-formed crystals of BFDC to a solution of PAA resulted in a high resolution (1.34 {angstrom}) structure of the BFDC-bound adduct of ThDP with PAA confirming the tetrahedral nature at the C2{alpha} atom, rather than of the enamine, and supporting the assignment of the {lambda}{sub max} at 473 nm to the PAA-ThDP adduct. The structure of the PAA-ThDP covalent complex is the first example of a product-ThDP adduct on BFDC. Similar studies with 3-PKB indicated that decarboxylation had taken place. Evidence was also obtained for the slow formation of the enamine intermediate when BFDC was incubated with benzaldehyde, the product of the decarboxylation reaction thus confirming its presence on the reaction pathway.

  6. Bound Indoleacetic Acid in Avena Coleoptiles 1

    PubMed Central

    Winter, Alan; Thimann, Kenneth V.

    1966-01-01

    When C14 carboxyl indoleacetic acid (IAA) is transported through Avena coleoptile sections a fraction of the activity becomes bound. The nature of this bound IAA has been investigated. Upon extraction with solvents and chromatography a substance having the RF of IAA in 4 solvents was detected. No evidence could be found for the formation of indoleacetyl conjugates. In pea stem sections subjected to a similar experimental regime good evidence was obtained for the occurrence of conjugates. When IAA was supplied exogenously to coleoptile sections floating in solutions the occurrence of conjugates was shown to be dependent on the presence of the primary leaf. In its absence no conjugates could be detected. On grinding coleoptile sections and subsequent centrifugation at 240 × g the radioactivity was found to be in the tissue fraction as opposed to the supernatant. The radioactivity cannot be removed from the tissue by extraction with water, buffer solution or treatment with ribonuclease. It is readily removed by 10% urea, crystalline trypsin and chymotrypsin. It is therefore concluded that IAA becomes bound to a protein. Bound IAA does not appear to be able to cause growth in Avena coleoptile sections. PMID:16656259

  7. Probing Protein Structure by Amino Acid-Specific Covalent Labeling and Mass Spectrometry

    PubMed Central

    Mendoza, Vanessa Leah; Vachet, Richard W.

    2009-01-01

    For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies. PMID:19016300

  8. Isoamylacetate production by entrapped and covalently bound Candida rugosa and porcine pancreatic lipases.

    PubMed

    Ozyilmaz, Gul; Yağız, Esra

    2012-12-15

    Candida rugosa lipase (CRL) and porcine pancreatic lipase (PPL) were immobilised by entrapping and also by covalent binding for use in synthesis of isoamyl acetate (IAAc), which has a typical banana flavour. Lipase entrapment was carried out by dripping sodium alginate (Na-Alg)-chitosan (Chi)-lipase mixture into CaCl(2)-glutaraldehyde (GAL) solution to obtain Ca-Alg/Chi(CRL/PPL). Immobilisation conditions were optimised as 1.5% Na-Alg, 1.5% chitosan and 0.15% GAL. Ca-Alg/Chi(CRL/PPL) samples showed the highest activity when they were dried upon reaching 27% of their initial weights. Covalent binding was achived with Chi modified with spacerarm via glutaraldehyde to get Chi(CRL/PPL). The highest IAAc production was observed when 1,3-diaminopropane was used as a spacer arm. The best ester yield was achieved in heptane, at 40 and 45°C reaction temperatures, 50mM IAA and 50 or 75 mM AA concentrations. The amount of IAAc was nearly 10 times higher for the batch type than for the continuous packed bed column reactor. PMID:22980809

  9. Photophysics and photochemistry of the UV filter kynurenine covalently attached to amino acids and to a model protein.

    PubMed

    Sherin, Peter S; Grilj, Jakob; Kopylova, Lyudmila V; Yanshole, Vadim V; Tsentalovich, Yuri P; Vauthey, Eric

    2010-09-16

    The photophysics and photochemistry of kynurenine (KN) covalently bound to the amino acids lysine, cysteine, and histidine, the antioxidant glutathione, and the protein lysozyme have been studied by optical spectroscopy with femto- and nanosecond time resolution. The fluorescence quantum yield of the adducts of KN to amino acids is approximately 2 times higher than that of the free KN in solution; KN attached to protein exhibits a 7-fold increase in the fluorescence quantum yield. The S(1) state dynamics of KN-modified lysozyme reveals a multiphasic decay with a broad dispersion of time constants from 1 ps to 2 ns. An increase of the triplet yield of KN bound to lysozyme is also observed; the triplet state undergoes fast intramolecular decay. The obtained results reveal an increase of the photochemical activity of KN after its covalent attachment to amino acids and proteins, which may contribute to the development of oxidative stress in the human lenses-the main causative factor for the cataract onset.

  10. Fluorescent silica nanoparticles containing covalently bound dyes for reporter, marker, and sensor applications

    NASA Astrophysics Data System (ADS)

    Patonay, Gabor; Henary, Maged; Chapman, Gala; Emer, Kyle; Crow, Sidney

    2016-03-01

    Silica nanoparticles have proven to be useful in many bioanalytical and medical applications and have been used in numerous applications during the last decade. Combining the properties of silica nanoparticles and fluorescent dyes that may be used as chemical probes or labels can be relatively easy by simply soaking porous silica nanoparticles in a solution of the dye of interest. Under proper conditions the entrapped dye can stay inside the silica nanoparticle for several hours resulting in a useful probe. In spite of the relative durability of these probes, leaching can still occur. A much better approach is to synthesize silica nanoparticles that have the fluorescent dye covalently attached to the backbone structure of the silica nanoparticle. This can be achieved by using appropriately modified tetraethyl orthosilicate (TEOS) analogues during the silica nanoparticle synthesis. The molar ratio of TEOS and modified TEOS will determine the fluorescent dye load in the silica nanoparticle. Dependent on the chemical stability of the reporting dye either reverse micellar (RM) or Stöber method can be used for silica nanoparticle synthesis. If dye stability allows RM procedure is preferred as it results in a much easier control of the silica nanoparticle reaction itself. Also controlling the size and uniformity of the silica nanoparticles are much easier using RM method. Dependent on the functional groups present in the reporting dye used in preparation of the modified TEOS, the silica nanoparticles can be utilized in many applications such as pH sensor, metal ion sensors, labels, etc. In addition surface activated silica nanoparticles with reactive moieties are also excellent reporters or they can be used as bright fluorescent labels. Many different fluorescent dyes can be used to synthesize silica nanoparticles including visible and NIR dyes. Several bioanalytical applications are discussed including studying amoeba phagocytosis.

  11. Growth of hydrogel nano- and microlayers covalently bounded onto PE surface

    NASA Astrophysics Data System (ADS)

    Silva, Rafael; Muniz, Edvani C.; Rubira, Adley F.

    2009-04-01

    Surface modifying strategies were developed to immobilize PAA cross-linked layers (hydrogel layers) with different thicknesses by chemical binding to the surface of polyethylene (PE). Polyethylene films were functionalized by two methods, chromic acid oxidation and maleic anhydride grafting. The reaction of the functional groups placed onto the film surface with ethylenediamine promoted the formation of an amine-functionalized surface. The thickness of the hydrogel layer was correlated with the presence and the release of impregnated ethylenediamine during the immobilization of the PAA chains by thermal esterification. Ethylenediamine acts as a cross-linking agent between different PAA chains. Attenuated total reflectance (ATR) FTIR spectroscopy and scanning electron microscopy (SEM) were used to characterize the chemical composition and the morphologies of the modified film surface.

  12. Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine

    SciTech Connect

    Pletnev, Vladimir Z. Pletneva, Nadya V.; Lukyanov, Konstantin A.; Souslova, Ekaterina A.; Fradkov, Arkady F.; Chudakov, Dmitry M.; Chepurnykh, Tatyana; Yampolsky, Ilia V.; Wlodawer, Alexander; Dauter, Zbigniew; Pletnev, Sergei

    2013-09-01

    The crystal structure of the novel red emitting fluorescent protein from lancelet Branchiostoma lanceolatum (Chordata) revealed an unusual five residues cyclic unit comprising Gly58-Tyr59-Gly60 chromophore, the following Phe61 and Tyr62 covalently bound to chromophore Tyr59. A key property of proteins of the green fluorescent protein (GFP) family is their ability to form a chromophore group by post-translational modifications of internal amino acids, e.g. Ser65-Tyr66-Gly67 in GFP from the jellyfish Aequorea victoria (Cnidaria). Numerous structural studies have demonstrated that the green GFP-like chromophore represents the ‘core’ structure, which can be extended in red-shifted proteins owing to modifications of the protein backbone at the first chromophore-forming position. Here, the three-dimensional structures of green laGFP (λ{sub ex}/λ{sub em} = 502/511 nm) and red laRFP (λ{sub ex}/λ{sub em} ≃ 521/592 nm), which are fluorescent proteins (FPs) from the lancelet Branchiostoma lanceolatum (Chordata), were determined together with the structure of a red variant laRFP-ΔS83 (deletion of Ser83) with improved folding. Lancelet FPs are evolutionarily distant and share only ∼20% sequence identity with cnidarian FPs, which have been extensively characterized and widely used as genetically encoded probes. The structure of red-emitting laRFP revealed three exceptional features that have not been observed in wild-type fluorescent proteins from Cnidaria reported to date: (i) an unusual chromophore-forming sequence Gly58-Tyr59-Gly60, (ii) the presence of Gln211 at the position of the conserved catalytic Glu (Glu222 in Aequorea GFP), which proved to be crucial for chromophore formation, and (iii) the absence of modifications typical of known red chromophores and the presence of an extremely unusual covalent bond between the Tyr59 C{sup β} atom and the hydroxyl of the proximal Tyr62. The impact of this covalent bond on the red emission and the large Stokes shift (

  13. Ionic and covalent stabilization of intermediates and transition states in catalysis by solid acids.

    PubMed

    Deshlahra, Prashant; Carr, Robert T; Iglesia, Enrique

    2014-10-29

    Reactivity descriptors describe catalyst properties that determine the stability of kinetically relevant transition states and adsorbed intermediates. Theoretical descriptors, such as deprotonation energies (DPE), rigorously account for Brønsted acid strength for catalytic solids with known structure. Here, mechanistic interpretations of methanol dehydration turnover rates are used to assess how charge reorganization (covalency) and electrostatic interactions determine DPE and how such interactions are recovered when intermediates and transition states interact with the conjugate anion in W and Mo polyoxometalate (POM) clusters and gaseous mineral acids. Turnover rates are lower and kinetically relevant species are less stable on Mo than W POM clusters with similar acid strength, and such species are more stable on mineral acids than that predicted from W-POM DPE-reactivity trends, indicating that DPE and acid strength are essential but incomplete reactivity descriptors. Born-Haber thermochemical cycles indicate that these differences reflect more effective charge reorganization upon deprotonation of Mo than W POM clusters and the much weaker reorganization in mineral acids. Such covalency is disrupted upon deprotonation but cannot be recovered fully upon formation of ion pairs at transition states. Predictive descriptors of reactivity for general classes of acids thus require separate assessments of the covalent and ionic DPE components. Here, we describe methods to estimate electrostatic interactions, which, taken together with energies derived from density functional theory, give the covalent and ionic energy components of protons, intermediates, and transition states. In doing so, we provide a framework to predict the reactive properties of protons for chemical reactions mediated by ion-pair transition states.

  14. Ionic and Covalent Stabilization of Intermediates and Transition States in Catalysis by Solid Acids

    SciTech Connect

    Deshlahra, Prashant; Carr, Robert T.; Iglesia, Enrique

    2014-10-29

    Reactivity descriptors describe catalyst properties that determine the stability of kinetically relevant transition states and adsorbed intermediates. Theoretical descriptors, such as deprotonation energies (DPE), rigorously account for Brønsted acid strength for catalytic solids with known structure. Here, mechanistic interpretations of methanol dehydration turnover rates are used to assess how charge reorganization (covalency) and electrostatic interactions determine DPE and how such interactions are recovered when intermediates and transition states interact with the conjugate anion in W and Mo polyoxometalate (POM) clusters and gaseous mineral acids. Turnover rates are lower and kinetically relevant species are less stable on Mo than W POM clusters with similar acid strength, and such species are more stable on mineral acids than that predicted from W-POM DPE–reactivity trends, indicating that DPE and acid strength are essential but incomplete reactivity descriptors. Born–Haber thermochemical cycles indicate that these differences reflect more effective charge reorganization upon deprotonation of Mo than W POM clusters and the much weaker reorganization in mineral acids. Such covalency is disrupted upon deprotonation but cannot be recovered fully upon formation of ion pairs at transition states. Predictive descriptors of reactivity for general classes of acids thus require separate assessments of the covalent and ionic DPE components. Here, we describe methods to estimate electrostatic interactions, which, taken together with energies derived from density functional theory, give the covalent and ionic energy components of protons, intermediates, and transition states. In doing so, we provide a framework to predict the reactive properties of protons for chemical reactions mediated by ion-pair transition states.

  15. Quantum mechanics/molecular mechanics modeling of fatty acid amide hydrolase reactivation distinguishes substrate from irreversible covalent inhibitors.

    PubMed

    Lodola, Alessio; Capoferri, Luigi; Rivara, Silvia; Tarzia, Giorgio; Piomelli, Daniele; Mulholland, Adrian; Mor, Marco

    2013-03-28

    Carbamate and urea derivatives are important classes of fatty acid amide hydrolase (FAAH) inhibitors that carbamoylate the active-site nucleophile Ser241. In the present work, the reactivation mechanism of carbamoylated FAAH is investigated by means of a quantum mechanics/molecular mechanics (QM/MM) approach. The potential energy surfaces for decarbamoylation of FAAH covalent adducts, derived from the O-aryl carbamate URB597 and from the N-piperazinylurea JNJ1661610, were calculated and compared to that for deacylation of FAAH acylated by the substrate oleamide. Calculations show that a carbamic group bound to Ser241 prevents efficient stabilization of transition states of hydrolysis, leading to large increments in the activation barrier. Moreover, the energy barrier for the piperazine carboxylate was significantly lower than that for the cyclohexyl carbamate derived from URB597. This is consistent with experimental data showing slowly reversible FAAH inhibition for the N-piperazinylurea inhibitor and irreversible inhibition for URB597.

  16. Coffee bean arabinogalactans: acidic polymers covalently linked to protein.

    PubMed

    Redgwell, Robert J; Curti, Delphine; Fischer, Monica; Nicolas, Pierre; Fay, Laurent B

    2002-02-11

    The arabinogalactan content of green coffee beans (Coffea arabica var. Yellow Caturra) was released by a combination of chemical extraction and enzymatic hydrolysis of the mannan-cellulose component of the wall. Several arabinogalactan fractions were isolated, purified by gel-permeation and ion-exchange chromatography and characterised by compositional and linkage analysis. The AG fractions contained between 6 and 8% glucuronic acid, and gave a positive test for the beta-glucosyl-Yariv reagent, a stain specific for arabinogalactan-proteins. The protein component accounted for between 0.5 and 2.0% of the AGPs and contained between 7 and 12% hydroxyproline. The AG moieties displayed considerable heterogeneity with regard to their degree of arabinosylation and the extent and composition of their side-chains. They possessed a MW average of 650 kDa which ranged between 150 and 2000 kDa. An investigation of the structural features of the major AG fraction, released following enzymatic hydrolysis of the mannan-cellulose polymers, allowed a partial structure of coffee arabinogalactan to be proposed.

  17. Thiolation of protein-bound carcinogenic aldehyde. An electrophilic acrolein-lysine adduct that covalently binds to thiols.

    PubMed

    Furuhata, Atsunori; Nakamura, Mitsuhiro; Osawa, Toshihiko; Uchida, Koji

    2002-08-01

    Acrolein, a representative carcinogenic aldehyde that could be ubiquitously generated in biological systems under oxidative stress, shows facile reactivity with the epsilon-amino group of lysine to form N(epsilon)-(3-formyl-3,4-dehydropiperidino)lysine (FDP-lysine) as the major product (Uchida, K., Kanematsu, M., Morimitsu, Y., Osawa, T., Noguchi, N., and Niki, E. (1998) J. Biol. Chem. 273, 16058-16066). In the present study, we determined the electrophilic potential of FDP-lysine and established a novel mechanism of protein thiolation in which the FDP-lysine generated in the acrolein-modified protein reacts with sulfhydryl groups to form thioether adducts. When a sulfhydryl enzyme, glyceraldehyde-3-phosphate dehydrogenase, was incubated with acrolein-modified bovine serum albumin in sodium phosphate buffer (pH 7.2) at 37 degrees C, a significant loss of sulfhydryl groups, which was accompanied by the loss of enzyme activity and the formation of high molecular mass protein species (>200 kDa), was observed. The FDP-lysine adduct generated in the acrolein-modified protein was suggested to represent a thiol-reactive electrophile based on the following observations. (i) N(alpha)-acetyl-FDP-lysine, prepared from the reaction of N(alpha)-acetyl lysine with acrolein, was covalently bound to glyceraldehyde-3-phosphate dehydrogenase. (ii) The FDP-lysine derivative reacted with glutathione to form a GSH conjugate. (iii) The acrolein-modified bovine serum albumin significantly reacted with GSH to form a glutathiolated protein. Furthermore, the observation that the glutathiolated acrolein-modified protein showed decreased immunoreactivity with an anti-FDP-lysine monoclonal antibody suggested that the FDP-lysine residues in the acrolein-modified protein served as the binding site of GSH. These data suggest that thiolation of the protein-bound acrolein may be involved in redox alteration under oxidative stress, whereby oxidative stress generates the increased production of

  18. Spin Labeling ESR Investigation of a Role of Humic Acids at Covalent Binding of Xenobiotics to Soil

    NASA Astrophysics Data System (ADS)

    Aleksandrova, Olga

    2014-05-01

    The environmental risk of organic xenobiotic chemicals released into soils is controlled by their sorption and binding processes. However, the molecular mechanisms of reversible and irreversible interactions of xenobiotics with soil constituents and an influence of humic substances on this interaction are only partly understood. New methods and approaches aimed at understanding of molecular mechanisms in the soil environment and a role of humic substances in the sorption and binding processes are today required to manage and keep the quality of soil used and fertilized in agricultural industry. The paper presents a new approach of using stable ESR spin labels to investigate a role of humic substances in the interactions of organic xenobiotic chemicals with constituents of natural soil via the typical functional groups of xenobiotics, such as Amines. At the experiment, the nitroxide spin labels, such as TEMPO (2,2,6,6-Tetramethylpiperidin-1-oxyl), Amino-TEMPO (4-amino-2,2,6,6-Tetramethylpiperidin-1-oxyl) and Aniline spin labels (2,5,5-Trimethyl-2-(3-aminophenyl)pyrrolidin-1-oxyl), were added to samples of different natural soils, such luvisol, cambisol and chernozem. Amino-TEMPO and Aniline spin labels include the aliphatic amino and aromatic amino functional groups, respectively. A significant broadening of the ESR spectrum of Aniline spin labels incubated in different soils indicated a stable effect of covalent binding of the spin labels to soil constituents via the aromatic amino, whereas the ESR spectra of the other two spin labels were not broadened that pointed at the absence of covalent binding of spin labels via the aliphatic amino. As shown, a part of bound spin labels via the aromatic amino increased with increasing of the concentration of humic acids in soil. The same broadened signals were also be detected with the humic acids extracted from the investigated soils. A strong covalent binding of spin labels to humic substances via the aromatic amines was

  19. Synthesis and immunological properties of conjugates composed of group B streptococcus type III capsular polysaccharide covalently bound to tetanus toxoid.

    PubMed

    Lagergard, T; Shiloach, J; Robbins, J B; Schneerson, R

    1990-03-01

    A synthetic scheme for covalently binding group B streptococcus type III to tetanus toxoid (TT), using adipic acid dihydrazide as a spacer, is described. Type III alone or as a conjugate with TT was injected subcutaneously into laboratory mice, and the type-specific and TT antibody responses elicited by these immunogens were assayed. Type III-TT elicited significantly higher levels of type-specific antibodies after each immunization than did the type III alone. These levels were related to the dosage of the conjugate, enhanced by Freund adjuvant, and exhibited booster responses. Type III alone elicited only immunoglobulin M (IgM) antibodies in Swiss albino mice and mostly IgM and low levels of IgG antibodies of the IgG3 subclass in BALB/c mice. Type III-TT conjugates, in contrast, elicited mostly IgG antibodies in both strains of mice. IgA type III antibodies were not detected. The first two immunizations with the conjugates elicited type III antibodies in the IgG1 and in the IgG3 subclasses. Low levels of IgG2a type III antibodies were detected after a third injection of type III-TT. Conjugate-induced antibodies facilitated opsonization of group B streptococcus type III organisms and did not react with the structurally related pneumococcus type 14. TT alone or as a component of type III-TT induced mostly antibodies of the IgG class: IgG1 levels were the highest of the four subclasses. No IgA TT antibodies were detected. The conjugation procedure, therefore, enhanced the immunogenicity of and conferred T-cell dependent properties to the type III while preserving the immunogenicity of the TT component. The T-cell dependent properties of the conjugates were responsible for stimulating IgG type III antibodies which could be boosted. Evaluation of type III-TT conjugates in antibody-negative women of child-bearing age is planned. PMID:2407652

  20. Amino acids and their Cu complexes covalently grafted onto a polystyrene resin A vibrational spectroscopic study

    NASA Astrophysics Data System (ADS)

    Korbély, B.; Kiss, J. T.; Hernadi, K.; Pálinkó, I.

    2007-05-01

    Immobilised Cu(II)- L-tyrosine methylester and Cu(II)-BOC- L-histidine complexes were prepared through covalently grafting the amino acid ligands onto chlorine-functionalised polystyrene. The steps of the syntheses were followed by IR spectroscopy. The ligand to central ion ratio was four in both anchored complexes, and the most probable coordination sites were the carboxylic, the amino and the phenolic OH groups and the imidazole nitrogens for the tyrosine methylester and the BOC- L-histidine, respectively.

  1. Disruption of heme-peptide covalent cross-linking in mammalian peroxidases by hypochlorous acid

    PubMed Central

    Abu-Soud, Husam M.; Maitra, Dhiman; Shaeib, Faten; Khan, Sana; Byun, Jaeman; Abdulhamid, Ibrahim; Yang, Zhe; Saed, Ghassan M.; Diamond, Michael P.; Andreana, Peter R.; Pennathur, Subramaniam

    2015-01-01

    Myeloperoxidase (MPO), lactoperoxidase (LPO) and eosinophil peroxidase (EPO) play a central role in oxidative damage in inflammatory disorders by utilizing hydrogen peroxide and halides/pseudo halides to generate the corresponding hypohalous acid. The catalytic sites of these enzymes contain a covalently modified heme group, which is tethered to the polypeptide chain at two ester linkages via the methyl group (MPO, EPO and LPO) and one sulfonium bond via the vinyl group (MPO only). Covalent cross-linking of the catalytic site heme to the polypeptide chain in peroxidases is thought to play a protective role, since it renders the heme moiety less susceptible to the oxidants generated by these enzymes. Mass-spectrometric analysis revealed the following possible pathways by which hypochlorous acid (HOCl) disrupts the heme-protein cross-linking: (1) the methyl-ester bond is cleaved to form an alcohol; (2) the alcohol group undergoes an oxygen elimination reaction via the formation of an aldehyde intermediate or undergoes a demethylation reaction to lose the terminal CH2 group; and (3) the oxidative cleavage of the vinyl-sulfonium linkage. Once the heme moiety is released it undergoes cleavage at the carbon-methyne bridge either along the δ-β or a α-γ axis to form different pyrrole derivatives. These results indicate that covalent cross-linking is not enough to protect the enzymes from HOCl mediated heme destruction and free iron release. Thus, the interactions of mammalian peroxidases with HOCl modulates their activity and sets a stage for initiation of the Fenton reaction, further perpetuating oxidative damage at sites of inflammation. PMID:25193127

  2. Photogeneration of singlet oxygen by the phenothiazine derivatives covalently bound to the surface-modified glassy carbon

    NASA Astrophysics Data System (ADS)

    Blacha-Grzechnik, Agata; Piwowar, Katarzyna; Krukiewicz, Katarzyna; Koscielniak, Piotr; Szuber, Jacek; Zak, Jerzy K.

    2016-05-01

    The selected group of four amine-derivatives of phenothiazine was covalently grafted to the glassy carbon surface in the four-step procedure consisting of the electrochemical reduction of the diazonium salt followed by the electrochemical and chemical post-modification steps. The proposed strategy involves the bonding of linker molecule to which the photosensitizer is attached. The synthesized organic layers were characterized by means of cyclic voltammetry, XPS and Raman Spectroscopy. It was shown that the phenothiazines immobilized via proposed strategy retain their photochemical properties and are able to generate 1O2 when activated by the laser radiation. The effectiveness of in situ singlet oxygen generation by those new solid photoactive materials was determined by means of UVVis spectroscopy. The reported, covalently modified solid surfaces may find their application as the singlet oxygen photogenerators in the fine chemicals' synthesis or in the wastewater treatment.

  3. Nitrooxyacyl derivatives of salicylic acid: aspirin-like molecules that covalently inactivate cyclooxygenase-1.

    PubMed

    Cena, Clara; Tosco, Paolo; Marini, Elisabetta; Lazzarato, Loretta; Piccinini, Marco; Ramondetti, Cristina; Lupino, Elisa; Fruttero, Roberta; Gasco, Alberto

    2011-03-01

    A recently described series of nitrooxyacyl derivatives of salicylic acid, displaying aspirin-like anti-inflammatory and platelet anti-aggregatory properties, were evaluated for their abilities to inhibit cyclooxygenase (COX). A number of these compounds irreversibly inhibited both COX-1 and COX-2 isoforms when tested in isolated human platelets and monocytes. Further studies using COX-1 expressed in human HEK293T cells showed that this inhibition mechanism is similar to that of aspirin; namely, the products are able to covalently bind to the Ser 530 residue present in the active cleft of the enzyme. Molecular modeling enabled us to rationalize this behavior. Because these products were previously found to display NO-dependent properties in rat animal models, particularly as they decreased in vivo gastrotoxicity and induced in vitro vasodilation, they represent a new and interesting class of potential aspirin-like antithrombotic agents worthy of further study.

  4. Layer by layer assembly of a biocatalytic packaging film: lactase covalently bound to low-density polyethylene.

    PubMed

    Wong, Dana E; Talbert, Joey N; Goddard, Julie M

    2013-06-01

    Active packaging is utilized to overcome limitations of traditional processing to enhance the health, safety, economics, and shelf life of foods. Active packaging employs active components to interact with food constituents to give a desired effect. Herein we describe the development of an active package in which lactase is covalently attached to low-density polyethylene (LDPE) for in-package production of lactose-free dairy products. The specific goal of this work is to increase the total protein content loading onto LDPE using layer by layer (LbL) deposition, alternating polyethylenimine, glutaraldehyde (GL), and lactase, to enhance the overall activity of covalently attached lactase. The films were successfully oxidized via ultraviolet light, functionalized with polyethylenimine and glutaraldehyde, and layered with immobilized purified lactase. The total protein content increased with each additional layer of conjugated lactase, the 5-layer sample reaching up to 1.3 μg/cm2 . However, the increase in total protein did not lend to an increase in overall lactase activity. Calculated apparent Km indicated the affinity of immobilized lactase to substrate remains unchanged when compared to free lactase. Calculated apparent turnover numbers (kcat ) showed with each layer of attached lactase, a decrease in substrate turnover was experienced when compared to free lactase; with a decrease from 128.43 to 4.76 s(-1) for a 5-layer conjugation. Our results indicate that while LbL attachment of lactase to LDPE successfully increases total protein mass of the bulk material, the adverse impact in enzyme efficiency may limit the application of LbL immobilization chemistry for bioactive packaging use.

  5. Covalent attachment of diamondoid phosphonic acid dichlorides to tungsten oxide surfaces.

    PubMed

    Li, Fei Hua; Fabbri, Jason D; Yurchenko, Raisa I; Mileshkin, Alexander N; Hohman, J Nathan; Yan, Hao; Yuan, Hongyuan; Tran, Ich C; Willey, Trevor M; Bagge-Hansen, Michael; Dahl, Jeremy E P; Carlson, Robert M K; Fokin, Andrey A; Schreiner, Peter R; Shen, Zhi-Xun; Melosh, Nicolas A

    2013-08-01

    Diamondoids (nanometer-sized diamond-like hydrocarbons) are a novel class of carbon nanomaterials that exhibit negative electron affinity (NEA) and strong electron-phonon scattering. Surface-bound diamondoid monolayers exhibit monochromatic photoemission, a unique property that makes them ideal electron sources for electron-beam lithography and high-resolution electron microscopy. However, these applications are limited by the stability of the chemical bonding of diamondoids on surfaces. Here we demonstrate the stable covalent attachment of diamantane phosphonic dichloride on tungsten/tungsten oxide surfaces. X-ray photoelectron spectroscopy (XPS) and Fourier-transform infrared (FTIR) spectroscopy revealed that diamondoid-functionalized tungsten oxide films were stable up to 300-350 °C, a substantial improvement over conventional diamondoid thiolate monolayers on gold, which dissociate at 100-200 °C. Extreme ultraviolet (EUV) light stimulated photoemission from these diamondoid phosphonate monolayers exhibited a characteristic monochromatic NEA peak with 0.2 eV full width at half-maximum (fwhm) at room temperature, showing that the unique monochromatization property of diamondoids remained intact after attachment. Our results demonstrate that phosphonic dichloride functionality is a promising approach for forming stable diamondoid monolayers for elevated temperature and high-current applications such as electron emission and coatings in micro/nano electromechanical systems (MEMS/NEMS).

  6. Transfer of a weakly bound electron in collisions of Rydberg atoms with neutral particles. I. Long-range interaction effects in the ionic-covalent coupling

    SciTech Connect

    Lebedev, V. S. Narits, A. A.

    2013-10-15

    Ion-pair formation processes are studied in collisions of Rydberg atoms with neutral particles possessing small electron affinities. Nonadiabatic transitions from a Rydberg covalent term to an ionic term of a quasi-molecule are considered using the modified Landau-Zener theory supplemented with calculation of survival factors of an anion decaying in the Coulomb field of a positive ion core. Using the technique of irreducible tensor operators and the momentum representation of the wavefunction of a highly excited atom, exact expressions are obtained for transition matrix elements and the ionic-covalent coupling parameter. The approach developed in the paper provides the description beyond the scope of a conventional assumption about a small variation of the wavefunction of the Rydberg atom on the range of electron coordinates determined by the characteristic radius of the wavefunction of the anion. This allows one to correctly consider long-range effects of the interaction between a weakly bound electron and the neutral core of a negative ion in processes under study. It is shown by the example of thermal collisions of Xe(nf) atoms with CH{sub 3}CN molecules that this is very important for a reliable quantitative description of anion formation with a low binding energy. The results are compared with experiments and calculations performed within the framework of a number of approximate methods.

  7. Covalent triazine-based framework: A promising adsorbent for removal of perfluoroalkyl acids from aqueous solution.

    PubMed

    Wang, Bingyu; Lee, Linda S; Wei, Chenhui; Fu, Heyun; Zheng, Shourong; Xu, Zhaoyi; Zhu, Dongqiang

    2016-09-01

    Perfluoroalkyl acids (PFAAs) are highly stable, persistent, and ubiquitous in the environment with significant concerns growing with regards to both human and ecosystem health. Due to the high stability to both biological and chemical attack, the only currently feasible approach for their removal from water is adsorbent technology. The main objective of this study was to assess a covalent triazine-based framework (CTF) adsorbent for removal from aqueous solutions of perfluoro C4, C6, and C8 carboxylates and sulfonates including the two C8s most commonly monitored, perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS). Adsorption affinity and capacity were quantified and compared to three commonly used sorbents: pulverized microporous activated carbon, single-walled carbon nanotubes, and Amberlite IRA-400 anion-exchange resin. CTF adsorbent exhibited pronouncedly higher adsorption affinity and capacity of PFAAs than other test sorbents. The remarkably strong adsorption to CTF can be attributed to the favored electrostatic interaction between the protonated triazine groups on the inner wall of the hydrophobic CTF pore and the negatively charged head groups of the PFAAs intercalated between the CTF layers. The homogeneous, nanosized pores (1.2 nm) of CTF hindered adsorption of a large-sized dissolved humic acid, thus minimizing the suppression of PFAA adsorption. Additionally, regeneration of CTF was easily accomplished by simply raising pH > 11, which inhibited the electrostatic adsorptive interaction of PFAAs. PMID:27389552

  8. Efficient production of hydrogen from formic acid using a covalent triazine framework supported molecular catalyst.

    PubMed

    Bavykina, A V; Goesten, M G; Kapteijn, F; Makkee, M; Gascon, J

    2015-03-01

    A heterogeneous molecular catalyst based on Ir(III) Cp* (Cp*=pentamethylcyclopentadienyl) attached to a covalent triazine framework (CTF) is reported. It catalyses the production of hydrogen from formic acid with initial turnover frequencies (TOFs) up to 27,000 h(-1) and turnover numbers (TONs) of more than one million in continuous operation. The CTF support, with a Brunauer-Emmett-Teller (BET) surface area of 1800 m(2)  g(-1), was constructed from an optimal 2:1 ratio of biphenyl and pyridine carbonitrile building blocks. Biphenyl building blocks induce mesoporosity and, therefore, facilitate diffusion of reactants and products whereas free pyridinic sites activate formic acid towards β-hydride elimination at the metal, rendering unprecedented rates in hydrogen production. The catalyst is air stable, produces CO-free hydrogen, and is fully recyclable. Hydrogen production rates of more than 60 mol L(-1)  h(-1) were obtained at high catalyst loadings of 16 wt % Ir, making it attractive towards process intensification.

  9. Building, characterising and catalytic activity testing of Co-C-protected amino acid complexes covalently grafted onto chloropropylated silica gel

    NASA Astrophysics Data System (ADS)

    Varga, G.; Timár, Z.; Csendes, Z.; Bajnóczi, É. G.; Carlson, S.; Canton, S. E.; Bagi, L.; Sipos, P.; Pálinkó, I.

    2015-06-01

    Co-C-protected amino acid (C-protected L-histidine, L-tyrosine, L-cysteine and L-cystine) complexes were covalently grafted onto chloropropylated silica gel, and the materials thus obtained were structurally characterised by mid/far IR and X-ray absorption spectroscopies. The superoxide dismutase-like activities of the substances were determined via the Beauchamp-Fridovich test reaction. It was found that covalent grafting and the preparation of the anchored complexes were successful in most cases. The coordinating groups varied upon changing the conditions of the syntheses. All materials displayed catalytic activity, although catalytic activities differed widely.

  10. Covalent grafting of copper amino acid complexes onto chloropropylated silica gel—an FT-IR study

    NASA Astrophysics Data System (ADS)

    Jakab, N. I.; Hernadi, K.; Kiss, J. T.; Pálinkó, I.

    2005-06-01

    Cu(amino acid) complexes were immobilised on silica gel by covalent anchoring. The amino acids were L-histidine and L-tyrosine and their BOC—( tert-butoxycarbonyl) or methyl ester protected derivatives. To gain control over the synthesis the appropriately protected amino acid was reacted with chloropropylated silica gel first. This modified material as is, or after deprotecting the anchored amino acids, was used in further steps of building the immobilised Cu(II) complex. The covalently grafted complexes were studied by FT-IR spectroscopy and computer modelling. Materials containing protected histidine ligands showed catalase activity (decomposition of H 2O 2), those containing protected or unprotected tyrosine ligands displayed tyrosinase activity (the decomposed H 2O 2 oxidised the tyrosine skeleton to a quinoidal structure).

  11. Hyaluronic acid and alginate covalent nanogels by template cross-linking in polyion complex micelle nanoreactors.

    PubMed

    De Santis, Serena; Diociaiuti, Marco; Cametti, Cesare; Masci, Giancarlo

    2014-01-30

    Hyaluronic acid (HA) and alginate (AL) covalent nanogels cross-linked with l-lysine ethyl ester were prepared by template chemical cross-linking of the polysaccharide in polyion complex micelle (PIC) nanoreactors. By using this method we were able to prepare HA and AL nanogels without organic solvents. PICs were prepared by using poly(ethylene oxide)-block-poly[(3-acrylamidopropyl)-trimethylammonium chloride] (PEO-b-PAMPTMA) or poly[(N-isopropylacrylamide)-block-PAMPTMA] (PNIPAAM-b-PAMPTMA). Only PNIPAAM-b-PAMPTMA block copolymers allowed to prepare PIC with small and controlled size. Short polysaccharide chains (Xn=50 and 63 for AL and HA, respectively, where Xn is the number of monosaccharidic units present in the polysaccharide) where used to optimize PIC formation. The remarkable difference in charge density and rigidity of HA and AL did not have a significant influence on the formation of PICs. PICs with small size (diameter of about 50-80 nm) and low polydispersity were obtained up to 5mg/mL of polymer. After cross-linking with l-lysine ethyl ester, the nanoreactors were dissociated by adding NaCl. The nanogels were easily purified and isolated by dialysis. The dissociation of the nanoreactors and the formation of the nanogels were confirmed by (1)H NMR, DLS, TEM and ζ-potential measurements. The size of the smallest nanogels in solution in the swollen state was 50-70 nm in presence of salt and 80-100 nm in water.

  12. Examination of stability of mutant photosynthetic reaction center of Rhodobacter sphaeroides I(L177)H and determination of location of bacteriochlorophyll covalently bound to the protein.

    PubMed

    Fufina, T Y; Vasilieva, L G; Shuvalov, V A

    2010-02-01

    We demonstrated earlier that as a result of the I(L177)H mutation in the photosynthetic reaction center (RC) of the bacterium Rhodobacter sphaeroides, one of the bacteriochlorophylls (BChl) binds with the L-subunit, simultaneously raising coordination stability of the central magnesium atom of the bacteriochlorophyll associated with the protein. In this study, spectral properties of wild type RC and I(L177)H in the presence of urea and SDS as well as at 48 degrees C were examined. It is shown that the I(L177)H mutation decreases the RC stability. Under denaturing conditions, some changes indicating breakdown of oligomeric structure of the complex and loss of interaction between pigments and their protein environment are observed in I(L177)H RC spectra. In addition, pheophytinization of bacteriochlorophylls occurs in both types of RC in the presence of SDS. However, an 811-nm band is observed in the spectrum of the mutant RC under these conditions, which indicates retention of one of the BChl molecules in the protein binding site and stable coordination of its central magnesium atom. It is shown that in both types of RC, monomeric BChl B(B) can be modified by sodium borohydride treatment and then extracted by acetone-methanol mixture. Spectral properties of the BChl covalently bound with the protein in I(L177)H RC do not change. The results demonstrate that BChl P(A) is the molecule of BChl tightly bound with the L-subunit in mutant RC as it was supposed earlier. PMID:20367608

  13. Self-quenched covalent fluorescent dye-nucleic acid conjugates as polymeric substrates for enzymatic nuclease assays.

    PubMed

    Trubetskoy, Vladimir S; Hagstrom, James E; Budker, Vladimir G

    2002-01-01

    A fluorescent method is described for assessing nuclease activity. The technique is based on the preparation of quenched fluorophore-nucleic acid covalent conjugates and their subsequent dequenching due to degradation by nucleases. The resulting fluorescence increase can be measured by a spectrofluorometer and exhibits subpicogram per milliliter sensitivity level for RNase A and low picogram per milliliter level for DNase I. The method is adaptable for quantitative nuclease inhibitor testing.

  14. Covalently stabilized trimethyl chitosan-hyaluronic acid nanoparticles for nasal and intradermal vaccination.

    PubMed

    Verheul, Rolf J; Slütter, Bram; Bal, Suzanne M; Bouwstra, Joke A; Jiskoot, Wim; Hennink, Wim E

    2011-11-30

    The physical stability of polyelectrolyte nanocomplexes composed of trimethyl chitosan (TMC) and hyaluronic acid (HA) is limited in physiological conditions. This may minimize the favorable adjuvant effects associated with particulate systems for nasal and intradermal immunization. Therefore, covalently stabilized nanoparticles loaded with ovalbumin (OVA) were prepared with thiolated TMC and thiolated HA via ionic gelation followed by spontaneous disulfide formation after incubation at pH 7.4 and 37°C. Also, maleimide PEG was coupled to the remaining thiol-moieties on the particles to shield their surface charge. OVA-loaded TMC/HA nanoparticles had a size of around 250-350nm, a positive zeta potential and OVA loading efficiencies up to 60%. Reacting the thiolated particles with maleimide PEG resulted in a slight reduction of zeta potential (from +7 to +4mV) and a minor increase in particle size. Stabilized TMC-S-S-HA particles (PEGylated or not) showed superior stability in saline solutions compared to non-stabilized particles (composed of nonthiolated polymers) but readily disintegrated upon incubation in a saline buffer containing 10mM dithiothreitol. In both the nasal and intradermal immunization study, OVA loaded stabilized TMC-S-S-HA particles demonstrated superior immunogenicity compared to non-stabilized particles (indicated by higher IgG titers). Intranasal, PEGylation completely abolished the beneficial effects of stabilization and it induced no enhanced immune responses against OVA after intradermal administration. In conclusion, stabilization of the TMC/HA particulate system greatly enhances the immunogenicity of OVA in nasal and intradermal vaccination.

  15. Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine

    PubMed Central

    Pletnev, Vladimir Z.; Pletneva, Nadya V.; Lukyanov, Konstantin A.; Souslova, Ekaterina A.; Fradkov, Arkady F.; Chudakov, Dmitry M.; Chepurnykh, Tatyana; Yampolsky, Ilia V.; Wlodawer, Alexander; Dauter, Zbigniew; Pletnev, Sergei

    2013-01-01

    A key property of proteins of the green fluorescent protein (GFP) family is their ability to form a chromophore group by post-translational modifications of internal amino acids, e.g. Ser65-Tyr66-Gly67 in GFP from the jellyfish Aequorea victoria (Cnidaria). Numerous structural studies have demonstrated that the green GFP-like chromophore represents the ‘core’ structure, which can be extended in red-shifted proteins owing to modifications of the protein backbone at the first chromophore-forming position. Here, the three-dimensional structures of green laGFP (λex/λem = 502/511 nm) and red laRFP (λex/λem ≃ 521/592 nm), which are fluorescent proteins (FPs) from the lancelet Branchiostoma lanceolatum (Chordata), were determined together with the structure of a red variant laRFP-ΔS83 (deletion of Ser83) with improved folding. Lancelet FPs are evolutionarily distant and share only ∼20% sequence identity with cnidarian FPs, which have been extensively characterized and widely used as genetically encoded probes. The structure of red-emitting laRFP revealed three exceptional features that have not been observed in wild-type fluorescent proteins from Cnidaria reported to date: (i) an unusual chromophore-forming sequence Gly58-Tyr59-Gly60, (ii) the presence of Gln211 at the position of the conserved catalytic Glu (Glu222 in Aequorea GFP), which proved to be crucial for chromophore formation, and (iii) the absence of modifications typical of known red chromophores and the presence of an extremely unusual covalent bond between the Tyr59 Cβ atom and the hydroxyl of the proximal Tyr62. The impact of this covalent bond on the red emission and the large Stokes shift (∼70 nm) of laRFP was verified by extensive structure-based site-directed mutagenesis. PMID:23999308

  16. Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine.

    PubMed

    Pletnev, Vladimir Z; Pletneva, Nadya V; Lukyanov, Konstantin A; Souslova, Ekaterina A; Fradkov, Arkady F; Chudakov, Dmitry M; Chepurnykh, Tatyana; Yampolsky, Ilia V; Wlodawer, Alexander; Dauter, Zbigniew; Pletnev, Sergei

    2013-09-01

    A key property of proteins of the green fluorescent protein (GFP) family is their ability to form a chromophore group by post-translational modifications of internal amino acids, e.g. Ser65-Tyr66-Gly67 in GFP from the jellyfish Aequorea victoria (Cnidaria). Numerous structural studies have demonstrated that the green GFP-like chromophore represents the `core' structure, which can be extended in red-shifted proteins owing to modifications of the protein backbone at the first chromophore-forming position. Here, the three-dimensional structures of green laGFP (λex/λem = 502/511 nm) and red laRFP (λex/λem ≃ 521/592 nm), which are fluorescent proteins (FPs) from the lancelet Branchiostoma lanceolatum (Chordata), were determined together with the structure of a red variant laRFP-ΔS83 (deletion of Ser83) with improved folding. Lancelet FPs are evolutionarily distant and share only ∼20% sequence identity with cnidarian FPs, which have been extensively characterized and widely used as genetically encoded probes. The structure of red-emitting laRFP revealed three exceptional features that have not been observed in wild-type fluorescent proteins from Cnidaria reported to date: (i) an unusual chromophore-forming sequence Gly58-Tyr59-Gly60, (ii) the presence of Gln211 at the position of the conserved catalytic Glu (Glu222 in Aequorea GFP), which proved to be crucial for chromophore formation, and (iii) the absence of modifications typical of known red chromophores and the presence of an extremely unusual covalent bond between the Tyr59 C(β) atom and the hydroxyl of the proximal Tyr62. The impact of this covalent bond on the red emission and the large Stokes shift (∼70 nm) of laRFP was verified by extensive structure-based site-directed mutagenesis.

  17. Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine.

    PubMed

    Pletnev, Vladimir Z; Pletneva, Nadya V; Lukyanov, Konstantin A; Souslova, Ekaterina A; Fradkov, Arkady F; Chudakov, Dmitry M; Chepurnykh, Tatyana; Yampolsky, Ilia V; Wlodawer, Alexander; Dauter, Zbigniew; Pletnev, Sergei

    2013-09-01

    A key property of proteins of the green fluorescent protein (GFP) family is their ability to form a chromophore group by post-translational modifications of internal amino acids, e.g. Ser65-Tyr66-Gly67 in GFP from the jellyfish Aequorea victoria (Cnidaria). Numerous structural studies have demonstrated that the green GFP-like chromophore represents the `core' structure, which can be extended in red-shifted proteins owing to modifications of the protein backbone at the first chromophore-forming position. Here, the three-dimensional structures of green laGFP (λex/λem = 502/511 nm) and red laRFP (λex/λem ≃ 521/592 nm), which are fluorescent proteins (FPs) from the lancelet Branchiostoma lanceolatum (Chordata), were determined together with the structure of a red variant laRFP-ΔS83 (deletion of Ser83) with improved folding. Lancelet FPs are evolutionarily distant and share only ∼20% sequence identity with cnidarian FPs, which have been extensively characterized and widely used as genetically encoded probes. The structure of red-emitting laRFP revealed three exceptional features that have not been observed in wild-type fluorescent proteins from Cnidaria reported to date: (i) an unusual chromophore-forming sequence Gly58-Tyr59-Gly60, (ii) the presence of Gln211 at the position of the conserved catalytic Glu (Glu222 in Aequorea GFP), which proved to be crucial for chromophore formation, and (iii) the absence of modifications typical of known red chromophores and the presence of an extremely unusual covalent bond between the Tyr59 C(β) atom and the hydroxyl of the proximal Tyr62. The impact of this covalent bond on the red emission and the large Stokes shift (∼70 nm) of laRFP was verified by extensive structure-based site-directed mutagenesis. PMID:23999308

  18. 5-amino salicylic acid bound nanoparticles for the therapy of inflammatory bowel disease.

    PubMed

    Pertuit, David; Moulari, Brice; Betz, Thomas; Nadaradjane, Arulraj; Neumann, Dirk; Ismaïli, Lhassane; Refouvelet, Bernard; Pellequer, Yann; Lamprecht, Alf

    2007-11-20

    Nanoparticles (NP) are known for their specific accumulation in the inflamed tissues in the colon and may therefore allow a selective delivery to the site of inflammation including a reduction of adverse effects. 5-amino salicylic acid (5ASA) loaded NP were designed in order to investigate their therapeutic potential in the treatment of inflammatory bowel disease. 5ASA was covalently bound to poly(caprolactone) prior to all formulation steps. Oil/water emulsification or nanoprecipitation methods were used for the NP formulation. Particle diameters were either 200 or 350 nm for emulsification or nanoprecipitation, respectively. In-vitro drug release demonstrated a significant drug retention inside the NP formulation. Toxicity of the different formulations was evaluated on Caco-2 and HEK cell culture which was slightly increased for 5ASA grafted NP in comparison to blank NP (Me5ASA-NP: 75 microg/l; blank NP: 210 microg/l). In-vivo, clinical activity score and myeloperoxidase activity decreased after administration of all 5ASA containing formulations (untreated control: 28.0+/-5.6 U/mg; 5ASA-NP (0.5 mg/kg): 15.2+/-5.6 U/mg; 5ASA solution (30 mg/kg): 16.2+/-3.6 U/mg). NP formulations allowed to lower significantly the dose of 5ASA. These oral NP formulations demonstrated their therapeutic potential and appear to be an interesting approach for the therapy of inflammatory bowel disease.

  19. Hyaluronic Acid-Based Hydrogels Containing Covalently Integrated Drug Depots: Implication for Controlling Inflammation in Mechanically Stressed Tissues

    PubMed Central

    Xiao, Longxi; Tong, Zhixiang; Chen, Yingchao; Pochan, Darrin J.; Sabanayagam, Chandran R.; Jia, Xinqiao

    2013-01-01

    Synthetic hydrogels containing covalently-integrated soft and deformable drug depots capable of releasing therapeutic molecules in response to mechanical forces are attractive candidates for the treatment of degenerated tissues that are normally load bearing. Herein, radically crosslinkable block copolymer micelles (xBCM) assembled from an amphiphilic block copolymer consisting of hydrophilic poly(acrylic acid) (PAA) partially modified with 2-hydroxyethyl acrylate, and hydrophobic poly(n-butyl acryclate) (PnBA) were employed as the drug depots and the microscopic crosslinkers for the preparation of hyaluronic acid (HA)-based, hydrogels. HA hydrogels containing covalently integrated micelles (HAxBCM) were prepared by radical polymerization of glycidyl methacrylate (GMA)-modified HA (HAGMA) in the presence of xBCMs. When micelles prepared from the parent PAA-b-PnBA without any polymerizable double bonds were used, hydrogels containing physically entrapped micelles (HApBCM) were obtained. The addition of xBCMs to a HAGMA precursor solution accelerated the gelation kinetics and altered the hydrogel mechanical properties. The resultant HAxBCM gels exhibit an elastic modulus of 847 ± 43 Pa and a compressive modulus of 9.2 ± 0.7 kPa. Diffusion analysis of Nile Red (NR)-labeled xBCMs employing fluorescence correlation spectroscopy confirmed the covalent immobilization of xBCMs in HA networks. Covalent integration of dexamethasone (DEX)-loaded xBCMs in HA gels significantly reduced the initial burst release and provided sustained release over a prolonged period. Importantly, DEX release from HAxBCM gels was accelerated by intermittently-applied external compression in a strain-dependent manner. Culturing macrophages in the presence of DEX-releasing HAxBCM gels significantly reduced cellular production of inflammatory cytokines. Incorporating mechano-responsive modules in synthetic matrices offers a novel strategy to harvest mechanical stress present in the healing wounds

  20. Hyaluronic acid-based hydrogels containing covalently integrated drug depots: implication for controlling inflammation in mechanically stressed tissues.

    PubMed

    Xiao, Longxi; Tong, Zhixiang; Chen, Yingchao; Pochan, Darrin J; Sabanayagam, Chandran R; Jia, Xinqiao

    2013-11-11

    Synthetic hydrogels containing covalently integrated soft and deformable drug depots capable of releasing therapeutic molecules in response to mechanical forces are attractive candidates for the treatment of degenerated tissues that are normally load bearing. Herein, radically cross-linkable block copolymer micelles (xBCM) assembled from an amphiphilic block copolymer consisting of hydrophilic poly(acrylic acid) (PAA) partially modified with 2-hydroxyethyl acrylate, and hydrophobic poly(n-butyl acryclate) (PnBA) were employed as the drug depots and the microscopic cross-linkers for the preparation of hyaluronic acid (HA)-based, hydrogels. HA hydrogels containing covalently integrated micelles (HAxBCM) were prepared by radical polymerization of glycidyl methacrylate (GMA)-modified HA (HAGMA) in the presence of xBCMs. When micelles prepared from the parent PAA-b-PnBA without any polymerizable double bonds were used, hydrogels containing physically entrapped micelles (HApBCM) were obtained. The addition of xBCMs to a HAGMA precursor solution accelerated the gelation kinetics and altered the hydrogel mechanical properties. The resultant HAxBCM gels exhibit an elastic modulus of 847 ± 43 Pa and a compressive modulus of 9.2 ± 0.7 kPa. Diffusion analysis of Nile Red (NR)-labeled xBCMs employing fluorescence correlation spectroscopy confirmed the covalent immobilization of xBCMs in HA networks. Covalent integration of dexamethasone (DEX)-loaded xBCMs in HA gels significantly reduced the initial burst release and provided sustained release over a prolonged period. Importantly, DEX release from HAxBCM gels was accelerated by intermittently applied external compression in a strain-dependent manner. Culturing macrophages in the presence of DEX-releasing HAxBCM gels significantly reduced cellular production of inflammatory cytokines. Incorporating mechano-responsive modules in synthetic matrices offers a novel strategy to harvest mechanical stress present in the healing

  1. Label-free fluorescent molecular beacon based on a small fluorescent molecule non-covalently bound to the intentional gap site in the stem moiety.

    PubMed

    Gao, Qiang; Lin, Kai; Zhang, Hongge; Qi, Honglan; Zhang, Chengxiao

    2010-12-15

    A label-free fluorescent molecular beacon (MB) based on a fluorescent molecule, 5,6,7-trimethyl-1,8-naphthyridin-2-ylamine (ATMND) which is non-covalently bound to the intentional gap site in the stem moiety of the label-free MB, was developed. In the absence of a cDNA, ATMND fluorescence is significantly quenched because it binds to the unpaired cytosine at the gap site by hydrogen bonding. As a result, the label-free MB shows almost no fluorescence. Upon hybridization with cDNA, the label-free MB undergoes a conformational change to destroy the gap site. This results in an effective fluorescent enhancement because of the release of the ATMND from the gap site to the solution. Fluorescence titration shows that ATMND strongly binds to the cytosine at the gap site (K(11)>10(6)). Circular-dichroism spectroscopy indicates that the binding of ATMND at the gap site of the stem moiety does not induce a significant conformational change to the hairpin DNA. Under optimal conditions, the fluorescent intensity of the label-free MB increases with an increase in cDNA concentration from 50 nM to 1.5 μM. A detection limit of 20 nM cDNA was achieved. A single mismatched target ss-DNA can be effectively discriminated from cDNA. The advantage of the label-free MB is that both its ends can be left free to introduce other useful functionalities. In addition, the label-free MB synthesis introduced in this paper is relatively simple and inexpensive because no label is required.

  2. Conformational Analysis of Free and Bound Retinoic Acid

    PubMed Central

    Fu, Zheng; Li, Xue; Merz, Kenneth M.

    2012-01-01

    The conformational profiles of unbound all-trans and 9-cis retinoic acid (RA) have been determined using classical and quantum mechanical calculations. Sixty-six all-trans-RA (ATRA) and forty-eight 9-cis-RA energy minimum conformers were identified via HF/6-31G* geometry optimizations in vacuo. Their relative conformational energies were estimated utilizing the M06, M06-2x and MP2 methods combined with the 6-311+G(d,p), aug-cc-pVDZ and aug-cc-pVTZ basis sets, as well as complete basis set MP2 extrapolations using the latter two basis sets. Single-point energy calculations performed with the M06-2x density functional were found to yield similar results to MP2/CBS for the low-energy retinoic acid conformations. Not unexpectedly, the conformational propensities of retinoic acid were governed by the orientation and arrangement of the torsion angles associated with the polyene tail. We also used previously reported QM/MM X-ray refinement results on four ATRA-protein crystal structures plus one newly refined 9-cis-RA complex (PDB ID 1XDK) in order to investigate the conformational preferences of bound retinoic acid. In the re-refined RA conformers the conjugated double bonds are nearly coplanar, which is consistent with the global minimum identified by the Omega/QM method rather than the corresponding crystallographically determined conformations given in the PDB. Consequently, a 91.3% average reduction of the local strain energy in the gas phase, as well as 92.1% in PCM solvent, was observed using the QM/MM refined structures versus the PDB deposited RA conformations. These results thus demonstrate that our QM/MM X-ray refinement approach can significantly enhance the quality of X-ray crystal structures refined by conventional refinement protocols, thereby providing reliable drug-target structural information for use in structure-based drug discovery applications. PMID:22844234

  3. Synthesis of a Sulfonated Two-Dimensional Covalent Organic Framework as an Efficient Solid Acid Catalyst for Biobased Chemical Conversion.

    PubMed

    Peng, Yongwu; Hu, Zhigang; Gao, Yongjun; Yuan, Daqiang; Kang, Zixi; Qian, Yuhong; Yan, Ning; Zhao, Dan

    2015-10-12

    Because of limited framework stability tolerance, de novo synthesis of sulfonated covalent organic frameworks (COFs) remains challenging and unexplored. Herein, a sulfonated two-dimensional crystalline COF, termed TFP-DABA, was synthesized directly from 1,3,5-triformylphloroglucinol and 2,5-diaminobenzenesulfonic acid through a previously reported Schiff base condensation reaction, followed by irreversible enol-to-keto tautomerization, which strengthened its structural stability. TFP-DABA is a highly efficient solid acid catalyst for fructose conversion with remarkable yields (97 % for 5-hydroxymethylfurfural and 65 % for 2,5-diformylfuran), good chemoselectivity, and good recyclability. The present study sheds light on the de novo synthesis of sulfonated COFs as novel solid acid catalysts for biobased chemical conversion.

  4. Synthesis of a Sulfonated Two-Dimensional Covalent Organic Framework as an Efficient Solid Acid Catalyst for Biobased Chemical Conversion.

    PubMed

    Peng, Yongwu; Hu, Zhigang; Gao, Yongjun; Yuan, Daqiang; Kang, Zixi; Qian, Yuhong; Yan, Ning; Zhao, Dan

    2015-10-12

    Because of limited framework stability tolerance, de novo synthesis of sulfonated covalent organic frameworks (COFs) remains challenging and unexplored. Herein, a sulfonated two-dimensional crystalline COF, termed TFP-DABA, was synthesized directly from 1,3,5-triformylphloroglucinol and 2,5-diaminobenzenesulfonic acid through a previously reported Schiff base condensation reaction, followed by irreversible enol-to-keto tautomerization, which strengthened its structural stability. TFP-DABA is a highly efficient solid acid catalyst for fructose conversion with remarkable yields (97 % for 5-hydroxymethylfurfural and 65 % for 2,5-diformylfuran), good chemoselectivity, and good recyclability. The present study sheds light on the de novo synthesis of sulfonated COFs as novel solid acid catalysts for biobased chemical conversion. PMID:26448524

  5. A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct.

    PubMed

    Arjunan, Palaniappa; Sax, Martin; Brunskill, Andrew; Chandrasekhar, Krishnamoorthy; Nemeria, Natalia; Zhang, Sheng; Jordan, Frank; Furey, William

    2006-06-01

    The crystal structure of the E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc) has been determined with phosphonolactylthiamin diphosphate (PLThDP) in its active site. PLThDP serves as a structural and electrostatic analogue of the natural intermediate alpha-lactylthiamin diphosphate (LThDP), in which the carboxylate from the natural substrate pyruvate is replaced by a phosphonate group. This represents the first example of an experimentally determined, three-dimensional structure of a thiamin diphosphate (ThDP)-dependent enzyme containing a covalently bound, pre-decarboxylation reaction intermediate analogue and should serve as a model for the corresponding intermediates in other ThDP-dependent decarboxylases. Regarding the PDHc-specific reaction, the presence of PLThDP induces large scale conformational changes in the enzyme. In conjunction with the E1-PLThDP and E1-ThDP structures, analysis of a H407A E1-PLThDP variant structure shows that an interaction between His-407 and PLThDP is essential for stabilization of two loop regions in the active site that are otherwise disordered in the absence of intermediate analogue. This ordering completes formation of the active site and creates a new ordered surface likely involved in interactions with the lipoyl domains of E2s within the PDHc complex. The tetrahedral intermediate analogue is tightly held in the active site through direct hydrogen bonds to residues His-407, Tyr-599, and His-640 and reveals a new, enzyme-induced, strain-related feature that appears to aid in the decarboxylation process. This feature is almost certainly present in all ThDP-dependent decarboxylases; thus its inclusion in our understanding of general thiamin catalysis is important. PMID:16531404

  6. Covalent attachment and dissociative loss of sinapinic acid to/from cysteine-containing proteins from bacterial cell lysates analyzed by MALDI-TOF-TOF mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Portions of this work were presented earlier as an oral presentation on June 2nd 2009 at the 57th American Society of Mass Spectrometry Conference (May 31-June 4, 2009, Philadelphia, PA). We report covalent attachment via a thiol ester linkage of 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid...

  7. Structures of the Michaelis Complex (1.2A) and the Covalent Acyl Intermediate (2.0A ) of Cefamandole Bound in the Active Sites of the Mycobacterium tuberculosis beta-Lactamase K72A and E166A Mutants

    SciTech Connect

    L Tremblay; h Xu; J Blanchard

    2011-12-31

    The genome of Mycobacterium tuberculosis (TB) contains a gene that encodes a highly active {beta}-lactamase, BlaC, that imparts TB with resistance to {beta}-lactam chemotherapy. The structure of covalent BlaC-{beta}-lactam complexes suggests that active site residues K73 and E166 are essential for acylation and deacylation, respectively. We have prepared the K73A and E166A mutant forms of BlaC and have determined the structures of the Michaelis complex of cefamandole and the covalently bound acyl intermediate of cefamandole at resolutions of 1.2 and 2.0 {angstrom}, respectively. These structures provide insight into the details of the catalytic mechanism.

  8. Covalent immobilization of redox enzyme on electrospun nonwoven poly(acrylonitrile-co-acrylic acid) nanofiber mesh filled with carbon nanotubes: a comprehensive study.

    PubMed

    Wang, Zhen-Gang; Ke, Bei-Bei; Xu, Zhi-Kang

    2007-07-01

    In this work, novel conductive composite nanofiber mesh possessing reactive groups was electrospun from solutions containing poly(acrylonitrile-co-acrylic acid) (PANCAA) and multi-walled carbon nanotubes (MWCNTs) for redoxase immobilization, assuming that the incorporated MWCNTs could behave as electrons transferor during enzyme catalysis. The covalent immobilization of catalase from bovine liver on the neat PANCAA nanofiber mesh or the composite one was processed in the presence of EDC/NHS. Results indicated that both the amount and activity retention of bound catalase on the composite nanofiber mesh were higher than those on the neat PANCAA nanofiber mesh, and the activity increased up to 42%. Kinetic parameters, K(m) and V(max), for the catalases immobilized on the composite nanofiber mesh were lower and higher than those on the neat one, respectively. This enhanced activity might be ascribed to either promoted electron transfer through charge-transfer complexes and the pi system of carbon nanotubes or rendered biocompatibility by modified MWCNTs. Furthermore, the immobilized catalases revealed much more stability after MWCNTs were incorporated into the polymer nanofiber mesh. However, there was no significant difference in optimum pH value and temperature, thermal stability and operational stability between these two immobilized preparations, while the two ones appeared more advantageous than the free in these properties. The effect of MWCNTs incorporation on another redox enzyme, peroxidase, was also studied and it was found that the activity increased by 68% in comparison of composite one with neat preparation. PMID:17171660

  9. 15N NMR investigation of the covalent binding of reduced TNT amines to soil humic acid, model compounds, and lignocellulose

    USGS Publications Warehouse

    Thorn, K.A.; Kennedy, K.R.

    2002-01-01

    The five major reductive degradation products of TNT-4ADNT (4-amino-2,6-dinitrotoluene), 2ADNT (2-amino-4,6-dinitrotoluene), 2,4DANT (2,4-diamino-6-nitrotoluene), 2,6DANT (2,6-diamino-4-nitrotoluene), and TAT (2,4,6-triaminotoluene)-labeled with 15N in the amine positions, were reacted with the IHSS soil humic acid and analyzed by 15N NMR spectrometry. In the absence of catalysts, all five amines underwent nucleophilic addition reactions with quinone and other carbonyl groups in the soil humic acid to form both heterocyclic and nonheterocyclic condensation products. Imine formation via 1,2-addition of the amines to quinone groups in the soil humic acid was significant with the diamines and TAT but not the monoamines. Horseradish peroxidase (HRP) catalyzed an increase in the incorporation of all five amines into the humic acid. In the case of the diamines and TAT, HRP also shifted the binding away from heterocyclic condensation product toward imine formation. A comparison of quantitative liquid phase with solid-state CP/MAS 15N NMR indicated that the CP experiment underestimated imine and heterocyclic nitrogens in humic acid, even with contact times optimal for observation of these nitrogens. Covalent binding of the mono- and diamines to 4-methylcatechol, the HRP catalyzed condensation of 4ADNT and 2,4DANT to coniferyl alcohol, and the binding of 2,4DANT to lignocellulose with and without birnessite were also examined.

  10. Breaking the dogma: PCB-derived semiquinone free radicals do not form covalent adducts with DNA, GSH, and amino acids.

    PubMed

    Wangpradit, Orarat; Rahaman, Asif; Mariappan, S V Santhana; Buettner, Garry R; Robertson, Larry W; Luthe, Gregor

    2016-02-01

    Covalent bond formations of free radical metabolites with biomolecules like DNA and proteins are thought to constitute a major mechanism of toxicity and carcinogenesis. Glutathione (GSH) is generally accepted as a radical scavenger protecting the cell. In the present study, we investigated a semiquinone radical (SQ(●-)) metabolite of the semivolatile 4-chlorobiphenyl, using electron paramagnetic resonance spectroscopy, and oxygen consumption. Proton nuclear magnetic resonance ((1)H NMR) and liquid chromatography-mass spectrometry (LC-MS) were also employed to elucidate the radical interaction with DNA, amino acids, and GSH. We found that DNA and oligonucleotides stabilized SQ(●-) by electron delocalization in the π-stacking system, resulting in persistent radical intercalated, rather than forming a covalent bond with SQ(●-). This finding was strongly supported by the semiempirical calculation of the semioccupied molecular orbital and the linear combination of the atomic orbitals, indicating 9.8 kcal mol(-1) energy gain. The insertion of SQ(●-) into the DNA strand may result in DNA strand breaks and interruption of DNA replication process or even activate radical mediated secondary reactions. The presence of amino acids resulted in a decrease of the electron paramagnetic resonance (EPR) signal of SQ(●-) and correlated with their isoelectric points. The pH shifts the equilibrium of the dianions of hydroquinone and influenced indirectly the formation of SQ(●-). Similar findings were observed with GSH and Cys. GSH and Cys functioned as indirect radical scavengers; their activities depend on their chemical equilibria with the corresponding quinones, and their further reaction via Michael addition. The generally accepted role of GSH as radical scavenger in biological systems should be reconsidered based upon these findings, questioning the generally accepted view of radical interaction of semiquinones with biologically active compounds, like DNA, amino acids

  11. Ferrocene-terminated monolayers covalently bound to hydrogen-terminated silicon surfaces. Toward the development of charge storage and communication devices.

    PubMed

    Fabre, Bruno

    2010-12-21

    The combination of monocrystalline silicon's well-defined structure and the ability to prepare hydrogen-terminated surfaces (Si-H) easily and reproducibly has made this material a very attractive substrate for immobilizing functional molecules. The functionalization of Si-H using the covalent attachment of organic monolayers has received intense attention due to the numerous potential applications of controlled and robust organic/Si interfaces. Researchers have investigated these materials in diverse fields such as molecular electronics, chemistry, and bioanalytical chemistry. Applications include the preparation of surface insulators, the incorporation of chemical or biochemical functionality at interfaces for use in photovoltaic conversion, and the development of new chemical and biological sensing devices. Unlike those of gold, silicon's electronic properties are tunable, and researchers can directly integrate silicon-based devices within electronic circuitry. Moreover, the technological processes used for the micro- and nanopatterning of silicon are numerous and mature enough for producing highly miniaturized functional electronic components. In this Account, we describe a powerful approach that integrates redox-active molecules, such as ferrocene, onto silicon toward electrically addressable systems devoted to information storage or transfer. Ferrocene exhibits attractive electrochemical characteristics: fast electron-transfer rate, low oxidation potential, and two stable redox states (neutral ferrocene and oxidized ferrocenium). Accordingly, ferrocene-modified silicon surfaces could be used as charge storage components with the bound ferrocene center as the memory element. Upon application of a positive potential to silicon, ferrocene is oxidized to its corresponding ferrocenium form. This redox change is equivalent to the change of a bit of information from the "0" to "1" state. To erase the stored charge and return the device to its initial state, a low

  12. 9-O-Acetylation of sialic acids is catalysed by CASD1 via a covalent acetyl-enzyme intermediate.

    PubMed

    Baumann, Anna-Maria T; Bakkers, Mark J G; Buettner, Falk F R; Hartmann, Maike; Grove, Melanie; Langereis, Martijn A; de Groot, Raoul J; Mühlenhoff, Martina

    2015-01-01

    Sialic acids, terminal sugars of glycoproteins and glycolipids, play important roles in development, cellular recognition processes and host-pathogen interactions. A common modification of sialic acids is 9-O-acetylation, which has been implicated in sialoglycan recognition, ganglioside biology, and the survival and drug resistance of acute lymphoblastic leukaemia cells. Despite many functional implications, the molecular basis of 9-O-acetylation has remained elusive thus far. Following cellular approaches, including selective gene knockout by CRISPR/Cas genome editing, we here show that CASD1--a previously identified human candidate gene--is essential for sialic acid 9-O-acetylation. In vitro assays with the purified N-terminal luminal domain of CASD1 demonstrate transfer of acetyl groups from acetyl-coenzyme A to CMP-activated sialic acid and formation of a covalent acetyl-enzyme intermediate. Our study provides direct evidence that CASD1 is a sialate O-acetyltransferase and serves as key enzyme in the biosynthesis of 9-O-acetylated sialoglycans. PMID:26169044

  13. Studies of optimum conditions for covalent immobilization of Candida rugosa lipase on poly(gamma-glutamic acid) by RSM.

    PubMed

    Chang, S-W; Shaw, J-F; Yang, K-H; Chang, S-F; Shieh, C-J

    2008-05-01

    Poly(gamma-glutamic acid) (gamma-PGA) is a material of polymer. Immobilization of Candida rugosa lipase (Lipase AY-30) by covalent binding on gamma-PGA led to a markedly improved performance of the enzyme. Response surface methodology (RSM) and 3-level-3-factor fractional factorial design were employed to evaluate the effects of immobilization parameters, such as immobilization time (2-6h), immobilization temperature (0-26 degrees C), and enzyme/support ratio (0.1-0.5, w/w). Based on the analysis of ridge max, the optimum immobilization conditions were as follows: immobilization time 2.3h, immobilization temperature 13.3 degrees C, and enzyme/support ratio 0.41 (w/w); the highest lipase activity obtained was 1196 U/mg-protein.

  14. Gas-phase ion/ion reactions of peptides and proteins: acid/base, redox, and covalent chemistries.

    PubMed

    Prentice, Boone M; McLuckey, Scott A

    2013-02-01

    Gas-phase ion/ion reactions are emerging as useful and flexible means for the manipulation and characterization of peptide and protein biopolymers. Acid/base-like chemical reactions (i.e., proton transfer reactions) and reduction/oxidation (redox) reactions (i.e., electron transfer reactions) represent relatively mature classes of gas-phase chemical reactions. Even so, especially in regards to redox chemistry, the widespread utility of these two types of chemistries is undergoing rapid growth and development. Additionally, a relatively new class of gas-phase ion/ion transformations is emerging which involves the selective formation of functional-group-specific covalent bonds. This feature details our current work and perspective on the developments and current capabilities of these three areas of ion/ion chemistry with an eye towards possible future directions of the field.

  15. Fabricating an Amperometric Cholesterol Biosensor by a Covalent Linkage between Poly(3-thiopheneacetic acid) and Cholesterol Oxidase

    PubMed Central

    Nien, Po-Chin; Chen, Po-Yen; Ho, Kuo-Chuan

    2009-01-01

    In this study, use of the covalent enzyme immobilization method was proposed to attach cholesterol oxidase (ChO) on a conducting polymer, poly(3-thiopheneacetic acid), [poly(3-TPAA)]. Three red-orange poly(3-TPAA) films, named electrodes A, B and C, were electropolymerized on a platinum electrode by applying a constant current of 1.5 mA, for 5, 20 and 100 s, respectively. Further, 1-ethyl-3-(3-dimethylamiopropyl)carbodiimide hydrochloride (EDC · HCl) and N-hydroxysuccinimide (NHS) were used to activate the free carboxylic groups of the conducting polymer. Afterwards, the amino groups of the cholesterol oxidase were linked on the activated groups to form peptide bonds. The best sensitivity obtained for electrode B is 4.49 mA M−1 cm−2, with a linear concentration ranging from 0 to 8 mM, which is suitable for the analysis of cholesterol in humans. The response time (t95) is between 70 and 90 s and the limit of detection is 0.42 mM, based on the signal to noise ratio equal to 3. The interference of species such as ascorbic acid and uric acid increased to 5.2 and 10.3% of the original current response, respectively, based on the current response of cholesterol (100%). With respect to the long-term stability, the sensing response retains 88% of the original current after 13 days. PMID:22573987

  16. Kinetics of rapid covalent bond formation of aniline with humic acid: ESR investigations with nitroxide spin labels

    NASA Astrophysics Data System (ADS)

    Glinka, Kevin; Matthies, Michael; Theiling, Marius; Hideg, Kalman; Steinhoff, Heinz-Jürgen

    2016-04-01

    Sulfonamide antibiotics used in livestock farming are distributed to farmland by application of slurry as fertilizer. Previous work suggests rapid covalent binding of the aniline moiety to humic acids found in soil. In the current work, kinetics of this binding were measured in X-band EPR spectroscopy by incubating Leonardite humic acid (LHA) with a paramagnetic aniline spin label (anilino-NO (2,5,5-Trimethyl-2-(3-aminophenyl)pyrrolidin-1-oxyl)). Binding was detected by a pronounced broadening of the spectral lines after incubation of LHA with anilino-NO. The time evolution of the amplitude of this feature was used for determining the reaction kinetics. Single- and double-exponential models were fitted to the data obtained for modelling one or two first-order reactions. Reaction rates of 0.16 min-1 and 0.012 min-1, were found respectively. Addition of laccase peroxidase did not change the kinetics but significantly enhanced the reacting fraction of anilino-NO. This EPR-based method provides a technically simple and effective method for following rapid binding processes of a xenobiotic substance to humic acids.

  17. Hierarchically structured, hyaluronic acid-based hydrogel matrices via the covalent integration of microgels into macroscopic networks$

    PubMed Central

    Jha, Amit K.; Malik, Manisha S.; Farach-Carson, Mary C.; Duncan, Randall L.; Jia, Xinqiao

    2010-01-01

    We aimed to develop biomimetic hydrogel matrices that not only exhibit structural hierarchy and mechanical integrity, but also present biological cues in a controlled fashion. To this end, photocrosslinkable, hyaluronic acid (HA)-based hydrogel particles (HGPs) were synthesized via an inverse emulsion crosslinking process followed by chemical modification with glycidyl methacrylate (GMA). HA modified with GMA (HA-GMA) was employed as the soluble macromer. Macroscopic hydrogels containing covalently integrated hydrogel particles (HA-c-HGP) were prepared by radical polymerization of HA-GMA in the presence of crosslinkable HGPs. The covalent linkages between the hydrogel particles and the secondary HA matrix resulted in the formation of a diffuse, fibrilar interface around the particles. Compared to the traditional bulk gels synthesized by photocrosslinking of HA-GMA, these hydrogels exhibited a reduced sol fraction and a lower equilibrium swelling ratio. When tested under uniaxial compression, the HA-c-HGP gels were more pliable than the HA-p-HGP gels and fractured at higher strain than the HA-GMA gels. Primary bovine chondrocytes were photoencapsulated in the HA matrices with minimal cell damage. The 3D microenvironment created by HA-GMA and HA HGPs not only maintained the chondrocyte phenotype but also fostered the production of cartilage specific extracellular matrix. To further improve the biological activities of the HA-c-HGP gels, bone morphogenetic protein 2 (BMP-2) was loaded into the immobilized HGPs. BMP-2 was released from the HA-c-HGP gels in a controlled manner with reduced initial burst over prolonged periods of time. The HA-c-HGP gels are promising candidates for use as bioactive matrices for cartilage tissue engineering. PMID:20936090

  18. ABS polymer electroless plating through a one-step poly(acrylic acid) covalent grafting.

    PubMed

    Garcia, Alexandre; Berthelot, Thomas; Viel, Pascal; Mesnage, Alice; Jégou, Pascale; Nekelson, Fabien; Roussel, Sébastien; Palacin, Serge

    2010-04-01

    A new, efficient, palladium- and chromium-free process for the electroless plating of acrylonitrile-butadiene-styrene (ABS) polymers has been developed. The process is based on the ion-exchange properties of poly(acrylic acid) (PAA) chemically grafted onto ABS via a simple and one-step method that prevents using classical surface conditioning. Hence, ABS electroless plating can be obtained in three steps, namely: (i) the grafting of PAA onto ABS, (ii) the copper Cu(0) seeding of the ABS surface, and (iii) the nickel or copper metallization using commercial-like electroless plating bath. IR, XPS, and SEM were used to characterize each step of the process, and the Cu loading was quantified by atomic absorption spectroscopy. This process successfully compares with the commercial one based on chromic acid etching and palladium-based seed layer, because the final metallic layer showed excellent adhesion with the ABS substrate. PMID:20361751

  19. Dynamic nuclear polarization of nucleic acid with endogenously bound manganese.

    PubMed

    Wenk, Patricia; Kaushik, Monu; Richter, Diane; Vogel, Marc; Suess, Beatrix; Corzilius, Björn

    2015-09-01

    We report the direct dynamic nuclear polarization (DNP) of (13)C nuclei of a uniformly [(13)C,(15)N]-labeled, paramagnetic full-length hammerhead ribozyme (HHRz) complex with Mn(2+) where the enhanced polarization is fully provided by the endogenously bound metal ion and no exogenous polarizing agent is added. A (13)C enhancement factor of ε = 8 was observed by intra-complex DNP at 9.4 T. In contrast, "conventional" indirect and direct DNP experiments were performed using AMUPol as polarizing agent where we obtained a (1)H enhancement factor of ε ≈ 250. Comparison with the diamagnetic (Mg(2+)) HHRz complex shows that the presence of Mn(2+) only marginally influences the (DNP-enhanced) NMR properties of the RNA. Furthermore two-dimensional correlation spectra ((15)N-(13)C and (13)C-(13)C) reveal structural inhomogeneity in the frozen, amorphous state indicating the coexistence of several conformational states. These demonstrations of intra-complex DNP using an endogenous metal ion as well as DNP-enhanced MAS NMR of RNA in general yield important information for the development of new methods in structural biology. PMID:26219517

  20. Acidity and hydrogen exchange dynamics of iron(II)-bound nitroxyl in aqueous solution.

    PubMed

    Gao, Yin; Toubaei, Abouzar; Kong, Xianqi; Wu, Gang

    2014-10-20

    Nitroxyl-iron(II) (HNO-Fe(II)) complexes are often unstable in aqueous solution, thus making them very difficult to study. Consequently, many fundamental chemical properties of Fe(II)-bound HNO have remained unknown. Using a comprehensive multinuclear ((1)H, (15)N, (17)O) NMR approach, the acidity of the Fe(II)-bound HNO in [Fe(CN)5(HNO)](3-) was investigated and its pK(a) value was determined to be greater than 11. Additionally, HNO undergoes rapid hydrogen exchange with water in aqueous solution and this exchange process is catalyzed by both acid and base. The hydrogen exchange dynamics for the Fe(II)-bound HNO have been characterized and the obtained benchmark values, when combined with the literature data on proteins, reveal that the rate of hydrogen exchange for the Fe(II)-bound HNO in the interior of globin proteins is reduced by a factor of 10(6). PMID:25205463

  1. Free and bound cinnamic acid derivatives in corsica sweet blond oranges.

    PubMed

    Carrera, Eric; El Kebir, Mohamed Vall Ould; Jacquemond, Camille; Luro, François; Lozano, Yves; Gaydou, Emile M

    2010-03-01

    Total determination of cinnamic acids (CA), including hydroxycinnamic acid derivatives is generally not accurate since, during hydrolysis, a possible degradation of dihydroxy CA such as caffeic acid could occur. Evaluations of CA (ferulic, p-coumaric, sinapic, cinnamic and caffeic acids) before and after hydrolysis have been undertaken using standards and either with or without addition of ascorbic acid and EDTA. The method was then applied to the determination of free and bound CA in five blond cultivars (Navelina, Washington navel, Pera, Salustiana and Valencia late) of sweet oranges [Citrus sinensis (L.) Osb.]. Four parts of the fruits (peel juice, flavedo, albedo and juice) have been investigated. Results show that CA are mainly bound (86% up to 92%) in the four fruit parts. The mean of total CA contents was found to be higher in peel juice (1.5 g kg(-1)) in comparison with flavedo (0.7 g kg(-1)), albedo (0.1 g kg(-1)) and juice (0.6 g kg(-1)). Free and bound ferulic acid represented 55-70% of CA in juices, followed by p-coumaric acid (20%), sinapic acid (10%) and caffeic acid (9%). Total contents of each CA in the four fruit parts are discussed and show the potential interest in orange peel wastes. PMID:20420324

  2. Structure-based non-canonical amino acid design to covalently crosslink an antibody–antigen complex

    PubMed Central

    Xu, Jianqing; Tack, Drew; Hughes, Randall A.; Ellington, Andrew D.; Gray, Jeffrey J.

    2014-01-01

    Engineering antibodies to utilize non-canonical amino acids (NCAA) should greatly expand the utility of an already important biological reagent. In particular, introducing crosslinking reagents into antibody complementarity determining regions (CDRs) should provide a means to covalently crosslink residues at the antibody–antigen interface. Unfortunately, finding the optimum position for crosslinking two proteins is often a matter of iterative guessing, even when the interface is known in atomic detail. Computer-aided antibody design can potentially greatly restrict the number of variants that must be explored in order to identify successful crosslinking sites. We have therefore used Rosetta to guide the introduction of an oxidizable crosslinking NCAA, l-3,4-dihydroxyphenylalanine (l-DOPA), into the CDRs of the anti-protective antigen scFv antibody M18, and have measured crosslinking to its cognate antigen, domain 4 of the anthrax protective antigen. Computed crosslinking distance, solvent accessibility, and interface energetics were three factors considered that could impact the efficiency of l-DOPA-mediated crosslinking. In the end, 10 variants were synthesized, and crosslinking efficiencies were generally 10% or higher, with the best variant crosslinking to 52% of the available antigen. The results suggest that computational analysis can be used in a pipeline for engineering crosslinking antibodies. The rules learned from l-DOPA crosslinking of antibodies may also be generalizable to the formation of other crosslinked interfaces and complexes. PMID:23680795

  3. Dynamic Covalent Chemistry-based Sensing: Pyrenyl Derivatives of Phenylboronic Acid for Saccharide and Formaldehyde

    NASA Astrophysics Data System (ADS)

    Chang, Xingmao; Fan, Jiayun; Wang, Min; Wang, Zhaolong; Peng, Haonan; He, Gang; Fang, Yu

    2016-08-01

    We synthesized two specially designed pyrenyl (Py) derivatives of phenylboronic acid, PSNB1 and PSNB2, of which PSNB2 self-assemble to form dynamic aggregate in methanol-water mixture (1:99, v/v) via intermolecular H-bonding and pi-pi stacking. Interestingly, the dynamic aggregate shows smart response to presence of fructose (F) as evidenced by fluorescence color change from green to blue. More interestingly, the fluorescence emission of the resulted PSNB2-F changes from blue to green with the addition of formaldehyde (FA). The reason behind is formation of a PSNB2-F dimer via FA cross-linking. Based upon the reactions as found, sensitive and fast sensing of F and FA in water was realized, of which the experimental DLs could be significantly lower than 10 μM for both analytes, and the response times are less than 1 min. It is believed that not only the materials as created may have the potential to find real-life applications but also the strategy as developed can be adopted to develop other dynamic materials.

  4. Dynamic Covalent Chemistry-based Sensing: Pyrenyl Derivatives of Phenylboronic Acid for Saccharide and Formaldehyde

    PubMed Central

    Chang, Xingmao; Fan, Jiayun; Wang, Min; Wang, Zhaolong; Peng, Haonan; He, Gang; Fang, Yu

    2016-01-01

    We synthesized two specially designed pyrenyl (Py) derivatives of phenylboronic acid, PSNB1 and PSNB2, of which PSNB2 self-assemble to form dynamic aggregate in methanol-water mixture (1:99, v/v) via intermolecular H-bonding and pi-pi stacking. Interestingly, the dynamic aggregate shows smart response to presence of fructose (F) as evidenced by fluorescence color change from green to blue. More interestingly, the fluorescence emission of the resulted PSNB2-F changes from blue to green with the addition of formaldehyde (FA). The reason behind is formation of a PSNB2-F dimer via FA cross-linking. Based upon the reactions as found, sensitive and fast sensing of F and FA in water was realized, of which the experimental DLs could be significantly lower than 10 μM for both analytes, and the response times are less than 1 min. It is believed that not only the materials as created may have the potential to find real-life applications but also the strategy as developed can be adopted to develop other dynamic materials. PMID:27498703

  5. Dynamic Covalent Chemistry-based Sensing: Pyrenyl Derivatives of Phenylboronic Acid for Saccharide and Formaldehyde.

    PubMed

    Chang, Xingmao; Fan, Jiayun; Wang, Min; Wang, Zhaolong; Peng, Haonan; He, Gang; Fang, Yu

    2016-01-01

    We synthesized two specially designed pyrenyl (Py) derivatives of phenylboronic acid, PSNB1 and PSNB2, of which PSNB2 self-assemble to form dynamic aggregate in methanol-water mixture (1:99, v/v) via intermolecular H-bonding and pi-pi stacking. Interestingly, the dynamic aggregate shows smart response to presence of fructose (F) as evidenced by fluorescence color change from green to blue. More interestingly, the fluorescence emission of the resulted PSNB2-F changes from blue to green with the addition of formaldehyde (FA). The reason behind is formation of a PSNB2-F dimer via FA cross-linking. Based upon the reactions as found, sensitive and fast sensing of F and FA in water was realized, of which the experimental DLs could be significantly lower than 10 μM for both analytes, and the response times are less than 1 min. It is believed that not only the materials as created may have the potential to find real-life applications but also the strategy as developed can be adopted to develop other dynamic materials. PMID:27498703

  6. A FRET-based probe for epidermal growth factor receptor bound non-covalently to a pair of synthetic amphipathic helixes

    SciTech Connect

    Itoh, Reina E.; Kurokawa, Kazuo; Fujioka, Aki; Sharma, Alok; Mayer, Bruce J.; Matsuda, Michiyuki . E-mail: matsudam@biken.osaka-u.ac.jp

    2005-07-01

    Epidermal growth factor (EGF) receptor plays a pivotal role in a variety of cellular functions, such as proliferation, differentiation, and migration. To monitor the EGF receptor (EGFR) activity in living cells, we developed a probe for EGFR activity based on the principle of fluorescence resonance energy transfer (FRET). Previously, we developed a probe designated as Picchu (Phosphorylation indicator of the CrkII chimeric unit), which detects the tyrosine phosphorylation of the CrkII adaptor protein. We used a pair of synthetic amphipathic helixes, WinZipA2 and WinZipB1, to bind Picchu non-covalently to the carboxyl-terminus of the EGFR. Using this modified probe named Picchu-Z, the activity of EGFR was followed in EGF-stimulated Cos7 cells. We found that a high level of tyrosine phosphorylation of Picchu-Z probe remained after endocytosis until the point when the EGFR was translocated to the perinuclear region. These findings are in agreement with the previously reported 'signaling endosome' model. Furthermore, by pulse stimulation with EGF and by acute ablation of EGFR activity with AG1478, it was suggested that the phosphorylation of Picchu-Z probe, and probably the phosphorylation of EGFR also, underwent a rapid equilibrium ({tau} {sub 1/2} < 2 min) between the phosphorylated and dephosphorylated states in the presence of EGF.

  7. Seven supramolecular frameworks constructed from combination of hydrogen-bonds and other non-covalent associations between organic acids and bis-imidazoles

    NASA Astrophysics Data System (ADS)

    Jin, Shouwen; Zhang, Huan; Zhao, Ying; Jin, Li; Ye, Xianghang; Liu, Hui; Wang, Daqi

    2015-11-01

    Seven crystalline organic acid-base adducts derived from bis(N-imidazolyl) and organic acids (2,4,6-trinitrophenol, p-nitrobenzoic acid, 3,5-dinitrobenzoic acid, oxalic acid, m-phthalic acid, and 1,5-naphthalenedisulfonic acid) were prepared and characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. The seven compounds are all organic salts. In salts 1, and 3, the L1 are monoprotonated, while in 4 and 6 the L1 are diprotonated. All supramolecular architectures involve extensive classical hydrogen bonds and C-H⋯O interactions. The role of weak and strong non-covalent interactions in the crystal packing is analyzed. The complexes displayed 2D-3D framework structures for the synergistic effect of the various non-covalent interactions. The results presented herein indicate that the strength and directionality of the N-H⋯N, N-H⋯O, O-H⋯O, O-H⋯N, N-H⋯S, and O-H⋯S hydrogen bonds between the organic acids and the ditopic imidazoles are sufficient to bring about the formation of binary organic salts.

  8. Covalently bonded sulfonic acid magnetic graphene oxide: Fe3O4@GO-Pr-SO3H as a powerful hybrid catalyst for synthesis of indazolophthalazinetriones.

    PubMed

    Doustkhah, Esmail; Rostamnia, Sadegh

    2016-09-15

    Multistep synthesis of covalently sulfonated magnetic graphene oxide was achieved by starting from Hummer's method to produce graphene oxide (GO) from chemical oxidation of graphite. Then, GO nanosheets were applied to support Fe3O4 nanoparticles (Fe3O4@GO) using co-precipitation method in the presence of GO sheets. This strategy led to formation of uniform particles of Fe3O4 on the surface of GO sheets. Then, it was sulfonated (Fe3O4@GO-Pr-SO3H) through modification with 3-mercaptopropyltrimethoxysilane (MPTMS) and subsequent oxidation with hydrogen peroxide (H2O2). In comparison, the covalently bonded propyl sulfonic acid groups were more prevailing rather to sulfonic acids of GO itself. The proposed catalyst was more active and recyclable at least for 11 runs.

  9. Covalently bonded sulfonic acid magnetic graphene oxide: Fe3O4@GO-Pr-SO3H as a powerful hybrid catalyst for synthesis of indazolophthalazinetriones.

    PubMed

    Doustkhah, Esmail; Rostamnia, Sadegh

    2016-09-15

    Multistep synthesis of covalently sulfonated magnetic graphene oxide was achieved by starting from Hummer's method to produce graphene oxide (GO) from chemical oxidation of graphite. Then, GO nanosheets were applied to support Fe3O4 nanoparticles (Fe3O4@GO) using co-precipitation method in the presence of GO sheets. This strategy led to formation of uniform particles of Fe3O4 on the surface of GO sheets. Then, it was sulfonated (Fe3O4@GO-Pr-SO3H) through modification with 3-mercaptopropyltrimethoxysilane (MPTMS) and subsequent oxidation with hydrogen peroxide (H2O2). In comparison, the covalently bonded propyl sulfonic acid groups were more prevailing rather to sulfonic acids of GO itself. The proposed catalyst was more active and recyclable at least for 11 runs. PMID:27309948

  10. A GC-ECD method for estimation of free and bound amino acids, gamma-aminobutyric acid, salicylic acid, and acetyl salicylic acid from Solanum lycopersicum (L.).

    PubMed

    Meher, Hari Charan; Gajbhiye, Vijay T; Singh, Ghanendra

    2011-01-01

    A gas chromatograph with electron capture detection method for estimation of selected metabolites--amino acids (free and bound), gamma-aminobutyric acid (GABA), salicylic acid (SA), and acetyl salicylic acid (ASA) from tomato--is reported. The method is based on nitrophenylation of the metabolites by 1-fluoro-2, 4-dinitrobenzene under aqueous alkaline conditions to form dinitophenyl derivatives. The derivatives were stable under the operating conditions of GC. Analysis of bound amino acids comprised perchloric acid precipitation of protein, alkylation (carboxymethylation) with iodoacetic acid, vapor-phase hydrolysis, and derivatization with 1-fluoro-2,4-dinitrobenzene in that order. The metabolites were resolved in 35 min, using a temperature-programmed run. The method is rapid, sensitive, and precise. It easily measured the typical amino acids (aspartate, asparagine, glutamate, glutamine, alanine, leucine, lysine, and phenylalanine) used for identification and quantification of a protein, resolved amino acids of the same mass (leucine and isoleucine), satisfactorily measured sulfur amino acid (methionine, cystine, and cysteine), and quantified GABA, SA, and ASA, as well. The developed method was validated for specificity, linearity, and precision. It has been applied and recommended for estimation of 25 metabolites from Solanum lycopersicum (L.).

  11. A GC-ECD method for estimation of free and bound amino acids, gamma-aminobutyric acid, salicylic acid, and acetyl salicylic acid from Solanum lycopersicum (L.).

    PubMed

    Meher, Hari Charan; Gajbhiye, Vijay T; Singh, Ghanendra

    2011-01-01

    A gas chromatograph with electron capture detection method for estimation of selected metabolites--amino acids (free and bound), gamma-aminobutyric acid (GABA), salicylic acid (SA), and acetyl salicylic acid (ASA) from tomato--is reported. The method is based on nitrophenylation of the metabolites by 1-fluoro-2, 4-dinitrobenzene under aqueous alkaline conditions to form dinitophenyl derivatives. The derivatives were stable under the operating conditions of GC. Analysis of bound amino acids comprised perchloric acid precipitation of protein, alkylation (carboxymethylation) with iodoacetic acid, vapor-phase hydrolysis, and derivatization with 1-fluoro-2,4-dinitrobenzene in that order. The metabolites were resolved in 35 min, using a temperature-programmed run. The method is rapid, sensitive, and precise. It easily measured the typical amino acids (aspartate, asparagine, glutamate, glutamine, alanine, leucine, lysine, and phenylalanine) used for identification and quantification of a protein, resolved amino acids of the same mass (leucine and isoleucine), satisfactorily measured sulfur amino acid (methionine, cystine, and cysteine), and quantified GABA, SA, and ASA, as well. The developed method was validated for specificity, linearity, and precision. It has been applied and recommended for estimation of 25 metabolites from Solanum lycopersicum (L.). PMID:21391500

  12. Non-covalent complexes of folic acid and oleic acid conjugated polyethylenimine: An efficient vehicle for antisense oligonucleotide delivery

    PubMed Central

    Yang, Shuang; Yang, Xuewei; Liu, Yan; Zheng, Bin; Meng, Lingjun; Lee, Robert J.; Xie, Jing; Teng, Lesheng

    2016-01-01

    Polyethylenimine (PEI) was conjugated to oleic acid (PEI-OA) and evaluated as a delivery agent for LOR-2501, an antisense oligonucleotide against ribonucleotide reductase R1 subunit. PEI-OA/LOR-2501 complexes were further coated with folic acid (FA/PEI-OA/LOR-2501) and evaluated in tumor cells. The level of cellular uptake of FA/PEI-OA/LOR-2501 was more than double that of PEI/LOR-2501 complexes, and was not affected by the expression level of folate receptor (FR) on the cell surface. Efficient delivery was seen in several cell lines. Furthermore, pathway specific cellular internalization inhibitors and markers were used to reveal the principal mechanism of cellular uptake. FA/PEI-OA/LOR-2501 significantly induced the downregulation of R1 mRNA and R1 protein. This novel formulation of FA/PEI-OA provides a reliable and highly efficient method for delivery of oligonucleotide and warrants further investigation. PMID:26263216

  13. Hydrogels with covalent and noncovalent crosslinks

    NASA Technical Reports Server (NTRS)

    Kilck, Kristi L. (Inventor); Yamaguchi, Nori (Inventor)

    2013-01-01

    A method for targeted delivery of therapeutic compounds from hydrogels is presented. The method involves administering to a cell a hydrogel in which a therapeutic compound is noncovalently bound to heparin. The hydrogel may contain covalent and non-covalent crosslinks.

  14. Seasonal and spatial changes of free and bound organic acids in total suspended particles in Guangzhou, China

    NASA Astrophysics Data System (ADS)

    Ma, Shexia; Peng, Ping'an; Song, Jianzhong; Bi, Xinhui; Zhao, Jinping; He, Lulu; Sheng, Guoying; Fu, Jiamo

    2010-12-01

    The concentrations and compositions of free and bound organic acids in total suspended particles from typical urban, suburban and forest park sites of Guangzhou were determined in this study. The free form of organic acids (solvent extractable) in aerosols in Guangzhou varied with site and season. The suburban samples contained the highest contents of alkanoic, alkenoic and dicarboxylic acids. These findings were consistent with a higher supply of hydrocarbons and NOx in the suburban area. However, concentrations of aromatic acids were similar in the urban, suburban and forest park sites. Generally, winter season samples of the acids from anthropogenic sources contained more organic acids than summer season samples due to stronger removal by wet deposition in the summer. For the acids from botanic sources, the summer season samples were higher. In addition to the free acids, bound acids (solvent non-extractable) mainly formed by esterification of free acids were also found in the samples. In general, bound acids were higher than free acids. Esterification is mainly controlled by the pKa of organic acids and the atmospheric pH value. This explains why aromatic and dicarboxylic acids occur mainly as bound forms and why the samples from urban sites contained high levels of bound acids as the pH of rain water can reach 4.53. Concentrations of alkanoic and alkenoic acids in the aerosols of Guangzhou were much higher than those in the other areas studied.

  15. Cytosolic and cell-wall-bound acid invertases from leaves of Urtica dioica L.: a comparison.

    PubMed

    Fahrendorf, T; Beck, E

    1990-01-01

    Two different forms of acid invertase (EC 3.2.1.26) were extracted from expanding leaves of the stinging nettle (Urtica dioica L.). One form was soluble and could be localized within the cytosol, whereas the other was ionically bound to the cell-wall and could not be detected in protoplasts. Both forms were purified, the latter to homogeneity. Western blotting with antibodies against the pure enzyme from cell walls was positive with the cell-wall enzyme but negative with the soluble form of acid invertase. Both forms are glycoproteins with identical molecular weights of 58 kDa. The Km values for sucrose (raffinose) are 5 mM (4.8 mM) for the soluble and 1.2 mM (3.6 mM) for the cell-wall-bound enzyme. The pH optimum of the latter is slightly more acidic (4.5) than that of the soluble invertase (5.5). Both forms could easily be distinguished by their isoelectric points which were determined at pH 4.6 for the soluble and pH 9.3 for the wall-bound enzyme. When extraction and purification were carried out in the absence of protease inhibitors, both acid invertases showed microheterogeneity ('multiple forms'). However, with benzamidine and phenylmethylsulfonylfluoride as protease inhibitors each invertase produced only one protein band upon isoelectric focusing and gel electrophoresis, respectively. PMID:24201951

  16. Extractive and oxidative removal of copper bound to humic acid in soil.

    PubMed

    Hwang, Bo-Ram; Kim, Eun-Jung; Yang, Jung-Seok; Baek, Kitae

    2015-04-01

    Copper (Cu) is often found strongly bound to natural organic matter (NOM) in soil through the formation of strong Cu-NOM complexes. Therefore, in order to successfully remediate Cu-contaminated soils, effective removal of Cu bound to soil organic matter should be considered. In this study, we investigated soil washing methods for Cu removal from a synthetic Cu-contaminated model silica soil coated with humic acid (HA) and from field contaminated soil. Various reagents were studied to extract Cu bound to NOM, which included oxidant (H2O2), base (NaOH), and chelating agents (citric acid and ethylenediaminetetraacetic acid (EDTA)). Among the wash reagents, EDTA extracted Cu most effectively since EDTA formed very strong complexes with Cu, and Cu-HA complexes were transformed into Cu-EDTA complexes. NaOH extracted slightly less Cu compared to EDTA. HA was effectively extracted from the model soil under strongly alkaline conditions with NaOH, which seemed to concurrently release Cu bound to HA. However, chemical oxidation with H2O2 was not effective at destroying Cu-HA complexes. Fourier transform infrared spectroscopy and elemental analysis revealed that chelating agents such as citrate and EDTA were adsorbed onto the model soil via possible complexation between HA and extraction agents. The extraction of Cu from a field contaminated soil sample was effective with chelating agents, while oxidative removal with H2O2 and extractive removal with NaOH separated negligible amounts of Cu from the soil. Based on these results, Cu bound to organic matter in soil could be effectively removed by chelating agents, although remnant agents may remain in the soil. PMID:25388560

  17. Extractive and oxidative removal of copper bound to humic acid in soil.

    PubMed

    Hwang, Bo-Ram; Kim, Eun-Jung; Yang, Jung-Seok; Baek, Kitae

    2015-04-01

    Copper (Cu) is often found strongly bound to natural organic matter (NOM) in soil through the formation of strong Cu-NOM complexes. Therefore, in order to successfully remediate Cu-contaminated soils, effective removal of Cu bound to soil organic matter should be considered. In this study, we investigated soil washing methods for Cu removal from a synthetic Cu-contaminated model silica soil coated with humic acid (HA) and from field contaminated soil. Various reagents were studied to extract Cu bound to NOM, which included oxidant (H2O2), base (NaOH), and chelating agents (citric acid and ethylenediaminetetraacetic acid (EDTA)). Among the wash reagents, EDTA extracted Cu most effectively since EDTA formed very strong complexes with Cu, and Cu-HA complexes were transformed into Cu-EDTA complexes. NaOH extracted slightly less Cu compared to EDTA. HA was effectively extracted from the model soil under strongly alkaline conditions with NaOH, which seemed to concurrently release Cu bound to HA. However, chemical oxidation with H2O2 was not effective at destroying Cu-HA complexes. Fourier transform infrared spectroscopy and elemental analysis revealed that chelating agents such as citrate and EDTA were adsorbed onto the model soil via possible complexation between HA and extraction agents. The extraction of Cu from a field contaminated soil sample was effective with chelating agents, while oxidative removal with H2O2 and extractive removal with NaOH separated negligible amounts of Cu from the soil. Based on these results, Cu bound to organic matter in soil could be effectively removed by chelating agents, although remnant agents may remain in the soil.

  18. Quantification of total content of non-esterified fatty acids bound to human serum albumin.

    PubMed

    Pavićević, Ivan D; Jovanović, Vesna B; Takić, Marija M; Aćimović, Jelena M; Penezić, Ana Z; Mandić, Ljuba M

    2016-09-10

    Non-esterified fatty acids bound to the human serum albumin (HSA) contribute to several HSAs properties of special concern in pathologies, for instance to the reactivity of the free HSA-Cys34 thiol group (important antioxidative thiol pool in plasma), and to the affinity for binding of molecules and ions (for example cobalt as a prominent biomarker in heart ischemia). Therefore, the method for determination of FAs bound to HSA was developed. FAs were released from HSA (previously isolated from serum by ammonium sulfate precipitation) using acidic copper(II) sulfate in phosphoric acid, extracted by n-heptane-chloroform (4:1, v/v) mixture, spotted on TL silica-gel and then developed with n-heptane-chloroform-acetic acid (5:3:0.3, v/v/v). Common office flatbed scanner and software solution for densitometric image analysis, developed in R, were used. The linearity of calibration curve in concentration range from 0.1 to 5.0mmol/L stearic acid was achieved. The method was proved to be precise (with RSD of 1.4-4.7%) and accurate. Accuracy was examined by standard addition method (recoveries 97.2-102.5%) and by comparison to results of GC. The method is sample saving, technically less demanding, and cheap, and therefore suitable for determination of FAs/HSA ratio when elevated concentrations of free FAs are reliable diagnostic/risk parameter of pathological states.

  19. Quantification of total content of non-esterified fatty acids bound to human serum albumin.

    PubMed

    Pavićević, Ivan D; Jovanović, Vesna B; Takić, Marija M; Aćimović, Jelena M; Penezić, Ana Z; Mandić, Ljuba M

    2016-09-10

    Non-esterified fatty acids bound to the human serum albumin (HSA) contribute to several HSAs properties of special concern in pathologies, for instance to the reactivity of the free HSA-Cys34 thiol group (important antioxidative thiol pool in plasma), and to the affinity for binding of molecules and ions (for example cobalt as a prominent biomarker in heart ischemia). Therefore, the method for determination of FAs bound to HSA was developed. FAs were released from HSA (previously isolated from serum by ammonium sulfate precipitation) using acidic copper(II) sulfate in phosphoric acid, extracted by n-heptane-chloroform (4:1, v/v) mixture, spotted on TL silica-gel and then developed with n-heptane-chloroform-acetic acid (5:3:0.3, v/v/v). Common office flatbed scanner and software solution for densitometric image analysis, developed in R, were used. The linearity of calibration curve in concentration range from 0.1 to 5.0mmol/L stearic acid was achieved. The method was proved to be precise (with RSD of 1.4-4.7%) and accurate. Accuracy was examined by standard addition method (recoveries 97.2-102.5%) and by comparison to results of GC. The method is sample saving, technically less demanding, and cheap, and therefore suitable for determination of FAs/HSA ratio when elevated concentrations of free FAs are reliable diagnostic/risk parameter of pathological states. PMID:27394177

  20. Intra-albumin migration of bound fatty acid probed by spin label ESR

    SciTech Connect

    Gurachevsky, Andrey . E-mail: a.gurachevsky@medinnovation.de; Shimanovitch, Ekaterina; Gurachevskaya, Tatjana; Muravsky, Vladimir

    2007-09-07

    Conventional ESR spectra of 16-doxyl-stearic acid bound to bovine and human serum albumin were recorded at different temperatures in order to investigate the status of spin-labeled fatty acid in the interior of the protein globule. A computer spectrum simulation of measured spectra, performed by non-linear least-squares fits, clearly showed two components corresponding to strongly and weakly immobilized fatty acid molecules. The two-component model was verified on spectra measured at different pH. Thermodynamic parameters of the spin probe exchange between two spin probe states were analyzed. It was concluded that at physiological conditions, fatty acid molecules permanently migrate in the globule interior between the specific binding sites and a space among albumin domains.

  1. A HSV-1 variant (1720) generates four equimolar isomers despite a 9200-bp deletion from TRL and sequences between 9200 np and 97,000 np in inverted orientation being covalently bound to sequences 94,000-126,372 np.

    PubMed

    Harland, J; Brown, S M

    1992-08-01

    The genome structure of a spontaneously generated HSV-1 strain 17 variant, 1720, has been determined by restriction endonuclease and Southern blot analysis. The short segment of 1720 is unaltered compared to the parental strain 17 genome, whereas the long segment is extensively rearranged. Almost all of TRL (approximately 9.2 kb) has been deleted and consequently IRL is converted into unique sequence. Sequences from approximately 9200 nucleotide position (np) to 97,000 np are present in inverted orientation, covalently bound to sequences in the prototype orientation from approximately 94,000 np to the L/S junction at 126,372 np. Thus, sequences from 94,000 np to 97,000 np are now diploid, with one copy in the normal orientation and location, and the other at the long terminus as an inverted repeat; no inversion of the intervening unique sequences occurs about this novel inverted repeat. In contrast, normal inversions of the long and short segments occur to give four equimolar genomic isomers, indicating that the novel long terminus has gained an "a" sequence. The duplication of sequences between 94,000 np and 97,000 np results in a genome containing two copies of UL43 and one complete and one partial copy each of genes UL42 and UL44 encoding the 65 kD DNA-binding protein and glycoprotein C, respectively. The variant has been shown to grow normally in vitro following high multiplicity infection.

  2. "Stereoscopic" 2D super-microporous phosphazene-based covalent organic framework: Design, synthesis and selective sorption towards uranium at high acidic condition.

    PubMed

    Zhang, Shuang; Zhao, Xiaosheng; Li, Bo; Bai, Chiyao; Li, Yang; Wang, Lei; Wen, Rui; Zhang, Meicheng; Ma, Lijian; Li, Shoujian

    2016-08-15

    So far, only five primary elements (C, H, O, N and B) and two types of spatial configuration (C2-C4, C6 and Td) are reported to build the monomers for synthesis of covalent organic frameworks (COFs), which have partially limited the route selection for accessing COFs with new topological structure and novel properties. Here, we reported the design and synthesis of a new "stereoscopic" 2D super-microporous phosphazene-based covalent organic framework (MPCOF) by using hexachorocyclotriphosphazene (a P-containing monomer in a C3-like spatial configuration) and p-phenylenediamine (a linker). The as-synthesized MPCOF shows high crystallinity, relatively high heat and acid stability and distinctive super-microporous structure with narrow pore-size distributions ranging from 1.0-2.1nm. The results of batch sorption experiments with a multi-ion solution containing 12 co-existing cations show that in the pH range of 1-2.5, MPCOF exhibits excellent separation efficiency for uranium with adsorption capacity more than 71mg/g and selectivity up to record-breaking 92%, and furthermore, an unreported sorption capacity (>50mg/g) and selectivity (>60%) were obtained under strong acidic condition (1M HNO3). Studies on sorption mechanism indicate that the uranium separation by MPCOF in acidic solution is realized mainly through both intra-particle diffusion and size-sieving effect. PMID:27107239

  3. "Stereoscopic" 2D super-microporous phosphazene-based covalent organic framework: Design, synthesis and selective sorption towards uranium at high acidic condition.

    PubMed

    Zhang, Shuang; Zhao, Xiaosheng; Li, Bo; Bai, Chiyao; Li, Yang; Wang, Lei; Wen, Rui; Zhang, Meicheng; Ma, Lijian; Li, Shoujian

    2016-08-15

    So far, only five primary elements (C, H, O, N and B) and two types of spatial configuration (C2-C4, C6 and Td) are reported to build the monomers for synthesis of covalent organic frameworks (COFs), which have partially limited the route selection for accessing COFs with new topological structure and novel properties. Here, we reported the design and synthesis of a new "stereoscopic" 2D super-microporous phosphazene-based covalent organic framework (MPCOF) by using hexachorocyclotriphosphazene (a P-containing monomer in a C3-like spatial configuration) and p-phenylenediamine (a linker). The as-synthesized MPCOF shows high crystallinity, relatively high heat and acid stability and distinctive super-microporous structure with narrow pore-size distributions ranging from 1.0-2.1nm. The results of batch sorption experiments with a multi-ion solution containing 12 co-existing cations show that in the pH range of 1-2.5, MPCOF exhibits excellent separation efficiency for uranium with adsorption capacity more than 71mg/g and selectivity up to record-breaking 92%, and furthermore, an unreported sorption capacity (>50mg/g) and selectivity (>60%) were obtained under strong acidic condition (1M HNO3). Studies on sorption mechanism indicate that the uranium separation by MPCOF in acidic solution is realized mainly through both intra-particle diffusion and size-sieving effect.

  4. Fatty acid preference of mycelium-bound lipase from a locally isolated strain of Geotrichum candidum.

    PubMed

    Loo, Joo Ling; Lai, Oi Mlng; Long, Kamariah; Ghazali, Hasanah Mohd

    2007-12-01

    Mycelium-bound lipase (MBL) was prepared using a strain of Geotrichum candidum isolated from local soil. At the time of maximum lipase activity (54 h), the mycelia to which the lipase was bound were harvested by filtration and centrifugation. Dry MBL was prepared by lyophilizing the mycelia obtained. The yield of MBL was 3.66 g/l with a protein content of 44.11 mg/g. The lipase activity and specific lipase activity were 22.59 and 510 U/g protein, respectively. The moisture content of the MBL was 3.85%. The activity of free (extracellular) lipase in the culture supernatant (after removal of mycelia) was less than 0.2 U/ml. The MBL showed selectivity for oleic acid over palmitic acid during hydrolysis of palm olein, indicating that the lipase from G. candidum displayed high substrate selectivity for unsaturated fatty acid containing a cis-9 double bond, even in crude form. This unique specificity of MBL could be a direct, simple and inexpensive way in the fats and oil industry for the selective hydrolysis or transesterification of cis-9 fatty acid residues in natural triacylglycerols.

  5. At low concentrations, 3,4-dihydroxyphenylacetic acid (DOPAC) binds non-covalently to alpha-synuclein and prevents its fibrillation.

    PubMed

    Zhou, Wenbo; Gallagher, Amy; Hong, Dong-Pyo; Long, Chunmei; Fink, Anthony L; Uversky, Vladimir N

    2009-05-01

    Several studies have shown that catecholamines can inhibit the fibrillation of alpha-synuclein (alpha-Syn), a small presynaptic protein whose aggregation is believed to be a critical step in the etiology of Parkinson's disease and several other neurodegenerative disorders. However, the mechanism of this inhibition is uncertain. We show here that substoichiometric concentrations of 3,4-dihydroxyphenylacetic acid (DOPAC), a normal product of the metabolism of dopamine, can inhibit the fibrillation of alpha-Syn, due to non-covalent binding of DOPAC to alpha-Syn monomer. Intriguingly, the presence of alpha-Syn accelerates the spontaneous oxidation of DOPAC, and the oxidized form of DOPAC (the quinone) is responsible for the fibrillation inhibition. In addition, the presence of DOPAC leads to the oxidation of the methionine residues of alpha-Syn, probably due to the H(2)O(2) production as a by-product of DOPAC oxidation. The lack of fibrillation results from the formation of stable oligomers, which are very similar to those observed transiently at early stages of the alpha-Syn fibrillation. A possible explanation for this phenomenon is that DOPAC stabilizes the normally transient oligomers and prevents them from subsequent fibril formation. The analysis of the alpha-Syn Y39W variant suggests that DOPAC binds non-covalently to the same N-terminal region of alpha-Syn as lipid vesicles, probably in the vicinity of residue 39. In contrast to the compounds with 1,2-dihydroxyphenyl groups (DOPAC and catechol), their 1,4-dihydroxyphenyl isomers (hydroquinone and homogentisic acid) are able to modify alpha-Syn covalently, probably due to the less steric hindrance in the Michael addition.

  6. Hybrid materials of MCM-41 functionalized by lanthanide (Tb{sup 3+}, Eu{sup 3+}) complexes of modified meta-methylbenzoic acid: Covalently bonded assembly and photoluminescence

    SciTech Connect

    Li Ying; Yan Bing

    2008-05-15

    Novel organic-inorganic mesoporous hybrid materials were synthesized by linking lanthanide (Tb{sup 3+}, Eu{sup 3+}) complexes to the mesoporous MCM-41 through the modified meta-methylbenzoic acid (MMBA-Si) using co-condensation method in the presence of the cetyltrimethylammonium bromide (CTAB) surfactant as template. The luminescence properties of these resulting materials (denoted as Ln-MMBA-MCM-41, Ln=Tb, Eu) were characterized in detail, and the results reveal that luminescent mesoporous materials have high surface area, uniformity in the ordered mesoporous structure. Moreover, the mesoporous material covalently bonded Tb{sup 3+} complex (Tb-MMBA-MCM-41) exhibits the stronger characteristic emission of Tb{sup 3+} and longer lifetime than Eu-MMBA-MCM-41 due to the triplet state energy of organic legend MMBA-Si matches with the emissive energy level of Tb{sup 3+} very well. - Graphical abstract: Novel organic-inorganic mesoporous luminescent materials were synthesized by linking lanthanide (Tb{sup 3+}, Eu{sup 3+}) complexes to covalently bond the functionalized ordered mesoporous MCM-41 with modified meta-methylbenzoic acid (MMBA)-Si by co-condensation of tetraethoxysilane (TEOS) in the presence of the cetyltrimethylammonium bromide (CTAB) surfactant as template.

  7. Bioremediation of soil contaminated with pentachlorophenol (PCP) using humic acids bound on zeolite.

    PubMed

    Dercová, Katarína; Sejáková, Zuzana; Skokanová, Marianna; Barancíková, Gabriela; Makovníková, Jaroslava

    2007-01-01

    We determined the toxicity of various chlorophenols, especially pentachlorophenol (PCP), on five bacterial strains and studied PCP biodegradation in soils amended with an organomineral complex (OMC) prepared from humic acids (organic part) bound on zeolite (inorganic part). Both components of OMC have excellent sorption properties and are of natural origin and therefore suitable to be used in the environment. Toxicity of chlorophenols depends not only on the number of chlorine atoms but also on their position on aromatic ring, and is thus regiospecific. Biodegradation of PCP was studied in three real completely characterized soil samples, Chernozem, Fluvisol, and Regosol, with and without the addition of OMC. The soils were sterilized and bioaugmented with the bacterial isolate Comamonas testosteroni CCM 7530. The immobilization effect of OMC in relation to PCP depends on the concentration of humic acids (HAs), the PCP concentration, and the content of organic carbon in soil. The microbial activity and the simulated action of acid rains led to the gradual release and biodegradation of the reversibly bound PCP without no initial toxic effect on indigenous or bioaugmented microorganisms. OMC appeared to be a good trap for PCP with potential applications in remediation technology because it reduces the potential toxicity of PCP to microbial community by lowering its bioavailability and thus facilitates its biodegradation.

  8. Relevant insight of surface characterization techniques to study covalent grafting of a biopolymer to titanium implant and its acidic resistance

    NASA Astrophysics Data System (ADS)

    D'Almeida, Mélanie; Amalric, Julien; Brunon, Céline; Grosgogeat, Brigitte; Toury, Bérangère

    2015-02-01

    Peri-implant bacterial infections are the main cause of complications in dentistry. Our group has previously proposed the attachment of chitosan on titanium implants via a covalent bond to improve its antibacterial properties while maintaining its biocompatibility. A better knowledge of the coating preparation process allows a better understanding of the bioactive coating in biological conditions. In this work, several relevant characterization techniques were used to assess an implant device during its production phase and its resistance in natural media at different pH. The titanium surface was functionalized with 3-aminopropyltriethoxysilane (APTES) followed by grafting of an organic coupling agent; succinic anhydride, able to form two covalent links, with the substrate through a Ti-O-Si bond and the biopolymer through a peptide bond. Each step of the coating synthesis as well as the presence confirmation of the biopolymer on titanium after saliva immersion was followed by FTIR-ATR, SEM, EDS, 3D profilometry, XPS and ToF-SIMS analyses. Results allowed to highlight the efficiency of each step of the process, and to propose a mechanism occurring during the chitosan coating degradation in saliva media at pH 5 and at pH 3.

  9. Construction of crystalline 2D covalent organic frameworks with remarkable chemical (acid/base) stability via a combined reversible and irreversible route.

    PubMed

    Kandambeth, Sharath; Mallick, Arijit; Lukose, Binit; Mane, Manoj V; Heine, Thomas; Banerjee, Rahul

    2012-12-01

    Two new chemically stable [acid and base] 2D crystalline covalent organic frameworks (COFs) (TpPa-1 and TpPa-2) were synthesized using combined reversible and irreversible organic reactions. Syntheses of these COFs were done by the Schiff base reactions of 1,3,5-triformylphloroglucinol (Tp) with p-phenylenediamine (Pa-1) and 2,5-dimethyl-p-phenylenediamine (Pa-2), respectively, in 1:1 mesitylene/dioxane. The expected enol-imine (OH) form underwent irreversible proton tautomerism, and only the keto-enamine form was observed. Because of the irreversible nature of the total reaction and the absence of an imine bond in the system, TpPa-1 and TpPa-2 showed strong resistance toward acid (9 N HCl) and boiling water. Moreover, TpPa-2 showed exceptional stability in base (9 N NaOH) as well.

  10. Sequential photochemical and microbial degradation of organic molecules bound to humic acid

    SciTech Connect

    Amador, J.A.; Zika, R.G. ); Alexander, M. )

    1989-11-01

    We studied the effects of photochemical processes on the mineralization by soil microorganisms of (2-{sup 14}C)glycine bound to soil humic acid. Microbial mineralization of these complexes in the dark increased inversely with the molecular weight of the complex molecules. Sunlight irradiation of glycine-humic acid complexes resulted in loss of absorbance in the UV range and an increase in the amount of {sup 14}C-labeled low-molecular-weight photoproducts and the rate and extent of mineralization. More than half of the radioactivity in the low-molecular-weight photoproducts appears to be associated with carboxylic acids. Microbial mineralization of the organic carbon increased with solar flux and was proportional to the loss of A{sub 330}. Mineralization was proportional to the percentage of the original complex that was converted to low-molecular-weight photoproducts. Only light at wavelengths below 380 nm had an effect on the molecular weight distribution of the products formed from the glycine-humic acid complexes and on the subsequent microbial mineralization. Our results indicate that photochemical processes generate low-molecular-weight, readily biodegradable molecules from high-molecular-weight complexes of glycine with humic acid.

  11. Sequential photochemical and microbial degradation of organic molecules bound to humic Acid.

    PubMed

    Amador, J A; Alexander, M; Zika, R G

    1989-11-01

    We studied the effects of photochemical processes on the mineralization by soil microorganisms of [2-C]glycine bound to soil humic acid. Microbial mineralization of these complexes in the dark increased inversely with the molecular weight of the complex molecules. Sunlight irradiation of glycine-humic acid complexes resulted in loss of absorbance in the UV range and an increase in the amount of C-labeled low-molecular-weight photoproducts and the rate and extent of mineralization. More than half of the radioactivity in the low-molecular-weight photoproducts appears to be associated with carboxylic acids. Microbial mineralization of the organic carbon increased with solar flux and was proportional to the loss of A(330). Mineralization was proportional to the percentage of the original complex that was converted to low-molecular-weight photoproducts. Only light at wavelengths below 380 nm had an effect on the molecular weight distribution of the products formed from the glycine-humic acid complexes and on the subsequent microbial mineralization. Our results indicate that photochemical processes generate low-molecular-weight, readily biodegradable molecules from high-molecular-weight complexes of glycine with humic acid.

  12. Crystal structure of a membrane-bound l-amino acid deaminase from Proteus vulgaris.

    PubMed

    Ju, Yingchen; Tong, Shuilong; Gao, Yongxiang; Zhao, Wei; Liu, Qi; Gu, Qiong; Xu, Jun; Niu, Liwen; Teng, Maikun; Zhou, Huihao

    2016-09-01

    l-amino acid oxidases/deaminases (LAAOs/LAADs) are a class of oxidoreductases catalyzing the oxidative deamination of l-amino acids to α-keto acids. They are widely distributed in eukaryotic and prokaryotic organisms, and exhibit diverse substrate specificity, post-translational modifications and cellular localization. While LAAOs isolated from snake venom have been extensively characterized, the structures and functions of LAAOs from other species are largely unknown. Here, we reported crystal structure of a bacterial membrane-bound LAAD from Proteus vulgaris (pvLAAD) in complex with flavin adenine dinucleotide (FAD). We found that the overall fold of pvLAAD does not resemble typical LAAOs. Instead it, is similar to d-amino acid oxidases (DAAOs) with an additional hydrophobic insertion module on protein surface. Structural analysis and liposome-binding assays suggested that the hydrophobic module serves as an extra membrane-binding site for LAADs. Bacteria from genera Proteus and Providencia were found to encode two classes of membrane-bound LAADs. Based on our structure, the key roles of residues Q278 and L317 in substrate selectivity were proposed and biochemically analyzed. While LAADs on the membrane were proposed to transfer electrons to respiratory chain for FAD re-oxidization, we observed that the purified pvLAAD could generate a significant amount of hydrogen peroxide in vitro, suggesting it could use dioxygen to directly re-oxidize FADH2 as what typical LAAOs usually do. These findings provide a novel insights for a better understanding this class of enzymes and will help developing biocatalysts for industrial applications. PMID:27422658

  13. Sialic Acid Is Required for Neuronal Inhibition by Soluble MAG but not for Membrane Bound MAG

    PubMed Central

    Al-Bashir, Najat; Mellado, Wilfredo; Filbin, Marie T.

    2016-01-01

    Myelin-Associated Glycoprotein (MAG), a major inhibitor of axonal growth, is a member of the immunoglobulin (Ig) super-family. Importantly, MAG (also known as Siglec-4) is a member of the Siglec family of proteins (sialic acid-binding, immunoglobulin-like lectins), MAG binds to complex gangliosides, specifically GD1a and/or GT1b. Therefore, it has been proposed as neuronal receptors for MAG inhibitory effect of axonal growth. Previously, we showed that MAG binds sialic acid through domain 1 at Arg118 and is able to inhibit axonal growth through domain 5. We developed a neurite outgrowth (NOG) assay, in which both wild type MAG and mutated MAG (MAG Arg118) are expressed on cells. In addition we also developed a soluble form NOG in which we utilized soluble MAG-Fc and mutated MAG (Arg118-Fc). Only MAG-Fc is able to inhibit NOG, but not mutated MAG (Arg118)-Fc that has been mutated at its sialic acid binding site. However, both forms of membrane bound MAG- and MAG (Arg118)- expressing cells still inhibit NOG. Here, we review various results from different groups regarding MAG’s inhibition of axonal growth. Also, we propose a model in which the sialic acid binding is not necessary for the inhibition induced by the membrane form of MAG, but it is necessary for the soluble form of MAG. This finding highlights the importance of understanding the different mechanisms by which MAG inhibits NOG in both the soluble fragmented form and the membrane-bound form in myelin debris following CNS damage. PMID:27065798

  14. 3-Nitropropionic Acid is a Suicide Inhibitor of MitochondrialRespiration that, Upon Oxidation by Complex II, Forms a Covalent AdductWith a Catalytic Base Arginine in the Active Site of the Enzyme

    SciTech Connect

    Huang, Li-shar; Sun, Gang; Cobessi, David; Wang, Andy C.; Shen,John T.; Tung, Eric Y.; Anderson, Vernon E.; Berry, Edward A.

    2005-12-01

    We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 {angstrom} resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site. In particular they support the role of Arg297 as a general base catalyst accepting a proton in the dehydrogenation of succinate. The dicarboxylate ligand in oxaloacetate-containing crystals appears to be the same as that reported for Shewanella flavocytochrome c treated with fumarate. The plant and fungal toxin 3-nitropropionic acid, an irreversible inactivator of succinate dehydrogenase, forms a covalent adduct with the side chain of Arg297. The modification eliminates a trypsin cleavage site in the flavoprotein, and tandem mass spectroscopic analysis of the new fragment shows the mass of Arg 297 to be increased by 83 Da and to have potential of losing 44 Da, consistent with decarboxylation, during fragmentation.

  15. Evidence for messenger ribonucleic acid of an ammonium-inducible glutamate dehydrogenase and synthesis, covalent modification, and degradation of enzyme subunits in uninduced Chlorella sorokiniana cells.

    PubMed Central

    Turner, K J; Bascomb, N F; Lynch, J J; Molin, W T; Thurston, C F; Schmidt, R R

    1981-01-01

    The cells of Chlorella sorokiniana cultured in nitrate medium contain no detectable catalytic activity of an ammonium-inducible nicotinamide adenine dinucleotide phosphate-specific glutamate dehydrogenase (NADP-GDH). However, several lines of experimental evidence indicated that the NADP-GDH messenger ribonucleic acid was present at high levels and was being translated in uninduced cells. First, binding studies with 125I-labeled anti-NADP-GDH immunoglobulin G and total polysomes isolated from uninduced and induced cells showed that NADP-GDH subunits were being synthesized on polysomes from both types of cells. Second, when polyadenylic acid-containing ribonucleic acid was extracted from polysomes from uninduced and induced cells and placed into a messenger ribonucleic acid-dependent in vitro translation system, NADP-GDH subunits were synthesized from the ribonucleic acid from both sources. Third, when ammonia was added to uninduced cells, NADP-GDH antigen accumulated without an apparent induction lag. Fourth, by use of a specific immunoprecipitation procedure coupled to pulse-chase studies with [35S]sulfate, it was shown that the NADP-GDH subunits are rapidly synthesized, covalently modified, and then degraded in uninduced cells. PMID:7217012

  16. Specific covalent immobilization of proteins through dityrosine cross-links.

    PubMed

    Endrizzi, Betsy J; Huang, Gang; Kiser, Patrick F; Stewart, Russell J

    2006-12-19

    Dityrosine cross-links are widely observed in nature in structural proteins such as elastin and silk. Natural oxidative cross-linking between tyrosine residues is catalyzed by a diverse group of metalloenzymes. Dityrosine formation is also catalyzed in vitro by metal-peptide complexes such as Gly-Gly-His-Ni(II). On the basis of these observations, a system was developed to specifically and covalently surface immobilize proteins through dityrosine cross-links. Methacrylate monomers of the catalytic peptide Gly-Gly-His-Tyr-OH (GGHY) and the Ni(II)-chelating group nitrilotriacetic acid (NTA) were copolymerized with acrylamide into microbeads. Green fluorescent protein (GFP), as a model protein, was genetically tagged with a tyrosine-modified His6 peptide on its carboxy terminus. GFP-YGH6, specifically associated with the NTA-Ni(II) groups, was covalently coupled to the bead surface through dityrosine bond formation catalyzed by the colocalized GGHY-Ni(II) complex. After extensive washing with EDTA to disrupt metal coordination bonds, we observed that up to 75% of the initially bound GFP-YGH6 remained covalently bound to the bead while retaining its structure and activity. Dityrosine cross-linking was confirmed by quenching the reaction with free tyrosine. The method may find particular utility in the construction and optimization of protein microarrays. PMID:17154619

  17. Amino acid residues interacting with both the bound quinone and coenzyme, pyrroloquinoline quinone, in Escherichia coli membrane-bound glucose dehydrogenase.

    PubMed

    Mustafa, Golam; Ishikawa, Yoshinori; Kobayashi, Kazuo; Migita, Catharina T; Elias, M D; Nakamura, Satsuki; Tagawa, Seiichi; Yamada, Mamoru

    2008-08-01

    The Escherichia coli membrane-bound glucose dehydrogenase (mGDH) as the primary component of the respiratory chain possesses a tightly bound ubiquinone (UQ) flanking pyrroloquinoline quinone (PQQ) as a coenzyme. Several mutants for Asp-354, Asp-466, and Lys-493, located close to PQQ, that were constructed by site-specific mutagenesis were characterized by enzymatic, pulse radiolysis, and EPR analyses. These mutants retained almost no dehydrogenase activity or ability of PQQ reduction. CD and high pressure liquid chromatography analyses revealed that K493A, D466N, and D466E mutants showed no significant difference in molecular structure from that of the wild-type mGDH but showed remarkably reduced content of bound UQ. A radiolytically generated hydrated electron (e(aq)(-)) reacted with the bound UQ of the wild enzyme and K493R mutant to form a UQ neutral semiquinone with an absorption maximum at 420 nm. Subsequently, intramolecular electron transfer from the bound UQ semiquinone to PQQ occurred. In K493R, the rate of UQ to PQQ electron transfer is about 4-fold slower than that of the wild enzyme. With D354N and D466N mutants, on the other hand, transient species with an absorption maximum at 440 nm, a characteristic of the formation of a UQ anion radical, appeared in the reaction of e(aq)(-), although the subsequent intramolecular electron transfer was hardly affected. This indicates that D354N and D466N are prevented from protonation of the UQ semiquinone radical. Moreover, EPR spectra showed that mutations on Asp-466 or Lys-493 residues changed the semiquinone state of bound UQ. Taken together, we reported here for the first time the existence of a semiquinone radical of bound UQ in purified mGDH and the difference in protonation of ubisemiquinone radical because of mutations in two different amino acid residues, located around PQQ. Furthermore, based on the present results and the spatial arrangement around PQQ, Asp-466 and Lys-493 are suggested to interact both

  18. Identification of a New Type of Covalent PPARγ Agonist using a Ligand-Linking Strategy.

    PubMed

    Ohtera, Anna; Miyamae, Yusaku; Yoshida, Kotaro; Maejima, Kazuhiro; Akita, Toru; Kakizuka, Akira; Irie, Kazuhiro; Masuda, Seiji; Kambe, Taiho; Nagao, Masaya

    2015-12-18

    Peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-activated transcription factor that plays an important role in adipogenesis and glucose metabolism. The ligand-binding pocket (LBP) of PPARγ has a large Y-shaped cavity with multiple subpockets where multiple ligands can simultaneously bind and cooperatively activate PPARγ. Focusing on this unique property of the PPARγ LBP, we describe a novel two-step cell-based strategy to develop PPARγ ligands. First, a combination of ligands that cooperatively activates PPARγ was identified using a luciferase reporter assay. Second, hybrid ligands were designed and synthesized. For proof of concept, we focused on covalent agonists, which activate PPARγ through a unique activation mechanism regulated by a covalent linkage with the Cys285 residue in the PPARγ LBP. Despite their biological significance and pharmacological potential, few covalent PPARγ agonists are known except for endogenous fatty acid metabolites. With our strategy, we determined that plant-derived cinnamic acid derivatives cooperatively activated PPARγ by combining with GW9662, an irreversible antagonist. GW9662 covalently reacts with the Cys285 residue. A docking study predicted that a cinnamic acid derivative can bind to the open cavity in GW9662-bound PPARγ LBP. On the basis of the putative binding mode, structures of both ligands were linked successfully to create a potent PPARγ agonist, which enhanced the transactivation potential of PPARγ at submicromolar levels through covalent modification of Cys285. Our approach could lead to the discovery of novel high-potency PPARγ agonists.

  19. Environmental risk assessment of acid rock drainage under uncertainty: The probability bounds and PHREEQC approach.

    PubMed

    Betrie, Getnet D; Sadiq, Rehan; Nichol, Craig; Morin, Kevin A; Tesfamariam, Solomon

    2016-01-15

    Acid rock drainage (ARD) is a major environmental problem that poses significant environmental risks during and after mining activities. A new methodology for environmental risk assessment based on probability bounds and a geochemical speciation model (PHREEQC) is presented. The methodology provides conservative and non-conservative ways of estimating risk of heavy metals posed to selected endpoints probabilistically, while propagating data and parameter uncertainties throughout the risk assessment steps. The methodology is demonstrated at a minesite located in British Columbia, Canada. The result of the methodology for the case study minesite shows the fate-and-transport of heavy metals is well simulated in the mine environment. In addition, the results of risk characterization for the case study show that there is risk due to transport of heavy metals into the environment.

  20. Hyaluronic acid-bound letrozole nanoparticles restore sensitivity to letrozole-resistant xenograft tumors in mice.

    PubMed

    Nair, Hareesh B; Huffman, Steven; Veerapaneni, Poornachand; Kirma, Nameer B; Binkley, Peter; Perla, Rao P; Evans, Dean B; Tekmal, Rajeshwar R

    2011-05-01

    Letrozole is a potent aromatase inhibitor and superior to other defined selective estrogen receptor modulators such as tamoxifen in treating hormone-responsive postmenopausal breast cancer patients. Patients who receive this drug may become insensitive to the effects of estrogen deprivation induced by letrozole. Letrozole has known side effects on bone metabolism due to systemic ablation of estrogen production. The purpose of this study was to examine the therapeutic efficacy of hyaluronic acid-bound letrozole nanoparticles (HA-Letr-NPs) in restoring sensitivity to letrozole-resistant (LTLT-Ca) cells. To target letrozole to LTLT-Ca cells, hyaluronic acid-bound letrozole nanoparticles were prepared by nanoprecipitation using biodegradable PLGA-PEG co-polymer. Binding specificity of HA to CD44 on the cell surface was analyzed in vitro using FITC-CD44 Ab and CD44 siRNA by flow cytometry. Effects on in vitro cytotoxicity and aromatase enzymatic activity of HA-Letr-NPs were performed in MCF-7 breast cancer cells, MCF-7 cells over-expressing aromatase (MCF-7/Aro), and LTLT-Ca cells resistant to letrozole. Preclinical efficacy of HA-Letr-NPs was examined in mice using LTLT-Ca xenograft tumors. HA-Letr-NPs were restricted to a maximum size of 100 nm. The in vitro drug release assay showed that the highest released concentration of letrozole occurred after 23 hours at 37 degrees C in phosphate-buffered saline. HA-Letr-NPs on MCF-7/Aro and LTLT-Ca cells showed an IC50 of 2 microM and 5 microM, respectively. HA-Letr-NPs were more efficacious in inhibiting tumor growth, reducing in vitro cellular and in vivo tumor aromatase enzyme activity more than the corresponding Letr-NPs or letrozole. HA-Letr-NPs restored and maintained a prolonged sensitivity and targeted delivery of letrozole in letrozole-resistant tumors in vivo. PMID:21780370

  1. Bound phenolics in foods, a review.

    PubMed

    Acosta-Estrada, Beatriz A; Gutiérrez-Uribe, Janet A; Serna-Saldívar, Sergio O

    2014-01-01

    Among phytochemicals, phenolic compounds have been extensively researched due to their diverse health benefits. Phenolic compounds occur mostly as soluble conjugates and insoluble forms, covalently bound to sugar moieties or cell wall structural components. Absorption mechanisms for bound phenolic compounds in the gastrointestinal tract greatly depend on the liberation of sugar moieties. Food processes such as fermentation, malting, thermoplastic extrusion or enzymatic, alkaline and acid hydrolyses occasionally assisted with microwave or ultrasound have potential to release phenolics associated to cell walls. Different kinds of wet chemistry methodologies to release and detect bound phenolic have been developed. These include harsh heat treatments, chemical modifications or biocatalysis. New protocols for processing and determining phenolics in food matrices must be devised in order to release bound phenolics and for quality control in the growing functional food industry.

  2. Improved hemocompatibility and endothelialization of vascular grafts by covalent immobilization of sulfated silk fibroin on poly(lactic-co-glycolic acid) scaffolds.

    PubMed

    Liu, Haifeng; Li, Xiaoming; Niu, Xufeng; Zhou, Gang; Li, Ping; Fan, Yubo

    2011-08-01

    Endothelialization of vascular grafts prior to implantation has been investigated widely to enhance biocompatibility and antithrombogenicity. Thrombosis of artificial vessels is typically caused by platelet adhesion and agglomeration following endothelial cells detachment when exposed to the shear stress of blood circulation. The present study thus aimed at preventing platelet adhesion and aggregation onto biomaterials before the endothelial confluence is fully achieved. We report this modification of poly(lactic-co-glycolic acid) (PLGA) scaffolds, both to impart hemocompatibility to prevent platelet adhesion and aggregation before the endothelial confluence is fully achieved and to support EC growth to accelerate endothelialization. The modification was achieved by covalent immobilization of sulfated silk fibroin on PLGA scaffolds using γ irradiation. Using phosphate-buffered saline (PBS) as an aging medium, it was demonstrated that the scaffolds prepared by γ irradiation had a good retention of sulfated silk fibroin. The systematic in vitro hemocompatibility evaluation revealed that sulfated silk fibroin covalently immobilized PLGA (S-PLGA) scaffolds-reduced platelet adhesion and activation, prolonged whole blood clotting time, activated partial thromboplastin time (APTT), thrombin time (TT), and prothrombin time (PT). To evaluate further in vitro cytocompatibility of the scaffolds, we seeded vascular ECs on the scaffolds and cultured them for 2 weeks. The ECs were seen to attach and proliferate well on S-PLGA scaffolds, forming cell aggregates that gradually increased in size and fused with adjacent cell aggregates to form a monolayer covering the scaffold surface. Moreover, it was demonstrated through the gene transcript levels and the protein expressions of EC-specific markers that the cell functions of ECs on S-PLGA scaffolds were better preserved than those on PLGA scaffolds. Therefore, this study has described the generation of a vascular graft that

  3. Covalent Defects Restrict Supramolecular Self-Assembly of Homopolypeptides: Case Study of β2-Fibrils of Poly-L-Glutamic Acid

    PubMed Central

    Fulara, Aleksandra; Hernik, Agnieszka; Nieznańska, Hanna; Dzwolak, Wojciech

    2014-01-01

    Poly-L-glutamic acid (PLGA) often serves as a model in studies on amyloid fibrils and conformational transitions in proteins, and as a precursor for synthetic biomaterials. Aggregation of PLGA chains and formation of amyloid-like fibrils was shown to continue on higher levels of superstructural self-assembly coinciding with the appearance of so-called β2-sheet conformation manifesting in dramatic redshift of infrared amide I′ band below 1600 cm−1. This spectral hallmark has been attributed to network of bifurcated hydrogen bonds coupling C = O and N-D (N-H) groups of the main chains to glutamate side chains. However, other authors reported that, under essentially identical conditions, PLGA forms the conventional in terms of infrared characteristics β1-sheet structure (exciton-split amide I′ band with peaks at ca. 1616 and 1683 cm−1). Here we attempt to shed light on this discrepancy by studying the effect of increasing concentration of intentionally induced defects in PLGA on the tendency to form β1/β2-type aggregates using infrared spectroscopy. We have employed carbodiimide-mediated covalent modification of Glu side chains with n-butylamine (NBA), as well as electrostatics-driven inclusion of polylysine chains, as two different ways to trigger structural defects in PLGA. Our study depicts a clear correlation between concentration of defects in PLGA and increasing tendency to depart from the β2-structure toward the one less demanding in terms of chemical uniformity of side chains: β1-structure. The varying predisposition to form β1- or β2-type aggregates assessed by infrared absorption was compared with the degree of morphological order observed in electron microscopy images. Our results are discussed in the context of latent covalent defects in homopolypeptides (especially with side chains capable of hydrogen-bonding) that could obscure their actual propensities to adopt different conformations, and limit applications in the field of synthetic

  4. The effect of covalently bonded conjugated linoleic acid on the reduction of oxidative stress and blood coagulation for polysulfone hemodialyzer membrane.

    PubMed

    Kung, Fu-Chen; Yang, Ming-Chine

    2006-05-30

    Conjugated linoleic acid (CLA) was covalently bonded to a layer of poly(acrylic acid) (PAA) grafted onto the surface of polysulfone (PSF) membranes. The effect of CLA-bonding on oxidative stress and blood coagulation was then evaluated. The surface was characterized with contact angle measurement and FTIR spectroscopy. Blood coagulation, platelet aggregation, and oxidative stress were evaluated using human blood. The complete blood count (CBC) and coagulation time (CT) were evaluated in vitro for hemocompatibility. The production of reactive oxygen species (ROS) was measured by the chemiluminescence (CL) method to evaluate the oxidative stress. The results showed that the CLA-bonding PSF membrane exhibited more stable CBC values, longer CT, and less adsorption of plasma proteins than the unmodified PSF membrane. In addition, the CL counts of hydrogen peroxide and superoxide values for CLA-bonding PSF membrane were more stable than for unmodified PSF membrane. These results demonstrate that CLA-bonding can improve the blood compatibility of PSF membrane. The CLA-bonding PSF membrane could offer protection for patients against oxidative stress and could also reduce the dosage of anticoagulant required during hemodialysis.

  5. Stimulation of proximal tubular cell apoptosis by albumin-bound fatty acids mediated by peroxisome proliferator activated receptor-gamma.

    PubMed

    Arici, Mustafa; Chana, Ravinder; Lewington, Andrew; Brown, Jez; Brunskill, Nigel John

    2003-01-01

    In nephrotic syndrome, large quantities of albumin enter the kidney tubule. This albumin carries with it a heavy load of fatty acids to which the proximal tubule cells are exposed at high concentration. It is postulated that exposure to fatty acids in this way is injurious to proximal tubule cells. This study has examined the ability of fatty acids to interact with peroxisome proliferator-activated receptors (PPAR) in primary cultures of human proximal tubule cells. Luciferase reporter assays in transiently transfected human proximal tubule cells were used to show that albumin bound fatty acids and other agonists activate PPARgamma in a dose-dependent manner. One of the consequences of this activation is apoptosis of the cells as determined by changes in cell morphology, evidence of PARP cleavage, and appearance of DNA laddering. Overexpression of PPARgamma in these cells also results in enhanced apoptosis. Both fatty acid-induced PPAR activation and apoptosis in these cells can be blocked by PPAR response element decoy oligonucleotides. Activation of PPARgamma by the specific agonist PGJ(2) is associated with inhibition of cell proliferation, whereas activation by albumin bound fatty acids is accompanied by increased proliferation. However, the net balance of apoptosis/proliferation favors deletion of cells. These results implicate albumin-bound fatty acids as important mediators of tubular injury in nephrosis and provide fresh impetus for pursuit of lipid-lowering strategies in proteinuric renal disease. PMID:12506134

  6. Transcriptional template activity of covalently modified DNA.

    PubMed

    Tolwińska-Stańczyk, Z; Wilmańska, D; Studzian, K; Gniazdowski, M

    1997-03-01

    The transcriptional template activity of covalent modified DNA is compared. 8-Methoxypsoralen (MOP), 3,4'dimethyl-8-methoxypsoralen (DMMOP) and benzopsoralen (BP) forming with DNA covalent complexes upon UV irradiation and exhibiting preference to pyrimidines, mostly thymines, differ in their cross-linking potency. MOP and DMMOP form both monoadducts and diadducts while no cross-links are formed by BP. Nitracrine (NC) forms covalent complexes with DNA upon reductive activation with dithiothreitol exhibiting a preference to purines and low cross-linking potency. Semilogarithmic plots of the relative template activity against the number of the drugs molecules covalently bound per 10(3) DNA nucleotides fit to regression lines corresponding to one-hit inactivation characteristics. The number of drug molecules decreasing RNA synthesis to 37% differ from 0.25 to 1.26 depending on the template used and the base preference but no dependence on the cross-linking potency was found. PMID:9067423

  7. Locking GTPases covalently in their functional states.

    PubMed

    Wiegandt, David; Vieweg, Sophie; Hofmann, Frank; Koch, Daniel; Li, Fu; Wu, Yao-Wen; Itzen, Aymelt; Müller, Matthias P; Goody, Roger S

    2015-01-01

    GTPases act as key regulators of many cellular processes by switching between active (GTP-bound) and inactive (GDP-bound) states. In many cases, understanding their mode of action has been aided by artificially stabilizing one of these states either by designing mutant proteins or by complexation with non-hydrolysable GTP analogues. Because of inherent disadvantages in these approaches, we have developed acryl-bearing GTP and GDP derivatives that can be covalently linked with strategically placed cysteines within the GTPase of interest. Binding studies with GTPase-interacting proteins and X-ray crystallography analysis demonstrate that the molecular properties of the covalent GTPase-acryl-nucleotide adducts are a faithful reflection of those of the corresponding native states and are advantageously permanently locked in a defined nucleotide (that is active or inactive) state. In a first application, in vivo experiments using covalently locked Rab5 variants provide new insights into the mechanism of correct intracellular localization of Rab proteins.

  8. Locking GTPases covalently in their functional states

    NASA Astrophysics Data System (ADS)

    Wiegandt, David; Vieweg, Sophie; Hofmann, Frank; Koch, Daniel; Li, Fu; Wu, Yao-Wen; Itzen, Aymelt; Müller, Matthias P.; Goody, Roger S.

    2015-07-01

    GTPases act as key regulators of many cellular processes by switching between active (GTP-bound) and inactive (GDP-bound) states. In many cases, understanding their mode of action has been aided by artificially stabilizing one of these states either by designing mutant proteins or by complexation with non-hydrolysable GTP analogues. Because of inherent disadvantages in these approaches, we have developed acryl-bearing GTP and GDP derivatives that can be covalently linked with strategically placed cysteines within the GTPase of interest. Binding studies with GTPase-interacting proteins and X-ray crystallography analysis demonstrate that the molecular properties of the covalent GTPase-acryl-nucleotide adducts are a faithful reflection of those of the corresponding native states and are advantageously permanently locked in a defined nucleotide (that is active or inactive) state. In a first application, in vivo experiments using covalently locked Rab5 variants provide new insights into the mechanism of correct intracellular localization of Rab proteins.

  9. Identification/quantification of free and bound phenolic acids in peel and pulp of apples (Malus domestica) using high resolution mass spectrometry (HRMS).

    PubMed

    Lee, Jihyun; Chan, Bronte Lee Shan; Mitchell, Alyson E

    2017-01-15

    Free and bound phenolic acids were measured in the pulp and peel of four varieties of apples using high resolution mass spectrometry. Twenty-five phenolic acids were identified and included: 8 hydroxybenzoic acids, 11 hydroxycinnamic acids, 5 hydroxyphenylacetic acids, and 1 hydoxyphenylpropanoic acid. Several phenolics are tentatively identified for the first time in apples and include: methyl gallate, ethyl gallate, hydroxy phenyl acetic acid, three phenylacetic acid isomers, 3-(4-hydroxyphenyl)propionic acid, and homoveratric acid. With exception of chlorogenic and caffeic acid, most phenolic acids were quantified for the first time in apples. Significant varietal differences (p<0.05) were observed in both peel and pulp. The levels of total phenolic acids were higher in the pulp as compared to apple peel (dry weight) in all varieties. Coumaroylquinic, protocatechuic, 4-hydroxybenzoic, vanillic and t-ferulic acids were present in free forms. With exception of chlorogenic acid, all other phenolic acids were present only as bound forms.

  10. Fischer carbene mediated covalent grafting of a peptide nucleic acid on gold surfaces and IR optical detection of DNA hybridization with a transition metalcarbonyl label

    NASA Astrophysics Data System (ADS)

    Srivastava, Pratima; Ghasemi, Mahsa; Ray, Namrata; Sarkar, Amitabha; Kocabova, Jana; Lachmanova, Stepanka; Hromadova, Magdalena; Boujday, Souhir; Cauteruccio, Silvia; Thakare, Pramod; Licandro, Emanuela; Fosse, Céline; Salmain, Michèle

    2016-11-01

    Amine-reactive surfaces comprising N-hydroxysuccinimide ester groups as well as much more unusual Fischer alkoxymetallocarbene groups were generated on gold-coated surfaces via self-assembled monolayers of carboxy- and azido-terminated thiolates, respectively. These functions were further used to immobilize homothymine peptide nucleic acid (PNA) decamer in a covalent fashion involving the primary amine located at its N-terminus. These stepwise processes were monitored by polarization modulation reflection - absorption infrared spectroscopy (PM-RAIRS) that gave useful information on the molecular composition of the organic layers. PNA grafting and hybridization with complementary DNA strand were successfully transduced by quartz crystal microbalance (QCM) measurements. Unfortunately, attempts to transduce the hybridization optically by IR in a label-free fashion were inconclusive. Therefore we undertook to introduce an IR reporter group, namely a transition metalcarbonyl (TMC) entity at the 5‧ terminus of complementary DNA. Evidence for the formation of PNA-DNA heteroduplex was brought by the presence of ν(Ctbnd O) bands in the 2000 cm-1 region of the IR spectrum of the gold surface owing to the metalcarbonyl label.

  11. Extending the Diffuse Layer Model of Surface Acidity Behavior: III. Estimating Bound Site Activity Coefficients

    EPA Science Inventory

    Although detailed thermodynamic analyses of the 2-pK diffuse layer surface complexation model generally specify bound site activity coefficients for the purpose of accounting for those non-ideal excess free energies contributing to bound site electrochemical potentials, in applic...

  12. Covalent modification of proteins by cocaine

    NASA Astrophysics Data System (ADS)

    Deng, Shi-Xian; Bharat, Narine; Fischman, Marian C.; Landry, Donald W.

    2002-03-01

    Cocaine covalently modifies proteins through a reaction in which the methyl ester of cocaine acylates the -amino group of lysine residues. This reaction is highly specific in vitro, because no other amino acid reacts with cocaine, and only cocaine's methyl ester reacts with the lysine side chain. Covalently modified proteins were present in the plasma of rats and human subjects chronically exposed to cocaine. Modified endogenous proteins are immunogenic, and specific antibodies were elicited in mouse and detected in the plasma of human subjects. Covalent modification of proteins could explain cocaine's autoimmune effects and provide a new biochemical approach to cocaine's long-term actions.

  13. Factors influencing the covalent binding of (+/-)-7 beta, 8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene to ribonucleic acids

    SciTech Connect

    Zytkovicz, T.H.; Liarakos, C.D.

    1984-09-01

    The covalent binding of the ultimate carcinogen (+/-)-7 beta, 8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10-tetrahydrobenzo (alpha)pyrene (BPDE) to enriched ovalbumin messenger RNA (mRNAov) of known sequence was examined. Incubation of mRNAov with elevated concentrations of labeled BPDE in TE buffer (0.02 M Tris X HCl, 1 mM EDTA, pH 7.2) containing 0.1 M KCl and 10 mM MgCl2 resulted in approximately 30 BPDEs covalently bound per RNA molecule. Covalent binding in the absence of KCl and MgCl2 resulted in a significant increase in binding to 110 BPDEs bound per molecule or modification of 12% of the total guanosine and adenosine nucleotides present. The nucleoside adducts formed were nearly all guanosine and adenosine in a ratio of 1.6:1.0. It was also observed that digestion of mRNAov with T2 RNase prior to reaction with BPDE resulted in a 52% decrease in guanosine adduct formation and a 93% decrease in adenosine adducts compared with undigested controls. Comparison of the binding of labeled BPDE to 18 S and 28 S ribosomal RNAs and to mRNAov revealed that the guanosine adduct to adenosine adduct ratio and the number of BPDEs bound increased with increasing G-C content. The results reported here show that ionic composition of the medium, G-C content, and the presence of a polymeric state can significantly influence the quantitative and/or qualitative nucleoside BPDE adducts formed.

  14. Development and Application of Pyrolysis Gas Chromatography/Mass Spectrometry for the Analysis of Bound Trinitrotoluene Residues in Soil

    USGS Publications Warehouse

    Weiss, J.M.; Mckay, A.J.; Derito, C.; Watanabe, C.; Thorn, K.A.; Madsen, E.L.

    2004-01-01

    TNT (trinitrotoluene) is a contaminant of global environmental significance, yet determining its environmental fate has posed longstanding challenges. To date, only differential extraction-based approaches have been able to determine the presence of covalently bound, reduced forms of TNT in field soils. Here, we employed thermal elution, pyrolysis, and gas chromatography/mass spectrometry (GC/MS) to distinguish between covalently bound and noncovalently bound reduced forms of TNT in soil. Model soil organic matter-based matrixes were used to develop an assay in which noncovalently bound (monomeric) aminodinitrotoluene (ADNT) and diaminonitrotoluene (DANT) were desorbed from the matrix and analyzed at a lower temperature than covalently bound forms of these same compounds. A thermal desorption technique, evolved gas analysis, was initially employed to differentiate between covalently bound and added 15N-labeled monomeric compounds. A refined thermal elution procedure, termed "double-shot analysis" (DSA), allowed a sample to be sequentially analyzed in two phases. In phase 1, all of an added 15N-labeled monomeric contaminant was eluted from the sample at relatively low temperature. In phase 2 during high-temperature pyrolysis, the remaining covalently bound contaminants were detected. DSA analysis of soil from the Louisiana Army Ammunition Plant (LAAP; ???5000 ppm TNT) revealed the presence of DANT, ADNT, and TNT. After scrutinizing the DSA data and comparing them to results from solvent-extracted and base/acid-hydrolyzed LAAP soil, we concluded that the TNT was a noncovalently bound "carryover" from phase 1. Thus, the pyrolysis-GC/MS technique successfully defined covalently bound pools of ADNT and DANT in the field soil sample.

  15. Composition of free and peptide-bound amino acids in beef chuck, loin, and round cuts.

    PubMed

    Wu, G; Cross, H R; Gehring, K B; Savell, J W; Arnold, A N; McNeill, S H

    2016-06-01

    Meat is a food for humans. However, beef consumption in the United States has steadily declined by >14% over the past decade due to a variety of factors, including insufficient knowledge of animal protein. This study quantified all proteinogenic AA as well as nutritionally and physiologically significant nonproteinogenic AA and small peptides in beef cuts from 3 subprimals (chuck, round, and loin). Beef carcasses ( = 10) were selected at 3 commercial packing plants in the United States. Retail-cut samples were analyzed for the nitrogenous substances after acid, alkaline, or enzymatic hydrolysis and after deproteinization. In these chuck, round, and loin cuts, total amounts of glutamate (free plus peptide bound) were the highest (69-75 mg/g dry weight) followed by lysine, leucine, arginine, and glutamine in descending order. This is the first study to determine aspartate, asparagine, glutamate, and glutamine in meat proteins of any animal species. In all the beef samples evaluated, glutamine was the most abundant free AA (4.0-5.7 mg/g dry weight) followed by taurine, alanine, glutamate, and β-alanine. Additionally, samples from all beef cuts had high concentrations of anserine, carnosine, and glutathione, which were 2.8 to 3.7, 15.2 to 24.2, and 0.68 to 0.79 mg/g dry weight, respectively. Beef top loin steaks appear to provide higher protein nutrition values than top round steaks and under blade roasts, but all are excellent sources of proteinogenic AA as well as antioxidant AA and peptides to improve human growth, development, and health. Our findings may help guide future decisions regarding human and animal nutrition. PMID:27285936

  16. Toward "stable-on-the-table" enzymes: improving key properties of catalase by covalent conjugation with poly(acrylic acid).

    PubMed

    Riccardi, Caterina M; Cole, Kyle S; Benson, Kyle R; Ward, Jessamyn R; Bassett, Kayla M; Zhang, Yiren; Zore, Omkar V; Stromer, Bobbi; Kasi, Rajeswari M; Kumar, Challa V

    2014-08-20

    Several key properties of catalase such as thermal stability, resistance to protease degradation, and resistance to ascorbate inhibition were improved, while retaining its structure and activity, by conjugation to poly(acrylic acid) (PAA, Mw 8000) via carbodiimide chemistry where the amine groups on the protein are appended to the carboxyl groups of the polymer. Catalase conjugation was examined at three different pH values (pH 5.0, 6.0, and 7.0) and at three distinct mole ratios (1:100, 1:500, and 1:1000) of catalase to PAA at each reaction pH. The corresponding products are labeled as Cat-PAA(x)-y, where x is the protein to polymer mole ratio and y is the pH used for the synthesis. The coupling reaction consumed about 60-70% of the primary amines on the catalase; all samples were completely water-soluble and formed nanogels, as evidenced by gel electrophoresis and electron microscopy. The UV circular dichroism (CD) spectra indicated substantial retention of protein secondary structure for all samples, which increased to 100% with increasing pH of the synthesis and polymer mole fraction. Soret CD bands of all samples indicated loss of ∼50% of band intensities, independent of the reaction pH. Catalytic activities of the conjugates increased with increasing synthesis pH, where 55-80% and 90-100% activity was retained for all samples synthesized at pH 5.0 and pH 7.0, respectively, and the Km or Vmax values of Cat-PAA(100)-7 did not differ significantly from those of the free enzyme. All conjugates synthesized at pH 7.0 were thermally stable even when heated to ∼85-90 °C, while native catalase denatured between 55 and 65 °C. All conjugates retained 40-90% of their original activities even after storing for 10 weeks at 8 °C, while unmodified catalase lost all of its activity within 2 weeks, under similar storage conditions. Interestingly, PAA surrounding catalase limited access to the enzyme from large molecules like proteases and significantly increased

  17. Inactivation of Matrix-bound MMPs by Cross-linking Agents in Acid Etched Dentin

    PubMed Central

    Scheffel, Débora Lopes Salles; Hebling, Josimeri; Scheffel, Régis Henke; Agee, Kelly A.; Turco, Gianluca; de Souza Costa, Carlos Alberto; Pashley, David H.

    2014-01-01

    Objectives Published TEM analysis of in vivo resin-dentin bonds shows that in 44 months almost 70% of collagen fibrils from the hybrid layer disappear. Matrix metalloproteinases (MMPs) play an important role in that process and are thought to be the main factor responsible for the solubitization of dentin collagen. Therefore, this study aimed to evaluate the inactivation of matrix-bound MMPs by carbodiimide (EDC) or proanthocyanidin (PA) both cross-linking agents, or the MMP-inhibitor, chlorhexidine (CHX), on acid-etched dentin using a simplified MMP assay method. Methods Dentin beams (1×1×6mm) were obtained from mid-coronal dentin of sound third molars and randomly divided into 6 groups (G) according to the dentin treatment: G1: Deionized water (control), G2: 0.1M EDC, G3: 0.5M EDC, G4: 0.5M EDC+35% HEMA, G5: 5% Proanthocyanidin (PA) and G6: 2% CHX. The beams were etched for 15s with 37% phosphoric acid, rinsed and then immersed for 60s in one of the treatment solutions. The total MMP activity of dentin was analyzed for 1 h by colorimetric assay (Sensolyte). Data were submitted to Wilcoxon non-parametric test and Mann-Whitney tests (p>0.05). Results All experimental cross-linking solutions significantly reduced MMP activity compared to control, except 0.1M EDC (53.6% ±16.1). No difference was observed between cross-linking agents and 2% CHX 0.5M EDC + 35% HEMA (92.3% ±8.0) was similar to 0.5M EDC (89.1% ±6.4), 5% PA (100.8% ±10.9) and 2% CHX (83.4% ±10.9). Conclusion Dentin treatment with cross-linking agents is effective to significantly reduce MMP activity. Mixing 0.5M EDC and 35% HEMA did not influence EDC inhibitor potential. PMID:23786610

  18. Comparative immunogenicity of conjugates composed of Escherichia coli O111 O-specific polysaccharide, prepared by treatment with acetic acid or hydrazine, bound to tetanus toxoid by two synthetic schemes.

    PubMed Central

    Gupta, R K; Egan, W; Bryla, D A; Robbins, J B; Szu, S C

    1995-01-01

    Escherichia coli O111, of various H types and virulence factors, causes enteritis throughout the world, especially in young children. This O type is found rarely in healthy individuals. Serum antibodies to the O-specific polysaccharide of O111 lipopolysaccharide (LPS) protect mice and dogs against infection with this E. coli serotype. The O111 O-specific polysaccharide is composed of a pentasaccharide repeat unit with two colitoses bound to the C-3 and C-6 of glucose in a trisaccharide backbone; this structure is identical to that of Salmonella adelaide (O35), another enteric pathogen. Nonpyrogenic O111 O-specific polysaccharide was prepared by treatment of its LPS with acetic acid (O-SP) or the organic base hydrazine (DeA-LPS). The O-SP had a reduced concentration of colitose. These products were derivatized with adipic acid dihydrazide (ADH) or thiolated with N-succinimidyl-3(2-pyridyldithio) propionate (SPDP). The four derivatives were covalently bound to tetanus toxoid (TT) by carbodiimide-mediated condensation or with SPDP to form conjugates. Immunization of BALB/c and general-purpose mice by a clinically acceptable route showed that DeA-LPS-TTADH, of the four conjugates, elicited the highest level of LPS antibodies. Possible reasons to explain this differential immunogenicity between the four conjugates are discussed. PMID:7542631

  19. Immobilization of a thermostable alpha-amylase by covalent binding to an alginate matrix increases high temperature usability.

    PubMed

    Tee, Boon L; Kaletunç, Gönül

    2009-01-01

    Thermostable alpha-amylase was covalently bound to calcium alginate matrix to be used for starch hydrolysis at liquefaction temperature of 95 degrees C. 1-ethyl-3-(3-dimethylamino-propyl) carbodiimide hydrochloride (EDAC) was used as crosslinker. EDAC reacts with the carboxylate groups on the calcium alginate matrix and the amine groups of the enzyme. Ethylenediamine tetraacetic acid (EDTA) treatment was applied to increase the number of available carboxylate groups on the calcium alginate matrix for EDAC binding. After the immobilization was completed, the beads were treated with 0.1 M calcium chloride solution to reinstate the bead mechanical strength. Enzyme loading efficiency, activity, and reusability of the immobilized alpha-amylase were investigated. Covalently bound thermostable alpha-amylase to calcium alginate produced a total of 53 g of starch degradation/mg of bound protein after seven consecutive starch hydrolysis cycles of 10 min each at 95 degrees C in a stirred batch reactor. The free and covalently bound alpha-amylase had maximum activity at pH 5.5 and 6.0, respectively. The Michaelis-Menten constant (K(m)) of the immobilized enzyme (0.98 mg/mL) was 2.5 times greater than that of the free enzyme (0.40 mg/mL). The maximum reaction rate (V(max)) of immobilized and free enzyme were determined to be 10.4-mg starch degraded/mL min mg bound protein and 25.7-mg starch degraded/mL min mg protein, respectively. The high cumulative activity and seven successive reuses obtained at liquefaction temperature make the covalently bound thermostable alpha-amylase to calcium alginate matrix, a promising candidate for use in industrial starch hydrolysis process. PMID:19353735

  20. Immobilization of a thermostable alpha-amylase by covalent binding to an alginate matrix increases high temperature usability.

    PubMed

    Tee, Boon L; Kaletunç, Gönül

    2009-01-01

    Thermostable alpha-amylase was covalently bound to calcium alginate matrix to be used for starch hydrolysis at liquefaction temperature of 95 degrees C. 1-ethyl-3-(3-dimethylamino-propyl) carbodiimide hydrochloride (EDAC) was used as crosslinker. EDAC reacts with the carboxylate groups on the calcium alginate matrix and the amine groups of the enzyme. Ethylenediamine tetraacetic acid (EDTA) treatment was applied to increase the number of available carboxylate groups on the calcium alginate matrix for EDAC binding. After the immobilization was completed, the beads were treated with 0.1 M calcium chloride solution to reinstate the bead mechanical strength. Enzyme loading efficiency, activity, and reusability of the immobilized alpha-amylase were investigated. Covalently bound thermostable alpha-amylase to calcium alginate produced a total of 53 g of starch degradation/mg of bound protein after seven consecutive starch hydrolysis cycles of 10 min each at 95 degrees C in a stirred batch reactor. The free and covalently bound alpha-amylase had maximum activity at pH 5.5 and 6.0, respectively. The Michaelis-Menten constant (K(m)) of the immobilized enzyme (0.98 mg/mL) was 2.5 times greater than that of the free enzyme (0.40 mg/mL). The maximum reaction rate (V(max)) of immobilized and free enzyme were determined to be 10.4-mg starch degraded/mL min mg bound protein and 25.7-mg starch degraded/mL min mg protein, respectively. The high cumulative activity and seven successive reuses obtained at liquefaction temperature make the covalently bound thermostable alpha-amylase to calcium alginate matrix, a promising candidate for use in industrial starch hydrolysis process.

  1. CovalentDock: automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints.

    PubMed

    Ouyang, Xuchang; Zhou, Shuo; Su, Chinh Tran To; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

    2013-02-01

    Covalent linkage formation is a very important mechanism for many covalent drugs to work. However, partly due to the limitations of proper computational tools for covalent docking, most covalent drugs are not discovered systematically. In this article, we present a new covalent docking package, the CovalentDock, built on the top of the source code of Autodock. We developed an empirical model of free energy change estimation for covalent linkage formation, which is compatible with existing scoring functions used in docking, while handling the molecular geometry constrains of the covalent linkage with special atom types and directional grid maps. Integrated preparation scripts are also written for the automation of the whole covalent docking workflow. The result tested on existing crystal structures with covalent linkage shows that CovalentDock can reproduce the native covalent complexes with significant improved accuracy when compared with the default covalent docking method in Autodock. Experiments also suggest that CovalentDock is capable of covalent virtual screening with satisfactory enrichment performance. In addition, the investigation on the results also shows that the chirality and target selectivity along with the molecular geometry constrains are well preserved by CovalentDock, showing great capability of this method in the application for covalent drug discovery.

  2. Detection of free and covalently bound microcystins in different tissues (liver, intestines, gills, and muscles) of rainbow trout (Oncorhynchus mykiss) by liquid chromatography-tandem mass spectrometry: method characterization.

    PubMed

    Cadel-Six, Sabrina; Moyenga, David; Magny, Stéphanie; Trotereau, Sophie; Edery, Marc; Krys, Sophie

    2014-02-01

    So far only a few publications have explored the development of extraction methods of cyanotoxin extracted from complex matrices. With regard to cyanobacterial microcystins (MCs), the data on the contamination of the flesh of aquatic organisms is hard to compare and very limited due to the lack of validated methods. In recent years, evidence that both free and bound fractions of toxin are found in these tissues has highlighted the need to develop effective methods of quantification. Several techniques do exist, but only the Lemieux oxidation has so far been used to investigate complex tissue matrices. In this study, protocols based on the Lemieux approach were adapted for the quantitative chemical analysis of free MC-LR and MMPB derived from bound toxin in the tissues of juvenile trout gavaged with MC-LR. Afterwards, the NF V03 110 guideline was used to characterize the protocols elaborated and evaluate their effectiveness.

  3. Hydrogen Isotopic Composition of Particulate-Bound Fatty Acids From the California Borderland Basins

    NASA Astrophysics Data System (ADS)

    Jones, A. A.; Sessions, A. L.; Campbell, B. J.; Valentine, D. L.

    2006-12-01

    We examined the hydrogen-isotopic composition of fatty acids associated with particulate organic matter (POM) from depth transects in three California Borderland stations. Our goals were to determine (1) the natural variability of δD values in POM-associated fatty acids and (2) the magnitude of isotopic fractionations associated with fatty acid degradation in the marine environment. Some differences in molecular abundance were observed between completely ventilated and occasionally suboxic sites, but no corresponding shifts in δD values were measured. Values of δD for specific fatty acids were generally consistent between stations. Saturated fatty acids (C14, C16, and C18) yielded δD values ranging from -230‰ to -132‰, with δD values generally decreasing with chain length. We found no evidence of extreme D-enrichment of the C18 fatty acid as has been observed in studies of isolated macroalgae (Chikaraishi, et al, 2004). The unsaturated C16 and C18 fatty acids showed a similar trend while the polyunsaturated fatty acid 22:6 was somewhat enriched in D (δD values ranging from -186‰ to -68‰) relative to 20:5 (-208‰ to -93‰). Unsaturated fatty acids tended to have more positive δD values than their saturated counterparts, opposite the trend observed in sediments from the same location. The bacterial fatty acid C15 showed even greater deuterium enrichment with δD values ranging from - 145‰ to -88‰. This offset can likely be attributed to differences in biosynthetic fractionation between bacteria and eukaryotes, to differences in hydrogen isotopic composition of the food sources of these organisms, or some combination of these two factors. Within the surface waters, fatty acids become enriched with depth by an average of 25‰. The C18:0 acid is a significant exception, becoming depleted by 48‰ over that same interval. Below 100 meters depth, all fatty acids tend to become slightly depleted in D with increasing depth. The difference in δD values

  4. Renoprotective effect of DPP-4 inhibitors against free fatty acid-bound albumin-induced renal proximal tubular cell injury.

    PubMed

    Tanaka, Yuki; Kume, Shinji; Chin-Kanasaki, Masami; Araki, Hisazumi; Araki, Shin-ichi; Ugi, Satoshi; Sugaya, Takeshi; Uzu, Takashi; Maegawa, Hiroshi

    2016-02-12

    Dipeptidyl peptidase (DPP)-4 inhibitors, a new class of antidiabetic agent, have recently been suggested to exert pleiotropic effects beyond glucose lowering. Renal prognosis in patients with diabetic nephropathy depends on the severity of tubulointerstitial injury induced by massive proteinuria. We thus examined the renoprotective effect of DPP-4 inhibitors on inflammation in cultured mouse proximal tubular cells stimulated with free fatty acid (FFA)-bound albumin. Linagliptin and higher concentrations of sitagliptin, vildagliptin, and alogliptin all inhibited FFA-bound albumin-induced increases in mRNA expression of MCP-1 in cultured mouse proximal tubular cells. Furthermore, linagliptin significantly inhibited tubulointerstitial injury induced by peritoneal injection of FFA-bound albumin, such as inflammation, fibrosis, and apoptosis, in mice without altering systemic characteristics including body weight, fasting blood glucose, and food intake. These results indicate that DPP-4 inhibitors pleiotropically exert a direct renoprotective effect, and may serve as an additional therapeutic strategy to protect proximal tubular cells against proteinuria in patients with diabetic nephropathy. PMID:26802469

  5. Binding of the Covalent Flavin Assembly Factor to the Flavoprotein Subunit of Complex II.

    PubMed

    Maklashina, Elena; Rajagukguk, Sany; Starbird, Chrystal A; McDonald, W Hayes; Koganitsky, Anna; Eisenbach, Michael; Iverson, Tina M; Cecchini, Gary

    2016-02-01

    Escherichia coli harbors two highly conserved homologs of the essential mitochondrial respiratory complex II (succinate:ubiquinone oxidoreductase). Aerobically the bacterium synthesizes succinate:quinone reductase as part of its respiratory chain, whereas under microaerophilic conditions, the quinol:fumarate reductase can be utilized. All complex II enzymes harbor a covalently bound FAD co-factor that is essential for their ability to oxidize succinate. In eukaryotes and many bacteria, assembly of the covalent flavin linkage is facilitated by a small protein assembly factor, termed SdhE in E. coli. How SdhE assists with formation of the covalent flavin bond and how it binds the flavoprotein subunit of complex II remain unknown. Using photo-cross-linking, we report the interaction site between the flavoprotein of complex II and the SdhE assembly factor. These data indicate that SdhE binds to the flavoprotein between two independently folded domains and that this binding mode likely influences the interdomain orientation. In so doing, SdhE likely orients amino acid residues near the dicarboxylate and FAD binding site, which facilitates formation of the covalent flavin linkage. These studies identify how the conserved SdhE assembly factor and its homologs participate in complex II maturation.

  6. Protein-bound advanced glycation endproducts (AGEs) as bioactive amino acid derivatives in foods.

    PubMed

    Henle, T

    2005-12-01

    The Maillard reaction or nonenzymatic browning is of outstanding importance for the formation of flavour and colour of heated foods. Corresponding reactions, also referred to as "glycation", are known from biological systems, where the formation of advanced glycation endproducts (AGEs) shall play an important pathophysiological role in diabetes and uremia. In this review, pathways leading to the formation of individual protein-bound lysine and arginine derivatives in foods are described and nutritional consequences resulting from this posttranslational modifications of food proteins are discussed. PMID:15997413

  7. Ether- and ester-bound iso-diabolic acid and other lipids in members of acidobacteria subdivision 4.

    PubMed

    Sinninghe Damsté, Jaap S; Rijpstra, W Irene C; Hopmans, Ellen C; Foesel, Bärbel U; Wüst, Pia K; Overmann, Jörg; Tank, Marcus; Bryant, Donald A; Dunfield, Peter F; Houghton, Karen; Stott, Matthew B

    2014-09-01

    Recently, iso-diabolic acid (13,16-dimethyl octacosanedioic acid) has been identified as a major membrane-spanning lipid of subdivisions 1 and 3 of the Acidobacteria, a highly diverse phylum within the Bacteria. This finding pointed to the Acidobacteria as a potential source for the bacterial glycerol dialkyl glycerol tetraethers that occur ubiquitously in peat, soil, lakes, and hot springs. Here, we examined the lipid composition of seven phylogenetically divergent strains of subdivision 4 of the Acidobacteria, a bacterial group that is commonly encountered in soil. Acid hydrolysis of total cell material released iso-diabolic acid derivatives in substantial quantities (11 to 48% of all fatty acids). In contrast to subdivisions 1 and 3 of the Acidobacteria, 6 out of the 7 species of subdivision 4 (excepting "Candidatus Chloracidobacterium thermophilum") contained iso-diabolic acid ether bound to a glycerol in larger fractional abundance than iso-diabolic acid itself. This is in agreement with the analysis of intact polar lipids (IPLs) by high-performance liquid chromatography-mass spectrometry (HPLC-MS), which showed the dominance of mixed ether-ester glycerides. iso-Diabolic acid-containing IPLs were not identified, because these IPLs are not released with a Bligh-Dyer extraction, as observed before when studying lipid compositions of subdivisions 1 and 3 of the Acidobacteria. The presence of ether bonds in the membrane lipids does not seem to be an adaptation to temperature, because the five mesophilic isolates contained a larger amount of ether lipids than the thermophile "Ca. Chloracidobacterium thermophilum." Furthermore, experiments with Pyrinomonas methylaliphatogenes did not reveal a major influence of growth temperature over the 50 to 69°C range. PMID:24928878

  8. A heteromeric membrane-bound prenyltransferase complex from hop catalyzes three sequential aromatic prenylations in the bitter acid pathway.

    PubMed

    Li, Haoxun; Ban, Zhaonan; Qin, Hao; Ma, Liya; King, Andrew J; Wang, Guodong

    2015-03-01

    Bitter acids (α and β types) account for more than 30% of the fresh weight of hop (Humulus lupulus) glandular trichomes and are well known for their contribution to the bitter taste of beer. These multiprenylated chemicals also show diverse biological activities, some of which have potential benefits to human health. The bitter acid biosynthetic pathway has been investigated extensively, and the genes for the early steps of bitter acid synthesis have been cloned and functionally characterized. However, little is known about the enzyme(s) that catalyze three sequential prenylation steps in the β-bitter acid pathway. Here, we employed a yeast (Saccharomyces cerevisiae) system for the functional identification of aromatic prenyltransferase (PT) genes. Two PT genes (HlPT1L and HlPT2) obtained from a hop trichome-specific complementary DNA library were functionally characterized using this yeast system. Coexpression of codon-optimized PT1L and PT2 in yeast, together with upstream genes, led to the production of bitter acids, but no bitter acids were detected when either of the PT genes was expressed by itself. Stepwise mutation of the aspartate-rich motifs in PT1L and PT2 further revealed the prenylation sequence of these two enzymes in β-bitter acid biosynthesis: PT1L catalyzed only the first prenylation step, and PT2 catalyzed the two subsequent prenylation steps. A metabolon formed through interactions between PT1L and PT2 was demonstrated using a yeast two-hybrid system, reciprocal coimmunoprecipitation, and in vitro biochemical assays. These results provide direct evidence of the involvement of a functional metabolon of membrane-bound prenyltransferases in bitter acid biosynthesis in hop. PMID:25564559

  9. Ether- and Ester-Bound iso-Diabolic Acid and Other Lipids in Members of Acidobacteria Subdivision 4

    PubMed Central

    Rijpstra, W. Irene C.; Hopmans, Ellen C.; Foesel, Bärbel U.; Wüst, Pia K.; Overmann, Jörg; Tank, Marcus; Bryant, Donald A.; Dunfield, Peter F.; Houghton, Karen; Stott, Matthew B.

    2014-01-01

    Recently, iso-diabolic acid (13,16-dimethyl octacosanedioic acid) has been identified as a major membrane-spanning lipid of subdivisions 1 and 3 of the Acidobacteria, a highly diverse phylum within the Bacteria. This finding pointed to the Acidobacteria as a potential source for the bacterial glycerol dialkyl glycerol tetraethers that occur ubiquitously in peat, soil, lakes, and hot springs. Here, we examined the lipid composition of seven phylogenetically divergent strains of subdivision 4 of the Acidobacteria, a bacterial group that is commonly encountered in soil. Acid hydrolysis of total cell material released iso-diabolic acid derivatives in substantial quantities (11 to 48% of all fatty acids). In contrast to subdivisions 1 and 3 of the Acidobacteria, 6 out of the 7 species of subdivision 4 (excepting “Candidatus Chloracidobacterium thermophilum”) contained iso-diabolic acid ether bound to a glycerol in larger fractional abundance than iso-diabolic acid itself. This is in agreement with the analysis of intact polar lipids (IPLs) by high-performance liquid chromatography-mass spectrometry (HPLC-MS), which showed the dominance of mixed ether-ester glycerides. iso-Diabolic acid-containing IPLs were not identified, because these IPLs are not released with a Bligh-Dyer extraction, as observed before when studying lipid compositions of subdivisions 1 and 3 of the Acidobacteria. The presence of ether bonds in the membrane lipids does not seem to be an adaptation to temperature, because the five mesophilic isolates contained a larger amount of ether lipids than the thermophile “Ca. Chloracidobacterium thermophilum.” Furthermore, experiments with Pyrinomonas methylaliphatogenes did not reveal a major influence of growth temperature over the 50 to 69°C range. PMID:24928878

  10. Synergistic transcriptional enhancement does not depend on the number of acidic activation domains bound to the promoter.

    PubMed Central

    Oliviero, S; Struhl, K

    1991-01-01

    Many eukaryotic transcriptional activator proteins contain a DNA-binding domain that interacts with specific promoter sequences and an acidic activation region that is required to stimulate transcription. Transcriptional enhancement by such activator proteins is often synergistic and promiscuous; promoters containing multiple binding sites for an individual protein or even for unrelated proteins can be 10-100 times more active than promoters with single sites. It has been suggested that such synergy reflects a nonlinear response of the basic transcription machinery to the number and/or quality of acidic activation regions. Here, we determine the transcriptional activity of Jun-Fos heterodimers containing one or two GCN4 acidic activation regions on promoters containing one or two Ap-1 target sites. Surprisingly, heterodimers with one or two acidic regions activate transcription with similar efficiency and are equally synergistic (10- to 15-fold) on promoters containing two target sites. Thus, transcriptional synergy does not depend on the number of acidic activation regions but rather on the number of proteins bound to the promoter. This suggests that synergy is mediated either by cooperative DNA binding or by alternative mechanisms in which the DNA-binding domain plays a more direct role in transcription (e.g., changes in DNA structure, nucleosome displacement, or direct interactions with the transcriptional machinery). Images PMID:1898773

  11. Covalent immobilization of liposomes on plasma functionalized metallic surfaces.

    PubMed

    Mourtas, S; Kastellorizios, M; Klepetsanis, P; Farsari, E; Amanatides, E; Mataras, D; Pistillo, B R; Favia, P; Sardella, E; d'Agostino, R; Antimisiaris, S G

    2011-05-01

    A method was developed to functionalize biomedical metals with liposomes. The novelty of the method includes the plasma-functionalization of the metal surface with proper chemical groups to be used as anchor sites for the covalent immobilization of the liposomes. Stainless steel (SS-316) disks were processed in radiofrequency glow discharges fed with vapors of acrylic acid to coat them with thin adherent films characterized by surface carboxylic groups, where liposomes were covalently bound through the formation of amide bonds. For this, liposomes decorated with polyethylene glycol molecules bearing terminal amine-groups were prepared. After ensuring that the liposomes remain intact, under the conditions applying for immobilization; different attachment conditions were evaluated (incubation time, concentration of liposome dispersion) for optimization of the technique. Immobilization of calcein-entrapping liposomes was evaluated by monitoring the percent of calcein attached on the surfaces. Best results were obtained when liposome dispersions with 5mg/ml (liposomal lipid) concentration were incubated on each disk for 24h at 37°C. The method is proposed for developing drug-eluting biomedical materials or devices by using liposomes that have appropriate membrane compositions and are loaded with drugs or other bioactive agents. PMID:21273051

  12. Determination of seleno-amino acids bound to proteins in extra virgin olive oils.

    PubMed

    Torres, Sabier; Gil, Raul; Silva, María Fernanda; Pacheco, Pablo

    2016-04-15

    An analytical method has been developed to determine seleno-amino acids in proteins extracted from extra virgin olive oils (EVOOs). Different aqueous/organic solvents were tested to isolate proteins, an acetone:n-hexane combination being the best protein precipitant. In a first dimension chromatography, extracted proteins were analysed by size exclusion chromatography (SEC) coupled to inductively coupled plasma mass spectrometry (ICP-MS) to identify S and Se associations as proteins marker. Two fractions of 66 kDa (A) and 443 kDa (B) were identified. These fractions were submitted to microwave-assisted acid hydrolysis (MAAH) to release seleno-amino acids. In a second dimension chromatography seleno-amino acids were determined by reversed-phase chromatography (RPC) coupled to ICP-MS. Seleno-methylselenocysteine was determined with values ranging from 1.03-2.03±0.2 μg kg(-1) and selenocysteine at a concentration of 1.47±0.1 μg kg(-1). Variations of protein and seleno-amino acid concentrations were observed between EVOO varieties, contributing to EVOO cultivar differentiation. PMID:26616967

  13. Identification/quantification of free and bound phenolic acids in peel and pulp of apples (Malus domestica) using high resolution mass spectrometry (HRMS).

    PubMed

    Lee, Jihyun; Chan, Bronte Lee Shan; Mitchell, Alyson E

    2017-01-15

    Free and bound phenolic acids were measured in the pulp and peel of four varieties of apples using high resolution mass spectrometry. Twenty-five phenolic acids were identified and included: 8 hydroxybenzoic acids, 11 hydroxycinnamic acids, 5 hydroxyphenylacetic acids, and 1 hydoxyphenylpropanoic acid. Several phenolics are tentatively identified for the first time in apples and include: methyl gallate, ethyl gallate, hydroxy phenyl acetic acid, three phenylacetic acid isomers, 3-(4-hydroxyphenyl)propionic acid, and homoveratric acid. With exception of chlorogenic and caffeic acid, most phenolic acids were quantified for the first time in apples. Significant varietal differences (p<0.05) were observed in both peel and pulp. The levels of total phenolic acids were higher in the pulp as compared to apple peel (dry weight) in all varieties. Coumaroylquinic, protocatechuic, 4-hydroxybenzoic, vanillic and t-ferulic acids were present in free forms. With exception of chlorogenic acid, all other phenolic acids were present only as bound forms. PMID:27542479

  14. Tissue Plasminogen Activator Binding to Superparamagnetic Iron Oxide Nanoparticle-Covalent Versus Adsorptive Approach.

    PubMed

    Friedrich, Ralf P; Zaloga, Jan; Schreiber, Eveline; Tóth, Ildikó Y; Tombácz, Etelka; Lyer, Stefan; Alexiou, Christoph

    2016-12-01

    Functionalized superparamagnetic iron oxide nanoparticles are frequently used to develop vehicles for drug delivery, hyperthermia, and photodynamic therapy and as tools used for magnetic separation and purification of proteins or for biomolecular imaging. Depending on the application, there are various possible covalent and non-covalent approaches for the functionalization of particles, each of them shows different advantages and disadvantages for drug release and activity at the desired location.Particularly important for the production of adsorptive and covalent bound drugs to nanoparticles is the pureness of the involved formulation. Especially the covalent binding strategy demands defined chemistry of the drug, which is stabilized by excess free amino acids which could reduce reaction efficiency. In this study, we therefore used tangential flow filtration (TFF) method to purify the drugs before the reaction and used the frequently applied and clinically available recombinant tissue plasminogen activator (tPA; Actilyse(®)) as a proof of concept. We then coupled the tPA preparation to polyacrylic acid-co-maleic acid (PAM)-coated superparamagnetic iron oxide nanoparticles (SPIONs) using an amino-reactive activated ester reaction and compared these particles to PAM-coated SPIONs with electrostatically adsorbed tPA.Using dynamic light scattering (DLS) and pH-dependent electrokinetic mobility measurements, we showed that surface properties of the SPIONs were significantly greater affected after activation of the particles compared to the adsorption controls. Different in vitro assays were used to investigate the activity of tPA after coupling to the particles and purification of the ferrofluid. Covalent linkage significantly improves the reactivity and long-term stability of the conjugated SPION-tPA system compared to simple adsorption. In conclusion, we have shown an effective way to produce SPIONs with covalent and non-covalent ultra-filtrated drugs. We showed

  15. Simultaneous GC-MS Determination of Free and Bound Phenolic Acids in Slovenian Red Wines and Chemometric Characterization.

    PubMed

    Ivanović, Milena; Islamčević Razboršek, Maša; Kolar, Mitja

    2016-01-01

    Several phenolic acids (PAs), caffeic, vanillic, syringic, p-coumaric and ferulic acid, found in Slovenian red wines were studied using gas chromatography and mass spectrometry. For isolation of the PAs from wine samples, solid phase extraction using hydrophilic modified styrene - HLB cartridges was used. The bound PAs were extracted after basic hydrolysis and o-coumaric acid was used as the internal standard. The developed method was validated and the linear concentration range for all analytes was from 1 to 100 mg L-1 with correlation coefficients above 0.999. We show that the method is repeatable (RSD<2%), recoveries were above 96%, and LOD and LOQ values were acceptable. In all of the wine samples tested, caffeic and p-coumaric acid were determined to be the predominant PAs (17-72 mg L-1), while other compounds were found in lower concentrations. Principal Component Analysis and Cluster Analysis were used to study differences between wines related towards varieties and Slovenian wine regions. The results demonstrate that variety has more influence on PAs content than wine regions in Slovenian red wines. PMID:27640394

  16. Soluble and cell wall-bound phenolic acids and ferulic acid dehydrodimers in rye flour and five bread model systems: insight into mechanisms of improved availability

    PubMed Central

    Dynkowska, Wioletta M; Cyran, Malgorzata R; Ceglińska, Alicja

    2015-01-01

    Background The bread-making process influences bread components, including phenolics that significantly contribute to its antioxidant properties. Five bread model systems made from different rye cultivars were investigated to compare their impact on concentration of ethanol-soluble (free and ester-bound) and insoluble phenolics. Results Breads produced by a straight dough method without acid addition (A) and three-stage sourdough method with 12 h native starter preparation (C) exhibited the highest, genotype-dependent concentrations of free phenolic acids. Dough acidification by direct acid addition (method B) or by gradual production during prolonged starter fermentation (24 and 48 h, for methods D and E) considerably decreased their level. However, breads B were enriched in soluble ester-bound fraction. Both direct methods, despite substantial differences in dough pH, caused a similar increase in the amount of insoluble ester-bound fraction. The contents of phenolic fractions in rye bread were positively related to activity level of feruloyl esterase and negatively to those of arabinoxylan-hydrolysing enzymes in wholemeal flour. Conclusion The solubility of rye bread phenolics may be enhanced by application of a suitable bread-making procedure with respect to rye cultivar, as the mechanisms of this process are also governed by a response of an individual genotype with specific biochemical profile. © 2014 Plant Breeding and Acclimatization Institute, National Research Institute. © 2014 The Authors. Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. PMID:25410263

  17. Comparison of enzymatic and acid hydrolysis of bound flavor compounds in model system and grapes.

    PubMed

    Dziadas, Mariusz; Jeleń, Henryk H

    2016-01-01

    Four synthesized terpenyl-ß-D-glycopyranosides (geranyl, neryl, citronellyl, myrtenyl) were subjected to enzymatic (AR 2000, pH 5.5) and acid (citric buffer, pH 2.5) hydrolysis. Decrease of glycosides was measured by HPLC and the volatiles released--by comprehensive gas chromatography-mass spectrometry (GC × GC-ToF-MS). Enzymatic hydrolysis performed for 21 h yielded 100% degree of hydrolysis for all glycosides but citronellyl (97%). Degree of acid hydrolysis was highly dependent on type of aglycone and the conditions. The highest degree was achieved for geraniol, followed by citronellol and nerol. Myrtenylo-ß-D-glycopyranoside was the most resistant glycoside to hydrolysis. Acid hydrolysis degree was also related to temperature/time combination, the highest being for 100 °C and 2 h. In a result of enzymatic hydrolysis 85-91% of total peak areas was terpene aglycone, whereas for acid hydrolysis the area of released terpene aglycone did not exceed 1.3% of total peak area indicating almost complete decomposition/transformation of terpenyl aglycone.

  18. Locking GTPases covalently in their functional states

    PubMed Central

    Wiegandt, David; Vieweg, Sophie; Hofmann, Frank; Koch, Daniel; Li, Fu; Wu, Yao-Wen; Itzen, Aymelt; Müller, Matthias P.; Goody, Roger S.

    2015-01-01

    GTPases act as key regulators of many cellular processes by switching between active (GTP-bound) and inactive (GDP-bound) states. In many cases, understanding their mode of action has been aided by artificially stabilizing one of these states either by designing mutant proteins or by complexation with non-hydrolysable GTP analogues. Because of inherent disadvantages in these approaches, we have developed acryl-bearing GTP and GDP derivatives that can be covalently linked with strategically placed cysteines within the GTPase of interest. Binding studies with GTPase-interacting proteins and X-ray crystallography analysis demonstrate that the molecular properties of the covalent GTPase–acryl–nucleotide adducts are a faithful reflection of those of the corresponding native states and are advantageously permanently locked in a defined nucleotide (that is active or inactive) state. In a first application, in vivo experiments using covalently locked Rab5 variants provide new insights into the mechanism of correct intracellular localization of Rab proteins. PMID:26178622

  19. An efficient algorithm for upper bound on the partition function of nucleic acids.

    PubMed

    Chitsaz, Hamidreza; Forouzmand, Elmirasadat; Haffari, Gholamreza

    2013-07-01

    It has been shown that minimum free-energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble-based quantities such as melting temperature and equilibrium concentrations can be more reliably predicted. Even structure prediction by sampling from the ensemble and clustering those structures by Sfold has proven to be more reliable than minimum free energy structure prediction. The main obstacle for ensemble-based approaches is the computational complexity of the partition function and base-pairing probabilities. For instance, the space complexity of the partition function for RNA-RNA interaction is O(n4) and the time complexity is O(n6), which is prohibitively large. Our goal in this article is to present a fast algorithm, based on sparse folding, to calculate an upper bound on the partition function. Our work is based on the recent algorithm of Hazan and Jaakkola (2012). The space complexity of our algorithm is the same as that of sparse folding algorithms, and the time complexity of our algorithm is O(MFE(n)ℓ) for single RNA and O(MFE(m, n)ℓ) for RNA-RNA interaction in practice, in which MFE is the running time of sparse folding and ℓ≤n (ℓ≤n+m) is a sequence-dependent parameter.

  20. Effects of carboxylic acids on the uptake of non-transferrin-bound iron by astrocytes.

    PubMed

    Keenan, Belinda M; Robinson, Stephen R; Bishop, Glenda M

    2010-01-01

    The concentrations of non-transferrin-bound iron are elevated in the brain during pathological conditions such as stroke and Alzheimer's disease. Astrocytes are specialised for sequestering this iron, however little is known about the mechanisms involved. Carboxylates, such as citrate, have been reported to facilitate iron uptake by intestinal cells. Citrate binds iron and limits its redox activity. The presence of high citrate concentrations in the interstitial fluid of the brain suggests that citrate may be an important ligand for iron transport by astrocytes. This study investigates whether iron accumulation by cultured rat astrocytes is facilitated by citrate or other carboxylates. Contrary to expectations, citrate, tartrate and malate were found to block iron accumulation in a concentration-dependent manner; alpha-ketoglutarate had limited effects, while fumarate, succinate and glutarate had no effect. This blockade was not due to an inhibition of ferric reductase activity. Instead, it appeared to be related to the capacity of these carboxylates to bind iron, since phosphate, which also binds iron, diminished the capacity of citrate, tartrate and malate to block the cellular accumulation of iron. These findings raise the possibility that citrate may have therapeutic potential in the management of neurodegenerative conditions that involve cellular iron overload.

  1. Charge transport through dicarboxylic-acid-terminated alkanes bound to graphene-gold nanogap electrodes

    NASA Astrophysics Data System (ADS)

    Liu, Longlong; Zhang, Qian; Tao, Shuhui; Zhao, Cezhou; Almutib, Eman; Al-Galiby, Qusiy; Bailey, Steven W. D.; Grace, Iain; Lambert, Colin J.; Du, Jun; Yang, Li

    2016-07-01

    Graphene-based electrodes are attractive for single-molecule electronics due to their high stability and conductivity and reduced screening compared with metals. In this paper, we use the STM-based matrix isolation I(s) method to measure the performance of graphene in single-molecule junctions with one graphene electrode and one gold electrode. By measuring the length dependence of the electrical conductance of dicarboxylic-acid-terminated alkanes, we find that the transport is consistent with phase-coherent tunneling, but with an attenuation factor of βN = 0.69 per methyl unit, which is lower than the value measured for Au-molecule-Au junctions. Comparison with density-functional-theory calculations of electron transport through graphene-molecule-Au junctions and Au-molecule-Au junctions reveals that this difference is due to the difference in Fermi energies of the two types of junction, relative to the frontier orbitals of the molecules. For most molecules, their electrical conductance in graphene-molecule-Au junctions is higher than that in Au-molecule-Au junctions, which suggests that graphene offers superior electrode performance, when utilizing carboxylic acid anchor groups.Graphene-based electrodes are attractive for single-molecule electronics due to their high stability and conductivity and reduced screening compared with metals. In this paper, we use the STM-based matrix isolation I(s) method to measure the performance of graphene in single-molecule junctions with one graphene electrode and one gold electrode. By measuring the length dependence of the electrical conductance of dicarboxylic-acid-terminated alkanes, we find that the transport is consistent with phase-coherent tunneling, but with an attenuation factor of βN = 0.69 per methyl unit, which is lower than the value measured for Au-molecule-Au junctions. Comparison with density-functional-theory calculations of electron transport through graphene-molecule-Au junctions and Au

  2. Potent and selective activation of abscisic acid receptors in vivo by mutational stabilization of their agonist-bound conformation

    PubMed Central

    Mosquna, Assaf; Peterson, Francis C.; Park, Sang-Youl; Lozano-Juste, Jorge; Volkman, Brian F.; Cutler, Sean R.

    2011-01-01

    Pyrabactin resistance (PYR) 1 and its relatives belong to a family of soluble abscisic acid (ABA) receptors that inhibit type 2C protein phosphatases (PP2C) when in their agonist-stabilized conformation. Given their switch-like properties, we envisioned that mutations that stabilize their agonist-bound conformation could be used to activate signaling in vivo. To identify such mutations, we subjected PYR1 to site-saturation mutagenesis at 39 highly conserved residues that participate in ABA or PP2C contacts. All 741 possible single amino acid substitutions at these sites were tested to identify variants that increase basal PYR1-PP2C interactions, which uncovered activating mutations in 10 residues that preferentially cluster in PYR1's gate loop and C-terminal helix. The mutations cause measurable but incomplete receptor activation in vitro; however, specific triple and quadruple mutant combinations were constructed that promote an agonist-bound conformation, as measured by heteronuclear single quantum coherence NMR, and lead to full receptor activation. Moreover, these mutations retain functionality when introduced into divergent family members, and can therefore be used to dissect individual receptor function in vivo, which has been problematic because of redundancy and family size. Expression of activated PYL2 in Arabidopsis seeds activates ABA signaling by a number of measures: modulation of ABA-regulated gene expression, induction of hyperdormancy, and suppression of ABA deficiency phenotypes in the aba2-1 mutant. Our results set the stage for systematic gain-of-function studies of PYR1 and related ABA receptors and reveal that, despite the large number of receptors, activation of a single receptor is sufficient to activate signaling in planta. PMID:22139369

  3. Preparation and evaluation of a chiral stationary phase covalently bound with a chiral pseudo-18-crown-6 ether having a phenolic hydroxy group for enantiomer separation of amino compounds.

    PubMed

    Yongzhu, Jin; Hirose, Keiji; Nakamura, Takashi; Nishioka, Ryota; Ueshige, Tetsuro; Tobe, Yoshito

    2006-10-01

    In order to develop a chiral stationary phase (CSP), which has even higher separation ability than the corresponding commercially available crown ether based CSP (OA-8000 having a pseudo-18-crown-6 ether with an OMe group as a selector), chemically bonded type CSP having a phenolic OH group on a crown ring was developed. Normal mobile phases with or without acid additive can be used with this OH type CSP in contrast to the conventional OMe type CSP which has a neutral chiral selector. Enantiomers of 25 out of 27 amino compounds, including 20 amino acids, 5 amino alcohols, and 2 lipophilic amines, were efficiently separated on a column with this CSP. Nine amino compounds out of 27 were separated with better separation factors than the corresponding OMe type CSP. It is noteworthy that the chromatography on this CSP exhibited excellent enantiomer-separations for amines and amino alcohols when triethyl amine was used as an additive in the mobile phase. Comparison of enantiomer separation ability on this OH type of CSP and on the OMe type of CSP and correlation between the enantioselectivity in chiral chromatography and that of the corresponding model compounds in solution imply that the chiral separation arose from chiral recognition in host guest interactions.

  4. Loosely-Bound Diatomic Molecules.

    ERIC Educational Resources Information Center

    Balfour, W. J.

    1979-01-01

    Discusses concept of covalent bonding as related to homonuclear diatomic molecules. Article draws attention to the existence of bound rare gas and alkaline earth diatomic molecules. Summarizes their molecular parameters and offers spectroscopic data. Strength and variation with distance of interatomic attractive forces is given. (Author/SA)

  5. Investigating the role of mineral-bound humic acid in phenanthrene sorption.

    PubMed

    Feng, Xiaojuan; Simpson, André J; Simpson, Myrna J

    2006-05-15

    Contaminant-soil interaction studies have indicated that physical conformation of organic matter atthe solid-aqueous interface is important in governing hydrophobic organic compound (HOC) sorption. To testthis, organo-clay complexes were constructed by coating montmorillonite and kaolinite with peat humic acid (PHA) in Na+ or Ca2+ dominated solutions with varying pH and ionic strength values. The solution conditions encouraged the dissolved PHA to adopt a "coiled" or "stretched" conformation prior to interacting with the clay mineral surface. Both kaolinite and montmorillonite organo-clay complexes exhibited higher phenanthrene sorption (Koc values) with decreasing pH, indicating that the coiled configuration provided more favorable sorption conditions. Evidence from 1H high-resolution magic angle spinning (HR-MAS) nuclear magnetic resonance (NMR) indicated that polymethylene groups were prevalent at the surface of the organo-clay complexes and may enhance sorptive interactions. Preferential sorption of polymethylene groups on kaolinite and aromatic compounds on montmorillonite may also contribute to the difference in phenanthrene sorption by PHA associated with these two types of clay. This study demonstrates the importance of solution conditions in the sorption of nonionic, hydrophobic organic contaminants and also provides evidence for the indirect role of clay minerals in sorption of contaminants at the soil-water interface. PMID:16749691

  6. Origin and vertical variation of the bound fatty acids in core sediments of Lake Dianchi in Southwest China.

    PubMed

    Wang, Lifang; Wu, Fengchang; Xiong, Yongqiang; Fang, Jidun

    2013-04-01

    Based on the molecular distribution of bound fatty acid (BFA) compound classes in core sediments of Lake Dianchi combined with the compound-specific δ(13)C values of the straight-chain BFAs, origin and vertical changes of organic matters in the sediments were investigated. The results indicated a significant change of BFA sources over the past 700 years. Contrast to the low concentrations of the terrestrial BFAs, the abundance of BFAs derived from the plankton/bacteria in the top sections (1944-recent) was more than 80%. The increasing proportions of the branched and unsaturated BFAs in total fatty acids were closely correlated with the heavy eutrophication and the frequent algal blooms in the decades. Furthermore, the positive shift of δ (13)C of C16 and C18 (~2‰) in the upper section might be an indicator of the excess phytoplankton productivity. However, it was found that the plankton/bacteria-derived BFAs were more easily degraded during the early diagenetic process. The special compound carbon isotopic compositions of the long straight-chain BFAs (C24 and C26) in the sediments showed a depletion of heavier δ (13)C values (ca. -30‰) in the midsections (1559-1787), reflecting a relatively growing contribution of C3 plants to C4 plants or that C4 plant growth was inhibited in cold and arid climates during the period. PMID:22903813

  7. Fluorescence anisotropy metrology of electrostatically and covalently labelled silica nanoparticles

    NASA Astrophysics Data System (ADS)

    Yip, Philip; Karolin, Jan; Birch, David J. S.

    2012-08-01

    We compare determining the size of silica nanoparticles using the time-resolved fluorescence anisotropy decay of dye molecules when electrostatically and covalently bound to stable silica nanoparticles. Covalent labelling is shown to offer advantages by simplifying the dye rotational kinetics and the appropriateness of various kinetic models is discussed. Silica nanoparticles produced using Stöber synthesis of tetraethylorthosilicate (TEOS) are found to be controllable between ˜3.1 and 3.8 nm radius by adjusting the relative water:TEOS concentration. Covalent labelling with fluorescein 5(6)-isothiocyanate (FITC) bound to (3-aminopropyl) trimethoxysilane (FITC-APS) predicts a larger particle than electrostatically labelling with rhodamine 6G. The difference is attributed to the presence of an additional depolarization mechanism to Brownian rotation of the nanoparticle and dye wobbling with electrostatic labelling in the form of dye diffusion on the surface of the nanoparticle.

  8. Assessment of total (free and bound) phenolic compounds in spent coffee extracts.

    PubMed

    Monente, Carmen; Ludwig, Iziar A; Irigoyen, Angel; De Peña, María-Paz; Cid, Concepción

    2015-05-01

    Spent coffee is the main byproduct of the brewing process and a potential source of bioactive compounds, mainly phenolic acids easily extracted with water. Free and bound caffeoylquinic (3-CQA, 4-CQA, 5-CQA), dicaffeoylquinic (3,4-diCQA, 3,5-diCQA, 4,5-diCQA), caffeic, ferulic, p-coumaric, sinapic, and 4-hydroxybenzoic acids were measured by HPLC, after the application of three treatments (alkaline, acid, saline) to spent coffee extracts. Around 2-fold higher content of total phenolics has been estimated in comparison to free compounds. Phenolic compounds with one or more caffeic acid molecules were approximately 54% linked to macromolecules such as melanoidins, mainly by noncovalent interactions (up to 81% of bound phenolic compounds). The rest of the quantitated phenolic acids were mainly attached to other structures by covalent bonds (62-97% of total bound compounds). Alkaline hydrolysis and saline treatment were suitable to estimate total bound and ionically bound phenolic acids, respectively, whereas acid hydrolysis is an inadequate method to quantitate coffee phenolic acids.

  9. Bound Phenolics of Quinoa Seeds Released by Acid, Alkaline, and Enzymatic Treatments and Their Antioxidant and α-Glucosidase and Pancreatic Lipase Inhibitory Effects.

    PubMed

    Tang, Yao; Zhang, Bing; Li, Xihong; Chen, Peter X; Zhang, Hua; Liu, Ronghua; Tsao, Rong

    2016-03-01

    Unextractable phenolics from plant foods and their role in health benefits have become increasingly important. Meal residues of three quinoa seeds free of fat and extractable phenolics were subjected to acid, alkaline, and enzymatic hydrolyses. The total and individual phenolic compounds released were analyzed, and 19 phenolics, predominantly phenolic acids and several flavonoids, were identified. The concentration of bound phenolics was highest in black quinoa followed by red and white, regardless of the hydrolysis method. Higher phenolic contents also showed stronger antioxidant activities and inhibition of α-glucosidase and pancreatic lipase activities. Carbohydrases, that is, pectinase, xylanase and feruloyl esterase, which effectively liberated bound phenolics are known to be secreted by colonic bacteria, suggesting potential antioxidant and anti-inflammatory effects by these compounds in the large intestine during colonic fermentation. These results can also be applied to treat foods high in bound phenolics to enhance bioaccessibility.

  10. Bound Phenolics of Quinoa Seeds Released by Acid, Alkaline, and Enzymatic Treatments and Their Antioxidant and α-Glucosidase and Pancreatic Lipase Inhibitory Effects.

    PubMed

    Tang, Yao; Zhang, Bing; Li, Xihong; Chen, Peter X; Zhang, Hua; Liu, Ronghua; Tsao, Rong

    2016-03-01

    Unextractable phenolics from plant foods and their role in health benefits have become increasingly important. Meal residues of three quinoa seeds free of fat and extractable phenolics were subjected to acid, alkaline, and enzymatic hydrolyses. The total and individual phenolic compounds released were analyzed, and 19 phenolics, predominantly phenolic acids and several flavonoids, were identified. The concentration of bound phenolics was highest in black quinoa followed by red and white, regardless of the hydrolysis method. Higher phenolic contents also showed stronger antioxidant activities and inhibition of α-glucosidase and pancreatic lipase activities. Carbohydrases, that is, pectinase, xylanase and feruloyl esterase, which effectively liberated bound phenolics are known to be secreted by colonic bacteria, suggesting potential antioxidant and anti-inflammatory effects by these compounds in the large intestine during colonic fermentation. These results can also be applied to treat foods high in bound phenolics to enhance bioaccessibility. PMID:26853559

  11. Initiators Based on Benzaldoximes: Bimolecular and Covalently Bound Systems

    PubMed Central

    2012-01-01

    Typical bimolecular photoinitiators (PIs) for radical polymerization of acrylates show only poor photoreactivity because of the undesired effect of back electron transfer. To overcome this limitation, PIs consisting of a benzaldoxime ester and various sensitizers based on aromatic ketones were introduced. The core of the photoinduced reactivity was established by laser flash photolysis, photo-CIDNP, and EPR experiments at short time scales. According to these results, the primarily formed iminyl radicals are not particularly active. The polymerization is predominantly initiated by C-centered radicals. Photo-DSC experiments show reactivities comparable to that of classical monomolecular type I PIs like Darocur 1173. PMID:23378672

  12. Tecto-dendrimers: a study of covalently bound nanospheres

    SciTech Connect

    Welch, Paul M; Welch, Cynthia F

    2008-01-01

    We present a computational and theoretical study of the size, shape, and solution properties of tecto-dendrimers. This class of polymer, composed of a central dendrimer with multiple dendrimers attached at its periphery, holds promise for multi-drug delivery and environmental remediation applications. We find (i) that the maximum number of tecto-units that may be attached to the central core varies logarightmically with the ratio of the sizes of the dendrimers, (ii) that their density profiles display a minimum near the junction of the tecto-units with the core, (iii) that a simple expression captures their radius of gyration, (iv) that their intrinsic viscosity will display a maximum as a function of the number of tecto-units attached, and (v) that their sphericity increases with increasing number of attached tecto-units. These results should bear upon both the synthesis and application of these materials.

  13. Thiophene-based covalent organic frameworks

    PubMed Central

    Bertrand, Guillaume H. V.; Michaelis, Vladimir K.; Ong, Ta-Chung; Griffin, Robert G.; Dincă, Mircea

    2013-01-01

    We report the synthesis and characterization of covalent organic frameworks (COFs) incorporating thiophene-based building blocks. We show that these are amenable to reticular synthesis, and that bent ditopic monomers, such as 2,5-thiophenediboronic acid, are defect-prone building blocks that are susceptible to synthetic variations during COF synthesis. The synthesis and characterization of an unusual charge transfer complex between thieno[3,2-b]thiophene-2,5-diboronic acid and tetracyanoquinodimethane enabled by the unique COF architecture is also presented. Together, these results delineate important synthetic advances toward the implementation of COFs in electronic devices. PMID:23479656

  14. Thiophene-based covalent organic frameworks.

    PubMed

    Bertrand, Guillaume H V; Michaelis, Vladimir K; Ong, Ta-Chung; Griffin, Robert G; Dincă, Mircea

    2013-03-26

    We report the synthesis and characterization of covalent organic frameworks (COFs) incorporating thiophene-based building blocks. We show that these are amenable to reticular synthesis, and that bent ditopic monomers, such as 2,5-thiophenediboronic acid, are defect-prone building blocks that are susceptible to synthetic variations during COF synthesis. The synthesis and characterization of an unusual charge transfer complex between thieno[3,2-b]thiophene-2,5-diboronic acid and tetracyanoquinodimethane enabled by the unique COF architecture is also presented. Together, these results delineate important synthetic advances toward the implementation of COFs in electronic devices.

  15. Characterization of 19 Genes Encoding Membrane-Bound Fatty Acid Desaturases and their Expression Profiles in Gossypium raimondii Under Low Temperature.

    PubMed

    Liu, Wei; Li, Wei; He, Qiuling; Daud, Muhammad Khan; Chen, Jinhong; Zhu, Shuijin

    2015-01-01

    To produce unsaturated fatty acids, membrane-bound fatty acid desaturases (FADs) can be exploited to introduce double bonds into the acyl chains of fatty acids. In this study, 19 membrane-bound FAD genes were identified in Gossypium raimondii through database searches and were classified into four different subfamilies based on phylogenetic analysis. All 19 membrane-bound FAD proteins shared three highly conserved histidine boxes, except for GrFAD2.1, which lost the third histidine box in the C-terminal region. In the G. raimondii genome, tandem duplication might have led to the increasing size of the FAD2 cluster in the Omega Desaturase subfamily, whereas segmental duplication appeared to be the dominant mechanism for the expansion of the Sphingolipid and Front-end Desaturase subfamilies. Gene expression analysis showed that seven membrane-bound FAD genes were significantly up-regulated and that five genes were greatly suppressed in G. raimondii leaves exposed to low temperature conditions.

  16. Characterization of 19 Genes Encoding Membrane-Bound Fatty Acid Desaturases and their Expression Profiles in Gossypium raimondii Under Low Temperature

    PubMed Central

    He, Qiuling; Daud, Muhammad Khan; Chen, Jinhong; Zhu, Shuijin

    2015-01-01

    To produce unsaturated fatty acids, membrane-bound fatty acid desaturases (FADs) can be exploited to introduce double bonds into the acyl chains of fatty acids. In this study, 19 membrane-bound FAD genes were identified in Gossypium raimondii through database searches and were classified into four different subfamilies based on phylogenetic analysis. All 19 membrane-bound FAD proteins shared three highly conserved histidine boxes, except for GrFAD2.1, which lost the third histidine box in the C-terminal region. In the G. raimondii genome, tandem duplication might have led to the increasing size of the FAD2 cluster in the Omega Desaturase subfamily, whereas segmental duplication appeared to be the dominant mechanism for the expansion of the Sphingolipid and Front-end Desaturase subfamilies. Gene expression analysis showed that seven membrane-bound FAD genes were significantly up-regulated and that five genes were greatly suppressed in G. raimondii leaves exposed to low temperature conditions. PMID:25894196

  17. Covalently networked monolayer-protected nanoparticle films.

    PubMed

    Tognarelli, D J; Miller, Robert B; Pompano, Rebecca R; Loftus, Andrew F; Sheibley, Daniel J; Leopold, Michael C

    2005-11-22

    Covalently networked films of nanoparticles can be assembled on various substrates from functionalized monolayer-protected clusters (MPCs) via ester coupling reactions. Exposure of a specifically modified substrate to alternating solutions of 11-mercaptoundecanoic acid exchanged and 11-mercaptoundecanol exchanged MPCs, in the presence of ester coupling reagents, 1,3-dicyclohexylcarbodiimide and 4-(dimethylamino)pyridine, results in the formation of a multilayer film with ester bridges between individual nanoparticles. These films can be grown in a controlled manner to various thicknesses and exhibit certain properties that are consistent with films having other types of interparticle connectivity, including chemical vapor response behavior and quantized double layer charging. Ester coupling of MPCs into assembled films is a straightforward and highly versatile approach that results in robust films that can endure harsher chemical environments than other types of films. The stability of these covalent films is assessed and compared to other more traditional MPC film assemblies.

  18. Reversible Control of Nanoparticle Functionalization and Physicochemical Properties by Dynamic Covalent Exchange†

    PubMed Central

    della Sala, Flavio

    2015-01-01

    Abstract Existing methods for the covalent functionalization of nanoparticles rely on kinetically controlled reactions, and largely lack the sophistication of the preeminent oligonucleotide‐based noncovalent strategies. Here we report the application of dynamic covalent chemistry for the reversible modification of nanoparticle (NP) surface functionality, combining the benefits of non‐biomolecular covalent chemistry with the favorable features of equilibrium processes. A homogeneous monolayer of nanoparticle‐bound hydrazones can undergo quantitative dynamic covalent exchange. The pseudomolecular nature of the NP system allows for the in situ characterization of surface‐bound species, and real‐time tracking of the exchange reactions. Furthermore, dynamic covalent exchange offers a simple approach for reversibly switching—and subtly tuning—NP properties such as solvophilicity. PMID:27346895

  19. Reversible Control of Nanoparticle Functionalization and Physicochemical Properties by Dynamic Covalent Exchange**

    PubMed Central

    della Sala, Flavio; Kay, Euan R

    2015-01-01

    Existing methods for the covalent functionalization of nanoparticles rely on kinetically controlled reactions, and largely lack the sophistication of the preeminent oligonucleotide-based noncovalent strategies. Here we report the application of dynamic covalent chemistry for the reversible modification of nanoparticle (NP) surface functionality, combining the benefits of non-biomolecular covalent chemistry with the favorable features of equilibrium processes. A homogeneous monolayer of nanoparticle-bound hydrazones can undergo quantitative dynamic covalent exchange. The pseudomolecular nature of the NP system allows for the in situ characterization of surface-bound species, and real-time tracking of the exchange reactions. Furthermore, dynamic covalent exchange offers a simple approach for reversibly switching—and subtly tuning—NP properties such as solvophilicity. PMID:25973468

  20. Covalent attachment of heme to the protein moiety in an insect E75 nitric oxide sensor

    PubMed Central

    Aicart-Ramos, Clara; Valhondo-Falcón, Margarita; Ortiz de Montellano, Paul R.; Rodriguez-Crespo, Ignacio

    2012-01-01

    We have recombinantly expressed and purified the ligand binding domains (LBDs) of four insect nuclear receptors of the E75 family. The Drosophila melanogaster and Bombyx mori nuclear receptors were purified as ferric hemoproteins with Soret maxima at 424 nm, whereas their ferrous form had a Soret maximum at 425 nm that responds to ·NO and CO binding. In contrast, the purified LBD of Oncopeltus fasciatus displayed a Soret maximum at 415 nm for the ferric protein that shifted to 425 nm in its ferrous state. Binding of ·NO to the heme moiety of D. melanogaster and B. mori E75 LBD resulted in the appearance of a peak at 385 nm, whereas this peak appeared at 416 nm in the case of the O. fasciatus hemoprotein, resembling the behaviour displayed by its human homolog Rev-erbβ. HPLC analysis revealed that, unlike the D. melanogaster and B. mori counterparts, the heme group of O. fasciatus is covalently attached to the protein through the side-chains of two amino acids. The large sequence homology with O. fasciatus E75 led us to clone and express the LBD of Blattella germanica, which established that its spectral properties closely resemble those of O. fasciatus and that it also has the heme group covalently bound to the protein. Hence, ·NO/CO regulation of the transcriptional activity of these nuclear receptors might be differently controlled among various insect species. In addition, covalent heme binding provides strong evidence that at least some of these nuclear receptors function as diatomic gas sensors rather than heme sensors. Finally, our findings expand the classes of hemoproteins in which the heme group is normally covalently attached to the polypeptide chain. PMID:22946928

  1. Covalent deposition of zwitterionic polymer and citric acid by click chemistry-enabled layer-by-layer assembly for improving the blood compatibility of polysulfone membrane.

    PubMed

    Xiang, Tao; Wang, Rui; Zhao, Wei-Feng; Sun, Shu-Dong; Zhao, Chang-Sheng

    2014-05-13

    Development of blood compatible membranes is critical for biomedical applications. Zwitterionic polymers have been proved to be resistant to nonspecific protein adsorption and platelet adhesion. In this work, two kinds of zwitterionic copolymers bearing alkynyl and azide groups are synthesized by atom transfer radical polymerization (ATRP) and subsequent reactions, namely alkynyl-poly(sulfobetaine methacrylate) (alkynyl-PSBMA) and azide-poly(sulfobetaine methacrylate) (azide-PSBMA). The copolymers are directly used to modify azido-functionalized polysulfone (PSf-N3) membrane via click chemistry-enabled layer-by-layer (LBL) assembly. Alkynyl-citric acid is then clicked onto the membrane when the outermost layer was azide-PSBMA. The chemical compositions, surface morphologies, and hydrophilicity of the zwitterionic polymer and citric acid multilayer modified membranes are characterized. The composite multilayer is resistant to protein adsorption and platelet adhesion and also prolongs clotting times, indicating that the blood compatibility is improved. Moreover, after clicking the small molecule anticoagulant alkynyl-citric acid onto the outermost of the zwitterionic multilayer, the membrane shows further improved anticoagulant property. The deposition of zwitterionic polymer and citric acid via click chemistry-enabled LBL assembly can improve the blood compatibility of the PSf membrane. PMID:24754639

  2. Covalent deposition of zwitterionic polymer and citric acid by click chemistry-enabled layer-by-layer assembly for improving the blood compatibility of polysulfone membrane.

    PubMed

    Xiang, Tao; Wang, Rui; Zhao, Wei-Feng; Sun, Shu-Dong; Zhao, Chang-Sheng

    2014-05-13

    Development of blood compatible membranes is critical for biomedical applications. Zwitterionic polymers have been proved to be resistant to nonspecific protein adsorption and platelet adhesion. In this work, two kinds of zwitterionic copolymers bearing alkynyl and azide groups are synthesized by atom transfer radical polymerization (ATRP) and subsequent reactions, namely alkynyl-poly(sulfobetaine methacrylate) (alkynyl-PSBMA) and azide-poly(sulfobetaine methacrylate) (azide-PSBMA). The copolymers are directly used to modify azido-functionalized polysulfone (PSf-N3) membrane via click chemistry-enabled layer-by-layer (LBL) assembly. Alkynyl-citric acid is then clicked onto the membrane when the outermost layer was azide-PSBMA. The chemical compositions, surface morphologies, and hydrophilicity of the zwitterionic polymer and citric acid multilayer modified membranes are characterized. The composite multilayer is resistant to protein adsorption and platelet adhesion and also prolongs clotting times, indicating that the blood compatibility is improved. Moreover, after clicking the small molecule anticoagulant alkynyl-citric acid onto the outermost of the zwitterionic multilayer, the membrane shows further improved anticoagulant property. The deposition of zwitterionic polymer and citric acid via click chemistry-enabled LBL assembly can improve the blood compatibility of the PSf membrane.

  3. Synthetic Covalent and Non-Covalent 2D Materials.

    PubMed

    Boott, Charlotte E; Nazemi, Ali; Manners, Ian

    2015-11-16

    The creation of synthetic 2D materials represents an attractive challenge that is ultimately driven by their prospective uses in, for example, electronics, biomedicine, catalysis, sensing, and as membranes for separation and filtration. This Review illustrates some recent advances in this diverse field with a focus on covalent and non-covalent 2D polymers and frameworks, and self-assembled 2D materials derived from nanoparticles, homopolymers, and block copolymers.

  4. A tightly bound quinone functions in the ubiquinone reaction sites of quinoprotein alcohol dehydrogenase of an acetic acid bacterium, Gluconobacter suboxydans.

    PubMed

    Matsushita, Kazunobu; Kobayashi, Yoshiki; Mizuguchi, Mitsuhiro; Toyama, Hirohide; Adachi, Osao; Sakamoto, Kimitoshi; Miyoshi, Hideto

    2008-10-01

    Quinoprotein alcohol dehydrogenase (ADH) of acetic acid bacteria is a membrane-bound enzyme that functions as the primary dehydrogenase in the ethanol oxidase respiratory chain. It consists of three subunits and has a pyrroloquinoline quinone (PQQ) in the active site and four heme c moieties as electron transfer mediators. Of these, three heme c sites and a further site have been found to be involved in ubiquinone (Q) reduction and ubiquinol (QH2) oxidation respectively (Matsushita et al., Biochim. Biophys. Acta, 1409, 154-164 (1999)). In this study, it was found that ADH solubilized and purified with dodecyl maltoside, but not with Triton X-100, had a tightly bound Q, and thus two different ADHs, one having the tightly bound Q (Q-bound ADH) and Q-free ADH, could be obtained. The Q-binding sites of both the ADHs were characterized using specific inhibitors, a substituted phenol PC16 (a Q analog inhibitor) and antimycin A. Based on the inhibition kinetics of Q2 reductase and ubiquinol-2 (Q2H2) oxidase activities, it was suggested that there are one and two PC16-binding sites in Q-bound ADH and Q-free ADH respectively. On the other hand, with antimycin A, only one binding site was found for Q2 reductase and Q2H2 oxidase activities, irrespective of the presence of bound Q. These results suggest that ADH has a high-affinity Q binding site (QH) besides low-affinity Q reduction and QH2 oxidation sites, and that the bound Q in the QH site is involved in the electron transfer between heme c moieties and bulk Q or QH2 in the low-affinity sites.

  5. Covalent attachment of Mn-porphyrin onto doxorubicin-loaded poly(lactic acid) nanoparticles for potential magnetic resonance imaging and pH-sensitive drug delivery.

    PubMed

    Jing, Lijia; Liang, Xiaolong; Li, Xiaoda; Yang, Yongbo; Dai, Zhifei

    2013-12-01

    In this paper, theranostic nanoparticles (MnP-DOX NPs) were fabricated by conjugating Mn-porphyrin onto the surface of doxorubicin (DOX)-loaded poly(lactic acid) (PLA) nanoparticles (DOX NPs) for potential T1 magnetic resonance imaging and pH-sensitive drug delivery. An in vitro drug release study showed that the release rate of DOX from MnP-DOX NPs was slow at neutral pH but accelerated significantly in acidic conditions. It was found that MnP-DOX NPs could be easily internalized by HeLa cells and effectively suppressed the growth of HeLa cells and HT-29 cells due to the accelerated drug release in acidic lysosomal compartments. Magnetic resonance imaging (MRI) scanning analysis demonstrated that MnP-DOX NPs had much higher longitudinal relaxivity in water (r1 value of 27.8 mM(-1) s(-1) of Mn(3+)) than Mn-porphyrin (Mn(III)TPPS3NH2; r1 value of 6.70 mM(-1) s(-1) of Mn(3+)), behaving as an excellent contrast agent for T1-weighted MRI both in vitro and in vivo. In summary, such a smart and promising nanoplatform integrates multiple capabilities for effective cancer diagnosis and therapy.

  6. Lack of release of bound anthocyanins and phenolic acids from carrot plant cell walls and model composites during simulated gastric and small intestinal digestion.

    PubMed

    Padayachee, Anneline; Netzel, Gabriele; Netzel, Michael; Day, Li; Mikkelsen, Deirdre; Gidley, Michael J

    2013-06-01

    Separately, polyphenols and plant cell walls (PCW) are important contributors to the health benefits associated with fruits and vegetables. However, interactions with PCW which occur either during food preparation or mastication may affect bioaccessibility and hence bioavailability of polyphenols. Binding interactions between anthocyanins, phenolic acids (PAs) and PCW components, were evaluated using both a bacterial cellulose-pectin model system and a black carrot puree system. The majority of available polyphenols bound to PCW material with 60-70% of available anthocyanins and PAs respectively binding to black carrot puree PCW matter. Once bound, release of polyphenols using acidified methanol is low with only ∼20% of total anthocyanins to ∼30% of PAs being released. Less than 2% of bound polyphenol was released after in vitro gastric and small intestinal (S.I.) digestion for both the model system and the black carrot puree PCW matter. Confocal laser scanning microscopy shows localised binding of anthocyanins to PCW. Very similar patterns of binding for anthocyanins and PAs suggest that PAs form complexes with anthocyanins and polysaccharides. Time dependent changes in extractability with acidified methanol but not the total bound fraction suggests that initial non-specific deposition on cellulose surfaces is followed by rearrangement of the bound molecules. Minimal release of anthocyanins and PAs after simulated gastric and S.I. digestion indicates that polyphenols in fruits and vegetables which bind to the PCW will be transported to the colon where they would be expected to be released by the action of cell wall degrading bacteria.

  7. Peroxidase-catalyzed metabolism of etoposide (VP-16-213) and covalent binding of reactive intermediates to cellular macromolecules

    SciTech Connect

    Haim, N.; Nemec, J.; Roman, J.; Sinha, B.K.

    1987-11-15

    The horseradish peroxidase- and prostaglandin synthetase-catalyzed oxidative metabolism of the highly active anticancer drug, etoposide (VP-16-213), has been studied in vitro. This oxidation of VP-16 resulted in the formation of VP-16 quinone, an aromatic VP-16 derivative and the corresponding aromatic VP-16 quinone. This oxidative metabolism of VP-16 also resulted in the formation of reactive species that covalently bound to exogenously added DNA and heat-inactivated microsomal proteins. The peroxidase-catalyzed binding was time dependent and required the presence of cofactors (hydrogen peroxide or arachidonic acid). The prostaglandin synthetase/arachidonic acid-catalyzed metabolism and binding of VP-16 were inhibited by indomethacin, an inhibitor of the cyclooxygenase, and were shown to involve the peroxidative arm of prostaglandin synthetase. Our studies show that the protein covalent binding species were formed as a result of O-demethylation of the drug as shown by the loss of specifically labeled (O-/sup 14/CH/sub 3/) radioactivity from O-methoxy group and by incubating proteins with VP-16 quinones. In contrast, the covalent binding intermediates for DNA appeared to be different and VP-16-derived quinone methides are suggested as DNA binding species. Co-oxidation of VP-16 and the related drug, VM-26, during prostaglandin biosynthesis may be an important pathway for the metabolism of these agents and may play a role in their cytotoxic properties.

  8. Nano-architectures by covalent assembly of molecular building blocks.

    PubMed

    Grill, Leonhard; Dyer, Matthew; Lafferentz, Leif; Persson, Mats; Peters, Maike V; Hecht, Stefan

    2007-11-01

    The construction of electronic devices from single molecular building blocks, which possess certain functions such as switching or rectifying and are connected by atomic-scale wires on a supporting surface, is an essential goal of molecular electronics. A key challenge is the controlled assembly of molecules into desired architectures by strong, that is, covalent, intermolecular connections, enabling efficient electron transport between the molecules and providing high stability. However, no molecular networks on surfaces 'locked' by covalent interactions have been reported so far. Here, we show that such covalently bound molecular nanostructures can be formed on a gold surface upon thermal activation of porphyrin building blocks and their subsequent chemical reaction at predefined connection points. We demonstrate that the topology of these nanostructures can be precisely engineered by controlling the chemical structure of the building blocks. Our results represent a versatile route for future bottom-up construction of sophisticated electronic circuits and devices, based on individual functionalized molecules.

  9. Nuclear magnetic resonance studies on covalent modification of amino acids thiol and amino residues by monofunctional aryl 13C-isocyanates, models of skin and respiratory sensitizers: transformation of thiocarbamates into urea adducts.

    PubMed

    Fleischel, Olivier; Giménez-Arnau, Elena; Lepoittevin, Jean-Pierre

    2009-06-01

    Exposure to aryl isocyanates, intermediates in the manufacture of polyurethanes, provokes lung sensitization and asthma but also occupational allergic contact dermatitis, sensitization occurring from a single accidental exposure. The initial step in the sensitization process is believed to be the covalent binding of the -N triple bond C triple bond O group with nucleophilic residues on proteins. While a wide knowledge exists on the reactivity of skin sensitizers toward amino acids, little is known about respiratory sensitizers such as aryl isocyanates. (13)C-Labeled monofunctional aryl isocyanates were synthesized, and their reactivities toward nucleophilic amino acids, GSH, and a model peptide were studied by (13)C and [(1)H-(13)C] NMR spectroscopy. An acetonitrile/buffer solution was used as a solvent to avoid the hampering of the follow up of the reactivity by the isocyanate hydrolysis competing reaction. The compounds reacted with thiol groups, through the formation of thiocarbamate bonds and with amino groups to form urea derivatives. The reactivity was confirmed with GSH, containing both free amino and thiol groups, and with a model peptide, particularly in the case of the reaction with lysine. The use of (13)C NMR to follow the aryl isocyanates reversible conjugation with thiol groups is also reported. Particularly, it is shown that thiocarbamate adducts can be converted into adducts of the urea kind by reaction with amino groups. These results confirmed the hypothesis by which thiol-containing peptides/proteins may act as carriers of isocyanates for possible reaction at a later time and/or place with other nucleophiles and confirmed the role of lysine as a good competing nucleophilic amino acid. The reactivity of aryl isocyanates with thiol and amino groups needs thus to be considered in their assigned sensitization processes.

  10. Covalent binding of aniline to humic substances. 2. 15N NMR studies of nucleophilic addition reactions

    USGS Publications Warehouse

    Thorn, K.A.; Pettigrew, P.J.; Goldenberg, W.S.; Weber, E.J.

    1996-01-01

    Aromatic amines are known to undergo covalent binding with humic substances in the environment. Although previous studies have examined reaction conditions and proposed mechanisms, there has been no direct spectroscopic evidence for the covalent binding of the amines to the functional groups in humic substances. In order to further elucidate the reaction mechanisms, the Suwannee River and IHSS soil fulvic and humic acids were reacted with 15N-labeled aniline at pH 6 and analyzed using 15N NMR spectrometry. Aniline underwent nucleophilic addition reactions with the quinone and other carbonyl groups in the samples and became incorporated in the form of anilinohydroquinone, anilinoquinone, anilide, imine, and heterocyclic nitrogen, the latter comprising 50% or more of the bound amine. The anilide and anilinohydroquinone nitrogens were determined to be susceptible to chemical exchange by ammonia. In the case of Suwannee River fulvic acid, reaction under anoxic conditions and pretreatment with sodium borohydride or hydroxylamine prior to reaction under oxic conditions resulted in a decrease in the proportion of anilinohydroquinone nitrogen incorporated. The relative decrease in the incorporation of anilinohydroquinone nitrogen with respect to anilinoquinone nitrogen under anoxic conditions suggested that inter- or intramolecular redox reactions accompanied the nucleophilic addition reactions.

  11. Covalent binding of reduced metabolites of [{sup 15}N{sub 3}]TNT to soil organic matter during a bioremediation process analyzed by {sup 15}N NMR spectroscopy

    SciTech Connect

    Achtnich, C.; Fernandes, E.; Bollag, J.M.; Knackmuss, H.J.; Lenke, H.

    1999-12-15

    Evidence is presented for the covalent binding of biologically reduced metabolites of 2,4,6-{sup 15}N{sub 3}-trinitrotoluene (TNT) to different soil fractions, using liquid {sup 15}N NMR spectroscopy. A silylation procedure was used to release soil organic matter from humin and whole soil for spectroscopic measurements. TNT-contaminated soil was spiked with 2,4,6-{sup 15}N{sub 3}-trinitrotoluene and {sup 14}C-ring labeled TNT, before treatment in a soil slurry reactor. During the anaerobic/aerobic incubation the amount of radioactivity detected in the fulvic and humic acid fractions did not change significantly whereas the radioactivity bound to humin increased to 71%. The {sup 15}N NMR spectra of the fulvic acid samples were dominated by a large peak that corresponded to aliphatic amines or ammonia. In the early stages of incubation, {sup 15}N NMR analysis of the humic acids indicated bound azoxy compounds. The signals arising from nitro and azoxy groups disappeared with further anaerobic treatment. At the end of incubation, the NMR shifts showed that nitrogen was covalently bound to humic acid as substituted amines and amides. The NMR spectra of the silylated humin suggest formation of azoxy compounds and imine linkages. Bound metabolites possessing nitro groups were also detected. Primary amines formed during the anaerobic incubation disappeared during the aerobic treatment. Simultaneously, the amount of amides and tertiary amines increased. Nitro and azoxy groups of bound molecules were still present in humin at the end of the incubation period. Formation of azoxy compounds from partially reduced TNT followed by binding and further reduction appears to be an important mechanism for the immobilization of metabolites of TNT to soil.

  12. The influence of dissolved and surface-bound humic acid on the toxicity of TiO₂ nanoparticles to Chlorella sp.

    PubMed

    Lin, Daohui; Ji, Jing; Long, Zhifeng; Yang, Kun; Wu, Fengchang

    2012-09-15

    NOM is likely to coat TiO₂ nanoparticles (nano-TiO₂) discharged into the aquatic environment and influence the nanotoxicity to aquatic organisms, which however has not been well investigated. This study explored the influence of nanoparticle surface-bound humic acid (HA, as a model NOM) as well as dissolved HA on the toxicity of nano-TiO₂ to Chlorella sp., with a specific focus on adhesion of the nanoparticles to the algae. Results showed that nano-TiO₂ and the dissolved HA could inhibit the algal growth with an IC₅₀ of 4.9 and 8.4 mg L⁻¹, respectively, while both dissolved and nanoparticle surface-bound HA could significantly alleviate the algal toxicity of nano-TiO₂. IC₅₀ of nano-TiO₂ increased to 18 mg L⁻¹ in the presence of 5 mg L⁻¹ of the dissolved HA and to 48 mg L⁻¹ as the result of surface-saturation by HA. Co-precipitation experiment and transmission electron microscopy observation revealed that both dissolved and nanoparticle surface-bound HA prevented the adhesion of nano-TiO₂ to the algal cells due to the increased electrosteric repulsion. The generation of intracellular reactive oxygen species (ROS) was significantly limited by the dissolved and nanoparticle surface-bound HA. The prevention of adhesion and inhibition of ROS generation could account for the HA-mitigated nanotoxicity.

  13. Trapping and partial characterization of an adduct postulated to be the covalent catalytic ternary complex of thymidylate synthetase

    SciTech Connect

    Ahmed, F.; Moore, M.A.; Dunlap, R.B.

    1986-05-01

    The proposed mechanism of action of thymidylate synthetase envisages the formation of a covalent ternary complex of the enzyme via the active site cysteine with dUMP and 5,10-methylenetetrahydrofolate (CH/sub 2/H/sub 4/folate). The authors recent success in using trichloroacetic acid to trap the covalent enzyme-FdUMP binary and ternary (enzyme-FdUMP-CH/sub 2/H/sub 4/folate) complexes led to the use of this technique in attempts to trap the transient covalent catalytic ternary complex. Experiments performed with (2-C/sup 14/)dUMP and /sup 3/H-CH/sub 2/H/sub 4/folate show that both these ligands remained bound to the enzyme after trichloroacetic acid precipitation. The trapped covalent catalytic ternary complex was subjected to CNBr fragmentation, and the peptides were fractionated by HPLC. The isolated active-site peptide was shown to retain the two ligands and was subjected to a limited sequence analysis by the dansyl-Edman procedure. The inhibitory ternary complex formed with /sup 14/C-FdUMP and /sup 3/H-CH/sub 2/ /sub 4/folate served as a control. The active-site peptides isolated from the CNBr treated inhibitory ternary complex and the catalytic complex exhibited identical sequences for the first four N-terminal residues, Ala-Leu-Pro-Pro, and the fifth residue was found to be associated with the labeled ligands. Sequence analysis of the active site peptide derived from the carboxymethylated enzyme confirmed this sequence and the 5th residue was shown to be Cm-Cys.

  14. [Bounds of change in unsaturation index of fatty acid composition of phospholipids at adaptation of molluscs to biogenic and abiogenic factors of external medium].

    PubMed

    Chebotareva, M A; Zabelinskiĭ, S A; Shukoliukova, E P; Krivchenko, A I

    2011-01-01

    Comparative study of fatty acid composition of total phospholipids, as well as of phosphatidylcholine and phosphatidylethanolamine from hepatopancreas and leg muscle was performed on several representatives of gasteropods (Gastropoda) molluscs and bivalve (Bivalvia) mussel (Mytilus edulus). The objects of our study were marine litorins (Littorina saxsatilis) adapted to different temperature conditions of White Sea and Barents Sea, freshwater lymnaea (Lymnaea stagnalis) infested by Trematoda and mussels from White Sea and Black Sea. It was shown that depending on the existence conditions of studied tissue or lipid, the maximal change is observed in the percentage of saturated acids (4-83 %), the percentage of unsaturated acids was less expressed (1-14 %) and the changes in unsaturation index (UI) did not exceed 20 % on average. It was supposed that observed quantitative bounds of UI change under the action of different external factors is utmost for maintenance of membrane fluidity necessary for normal vital activity of cell, particularly in studied ectothermic molluscs. PMID:22145319

  15. Structural investigation of the covalent and electrostatic binding of yeast cytochrome c to the surface of various ultrathin lipid multilayers using x-ray diffraction.

    PubMed Central

    Pachence, J M; Blasie, J K

    1991-01-01

    X-Ray diffraction was used to characterize the profile structures of ultrathin lipid multilayers having a bound surface layer of cytochrome c. The lipid multilayers were formed on an alkylated glass surface, using the Langmuir-Blodgett method. The ultrathin lipid multilayers of this study were: five monolayers of arachidic acid, four monolayers of arachidic acid with a surface monolayer of dimyristoyl phosphatidylserine, and four monolayers of arachidic acid acid with a surface monolayer of thioethyl stearate. Both the phosphatidylserine and the thioethyl stearate surfaces were found previously to covalently bind yeast cytochrome c, while the arachidic acid surface electrostatically binds yeast cytochrome c. Meridional x-ray diffraction data were collected from these lipid multilayer films with and without a bound yeast cytochrome c surface layer. A box refinement technique, previously shown to be effective in deriving the profile structures of ultrathin multilayer lipid films with and without electrostatically bound cytochrome c, was used to determine the multilayer electron density profiles. The surface monolayer of bound cytochrome c was readily apparent upon comparison of the multilayer electron density profiles for the various pairs of ultrathin multilayer films plus/minus cytochrome c for all cases. In addition, cytochrome c binding to the multilayer surface significantly perturbs the underlying lipid monolayers. PMID:1648415

  16. Strong covalent hydration of terephthalaldehyde.

    PubMed

    Baymak, Melek S; Vercoe, Kellie L; Zuman, Petr

    2005-11-24

    Spectrophotometric and electroanalytical studies indicate that one of the formyl groups of terephthalaldehyde in aqueous solution is present in about 23% as a geminal diol. Stronger covalent hydration of CHO in terephthalaldehyde than in p-nitrobenzaldehyde is attributed to a strong resonance interaction between the two formyl groups.

  17. Chemistry of Covalent Organic Frameworks.

    PubMed

    Waller, Peter J; Gándara, Felipe; Yaghi, Omar M

    2015-12-15

    Linking organic molecules by covalent bonds into extended solids typically generates amorphous, disordered materials. The ability to develop strategies for obtaining crystals of such solids is of interest because it opens the way for precise control of the geometry and functionality of the extended structure, and the stereochemical orientation of its constituents. Covalent organic frameworks (COFs) are a new class of porous covalent organic structures whose backbone is composed entirely of light elements (B, C, N, O, Si) that represent a successful demonstration of how crystalline materials of covalent solids can be achieved. COFs are made by combination of organic building units covalently linked into extended structures to make crystalline materials. The attainment of crystals is done by several techniques in which a balance is struck between the thermodynamic reversibility of the linking reactions and their kinetics. This success has led to the expansion of COF materials to include organic units linked by these strong covalent bonds: B-O, C-N, B-N, and B-O-Si. Since the organic constituents of COFs, when linked, do not undergo significant change in their overall geometry, it has been possible to predict the structures of the resulting COFs, and this advantage has facilitated their characterization using powder X-ray diffraction (PXRD) techniques. It has also allowed for the synthesis of COF structures by design and for their formation with the desired composition, pore size, and aperture. In practice, the modeled PXRD pattern for a given expected COF is compared with the experimental one, and depending on the quality of the match, this is used as a starting point for solving and then refining the crystal structure of the target COF. These characteristics make COFs an attractive class of new porous materials. Accordingly, they have been used as gas storage materials for energy applications, solid supports for catalysis, and optoelectronic devices. A large and

  18. Covalent binding of aniline to humic substances. 1. Kinetic studies

    USGS Publications Warehouse

    Weber, E.J.; Spidle, D.L.; Thorn, K.A.

    1996-01-01

    The reaction kinetics for the covalent binding of aniline with reconstituted IHSS humic and fulvic acids, unfractionated DOM isolated from Suwannee River water, and whole samples of Suwannee River water have been investigated. The reaction kinetics in each of these systems can be adequately described by a simple second-order rate expression. The effect of varying the initial concentration of aniline on reaction kinetics suggested that approximately 10% of the covalent binding sites associated with Suwannee River fulvic acid are highly reactive sites that are quickly saturated. Based on the kinetic parameters determined for the binding of aniline with the Suwannee River fulvic and humic acid isolates, it was estimated that 50% of the aniline concentration decrease in a Suwannee River water sample could be attributed to reaction with the fulvic and humic acid components of the whole water sample. Studies with Suwannee River fulvic acid demonstrated that the rate of binding decreased with decreasing pH, which parallels the decrease in the effective concentration of the neutral form, or reactive nucleophilic species of aniline. The covalent binding of aniline with Suwannee River fulvic acid was inhibited by prior treatment of the fulvic acid with hydrogen sulfide, sodium borohydride, or hydroxylamine. These observations are consistent with a reaction pathway involving nucleophilic addition of aniline to carbonyl moieties present in the fulvic acid.

  19. Reductive transformation of bound trinitrophenyl residues and free TNT during a bioremediation process analyzed by immunoassay

    SciTech Connect

    Achtnich, C.; Pfortner, P.; Weller, M.G.; Niessner, R.; Lenke, H.; Knackmuss, H.J.

    1999-10-01

    To follow the fate of bound metabolites of TNT in soil, a synthetic trinitrophenyl residue covalently linked to humic acids was used as model compound. A selective monoclonal antibody was able to detect chemical changes of the nitro groups of the bound residues. The general possibility of reductive transformations of nitro groups of bound molecules and the reduction rates should be determined. In comparison to the reduction of free TNT and its metabolites, the reductive transformation of the bound trinitrophenyl residue was delayed, and the transformation rate was considerably slower. Trinitrophenyl residues also could be detected by the immunoassay in humic acids extracted from TNT contaminated soil. The reductive transformation of these trinitrophenyl residues started after the reduction of free TNT. At the end of the treatment, small amounts of these residues were still detectable indicating that some of these structures were not completely reduced during the process. From present results one can conclude that the further reduction of nitro groups of bound metabolites requires a prolonged anaerobic treatment. Not only the monitoring of free nitroaromatic compounds is recommended during the bioremediation process but also the measurement of bound residues to determine the optimal conditions and duration of the treatment.

  20. A Heteromeric Membrane-Bound Prenyltransferase Complex from Hop Catalyzes Three Sequential Aromatic Prenylations in the Bitter Acid Pathway1[OPEN

    PubMed Central

    Li, Haoxun; Ban, Zhaonan; Qin, Hao; Ma, Liya; King, Andrew J.

    2015-01-01

    Bitter acids (α and β types) account for more than 30% of the fresh weight of hop (Humulus lupulus) glandular trichomes and are well known for their contribution to the bitter taste of beer. These multiprenylated chemicals also show diverse biological activities, some of which have potential benefits to human health. The bitter acid biosynthetic pathway has been investigated extensively, and the genes for the early steps of bitter acid synthesis have been cloned and functionally characterized. However, little is known about the enzyme(s) that catalyze three sequential prenylation steps in the β-bitter acid pathway. Here, we employed a yeast (Saccharomyces cerevisiae) system for the functional identification of aromatic prenyltransferase (PT) genes. Two PT genes (HlPT1L and HlPT2) obtained from a hop trichome-specific complementary DNA library were functionally characterized using this yeast system. Coexpression of codon-optimized PT1L and PT2 in yeast, together with upstream genes, led to the production of bitter acids, but no bitter acids were detected when either of the PT genes was expressed by itself. Stepwise mutation of the aspartate-rich motifs in PT1L and PT2 further revealed the prenylation sequence of these two enzymes in β-bitter acid biosynthesis: PT1L catalyzed only the first prenylation step, and PT2 catalyzed the two subsequent prenylation steps. A metabolon formed through interactions between PT1L and PT2 was demonstrated using a yeast two-hybrid system, reciprocal coimmunoprecipitation, and in vitro biochemical assays. These results provide direct evidence of the involvement of a functional metabolon of membrane-bound prenyltransferases in bitter acid biosynthesis in hop. PMID:25564559

  1. Influence of amino acid replacement at position 198 on catalytic properties of zinc-bound water in human carbonic anhydrase III.

    PubMed

    LoGrasso, P V; Tu, C; Chen, X; Taoka, S; Laipis, P J; Silverman, D N

    1993-06-01

    Carbonic anhydrase III, found predominantly in skeletal muscle, is the least efficient of the mammalian carbonic anhydrases in catalyzing the hydration of CO2. Phenylalanine-198 is located on the hydrophobic side of the active-site cavity with its phenyl ring in the proximity of the catalytically active zinc-bound water. We replaced phenylalanine-198 in human carbonic anhydrase III with seven other amino acids (Ala, Asn, Asp, His, Leu, Tyr, Val) using site-directed mutagenesis. The catalytic properties of these enzymes were determined by stopped-flow spectrophotometry, and the exchange of 18O between CO2 and water was measured by mass spectrometry. All of the mutants had maximal values of kcat/Km for the hydration of CO2 enhanced, and five of the mutants had the pKa of the zinc-bound water increased compared with the wild-type enzyme. The largest effects were observed with the replacement Phe-198-->Asp which increased the maximal kcat/Km 140-fold and increased the pKa of the zinc-bound water from near 5 to 9.2. A Brønsted correlation was observed between log(kcat/Km) for hydration of CO2 and the pKa of the zinc-bound water (correlation coefficient r = 0.92); in addition, this pKa was inversely correlated with hydrophobicity of the residue at 198 (correlation coefficient r = -0.83). A direct correlation between the logarithm of the maximal kcat/Km for hydration and the logarithm of the pH-independent value of Ki for inhibition by cyanate (r = 0.95) indicated that the effect of the mutations at residue 198 occurred in large part by enhancement of the rate of dissociation of the enzyme-bicarbonate complex. PMID:8504098

  2. Atomic Covalent Functionalization of Graphene

    PubMed Central

    Johns, James E.; Hersam, Mark C.

    2012-01-01

    Conspectus Although graphene’s physical structure is a single atom thick, two-dimensional, hexagonal crystal of sp2 bonded carbon, this simple description belies the myriad interesting and complex physical properties attributed to this fascinating material. Because of its unusual electronic structure and superlative properties, graphene serves as a leading candidate for many next generation technologies including high frequency electronics, broadband photodetectors, biological and gas sensors, and transparent conductive coatings. Despite this promise, researchers could apply graphene more routinely in real-world technologies if they could chemically adjust graphene’s electronic properties. For example, the covalent modification of graphene to create a band gap comparable to silicon (~1 eV) would enable its use in digital electronics, and larger band gaps would provide new opportunities for graphene-based photonics. Towards this end, researchers have focused considerable effort on the chemical functionalization of graphene. Due to its high thermodynamic stability and chemical inertness, new methods and techniques are required to create covalent bonds without promoting undesirable side reactions or irreversible damage to the underlying carbon lattice. In this Account, we review and discuss recent theoretical and experimental work studying covalent modifications to graphene using gas phase atomic radicals. Atomic radicals have sufficient energy to overcome the kinetic and thermodynamic barriers associated with covalent reactions on the basal plane of graphene but lack the energy required to break the C-C sigma bonds that would destroy the carbon lattice. Furthermore, because they are atomic species, radicals substantially reduce the likelihood of unwanted side reactions that confound other covalent chemistries. Overall, these methods based on atomic radicals show promise for the homogeneous functionalization of graphene and the production of new classes of two

  3. RNA Bound to a Solid Phase can Select an Amino Acid and Facilitate Subsequent Amide Bond Formation

    NASA Astrophysics Data System (ADS)

    Mellersh, Anthony; Wilkinson, Alan-Shaun

    2000-01-01

    Polyadenylic acid (Poly A) immobilised on silica gel stereoselectively binds L-lysine from dilute aqueous solution. When the resulting complex is suspended in an organic solvent and liquid ammonia added, lysinamide is formed.

  4. Stochastic sensing through covalent interactions

    DOEpatents

    Bayley, Hagan; Shin, Seong-Ho; Luchian, Tudor; Cheley, Stephen

    2013-03-26

    A system and method for stochastic sensing in which the analyte covalently bonds to the sensor element or an adaptor element. If such bonding is irreversible, the bond may be broken by a chemical reagent. The sensor element may be a protein, such as the engineered P.sub.SH type or .alpha.HL protein pore. The analyte may be any reactive analyte, including chemical weapons, environmental toxins and pharmaceuticals. The analyte covalently bonds to the sensor element to produce a detectable signal. Possible signals include change in electrical current, change in force, and change in fluorescence. Detection of the signal allows identification of the analyte and determination of its concentration in a sample solution. Multiple analytes present in the same solution may be detected.

  5. Enhanced enzyme stability through site-directed covalent immobilization.

    PubMed

    Wu, Jeffrey Chun Yu; Hutchings, Christopher Hayden; Lindsay, Mark Jeffrey; Werner, Christopher James; Bundy, Bradley Charles

    2015-01-10

    Breakthroughs in enzyme immobilization have enabled increased enzyme recovery and reusability, leading to significant decreases in the cost of enzyme use and fueling biocatalysis growth. However, current enzyme immobilization techniques suffer from leaching, enzyme stability, and recoverability and reusability issues. Moreover, these techniques lack the ability to control the orientation of the immobilized enzymes. To determine the impact of orientation on covalently immobilized enzyme activity and stability, we apply our PRECISE (Protein Residue-Explicit Covalent Immobilization for Stability Enhancement) system to a model enzyme, T4 lysozyme. The PRECISE system uses non-canonical amino acid incorporation and the Huisgen 1,3-dipolar cycloaddition "click" reaction to enable directed enzyme immobilization at rationally chosen residues throughout an enzyme. Unlike previous site-specific systems, the PRECISE system is a truly covalent immobilization method. Utilizing this system, enzymes immobilized at proximate and distant locations from the active site were tested for activity and stability under denaturing conditions. Our results demonstrate that orientation control of covalently immobilized enzymes can provide activity and stability benefits exceeding that of traditional random covalent immobilization techniques. PRECISE immobilized enzymes were 50 and 73% more active than randomly immobilized enzymes after harsh freeze-thaw and chemical denaturant treatments.

  6. Photoinduced covalent binding of frusemide and frusemide glucuronide to human serum albumin

    PubMed Central

    Mizuma, Takashi; McDonagh, Antony F; Lin, Emil T; Benet, Leslie Z

    1999-01-01

    Aims To study reaction of photoactivated frusemide (F) and F glucuronide (Fgnd metabolite) with human serum albumin in order to find a clue to clarify a mechanism of phototoxic blisters from high frusemide dosage. Methods F was exposed to light in the presence of human serum albumin (HSA). HSA treated with this method (TR-HSA) was characterized by fluorescence spectroscopic experiment, alkali treatment and reversible binding experiment. Results Less 4-hydroxyl-N-furfuryl-5-sulphamoylanthranilic acid (4HFSA, a photodegradation product of F) was formed in the presence of HSA than in the absence of HSA. A new fluorescence spectrum excited at 320 nm was observed for TR-HSA. Alkali treatment of TR-HSA released 4HFSA. Quenching of the fluorescence due to the lone tryptophan near the warfarin-binding site of HSA was observed in TR-HSA. The reversible binding of F or naproxen to the warfarin-binding site of TR-HSA was less than to that of native HSA. These results indicate the photoactivated F was covalently bound to the warfarin-binding site of HSA. The covalent binding of Fgnd, which is also reversibly bound to the wafarin-binding site of HSA, was also induced by exposure to sunlight. Fgnd was more photoactive than F, indicating that F could be activated by glucuronidation to become a more photoactive compound. Conclusions The reactivity of photoactivated F and Fgnd to HSA and/or to other endogenous compounds may cause the phototoxic blisters that result at high F dosage. PMID:10383564

  7. The effect of covalently linked RGD peptide on the conformation of polysaccharides in aqueous solutions.

    PubMed

    Bernstein-Levi, Ortal; Ochbaum, Guy; Bitton, Ronit

    2016-01-01

    Covalently modified polysaccharides are routinely used in tissue engineering due to their tailored biofunctionality. Understanding the effect of single-chain level modification on the solution conformation of the single chain, and more importantly on the self-assembly and aggregation of the ensemble of chains is expected to improve our ability to control network topology and the properties of the resulting gels. Attaching an RGD peptide to a polysaccharide backbone is a common procedure used to promote cell adhesion in hydrogel scaffolds. Recently it has been shown that the spatial presentation of the RGD sequences affects the cell behavior; thus, understanding the effects of grafted RGD on the conformational properties of the solvated polysaccharide chains is a prerequisite for rational design of polysaccharide-peptide based biomaterials. Here we investigate the effect of covalently linked G4RGDS on the conformational state of the individual chain and chain assemblies of alginate, chitosan, and hyaluronic acid (HA) in aqueous solutions. Two peptide fractions were studied using small-angle X-ray scattering (SAXS) and rheology. In all cases, upon peptide conjugation structural differences were observed. Analysis of the scattering data shows evidence of clustering for a higher fraction of bound peptide. Moreover for all three polysaccharides the typical shear thinning behavior of the natural polysaccharide solutions is replaced by a Newtonian fluid behavior for the lower fraction conjugated peptide while a more pronounced shear thinning behavior is observed for the higher fraction. These results indicate that the fraction of the bounded peptide, determines the behavior of a polysaccharide-peptide conjugates in solution, regardless of the specific nature of the polysaccharide. PMID:26215906

  8. Gas chromatographic mass spectrometric detection of dihydroxy fatty acids preserved in the 'bound' phase of organic residues of archaeological pottery vessels.

    PubMed

    Hansel, Fabricio A; Bull, Ian D; Evershed, Richard P

    2011-07-15

    A methodology is presented for the determination of dihydroxy fatty acids preserved in the 'bound' phase of organic residues preserved in archaeological potsherds. The method comprises saponification, esterification, silica gel column chromatographic fractionation, and analysis by gas chromatography/mass spectrometry. The electron ionisation mass spectra of the trimethylsilyl ether methyl ester derivatives are characterised by fragment ions arising from cleavage of the bond between the two vicinal trimethylsiloxy groups. Other significant fragment ions are [M-15](+.), [M-31](+.), m/z 147 and ions characteristic of vicinal disubstituted (trimethylsiloxy) TMSO- groups (Δ(7,8), Δ(9,10), Δ(11,12) and Δ(13,14): m/z 304, 332, 360 and 388, respectively). The dihydroxy fatty acids identified in archaeological extracts exhibited carbon numbers ranging from C(16) to C(22) and concentrations varying from 0.05 to 14.05 µg g(-1) . The wide range of dihydroxy fatty acids observed indicates that this approach may be applied confidently in screening archaeological potsherds for the degradation products of monounsaturated fatty acids derived from commodities processed in archaeological pottery vessels.

  9. Technique for measuring picomolar amounts of bound and unbound amino acids obtained from myogenic cell cultures of skeletal muscle

    SciTech Connect

    Bullaro, J.C.

    1981-10-01

    A procedure is described that compares the isotope dilution method of measuring picomolar amounts of amino acids obtained from cellular extracts with a direct method of analysis. Evidence is provided that shows that the direct method is at least as accurate as the isotope dilution method. In addition the direct method is as expedient an requires but a single isotope and fewer chromatograms for analysis. A procedure also is described for selecting the appropriate conditions for dansylation and for measuring the loss of dansyl amino acid due to decomposition.

  10. Effect of feeding lipids recovered from fish processing waste by lactic acid fermentation and enzymatic hydrolysis on antioxidant and membrane bound enzymes in rats.

    PubMed

    Rai, Amit Kumar; Bhaskar, N; Baskaran, V

    2015-06-01

    Fish oil recovered from fresh water fish visceral waste (FVW-FO) through lactic acid fermentation (FO-LAF) and enzymatic hydrolysis (FO-EH) were fed to rats to study their influence on lipid peroxidation and activities of antioxidant and membrane bound enzyme in liver, heart and brain. Feeding of FO-LAF and FO-EH resulted in increase (P < 0.05) in lipid peroxides level in serum, liver, brain and heart tissues compared to ground nut oil (control). Activity of catalase (40-235 %) and superoxide dismutase (17-143 %) also increased (P < 0.05) with incremental level of EPA + DHA in diet. The increase was similar to cod liver oil fed rats at same concentration of EPA + DHA. FO-LAF and FO-EH increased (P < 0.05) the Na(+)K(+) ATPase activity in liver and brain microsomes, Ca(+)Mg(+) ATPase in heart microsome and acetylcholine esterase in brain microsomes when fed with 5 % EPA + DHA. There was also significant change in fatty acid composition and cholesterol/phospholipid ratio in microsomes of rat fed with FVW-FO. Feeding FVW-FO recovered by biotechnological approaches enhanced the activity of antioxidant enzymes in tissues, modulates the activities of membrane bound enzymes and improved the fatty acid composition in microsomes of tissues similar to CLO. Utilization of these processing wastes for the production of valuable biofunctional products can reduce the mounting economic values of fish oil and minimize the environmental pollution problems.

  11. Covalent biofunctionalization of silicon nitride surfaces.

    PubMed

    Arafat, Ahmed; Giesbers, Marcel; Rosso, Michel; Sudhölter, Ernst J R; Schroën, Karin; White, Richard G; Yang, Li; Linford, Matthew R; Zuilhof, Han

    2007-05-22

    Covalently attached organic monolayers on etched silicon nitride (SixN4; x >/= 3) surfaces were prepared by reaction of SixN4-coated wafers with neat or solutions of 1-alkenes and 1-alkynes in refluxing mesitylene. The surface modification was monitored by measurement of the static water contact angle, XPS, IRRAS, AFM, and ToF-SIMS, and evidence for the formation of Si-C bonds is presented. The etching can be achieved by dilute HF solutions and yields both Si-H and N-H moieties. The resulting etched SixN4 surfaces are functionalized by terminal carboxylic acid groups in either of two ways: (a) via attachment of a 10-undecenoic acid 2,2,2-trifluoroethyl ester (trifluoro ethanol ester) and subsequent thermal acid hydrolysis; (b) through attachment of a photocleavable ester, and subsequent photochemical cleavage, as this would allow photopatterned functionalized SixN4. The carboxylic acids are successfully used for the attachment of oligopeptides (aspartame) and complete proteins using EDC/NHS chemistry. Finally, an amino-terminated organic monolayer can be formed by reaction of HF-treated SixN4 surfaces with a N-(omega-undecylenyl)phthalimide, which yields an amino-terminated surface upon deprotection with hydrazine.

  12. Outward Bound.

    ERIC Educational Resources Information Center

    Outward Bound, Inc., Andover, MA.

    The Outward Bound concept was developed in Germany and Great Britain with the saving of human life as the ultimate goal. Courses are designed to help students discover their true physical and mental limits through development of skills including emergency medical aid, firefighting, search and rescue, mountaineering, and sailing. Five Outward Bound…

  13. Improved Quantification of Free and Ester-Bound Gallic Acid in Foods and Beverages by UHPLC-MS/MS.

    PubMed

    Newsome, Andrew G; Li, Yongchao; van Breemen, Richard B

    2016-02-17

    Hydrolyzable tannins are measured routinely during the characterization of food and beverage samples. Most methods for the determination of hydrolyzable tannins use hydrolysis or methanolysis to convert complex tannins to small molecules (gallic acid, methyl gallate, and ellagic acid) for quantification by HPLC-UV. Often unrecognized, analytical limitations and variability inherent in these approaches for the measurement of hydrolyzable tannins include the variable mass fraction (0-0.90) that is released as analyte, contributions of sources other than tannins to hydrolyzable gallate (can exceed >10 wt %/wt), the measurement of both free and total analyte, and lack of controls to account for degradation. An accurate, specific, sensitive, and higher-throughput approach for the determination of hydrolyzable gallate based on ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) that overcomes these limitations was developed. PMID:26804199

  14. Improved Quantification of Free and Ester-Bound Gallic Acid in Foods and Beverages by UHPLC-MS/MS.

    PubMed

    Newsome, Andrew G; Li, Yongchao; van Breemen, Richard B

    2016-02-17

    Hydrolyzable tannins are measured routinely during the characterization of food and beverage samples. Most methods for the determination of hydrolyzable tannins use hydrolysis or methanolysis to convert complex tannins to small molecules (gallic acid, methyl gallate, and ellagic acid) for quantification by HPLC-UV. Often unrecognized, analytical limitations and variability inherent in these approaches for the measurement of hydrolyzable tannins include the variable mass fraction (0-0.90) that is released as analyte, contributions of sources other than tannins to hydrolyzable gallate (can exceed >10 wt %/wt), the measurement of both free and total analyte, and lack of controls to account for degradation. An accurate, specific, sensitive, and higher-throughput approach for the determination of hydrolyzable gallate based on ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) that overcomes these limitations was developed.

  15. Protein covalent immobilization via its scarce thiol versus abundant amine groups: Effect on orientation, cell binding domain exposure and conformational lability.

    PubMed

    Ba, O M; Hindie, M; Marmey, P; Gallet, O; Anselme, K; Ponche, A; Duncan, A C

    2015-10-01

    Quantity, orientation, conformation and covalent linkage of naturally cell adhesive proteins adsorbed or covalently linked to a surface, are known to influence the preservation of their subsequent long term cell adhesion properties and bioactivity. In the present work, we explore two different strategies for the covalent linking of plasma fibronectin (pFN) - used as a cell adhesive model protein, onto a polystyrene (PS) surface. One is aimed at tethering the protein to the surface in a semi-oriented fashion (via one of the 4 free thiol reactive groups on the protein) with a heterofunctional coupling agent (SSMPB method). The other aims to immobilize the protein in a more random fashion by reaction between the abundant pendant primary amine bearing amino acids of the pFN and activated carboxylic surface functions obtained after glutaric anhydride surface treatment (GA method). The overall goal will be to verify the hypothesis of a correlation between covalent immobilization of a model cell adhesive protein to a PS surface in a semi-oriented configuration (versus randomly oriented) with promotion of enhanced exposure of the protein's cell binding domain. This in turn would lead to enhanced cell adhesion. Ideally the goal is to elaborate substrates exhibiting a long term stable protein monolayer with preserved cell adhesive properties and bioactivity for biomaterial and/or cell adhesion commercial plate applications. However, the initial restrictive objective of this paper is to first quantitatively and qualitatively investigate the reversibly (merely adsorbed) versus covalently irreversibly bound protein to the surface after the immobilization procedure. Although immobilized surface amounts were similar (close to the monolayer range) for all immobilization approaches, covalent grafting showed improved retention and stronger "tethering" of the pFN protein to the surface (roughly 40%) after SDS rinsing compared to that for mere adsorption (0%) suggesting an added value

  16. Functional systems with orthogonal dynamic covalent bonds.

    PubMed

    Wilson, Adam; Gasparini, Giulio; Matile, Stefan

    2014-03-21

    This review summarizes the use of orthogonal dynamic covalent bonds to build functional systems. Dynamic covalent bonds are unique because of their dual nature. They can be as labile as non-covalent interactions or as permanent as covalent bonds, depending on conditions. Examples from nature, reaching from the role of disulfides in protein folding to thioester exchange in polyketide biosynthesis, indicate how dynamic covalent bonds are best used in functional systems. Several synthetic functional systems that employ a single type of dynamic covalent bonds have been reported. Considering that most functional systems make simultaneous use of several types of non-covalent interactions together, one would expect the literature to contain many examples in which different types of dynamic covalent bonds are similarly used in tandem. However, the incorporation of orthogonal dynamic covalent bonds into functional systems is a surprisingly rare and recent development. This review summarizes the available material comprehensively, covering a remarkably diverse collection of functions. However, probably more revealing than the specific functions addressed is that the questions asked are consistently quite unusual, very demanding and highly original, focusing on molecular systems that can self-sort, self-heal, adapt, exchange, replicate, transcribe, or even walk and "think" (logic gates). This focus on adventurous chemistry off the beaten track supports the promise that with orthogonal dynamic covalent bonds we can ask questions that otherwise cannot be asked. The broad range of functions and concepts covered should appeal to the supramolecular organic chemist but also to the broader community. PMID:24287608

  17. Gallic acid-based alkyl esters synthesis in a water-free system by celite-bound lipase of Bacillus licheniformis SCD11501.

    PubMed

    Sharma, Shivika; Kanwar, Shamsher S; Dogra, Priyanka; Chauhan, Ghanshyam S

    2015-01-01

    Gallic acid (3, 4, 5- trihydroxybenzoic acid) is an important antioxidant, anti-inflammatory, and radical scavenging agent. In the present study, a purified thermo-tolerant extra-cellular lipase of Bacillus licheniformis SCD11501 was successfully immobilized by adsorption on Celite 545 gel matrix followed by treatment with a cross-linking agent, glutaraldehyde. The celite-bound lipase treated with glutaraldehyde showed 94.8% binding/retention of enzyme activity (36 U/g; specific activity 16.8 U/g matrix; relative increase in enzyme activity 64.7%) while untreated matrix resulted in 88.1% binding/retention (28.0 U/g matrix; specific activity 8.5 U/g matrix) of lipase. The celite-bound lipase was successfully used to synthesis methyl gallate (58.2%), ethyl gallate (66.9%), n-propyl gallate (72.1%), and n-butyl gallate (63.8%) at 55(o) C in 10 h under shaking (150 g) in a water-free system by sequentially optimizing various reaction parameters. The low conversion of more polar alcohols such as methanol and ethanol into their respective gallate esters might be due to the ability of these alcohols to severely remove water from the protein hydration shell, leading to enzyme inactivation. Molecular sieves added to the reaction mixture resulted in enhanced yield of the alkyl ester(s). The characterization of synthesised esters was done through fourier transform infrared (FTIR) spectroscopy and (1) H NMR spectrum analysis.

  18. Thermochemolysis of the Murchison meteorite: identification of oxygen bound and occluded units in the organic macromolecule

    NASA Astrophysics Data System (ADS)

    Watson, Jonathan S.; Sephton, Mark A.; Gilmour, Iain

    2010-10-01

    An organic macromolecular residue, prepared from the Murchison meteorite by treatment with hydrofluoric and hydrochloric acids, was subjected to online thermochemolysis with tetramethylammonium hydroxide (TMAH). The most abundant compound released by thermochemolysis was benzoic acid. Other abundant compounds include methyl and dimethyl benzoic acids as well as methoxy benzoic acids. Short chain dicarboxylic acids (C4-8) were also released from the organic macromolecule. Within the C1 and C2 benzoic acids all possible structural isomers are present reflecting the abiotic origin of these units. The most abundant isomers include 3,4-dimethylbenzoic acid (DMBA), 3,5-DMBA, 2,6-DMBA and phenylacetic acid. Thermochemolysis also liberates hydrocarbons that are not observed during thermal desorption; these compounds include naphthalene, methylnaphthalenes, biphenyl, methylbiphenyls, acenaphthylene, acenaphthene, phenanthrene, anthracene, fluoranthene and pyrene. The lack of oxygen containing functional groups in these hydrocarbons indicates that they represent non-covalently bound, occluded molecules within the organic framework. This data provides a valuable insight into oxygen bound and physically occluded moieties in the Murchison organic macromolecule and implies a relative order of synthesis or agglomeration for the detected organic constituents.

  19. Covalent attachment of 1-alkenes to oxidized platinum surfaces.

    PubMed

    Alonso, Jose Maria; Fabre, Bruno; Trilling, Anke K; Scheres, Luc; Franssen, Maurice C R; Zuilhof, Han

    2015-03-10

    We report the formation of covalently bound alkyl layers onto oxidized Pt (PtOx) substrates by reaction with 1-alkenes as a novel way to bind organic molecules to metal surfaces. The organic layers were characterized by static contact angle, infrared reflection absorption spectroscopy (IRRAS), X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM). The grafted alkyl layers display a hydrolytic stability that is comparable to that of alkyl thiols on Au. PtOx-alkene attachment is compatible with terminal ester moieties enabling further anchoring of functional groups, such as redox-active ferrocene, and thus has great potential to extend monolayer chemistry on noble metals.

  20. Factors Affecting Peptide Interactions with Surface-Bound Microgels.

    PubMed

    Nyström, Lina; Nordström, Randi; Bramhill, Jane; Saunders, Brian R; Álvarez-Asencio, Rubén; Rutland, Mark W; Malmsten, Martin

    2016-02-01

    Effects of electrostatics and peptide size on peptide interactions with surface-bound microgels were investigated with ellipsometry, confocal microscopy, and atomic force microscopy (AFM). Results show that binding of cationic poly-L-lysine (pLys) to anionic, covalently immobilized, poly(ethyl acrylate-co-methacrylic acid) microgels increased with increasing peptide net charge and microgel charge density. Furthermore, peptide release was facilitated by decreasing either microgel or peptide charge density. Analogously, increasing ionic strength facilitated peptide release for short peptides. As a result of peptide binding, the surface-bound microgels displayed pronounced deswelling and increased mechanical rigidity, the latter quantified by quantitative nanomechanical mapping. While short pLys was found to penetrate the entire microgel network and to result in almost complete charge neutralization, larger peptides were partially excluded from the microgel network, forming an outer peptide layer on the microgels. As a result of this difference, microgel flattening was more influenced by the lower Mw peptide than the higher. Peptide-induced deswelling was found to be lower for higher Mw pLys, the latter effect not observed for the corresponding microgels in the dispersed state. While the effects of electrostatics on peptide loading and release were similar to those observed for dispersed microgels, there were thus considerable effects of the underlying surface on peptide-induced microgel deswelling, which need to be considered in the design of surface-bound microgels as carriers of peptide loads, for example, in drug delivery or in functionalized biomaterials. PMID:26750986

  1. Simultaneous covalent and noncovalent hybrid polymerizations

    NASA Astrophysics Data System (ADS)

    Yu, Zhilin; Tantakitti, Faifan; Yu, Tao; Palmer, Liam C.; Schatz, George C.; Stupp, Samuel I.

    2016-01-01

    Covalent and supramolecular polymers are two distinct forms of soft matter, composed of long chains of covalently and noncovalently linked structural units, respectively. We report a hybrid system formed by simultaneous covalent and supramolecular polymerizations of monomers. The process yields cylindrical fibers of uniform diameter that contain covalent and supramolecular compartments, a morphology not observed when the two polymers are formed independently. The covalent polymer has a rigid aromatic imine backbone with helicoidal conformation, and its alkylated peptide side chains are structurally identical to the monomer molecules of supramolecular polymers. In the hybrid system, covalent chains grow to higher average molar mass relative to chains formed via the same polymerization in the absence of a supramolecular compartment. The supramolecular compartments can be reversibly removed and re-formed to reconstitute the hybrid structure, suggesting soft materials with novel delivery or repair functions.

  2. Simultaneous covalent and noncovalent hybrid polymerizations.

    PubMed

    Yu, Zhilin; Tantakitti, Faifan; Yu, Tao; Palmer, Liam C; Schatz, George C; Stupp, Samuel I

    2016-01-29

    Covalent and supramolecular polymers are two distinct forms of soft matter, composed of long chains of covalently and noncovalently linked structural units, respectively. We report a hybrid system formed by simultaneous covalent and supramolecular polymerizations of monomers. The process yields cylindrical fibers of uniform diameter that contain covalent and supramolecular compartments, a morphology not observed when the two polymers are formed independently. The covalent polymer has a rigid aromatic imine backbone with helicoidal conformation, and its alkylated peptide side chains are structurally identical to the monomer molecules of supramolecular polymers. In the hybrid system, covalent chains grow to higher average molar mass relative to chains formed via the same polymerization in the absence of a supramolecular compartment. The supramolecular compartments can be reversibly removed and re-formed to reconstitute the hybrid structure, suggesting soft materials with novel delivery or repair functions. PMID:26823427

  3. The Phosphorylation of Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) by Engineered Surfaces with Electrostatically or Covalently Immobilized VEGF

    PubMed Central

    Anderson, Sean M.; Chen, Tom T.; Iruela-Arispe, M. Luisa; Segura, Tatiana

    2010-01-01

    Growth factors are a class of signaling proteins that direct cell fate through interaction with cell surface receptors. Although a myriad of possible cell fates stem from a growth factor binding to its receptor, the signaling cascades that result in one fate over another are still being elucidated. One possible mechanism by which nature modulates growth factor signaling is through the method of presentation of the growth factor – soluble or immobilized (matrix bound). Here we present the methodology to study signaling of soluble versus immobilized VEGF through VEGFR-2. We have designed a strategy to covalently immobilize VEGF using its heparin-binding domain to orient the molecule (bind) and a secondary functional group to mediate covalent binding (lock). This bind-and-lock approach aims to allow VEGF to assume a bioactive orientation before covalent immobilization. Surface plasmon resonance (SPR) demonstrated heparin and VEGF binding with surface densities of 60 ng/cm2 and 100 pg/cm2, respectively. ELISA experiments confirmed VEGF surface density and showed that electrostatically bound VEGF releases in cell medium and heparin solutions while covalently bound VEGF remains immobilized. Electrostatically bound VEGF and covalently bound VEGF phosphorylate VEGFR-2 in both VEGFR-2 transfected cells and VEGFR-2 endogenously producing cells. HUVECs plated on VEGF functionalized surfaces showed different morphologies between surface-bound VEGF and soluble VEGF. The surfaces synthesized in these studies allow for the study of VEGF/VEGFR-2 signaling induced by covalently bound, electrostatically bound, and soluble VEGF and may provide further insight into the design of materials for the generation of a mature and stable vasculature. PMID:19540581

  4. Semisynthetic Nanoreactor for Reversible Single-Molecule Covalent Chemistry.

    PubMed

    Lee, Joongoo; Boersma, Arnold J; Boudreau, Marc A; Cheley, Stephen; Daltrop, Oliver; Li, Jianwei; Tamagaki, Hiroko; Bayley, Hagan

    2016-09-27

    Protein engineering has been used to remodel pores for applications in biotechnology. For example, the heptameric α-hemolysin pore (αHL) has been engineered to form a nanoreactor to study covalent chemistry at the single-molecule level. Previous work has been confined largely to the chemistry of cysteine side chains or, in one instance, to an irreversible reaction of an unnatural amino acid side chain bearing a terminal alkyne. Here, we present four different αHL pores obtained by coupling either two or three fragments by native chemical ligation (NCL). The synthetic αHL monomers were folded and incorporated into heptameric pores. The functionality of the pores was validated by hemolysis assays and by single-channel current recording. By using NCL to introduce a ketone amino acid, the nanoreactor approach was extended to an investigation of reversible covalent chemistry on an unnatural side chain at the single-molecule level. PMID:27537396

  5. Semisynthetic Nanoreactor for Reversible Single-Molecule Covalent Chemistry

    PubMed Central

    2016-01-01

    Protein engineering has been used to remodel pores for applications in biotechnology. For example, the heptameric α-hemolysin pore (αHL) has been engineered to form a nanoreactor to study covalent chemistry at the single-molecule level. Previous work has been confined largely to the chemistry of cysteine side chains or, in one instance, to an irreversible reaction of an unnatural amino acid side chain bearing a terminal alkyne. Here, we present four different αHL pores obtained by coupling either two or three fragments by native chemical ligation (NCL). The synthetic αHL monomers were folded and incorporated into heptameric pores. The functionality of the pores was validated by hemolysis assays and by single-channel current recording. By using NCL to introduce a ketone amino acid, the nanoreactor approach was extended to an investigation of reversible covalent chemistry on an unnatural side chain at the single-molecule level. PMID:27537396

  6. Covalent bonding: the fundamental role of the kinetic energy.

    PubMed

    Bacskay, George B; Nordholm, Sture

    2013-08-22

    This work addresses the continuing disagreement between two prevalent schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg, and Kutzelnigg, a lowering of the kinetic energy associated with electron delocalization is the key stabilization mechanism. The opposing view of Slater, Feynman, and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei. Despite the large body of accurate quantum chemical work on a range of molecules, the debate concerning the origin of bonding continues unabated, even for H2(+), the simplest of covalently bound molecules. We therefore present here a detailed study of H2(+), including its formation, that uses a sequence of computational methods designed to reveal the relevant contributing mechanisms as well as the spatial density distributions of the kinetic and potential energy contributions. We find that the electrostatic mechanism fails to provide real insight or explanation of bonding, while the kinetic energy mechanism is sound and accurate but complex or even paradoxical to those preferring the apparent simplicity of the electrostatic model. We further argue that the underlying mechanism of bonding is in fact of dynamical character, and analyses that focus on energy do not reveal the origin of covalent bonding in full clarity. PMID:23859401

  7. Athermal fracture of covalent bonds

    SciTech Connect

    Gilman, J.J.

    1999-08-01

    Most fracture is athermal. Either because it occurs at low temperatures or because it occurs too fast for thermal activation to be effective. Thus it must be directly activated by applied stresses. This can occur via quantum tunneling when the chemical bonding of a solid resides in localized (covalent) bonds. Then applied stresses can cause the bonding electrons to become delocalized (anti-bonded) through quantum tunneling. That is, the bonds become broken. The process is related to the Zener tunneling process that is thought to be responsible for dielectric breakdown in semiconductors. Under a driving force, bonding electrons tunnel at constant energy from their bonding states into anti-bonding states through the forbidden gap in the bonding energy spectrum.

  8. Transfection of cells mediated by biodegradable polymer materials with surface-bound polyethyleneimine.

    PubMed

    Zheng, J; Manuel, W S; Hornsby, P J

    2000-01-01

    Poly(epsilon-CBZ-L-lysine) can be mixed with biodegradable polymers such as poly(D,L-lactic-co-glycolic acid) or poly(L-lactic acid) and formed into films, foams, or microspheres. Surface amino groups may then be deprotected with acid or lithium/liquid ammonia. The amino groups serve as a method to modify the surface by attachment of other molecules. In the present experiments, we show that these polymer materials, as films or foams, may be surface modified by the attachment of polyethyleneimine (PEI). Plasmid DNA attached to the PEI can transfect cells plated on the surface over several days. Covalent atachment of PEI was required for transfection to be efficient. PEI was also attached to surface-bound collagen on cell culture plates and was shown to mediate transfection.

  9. Stimulation of Tetrabromobisphenol A Binding to Soil Humic Substances by Birnessite and the Chemical Structure of the Bound Residues.

    PubMed

    Tong, Fei; Gu, Xueyuan; Gu, Cheng; Xie, Jinyu; Xie, Xianchuan; Jiang, Bingqi; Wang, Yongfeng; Ertunc, Tanya; Schäffer, Andreas; Ji, Rong

    2016-06-21

    Studies have shown the main fate of the flame retardant tetrabromobisphenol A (TBBPA) in soils is the formation of bound residues, and mechanisms on it are less-understood. This study investigated the effect of birnessite (δ-MnO2), a naturally occurring oxidant in soils, on the formation of bound residues. (14)C-labeled TBBPA was used to investigate the pH dependency of TBBPA bound-residue formation to two soil humic acids (HAs), Elliott soil HA and Steinkreuz soil HA, in the presence of δ-MnO2. The binding of TBBPA and its transformation products to both HAs was markedly increased (3- to 17-fold) at all pH values in the presence of δ-MnO2. More bound residues were formed with the more aromatic Elliott soil HA than with Steinkreuz soil HA. Gel-permeation chromatography revealed a uniform distribution of the bound residues within Steinkreuz soil HA and a nonuniform distribution within Elliott soil HA. (13)C NMR spectroscopy of (13)C-TBBPA residues bound to (13)C-depleted HA suggested that in the presence of δ-MnO2, binding occurred via ester and ether and other types of covalent bonds besides HA sequestration. The insights gained in this study contribute to an understanding of the formation of TBBPA bound residues facilitated by δ-MnO2. PMID:27223831

  10. Membrane-bound guaiacol peroxidases from maize (Zea mays L.) roots are regulated by methyl jasmonate, salicylic acid, and pathogen elicitors.

    PubMed

    Mika, Angela; Boenisch, Marike Johanne; Hopff, David; Lüthje, Sabine

    2010-03-01

    Plant peroxidases are involved in numerous cellular processes in plant development and stress responses. Four plasma membrane-bound peroxidases have been identified and characterized in maize (Zea mays L.) roots. In the present study, maize seedlings were treated with different stresses and signal compounds, and a functional analysis of these membrane-bound class III peroxidases (pmPOX1, pmPOX2a, pmPOX2b, and pmPOX3) was carried out. Total guaiacol peroxidase activities from soluble and microsomal fractions of maize roots were compared and showed weak changes. By contrast, total plasma membrane and washed plasma membrane peroxidase activities, representing peripheral and integral membrane proteins, revealed strong changes after all of the stresses applied. A proteomic approach using 2D-PAGE analysis showed that pmPOX3 was the most abundant class III peroxidase at plasma membranes of control plants, followed by pmPOX2a >pmPOX2b >pmPOX1. The molecular mass (63 kDa) and the isoelectric point (9.5) of the pmPOX2a monomer were identified for the first time. The protein levels of all four enzymes changed in response to multiple stresses. While pmPOX2b was the only membrane peroxidase down-regulated by wounding, all four enzymes were differentially but strongly stimulated by methyl jasmonate, salicylic acid, and elicitors (Fusarium graminearum and Fusarium culmorum extracts, and chitosan) indicating their function in pathogen defence. Oxidative stress applied as H(2)O(2) treatment up-regulated pmPOX2b >pmPOX2a, while pmPOX3 was down-regulated. Treatment with the phosphatase inhibitor chantharidin resulted in distinct responses.

  11. Cell wall bound anionic peroxidases from asparagus byproducts.

    PubMed

    Jaramillo-Carmona, Sara; López, Sergio; Vazquez-Castilla, Sara; Jimenez-Araujo, Ana; Rodriguez-Arcos, Rocio; Guillen-Bejarano, Rafael

    2014-10-01

    Asparagus byproducts are a good source of cationic soluble peroxidases (CAP) useful for the bioremediation of phenol-contaminated wastewaters. In this study, cell wall bound peroxidases (POD) from the same byproducts have been purified and characterized. The covalent forms of POD represent >90% of the total cell wall bound POD. Isoelectric focusing showed that whereas the covalent fraction is constituted primarily by anionic isoenzymes, the ionic fraction is a mixture of anionic, neutral, and cationic isoenzymes. Covalently bound peroxidases were purified by means of ion exchange chromatography and affinity chromatography. In vitro detoxification studies showed that although CAP are more effective for the removal of 4-CP and 2,4-DCP, anionic asparagus peroxidase (AAP) is a better option for the removal of hydroxytyrosol (HT), the main phenol present in olive mill wastewaters.

  12. Covalently Cross-Linked Arabinoxylans Films for Debaryomyces hansenii Entrapment.

    PubMed

    González-Estrada, Ramsés; Calderón-Santoyo, Montserrat; Carvajal-Millan, Elizabeth; Ascencio Valle, Felipe de Jesús; Ragazzo-Sánchez, Juan Arturo; Brown-Bojorquez, Francisco; Rascón-Chu, Agustín

    2015-01-01

    In the present study, wheat water extractable arabinoxylans (WEAX) were isolated and characterized, and their capability to form covalently cross-linked films in presence of Debaryomyces hansenii was evaluated. WEAX presented an arabinose to xylose ratio of 0.60, a ferulic acid and diferulic acid content of 2.1 and 0.04 µg∙mg(-1) WEAX, respectively and a Fourier Transform Infra-Red (FT-IR) spectrum typical of WEAX. The intrinsic viscosity and viscosimetric molecular weight values for WEAX were 3.6 dL∙g(-1) and 440 kDa, respectively. The gelation of WEAX (1% w/v) with and without D. hansenii (1 × 10(7) CFU∙cm(-2)) was rheologically investigated by small amplitude oscillatory shear. The entrapment of D. hansenii decreased gel elasticity from 1.4 to 0.3 Pa, probably by affecting the physical interactions between WEAX chains. Covalently cross-linked WEAX films containing D. hansenii were prepared by casting. Scanning electron microscopy images show that WEAX films containing D. hansenii were porous and consisted of granular-like and fibre microstructures. Average tensile strength, elongation at break and Young's modulus values dropped when D. hansenii was present in the film. Covalently cross-lined WEAX containing D. hansenii could be a suitable as a functional entrapping film. PMID:26102070

  13. Interaction of functionally bound vitamins in the distribution and metabolism of (/sup 14/C)nicotinic acid in tissues and blood cells

    SciTech Connect

    Rozanov, A.Ya.; Yakubik, E.Yu.

    1986-03-10

    Leukocytes absorb two orders of magnitude more of labeled nicotinic acid ((/sup 14/C)NA) than erythrocytes (recalculated per cell). The dynamics of the binding of the labeled vitamin by leukocytes is biphasic, with the formation chiefly of (/sup 14/C)-nicotinic coenzymes in the shortest periods after its injection into rats. At the same time, injected thiamine, riboflavin, lipoate, and pantothenate increase the accumulation of labeled metabolites of nicotinate in the blood and leukocytes of rats by a factor of 2.1 and 4.1, respectively. The metabolism of subcutaneously injected (/sup 14/C)NA occurs chiefly in the digestive system, with a pronounced biphasic dynamics of the changes in the content of labeled metabolites in the liver and small intestine, with secretion of substantial amounts of them with the digestive juices. At the same time, functionally bound vitamins introduced increase the incorporation of the total label into liver tissue (to 45% of the introduced dose, versus 33% in the control) and the rise in the content of (/sup 14/C)-pyridine nucleotides. Analogous effects were also observed in the accumulation of labeled metabolites of (/sup 14/C)NA in the membranes of the small intestine.

  14. Covalently crosslinked diels-alder polymer networks.

    SciTech Connect

    Bowman, Christopher; Adzima, Brian J.; Anderson, Benjamin John

    2011-09-01

    This project examines the utility of cycloaddition reactions for the synthesis of polymer networks. Cycloaddition reactions are desirable because they produce no unwanted side reactions or small molecules, allowing for the formation of high molecular weight species and glassy crosslinked networks. Both the Diels-Alder reaction and the copper-catalyzed azide-alkyne cycloaddition (CuAAC) were studied. Accomplishments include externally triggered healing of a thermoreversible covalent network via self-limited hysteresis heating, the creation of Diels-Alder based photoresists, and the successful photochemical catalysis of CuAAC as an alternative to the use of ascorbic acid for the generation of Cu(I) in click reactions. An analysis of the results reveals that these new methods offer the promise of efficiently creating robust, high molecular weight species and delicate three dimensional structures that incorporate chemical functionality in the patterned material. This work was performed under a Strategic Partnerships LDRD during FY10 and FY11 as part of a Sandia National Laboratories/University of Colorado-Boulder Excellence in Science and Engineering Fellowship awarded to Brian J. Adzima, a graduate student at UC-Boulder. Benjamin J. Anderson (Org. 1833) was the Sandia National Laboratories point-of-contact for this fellowship.

  15. Production of a covalent flavin linkage in lipoamide dehydrogenase. Reaction with 8-Cl-FAD.

    PubMed

    Moore, E G; Cardemil, E; Massey, V

    1978-09-25

    A method is described for preparation of apolipoamide dehydrogenase which gives quantitative removal of FAD. Active holoenzyme can be reconstituted by incubation with FAD. Reconstitution of apoenzyme with 8-Cl-FAD results in the fixation of most of the flavin to the protein in a covalently bound form. The portion noncovalently bound was shown to be unmodified 8-Cl-FAD. The covalently bound flavin has an absorption spectrum quite different from that of 8-Cl-FAD. It has a single band in the visible with a maximum at 459 nm (extinction coefficient of 22 mM-1 cm-1) and a shoulder at 480 nm. Model reactions between 8-Cl-Flavin (riboflavin or FAD) and organic thiols (thiophenol, beta-mercaptoethanol, or N-acetylcysteine) give products with spectra which are similar to that of FAD covalently bound to lipoamide dehydrogenase. The products of the model reactions have a single visible band with a maximum at 480 nm (extinction coefficient of 23.6 mM-1 cm-1 to 28.4 mM-1 cm-1) and a shoulder at 460 nm. The products of the model reaction and the covalently bound FAD of lipoamide dehydrogenase appear to be the result of a nucleophilic attack on the carbon at position 8 of the flavin ring by a thiolate anion, displacing the chloride. Thus, the product of the model reaction is 8-(RS)-flavin, and the product of the reaction between 8-Cl-FAD and protein probably has a cysteinyl residue covalently attacked at position 8 of FAD. Reconstitution of apoliopoamide dehydrogenase with 8-Cl-FAD gives two enzyme products which are fractionated by ammonium sulfate. Enzyme fractionating between 20% and 45% ammonium sulfate is monomeric and contains covanently bound FAD. Enzyme fractionating between 55% and 75% ammonium sulfate is dimeric and contains both covalently bound FAD and noncovalently bound 8-Cl-FAD. Both protein fractions contain one FAD per protein subunit and both are active with physiological substrates with Km values for NAD and dihydrolipoamide similar to those of native lipoamide

  16. Production of a covalent flavin linkage in lipoamide dehydrogenase. Reaction with 8-Cl-FAD.

    PubMed

    Moore, E G; Cardemil, E; Massey, V

    1978-09-25

    A method is described for preparation of apolipoamide dehydrogenase which gives quantitative removal of FAD. Active holoenzyme can be reconstituted by incubation with FAD. Reconstitution of apoenzyme with 8-Cl-FAD results in the fixation of most of the flavin to the protein in a covalently bound form. The portion noncovalently bound was shown to be unmodified 8-Cl-FAD. The covalently bound flavin has an absorption spectrum quite different from that of 8-Cl-FAD. It has a single band in the visible with a maximum at 459 nm (extinction coefficient of 22 mM-1 cm-1) and a shoulder at 480 nm. Model reactions between 8-Cl-Flavin (riboflavin or FAD) and organic thiols (thiophenol, beta-mercaptoethanol, or N-acetylcysteine) give products with spectra which are similar to that of FAD covalently bound to lipoamide dehydrogenase. The products of the model reactions have a single visible band with a maximum at 480 nm (extinction coefficient of 23.6 mM-1 cm-1 to 28.4 mM-1 cm-1) and a shoulder at 460 nm. The products of the model reaction and the covalently bound FAD of lipoamide dehydrogenase appear to be the result of a nucleophilic attack on the carbon at position 8 of the flavin ring by a thiolate anion, displacing the chloride. Thus, the product of the model reaction is 8-(RS)-flavin, and the product of the reaction between 8-Cl-FAD and protein probably has a cysteinyl residue covalently attacked at position 8 of FAD. Reconstitution of apoliopoamide dehydrogenase with 8-Cl-FAD gives two enzyme products which are fractionated by ammonium sulfate. Enzyme fractionating between 20% and 45% ammonium sulfate is monomeric and contains covanently bound FAD. Enzyme fractionating between 55% and 75% ammonium sulfate is dimeric and contains both covalently bound FAD and noncovalently bound 8-Cl-FAD. Both protein fractions contain one FAD per protein subunit and both are active with physiological substrates with Km values for NAD and dihydrolipoamide similar to those of native lipoamide

  17. Synergistic Assembly of Covalent and Supramolecular Polymers.

    PubMed

    Bai, Linyi; Zhao, Yanli

    2016-06-01

    Integrating irreplaceable features of both covalent chemistry and noncovalent interactions into a single entity to maximize the applicability is highly desired. Here, a discovery of this type of hybrid, developed by Stupp and co-workers, is developed, where a synergistic combination of covalent and noncovalent compartments enables them to assemble by each other perfectively. The covalent compartments can grow into polymer chains assisted by a supramolecular compartment. The supramolecular compartments can be reversibly removed and re-formed to reconstitute the hybrid structure. The obtained soft materials can serve as functional platforms for molecular delivery or self-repairing materials. PMID:27076255

  18. Self-assembling of cytosine nucleoside into triply-bound dimers in acid media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, X-rays diffractometry, and theoretical calculations.

    PubMed

    Armentano, Donatella; De Munno, Giovanni; Di Donna, Leonardo; Sindona, Giovanni; Giorgi, Gianluca; Salvini, Laura; Napoli, Anna

    2004-02-01

    Electrospray tandem mass spectrometry (ESI-MS/MS) is used to evaluate the assembling of cytosine and thymine nucleosides in the gas phase, through the formation of hydrogen bonded supermolecules. Mixtures of cytidine analogues and homologues deliver in the gas phase proton-bound heterodimers stabilized by multiple interactions, as proven by the kinetics of their dissociation into the corresponding protonated monomers. Theoretical calculations, performed on initial structures of methylcytosine homodimers available in the literature, converged to a minimized structure whereby the two pyrimidine rings interact through the formation of three hydrogen bonds of similar energy. The crystallographic data here reported show the equivalency of the two interacting pyrimidines which is attributable to the presence of an inversion center. Thymine and uracil pyrimidyl nucleosides form, by ESI, gaseous proton-bound dimers. The kinetic of their dissociation into the related protonated monomers shows that the nucleobases are weekly interacting through a single hydrogen bond. The minimized structure of the protonated heterodimer formed by thymine and N-1-methylthymine confirmed the existence of mainly one hydrogen bond which links the two nucleobases through the O4 oxygens. No crystallographic data exists on thymine proton-bound species, nor have we been able to obtain these aggregates in the solid phase. The gaseous phase, under high vacuum conditions, seems therefore a suitable environment where vanishing structures produced by ESI can be studied with a good degree of approximation.

  19. Peptide immobilization onto radiation grafted PVDF-g-poly(acrylic acid) films

    NASA Astrophysics Data System (ADS)

    Clochard, M.-C.; Betz, N.; Goncalves, M.; Bittencourt, C.; Pireaux, J.-J.; Gionnet, K.; Déléris, G.; Moël, A. Le

    2005-07-01

    Introducing hydrophilic functions on poly(vinylidene fluoride) (PVDF) films surface allows the covalent immobilization of peptides. Therefore radiation grafting of acrylic acid (AA) in pre-irradiated PVDF films was achieved to allow surface functionalization with linear and cyclic peptides. Peptides were bound via spacer molecules using EDC as a coupling agent. The reactions were followed by Fourier Transform Infrared (FTIR) spectroscopy in attenuated total reflection (ATR) mode. The amount of immobilized peptides was determined by UV spectroscopy. As well, an uncommon method for PVDF characterization and reactions quantification was used: high-resolution-magic angle spinning nuclear mass spectroscopy (HR-MAS NMR). Spacer saturation of the film surface corresponded to 25 mol% yield meaning that one spacer on 4 carboxylic acids was covalently bound. XPS experiments were also performed to deepen analysis of the surface composition. Peptide density is governed by steric hindrance. ELISA tests showed that the peptides' activity is maintained.

  20. Cellular delivery of quantum dot-bound hybridization probe for detection of intracellular pre-microRNA using chitosan/poly(γ-glutamic acid) complex as a carrier.

    PubMed

    Geng, Yao; Lin, Dajie; Shao, Lijia; Yan, Feng; Ju, Huangxian

    2013-01-01

    A quantum dot (QD)-bound hybridization probe was designed for detection of intracellular pre-miRNA using chitosan (CS)/poly(γ-glutamic acid) (γ-PGA) complex as a gene vector. The probe was prepared by assembling thiolated RNA to gold nanoparticle (Au NP) via Au-S bond and then binding 3'-end amine of the RNA to the carboxy group capped on quantum dot surface. The QD-RNA-Au NP probe was assembled on the vector by mixing with aqueous γ-PGA solution and then CS solution to construct a gene delivery system for highly effective cellular uptake and delivery. After the probe was released from CS/γ-PGA complex to the cytoplasm by electrostatic repulsion at intracellular pH, it hybridized with pre-miRNA precursor as target. The formed product was then cleaved by RNase III Dicer, leading to the separation of QDs from Au NPs and fluorescence emission of QDs, which could be detected by confocal microscopic imaging to monitor the amount of the intracellular pre-miRNA precursor. The in vitro assays revealed that the QD-RNA-Au NP was a robust, sensitive and selective probe for quantitative detection of target pre-miRNA. Using MDA-MB231 and MCF-7 breast cancer cells as models, the relative amount of pre-miRNA let-7a could be successfully compared. Since the amount of miRNA is related to the progress and prognosis of cancer, this strategy could be expected to hold promising application potential in medical research and clinical diagnostics.

  1. Vertical distributions of bound saturated fatty acids and compound-specific stable carbon isotope compositions in sediments of two lakes in China: implication for the influence of eutrophication.

    PubMed

    Wang, Lifang; Xiong, Yongqiang; Wu, Fengchang; Li, Qiuhua; Lin, Tian; Giesy, John P

    2014-11-01

    Lakes Dianchi (DC) and Bosten (BST) were determined to be at different stages of eutrophication, by use of total organic carbon content, bulk carbon isotopic composition, bulk nitrogen isotopic composition, and bound saturated fatty acid (BSFA) concentrations in sediment cores. A rapid increase in the supply of organic matter (OM) to DC began after the 1950s, while the environment and trophic status of BST remained constant as indicated by characteristics of OM input to sediments. The BSFA ratios of nC14 + nC16 + nC18/nC24 + nC26 + nC28 increase upward from 7 to 13 in the DC core, which are significantly greater than those from BST (2 to 3). This result is consistent with algae or bacteria being the dominant contribution of the OM increase induced by eutrophication in DC. The positive shift of nC16 compound-specific δ (13)C in the upper section might be an indicator of excess algal productivity, which was observed in the two lakes. The positive shifts of compound-specific δ (13)C of other BSFAs were also observed in the upper section of the core only from DC. The observed trends of compound-specific δ(13)C of BSFA originated from different sources became more consistent, which reflected the intensified eutrophication had profoundly affected production and preservation of OM in DC. The results observed for BST indicated that accumulation of algae did not affect the entire aquatic ecosystem until now.

  2. Reversible Michael additions: covalent inhibitors and prodrugs.

    PubMed

    Johansson, Martin H

    2012-11-01

    Covalent inhibition is an efficient molecular mechanism for inhibiting enzymes or modulating the function of proteins and is found in the action of many drugs and biologically active natural products. However, it is has been less appreciated that the formation of covalent bonds can be reversible or irreversible. This review focuses on biologically active compounds that are Michael acceptors and how the reversible nature of the Michael addition reaction influences biological activity and how this can be exploited in designing prodrugs.

  3. Effects of niacin-bound chromium, Maitake mushroom fraction SX and (-)-hydroxycitric acid on the metabolic syndrome in aged diabetic Zucker fatty rats.

    PubMed

    Talpur, Nadeem; Echard, Bobby W; Yasmin, Taharat; Bagchi, Debasis; Preuss, Harry G

    2003-10-01

    Previous studies in our laboratories have demonstrated that niacin-bound chromium (NBC), Maitake mushroom and (-)-hydroxycitric acid (HCA-SX) can ameliorate hypertension, dyslipidemias and diabetes mellitus, and therefore may be useful in weight management. In the present study, we used aged, diabetic Zucker fatty rats (ZFR) (70-75 weeks) in order to determine whether NBC, fraction SX of Maitake mushroom (MSX) and 60% (-)-hydroxycitric acid (HCA-SX) from Garcinia cambogia, alone or in combination, can affect certain aspects of the metabolic syndrome. Syndrome X or metabolic syndrome has been described as a concurrence of disturbed glucose and insulin metabolism, overweight and abdominal fat distribution, mild dyslipidemia, and hypertension, which are associated with subsequent development of type 2 diabetes mellitus and cardiovascular disease. Four groups of eight ZFR were gavaged daily with different supplements. For the initial three weeks, the control group of ZFR received only water, the second group received NBC 40 mcg elemental chromium/day, the third group received MSX 100 mg/day and the last group received HCA-SX 200 mg/day. During weeks 4-6, the doses of each treatment were doubled. The control animals lost approximately 50 g body weight (BW) per rat over 6 weeks of treatment, which is characteristic of these animals in declining health. In contrast, eight ZFR receiving NBC lost approximately 9 g BW per rat, while rats consuming MSX lost 16 g BW per rat. However, ZFR receiving HCA-SX simulated the pattern in the control group because these animals lost approximately 46 g BW per rat. The wide individual variations resulted in a lack of statistical significance among groups. Nevertheless, 75% of the ZFR in the control group lost more than 50 g BW over the 6 weeks duration, whereas none of the ZFR receiving NBC, 25% of the ZFR receiving MSX and 57% of the ZFR receiving HCA-SX lost over 50 g BW over the 6 weeks of the study. ZFR in all 3 treatment groups

  4. Structure of EstA esterase from psychrotrophic Pseudoalteromonas sp. 643A covalently inhibited by monoethylphosphonate

    SciTech Connect

    Brzuszkiewicz, Anna; Nowak, Elzbieta; Dauter, Zbigniew; Dauter, Miroslawa; Cieslinski, Hubert; Dlugolecka, Anna; Kur, Józef

    2010-10-28

    The crystal structure of the esterase EstA from the cold-adapted bacterium Pseudoalteromonas sp. 643A was determined in a covalently inhibited form at a resolution of 1.35 {angstrom}. The enzyme has a typical SGNH hydrolase structure consisting of a single domain containing a five-stranded {beta}-sheet, with three helices at the convex side and two helices at the concave side of the sheet, and is ornamented with a couple of very short helices at the domain edges. The active site is located in a groove and contains the classic catalytic triad of Ser, His and Asp. In the structure of the crystal soaked in diethyl p-nitrophenyl phosphate (DNP), the catalytic serine is covalently connected to a phosphonate moiety that clearly has only one ethyl group. This is the only example in the Protein Data Bank of a DNP-inhibited enzyme with covalently bound monoethylphosphate.

  5. How Cellulose Stretches: Synergism between Covalent and Hydrogen Bonding

    PubMed Central

    2014-01-01

    Cellulose is the most familiar and most abundant strong biopolymer, but the reasons for its outstanding mechanical performance are not well understood. Each glucose unit in a cellulose chain is joined to the next by a covalent C–O–C linkage flanked by two hydrogen bonds. This geometry suggests some form of cooperativity between covalent and hydrogen bonding. Using infrared spectroscopy and X-ray diffraction, we show that mechanical tension straightens out the zigzag conformation of the cellulose chain, with each glucose unit pivoting around a fulcrum at either end. Straightening the chain leads to a small increase in its length and is resisted by one of the flanking hydrogen bonds. This constitutes a simple form of molecular leverage with the covalent structure providing the fulcrum and gives the hydrogen bond an unexpectedly amplified effect on the tensile stiffness of the chain. The principle of molecular leverage can be directly applied to certain other carbohydrate polymers, including the animal polysaccharide chitin. Related but more complex effects are possible in some proteins and nucleic acids. The stiffening of cellulose by this mechanism is, however, in complete contrast to the way in which hydrogen bonding provides toughness combined with extensibility in protein materials like spider silk. PMID:24568640

  6. How cellulose stretches: synergism between covalent and hydrogen bonding.

    PubMed

    Altaner, Clemens M; Thomas, Lynne H; Fernandes, Anwesha N; Jarvis, Michael C

    2014-03-10

    Cellulose is the most familiar and most abundant strong biopolymer, but the reasons for its outstanding mechanical performance are not well understood. Each glucose unit in a cellulose chain is joined to the next by a covalent C-O-C linkage flanked by two hydrogen bonds. This geometry suggests some form of cooperativity between covalent and hydrogen bonding. Using infrared spectroscopy and X-ray diffraction, we show that mechanical tension straightens out the zigzag conformation of the cellulose chain, with each glucose unit pivoting around a fulcrum at either end. Straightening the chain leads to a small increase in its length and is resisted by one of the flanking hydrogen bonds. This constitutes a simple form of molecular leverage with the covalent structure providing the fulcrum and gives the hydrogen bond an unexpectedly amplified effect on the tensile stiffness of the chain. The principle of molecular leverage can be directly applied to certain other carbohydrate polymers, including the animal polysaccharide chitin. Related but more complex effects are possible in some proteins and nucleic acids. The stiffening of cellulose by this mechanism is, however, in complete contrast to the way in which hydrogen bonding provides toughness combined with extensibility in protein materials like spider silk. PMID:24568640

  7. Breast cancer photothermal therapy based on gold nanorods targeted by covalently-coupled bombesin peptide

    NASA Astrophysics Data System (ADS)

    Heidari, Zahra; Salouti, Mojtaba; Sariri, Reyhaneh

    2015-05-01

    Photothermal therapy, a minimally invasive treatment method for killing cancers cells, has generated a great deal of interest. In an effort to improve treatment efficacy and reduce side effects, better targeting of photoabsorbers to tumors has become a new concept in the battle against cancer. In this study, a bombesin (BBN) analog that can bind to all gastrin-releasing peptide (GRP) receptor subtypes was bound covalently with gold nanorods (GNRs) using Nanothinks acid as a link. The BBN analog was also coated with poly(ethylene glycol) to increase its stability and biocompatibility. The interactions were confirmed by ultraviolet-visible and Fourier transform infrared spectroscopy. A methylthiazol tetrazolium assay showed no cytotoxicity of the PEGylated GNR-BBN conjugate. The cell binding and internalization studies showed high specificity and uptake of the GNR-BBN-PEG conjugate toward breast cancer cells of the T47D cell line. The in vitro study revealed destruction of the T47D cells exposed to the new photothermal agent combined with continuous-wave near-infrared laser irradiation. The biodistribution study showed significant accumulation of the conjugate in the tumor tissue of mice with breast cancer. The in vivo photothermal therapy showed the complete disappearance of xenographted breast tumors in the mouse model.

  8. Effect of photocurrent enhancement in porphyrin-graphene covalent hybrids.

    PubMed

    Tang, Jianguo; Niu, Lin; Liu, Jixian; Wang, Yao; Huang, Zhen; Xie, Shiqiang; Huang, Linjun; Xu, Qingsong; Wang, Yuan; Belfiore, Laurence A

    2014-01-01

    Graphene oxide (GO) sheets were covalently functionalized with 5-p-aminophenyl-10,15,20-triphenylporphyrin (NH2TPP) by an amidation reaction between the amino group in NH2TPP and carboxyl groups in GO. The Fourier transform infrared spectroscopy, nuclear magnetic resonance, scanning and transmission electron microscopies reveal that NH2TPP covalent bonds form on the double surface of graphene oxide sheets, generating a unique nano-framework, i.e., NH2TPP-graphene-NH2TPP. Its UV-visible spectroscopy reveals that the absorption spectrum is not a linear superposition of the spectra of NH2TPP and graphene oxide, because a 59nm red shift of the strong graphene oxide absorption is observed from 238 to 297nm, with significant spectral broadening between 300 and 700nm. Fluorescence emission spectroscopy indicates efficient quenching of NH2TPP photoluminescence in this hybrid material, suggesting that photo-induced electron transfer occurs at the interface between NH2TPP and GO. A reversible on/off photo-current density of 47mA/cm(2) is observed when NH2TPP-graphene-NH2TPP hybrid sandwiches are subjected to pulsed white-light illumination. Covalently-bound porphyrins decrease the optical HOMO/LUMO band gap of graphene oxide by ≈1eV, according to UV-visible spectroscopy. Cyclic voltammetry predicts a small HOMO/LUMO band gap of 0.84eV for NH2TPP-graphene-NH2TPP hybrid sandwiches, which is consistent with efficient electron transfer and fluorescence quenching.

  9. Functionalized membrane supports for covalent protein microsequence analysis

    SciTech Connect

    Coull, J.M.; Pappin, D.J.; Mark, J.; Aebersold, R.; Koester, H. )

    1991-04-01

    Methods were developed for high yield covalent attachment of peptides and proteins to isothiocyanate and arylamine-derivatized poly(vinylidene difluoride) membranes for solid-phase sequence analysis. Solutions of protein or peptide were dried onto 8-mm membrane disks such that the functional groups on the surface and the polypeptide were brought into close proximity. In the case of the isothiocyanate membrane, reaction between polypeptide amino groups and the surface isothiocyanate moieties was promoted by application of aqueous N-methylmorpholine. Attachment of proteins and peptides to the arylamine surface was achieved by application of water-soluble carbodiimide in a pH 5.0 buffer. Edman degradation of covalently bound polypeptides was accomplished with initial and repetitive sequence yields ranging from 33 to 75% and 88.5 to 98.5%, respectively. The yields were independent of the sample load (20 pmol to greater than 1 nmol) for either surface. Significant loss of material was not observed when attachment residues were encountered during sequence runs. Application of bovine beta-lactoglobulin A chain, staphylococcus protein A, or the peptide melittin to the isothiocyanate membrane allowed for extended N-terminal sequence identification (35 residues from 20 pmol of beta-lactoglobulin). A number of synthetic and naturally occurring peptides were sequenced to the C-terminal residue following attachment to the arylamine surface. In one example, 10 micrograms of bovine alpha-casein was digested with staphylococcal protease V8 and the peptides were separated by reverse-phase chromatography. Peptide fractions were then directly applied to arylamine membrane disks for covalent sequence analysis. From as little as 2 pmol of initial signal it was possible to determine substantial sequence information (greater than 10 residues).

  10. Acetaminophen structure-toxicity studies: In vivo covalent binding of a nonhepatotoxic analog, 3-hydroxyacetanilide

    SciTech Connect

    Roberts, S.A.; Price, V.F.; Jollow, D.J. )

    1990-09-01

    High doses of 3-hydroxyacetanilide (3HAA), a structural isomer of acetaminophen, do not produce hepatocellular necrosis in normal male hamsters or in those sensitized to acetaminophen-induced liver damage by pretreatment with a combination of 3-methylcholanthrene, borneol, and diethyl maleate. Although 3HAA was not hepatotoxic, the administration of acetyl-labeled (3H or 14C)3HAA (400 mg/kg, ip) produced levels of covalently bound radiolabel that were similar to those observed after an equimolar, hepatotoxic dose of (G-3H)acetaminophen. The covalent nature of 3HAA binding was demonstrated by retention of the binding after repetitive organic solvent extraction following protease digestion. Hepatic and renal covalent binding after 3HAA was approximately linear with both dose and time. In addition, 3HAA produced only a modest depletion of hepatic glutathione, suggesting the lack of a glutathione threshold. 3-Methylcholanthrene pretreatment increased and pretreatment with cobalt chloride and piperonyl butoxide decreased the hepatic covalent binding of 3HAA, indicating the involvement of cytochrome P450 in the formation of the 3HAA reactive metabolite. The administration of multiple doses or a single dose of (ring-3H)3HAA to hamsters pretreated with a combination of 3-methylcholanthrene, borneol, and diethyl maleate produced hepatic levels of 3HAA covalent binding that were in excess of those observed after a single, hepatotoxic acetaminophen dose. These data suggest that the nature and/or the intracellular processing of the reactive metabolites of acetaminophen and 3HAA are different. These data also demonstrate that absolute levels of covalently bound xenobiotic metabolites cannot be utilized as absolute predictors of cytotoxic potential.

  11. Biocompatible hydrogel nanocomposite with covalently embedded silver nanoparticles.

    PubMed

    García-Astrain, Clara; Chen, Cheng; Burón, María; Palomares, Teodoro; Eceiza, Arantxa; Fruk, Ljiljana; Corcuera, M Ángeles; Gabilondo, Nagore

    2015-04-13

    Bionanocomposite materials, combining the properties of biopolymers and nanostructured materials, are attracting interest of the wider scientific community due to their potential application in design of implants, drug delivery systems, and tissue design platforms. Herein, we report on the use of maleimide-coated silver nanoparticles (Ag NPs) as cocross-linkers for the preparation of a bionanocomposite gelatin based hydrogel. Diels-Alder cycloaddition of benzotriazole maleimide (BTM) functionalized Ag NPs and furan containing gelatin in combination with additional amide coupling resulted in stable and biocompatible hybrid nanocomposite. The storage moduli values for the hydrogel are nearly three times higher than that of control hydrogel without NPs indicating a stabilizing role of the covalently bound NPs. Finally, the swelling and drug release properties of the materials as well as the biocompatibility and toxicity tests indicate the biomedical potential of this type of material.

  12. Prolonged and tunable residence time using reversible covalent kinase inhibitors

    PubMed Central

    Bradshaw, J. Michael; McFarland, Jesse M.; Paavilainen, Ville O.; Bisconte, Angelina; Tam, Danny; Phan, Vernon T.; Romanov, Sergei; Finkle, David; Shu, Jin; Patel, Vaishali; Ton, Tony; Li, Xiaoyan; Loughhead, David G.; Nunn, Philip A.; Karr, Dane E.; Gerritsen, Mary E.; Funk, Jens Oliver; Owens, Timothy D.; Verner, Erik; Brameld, Ken A.; Hill, Ronald J.; Goldstein, David M.; Taunton, Jack

    2015-01-01

    Drugs with prolonged, on-target residence time often show superior efficacy, yet general strategies for optimizing drug-target residence time are lacking. Here, we demonstrate progress toward this elusive goal by targeting a noncatalytic cysteine in Bruton's tyrosine kinase (BTK) with reversible covalent inhibitors. Utilizing an inverted orientation of the cysteine-reactive cyanoacrylamide electrophile, we identified potent and selective BTK inhibitors that demonstrate biochemical residence times spanning from minutes to 7 days. An inverted cyanoacrylamide with prolonged residence time in vivo remained bound to BTK more than 18 hours after clearance from the circulation. The inverted cyanoacrylamide strategy was further utilized to discover fibroblast growth factor receptor (FGFR) kinase inhibitors with residence times of several days, demonstrating generalizability of the approach. Targeting noncatalytic cysteines with inverted cyanoacrylamides may serve as a broadly applicable platform that facilitates “residence time by design”, the ability to modulate and improve the duration of target engagement in vivo. PMID:26006010

  13. Synthesis of Polymers Containing Covalently Bonded NLO Chromophores

    NASA Technical Reports Server (NTRS)

    Denga, Xiao-Hua; Sanghadasa, Mohan; Walton, Connie; Penn, Benjamin B.; Amai, Robert L. S.; Clark, Ronald D.

    1998-01-01

    Polymers containing covalently bonded nonlinear optical (NLO) chromophores are expected to possess special properties such as greater stability, better mechanical processing, and easier film formation than their non-polymeric equivalent. For the present work, polymethylmethacrylate (PMMA) was selected as the basic polymer unit on which to incorporate different NLO chromophores. The NLO components were variations of DIVA {[2-methoxyphenyl methylidene]-propanedinitrile} which we prepared from vanillin derivatives and malononitrile. These were esterified with methacrylic acid and polymerized either directly or with methyl methacrylate to form homopolymers or copolymers respectively. Characterization of the polymers and NLO property studies are underway.

  14. Stabilization of human prostatic acid phosphatase by coupling with chondroitin sulfate.

    PubMed

    Luchter-Wasylewska, E; Dulińska, J; Ostrowski, W S; Torchilin, V P; Trubetskoy, V S

    1991-02-01

    Human prostatic acid phosphatase (PAP) (EC 3.1.3.2) was covalently linked to chondroitin sulfate A from whale cartilage. In order to bind the protein amino groups with the preactivated carboxyl groups of chondroitin sulfate, 1-ethyl-3-(3'-dimethylaminepropyl)carbodiimide and N-hydroxysulfosuccinimide were used as coupling agents. The product was soluble and enzymatically active. The activity was on average 25% higher than that of the free enzyme. The product was heterogeneous in respect to charge and Mr (50-1500) kDa, as determined by chromatography on Sephacryl S 300 and polyacrylamide gel electrophoresis. The resulting polymers contained covalently bound chondroitin sulfate, as shown by the biotin-avidin test. The modified enzyme is more resistant against various denaturing agents, e.g., urea, ethanol, and heat. Thus covalent modification of PAP by cross-linking to chondroitin sulfate could be the preferred method for stabilization of its biological activity.

  15. Benchmarking in vitro covalent binding burden as a tool to assess potential toxicity caused by nonspecific covalent binding of covalent drugs.

    PubMed

    Dahal, Upendra P; Obach, R Scott; Gilbert, Adam M

    2013-11-18

    Despite several advantages of covalent inhibitors (such as increased biochemical efficiency, longer duration of action on the target, and lower efficacious doses) over their reversible binding counterparts, there is a reluctance to use covalent inhibitors as a drug design strategy in pharmaceutical research. This reluctance is due to their anticipated reactions with nontargeted macromolecules. We hypothesized that there may be a threshold limit for nonspecific covalent binding, below which a covalent binding drug may be less likely to cause toxicity due to irreversible binding to off-target macromolecules. Estimation of in vivo covalent binding burden from in vitro data has previously been used as an approach to distinguish those agents more likely to cause toxicity (e.g., hepatotoxicity) via metabolic activation to reactive metabolites. We have extended this approach to nine covalent binding drugs to determine in vitro covalent binding burden. In vitro covalent binding burden was determined by incubating radiolabeled drugs with pooled human hepatocytes. These data were scaled to an estimate of in vivo covalent binding burden by combining the in vitro data with daily dose. Scaled in vivo daily covalent binding burden of marketed covalent drugs was found to be under 10 mg/day, which is in agreement with previously reported threshold value for metabolically activated reversible drugs. Covalent binding was also compared to the intrinsic reactivities of the covalent inhibitors assessed using nucleophiles glutathione and N-α-acetyl lysine. The intrinsic reactivity did not correlate with observed in vitro covalent binding, which demonstrated that the intrinsic reactivity of the electrophilic groups of covalent drugs does not exclusively account for the extent of covalent binding. The ramifications of these findings for consideration of using a covalent strategy in drug design are discussed. PMID:24164572

  16. CovalentDock Cloud: a web server for automated covalent docking

    PubMed Central

    Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

    2013-01-01

    Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/. PMID:23677616

  17. Platinum-modified covalent triazine frameworks hybridized with carbon nanoparticles as methanol-tolerant oxygen reduction electrocatalysts

    PubMed Central

    Kamiya, Kazuhide; Kamai, Ryo; Hashimoto, Kazuhito; Nakanishi, Shuji

    2014-01-01

    Covalent triazine frameworks, which are crosslinked porous polymers with two-dimensional molecular structures, are promising materials for heterogeneous catalysts. However, the application of the frameworks as electrocatalysts has not been achieved to date because of their poor electrical conductivity. Here we report that platinum-modified covalent triazine frameworks hybridized with conductive carbon nanoparticles are successfully synthesized by introducing carbon nanoparticles during the polymerization process of covalent triazine frameworks. The resulting materials exhibit clear electrocatalytic activity for oxygen reduction reactions in acidic solutions. More interestingly, the platinum-modified covalent triazine frameworks show almost no activity for methanol oxidation, in contrast to commercial carbon-supported platinum. Thus, platinum-modified covalent triazine frameworks hybridized with carbon nanoparticles exhibit selective activity for oxygen reduction reactions even in the presence of high concentrations of methanol, which indicates potential utility as a cathode catalyst in direct methanol fuel cells. PMID:25242214

  18. Platinum-modified covalent triazine frameworks hybridized with carbon nanoparticles as methanol-tolerant oxygen reduction electrocatalysts

    NASA Astrophysics Data System (ADS)

    Kamiya, Kazuhide; Kamai, Ryo; Hashimoto, Kazuhito; Nakanishi, Shuji

    2014-09-01

    Covalent triazine frameworks, which are crosslinked porous polymers with two-dimensional molecular structures, are promising materials for heterogeneous catalysts. However, the application of the frameworks as electrocatalysts has not been achieved to date because of their poor electrical conductivity. Here we report that platinum-modified covalent triazine frameworks hybridized with conductive carbon nanoparticles are successfully synthesized by introducing carbon nanoparticles during the polymerization process of covalent triazine frameworks. The resulting materials exhibit clear electrocatalytic activity for oxygen reduction reactions in acidic solutions. More interestingly, the platinum-modified covalent triazine frameworks show almost no activity for methanol oxidation, in contrast to commercial carbon-supported platinum. Thus, platinum-modified covalent triazine frameworks hybridized with carbon nanoparticles exhibit selective activity for oxygen reduction reactions even in the presence of high concentrations of methanol, which indicates potential utility as a cathode catalyst in direct methanol fuel cells.

  19. Platinum-modified covalent triazine frameworks hybridized with carbon nanoparticles as methanol-tolerant oxygen reduction electrocatalysts.

    PubMed

    Kamiya, Kazuhide; Kamai, Ryo; Hashimoto, Kazuhito; Nakanishi, Shuji

    2014-01-01

    Covalent triazine frameworks, which are crosslinked porous polymers with two-dimensional molecular structures, are promising materials for heterogeneous catalysts. However, the application of the frameworks as electrocatalysts has not been achieved to date because of their poor electrical conductivity. Here we report that platinum-modified covalent triazine frameworks hybridized with conductive carbon nanoparticles are successfully synthesized by introducing carbon nanoparticles during the polymerization process of covalent triazine frameworks. The resulting materials exhibit clear electrocatalytic activity for oxygen reduction reactions in acidic solutions. More interestingly, the platinum-modified covalent triazine frameworks show almost no activity for methanol oxidation, in contrast to commercial carbon-supported platinum. Thus, platinum-modified covalent triazine frameworks hybridized with carbon nanoparticles exhibit selective activity for oxygen reduction reactions even in the presence of high concentrations of methanol, which indicates potential utility as a cathode catalyst in direct methanol fuel cells. PMID:25242214

  20. Ring-Closing and Cross-Metathesis with Artificial Metalloenzymes Created by Covalent Active Site-Directed Hybridization of a Lipase.

    PubMed

    Basauri-Molina, Manuel; Verhoeven, Dide G A; van Schaik, Arnoldus J; Kleijn, Henk; Klein Gebbink, Robertus J M

    2015-10-26

    A series of Grubbs-type catalysts that contain lipase-inhibiting phosphoester functionalities have been synthesized and reacted with the lipase cutinase, which leads to artificial metalloenzymes for olefin metathesis. The resulting hybrids comprise the organometallic fragment that is covalently bound to the active amino acid residue of the enzyme host in an orthogonal orientation. Differences in reactivity as well as accessibility of the active site by the functionalized inhibitor became evident through variation of the anchoring motif and substituents on the N-heterocyclic carbene ligand. Such observations led to the design of a hybrid that is active in the ring-closing metathesis and the cross-metathesis of N,N-diallyl-p-toluenesulfonamide and allylbenzene, respectively, the latter being the first example of its kind in the field of artificial metalloenzymes.

  1. Non-covalent interactions of nitrous oxide with aromatic compounds: Spectroscopic and computational evidence for the formation of 1:1 complexes

    SciTech Connect

    Cao, Qian; Gor, Gennady Y.; Krogh-Jespersen, Karsten; Khriachtchev, Leonid

    2014-04-14

    We present the first study of intermolecular interactions between nitrous oxide (N{sub 2}O) and three representative aromatic compounds (ACs): phenol, cresol, and toluene. The infrared spectroscopic experiments were performed in a Ne matrix and were supported by high-level quantum chemical calculations. Comparisons of the calculated and experimental vibrational spectra provide direct identification and characterization of the 1:1 N{sub 2}O-AC complexes. Our results show that N{sub 2}O is capable of forming non-covalently bonded complexes with ACs. Complex formation is dominated by dispersion forces, and the interaction energies are relatively low (about −3 kcal mol{sup −1}); however, the complexes are clearly detected by frequency shifts of the characteristic bands. These results suggest that N{sub 2}O can be bound to the amino-acid residues tyrosine or phenylalanine in the form of π complexes.

  2. Non-covalent interactions of nitrous oxide with aromatic compounds: Spectroscopic and computational evidence for the formation of 1:1 complexes

    NASA Astrophysics Data System (ADS)

    Cao, Qian; Gor, Gennady Y.; Krogh-Jespersen, Karsten; Khriachtchev, Leonid

    2014-04-01

    We present the first study of intermolecular interactions between nitrous oxide (N2O) and three representative aromatic compounds (ACs): phenol, cresol, and toluene. The infrared spectroscopic experiments were performed in a Ne matrix and were supported by high-level quantum chemical calculations. Comparisons of the calculated and experimental vibrational spectra provide direct identification and characterization of the 1:1 N2O-AC complexes. Our results show that N2O is capable of forming non-covalently bonded complexes with ACs. Complex formation is dominated by dispersion forces, and the interaction energies are relatively low (about -3 kcal mol-1); however, the complexes are clearly detected by frequency shifts of the characteristic bands. These results suggest that N2O can be bound to the amino-acid residues tyrosine or phenylalanine in the form of π complexes.

  3. Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design

    PubMed Central

    Wang, Ling; Althoff, Eric A.; Bolduc, Jill; Jiang, Lin; Moody, James; Lassila, Jonathan K.; Giger, Lars; Hilvert, Donald; Stoddard, Barry; Baker, David

    2012-01-01

    We report the cocrystal structures of a computationally designed and experimentally optimized retro-aldol enzyme with covalently bound substrate analogs. The structure with covalently bound substrate analog is similar but not identical to the design model, with an RMSD over the active site residues and equivalent substrate atoms of 1.4Å. As in the design model, the binding pocket orients the substrate through hydrophobic interactions with the naphthyl moiety such that the oxygen atoms analogous to the carbinolamine and β-hydroxyl oxygens are positioned near a network of bound waters. However, there are differences between the design model and the structure: the orientation of the naphthyl group and the conformation of the catalytic lysine are slightly different; the bound water network appears to be more extensive; and the bound substrate analog exhibits more conformational heterogeneity than in typical native enzyme-inhibitor complexes. Alanine scanning of the active site residues shows that both the catalytic lysine and the residues around the binding pocket for the substrate naphthyl group make critical contributions to catalysis. Mutating the set of water-coordinating residues also significantly reduces catalytic activity. The crystal structure of the enzyme with a smaller substrate analogue that lacks the naphthyl rings shows the catalytic lysine to be more flexible than in the naphthyl substrate complex; increased preorganization of the active site would likely improve catalysis. The covalently bound complex structures and mutagenesis data highlight strengths and weaknesses of the de novo enzyme design strategy. PMID:22075445

  4. Multiple-component covalent organic frameworks

    NASA Astrophysics Data System (ADS)

    Huang, Ning; Zhai, Lipeng; Coupry, Damien E.; Addicoat, Matthew A.; Okushita, Keiko; Nishimura, Katsuyuki; Heine, Thomas; Jiang, Donglin

    2016-07-01

    Covalent organic frameworks are a class of crystalline porous polymers that integrate molecular building blocks into periodic structures and are usually synthesized using two-component [1+1] condensation systems comprised of one knot and one linker. Here we report a general strategy based on multiple-component [1+2] and [1+3] condensation systems that enable the use of one knot and two or three linker units for the synthesis of hexagonal and tetragonal multiple-component covalent organic frameworks. Unlike two-component systems, multiple-component covalent organic frameworks feature asymmetric tiling of organic units into anisotropic skeletons and unusually shaped pores. This strategy not only expands the structural complexity of skeletons and pores but also greatly enhances their structural diversity. This synthetic platform is also widely applicable to multiple-component electron donor-acceptor systems, which lead to electronic properties that are not simply linear summations of those of the conventional [1+1] counterparts.

  5. Grass cell wall feruloylation: distribution of bound ferulate and candidate gene expression in Brachypodium distachyon.

    PubMed

    Molinari, Hugo B C; Pellny, Till K; Freeman, Jackie; Shewry, Peter R; Mitchell, Rowan A C

    2013-01-01

    The cell walls of grasses such as wheat, maize, rice, and sugar cane, contain large amounts of ferulate that is ester-linked to the cell wall polysaccharide glucuronoarabinoxylan (GAX). This ferulate is considered to limit the digestibility of polysaccharide in grass biomass as it forms covalent linkages between polysaccharide and lignin components. Candidate genes within a grass-specific clade of the BAHD acyl-coA transferase superfamily have been identified as being responsible for the ester linkage of ferulate to GAX. Manipulation of these BAHD genes may therefore be a biotechnological target for increasing efficiency of conversion of grass biomass into biofuel. Here, we describe the expression of these candidate genes and amounts of bound ferulate from various tissues and developmental stages of the model grass Brachypodium distachyon. BAHD candidate transcripts and significant amounts of bound ferulate were present in every tissue and developmental stage. We hypothesize that BAHD candidate genes similar to the recently described Oryza sativa p-coumarate monolignol transferase (OsPMT) gene (PMT sub-clade) are principally responsible for the bound para-coumaric acid (pCA), and that other BAHD candidates (non-PMT sub-clade) are responsible for bound ferulic acid (FA). There were some similarities with between the ratio of expression non-PMT/PMT genes and the ratio of bound FA/pCA between tissue types, compatible with this hypothesis. However, much further work to modify BAHD genes in grasses and to characterize the heterologously expressed proteins is required to demonstrate their function.

  6. Interfacial welding of dynamic covalent network polymers

    NASA Astrophysics Data System (ADS)

    Yu, Kai; Shi, Qian; Li, Hao; Jabour, John; Yang, Hua; Dunn, Martin L.; Wang, Tiejun; Qi, H. Jerry

    2016-09-01

    Dynamic covalent network (or covalent adaptable network) polymers can rearrange their macromolecular chain network by bond exchange reactions (BERs) where an active unit replaces a unit in an existing bond to form a new bond. Such macromolecular events, when they occur in large amounts, can attribute to unusual properties that are not seen in conventional covalent network polymers, such as shape reforming and surface welding; the latter further enables the important attributes of material malleability and powder-based reprocessing. In this paper, a multiscale modeling framework is developed to study the surface welding of thermally induced dynamic covalent network polymers. At the macromolecular network level, a lattice model is developed to describe the chain density evolution across the interface and its connection to bulk stress relaxation due to BERs. The chain density evolution rule is then fed into a continuum level interfacial model that takes into account surface roughness and applied pressure to predict the effective elastic modulus and interfacial fracture energy of welded polymers. The model yields particularly accessible results where the moduli and interfacial strength of the welded samples as a function of temperature and pressure can be predicted with four parameters, three of which can be measured directly. The model identifies the dependency of surface welding efficiency on the applied thermal and mechanical fields: the pressure will affect the real contact area under the consideration of surface roughness of dynamic covalent network polymers; the chain density increment on the real contact area of interface is only dependent on the welding time and temperature. The modeling approach shows good agreement with experiments and can be extended to other types of dynamic covalent network polymers using different stimuli for BERs, such as light and moisture etc.

  7. The effect of Plantago major Linnaeus on serum total sialic acid, lipid-bound sialic acid, some trace elements and minerals after administration of 7,12-dimethylbenz(a)anthracene in rats.

    PubMed

    Oto, Gokhan; Ekin, Suat; Ozdemir, Hulya; Levent, Abdulkadir; Berber, Ismet

    2012-05-01

    The present study was designed to evaluate the effect of Plantago major Linnaeus (PM) extract on serum total sialic acid (TSA), lipid-bound sialic acid (LSA), some trace elements (copper (Cu), zinc (Zn) and iron) and mineral levels (magnesium, calcium and sodium) in Wistar albino rat administrated 7,12-dimethylbenz(a)anthracene (DMBA). Rats were divided into three equal groups (n = 6). Group I comprised the control group, group II was treated with DMBA (100 mg/kg, single dose) and group III was treated with DMBA (100 mg/kg single dose) and aqueous extract of PM 100 mg/kg/day for 60 days. After 60 days, statistical analyses showed that TSA and LSA levels in DMBA and DMBA + PM groups were significantly higher compared to the control group (TSA: p < 0.01, p < 0.05; LSA: p < 0.05, p < 0.05, respectively). Serum Zn levels were decreased in subjects treated with DMBA (p < 0.01) and DMBA + PM (p < 0.05) compared to the control group values. Serum Cu levels were increased in DMBA group and PM-treated group compared to the control group values. The results of this investigation showed that the levels of TSA and LSA changed significantly, which are sensitive markers for detecting the toxic effects of DMBA. On the other hand, observed decline in Zn levels in rats from DMBA + PM group might be due to decreased generation of free radicals and oxidative stress. Results from this study suggest that PM may be partially effective in preventing carcinogenesis initiated by environmental carcinogen DMBA.

  8. The effect of Plantago major Linnaeus on serum total sialic acid, lipid-bound sialic acid, some trace elements and minerals after administration of 7,12-dimethylbenz(a)anthracene in rats.

    PubMed

    Oto, Gokhan; Ekin, Suat; Ozdemir, Hulya; Levent, Abdulkadir; Berber, Ismet

    2012-05-01

    The present study was designed to evaluate the effect of Plantago major Linnaeus (PM) extract on serum total sialic acid (TSA), lipid-bound sialic acid (LSA), some trace elements (copper (Cu), zinc (Zn) and iron) and mineral levels (magnesium, calcium and sodium) in Wistar albino rat administrated 7,12-dimethylbenz(a)anthracene (DMBA). Rats were divided into three equal groups (n = 6). Group I comprised the control group, group II was treated with DMBA (100 mg/kg, single dose) and group III was treated with DMBA (100 mg/kg single dose) and aqueous extract of PM 100 mg/kg/day for 60 days. After 60 days, statistical analyses showed that TSA and LSA levels in DMBA and DMBA + PM groups were significantly higher compared to the control group (TSA: p < 0.01, p < 0.05; LSA: p < 0.05, p < 0.05, respectively). Serum Zn levels were decreased in subjects treated with DMBA (p < 0.01) and DMBA + PM (p < 0.05) compared to the control group values. Serum Cu levels were increased in DMBA group and PM-treated group compared to the control group values. The results of this investigation showed that the levels of TSA and LSA changed significantly, which are sensitive markers for detecting the toxic effects of DMBA. On the other hand, observed decline in Zn levels in rats from DMBA + PM group might be due to decreased generation of free radicals and oxidative stress. Results from this study suggest that PM may be partially effective in preventing carcinogenesis initiated by environmental carcinogen DMBA. PMID:21996710

  9. Binding of cationic peptides (KX)4K to DPPG bilayers. Increasing the hydrophobicity of the uncharged amino acid X drives formation of membrane bound β-sheets: A DSC and FT-IR study.

    PubMed

    Hädicke, André; Blume, Alfred

    2016-06-01

    The binding of cationic peptides of the sequence (KX)4K to lipid vesicles of negatively charged dipalmitoyl-phosphatidylglycerol (DPPG) was investigated by differential scanning calorimetry (DSC) and temperature dependent Fourier-transformed infrared (FT-IR) spectroscopy. The hydrophobicity of the uncharged amino acid X was changed from G (glycine) over A (alanine), Abu (α-aminobutyric acid), V (valine) to L (leucine). The binding of the peptides caused an increase of the phase transition temperature (Tm) of DPPG by up to 20°C. The shift depended on the charge ratio and on the hydrophobicity of the amino acid X. Unexpectedly, the upward shift of Tm increased with increasing hydrophobicity of X. FT-IR spectroscopy showed a shift of the CH2 stretching vibrations of DPPG to lower frequency, particularly for bilayers in the liquid-crystalline phase, indicating an ordering of the hydrocarbon chains when the peptides were bound. Changes in the lipid C=O vibrational band indicated a dehydration of the lipid headgroup region after peptide binding. (KG)4K was bound in an unordered structure at all temperatures. All other peptides formed intermolecular antiparallel β-sheets, when bound to gel phase DPPG. However, for (KA)4K and (KAbu)4K, the β-sheets converted into an unordered structure above Tm. In contrast, the β-sheet structures of (KV)4K and (KL)4K remained stable even at 80°C when bound to the liquid-crystalline phase of DPPG. Strong aggregation of DPPG vesicles occurred after peptide binding. For the aggregates, we suggest a structure, where aggregated single β-sheets are sandwiched between opposing DPPG bilayers with a dehydrated interfacial region.

  10. Formation of "bound

    NASA Astrophysics Data System (ADS)

    Nowak, K.; Kästner, M.; Miltner, A.

    2009-04-01

    During degradation of organic pollutants in soil, metabolites, microbial biomass, CO2and "bound" residues ("non-extractable" residues in soil organic matter) are formed. Enhanced transformation of these contaminants into "bound" residues has been proposed as an alternative remediation method for polluted soils. However, this kind of residues may pose a potential risk for the environment due to their chemical structure and possible remobilization under different conditions. Therefore particular attention is given actually to "bound" residues. Part of these non-extractable residues may be "biogenic," because microorganisms use the carbon from the pollutant to form their biomass components (fatty acids, amino acids, amino sugars), which subsequently may be incorporated into soil organic matter. Furthermore, the CO2 originating from mineralization of xenobiotics, can be re-assimilated by microorganisms and also incorporated into "biogenic residue". The hazard posed by "bound" residues may be overestimated because they are "biogenic" (contain microbial fatty acids and amino acids). The knowledge about the pathways of "biogenic residue" formation is necessary for a proper assessment of the fate of tested pollutants and their turnover in the soil environment. Moreover, these data are needed to establish the realistic degradation rates of the contaminants in soil. The main objectives of this study are: to quantify the extent of "biogenic residue" (fatty acids, amino acids, amino sugars) formation during the degradation of a model pollutant (2,4-dichlorophenoxyacetic acid = 2,4-D) and during CO2 assimilation by microorganisms and to evaluate which components are mainly incorporated into "bound" residues. To investigate the extent of "biogenic residue" formation in soil during the degradation of 2,4-D, experiments with either 14C-U-ring and 13C6-2,4-D or carboxyl-14C 2,4-D were performed. The incubation experiments were performed according to OECD test guideline 307, in the

  11. Mutagenesis and biochemical studies on AuaA confirmed the importance of the two conserved aspartate-rich motifs and suggested difference in the amino acids for substrate binding in membrane-bound prenyltransferases.

    PubMed

    Stec, Edyta; Li, Shu-Ming

    2012-07-01

    AuaA is a membrane-bound farnesyltransferase from the myxobacterium Stigmatella aurantiaca involved in the biosynthesis of aurachins. Like other known membrane-bound aromatic prenyltransferases, AuaA contains two conserved aspartate-rich motifs. Several amino acids in the first motif NXxxDxxxD were proposed to be responsible for prenyl diphosphate binding via metal ions like Mg(2+). Site-directed mutagenesis experiments demonstrated in this study that asparagine, but not the arginine residue in NRxxDxxxD, is important for the enzyme activity of AuaA, differing from the importance of NQ or ND residues in the NQxxDxxxD or NDxxDxxxD motifs observed in some membrane-bound prenyltransferases. The second motif of known membrane-bound prenyltransferases was proposed to be involved in the binding of their aromatic substrates. KDIxDxEGD, also found in AuaA, had been previously speculated to be characteristic for binding of flavonoids or homogenisate. Site-directed mutagenesis experiments with AuaA showed that KDIxDxEGD was critical for the enzyme activity. However, this motif is very likely not specific for flavonoid or homogenisate prenyltransferases, because none of the tested flavonoids was accepted by AuaA or its mutant R53A in the presence of farnesyl, geranyl or dimethylallyl diphosphate.

  12. Theoretical Insights into Covalency Driven f Element Separations

    SciTech Connect

    Lindsay E. Roy; Nicholas J. Bridges; Leigh R. Martin

    2013-02-01

    The lanthanide series, Am, and Cm are predominantly found in the trivalent oxidation state in aqueous solutions making their separation very difficult to achieve. To date, one of the mostly promising separation processes for transplutonium elements from the lanthanides is the TALSPEAK process. Though the mechanism of the TALSPEAK process is not fully understood, it has been demonstrated to provide excellent separation factors between the lanthanides and the trivalent lanthanides. Through Density Function Theory (DFT) calculations of di 2-ethylenetriamine-N,N,N',N”,N”-pentaacetic acid (DTPA), we set out to understand the structures and stabilities of the aqueous phase complexes [MIII(DTPA)-H2O]2- (M = Nd, Am) as well as the changes in Gibbs free energy for complexation in the gas phase and aqueous solution. Mulliken population analysis, Bader’s Atoms-in-Molecules (AIM) approach, and Natural Bond Orbital (NBO) analysis were then used to analyze the bonding in both molecules. The results discussed below suggest that the preference of the DTPA5- ligand for Am over Nd is mainly due to electrostatic and covalent interactions from the oxygen atoms with the nitrogen chelates provide an additional, yet small, covalent interaction. These results question the exclusive use of hard and soft acids and bases (HSAB) concepts for the design of extracting reagents and suggest that hard-soft interactions play more of a role in the separations process than previously thought.

  13. Covalent linkage of prosthetic heme to CYP4 family P450 enzymes.

    PubMed

    Henne, K R; Kunze, K L; Zheng, Y M; Christmas, P; Soberman, R J; Rettie, A E

    2001-10-30

    An extensive body of research on the structural properties of cytochrome P450 enzymes has established that these proteins possess a b-type heme prosthetic group which is noncovalently bound at the active site. Coordinate, electrostatic, and hydrogen bond interactions between the protein backbone and heme functional groups are readily overcome upon mild acid treatment of the enzyme, which releases free heme from the protein. In the present study, we have used a combination of HPLC, LC/ESI-MS, and SDS-PAGE techniques to demonstrate that members of the mammalian CYP4B, CYP4F, and CYP4A subfamilies bind their heme in an unusually tight manner. HPLC chromatography of CYP4B1 on a POROS R2 column under mild acidic conditions caused dissociation of less than one-third of the heme from the protein. Moreover, heme was not substantially removed from CYP4B1 under electrospray or electrophoresis conditions that readily release the prosthetic group from other non-CYP4 P450 isoforms. This was evidenced by an intact protein mass value of 59,217 +/- 3 amu for CYP4B1 (i.e., apoprotein plus heme) and extensive staining of this approximately 60 kDa protein with tetramethylbenzidine/H(2)O(2) following SDS-PAGE. In addition, treatment of CYP4B1, CYP4F3, and CYP4A5/7 with strong base generated a new, chromatographically distinct, polar heme species with a mass of 632.3 amu rather than 616.2 amu. This mass shift is indicative of the incorporation of an oxygen atom into the heme nucleus and is consistent with the presence of a novel covalent ester linkage between the protein backbone of the CYP4 family of mammalian P450s and their heme catalytic center.

  14. Covalent bonding of polycations to small polymeric particles

    NASA Technical Reports Server (NTRS)

    Rembaum, A.

    1975-01-01

    Process produces small spherical polymeric particles which have polycations bound to them. In emulsion form, particles present large positively charged surface which is available to absorb polyanions. This properly can be used in removing heparin from blood or bile acids from the digestive tract. Other anions, such as DNA and RNA, can also be removed from aqueous solutions.

  15. Covalent functionalization of graphene with reactive intermediates.

    PubMed

    Park, Jaehyeung; Yan, Mingdi

    2013-01-15

    Graphene, a material made exclusively of sp(2) carbon atoms with its π electrons delocalized over the entire 2D network, is somewhat chemically inert. Covalent functionalization can enhance graphene's properties including opening its band gap, tuning conductivity, and improving solubility and stability. Covalent functionalization of pristine graphene typically requires reactive species that can form covalent adducts with the sp(2) carbon structures in graphene. In this Account, we describe graphene functionalization reactions using reactive intermediates of radicals, nitrenes, carbenes, and arynes. These reactive species covalently modify graphene through free radical addition, CH insertion, or cycloaddition reactions. Free radical additions are among the most common reaction, and these radicals can be generated from diazonium salts and benzoyl peroxide. Electron transfer from graphene to aryl diazonium ion or photoactivation of benzoyl peroxide yields aryl radicals that subsequently add to graphene to form covalent adducts. Nitrenes, electron-deficient species generated by thermal or photochemical activation of organic azides, can functionalize graphene very efficiently. Because perfluorophenyl nitrenes show enhanced bimolecular reactions compared with alkyl or phenyl nitrenes, perfluorophenyl azides are especially effective. Carbenes are used less frequently than nitrenes, but they undergo CH insertion and C═C cycloaddition reactions with graphene. In addition, arynes can serve as a dienophile in a Diels-Alder type reaction with graphene. Further study is needed to understand and exploit the chemistry of graphene. The generation of highly reactive intermediates in these reactions leads to side products that complicate the product composition and analysis. Fundamental questions remain about the reactivity and regioselectivity of graphene. The differences in the basal plane and the undercoordinated edges of graphene and the zigzag versus arm-chair configurations

  16. Photodynamic targeting of human retinoblastoma cells using covalent low-density lipoprotein conjugates.

    PubMed Central

    Schmidt-Erfurth, U.; Diddens, H.; Birngruber, R.; Hasan, T.

    1997-01-01

    Combination of photosensitizers with carrier molecules has been shown to enhance the efficiency of photodynamic therapy (PDT). Owing to an increased expression of their receptors on some malignant and proliferating cells, low-density lipoproteins (LDLs) are potential endogenous carriers. A photosensitizer, chlorin e6 (Ce6), was covalently bound to LDL via carbodiimide activation. The Ce6-LDL conjugate was evaluated on a fibroblast cell line with defined LDL receptor expression and a retinoblastoma cell line (Y79). Uptake of free Ce6 and Ce6 either covalently bound to or complexed with LDL was measured by spectrofluorimetry. Phototoxicity after irradiation at 660 nm was determined by a mitochondrial activity assay (MTT). Covalent binding to LDL significantly increased the uptake of Ce6 for both cell lines by a factor of 4-5. A Ce6: LDL binding ratio of 50:1 was optimal. A receptor-mediated uptake was demonstrated by saturability and competitive inhibition by free LDL. Binding also occurred at 2 degrees C and was attributed to non-specific associations. Irradiation with 10 J cm-2 of 660 nm light after treatment of cells with Ce6-LDL conjugate reduced the MTT activity by 80%, while free or mixed Ce6 induced a maximum of 10% reduction in the MTT activity following identical treatment conditions. These data suggest that targeting of LDL receptor-bearing cells using covalently bound carriers, such as LDL, might increase the efficiency and selectivity of PDT. Intraocular tumours such as retinoblastomas could be appropriate targets for such an approach owing to the ease of access of light sources and the need for non-invasive approaches in sensitive ocular sites. PMID:9000598

  17. Formation of 4-keto-D-aldopentoses and 4-pentulosonates (4-keto-D-pentonates) with unidentified membrane-bound enzymes from acetic acid bacteria.

    PubMed

    Adachi, Osao; Hours, Roque A; Shinagawa, Emiko; Akakabe, Yoshihiko; Yakushi, Toshiharu; Matsushita, Kazunobu

    2011-01-01

    In our previous study, a new microbial reaction yielding 4-keto-D-arabonate from 2,5-diketo-D-gluconate was identified with Gluconacetobacter liquefaciens RCTMR 10. It appeared that decarboxylation and dehydrogenation took place together in the reaction. To analyze the nature of the reaction, investigations were done with the membrane fraction of the organism, and 4-keto-D-arabinose was confirmed as the direct precursor of 4-keto-D-arabonate. Two novel membrane-bound enzymes, 2,5-diketo-D-gluconate decarboxylase and 4-keto-D-aldopentose 1-dehydrogenase, were involved in the reaction. Alternatively, D-arabonate was oxidized to 4-keto-D-arabonate by another membrane-bound enzyme, D-arabonate 4-dehydrogenase. More directly, D-arabinose oxidation was examined with growing cells and with the membrane fraction of G. suboxydans IFO 12528. 4-Keto-D-arabinose, the same intermediate as that from 2,5-diketo-D-gluconate, was detected, and it was oxidized to 4-keto-D-arabonate. Likewise, D-ribose was oxidized to 4-keto-D-ribose and then it was oxidized to 4-keto-D-ribonate. In addition to 4-keto-D-aldopentose 1-dehydrogenase, the presence of a novel membrane-bound enzyme, D-aldopentose 4-dehydrogenase, was confirmed in the membrane fraction. The formation of 4-keto-D-aldopentoses and 4-keto-D-pentonates (4-pentulosonates) was finally confirmed as reaction products of four different novel membrane-bound enzymes.

  18. Formation of 4-keto-D-aldopentoses and 4-pentulosonates (4-keto-D-pentonates) with unidentified membrane-bound enzymes from acetic acid bacteria.

    PubMed

    Adachi, Osao; Hours, Roque A; Shinagawa, Emiko; Akakabe, Yoshihiko; Yakushi, Toshiharu; Matsushita, Kazunobu

    2011-01-01

    In our previous study, a new microbial reaction yielding 4-keto-D-arabonate from 2,5-diketo-D-gluconate was identified with Gluconacetobacter liquefaciens RCTMR 10. It appeared that decarboxylation and dehydrogenation took place together in the reaction. To analyze the nature of the reaction, investigations were done with the membrane fraction of the organism, and 4-keto-D-arabinose was confirmed as the direct precursor of 4-keto-D-arabonate. Two novel membrane-bound enzymes, 2,5-diketo-D-gluconate decarboxylase and 4-keto-D-aldopentose 1-dehydrogenase, were involved in the reaction. Alternatively, D-arabonate was oxidized to 4-keto-D-arabonate by another membrane-bound enzyme, D-arabonate 4-dehydrogenase. More directly, D-arabinose oxidation was examined with growing cells and with the membrane fraction of G. suboxydans IFO 12528. 4-Keto-D-arabinose, the same intermediate as that from 2,5-diketo-D-gluconate, was detected, and it was oxidized to 4-keto-D-arabonate. Likewise, D-ribose was oxidized to 4-keto-D-ribose and then it was oxidized to 4-keto-D-ribonate. In addition to 4-keto-D-aldopentose 1-dehydrogenase, the presence of a novel membrane-bound enzyme, D-aldopentose 4-dehydrogenase, was confirmed in the membrane fraction. The formation of 4-keto-D-aldopentoses and 4-keto-D-pentonates (4-pentulosonates) was finally confirmed as reaction products of four different novel membrane-bound enzymes. PMID:21897028

  19. Use of (2-/sup 14/C)mevalonate and saponin-bound (/sup 14/C)-3-hydroxy-3-methylglutaric acid for the biosynthesis of terpenoids in leaves of Dioscorea deltoidea

    SciTech Connect

    Gurielidze, K.G.; Paseshnichenko, V.A.; Vasil'eva, I.S.

    1986-03-20

    After the introduction of (2-/sup 14/C)acetate into leaves of Dioscorea deltoidea, a radioactive furonanalog of deltafolin - protodeltofolin, containing two-thirds of the label in the 3-hydroxy-3-methylglutaryl portion - was isolated from them. Radioactive ..beta..-careotene and sterols were isolated from cut young leaves of Dioscorea 24 h after the introduction of (/sup 14/C) protodeltofolin into them, using chromatography on a column of silica gel and precipitation of sterols in the form of digitonins for this purpose. The incorporation of radioactivity from (/sup 14/C)-3-hydroxy-3-methyl-glutaric acid, bound in the form of a saponin, and ..beta..-carotene came to 0.18-0.80%, while incorporation into sterols came to 0.07-2.86% of the radioactivity of the alcohol extract. Thereby it was shown that 3-hydroxyl-3-methylglutaric acid, bound in the form of the saponin, can be used to form terpenoids in Dioscorea leaves. It was suggested that the binding of hydroxymethylglutaric acid to saponin represents one of the mechanisms of regulation of the rate of terpenoid biosynthesis in Dioscorea leaves.

  20. β-Lactoglobulin as nanotransporter--Part II: Characterization of the covalent protein modification by allicin and diallyl disulfide.

    PubMed

    Wilde, Sandra Catharina; Treitz, Christian; Keppler, Julia Katharina; Koudelka, Tomas; Palani, Kalpana; Tholey, Andreas; Rawel, Harshadrai M; Schwarz, Karin

    2016-04-15

    The whey protein β-lactoglobulin has been proposed as a transporter for covalent bound bioactive compounds in order to enhance their stability and reduce their sensory perception. The garlic derived compounds allicin and diallyl disulfide were bound covalently to the native and heat denatured protein. The binding site and the influence of the modification on the digestibility were determined by mass spectrometric analysis of the modified β-lactoglobulin. Further, the conformation of the modified protein was assessed by circular dichroism and dynamic light scattering. The free thiol group of Cys(121) turned out to be the major binding site. After proteolysis with trypsin at pH 7 but not with pepsin at pH 2, a limited transfer to other cysteinyl residues was observed. The covalently bound ligands did not mask any proteolytic cleavage sites of pepsin, trypsin or chymotrypsin. The modified β-lactoglobulin showed a native like conformation, besides a moderate loosening of protein folding. The covalent binding of organosulfur compounds to β-lactoglobulin provides a bioactive ingredient without impairing the digestibility and functional properties of the protein. PMID:26617049

  1. β-Lactoglobulin as nanotransporter--Part II: Characterization of the covalent protein modification by allicin and diallyl disulfide.

    PubMed

    Wilde, Sandra Catharina; Treitz, Christian; Keppler, Julia Katharina; Koudelka, Tomas; Palani, Kalpana; Tholey, Andreas; Rawel, Harshadrai M; Schwarz, Karin

    2016-04-15

    The whey protein β-lactoglobulin has been proposed as a transporter for covalent bound bioactive compounds in order to enhance their stability and reduce their sensory perception. The garlic derived compounds allicin and diallyl disulfide were bound covalently to the native and heat denatured protein. The binding site and the influence of the modification on the digestibility were determined by mass spectrometric analysis of the modified β-lactoglobulin. Further, the conformation of the modified protein was assessed by circular dichroism and dynamic light scattering. The free thiol group of Cys(121) turned out to be the major binding site. After proteolysis with trypsin at pH 7 but not with pepsin at pH 2, a limited transfer to other cysteinyl residues was observed. The covalently bound ligands did not mask any proteolytic cleavage sites of pepsin, trypsin or chymotrypsin. The modified β-lactoglobulin showed a native like conformation, besides a moderate loosening of protein folding. The covalent binding of organosulfur compounds to β-lactoglobulin provides a bioactive ingredient without impairing the digestibility and functional properties of the protein.

  2. Covalent assembly of molecular building blocks by ``on-surface-synthesis''

    NASA Astrophysics Data System (ADS)

    Grill, Leonhard; Lafferentz, Leif; Bombis, Christian; Dyer, Matthew; Persson, Mats; Peters, Maike; Yu, Hao; Hecht, Stefan

    2010-03-01

    A key challenge in the field of molecular electronics is the bottom-up construction of stable molecular networks with pre-defined topology and shape, whereas covalent bonds are desired due to stability and charge transport requirements. We have developed the method of ``on-surface-synthesis,'' which allows the formation of covalent bonds by controlling the synthetic process directly on the surface. This technique has been used successfully for the controlled formation of covalently bound networks of porphyrin molecules on a gold surface, which were then characterized by low temperature scanning tunnelling microscopy (STM). The covalent character of the intermolecular bonds has been proven by manipulation and spectroscopy and is in agreement with calculations. We demonstrate that the dimensions and shape of these nanostructures can be precisely engineered, because the resulting nanostructures directly reflect the chemical structure of the individual building blocks, which makes this method highly interesting for functional molecules. Very recently, we have deposited ultrathin NaCl films on the metallic surface in order to achieve the interesting hybrid configuration of molecular wires on insulating films.

  3. Syntheses of covalently-linked porphyria-quinone complexes. I

    SciTech Connect

    Kong, J.L.Y.; Loach, P.A.

    1980-06-01

    A synthetic route for the preparation of covalently-linked prophyin-quinone and metalloporphyrinquinone complexes as models for the phototrap in bacterial photosynthesis is described. 5(5-Carboxyphenyl)-10,15,20-tritolylporphyrin, prepared by a mixed aldehyde approach, was attached to benzoquinone center with a propanediol bridge by means of ester linkages. The starting point for the benzoquinone moiety was 2,5-dihydroxyphenylacetic acid, whose hydroquinone function was first protected by preparing its dimethyl ether. The spacing between the two centers of the complex could be altered simply by varying the length of the bridging group (a diol) employed. Boron tribomide was used to unmask the quinol derivatives in the final coupled products. The zinc(II) derivative of porphyrin-quinone complex was prepared by addition of a saturated solution of zinc acetate in methanol to a solution of the corresponding prophyrin-hydroqyuinone complex in dichloromethane at room temperature. The structures of these complexes were confirmed by nmr spectroscopy, uv-visible absorption, and mass spectroscopy. Oxidation of the quinol moiety in the covalently-linked complex to its corresponding quinonoid derivative was accomplished by treating a solution of the complex in dichloromethane with a stoichiometric amount of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone, a high potential benzoquinone.

  4. Short peptide tag for covalent protein labeling based on coiled coils.

    PubMed

    Wang, Jianpeng; Yu, Yongsheng; Xia, Jiang

    2014-01-15

    To label proteins covalently, one faces a trade-off between labeling a protein specifically and using a small tag. Often one must compromise one parameter for the other or use additional components, such as an enzyme, to satisfy both requirements. Here, we report a new reaction that covalently labels proteins by using engineered coiled-coil peptides. Harnessing the concept of "proximity-induced reactivity", the 21-amino-acid three-heptad peptides CCE/CCK were modified with a nucleophilic cysteine and an α-chloroacetyl group at selected positions. When pairs of coiled coils associated, an irreversible covalent bond spontaneously formed between the peptides. The specificity of the cross-linking reaction was characterized, the probes were improved by making them bivalent, and the system was used to label a protein in vitro and receptors on the surface of mammalian cells. PMID:24341800

  5. Semiempirical model of covalent bonding in silicon

    NASA Astrophysics Data System (ADS)

    Ackland, Graeme

    1989-11-01

    A simple, analytic model for energetics in silicon is presented. The model incorporates ionic core repulsions written as a pairwise repulsion between ions, and a cohesive energy written as a sum over valence-electron energies. The electrons form covalent bonds represented by pair potentials, and other interactions by a simple repulsive pair potential. The resulting model has a simpler interpretation and fewer parameters than previously published empirical potentials, yet yields structural results in better agreement with density-functional calculations and experimental observations. This shows that by representing cohesion in silicon explicitly in terms of electron bonds, and not by effective interactions between ions as has been done previously, a simple mathematical model can give a better insight into the physics of covalent bonding.

  6. Non-Covalent Derivatives: Cocrystals and Eutectics.

    PubMed

    Stoler, Emily; Warner, John C

    2015-01-01

    Non-covalent derivatives (NCDs) are formed by incorporating one (or more) coformer molecule(s) into the matrix of a parent molecule via non-covalent forces. These forces can include ionic forces, Van der Waals forces, hydrogen bonding, lipophilic-lipophilic interactions and pi-pi interactions. NCDs, in both cocrystal and eutectic forms, possess properties that are unique to their supramolecular matrix. These properties include critical product performance factors such as solubility, stability and bioavailability. NCDs have been used to tailor materials for a variety of applications and have the potential to be used in an even broader range of materials and processes. NCDs can be prepared using little or no solvent and none of the reagents typical to synthetic modifications. Thus, NCDs represent a powerfully versatile, environmentally-friendly and cost-effective opportunity. PMID:26287141

  7. Covalent immobilization of glucose oxidase onto new modified acrylonitrile copolymer/silica gel hybrid supports.

    PubMed

    Godjevargova, Tzonka; Nenkova, Ruska; Dimova, Nedyalka

    2005-08-12

    New polymer/silica gel hybrid supports were prepared by coating high surface area of silica gel with modified acrylonitrile copolymer. The concentrations of the modifying agent (NaOH) and the modified polymer were varied. GOD was covalently immobilized on these hybrid supports and the relative activity and the amount of bound protein were determined. The highest relative activity and sufficient amount of bound protein of the immobilized GOD were achieved in 10% NaOH and 2% solution of modified acrylonitrile copolymer. The influence of glutaraldehyde concentration and the storage time on enzyme efficiency were examined. Glutaraldehyde concentration of 0.5% is optimal for the immobilized GOD. It was shown that the covalently bound enzyme (using 0.5% glutaraldehyde) had higher relative activity than the activity of the adsorbed enzyme. Covalently immobilized GOD with 0.5% glutaraldehyde was more stable for four months in comparison with the one immobilized on pure silica gel, hybrid support with 10% glutaraldehyde and the free enzyme. The effect of the pore size on the enzyme efficiency was studied on four types of silica gel with different pore size. Silica with large pores (CPC-Silica carrier, 375 A) presented higher relative activity than those with smaller pore size (Silica gel with 4, 40 and 100 A). The amount of bound protein was also reduced with decreasing the pore size. The effect of particle size was studied and it was found out that the smaller the particle size was, the greater the activity and the amount of immobilized enzyme were. The obtained results proved that these new polymer/silica gel hybrid supports were suitable for GOD immobilization. PMID:16080168

  8. Covalent Sidewall Functionalization of Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Chiang, I.W.; Saini, R. K.; Mickelson, E. T.; Billups, W. E.; Hauge, R. H.; Margrave, J. L.

    2001-01-01

    Progress of fluorination of single-wall carbon nanotubes is being reported. Covalent attachment of alkyl groups including methyl, n-butyl and n-hexyl groups to the sidewalls of single wall carbon nanotubes (SWNTs) has been achieved. Quantitative measurement of the alkylation was done by thermal gravimetric analysis. FTIR, Raman and UV-Vis-NIR were used to characterize these alkylated SWNTs. Application of these nanotubes are being investigated-fibers, composites, batteries, lubricants, etc.

  9. Multiple-component covalent organic frameworks

    PubMed Central

    Huang, Ning; Zhai, Lipeng; Coupry, Damien E.; Addicoat, Matthew A.; Okushita, Keiko; Nishimura, Katsuyuki; Heine, Thomas; Jiang, Donglin

    2016-01-01

    Covalent organic frameworks are a class of crystalline porous polymers that integrate molecular building blocks into periodic structures and are usually synthesized using two-component [1+1] condensation systems comprised of one knot and one linker. Here we report a general strategy based on multiple-component [1+2] and [1+3] condensation systems that enable the use of one knot and two or three linker units for the synthesis of hexagonal and tetragonal multiple-component covalent organic frameworks. Unlike two-component systems, multiple-component covalent organic frameworks feature asymmetric tiling of organic units into anisotropic skeletons and unusually shaped pores. This strategy not only expands the structural complexity of skeletons and pores but also greatly enhances their structural diversity. This synthetic platform is also widely applicable to multiple-component electron donor–acceptor systems, which lead to electronic properties that are not simply linear summations of those of the conventional [1+1] counterparts. PMID:27460607

  10. Multiple-component covalent organic frameworks.

    PubMed

    Huang, Ning; Zhai, Lipeng; Coupry, Damien E; Addicoat, Matthew A; Okushita, Keiko; Nishimura, Katsuyuki; Heine, Thomas; Jiang, Donglin

    2016-01-01

    Covalent organic frameworks are a class of crystalline porous polymers that integrate molecular building blocks into periodic structures and are usually synthesized using two-component [1+1] condensation systems comprised of one knot and one linker. Here we report a general strategy based on multiple-component [1+2] and [1+3] condensation systems that enable the use of one knot and two or three linker units for the synthesis of hexagonal and tetragonal multiple-component covalent organic frameworks. Unlike two-component systems, multiple-component covalent organic frameworks feature asymmetric tiling of organic units into anisotropic skeletons and unusually shaped pores. This strategy not only expands the structural complexity of skeletons and pores but also greatly enhances their structural diversity. This synthetic platform is also widely applicable to multiple-component electron donor-acceptor systems, which lead to electronic properties that are not simply linear summations of those of the conventional [1+1] counterparts. PMID:27460607

  11. Two supramolecular complexes based on polyoxometalates and Co-EDTA units via covalent connection or non-covalent interaction

    NASA Astrophysics Data System (ADS)

    Teng, Chunlin; Xiao, Hanxi; Cai, Qing; Tang, Jianting; Cai, Tiejun; Deng, Qian

    2016-11-01

    Two new 3D network organic-inorganic hybrid supramolecular complexes {[Na6(CoEDTA)2(H2O)13]·(H2SiW12O40)·xH2O}n (1) and [CoH4EDTA(H2O)]2(SiW12O40)·15H2O (2) (H4EDTA=Ethylenediamine tetraacetic acid) have been successfully synthesized by solution method, and characterized by infrared spectrum (IR), thermogravimetric-differential thermal analysis (TG-DTA), cyclic voltammetry (CV) and single-crystal X-ray diffraction (XRD). Both of the complexes are the supramolecules, but with different liking mode, they are two representative models of supramolecule. complex (1) is a 3D infinite network supramolecular coordination polymer with a rare multi-metal sturcture of sodium-cobalt-containing, which is mainly linked through coordinate-covalent bonds. While complex (2) is normal supramolecule, which linked by non-covalent interactions, such as H-bonding interaction, electrostatic interaction and van der waals force. Both of complex (1) and (2) exhibit good catalytic activities for catalytic oxidation of methanol, when the initial concentration of methanol is 3.0 g m-3, flow rate is 10 mL min-1, and the quality of catalyst is 0.2 g, for complex (1) and complex (2) the maximum elimination rates of methanol are 85% (150 °C) and 92% (120 °C), respectively.

  12. Photophysical and theoretical insights on non-covalently linked fullerene-zinc phthalocyanine complexes.

    PubMed

    Ray, A; Chattopadhyay, S; Bhattacharya, S

    2011-09-01

    The photo-physical aspects of non-covalently linked assemblies of a series of fullerenes, namely, C60, C70, tert-butyl-(1,2-methanofullerene)-61-carboxylate (1) and [6,6]-phenyl C70 butyric acid methyl ester (2) with a designed zinc phthalocyanine (ZnPc), viz., zinc-1,4,8,11,15,18,22,25-octabutoxy-29H,31H-phthalocyanine (3) in toluene medium are studied employing absorption spectrophotometric, steady state and time resolved fluorescence spectroscopic measurements. Of central interest in these investigations is the preferential binding of various fullerenes with ZnPc in toluene. The ground state interaction between fullerenes and 3 is first evidenced from UV-Vis measurements. Steady state fluorescence experiment reveals efficient quenching of the excited singlet state of 3 in presence of both underivatized and derivatized fullerenes. K values for the complexes of C60, C70, 1 and 2 with 3 are determined to be 6500, 22,230, 47,800 and 54,770 dm3 mol(-1), respectively. The magnitude of K suggests that 3 preferentially binds C70 and derivatized C70 in comparison to C60 and 1. Time resolved emission measurements establish that C(70)-3 and 2-3 complexes are stabilized much more in comparison to C(60)-3 and 1-3 systems in terms of charge separation process. Semi empirical calculations employing third parametric method substantiate the strong binding of C70 and its derivative with 3 in terms of heat of formation values of the respective complexes, and at the same time, determine the orientation of bound guest (here fullerenes) with the molecular plane of 3.

  13. Antioxidant activity of albumin-bound bilirubin.

    PubMed Central

    Stocker, R; Glazer, A N; Ames, B N

    1987-01-01

    Bilirubin, when bound to human albumin and at concentrations present in normal human plasma, protects albumin-bound linoleic acid from peroxyl radical-induced oxidation in vitro. Initially, albumin-bound bilirubin (Alb-BR) is oxidized at the same rate as peroxyl radicals are formed and biliverdin is produced stoichiometrically as the oxidation product. On an equimolar basis, Alb-BR successfully competes with uric acid for peroxyl radicals but is less efficient in scavenging these radicals than vitamin C. These results show that 1 mol of Alb-BR can scavenge 2 mol of peroxyl radicals and that small amounts of plasma bilirubin are sufficient to prevent oxidation of albumin-bound fatty acids as well as of the protein itself. The data indicate a role for Alb-BR as a physiological antioxidant in plasma and the extravascular space. PMID:3475708

  14. A matrix lower bound

    SciTech Connect

    Grcar, Joseph F.

    2002-02-04

    A matrix lower bound is defined that generalizes ideas apparently due to S. Banach and J. von Neumann. The matrix lower bound has a natural interpretation in functional analysis, and it satisfies many of the properties that von Neumann stated for it in a restricted case. Applications for the matrix lower bound are demonstrated in several areas. In linear algebra, the matrix lower bound of a full rank matrix equals the distance to the set of rank-deficient matrices. In numerical analysis, the ratio of the matrix norm to the matrix lower bound is a condition number for all consistent systems of linear equations. In optimization theory, the matrix lower bound suggests an identity for a class of min-max problems. In real analysis, a recursive construction that depends on the matrix lower bound shows that the level sets of continuously differential functions lie asymptotically near those of their tangents.

  15. Post-Synthetic Decoupling of On-Surface-Synthesized Covalent Nanostructures from Ag(111).

    PubMed

    Rastgoo-Lahrood, Atena; Björk, Jonas; Lischka, Matthias; Eichhorn, Johanna; Kloft, Stephan; Fritton, Massimo; Strunskus, Thomas; Samanta, Debabrata; Schmittel, Michael; Heckl, Wolfgang M; Lackinger, Markus

    2016-06-27

    The on-surface synthesis of covalent organic nanosheets driven by reactive metal surfaces leads to strongly adsorbed organic nanostructures, which conceals their intrinsic properties. Hence, reducing the electronic coupling between the organic networks and commonly used metal surfaces is an important step towards characterization of the true material. We demonstrate that post-synthetic exposure to iodine vapor leads to the intercalation of an iodine monolayer between covalent polyphenylene networks and Ag(111) surfaces. The experimentally observed changes from surface-bound to detached nanosheets are reproduced by DFT simulations. These findings suggest that the intercalation of iodine provides a material that shows geometric and electronic properties substantially closer to those of the freestanding network.

  16. Covalent immobilization of Pseudomonas cepacia lipase on semiconducting materials

    NASA Astrophysics Data System (ADS)

    Fernandez, Renny Edwin; Bhattacharya, Enakshi; Chadha, Anju

    2008-05-01

    Lipase from Pseudomonas cepacia was covalently immobilized on crystalline silicon, porous silicon and silicon nitride surfaces. The various stages of immobilization were characterized using FTIR (Fourier transform infrared) spectroscopy. The surface topography of the enzyme immobilized surfaces was investigated using scanning electron microscopy (SEM). The quantity of the immobilized active enzyme was estimated by the para-nitrophenyl palmitate (pNPP) assay. The immobilized lipase was used for triglyceride hydrolysis and the acid produced was detected by a pH sensitive silicon nitride surface as a shift in the C- V (capacitance-voltage) characteristics of an electrolyte-insulator-semiconductor capacitor (EISCAP) thus validating the immobilization method for use as a biosensor.

  17. Dual-Mode HDAC Prodrug for Covalent Modification and Subsequent Inhibitor Release

    PubMed Central

    2016-01-01

    Histone deacetylase inhibitors (HDACi) target abnormal epigenetic states associated with a variety of pathologies, including cancer. Here, the development of a prodrug of the canonical broad-spectrum HDACi suberoylanilide hydroxamic acid (SAHA) is described. Although hydroxamic acids are utilized universally in the development of metalloenzyme inhibitors, they are considered to be poor pharmacophores with reduced activity in vivo. We developed a prodrug of SAHA by appending a promoiety, sensitive to thiols, to the hydroxamic acid warhead (termed SAHA-TAP). After incubation of SAHA-TAP with an HDAC, the thiol of a conserved HDAC cysteine residue becomes covalently tagged with the promoiety, initiating a cascade reaction that leads to the release of SAHA. Mass spectrometry and enzyme kinetics experiments validate that the cysteine residue is covalently appended with the TAP promoiety. SAHA-TAP demonstrates cytotoxicity activity against various cancer cell lines. This strategy represents an original prodrug design with a dual mode of action for HDAC inhibition. PMID:25974739

  18. Facile Method for the Site-Specific, Covalent Attachment of full-length IgG onto Nanoparticles

    PubMed Central

    Hui, James Zhe; Al Zaki, Ajlan; Cheng, Zhiliang; Popik, Vladimir; Zhang, Hongtao; Luning Prak, Eline T.

    2014-01-01

    Antibodies, most commonly IgGs, have been widely used as targeting ligands in research and therapeutic applications due to their wide array of targets, high specificity and proven efficacy. Many of these applications require antibodies to be conjugated onto surfaces (e.g. nanoparticles and microplates); however, most conventional bioconjugation techniques exhibit low crosslinking efficiencies, reduced functionality due to non-site-specific labeling and random surface orientation, and/or require protein engineering (e.g. cysteine handles), which can be technically challenging. To overcome these limitations, we have recombinantly expressed Protein Z, which binds the Fc region of IgG, with an UV active non-natural amino acid benzoylphenyalanine (BPA) within its binding domain. Upon exposure to long wavelength UV light, the BPA is activated and forms a covalent link between the Protein Z and the bound Fc region of IgG. This technology was combined with expressed protein ligation (EPL), which allowed for the introduction of a fluorophore and click chemistry-compatible azide group onto the C-terminus of Protein Z during the recombinant protein purification step. This enabled crosslinked-Protein Z-IgG complexes to be efficiently and site-specifically attached to aza-dibenzycyclooctyne-modified nanoparticles, via copper-free click chemistry. PMID:24729432

  19. Transduction of proteins into leishmania tarentolae by formation of non-covalent complexes with cell-penetrating peptides.

    PubMed

    Keller, Andrea-Anneliese; Breitling, Reinhard; Hemmerich, Peter; Kappe, Katarina; Braun, Maria; Wittig, Berith; Schaefer, Buerk; Lorkowski, Stefan; Reissmann, Siegmund

    2014-02-01

    Cell-penetrating peptides (CPPs) are used to transport peptides, proteins, different types of ribonucleic acids (or mimics of these molecules), and DNA into live cells, both plant and mammalian. Leishmania belongs to the class of protozoa having, in comparison to mammalian cells, a different lipid composition of the membrane, proteoglycans on the surface, and signal pathways. We investigated the uptake of two different and easily detectable proteins into the non-pathogenic strain Leishmania tarentolae. From the large number of CPPs available, six and a histone were chosen specifically for their ability to form non-covalent complexes. For Leishmania we used the enzyme β-galactosidase and fluorescent labeled bovine serum albumin as cargoes. The results are compared to similar internalization studies using mammalian cells [Mussbach et al., ]. Leishmania cells can degrade CPPs by a secreted and membrane-bound chymotrypsin-like protease. Both cargo proteins were internalized with sufficient efficiency and achieved intramolecular concentrations similar to mammalian cells. The transport efficiencies of the CPPs differed from each other, and showed a different rank order for both cargoes. The intracellular distribution of fluorescent-labeled bovine serum albumin showed highest concentrations in the nucleus and kinetoplast. Leishmania are susceptible to high concentrations of some CPPs, although comparably dissimilar to mammalian cells. MPG-peptides are more cytotoxic in Leishmania than in mammalian cells, acting as antimicrobial peptides. Our results contribute to a better understanding of molecular interactions in Leishmania cells and possibly to new treatments of leishmaniasis.

  20. Development of covalent inhibitors that can overcome resistance to first-generation FGFR kinase inhibitors

    PubMed Central

    Tan, Li; Wang, Jun; Tanizaki, Junko; Huang, Zhifeng; Aref, Amir R.; Rusan, Maria; Zhu, Su-Jie; Zhang, Yiyun; Ercan, Dalia; Liao, Rachel G.; Capelletti, Marzia; Zhou, Wenjun; Hur, Wooyoung; Kim, NamDoo; Sim, Taebo; Gaudet, Suzanne; Barbie, David A.; Yeh, Jing-Ruey Joanna; Yun, Cai-Hong; Hammerman, Peter S.; Mohammadi, Moosa; Jänne, Pasi A.; Gray, Nathanael S.

    2014-01-01

    The human FGF receptors (FGFRs) play critical roles in various human cancers, and several FGFR inhibitors are currently under clinical investigation. Resistance usually results from selection for mutant kinases that are impervious to the action of the drug or from up-regulation of compensatory signaling pathways. Preclinical studies have demonstrated that resistance to FGFR inhibitors can be acquired through mutations in the FGFR gatekeeper residue, as clinically observed for FGFR4 in embryonal rhabdomyosarcoma and neuroendocrine breast carcinomas. Here we report on the use of a structure-based drug design to develop two selective, next-generation covalent FGFR inhibitors, the FGFR irreversible inhibitors 2 (FIIN-2) and 3 (FIIN-3). To our knowledge, FIIN-2 and FIIN-3 are the first inhibitors that can potently inhibit the proliferation of cells dependent upon the gatekeeper mutants of FGFR1 or FGFR2, which confer resistance to first-generation clinical FGFR inhibitors such as NVP-BGJ398 and AZD4547. Because of the conformational flexibility of the reactive acrylamide substituent, FIIN-3 has the unprecedented ability to inhibit both the EGF receptor (EGFR) and FGFR covalently by targeting two distinct cysteine residues. We report the cocrystal structure of FGFR4 with FIIN-2, which unexpectedly exhibits a “DFG-out” covalent binding mode. The structural basis for dual FGFR and EGFR targeting by FIIN3 also is illustrated by crystal structures of FIIN-3 bound with FGFR4 V550L and EGFR L858R. These results have important implications for the design of covalent FGFR inhibitors that can overcome clinical resistance and provide the first example, to our knowledge, of a kinase inhibitor that covalently targets cysteines located in different positions within the ATP-binding pocket. PMID:25349422

  1. Mechanism of benzaldehyde lyase studied via thiamin diphosphate-bound intermediates and kinetic isotope effects.

    PubMed

    Chakraborty, Sumit; Nemeria, Natalia; Yep, Alejandra; McLeish, Michael J; Kenyon, George L; Jordan, Frank

    2008-03-25

    Direct spectroscopic observation of thiamin diphosphate-bound intermediates was achieved on the enzyme benzaldehyde lyase, which carries out reversible and highly enantiospecific conversion of ( R)-benzoin to benzaldehyde. The key enamine intermediate could be observed at lambda max 393 nm in the benzoin breakdown direction and in the decarboxylase reaction starting with benzoylformate. With benzaldehyde as substrate, no intermediates could be detected, only formation of benzoin at 314 nm. To probe the rate-limiting step in the direction of ( R)-benzoin synthesis, the (1)H/ (2)H kinetic isotope effect was determined for benzaldehyde labeled at the aldehyde position and found to be small (1.14 +/- 0.03), indicating that ionization of the C2alphaH from C2alpha-hydroxybenzylthiamin diphosphate is not rate limiting. Use of the alternate substrates benzoylformic and phenylpyruvic acids (motivated by the observation that while a carboligase, benzaldehyde lyase could also catalyze the slow decarboxylation of 2-oxo acids) enabled the observation of the substrate-thiamin covalent intermediate via the 1',4'-iminopyrimidine tautomer, characteristic of all intermediates with a tetrahedral C2 substituent on ThDP. The reaction of benzaldehyde lyase with the chromophoric substrate analogue ( E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid and its decarboxylated product ( E)-3-(pyridine-3-yl)acrylaldehyde enabled the detection of covalent adducts with both. Neither adduct underwent further reaction. An important finding of the studies is that all thiamin-related intermediates are in a chiral environment on benzaldehyde lyase as reflected by their circular dichroism signatures.

  2. In vitro covalent binding of 3-(/sup 14/C)methylindole metabolites in goat tissues

    SciTech Connect

    Bray, T.M.; Carlson, J.R.; Nocerini, M.R.

    1984-05-01

    Covalent binding of 3-(/sup 14/C)methylindole (3(/sup 14/C)MI) in crude microsomal preparations of goat lung, liver, and kidney was measured to determine if a reactive intermediate was formed during the in vitro metabolism of 3-methylindole (3MI). The bound radioactivity was highest in lung compared to liver and kidney. The amount of bound radioactivity per nanomole of cytochrome P-450 was approximately 10 times higher in the lung compared to the liver. No detectable bound radioactivity was found when 3-(/sup 3/H)methyloxindole was used as the substrate. Cofactor requirements and the effects of inhibitors indicate that a mixed function oxidase (MFO) system is involved in formation of a reactive intermediate. Inhibitors and conjugating agents that are known to reduce the severity of 3MI-induced lung injury such as piperonyl butoxide (MFO inhibitor) and glutathione (conjugating agent) significantly decreased the in vitro binding of 3(/sup 14/C)MI. The results indicate that a reactive intermediate is produced during the metabolism of 3MI by the MFO system. The organ specificity in binding suggests that covalent binding by lung microsomes may be related to the mechanism of 3MI-induced lung injury.

  3. Targeting to cells of fluorescent liposomes covalently coupled with monoclonal antibody or protein A

    NASA Astrophysics Data System (ADS)

    Leserman, Lee D.; Barbet, Jacques; Kourilsky, François; Weinstein, John N.

    1980-12-01

    Many applications envisioned for liposomes in cell biology and chemotherapy require their direction to specific cellular targets1-3. The ability to use antibody as a means of conferring specificity to liposomes would markedly increase their usefulness. We report here a method for covalently coupling soluble proteins, including monoclonal antibody and Staphylococcus aureus protein A (ref. 4), to small sonicated liposomes, by using the heterobifunctional cross-linking reagent N-hydroxysuccinimidyl 3-(2-pyridyldithio)propionate (SPDP, Pharmacia). Liposomes bearing covalently coupled mouse monoclonal antibody against human β2-microglobulin [antibody B1.1G6 (IgG2a, κ) (B. Malissen et al., in preparation)] bound specifically to human, but not to mouse cells. Liposomes bearing protein A became bound to human cells previously incubated with the B1.1G6 antibody, but not to cells incubated without antibody. The coupling method results in efficient binding of protein to the liposomes without aggregation and without denaturation of the coupled ligand; at least 60% of liposomes bound functional protein. Further, liposomes did not leak encapsulated carboxyfluorescein (CF) as a consequence of the reaction.

  4. Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers

    DOEpatents

    Alivisatos, A. Paul; Colvin, Vicki L.

    1998-01-01

    Methods are described for attaching semiconductor nanocrystals to solid inorganic surfaces, using self-assembled bifunctional organic monolayers as bridge compounds. Two different techniques are presented. One relies on the formation of self-assembled monolayers on these surfaces. When exposed to solutions of nanocrystals, these bridge compounds bind the crystals and anchor them to the surface. The second technique attaches nanocrystals already coated with bridge compounds to the surfaces. Analyses indicate the presence of quantum confined clusters on the surfaces at the nanolayer level. These materials allow electron spectroscopies to be completed on condensed phase clusters, and represent a first step towards synthesis of an organized assembly of clusters. These new products are also disclosed.

  5. Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers

    DOEpatents

    Alivisatos, A.P.; Colvin, V.L.

    1998-05-12

    Methods are described for attaching semiconductor nanocrystals to solid inorganic surfaces, using self-assembled bifunctional organic monolayers as bridge compounds. Two different techniques are presented. One relies on the formation of self-assembled monolayers on these surfaces. When exposed to solutions of nanocrystals, these bridge compounds bind the crystals and anchor them to the surface. The second technique attaches nanocrystals already coated with bridge compounds to the surfaces. Analyses indicate the presence of quantum confined clusters on the surfaces at the nanolayer level. These materials allow electron spectroscopies to be completed on condensed phase clusters, and represent a first step towards synthesis of an organized assembly of clusters. These new products are also disclosed. 10 figs.

  6. Chirality sensing and size recognition of N-Boc-amino acids by cage-type dimeric lanthanide complexes: chirality detection of N-Boc-aspartate anions via luminescence colour change.

    PubMed

    Ito, Hiroshi; Shinoda, Satoshi

    2015-03-01

    Chiral luminescent lanthanide complexes, characterized by covalently-linked face-to-face octadentate cyclen (tetraaza-12-crown-4) ligands, specifically bound a chiral N-Boc-aspartate among various N-Boc amino acid anions to enhance Eu(III) luminescence intensity at 615 nm. The combination of Tb(III) and Eu(III) complexes enabled naked-eye discrimination of N-Boc-D- and L-aspartates via the luminescence colour change.

  7. Nuclear Clusters and Covalent Molecules on the femto-scale

    SciTech Connect

    Oertzen, Wolfram von

    2010-04-30

    Nuclear clusters like alpha-particles light N = Z nuclei are the building blocks of nuclear molecules. With additional 'valence' neutrons, which find there place in quantum mechanical two-center orbits a variety of covalently bound states in nuclei have been established in the last decade: in isotopes of {sup 9-12}Be, {sup 13-14}C and {sup 21}Ne. More recently we have studied molecular states in {sup 18,19,20}O-isotopes using the ({sup 7}Li,p) reaction on {sup 12,13,14}C targets at E{sub lab}({sup 7}Li) = 44 MeV. The systematics of the energies and cross sections show rotational bands with high moments of inertia. These are characteristic of large deformations or molecular structures where the clusters are well separated. Generally the large scale shell model calculations are unable to reproduce these cluster bands. With two clusters of different size (e.g. ({sup 14}C x {sup 4}He), or ({sup 16}O x {sup 4}He)) intrinsically reflection asymmetric shapes arise. The molecular structures appear as rotational bands split into parity inversion doublets.

  8. Physical Uncertainty Bounds (PUB)

    SciTech Connect

    Vaughan, Diane Elizabeth; Preston, Dean L.

    2015-03-19

    This paper introduces and motivates the need for a new methodology for determining upper bounds on the uncertainties in simulations of engineered systems due to limited fidelity in the composite continuum-level physics models needed to simulate the systems. We show that traditional uncertainty quantification methods provide, at best, a lower bound on this uncertainty. We propose to obtain bounds on the simulation uncertainties by first determining bounds on the physical quantities or processes relevant to system performance. By bounding these physics processes, as opposed to carrying out statistical analyses of the parameter sets of specific physics models or simply switching out the available physics models, one can obtain upper bounds on the uncertainties in simulated quantities of interest.

  9. The covalent bond in Particle Spectroscopy

    SciTech Connect

    Bugg, D. V.

    2010-08-05

    Meson resonances are linear combinations of qq-bar and meson-meson (MM) baryon resonances are combinations of qqq and meson-baryon. Mixing between these combinations arises via decays of confined states to meson-meson or meson-baryon. There is a useful analogy with the covalent bond in molecular physics. One eigenstate is lowered by the mixing. Cusps arise at thresholds. At sharp thresholds due to S-wave 2-particle decays, these cusps play a conspicuous role in many sets of data.

  10. Potentials and bound states

    SciTech Connect

    Buell, W.F. ); Shadwick, B.A. )

    1995-03-01

    We discuss several quantum mechanical potential problems, focusing on those which highlight commonly held misconceptions about the existence of bound states. We present a proof, based on the variational principle, that certain one dimensional potentials always support at least one bound state, regardless of the potential's strength. We examine arguments concerning the existence of bound states based on the uncertainty principle and demonstrate, by explicit calculations, that such arguments must be viewed with skepticism.

  11. Protocol for rational design of covalently interacting inhibitors.

    PubMed

    Schmidt, Thomas C; Welker, Armin; Rieger, Max; Sahu, Prabhat K; Sotriffer, Christoph A; Schirmeister, Tanja; Engels, Bernd

    2014-10-20

    The inhibition potencies of covalent inhibitors mainly result from the formation of a covalent bond to the enzyme during the inhibition mechanism. This class of inhibitors has essentially been ignored in previous target-directed drug discovery projects because of concerns about possible side effects. However, their advantages, such as higher binding energies and longer drug-target residence times moved them into the focus of recent investigations. While the rational design of non-covalent inhibitors became standard the corresponding design of covalent inhibitors is still in its early stages. Potent covalent inhibitors can be retrieved from large compound libraries by covalent docking approaches but protocols are missing that can reliably predict the influence of variations in the substitution pattern on the affinity and/or reactivity of a given covalent inhibitor. Hence, the wanted property profile can only be obtained from trial-and-error proceedings. This paper presents an appropriate protocol which is able to predict improved covalent inhibitors. It uses hybrid approaches, which mix quantum mechanical (QM) and molecular mechanical (MM) methods to predict variations in the reactivity of the inhibitor. They are also used to compute the required information about the non-covalent enzyme-inhibitor complex. Docking tools are employed to improve the inhibitor with respect to the non-covalent interactions formed in the binding site. PMID:25251382

  12. Dataset for the NMR structure of the intrinsically disordered acidic region of XPC bound to the PH domain of TFIIH p62

    PubMed Central

    Okuda, Masahiko; Nishimura, Yoshifumi

    2016-01-01

    The global genome nucleotide excision repair factor XPC firstly detects DNA lesions and then recruits a ten-subunit complex TFIIH through binding to the subunit p62 to unwind the damaged DNA for excision repair. This data article contains detailed nuclear magnetic resonance (NMR) restraints (nuclear Overhauser enhancement (NOE)-derived distance restraints, dihedral angle restraints, and hydrogen bond restraints) used for the structure determination of the complex formed between the intrinsically disordered acidic region of XPC and the pleckstrin homology (PH) domain of TFIIH p62, related to the recent work entitled “Structural insight into the mechanism of TFIIH recognition by the acidic string of the nucleotide excision repair factor XPC.” [1]. PMID:26909369

  13. Arabinose 5-phosphate covalently inhibits transaldolase.

    PubMed

    Light, Samuel H; Anderson, Wayne F

    2014-03-01

    Arabinose 5-phosphate (A5P) is the aldopentose version of the ketohexose fructose 6-phosphate (F6P), having identical stereochemistry but lacking atoms corresponding to the 1-carbon and 1-hydroxyl. Despite structural similarity and conservation of the reactive portion of F6P, F6P acts as a substrate whereas A5P is reported to be an inhibitor of transaldolase. To address the lack of A5P reactivity we determined a crystal structure of the Francisella tularensis transaldolase in complex with A5P. This structure reveals that like F6P, A5P forms a covalent Schiff base with active site Lys135. Unlike F6P, A5P binding fails to displace an ordered active site water molecule. Retaining this water necessitates conformational changes at the A5P-protein linkage that possibly hinder reactivity. The findings presented here show the basis of A5P inhibition and suggest an unusual mechanism of competitive, reversible-covalent transaldolase regulation.

  14. Sharing in covalent and hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Perhacs, Pablo

    1998-11-01

    The sharing of a single electron between two spatial and spin coordinates ζ and ζsp/prime in a many electron system is discussed in terms of the single particle sharing amplitude, Covalent bonding is distinguished from non-bonding and anti- bonding. Molecules studied are the diatomics of seven of the first nine elements and the hydrides of the first row of eight elements. Analysis is extended to the complex of methane and hydrogen fluoride and to pairs of hydrogen fluoride, water, and ammonia. The behavior of covalent bonding. The ammonia dimer is shown not to be hydrogen bonded.

  15. Comparative immunogenicity of conjugates composed of the Staphylococcus aureus type 8 capsular polysaccharide bound to carrier proteins by adipic acid dihydrazide or N-succinimidyl-3-(2-pyridyldithio)propionate.

    PubMed Central

    Fattom, A; Shiloach, J; Bryla, D; Fitzgerald, D; Pastan, I; Karakawa, W W; Robbins, J B; Schneerson, R

    1992-01-01

    Staphylococcus aureus type 8 capsular polysaccharide (CP) was conjugated either to diphtheria toxoid or to Pseudomonas aeruginosa recombinant exoprotein A by using adipic acid dihydrazide (ADH) or N-succinimidyl-3-(2-pyridyldithio)propionate (SPDP) as the joining reagent. The polysaccharide/protein ratios of these two pairs of conjugates were similar. The two synthetic schemes bound the linker to the carboxyls of the type 8 CP by carbodiimide-mediated condensation. ADH was bound to the carboxyls of the protein, whereas SPDP reacted with the amino groups of the protein. Intermolecular linking of the carrier protein, caused by the carbodiimide during the conjugation reaction with the type 8 CP derivative, probably accounts for the larger size of the conjugates formed with ADH compared with those formed with SPDP. Both conjugates synthesized with ADH elicited higher levels of CP antibodies, especially after the first immunization, than did those prepared with SPDP. Similar levels of exoprotein A antibodies were elicited by both conjugates. Higher levels of diphtheria toxoid antibodies were elicited by the conjugate prepared with SPDP than by the one prepared with ADH. The basis for the differences in the immunogenicities of these two pairs of S. aureus type 8 CP conjugates is discussed. PMID:1730492

  16. Comparative immunogenicity of conjugates composed of the Staphylococcus aureus type 8 capsular polysaccharide bound to carrier proteins by adipic acid dihydrazide or N-succinimidyl-3-(2-pyridyldithio)propionate.

    PubMed

    Fattom, A; Shiloach, J; Bryla, D; Fitzgerald, D; Pastan, I; Karakawa, W W; Robbins, J B; Schneerson, R

    1992-02-01

    Staphylococcus aureus type 8 capsular polysaccharide (CP) was conjugated either to diphtheria toxoid or to Pseudomonas aeruginosa recombinant exoprotein A by using adipic acid dihydrazide (ADH) or N-succinimidyl-3-(2-pyridyldithio)propionate (SPDP) as the joining reagent. The polysaccharide/protein ratios of these two pairs of conjugates were similar. The two synthetic schemes bound the linker to the carboxyls of the type 8 CP by carbodiimide-mediated condensation. ADH was bound to the carboxyls of the protein, whereas SPDP reacted with the amino groups of the protein. Intermolecular linking of the carrier protein, caused by the carbodiimide during the conjugation reaction with the type 8 CP derivative, probably accounts for the larger size of the conjugates formed with ADH compared with those formed with SPDP. Both conjugates synthesized with ADH elicited higher levels of CP antibodies, especially after the first immunization, than did those prepared with SPDP. Similar levels of exoprotein A antibodies were elicited by both conjugates. Higher levels of diphtheria toxoid antibodies were elicited by the conjugate prepared with SPDP than by the one prepared with ADH. The basis for the differences in the immunogenicities of these two pairs of S. aureus type 8 CP conjugates is discussed. PMID:1730492

  17. Designing Covalently Linked Heterodimeric Four-Helix Bundles.

    PubMed

    Chino, M; Leone, L; Maglio, O; Lombardi, A

    2016-01-01

    De novo design has proven a powerful methodology for understanding protein folding and function, and for mimicking or even bettering the properties of natural proteins. Extensive progress has been made in the design of helical bundles, simple structural motifs that can be nowadays designed with a high degree of precision. Among helical bundles, the four-helix bundle is widespread in nature, and is involved in numerous and fundamental processes. Representative examples are the carboxylate bridged diiron proteins, which perform a variety of different functions, ranging from reversible dioxygen binding to catalysis of dioxygen-dependent reactions, including epoxidation, desaturation, monohydroxylation, and radical formation. The "Due Ferri" (two-irons; DF) family of proteins is the result of a de novo design approach, aimed to reproduce in minimal four-helix bundle models the properties of the more complex natural diiron proteins, and to address how the amino acid sequence modulates their functions. The results so far obtained point out that asymmetric metal environments are essential to reprogram functions, and to achieve the specificity and selectivity of the natural enzymes. Here, we describe a design method that allows constructing asymmetric four-helix bundles through the covalent heterodimerization of two different α-helical harpins. In particular, starting from the homodimeric DF3 structure, we developed a protocol for covalently linking the two α2 monomers by using the Cu(I) catalyzed azide-alkyne cycloaddition. The protocol was then generalized, in order to include the construction of several linkers, in different protein positions. Our method is fast, low cost, and in principle can be applied to any couple of peptides/proteins we desire to link. PMID:27586346

  18. Bounding species distribution models

    USGS Publications Warehouse

    Stohlgren, T.J.; Jarnevich, C.S.; Esaias, W.E.; Morisette, J.T.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used. ?? 2011 Current Zoology.

  19. Bounding Species Distribution Models

    NASA Technical Reports Server (NTRS)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  20. Covalently functionalized carbon nanostructures and methods for their separation

    DOEpatents

    Wang, YuHuang; Brozena, Alexandra H; Deng, Shunliu; Zhang, Yin

    2015-03-17

    The present invention is directed to carbon nanostructures, e.g., carbon nanotubes, methods of covalently functionalizing carbon nanostructures, and methods of separating and isolating covalently functionalized carbon. In some embodiments, carbon nanotubes are reacted with alkylating agents to provide water soluble covalently functionalized carbon nanotubes. In other embodiments, carbon nanotubes are reacted with a thermally-responsive agent and exposed to light in order to separate carbon nanotubes of a specific chirality from a mixture of carbon nanotubes.

  1. Photoinduced electron transfer and fluorescence mechanisms in covalently linked polynuclear aromatic-nucleotide complexes

    SciTech Connect

    Geacintov, N.E.; Mao, Bing; Zhao, Rushen; Chen, Junxin; Liu, Tong Ming; Ya, Nai-Qi; France, L.L.; Sutherland, J.D.

    1992-04-01

    The fluorescence of polycyclic aromatic hydrocarbon-nucleic acid complexes is quenched by photoinduced electron transfer mechanisms in aqueous solutions at ambient temperatures. These effects are illustrated with the biologically important compound benzo[a]pyrene-7,8-diol-9,10-epoxide (BPDE), a mutagenic and carcinogenic metabolite of the environmental pollutant benzo[a]pyrene, which forms covalent mutagenic lesions with 2{prime}-deoxyguanosine (dG) residues in DNA. The dependence of the fluroescence yeild and fluorescence decay times of the covalent model adduct (+)-trans-BPDE-N{sup 2}-dG as a function of temperature and methanol/water composition are described. Because of the sensitivity of the fluorescence of the pyrenyl residue to the polarity of the microenvironment, the magnitude of the fluorescence yield can be used to distinguish between highly hydrophobic (e.g. intercalation) and other more solvent-exposed BPDE-nucleic acid binding sites.

  2. Photoinduced electron transfer and fluorescence mechanisms in covalently linked polynuclear aromatic-nucleotide complexes

    SciTech Connect

    Geacintov, N.E.; Mao, Bing; Zhao, Rushen; Chen, Junxin; Liu, Tong Ming; Ya, Nai-Qi . Dept. of Chemistry); France, L.L.; Sutherland, J.D. )

    1992-01-01

    The fluorescence of polycyclic aromatic hydrocarbon-nucleic acid complexes is quenched by photoinduced electron transfer mechanisms in aqueous solutions at ambient temperatures. These effects are illustrated with the biologically important compound benzo(a)pyrene-7,8-diol-9,10-epoxide (BPDE), a mutagenic and carcinogenic metabolite of the environmental pollutant benzo(a)pyrene, which forms covalent mutagenic lesions with 2{prime}-deoxyguanosine (dG) residues in DNA. The dependence of the fluroescence yeild and fluorescence decay times of the covalent model adduct (+)-trans-BPDE-N{sup 2}-dG as a function of temperature and methanol/water composition are described. Because of the sensitivity of the fluorescence of the pyrenyl residue to the polarity of the microenvironment, the magnitude of the fluorescence yield can be used to distinguish between highly hydrophobic (e.g. intercalation) and other more solvent-exposed BPDE-nucleic acid binding sites.

  3. Relativistic four-component potential energy curves for the lowest 23 covalent states of molecular bromine (Br2).

    PubMed

    Gomes, José da Silva; Gargano, Ricardo; Martins, João B L; M de Macedo, Luiz Guilherme

    2014-08-01

    The covalent excited states and ground state of the Br2 molecule has been investigated by using four-component relativistic COSCI and MRCISD methods. These methods were performed for all covalent states in the representation Ω((±)). Calculated potential energy curves (PECs) were obtained at the four-component COSCI level, and spectroscopic constants (R(e), D(e), D0, ω(e), ω(e)x(e), ω(e)y(e), B(e), α(e), γ(e), Te, Dv) for bounded states are reported. The vertical excitations for all covalent states are reported at COSCI, MRCISD, and MRCISD+Q levels. We also present spectroscopic constants for two weakly bounded states (A':(1)2u and B':(1)0(-)u) not yet reported in the literature, as well as accurate analytical curves for all five relativistic molecular bounded sates [the ground state X:0 g(+) and the excited states A:(1)1(u), B:(1)0(u)(+), C:(2)1(u), and B':(1)0(u)(-)] found in this work.

  4. Purification and characterization of a 14-kilodalton protein that is bound to the surface of polyhydroxyalkanoic acid granules in Rhodococcus ruber.

    PubMed Central

    Pieper-Fürst, U.; Madkour, M. H.; Mayer, F.; Steinbüchel, A.

    1994-01-01

    The N-terminal amino acid sequence of the polyhydroxyalkanoic acid (PHA) granule-associated M(r)-15,500 protein of Rhodococcus ruber (the GA14 protein) was analyzed. The sequence revealed that the corresponding structural gene is represented by open reading frame 3, encoding a protein with a calculated M(r) of 14,175 which was recently localized downstream of the PHA synthase gene (U. Pieper and A. Steinbüchel, FEMS Microbiol. Lett. 96:73-80, 1992). A recombinant strain of Escherichia coli XL1-Blue carrying the hybrid plasmid (pSKXA10*) with open reading frame 3 overexpressed the GA14 protein. The GA14 protein was subsequently purified in a three-step procedure including chromatography on DEAE-Sephacel, phenyl-Sepharose CL-4B, and Superose 12. Determination of the molecular weight by gel filtration as well as electron microscopic studies indicates that a tetrameric structure of the recombinant, native GA14 protein is most likely. Immunoelectron microscopy demonstrated a localization of the GA14 protein at the periphery of PHA granules as well as close to the cell membrane in R. ruber. Investigations of PHA-leaky and PHA-negative mutants of R. ruber indicated that expression of the GA14 protein depended strongly on PHA synthesis. Images PMID:8021220

  5. Covalent binding of single-walled carbon nanotubes to polyamide membranes for antimicrobial surface properties.

    PubMed

    Tiraferri, Alberto; Vecitis, Chad D; Elimelech, Menachem

    2011-08-01

    We propose an innovative approach to impart nanomaterial-specific properties to the surface of thin-film composite membranes. Specifically, biocidal properties were obtained by covalently binding single-walled carbon nanotubes (SWNTs) to the membrane surface. The SWNTs were first modified by purification and ozonolysis to increase their sidewall functionalities, maximize cytotoxic properties, and achieve dispersion in aqueous solution. A tailored reaction protocol was developed to exploit the inherent moieties of hand-cast polyamide membrane surfaces and create covalent amide bonds with the functionalized SWNTs. The reaction is entirely aqueous-based and entails activation of the carboxylate groups of both the membrane and the nanomaterials to maximize reaction with ethylenediamine. The presence of SWNTs was verified after sonication of the membranes, confirming the strength of the bond between the SWNTs and the membrane surface. Characterization of the SWNT-functionalized surfaces demonstrated the attainment of membranes with novel properties that continued to exhibit high performance in water separation processes. The presence of surface-bound antimicrobial SWNTs was confirmed by experiments using E. coli cells that demonstrated an enhanced bacterial cytotoxicity for the SWNT-coated membranes. The SWNT membranes were observed to achieve up to 60% inactivation of bacteria attached to the membrane within 1 h of contact time. Our results suggest the potential of covalently bonded SWNTs to delay the onset of membrane biofouling during operation.

  6. Bound infragravity waves

    NASA Astrophysics Data System (ADS)

    Okihiro, Michele; Guza, R. T.; Seymour, R. J.

    1992-07-01

    Model predictions of bound (i.e., nonlinearly forced by and coupled to wave groups) infragravity wave energy are compared with about 2 years of observations in 8- to 13-m depths at Imperial Beach, California, and Barbers Point, Hawaii. Frequency-directional spectra of free waves at sea and swell frequencies, estimated with a small array of four pressure sensors, are used to predict the bound wave spectra below 0.04 Hz. The predicted total bound wave energy is always less than the observed infragravity energy, and the underprediction increases with increasing water depth and especially with decreasing swell energy. At most half, and usually much less, of the observed infragravity energy is bound. Bound wave spectra are also predicted with data from a single wave gage in 183-m depth at Point Conception, California, and the assumption of unidirectional sea and swell. Even with energetic swell, less than 10% of the total observed infragravity energy in 183-m depth is bound. Free waves, either leaky or edge waves, are more energetic than bound waves at both the shallow and deep sites. The low level of infragravity energy observed in 183-m depth compared with 8- to 13-m depths, with similarly moderate sea and swell energy, suggests that leaky (and very high-mode edge) waves contribute less than 10% of the infragravity energy in 8-13 m. Most of the free infragravity energy in shallow water is refractively trapped and does not reach deep water.

  7. Oriented Thin Films of a Benzodithiophene Covalent Organic Framework

    PubMed Central

    2014-01-01

    A mesoporous electron-donor covalent organic framework based on a benzodithiophene core, BDT-COF, was obtained through condensation of a benzodithiophene-containing diboronic acid and hexahydroxytriphenylene (HHTP). BDT-COF is a highly porous, crystalline, and thermally stable material, which can be handled in air. Highly porous, crystalline oriented thin BDT-COF films were synthesized from solution on different polycrystalline surfaces, indicating the generality of the synthetic strategy. The favorable orientation, crystallinity, porosity, and the growth mode of the thin BDT-COF films were studied by means of X-ray diffraction (XRD), 2D grazing incidence diffraction (GID), transmission and scanning electron microscopy (TEM, SEM), and krypton sorption. The highly porous thin BDT-COF films were infiltrated with soluble fullerene derivatives, such as [6,6]-phenyl C61 butyric acid methyl ester (PCBM), to obtain an interpenetrated electron-donor/acceptor host–guest system. Light-induced charge transfer from the BDT-framework to PCBM acceptor molecules was indicated by efficient photoluminescence quenching. Moreover, we monitored the dynamics of photogenerated hole-polarons via transient absorption spectroscopy. This work represents a combined study of the structural and optical properties of highly oriented mesoporous thin COF films serving as host for the generation of periodic interpenetrated electron-donor and electron-acceptor systems. PMID:24559375

  8. Novel hydroxyapatite biomaterial covalently linked to raloxifene.

    PubMed

    Meme, L; Santarelli, A; Marzo, G; Emanuelli, M; Nocini, P F; Bertossi, D; Putignano, A; Dioguardi, M; Lo Muzio, L; Bambini, F

    2014-01-01

    Since raloxifene, a drug used in osteoporosis therapy, inhibits osteoclast, but not osteoblast functions, it has been suggested to improve recovery during implant surgery. The present paper describes an effective method to link raloxifene, through a covalent bond, to a nano-Hydroxyapatite-based biomaterial by interfacing with (3-aminopropyl)-Triethoxysilane as assessed by Infra Red-Fourier Transformed (IR-FT) spectroscopy and Scanning Electron Microscope (SEM). To evaluate the safety of this modified new material, the vitality of osteoblast-like cells cultured with the new biomaterial was then investigated. Raloxifene-conjugated HAbiomaterial has been shown to be a safe material easy to obtain which could be an interesting starting point for the use of a new functional biomaterial suitable in bone regeneration procedures. PMID:25280036

  9. Cell Signalling Through Covalent Modification and Allostery

    NASA Astrophysics Data System (ADS)

    Johnson, Louise N.

    Phosphorylation plays essential roles in nearly every aspect of cell life. Protein kinases catalyze the transfer of the γ-phosphate of ATP to a serine, threonine or tyrosine residue in protein substrates. This covalent modification allows activation or inhibition of enzyme activity, creates recognition sites for other proteins and promotes order/disorder or disorder/order transitions. These properties regulate ­signalling pathways and cellular processes that mediate metabolism, transcription, cell cycle progression, differentiation, cytoskeleton arrangement and cell movement, apoptosis, intercellular communication, and neuronal and immunological functions. In this lecture I shall review the structural consequences of protein phosphorylation using our work on glycogen phosphorylase and the cell cycle cyclin dependent protein kinases as illustrations. Regulation of protein phosphorylation may be disrupted in the diseased state and protein kinases have become high profile targets for drug development. To date there are 11 compounds that have been approved for clinical use in the treatment of cancer.

  10. Covalent Polymers Containing Discrete Heterocyclic Anion Receptors

    PubMed Central

    Rambo, Brett M.; Silver, Eric S.; Bielawski, Christopher W.; Sessler, Jonathan L.

    2010-01-01

    This chapter covers recent advances in the development of polymeric materials containing discrete heterocyclic anion receptors, and focuses on advances in anion binding and chemosensor chemistry. The development of polymers specific for anionic species is a relatively new and flourishing area of materials chemistry. The incorporation of heterocyclic receptors capable of complexing anions through non-covalent interactions (e.g., hydrogen bonding and electrostatic interactions) provides a route to not only sensitive but also selective polymer materials. Furthermore, these systems have been utilized in the development of polymers capable of extracting anionic species from aqueous environments. These latter materials may lead to advances in water purification and treatment of diseases resulting from surplus ions. PMID:20871791

  11. Biofunctional Paper via Covalent Modification of Cellulose

    PubMed Central

    Yu, Arthur; Shang, Jing; Cheng, Fang; Paik, Bradford A.; Kaplan, Justin M.; Andrade, Rodrigo B.; Ratner, Daniel M.

    2012-01-01

    Paper-based analytical devices are the subject of growing interest for the development of low-cost point-of-care diagnostics, environmental monitoring technologies and research tools for limited-resource settings. However, there are limited chemistries available for the conjugation of biomolecules to cellulose for use in biomedical applications. Herein, divinyl sulfone (DVS) chemistry was demonstrated to covalently immobilize small molecules, proteins and DNA onto the hydroxyl groups of cellulose membranes through nucleophilic addition. Assays on modified cellulose using protein-carbohydrate and protein-glycoprotein interactions as well as oligonucleotide hybridization showed that the membrane’s bioactivity was specific, dose-dependent, and stable over a long period of time. Use of an inkjet printer to form patterns of biomolecules on DVS-activated cellulose illustrates the adaptability of the DVS functionalization technique to pattern sophisticated designs, with potential applications in cellulose-based lateral flow devices. PMID:22708701

  12. Crystallization and preliminary X-ray analysis of a bacterial l-amino-acid oxidase from Rhodococcus opacus

    SciTech Connect

    Faust, Annette; Geueke, Birgit; Niefind, Karsten; Hummel, Werner; Schomburg, Dietmar

    2006-03-01

    The crystallization and preliminary X-ray analysis of a bacterial l-amino acid oxidase from R. opacus is described. The homodimeric protein contains one molecule of non-covalently bound FAD per monomer. Crystals with good diffraction properties were grown in two different orthorhombic space groups (P2{sub 1}2{sub 1}2{sub 1} and C222{sub 1}). l-Amino-acid oxidases (EC 1.4.3.2) catalyse the stereospecific oxidative deamination of an l-amino-acid substrate to an α-keto acid with the production of ammonia and hydrogen peroxide. In this study, the crystallization and preliminary X-ray analysis of a bacterial l-amino-acid oxidase from Rhodococcus opacus (RoLAAO) is described. RoLAAO is a dimeric protein consisting of two identical subunits of 489 amino acids with a calculated molecular weight of 54.2 kDa and a non-covalently bound FAD molecule. RoLAAO was crystallized by the vapour-diffusion method in two different space groups: P2{sub 1}2{sub 1}2{sub 1} (unit-cell parameters a = 65.7, b = 109.7, c = 134.4 Å) and C222{sub 1} (unit-cell parameters a = 68.3, b = 88.4, c = 186.6 Å). Both crystal forms diffracted X-rays to a resolution of at least 1.6 Å.

  13. DNA Linked To Single Wall Carbon Nanotubes: Covalent Versus Non-Covalent Approach

    NASA Astrophysics Data System (ADS)

    Chung, C.-L.; Nguyen, K.; Lyonnais, S.; Streiff, S.; Campidelli, S.; Goux-Capes, L.; Bourgoin, J.-P.; Filoramo, A.

    2008-10-01

    Nanometer-scale structures represent a novel and intriguing field, where scientists and engineers manipulate materials at the atomic and molecular scale levels to produce innovative materials. Carbon nanotubes constitute a relatively new class of materials exhibiting exceptional mechanical and electronic properties and were found to be promising candidates for molecular electronics, sensing or biomedical applications. Considering the bottom-up strategy in nanotechnology, the combination of the recognition properties of DNA with the electronic properties of single walled carbon nanotubes (SWNTs) seems to be a promising approach for the future of electronics. With the aim to assemble DNA with SWNTs, two complementary strategies have been envisioned: the covalent linkage of DNA on carboxylic groups of SWNTs under classical coupling condition and the non-covalent approach based on biotin-streptavidin molecular recognition properties. Here, we present and compare the results that we obtained with these two different methods; we want to objectively show the advantages and disadvantages of each approach.

  14. Identification of charge transfer transitions related to thiamin-bound intermediates on enzymes provides a plethora of signatures useful in mechanistic studies.

    PubMed

    Patel, Hetalben; Nemeria, Natalia S; Andrews, Forest H; McLeish, Michael J; Jordan, Frank

    2014-04-01

    Identification of enzyme-bound intermediates via their spectroscopic signatures, which then allows direct monitoring of the kinetic fate of these intermediates, poses a continuing challenge. As an electrophilic covalent catalyst, the thiamin diphosphate (ThDP) coenzyme forms a number of noncovalent and covalent intermediates along its reaction pathways, and multiple UV-vis and circular dichroism (CD) bands have been identified at Rutgers pertinent to several among them. These electronic transitions fall into two classes: those for which the conjugated system provides a reasonable guide to the observed λmax and others in which there is no corresponding conjugated system and the observed CD bands are best ascribed to charge transfer (CT) transitions. Herein is reported the reaction of four ThDP enzymes with alternate substrates: (a) acetyl pyruvate, its methyl ester, and fluoropyruvate, these providing the shortest side chains attached at the thiazolium C2 atom and leading to CT bands with λmax values of >390 nm, not pertinent to any on-pathway conjugated systems (estimated λmax values of <330 nm), and (b) (E)-4-(4-chlorophenyl)-2-oxo-3-butenoic acid displaying both a conjugated enamine (430 nm) and a CT transition (480 nm). We suggest that the CT transitions result from an interaction of the π bond on the ThDP C2 side chain as a donor, and the positively charged thiazolium ring as an acceptor, and correspond to covalent ThDP-bound intermediates. Time resolution of these bands allows the rate constants for individual steps to be determined. These CD methods can be applied to the entire ThDP superfamily of enzymes and should find applications with other enzymes.

  15. Identification of Charge Transfer Transitions Related to Thiamin-Bound Intermediates on Enzymes Provides a Plethora of Signatures Useful in Mechanistic Studies

    PubMed Central

    2015-01-01

    Identification of enzyme-bound intermediates via their spectroscopic signatures, which then allows direct monitoring of the kinetic fate of these intermediates, poses a continuing challenge. As an electrophilic covalent catalyst, the thiamin diphosphate (ThDP) coenzyme forms a number of noncovalent and covalent intermediates along its reaction pathways, and multiple UV–vis and circular dichroism (CD) bands have been identified at Rutgers pertinent to several among them. These electronic transitions fall into two classes: those for which the conjugated system provides a reasonable guide to the observed λmax and others in which there is no corresponding conjugated system and the observed CD bands are best ascribed to charge transfer (CT) transitions. Herein is reported the reaction of four ThDP enzymes with alternate substrates: (a) acetyl pyruvate, its methyl ester, and fluoropyruvate, these providing the shortest side chains attached at the thiazolium C2 atom and leading to CT bands with λmax values of >390 nm, not pertinent to any on-pathway conjugated systems (estimated λmax values of <330 nm), and (b) (E)-4-(4-chlorophenyl)-2-oxo-3-butenoic acid displaying both a conjugated enamine (430 nm) and a CT transition (480 nm). We suggest that the CT transitions result from an interaction of the π bond on the ThDP C2 side chain as a donor, and the positively charged thiazolium ring as an acceptor, and correspond to covalent ThDP-bound intermediates. Time resolution of these bands allows the rate constants for individual steps to be determined. These CD methods can be applied to the entire ThDP superfamily of enzymes and should find applications with other enzymes. PMID:24628377

  16. Chromatographic separation of proteins on metal immobilized iminodiacetic acid-bound molded monolithic rods of macroporous poly(glycidyl methacrylate-co-ethylene dimethacrylate).

    PubMed

    Luo, Q; Zou, H; Xiao, X; Guo, Z; Kong, L; Mao, X

    2001-08-17

    Continuous rod of macroporous poly(glycidyl methacrylate-co-ethylene dimethacrylate) was prepared by a free radical polymerization within the confines of a stainless-steel column. The epoxide groups of the rod were modified by a reaction with iminodiacetic acid (IDA) that affords the active site to form metal IDA chelates used for immobilized metal affinity chromatography (IMAC). The efficiency of coupling of IDA to the epoxide-contained matrix was studied as a function of reaction time and temperature. High-performance separation of proteins, based on immobilized different metals on the column, were described. The influence of pH on the adsorption capacity of bovine serum albumin on the Cu2+-IDA continuous rod column was investigated in the range from 5.0 to 9.0. Purification of lysozyme from egg white and human serum albumin (HSA) on the commercially available HSA solution were performed on the naked IDA and Cu2+-IDA continuous rod columns, respectively; and the purity of the obtained fractions was detected by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. PMID:11556331

  17. Covalent anthocyanin-flavonol complexes from the violet-blue flowers of Allium 'Blue Perfume'.

    PubMed

    Saito, Norio; Nakamura, Maiko; Shinoda, Koichi; Murata, Naho; Kanazawa, Toshinari; Kato, Kazuhisa; Toki, Kenjiro; Kasai, Hiroko; Honda, Toshio; Tatsuzawa, Fumi

    2012-08-01

    Three covalent anthocyanin-flavonol complexes (pigments 1-3) were extracted from the violet-blue flower of Allium 'Blue Perfume' with 5% acetic acid-MeOH solution, in which pigment 1 was the dominant pigment. These three pigments are based on delphinidin 3-glucoside as their deacylanthocyanin and were acylated with malonyl kaempferol 3-sophoroside-7-glucosiduronic acid or malonyl-kaempferol 3-p-coumaroyl-tetraglycoside-7-glucosiduronic acid in addition to acylation with acetic acid. By spectroscopic and chemical methods, the structures of these three pigments 1-3 were determined to be: pigment 1, (6(I)-O-(delphinidin 3-O-(3(I)-O-(acetyl)-β-glucopyranoside(I))))(2(VI)-O-(kaempferol 3-O-(2(II)-O-(3(III)-O-(β-glucopyranosyl(V))-β-glucopyranosyl(III))-4(II)-O-(trans-p-coumaroyl)-6(II)-O-(β-glucopyranosyl(IV))-β-glucopyranoside(II))-7-O-(β-glucosiduronic acid(VI)))) malonate; pigment 2, (6(I)-O-(delphinidin 3-O-(3(I)-O-(acetyl)-β-glucopyranoside(I))))(2(VI)-O-(kaempferol 3-O-(2(II)-O-β-glucopyranosyl(III))-β-glucopyranoside(II))-7-O-(β-glucosiduronic acid(VI)))); and pigment 3, (6(I)-O-(delphinidin 3-O-(3(I)-O-(acetyl)-β-glucopyranoside(I))))(2(VI)-O-(kaempferol 3-O-(2(II)-O-(3(III)-O-(β-glucopyranosyl(V))-β-glucopyranosyl(III))-4(II)-O-(cis-p-coumaroyl)-6(II)-O-(β-glucopyranosyl(IV))-β-glucopyranoside(II))-7-O-(β-glucosiduronic acid(VI)))) malonate. The structure of pigment 2 was analogous to that of a covalent anthocyanin-flavonol complex isolated from Allium schoenoprasum where delphinidin was observed in place of cyanidin. The three covalent anthocyanin-flavonol complexes (pigment 1-3) had a stable violet-blue color with three characteristic absorption maxima at 540, 547 and 618nm in pH 5-6 buffer solution. From circular dichroism measurement of pigment 1 in the pH 6.0 buffer solution, cotton effects were observed at 533 (+), 604 (-) and 638 (-) nm. Based on these results, these covalent anthocyanin-flavonol complexes were presumed to maintain a

  18. Effects of bound versus soluble pentosan polysulphate in PEG/HA-based hydrogels tailored for intervertebral disc regeneration.

    PubMed

    Frith, Jessica E; Menzies, Donna J; Cameron, Andrew R; Ghosh, P; Whitehead, Darryl L; Gronthos, S; Zannettino, Andrew C W; Cooper-White, Justin J

    2014-01-01

    Previous reports in the literature investigating chondrogenesis in mesenchymal progenitor cell (MPC) cultures have confirmed the chondro-inductive potential of pentosan polysulphate (PPS), a highly sulphated semi-synthetic polysaccharide, when added as a soluble component to culture media under standard aggregate-assay conditions or to poly(ethylene glycol)/hyaluronic acid (PEG/HA)-based hydrogels, even in the absence of inductive factors (e.g. TGFβ). In this present study, we aimed to assess whether a 'bound' PPS would have greater activity and availability over a soluble PPS, as a media additive or when incorporated into PEG/HA-based hydrogels. We achieved this by covalently pre-binding the PPS to the HA component of the gel (forming a new molecule, HA-PPS). We firstly investigated the activity of HA-PPS compared to free PPS, when added as a soluble factor to culture media. Cell proliferation, as determined by CCK8 and EdU assay, was decreased in the presence of either bound or free PPS whilst chondrogenic differentiation, as determined by DMMB assay and histology, was enhanced. In all cases, the effect of the bound PPS (HA-PPS) was more potent than that of the unbound form. These results alone suggest wider applications for this new molecule, either as a culture supplement or as a coating for scaffolds targeted at chondrogenic differentiation or maturation. We then investigated the incorporation of HA-PPS into a PEG/HA-based hydrogel system, by simply substituting some of the HA for HA-PPS. Rheological testing confirmed that incorporation of either HA-PPS or PPS did not significantly affect gelation kinetics, final hydrogel modulus or degradation rate but had a small, but significant, effect on swelling. When encapsulated in the hydrogels, MPCs retained good viability and rapidly adopted a rounded morphology. Histological analysis of both GAG and collagen deposition after 21 days showed that the incorporation of the bound-PPS into the hydrogel resulted in

  19. Covalent Docking Predicts Substrates for Haloalkanoate Dehalogenase Superfamily Phosphatases

    PubMed Central

    2015-01-01

    Enzyme function prediction remains an important open problem. Though structure-based modeling, such as metabolite docking, can identify substrates of some enzymes, it is ill-suited to reactions that progress through a covalent intermediate. Here we investigated the ability of covalent docking to identify substrates that pass through such a covalent intermediate, focusing particularly on the haloalkanoate dehalogenase superfamily. In retrospective assessments, covalent docking recapitulated substrate binding modes of known cocrystal structures and identified experimental substrates from a set of putative phosphorylated metabolites. In comparison, noncovalent docking of high-energy intermediates yielded nonproductive poses. In prospective predictions against seven enzymes, a substrate was identified for five. For one of those cases, a covalent docking prediction, confirmed by empirical screening, and combined with genomic context analysis, suggested the identity of the enzyme that catalyzes the orphan phosphatase reaction in the riboflavin biosynthetic pathway of Bacteroides. PMID:25513739

  20. A Photoresponsive Surface Covalent Organic Framework: Surface-Confined Synthesis, Isomerization, and Controlled Guest Capture and Release.

    PubMed

    Liu, Chunhua; Zhang, Wei; Zeng, Qingdao; Lei, Shengbin

    2016-05-10

    By introducing an azobenzene group to the backbone of diboronic acid, we have obtained a surface-confined, photoresponsive single-layer covalent organic framework with long-range order and almost entire surface coverage. Scanning tunneling microscopic characterization indicates that though the covalent linkage provides a significant locking effect, isomerization can still happen under UV irradiation, which causes destruction of the surface COF. Furthermore, the decomposed surface COF can recover upon annealing. This photoinduced decomposition provides a facile approach for the controlled capture and release of targeted objects using these nanoporous surface COFs as a host, which has been demonstrated in this work using copper phthalocyanine as a model guest. PMID:26990558

  1. Ab initio study of chemical bond interactions between covalently functionalized carbon nanotubes via amide, ester and anhydride linkages

    NASA Astrophysics Data System (ADS)

    Ben Doudou, Bessem; Chen, Jun; Vivet, Alexandre; Poilâne, Christophe

    2016-03-01

    In this paper, we have investigated the chemical bond interactions between covalently functionalized zigzag (5,0) and (8,0) SWCNT-SWCNT via various covalent linkages. Side-to-side junctions connected via amide, ester and anhydride linkages were particularly studied. The geometries and energy of the forming reaction were investigated using first-principles density functional theory. Furthermore, the band structures and the total density of states (DOS) of the junctions have also been analyzed. Our results show that several promising structures could be obtained by using chemical connection strategy and particularly the junctions formed by coupling amino functionalized SWCNT and carboxylic acid functionalized SWCNT was more favorable.

  2. Covalency-reinforced oxygen evolution reaction catalyst

    NASA Astrophysics Data System (ADS)

    Yagi, Shunsuke; Yamada, Ikuya; Tsukasaki, Hirofumi; Seno, Akihiro; Murakami, Makoto; Fujii, Hiroshi; Chen, Hungru; Umezawa, Naoto; Abe, Hideki; Nishiyama, Norimasa; Mori, Shigeo

    2015-09-01

    The oxygen evolution reaction that occurs during water oxidation is of considerable importance as an essential energy conversion reaction for rechargeable metal-air batteries and direct solar water splitting. Cost-efficient ABO3 perovskites have been studied extensively because of their high activity for the oxygen evolution reaction; however, they lack stability, and an effective solution to this problem has not yet been demonstrated. Here we report that the Fe4+-based quadruple perovskite CaCu3Fe4O12 has high activity, which is comparable to or exceeding those of state-of-the-art catalysts such as Ba0.5Sr0.5Co0.8Fe0.2O3-δ and the gold standard RuO2. The covalent bonding network incorporating multiple Cu2+ and Fe4+ transition metal ions significantly enhances the structural stability of CaCu3Fe4O12, which is key to achieving highly active long-life catalysts.

  3. Covalency-reinforced oxygen evolution reaction catalyst

    PubMed Central

    Yagi, Shunsuke; Yamada, Ikuya; Tsukasaki, Hirofumi; Seno, Akihiro; Murakami, Makoto; Fujii, Hiroshi; Chen, Hungru; Umezawa, Naoto; Abe, Hideki; Nishiyama, Norimasa; Mori, Shigeo

    2015-01-01

    The oxygen evolution reaction that occurs during water oxidation is of considerable importance as an essential energy conversion reaction for rechargeable metal–air batteries and direct solar water splitting. Cost-efficient ABO3 perovskites have been studied extensively because of their high activity for the oxygen evolution reaction; however, they lack stability, and an effective solution to this problem has not yet been demonstrated. Here we report that the Fe4+-based quadruple perovskite CaCu3Fe4O12 has high activity, which is comparable to or exceeding those of state-of-the-art catalysts such as Ba0.5Sr0.5Co0.8Fe0.2O3−δ and the gold standard RuO2. The covalent bonding network incorporating multiple Cu2+ and Fe4+ transition metal ions significantly enhances the structural stability of CaCu3Fe4O12, which is key to achieving highly active long-life catalysts. PMID:26354832

  4. Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism

    NASA Astrophysics Data System (ADS)

    Kidd, Philip B.; Wingreen, Ned S.

    2010-03-01

    In the bacterium Escherichia coli, the enzyme glutamine synthetase (GS) converts ammonium into the amino acid glutamine. GS is principally active when the cell is experiencing nitrogen limitation, and its activity is regulated by a bicyclic covalent modification cascade. The advantages of this bicyclic-cascade architecture are poorly understood. We analyze a simple model of the GS cascade in comparison to other regulatory schemes and conclude that the bicyclic cascade is suboptimal for maintaining metabolic homeostasis of the free glutamine pool. Instead, we argue that the lag inherent in the covalent modification of GS slows the response to an ammonium shock and thereby allows GS to transiently detoxify the cell, while maintaining homeostasis over longer times.

  5. Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism

    PubMed Central

    Kidd, Philip B

    2013-01-01

    In the bacterium Escherichia coli, the enzyme glutamine synthetase (GS) converts ammonium into the amino acid glutamine. GS is principally active when the cell is experiencing nitrogen limitation, and its activity is regulated by a bicyclic covalent modification cascade. The advantages of this bicyclic-cascade architecture are poorly understood. We analyze a simple model of the GS cascade in comparison to other regulatory schemes and conclude that the bicyclic cascade is suboptimal for maintaining metabolic homeostasis of the free glutamine pool. Instead, we argue that the lag inherent in the covalent modification of GS slows the response to an ammonium shock and thereby allows GS to transiently detoxify the cell, while maintaining homeostasis over longer times. PMID:20057006

  6. DNA profiling by capillary array electrophoresis with non-covalent fluorescent labeling.

    PubMed

    Olson, Nels A; Khandurina, Julia; Guttman, Andras

    2004-10-01

    Increasing need for large-scale DNA profiling necessitated the development of automated electrophoresis based methods enabling rapid, high performance analysis of nucleic acids in a wide molecular-mass range. In this paper, we report on the adaptation of a commercial 96-capillary array electrophoresis (CAE) instrument for high-throughput DNA fragment analysis and the evaluation of the effects of different non-covalent DNA staining dyes on separation efficiency. The applicability of different color internal fluorescent standards is shown with mathematical spectral overlap correction algorithms. Large-scale quality control assessment of oligonucleotide probes using non-covalent fluorophore labeling is also demonstrated. The method requires small sample amounts, offers automation and quantification capabilities to accommodate modern biotechnology industry needs.

  7. Second-Generation Non-Covalent NAAA Inhibitors are Protective in a Model of Multiple Sclerosis.

    PubMed

    Migliore, Marco; Pontis, Silvia; Fuentes de Arriba, Angel Luis; Realini, Natalia; Torrente, Esther; Armirotti, Andrea; Romeo, Elisa; Di Martino, Simona; Russo, Debora; Pizzirani, Daniela; Summa, Maria; Lanfranco, Massimiliano; Ottonello, Giuliana; Busquet, Perrine; Jung, Kwang-Mook; Garcia-Guzman, Miguel; Heim, Roger; Scarpelli, Rita; Piomelli, Daniele

    2016-09-01

    Palmitoylethanolamide (PEA) and oleoylethanolamide (OEA) are endogenous lipid mediators that suppress inflammation. Their actions are terminated by the intracellular cysteine amidase, N-acylethanolamine acid amidase (NAAA). Even though NAAA may offer a new target for anti-inflammatory therapy, the lipid-like structures and reactive warheads of current NAAA inhibitors limit the use of these agents as oral drugs. A series of novel benzothiazole-piperazine derivatives that inhibit NAAA in a potent and selective manner by a non-covalent mechanism are described. A prototype member of this class (8) displays high oral bioavailability, access to the central nervous system (CNS), and strong activity in a mouse model of multiple sclerosis (MS). This compound exemplifies a second generation of non-covalent NAAA inhibitors that may be useful in the treatment of MS and other chronic CNS disorders. PMID:27404798

  8. Changes in Dehydrodiferulic Acids and Peroxidase Activity against Ferulic Acid Associated with Cell Walls during Growth of Pinus pinaster Hypocotyl.

    PubMed Central

    Sanchez, M.; Pena, M. J.; Revilla, G.; Zarra, I.

    1996-01-01

    Hydroxycinnamic acids associated with hypocotyl cell walls of dark-grown seedlings of Pinus pinaster Aiton were extracted with 1 N NaOH and identified by gas chromatography-mass spectrometry. The main hydroxycinnamic acid found was ferulic acid. Diferulic acid dehydrodimers were also found, with the 8,8-coupled isomer (compound 11) being the dehydrodiferulate present in the highest amount. However, the 5,5-coupled isomer, commonly referred to referred to as diferulic acid, was not detected. Two truxillic acids, 4-4[prime]-dihydroxy-3-3[prime]-dimethoxy-[alpha]-truxillic acids I and II, were tentatively identified. The 8,8-coupled dehydrodiferulic acid (compound 11) was the phenolic acid that showed the most conspicuous changes with hypocotyl age as well as along the hypocotyl axis. Peroxidase activity against ferulic acid was found in the apoplastic fluid as well as being ionically and covalently bound to the cell walls. The peroxidase activity increased with hypocotyl age as well as from the subapical toward the basal region of the hypocotyls. A key role in the cell-wall stiffening of 8,8 but not 5,5 dimerization of ferulic acid catalyzed by cell-wall peroxidases is proposed. PMID:12226339

  9. Validation of EMP bounds

    SciTech Connect

    Warne, L.K.; Merewether, K.O.; Chen, K.C.; Jorgenson, R.E.; Morris, M.E.; Solberg, J.E.; Lewis, J.G.; Derr, W.

    1996-07-01

    Test data on canonical weapon-like fixtures are used to validate previously developed analytical bounding results. The test fixtures were constructed to simulate (but be slightly worse than) weapon ports of entry but have known geometries (and electrical points of contact). The exterior of the test fixtures exhibited exterior resonant enhancement of the incident fields at the ports of entry with magnitudes equal to those of weapon geometries. The interior consisted of loaded transmission lines adjusted to maximize received energy or voltage but incorporating practical weapon geometrical constraints. New analytical results are also presented for bounding the energies associated with multiple bolt joints and for bounding the exterior resonant enhancement of the exciting fields.

  10. A novel tyrosine-heme C−O covalent linkage in F43Y myoglobin: a new post-translational modification of heme proteins.

    PubMed

    Yan, Dao-Jing; Li, Wei; Xiang, Yu; Wen, Ge-Bo; Lin, Ying-Wu; Tan, Xiangshi

    2015-01-01

    Heme post-translational modification plays a key role in tuning the structure and function of heme proteins. We herein report a novel tyrosine-heme covalent C−O bond in an artificially produced sperm whale myoglobin (Mb) mutant, F43Y Mb, which formed spontaneously in vivo between the Tyr43 hydroxy group and the heme 4-vinyl group. This highlights the diverse chemistry of heme post-translational modifications, and lays groundwork for further investigation of the structural and functional diversity of covalently-bound heme proteins. PMID:25392956

  11. A novel tyrosine-heme C−O covalent linkage in F43Y myoglobin: a new post-translational modification of heme proteins.

    PubMed

    Yan, Dao-Jing; Li, Wei; Xiang, Yu; Wen, Ge-Bo; Lin, Ying-Wu; Tan, Xiangshi

    2015-01-01

    Heme post-translational modification plays a key role in tuning the structure and function of heme proteins. We herein report a novel tyrosine-heme covalent C−O bond in an artificially produced sperm whale myoglobin (Mb) mutant, F43Y Mb, which formed spontaneously in vivo between the Tyr43 hydroxy group and the heme 4-vinyl group. This highlights the diverse chemistry of heme post-translational modifications, and lays groundwork for further investigation of the structural and functional diversity of covalently-bound heme proteins.

  12. Covalent functionalization of silica surface using "inert" poly(dimethylsiloxanes).

    PubMed

    Graffius, Gabriel; Bernardoni, Frank; Fadeev, Alexander Y

    2014-12-16

    Methyl-terminated poly(dimethylsiloxanes) (PDMSs) are typically considered to be inert and not suitable for surface functionalization reactions because of the absence of readily hydrolyzable groups. Nevertheless, these siloxanes do react with silica and other oxides, producing chemically grafted organic surfaces. Known since the 1970s and then forgotten and recently rediscovered, this reaction provides a versatile yet simple method for the covalent functionalization of inorganic surfaces. In this work, we have explored the reactions of linear methyl-terminated and cyclic PDMS and bis-fluoroalkyl disiloxanes for the surface functionalization of mesoporous silica (Dpore ≈ 30-35 nm). The optimal reaction conditions included 24 h of contact of neat siloxane liquids and silica at 120-250 °C (depending on the siloxane). A study of the reactions of silicas with different extents of hydration demonstrated the critical role of water in facilitating the grafting of the siloxanes. The proposed reaction mechanism involved the hydrolysis of the adsorbed siloxanes by the Lewis acidic centers (presumably formed by water adsorbed onto surface defects) followed by the coupling of silanols to the surface to produce grafted siloxanes. For rigorously dehydrated silicas (calcination ∼1000 °C), an alternative pathway that did not require water and involved the reaction of the siloxanes with the strained siloxane rings was also plausible. According to FTIR and chemical analysis, the reactions of bis-fluoroalkyl disiloxanes and cyclic PDMS (D3-D5) produced covalently-attached monolayer surfaces, and the reactions of high-MM methyl-terminated PDMS produced polymeric grafted silicas with a PDMS mass content of up to 50%. As evidenced by the high contact angles of ∼130°/100° (adv/rec) and the negligible amount of water adsorption over the entire range of relative pressures, including saturation (p/p0 → 1), the siloxane-grafted porous silicas show uniform, high-quality hydrophobic

  13. Non-covalent and covalent functionalization of graphene for device applications

    NASA Astrophysics Data System (ADS)

    Jandhyala, Srikar

    In order to continue improving the performance of electronic devices and also to increase functionality, incorporation of alternative channel materials into the current silicon based technology is inevitable. Graphene is one such material which is being heavily investigated owing to its high carrier mobility, one atom thickness, and other electronic as well as physical attributes. There are various architectures proposed for graphene based devices. This dissertation focuses on one of the challenges in integrating graphene based devices, i.e. gate dielectrics. For the more common device architectures utilizing electric field-effect in graphene, a thin and high dielectric constant (high-kappa) material is desired for gate dielectric applications. Although, atomic layer deposition (ALD) is the most suitable technique for depositing such dielectrics on various substrates, it is difficult to initiate dielectric growth using ALD on graphene because it lacks out-of-plane bonds owing to the sp2 hybridization of carbon atoms. An approach involving non-covalent functionalization of graphene surface with ozone (O3) at room temperature is studied for depositing high-kappa oxides with ALD. A scheme was developed for in-situ electrical monitoring of transport properties of back-gate graphene field-effect transistors (GFETs) during the ALD process. It was established that O 3 is mostly physisorbed on (high-quality) graphene at room temperature and its effects on graphene properties are reversed upon introduction of metal precursor which reacts with the adsorbed O3 molecules resulting in oxide deposition. Utilizing this knowledge, a high-pressure O3 functionalization approach was developed for depositing oxide gate dielectrics on graphene using ALD and top-gate GFETs with dielectric thickness below 5 nm were demonstrated. A low-kappa tunnel dielectric is the proposed requirement for certain graphene based devices. Covalent functionalization of graphene with fluorine through plasma

  14. O2 reduction reaction by biologically relevant anionic ligand bound iron porphyrin complexes.

    PubMed

    Samanta, Subhra; Das, Pradip Kumar; Chatterjee, Sudipta; Sengupta, Kushal; Mondal, Biswajit; Dey, Abhishek

    2013-11-18

    Iron porphyrin complex with a covalently attached thiolate ligand and another with a covalently attached phenolate ligand has been synthesized. The thiolate bound complex shows spectroscopic features characteristic of P450, including the hallmark absorption spectrum of the CO adduct. Electrocatalytic O2 reduction by this complex, which bears a terminal alkyne group, is investigated by both physiabsorbing on graphite surfaces (fast electron transfer rates) and covalent attachment to azide terminated self-assembled monolayer (physiologically relevant electron transfer rates) using the terminal alkyne group. Analysis of the steady state electrochemical kinetics reveals that this catalyst can selectively reduce O2 to H2O with a second-order k(cat.) ~10(7) M(-1 )s(-1) at pH 7. The analogous phenolate bound iron porphyrin complex reduces O2 with a second-order rate constant of 10(5) M(-1) s(-1) under the same conditions. The anionic ligand bound iron porphyrin complexes catalyze oxygen reduction reactions faster than any known synthetic heme porphyrin analogues. The kinetic parameters of O2 reduction of the synthetic thiolate bound complex, which is devoid of any second sphere effects present in protein active sites, provide fundamental insight into the role of the protein environment in tuning the reactivity of thiolate bound iron porphyrin containing metalloenzymes. PMID:24171513

  15. X-ray crystallographic analysis of adipocyte fatty acid binding protein (aP2) modified with 4-hydroxy-2-nonenal

    SciTech Connect

    Hellberg, Kristina; Grimsrud, Paul A.; Kruse, Andrew C.; Banaszak, Leonard J.; Ohlendorf, Douglas H.; Bernlohr, David A.

    2012-07-11

    Fatty acid binding proteins (FABP) have been characterized as facilitating the intracellular solubilization and transport of long-chain fatty acyl carboxylates via noncovalent interactions. More recent work has shown that the adipocyte FABP is also covalently modified in vivo on Cys117 with 4-hydroxy-2-nonenal (4-HNE), a bioactive aldehyde linked to oxidative stress and inflammation. To evaluate 4-HNE binding and modification, the crystal structures of adipocyte FABP covalently and noncovalently bound to 4-HNE have been solved to 1.9 {angstrom} and 2.3 {angstrom} resolution, respectively. While the 4-HNE in the noncovalently modified protein is coordinated similarly to a carboxylate of a fatty acid, the covalent form show a novel coordination through a water molecule at the polar end of the lipid. Other defining features between the two structures with 4-HNE and previously solved structures of the protein include a peptide flip between residues Ala36 and Lys37 and the rotation of the side chain of Phe57 into its closed conformation. Representing the first structure of an endogenous target protein covalently modified by 4-HNE, these results define a new class of in vivo ligands for FABPs and extend their physiological substrates to include bioactive aldehydes.

  16. Renaturation of denatured, covalently closed circular DNA.

    PubMed

    Strider, W; Camien, M N; Warner, R C

    1981-08-10

    The rate of renaturation of denatured, covalently closed, circular DNA (form Id DNA) of the phi X174 replicative form has been investigated as a function of pH, temperature, and ionic strength. The rate at a constant temperature is a sharply peaked function of pH in the range of pH 9 to 12. The position on the pH scale of the maximum rate decreases as the temperature is increased and as the ionic strength is increased. The kinetic course of renaturation is pseudo-first order: it is independent of DNA concentration, but falls off in rate from a first order relationship as the reaction proceeds. The rate of renaturation depends critically on the temperature at which the denaturation is carried out. Form Id, prepared at an alkaline pH at 0 degrees C, renatures from 5 to more than 100 times more rapidly than that similarly prepared at 50 degrees C. Both the heterogeneity in rate and the effect of the temperature of denaturation depend, in part, on the degree of supercoiling of the form I DNA from which the form Id is prepared. However, it is concluded that a much larger contribution to both arises from a configurational heterogeneity introduced in the denaturation reaction. The renaturation rate was determined by neutralization of the alkaline reaction and analytical ultracentrifugal analysis of the amounts of forms I and Id. The nature of the proximate renatured species at the temperature and alkaline pH of renaturation was investigated by spectrophotometric titration and analytical ultracentrifugation. It is concluded that the proximate species are the same as the intermediate species defined by an alkaline sedimentation titration of the kind first done by Vinograd et al. ((1965) Proc. Natl. Acad. Sci. U. S. A. 53, 1104-1111). Observations are included on the buoyant density of form Id and on depurination of DNA at alkaline pH values and high temperatures.

  17. Lipid bilayers covalently anchored to carbon nanotubes.

    PubMed

    Dayani, Yasaman; Malmstadt, Noah

    2012-05-29

    The unique physical and electrical properties of carbon nanotubes make them an exciting material for applications in various fields such as bioelectronics and biosensing. Due to the poor water solubility of carbon nanotubes, functionalization for such applications has been a challenge. Of particular need are functionalization methods for integrating carbon nanotubes with biomolecules and constructing novel hybrid nanostructures for bionanoelectronic applications. We present a novel method for the fabrication of dispersible, biocompatible carbon nanotube-based materials. Multiwalled carbon nanotubes (MWCNTs) are covalently modified with primary amine-bearing phospholipids in a carbodiimide-activated reaction. These modified carbon nanotubes have good dispersibility in nonpolar solvents. Fourier transform infrared (FTIR) spectroscopy shows peaks attributable to the formation of amide bonds between lipids and the nanotube surface. Simple sonication of lipid-modified nanotubes with other lipid molecules leads to the formation of a uniform lipid bilayer coating the nanotubes. These bilayer-coated nanotubes are highly dispersible and stable in aqueous solution. Confocal fluorescence microscopy shows labeled lipids on the surface of bilayer-modified nanotubes. Transmission electron microscopy (TEM) shows the morphology of dispersed bilayer-coated MWCNTs. Fluorescence quenching of lipid-coated MWCNTs confirms the bilayer configuration of the lipids on the nanotube surface, and fluorescence anisotropy measurements show that the bilayer is fluid above the gel-to-liquid transition temperature. The membrane protein α-hemolysin spontaneously inserts into the MWCNT-supported bilayer, confirming the biomimetic membrane structure. These biomimetic nanostructures are a promising platform for the integration of carbon nanotube-based materials with biomolecules.

  18. Chloramphenicol Biosynthesis: The Structure of CmlS, a Flavin-Dependent Halogenase Shwing a Covalent Flavin-Aspartate Bond

    SciTech Connect

    Podzelinska, K.; Latimer, R; Bhattacharya, A; Vining, L; Zechel, D; Jia, Z

    2010-01-01

    Chloramphenicol is a halogenated natural product bearing an unusual dichloroacetyl moiety that is critical for its antibiotic activity. The operon for chloramphenicol biosynthesis in Streptomyces venezuelae encodes the chloramphenicol halogenase CmlS, which belongs to the large and diverse family of flavin-dependent halogenases (FDH's). CmlS was previously shown to be essential for the formation of the dichloroacetyl group. Here we report the X-ray crystal structure of CmlS determined at 2.2 {angstrom} resolution, revealing a flavin monooxygenase domain shared by all FDHs, but also a unique 'winged-helix' C-terminal domain that creates a T-shaped tunnel leading to the halogenation active site. Intriguingly, the C-terminal tail of this domain blocks access to the halogenation active site, suggesting a structurally dynamic role during catalysis. The halogenation active site is notably nonpolar and shares nearly identical residues with Chondromyces crocatus tyrosyl halogenase (CndH), including the conserved Lys (K71) that forms the reactive chloramine intermediate. The exception is Y350, which could be used to stabilize enolate formation during substrate halogenation. The strictly conserved residue E44, located near the isoalloxazine ring of the bound flavin adenine dinucleotide (FAD) cofactor, is optimally positioned to function as a remote general acid, through a water-mediated proton relay, which could accelerate the reaction of the chloramine intermediate during substrate halogenation, or the oxidation of chloride by the FAD(C4{alpha})-OOH intermediate. Strikingly, the 8{alpha} carbon of the FAD cofactor is observed to be covalently attached to D277 of CmlS, a residue that is highly conserved in the FDH family. In addition to representing a new type of flavin modification, this has intriguing implications for the mechanism of FDHs. Based on the crystal structure and in analogy to known halogenases, we propose a reaction mechanism for CmlS.

  19. Synthesis and Photophysical Study of a [NiFe] Hydrogenase Biomimetic Compound Covalently Linked to a Re-diimine Photosensitizer

    PubMed Central

    2015-01-01

    The synthesis, photophysics, and photochemistry of a linked dyad ([Re]-[NiFe2]) containing an analogue ([NiFe2]) of the active site of [NiFe] hydrogenase, covalently bound to a Re-diimine photosensitizer ([Re]), are described. Following excitation, the mechanisms of electron transfer involving the [Re] and [NiFe2] centers and the resulting decomposition were investigated. Excitation of the [Re] center results in the population of a diimine-based metal-to-ligand charge transfer excited state. Reductive quenching by NEt3 produces the radically reduced form of [Re], [Re]− (kq = 1.4 ± 0.1 × 107 M–1 s–1). Once formed, [Re]− reduces the [NiFe2] center to [NiFe2]−, and this reduction was followed using time-resolved infrared spectroscopy. The concentration dependence of the electron transfer rate constants suggests that both inter- and intramolecular electron transfer pathways are involved, and the rate constants for these processes have been estimated (kinter = 5.9 ± 0.7 × 108 M–1 s–1, kintra = 1.5 ± 0.1 × 105 s–1). For the analogous bimolecular system, only intermolecular electron transfer could be observed (kinter = 3.8 ± 0.5 × 109 M–1 s–1). Fourier transform infrared spectroscopic studies confirms that decomposition of the dyad occurs upon prolonged photolysis, and this appears to be a major factor for the low activity of the system toward H2 production in acidic conditions. PMID:26605700

  20. COVALENT BINDING OF REDUCED METABOLITES OF [15N3] TNT TO SOIL ORGANIC MATTER DURING A BIOREMEDIATION PROCESS ANALYZED BY 15N NMR SPECTROSCOPY. (R826646)

    EPA Science Inventory

    Evidence is presented for the covalent binding of
    biologically reduced metabolites of 2,4,6-15N3-trinitrotoluene
    (TNT) to different soil fractions (humic acids, fulvic
    acids, and humin) using liquid 15N NMR spectroscopy. A
    silylation p...

  1. X-ray Crystallography Reveals a Reduced Substrate Complex of UDP-Galactopyranose Mutase Poised for Covalent Catalysis by Flavin

    SciTech Connect

    Gruber, Todd D.; Westler, William M.; Kiessling, Laura L.; Forest, Katrina T.

    2009-11-04

    The flavoenzyme uridine 5'-diphosphate galactopyranose mutase (UGM or Glf) catalyzes the interconversion of UDP-galactopyranose and UDP-galactofuranose. The latter is a key building block for cell wall construction in numerous pathogens, including Mycobacterium tuberculosis. Mechanistic studies of UGM suggested a novel role for the flavin, and we previously provided evidence that the catalytic mechanism proceeds through a covalent flavin-galactose iminium. Here, we describe 2.3 and 2.5 {angstrom} resolution X-ray crystal structures of the substrate-bound enzyme in oxidized and reduced forms, respectively. In the latter, C1 of the substrate is 3.6 {angstrom} from the nucleophilic flavin N5 position. This orientation is consistent with covalent catalysis by flavin.

  2. Supramolecular motifs in dynamic covalent PEG-hemiaminal organogels

    PubMed Central

    Fox, Courtney H.; ter Hurrne, Gijs M.; Wojtecki, Rudy J.; Jones, Gavin O.; Horn, Hans W.; Meijer, E. W.; Frank, Curtis W.; Hedrick, James L.; García, Jeannette M.

    2015-01-01

    Dynamic covalent materials are stable materials that possess reversible behaviour triggered by stimuli such as light, redox conditions or temperature; whereas supramolecular crosslinks depend on the equilibrium constant and relative concentrations of crosslinks as a function of temperature. The combination of these two reversible chemistries can allow access to materials with unique properties. Here, we show that this combination of dynamic covalent and supramolecular chemistry can be used to prepare organogels comprising distinct networks. Two materials containing hemiaminal crosslink junctions were synthesized; one material is comprised of dynamic covalent junctions and the other contains hydrogen-bonding bis-hemiaminal moieties. Under specific network synthesis conditions, these materials exhibited self-healing behaviour. This work reports on both the molecular-level detail of hemiaminal crosslink junction formation as well as the macroscopic behaviour of hemiaminal dynamic covalent network (HDCN) elastomeric organogels. These materials have potential applications as elastomeric components in printable materials, cargo carriers and adhesives. PMID:26174864

  3. Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity

    SciTech Connect

    Pegan, Scott D.; Serrano, Hector; Whitman, Christian P.; Mesecar, Andrew D.

    2008-12-01

    The X-ray structure of a noncovalently modified trans-3-chloroacrylic acid dehalogenase with a substrate-homolog acetate bound in the active site has been determined to 1.7 Å resolution. Elucidation of catalytically important water is reported and multiple conformations of the catalytic residue αGlu52 are observed. Trans-3-chloroacrylic acid dehalogenase (CaaD) is a critical enzyme in the trans-1, 3-dichloropropene (DCP) degradation pathway in Pseudomonas pavonaceae 170. This enzyme allows bacteria to use trans-DCP, a common component in commercially produced fumigants, as a carbon source. CaaD specifically catalyzes the fourth step of the pathway by cofactor-independent dehalogenation of a vinyl carbon–halogen bond. Previous studies have reported an X-ray structure of CaaD under acidic conditions with a covalent modification of the catalytic βPro1 residue. Here, the 1.7 Å resolution X-ray structure of CaaD under neutral (pH 6.5) conditions is reported without the presence of the covalent adduct. In this new structure, a substrate-like acetate molecule is bound within the active site in a position analogous to the putative substrate-binding site. Additionally, a catalytically important water molecule was identified, consistent with previously proposed reaction schemes. Finally, flexibility of the catalytically relevant side chain αGlu52 is observed in the structure, supporting its role in the catalytic mechanism.

  4. Mass Spectrometric and Spectrofluorometric Studies of the Interaction of Aristolochic Acids with Proteins

    PubMed Central

    Li, Weiwei; Hu, Qin; Chan, Wan

    2015-01-01

    Aristolochic acid (AA) is a potent carcinogen and nephrotoxin and is associated with the development of “Chinese herb nephropathy” and Balkan endemic nephropathy. Despite decades of research, the specific mechanism of the observed nephrotoxicity has remained elusive and the potential effects on proteins due to the observed toxicity of AA are not well-understood. To better understand the pharmacotoxicological features of AA, we investigated the non-covalent interactions of AA with proteins. The protein-binding properties of AA with bovine serum albumin (BSA) and lysozyme were characterized using spectrofluorometric and mass spectrometric (MS) techniques. Moreover, the protein-AA complexes were clearly identified by high-resolution MS analyses. To the best of our knowledge, this is the first direct evidence of non-covalently bound protein-AA complexes. An analysis of the spectrofluorometric data by a modified Stern−Volmer plot model also revealed that both aristolochic acid I (AAI) and aristolochic acid II (AAII) were bound to BSA and lysozyme in 1:1 stoichiometries. A significantly stronger protein binding property was observed in AAII than in AAI as evidenced by the spectrofluorometric and MS analyses, which may explain the observed higher mutagenicity of AAII. PMID:26471474

  5. Mass Spectrometric and Spectrofluorometric Studies of the Interaction of Aristolochic Acids with Proteins

    NASA Astrophysics Data System (ADS)

    Li, Weiwei; Hu, Qin; Chan, Wan

    2015-10-01

    Aristolochic acid (AA) is a potent carcinogen and nephrotoxin and is associated with the development of “Chinese herb nephropathy” and Balkan endemic nephropathy. Despite decades of research, the specific mechanism of the observed nephrotoxicity has remained elusive and the potential effects on proteins due to the observed toxicity of AA are not well-understood. To better understand the pharmacotoxicological features of AA, we investigated the non-covalent interactions of AA with proteins. The protein-binding properties of AA with bovine serum albumin (BSA) and lysozyme were characterized using spectrofluorometric and mass spectrometric (MS) techniques. Moreover, the protein-AA complexes were clearly identified by high-resolution MS analyses. To the best of our knowledge, this is the first direct evidence of non-covalently bound protein-AA complexes. An analysis of the spectrofluorometric data by a modified Stern-Volmer plot model also revealed that both aristolochic acid I (AAI) and aristolochic acid II (AAII) were bound to BSA and lysozyme in 1:1 stoichiometries. A significantly stronger protein binding property was observed in AAII than in AAI as evidenced by the spectrofluorometric and MS analyses, which may explain the observed higher mutagenicity of AAII.

  6. A New Staple: Peptide-Targeted Covalent Inhibitors.

    PubMed

    Leverson, Joel D

    2016-09-22

    In this issue of Cell Chemical Biology, Huhn et al. (2016) unveil a clever strategy for selectively and irreversibly inhibiting an anti-apoptotic protein, BFL-1. The authors describe stapled peptides bearing carefully placed electrophiles that target a unique cysteine residue in BFL-1 via covalent modification, thus representing an extension of the stapled peptide concept into the covalent inhibitor space. PMID:27662249

  7. Non-covalent interactions between carbon nanotubes and conjugated polymers.

    PubMed

    Tuncel, Dönüs

    2011-09-01

    Carbon nanotubes (CNTs) are interest to many different disciplines including chemistry, physics, biology, material science and engineering because of their unique properties and potential applications in various areas spanning from optoelectronics to biotechnology. However, one of the drawbacks associated with these materials is their insolubility which limits their wide accessibility for many applications. Various approaches have been adopted to circumvent this problem including modification of carbon nanotube surfaces by non-covalent and covalent attachments of solubilizing groups. Covalent approach modification may alter the intrinsic properties of carbon nanotubes and, in turn make them undesirable for many applications. On the other hand, a non-covalent approach helps to improve the solubility of CNTs while preserving their intrinsic properties. Among many non-covalent modifiers of CNTs, conjugated polymers are receiving increasing attention and highly appealing because of a number of reasons. To this end, the aim of this feature article is to review the recent results on the conjugated polymer-based non-covalent functionalization of CNTs with an emphasis on the effect of conjugated polymers in the dispersibility/solubility, optical, thermal and mechanical properties of carbon nanotubes as well as their usage in the purification and isolation of a specific single-walled nanotube from the mixture of the various tubes.

  8. Immunodetection of human topoisomerase I-DNA covalent complexes.

    PubMed

    Patel, Anand G; Flatten, Karen S; Peterson, Kevin L; Beito, Thomas G; Schneider, Paula A; Perkins, Angela L; Harki, Daniel A; Kaufmann, Scott H

    2016-04-01

    A number of established and investigational anticancer drugs slow the religation step of DNA topoisomerase I (topo I). These agents induce cytotoxicity by stabilizing topo I-DNA covalent complexes, which in turn interact with advancing replication forks or transcription complexes to generate lethal lesions. Despite the importance of topo I-DNA covalent complexes, it has been difficult to detect these lesions within intact cells and tumors. Here, we report development of a monoclonal antibody that specifically recognizes covalent topo I-DNA complexes, but not free topo I or DNA, by immunoblotting, immunofluorescence or flow cytometry. Utilizing this antibody, we demonstrate readily detectable topo I-DNA covalent complexes after treatment with camptothecins, indenoisoquinolines and cisplatin but not nucleoside analogues. Topotecan-induced topo I-DNA complexes peak at 15-30 min after drug addition and then decrease, whereas indotecan-induced complexes persist for at least 4 h. Interestingly, simultaneous staining for covalent topo I-DNA complexes, phospho-H2AX and Rad51 suggests that topotecan-induced DNA double-strand breaks occur at sites distinct from stabilized topo I-DNA covalent complexes. These studies not only provide new insight into the action of topo I-directed agents, but also illustrate a strategy that can be applied to study additional topoisomerases and their inhibitors in vitro and in vivo.

  9. Bound Exciton Complexes

    NASA Astrophysics Data System (ADS)

    Meyer, B. K.

    In the preceding chapter, we concentrated on the properties of free excitons. These free excitons may move through the sample and hit a trap, a nonradiative or a radiative recombination center. At low temperatures, the latter case gives rise to either deep center luminescence, mentioned in Sect. 7.1 and discussed in detail in Chap. 9, or to the luminescence of bound exciton complexes (BE or BEC). The chapter continues with the most prominent of these BECs, namely A-excitons bound to neutral donors. The next aspects are the more weakly BEs at ionized donors. The Sect. 7.4 treats the binding or localization energies of BEC from a theoretical point of view, while Sect. 7.5 is dedicated to excited states of BECs, which contain either holes from deeper valence bands or an envelope function with higher quantum numbers. The last section is devoted to donor-acceptor pair transitions. There is no section devoted specifically to excitons bound to neutral acceptors, because this topic is still partly controversially discussed. Instead, information on these A0X complexes is scattered over the whole chapter, however, with some special emphasis seen in Sects. 7.1, 7.4, and 7.5.

  10. Progress in the experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations.

    PubMed

    Jordan, Frank; Nemeria, Natalia S

    2014-12-01

    Thiamin diphosphate (ThDP), the vitamin B1 coenzyme is an excellent representative of coenzymes, which carry out electrophilic catalysis by forming a covalent complex with their substrates. The function of ThDP is to greatly increase the acidity of two carbon acids by stabilizing their conjugate bases, the ylide/carbene/C2-carbanion of the thiazolium ring and the C2α-carbanion/enamine, once the substrate binds to ThDP. In recent years, several ThDP-bound intermediates on such pathways have been characterized by both solution and solid-state methods. Prominent among these advances are X-ray crystallographic results identifying both oxidative and non-oxidative intermediates, rapid chemical quench followed by NMR detection of several intermediates which are stable under acidic conditions, solid-state NMR and circular dichroism detection of the states of ionization and tautomerization of the 4'-aminopyrimidine moiety of ThDP in some of the intermediates. These methods also enabled in some cases determination of the rate-limiting step in the complex series of steps. This review is an update of a review with the same title published by the authors in 2005 in this Journal. Much progress has been made in the intervening decade in the identification of the intermediates and their application to gain additional mechanistic insight.

  11. Covalent assembly of a soluble T cell receptor-peptide-major histocompatibility class I complex.

    PubMed Central

    Grégoire, C; Lin, S Y; Mazza, G; Rebai, N; Luescher, I F; Malissen, B

    1996-01-01

    We used stepwise photochemical cross-linking for specifically assembling soluble and covalent complexes made of a T-cell antigen receptor (TCR) and a class I molecule of the major histocompatibility complex (MHC) bound to an antigenic peptide. For that purpose, we have produced in myeloma cells a single-chain Fv construct of a TCR specific for a photoreactive H-2Kd-peptide complex. Photochemical cross-linking of this TCR single-chain Fv with a soluble form of the photoreactive H-2Kd-peptide ligand resulted in the formation of a ternary covalent complex. We have characterized the soluble ternary complex and showed that it reacted with antibodies specific for epitopes located either on the native TCR or on the Kd molecules. By preventing the fast dissociation kinetics observed with most T cell receptors, this approach provides a means of preparing soluble TCR-peptide-MHC complexes on large-scale levels. Images Fig. 3 Fig. 4 PMID:8692966

  12. Covalent modification of mushroom tyrosinase with different amphiphic polymers for pharmaceutical and biocatalysis applications

    SciTech Connect

    Morpurgo, M.; Schiavon, O.; Caliceti, P.

    1996-01-01

    Two different poly(ethylene glycol) derivatives (linear, mol wt 5000 and a branched form, mol wt 10000) and a new polymer (poly-[acryloylmorfoline], mol wt 5500) were covalently bound to the enzyme tyrosinase. The polymer-protein conjugates were studied with a view to their potential pharmaceutical application and to their use for the bioconversion of phenolic substrates in organic solvents. V{sub max} and K{sub m} for the dopa-dopaquinone conversion, thermostability, stability toward inactivation by dopa oxidation products, half-life in blood circulation, and behavior in organic solvents for the different adducts were investigated. Arrhenius plots for the dopa-dopaquinone conversion were also obtained in order to study the effects of temperature on the different enzyme forms. Covalent attachment of the polymers increased enzyme stability in aqueous solution and the solubility in organic solvents. However, organic solvent solubilization brought about loss of enzyme conformation as assessed by CD measurements, which is accompanied by a nonreversible loss of catalytic activity. 30 refs., 4 figs., 4 tabs.

  13. Covalent linkage of nanodiamond-paclitaxel for drug delivery and cancer therapy

    NASA Astrophysics Data System (ADS)

    Liu, Kuang-Kai; Zheng, Wen-Wei; Wang, Chi-Ching; Chiu, Yu-Chung; Cheng, Chia-Liang; Lo, Yu-Shiu; Chen, Chinpiao; Chao, Jui-I.

    2010-08-01

    A nanoparticle-conjugated cancer drug provides a novel strategy for cancer therapy. In this study, we manipulated nanodiamond (ND), a carbon nanomaterial, to covalently link paclitaxel for cancer drug delivery and therapy. Paclitaxel was bound to the surface of 3-5 nm sized ND through a succession of chemical modifications. The ND-paclitaxel conjugation was measured by atomic force microscope and nuclear magnetic resonance spectroscopy, and confirmed with infrared spectroscopy by the detection of deuterated paclitaxel. Treatment with 0.1-50 µg ml - 1 ND-paclitaxel for 48 h significantly reduced the cell viability in the A549 human lung carcinoma cells. ND-paclitaxel induced both mitotic arrest and apoptosis in A549 cells. However, ND alone or denatured ND-paclitaxel (after treatment with strong alkaline solution, 1 M NaOH) did not induce the damage effects on A549 cells. ND-paclitaxel was taken into lung cancer cells in a concentration-dependent manner using flow cytometer analysis. The ND-paclitaxel particles were located in the microtubules and cytoplasm of A549 cells observed by confocal microscopy. Furthermore, ND-paclitaxel markedly blocked the tumor growth and formation of lung cancer cells in xenograft SCID mice. Together, we provide a functional covalent conjugation of ND-paclitaxel, which can be delivered into lung carcinoma cells and preserves the anticancer activities on the induction of mitotic blockage, apoptosis and anti-tumorigenesis.

  14. Tendon chitosan tubes covalently coupled with synthesized laminin peptides facilitate nerve regeneration in vivo.

    PubMed

    Suzuki, Masumi; Itoh, Soichiro; Yamaguchi, Isamu; Takakuda, Kazuo; Kobayashi, Hisatoshi; Shinomiya, Kenichi; Tanaka, Junzo

    2003-06-01

    We have developed tendon chitosan tubes having the ability to bind peptides covalently, and the effectiveness of laminin peptides coupled to these tubular wall on nerve regeneration was examined in vivo. Bridge graft implantation (15 mm) into the sciatic nerve of SD rats was carried out using chitosan tubes having a triangular cross section containing either covalently bound intact laminin or the laminin peptides CDPGYIGSR or CSRARKQAASIKVAVSAD or being nontreated (N = 20 in each group). As a control, isografting (N = 5) was carried out. Three rats in each experimental group were sacrificed for histology observations after 1, 2, 4, 6, and 8 weeks. The total area of regenerating tissue in the tube and the length of the area where regenerating tissue attached to the inner surface of the tube were measured. In five rats from each experimental and control group, the latency quotient between the implanted and the nontreated site was determined 12 weeks after implantation. Furthermore, the percentage of myelinated axon area was measured at a 10-mm distance from the distal anastomosed site. Histological findings suggest that the immobilized laminin, confirmed by immunostaining as long as 12 weeks postoperatively, as well as laminin oligopeptides may effectively assist nerve tissue extension. According to statistical analysis of the percentage neural tissue found in relation to evoked action potentials, the sequential treatments with YIGSR first followed by IKVAV matched the effectiveness of intact laminin in enhancing nerve regeneration. However, when compared with that after isografting, the enhancement of regenerated axon growth was less sufficient.

  15. Covalent Immobilization of Bacillus licheniformis γ-Glutamyl Transpeptidase on Aldehyde-Functionalized Magnetic Nanoparticles

    PubMed Central

    Chen, Yi-Yu; Tsai, Ming-Gen; Chi, Meng-Chun; Wang, Tzu-Fan; Lin, Long-Liu

    2013-01-01

    This work presents the synthesis and use of surface-modified iron oxide nanoparticles for the covalent immobilization of Bacillus licheniformis γ-glutamyl transpeptidase (BlGGT). Magnetic nanoparticles were prepared by an alkaline solution of divalent and trivalent iron ions, and they were subsequently treated with 3-aminopropyltriethoxysilane (APES) to obtain the aminosilane-coated nanoparticles. The functional group on the particle surface and the amino group of BlGGT was then cross-linked using glutaraldehyde as the coupling reagent. The loading capacity of the prepared nanoparticles for BlGGT was 34.2 mg/g support, corresponding to 52.4% recovery of the initial activity. Monographs of transmission electron microscopy revealed that the synthesized nanoparticles had a mean diameter of 15.1 ± 3.7 nm, and the covalent cross-linking of the enzyme did not significantly change their particle size. Fourier transform infrared spectroscopy confirmed the immobilization of BlGGT on the magnetic nanoparticles. The chemical and kinetic behaviors of immobilized BlGGT are mostly consistent with those of the free enzyme. The immobilized enzyme could be recycled ten times with 36.2% retention of the initial activity and had a comparable stability respective to free enzyme during the storage period of 30 days. Collectively, the straightforward synthesis of aldehyde-functionalized nanoparticles and the efficiency of enzyme immobilization offer wide perspectives for the practical use of surface-bound BlGGT. PMID:23443161

  16. Direct detection and kinetic analysis of covalent intermediate formation in the 4-amino-4-deoxychorismate synthase catalyzed reaction.

    PubMed

    He, Ze; Toney, Michael D

    2006-04-18

    Chorismate-utilizing enzymes catalyze diverse reactions, providing critical physiological functions unique to plants, bacteria, fungi, and some parasites. Their absence in animals makes them excellent targets for antimicrobials and herbicides. 4-Amino-4-deoxychorismate synthase (ADCS) catalyzes the first step in folate biosynthsis and shares a common core mechanism with isochorismate synthase (IS) and anthranilate synthase (AS), in which nucleophile addition at C2 initiates these reactions. Evidence was presented previously [He, Z., Stigers Lavoie, K. D., Bartlett, P. A., and Toney, M. D. (2004) J. Am. Chem. Soc. 126, 2378-2385] that K274 is the nucleophile in ADCS, implying formation of a covalent intermediate. Herein, we report the direct detection of this covalent intermediate formed in ADCS-catalyzed reactions by ESI-MS. Difference spectra show the covalent intermediate has an absorption maximum at 310 nm. This was used to study the pre-steady-state kinetics of covalent intermediate formation under various conditions. Additionally, E258 in ADCS was shown to be critical to formation of the covalent intermediate by acting as a general acid catalyst for loss of the C4 hydroxyl group. The E258A/D mutants both exhibit very low activity. Acetate is a poor chemical rescue agent for E258D but an excellent one for E258A, with a 20000-fold and 3000-fold rate increase for Gln-dependent and NH(4)(+)-dependent activities, respectively. Lastly, A213 in IS (structurally homologous to K274 in ADCS) was changed to lysine in an attempt to convert IS to an ADCS-like enzyme. HPLC studies support the formation of a covalent intermediate with this mutant. PMID:16605270

  17. Cadaverine covalently linked to peptidoglycan is required for interaction between the peptidoglycan and the periplasm-exposed S-layer-homologous domain of major outer membrane protein Mep45 in Selenomonas ruminantium.

    PubMed

    Kojima, Seiji; Ko, Kyong-Cheol; Takatsuka, Yumiko; Abe, Naoki; Kaneko, Jun; Itoh, Yoshifumi; Kamio, Yoshiyuki

    2010-11-01

    The peptidoglycan of Selenomonas ruminantium is covalently bound to cadaverine (PG-cadaverine), which likely plays a significant role in maintaining the integrity of the cell surface structure. The outer membrane of this bacterium contains a 45-kDa major protein (Mep45) that is a putative peptidoglycan-associated protein. In this report, we determined the nucleotide sequence of the mep45 gene and investigated the relationship between PG-cadaverine, Mep45, and the cell surface structure. Amino acid sequence analysis showed that Mep45 is comprised of an N-terminal S-layer-homologous (SLH) domain followed by α-helical coiled-coil region and a C-terminal β-strand-rich region. The N-terminal SLH domain was found to be protruding into the periplasmic space and was responsible for binding to peptidoglycan. It was determined that Mep45 binds to the peptidoglycan in a manner dependent on the presence of PG-cadaverine. Electron microscopy revealed that defective PG-cadaverine decreased the structural interactions between peptidoglycan and the outer membrane, consistent with the proposed role for PG-cadaverine. The C-terminal β-strand-rich region of Mep45 was predicted to be a membrane-bound unit of the 14-stranded β-barrel structure. Here we propose that PG-cadaverine possesses functional importance to facilitate the structural linkage between peptidoglycan and the outer membrane via specific interaction with the SLH domain of Mep45.

  18. Micelle-bound structures and dynamics of the hinge deleted analog of melittin and its diastereomer: implications in cell selective lysis by D-amino acid containing antimicrobial peptides.

    PubMed

    Saravanan, Rathi; Bhunia, Anirban; Bhattacharjya, Surajit

    2010-02-01

    Melittin, the major component of the honey bee venom, is a 26-residue hemolytic and membrane active peptide. Structures of melittin determined either in lipid environments by NMR or by use of X-ray demonstrated two helical regions at the N- and C-termini connected by a hinge or a bend at the middle. Here, we show that deletion of the hinge residues along with two C-terminal terminal Gln residues (Q25 and Q26), yielding a peptide analog of 19-residue or Mel-H, did not affect antibacterial activity but resulted in a somewhat reduced hemolytic activity. A diastereomer of Mel-H or Mel-(d)H containing d-amino acids [(d)V5, (d)V8, (d)L11 and (d)K16] showed further reduction in hemolytic activity without lowering antibacterial activity. We have carried out NMR structures, dynamics (H-D exchange and proton relaxation), membrane localization by spin labeled lipids, pulse-field-gradient (PFG) NMR and isothermal titration calorimetry (ITC) in dodecylphosphocholine (DPC) micelles, as a mimic to eukaryotic membrane, to gain insights into cell selectivity of these melittin analogs. PFG-NMR showed Mel-H and Mel-(d)H both were similarly partitioned into DPC micelles. ITC demonstrated that Mel-H and Mel-(d)H interact with DPC with similar affinity. The micelle-bound structure of Mel-H delineated a straight helical conformation, whereas Mel-(d)H showed multiple beta-turns at the N-terminus and a short helix at the C-terminus. The backbone amide-proton exchange with solvent D(2)O demonstrated a large difference in dynamics between Mel-H and Mel-(d)H, whereby almost all backbone protons of Mel-(d)H showed a much faster rate of exchange as compared to Mel-H. Proton T(1) relaxation had suggested a mobile backbone of Mel-(d)H peptide in DPC micelles. Resonance perturbation by paramagnetic lipids indicated that Mel-H inserted deeper into DPC micelles, whereas Mel-(d)H is largely located at the surface of the micelle. Taken together, results presented in this study demonstrated that the

  19. Synthesis and characterization of covalently immobilized bis-crown ether based potassium ionophore.

    PubMed

    Bereczki, Róbert; Gyurcsányi, Róbert E; Agai, Béla; Tóth, Klára

    2005-01-01

    The synthesis of a novel covalently immobilized crown ether based potassium ionophore is presented. Apart from previously proposed methods for the preparation of PVC linked ionophores based on the chemical modification of functionalized PVC polymers, the hereby proposed procedure involves the direct copolymerization of a suitable derivative of the bis-crown ether type potassium ionophore (BME 44) and vinyl chloride monomer. The analytical performance of the potentiometric ion selective electrodes incorporating the PVC bound ionophore were optimized and determined. Compared with electrodes based on other bis-crown ether type immobilized potassium selective ionophores a slightly improved logK(K, Na)(Pot) and a longer lifetime was found. Spectral imaging and chronoamperometry were used to study the mobility of different bis-crown ether derivatives in plasticized PVC membranes.

  20. Computational, electrochemical, and spectroscopic, studies of acetycholinesterase covalently attached to carbon nanotubes.

    PubMed

    Cabral, Murilo F; Barrios, Joseph D; Kataoka, Erica M; Machado, Sergio A S; Carrilho, Emanuel; Garcia, Carlos D; Ayon, Arturo A

    2013-03-01

    This manuscript describes results related to the characterization of electrodes modified with a composite of acetylcholinesterase covalently bound to carbon nanotubes (CNT). The characterization was performed by computational methods and complemented by cyclic voltammetry, infrared spectroscopy, and electrochemical impedance spectroscopy. In-silico simulations enabled the identification of the binding site and the calculation of the interaction energy. Besides complementing the computational studies, experimental results obtained by cyclic voltammetry showed that the addition of CNT to the surface of electrodes yielded significant increases in effective area and greatly facilitated the electron transfer reactions. These results are also in agreement with impedance spectroscopy data, which indicated a high apparent rate constant, even after the immobilization of the enzyme. These results lend new information about the physical and chemical properties of biointerfaces at the molecular level, specifically about the mechanism and consequences of the interaction of a model enzyme with CNT. PMID:23274156

  1. Crystalline fibres of a covalent organic framework through bottom-up microfluidic synthesis.

    PubMed

    Rodríguez-San-Miguel, David; Abrishamkar, Afshin; Navarro, Jorge A R; Rodriguez-Trujillo, Romen; Amabilino, David B; Mas-Ballesté, Ruben; Zamora, Félix; Puigmartí-Luis, Josep

    2016-07-28

    A microfluidic chip has been used to prepare fibres of a porous polymer with high structural order, setting a precedent for the generation of a wide variety of materials using this reagent mixing approach that provides unique materials not accessible easily through bulk processes. The reaction between 1,3,5-tris(4-aminophenyl)benzene and 1,3,5-benzenetricarbaldehyde in acetic acid under continuous microfluidic flow conditions leads to the formation of a highly crystalline and porous covalent organic framework (hereafter denoted as MF-COF-1), consisting of fibrillar micro-structures, which have mechanical stability that allows for direct drawing of objects on a surface.

  2. Universal bounds on current fluctuations

    NASA Astrophysics Data System (ADS)

    Pietzonka, Patrick; Barato, Andre C.; Seifert, Udo

    2016-05-01

    For current fluctuations in nonequilibrium steady states of Markovian processes, we derive four different universal bounds valid beyond the Gaussian regime. Different variants of these bounds apply to either the entropy change or any individual current, e.g., the rate of substrate consumption in a chemical reaction or the electron current in an electronic device. The bounds vary with respect to their degree of universality and tightness. A universal parabolic bound on the generating function of an arbitrary current depends solely on the average entropy production. A second, stronger bound requires knowledge both of the thermodynamic forces that drive the system and of the topology of the network of states. These two bounds are conjectures based on extensive numerics. An exponential bound that depends only on the average entropy production and the average number of transitions per time is rigorously proved. This bound has no obvious relation to the parabolic bound but it is typically tighter further away from equilibrium. An asymptotic bound that depends on the specific transition rates and becomes tight for large fluctuations is also derived. This bound allows for the prediction of the asymptotic growth of the generating function. Even though our results are restricted to networks with a finite number of states, we show that the parabolic bound is also valid for three paradigmatic examples of driven diffusive systems for which the generating function can be calculated using the additivity principle. Our bounds provide a general class of constraints for nonequilibrium systems.

  3. Enzyme directed formation of un-natural side-chains for covalent surface attachment of proteins.

    PubMed

    Cho, Hwayoung; Jaworski, Justyn

    2014-10-01

    The covalent immobilization of proteins onto surfaces is an essential aspect of several fields of research, including proteomics, sensing, heterogeneous biocatalysis, and more broadly biotechnology. Site-specific, covalent attachment of proteins has been achieved in recent years by the use of expanded genetic codes to produce proteins with controlled placement of un-natural amino acids bearing bio-orthogonal functional groups. Unfortunately, the complexity of developing such systems is impractical for most laboratories; hence, a less complicated approach to generating un-natural amino acid side-chains has been employed. Utilizing a straightforward reaction with formylglycine generating enzyme, we use the site-specific modification of engineered proteins to yield un-natural amino acid side-chains for protein immobilization. Using this approach, we demonstrate the controlled immobilization of various enzymes onto a variety of amine coated surfaces. Our results reveal reusability of the immobilized enzymes via this strategy, and furthermore, we find the activity of the immobilized enzymes to remain even after a month of use indicating significant stability of the linkage.

  4. Bound anionic states of adenine

    SciTech Connect

    Haranczyk, Maciej; Gutowski, Maciej S; Li, Xiang; Bowen, Kit H

    2007-03-20

    Anionic states of nucleic acid bases are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases, are thought to be adiabatically unbound. Contrary to this expectation, we have demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the new-found anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The discovery of these valence anionic states of adenine was facilitated by the development of: (i) a new experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (ii) a new combinatorial/ quantum chemical approach for identification of the most stable tautomers of organic molecules. The computational portion of this work was supported by the: (i) Polish State Committee for Scientific Research (KBN) Grants: DS/8000-4-0140-7 (M.G.) and N204 127 31/2963 (M.H.), (ii) European Social Funds (EFS) ZPORR/2.22/II/2.6/ARP/U/2/05 (M.H.), and (iii) US DOE Office of Biological and Environmental Research, Low Dose Radiation Research Program (M.G.). M.H. holds the Foundation for Polish Science (FNP) award for young scientists. The calculations were performed at the Academic

  5. Synthesis and anti-cancer activity of covalent conjugates of artemisinin and a transferrin-receptor targeting peptide.

    PubMed

    Oh, Steve; Kim, Byung Ju; Singh, Narendra P; Lai, Henry; Sasaki, Tomikazu

    2009-02-01

    Artemisinin, a natural product isolated from Artemisia annua L., shows a unique anti-cancer activity by an iron dependent mechanism. Artemisinin was covalently conjugated to a transferrin-receptor targeting peptide, HAIYPRH that binds to a cavity on the surface of transferrin receptor. This enables artemisinin to be co-internalized with receptor-bound transferrin. The iron released from transferrin can activate artemisinin to generate toxic radical species to kill cells. The artemisinin-peptide conjugates showed potent anti-cancer activity against Molt-4 leukemia cells with a significantly improved cancer/normal cells selectivity. PMID:18838215

  6. Blog life: Entropy Bound

    NASA Astrophysics Data System (ADS)

    Steinberg, Peter

    2008-06-01

    Who is the blog written by? Peter Steinberg is a nuclear physicist at the Brookhaven National Laboratory in New York, US. He is acting project manager of the PHOBOS experiment, which used Brookhaven's Relativistic Heavy Ion Collider (RHIC) to search for unusual events produced during collisions between gold nuclei. He is also involved with the PHENIX experiment, which seeks to discover a new state of matter known as the quark-gluon plasma. In addition to his own blog Entropy Bound, Steinberg is currently blogging on a website that was set up last year to publicize the involvement of US scientists with the Large Hadron Collider (LHC) at CERN.

  7. A bound on chaos

    NASA Astrophysics Data System (ADS)

    Maldacena, Juan; Shenker, Stephen H.; Stanford, Douglas

    2016-08-01

    We conjecture a sharp bound on the rate of growth of chaos in thermal quantum systems with a large number of degrees of freedom. Chaos can be diagnosed using an out-of-time-order correlation function closely related to the commutator of operators separated in time. We conjecture that the influence of chaos on this correlator can develop no faster than exponentially, with Lyapunov exponent λ L ≤ 2π k B T/ℏ. We give a precise mathematical argument, based on plausible physical assumptions, establishing this conjecture.

  8. Subunit Movements in Single Membrane-bound H+-ATP Synthases from Chloroplasts during ATP Synthesis

    PubMed Central

    Bienert, Roland; Rombach-Riegraf, Verena; Diez, Manuel; Gräber, Peter

    2009-01-01

    Subunit movements within the H+-ATP synthase from chloroplasts (CF0F1) are investigated during ATP synthesis. The γ-subunit (γCys-322) is covalently labeled with a fluorescence donor (ATTO532). A fluorescence acceptor (adenosine 5′-(β,γ-imino)triphosphate (AMPPNP)-ATTO665) is noncovalently bound to a noncatalytic site at one α-subunit. The labeled CF0F1 is integrated into liposomes, and a transmembrane pH difference is generated by an acid base transition. Single-pair fluorescence resonance energy transfer is measured in freely diffusing proteoliposomes with a confocal two-channel microscope. The fluorescence time traces reveal a repetitive three-step rotation of the γ-subunit relative to the α-subunit during ATP synthesis. Some traces show splitting into sublevels with fluctuations between the sublevels. During catalysis the central stalk interacts, with equal probability, with each αβ-pair. Without catalysis the central stalk interacts with only one specific αβ-pair, and no stepping between FRET levels is observed. Two inactive states of the enzyme are identified: one in the presence of AMPPNP and one in the presence of ADP. PMID:19864418

  9. Subunit movements in single membrane-bound H+-ATP synthases from chloroplasts during ATP synthesis.

    PubMed

    Bienert, Roland; Rombach-Riegraf, Verena; Diez, Manuel; Gräber, Peter

    2009-12-25

    Subunit movements within the H(+)-ATP synthase from chloroplasts (CF(0)F(1)) are investigated during ATP synthesis. The gamma-subunit (gammaCys-322) is covalently labeled with a fluorescence donor (ATTO532). A fluorescence acceptor (adenosine 5'-(beta,gamma-imino)triphosphate (AMPPNP)-ATTO665) is noncovalently bound to a noncatalytic site at one alpha-subunit. The labeled CF(0)F(1) is integrated into liposomes, and a transmembrane pH difference is generated by an acid base transition. Single-pair fluorescence resonance energy transfer is measured in freely diffusing proteoliposomes with a confocal two-channel microscope. The fluorescence time traces reveal a repetitive three-step rotation of the gamma-subunit relative to the alpha-subunit during ATP synthesis. Some traces show splitting into sublevels with fluctuations between the sublevels. During catalysis the central stalk interacts, with equal probability, with each alphabeta-pair. Without catalysis the central stalk interacts with only one specific alphabeta-pair, and no stepping between FRET levels is observed. Two inactive states of the enzyme are identified: one in the presence of AMPPNP and one in the presence of ADP.

  10. Nevirapine bioactivation and covalent binding in the skin.

    PubMed

    Sharma, Amy M; Klarskov, Klaus; Uetrecht, Jack

    2013-03-18

    Nevirapine (NVP) treatment is associated with serious skin rashes that appear to be immune-mediated. We previously developed a rat model of this skin rash that is immune-mediated and is very similar to the rash in humans. Treatment of rats with the major NVP metabolite, 12-OH-NVP, also caused the rash. Most idiosyncratic drug reactions are caused by reactive metabolites; 12-OH-NVP forms a benzylic sulfate, which was detected in the blood of animals treated with NVP or 12-OH-NVP. This sulfate is presumably formed in the liver; however, the skin also has significant sulfotransferase activity. In this study, we used a serum against NVP to detect covalent binding in the skin of rats. There was a large artifact band in immunoblots of whole skin homogenates that interfered with detection of covalent binding; however, when the skin was separated into dermal and epidermal fractions, covalent binding was clearly present in the epidermis, which is also the location of sulfotransferases. In contrast to rats, treatment of mice with NVP did not result in covalent binding in the skin or skin rash. Although the reaction of 12-OH-NVP sulfate with nucleophiles such as glutathione is slow, incubation of this sulfate with homogenized human and rat skin led to extensive covalent binding. Incubations of 12-OH-NVP with the soluble fraction from a 9,000g centrifugation (S9) of rat or human skin homogenate in the presence of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) produced extensive covalent binding, but no covalent binding was detected with mouse skin S9, which suggests that the reason mice do not develop a rash is that they lack the required sulfotransferase. This is the first study to report covalent binding of NVP to rat and human skin. These data provide strong evidence that covalent binding of NVP in the skin is due to 12-OH-NVP sulfate, which is likely responsible for NVP-induced skin rash. Sulfation may represent a bioactivation pathway for other drugs that cause a skin rash

  11. Covalent attachment of lactase to low-density polyethylene films.

    PubMed

    Goddard, J M; Talbert, J N; Hotchkiss, J H

    2007-01-01

    Polymer films to which bioactive compounds such as enzymes are covalently attached offer potential for in-package processing of food. Beta-galactosidase (lactase) was covalently attached to surface-functionalized low-density polyethylene films. A two-step wet chemical functionalization introduced 15.7 nmol/cm2 primary amines to the film surface. Contact angle, dye assays, X-ray photoelectron spectroscopy, and appropriate protein assays were used to characterize changes in film surface chemistry after each step in the process of attachment. Glutaraldehyde was used to covalently attach lactase to the surface at a density of 6.0 microg protein per cm2 via reductive amination. The bond between the covalently attached lactase and the functionalized polyethylene withstood heat treatment in the presence of an ionic denaturant with 74% enzyme retention, suggesting that migration of the enzyme into the food product would be unlikely. The resulting polyethylene had an enzyme activity of 0.020 lactase units (LU)/cm2 (approximately 4500 LU/g). These data suggest that enzymes that may have applications in foods can be covalently attached to inert polymer surfaces, retain significant activity, and thus have potential as a nonmigratory active packaging materials.

  12. Evidence for specific and non-covalent binding of lipids to natural and recombinant Mycobacterium bovis BCG hsp60 proteins, and to the Escherichia coli homologue GroEL.

    PubMed

    De Bruyn, J; Soetaert, K; Buyssens, P; Calonne, I; De Coene, J L; Gallet, X; Brasseur, R; Wattiez, R; Falmagne, P; Montrozier, H; Lanéelle, M A; Daffé, M

    2000-07-01

    Heat-shock proteins (Hsps) from various origins are known to share a conserved structure and are assumed to be key partners in the biogenesis of proteins. Fractionation of the mycobacterial Hsp60, a 65 kDa protein also called Cpn60, from Mycobacterium bovis BCG zinc-deficient culture filtrate on phenyl-Sepharose followed by Western blotting revealed the existence of four Hsp60-1 and Hsp60-2 forms, based on their hydrophobicity behaviour. Hsp60-2 species were further purified by ion-exchange chromatography and partial amino acid sequences of cyanogen bromide (CNBr) peptides of purified Hsp60-2 species showed identity with the amino acid sequence deduced from the hsp60-2 gene, indicating that the various Hsp60-2 forms are encoded by the same gene. In addition, the mycobacterial Hsp60-2 was overexpressed in E. coli using the pRR3Hsp60-2 plasmid and analysed on phenyl-Sepharose. The elution pattern of the recombinant Hsp60-2, as well as that of Escherichia coli GroEL, was similar to that of the native Hsp60-2 from the culture filtrate of M. bovis BCG and entirely different from that of the mycobacterial antigen 85. Extraction of mycobacterial Hsp60-2 forms, recombinant BCG Hsp60-2 and E. coli GroEL with organic solvents releases various amounts of non-covalently bound lipids. The presence of lipids on Hsp60-2 was confirmed by labelling M. bovis BCG with radioactive palmitate. The radioactivity was specifically associated with Hsp60 in the aqueous phase and the 19 and 38 kDa lipoproteins in the Triton X-114 phase. Analysis of the lipids extracted from purified Hsp60-2, recombinant BCG Hsp60-2 and E. coli GroEL by TLC showed the same pattern for all the samples. Acid methanolysis of the lipids followed by GC analysis led to the identification of C(16:0), C(18:0) and C(18:1) as the major fatty acyl constituents, and of methylglycoside in these proteins. Altogether, these data demonstrate that lipids are non-covalently bound to Hsp60-2 and homologous proteins. PMID

  13. Increased Protein Structural Resolution from Diethylpyrocarbonate-based Covalent Labeling and Mass Spectrometric Detection

    NASA Astrophysics Data System (ADS)

    Zhou, Yuping; Vachet, Richard W.

    2012-04-01

    Covalent labeling and mass spectrometry are seeing increased use together as a way to obtain insight into the 3-dimensional structure of proteins and protein complexes. Several amino acid specific (e.g., diethylpyrocarbonate) and non-specific (e.g., hydroxyl radicals) labeling reagents are available for this purpose. Diethylpyrocarbonate (DEPC) is a promising labeling reagent because it can potentially probe up to 30% of the residues in the average protein and gives only one reaction product, thereby facilitating mass spectrometric analysis. It was recently reported, though, that DEPC modifications are labile for some amino acids. Here, we show that label loss is more significant and widespread than previously thought, especially for Ser, Thr, Tyr, and His residues, when relatively long protein digestion times are used. Such label loss ultimately decreases the amount of protein structural information that is obtainable with this reagent. We find, however, that the number of DEPC modified residues and, thus, protein structural information, can be significantly increased by decreasing the time between the covalent labeling reaction and the mass spectrometric analysis. This is most effectively accomplished using short (e.g., 2 h) proteolytic digestions with enzymes such as immobilized chymotrypsin or Glu-C rather than using methods (e.g., microwave or ultrasonic irradiation) that accelerate proteolysis in other ways. Using short digestion times, we show that the percentage of solvent accessible residues that can be modified by DEPC increases from 44% to 67% for cytochrome c, 35% to 81% for myoglobin, and 76% to 95% for β-2-microglobulin. In effect, these increased numbers of modified residues improve the protein structural resolution available from this covalent labeling method. Compared with typical overnight digestion conditions, the short digestion times decrease the average distance between modified residues from 11 to 7 Å for myoglobin, 13 to 10 Å for

  14. A Highly-Ordered 3D Covalent Fullerene Framework**

    PubMed Central

    Minar, Norma K; Hou, Kun; Westermeier, Christian; Döblinger, Markus; Schuster, Jörg; Hanusch, Fabian C; Nickel, Bert; Ozin, Geoffrey A; Bein, Thomas

    2015-01-01

    A highly-ordered 3D covalent fullerene framework is presented with a structure based on octahedrally functionalized fullerene building blocks in which every fullerene is separated from the next by six functional groups and whose mesoporosity is controlled by cooperative self-assembly with a liquid-crystalline block copolymer. The new fullerene-framework material was obtained in the form of supported films by spin coating the synthesis solution directly on glass or silicon substrates, followed by a heat treatment. The fullerene building blocks coassemble with a liquid-crystalline block copolymer to produce a highly ordered covalent fullerene framework with orthorhombic Fmmm symmetry, accessible 7.5 nm pores, and high surface area, as revealed by gas adsorption, NMR spectroscopy, small-angle X-ray scattering (SAXS), and TEM. We also note that the 3D covalent fullerene framework exhibits a dielectric constant significantly lower than that of the nonporous precursor material. PMID:25958846

  15. Noncovalent Interaction Energies in Covalent Complexes: TEM-1 beta-Lactamase and beta-Lactams

    SciTech Connect

    Wang, Xiaojun; Minasov, George; Shoichet, Brian K.

    2010-03-08

    The class A {beta}-lactamase TEM-1 is a key bacterial resistance enzyme against {beta}-lactam antibiotics, but little is known about the energetic bases for complementarity between TEM-1 and its inhibitors. Most inhibitors form a covalent adduct with the catalytic Ser70, making the measurement of equilibriumconstants, and hence interaction energies, technically difficult. This study evaluates noncovalent interactions withincovalent complexes by examining the differential stability of TEM-1 and its inhibitor adducts. The thermal denaturation of TEM-1 follows a two-state, reversible model with a melting temperature (T{sub m}) of 51.6 C and a van't Hoff enthalpy of unfolding ({Delta}H{sub VH}) of 146.2 kcal/mol at pH 7.0. The stability of the enzyme changes on forming an inhibitor adduct. As expected, some inhibitors stabilize TEM-1; transition-state analogues increase the T{sub m} by up to 3.7 C(1.7 kcal/mol). Surprisingly, all {beta}-lactam covalent acyl-enzyme complexes tested destabilize TEM-1 significantly relative to the apoenzyme. For instance, the clinically used inhibitor clavulanic acid and the {beta}-lactamase-resistant {beta}-lactams moxalactam and imipenem destabilize TEM-1 by over 2.6 C (1.2 kcal/mol) in their covalent adducts. Based on the structure of the TEM-1/imipenem complex (Maveyraud et al., J Am Chem Soc 1998;120:9748-52), destabilization by moxalactam and imipenem is thought to be caused by a steric clash between the side-chain of Asn132 and the 6(7)-{alpha} group of these {beta}-lactams. To test this hypothesis, the mutant enzyme N132A was made. In contrast with wild-type, the covalent complexes between N132A and both imipenem and moxalactam stabilize the enzyme, consistent with the hypothesis. To investigate the structural bases of this dramatic change instability, the structure of N132A/imipenem was determined by X-ray crystallography. In the complex with N132A, imipenemadopts a very different conformation from that observed in the wild

  16. Photochemistry of triarylmethane dyes bound to proteins

    NASA Astrophysics Data System (ADS)

    Indig, Guilherme L.

    1996-04-01

    Triarylmethanes represent a class of cationic dyes whose potential as photosensitizers for use in photodynamic therapy of neoplastic diseases has never been comprehensively evaluated. Here, the laser-induced photodecomposition of three triarylmethane dyes, crystal violet, ethyl violet, and malachite green, non-covalently bound to bovine serum albumin (a model biological target) was investigated. Upon laser excitation at 532 nm, the bleaching of the corresponding dye-protein molecular complexes follows spectroscopic patterns that suggest the formation of reduced forms of the dyes as major reaction photoproducts. That implies that an electron or hydrogen atom transfer from the protein to the dye's moiety within the guest-host complex is the first step of the photobleaching process. Since the availability of dissolved molecular oxygen was not identified as a limiting factor for the phototransformations to occur, these dyes can be seen as potential phototherapeutic agents for use in hypoxic areas of tumors. These triarylmethane dyes strongly absorb at relatively long wavelengths (absorption maximum around 600 nm; (epsilon) max approximately equals 105 M-1 cm-1), and only minor changes in their absorption characteristics are observed upon binding to the protein. However the binding event leads to a remarkable increase in their fluorescence quantum yield and photoreactivity.

  17. Insoluble-Bound Phenolics in Food.

    PubMed

    Shahidi, Fereidoon; Yeo, Ju-Dong

    2016-01-01

    This contribution provides a review of the topic of insoluble-bound phenolics, especially their localization, synthesis, transfer and formation in plant cells, as well as their metabolism in the human digestive system and corresponding bioactivities. In addition, their release from the food matrix during food processing and extraction methods are discussed. The synthesis of phenolics takes place mainly at the endoplasmic reticulum and they are then transferred to each organ through transport proteins such as the ATP-binding cassette (ABC) and multidrug and toxic compound extrusion (MATE) transporter at the organ's compartment membrane or via transport vesicles such as cytoplasmic and Golgi vesicles, leading to the formation of soluble and insoluble-bound phenolics at the vacuole and cell wall matrix, respectively. This part has not been adequately discussed in the food science literature, especially regarding the synthesis site and their transfer at the cellular level, thus this contribution provides valuable information to the involved scientists. The bound phenolics cannot be absorbed at the small intestine as the soluble phenolics do (5%-10%), thus passing into the large intestine and undergoing fermentation by a number of microorganisms, partially released from cell wall matrix of foods. Bound phenolics such as phenolic acids and flavonoids display strong bioactivities such as anticancer, anti-inflammation and cardiovascular disease ameliorating effects. They can be extracted by several methods such as acid, alkali and enzymatic hydrolysis to quantify their contents in foods. In addition, they can also be released from the cell wall matrix during food processing procedures such as fermentation, germination, roasting, extrusion cooking and boiling. This review provides critical information for better understanding the insoluble-bound phenolics in food and fills an existing gap in the literature. PMID:27626402

  18. Constructing covalent interface in rubber/clay nanocomposite by combining structural modification and interlamellar silylation of montmorillonite.

    PubMed

    Zha, Chao; Wang, Wencai; Lu, Yonglai; Zhang, Liqun

    2014-11-12

    Strong interfacial interaction and nanodispersion are necessary for polymer nanocomposites with expectations on mechanical performance. In this work, montmorillonite (MMT) was first structurally modified by acid treatment to produce more silanol groups on the layer surface. This was followed by chemical modification of γ-methacryloxy propyl trimethoxysilane molecule (KH570) through covalent grafting with the silanol groups. (29)Si and (27)Al magic angle spinning (MAS) NMR results revealed the microstructural changes of MMT after acid treatment and confirmed the increase of silanol groups on acid-treated MMT surfaces. Thermogravimetric analysis indicated an increase in the grafted amount of organosilane on the MMT surface. X-ray diffraction (XRD) showed that the functionalization process changed the highly ordered stacking structure of the MMT mineral into a highly disordered structure, indicating successful grafting of organosilane to the interlayer surface of the crystalline sheets. The styrene-butadiene rubber (SBR)/MMT nanocomposites were further prepared by co-coagulating with SBR latex and grafted-MMT aqueous suspension. During vulcanization, a covalent interface between modified MMT and rubber was established through peroxide-radical-initiated reactions, and layer aggregation was effectively prevented. The SBR/MMT nanocomposites had highly and uniformly dispersed MMT layers, and the covalent interfacial interaction was finally achieved and exhibited high performance. PMID:25322875

  19. Covalent organic frameworks as pH responsive signaling scaffolds.

    PubMed

    Zhang, Yuwei; Shen, Xiaochen; Feng, Xiao; Xia, Hong; Mu, Ying; Liu, Xiaoming

    2016-09-25

    A β-ketoenamine based covalent organic framework, COF-JLU4, was synthesized by condensation of 2,5-dimethoxyterephthalohydrazide with triformylphloroglucinol under solvothermal conditions. This COF has strong crystallinity, good porosity, photoluminescence properties and wettability for water. It can serve as the first COF-based fluorescent pH sensor in aqueous solutions. PMID:27545686

  20. Fluoroquinolones as potential photochemotherapeutic agents: covalent addition to guanosine monophosphate.

    PubMed

    Fasani, Elisa; Manet, Ilse; Capobianco, Massimo L; Monti, Sandra; Pretali, Luca; Albini, Angelo

    2010-08-21

    The triplet aryl cation photochemically generated from fluoroquinolones bearing a fluoro atom at position 8 attacks guanosine monophosphate (k(r) > 10(9) M(-1)s(-1)) and forms covalent adducts. The reaction is a model for the implementation of oxygen-independent photochemotherapy. PMID:20571620

  1. Repeatable mechanochemical activation of dynamic covalent bonds in thermoplastic elastomers.

    PubMed

    Imato, Keiichi; Kanehara, Takeshi; Nojima, Shiki; Ohishi, Tomoyuki; Higaki, Yuji; Takahara, Atsushi; Otsuka, Hideyuki

    2016-08-18

    Repeated mechanical scission and recombination of dynamic covalent bonds incorporated in segmented polyurethane elastomers are demonstrated by utilizing a diarylbibenzofuranone-based mechanophore and by the design of the segmented polymer structures. The repeated mechanochemical reactions can accompany clear colouration and simultaneous fading.

  2. Valence, Covalence, Hypervalence, Oxidation State, and Coordination Number

    ERIC Educational Resources Information Center

    Smith, Derek W.

    2005-01-01

    Valence as a numerical measure of an atom's combining power, expressed by the number of bonds it forms in a molecular formulation of the compound in question, was unable to cope with coordination compounds. The covalence of an atom is the nearest model equivalent, but is subject to ambiguity since it often depends on which bonding model is being…

  3. Repeatable mechanochemical activation of dynamic covalent bonds in thermoplastic elastomers.

    PubMed

    Imato, Keiichi; Kanehara, Takeshi; Nojima, Shiki; Ohishi, Tomoyuki; Higaki, Yuji; Takahara, Atsushi; Otsuka, Hideyuki

    2016-08-18

    Repeated mechanical scission and recombination of dynamic covalent bonds incorporated in segmented polyurethane elastomers are demonstrated by utilizing a diarylbibenzofuranone-based mechanophore and by the design of the segmented polymer structures. The repeated mechanochemical reactions can accompany clear colouration and simultaneous fading. PMID:27424868

  4. In vitro degradation of covalently cross-linked arabinoxylan hydrogels by bifidobacteria.

    PubMed

    Martínez-López, Ana L; Carvajal-Millan, Elizabeth; Micard, Valérie; Rascón-Chu, Agustín; Brown-Bojorquez, Francisco; Sotelo-Cruz, Norberto; López-Franco, Yolanda L; Lizardi-Mendoza, Jaime

    2016-06-25

    Arabinoxylan gels with different cross-linking densities, swelling ratios, and rheological properties were obtained by increasing the concentration of arabinoxylan from 4 to 6% (w/v) during oxidative gelation by laccase. The degradation of these covalently cross-linked gels by a mixture of two Bifidobacterium strains (Bifidobacterium longum and Bifidobacterium adolescentis) was investigated. The kinetics of the evolution of structural morphology of the arabinoxylan gel, the carbohydrate utilization profiles and the bacterial production of short-acid fatty acid (SCFA) were measured. Scanning electron microscopy analysis of the degraded gels showed multiple cavity structures resulting from the bacterial action. The total SCFA decreased when the degree of cross-linking increased in the gels. A slower fermentation of arabinoxylan chains was obtained for arabinoxylan gels with more dense network structures. These results suggest that the differences in the structural features and properties studied in this work affect the degradation time of the arabinoxylan gels. PMID:27083795

  5. Mechanoassisted Synthesis of Sulfonated Covalent Organic Frameworks with High Intrinsic Proton Conductivity.

    PubMed

    Peng, Yongwu; Xu, Guodong; Hu, Zhigang; Cheng, Youdong; Chi, Chenglong; Yuan, Daqiang; Cheng, Hansong; Zhao, Dan

    2016-07-20

    It is challenging to introduce pendent sulfonic acid groups into modularly built crystalline porous frameworks for intrinsic proton conduction. Herein, we report the mechanoassisted synthesis of two sulfonated covalent organic frameworks (COFs) possessing one-dimensional nanoporous channels decorated with pendent sulfonic acid groups. These COFs exhibit high intrinsic proton conductivity as high as 3.96 × 10(-2) S cm(-1) with long-term stability at ambient temperature and 97% relative humidity (RH). In addition, they were blended with nonconductive polyvinylidene fluoride (PVDF) affording a series of mixed-matrix membranes (MMMs) with proton conductivity up to 1.58 × 10(-2) S cm(-1) and low activation energy of 0.21 eV suggesting the Grotthuss mechanism for proton conduction. Our study has demonstrated the high intrinsic proton conductivity of COFs shedding lights on their wide applications in proton exchange membranes.

  6. Mechanoassisted Synthesis of Sulfonated Covalent Organic Frameworks with High Intrinsic Proton Conductivity.

    PubMed

    Peng, Yongwu; Xu, Guodong; Hu, Zhigang; Cheng, Youdong; Chi, Chenglong; Yuan, Daqiang; Cheng, Hansong; Zhao, Dan

    2016-07-20

    It is challenging to introduce pendent sulfonic acid groups into modularly built crystalline porous frameworks for intrinsic proton conduction. Herein, we report the mechanoassisted synthesis of two sulfonated covalent organic frameworks (COFs) possessing one-dimensional nanoporous channels decorated with pendent sulfonic acid groups. These COFs exhibit high intrinsic proton conductivity as high as 3.96 × 10(-2) S cm(-1) with long-term stability at ambient temperature and 97% relative humidity (RH). In addition, they were blended with nonconductive polyvinylidene fluoride (PVDF) affording a series of mixed-matrix membranes (MMMs) with proton conductivity up to 1.58 × 10(-2) S cm(-1) and low activation energy of 0.21 eV suggesting the Grotthuss mechanism for proton conduction. Our study has demonstrated the high intrinsic proton conductivity of COFs shedding lights on their wide applications in proton exchange membranes. PMID:27385672

  7. Silane modified starch for compatible reactive blend with poly(lactic acid).

    PubMed

    Jariyasakoolroj, Piyawanee; Chirachanchai, Suwabun

    2014-06-15

    A reactive blend of poly(lactic acid) (PLA) and a surface modified starch by silane coupling agent to achieve compatibility is proposed. A detailed structural analysis by using (1)H-(1)H TOCSY NMR spectrum clarifies, for the first time, that chloropropyl trimethoxysilane (CPMS) forms covalent bonds with starch during starch modification and consequently forms covalent bonds with PLA in the step of blending to produce a reactive blend of PLA and CP-starch. The CP-starch covalently bound with PLA provides the compatibility between PLA and starch and also plays the role as nucleating agent as identified from a significant increase of degree of crystallinity (as high as 10-15 times), as well as induces chain mobility, as identified from a slight decrease in glass transition temperature (∼5-10°C). The PLA/CP-starch film performed as well as neat PLA with slight increases in tensile strength and elongation at break, as compared to other PLA/silane modified starch films. PMID:24721076

  8. Silane modified starch for compatible reactive blend with poly(lactic acid).

    PubMed

    Jariyasakoolroj, Piyawanee; Chirachanchai, Suwabun

    2014-06-15

    A reactive blend of poly(lactic acid) (PLA) and a surface modified starch by silane coupling agent to achieve compatibility is proposed. A detailed structural analysis by using (1)H-(1)H TOCSY NMR spectrum clarifies, for the first time, that chloropropyl trimethoxysilane (CPMS) forms covalent bonds with starch during starch modification and consequently forms covalent bonds with PLA in the step of blending to produce a reactive blend of PLA and CP-starch. The CP-starch covalently bound with PLA provides the compatibility between PLA and starch and also plays the role as nucleating agent as identified from a significant increase of degree of crystallinity (as high as 10-15 times), as well as induces chain mobility, as identified from a slight decrease in glass transition temperature (∼5-10°C). The PLA/CP-starch film performed as well as neat PLA with slight increases in tensile strength and elongation at break, as compared to other PLA/silane modified starch films.

  9. NCIPLOT: a program for plotting non-covalent interaction regions

    PubMed Central

    Contreras-García, Julia; Johnson, Erin R.; Keinan, Shahar; Chaudret, Robin; Piquemal, Jean-Philip; Beratan, David N.; Yang, Weitao

    2011-01-01

    Non-covalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these non-covalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define non-covalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their van der Waals radii. We recently developed an alternative perspective, derived from the electronic density: the Non-Covalent Interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of non-covalent interactions is of great potential value. Here, we describe the NCI computational algorithms and their implementation for the analysis and visualization of weak interactions, using both self-consistent fully quantum-mechanical, as well as promolecular, densities. A wide range of options for tuning the range of interactions to be plotted is also presented. To demonstrate the capabilities of our approach, several examples are given from organic, inorganic, solid state, and macromolecular chemistry, including cases where NCI analysis gives insight into unconventional chemical bonding. The NCI code and its manual are available for download at http://www.chem.duke.edu/~yang/software.htm PMID:21516178

  10. Computational studies on non-covalent interactions of carbon and boron fullerenes with graphene.

    PubMed

    Manna, Arun K; Pati, Swapan K

    2013-06-24

    First-principles DFT calculations are carried out to study the changes in structures and electronic properties of two-dimensional single-layer graphene in the presence of non-covalent interactions induced by carbon and boron fullerenes (C60, C70, C80 and B80). Our study shows that larger carbon fullerene interacts more strongly than the smaller fullerene, and boron fullerene interacts more strongly than that of its carbon analogue with the same nuclearity. We find that van der Waals interactions play a major role in governing non-covalent interactions between the adsorbed fullerenes and graphene. Moreover, a greater extent of van der Waals interactions found for the larger fullerenes, C80 and B80, relative to smaller C60, and consequently, results in higher stabilisation. We find a small amount of electron transfer from graphene to fullerene, which gives rise to a hole-doped material. We also find changes in the graphene electronic band structures in the presence of these surface-decorated fullerenes. The Dirac cone picture, such as that found in pristine graphene, is significantly modified due to the re-hybridisation of graphene carbon orbitals with fullerenes orbitals near the Fermi energy. However, all of the composites exhibit perfect conducting behaviour. The simulated absorption spectra for all of the graphene-fullerene hybrids do not exhibit a significant change in the absorption peak positions with respect to the pristine graphene absorption spectrum. Additionally, we find that the hole-transfer integral between graphene and C60 is larger than the electron-transfer integrals and the extent of these transfer integrals can be significantly tuned by graphene edge functionalisation with carboxylic acid groups. Our understanding of the non-covalent functionalisation of graphene with various fullerenes would promote experimentalists to explore these systems, for their possible applications in electronic and opto-electronic devices.

  11. Model of early self-replication based on covalent complementarity for a copolymer of glycerate-3-phosphate and glycerol-3-phosphate

    NASA Technical Reports Server (NTRS)

    Weber, Arthur L.

    1989-01-01

    Glyceraldehyde-3-phosphate acts as the substrate in a model of early self-replication of a phosphodiester copolymer of glycerate-3-phosphate and glycerol-3-phosphate. This model of self-replication is based on covalent complementarity in which information transfer is mediated by a single covalent bond, in contrast to multiple weak interactions that establish complementarity in nucleic acid replication. This replication model is connected to contemporary biochemistry through its use of glyceraldehyde-3-phosphate, a central metabolite of glycolysis and photosynthesis.

  12. COVALENT BINDING OF TRICHLOROETHYLENE TO PROTEINS IN HUMAN AND RAT HEPATOCYTES. (R826409)

    EPA Science Inventory

    The environmental contaminant and occupational solvent trichloroethylene is metabolized to a reactive intermediate that covalently binds to specific hepatic proteins in exposed mice and rats. In order to compare covalent binding between humans and rodents, primary hepatocyte c...

  13. Covalent bonding modulated graphene-metal interfacial thermal transport

    NASA Astrophysics Data System (ADS)

    Jiang, Tao; Zhang, Xueqiang; Vishwanath, Suresh; Mu, Xin; Kanzyuba, Vasily; Sokolov, Denis A.; Ptasinska, Sylwia; Go, David B.; Xing, Huili Grace; Luo, Tengfei

    2016-05-01

    We report the covalent bonding enabled modulation of the interfacial thermal conductance between graphene and metals Cu, Al, and Pt by controlling the oxidation of graphene. By combining comprehensive X-ray photoelectron spectroscopy (XPS) analysis and time-domain thermoreflectance measurements, we quantify the effect of graphene oxidation on interfacial thermal conductance. It was found that thermal conductance increases with the degree of graphene oxidation until a peak value is obtained at an oxygen/carbon atom percentage of ~7.7%. The maximum enhancement in thermal conductance was measured to be 55%, 38%, and 49% for interfaces between oxidized graphene and Cu, Al, and Pt, respectively. In situ XPS measurements show that oxygen covalently binds to Cu and graphene simultaneously, forming a highly efficient bridge to enhance the thermal transport. Our molecular dynamics simulations verify that strong interfacial covalent bonds are the key to the thermal conductance enhancement. This work provides valuable insights into the mechanism of functionalization-induced thermal conductance enhancement and design guidelines for graphene-based devices.We report the covalent bonding enabled modulation of the interfacial thermal conductance between graphene and metals Cu, Al, and Pt by controlling the oxidation of graphene. By combining comprehensive X-ray photoelectron spectroscopy (XPS) analysis and time-domain thermoreflectance measurements, we quantify the effect of graphene oxidation on interfacial thermal conductance. It was found that thermal conductance increases with the degree of graphene oxidation until a peak value is obtained at an oxygen/carbon atom percentage of ~7.7%. The maximum enhancement in thermal conductance was measured to be 55%, 38%, and 49% for interfaces between oxidized graphene and Cu, Al, and Pt, respectively. In situ XPS measurements show that oxygen covalently binds to Cu and graphene simultaneously, forming a highly efficient bridge to enhance

  14. Covalent attachment of functionalized lipid bilayers to planar waveguides for measuring protein binding to biomimetic membranes.

    PubMed Central

    Heyse, S.; Vogel, H.; Sänger, M.; Sigrist, H.

    1995-01-01

    A new method is presented for measuring sensitively the interactions between ligands and their membrane-bound receptors in situ using integrated optics, thus avoiding the need for additional labels. Phospholipid bilayers were attached covalently to waveguides by a novel protocol, which can in principle be used with any glass-like surface. In a first step, phospholipids carrying head-group thiols were covalently immobilized onto SiO2-TiO2 waveguide surfaces. This was accomplished by acylation of aminated waveguides with the heterobifunctional crosslinker N-succinimidyl-3-maleimidopropionate, followed by the formation of thioethers between the surface-grafted maleimides and the synthetic thiolipids. The surface-attached thiolipids served as hydrophobic templates and anchors for the deposition of a complete lipid bilayer either by fusion of lipid vesicles or by lipid self-assembly from mixed lipid/detergent micelles. The step-by-step lipid bilayer formation on the waveguide surface was monitored in situ by an integrated optics technique, allowing the simultaneous determination of optical thickness and one of the two refractive indices of the adsorbed organic layers. Surface coverages of 50-60% were calculated for thiolipid layers. Subsequent deposition of POPC resulted in an overall lipid layer thickness of 45-50 A, which corresponds to the thickness of a fluid bilayer membrane. Specific recognition reactions occurring at cell membrane surfaces were modeled by the incorporation of lipid-anchored receptor molecules into the supported bilayer membranes. (1) The outer POPC layer was doped with biotinylated phosphatidylethanolamine. Subsequent specific binding of streptavidin was optically monitored. (2) A lipopeptide was incorporated in the outer POPC monolayer. Membrane binding of monoclonal antibodies, which were directed against the peptide moiety of the lipopeptide, was optically detected. The specific antibody binding correlated well with the lipopepitde

  15. Ions colliding with clusters of fullerenes—Decay pathways and covalent bond formations

    NASA Astrophysics Data System (ADS)

    Seitz, F.; Zettergren, H.; Rousseau, P.; Wang, Y.; Chen, T.; Gatchell, M.; Alexander, J. D.; Stockett, M. H.; Rangama, J.; Chesnel, J. Y.; Capron, M.; Poully, J. C.; Domaracka, A.; Méry, A.; Maclot, S.; Vizcaino, V.; Schmidt, H. T.; Adoui, L.; Alcamí, M.; Tielens, A. G. G. M.; Martín, F.; Huber, B. A.; Cederquist, H.

    2013-07-01

    We report experimental results for the ionization and fragmentation of weakly bound van der Waals clusters of n C60 molecules following collisions with Ar2 +, He2 +, and Xe20 + at laboratory kinetic energies of 13 keV, 22.5 keV, and 300 keV, respectively. Intact singly charged C60 monomers are the dominant reaction products in all three cases and this is accounted for by means of Monte Carlo calculations of energy transfer processes and a simple Arrhenius-type [C_{60}]_n^+ → C_{60}+ + (n-1)C_{60} evaporation model. Excitation energies in the range of only ˜0.7 eV per C60 molecule in a [C_{60}]_{13}^+ cluster are sufficient for complete evaporation and such low energies correspond to ion trajectories far outside the clusters. Still we observe singly and even doubly charged intact cluster ions which stem from even more distant collisions. For penetrating collisions the clusters become multiply charged and some of the individual molecules may be promptly fragmented in direct knock-out processes leading to efficient formations of new covalent systems. For Ar2 + and He2 + collisions, we observe very efficient C_{119}+ and C_{118}+ formation and molecular dynamics simulations suggest that they are covalent dumb-bell systems due to bonding between C_{59}+ or C_{58}+ and C60 during cluster fragmentation. In the Ar2 + case, it is possible to form even smaller C_{120-2m}+ molecules (m = 2-7), while no molecular fusion reactions are observed for the present Xe20 + collisions.

  16. Ions colliding with clusters of fullerenes-Decay pathways and covalent bond formations

    SciTech Connect

    Seitz, F.; Zettergren, H.; Chen, T.; Gatchell, M.; Alexander, J. D.; Stockett, M. H.; Schmidt, H. T.; Cederquist, H.; Rousseau, P.; Chesnel, J. Y.; Capron, M.; Poully, J. C.; Mery, A.; Maclot, S.; Adoui, L.; Wang, Y.; Martin, F.; Rangama, J.; Domaracka, A.; Vizcaino, V. [CIMAP, UMR 6252, CEA and others

    2013-07-21

    We report experimental results for the ionization and fragmentation of weakly bound van der Waals clusters of n C{sub 60} molecules following collisions with Ar{sup 2+}, He{sup 2+}, and Xe{sup 20+} at laboratory kinetic energies of 13 keV, 22.5 keV, and 300 keV, respectively. Intact singly charged C{sub 60} monomers are the dominant reaction products in all three cases and this is accounted for by means of Monte Carlo calculations of energy transfer processes and a simple Arrhenius-type [C{sub 60}]{sub n}{sup +}{yields}C{sub 60}{sup +}+(n-1)C{sub 60} evaporation model. Excitation energies in the range of only {approx}0.7 eV per C{sub 60} molecule in a [C{sub 60}]{sub 13}{sup +} cluster are sufficient for complete evaporation and such low energies correspond to ion trajectories far outside the clusters. Still we observe singly and even doubly charged intact cluster ions which stem from even more distant collisions. For penetrating collisions the clusters become multiply charged and some of the individual molecules may be promptly fragmented in direct knock-out processes leading to efficient formations of new covalent systems. For Ar{sup 2+} and He{sup 2+} collisions, we observe very efficient C{sub 119}{sup +} and C{sub 118}{sup +} formation and molecular dynamics simulations suggest that they are covalent dumb-bell systems due to bonding between C{sub 59}{sup +} or C{sub 58}{sup +} and C{sub 60} during cluster fragmentation. In the Ar{sup 2+} case, it is possible to form even smaller C{sub 120-2m}{sup +} molecules (m= 2-7), while no molecular fusion reactions are observed for the present Xe{sup 20+} collisions.

  17. Contribution of flavin covalent linkage with histidine 99 to the reaction catalyzed by choline oxidase.

    PubMed

    Quaye, Osbourne; Cowins, Sharonda; Gadda, Giovanni

    2009-06-19

    The FAD-dependent choline oxidase has a flavin cofactor covalently attached to the protein via histidine 99 through an 8alpha-N(3)-histidyl linkage. The enzyme catalyzes the four-electron oxidation of choline to glycine betaine, forming betaine aldehyde as an enzyme-bound intermediate. The variant form of choline oxidase in which the histidine residue has been replaced with asparagine was used to investigate the contribution of the 8alpha-N(3)-histidyl linkage of FAD to the protein toward the reaction catalyzed by the enzyme. Decreases of 10-fold and 30-fold in the k(cat)/K(m) and k(cat) values were observed as compared with wild-type choline oxidase at pH 10 and 25 degrees C, with no significant effect on k(cat)/K(O) using choline as substrate. Both the k(cat)/K(m) and k(cat) values increased with increasing pH to limiting values at high pH consistent with the participation of an unprotonated group in the reductive half-reaction and the overall turnover of the enzyme. The pH independence of both (D)(k(cat)/K(m)) and (D)k(cat), with average values of 9.2 +/- 3.3 and 7.4 +/- 0.5, respectively, is consistent with absence of external forward and reverse commitments to catalysis, and the chemical step of CH bond cleavage being rate-limiting for both the reductive half-reaction and the overall enzyme turnover. The temperature dependence of the (D)k(red) values suggests disruption of the preorganization in the asparagine variant enzyme. Altogether, the data presented in this study are consistent with the FAD-histidyl covalent linkage being important for the optimal positioning of the hydride ion donor and acceptor in the tunneling reaction catalyzed by choline oxidase.

  18. Fractional diffusion on bounded domains

    SciTech Connect

    Defterli, Ozlem; D'Elia, Marta; Du, Qiang; Gunzburger, Max Donald; Lehoucq, Richard B.; Meerschaert, Mark M.

    2015-03-13

    We found that the mathematically correct specification of a fractional differential equation on a bounded domain requires specification of appropriate boundary conditions, or their fractional analogue. In this paper we discuss the application of nonlocal diffusion theory to specify well-posed fractional diffusion equations on bounded domains.

  19. Error Bounds for Interpolative Approximations.

    ERIC Educational Resources Information Center

    Gal-Ezer, J.; Zwas, G.

    1990-01-01

    Elementary error estimation in the approximation of functions by polynomials as a computational assignment, error-bounding functions and error bounds, and the choice of interpolation points are discussed. Precalculus and computer instruction are used on some of the calculations. (KR)

  20. Northwest Outward Bound Instructor's Manual.

    ERIC Educational Resources Information Center

    Northwest Outward Bound School, Portland, OR.

    Instructor responsibilities, procedures for completing activities safely, and instructional methods and techniques are outlined to assist instructors in the Northwest Outward Bound School (Portland, Oregon) as they strive for teaching excellence. Information is organized into six chapters addressing: history and philosophy of Outward Bound; course…

  1. Shear-Thinning Supramolecular Hydrogels with Secondary Autonomous Covalent Crosslinking to Modulate Viscoelastic Properties In Vivo

    PubMed Central

    Rodell, Christopher B.; MacArthur, John W.; Dorsey, Shauna M.; Wade, Ryan J.; Wang, Leo L.; Woo, Y. Joseph

    2015-01-01

    Clinical percutaneous delivery of synthetically engineered hydrogels remains limited due to challenges posed by crosslinking kinetics – too fast leads to delivery failure, too slow limits material retention. To overcome this challenge, we exploit supramolecular assembly to localize hydrogels at the injection site and introduce subsequent covalent crosslinking to control final material properties. Supramolecular gels were designed through the separate pendant modifications of hyaluronic acid (HA) by the guest-host pair cyclodextrin and adamantane, enabling shear-thinning injection and high target site retention (>98%). Secondary covalent crosslinking occurred via addition of thiols and Michael-acceptors (i.e., methacrylates, acrylates, vinyl sulfones) on HA and increased hydrogel moduli (E=25.0±4.5kPa) and stability (>3.5 fold in vivo at 28 days). Application of the dual-crosslinking hydrogel to a myocardial infarct model showed improved outcomes relative to untreated and supramolecular hydrogel alone controls, demonstrating its potential in a range of applications where the precise delivery of hydrogels with tunable properties is desired. PMID:26526097

  2. Rapid Covalent Modification of Silicon Oxide Surfaces through Microwave-Assisted Reactions with Alcohols.

    PubMed

    Lee, Austin W H; Gates, Byron D

    2016-07-26

    We demonstrate the method of a rapid covalent modification of silicon oxide surfaces with alcohol-containing compounds with assistance by microwave reactions. Alcohol-containing compounds are prevalent reagents in the laboratory, which are also relatively easy to handle because of their stability against exposure to atmospheric moisture. The condensation of these alcohols with the surfaces of silicon oxides is often hindered by slow reaction kinetics. Microwave radiation effectively accelerates this condensation reaction by heating the substrates and/or solvents. A variety of substrates were modified in this demonstration, such as silicon oxide films of various thicknesses, glass substrates such as microscope slides (soda lime), and quartz. The monolayers prepared through this strategy demonstrated the successful formation of covalent surface modifications of silicon oxides with water contact angles of up to 110° and typical hysteresis values of 2° or less. An evaluation of the hydrolytic stability of these monolayers demonstrated their excellent stability under acidic conditions. The techniques introduced in this article were successfully applied to tune the surface chemistry of silicon oxides to achieve hydrophobic, oleophobic, and/or charged surfaces. PMID:27396288

  3. A Covalent Linker Allows for Membrane Targeting of An Oxylipin Biosynthetic Complex

    SciTech Connect

    Gilbert, N.C.; Niebuhr, M.; Tsuruta, H.; Bordelon, T.; Ridderbusch, O.; Dassey, A.; Brash, A.R.; Bartlett, S.G.; Newcomer, M.E.

    2009-05-18

    A naturally occurring bifunctional protein from Plexaura homomalla links sequential catalytic activities in an oxylipin biosynthetic pathway. The C-terminal lipoxygenase (LOX) portion of the molecule catalyzes the transformation of arachidonic acid (AA) to the corresponding 8R-hydroperoxide, and the N-terminal allene oxide synthase (AOS) domain promotes the conversion of the hydroperoxide intermediate to the product allene oxide (AO). Small-angle X-ray scattering data indicate that in the absence of a covalent linkage the two catalytic domains that transform AA to AO associate to form a complex that recapitulates the structure of the bifunctional protein. The SAXS data also support a model for LOX and AOS domain orientation in the fusion protein inferred from a low-resolution crystal structure. However, results of membrane binding experiments indicate that covalent linkage of the domains is required for Ca2+-dependent membrane targeting of the sequential activities, despite the noncovalent domain association. Furthermore, membrane targeting is accompanied by a conformational change as monitored by specific proteolysis of the linker that joins the AOS and LOX domains. Our data are consistent with a model in which Ca2+-dependent membrane binding relieves the noncovalent interactions between the AOS and LOX domains and suggests that the C2-like domain of LOX mediates both protein-protein and protein-membrane interactions.

  4. Reagent Cluster Anions for Multiple Gas-Phase Covalent Modifications of Peptide and Protein Cations

    NASA Astrophysics Data System (ADS)

    Prentice, Boone M.; Stutzman, John R.; McLuckey, Scott A.

    2013-07-01

    Multiple gas phase ion/ion covalent modifications of peptide and protein ions are demonstrated using cluster-type reagent anions of N-hydroxysulfosuccinimide acetate (sulfo-NHS acetate) and 2-formyl-benzenesulfonic acid (FBMSA). These reagents are used to selectively modify unprotonated primary amine functionalities of peptides and proteins. Multiple reactive reagent molecules can be present in a single cluster ion, which allows for multiple covalent modifications to be achieved in a single ion/ion encounter and at the `cost' of only a single analyte charge. Multiple derivatizations are demonstrated when the number of available reactive sites on the analyte cation exceeds the number of reagent molecules in the anionic cluster (e.g., data shown here for reactions between the polypeptide [K10 + 3H]3+ and the reagent cluster [5R5Na - Na]-). This type of gas-phase ion chemistry is also applicable to whole protein ions. Here, ubiquitin was successfully modified using an FBMSA cluster anion which, upon collisional activation, produced fragment ions with various numbers of modifications. Data for the pentamer cluster are included as illustrative of the results obtained for the clusters comprised of two to six reagent molecules.

  5. A new family of covalent inhibitors block nucleotide binding to the active site of pyruvate kinase

    PubMed Central

    Morgan, Hugh P.; Walsh, Martin J.; Blackburn, Elizabeth A.; Wear, Martin A.; Boxer, Matthew B.; Shen, Min; Mcnae, Iain W.; Nowicki, Matthew W.; Michels, Paul A. M.; Auld, Douglas S.; Fothergill-Gilmore, Linda A.; Walkinshaw, Malcolm D.

    2012-01-01

    SYNOPSIS Pyruvate kinase (PYK) plays a central role in the metabolism of many organisms and cell types, but the elucidation of the details of its function in a systems biology context has been hampered by the lack of specific high-affinity small molecule inhibitors. High-throughput screening has been used to identify a family of saccharin derivatives which inhibit Leishmania mexicana PYK (LmPYK) activity in a time- (and dose-) dependent manner; a characteristic of irreversible inhibition. The crystal structure of 4-[(1,1-dioxo-1,2-benzothiazol-3-yl)sulfanyl]benzoic acid (DBS) complexed with LmPYK shows that the saccharin moiety reacts with an active-site lysine residue (Lys335), forming a covalent bond and sterically hindering the binding of ADP/ATP. Mutation of the lysine residue to an arginine residue eliminated the effect of the inhibitor molecule, providing confirmation of the proposed inhibitor mechanism. This lysine residue is conserved in the active sites of the four human PYK isoenzymes, which were also found to be irreversibly inhibited by DBS. X-ray structures of PYK isoforms show structural differences at the DBS binding pocket, and this covalent inhibitor of PYK provides a chemical scaffold for the design of new families of potentially isoform-specific irreversible inhibitors. PMID:22906073

  6. Mechanistic studies of two-dimensional covalent organic frameworks rapidly polymerized from initially homogenous conditions.

    PubMed

    Smith, Brian J; Dichtel, William R

    2014-06-18

    Covalent organic frameworks (COFs) are periodic two- and three-dimensional (2D and 3D) polymer networks with high surface areas, low densities, and designed structures. Despite intense interest in framework materials, the nucleation and growth processes of COFs, and even of more established metal-organic frameworks (MOFs), are poorly understood. The kinetics of COF growth under varied reaction conditions provides mechanistic insight needed to improve their crystallinity and rationally synthesize new materials. Such kinetic measurements are unprecedented and difficult to perform on typical heterogeneous COF reaction mixtures. Here we synthesize 2D boronate ester-linked COF-5 under conditions in which the monomers are fully soluble. These homogeneous growth conditions provide equal or better material quality compared to any previous report and enable the first rigorous studies of the early stages of COF growth. COF-5 forms within minutes, and the precipitation rate is readily quantified from optical turbidity measurements. COF-5 formation follows an Arrhenius temperature dependence between 60-90 °C with an activation energy of 22-27 kcal/mol. The measured rate law includes a second order in both boronic acid and catechol moieties, and inverse second order in MeOH concentration. A competitive monofunctional catechol slows COF-5 formation but does not redissolve already precipitated COF, indicating both dynamic covalent bond formation and irreversible precipitation. Finally, stoichiometric H2O provides a 4-fold increase in crystallite domain areas, representing the first rational link between reaction conditions and material quality. PMID:24892961

  7. Cysteine-reactive covalent capture tags for enrichment of cysteine-containing peptides.

    PubMed

    Giron, Priscille; Dayon, Loïc; Mihala, Nikolett; Sanchez, Jean-Charles; Rose, Keith

    2009-11-01

    Considering the tremendous complexity and the wide dynamic range of protein samples from biological origin and their proteolytic peptide mixtures, proteomics largely requires simplification strategies. One common approach to reduce sample complexity is to target a particular amino acid in proteins or peptides, such as cysteine (Cys), with chemical tags in order to reduce the analysis to a subset of the whole proteome. The present work describes the synthesis and the use of two new cysteinyl tags, so-called cysteine-reactive covalent capture tags (C3T), for the isolation of Cys-containing peptides. These bifunctional molecules were specifically designed to react with cysteines through iodoacetyl and acryloyl moieties and permit efficient selection of the tagged peptides. To do so, a thioproline was chosen as the isolating group to form, after a deprotection/activation step, a thiazolidine with an aldehyde resin by the covalent capture (CC) method. The applicability of the enrichment strategy was demonstrated on small synthetic peptides as well as on peptides derived from digested proteins. Mass spectrometric (MS) analysis and tandem mass spectrometric (MS/MS) sequencing confirmed the efficient and straightforward selection of the cysteine-containing peptides. The combination of C3T and CC methods provides an effective alternative to reduce sample complexity and access low abundance proteins. PMID:19813279

  8. Covalent immobilization of lysozyme on ethylene vinyl alcohol films for nonmigrating antimicrobial packaging applications.

    PubMed

    Muriel-Galet, V; Talbert, J N; Hernandez-Munoz, P; Gavara, R; Goddard, J M

    2013-07-10

    The objective of this study was to develop a new antimicrobial film, in which lysozyme was covalently attached onto two different ethylene vinyl alcohol copolymers (EVOH 29 and EVOH 44). The EVOH surface was modified with UV irradiation treatment to generate carboxylic acid groups, and lysozyme was covalently attached to the functionalized polymer surface. Surface characterization of control and modified films was performed using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) and dye assay. The value of protein loading after attachment on the surface was 8.49 μg protein/cm(2) and 5.74 μg protein/cm(2) for EVOH 29 and EVOH 44, respectively, after 10 min UV irradiation and bioconjugation. The efficacy of the EVOH-lysozyme films was assessed using Micrococcus lysodeikticus. The antimicrobial activity of the films was tested against Listeria monocytogenes and was similar to an equivalent amount of free enzyme. The reduction was 1.08 log for EVOH 29-lysozyme, 0.95 log for EVOH 44-lysozyme, and 1.34 log for free lysozyme. This work confirmed the successful use of lysozyme immobilization on the EVOH surface for antimicrobial packaging.

  9. Rapid Covalent Modification of Silicon Oxide Surfaces through Microwave-Assisted Reactions with Alcohols.

    PubMed

    Lee, Austin W H; Gates, Byron D

    2016-07-26

    We demonstrate the method of a rapid covalent modification of silicon oxide surfaces with alcohol-containing compounds with assistance by microwave reactions. Alcohol-containing compounds are prevalent reagents in the laboratory, which are also relatively easy to handle because of their stability against exposure to atmospheric moisture. The condensation of these alcohols with the surfaces of silicon oxides is often hindered by slow reaction kinetics. Microwave radiation effectively accelerates this condensation reaction by heating the substrates and/or solvents. A variety of substrates were modified in this demonstration, such as silicon oxide films of various thicknesses, glass substrates such as microscope slides (soda lime), and quartz. The monolayers prepared through this strategy demonstrated the successful formation of covalent surface modifications of silicon oxides with water contact angles of up to 110° and typical hysteresis values of 2° or less. An evaluation of the hydrolytic stability of these monolayers demonstrated their excellent stability under acidic conditions. The techniques introduced in this article were successfully applied to tune the surface chemistry of silicon oxides to achieve hydrophobic, oleophobic, and/or charged surfaces.

  10. Photosensitivity and line-edge roughness of novel polymer-bound PAG photoresists

    NASA Astrophysics Data System (ADS)

    Lee, Cheng-Tsung; Wang, Mingxing; Jarnagin, Nathan D.; Gonsalves, Kenneth E.; Roberts, Jeanette M.; Yueh, Wang; Henderson, Clifford L.

    2007-03-01

    Substantially improved photoresist material designs, which can provide higher photosensitivity and precise critical dimension and edge roughness control, will be required to enable the application of next generation lithography technology to the production of future sub-65 nm node IC device generations. The development and characterization of novel material platforms that solve the aforementioned basic problems with chemically amplified resists (CARs) is essential and is already one of the major subjects of modern lithography research. In that regard, we have pursued development of a variety of 193 nm and EUV CARs that contain photoacid generator (PAG) units covalently bonded directly to the resin polymer backbone. However, the detailed structure-property relationships that result from this direct attachment of the PAG functional group to the polymer have previously not yet been rigorously characterized. In this work, the lithographic properties of a polymer-bound PAG CAR (GBLMA-co-EAMA-co-F4-MBS.TPS) and its blended-PAG analog resist (GBLMA-co-EAMA blend F4-IBBS.TPS) were studied and compared. The direct incorporation of PAG functionality into the resist polymer, where the resulting photoacid remains bound to the polymer, showed improved photosensitivity, resolution, and lower LER as compared with the analogous blended-PAG resist. The improved resolution and LER were expected due to the restricted photoacid diffusion and uniform PAG distribution provided by direct incorporation of the PAG into the polymer backbone to make a single-component resist material. The ability to load higher levels of PAG into the resist provided by this PAG incorporation into the polymer, as compared to the low PAG concentrations attainable by traditional blending approaches, overcomes the sensitivity loss that should result from reduction in photoacid diffusivity and concomitant smaller acid-catalytic chain lengths. In fact, the polymer-bound PAG resist achieves a faster photospeed than

  11. Structure-based design of covalent Siah inhibitors.

    PubMed

    Stebbins, John L; Santelli, Eugenio; Feng, Yongmei; De, Surya K; Purves, Angela; Motamedchaboki, Khatereh; Wu, Bainan; Ronai, Ze'ev A; Liddington, Robert C; Pellecchia, Maurizio

    2013-08-22

    The E3 ubiquitin ligase Siah regulates key cellular events that are central to cancer development and progression. A promising route to Siah inhibition is disrupting its interactions with adaptor proteins. However, typical of protein-protein interactions, traditional unbiased approaches to ligand discovery did not produce viable hits against this target, despite considerable effort and a multitude of approaches. Ultimately, a rational structure-based design strategy was successful for the identification of Siah inhibitors in which peptide binding drives specific covalent bond formation with the target. X-ray crystallography, mass spectrometry, and functional data demonstrate that these peptide mimetics are efficient covalent inhibitors of Siah and antagonize Siah-dependent regulation of Erk and Hif signaling in the cell. The proposed strategy may result useful as a general approach to the design of peptide-based inhibitors of other protein-protein interactions.

  12. The alternative strategy for designing covalent drugs through kinetic effects of pi-stacking on the self-assembled nanoparticles: a model study with antibiotics.

    PubMed

    Du, Libo; Suo, Siqingaowa; Zhang, Han; Jia, Hongying; Liu, Ke Jian; Zhang, Xue Ji; Liu, Yang

    2016-11-01

    It is still a huge challenge to find a new strategy for rationally designing covalent drugs because most of them are discovered by serendipity. Considering that the effect of covalent drugs is closely associated with the kinetics of the reaction between drug molecule and its target protein, here we first demonstrate an example of the kinetic effect of pi-stacking of drug molecules on covalent antimicrobial drug design. When PEGylated 7-aminocephalosporanic acid (PEG-ACA) is used as a substrate drug, pi-stacking of  the ACA group via the self-assembly of PEG-ACA on the surface of gold nanoparticles (i.e. Au@ACA) exhibits antibacterial activity against E. coli fourfold higher than a PEG-ACA monomer does. The reason can be reasonably attributed to the kinetic rate enhancement for the covalent reaction between Au@ACA and penicillin binding proteins. We believe that the self-assembly of functional groups onto the surface of gold nanoparticles represents a new strategy for covalent drug design. PMID:27673346

  13. The alternative strategy for designing covalent drugs through kinetic effects of pi-stacking on the self-assembled nanoparticles: a model study with antibiotics

    NASA Astrophysics Data System (ADS)

    Du, Libo; Suo, Siqingaowa; Zhang, Han; Jia, Hongying; Liu, Ke Jian; Zhang, Xue Ji; Liu, Yang

    2016-11-01

    It is still a huge challenge to find a new strategy for rationally designing covalent drugs because most of them are discovered by serendipity. Considering that the effect of covalent drugs is closely associated with the kinetics of the reaction between drug molecule and its target protein, here we first demonstrate an example of the kinetic effect of pi-stacking of drug molecules on covalent antimicrobial drug design. When PEGylated 7-aminocephalosporanic acid (PEG-ACA) is used as a substrate drug, pi-stacking of the ACA group via the self-assembly of PEG-ACA on the surface of gold nanoparticles (i.e. Au@ACA) exhibits antibacterial activity against E. coli fourfold higher than a PEG-ACA monomer does. The reason can be reasonably attributed to the kinetic rate enhancement for the covalent reaction between Au@ACA and penicillin binding proteins. We believe that the self-assembly of functional groups onto the surface of gold nanoparticles represents a new strategy for covalent drug design.

  14. The alternative strategy for designing covalent drugs through kinetic effects of pi-stacking on the self-assembled nanoparticles: a model study with antibiotics.

    PubMed

    Du, Libo; Suo, Siqingaowa; Zhang, Han; Jia, Hongying; Liu, Ke Jian; Zhang, Xue Ji; Liu, Yang

    2016-11-01

    It is still a huge challenge to find a new strategy for rationally designing covalent drugs because most of them are discovered by serendipity. Considering that the effect of covalent drugs is closely associated with the kinetics of the reaction between drug molecule and its target protein, here we first demonstrate an example of the kinetic effect of pi-stacking of drug molecules on covalent antimicrobial drug design. When PEGylated 7-aminocephalosporanic acid (PEG-ACA) is used as a substrate drug, pi-stacking of  the ACA group via the self-assembly of PEG-ACA on the surface of gold nanoparticles (i.e. Au@ACA) exhibits antibacterial activity against E. coli fourfold higher than a PEG-ACA monomer does. The reason can be reasonably attributed to the kinetic rate enhancement for the covalent reaction between Au@ACA and penicillin binding proteins. We believe that the self-assembly of functional groups onto the surface of gold nanoparticles represents a new strategy for covalent drug design.

  15. Editorial - Proceedings on Basic Research on Ionic-Covalent Materials

    NASA Astrophysics Data System (ADS)

    2016-05-01

    The third symposium on Basic Research on Ionic-Covalent Materials for Nuclear Applications, originally initiated at the EMRS in Nice (May 2011), attracted 80 registered participants. During 4 days, 54 oral talks and 22 posters were presented. The overall high quality of the majority of the contributions was appreciated, in particular the great efforts of the invited speakers to convey their expertise in an excellent tutorial way.

  16. Dislocation dynamics in solid solutions of covalent crystals

    NASA Astrophysics Data System (ADS)

    Petukhov, B. V.

    2016-09-01

    The dislocation mechanism of solid solution strengthening of covalent semiconductor crystals has been studied. The change in the regularities of dislocation dynamics in solid solutions from those in the components of the solution is connected with the manifestation of the nonlinear drift of dislocation kinks. The theory developed suggests an explanation of specificities of the dislocation mobility in a Ge1- c Si c solid solution.

  17. Covalent intermolecular interaction of the nitric oxide dimer (NO)2

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Zheng, Gui-Li; Lv, Gang; Geng, Yi-Zhao; Ji, Qing

    2015-09-01

    Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer, (NO)2, in its most stable conformation, a cis conformation. The natural bond orbital (NBO) analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the π bonds with bond order 0.5 of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics (MM) calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics (QM). The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary. Project supported by the National Natural Science Foundation of China (Grant Nos. 90403007 and 10975044), the Key Subject Construction Project of Hebei Provincial Universities, China, the Research Project of Hebei Education Department, China (Grant Nos. Z2012067 and Z2011133), the National Natural Science Foundation of China (Grant No. 11147103), and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5

  18. Boronic acid-modified magnetic materials for antibody purification

    PubMed Central

    Dhadge, Vijaykumar L.; Hussain, Abid; Azevedo, Ana M.; Aires-Barros, Raquel; Roque, Ana C. A.

    2014-01-01

    Aminophenyl boronic acids can form reversible covalent ester interactions with cis-diol-containing molecules, serving as a selective tool for binding glycoproteins as antibody molecules that possess oligosaccharides in both the Fv and Fc regions. In this study, amino phenyl boronic acid (APBA) magnetic particles (MPs) were applied for the magnetic separation of antibody molecules. Iron oxide MPs were firstly coated with dextran to avoid non-specific binding and then with 3-glycidyloxypropyl trimethoxysilane to allow further covalent coupling of APBA (APBA_MP). When contacted with pure protein solutions of human IgG (hIgG) and bovine serum albumin (BSA), APBA_MP bound 170 ± 10 mg hIgG g−1 MP and eluted 160 ± 5 mg hIgG g−1 MP, while binding only 15 ± 5 mg BSA g−1 MP. The affinity constant for the interaction between hIgG and APBA_MP was estimated as 4.9 × 105 M−1 (Ka) with a theoretical maximum capacity of 492 mg hIgG adsorbed g−1 MP (Qmax), whereas control particles bound a negligible amount of hIgG and presented an estimated theoretical maximum capacity of 3.1 mg hIgG adsorbed g−1 MP (Qmax). APBA_MPs were also tested for antibody purification directly from CHO cell supernatants. The particles were able to bind 98% of IgG loaded and to recover 95% of pure IgG (purity greater than 98%) at extremely mild conditions. PMID:24258155

  19. Boronic acid-modified magnetic materials for antibody purification.

    PubMed

    Dhadge, Vijaykumar L; Hussain, Abid; Azevedo, Ana M; Aires-Barros, Raquel; Roque, Ana C A

    2014-02-01

    Aminophenyl boronic acids can form reversible covalent ester interactions with cis-diol-containing molecules, serving as a selective tool for binding glycoproteins as antibody molecules that possess oligosaccharides in both the Fv and Fc regions. In this study, amino phenyl boronic acid (APBA) magnetic particles (MPs) were applied for the magnetic separation of antibody molecules. Iron oxide MPs were firstly coated with dextran to avoid non-specific binding and then with 3-glycidyloxypropyl trimethoxysilane to allow further covalent coupling of APBA (APBA_MP). When contacted with pure protein solutions of human IgG (hIgG) and bovine serum albumin (BSA), APBA_MP bound 170 ± 10 mg hIgG g(-1) MP and eluted 160 ± 5 mg hIgG g(-1) MP, while binding only 15 ± 5 mg BSA g(-1) MP. The affinity constant for the interaction between hIgG and APBA_MP was estimated as 4.9 × 10(5) M(-1) (Ka) with a theoretical maximum capacity of 492 mg hIgG adsorbed g(-1) MP (Qmax), whereas control particles bound a negligible amount of hIgG and presented an estimated theoretical maximum capacity of 3.1 mg hIgG adsorbed g(-1) MP (Qmax). APBA_MPs were also tested for antibody purification directly from CHO cell supernatants. The particles were able to bind 98% of IgG loaded and to recover 95% of pure IgG (purity greater than 98%) at extremely mild conditions.

  20. The mitochondrial acyl carrier protein (ACP) coordinates mitochondrial fatty acid synthesis with iron sulfur cluster biogenesis

    PubMed Central

    Van Vranken, Jonathan G; Jeong, Mi-Young; Wei, Peng; Chen, Yu-Chan; Gygi, Steven P; Winge, Dennis R; Rutter, Jared

    2016-01-01

    Mitochondrial fatty acid synthesis (FASII) and iron sulfur cluster (FeS) biogenesis are both vital biosynthetic processes within mitochondria. In this study, we demonstrate that the mitochondrial acyl carrier protein (ACP), which has a well-known role in FASII, plays an unexpected and evolutionarily conserved role in FeS biogenesis. ACP is a stable and essential subunit of the eukaryotic FeS biogenesis complex. In the absence of ACP, the complex is destabilized resulting in a profound depletion of FeS throughout the cell. This role of ACP depends upon its covalently bound 4’-phosphopantetheine (4-PP)-conjugated acyl chain to support maximal cysteine desulfurase activity. Thus, it is likely that ACP is not simply an obligate subunit but also exploits the 4-PP-conjugated acyl chain to coordinate mitochondrial fatty acid and FeS biogenesis. DOI: http://dx.doi.org/10.7554/eLife.17828.001 PMID:27540631

  1. The mitochondrial acyl carrier protein (ACP) coordinates mitochondrial fatty acid synthesis with iron sulfur cluster biogenesis.

    PubMed

    Van Vranken, Jonathan G; Jeong, Mi-Young; Wei, Peng; Chen, Yu-Chan; Gygi, Steven P; Winge, Dennis R; Rutter, Jared

    2016-01-01

    Mitochondrial fatty acid synthesis (FASII) and iron sulfur cluster (FeS) biogenesis are both vital biosynthetic processes within mitochondria. In this study, we demonstrate that the mitochondrial acyl carrier protein (ACP), which has a well-known role in FASII, plays an unexpected and evolutionarily conserved role in FeS biogenesis. ACP is a stable and essential subunit of the eukaryotic FeS biogenesis complex. In the absence of ACP, the complex is destabilized resulting in a profound depletion of FeS throughout the cell. This role of ACP depends upon its covalently bound 4'-phosphopantetheine (4-PP)-conjugated acyl chain to support maximal cysteine desulfurase activity. Thus, it is likely that ACP is not simply an obligate subunit but also exploits the 4-PP-conjugated acyl chain to coordinate mitochondrial fatty acid and FeS biogenesis. PMID:27540631

  2. Covalent assembly of gold nanoparticles for nonvolatile memory applications.

    PubMed

    Gupta, Raju Kumar; Kusuma, Damar Yoga; Lee, P S; Srinivasan, M P

    2011-12-01

    This work reports a versatile approach for enhancing the stability of nonvolatile memory devices through covalent assembly of functionalized gold nanoparticles. 11-mercapto-1-undecanol functionalized gold nanoparticles (AuNPs) with a narrow size distribution and particle size of about 5 nm were synthesized. Then, the AuNPs were immobilized on a SiO(2) substrate using a functionalized polymer as a surface modifier. Microscopic and spectroscopic techniques were used to characterize the AuNPs and their morphology before and after immobilization. Finally, a metal-insulator-semiconductor (MIS) type memory device with such covalently anchored AuNPs as a charge trapping layer was fabricated. The MIS structure showed well-defined counterclockwise C-V hysteresis curves indicating a good memory effect. The flat band voltage shift was 1.64 V at a swapping voltage between ±7 V. Furthermore, the MIS structure showed a good retention characteristic up to 20,000 s. The present synthetic route to covalently immobilize gold nanoparticles system will be a step towards realization for the nanoparticle-based electronic devices and related applications.

  3. Covalent bonding modulated graphene-metal interfacial thermal transport.

    PubMed

    Jiang, Tao; Zhang, Xueqiang; Vishwanath, Suresh; Mu, Xin; Kanzyuba, Vasily; Sokolov, Denis A; Ptasinska, Sylwia; Go, David B; Xing, Huili Grace; Luo, Tengfei

    2016-06-01

    We report the covalent bonding enabled modulation of the interfacial thermal conductance between graphene and metals Cu, Al, and Pt by controlling the oxidation of graphene. By combining comprehensive X-ray photoelectron spectroscopy (XPS) analysis and time-domain thermoreflectance measurements, we quantify the effect of graphene oxidation on interfacial thermal conductance. It was found that thermal conductance increases with the degree of graphene oxidation until a peak value is obtained at an oxygen/carbon atom percentage of ∼7.7%. The maximum enhancement in thermal conductance was measured to be 55%, 38%, and 49% for interfaces between oxidized graphene and Cu, Al, and Pt, respectively. In situ XPS measurements show that oxygen covalently binds to Cu and graphene simultaneously, forming a highly efficient bridge to enhance the thermal transport. Our molecular dynamics simulations verify that strong interfacial covalent bonds are the key to the thermal conductance enhancement. This work provides valuable insights into the mechanism of functionalization-induced thermal conductance enhancement and design guidelines for graphene-based devices.

  4. Saturating the holographic entropy bound

    SciTech Connect

    Bousso, Raphael; Freivogel, Ben; Leichenauer, Stefan

    2010-10-15

    The covariant entropy bound states that the entropy, S, of matter on a light sheet cannot exceed a quarter of its initial area, A, in Planck units. The gravitational entropy of black holes saturates this inequality. The entropy of matter systems, however, falls short of saturating the bound in known examples. This puzzling gap has led to speculation that a much stronger bound, S < or approx. A{sup 3/4}, may hold true. In this note, we exhibit light sheets whose entropy exceeds A{sup 3/4} by arbitrarily large factors. In open Friedmann-Robertson-Walker universes, such light sheets contain the entropy visible in the sky; in the limit of early curvature domination, the covariant bound can be saturated but not violated. As a corollary, we find that the maximum observable matter and radiation entropy in universes with positive (negative) cosmological constant is of order {Lambda}{sup -1} ({Lambda}{sup -2}), and not |{Lambda}|{sup -3/4} as had hitherto been believed. Our results strengthen the evidence for the covariant entropy bound, while showing that the stronger bound S < or approx. A{sup 3/4} is not universally valid. We conjecture that the stronger bound does hold for static, weakly gravitating systems.

  5. Poly(ethylene glycol) (PEG)-lactic acid nanocarrier-based degradable hydrogels for restoring the vaginal microenvironment.

    PubMed

    Sundara Rajan, Sujata; Turovskiy, Yevgeniy; Singh, Yashveer; Chikindas, Michael L; Sinko, Patrick J

    2014-11-28

    Women with bacterial vaginosis (BV) display reduced vaginal acidity, which make them susceptible to associated infections such as HIV. In the current study, poly(ethylene glycol) (PEG) nanocarrier-based degradable hydrogels were developed for the controlled release of lactic acid in the vagina of BV-infected women. PEG-lactic acid (PEG-LA) nanocarriers were prepared by covalently attaching lactic acid to 8-arm PEG-SH via cleavable thioester bonds. PEG-LA nanocarriers with 4 copies of lactic acid per molecule provided controlled release of lactic acid with a maximum release of 23% and 47% bound lactic acid in phosphate buffered saline (PBS, pH7.4) and acetate buffer (AB, pH4.3), respectively. The PEG nanocarrier-based hydrogels were formed by cross-linking the PEG-LA nanocarriers with 4-arm PEG-NHS via degradable thioester bonds. The nanocarrier-based hydrogels formed within 20 min under ambient conditions and exhibited an elastic modulus that was 100-fold higher than the viscous modulus. The nanocarrier-based degradable hydrogels provided controlled release of lactic acid for several hours; however, a maximum release of only 10%-14% bound lactic acid was observed possibly due to steric hindrance of the polymer chains in the cross-linked hydrogel. In contrast, hydrogels with passively entrapped lactic acid showed burst release with complete release within 30 min. Lactic acid showed antimicrobial activity against the primary BV pathogen Gardnerella vaginalis with a minimum inhibitory concentration (MIC) of 3.6 mg/ml. In addition, the hydrogels with passively entrapped lactic acid showed retained antimicrobial activity with complete inhibition G. vaginalis growth within 48 h. The results of the current study collectively demonstrate the potential of PEG nanocarrier-based hydrogels for vaginal administration of lactic acid for preventing and treating BV.

  6. Ionic complexation as a non-covalent approach for the design of folate anchored rifampicin Gantrez nanoparticles.

    PubMed

    Date, Praveen V; Patel, Mitesh D; Majee, Sharmila B; Samad, Abdul; Devarajan, Padma V

    2013-05-01

    The present study discloses the design of folate anchored Rifampicin-Poly methylvinylether maleic anhydride copolymer (Gantrez AN-119, Gantrez) nanoparticles (RFMGzFa) by ionic complexation. Folic acid was anchored to the preformed drug loaded nanoparticles. Folic acid was anchored in different concentration by simply varying the amount of folic acid added during preparation. RFMGzFa nanoparticles were prepared by emulsion solvent diffusion method. Gantrez AN-119 rapidly hydrolyzes in aqueous medium releasing carboxylic acid groups, to create an acidic environment. This facilitates protonation and subsequent ionic complexation of folic acid with the carboxylic groups, to enable anchoring. FTIR spectra confirmed this interaction. Infrared imaging revealed distribution of folic acid across the nanoparticle surface. Nanoparticles were obtained in the size range 350-450 nm with RFM loading of 12-14% w/w. Zeta potential confirmed colloidal stability. TEM/SEM revealed spherical morphology. RFMGzFa nanoparticles exhibited sustained release of RFM and folic acid. Folic acid showed sustained release upto 12 h, which was ion exchange mediated. A 480% enhancement in RFM uptake with RFMGzFa nanoparticles compared to 300% with RFMGz nanoparticles in-vitro, in human macrophage cell line U-937, suggested the role of folic acid in folate receptor mediated uptake. Ionic complexation represents a simple non-covalent approach for anchoring folic acid on polymeric nanoparticles of Gantrez.

  7. Reactivity of Metal Ions Bound to Water-Soluble Polymers

    SciTech Connect

    Sauer, N.N.; Watkins, J.G.; Lin, M.; Birnbaum, E.R.; Robison, T.W.; Smith, B.F.; Gohdes, J.W.; McDonald, J.G.

    1999-06-29

    The intent of this work is to determine the effectiveness of catalysts covalently bound to polymers and to understand the consequences of supporting the catalysts on catalyst efficiency and selectivity. Rhodium phosphine complexes with functional groups for coupling to polymers were prepared. These catalyst precursors were characterized using standard techniques including IR, NMR, and elemental analysis. Studies on the modified catalysts showed that they were still active hydrogenation catalysts. However, tethering of the catalysts to polyamines gave systems with low hydrogenation activity. Analogous biphasic systems were also explored. Phosphine ligands with a surfactant-like structure have been synthesized and used to prepare catalytically active complexes of palladium. The palladium complexes were utilized in Heck-type coupling reactions (e.g. coupling of iodobenzene and ethyl acrylate to produce ethyl cinnamate) under vigorously stirred biphasic reaction conditions, and were found to offer superior performance over a standard water-soluble palladium catalyst under analogous conditions.

  8. Covalency-Driven Dimerization of Plutonium(IV) in a Hydroxamate Complex.

    PubMed

    Silver, Mark A; Cary, Samantha K; Stritzinger, Jared T; Parker, T Gannon; Maron, Laurent; Albrecht-Schmitt, Thomas E

    2016-06-01

    The reaction of formohydroxamic acid [NH(OH)CHO, FHA] with Pu(III) should result in stabilization of the trivalent oxidation state. However, slow oxidation to Pu(IV) occurs, which leads to formation of the dimeric plutonium(IV) formohydroxamate complex Pu2(FHA)8. In addition to being reductants, hydroxamates are also strong π-donor ligands. Here we show that formation of the Pu2(FHA)8 dimer occurs via covalency between the 5f orbitals on plutonium and the π* orbitals of FHA(-) anions, which gives rise to a broad and intense ligand-to-metal charge-transfer feature. Time-dependent density functional theory calculations corroborate this assignment. PMID:27228095

  9. Polyvinylamine-graft-TEMPO adsorbs onto, oxidizes, and covalently bonds to wet cellulose.

    PubMed

    Pelton, Robert; Ren, Pengchao; Liu, Jieyi; Mijolovic, Darijo

    2011-04-11

    Described is a new, greener approach to increasing adhesion between wet cellulose surfaces. Polyvinylamine (PVAm) with grafted TEMPO spontaneously adsorbs onto cellulose and oxidizes the C6 hydroxyl to aldehyde groups that react to form covalent bonds with primary amines on PVAm. Grafted TEMPO offers two important advantages over solutions of low-molecular-weight water-soluble TEMPO derivatives. First, the oxidation of porous cellulose wood fibers is restricted to the exterior surfaces accessible to high-molecular-weight PVAm. Thus, fibers are not weakened by excessive oxidation of the interior fiber wall surfaces. The second advantage of tethered TEMPO is that the total dose of TEMPO required to oxidize dilute fiber suspensions is much less than that required by water-soluble TEMPO derivatives. PVAm-TEMPO is stable under oxidizing conditions. The oxidation activity of the immobilized TEMPO was demonstrated by the conversion of methylglyoxal to pyruvic acid.

  10. Covalent Triazine-Based Frameworks as Visible Light Photocatalysts for the Splitting of Water.

    PubMed

    Bi, Jinhong; Fang, Wei; Li, Liuyi; Wang, Jinyun; Liang, Shijing; He, Yunhui; Liu, Minghua; Wu, Ling

    2015-10-01

    Covalent triazine-based frameworks (CTFs) with a graphene-like layered morphology have been controllably synthesized by the trifluoromethanesulfonic acid-catalyzed nitrile trimerization reactions at room temperature via selecting different monomers. Platinum nanoparticles are well dispersed in CTF-T1, which is ascribed to the synergistic effects of the coordination of triazine moieties and the nanoscale confinement effect of CTFs. CTF-T1 exhibits excellent photocatalytic activity and stability for H2 evolution in the presence of platinum under visible light irradiation (λ ≥ 420 nm). The activity and stability of CTF-T1 are comparable to those of g-C3 N4 . Importantly, as a result of the tailorable electronic and spatial structures of CTFs that can be achieved through the judicial selection of monomers, CTFs not only show great potential as organic semiconductor for photocatalysis but also may provide a molecular-level understanding of the inherent heterogeneous photocatalysis.

  11. Robustness and modularity properties of a non-covalent DNA catalytic reaction

    PubMed Central

    Zhang, David Yu

    2010-01-01

    The biophysics of nucleic acid hybridization and strand displacement have been used for the rational design of a number of nanoscale structures and functions. Recently, molecular amplification methods have been developed in the form of non-covalent DNA catalytic reactions, in which single-stranded DNA (ssDNA) molecules catalyze the release of ssDNA product molecules from multi-stranded complexes. Here, we characterize the robustness and specificity of one such strand displacement-based catalytic reaction. We show that the designed reaction is simultaneously sensitive to sequence mutations in the catalyst and robust to a variety of impurities and molecular noise. These properties facilitate the incorporation of strand displacement-based DNA components in synthetic chemical and biological reaction networks. PMID:20194118

  12. Bounding the elliptic Mahler measure

    NASA Astrophysics Data System (ADS)

    Pinner, Christopher

    1998-11-01

    We give a simple inequality relating the elliptic Mahler measure of a polynomial to the traditional Mahler measure (via the length of the polynomial). These bounds are essentially sharp. We also give the corresponding result for polynomials in several variables.

  13. Eriocalyxin B Inhibits STAT3 Signaling by Covalently Targeting STAT3 and Blocking Phosphorylation and Activation of STAT3.

    PubMed

    Yu, Xiaokui; He, Li; Cao, Peng; Yu, Qiang

    2015-01-01

    Activated STAT3 plays an important role in oncogenesis by stimulating cell proliferation and resisting apoptosis. STAT3 therefore is an attractive target for cancer therapy. We have screened a traditional Chinese herb medicine compound library and found Eriocalyxin B (EB), a diterpenoid from Isodon eriocalyx, as a specific inhibitor of STAT3. EB selectively inhibited constitutive as well as IL-6-induced phosphorylation of STAT3 and induced apoptosis of STAT3-dependent tumor cells. EB did not affect the upstream protein tyrosine kinases or the phosphatase (PTPase) of STAT3, but rather interacted directly with STAT3. The effects of EB could be abolished by DTT or GSH, suggesting a thiol-mediated covalent linkage between EB and STAT3. Site mutagenesis of cysteine in and near the SH2 domain of STAT3 identified Cys712 to be the critical amino acid for the EB-induced inactivation of STAT3. Furthermore, LC/MS/MS analyses demonstrated that an α, β-unsaturated carbonyl of EB covalently interacted with the Cys712 of STAT3. Computational modeling analyses also supported a direct interaction between EB and the Cys712 of STAT3. These data strongly suggest that EB directly targets STAT3 through a covalent linkage to inhibit the phosphorylation and activation of STAT3 and induces apoptosis of STAT3-dependent tumor cells. PMID:26010889

  14. Eriocalyxin B Inhibits STAT3 Signaling by Covalently Targeting STAT3 and Blocking Phosphorylation and Activation of STAT3

    PubMed Central

    Yu, Xiaokui; He, Li; Cao, Peng; Yu, Qiang

    2015-01-01

    Activated STAT3 plays an important role in oncogenesis by stimulating cell proliferation and resisting apoptosis. STAT3 therefore is an attractive target for cancer therapy. We have screened a traditional Chinese herb medicine compound library and found Eriocalyxin B (EB), a diterpenoid from Isodon eriocalyx, as a specific inhibitor of STAT3. EB selectively inhibited constitutive as well as IL-6-induced phosphorylation of STAT3 and induced apoptosis of STAT3-dependent tumor cells. EB did not affect the upstream protein tyrosine kinases or the phosphatase (PTPase) of STAT3, but rather interacted directly with STAT3. The effects of EB could be abolished by DTT or GSH, suggesting a thiol-mediated covalent linkage between EB and STAT3. Site mutagenesis of cysteine in and near the SH2 domain of STAT3 identified Cys712 to be the critical amino acid for the EB-induced inactivation of STAT3. Furthermore, LC/MS/MS analyses demonstrated that an α, β-unsaturated carbonyl of EB covalently interacted with the Cys712 of STAT3. Computational modeling analyses also supported a direct interaction between EB and the Cys712 of STAT3. These data strongly suggest that EB directly targets STAT3 through a covalent linkage to inhibit the phosphorylation and activation of STAT3 and induces apoptosis of STAT3-dependent tumor cells. PMID:26010889

  15. Assessment of novel chemical strategies for covalent attachment of adhesive peptides to rough titanium surfaces: XPS analysis and biological evaluation.

    PubMed

    Dettin, Monica; Herath, Thushari; Gambaretto, Roberta; Iucci, Giovanna; Battocchio, Chiara; Bagno, Andrea; Ghezzo, Francesca; Di Bello, Carlo; Polzonetti, Giovanni; Di Silvio, Lucy

    2009-11-01

    Bioactive molecules have been proposed to promote beneficial interactions at bone-implant interfaces for enhancing integration. The main objective of this study was to develop novel methods to functionalize oxidized titanium surfaces by the covalent immobilization of bioactive peptides, through selective reaction involving single functional groups. In the first protocol, an aminoalkylsilane was covalently linked to the Ti oxide layer, followed by covalent binding of glutaric anhydride to the free NH(2) groups. The carboxylic group of glutaric anhydride was used to condense the free N-terminal group of the side-chain protected peptide sequence. Finally, the surface was treated with trifluoroacetic acid to deprotect side-chain groups. In the second protocol, the peptide was directly anchored to the Ti oxide surface via UV activation of an arylazide peptide analogue. X-ray photoelectron spectroscopy analyses confirmed that modifications induced onto surface composition were in agreement with the reactions performed. The peptide density of each biomimetic surface was determined on the basis of radiolabeling and XPS derived reaction yields. The in vitro cellular response of the biomimetic surfaces was evaluated using a primary human osteoblast cell model. Cell adhesion, proliferation, differentiation, and mineralization were examined at initial-, short-, and long-time periods. In was shown that the biomimetic surface obtained through photoprobe-marked analogue that combines an easily-performed modification provides a favorable surface for an enhanced cellular response.

  16. The number of copies of ribosome-bound proteins L7 and L12 required for protein synthesis activity.

    PubMed

    Lee, C C; Cantor, C R; Wittmann-Liebold, B

    1981-01-10

    Poly(U)-dependent poly(Phe) synthesis and elongation factor G (EF-G)-dependent GTPase activity were used to study the partial reconstitution of L7/L12-deficient ribosomes with proteins L7/L12 and fluorescent conjugates. Seventy-five per cent of these activities are restored when unmodified L7/L12 dimer is added to L7/L12-deficient cores at a ratio of 1:1. Various covalent fluorescent conjugates of L7/L12 bind to these cores about as well as unmodified protein. A fluorescein-5-isothiocyanate derivative of L12 shows almost no functional activity when bound. However, mixed reconstitutes of this conjugate and unmodified L12 have 75% functional activity when half the protein is unmodified. These results can be explained by a model in which there are two independent binding sites on the ribosome for two dimers of L7/L12. The binding of dimers to ribosomes is totally random and complete; the particle is 100% active so long as it has one active dimer bound to either one of the two sites. However, more complex models cannot be ruled out. An 5-(iodoacetamidoethyl)-aminonaphthalene-1-sulfonic acid (IAEDANS) derivative of L7 is labeled semispecifically at the COOH terminus. This conjugate shows partial functional activity. When assay results are analyzed using the above model, it appears that the specific COOH-terminal modification has no effect on activity. However, all but a small fraction of the nonspecific IAEDANS modifications lead to inactivation.

  17. Determination of the solution-bound conformation of an amino acid binding protein by NMR paramagnetic relaxation enhancement: use of a single flexible paramagnetic probe with improved estimation of its sampling space.

    PubMed

    Bermejo, Guillermo A; Strub, Marie-Paule; Ho, Chien; Tjandra, Nico

    2009-07-15

    We demonstrate the feasibility of elucidating the bound ("closed") conformation of a periplasmic binding protein, the glutamine-binding protein (GlnBP), in solution, using paramagnetic relaxation enhancements (PREs) arising from a single paramagnetic group. GlnBP consists of two globular domains connected by a hinge. Using the ligand-free ("open") conformation as a starting point, conjoined rigid-body/torsion-angle simulated annealing calculations were performed using backbone (1)H(N)-PREs as a major source of distance information. Paramagnetic probe flexibility was accounted for via a multiple-conformer representation. A conventional approach where the entire PRE data set is enforced at once during simulated annealing yielded poor results due to inappropriate conformational sampling of the probe. On the other hand, significant improvements in coordinate accuracy were obtained by estimating the probe sampling space prior to structure calculation. Such sampling is achieved by refining the ensemble of probe conformers with intradomain PREs only, keeping the protein backbone fixed in the open form. Subsequently, while constraining the probe to the previously found conformations, the domains are allowed to move relative to each other under the influence of the non-intradomain PREs, giving the hinge region torsional degrees of freedom. Thus, by partitioning the protocol into "probe sampling" and "backbone sampling" stages, structures significantly closer to the X-ray structure of ligand-bound GlnBP were obtained.

  18. Discovery of Covalent Ligands via Noncovalent Docking by Dissecting Covalent Docking Based on a "Steric-Clashes Alleviating Receptor (SCAR)" Strategy.

    PubMed

    Ai, Yuanbao; Yu, Lingling; Tan, Xiao; Chai, Xiaoying; Liu, Sen

    2016-08-22

    Covalent ligands modulating protein activities/signals have attracted unprecedented attention in recent years, but the insufficient understanding of their advantages in the early days of drug discovery has hindered their rational discovery and development. This also left us inadequate knowledge on the rational design of covalent ligands, e.g., how to balance the contribution from the covalent group and the noncovalent group, respectively. In this work, we dissected the noncovalent docking from covalent docking by creating SCARs (steric-clashes alleviating receptors). We showed that the SCAR method outperformed those specifically developed but more complicated covalent docking protocols. We furthermore provided a "proof-of-principle" example by implementing this method in the first high-throughput screening and discovery of novel covalent inhibitors of S-adenosylmethionine decarboxylase. This work demonstrated that noncovalent groups play a predeterminate role in the design of covalent ligands, and would be of great value in accelerating the discovery and development of covalent ligands. PMID:27411028

  19. Uncoupling protein 1 binds one nucleotide per monomer and is stabilized by tightly bound cardiolipin

    PubMed Central

    Lee, Yang; Willers, Chrissie; Kunji, Edmund R. S.; Crichton, Paul G.

    2015-01-01

    Uncoupling protein 1 (UCP1) catalyzes fatty acid-activated, purine nucleotide-sensitive proton leak across the mitochondrial inner membrane of brown adipose tissue to produce heat, and could help combat obesity and metabolic disease in humans. Studies over the last 30 years conclude that the protein is a dimer, binding one nucleotide molecule per two proteins, and unlike the related mitochondrial ADP/ATP carrier, does not bind cardiolipin. Here, we have developed novel methods to purify milligram amounts of UCP1 from native sources by using covalent chromatography that, unlike past methods, allows the protein to be prepared in defined conditions, free of excess detergent and lipid. Assessment of purified preparations by TLC reveal that UCP1 retains tightly bound cardiolipin, with a lipid phosphorus content equating to three molecules per protein, like the ADP/ATP carrier. Cardiolipin stabilizes UCP1, as demonstrated by reconstitution experiments and thermostability assays, indicating that the lipid has an integral role in the functioning of the protein, similar to other mitochondrial carriers. Furthermore, we find that UCP1 is not dimeric but monomeric, as indicated by size exclusion analysis, and has a ligand titration profile in isothermal calorimetric measurements that clearly shows that one nucleotide binds per monomer. These findings reveal the fundamental composition of UCP1, which is essential for understanding the mechanism of the protein. Our assessment of the properties of UCP1 indicate that it is not unique among mitochondrial carriers and so is likely to use a common exchange mechanism in its primary function in brown adipose tissue mitochondria. PMID:26038550

  20. Functionalization of SnO₂ crystals with a covalently-assembled porphyrin monolayer.

    PubMed

    Cristaldi, Domenico A; Gulino, Antonino

    2013-06-01

    The functionalization of micro- and nano-sized metal-oxide powders offers many advantages because of their large surface areas and, therefore, the large number of functional molecules that can be grafted onto the grain surfaces. Porphyrin molecules on large band-gap semiconducting metal oxides represent key materials for many different optical and electronic applications. Herein, we have proposed a general two-step procedure for the functionalization of metal-oxide crystals with dye-sensitizers. In particular, we functionalized SnO₂ nanoparticles with a monolayer of the bifunctional trichloro[4-(chloromethyl)phenyl]silane. Then, a monolayer of 5,10,15,20-tetrakis(4-hydroxyphenyl)-21H,23H-porphyne was covalently bound to the silanized SnO₂ grains. IR, UV/Vis, and luminescence measurements were used for optical characterization. The measured footprint of the grafted porphyrin molecules indicated total surface coverage of the grains. The surface electronic characterization was performed by using X-ray photoelectron spectroscopy. Emission measurements revealed two strong bands at 664.1 and 721.0 nm that were attributed to the porphyrin monolayer assembled on the surface of the SnO₂ crystals.

  1. Gluing together metallic and covalent layers to form Ru2C under ambient conditions.

    PubMed

    Sun, Weiwei; Li, Yunguo; Zhu, Li; Ma, Yanming; Di Marco, Igor; Johansson, Börje; Korzhavyi, Pavel

    2015-04-21

    Ru2C has recently been synthesised at high pressure and high temperature, and was assumed to have a structure with space group P3̅m1. However, subsequent theoretical work has revealed that this structure is unstable under ambient conditions, which motivated us to look for the stable structure. In this work, we explore the structures of Ru2C by using an unbiased swarm structure searching algorithm. The structures with R3m and R3̅m symmetries have been found to be lower in energy than the P3̅m1 structure, at the same time being dynamically stable under ambient conditions. These layered structures consist of alternating Ru bilayers and C monolayers in the R3m structure, and alternating Ru tetra-layers and C bilayers in the R3̅m structure. The C layers are more evenly distributed and more covalently bound to the Ru layers in the R3m structure than in the R3̅m structure. Instead, in the R3̅m structure there exists more Ru-Ru metallic bonding, which has a crucial role in diminishing the hardness of this material. Our findings should stimulate further explorations of the structures and properties of the heavy transition metal carbides and nitrides, potentially leading to industrial applications.

  2. Ibrutinib: a first in class covalent inhibitor of Bruton’s tyrosine kinase

    PubMed Central

    Davids, Matthew S; Brown, Jennifer R

    2015-01-01

    Ibrutinib (formerly PCI-32765) is a potent, covalent inhibitor of Bruton’s tyrosine kinase, a kinase downstream of the B-cell receptor that is critical for B-cell survival and proliferation. In preclinical studies, ibrutinib bound to Bruton’s tyrosine kinase with high affinity, leading to inhibition of B-cell receptor signaling, decreased B-cell activation and induction of apoptosis. In clinical studies, ibrutinib has been well-tolerated and has demonstrated profound anti-tumor activity in a variety of hematologic malignancies, most notably chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL), leading to US FDA approval for relapsed CLL and MCL. Ongoing studies are evaluating ibrutinib in other types of non-Hodgkin’s lymphoma, such as diffuse large B-cell lymphoma and Waldenström’s macrogobulinemia, in larger Phase III studies in CLL and MCL, and in combination studies with monoclonal antibodies and chemotherapy. Future studies will combine ibrutinib with other promising novel agents currently in development in hematologic malignancies. PMID:24941982

  3. An Efficient Covalent Coating on Glass Slides for Preparation of Optical Oligonucleotide Microarrays

    PubMed Central

    Pourjahed, Atefeh; Rabiee, Mohammad; Tahriri, Mohammadreza

    2013-01-01

    Objective(s): Microarrays are potential analyzing tools for genomics and proteomics researches, which is in needed of suitable substrate for coating and also hybridization of biomolecules. Materials and Methods: In this research, a thin film of oxidized agarose was prepared on the glass slides which previously coated with poly-L-lysine (PLL). Some of the aldehyde groups of the activated agarose linked covalently to PLL amine groups; also bound to the amino groups of biomolecules. These linkages were fixed by UV irradiation. The prepared substrates were compared to only agarose-coated and PLL-coated slides. Results: Results on atomic force microscope (AFM) demonstrated that agarose provided three-dimensional surface which had higher loading and bindig capacity for biomolecules than PLL-coated surface which had two-dimensional surface. In addition, the signal-to-noise ratio in hybridization reactions performed on the agarose-PLL coated substrates increased two fold and four fold compared to agarose and PLL coated substrates, respectively. Conclusion: The agarose-PLL microarrays had the highest signal (2546) and lowest background signal (205) in hybridization, suggesting that the prepared slides are suitable in analyzing wide concentration range of analytes. PMID:24570832

  4. The Search for Covalently Ligandable Proteins in Biological Systems.

    PubMed

    Badshah, Syed Lal; Mabkhot, Yahia Nasser

    2016-01-01

    This commentary highlights the recent article published in Nature, June 2016, titled: "Proteome-wide covalent ligand discovery in native biological systems". They screened the whole proteome of different human cell lines and cell lysates. Around 700 druggable cysteines in the whole proteome were found to bind the electrophilic fragments in both active and inactive states of the proteins. Their experiment and computational docking results agreed with one another. The usefulness of this study in terms of bringing a change in medicinal chemistry is highlighted here. PMID:27598117

  5. The Synthesis, Structures and Chemical Properties of Macrocyclic Ligands Covalently Bonded into Layered Arrays

    SciTech Connect

    Clearfield, Abraham

    2003-10-09

    OAK-B135 The immobilization of crown ethers tends to limit the leveling effect of solvents making the macrocycles more selective. In addition immobilization has the added advantage of relative ease of recovery of the otherwise soluble crown. We have affixed CH2PO3H2 groups to azacrown ethers. The resultant phosphorylated macrocycles may spontaneously aggregate into crystalline supramolecular linear arrays or contacted with cations produce layered or linear polymers. In the linear polymers the metal and phosphonic acids covalently bond into a central stem with the macrocyclic rings protruding from the stem as leaves on a twig. Two types of layered compounds were obtained with group 4 metals. Monoaza-crown ethers form a bilayer where the M4+ plus phosphonic acid groups build the layer and the rings fill the interlayer space. 1, 10-diazadiphosphonic acids cross-link the metal phosphonate layers forming a three-dimensional array of crown ethers. In order to improve diffusion into these 3-D arrays they are spaced by inclusion of phosphate or phosphate groups. Two series of azamacrocylic crown ethers were prepared containing rings with 20 to 32 atoms. These larger rings can complex two cations per ring. Methylene phosphonic acid groups have been bonded to the aza ring atoms to increase the complexing ability of these ligands. Our approach is to carry out acid-base titrations in the absence and presence of cations to determine the pKa values of the protons, both those bonded to aza groups and those associated with the phosphonic acid groups. From the differences in the titration curves obtained with and without the cations present we obtain the stoichiometry of complex formation and the complex stability constants. Some of the applications we are targeting include phase transfer catalysis, separation of cations and the separation of radioisotopes for diagnostic and cancer therapeutic purposes.

  6. How covalent heme to protein bonds influence the formation and reactivity of redox intermediates of a bacterial peroxidase.

    PubMed

    Auer, Markus; Nicolussi, Andrea; Schütz, Georg; Furtmüller, Paul G; Obinger, Christian

    2014-11-01

    The most striking feature of mammalian peroxidases, including myeloperoxidase and lactoperoxidase (LPO) is the existence of covalent bonds between the prosthetic group and the protein, which has a strong impact on their (electronic) structure and biophysical and chemical properties. Recently, a novel bacterial heme peroxidase with high structural and functional similarities to LPO was described. Being released from Escherichia coli, it contains mainly heme b, which can be autocatalytically modified and covalently bound to the protein by incubation with hydrogen peroxide. In the present study, we investigated the reactivity of these two forms in their ferric, compound I and compound II state in a multi-mixing stopped-flow study. Upon heme modification, the reactions between the ferric proteins with cyanide or H2O2 were accelerated. Moreover, apparent bimolecular rate constants of the reaction of compound I with iodide, thiocyanate, bromide, and tyrosine increased significantly and became similar to LPO. Kinetic data are discussed and compared with known structure-function relationships of the mammalian peroxidases LPO and myeloperoxidase.

  7. How Covalent Heme to Protein Bonds Influence the Formation and Reactivity of Redox Intermediates of a Bacterial Peroxidase*

    PubMed Central

    Auer, Markus; Nicolussi, Andrea; Schütz, Georg; Furtmüller, Paul G.; Obinger, Christian

    2014-01-01

    The most striking feature of mammalian peroxidases, including myeloperoxidase and lactoperoxidase (LPO) is the existence of covalent bonds between the prosthetic group and the protein, which has a strong impact on their (electronic) structure and biophysical and chemical properties. Recently, a novel bacterial heme peroxidase with high structural and functional similarities to LPO was described. Being released from Escherichia coli, it contains mainly heme b, which can be autocatalytically modified and covalently bound to the protein by incubation with hydrogen peroxide. In the present study, we investigated the reactivity of these two forms in their ferric, compound I and compound II state in a multi-mixing stopped-flow study. Upon heme modification, the reactions between the ferric proteins with cyanide or H2O2 were accelerated. Moreover, apparent bimolecular rate constants of the reaction of compound I with iodide, thiocyanate, bromide, and tyrosine increased significantly and became similar to LPO. Kinetic data are discussed and compared with known structure-function relationships of the mammalian peroxidases LPO and myeloperoxidase. PMID:25246525

  8. Non-Covalent Fluorescent Labeling of Hairpin DNA Probe Coupled with Hybridization Chain Reaction for Sensitive DNA Detection.

    PubMed

    Song, Luna; Zhang, Yonghua; Li, Junling; Gao, Qiang; Qi, Honglan; Zhang, Chengxiao

    2016-04-01

    An enzyme-free signal amplification-based assay for DNA detection was developed using fluorescent hairpin DNA probes coupled with hybridization chain reaction (HCR). The hairpin DNAs were designed to contain abasic sites in the stem moiety. Non-covalent labeling of the hairpin DNAs was achieved when a fluorescent ligand was bound to the abasic sites through hydrogen bonding with the orphan cytosine present on the complementary strand, accompanied by quench of ligand fluorescence. As a result, the resultant probes, the complex formed between the hairpin DNA and ligand, showed almost no fluorescence. Upon hybridization with target DNA, the probe underwent a dehybridization of the stem moiety containing an abasic site. The release of ligand from the abasic site to the solution resulted in an effective fluorescent enhancement, which can be used as a signal. Compared with a sensing system without HCR, a 20-fold increase in the sensitivity was achieved using the sensing system with HCR. The fluorescent intensity of the sensing system increased with the increase in target DNA concentration from 0.5 nM to 100 nM. A single mismatched target ss-DNA could be effectively discriminated from complementary target DNA. Genotyping of a G/C single-nucleotide polymorphism of polymerase chain reaction (PCR) products was successfully demonstrated with the sensing system. Therefore, integrating HCR strategy with non-covalent labeling of fluorescent hairpin DNA probes provides a sensitive and cost-effective DNA assay.

  9. Non-covalent functionalization of single-walled carbon nanotubes with modified polyethyleneimines for efficient gene delivery.

    PubMed

    Behnam, Behzad; Shier, Wayne T; Nia, Azadeh Hashem; Abnous, Khalil; Ramezani, Mohammad

    2013-09-15

    Functionalized carbon nanotubes (CNTs) have been recently emerged as important class of vectors for delivery of DNA and other biomolecules into various cells. In this study, single-walled carbon nanotubes (SWNTs) were functionalized by non-covalent binding of hydrophobic moieties, which were covalently linked to polyethyleneimines (PEIs). PEIs of three molecular weights (25, 10 and 1.8kDa) were used. CNTs were functionalized with the PEI series either through phospholipid moiety (via a polyethyleneglycol linker) or through directly-attached long (18 carbons) or intermediate (10 carbons) hydrophobic alkyl moieties. All PEI-functionalized CNTs exhibited good stability and dispersibility in biological media. Visualizing of functionalized CNTs and lack of aggregation were confirmed by atomic force microscopy. The PEI derivatives bound to CNTs retained the ability to fully condense plasmid DNA at low N/P ratios and substantial buffering capacity in the endosomal pH range. PEI-functionalized CNTs exhibited increased transfection efficiency compared to underivatized PEIs up to 19-fold increase being observed in the functionalized CNT with the smallest PEI tested, the smallest hydrophobic attachment moiety tested and no linker. Also PEI-functionalized CNTs were effective gene delivery vectors in vivo following tail vein injection in mice with the largest expression occurring with the vector PEI-functionalized through a polyethyleneglycol linker.

  10. Characterization of ellagitannins, gallotannins, and bound proanthocyanidins from California almond (Prunus dulcis) varieties.

    PubMed

    Xie, Liyang; Roto, Anna V; Bolling, Bradley W

    2012-12-12

    Extractable and bound proanthocyanidins and hydrolyzable tannins were characterized in Nonpareil, Carmel, and Butte almond varieties from California, with n = 3 samples/variety. Bound proanthocyanidins were recovered from extracted defatted almond residue by hydrolysis with 4 N sodium hydroxide and represented 3-21% of the total proanthocyanidin content among varieties. The bound proanthocyanidins were recovered primarily as monomers and dimers. In contrast, acid hydrolysis of extracted almond residue did not yield bound proanthocyanidins. Hydrolyzable tannins were characterized in aqueous acetone extracts of defatted almond using two-dimensional TLC and further quantitated by HPLC following acid hydrolysis. Almond hydrolyzable tannin content was 54.7 ± 2.3 mg ellagic acid and 27.4 ± 7.3 mg gallic acid per 100 g almond among varieties. The tannin contents of Nonpareil, Carmel, and Butte almond varieties were not significantly different. Thus, bound proanthocyanidins and hydrolyzable tannins significantly contribute to almond polyphenol content.

  11. The use of native chemical functional groups presented by wound beds for the covalent attachment of polymeric microcarriers of bioactive factors

    PubMed Central

    Jain, Rishabh; Agarwal, Ankit; Kierski, Patricia R.; Schurr, Michael J.; Murphy, Christopher J.; McAnulty, Jonathan F.; Abbott, Nicholas L.

    2012-01-01

    The development of versatile methods that provide spatial and temporal control over the presentation of physical and biochemical cues on wound beds can lead to new therapeutic approaches that expedite wound healing by favorably influencing cellular behaviors. Towards that goal, we report that native chemical functional groups presented by wound beds can be utilized for direct covalent attachment of polymeric microbeads. Specifically, we demonstrated the covalent attachment of maleimide-functionalized and catechol-functionalized microbeads, made of either polystyrene (non-degradable) or poly(lactic-co-glycolic acid) ((PLGA), degradable), to sulfhydryl and amine groups present on porcine dermis used here as an ex vivo model wound bed. A pronounced increase (10–70 fold) in the density and persistence of the covalently reactive microbeads was observed relative to microbeads that adsorb via non-covalent interactions. Complementary characterization of the surface chemistry of the ex vivo wound beds using Raman microspectroscopy provides support for our conclusion that the increased adherence of the maleimide-functionalized beads results from their covalent bond formation with sulfhydryl groups on the wound bed. The attachment of maleimide-functionalized microbeads to wounds created in live wild-type and diabetic mice led to observations of differential immobilization of microbeads on them and were consistent with anticipated differences in the presentation of sulfhydryl groups on the two different wound types. Finally, the incorporation of maleimide-functionalized microbeads in wounds created in wild-type mice did not impair the rate of wound closure relative to an untreated wound. Overall, the results presented in this paper enable a general and facile approach to the engineering of wound beds in which microbeads are covalently immobilized to wound beds. Such immobilized microbeads could be used in future studies to release bioactive factors (e.g., antimicrobial

  12. Gold nanoparticles for nucleic acid delivery.

    PubMed

    Ding, Ya; Jiang, Ziwen; Saha, Krishnendu; Kim, Chang Soo; Kim, Sung Tae; Landis, Ryan F; Rotello, Vincent M

    2014-06-01

    Gold nanoparticles provide an attractive and applicable scaffold for delivery of nucleic acids. In this review, we focus on the use of covalent and noncovalent gold nanoparticle conjugates for applications in gene delivery and RNA-interference technologies. We also discuss challenges in nucleic acid delivery, including endosomal entrapment/escape and active delivery/presentation of nucleic acids in the cell. PMID:24599278

  13. Detection of bound residues in soils by sandwich-immunoassay

    SciTech Connect

    Dosch, M.; Weller, M.G.; Niessner, R.

    1995-12-31

    Immunoassays are useful analytical instruments for the detection of many environmental compounds. This method was not introduced for the detection of non-extractable compounds in soil. So-called ``bound residues`` consist of a soil component, e.g. humic acids and an irreversibly bound pollutant. Because of the complexity of those macromolecules conventional analytical methods in general do not work. Enzyme immunoassays, in contrast, seem to have a large potential for applications and further developments in this field. The use of antibodies with high affinity to the analytes makes a selective detection of environmental pollutants possible. With the development of an enzyme-labeled sandwich-immunoassay polycyclic aromatic hydrocarbons (PAHs) irreversibly bound to humic acids were determined for the first time.

  14. Detection of bound residues in soils by sandwich-immunoassay

    NASA Astrophysics Data System (ADS)

    Dosch, M.; Weller, Michael G.; Niessner, Reinhard

    1995-10-01

    Immunoassays are useful analytical instruments for the detection of many environmental compounds. This method is now introduced for the detection of non-extractable compounds in soil. So-called 'bound residues' consist of a soil component, e.g. humic acids, and an irreversibly bound pollutant. Because of the complexity of those macromolecules conventional analytical methods in general do not work. Enzyme immunoassays, in contrast, seem to have a large potential for applications and further developments in this field. The use of antibodies with high affinity to the analytes makes a selective detection of environmental pollutants possible. With the development of an enzyme-labeled sandwich-immunoassay polycyclic aromatic hydrocarbons (PAHs), irreversibly bound to humic acids, were determined for the first time.

  15. Covalent cross-links in polyampholytic chitosan fibers enhances bone regeneration in a rabbit model.

    PubMed

    Ghosh, Paulomi; Rameshbabu, Arun Prabhu; Das, Dipankar; Francis, Nimmy K; Pawar, Harpreet Singh; Subramanian, Bhuvaneshwaran; Pal, Sagar; Dhara, Santanu

    2015-01-01

    Chitosan fibers were prepared in citric acid bath, pH 7.4 and NaOH solution at pH 13, to form ionotropically cross-linked and uncross-linked fibers, respectively. The fibers formed in citric acid bath were further cross-linked via carbodiimide chemistry; wherein the pendant carboxyl moieties of citric acid were used for new amide bond formation. Moreover, upon covalent cross-linking in the ionically gelled citrate-chitosan fibers, incomplete conversion of the ion pairs to amide linkages took place resulting in the formation of a dual network structure. The dual cross-linked fibers displayed improved mechanical property, higher stability against enzymatic degradation, hydrophobicity and superior bio-mineralization compared to the uncross-linked and native citrate cross-linked fibers. Additionally, upon cyclic loading, the ion pairs in the dual cross-linked fibers dissociated by dissipating energy and reformed during the relaxation period. The twin property of elasticity and energy dissipation mechanism makes the dual cross-linked fiber unique under dynamic mechanical conditions. The differences in the physico-chemical characteristics were reflected in protein adsorption, which in turn influenced the cellular activities on the fibers. Compared to the uncross-linked and ionotropically cross-linked fibers, the dual cross-linked fibers demonstrated higher proliferation and osteogenic differentiation of the MSCs in vitro as well as better osseous tissue regeneration in a rabbit model. PMID:25483844

  16. Tandem Mass Spectrometry for Characterization of Covalent Adducts of DNA with Anti-cancer Therapeutics

    PubMed Central

    Silvestri, Catherine; Brodbelt, Jennifer S.

    2012-01-01

    The chemotherapeutic activities of many anticancer and antibacterial drugs arise from their interactions with nucleic acid substrates. Some of these ligands interact with DNA in a way that causes conformational changes or damage to the nucleic acid targets, ultimately altering recognition by key DNA-specific enzymes, interfering with DNA transcription or prohibiting replication, and terminating cell growth and proliferation. The design and synthesis of ligands that bind to nucleic acids remains a dynamic field in medicinal chemistry and pharmaceutical research. The quest for more selective and efficacious DNA-interactive anti-cancer chemotherapeutics has likewise catalyzed the need for sensitive analytical methods that can provide structural information about the nature of the resulting DNA adducts and provide insight into the mechanistic pathways of the DNA/drug interactions and the impact on the cellular processes in biological systems. This review focuses on the array of tandem mass spectrometric strategies developed and applied for characterization of covalent adducts formed between DNA and anti-cancer ligands. PMID:23150278

  17. Suicide inactivation of covalent peroxidase-mimicking DNAzyme with hydrogen peroxide and its protection by a reductant substrate.

    PubMed

    Gribas, Anastasia V; Zatsepin, Timofey S; Korolev, Sergey P; Gottikh, Marina B; Sakharov, Ivan Yu

    2016-08-01

    Recently a covalent peroxidase-mimicking DNAzyme (cPMDNAzyme) with the improved catalytic activity was prepared. Here we demonstrate that hydrogen peroxide, the oxidant substrate of cPMDNAzyme is an inactivating agent of this catalyst. Presence of the reductant substrate, 2,2'-azino-bis(3-ethylbenthothiazoline-6-sulfonic acid (ABTS) prevents the inactivation of cPMDNAzyme. The experimental conditions (pH-optimum, concentrations of ABTS and H2O2) for the determination of cPMDNAzyme activity were optimized that allows a construction of the colorimetric cPMDNAzyme-based biosensors and assays with improved sensitivity. PMID:27216675

  18. Detection, purification, and characterization of two species of covalently closed circular proviral DNA molecules of bovine leukemia virus.

    PubMed Central

    Kashmiri, S V; Mehdi, R; Ferrer, J F

    1983-01-01

    Cocultivation of uninfected and bovine leukemia virus-producing bat cells yielded, in addition to the unintegrated linear DNA duplex, DNA molecules that migrated as 4.4- and 4.8-kilobase-pair DNA fragments in gel electrophoresis. These DNA molecules were purified by acid-phenol extraction and cleaved with restriction endonucleases EcoRI, and HindIII, which have one recognition site each on the bovine leukemia virus proviral DNA. Such cleavage generated DNA molecules of approximately 10.0 and 9.4 kilobase pairs, thus indicating the existence of two species of covalently closed circular molecules of bovine leukemia virus proviral DNA. Images PMID:6300454

  19. Covalent Design for Dye-Sensitized H2-Evolving Photocathodes Based on a Cobalt Diimine-Dioxime Catalyst.

    PubMed

    Kaeffer, Nicolas; Massin, Julien; Lebrun, Colette; Renault, Olivier; Chavarot-Kerlidou, Murielle; Artero, Vincent

    2016-09-28

    Dye-sensitized photoelectrochemical cells (DS-PECs) for water splitting hold promise for the large-scale storage of solar energy in the form of (solar) fuels, owing to the low cost and ease to process of their constitutive photoelectrode materials. The efficiency of such systems ultimately depends on our capacity to promote unidirectional light-driven electron transfer from the electrode substrate to a catalytic moiety. We report here on the first noble-metal free and covalent dye-catalyst assembly able to achieve photoelectrochemical visible light-driven H2 evolution in mildly acidic aqueous conditions when grafted onto p-type NiO electrode substrate. PMID:27595317

  20. Probing the Active Center of Benzaldehyde Lyase with Substitutions and the Pseudosubstrate Analogue Benzoylphosphonic Acid Methyl Ester

    SciTech Connect

    Brandt, Gabriel S.; Nemeria, Natalia; Chakraborty, Sumit; McLeish, Michael J.; Yep, Alejandra; Kenyon, George L.; Petsko, Gregory A.; Jordan, Frank; Ringe, Dagmar

    2008-07-28

    Benzaldehyde lyase (BAL) catalyzes the reversible cleavage of (R)-benzoin to benzaldehyde utilizing thiamin diphosphate and Mg{sup 2+} as cofactors. The enzyme is important for the chemoenzymatic synthesis of a wide range of compounds via its carboligation reaction mechanism. In addition to its principal functions, BAL can slowly decarboxylate aromatic amino acids such as benzoylformic acid. It is also intriguing mechanistically due to the paucity of acid-base residues at the active center that can participate in proton transfer steps thought to be necessary for these types of reactions. Here methyl benzoylphosphonate, an excellent electrostatic analogue of benzoylformic acid, is used to probe the mechanism of benzaldehyde lyase. The structure of benzaldehyde lyase in its covalent complex with methyl benzoylphosphonate was determined to 2.49 {angstrom} (Protein Data Bank entry 3D7K) and represents the first structure of this enzyme with a compound bound in the active site. No large structural reorganization was detected compared to the complex of the enzyme with thiamin diphosphate. The configuration of the predecarboxylation thiamin-bound intermediate was clarified by the structure. Both spectroscopic and X-ray structural studies are consistent with inhibition resulting from the binding of MBP to the thiamin diphosphate in the active centers. We also delineated the role of His29 (the sole potential acid-base catalyst in the active site other than the highly conserved Glu50) and Trp163 in cofactor activation and catalysis by benzaldehyde lyase.

  1. Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester.

    PubMed

    Brandt, Gabriel S; Nemeria, Natalia; Chakraborty, Sumit; McLeish, Michael J; Yep, Alejandra; Kenyon, George L; Petsko, Gregory A; Jordan, Frank; Ringe, Dagmar

    2008-07-22

    Benzaldehyde lyase (BAL) catalyzes the reversible cleavage of ( R)-benzoin to benzaldehyde utilizing thiamin diphosphate and Mg (2+) as cofactors. The enzyme is important for the chemoenzymatic synthesis of a wide range of compounds via its carboligation reaction mechanism. In addition to its principal functions, BAL can slowly decarboxylate aromatic amino acids such as benzoylformic acid. It is also intriguing mechanistically due to the paucity of acid-base residues at the active center that can participate in proton transfer steps thought to be necessary for these types of reactions. Here methyl benzoylphosphonate, an excellent electrostatic analogue of benzoylformic acid, is used to probe the mechanism of benzaldehyde lyase. The structure of benzaldehyde lyase in its covalent complex with methyl benzoylphosphonate was determined to 2.49 A (Protein Data Bank entry 3D7K ) and represents the first structure of this enzyme with a compound bound in the active site. No large structural reorganization was detected compared to the complex of the enzyme with thiamin diphosphate. The configuration of the predecarboxylation thiamin-bound intermediate was clarified by the structure. Both spectroscopic and X-ray structural studies are consistent with inhibition resulting from the binding of MBP to the thiamin diphosphate in the active centers. We also delineated the role of His29 (the sole potential acid-base catalyst in the active site other than the highly conserved Glu50) and Trp163 in cofactor activation and catalysis by benzaldehyde lyase.

  2. One-Step Dipping Method for Covalently Grafting Polymer Films onto a Si Surface from Aqueous Media.

    PubMed

    Zhang, Junhong; Li, Ming; Zhang, Wenqi; Cao, Liqiang

    2016-08-30

    A facile and one-pot dipping method was proposed in this article for the first time to prepare vinylic polymer films on a silicon (Si) surface. This novel process was conducted in acidic aqueous media containing 4-nitrobenzene diazonium (NBD) tetrafluoroborate, hydrofluoric acid (HF), and vinylic monomers at room temperature in the open air and without any apparatus requirement. The formation of the polyvinyl film was confirmed by corroborating evidence from ellipsometry, Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and atomic force microscope (AFM) analysis. The results revealed that both polymers of poorly water soluble methyl methacrylate (MMA) and water-soluble acrylic acid (AA) monomers were covalently grafted onto the Si surface via this simple process. The polyvinyl film was composed of polynitrophenyl (PNP) and polyvinyl, where PNP was doped into polyvinyl chains throughout the entire film. From a mechanistic point of view, the simple dipping method took advantage of the ability of the NBD cation to be spontaneously reduced at the Si surface at open circuit potential, providing aryl radicals. These radicals can be covalently bonded to the Si surface to form the PNP primer layer. Although the PNP sublayer was thinner and difficult to detect, it was necessary to graft polyvinyl chains. Furthermore, the aryl radicals were used to initiate the polymerization of vinylic monomers. The radical-terminated polyvinyl chains formed in the solution were then added to the aromatic rings of the primer layer to form the expected polyvinyl film. PMID:27441573

  3. Poly(DL-lactic acid) film surface modification with heparin for improving hemocompatibility of blood-contacting bioresorbable devices.

    PubMed

    Sharkawi, Tahmer; Darcos, Vincent; Vert, Michel

    2011-07-01

    This work describes a simple method to immobilize heparin by covalent bonding to the surface of poly(lactic acid) film with the aim of showing improved hemocompatibility. Carboxyl groups present in heparin molecules were activated by reaction with N-hydroxy-succinimide and allowed to react with free amino groups created at the surface of poly(DL-lactic acid) films by controlled aminolysis. Contact angle measurements and XPS analysis confirmed the binding. Quantification was determined by radioactivity using heparin labeled with tritium. The surface exhibited anti factor Xa activity, thus confirming the presence of bounded heparin that kept some biological activity. Finally platelets adhesion showed less platelet adhesion on heparin modified films as well as preserved morphology.

  4. Experimental activation of bound entanglement.

    PubMed

    Kaneda, Fumihiro; Shimizu, Ryosuke; Ishizaka, Satoshi; Mitsumori, Yasuyoshi; Kosaka, Hideo; Edamatsu, Keiichi

    2012-07-27

    Entanglement is one of the essential resources in quantum information and communication technology (QICT). The entanglement thus far explored and applied to QICT has been pure and distillable entanglement. Yet, there is another type of entanglement, called "bound entanglement," which is not distillable by local operations and classical communication. We demonstrate the experimental "activation" of the bound entanglement held in the four-qubit Smolin state, unleashing its immanent entanglement in distillable form, with the help of auxiliary two-qubit entanglement and local operations and classical communication. We anticipate that it opens the way to a new class of QICT applications that utilize more general classes of entanglement than ever, including bound entanglement.

  5. Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity

    SciTech Connect

    Pegan, Scott D.; Serrano, Hector; Whitman, Christian P.; Mesecar, Andrew D.

    2009-03-04

    Trans-3-chloroacrylic acid dehalogenase (CaaD) is a critical enzyme in the trans-1,3-dichloropropene (DCP) degradation pathway in Pseudomonas pavonaceae 170. This enzyme allows bacteria to use trans-DCP, a common component in commercially produced fumigants, as a carbon source. CaaD specifically catalyzes the fourth step of the pathway by cofactor-independent dehalogenation of a vinyl carbon-halogen bond. Previous studies have reported an X-ray structure of CaaD under acidic conditions with a covalent modification of the catalytic {beta}Pro1 residue. Here, the 1.7 {angstrom} resolution X-ray structure of CaaD under neutral (pH 6.5) conditions is reported without the presence of the covalent adduct. In this new structure, a substrate-like acetate molecule is bound within the active site in a position analogous to the putative substrate-binding site. Additionally, a catalytically important water molecule was identified, consistent with previously proposed reaction schemes. Finally, flexibility of the catalytically relevant side chain {alpha}Glu52 is observed in the structure, supporting its role in the catalytic mechanism.

  6. Enzymatic modification of chitosan by cinnamic acids: Antibacterial activity against Ralstonia solanacearum.

    PubMed

    Yang, Caifeng; Zhou, Yu; Zheng, Yu; Li, Changlong; Sheng, Sheng; Wang, Jun; Wu, Fuan

    2016-06-01

    This study aimed to identify chitosan polymers that have antibacterial activity against the bacterial wilt pathogen. The chitosan polymers were enzymatically synthesized using chitosan and five cinnamic acids (CADs): caffeic acid (CA), ferulic acid (FA), cinnamic acid (CIA), p-coumaric acid (COA) and chlorogenic acid (CHA), using laccase from Pleurotus ostreatus as a catalyst. The reaction was performed in a phosphate buffered solution under heterogenous reaction conditions. The chitosan derivatives (CTS-g-CADs) were characterized by FT-IR, XRD, TGA and SEM. FT-IR demonstrated that the reaction products bound covalently to the free amino groups or hydroxyl groups of chitosan via band of amide I or ester band. XRD showed a reduced packing density for grafted chitosan comparing to original chitosan. TGA demonstrated that CTS-g-CADs have a higher thermostability than chitosan. Additionally, chitosan and its derivatives showed similar antibacterial activity. However, the IC50 value of the chitosan-caffeic acid derivative (CTS-g-CA) against the mulberry bacterial wilt pathogen RS-5 was 0.23mg/mL, which was two-fifths of the IC50 value of chitosan. Therefore, the enzymatically synthesized chitosan polymers can be used to control plant diseases in biotechnological domains. PMID:26993531

  7. Enzymatic modification of chitosan by cinnamic acids: Antibacterial activity against Ralstonia solanacearum.

    PubMed

    Yang, Caifeng; Zhou, Yu; Zheng, Yu; Li, Changlong; Sheng, Sheng; Wang, Jun; Wu, Fuan

    2016-06-01

    This study aimed to identify chitosan polymers that have antibacterial activity against the bacterial wilt pathogen. The chitosan polymers were enzymatically synthesized using chitosan and five cinnamic acids (CADs): caffeic acid (CA), ferulic acid (FA), cinnamic acid (CIA), p-coumaric acid (COA) and chlorogenic acid (CHA), using laccase from Pleurotus ostreatus as a catalyst. The reaction was performed in a phosphate buffered solution under heterogenous reaction conditions. The chitosan derivatives (CTS-g-CADs) were characterized by FT-IR, XRD, TGA and SEM. FT-IR demonstrated that the reaction products bound covalently to the free amino groups or hydroxyl groups of chitosan via band of amide I or ester band. XRD showed a reduced packing density for grafted chitosan comparing to original chitosan. TGA demonstrated that CTS-g-CADs have a higher thermostability than chitosan. Additionally, chitosan and its derivatives showed similar antibacterial activity. However, the IC50 value of the chitosan-caffeic acid derivative (CTS-g-CA) against the mulberry bacterial wilt pathogen RS-5 was 0.23mg/mL, which was two-fifths of the IC50 value of chitosan. Therefore, the enzymatically synthesized chitosan polymers can be used to control plant diseases in biotechnological domains.

  8. Covalent bonds against magnetism in transition metal compounds.

    PubMed

    Streltsov, Sergey V; Khomskii, Daniel I

    2016-09-20

    Magnetism in transition metal compounds is usually considered starting from a description of isolated ions, as exact as possible, and treating their (exchange) interaction at a later stage. We show that this standard approach may break down in many cases, especially in 4d and 5d compounds. We argue that there is an important intersite effect-an orbital-selective formation of covalent metal-metal bonds that leads to an "exclusion" of corresponding electrons from the magnetic subsystem, and thus strongly affects magnetic properties of the system. This effect is especially prominent for noninteger electron number, when it results in suppression of the famous double exchange, the main mechanism of ferromagnetism in transition metal compounds. We study this mechanism analytically and numerically and show that it explains magnetic properties of not only several 4d-5d materials, including Nb2O2F3 and Ba5AlIr2O11, but can also be operative in 3d transition metal oxides, e.g., in CrO2 under pressure. We also discuss the role of spin-orbit coupling on the competition between covalency and magnetism. Our results demonstrate that strong intersite coupling may invalidate the standard single-site starting point for considering magnetism, and can lead to a qualitatively new behavior. PMID:27601669

  9. Optimization of covalent antibody immobilization on macroporous silicon solid supports

    NASA Astrophysics Data System (ADS)

    Das, R. Dev; Maji, S.; Das, S.; RoyChaudhuri, C.

    2010-08-01

    In this paper, optimization of the protocol for covalent antibody immobilization on macroporous silicon solid supports of various porosities, which is recently being employed as a promising substrate for biosensors, has been reported. Covalent binding of antibody has been carried out by silanization and crosslinker attachment on the substrate. For maximum antibody immobilization on macroporous silicon, all the individual processes have been separately optimized for the first time in terms of treatment time, pH, concentration, incubation time and others with the help of optical density measurements. The optimum treatment of the surface after every step has been further reconfirmed by detailed EDX analysis, SEM measurements and contact angle measurements. It has been observed that the density of antibody binding increases with increasing porosity and for a 70% porosity macroporous sample it is almost three times more than that of planar silicon which is significantly higher than the previous comparative reports on planar silicon and macroporous silicon. The amount of properly oriented HIgG antibodies has been estimated by quantification of the alkaline phosphate conjugated protein A binding by optical density measurements.

  10. Discovery of potent and selective covalent inhibitors of JNK

    PubMed Central

    Zhang, Tinghu; Inesta-Vaquera, Francisco; Niepel, Mario; Zhang, Jianming; Ficarro, Scott B.; Machleidt, Thomas; Xie, Ting; Marto, Jarrod A.; Kim, NamDoo; Sim, Taebo; Laughlin, John D; Park, Hajeung; LoGrasso, Philip V.; Patricelli, Matt; Nomanbhoy, Tyzoon K.; Sorger, Peter K.; Alessi, Dario R.; Gray, Nathanael S.

    2012-01-01

    The mitogen activated kinases JNK1/2/3 are key enzymes in signaling modules that transduce and integrate extracellular stimuli into coordinated cellular response. Here we report the discovery of the first irreversible inhibitors of JNK1/2/3. We describe two JNK3 co-crystal structures at 2.60 and 2.97 Å resolutions that show the compounds form covalent bonds with a conserved cysteine residue. JNK-IN-8 is a selective JNK inhibitor that inhibits phosphorylation of c-Jun, a direct substrate of JNK kinase, in cells exposed to sub-micromolar drug in a manner that depends on covalent modification of the conserved cysteine residue. Extensive biochemical, cellular and pathway-based profiling establish the selectivity of JNK-IN-8 for JNK and suggest that the compound will be broadly useful as a pharmacological probe of JNK-dependent signal transduction. Potential lead compounds have also been identified for kinases including IRAK1, PIK3C3, PIP4K2C, and PIP5K3. PMID:22284361

  11. Human IgG2 can form covalent dimers.

    PubMed

    Yoo, Esther M; Wims, Letitia A; Chan, Lisa A; Morrison, Sherie L

    2003-03-15

    Unlike IgA and IgM, IgG has not yet been shown to form covalent polymers. However in the presence of specific Ag, murine IgG3 has been shown to polymerize through noncovalent interactions. In contrast to the noncovalent oligomers found with murine IgG3, we have detected covalent dimers in three different recombinant human IgG2 Abs produced in myeloma cells. Both IgG2,kappa and IgG2,lambda can form dimers. In addition, analysis of pooled human gamma globulin and several normal sera revealed the presence of IgG2 dimers. The IgG2 dimers are in contrast to the noncovalent IgG dimers found in pooled sera of multiple donors resulting from idiotype/anti-idiotype (Id/anti-Id) interactions. Cyanogen bromide cleavage analysis suggests that one or more Cys residues in the gamma 2 hinge are involved in dimer assembly. The potential role of IgG2 dimers in immunity against carbohydrate Ags is discussed.

  12. Covalent bonds against magnetism in transition metal compounds.

    PubMed

    Streltsov, Sergey V; Khomskii, Daniel I

    2016-09-20

    Magnetism in transition metal compounds is usually considered starting from a description of isolated ions, as exact as possible, and treating their (exchange) interaction at a later stage. We show that this standard approach may break down in many cases, especially in 4d and 5d compounds. We argue that there is an important intersite effect-an orbital-selective formation of covalent metal-metal bonds that leads to an "exclusion" of corresponding electrons from the magnetic subsystem, and thus strongly affects magnetic properties of the system. This effect is especially prominent for noninteger electron number, when it results in suppression of the famous double exchange, the main mechanism of ferromagnetism in transition metal compounds. We study this mechanism analytically and numerically and show that it explains magnetic properties of not only several 4d-5d materials, including Nb2O2F3 and Ba5AlIr2O11, but can also be operative in 3d transition metal oxides, e.g., in CrO2 under pressure. We also discuss the role of spin-orbit coupling on the competition between covalency and magnetism. Our results demonstrate that strong intersite coupling may invalidate the standard single-site starting point for considering magnetism, and can lead to a qualitatively new behavior.

  13. Orbital reconstruction and covalent bonding at an oxide interface.

    SciTech Connect

    Chakhalian, J.; Freeland, J. W.; Habermeier, H.-U.; Cristiani, G.; Khaliullin, G.; van Veenendaal, M.; Keimer, B.; X-Ray Science Division; Univ. of Arkansas; Max Planck Inst.for Solid State Research; Northern Illinois Univ.

    2007-11-16

    Orbital reconstructions and covalent bonding must be considered as important factors in the rational design of oxide heterostructures with engineered physical properties. We have investigated the interface between high-temperature superconducting (Y,Ca)Ba{sub 2}Cu{sub 3}O{sub 7} and metallic La{sub 0.67}Ca{sub 0.33}MnO{sub 3} by resonant x-ray spectroscopy. A charge of about -0.2 electron is transferred from Mn to Cu ions across the interface and induces a major reconstruction of the orbital occupation and orbital symmetry in the interfacial CuO{sub 2} layers. In particular, the Cu d{sub 3z{sup 2}-r{sup 2}} orbital, which is fully occupied and electronically inactive in the bulk, is partially occupied at the interface. Supported by exact-diagonalization calculations, these data indicate the formation of a strong chemical bond between Cu and Mn atoms across the interface. Orbital reconstructions and associated covalent bonding are thus important factors in determining the physical properties of oxide heterostructures.

  14. Non-covalent and reversible functionalization of carbon nanotubes

    PubMed Central

    Di Crescenzo, Antonello; Ettorre, Valeria

    2014-01-01

    Summary Carbon nanotubes (CNTs) have been proposed and actively explored as multipurpose innovative nanoscaffolds for applications in fields such as material science, drug delivery and diagnostic applications. Their versatile physicochemical features are nonetheless limited by their scarce solubilization in both aqueous and organic solvents. In order to overcome this drawback CNTs can be easily non-covalently functionalized with different dispersants. In the present review we focus on the peculiar hydrophobic character of pristine CNTs that prevent them to easily disperse in organic solvents. We report some interesting examples of CNTs dispersants with the aim to highlight the essential features a molecule should possess in order to act as a good carbon nanotube dispersant both in water and in organic solvents. The review pinpoints also a few examples of dispersant design. The last section is devoted to the exploitation of the major quality of non-covalent functionalization that is its reversibility and the possibility to obtain stimuli-responsive precipitation or dispersion of CNTs. PMID:25383279

  15. Covalent attachment of nanoparticles to copolymer surfaces to control structure-property relationships

    NASA Astrophysics Data System (ADS)

    McConnell, Marla D.

    Interest in functional nanoparticles has increased in recent years, because their small size gives them unique properties. Surface assembly of nanoparticles is particularly appealing, because it can create surfaces with tunable wetting and optical properties. This thesis presents a novel method for the covalent assembly of silica nanoparticles on random copolymer films via covalent bonding, and the subsequent analysis of the wetting and optical properties of these functionalized surfaces. First, the kinetics of the covalent attachment of amine-modified silica nanoparticles to poly(styrene-ran-acrylic acid) were investigated. The surface swelling of the copolymer films upon exposure to reaction solvents was studied with in situ AFM. The films' surface roughness controlled the nanoparticle attachment kinetics, as well as the final nanoparticle coverage. For particle diameters on the order of the roughness features, 70% surface coverage was achieved, while particles with diameters much larger than the surface features reached only 30% coverage. The wetting properties of the nanoparticle surfaces were investigated as a function of particle coverage and diameter. At low coverages of small particles, the surfaces exhibited Wenzel-type wetting behavior. At high particle coverages, the surfaces showed Cassie-type wetting. Finally, the particles were observed to sink into the polymer film with increasing reaction time. This sinking, as well as the magnitude of the contact angles achieved at high particle coverages, led to the hypothesis that polymer chains wet onto the surface of the silica particles. Core-shell Janus particles were prepared by electrostatic assembly of gold nanoparticles on the unprotected surfaces of the silica particles. The plasmon resonance absorption of the gold particles underwent a red shift upon formation of closely-packed networks on the silica particle surfaces. By applying gold, chromium, and gold:palladium coatings to the Janus particles and

  16. Bounds for nonlocality distillation protocols

    SciTech Connect

    Forster, Manuel

    2011-06-15

    Nonlocality can be quantified by the violation of a Bell inequality. Since this violation may be amplified by local operations, an alternative measure has been proposed--distillable nonlocality. The alternative measure is difficult to calculate exactly due to the double exponential growth of the parameter space. In this paper, we give a way to bound the distillable nonlocality of a resource by the solutions to a related optimization problem. Our upper bounds are exponentially easier to compute than the exact value and are shown to be meaningful in general and tight in some cases.

  17. Upper Bound for Induced Gravitation

    NASA Astrophysics Data System (ADS)

    Khuri, N. N.

    1982-08-01

    Given the assumption that Gind-1 given by the Adler-Zee formula is positive, an explicit and rigorous upper bound is derived for it. For pure SU(N) gauge theory, (16πG)-1<=(2512π2)(N2-1)ΛN2 is obtained where ΛN is the mass scale. In general the bound (16πG)-1<=25(π2144)CψΛ2 is obtained, where Cψ is the coefficient of the most singular anomaly contribution in x space, a constant easily determined by low-order perturbation theory for any gauge group.

  18. On lower bounds for polarisability

    NASA Astrophysics Data System (ADS)

    Montgomery, H. E.; Pupyshev, V. I.

    2013-09-01

    The response of molecular systems to external fields was one of the first areas studied after development of the new quantum mechanics. Early work by Kirkwood and Buckingham developed polarisability lower bounds that are still used today. This work uses an inequality proposed by Linderberg to develop a treatment of polarisability lower bounds that unifies the work of Kirkwood and Buckingham with Hylleraas' variational perturbation theory. In particular, the prehistory of the works of Kirkwood and Buckingham is described. Numerical examples are presented to demonstrate the convergence of approximate wavefunctions in the confined atom problem. The applicability of dimensional scaling and its utility in the analysis of confined systems are also discussed.

  19. Chemisorption of Perfluorooctanoic Acid on Powdered Activated Carbon Initiated by Persulfate in Aqueous Solution.

    PubMed

    Sun, Bo; Ma, Jun; Sedlak, David L

    2016-07-19

    Perfluorooctanoic acid (PFOA) is a perfluorocarboxylic acid that is difficult to treat by most conventional methods. As a result, it is often removed from solution by adsorption on powdered activated carbon (PAC), followed by incineration of the spent carbon. To provide a new approach for treatment, PFOA was exposed to sulfate radicals (SO4(-•)) produced by thermolysis of persulfate (S2O8(2-)) in the presence of PAC. Under acidic conditions, thermal activation of persulfate resulted in transformation of PFOA to shorter-chain-length perfluorinated compounds, as previously reported. However, when thermolysis of persulfate occurred under circumneutral pH conditions in the presence of PAC, a new removal pathway for PFOA was observed. Under these conditions, the removal of PFOA was attributable to chemisorption, a process in which PAC catalyzed persulfate decomposition and reacted with the transformation products to produce covalently bound PFOA. At PAC concentrations between 200 and 1000 mg/L and an initial PFOA concentration of 0.5 μM, covalent bonding resulted in removal of 10-40% of the PFOA. Under these conditions, the process resulted in removal of more than half of a more hydrophilic perfluoroalkyl acid (i.e., perfluorobutanoic acid, PFBA), which was greater than the amount of PFBA removed by physical adsorption on PAC. Although the high reaction temperatures (i.e., 80 °C) and relatively high doses of PAC used in this study may be impractical for drinking water treatment, this process may be applied to the treatment of these recalcitrant compounds in industrial wastewater, reverse osmosis concentrate, and other waters that contain high concentrations of PFOA and other perfluorocarboxylic acids. PMID:27336204

  20. INACTIVATION OF MYELOPEROXIDASE BY BENZOIC ACID HYDRAZIDE*

    PubMed Central

    Huang, Jiansheng; Smith, Forrest; Panizzi, Jennifer R.; Goodwin, Douglas C.; Panizzi, Peter

    2015-01-01

    Myeloperoxidase (MPO) is expressed by myeloid cells for the purpose of catalyzing the formation of hypochlorous acid, from chloride ions and reaction with a hydrogen peroxide-charged heme covalently bound to the enzyme. Most peroxidase enzymes both plant and mammalian are inhibited by benzoic acid hydrazide (BAH)-containing compounds, but the mechanism underlying MPO inhibition by BAH compounds is largely unknown. Recently, we reported MPO inhibition by BAH and 4-(trifluoromethyl)-BAH was due to hydrolysis of the ester bond between MPO heavy chain glutamate 242 (Glu242) residue and the heme pyrrole A ring, freeing the heme linked light chain MPO subunit from the larger remaining heavy chain portion. Here we probed the structure and function relationship behind this ester bond cleavage using a panel of BAH analogs to gain insight into the constraints imposed by the MPO active site and channel leading to the buried protoporphyrin IX ring. In addition, we show evidence that destruction of the heme ring does not occur by tracking the heme prosthetic group and provide evidence that the mechanism of hydrolysis follows a potential attack of the Glu242 carbonyl leading to a rearrangement causing the release of the vinyl-sulfonium linkage between HC-Met243 and the pyrrole A ring. PMID:25688920