Sample records for carbohydrate side chains

  1. The molecular mechanism of N-acetylglucosamine side-chain attachment to the Lancefield group A Carbohydrate in Streptococcus pyogenes. (United States)

    Rush, Jeffrey S; Edgar, Rebecca J; Deng, Pan; Chen, Jing; Zhu, Haining; van Sorge, Nina M; Morris, Andrew J; Korotkov, Konstantin V; Korotkova, Natalia


    In many Lactobacillales species (i.e. lactic acid bacteria), peptidoglycan is decorated by polyrhamnose polysaccharides that are critical for cell envelope integrity and cell shape and also represent key antigenic determinants. Despite the biological importance of these polysaccharides, their biosynthetic pathways have received limited attention. The important human pathogen, Streptococcus pyogenes, synthesizes a key antigenic surface polymer-the Lancefield group A carbohydrate (GAC). GAC is covalently attached to peptidoglycan and consists of a polyrhamnose polymer, with N-acetylglucosamine (GlcNAc) side chains, which is an essential virulence determinant. The molecular details of the mechanism of polyrhamnose modification with GlcNAc are currently unknown. In this report, using molecular genetics, analytical chemistry and mass spectrometry analysis, we demonstrated that GAC biosynthesis requires two distinct undecaprenol-linked GlcNAc-lipid intermediates: GlcNAc-pyrophosphoryl-undecaprenol (GlcNAc-P-P-Und) produced by the GlcNAc-phosphate transferase GacO and GlcNAc-phosphate-undecaprenol (GlcNAc-P-Und) produced by the glycosyltransferase GacI. Further investigations revealed that the GAC polyrhamnose backbone is assembled on GlcNAc-P-P-Und. Our results also suggested that a GT-C glycosyltranferase, GacL, transfers GlcNAc from GlcNAc-P-Und to polyrhamnose. Moreover, GacJ, a small membrane-associated protein, formed a complex with GacI and significantly stimulated its catalytic activity. Of note, we observed that GacI homologs perform a similar function in Streptococcus agalactiae and Enterococcus faecalis. In conclusion, the elucidation of GAC biosynthesis in S. pyogenes reported here enhances our understanding of how other Gram-positive bacteria produce essential components of their cell wall. Copyright © 2017, The American Society for Biochemistry and Molecular Biology.

  2. Methods for Shortening and Extending the Carbon Chain in Carbohydrates

    DEFF Research Database (Denmark)

    Monrad, Rune Nygaard


    Carbohydrates play a central role in a variety of physiological and pathological processes such as HIV, cancer and diabetes. The understanding of these processes and the development of specific therapeutic agents is relying on the ability to chemically synthesize unnatural sugars, glycoconjugates...... and carbohydrate mimetics. Such polyhydroxylated compounds are conveniently synthesized from carbohydrates, however, due to the scarcity of many sugars from nature, efficient methods for transformation of readily available carbohydrates into valuable chiral building blocks are required. The work presented...... in this thesis focuses on the development and application of transition metal mediated methods for shortening and extending the carbon chain in carbohydrates thereby providing access to lower and higher sugars.A new catalytic procedure for shortening unprotected sugars by one carbon atom has been developed...

  3. Side chain polysiloxanes with phthalocyanine moieties

    Directory of Open Access Journals (Sweden)

    T. Ganicz


    Full Text Available Side chain polysiloxane with 5-(pentyloxy-3-methyloxy-9,10,16,17,23,24-hexakis(octenyloxyphthalocyanine moieties is synthesized by hydrosilylation reaction. The phase behavior and thermooptical properties of the polysiloxane and starting 2-(pent-4-enyloxy-3-methyloxy-9,10,16,17,23,24-hexakis(octenyloxyphthalocyanine is examined by POM (Polarizing optical microscopy, TOA (thermooptical analysis, DSC (differential scanning calorimetry, AFM (atomic force microscopy and SAXS (small angle X-ray scattering studies. The effect of the attachment of phthalocyanine to polysiloxane chains over phase transitions and phase morphology is discussed in details.

  4. Side Chain Cyclized Aromatic Amino Acids

    DEFF Research Database (Denmark)

    Van der Poorten, Olivier; Knuhtsen, Astrid; Sejer Pedersen, Daniel


    Constraining the conformation of flexible peptides is a proven strategy to increase potency, selectivity, and metabolic stability. The focus has mostly been on constraining the backbone dihedral angles; however, the correct orientation of the amino acid side chains (χ-space) that constitute...... the peptide pharmacophore is equally important. Control of χ-space utilizes conformationally constrained amino acids that favor, disfavor, or exclude the gauche (-), the gauche (+), or the trans conformation. In this review we focus on cyclic aromatic amino acids in which the side chain is connected...... to the peptide backbone to provide control of χ(1)- and χ(2)-space. The manifold applications for cyclized analogues of the aromatic amino acids Phe, Tyr, Trp, and His within peptide medicinal chemistry are showcased herein with examples of enzyme inhibitors and ligands for G protein-coupled receptors....

  5. Quantifying side-chain conformational variations in protein structure (United States)

    Miao, Zhichao; Cao, Yang


    Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

  6. Side Chain Engineering in Solution-Processable Conjugated Polymers

    KAUST Repository

    Mei, Jianguo


    Side chains in conjugated polymers have been primarily utilized as solubilizing groups. However, these side chains have roles that are far beyond. We advocate using side chain engineering to tune a polymer\\'s physical properties, including absorption, emission, energy level, molecular packing, and charge transport. To date, numerous flexible substituents suitable for constructing side chains have been reported. In this Perspective article, we advocate that the side chain engineering approach can advance better designs for next-generation conjugated polymers. © 2013 American Chemical Society.

  7. Steroid Carbon Skeletons with Unusually Branched C-3 Alkyl Side Chains in Sulphur-Rich Sediments (United States)

    Schouten, Stefan; Sephton, Sarah; Baas, Marianne; Sinninghe Damsté, Jaap S.


    A novel series of thiophenes with C-3 alkylated steroid carbon skeletons has been identified in sediments of the Miocene Monterey Formation (California, USA) and in the Turonian Tarfaya basin (Morocco). Their carbon skeletons are unusual in the sense that the alkyl side-chains at C-3 are almost exclusively isopentyl, 3-methylpentyl, and 2,3-dimethylbutyl moieties whilst n-alkyl (pentyl or hexyl) moieties are almost absent. Although they occur as thiophenes, the number of carbon atoms in the C-3 alkyl side chain and their carbon isotopic compositions point towards an origin from carbohydrates for the C-3 alkyl side chain. However, the branched structures of the C-3 alkyl side chains points to a different biosynthetic pathway, possibly starting from the addition of isopentylpyrophosphate to sterols.

  8. Protein side chain conformation predictions with an MMGBSA energy function. (United States)

    Gaillard, Thomas; Panel, Nicolas; Simonson, Thomas


    The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an "MMGBSA" energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803-819. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  9. Pendant triazole ring assisted mesogen containing side chain liquid ...

    Indian Academy of Sciences (India)

    yl containing side- chain liquid-crystalline polymethacrylates were synthesized by free radical polymerization technique. Mesogen was linked to backbone through various spacer units. Monomers and polymers were characterized by FT-IR, 1H ...

  10. Holographic Gratings in Azobenzene Side-Chain Polymethacrylates

    DEFF Research Database (Denmark)

    Andruzzi, Luisa; Altomare, Angelina; Ciardelli, Francesco


    Optical storage properties of thin unoriented liquid crystalline and amorphous side-chain azobenzene polymethacrylate films are examined by polarization holographic measurements. The investigated materials are free radical copolymers derived from two photochromic monomers, 6-(4-oxy-4...

  11. Antibody side chain conformations are position-dependent. (United States)

    Leem, Jinwoo; Georges, Guy; Shi, Jiye; Deane, Charlotte M


    Side chain prediction is an integral component of computational antibody design and structure prediction. Current antibody modelling tools use backbone-dependent rotamer libraries with conformations taken from general proteins. Here we present our antibody-specific rotamer library, where rotamers are binned according to their immunogenetics (IMGT) position, rather than their local backbone geometry. We find that for some amino acid types at certain positions, only a restricted number of side chain conformations are ever observed. Using this information, we are able to reduce the breadth of the rotamer sampling space. Based on our rotamer library, we built a side chain predictor, position-dependent antibody rotamer swapper (PEARS). On a blind test set of 95 antibody model structures, PEARS had the highest average χ 1 and χ1+2 accuracy (78.7% and 64.8%) compared to three leading backbone-dependent side chain predictors. Our use of IMGT position, rather than backbone ϕ/ψ, meant that PEARS was more robust to errors in the backbone of the model structure. PEARS also achieved the lowest number of side chain-side chain clashes. PEARS is freely available as a web application at © 2018 Wiley Periodicals, Inc.

  12. A protein-dependent side-chain rotamer library.

    KAUST Repository

    Bhuyan, M.S.


    Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.

  13. Integrated planning in supply chains with buy-side and sell-side ...

    Indian Academy of Sciences (India)

    In this paper we develop a quadratic programming model for partner selection and planning in integrated supply chain networks embedded with both sell-side and buy-side electronic marketplaces. Such a scenario arises in several practical applications. In particular, we consider a contract manufacturer who procures ...

  14. Effect of protein crystal hydration on side chain conformational heterogeneity (United States)

    Atakisi, Hakan; Moreau, David; Hopkins, Jesse; Thorne, Robert; Robert Thorne's Group Team

    The structure of protein crystals is determined in part by water-mediated interactions involving both protein surface-ordered (hydration) and bulk water, and so is sensitive to the relative humidity of the environment. Monoclinic lysozyme provides a remarkable model for studying structural changes induced by dehydration, as it maintains excellent order for relative humidities (r.h.) down to 5%, corresponding to solvent content of 9% by volume, much smaller than the 88% (22% by volume) at which lysozyme loses its enzymatic activity. Although the main chain conformation does not change significantly, the effect of dehydration on side chain conformations has not been systematically studied. High resolution (1.1 to 1.7 A) structural data sets for monoclinic lysozyme at r.h. between 99% and 11% have been analyzed to identify major and minor side chain conformers at each humidity, and to map out how the side chain conformational ensemble evolves with hydration. Modest dehydration produces comparable overall effects to cooling to T =100 K, but with conformational changes largely confined to solvent-exposed residues. The largest side chain conformation changes occur at humidities that deplete water within the first two hydration shells.

  15. Simultaneous in vivo truncation of pectic side chains

    DEFF Research Database (Denmark)

    Øbro, Jens; Borkhardt, Bernhard; Harholt, Jesper


    Despite the wide occurrence of pectin in nature only a few source materials have been used to produce commercial pectins. One of the reasons for this is that many plant species contain pectins with high levels of neutral sugar side chains or that are highly substituted with acetyl or other groups...

  16. Banana-shaped side chain liquid crystalline siloxanes

    NARCIS (Netherlands)

    Achten, R.; Koudijs, A.; Giesbers, M.; Reddy, R.A.; Verhulst, T.; Tschierske, C.; Marcelis, A.T.M.; Sudhölter, E.J.R.


    Eight banana-shaped side chain liquid crystalline oligomers and polymers have been synthesized by hydrosilylation of vinyl-terminated bent-core mesogens with trimethylsilyl-terminated siloxanes. The synthesized oligomers and polymers, and their olefinic precursors, were investigated by polarizing

  17. Well-defined side-chain liquid-crystalline polysiloxanes

    NARCIS (Netherlands)

    Hempenius, Mark A.; Lammertink, Rob G.H.; Vancso, Gyula J.


    A route to well-defined side-chain liquid-crystalline polysiloxanes (ratio of weight-to number-average molar masses Mw/Mn < 1.2 is reported. Anionic ring-opening polymerization of pentamethylvinylcyclotrisiloxane yielded a poly(dimethylsiloxane-co-methylvinylsiloxane) backbone. A flexible disiloxane

  18. Three entropic classes of side chain in a globular protein

    Energy Technology Data Exchange (ETDEWEB)

    Glass, Dennis C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Krishnan, Marimuthu [International Institute of Information Technology, Hyderbad (India); Smith, Jeremy C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Baudry, Jerome Y. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)


    The relationship between the NMR methyl group axial order parameter and the side chain conformational entropy is investigated in inhibitor-bound and apo human HIV protease using molecular dynamics simulation. Three distinct entropic classes of methyl-bearing side chains, determined by the topological distance of the methyl group from the protein backbone (i.e., the number of -bonds between the C and the carbon of the CH3 group), are revealed by atomistic trajectory analyses performed in the local frame of reference of individual methyl probes. The results demonstrate that topologically equivalent methyl groups experience similar nonbonded microenvironments regardless of the type of residues to which they are attached. Similarly, methyl groups that belong to the same side chain but that are not topologically equivalent exhibit different thermodynamic and dynamic properties. As a result, the two-parameter classification (based upon entropy and methyl axial order parameter) of side chains described here permits improved estimates of the conformational entropies of proteins from NMR motional parameters.

  19. Identification of a tetrasialylated monofucosylated tetraantennary N-linked carbohydrate chain in human platelet glycocalicin

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Korrel, S.A.M.; Clemetson, K.J.; Halbeek, H. van; Kamerling, J.P.; Sixma, J.J.


    Glycocalicin (140 kDa), the main constituent of the glycoprotein Ib alpha-chain (150 kDa) of the human platelet membrane, contains 4 putative N-glycosylation sites. For the structural analysis of the N-glycosidic carbohydrate chains of glycocalicin, the glycoprotein has been subjected to the

  20. Light scattering of thin azobenzene side-chain polyester layers

    DEFF Research Database (Denmark)

    Kerekes, Á.; Lörincz, E.; Ramanujam, P.S.


    Light scattering properties of liquid crystalline and amorphous azobenzene side-chain polyester layers used for optical data storage were examined by means of transmissive scatterometry. Comparative experiments show that the amorphous polyester has significantly lower light scattering characteris...... for the domain size in thin liquid crystalline polyester layers being responsible for the dominant light scattering. The characteristic domain Sizes obtained from the Fourier transformation of polarization microscopic Pictures confirm these values.......Light scattering properties of liquid crystalline and amorphous azobenzene side-chain polyester layers used for optical data storage were examined by means of transmissive scatterometry. Comparative experiments show that the amorphous polyester has significantly lower light scattering...... characteristics than the liquid crystalline polyester. The amorphous samples have negligible polarization part orthogonal to the incident beam. the liquid crystalline samples have relative high orthogonal polarization part in light scattering, The light scattering results can be used to give a lower limit...

  1. Peptide Nucleic Acids Having Amino Acid Side Chains

    DEFF Research Database (Denmark)


    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than the corresponding DNA or RNA strands, and exhibit increased sequence specificity and solubility. The peptide nucleic acids comprise ligands selected from a group consisting of nat...... of naturally-occurring nucleobases and non-naturally-occurring nucleobases attached to a polyamide backbone, and contain alkylamine side chains....

  2. Side-chain liquid crystalline polyesters for optical information storage

    DEFF Research Database (Denmark)

    Ramanujam, P.S.; Holme, Christian; Hvilsted, Søren


    and holographic storage in one particular polyester are described in detail and polarized Fourier transform infrared spectroscopic data complementing the optical data are presented. Optical and atomic force microscope investigations point to a laser-induced aggregation as responsible for permanent optical storage.......Azobenzene side-chain liquid crystalline polyester structures suitable for permanent optical storage are described. The synthesis and characterization of the polyesters together with differential scanning calorimetry and X-ray investigations are discussed. Optical anisotropic investigations...

  3. Highly conductive side chain block copolymer anion exchange membranes. (United States)

    Wang, Lizhu; Hickner, Michael A


    Block copolymers based on poly(styrene) having pendent trimethyl styrenylbutyl ammonium (with four carbon ring-ionic group alkyl linkers) or benzyltrimethyl ammonium groups with a methylene bridge between the ring and ionic group were synthesized by reversible addition-fragmentation radical (RAFT) polymerization as anion exchange membranes (AEMs). The C4 side chain polymer showed a 17% increase in Cl(-) conductivity of 33.7 mS cm(-1) compared to the benzyltrimethyl ammonium sample (28.9 mS cm(-1)) under the same conditions (IEC = 3.20 meq. g(-1), hydration number, λ = ∼7.0, cast from DMF/1-propanol (v/v = 3 : 1), relative humidity = 95%). As confirmed by small angle X-ray scattering (SAXS), the side chain block copolymers with tethered ammonium cations showed well-defined lamellar morphologies and a significant reduction in interdomain spacing compared to benzyltrimethyl ammonium containing block copolymers. The chemical stabilities of the block copolymers were evaluated under severe, accelerated conditions, and degradation was observed by (1)H NMR. The block copolymer with C4 side chain trimethyl styrenylbutyl ammonium motifs displayed slightly improved stability compared to that of a benzyltrimethyl ammonium-based AEM at 80 °C in 1 M NaOD aqueous solution for 30 days.

  4. Carbohydrates (United States)

    Carbohydrates are one of the main types of nutrients. They are the most important source of energy for your body. Your digestive system changes carbohydrates into glucose (blood sugar). Your body uses this ...

  5. Protection of the amide side-chain of asparagine with the 1-tetralinyl ...

    African Journals Online (AJOL)


    made more efficient with the development of solid-phase peptide synthetic methods. (SPPS).3,4. Side-chain amide protection of asparagine (Asn) or glutamine (Gln) has been considered optional.5 These amide side-chains are liable to undergo dehydration during the coupling steps.6–8 This side reaction does not occur ...

  6. Soluble Polyimides Bearing Long-Chain Alkyl Groups on Their Side Chain via Polymer Reaction

    Directory of Open Access Journals (Sweden)

    Yusuke Tsuda


    Full Text Available Novel soluble polyimides having long-chain alkyl groups on their side chain were synthesized via polymer reaction with the polyimides having phenolic OH groups and 3,4,5-tris(dodecyloxybenzoic acid (12GA using N,N′-dicyclohexylcarbodiimide (DCC as a dehydration reagent. The polyimides having phenolic OH groups were synthesized from the tetracarboxylic dianhydrides such as 5-(2,5-dioxotetrahydrofuryl-3-methyl-3-cyclohexene-1,2-dicarboxylic anhydride (cyclohexene-DA, 4,4′-hexafluoroisopropylidendi(phthalic anhydride (6FDA, and 3,3′,4,4′-diphenylsulfone tetracarboxylic dianhydride (DSDA and aromatic diamines such as 4,4′-diamino-3,3′-dihydroxybiphenyl (HAB. The polymer reactions were carried out in NMP and the progresses of polymer reactions were quantitatively monitored by 1H NMR measurements (conversion; 12.2–98.7%. The obtained polyimides bearing long-chain alkyl groups have enough molecular weights, good film-forming ability, good solubility for various organic solvents, and enough thermal stability. The water contact angles of the polyimide films were investigated, and it is noted that the introduction of long-chain alkyl groups increases the hydrophobicity of polyimide surface. These polyimides are expected to be applicable as the functional materials for microelectronics such as the alignment layers of LCDs.

  7. Beta-scission of side-chain alkoxyl radicals on peptides and proteins results in the loss of side-chains as aldehydes and ketones

    DEFF Research Database (Denmark)

    Headlam, Henrietta A; Davies, Michael Jonathan


    Exposure of proteins to radicals in the presence of O(2) results in side-chain oxidation and backbone fragmentation; the interrelationship between these processes is not fully understood. Recently, initial attack on Ala side-chains was shown to give alpha-carbon radicals (and hence backbone...... cleavage) and formaldehyde, via the formation and subsequent beta-scission, of C-3 alkoxyl radicals. We now show that this side-chain to backbone damage transfer, is a general mechanism for aliphatic side-chains. Oxidation of Val, Leu, and Asp residues by HO(*)/O(2) results in the release of a family...... of carbonyls (including formaldehyde, acetone, isobutyraldehyde, and glyoxylic acid) via the formation, and subsequent beta-scission of alkoxyl radicals. The concentration of these products increases with the HO(*) flux. The release of multiple carbonyls confirms the occurrence of oxidation at C-3 and C-4...

  8. Role of the carbohydrate chain and two phosphate moieties in the heat-induced aggregation of hen ovalbumin. (United States)

    Tani, Fumito; Shirai, Nobuaki; Nakanishi, Yukiko; Yasumoto, Kyoden; Kitabatake, Naofumi


    We investigated the effect of the carbohydrate chain and two phosphate moieties on heat-induced aggregation of hen ovalbumin. The dephosphorylated form of ovalbumin was obtained by treating the original protein with acid phosphatase. The single carbohydrate chain was removed by digestion of heat-denatured ovalbumin with glycopeptidase F, and the resulting polypeptide without this carbohydrate chain was correctly refolded to acquire protease-resistance. Thermal unfolding can be approximated by a mechanism involving a two-state transition between the folded and unfolded states with a midpoint temperature of 76 degrees C for the original form, of 74 degrees C for the dephosphorylated form, and of 71 degrees C for the carbohydrate-free form. The conformational stability of the original form was higher than that of the carbohydrate-free form. When the three forms of ovalbumin were heated to 80 degrees C and then cooled rapidly in an ice bath, the polypeptide chains were compactly collapsed to metastable intermediates with secondary structures whose properties were indistinguishable. Upon incubation at 60 degrees C, renaturation was possible for a large portion of the intermediates of the original form, but for only a small portion of those of the carbohydrate-free form. Light scattering experiments showed that in the presence of sulfate anions, the intermediates of the carbohydrate-free form aggregated to a greater extent than did those of the original form. The intermediates of the carbohydrate-free form bound to the chaperonin GroEL with about 10-fold higher affinity than those of the original form. It follows that the carbohydrate chain and the two phosphate moieties do not affect hydrophobic collapse in the kinetic refolding of hen ovalbumin but play an important role in the slow rearrangement. They block the off-pathway reaction that competes with correct refolding by effectively decreasing surface hydrophobicity.

  9. Charge photogeneration and transport in side-chain carbazole polymers and co-polymers

    KAUST Repository

    Li, Huawei


    The photoconductivity, hole mobility and charge photogeneration efficiency of a series of side-chain carbazole homopolymers and copolymers (with azo side-chains) have been investigated. Cyclic voltammetry measurement of frontier orbitals energies show that the HOMO energy is determined by the nature and the position of attachment of the linker between the main chain and the carbazole, the azo-moiety being not relevant in this respect. Hole mobility is not influenced by the HOMO energy but seems to depend on the degree of conformational mobility of the side-chains, reaching values of the order of 10-3cm2V-1s-1 in the best cases. The HOMO energy is instead extremely important when considering photogeneration efficiency, that can change by 10 orders of magnitude depending on the density of the carbazole side-chains in co-polymers and on the linker nature and attachment position. © 2011 Elsevier B.V. All rights reserved.

  10. Side-chain crystallization in alkyl-substituted cellulose esters and hydroxypropyl cellulose esters. (United States)

    Chen, Xi; Zheng, Nan; Wang, Qiao; Liu, Lingzhi; Men, Yongfeng


    The differences in side chain crystallization behavior between cellulose esters (CEs) and hydroxypropyl cellulose esters (HPCEs) were systematically investigated by a combination of differential scanning calorimetry (DSC) and small and wide-angle X-ray scattering techniques. DSC investigation indicated that under the same side chain length, the fusion enthalpy and the number of crystallized CH 2 of CEs were smaller than HPCEs. At the same time, their d-spacing and molecular arrangements were also different from each other. For the CEs, the side chains are perpendicular to the main chain, while the side chains most probably tend to tilt to main chain in the HPCEs as was evidenced by X-ray scattering results. The phenomenon can be understood as a consequence of different flexibility of attachment bridges in both kinds of side chain polymers and the steric hindrance of methyl group in the hydroxypropyl group in HPCEs. In addition, the added hydroxypropyl substituents make the side chain length increasing. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Product ion tandem mass spectrometric differentiation of regioisomeric side-chain groups in cathinone derivatives. (United States)

    Abiedalla, Younis; DeRuiter, Jack; Clark, C Randall


    Precursor materials are available to prepare aminoketone drugs containing regioisomeric propyl and isopropyl side-chain groups related to the drug alpha-pyrrovalerone (Flakka) and MDPV (3,4-methylenedioxypyrrovalerone). These compounds yield equivalent regioisomeric iminium cation base peaks in electron ionization mass spectrometry (EI-MS). The propyl and isopropyl side-chain groups related to alpha-pyrrovalerone and MDPV were prepared and evaluated in EI-MS and tandem mass spectrometry (MS/MS) product ion experiments. Deuterium labeling in both the pyrrolidine and alkyl side-chain groups allowed for the confirmation of the structures for the major product ions formed from the regioisomeric EI-MS iminium cation base peaks. These iminium cation base peaks show characteristic product ion spectra which allow differentiation of the side-chain propyl and isopropyl groups in the structure. The n-propyl side chain containing iminium cation base peak (m/z 126) in the EI-MS spectrum yields a major product ion at m/z 84 while the regioisomeric m/z 126 base peak for the isopropyl side chain yields a characteristic product ion at m/z 70. Deuterium labeling in both the pyrrolidine ring and the alkyl side chain confirmed the process for the formation of these major product ions. Product ion fragmentation provides useful data for differentiation of n-propyl and isopropyl side-chain iminium cations from cathinone derivative drugs of abuse. Regioisomeric n-propyl and isopropyl iminium cations of equal mass yield characteristic product ions identifying the alkyl side-chain regioisomers in the pyrrolidine cathinone derivatives. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  12. Solid-phase and solution-phase syntheses of oligomeric guanidines bearing peptide side chains. (United States)

    Zhang, Zhongsheng; Fan, Erkang


    [reaction: see text] Synthetic strategies for preparing N,N'-bridged oligomeric guanidines bearing peptide side chains both on solid support and in solution are presented. Monomers are prepared from common alpha-amino acids and therefore contain conventionally protected peptide side chains. The side chains include alkyl, aromatic, hydroxyl, amino, carboxylic acid, and amide functional groups. Oligomer elongation utilizes acid-sensitive sulfonyl activated thiourea through the formation of carbodiimide intermediate. With proper preparation of monomers, synthesis of oligomer can be performed in two directions (equivalent to N to C terminal or C to N terminal in a peptide sequence) with excellent efficiency.

  13. Polypropylene non-woven meshes with conformal glycosylated layer for lectin affinity adsorption: the effect of side chain length. (United States)

    Ye, Xiang-Yu; Huang, Xiao-Jun; Xu, Zhi-Kang


    The unique characteristics of polypropylene non-woven meshes (PPNWMs), like random network of overlapped fibers, multiple connected pores and overall high porosity, make them high potentials for use as separation or adsorption media. Meanwhile, carbohydrates can specifically recognize certain lectin through multivalent interactions. Therefore glycosylated PPNWMs, combing the merits of both, can be regarded as superior affinity membranes for lectin adsorption and purification. Here, we describe a versatile strategy for the glycosylation of PPNWMs. Two hydrophilic polymers with different side chain length, poly(2-hydroxyethyl methacrylate) (PHEMA) and poly(oligo(ethylene glycol) methacrylate) (POEGMA), were first conformally tethered on the polypropylene fiber surface by a modified plasma pretreatment and benzophenone (BP) entrapment UV irradiation process. Then glucose ligands were bound through the reaction between the hydroxyl group and acetyl glucose. Chemical changes of the PPNWMs surface were monitored by FT-IR/ATR. SEM pictures show that conformal glucose ligands can be achieved through the modified process. After deprotection, the glycosylated PPNWMs became superhydrophilic and had high specific recognition capability toward Concanavalin A (Con A). Static Con A adsorption experiments were further performed and the results indicate that fast adsorption kinetics and high binding capacity can be accomplished at the same time. We also found that increasing the side chain length of polymer brushes had positive effect on protein binding capacity due to improved chain mobility. Model studies suggest a multilayer adsorption behavior of Con A. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains. (United States)

    Makowski, Mariusz; Liwo, Adam; Scheraga, Harold A


    The two-site coarse-grained model for the interactions of charged side chains, to be used with our coarse-grained UNRES force field for protein simulations proposed in the accompanying paper, has been extended to pairs of oppositely charged side chains. The potentials of mean force of four pairs of molecules modeling charged amino-acid side chains, i.e., propionate-n-pentylamine cation (for aspartic acid-lysine), butyrate-n-pentylamine cation (for glutamic acid-lysine), propionate-1-butylguanidine (for aspartic acid-arginine), and butyrate-1-butylguanidine (for glutamic acid-arginine) pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expression was fitted to the potentials of mean force. Compared to pairs of like-charged side chains discussed in the accompanying paper, an average quadrupole-quadrupole interaction term had to be introduced to reproduce the Coulombic interactions, and a multistate model of charge distribution had to be introduced to fit the potentials of mean force of all oppositely charged pairs well. The model reproduces all salt-bridge minima and, consequently, is likely to improve the performance of the UNRES force field. © 2011 American Chemical Society

  15. From labdanes to drimanes. Degradation of the side chain of dihydrozamoranic acid. (United States)

    Rodilla, Jesús M L; Díez, D; Urones, J G; Rocha, Pedro M


    A new route for the degradation of the saturated side chain of dihydrozamoranic acid has been devised, giving an advanced intermediate, compound 14, useful for the synthesis of insect antifeedants such as warburganal and polygodial.

  16. From Labdanes to Drimanes. Degradation of the Side Chain of Dihydrozamoranic Acid.

    Directory of Open Access Journals (Sweden)

    Pedro M. Rocha


    Full Text Available A new route for the degradation of the saturated side chain of dihydrozamoranic acid has been devised, giving an advanced intermediate, compound 14, useful for the synthesis of insect antifeedants such as warburganal and polygodial.

  17. Hydroxylation of steroids with nonpolar side chains with 11 alpha-hydroxylase of Rhizopus nigricans. (United States)

    Zakelj-Mavric, M; Kastelic-Suhadolc, T; Gottlieb, H E; Belic, I


    Steroids with nonpolar side chains with 2, 4 and 8 C atoms were used as substrates for the 11 alpha-hydroxylase of Rhizopus nigricans. Their bioconversion was compared to that of progesterone, which was found to be far the best substrate giving the highest total bioconversion. 3-keto-4-ene steroids with nonpolar side chains were converted to their hydroxylated products in a small yield or not at all. The absence of an oxygen function in the side chain did not affect the regio-specificity of the hydroxylation, but resulted in a much lower total bioconversion. The strong effect of the oxygen function and of the length of the side chain on hydroxylation with the 11 alpha-hydroxylase of Rhizopus nigricans was demonstrated.

  18. Synthesis and solution self-assembly of side-chain cobaltocenium-containing block copolymers. (United States)

    Ren, Lixia; Hardy, Christopher G; Tang, Chuanbing


    The synthesis of side-chain cobaltocenium-containing block copolymers and their self-assembly in solution was studied. Highly pure monocarboxycobaltocenium was prepared and subsequently attached to side chains of poly(tert-butyl acrylate)-block-poly(2-hydroxyethyl acrylate), yielding poly(tert-butyl acrylate)-block-poly(2-acryloyloxyethyl cobaltoceniumcarboxylate). The cobaltocenium block copolymers exhibited vesicle morphology in the mixture of acetone and water, while micelles of nanotubes were formed in the mixture of acetone and chloroform.

  19. Temperature dependence of amino acid side chain IR absorptions in the amide I' region. (United States)

    Anderson, Benjamin A; Literati, Alex; Ball, Borden; Kubelka, Jan


    Amide I' IR spectra are widely used for studies of structural changes in peptides and proteins as a function of temperature. Temperature dependent absorptions of amino acid side-chains that overlap the amide I' may significantly complicate the structural analyses. While the side-chain IR spectra have been investigated previously, thus far their dependence on temperature has not been reported. Here we present the study of the changes in the IR spectra with temperature for side-chain groups of aspartate, glutamate, asparagine, glutamine, arginine, and tyrosine in the amide I' region (in D2O). Band fitting analysis was employed to extract the temperature dependence of the individual spectral parameters, such as peak frequency, integrated intensity, band width, and shape. As expected, the side-chain IR bands exhibit significant changes with temperature. The majority of the spectral parameters, particularly the frequency and intensity, show linear dependence on temperature, but the direction and magnitude vary depending on the particular side-chain group. The exception is arginine, which exhibits a distinctly nonlinear frequency shift with temperature for its asymmetric CN3H5(+) bending signal, although a linear fit can account for this change to within ~1/3 cm(-1). The applicability of the determined spectral parameters for estimations of temperature-dependent side-chain absorptions in peptides and proteins are discussed. Copyright © 2013 Wiley Periodicals, Inc.

  20. Searching for low percolation thresholds within amphiphilic polymer membranes: The effect of side chain branching (United States)

    Dorenbos, G.


    Percolation thresholds for solvent diffusion within hydrated model polymeric membranes are derived from dissipative particle dynamics in combination with Monte Carlo (MC) tracer diffusion calculations. The polymer backbones are composed of hydrophobic A beads to which at regular intervals Y-shaped side chains are attached. Each side chain is composed of eight A beads and contains two identical branches that are each terminated with a pendant hydrophilic C bead. Four types of side chains are considered for which the two branches (each represented as [C], [AC], [AAC], or [AAAC]) are splitting off from the 8th, 6th, 4th, or 2nd A bead, respectively. Water diffusion through the phase separated water containing pore networks is deduced from MC tracer diffusion calculations. The percolation threshold for the architectures containing the [C] and [AC] branches is at a water volume fraction of ˜0.07 and 0.08, respectively. These are much lower than those derived earlier for linear architectures of various side chain length and side chain distributions. Control of side chain architecture is thus a very interesting design parameter to decrease the percolation threshold for solvent and proton transports within flexible amphiphilic polymer membranes.

  1. Side-chain modification and "grafting onto" via olefin cross-metathesis. (United States)

    de Espinosa, Lucas Montero; Kempe, Kristian; Schubert, Ulrich S; Hoogenboom, Richard; Meier, Michael A R


    Olefin cross-metathesis is introduced as a versatile polymer side-chain modification technique. The reaction of a poly(2-oxazoline) featuring terminal double bonds in the side chains with a variety of functional acrylates has been successfully performed in the presence of Hoveyda-Grubbs second-generation catalyst. Self-metathesis, which would lead to polymer-polymer coupling, can be avoided by using an excess of the cross-metathesis partner and a catalyst loading of 5 mol%. The results suggest that bulky acrylates reduce chain-chain coupling due to self-metathesis. Moreover, different functional groups such as alkyl chains, hydroxyl, and allyl acetate groups, as well as an oligomeric poly(ethylene glycol) and a perfluorinated alkyl chain have been grafted with quantitative conversions. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins. (United States)

    Soltan Ghoraie, Laleh; Burkowski, Forbes; Zhu, Mu


    Recent studies have highlighted the role of coupled side-chain fluctuations alone in the allosteric behavior of proteins. Moreover, examination of X-ray crystallography data has recently revealed new information about the prevalence of alternate side-chain conformations (conformational polymorphism), and attempts have been made to uncover the hidden alternate conformations from X-ray data. Hence, new computational approaches are required that consider the polymorphic nature of the side chains, and incorporate the effects of this phenomenon in the study of information transmission and functional interactions of residues in a molecule. These studies can provide a more accurate understanding of the allosteric behavior. In this article, we first present a novel approach to generate an ensemble of conformations and an efficient computational method to extract direct couplings of side chains in allosteric proteins, and provide sparse network representations of the couplings. We take the side-chain conformational polymorphism into account, and show that by studying the intrinsic dynamics of an inactive structure, we are able to construct a network of functionally crucial residues. Second, we show that the proposed method is capable of providing a magnified view of the coupled and conformationally polymorphic residues. This model reveals couplings between the alternate conformations of a coupled residue pair. To the best of our knowledge, this is the first computational method for extracting networks of side chains' alternate conformations. Such networks help in providing a detailed image of side-chain dynamics in functionally important and conformationally polymorphic sites, such as binding and/or allosteric sites. © 2014 Wiley Periodicals, Inc.

  3. Assessment of Protein Side-Chain Conformation Prediction Methods in Different Residue Environments (United States)

    Peterson, Lenna X.; Kang, Xuejiao; Kihara, Daisuke


    Computational prediction of side-chain conformation is an important component of protein structure prediction. Accurate side-chain prediction is crucial for practical applications of protein structure models that need atomic detailed resolution such as protein and ligand design. We evaluated the accuracy of eight side-chain prediction methods in reproducing the side-chain conformations of experimentally solved structures deposited to the Protein Data Bank. Prediction accuracy was evaluated for a total of four different structural environments (buried, surface, interface, and membrane-spanning) in three different protein types (monomeric, multimeric, and membrane). Overall, the highest accuracy was observed for buried residues in monomeric and multimeric proteins. Notably, side-chains at protein interfaces and membrane-spanning regions were better predicted than surface residues even though the methods did not all use multimeric and membrane proteins for training. Thus, we conclude that the current methods are as practically useful for modeling protein docking interfaces and membrane-spanning regions as for modeling monomers. PMID:24619909

  4. Side chains control dynamics and self-sorting in fluorescent organic nanoparticles. (United States)

    Kaeser, Adrien; Fischer, Irén; Abbel, Robert; Besenius, Pol; Dasgupta, Debarshi; Gillisen, Martijn A J; Portale, Giuseppe; Stevens, Amy L; Herz, Laura M; Schenning, Albertus P H J


    To develop fluorescent organic nanoparticles with tailored properties for imaging and sensing, full control over the size, fluorescence, stability, dynamics, and supramolecular organization of these particles is crucial. We have designed, synthesized, and fully characterized 12 nonionic fluorene co-oligomers that formed self-assembled fluorescent nanoparticles in water. In these series of molecules, the ratio of hydrophilic ethylene glycol and hydrophobic alkyl side chains was systematically altered to investigate its role on the above-mentioned properties. The nanoparticles consisting of π-conjugated oligomers containing polar ethylene glycol side chains were less stable and larger in size, while nanoparticles self-assembled from oligomers containing nonpolar pendant chains were more stable, smaller, and generally had a higher fluorescence quantum yield. Furthermore, the dynamics of the molecules between the nanoparticles was enhanced if the number of hydrophilic side chains increased. Energy transfer studies between naphthalene and benzothiadiazole fluorene co-oligomers with the same side chains showed no exchange of molecules between the particles for the apolar molecules. For the more polar systems, the exchange of molecules between nanoparticles took place at room temperature or after annealing. Self-assembled nanoparticles consisting of π-conjugated oligomers having different side chains caused self-sorting, resulting either in the formation of domains within particles or the formation of separate nanoparticles. Our results show that we can control the stability, fluorescence, dynamics, and self-sorting properties of the nanoparticles by simply changing the nature of the side chains of the π-conjugated oligomers. These findings are not only important for the field of self-assembled nanoparticles but also for the construction of well-defined multicomponent supramolecular materials in general.

  5. Azobenzene side-chain liquid crystalline polyesters with outstanding optical storage properties

    DEFF Research Database (Denmark)

    Hvilsted, Søren; Pedersen, M; Holme, NCR


    A flexible azobenzene side-chain liquid crystalline (SCLC) polyester architecture employed for reversible optical storage is described. The modular design allows four structural parameters to be individually modified. These parameters: i- the methylene side-chain spacer length, ii- the substituent......, information can be recorded either through polarization holography or as direct computer generated pattern (grey tones). Thus polarization holography results in high diffraction efficiency (> 50%) and high storage density (> 5000 lines/mm interference gratings) lasting presently well over 5 years without any......, the observed surface roughness is strongly dependent on the laser polarization. Polarization Fourier-Transform infrared studies of laser induced segmental motion in selectively deuterated SCLC cyanoazobenzene polyesters have revealed that not only the azobenzene chromophores but also main-chain and side...

  6. Entropy and enthalpy of interaction between amino acid side chains in nanopores

    CERN Document Server

    Vaitheeswaran, S


    Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientations between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by e...

  7. Record high hole mobility in polymer semiconductors via side-chain engineering. (United States)

    Kang, Il; Yun, Hui-Jun; Chung, Dae Sung; Kwon, Soon-Ki; Kim, Yun-Hi


    Charge carrier mobility is still the most challenging issue that should be overcome to realize everyday organic electronics in the near future. In this Communication, we show that introducing smart side-chain engineering to polymer semiconductors can facilitate intermolecular electronic communication. Two new polymers, P-29-DPPDBTE and P-29-DPPDTSE, which consist of a highly conductive diketopyrrolopyrrole backbone and an extended branching-position-adjusted side chain, showed unprecedented record high hole mobility of 12 cm(2)/(V·s). From photophysical and structural studies, we found that moving the branching position of the side chain away from the backbone of these polymers resulted in increased intermolecular interactions with extremely short π-π stacking distances, without compromising solubility of the polymers. As a result, high hole mobility could be achieved even in devices fabricated using the polymers at room temperature.

  8. Side-Chain Effects on the Thermoelectric Properties of Fluorene-Based Copolymers. (United States)

    Liang, Ansheng; Zhou, Xiaoyan; Zhou, Wenqiao; Wan, Tao; Wang, Luhai; Pan, Chengjun; Wang, Lei


    Three conjugated polymers with alkyl chains of different lengths are designed and synthesized, and their structure-property relationship as organic thermoelectric materials is systematically elucidated. All three polymers show similar photophysical properties, thermal properties, and mechanical properties; however, their thermoelectric performance is influenced by the length of their side chains. The length of the alkyl chain significantly influences the electrical conductivity of the conjugated polymers, and polymers with a short alkyl chain exhibit better conductivity than those with a long alkyl chain. The length of the alkyl chain has little effect on the Seebeck coefficient. Only a slight increase in the Seebeck coefficient is observed with the increasing length of the alkyl chain. The purpose of this study is to provide comprehensive insight into fine-tuning the thermoelectric properties of conjugated polymers as a function of side-chain engineering, thereby providing a novel perspective into the design of high-performance thermoelectric conjugated polymers. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Electro-optic side-chain polyimide system with large optical nonlinearity and high thermal stability (United States)

    Sotoyama, Wataru; Tatsuura, Satoshi; Yoshimura, Tetsuzo


    We report electro-optic (EO) efficiency and thermal stability of a poled polyimide system with nonlinear optical dyes as side chains. The side-chain polyimide system is synthesized from a dianhydride containing azobenzene dye and a diamine. The dye in the polymer is chemically stable for temperatures below 250 °C. The polymer can be poled simultaneously with or after imidization of the polyamic acid. Our sample poled after imidization shows a large EO coefficient (r33=10.8 pm/V at λ=1.3 μm) and long-term thermal stability at 120 °C.

  10. Exploring backbone-cation alkyl spacers for multi-cation side chain anion exchange membranes (United States)

    Zhu, Liang; Yu, Xuedi; Hickner, Michael A.


    In order to systematically study how the arrangement of cations on the side chain and length of alkyl spacers between cations impact the performance of multi-cation AEMs for alkaline fuel cells, a series of polyphenylene oxide (PPO)-based AEMs with different cationic side chains were synthesized. This work resulted in samples with two or three cations in a side chain pendant to the PPO backbone. More importantly, the length of the spacer between cations varied from 3 methylene (-CH2-) (C3) groups to 8 methylene (C8) groups. The highest conductivity, up to 99 mS/cm in liquid water at room temperature, was observed for the triple-cation side chain AEM with pentyl (C5) or hexyl (C6) spacers. The multi-cation AEMs were found to have decreased water uptake and ionic conductivity when the spacer chains between cations were lengthened from pentyl (C5) or hexyl (C6) to octyl (C8) linking groups. The triple-cation membranes with pentyl (C5) or hexyl (C6) groups between cations showed greatest stability after immersion in 1 M NaOH at 80 °C for 500 h.

  11. side chains

    African Journals Online (AJOL)


    ABSTRACT. The hydration structures of Co(III) and Fe(III) ions have been investigated by. Metropolis Monte Carlo (MC) simulations using only ion-water pair interaction potentials and by including up to three body correction terms. The hydration structures were evaluated in terms of radial distribution functions, coordination ...

  12. side chains

    African Journals Online (AJOL)


    The Fe(III)-H RDF confirms a strictly dipole oriented arrangement of the first-shell water ligands. Some characteristic values for Fe(III)-O and Fe(III)-H radial distribution functions are listed and compared with results obtained from experimental works and other simulations investigations in Table 2. Bull. Chem. Soc. Ethiop.

  13. side chains

    African Journals Online (AJOL)


    Commercial sources reagents (Aldrich and Fluka Chemicals) were used without further purification. Zn-Cu couple was prepared according to a literature procedure [23]. IR spectra were recorded in CH2Cl2 unless otherwise stated, using CaF2 optic on a Perkin-. Elmer 882 spectrophotometer. The 1H NMR, 13C NMR and ...

  14. side chains

    African Journals Online (AJOL)


    The cumene cracking belongs to the largely used catalytic reactions; it has been thoroughly studied on the zeolitic catalysts like ZSM-5 but rarely with mesoporous materials and especially. MCM-41. A series of experiments in which cumene converted were carried out on ZSM-5 zeolites with a different ionic exchange ...

  15. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. (United States)

    Holehouse, Alex S; Garai, Kanchan; Lyle, Nicholas; Vitalis, Andreas; Pappu, Rohit V


    In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones, and therefore, backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations of denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of side chains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that side chains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of side chain-mediated interactions as determinants

  16. Steroid carbon skeletons with unusually branched C-3 alkyl side chains in sulphur-rich sediments

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Schouten, S.; Sephton, S.; Baas, M.


    A novel series of thiophenes with C-3 alkylated steroid carbon skeletons has been identified in sediments of the Miocene Monterey Formation (California, USA) and in the Turonian Tarfaya basin (Morocco). Their carbon skeletons are unusual in the sense that the alkyl side-chains at C-3 are almost

  17. Novel biphotonic holographic storage in a side-chain liquid crystalline polyester

    DEFF Research Database (Denmark)

    Ramanujam, P.S.; Hvilsted, S.; Andruzzi, F.


    We report novel biphotonic holographic storage of text and gratings on unoriented films of a side-chain liquid crystalline polyester capable of high density storage and complete erasure. The holograms have a typical size of 1 mm. The recording utilizes unusual photochemistry involving azo dye...

  18. Determination of the Response Time of Photoanisotropy in Azobenzene Side-Chain Polyesters

    DEFF Research Database (Denmark)

    Bublitz, D.; Fleck, B.; Wenke, L.


    We present a method which allows the determination of the response time to polarized light of an azobenzene side-chain polyester. This method is based on the measurement of intensities in dependence on the delay time between a pump and a probe pulse. The described method does not need a very soph...

  19. Arabidopsis GUX Proteins Are Glucuronyltransferases Responsible for the Addition of Glucuronic Acid Side Chains onto Xylan (United States)

    Xylan, the second most abundant cell wall polysaccharide, is composed of a linear backbone of β-(1,4)-linked xylosyl residues that are often substituted with sugar side chains, such as glucuronic acid (GlcA) and methylglucuronic acid (MeGlcA). It has recently been shown that muta...

  20. Determination of monounsaturated alkyl side chain 2-alkylcyclobutanones in irradiated foods

    NARCIS (Netherlands)

    Horvatovich, Péter; Miesch, Michel; Hasselmann, Claude; Delincée, Henry; Marchioni, Eric


    The 2-alkylcyclobutanones (2-ACBs) are formed from triglycerides by irradiation treatment and may be used as markers for this type of food processing. This paper describes a detection method for the analysis of monounsaturated alkyl side chain 2-ACBs, which is formed upon irradiation from

  1. Light-induced circular birefringence in cyanoazobenzene side-chain liquid-crystalline polyester films

    DEFF Research Database (Denmark)

    Naydenova, I; Nikolova, L; Ramanujam, P.S.


    We report the inducement of large circular birefringence (optical activity) in films of a cyanoazobenzene side-chain liquid-crystalline polyester on illumination with circularly polarized light. The polyester has no chiral groups and is initially isotropic. The induced optical rotation is up to 5...

  2. Supramolecular control of self-assembling terthiophene-peptide conjugates through the amino acid side chain

    Energy Technology Data Exchange (ETDEWEB)

    Lehrman, Jessica A.; Cui, Honggang; Tsai, Wei-Wen; Moyer, Tyson J.; Stupp, Samuel I. [NWU


    The self-assembly of oligothiophene–peptide conjugates can be directed through the systematic variation of the peptide sequence into different nanostructures, including flat spicules, nanotubes, spiral sheets, and giant, flat sheets. Furthermore, the assembly of these molecules is not controlled by steric interactions between the amino acid side chains.

  3. Pectic arabinan side chains are essential for pollen cell wall integrity during pollen development

    DEFF Research Database (Denmark)

    Cankar, Katarina; Kortstee, Anne; Toonen, Marcel A.J.


    transgenes were not transmitted to the next generation when these lines were used as a pollen donor, suggesting male sterility. Viability of mature pollen was severely decreased in potato lines with reduced pectic arabinan, but not in lines with altered galactan side chains. Anthers and pollen of different...

  4. A paint removal concept with side-chain liquid crystalline polymers as primer material

    NARCIS (Netherlands)

    Wielen, van der M.W.J.; Cohen Stuart, M.A.; Fleer, G.J.; Nieuwhof, R.P.; Marcelis, A.T.M.; Sudhölter, E.J.R.


    A new paint removal concept is introduced making use of a polymer primer layer with a sharp softening temperature. For this, a new class of side-chain liquid crystalline polymers with polar moieties in the backbone has been developed and studied in thin films. These polymers form lamellar-ordered

  5. Side-chain liquid-crystalline polyesters for optical information storage

    DEFF Research Database (Denmark)

    Hvilsted, Søren; Andruzzi, F.; Ramanujam, P.S.


    We report erasable holographic recording with a resolution of at least 2500 lines/mm on unoriented films of side-chain liquid-crystalline polyesters. Recording energies of approximately 1 J/cm2 have been used. We have obtained a diffraction efficiency of approximately 30% with polarization...

  6. Influence of structures of polymer backbones on cooperative photoreorientation behavior of p-cyanoazobenzene side chains

    DEFF Research Database (Denmark)

    Han, Mina; Kidowaki, Masatoshi; Ichimura, Kunihiro


    Photoinduced orientational behavior of a polymethacrylate (CN6) and a polyester (p6a12) with p-cyanoazobenzene side chains was studied to reveal the structural effect of the liquid crystalline polymer backbones. Irradiation with linearly polarized W light resulted in the reorientation of the azob...

  7. Energetic, Structural, and Antimicrobial Analyses of [beta]-Lactam Side Chain Recognition by [beta]-Lactamases

    Energy Technology Data Exchange (ETDEWEB)

    Caselli, E.; Powers, R.A.; Blaszczak, L.C.; Wu, C.Y.E.; Prati, F.; Shoichet, B.K. (NWU)


    Penicillins and cephalosporins are among the most widely used and successful antibiotics. The emergence of resistance to these {beta}-lactams, most often through bacterial expression of {beta}-lactamases, threatens public health. To understand how {beta}-lactamases recognize their substrates, it would be helpful to know their binding energies. Unfortunately, these have been difficult to measure because {beta}-lactams form covalent adducts with {beta}-lactamases. This has complicated functional analyses and inhibitor design. To investigate the contribution to interaction energy of the key amide (R1) side chain of {beta}-lactam antibiotics, eight acylglycineboronic acids that bear the side chains of characteristic penicillins and cephalosporins, as well as four other analogs, were synthesized. These transition-state analogs form reversible adducts with serine {beta}-lactamases. Therefore, binding energies can be calculated directly from K{sub i} values. The K{sub i} values measured span four orders of magnitude against the Group I {beta}-lactamase AmpC and three orders of magnitude against the Group II {beta}-lactamase TEM-1. The acylglycineboronic acids have K{sub i} values as low as 20 nM against AmpC and as low as 390 nM against TEM-1. The inhibitors showed little activity against serine proteases, such as chymotrypsin. R1 side chains characteristic of {beta}-lactam inhibitors did not have better affinity for AmpC than did side chains characteristic of {beta}-lactam substrates. Two of the inhibitors reversed the resistance of pathogenic bacteria to {beta}-lactams in cell culture. Structures of two inhibitors in their complexes with AmpC were determined by X-ray crystallography to 1.90 {angstrom} and 1.75 {angstrom} resolution; these structures suggest interactions that are important to the affinity of the inhibitors. Acylglycineboronic acids allow us to begin to dissect interaction energies between {beta}-lactam side chains and {beta}-lactamases. Surprisingly

  8. Structure and dynamics of a conformationally constrained nitroxide side chain and applications in EPR spectroscopy. (United States)

    Fleissner, Mark R; Bridges, Michael D; Brooks, Evan K; Cascio, Duilio; Kálai, Tamás; Hideg, Kálmán; Hubbell, Wayne L


    A disulfide-linked nitroxide side chain (R1) is the most widely used spin label for determining protein topology, mapping structural changes, and characterizing nanosecond backbone motions by site-directed spin labeling. Although the internal motion of R1 and the number of preferred rotamers are limited, translating interspin distance measurements and spatial orientation information into structural constraints is challenging. Here, we introduce a highly constrained nitroxide side chain designated RX as an alternative to R1 for these applications. RX is formed by a facile cross-linking reaction of a bifunctional methanethiosulfonate reagent with pairs of cysteine residues at i and i + 3 or i and i + 4 in an α-helix, at i and i + 2 in a β-strand, or with cysteine residues in adjacent strands in a β-sheet. Analysis of EPR spectra, a crystal structure of RX in T4 lysozyme, and pulsed electron-electron double resonance (ELDOR) spectroscopy on an immobilized protein containing RX all reveal a highly constrained internal motion of the side chain. Consistent with the constrained geometry, interspin distance distributions between pairs of RX side chains are narrower than those from analogous R1 pairs. As an important consequence of the constrained internal motion of RX, spectral diffusion detected with ELDOR reveals microsecond internal motions of the protein. Collectively, the data suggest that the RX side chain will be useful for distance mapping by EPR spectroscopy, determining spatial orientation of helical segments in oriented specimens, and measuring structural fluctuations on the microsecond time scale.

  9. Conjugation of diisocyanate side chains to dimethacrylate reduces polymerization shrinkage and increases the hardness of composite resins

    Directory of Open Access Journals (Sweden)

    Yih-Dean Jan


    Conclusion: Conjugation of diisocyanate side chains to dimethacrylate represents an effective means of reducing polymerization shrinkage and increasing the surface hardness of dental composite resins.

  10. Primary structure of N-linked carbohydrate chains of a human chimeric plasminogen activator K2tu-PA expressed in Chinese hamster ovary cells

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Bergwerff, A.A.; Oostrum, J. van; Asselbergs, F.A.M.; Bürgi, R.; Hokke, C.H.; Kamerling, J.P.


    A recombinant human plasminogen activator hybrid variant K2tu-PA, expressed in Chinese hamster ovary cells, is partially glycosylated at Asn12 (A chain, kringle-2 domain) and completely glycosylated at Asn247 (B chain, protease domain). After release of the N-linked carbohydrate chains by

  11. Producing high-accuracy lattice models from protein atomic coordinates including side chains. (United States)

    Mann, Martin; Saunders, Rhodri; Smith, Cameron; Backofen, Rolf; Deane, Charlotte M


    Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models.

  12. Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes. (United States)

    Carpenter, Margaret A; Shaw, Martin; Cooper, Rebecca D; Frew, Tonya J; Butler, Ruth C; Murray, Sarah R; Moya, Leire; Coyne, Clarice J; Timmerman-Vaughan, Gail M


    Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea. To understand how allelic variation in the pea starch metabolic pathway affects starch structure and percent amylose, partial sequences of 25 candidate genes were characterized for polymorphisms using a panel of 92 diverse pea lines. Variation in the percent amylose composition of extracted seed starch and (amylopectin) chain length distribution, one measure of starch structure, were characterized for these lines. Association mapping was undertaken to identify polymorphisms associated with the variation in starch chain length distribution and percent amylose, using a mixed linear model that incorporated population structure and kinship. Associations were found for polymorphisms in seven candidate genes plus Mendel's r locus (which conditions the round versus wrinkled seed phenotype). The genes with associated polymorphisms are involved in the substrate supply, chain elongation and branching stages of the pea carbohydrate and starch metabolic pathways. The association of polymorphisms in carbohydrate and starch metabolic genes with variation in amylopectin chain length distribution and percent amylose may help to guide manipulation of pea seed starch structural and functional properties through plant breeding.

  13. Side Chain Cyclized Aromatic Amino Acids: Great Tools as Local Constraints in Peptide and Peptidomimetic Design. (United States)

    Van der Poorten, Olivier; Knuhtsen, Astrid; Sejer Pedersen, Daniel; Ballet, Steven; Tourwé, Dirk


    Constraining the conformation of flexible peptides is a proven strategy to increase potency, selectivity, and metabolic stability. The focus has mostly been on constraining the backbone dihedral angles; however, the correct orientation of the amino acid side chains (χ-space) that constitute the peptide pharmacophore is equally important. Control of χ-space utilizes conformationally constrained amino acids that favor, disfavor, or exclude the gauche (-), the gauche (+), or the trans conformation. In this review we focus on cyclic aromatic amino acids in which the side chain is connected to the peptide backbone to provide control of χ(1)- and χ(2)-space. The manifold applications for cyclized analogues of the aromatic amino acids Phe, Tyr, Trp, and His within peptide medicinal chemistry are showcased herein with examples of enzyme inhibitors and ligands for G protein-coupled receptors.

  14. Fuel cell catalyst layers containing short-side-chain perfluorosulfonic acid ionomers

    Energy Technology Data Exchange (ETDEWEB)

    Peron, Jennifer; Edwards, Dave; Haldane, Mark; Shi, Zhiqing [Institute for Fuel Cell Innovation, National Research Council (Canada); Luo, Xiaoyan [Department of Chemistry, Simon Fraser University, Burnaby, British Columbia (Canada); Zhang, Yongming [School of Chemistry and Chemical Technology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240 (China); Holdcroft, Steven [Institute for Fuel Cell Innovation, National Research Council (Canada); Department of Chemistry, Simon Fraser University, Burnaby, British Columbia (Canada)


    Porous catalyst layers (CLs) containing short-side-chain (SSC) perfluorosulfonic acid (PFSA) ionomers of different ion exchange capacity (IEC: 1.3, 1.4 and 1.5 meq g{sup -1}) were deposited onto Nafion 211 to form catalyst-coated membranes. The porosity of SSC-PFSA-based CLs is larger than Nafion-CL analogues. CLs incorporating SSC ionomer extend the current density of fuel cell polarization curves at elevated temperature and lower relative humidity compared to those based on long-side chain PFSA (e.g., Nafion)-based CLs. Fuel cell polarization performance was greatly improved at 110 C and 30% relative humidity (RH) when SSC PFSI was incorporated into the catalyst layer. (author)

  15. Histidine side-chain dynamics and protonation monitored by C-13 CPMG NMR relaxation dispersion

    DEFF Research Database (Denmark)

    Hass, M. A. S.; Yilmaz, A.; Christensen, Hans Erik Mølager


    the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from N-15 backbone relaxation measurements. Compared to measurements of backbone nuclei, C-13(epsilon 1) dispersion provides a more direct method to monitor interchanging protonation states...... or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the C-13(epsilon 1) dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains......The use of C-13 NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically C-13 labeled histidine residues in plastocyanin (PCu) from...

  16. Aqueous Processing for Printed Organic Electronics: Conjugated Polymers with Multistage Cleavable Side Chains. (United States)

    Schmatz, Brian; Yuan, Zhibo; Lang, Augustus W; Hernandez, Jeff L; Reichmanis, Elsa; Reynolds, John R


    The ability to process conjugated polymers via aqueous solution is highly advantageous for reducing the costs and environmental hazards of large scale roll-to-roll processing of organic electronics. However, maintaining competitive electronic properties while achieving aqueous solubility is difficult for several reasons: (1) Materials with polar functional groups that provide aqueous solubility can be difficult to purify and characterize, (2) many traditional coupling and polymerization reactions cannot be performed in aqueous solution, and (3) ionic groups, though useful for obtaining aqueous solubility, can lead to a loss of solid-state order, as well as a screening of any applied bias. As an alternative, we report a multistage cleavable side chain method that combines desirable aqueous processing attributes without sacrificing semiconducting capabilities. Through the attachment of cleavable side chains, conjugated polymers have for the first time been synthesized, characterized, and purified in organic solvents, converted to a water-soluble form for aqueous processing, and brought through a final treatment to cleave the polymer side chains and leave behind the desired electronic material as a solvent-resistant film. Specifically, we demonstrate an organic soluble polythiophene that is converted to an aqueous soluble polyelectrolyte via hydrolysis. After blade coating from an aqueous solution, UV irradiation is used to cleave the polymer's side chains, resulting in a solvent-resistant, electroactive polymer thin film. In application, this process results in aqueous printed materials with utility for solid-state charge transport in organic field effect transistors (OFETs), along with red to colorless electrochromism in ionic media for color changing displays, demonstrating its potential as a universal method for aqueous printing in organic electronics.

  17. Oxidative Degradations of the Side Chain of Unsaturated Ent-labdanes. Part I.

    Directory of Open Access Journals (Sweden)

    Karen Catalán Marín


    Full Text Available A selective route for the degradation of the unsaturated side chain of ent-labdanes has been devised, giving two useful synthons: 2β-acetoxy-14,15,17-trinor-ent-labdane-8,13- dione (5 and 2β-acetoxy-14,15-dinor-ent-labd-8(17-en-13-one (7, the use of which for the preparation of terpenylquinone derivatives shall be reported elsewhere.

  18. Aqueous Processing for Printed Organic Electronics: Conjugated Polymers with Multistage Cleavable Side Chains (United States)


    The ability to process conjugated polymers via aqueous solution is highly advantageous for reducing the costs and environmental hazards of large scale roll-to-roll processing of organic electronics. However, maintaining competitive electronic properties while achieving aqueous solubility is difficult for several reasons: (1) Materials with polar functional groups that provide aqueous solubility can be difficult to purify and characterize, (2) many traditional coupling and polymerization reactions cannot be performed in aqueous solution, and (3) ionic groups, though useful for obtaining aqueous solubility, can lead to a loss of solid-state order, as well as a screening of any applied bias. As an alternative, we report a multistage cleavable side chain method that combines desirable aqueous processing attributes without sacrificing semiconducting capabilities. Through the attachment of cleavable side chains, conjugated polymers have for the first time been synthesized, characterized, and purified in organic solvents, converted to a water-soluble form for aqueous processing, and brought through a final treatment to cleave the polymer side chains and leave behind the desired electronic material as a solvent-resistant film. Specifically, we demonstrate an organic soluble polythiophene that is converted to an aqueous soluble polyelectrolyte via hydrolysis. After blade coating from an aqueous solution, UV irradiation is used to cleave the polymer’s side chains, resulting in a solvent-resistant, electroactive polymer thin film. In application, this process results in aqueous printed materials with utility for solid-state charge transport in organic field effect transistors (OFETs), along with red to colorless electrochromism in ionic media for color changing displays, demonstrating its potential as a universal method for aqueous printing in organic electronics. PMID:28979937

  19. Quantitative profiling of feruloylated arabinoxylan side chains from graminaceous cell walls

    Directory of Open Access Journals (Sweden)

    Rachel R. Schendel


    Full Text Available Graminaceous arabinoxylans are distinguished by decoration with feruloylated monosaccha-ridic and oligosaccharidic side-chains. Although it is hypothesized that structural complexity and abundance of these feruloylated arabinoxylan side-chains may contribute, among other factors, to resistance of plant cell walls to enzymatic degradation, quantitative profiling ap-proaches for these structural units in plant cell wall materials have not been described yet. Here we report the development and application of a rapid and robust method enabling the quantitative comparison of feruloylated side-chain profiles in cell wall materials following mildly acidic hydrolysis, C18-SPE, reduction under aprotic conditions, and liquid chromatog-raphy with diode-array detection/mass spectrometry (LC-DAD/MS separation and detection. The method was applied to the insoluble fiber/cell wall materials isolated from twelve whole grains: wild rice (Zizania aquatica L., long-grain brown rice (Oryza sativa L., rye (Secale cereal L., kamut (Triticum turanicum Jakubz., wheat (Triticum aestivum L., spelt (Triticum spelta L., intermediate wheatgrass (Thinopyrum intermedium, maize (Zea mays L., popcorn (Zea mays L. var. everta, oat (Avena sativa L. (dehulled, barley (Hordeum vulgare L. (de-hulled, and proso millet (Panicum miliaceum L.. Between 51 and 96% of the total esterified monomeric ferulates were represented in the quantified compounds captured in the feruloylat-ed side-chain profiles, which confirms the significance of these structures to the global arabi-noxylan structure in terms of quantity. The method provided new structural insights into cere-al grain arabinoxylans, in particular, that the structural moiety α-L-galactopyranosyl-(1→2-β-D-xylopyranosyl-(1→2-5-O-trans-feruloyl-L-arabinofuranose (FAXG, which had previous-ly only been described in maize, is ubiquitous to cereal grains.

  20. Quantitative Profiling of Feruloylated Arabinoxylan Side-Chains from Graminaceous Cell Walls. (United States)

    Schendel, Rachel R; Meyer, Marleen R; Bunzel, Mirko


    Graminaceous arabinoxylans are distinguished by decoration with feruloylated monosaccharidic and oligosaccharidic side-chains. Although it is hypothesized that structural complexity and abundance of these feruloylated arabinoxylan side-chains may contribute, among other factors, to resistance of plant cell walls to enzymatic degradation, quantitative profiling approaches for these structural units in plant cell wall materials have not been described yet. Here we report the development and application of a rapid and robust method enabling the quantitative comparison of feruloylated side-chain profiles in cell wall materials following mildly acidic hydrolysis, C18-solid phase extraction (SPE), reduction under aprotic conditions, and liquid chromatography with diode-array detection/mass spectrometry (LC-DAD/MS) separation and detection. The method was applied to the insoluble fiber/cell wall materials isolated from 12 whole grains: wild rice (Zizania aquatica L.), long-grain brown rice (Oryza sativa L.), rye (Secale cereale L.), kamut (Triticum turanicum Jakubz.), wheat (Triticum aestivum L.), spelt (Triticum spelta L.), intermediate wheatgrass (Thinopyrum intermedium), maize (Zea mays L.), popcorn (Zea mays L. var. everta), oat (Avena sativa L.) (dehulled), barley (Hordeum vulgare L.) (dehulled), and proso millet (Panicum miliaceum L.). Between 51 and 96% of the total esterified monomeric ferulates were represented in the quantified compounds captured in the feruloylated side-chain profiles, which confirms the significance of these structures to the global arabinoxylan structure in terms of quantity. The method provided new structural insights into cereal grain arabinoxylans, in particular, that the structural moiety α-l-galactopyranosyl-(1→2)-β-d-xylopyranosyl-(1→2)-5-O-trans-feruloyl-l-arabinofuranose (FAXG), which had previously only been described in maize, is ubiquitous to cereal grains.

  1. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. (United States)

    Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S


    We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

  2. Exploiting the CNC side chain in heterocyclic rearrangements: synthesis of 4(5)-acylamino-imidazoles. (United States)

    Piccionello, Antonio Palumbo; Buscemi, Silvestre; Vivona, Nicolò; Pace, Andrea


    A new variation on the Boulton-Katritzky reaction is reported, namely, involving use of a CNC side chain. A novel Montmorillonite-K10 catalyzed nonreductive transamination of a 3-benzoyl-1,2,4-oxadiazole afforded a 3-(alpha-aminobenzyl)-1,2,4-oxadiazole, which was condensed with benzaldehydes to afford the corresponding imines. In the presence of strong base, these imines underwent Boulton-Katritzky-type rearrangement to afford novel 4(5)-acylaminoimidazoles.

  3. Applying Thienyl Side Chains and Different π-Bridge to Aromatic Side-Chain Substituted Indacenodithiophene-Based Small Molecule Donors for High-Performance Organic Solar Cells. (United States)

    Wang, Jin-Liang; Liu, Kai-Kai; Liu, Sha; Liu, Feng; Wu, Hong-Bin; Cao, Yong; Russell, Thomas P


    A pair of linear tetrafluorinated small molecular donors, named as ThIDTTh4F and ThIDTSe4F, which are with tetrathienyl-substituted IDT as electron-rich central core, electron-deficient difluorobenzothiadiazole as acceptor units, and donor end-capping groups, but having differences in the π-bridge (thiophene and selenophene), were successfully synthesized and evaluated as donor materials in organic solar cells. Such π-bridge and core units in these small molecules play a decisive role in the formation of the nanoscale separation of the blend films, which were systematically investigated through absorption spectra, grazing incidence X-ray diffraction pattern, transmission electron microscopy images, resonant soft X-ray scattering profiles, and charge mobility measurement. The ThIDTSe4F (with selenophene π-bridge)-based device exhibited superior performance than devices based on ThIDTh4F (with thiophene π-bridge) after post annealing treatment owing to optimized film morphology and improved charge transport. Power conversion efficiency of 7.31% and fill factor of ∼0.70 were obtained by using a blend of ThIDTSe4F and PC71BM with thermal annealing and solvent vapor annealing treatments, which is the highest PCE from aromatic side-chain substituted IDT-based small molecular solar cells. The scope of this study is to reveal the structure-property relationship of the aromatic side-chain substituted IDT-based donor materials as a function of π-bridge and the post annealing conditions.

  4. Cation alkyl side chain length and symmetry effects on the surface tension of ionic liquids. (United States)

    Almeida, Hugo F D; Freire, Mara G; Fernandes, Ana M; Lopes-da-Silva, José A; Morgado, Pedro; Shimizu, Karina; Filipe, Eduardo J M; Lopes, José N Canongia; Santos, Luís M N B F; Coutinho, João A P


    Aiming at providing a comprehensive study of the influence of the cation symmetry and alkyl side chain length on the surface tension and surface organization of ionic liquids (ILs), this work addresses the experimental measurements of the surface tension of two extended series of ILs, namely R,R'-dialkylimidazolium bis[(trifluoromethyl)sulfonyl]imide ([C(n)C(n)im][NTf2]) and R-alkyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide ([C(n)C(1)im][NTf2]), and their dependence with temperature (from 298 to 343 K). For both series of ILs the surface tension decreases with an increase in the cation side alkyl chain length up to aliphatic chains no longer than hexyl, here labeled as critical alkyl chain length (CACL). For ILs with aliphatic moieties longer than CACL the surface tension displays an almost constant value up to [C12C12im][NTf2] or [C16C1im][NTf2]. These constant values further converge to the surface tension of long chain n-alkanes, indicating that, for sufficiently long alkyl side chains, the surface ordering is strongly dominated by the aliphatic tails present in the IL. The enthalpies and entropies of surface were also derived and the critical temperatures were estimated from the experimental data. The trend of the derived thermodynamic properties highlights the effect of the structural organization of the IL at the surface with visible trend shifts occurring at a well-defined CACL in both symmetric and asymmetric series of ILs. Finally, the structure of a long-alkyl side chain IL at the vacuum-liquid interface was also explored using Molecular Dynamics simulations. In general, it was found that for the symmetric series of ILs, at the outermost polar layers, more cations point one of their aliphatic tails outward and the other inward, relative to the surface, than cations pointing both tails outward. The number of the former, while being the preferred conformation, exceeds the latter by around 75%.

  5. Controlling the mode of operation of organic transistors through side-chain engineering

    KAUST Repository

    Giovannitti, Alexander


    Electrolyte-gated organic transistors offer low bias operation facilitated by direct contact of the transistor channel with an electrolyte. Their operation mode is generally defined by the dimensionality of charge transport, where a field-effect transistor allows for electrostatic charge accumulation at the electrolyte/semiconductor interface, whereas an organic electrochemical transistor (OECT) facilitates penetration of ions into the bulk of the channel, considered a slow process, leading to volumetric doping and electronic transport. Conducting polymer OECTs allow for fast switching and high currents through incorporation of excess, hygroscopic ionic phases, but operate in depletion mode. Here, we show that the use of glycolated side chains on a thiophene backbone can result in accumulation mode OECTs with high currents, transconductance, and sharp subthreshold switching, while maintaining fast switching speeds. Compared with alkylated analogs of the same backbone, the triethylene glycol side chains shift the mode of operation of aqueous electrolyte-gated transistors from interfacial to bulk doping/transport and show complete and reversible electrochromism and high volumetric capacitance at low operating biases. We propose that the glycol side chains facilitate hydration and ion penetration, without compromising electronic mobility, and suggest that this synthetic approach can be used to guide the design of organic mixed conductors.

  6. Effects of side chains on thiazolothiazole-based copolymer semiconductors for high performance solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Subramaniyan, Selvam; Xin, Hao; Kim, Felix Sunjoo; Jenekhe, Samson A. [Department of Chemical Engineering and Department of Chemistry, University of Washington, Seattle, Washington (United States); Shoaee, Safa; Durrant, James R. [Department of Chemistry, Imperial College London, Exhibition Road, London (United Kingdom)


    New thiazolothiazole-dithienosilole copolymer semiconductors bearing side chains of different type, size, and topology were synthesized and used to demonstrate the influence of side chains on morphology, charge transport and photovoltaic properties. The field effect mobility of holes varied from 0.01-0.03 cm{sup 2}V{sup -1}s{sup -1} in PSOTT and PSEHTT to 0.12 cm{sup 2}V{sup -1}s{sup -1} in PSOxTT. The average power conversion efficiency of solar cells under 1.0 sun illumination could be varied from 2.1% in PSOxTT and 4.1% in PSOTT to 5.0% in PSEHTT. The highest photovoltaic efficiency achieved in PSEHTT, that has all-branched alkyl side chains and face-on {pi}-stacking orientation, was corroborated by its enhanced charge photogeneration observed by transient absorption spectroscopy. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. Side chain hydrophobicity modulates therapeutic activity and membrane selectivity of antimicrobial peptide mastoparan-X.

    Directory of Open Access Journals (Sweden)

    Jonas R Henriksen

    Full Text Available The discovery of new anti-infective compounds is stagnating and multi-resistant bacteria continue to emerge, threatening to end the "antibiotic era". Antimicrobial peptides (AMPs and lipo-peptides such as daptomycin offer themselves as a new potential class of antibiotics; however, further optimization is needed if AMPs are to find broad use as antibiotics. In the present work, eight analogues of mastoparan-X (MPX were investigated, having side chain modifications in position 1, 8 and 14 to modulate peptide hydrophobicity. The self-association properties of the peptides were characterized, and the peptide-membrane interactions in model membranes were compared with the bactericidal and haemolytic properties. Alanine substitution at position 1 and 14 resulted in higher target selectivity (red blood cells versus bacteria, but also decreased bactericidal potency. For these analogues, the gain in target selectivity correlated to biophysical parameters showing an increased effective charge and reduction in the partitioning coefficient for membrane insertion. Introduction of an unnatural amino acid, with an octyl side chain by amino acid substitution, at positions 1, 8 and 14 resulted in increased bactericidal potency at the expense of radically reduced membrane target selectivity. Overall, optimized membrane selectivity or bactericidal potency was achieved by changes in side chain hydrophobicity of MPX. However, enhanced potency was achieved at the expense of selectivity and vice versa in all cases.

  8. Improving proton conduction pathways in di- and triblock copolymer membranes: Branched versus linear side chains (United States)

    Dorenbos, G.


    Phase separation within a series of polymer membranes in the presence of water is studied by dissipative particle dynamics. Each polymer contains hydrophobic A beads and hydrophilic C beads. Three parent architectures are constructed from a backbone composed of connected hydrophobic A beads to which short ([C]), long ([A3C]), or symmetrically branched A5[AC][AC] side chains spring off. Three di-block copolymer derivatives are constructed by covalently bonding an A30 block to each parent architecture. Also three tri-blocks with A15 blocks attached to both ends of each parent architecture are modeled. Monte Carlo tracer diffusion calculations through the water containing pores for 1226 morphologies reveal that water diffusion for parent architectures is slowest and diffusion through the di-blocks is fastest. Furthermore, diffusion increases with side chain length and is highest for branched side chains. This is explained by the increase of water pore size with , which is the average number of bonds that A beads are separated from a nearest C bead. Optimization of within the amphiphilic parent architecture is expected to be essential in improving proton conduction in polymer electrolyte membranes.

  9. An exceptional series of phase transitions in hydrophobic amino acids with linear side chains

    Directory of Open Access Journals (Sweden)

    Carl Henrik Görbitz


    Full Text Available The solid-state phase transitions and intermediate structures of S-2-aminobutanoic acid (l-2-aminobutyric acid, S-2-aminopentanoic acid (l-norvaline, S-2-aminohexanoic acid (l-norleucine and l-methionine between 100 and 470 K, identified by differential scanning calorimetry, have been characterized in a comprehensive single-crystal X-ray diffraction investigation. Unlike other enantiomeric amino acids investigated until now, this group featuring linear side chains displays up to five distinct phases. The multiple transitions between them involve a number of different processes: alteration of the hydrogen-bond pattern, to our knowledge the first example of this observed for an amino acid, sliding of molecular bilayers, seen previously only for racemates and quasiracemates, concerted side-chain rearrangements and abrupt as well as gradual modifications of the side-chain disorder. Ordering of l-norleucine upon cooling even proceeds via an incommensurately modulated structure. l-Methionine has previously been described as being fully ordered at room temperature. An accurate refinement now reveals extensive disorder for both molecules in the asymmetric unit, while two previously unknown phases occur above room temperature.

  10. Arginine side chains as a dispersant for individual single-wall carbon nanotubes. (United States)

    Hirano, Atsushi; Tanaka, Takeshi; Kataura, Hiromichi; Kameda, Tomoshi


    Charged peptides and proteins disperse single-wall carbon nanotubes (SWCNTs) in aqueous solutions. However, little is known about the role of their side chains in their interactions with SWCNTs. Homopolypeptide-SWCNT systems are ideal for investigating the mechanisms of such interactions. In this study, we demonstrate that SWCNTs are individually dispersed by poly-L-arginine (PLA). The debundled SWCNTs exhibited a distinct fluorescence. The dispersibility of SWCNTs with PLA was greater than that of SWCNTs with poly-L-lysine (PLL). Molecular dynamics simulations suggest that the side chains of PLA have stronger interactions with the sidewalls of SWCNTs compared with those of PLL. The guanidinium group at the end of the side chain of an arginine residue plays an important role in the interaction with SWCNTs, likely through hydrophobic, van der Waals, and π-π interactions. PLA can be useful as a tool for the dispersion of SWCNTs and can be used to non-covalently anchor materials to SWCNTs with strong binding. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Pectic arabinan side chains are essential for pollen cell wall integrity during pollen development. (United States)

    Cankar, Katarina; Kortstee, Anne; Toonen, Marcel A J; Wolters-Arts, Mieke; Houbein, Rudolf; Mariani, Celestina; Ulvskov, Peter; Jorgensen, Bodil; Schols, Henk A; Visser, Richard G F; Trindade, Luisa M


    Pectin is a complex polysaccharide and an integral part of the primary plant cell wall and middle lamella, contributing to cell wall mechanical strength and cell adhesion. To understand the structure-function relationships of pectin in the cell wall, a set of transgenic potato lines with altered pectin composition was analysed. The expression of genes encoding enzymes involved in pectin acetylation, degradation of the rhamnogalacturonan backbone and type and length of neutral side chains, arabinan and galactan in particular, has been altered. Upon crossing of different transgenic lines, some transgenes were not transmitted to the next generation when these lines were used as a pollen donor, suggesting male sterility. Viability of mature pollen was severely decreased in potato lines with reduced pectic arabinan, but not in lines with altered galactan side chains. Anthers and pollen of different developmental stages were microscopically examined to study the phenotype in more detail. Scanning electron microscopy of flowers showed collapsed pollen grains in mature anthers and in earlier stages cytoplasmic protrusions at the site of the of kin pore, eventually leading to bursting of the pollen grain and leaking of the cytoplasm. This phenomenon is only observed after the microspores are released and the tapetum starts to degenerate. Timing of the phenotype indicates a role for pectic arabinan side chains during remodelling of the cell wall when the pollen grain is maturing and dehydrating. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  12. Cylindrical polymer brushes with dendritic side chains by iterative anionic reactions

    KAUST Repository

    Zhang, Hefeng


    We report in this paper an easy method for the synthesis of cylindrical polymer brushes with dendritic side chains through anionic reaction. The synthesis is accomplished by iteratively grafting a living block copolymer, polyisoprene-. b-polystyrenyllithium (PI-. b-PSLi), to the main chain and subsequently to the branches in a divergent way. PI segment is short and serves as a precursor for multifunctional branching unit. The grafting reaction involves two successive steps: i) epoxidation of internal double bonds of PI segments, either in main chain or side chains; ii) ring-opening addition to the resulting epoxy group by the living PI-. b-PSLi. Repeating the two steps affords a series of cylindrical polymer brushes with up to 3rd generation and extremely high molecular weight. The branching multiplicity depends on the average number of oxirane groups per PI segment, usually ca. 8 in the present work. The high branching multiplicity leads to tremendous increase in molecular weights of the cylindrical products with generation growth. Several series of cylindrical polymer brushes with tunable aspect ratios are prepared using backbones and branches with controlled lengths. Shape anisotropy is investigated in dilute solution using light scattering technique. Worm-like single molecular morphology with large persistence length is observed on different substrates by atomic force microscopy.

  13. Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains. (United States)

    Makowski, Mariusz; Liwo, Adam; Scheraga, Harold A


    The physics-based potentials of side-chain-side-chain interactions corresponding to pairs composed of charged and polar, polar and polar, charged and hydrophobic, and hydrophobic and hydrophobic side chains have been determined. A total of 144 four-dimensional potentials of mean force (PMFs) of all possible pairs of molecules modeling these pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expressions were then fitted to the PMFs. Depending on the type of interacting sites, the analytical approximation to the PMF is a sum of terms corresponding to van der Waals interactions and cavity-creation involving the nonpolar sections of the side chains and van der Waals, cavity-creation, and electrostatic (charge-dipole or dipole-dipole) interaction energies and polarization energies involving the charged or polar sections of the side chains. The model used in this work reproduces all features of the interacting pairs. The UNited RESidue force field with the new side-chain-side-chain interaction potentials was preliminarily tested with the N-terminal part of the B-domain of staphylococcal protein A (PDBL 1BDD ; a three-α-helix bundle) and UPF0291 protein YnzC from Bacillus subtilis (PDB: 2HEP ; an α-helical hairpin).

  14. Absolute Side-chain Structure at Position 13 Is Required for the Inhibitory Activity of Bromein* (United States)

    Sawano, Yoriko; Hatano, Ken-ichi; Miyakawa, Takuya; Tanokura, Masaru


    Bromelain isoinhibitor (bromein), a cysteine proteinase inhibitor from pineapple stem, has a unique double-chain structure. The bromein precursor protein includes three homologous inhibitor domains, each containing an interchain peptide between the light and heavy chains. The interchain peptide in the single-chain precursor is immediately processed by bromelain, a target proteinase. In the present study, to clarify the essential inhibitory site of bromein, we constructed 44 kinds of site-directed and deletion mutants and investigated the inhibitory activity of each toward bromelain. As a result, the complete chemical structure of Leu13 in the light chain was revealed to be essential for inhibition. Pro12 prior to the leucine residue was also involved in the inhibitory activity and would control the location of the leucine side chain by the fixed φ dihedral angle of proline. Furthermore, the five-residue length of the interchain peptide was strictly required for the inhibitory activity. On the other hand, no inhibitory activity against bromelain was observed by the substitution of proline for the N terminus residue Thr15 of the interchain peptide. In summary, these mutational analyses of bromein demonstrated that the appropriate position and conformation of Leu13 are absolutely crucial for bromelain inhibition. PMID:18948264

  15. Dependence of crystallite formation and preferential backbone orientations on the side chain pattern in PBDTTPD polymers

    KAUST Repository

    El Labban, Abdulrahman


    (Figure Presented) Alkyl substituents appended to the π-conjugated main chain account for the solution-processability and film-forming properties of most π-conjugated polymers for organic electronic device applications, including field-effect transistors (FETs) and bulk-heterojunction (BHJ) solar cells. Beyond film-forming properties, recent work has emphasized the determining role that side-chain substituents play on polymer self-assembly and thin-film nanostructural order, and, in turn, on device performance. However, the factors that determine polymer crystallite orientation in thin-films, implying preferential backbone orientation relative to the device substrate, are a matter of some debate, and these structural changes remain difficult to anticipate. In this report, we show how systematic changes in the side-chain pattern of poly(benzo[1,2-b:4,5-b′]dithiophene-alt-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers can (i) influence the propensity of the polymer to order in the π-stacking direction, and (ii) direct the preferential orientation of the polymer crystallites in thin films (e.g., "face-on" vs "edge-on"). Oriented crystallites, specifically crystallites that are well-ordered in the π-stacking direction, are believed to be a key contributor to improved thin-film device performance in both FETs and BHJ solar cells.

  16. Amphiphilic polymer based on fluoroalkyl and PEG side chains for fouling release coating (United States)

    Cong, W. W.; Wang, K.; Yu, X. Y.; Zhang, H. Q.; Lv, Z.; Gui, T. J.


    Under static conditions, fouling release coating could not express good release property to marine organisms. Amphiphilic polymer with mixture of fluorinated monomer and short side group of polyethylene glycol (PEG) was synthesized. And also we studied the ability of amphiphilic polymer to influence the surface properties and how it controlled the adhesion of marine organisms to coated surfaces. By incorporating fluorinated monomer and PEG side chain into the polymer, the effect of incorporating both polar and non-polar groups on fouling-release coating could be studied. The dry surface was characterized by three-dimensional digital microscopy and scanning electron microscopy (SEM), and the morphology of the amphiphilic fouling release coating showed just like flaky petal. The amphiphilic polymer in fouling release coating tended to reconstruct in water, and the ability was examined by static contact angle, which was smaller than the PDMS (polydimethylsiloxane) fouling release coating. Also surface energy was calculated by three solvents, and surface energy of amphiphilic fouling release coating was higher than that of the PDMS fouling release coating. To understand more about its fouling release property, seawater exposure method was adopted in gulf of Qingdao port. Fewer diatoms Navicula were found in biofilm after using amphiphilic fouling release coating. In general, coating containing both PEG and fluorinated side chain possessed certain fouling release property.

  17. Unique contributions of an arginine side chain to ligand recognition in a glutamate-gated chloride channel

    DEFF Research Database (Denmark)

    Lynagh, Timothy; Komnatnyy, Vitaly V; Pless, Stephan A


    -gated chloride channel from the nematode Haemonchus contortus. Our data unveil a surprisingly small contribution of charge at a conserved arginine side chain previously suggested to form a salt bridge with the ligand, glutamate. Instead, our data show that Arg contributes crucially to ligand sensitivity via...... a hydrogen bond network, where Arg interacts both with agonist and with a conserved Thr side chain within the receptor. Together, the data provide a new explanation for the reliance of neurotransmitter receptors on Arg side chains and highlight the exceptional capacity of unnatural amino acid incorporation...

  18. Conformational studies on the N-linked carbohydrate chain of bromelain

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Bouwstra, J.B.; Spoelstra, E.C.; Waard, P. de; Leeflang, B.R.; Kamerling, J.P.


    1H- and 13C-NMR assignments for the carbohydrate part of the glycopeptide alpha-d-Man-(1->6)-[ß-d-Xyl-(1->2)]-ß-d-Man-(1->4)-ß-d-GlcNAc-(1->4)-[alpha-l-Fuc-(1->3)]-ß-d- GlcNAc-(1->N)-Asn~, derived from the proteolytic enzyme bromelain (EC, have been obtained using homo- and heteronuclear

  19. The binding mode of side chain- and C3-modified epothilones to tubulin. (United States)

    Erdélyi, Máté; Navarro-Vázquez, Armando; Pfeiffer, Bernhard; Kuzniewski, Christian N; Felser, Andrea; Widmer, Toni; Gertsch, Jürg; Pera, Benet; Díaz, José Fernando; Altmann, Karl-Heinz; Carlomagno, Teresa


    The tubulin-binding mode of C3- and C15-modified analogues of epothilone A (Epo A) was determined by NMR spectroscopy and computational methods and compared with the existing structural models of tubulin-bound natural Epo A. Only minor differences were observed in the conformation of the macrocycle between Epo A and the C3-modified analogues investigated. In particular, 3-deoxy- (compound 2) and 3-deoxy-2,3-didehydro-Epo A (3) were found to adopt similar conformations in the tubulin-binding cleft as Epo A, thus indicating that the 3-OH group is not essential for epothilones to assume their bioactive conformation. None of the available models of the tubulin-epothilone complex is able to fully recapitulate the differences in tubulin-polymerizing activity and microtubule-binding affinity between C20-modified epothilones 6 (C20-propyl), 7 (C20-butyl), and 8 (C20-hydroxypropyl). Based on the results of transferred NOE experiments in the presence of tubulin, the isomeric C15 quinoline-based Epo B analogues 4 and 5 show very similar orientations of the side chain, irrespective of the position of the nitrogen atom in the quinoline ring. The quinoline side chain stacks on the imidazole moiety of beta-His227 with equal efficiency in both cases, thus suggesting that the aromatic side chain moiety in epothilones contributes to tubulin binding through strong van der Waals interactions with the protein rather than hydrogen bonding involving the heteroaromatic nitrogen atom. These conclusions are in line with existing tubulin polymerization and microtubule-binding data for 4, 5, and Epo B.

  20. Influence of water solubility, side chain degradability and side chain configuration on the degradation of phthalic acid esters under methanogenic conditions

    Energy Technology Data Exchange (ETDEWEB)

    Alnervik, M.


    Water solubility and degradability of side chains estrifying phthalic acid are factors possible to influence the degradation of phthalic acid esters (PAEs). To investigate the importance of these factors degradation of butyl 2-ethylhexyl phthalate (BEHP), bis(2-ethylhexyl) phthalate (DEHP), dibutyl phthalate (DBP), dihexyl phthalate (DHP), dioctyl phthalate (DOP) and didecyl phthalate (DDP) were examined under methanogenic conditions as well as was the degradability of the alcohols estrifying these PAEs. We also investigated if the degradation of resistant PAEs could be stimulated by the addition of a degradable PAE. Synthesis of degradation intermediates and two methods for PAE analyses are presented. The investigation showed that all alcohols were degraded to methane and carbon dioxide and that the degradation of PAE occurred in incubations amended with BBP, BEHP, DHP and DBP, whilst DEHP, DOP and DDP were unaffected throughout the experimental period. BBP added to incubations with DEHP, could not stimulate DEHP degradation. In conclusion, the degradability of alcohols estrifying phthalic acid in this study does not affect the anaerobic degradability of PAEs. Water solubility of a PAE can not be rejected as a factor limiting phthalate degradation under methanogenic conditions. Anaerobic degradation of persistent PAEs can not be stimulated by mixing it with a degradable phthalate. 23 refs, 11 figs, 2 tabs

  1. Stability of photochromism in new bifunctional copolymers containing spiropyran and chalcone moiety in the side chain

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Dong Hoon; Ban, Si Young; Kim, Jae Hong [Kyunghee Univ., Suwon (Korea, Republic of)


    We synthesized three copolymers bearing photochromic spiropyran dye and chalcone moiety in the side chain for studying the dynamic properties of their photochromism. They contain methacrylate-spiropyran (MA-spiropyran) and methacrylate-chalcone) (MA-chalcone) with the different concentration. The photosensitivity of the newly synthesized copolymers was investigated by using UV-Vis absorption spectroscopy. We absorbed photodimerization and phtochromic behavior under UV irradiation at the same time. The effect of photocrosslink on the rate and stability of photochromism in three copolymers was considered in this study. This study might be helpful to design photochromic materials for irreversible optical memory by virtue of photocrosslinking reaction.

  2. Oxidative Degradations of the Side Chain of Unsaturated Ent-labdanes. Part II

    Directory of Open Access Journals (Sweden)

    María Cristina Chamy


    Full Text Available A route for the degradation of the side chain of ent-labdane derivatives has beendevised, giving the useful synthon 2β,12-dihydroxy-13,14,15,16,17-pentanor-ent-labdane-8-one (8. The use of this compound in the preparation of terpenylquinone derivatives shallbe reported elsewhere. In addition we have synthesized the compound 2β,12-diacetoxy-8β,17-epoxy-13,14,15,16-tetranor-ent-labdane (10, which upon catalytic epoxide ringopening in alkaline or acid media gave rise in all cases to the formation of tricycliccompounds.

  3. Two New Prenylated Stilbenes with an Irregular Sesquiterpenyl Side Chain from Propolis from Fiji Islands

    Directory of Open Access Journals (Sweden)

    Boryana Trusheva


    Full Text Available Two new prenylated stilbenes with an irregular sesquiterpenyl side chain, solomonin B (1 and solomonin C (2, together with four known compounds, glyasperin A (3, isolated for the first time from propolis, kumatakenin (4, macarangin (5 and mangiferolic acid (6 were isolated from ethanol extract of propolis from Fiji islands. The compounds structures were determined based on their spectral data analysis (1D- and 2D NMR, UV and HREIMS and comparison with literature data. The chemical composition of propolis from Fiji islands was determined for the first time.

  4. Ion-Exchange Membranes Based on Polynorbornenes with Fluorinated Imide Side Chain Groups

    Directory of Open Access Journals (Sweden)

    Arlette A. Santiago


    Full Text Available The electrochemical characteristics of cation-exchange membranes based on polynorbornenes with fluorinated and sulfonated dicarboximide side chain groups were reported. This study was extended to a block copolymer containing structural units with phenyl and 4-oxybenzenesulfonic acid, 2,3,5,6-tetrafluorophenyl moieties replacing the hydrogen atom of the dicarboximide group. A thorough study on the electrochemical characteristics of the membranes involving electromotive forces of concentration cells and proton conductivity is reported. The proton permselectivity of the membranes is also discussed.

  5. Recent advances in metathesis-derived polymers containing transition metals in the side chain

    Directory of Open Access Journals (Sweden)

    Ileana Dragutan


    Full Text Available This account critically surveys the field of side-chain transition metal-containing polymers as prepared by controlled living ring-opening metathesis polymerization (ROMP of the respective metal-incorporating monomers. Ferrocene- and other metallocene-modified polymers, macromolecules including metal-carbonyl complexes, polymers tethering early or late transition metal complexes, etc. are herein discussed. Recent advances in the design and syntheses reported mainly during the last three years are highlighted, with special emphasis on new trends for superior applications of these hybrid materials.

  6. Side chain packing below the fusion peptide strongly modulates triggering of the Hendra virus F protein. (United States)

    Smith, Everett Clinton; Dutch, Rebecca Ellis


    Triggering of the Hendra virus fusion (F) protein is required to initiate the conformational changes which drive membrane fusion, but the factors which control triggering remain poorly understood. Mutation of a histidine predicted to lie near the fusion peptide to alanine greatly reduced fusion despite wild-type cell surface expression levels, while asparagine substitution resulted in a moderate restoration in fusion levels. Slowed kinetics of six-helix bundle formation, as judged by sensitivity to heptad repeat B-derived peptides, was observed for all H372 mutants. These data suggest that side chain packing beneath the fusion peptide is an important regulator of Hendra virus F triggering.

  7. Novel side-chain liquid crystalline polyester architecture for reversible optical storage

    DEFF Research Database (Denmark)

    Hvilsted, Søren; Andruzzi, Fulvio; Kulinna, Chrisian


    New side-chain liquid crystalline polyesters have been prepared by melt transesterification of diphenyl tetradecanedioate and a series of mesogenic 2-[omega-[4-[(4-cyanophenyl)azo]phenoxyl] alkyl]-1,3-propanediols, where the alkyl spacer is hexa-, octa-, and decamethylene in turn. The polyesters...... for the cyanoazobenzene mesogens calculated. FTIR is also utilized to follow the temperature-dependent erasure of the induced orientation. Optical storage properties of thin unoriented polyester films are examined through measurements of polarization anisotropy and holography. A resolution of over 5000 lines...

  8. Synthesis and Intramolecular [4+2] Cycloaddition Reactions of 4-Pyridazinecarbonitriles with Alkyne Side Chains

    Directory of Open Access Journals (Sweden)

    Norbert Haider


    Full Text Available The preparation of a series of new 3-(alkynyl-X-substituted 4-pyridazinecarbonitriles 2-5 (X = O, NH is described. The compounds are shown to undergo thermally induced intramolecular Diels-Alder reactions with inverse electron demand, affording the fused benzonitriles 6-8. Incorporation of a 1,2-phenylene unit into the side chain, as in the case of compounds 10 and 13, results in a more favorable conformation of the dienophilic substructure and thus to a pronounced acceleration of the [4+2] cycloaddition reaction.

  9. Characterization of an aldolase involved in cholesterol side chain degradation in Mycobacterium tuberculosis. (United States)

    Gilbert, Stephanie; Hood, LaChae; Seah, Stephen Y K


    The heteromeric acyl-CoA dehydrogenase, FadE28-FadE29 and the enoyl CoA hydratase ChsH1-ChsH2, encoded by genes within the intracellular growth (igr) operon of Mycobacterium tuberculosis, catalyze the dehydrogenation of the 3-carbon side chain cholesterol metabolite, 3-OPC-CoA, and subsequent hydration of the product 3-oxo-4,17-pregnadiene-20-carboxyl-CoA (3-OPDC-CoA) to form 17-hydroxy-3-oxo-4-pregnene-20-carboxyl-CoA (17-HOPC-CoA). The gene downstream of chsH2, ltp2, was expressed in recombinant Rhodococcus jostii RHA1 in combination with other genes within the igr operon. His-tagged Ltp2 co-purified with untagged ChsH1-ChsH2, ChsH2 or the C-terminal domain of ChsH2 that contains a domain of unknown function (DUF35). Ltp2 in association with ChsH1-ChsH2 or just the DUF35 domain of ChsH2 were shown to catalyze the retro-aldol cleavage of 17-HOPC-CoA to form androst-4-ene-3,17-dione and propionyl-CoA. Steady state kinetic analysis using Ltp2-DUF35 complex showed that the aldolase has an optimum activity at pH 7.5 with Km of 6.54 ± 0.90 μM and kcat of 159 ± 8.50 s-1 ChsH1-ChsH2 can only hydrate about 30% of 3-OPDC-CoA, but this unfavourable equilibrium can be overcome when the aldolase was present to remove the hydrated product, providing a rationale for the close association between the aldolase with the hydratase. Homologs of ChsH1, ChsH2 and Ltp2 are found in steroid degrading Gram positive and Gram negative bacteria suggesting that side chains of diverse steroids may also be cleaved by aldolases in these bacteria.Importance The C-C bond cleavage of the D-ring side chain of cholesterol was shown to be catalyzed by an aldolase. The aldolase associates with the hydratase that catalyzes the preceding reaction in the cholesterol side chain degradation pathway. These enzymes are encoded by genes within the intracellular growth (igr) operon of M. tuberculosis and the operon was previously demonstrated to be linked to the pathogenicity and persistence of the bacteria

  10. Relationship between Side-Chain Polarity and the Self-Assembly Characteristics of Perylene Diimide Derivatives in Aqueous Solution. (United States)

    Schill, Jurgen; Milroy, Lech-Gustav; Lugger, Jody A M; Schenning, Albertus P H J; Brunsveld, Luc


    Perylene-3,4,9,10-tetracarboxylic acid diimides (PDIs) have recently gained considerable interest for water-based biosensing applications. PDIs have been studied intensively in the bulk state, but their physical properties in aqueous solution in interplay with side-chain polarity are, however, poorly understood. Therefore, three perylene diimide based derivatives were synthesized to study the relationship between side-chain polarity and their self-assembly characteristics in water. The polarity of the side chains was found to dictate the size and morphology of the formed aggregates. Side-chain polarity rendered the self-assembly and photophysical properties of the PDIs-both important for imminent water-based applications-and these were revealed to be especially responsive to changes in solvent composition.

  11. A new series of two-ring-based side chain liquid crystalline polymers: synthesis and mesophase characterization

    CSIR Research Space (South Africa)

    Reddy, GSM


    Full Text Available A new series of side chain liquid crystalline polymers containing a core, a butamethylenoxy spacer, ester groups, and terminal alkoxy groups were synthesised and their structures were confirmed. The core was constructed with two phenyl rings...

  12. Enabling high-mobility, ambipolar charge-transport in a DPP-benzotriazole copolymer by side-chain engineering

    DEFF Research Database (Denmark)

    Gruber, Mathias; Jung, Seok-Heon; Schott, Sam


    side-chain on the DPP-unit leads to an increase in thin-film order and charge-carrier mobility if a sufficiently solubilizing, branched, side chain is attached to the BTZ. We compare two different synthetic routes, direct arylation and Suzuki-polycondensation, by a direct comparison of polymers...... exceptionally high and near balanced average electron and hole mobilities >2 cm2 V-1 s-1 which are among the highest, robustly extracted mobility values reported for DPP copolymers in a top-gate configuration to date. Our results demonstrate clearly that linear side chain substitution of the DPP unit together...... with co-monomers that allow for the use of sufficiently long or branched solubilizing side chains can be an attractive design motif for solution processable, high mobility DPP copolymers....

  13. Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3 (United States)

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall


    One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0

  14. Relationship between Side?Chain Polarity and the Self?Assembly Characteristics of Perylene Diimide Derivatives in Aqueous Solution


    Schill, Jurgen; Milroy, Lech?Gustav; Lugger, Jody A. M.; Schenning, Albertus P. H. J.; Brunsveld, Luc


    Abstract Perylene?3,4,9,10?tetracarboxylic acid diimides (PDIs) have recently gained considerable interest for water?based biosensing applications. PDIs have been studied intensively in the bulk state, but their physical properties in aqueous solution in interplay with side?chain polarity are, however, poorly understood. Therefore, three perylene diimide based derivatives were synthesized to study the relationship between side?chain polarity and their self?assembly characteristics in water. T...

  15. Free Energy Perturbation Calculations of the Thermodynamics of Protein Side-Chain Mutations. (United States)

    Steinbrecher, Thomas; Abel, Robert; Clark, Anthony; Friesner, Richard


    Protein side-chain mutation is fundamental both to natural evolutionary processes and to the engineering of protein therapeutics, which constitute an increasing fraction of important medications. Molecular simulation enables the prediction of the effects of mutation on properties such as binding affinity, secondary and tertiary structure, conformational dynamics, and thermal stability. A number of widely differing approaches have been applied to these predictions, including sequence-based algorithms, knowledge-based potential functions, and all-atom molecular mechanics calculations. Free energy perturbation theory, employing all-atom and explicit-solvent molecular dynamics simulations, is a rigorous physics-based approach for calculating thermodynamic effects of, for example, protein side-chain mutations. Over the past several years, we have initiated an investigation of the ability of our most recent free energy perturbation methodology to model the thermodynamics of protein mutation for two specific problems: protein-protein binding affinities and protein thermal stability. We highlight recent advances in the field and outline current and future challenges. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Side-chain modification of cytokinins controls shoot growth in Arabidopsis. (United States)

    Kiba, Takatoshi; Takei, Kentaro; Kojima, Mikiko; Sakakibara, Hitoshi


    Cytokinins (CKs), a class of plant hormones, are central regulators of plant growth and development. Based on numerous physiological and genetic studies, the quantitative regulation of cytokinin levels is the major mechanism regulating cytokinin action in diverse developmental processes. Here, we identified a different mechanism with which the physiological function of CK is modulated through side-chain modification (trans-hydroxylation). The trans-hydroxylation that forms trans-zeatin (tZ)-type CK from N(6)-(Δ(2)-isopentenyl)adenine (iP)-type CK is catalyzed by the cytochrome P450 enzymes CYP735A1 and CYP735A2 in Arabidopsis. Deficiency in trans-hydroxylation activity results in dramatic retardation of shoot growth without affecting total CK quantity, while augmentation of the activity enhances shoot growth. Application of exogenous tZ but not iP recovers the wild-type phenotype in the mutants, indicating that trans-hydroxylation modifies the physiological function of CK. We propose that the control of cytokinin function by side-chain modification is crucial for shoot growth regulation in plants. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Roasting-induced changes in arabinotriose, a model of coffee arabinogalactan side chains. (United States)

    Moreira, Ana S P; Coimbra, Manuel A; Nunes, Fernando M; Domingues, M Rosário M


    Thermal processing can promote reactions that change the structure of food constituents, often by unknown mechanisms, such as those occurring in arabinose residues of coffee arabinogalactan side chains. Aiming to know more about these modifications, the structurally related α-(1→5)-l-arabinotriose was roasted at 200°C and the products obtained were identified by ESI-MS and MALDI-MS and characterised by ESI-MS(n). Depolymerised and polymerised oligosaccharides with up to 16 residues and new types of linkages were formed. Also, products resulting from dehydration, oxidation, and cleavage of a carbon-carbon bond at the reducing end of the corresponding non-modified oligosaccharide were formed, probably promoting the release of formaldehyde, formic acid, glycolaldehyde, glyoxal, acetic acid, glycolic acid, glyceraldehyde, 2-hydroxypropanedialdehyde and lactic acid. As many of these compounds have been reported to occur in roasted coffee beans and/or brews, it can be suggested that the degradation of coffee arabinogalactan side chains can contribute to their formation upon roasting. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Controlling Side Chain Density of Electron Donating Polymers for Improving VOC in Polymer Solar Cells (United States)

    Kim, B. J.; Kim, K. H.; Cho, C. H.; Kang, H.; Yoon, S. C.


    The ability to tune the LUMO/HOMO levels of electroactive materials in active layer of polymer solar cells is critical in controlling their optical and electrochemical properties because the HOMO and LUMO offsets between the polymer donor and the electron acceptor strongly affect charge separation and the open circuit voltage (VOC) of a solar cell. Here, we developed two series of electroactive materials for improving VOC in polymer solar cells. First, we enable facile control over the number of solubilizing groups ultimately tethered to the fullerene by tuning the molar ratio between reactants from 1:1 to 1:3, thus producing o-xylenyl C60 mono-, bis-, and tris-adducts (OXCMA, OXCBA, and OXCTA) as electron acceptors with different LUMO levels. As the number of solubilizing groups increased, VOC values of the P3HT-based BHJ solar cells increased from 0.63, 0.83, to 0.98 V. Second, we present a series of novel poly[3-(4-n-octyl)phenylthiophene] (POPT) derivatives (POPT, POPTT, and POTQT) as electron donors with different side-chain density. As a result of lower HOMO levels by decrease in the side-chain density of the polymers, the devices consisting of POPT, POPTT, and POPQT with PCBM showed increased VOC values of 0.58, 0.63, and 0.75 V, respectively.

  19. Absolute rate constants for the reaction of hypochlorous acid with protein side chains and peptide bonds

    DEFF Research Database (Denmark)

    Pattison, D I; Davies, Michael Jonathan


    , absolute second-order rate constants for the reactions of HOCl with protein side chains, model compounds, and backbone amide (peptide) bonds have been determined at physiological pH values. The reactivity of HOCl with potential reactive sites in proteins is summarized by the series: Met (3.8 x 10(7) M(-1......) x s(-1)) > backbone amides (10-10(-3) M(-1) x s(-1)) > Gln(0.03 M(-1) x s(-1)) approximately Asn (0.03 M(-1) x s(-1)). The rate constants for reaction of HOCl with backbone amides (peptide bonds) vary by 4 orders of magnitude with uncharged peptide bonds reacting more readily with HOCl than those....... Proteins are major targets for this oxidant, and such reaction results in side-chain modification, backbone fragmentation, and cross-linking. Despite a wealth of qualitative data for such reactions, little absolute kinetic data is available to rationalize the in vitro and in vivo data. In this study...

  20. Subcritical Water Hydrolysis of Peptides: Amino Acid Side-Chain Modifications (United States)

    Powell, Thomas; Bowra, Steve; Cooper, Helen J.


    Previously we have shown that subcritical water may be used as an alternative to enzymatic digestion in the proteolysis of proteins for bottom-up proteomics. Subcritical water hydrolysis of proteins was shown to result in protein sequence coverages greater than or equal to that obtained following digestion with trypsin; however, the percentage of peptide spectral matches for the samples treated with trypsin were consistently greater than for those treated with subcritical water. This observation suggests that in addition to cleavage of the peptide bond, subcritical water treatment results in other hydrolysis products, possibly due to modifications of amino acid side chains. Here, a model peptide comprising all common amino acid residues (VQSIKCADFLHYMENPTWGR) and two further model peptides (VCFQYMDRGDR and VQSIKADFLHYENPTWGR) were treated with subcritical water with the aim of probing any induced amino acid side-chain modifications. The hydrolysis products were analyzed by direct infusion electrospray tandem mass spectrometry, either collision-induced dissociation or electron transfer dissociation, and liquid chromatography collision-induced dissociation tandem mass spectrometry. The results show preferential oxidation of cysteine to sulfinic and sulfonic acid, and oxidation of methionine. In the absence of cysteine and methionine, oxidation of tryptophan was observed. In addition, water loss from aspartic acid and C-terminal amidation were observed in harsher subcritical water conditions. [Figure not available: see fulltext.

  1. Synthesis and property characterization of two novel side-chain isoindigo copolymers for polymer solar cells

    Directory of Open Access Journals (Sweden)

    X. Liu


    Full Text Available Two novel side-chain conjugated polymers, PTBT-TID and PTBT-TTID, based on the new synthetic thiophene-benzne-thiophene (TBT unit, side-chain isoindigo (ID unit, and the introduced thiophene π-bridge, have been designed and synthesized. The photophysical, electrochemical and photovoltaic properties of the two polymers have been systematically investigated. The two polymers possess relatively good solubility as well as excellent thermal stability up to 380°C, and all of the polymer solar cell (PSC devices based on the two polymers obtain high open circuit voltage (Voc of about 0.8 V. The polymer solar cells based on the polymer PTBT-TID show relatively higher efficiencies than the PTBT-TTID-based ones, due to the broader absorption spectrum, a relatively higher hole mobility, a lower HOMO (the highest occupied molecular orbital energy level, a stronger IPCE (the incident photon to current conversion efficiency response and a better microphase separation, Consequently, the device based on PTBT-TID:PC61BM (1:2, by weight gives the best power conversion efficiency (PCE of 2.04%, with a short-circuit current density (Jsc of 5.39 mA·cm–2, an open-circuit voltage (Voc of 0.83 V, and a fill factor (FF of 0.45.

  2. Effect of side-chain length on the side-chain dynamics of alpha-helical poly(L-glutamic acid) as probed by a fluorescence blob model. (United States)

    Ingratta, Mark; Duhamel, Jean


    Two series of pyrene-labeled poly(glutamic acid) (Py-PGA) were synthesized utilizing two different linkers for pyrene attachment, namely 1-pyrenemethylamine (PMA) and 1-pyrenebutylamine (PBA). Several Py-PGAs were synthesized for each series with pyrene contents ranging from 4 to 15 mol %. Py-PGA forms a rigid alpha-helix in DMF that effectively locks the backbone in place, thus enabling only side-chain or linker motions to be monitored by time-resolved fluorescence. Time-resolved fluorescence decays were acquired for the pyrene monomer of the Py-PGA constructs and the fluorescence blob model (FBM) was used to quantify the dynamics of the different linkers connecting pyrene to the backbone. Nitromethane was used to shorten the lifetime of the pyrene monomer, in effect controlling the probing time of the pyrene group, from 50 to 155 ns for PGA-PBA and from 50 to 215 ns for PGA-PMA. The FBM analysis of the fluorescence decays led to the conclusion that excimer formation around the rigid alpha-helix backbone takes place in a compact environment. The number of glutamic acid units within a blob, N blob, decreased only slightly with decreasing probing time for both Py-PGA constructs as a result of the compact distribution of the chromophores around the alpha-helix. The PGA alpha-helix was modeled using Hyperchem software and the ability of two pyrene groups to encounter was evaluated as they were separated by increasing numbers of amino acids along the alpha-helix. The number of amino acids required for two pyrenes to lose their ability to overlap and form excimer matched closely the N blob values retrieved using the FBM.

  3. Targeting Antibodies to Carbon Nanotube Field Effect Transistors by Pyrene Hydrazide Modification of Heavy Chain Carbohydrates

    Directory of Open Access Journals (Sweden)

    Steingrimur Stefansson


    Full Text Available Many carbon nanotube field-effect transistor (CNT-FET studies have used immobilized antibodies as the ligand binding moiety. However, antibodies are not optimal for CNT-FET detection due to their large size and charge. Their size can prevent ligands from reaching within the Debye length of the CNTs and a layer of charged antibodies on the circuits can drown out any ligand signal. In an attempt to minimize the antibody footprint on CNT-FETs, we examined whether pyrene hydrazide modification of antibody carbohydrates could reduce the concentration required to functionalize CNT circuits. The carbohydrates are almost exclusively on the antibody Fc region and this site-specific modification could mediate uniform antibody orientation on the CNTs. We compared the hydrazide modification of anti-E. coli O157:H7 polyclonal antibodies to pyrenebutanoic acid succinimidyl ester-coated CNTs and carbodiimide-mediated antibody CNT attachment. Our results show that the pyrene hydrazide modification was superior to those methods with respect to bacteria detection and less than 1 nM labeled antibody was required to functionalize the circuits.

  4. Methacrylate Copolymers with Liquid Crystalline Side Chains for Organic Gate Dielectric Applications. (United States)

    Berndt, Andreas; Pospiech, Doris; Jehnichen, Dieter; Häußler, Liane; Voit, Brigitte; Al-Hussein, Mahmoud; Plötner, Matthias; Kumar, Amit; Fischer, Wolf-Joachim


    Polymers for all-organic field-effect transistors are under development to cope with the increasing demand for novel materials for organic electronics. Besides the semiconductor, the dielectric layer determines the efficiency of the final device. Poly(methyl methacrylate) (PMMA) is a frequently used dielectric. In this work, the chemical structure of this material was stepwise altered by incorporation of cross-linkable and/or self-organizing comonomers to improve the chemical stability and the dielectric properties. Different types of cross-linking methods were used to prevent dissolution, swelling or intermixing of the dielectric e.g. during formation processes of top electrodes or semiconducting layers. Self-organizing comonomers were expected to influence the dielectric/semiconductor interface, and moreover, to enhance the chemical resistance of the dielectric. Random copolymers were obtained by free radical and reversible addition-fragmentation chain transfer (RAFT) polymerization. With 6-[4-(4'-cyanophenyl)phenoxy]alkyl side chains having hexyl or octyl spacer, thermotropic liquid crystalline (LC) behavior and nanophase separation into smectic layers was observed, while copolymerization with methyl methacrylate induced molecular disorder. In addition to chemical, thermal and structural properties, electrical characteristics like breakdown field strength (EBD) and relative permittivity (k) were determined. The dielectric films were studied in metal-insulator-metal setups. EBD appeared to be strongly dependent on the type of electrode used and especially the ink formulation. Cross-linking of PMMA yielded an increase in EBD up to 4.0 MV/cm with Ag and 5.7 MV/cm with PSS electrodes because of the increased solvent resistance. The LC side chains reduce the ability for cross-linking resulting in decreased breakdown field strengths.

  5. A major role for side-chain polyglutamine hydrogen bonding in irreversible ataxin-3 aggregation.

    Directory of Open Access Journals (Sweden)

    Antonino Natalello


    Full Text Available The protein ataxin-3 consists of an N-terminal globular Josephin domain (JD and an unstructured C-terminal region containing a stretch of consecutive glutamines that triggers the neurodegenerative disorder spinocerebellar ataxia type 3, when it is expanded beyond a critical threshold. The disease results from misfolding and aggregation, although the pathway and structure of the aggregation intermediates are not fully understood. In order to provide insight into the mechanism of the process, we monitored the aggregation of a normal (AT3Q24 ataxin-3, an expanded (AT3Q55 ataxin-3, and the JD in isolation. We observed that all of them aggregated, although the latter did so at a much slower rate. Furthermore, the expanded AT3Q55 displayed a substantially different behavior with respect to the two other variants in that at the latest stages of the process it was the only one that did the following: i lost its reactivity towards an anti-oligomer antibody, ii generated SDS-insoluble aggregates, iii gave rise to bundles of elongated fibrils, and iv displayed two additional bands at 1604 and 1656 cm(-1 in FTIR spectroscopy. Although these were previously observed in other aggregated polyglutamine proteins, no one has assigned them unambiguously, yet. By H/D exchange experiments we show for the first time that they can be ascribed to glutamine side-chain hydrogen bonding, which is therefore the hallmark of irreversibly SDS-insoluble aggregated protein. FTIR spectra also showed that main-chain intermolecular hydrogen bonding preceded that of glutamine side-chains, which suggests that the former favors the latter by reorganizing backbone geometry.

  6. A Major Role for Side-Chain Polyglutamine Hydrogen Bonding in Irreversible Ataxin-3 Aggregation (United States)

    Relini, Annalisa; Apicella, Alessandra; Invernizzi, Gaetano; Casari, Carlo; Gliozzi, Alessandra; Doglia, Silvia Maria; Tortora, Paolo; Regonesi, Maria Elena


    The protein ataxin-3 consists of an N-terminal globular Josephin domain (JD) and an unstructured C-terminal region containing a stretch of consecutive glutamines that triggers the neurodegenerative disorder spinocerebellar ataxia type 3, when it is expanded beyond a critical threshold. The disease results from misfolding and aggregation, although the pathway and structure of the aggregation intermediates are not fully understood. In order to provide insight into the mechanism of the process, we monitored the aggregation of a normal (AT3Q24) ataxin-3, an expanded (AT3Q55) ataxin-3, and the JD in isolation. We observed that all of them aggregated, although the latter did so at a much slower rate. Furthermore, the expanded AT3Q55 displayed a substantially different behavior with respect to the two other variants in that at the latest stages of the process it was the only one that did the following: i) lost its reactivity towards an anti-oligomer antibody, ii) generated SDS-insoluble aggregates, iii) gave rise to bundles of elongated fibrils, and iv) displayed two additional bands at 1604 and 1656 cm−1 in FTIR spectroscopy. Although these were previously observed in other aggregated polyglutamine proteins, no one has assigned them unambiguously, yet. By H/D exchange experiments we show for the first time that they can be ascribed to glutamine side-chain hydrogen bonding, which is therefore the hallmark of irreversibly SDS-insoluble aggregated protein. FTIR spectra also showed that main-chain intermolecular hydrogen bonding preceded that of glutamine side-chains, which suggests that the former favors the latter by reorganizing backbone geometry. PMID:21533208

  7. Controlling the Morphology and Efficiency of Hybrid ZnO : Polythiophene Solar Cells Via Side Chain Functionalization

    NARCIS (Netherlands)

    Oosterhout, Stefan D.; Koster, L. Jan Anton; van Bavel, Svetlana S.; Loos, Joachim; Stenzel, Ole; Thiedmann, Ralf; Schmidt, Volker; Campo, Bert; Cleij, Thomas J.; Lutzen, Laurence; Vanderzande, Dirk; Wienk, Martijn M.; Janssen, Rene A. J.


    The efficiency of polymer - metal oxide hybrid solar cells depends critically on the intimacy of mixing of the two semiconductors. The effect of side chain functionalization on the morphology and performance of conjugated polymer:ZnO solar cells is investigated. Using an ester-functionalized side

  8. Investigating the cationic side chains of the antimicrobial peptide tritrpticin: hydrogen bonding properties govern its membrane-disruptive activities

    NARCIS (Netherlands)

    Nguyen, Leonard T.; de Boer, Leonie; Zaat, Sebastian A. J.; Vogel, Hans J.


    The positively charged side chains of cationic antimicrobial peptides are generally thought to provide the initial long-range electrostatic attractive forces that guide them towards the negatively charged bacterial membranes. Peptide analogs were designed to examine the role of the four Arg side

  9. Carbohydrate-binding specificities of five lectins that bind to O-Glycosyl-linked carbohydrate chains. Quantitative analysis by frontal-affinity chromatography. (United States)

    Sueyoshi, S; Tsuji, T; Osawa, T


    The carbohydrate-binding specificities of lectins purified from Agaricus bisporus (ABA-I), Arachis hypogaea (PNA), Bauhinia purpurea (BPA), Glycine max (SBA), and Vicia villosa (VVA-B4) have been studied by affinity chromatography on columns of the immobilized lectins, and quantitatively analyzed by frontal affinity chromatography. These five lectins could be classified into two groups with respect to their reactivities with typical mucin-type glycopeptides, beta-D-Galp-(1----3)-alpha-D-GalpNAc-(1----3)-Ser/Thr (2) and alpha-D-GalpNAc-(1----3)-Ser/Thr (3). One group, which consists of ABA-I, PNA, and BPA, preferentially binds to 2, and the other, which consists of SBA and VVA-B4, shows higher affinity for 3 than for 2. Among the lectins tested, only ABA-I was found to bind to a sialylated glycopeptide, whic which was prepared from human erythrocyte glycophorin A and contains three three tetrasaccharide chains having the structure of alpha-NeuAc-(2----3)-beta-D-GAlp-(1----3)-NeuAC-(2----6)]-alpha-D-Galp NAc-(1----, with an association constant of 15 microM, whereas the association constants of the other four lectins for this sialylated glycopeptide were less than 3.5 mM. On the other hand, removal of the beta-D-galactopyranosyl group from a glycopeptide containing sequence 2 resulted in decreased association constants for the three lectins of the first group, especially ABA-I and PNA. The two lectins of the second group showed a high affinity for 3, but SBA preferentially interacted with oligosaccharides containing the alpha-D-GalpNAc-(1----3)-beta-D-Galp-(1----3)-D-GlapNAc sequence, prepared from a blood group A-active oligosaccharide.

  10. Quantification of fructans, galacto-oligosacharides and other short-chain carbohydrates in processed grains and cereals. (United States)

    Biesiekierski, J R; Rosella, O; Rose, R; Liels, K; Barrett, J S; Shepherd, S J; Gibson, P R; Muir, J G


    Wholegrain grains and cereals contain a wide range of potentially protective factors that are relevant to gastrointestinal health. The prebiotics best studied are fructans [fructooligosaccharides (FOS), inulin] and galactooligosaccharides (GOS). These and other short-chain carbohydrates can also be poorly absorbed in the small intestine (named fermentable oligo-, di- and monosaccharides and polyols; FODMAPs) and may have important implications for the health of the gut. In the present study, FODMAPs, including fructose in excess of glucose, FOS (nystose, kestose), GOS (raffinose, stachyose) and sugar polyols (sorbitol, mannitol), were quantified using high-performance liquid chromatography with an evaporative light scattering detector. Total fructan was quantified using an enzymic hydrolysis method. Fifty-five commonly consumed grains, breakfast cereals, breads, pulses and biscuits were analysed. Total fructan were the most common short-chain carbohydrate present in cereal grain products and ranged (g per portion as eaten) from 1.12 g in couscous to 0 g in rice; 0.6 g in dark rye bread to 0.07 g in spelt bread; 0.96 g in wheat-free muesli to 0.11 g in oats; and 0.81 g in muesli fruit bar to 0.05 g in potato chips. Raffinose and stachyose were most common in pulses.   Composition tables including FODMAPs and prebiotics (FOS and GOS) that are naturally present in food will greatly assist research aimed at understanding their physiological role in the gut. © 2011 The Authors. Journal compilation © 2011 The British Dietetic Association Ltd.

  11. Design of β-amino acid with backbone-side chain interactions: stabilization of 14/15-helix in α/β-peptides. (United States)

    Sharma, Gangavaram V M; Yadav, Thota Anupama; Choudhary, Madavi; Kunwar, Ajit C


    A new C-linked carbo-β-amino acid, (R)-β-Caa((r)), having a carbohydrate side chain with D-ribo configuration, was prepared from D-glucose by inverting the C-3 stereocenter to introduce constraints/interactions. From the NMR studies it was inferred that the new monomer may participate in additional electrostatic interactions, facilitating and enhancing novel folds in oligomeric peptides derived from it. The α/β-peptides, synthesized from alternating L-Ala and (R)-β-Caa((r)), have shown the presence of 14/15-helix by NMR (in CDCl(3), methanol-d(3) and CD(3)CN), CD and MD calculations. The hybrid peptides showed the presence of electrostatic interactions involving the intraresidue amide proton and the C3-OMe, which helped in the stabilization of the NH(i)···CO(i-4) H-bonds and adoption of 14/15-helix. The importance of such additional interactions has been well defined in recent times to stabilize the folding in a variety of peptidic foldamers. These observations suggest and emphasize that the side chain-backbone interactions are crucial in the stabilization of the desired folding propensity. The designed monomer thus enlarges the opportunities for the synthesis of peptides with novel conformations and expands the repertoire of the foldamers.

  12. Backbone and side chain chemical shift assignments of apolipophorin III from Galleria mellonella. (United States)

    Crowhurst, Karin A; Horn, James V C; Weers, Paul M M


    Apolipophorin III, a 163 residue monomeric protein from the greater wax moth Galleria mellonella (abbreviated as apoLp-IIIGM), has roles in upregulating expression of antimicrobial proteins as well as binding and deforming bacterial membranes. Due to its similarity to vertebrate apolipoproteins there is interest in performing atomic resolution analysis of apoLp-IIIGM as part of an effort to better understand its mechanism of action in innate immunity. In the first step towards structural characterization of apoLp-IIIGM, 99 % of backbone and 88 % of side chain (1)H, (13)C and (15)N chemical shifts were assigned. TALOS+ analysis of the backbone resonances has predicted that the protein is composed of five long helices, which is consistent with the reported structures of apolipophorins from other insect species. The next stage in the characterization of apoLp-III from G. mellonella will be to utilize these resonance assignments in solving the solution structure of this protein.

  13. Poly-dimethylsiloxane derivates side chains effect on syntan functionalized Polyamide fabric (United States)

    Migani, V.; Weiss, H.; Massafra, M. R.; Merlo, A.; Colleoni, C.; Rosace, G.


    Poly-dimethylsiloxane (PDMS) polymers finishing of Polyamide-6,6 (PA66) fabrics involves ionic interactions between reactive groups on the PDMS polymers and the ones of the textile fabric. Such interactions could be strengthened by a pretreatment with a fixing agent to promote either ion-ion and H-bonding and ion-dipole forces. These forces could contribute towards the building of substantial PDMS-PA66 systems and the achieving of better adhesion properties to fabrics. Four different silicone polymers based on PDMS were applied on a synthetic tanning agent (syntan) finished Polyamide-6,6 fabric under acid conditions. Soxhlet extraction method and ATR FT-IR technique were used to investigate the application conditions. The finishing parameters such as pH and temperature together with fastness, mechanical and performance properties of the treated samples were studied and related to PDMS side chains effect on syntan functionalized Polyamide fabric.

  14. Selectively deuterated liquid crystalline cyanoazobenzene side-chain polyesters. 2. Preparation and characterization of polyesters

    DEFF Research Database (Denmark)

    Kulinna, Christian; Hvilsted, Søren; Hendann, Claudia


    calorimetry. Whereas the polytetradecanedioates show a complex thermal behaviour with a number of different phases, the polyadipates are less complex and both nematic and smectic A phases have been identified by polarizing optical microscopy. Solution 1H, 13C and 2H NMR spectroscopy have been utilized......Two sets of specifically deuterated cyanoazobenzene side-chain polyadipates and polytetrade-canedioates have been prepared by transesterification in the melt. Combinations of three different, selectively deuterium labeled 2-[6-[4-[(4-cyanophenyl)azo]phenoxy]hexyl]-1,3-propanediols or the non...... for both polyester structural assessment and determination of deuterium distribution and content. FTIR spectroscopy has revealed suitable and characteristic vibrations which unequivocally represents the absorption behaviour of individual polyester segments or molecular structures in the different...

  15. Novel extended side-chain-unsaturated hopenes released from the kerogen macromolecules under artificial conditions

    Energy Technology Data Exchange (ETDEWEB)

    Qu, D.G.; Shi, J.Y.; Xiang, M.J. [Chinese Academy of Sciences, Guanzhou (China). Guanghou Inst. of Geochemistry


    This paper describes a novel family of hopanoids present in pyrolysates of solvent-extracted peat from the Caohai Basin, Southwestern China that have been tentatively identified on the basis of GC-MS data as C{sub 32}-C{sub 35} extended side-chain-unsaturated hopenes. These unsaturated pentacyclic triterpenoid compounds are produced by laboratory thermal decomposition of kerogen. The results of pyrolysis experiments suggest that these structures result from thermal release of bound C{sub 35} bacteriohopanepolyols which are bonded to the kerogen macromolecule via polyether or polyester linkages. This pyrolysis can provide information about the types of linkings and sites of bonding of hopane units to the macromolecular network and can provide information on the way that these hopane skeletons are released from a kerogen structure under thermal stress.

  16. High Performance All-Polymer Solar Cell via Polymer Side-Chain Engineering

    KAUST Repository

    Zhou, Yan


    An average PCE of 4.2% for all-polymer solar cells from 20 devices with an average J SC of 8.8 mA cm-2 are obtained with a donor-acceptor pair despite a low LUMO-LUMO energy offset of less than 0.1 eV. Incorporation of polystyrene side chains into the donor polymer is found to assist in reducing the phase separation domain length scale, and results in more than 20% enhancement of PCE. We observe a direct correlation between the short circuit current (J SC) and the length scale of BHJ phase separation, which is obtained by resonance soft X-ray scattering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Side chain and backbone contributions of Phe508 to CFTR folding

    Energy Technology Data Exchange (ETDEWEB)

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)


    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  18. Effect of temperature on the optical poling process in a side-chain polymer system (United States)

    Liu, Xuchun; Xu, Gang; Si, Jinhai; Ye, Peixian; Li, Zhao; Shen, Yuquan


    An improvement to the Fiorini and Nuzi's theory for all-optical poling is proposed. The influence of cis is taken into account in the photoinduced process. An analytical expression for the dynamic optical poling process is derived. Contrary to Fiorini and Nuzi's theory which is based on unique process, three processes exist in the time evolution of the photoinduced second-order susceptibility χ(2) during the optical poling: two of which are fast and the other one which is slow. Furthermore we discuss the influence of temperature on the poling process in a side-chain polymer system with a high glass transition temperature. It is predicted that the two fast processes will become even faster and their relative contribution to the magnitude of χ(2) will decrease with the increase of temperature. The prediction is verified by our experiment with disperse red 19-functionalized polyimide polymer.

  19. Protein native-state stabilization by placing aromatic side chains in N-glycosylated reverse turns. (United States)

    Culyba, Elizabeth K; Price, Joshua L; Hanson, Sarah R; Dhar, Apratim; Wong, Chi-Huey; Gruebele, Martin; Powers, Evan T; Kelly, Jeffery W


    N-glycosylation of eukaryotic proteins helps them fold and traverse the cellular secretory pathway and can increase their stability, although the molecular basis for stabilization is poorly understood. Glycosylation of proteins at naïve sites (ones that normally are not glycosylated) could be useful for therapeutic and research applications but currently results in unpredictable changes to protein stability. We show that placing a phenylalanine residue two or three positions before a glycosylated asparagine in distinct reverse turns facilitates stabilizing interactions between the aromatic side chain and the first N-acetylglucosamine of the glycan. Glycosylating this portable structural module, an enhanced aromatic sequon, in three different proteins stabilizes their native states by -0.7 to -2.0 kilocalories per mole and increases cellular glycosylation efficiency.

  20. Side-chain-controlled self-assembly of polystyrene-polypeptide miktoarm star copolymers

    KAUST Repository

    Junnila, Susanna


    We show how the self-assembly of miktoarm star copolymers can be controlled by modifying the side chains of their polypeptide arms, using A 2B and A 2B 2 type polymer/polypeptide hybrids (macromolecular chimeras). Initially synthesized PS 2PBLL and PS 2PBLL 2 (PS, polystyrene; PBLL, poly(ε-tert-butyloxycarbonyl-l-lysine) ) miktoarms were first deprotected to PS 2PLLHCl and PS 2PLLHCl 2 miktoarms (PLLHCl, poly(l-lysine hydrochloride)) and then complexed ionically with sodium dodecyl sulfonate (DS) to give the supramolecular complexes PS 2PLL(DS) and PS 2(PLL(DS)) 2. The solid-state self-assemblies of these six miktoarm systems were studied by transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and small- and wide-angle X-ray scattering (SAXS, WAXS). The side chains of the polypeptide arms were observed to have a large effect on the solubility, polypeptide conformation, and self-assembly of the miktoarms. Three main categories were observed: (i) lamellar self-assemblies at the block copolymer length scale with packed layers of α-helices in PS 2PBLL and PS 2PBLL 2; (ii) charge-clustered polypeptide micelles with less-defined conformations in a nonordered lattice within a PS matrix in PS 2PLLHCl and PS 2PLLHCl 2; (iii) lamellar polypeptide-surfactant self-assemblies with β-sheet conformation in PS 2PLL(DS) and PS 2(PLL(DS)) 2 which dominate over the formation of block copolymer scale structures. Differences between the 3- and 4-arm systems illustrate how packing frustration between the coil-like PS arms and rigid polypeptide conformations can be relieved by the right number of arms, leading to differences in the extent of order. © 2012 American Chemical Society.

  1. Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions

    Directory of Open Access Journals (Sweden)

    Inbar Yuval


    Full Text Available Abstract Background Accurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational protein design. Results Here we introduce a method for accurate protein structure modelling and evaluation based on a novel 4-distance description of residue-residue interaction geometry. Statistical 4-distance preferences were extracted from high-resolution protein structures and were used as a basis for a knowledge-based potential, called Hunter. We demonstrate that 4-distance description of side chain interactions can be used reliably to discriminate the native structure from a set of decoys. Hunter ranked the native structure as the top one in 217 out of 220 high-resolution decoy sets, in 25 out of 28 "Decoys 'R' Us" decoy sets and in 24 out of 27 high-resolution CASP7/8 decoy sets. The same concept was applied to side chain modelling in protein structures. On a set of very high-resolution protein structures the average RMSD was 1.47 Å for all residues and 0.73 Å for buried residues, which is in the range of attainable accuracy for a model. Finally, we show that Hunter performs as good or better than other top methods in homology modelling based on results from the CASP7 experiment. The supporting web site was developed to enable the use of Hunter and for visualization and interactive exploration of 4-distance distributions. Conclusions Our results suggest that Hunter can be used as a tool for evaluation and for accurate modelling of residue-residue interactions in protein structures. The same methodology is applicable to other areas involving high-resolution modelling of biomolecules.

  2. Determination of monounsaturated alkyl side chain 2-alkylcyclobutanones in irradiated foods. (United States)

    Horvatovich, Péter; Miesch, Michel; Hasselmann, Claude; Delincée, Henry; Marchioni, Eric


    The 2-alkylcyclobutanones (2-ACBs) are formed from triglycerides by irradiation treatment and may be used as markers for this type of food processing. This paper describes a detection method for the analysis of monounsaturated alkyl side chain 2-ACBs, which is formed upon irradiation from monounsaturated fatty acids which frequently are the most abundant fatty acids in foods. The estimated radioproduction yields of the cis-2-(dodec-5'-enyl)-cyclobutanones (cis-2-dDeCB) and the cis-2-(tetradec-5'-enyl)-cyclobutanones (cis-2-tDeCB) were 1.0 +/- 0.5 and 0.9 +/- 0.2 nmol.mmol(-1) precursor fatty acid.kGy(-1), respectively, being similar to that of saturated 2-ACBs. The stability study of the s- and mu-2-ACBs in poultry meat samples irradiated at 10 kGy and stored for 3-4 weeks at 4 degrees C and 25 degrees C showed that these compounds undergo some transformation, their amounts being reduced by about 50%. These storage losses did not depend on the saturation state of the alkyl side chain. The EI-MS detection limit of 2-tDeCB is 3 times higher (0.6 pmol) than that of 2-dodecylcyclobutanone (0.2 pmol). Consequently, when the oleic acid content of the analyzed food exceeds the content of palmitic acid by a factor of 3, it would be of an advantage to apply 2-tDeCB as a marker for detection of the irradiation treatment.

  3. Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures (United States)

    Genshaft, Alexander; Moser, Joe-Ann S.; D'Antonio, Edward L.; Bowman, Christine M.; Christianson, David W.


    The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular “switch” for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly-accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations. PMID:23401043

  4. Anchor side chains of short peptide fragments trigger ligand-exchange of class II MHC molecules.

    Directory of Open Access Journals (Sweden)

    Shashank Gupta

    Full Text Available Class II MHC molecules display peptides on the cell surface for the surveillance by CD4+ T cells. To ensure that these ligands accurately reflect the content of the intracellular MHC loading compartment, a complex processing pathway has evolved that delivers only stable peptide/MHC complexes to the surface. As additional safeguard, MHC molecules quickly acquire a 'non-receptive' state once they have lost their ligand. Here we show now that amino acid side chains of short peptides can bypass these safety mechanisms by triggering the reversible ligand-exchange. The catalytic activity of dipeptides such as Tyr-Arg was stereo-specific and could be enhanced by modifications addressing the conserved H-bond network near the P1 pocket of the MHC molecule. It affected both antigen-loading and ligand-release and strictly correlated with reported anchor preferences of P1, the specific target site for the catalytic side chain of the dipeptide. The effect was evident also in CD4+ T cell assays, where the allele-selective influence of the dipeptides translated into increased sensitivities of the antigen-specific immune response. Molecular dynamic calculations support the hypothesis that occupation of P1 prevents the 'closure' of the empty peptide binding site into the non-receptive state. During antigen-processing and -presentation P1 may therefore function as important "sensor" for peptide-load. While it regulates maturation and trafficking of the complex, on the cell surface, short protein fragments present in blood or lymph could utilize this mechanism to alter the ligand composition on antigen presenting cells in a catalytic way.

  5. DMFC Performance of Polymer Electrolyte Membranes Prepared from a Graft-Copolymer Consisting of a Polysulfone Main Chain and Styrene Sulfonic Acid Side Chains

    Directory of Open Access Journals (Sweden)

    Nobutaka Endo


    Full Text Available Polymer electrolyte membranes (PEMs for direct methanol fuel cell (DMFC applications were prepared from a graft-copolymer (PSF-g-PSSA consisting of a polysulfone (PSF main chain and poly(styrene sulfonic acid (PSSA side chains with various average distances between side chains (Lav and side chain lengths (Lsc. The polymers were synthesized by grafting ethyl p-styrenesulfonate (EtSS on macro-initiators of chloromethylated polysulfone with different contents of chloromethyl (CM groups, and by changing EtSS content in the copolymers by using atom transfer radical polymerization (ATRP. The DMFC performance tests using membrane electrode assemblis (MEAs with the three types of the PEMs revealed that: a PSF-g-PSSA PEM (SF-6 prepared from a graft copolymer with short average distances between side chains (Lav and medium Lsc had higher DMFC performance than PEMs with long Lav and long Lsc or with short Lav and short Lsc. SF-6 had about two times higher PDmax (68.4 mW/cm2 than Nafion® 112 at 30 wt % of methanol concentration. Furthermore, it had 58.2 mW/cm2 of PDmax at 50 wt % of methanol concentration because of it has the highest proton selectivity during DMFC operation of all the PSF-g-PSSA PEMs and Nafion® 112.

  6. Synthesis of β-1,4-Linked Galactan Side-Chains of Rhamnogalacturonan I

    DEFF Research Database (Denmark)

    Andersen, Mathias Christian Franch; Kracun, Stjepan; Rydahl, Maja


    with a covalent linker and immobilization on NHS-modified glass surfaces allows for the generation of carbohydrate microarrays. The glycan arrays enables the study of protein-carbohydrate interactions in a high throughput fashion, here demonstrated with binding to mAbs and CBMs....

  7. Isolation and structure determination of the intact sialylated N-linked carbohydrate chains of recombinant human follitropin expressed in Chinese hamster ovary cells

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Hård, K.; Mekking, A.; Damm, J.B.L.; Kamerling, J.P.; Boer, W. de; Wijnands, R.A.


    Biologically active recombinant human follitropin has been expressed in Chinese hamster ovary cells. The carbohydrate chains of the recombinant glycoprotein hormone were enzymatically released by peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase F. The oligosaccharides were separated from

  8. Genetic algorithm with alternating selection pressure for protein side-chain packing and pK(a) prediction. (United States)

    Comte, Pascal; Vassiliev, Sergei; Houghten, Sheridan; Bruce, Doug


    The prediction of protein side-chain conformation is central for understanding protein functions. Side-chain packing is a sub-problem of protein folding and its computational complexity has been shown to be NP-hard. We investigated the capabilities of a hybrid (genetic algorithm/simulated annealing) technique for side-chain packing and for the generation of an ensemble of low energy side-chain conformations. Our method first relies on obtaining a near-optimal low energy protein conformation by optimizing its amino-acid side-chains. Upon convergence, the genetic algorithm is allowed to undergo forward and "backward" evolution by alternating selection pressures between minimal and higher energy setpoints. We show that this technique is very efficient for obtaining distributions of solutions centered at any desired energy from the minimum. We outline the general concepts of our evolutionary sampling methodology using three different alternating selective pressure schemes. Quality of the method was assessed by using it for protein pK(a) prediction. Crown Copyright © 2011. Published by Elsevier Ireland Ltd. All rights reserved.

  9. Effects of carbohydrate, branched-chain amino acids, and arginine in recovery period on the subsequent performance in wrestlers

    Directory of Open Access Journals (Sweden)

    Jang Tsong-Rong


    Full Text Available Abstract Many athletes need to participate in multiple events in a single day. The efficient post-exercise glycogen recovery may be critical for the performance in subsequent exercise. This study examined whether post-exercise carbohydrate supplementation could restore the performance in the subsequent simulated wrestling match. The effect of branched-chain amino acids and arginine on glucose disposal and performance was also investigated. Nine well-trained male wrestlers participated in 3 trials in a random order. Each trial contained 3 matches with a 1-hr rest between match 1 and 2, and a 2-hr rest between match 2 and 3. Each match contained 3 exercise periods interspersed with 1-min rests. The subjects alternated 10-s all-out sprints and 20-s rests in each exercise period. At the end of match 2, 3 different supplementations were consumed: 1.2 g/kg glucose (CHO trial, 1 g/kg glucose + 0.1 g/kg Arg + 0.1 g/kg BCAA (CHO+AA trial, or water (placebo trial. The peak and average power in the 3 matches was similar in the 3 trials. After the supplementation, CHO and CHO+AA trial showed significantly higher glucose and insulin, and lower glycerol and non-esterified fatty acid concentrations than the placebo trial. There was no significant difference in these biochemical parameters between the CHO and CHO+AA trials. Supplementation of carbohydrate with or without BCAA and arginine during the post-match period had no effect on the performance in the following simulated match in wrestlers. In addition, BCAA and arginine did not provide additional insulinemic effect.

  10. Vibrational spectroscopic studies on fibrinogen adsorption at polystyrene/protein solution interfaces: hydrophobic side chain and secondary structure changes. (United States)

    Wang, Jie; Chen, Xiaoyun; Clarke, Matthew L; Chen, Zhan


    Structural changes of fibrinogen after adsorption to polystyrene (PS) were examined at the PS/protein solution interface in situ using sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). Different behaviors of hydrophobic side chains and secondary structures of adsorbed fibrinogen molecules have been observed. Our results indicate that upon adsorption, the hydrophobic PS surface induces fast structural changes of fibrinogen molecules by aligning some hydrophobic side chains in fibrinogen so that they face to the surface. Such structural changes of fibrinogen hydrophobic side chains are local changes and do not immediately induce significant changes of the protein secondary structures. Our research also shows that the interactions between adsorbed fibrinogen and the PS surface can induce significant changes of protein secondary structures or global conformations which occur on a much longer time scale.

  11. Selective carbon 13 enrichment of side chain carbons of ginkgo lignin traced by carbon 13 nuclear magnetic resonance

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Y. (Nagoya Univ. (Japan). Faculty of Agriculture); Robert, D.R. (CEA Centre d' Etudes de Grenoble, 38 (France). Dept. de Recherche Fondamentale sur la Matiere Condensee); Terashima, N. (Forest Products Lab., Madison, WI (United States))

    Although carbon 13 nuclear magnetic resonance spectroscopy ([sup 13]C-NMR) is widely used in lignin structural studies, serious difficulties are encountered in the assignments of [sup 13]C signals because of their extensive overlaps resulting from the complex structure of lignin and of delicate detection of minor structures. To overcome these difficulties, specifically [sup 13]C-enriched precursors of lignin biosynthesis, coniferin-[side chain-[beta]-[sup 13]C] and coniferin-[side chain-[gamma]-[sup 13]C], were administered to growing stems of ginkgo (Ginkgo biloba). The NMR analysis of the milled wood lignins isolated from the newly formed xylem showed that selective enrichment of specific carbons of protolignin in the cell wall was achieved without seriously disturbing the lignin biosynthesis. The presence of saturated methylene side chains in the protolignin was shown for the first time by this selective enrichment technique in combination with NMR analysis. (authors). 23 refs., 3 figs., 1 tab.

  12. From Semi- to Full-Two-Dimensional Conjugated Side-Chain Design: A Way toward Comprehensive Solar Energy Absorption

    Energy Technology Data Exchange (ETDEWEB)

    Chao, Pengjie [Department; School; Wang, Huan [Department; Qu, Shiwei [Department; Mo, Daize [Department; Meng, Hong [School; Chen, Wei [Materials; Institute; He, Feng [Department


    Two polymers with fully two-dimensional (2D) conjugated side chains, 2D-PTB-Th and 2D-PTB-TTh, were synthesized and characterized through simultaneously integrating the 2D-TT and the 2D-BDT monomers onto the polymer backbone. Resulting from the synergistic effect from the conjugated side chains on both monomers, the two polymers showed remarkably efficient absorption of the sunlight and improved pi-pi intermolecular interactions for efficient charge carrier transport. The optimized bulk heterojunction device based on 2D-PTB-Th and PC71BM shows a higher PCE of 9.13% compared to PTB7-Th with a PCE of 8.26%, which corresponds to an approximately 10% improvement in solar energy conversion. The fully 2D-conjugated side-chain concept reported here developed a new molecular design strategy for polymer materials with enhanced sunlight absorption and efficient solar energy conversion.

  13. Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance {sup 13}C NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Daley, Margaret E.; Sykes, Brian D. [University of Alberta, Department of Biochemistry, CIHR Group in Protein Structure and Function and Protein Engineering Network of Centres of Excellence (Canada)


    The dynamics of threonine side chains of the Tenebrio molitor antifreeze protein (TmAFP) were investigated using natural abundance {sup 13}C NMR. In TmAFP, the array of threonine residues on one face of the protein is responsible for conferring its ability to bind crystalline ice and inhibit its growth. Heteronuclear longitudinal and transverse relaxation rates and the {sup 1}H-{sup 13}C NOE were determined in this study. The C{alpha}H relaxation measurements were compared to the previously measured {sup 15}N backbone parameters and these are found to be in agreement. For the analysis of the threonine side chain motions, the model of restricted rotational diffusion about the {chi}{sub 1} dihedral angle was employed [London and Avitabile (1978) J. Am. Chem. Soc., 100, 7159-7165]. We demonstrate that the motion experienced by the ice binding threonine side chains is highly restricted, with an approximate upper limit of less than {+-}25 deg.

  14. Genes involved in cell wall localization and side chain formation of rhamnose-glucose polysaccharide in Streptococcus mutans. (United States)

    Yamashita, Y; Tsukioka, Y; Tomihisa, K; Nakano, Y; Koga, T


    We identified in Streptococcus mutans six new genes (rgpA through rgpF), whose disruption results in a loss of serotype-specific antigenicity, specified by the glucose side chains of rhamnose-glucose polysaccharide from the cell wall. Rhamnose and glucose content of the cell wall decreased drastically in all these disruption mutants, except that in the rgpE mutant only the glucose content decreased. RgpC and RgpD are homologous to ATP-binding cassette transporter components and may be involved in polysaccharide export, whereas RgpE may be a transferase of side chain glucose.

  15. Thermochemistry of alkali metal cation interactions with histidine: influence of the side chain. (United States)

    Armentrout, P B; Citir, Murat; Chen, Yu; Rodgers, M T


    The interactions of alkali metal cations (M(+) = Na(+), K(+), Rb(+), Cs(+)) with the amino acid histidine (His) are examined in detail. Experimentally, bond energies are determined using threshold collision-induced dissociation of the M(+)(His) complexes with xenon in a guided ion beam tandem mass spectrometer. Analyses of the energy dependent cross sections provide 0 K bond energies of 2.31 ± 0.11, 1.70 ± 0.08, 1.42 ± 0.06, and 1.22 ± 0.06 eV for complexes of His with Na(+), K(+), Rb(+), and Cs(+), respectively. All bond dissociation energy (BDE) determinations include consideration of unimolecular decay rates, internal energy of reactant ions, and multiple ion-neutral collisions. These experimental results are compared to values obtained from quantum chemical calculations conducted previously at the MP2(full)/6-311+G(2d,2p), B3LYP/6-311+G(2d,2p), and B3P86/6-311+G(2d,2p) levels with geometries and zero point energies calculated at the B3LYP/6-311+G(d,p) level where Rb and Cs use the Hay-Wadt effective core potential and basis set augmented with additional polarization functions (HW*). Additional calculations using the def2-TZVPPD basis set with B3LYP geometries were conducted here at all three levels of theory. Either basis set yields similar results for Na(+)(His) and K(+)(His), which are in reasonable agreement with the experimental BDEs. For Rb(+)(His) and Cs(+)(His), the HW* basis set and ECP underestimate the experimental BDEs, whereas the def2-TZVPPD basis set yields results in good agreement. The effect of the imidazole side chain on the BDEs is examined by comparing the present results with previous thermochemistry for other amino acids. Both polarizability and the local dipole moment of the side chain are influential in the energetics.

  16. Effect of side chain length and degree of polymerization on the decomposition and crystallization behaviour of chlorinated poly(vinyl ester) oligomers

    Energy Technology Data Exchange (ETDEWEB)

    Heinze, D.; Mang, Th. [Aachen University of Applied Sciences, Heinrich-Mussmann-Str. 1, 52428 Jülich (Germany); Popescu, C., E-mail: [KAO Germany GmbH, Pfungstädterstr. 98-100, 64297 Darmstadt (Germany); Weichold, O., E-mail: [Institute of Building Materials Research, Schinkelstr. 3, 52062 Aachen (Germany)


    Highlights: • Thermal behaviour of telomerized polyvinyl esters is investigated. • Thermal stability relies mainly on the contribution of side chains. • At equal molecular weights thermal stability is dictated by length of side chain. • Increasing the length of side chains improves also the packing degree of polymer. - Abstract: Four members of a homologous series of chlorinated poly(vinyl ester) oligomers CCl{sub 3}–(CH{sub 2}CH (OCO(CH{sub 2}){sub m}CH{sub 3})){sub n}–Cl with degrees of polymerization of 10 and 20 were prepared by telomerisation using carbon tetrachloride. The number of side chain carbon atoms ranges from 2 (poly(vinyl acetate) to 18 (poly(vinyl stearate)). The effect of the n-alkyl side chain length and of the degree of polymerization on the thermal stability and crystallization behaviour of the synthesized compounds was investigated. All oligomers degrade in two major steps by first losing HCl and side chains with subsequent breakdown of the backbone. The members with short side chains, up to poly(vinyl octanoate), are amorphous and show internal plasticization, whereas those with high number of side chain carbon atoms are semi-crystalline due to side-chain crystallization. A better packing for poly(vinyl stearate) is also noticeable. The glass transition and melting temperatures as well as the onset temperature of decomposition are influenced to a larger extent by the side chain length than by the degree of polymerization. Thermal stability is improved if both the size and number of side chains increase, but only a long side chain causes a significant increase of the resistance to degradation. This results in a stabilization of PVAc so that oligomers from poly(vinyl octanoate) on are stable under atmospheric conditions. Thus, the way to design stable, chlorinated PVEs oligomers is to use a long n-alkyl side chain.

  17. A rigid disulfide-linked nitroxide side chain simplifies the quantitative analysis of PRE data

    Energy Technology Data Exchange (ETDEWEB)

    Fawzi, Nicolas L. [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Fleissner, Mark R. [University of California, Jules Stein Eye Institute and Department of Chemistry and Biochemistry (United States); Anthis, Nicholas J. [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Kalai, Tamas; Hideg, Kalman [University of Pecs, Institute of Organic and Medicinal Chemistry (Hungary); Hubbell, Wayne L., E-mail: [University of California, Jules Stein Eye Institute and Department of Chemistry and Biochemistry (United States); Clore, G. Marius, E-mail: [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)


    The measurement of {sup 1}H transverse paramagnetic relaxation enhancement (PRE) has been used in biomolecular systems to determine long-range distance restraints and to visualize sparsely-populated transient states. The intrinsic flexibility of most nitroxide and metal-chelating paramagnetic spin-labels, however, complicates the quantitative interpretation of PREs due to delocalization of the paramagnetic center. Here, we present a novel, disulfide-linked nitroxide spin label, R1p, as an alternative to these flexible labels for PRE studies. When introduced at solvent-exposed {alpha}-helical positions in two model proteins, calmodulin (CaM) and T4 lysozyme (T4L), EPR measurements show that the R1p side chain exhibits dramatically reduced internal motion compared to the commonly used R1 spin label (generated by reacting cysteine with the spin labeling compound often referred to as MTSL). Further, only a single nitroxide position is necessary to account for the PREs arising from CaM S17R1p, while an ensemble comprising multiple conformations is necessary for those observed for CaM S17R1. Together, these observations suggest that the nitroxide adopts a single, fixed position when R1p is placed at solvent-exposed {alpha}-helical positions, greatly simplifying the interpretation of PRE data by removing the need to account for the intrinsic flexibility of the spin label.

  18. Phase biaxiality in nematic liquid crystalline side-chain polymers of various chemical constitutions. (United States)

    Severing, Kirsten; Stibal-Fischer, Elke; Hasenhindl, Alfred; Finkelmann, Heino; Saalwächter, Kay


    In a previous deuterium NMR study conducted on a liquid crystalline (LC) polymer with laterally attached book-shaped molecules as the mesogenic moiety, we have revealed a biaxial nematic phase below the conventional uniaxial nematic phase (Phys. Rev. Lett. 2004, 92, 125501). To elucidate details of its formation, we here report on deuterium NMR experiments that have been conducted on different types of LC side-chain polymers as well as on mixtures with low-molar-mass mesogens. Different parameters that affect the formation of a biaxial nematic phase, such as the geometry of the attachment, the spacer length between the polymer backbone and the mesogenic unit, as well as the polymer dynamics, were investigated. Surprisingly, also polymers with terminally attached mesogens (end-on polymers) are capable of forming biaxial nematic phases if the flexible spacer is short and thus retains a coupling between the polymer backbone and the LC phase. Furthermore, the most important parameter for the formation of a biaxial nematic phase is the dynamics of the polymer backbone, as the addition of a small percentage of low molar mass LC to the biaxial nematic polymer from the original study served to shift both the glass transition and the appearance of detectable biaxiality in a very similar fashion. Plotting different parameters for the investigated systems as a function of T/Tg also reveals the crucial role of the dynamics of the polymer backbone and hence the glass transition.

  19. Photo-induced deformations in azobenzene-containing side-chain polymers: molecular dynamics study

    Directory of Open Access Journals (Sweden)



    Full Text Available We perform molecular dynamics simulations of azobenzene containing side-chain liquid crystalline polymer subject to an external model field that mimicks the reorientations of the azobenzenes upon irradiation with polarized light. The smectic phase of the polymer is studied with the field applied parallel to the nematic director, forcing the trans isomers to reorient perpendicularly to the field (the direction of which can be assosiated with the light polarization. The coupling between the reorientation of azobenzenes and mechanical deformation of the sample is found to depend on the field strength. In a weak field the original smectic order is melted gradually with no apparent change in the simulation box shape, whereas in a strong field two regimes are observed. During the first one a rapid melting of the liquid crystalline order is accompanied by the contraction of the polymer along the field direction (the effect similar to the one observed experimentally in azobenzene containing elastomers. During the slower second regime, the smectic layers are rebuilt to accomodate the preferential direction of chromophores perperdicular to the field.

  20. Side chain NMR assignments in the membrane protein OmpX reconstituted in DHPC micelles. (United States)

    Hilty, Christian; Fernández, César; Wider, Gerhard; Wüthrich, Kurt


    Sequence-specific assignments have been obtained for side chain methyl resonances of Val, Leu and Ile in the outer membrane protein X (OmpX) from Escherichia coli reconstituted in 60 kDa micelles in aqueous solution. Using previously established techniques, OmpX was uniformly 2H,13C,15N-labeled with selectively protonated Val-gamma(1,2), Leu-delta(1,2) and Ile-delta1 methyl groups. The thus labeled protein was studied with the novel experiments 3D (H)C(CC)-TOCSY-(CO)-[15N,1H]-TROSY and 3D H(C)(CC)-TOCSY-(CO)-[15N,1H]-TROSY. Compared to the corresponding conventional experimental schemes, the TROSY-type experiments yielded a sensitivity gain of about 2 at 500 MHz. The overall sensitivity of the experiments was further enhanced more than two-fold by the use of a cryoprobe. Complete assignments of the proton and carbon chemical shifts were obtained for all isopropyl methyl groups of Val and Leu, as well as for the delta1-methyls of Ile. The present approach is applicable for soluble proteins or micelle-reconstituted membrane proteins in structures with overall molecular weights up to about 100 kDa, and adds to the potentialities of solution NMR for de novo structure determination as well as for functional studies, such as ligand screening with proteins in large structures.

  1. Improving ranking of models for protein complexes with side chain modeling and atomic potentials. (United States)

    Viswanath, Shruthi; Ravikant, D V S; Elber, Ron


    An atomically detailed potential for docking pairs of proteins is derived using mathematical programming. A refinement algorithm that builds atomically detailed models of the complex and combines coarse grained and atomic scoring is introduced. The refinement step consists of remodeling the interface side chains of the top scoring decoys from rigid docking followed by a short energy minimization. The refined models are then re-ranked using a combination of coarse grained and atomic potentials. The docking algorithm including the refinement and re-ranking, is compared favorably to other leading docking packages like ZDOCK, Cluspro, and PATCHDOCK, on the ZLAB 3.0 Benchmark and a test set of 30 novel complexes. A detailed analysis shows that coarse grained potentials perform better than atomic potentials for realistic unbound docking (where the exact structures of the individual bound proteins are unknown), probably because atomic potentials are more sensitive to local errors. Nevertheless, the atomic potential captures a different signal from the residue potential and as a result a combination of the two scores provides a significantly better prediction than each of the approaches alone. Copyright © 2012 Wiley Periodicals, Inc.

  2. The role of side chain conformational flexibility in surface recognition by Tenebrio molitor antifreeze protein (United States)

    Daley, Margaret E.; Sykes, Brian D.


    Two-dimensional nuclear magnetic resonance spectroscopy was used to investigate the flexibility of the threonine side chains in the β-helical Tenebrio molitor antifreeze protein (TmAFP) at low temperatures. From measurement of the 3Jαβ 1H-1H scalar coupling constants, the χ1 angles and preferred rotamer populations can be calculated. It was determined that the threonines on the ice-binding face of the protein adopt a preferred rotameric conformation at near freezing temperatures, whereas the threonines not on the ice-binding face sample many rotameric states. This suggests that TmAFP maintains a preformed ice-binding conformation in solution, wherein the rigid array of threonines that form the AFP-ice interface matches the ice crystal lattice. A key factor in binding to the ice surface and inhibition of ice crystal growth appears to be the close surface-to-surface complementarity between the AFP and crystalline ice, and the lack of an entropic penalty associated with freezing out motions in a flexible ligand. PMID:12824479

  3. High-performance polymer semiconducting heterostructure devices by nitrene-mediated photocrosslinking of alkyl side chains (United States)

    Png, Rui-Qi; Chia, Perq-Jon; Tang, Jie-Cong; Liu, Bo; Sivaramakrishnan, Sankaran; Zhou, Mi; Khong, Siong-Hee; Chan, Hardy S. O.; Burroughes, Jeremy H.; Chua, Lay-Lay; Friend, Richard H.; Ho, Peter K. H.


    Heterostructures are central to the efficient manipulation of charge carriers, excitons and photons for high-performance semiconductor devices. Although these can be formed by stepwise evaporation of molecular semiconductors, they are a considerable challenge for polymers owing to re-dissolution of the underlying layers. Here we demonstrate a simple and versatile photocrosslinking methodology based on sterically hindered bis(fluorophenyl azide)s. The photocrosslinking efficiency is high and dominated by alkyl side-chain insertion reactions, which do not degrade semiconductor properties. We demonstrate two new back-infiltrated and contiguous interpenetrating donor-acceptor heterostructures for photovoltaic applications that inherently overcome internal recombination losses by ensuring path continuity to give high carrier-collection efficiency. This provides the appropriate morphology for high-efficiency polymer-based photovoltaics. We also demonstrate photopatternable polymer-based field-effect transistors and light-emitting diodes, and highly efficient separate-confinement-heterostructure light-emitting diodes. These results open the way to the general development of high-performance polymer semiconductor heterostructures that have not previously been thought possible.

  4. Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains. (United States)

    Makowski, Mariusz; Liwo, Adam; Sobolewski, Emil; Scheraga, Harold A


    A new model of side-chain-side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parametrized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. © 2011 American Chemical Society

  5. Slow Structural Rearrangement of a Side-Chain Phthalocyanine Methacrylate Polymer at the Air-Water Interface

    NARCIS (Netherlands)

    Nostrum, C.F. van; Nolte, R.J.M.; Devillers, M.A.C.; Oostergetel, G.T.; Teerenstra, M.N.; Schouten, A.J.


    A polymethacrylate with dodecoxy-substituted phthalocyanine units in the side chains has been used to form Langmuir-Blodgett monolayers at the air-water interface. The monolayers are highly crystalline. They expand slowly even when a constant surface pressure is applied. The structural change

  6. Release and characterization of single side chains of white cabbage pectin and their complement-fixing activity

    NARCIS (Netherlands)

    Westereng, B.; Coenen, G.J.; Michaelsen, T.E.; Voragen, A.G.J.; Samuelsen, A.B.; Schols, H.A.; Knutsen, S.H.


    A mixture of single side chains from white cabbage pectin were obtained by anion exchange chromatography after applying mild chemical conditions promoting -elimination. These pectin fragments were characterized by their molecular weight distribution, sugar composition, 13C-NMR, and MALDI-TOF-MS

  7. Conjugation of diisocyanate side chains to dimethacrylate reduces polymerization shrinkage and increases the hardness of composite resins. (United States)

    Jan, Yih-Dean; Lee, Bor-Shiunn; Lin, Chun-Pin; Tseng, Wan-Yu


    Polymerization shrinkage is one of the main causes of dental restoration failure. This study tried to conjugate two diisocyanate side chains to dimethacrylate resins in order to reduce polymerization shrinkage and increase the hardness of composite resins. Diisocyanate, 2-hydroxyethyl methacrylate, and bisphenol A dimethacrylate were reacted in different ratios to form urethane-modified new resin matrices, and then mixed with 50 wt.% silica fillers. The viscosities of matrices, polymerization shrinkage, surface hardness, and degrees of conversion of experimental composite resins were then evaluated and compared with a non-modified control group. The viscosities of resin matrices increased with increasing diisocyanate side chain density. Polymerization shrinkage and degree of conversion, however, decreased with increasing diisocyanate side chain density. The surface hardness of all diisocyanate-modified groups was equal to or significantly higher than that of the control group. Conjugation of diisocyanate side chains to dimethacrylate represents an effective means of reducing polymerization shrinkage and increasing the surface hardness of dental composite resins. Copyright © 2012. Published by Elsevier B.V.

  8. Biliverdin amides reveal roles for propionate side chains in bilin reductase recognition and in holophytochrome assembly and photoconversion. (United States)

    Shang, Lixia; Rockwell, Nathan C; Martin, Shelley S; Lagarias, J Clark


    Linear tetrapyrroles (bilins) perform important antioxidant and light-harvesting functions in cells from bacteria to humans. To explore the role of the propionate moieties in bilin metabolism, we report the semisynthesis of mono- and diamides of biliverdin IXalpha and those of its non-natural XIIIalpha isomer. Initially, these were examined as substrates of two types of NADPH-dependent biliverdin reductase, BVR and BvdR, and of the representative ferredoxin-dependent bilin reductase, phycocyanobilin:ferredoxin oxidoreductase (PcyA). Our studies indicate that the NADPH-dependent biliverdin reductases are less accommodating to amidation of the propionic acid side chains of biliverdin IXalpha than PcyA, which does not require free carboxylic acid side chains to yield its phytobilin product, phycocyanobilin. Bilin amides were also assembled with BV-type and phytobilin-type apophytochromes, demonstrating a role for the 8-propionate in the formation of the spectroscopically native P(r) dark states of these biliprotein photosensors. Neither ionizable propionate side chain proved to be essential to primary photoisomerization for both classes of phytochromes, but an unsubstituted 12-propionate was required for full photointerconversion of phytobilin-type phytochrome Cph1. Taken together, these studies provide insight into the roles of the ionizable propionate side chains in substrate discrimination by two bilin reductase families while further underscoring the mechanistic differences between the photoconversions of BV-type and phytobilin-type phytochromes.

  9. A protocol for CABS-dock protein-peptide docking driven by side-chain contact information. (United States)

    Kurcinski, Mateusz; Blaszczyk, Maciej; Ciemny, Maciej Pawel; Kolinski, Andrzej; Kmiecik, Sebastian


    The characterization of protein-peptide interactions is a challenge for computational molecular docking. Protein-peptide docking tools face at least two major difficulties: (1) efficient sampling of large-scale conformational changes induced by binding and (2) selection of the best models from a large set of predicted structures. In this paper, we merge an efficient sampling technique with external information about side-chain contacts to sample and select the best possible models. In this paper we test a new protocol that uses information about side-chain contacts in CABS-dock protein-peptide docking. As shown in our recent studies, CABS-dock enables efficient modeling of large-scale conformational changes without knowledge about the binding site. However, the resulting set of binding sites and poses is in many cases highly diverse and difficult to score. As we demonstrate here, information about a single side-chain contact can significantly improve the prediction accuracy. Importantly, the imposed constraints for side-chain contacts are quite soft. Therefore, the developed protocol does not require precise contact information and ensures large-scale peptide flexibility in the broad contact area. The demonstrated protocol provides the extension of the CABS-dock method that can be practically used in the structure prediction of protein-peptide complexes guided by the knowledge of the binding interface.

  10. Amphiphilic Surface Active Triblock Copolymers with Mixed Hydrophobic and Hydrophilic Side Chains for Tuned Marine Fouling-Release Properties

    Energy Technology Data Exchange (ETDEWEB)

    Park, D.; Weinman, C; Finlay, J; Fletcher, B; Paik, M; Sundaram, H; Dimitriou, M; Sohn, K; Callow, M; et al.


    Two series of amphiphilic triblock surface active block copolymers (SABCs) were prepared through chemical modification of two polystyrene-block-poly(ethylene-ran-butylene)-block-polyisoprene ABC triblock copolymer precursors. The methyl ether of poly(ethylene glycol) [M{sub n} {approx} 550 g/mol (PEG550)] and a semifluorinated alcohol (CF{sub 3}(CF{sub 2}){sub 9}(CH{sub 2}){sub 10}OH) [F10H10] were attached at different molar ratios to impart both hydrophobic and hydrophilic groups to the isoprene segment. Coatings on glass slides consisting of a thin layer of the amphiphilic SABC deposited on a thicker layer of an ABA polystyrene-block-poly(ethylene-ran-butylene)-block-polystyrene thermoplastic elastomer were prepared for biofouling assays with algae. Dynamic water contact angle analysis, X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) measurements were utilized to characterize the surfaces. Clear differences in surface structure were realized as the composition of attached side chains was varied. In biofouling assays, the settlement (attachment) of zoospores of the green alga Ulva was higher for surfaces incorporating a large proportion of the hydrophobic F10H10 side chains, while surfaces with a large proportion of the PEG550 side chains inhibited settlement. The trend in attachment strength of sporelings (young plants) of Ulva did not show such an obvious pattern. However, amphiphilic SABCs incorporating a mixture of PEG550 and F10H10 side chains performed the best. The number of cells of the diatom Navicula attached after exposure to flow decreased as the content of PEG550 to F10H10 side chains increased.

  11. Enhancing the Performance of Polymer Solar Cells by Using Donor Polymers Carrying Discretely Distributed Side Chains. (United States)

    Gong, Xue; Li, Guangwu; Wu, Yang; Zhang, Jicheng; Feng, Shiyu; Liu, Yahui; Li, Cuihong; Ma, Wei; Bo, Zhishan


    Conjugated polymers with three components, P1-1 and P1-2, were prepared by one-pot Stille polymerization. The two-component polymer P1-0 is only composed of a 5-fluoro-6-alkyloxybenzothiadiazole (AFBT) acceptor unit and a thiophene donor unit, while the three-component polymers P1-1 and P1-2 contain 10% and 20% 5,6-difluorobenzothiadiazole (DFBT), respectively, as the third component. The incorporation of the third component, 5,6-difluorobenzothiadiazole, makes the side chains discretely distributed in the polymer backbones, which can enhance the π-π stacking of polymers in film, markedly increase the hole mobility of active layers, and improve the power-conversion efficiency (PCE) of devices. Influence of the third component on the morphology of active layer was also studied by X-ray diffraction (XRD), resonant soft X-ray scattering (R-SoXS), and transmission electron microscopy (TEM) experiments. P1-1/PC71BM-based PSCs gave a high PCE up to 7.25%, whereas similarly fabricated devices for P1-0/PC71BM only showed a PCE of 3.46%. The PCE of P1-1/PC71BM-based device was further enhanced to 8.79% after the use of 1,8-diiodooctane (DIO) as the solvent additive. Most importantly, after the incorporation of 10% 5,6-difluorobenzothiadiazole unit, P1-1 exhibited a marked tolerance to the blend film thickness. Devices with a thickness of 265 nm still showed a PCE above 8%, indicating that P1-1 is promising for future applications.

  12. Side chain NMR assignments in the membrane protein OmpX reconstituted in DHPC micelles

    Energy Technology Data Exchange (ETDEWEB)

    Hilty, Christian; Fernandez, Cesar; Wider, Gerhard; Wuethrich, Kurt [Institut fuer Molekularbiologie und Biophysik, Eidgenoessische Technische Hochschule Zuerich (Switzerland)], E-mail:


    Sequence-specific assignments have been obtained for side chain methyl resonances of Val, Leu and Ile in the outer membrane protein X (OmpX) from Escherichia colireconstituted in 60 kDa micelles in aqueous solution. Using previously established techniques, OmpX was uniformly {sup 2}H,{sup 13}C,{sup 15}N-labeled with selectively protonated Val-{gamma}{sup 1,2}, Leu-{delta}{sup 1,2}and Ile-{delta}{sup 1}methyl groups. The thus labeled protein was studied with the novel experiments 3D (H)C(CC)-TOCSY-(CO)-[{sup 15}N,{sup 1}H]-TROSY and 3D H(C)(CC)-TOCSY-(CO)-[{sup 15}N,{sup 1}H]-TROSY. Compared to the corresponding conventional experimental schemes, the TROSY-type experiments yielded a sensitivity gain of about 2 at 500 MHz. The overall sensitivity of the experiments was further enhanced more than two-fold by the use of a cryoprobe. Complete assignments of the proton and carbon chemical shifts were obtained for all isopropyl methyl groups of Val and Leu, as well as for the {delta}{sup 1}-methyls of Ile. The present approach is applicable for soluble proteins or micelle-reconstituted membrane proteins in structures with overall molecular weights up to about 100 kDa, and adds to the potentialities of solution NMR for de novostructure determination as well as for functional studies, such as ligand screening with proteins in large structures.

  13. ω-Turn: a novel β-turn mimic in globular proteins stabilized by main-chain to side-chain C−H···O interaction. (United States)

    Dhar, Jesmita; Chakrabarti, Pinak; Saini, Harpreet; Raghava, Gajendra Pal Singh; Kishore, Raghuvansh


    Mimicry of structural motifs is a common feature in proteins. The 10-membered hydrogen-bonded ring involving the main-chain C − O in a β-turn can be formed using a side-chain carbonyl group leading to Asx-turn. We show that the N − H component of hydrogen bond can be replaced by a C(γ) -H group in the side chain, culminating in a nonconventional C − H···O interaction. Because of its shape this β-turn mimic is designated as ω-turn, which is found to occur ∼ three times per 100 residues. Three residues (i to i + 2) constitute the turn with the C − H···O interaction occurring between the terminal residues, constraining the torsion angles ϕi + 1, ψi + 1, ϕi + 2 and χ'1(i + 2) (using the interacting C(γ) atom). Based on these angles there are two types of ω-turns, each of which can be further divided into two groups. C(β) -branched side-chains, and Met and Gln have high propensities to occur at i + 2; for the last two residues the carbonyl oxygen may participate in an additional interaction involving the S and amino group, respectively. With Cys occupying the i + 1 position, such turns are found in the metal-binding sites. N-linked glycosylation occurs at the consensus pattern Asn-Xaa-Ser/Thr; with Thr at i + 2, the sequence can adopt the secondary structure of a ω-turn, which may be the recognition site for protein modification. Location between two β-strands is the most common occurrence in protein tertiary structure, and being generally exposed ω-turn may constitute the antigenic determinant site. It is a stable scaffold and may be used in protein engineering and peptide design. © 2014 Wiley Periodicals, Inc.

  14. The interplay between transient a-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M


    The peptide backbones of disordered proteins are routinely characterized by NMR with respect to transient structure and dynamics. Little experimental information is, however, available about the side chain conformations and how structure in the backbone affects the side chains. Methyl chemical sh...

  15. Quantitative Analysis of Cu(I) Concentration in Click Chemistry : Biotinylation at Side Chain of Propargylglycine Using Click Chemistry under Heating Conditions


    Ogasawara, Yui; Murai, Yuta; Sakihama, Yasuko; Hashidoko, Yasuyuki; Hashimoto, Makoto


    The click reaction is one of the latest techniques for the chemical modification of bioactive compounds. Chemical modifications of α-amino acid side chains are gaining significance as useful and important tools for biochemical research. Biotinylation at side chain of propargylglycine using click reaction was examined. The detail quantitative analysis of Cu(I) concentration are performed to proceed the click reaction effectively.

  16. The NMR side-chain assignments and solution structure of enzyme IIBcellobiose of the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli

    NARCIS (Netherlands)

    AB, Eiso; Schuurman-Wolters, Gea; Reizer, Jonathan; Saier, Milton H.; Dijkstra, Klaas; Scheek, Ruud M.; Robillard, George T.

    The assignment of the side-chain Nh IR resonances and the determination of the three-dimensional solution structure of the C10S mutant of enzyme IIBcellobiose (IIBcel) of the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli are presented. The side-chain resonances were

  17. The Influence of Conjugated Polymer Side Chain Manipulation on the Efficiency and Stability of Polymer Solar Cells

    DEFF Research Database (Denmark)

    Heckler, Ilona Maria; Kesters, Jurgen; Defour, Maxime


    studies under constant sun irradiance showed a diminishing initial degradation rate for the BT-based devices upon including the alternative side chains, whereas the (more stable) TzTz-based devices degraded at a faster rate from the start of the experiment upon partly exchanging the side chains. No clear......]thiazole (TzTz) acceptor units, were selected toward effective device scalability by roll-coating. The influence of the partial exchange (5% or 10%) of the solubilizing 2-hexyldecyloxy by alternative 2-phenylethoxy groups on efficiency and stability was investigated. With an increasing 2-phenylethoxy ratio......, a decrease in solar cell efficiency was observed for the BT-based series, whereas the efficiencies for the devices based on the TzTz polymers remained approximately the same.The photochemical degradation rate for PSCs based on the TzTz polymers decreased with an increasing 2-phenylethoxy ratio. Lifetime...

  18. Siloxane-Terminated Solubilizing Side Chains: Bringing Conjugated Polymer Backbones Closer and Boosting Hole Mobilities in Thin-Film Transistors

    KAUST Repository

    Mei, Jianguo


    We introduce a novel siloxane-terminated solubilizing group and demonstrate its effectiveness as a side chain in an isoindigo-based conjugated polymer. An average hole mobility of 2.00 cm 2 V -1 s -1 (with a maximum mobility of 2.48 cm 2 V -1 s -1), was obtained from solution-processed thin-film transistors, one of the highest mobilities reported to date. In contrast, the reference polymer with a branched alkyl side chain gave an average hole mobility of 0.30 cm 2 V -1 s -1 and a maximum mobility of 0.57 cm 2 V -1 s -1. This is largely explained by the polymer packing: our new polymer exhibited a π-π stacking distance of 3.58 Å, while the reference polymer showed a distance of 3.76 Å. © 2011 American Chemical Society.

  19. The bulky side chain of antillatoxin is important for potent toxicity: rational design of photoresponsive cytotoxins based on SAR studies. (United States)

    Okura, Ken; Matsuoka, Shigeru; Inoue, Masayuki


    Antillatoxin is a cyclic peptide with potent neurotoxic and neuritogenic activities. We designed and synthesized six analogues that have photocleavable protecting groups at the terminus of the side chain. Among these compounds, the bis-o-nitrobenzyl acetal derivative was found to exhibit high toxicity and was effectively deactivated by photochemical removal, proving that the biological activity of antillatoxin was modulated by altering the size of the terminal group.

  20. Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization


    Lorenzen, Stephan; Zhang, Yang


    Structures of hitherto unknown protein complexes can be predicted by docking the solved protein monomers. Here, we present a method to refine initial docking estimates of protein complex structures by a Monte Carlo approach including rigid-body moves and side-chain optimization. The energy function used is comprised of van der Waals, Coulomb, and atomic contact energy terms. During the simulation, we gradually shift from a novel smoothed van der Waals potential, which prevents trapping in loc...

  1. In Situ Monitoring the Thermal Degradation of PCPDTBT Low Band Gap Polymers with Varying Alkyl Side-Chain Patterns


    Marin, Lidia; Penxten, Huguette; Van Mierloo, Sarah; Carleer, Robert; Lutsen, Laurence; Vanderzande, Dirk; Maes, Wouter


    The degradation pattern of a series of low band gap PCPDTBT polymers under thermal stress is investigated by in situ UV-vis and FT-IR techniques combined with thermal degradation analysis. Thermogravimetric analysis is used to predetermine the decomposition intervals, revealing that thermolysis occurs in two stages. TG-TD-GC/MS shows that loss of the alkyl side chains predominantly happens within the first temperature regime and degradation of the polymer backbone occurs thereafter. UV-vis sp...

  2. Fabrication of narrow surface relief features in a side-chain azobenzene polyester with a scanning near-field microscope

    DEFF Research Database (Denmark)

    Ramanujam, P.S.; Holme, N. C. R.; Pedersen, M.


    We show that it is possible to fabricate topographic submicron features in a side-chain azobenzene polyester with a scanning near-field optical microscope, Through irradiation at a wavelength of 488 run at intensity levels of 12 W/cm(2), topographic features as narrow as 240 nm and as high as 6 nm...... in high-density optical storage and high-resolution lithography....

  3. Interplay Between Side Chain Pattern, Polymer Aggregation, and Charge Carrier Dynamics in PBDTTPD:PCBM Bulk-Heterojunction Solar Cells

    KAUST Repository

    Dyer-Smith, Clare


    Poly(benzo[1,2-b:4,5-b′]dithiophene–alt–thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymer donors with linear side-chains yield bulk-heterojunction (BHJ) solar cell power conversion efficiencies (PCEs) of about 4% with phenyl-C71-butyric acid methyl ester (PC71BM) as the acceptor, while a PBDTTPD polymer with a combination of branched and linear substituents yields a doubling of the PCE to 8%. Using transient optical spectroscopy it is shown that while the exciton dissociation and ultrafast charge generation steps are not strongly affected by the side chain modifications, the polymer with branched side chains exhibits a decreased rate of nongeminate recombination and a lower fraction of sub-nanosecond geminate recombination. In turn the yield of long-lived charge carriers increases, resulting in a 33% increase in short circuit current (J sc). In parallel, the two polymers show distinct grazing incidence X-ray scattering spectra indicative of the presence of stacks with different orientation patterns in optimized thin-film BHJ devices. Independent of the packing pattern the spectroscopic data also reveals the existence of polymer aggregates in the pristine polymer films as well as in both blends which trap excitons and hinder their dissociation.

  4. Enzymic oxidation of. cap alpha. ,. beta. -unsaturated alcohols in the side chains of lignin-related aromatic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Iwahara, S. (Kagawa Univ., Kagawa-ken, Japan); Nishihira, T.; Jomori, T.; Kuwahara, M.; Higuchi, T.


    An enzyme which catalyzed oxidation of the ..cap alpha..,..beta..-unsaturated primary alcohol group in the side chain of dehydrodiconiferyl alcohol to the corresponding aldehyde was excreted into the culture media by several molds that degraded synthetic lignin-a dehydrogenation polymer of coniferyl alcohol and lignosulfonate. The enzyme produced by Fusarium solani M-13-1, partially purified by gel filtration, specifically oxidized ..cap alpha..,..beta..-unsaturated alcohols in the side chains of lignin-related aromatic compounds such as coniferyl alcohol, cinnamyl alcohol, dehydrodiconiferyl alcohol and guaiacylglycerol-..beta..-coniferyl ether, but did not oxidize aromatic alcohols such as benzyl o-, m- and p-methoxybenzyl, and vanillyl alcohols or aliphatic alcohols such as methanol, ethanol, butanol. The reaction required one mole of oxygen to oxidize one mole of substrate and produced one mole of hydrogen peroxide. It is suggested that this enzyme also oxidizes ..cap alpha..,..beta..-unsaturated alcohol groups in the side chains of high molecular weight lignins.

  5. The Influence of Conjugated Polymer Side Chain Manipulation on the Efficiency and Stability of Polymer Solar Cells

    Directory of Open Access Journals (Sweden)

    Ilona M. Heckler


    Full Text Available The stability of polymer solar cells (PSCs can be influenced by the introduction of particular moieties on the conjugated polymer side chains. In this study, two series of donor-acceptor copolymers, based on bis(thienyldialkoxybenzene donor and benzo[c][1,2,5]thiadiazole (BT or thiazolo[5,4-d]thiazole (TzTz acceptor units, were selected toward effective device scalability by roll-coating. The influence of the partial exchange (5% or 10% of the solubilizing 2-hexyldecyloxy by alternative 2-phenylethoxy groups on efficiency and stability was investigated. With an increasing 2-phenylethoxy ratio, a decrease in solar cell efficiency was observed for the BT-based series, whereas the efficiencies for the devices based on the TzTz polymers remained approximately the same. The photochemical degradation rate for PSCs based on the TzTz polymers decreased with an increasing 2-phenylethoxy ratio. Lifetime studies under constant sun irradiance showed a diminishing initial degradation rate for the BT-based devices upon including the alternative side chains, whereas the (more stable TzTz-based devices degraded at a faster rate from the start of the experiment upon partly exchanging the side chains. No clear trends in the degradation behavior, linked to the copolymer structural changes, could be established at this point, evidencing the complex interplay of events determining PSCs’ lifetime.

  6. The Influence of Conjugated Polymer Side Chain Manipulation on the Efficiency and Stability of Polymer Solar Cells. (United States)

    Heckler, Ilona M; Kesters, Jurgen; Defour, Maxime; Madsen, Morten V; Penxten, Huguette; D'Haen, Jan; Van Mele, Bruno; Maes, Wouter; Bundgaard, Eva


    The stability of polymer solar cells (PSCs) can be influenced by the introduction of particular moieties on the conjugated polymer side chains. In this study, two series of donor-acceptor copolymers, based on bis(thienyl)dialkoxybenzene donor and benzo[c][1,2,5]thiadiazole (BT) or thiazolo[5,4-d]thiazole (TzTz) acceptor units, were selected toward effective device scalability by roll-coating. The influence of the partial exchange (5% or 10%) of the solubilizing 2-hexyldecyloxy by alternative 2-phenylethoxy groups on efficiency and stability was investigated. With an increasing 2-phenylethoxy ratio, a decrease in solar cell efficiency was observed for the BT-based series, whereas the efficiencies for the devices based on the TzTz polymers remained approximately the same. The photochemical degradation rate for PSCs based on the TzTz polymers decreased with an increasing 2-phenylethoxy ratio. Lifetime studies under constant sun irradiance showed a diminishing initial degradation rate for the BT-based devices upon including the alternative side chains, whereas the (more stable) TzTz-based devices degraded at a faster rate from the start of the experiment upon partly exchanging the side chains. No clear trends in the degradation behavior, linked to the copolymer structural changes, could be established at this point, evidencing the complex interplay of events determining PSCs' lifetime.

  7. Effects of branched-chain amino acids and carbohydrate on fatigue during intermittent, high-intensity running. (United States)

    Davis, J M; Welsh, R S; De Volve, K L; Alderson, N A


    Experimental support for the hypothesized benefits of BCAA supplements on endurance performance is limited. However, it is theorized that the benefits may be enhanced if 1) BCAA are taken along with a pre-event carbohydrate meal as well as during exercise, and 2) the exercise is intermittent in nature. This study tested the effects of ingesting carbohydrate beverages with and without BCAA before and during intermittent high-intensity running to fatigue. Eight subjects performed 3 exercise trials consisting of intermittent shuttle running (walking, sprinting, and running) to fatigue. Subjects drank either carbohydrate drinks given 1 h before (5 mL/kg, 18% carbohydrate) and during exercise (2 mL/kg, 6% carbohydrate) (CHO), carbohydrate drinks with BCAA (7 g) added to the portions consumed 1 h before and immediately before exercise (CHO+BCAA), or flavored water placebos (P). Subjects ran longer when fed either CHO or CHO+BCAA as compared to P, with no differences between CHO and CHO+BCAA. CHO and CHO+BCAA also had higher plasma glucose and insulin, and lower FFA (p basketball, and hockey. They do not, however, support the hypothesis of an added benefit of BCAA supplements.

  8. Impact of the Nature of the Side-Chains on the Polymer-Fullerene Packing in the Mixed Regions of Bulk Heterojunction Solar Cells

    KAUST Repository

    Wang, Tonghui


    Polymer-fullerene packing in mixed regions of a bulk heterojunction solar cell is expected to play a major role in exciton-dissociation, charge-separation, and charge-recombination processes. Here, molecular dynamics simulations are combined with density functional theory calculations to examine the impact of nature and location of polymer side-chains on the polymer-fullerene packing in mixed regions. The focus is on poly-benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione (PBDTTPD) as electron-donating material and [6,6]-phenyl-C61-butyric acid methyl ester (PC61BM) as electron-accepting material. Three polymer side-chain patterns are considered: i) linear side-chains on both benzodithiophene (BDT) and thienopyrroledione (TPD) moieties; ii) two linear side-chains on BDT and a branched side-chain on TPD; and iii) two branched side-chains on BDT and a linear side-chain on TPD. Increasing the number of branched side-chains is found to decrease the polymer packing density and thereby to enhance PBDTTPD–PC61 BM mixing. The nature and location of side-chains are found to play a determining role in the probability of finding PC61BM molecules close to either BDT or TPD. The electronic couplings relevant for the exciton-dissociation and charge-recombination processes are also evaluated. Overall, the findings are consistent with the experimental evolution of the PBDTTPD–PC61BM solar-cell performance as a function of side-chain patterns. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

  9. Oxidative one-carbon cleavage of the octyl side chain of olanexidine, a novel antimicrobial agent, in dog liver microsomes. (United States)

    Umehara, K; Shimokawa, Y; Koga, T; Ohtani, T; Miyamoto, G


    1. The oxidative one-carbon cleavage reaction in the octyl side chain of olanexidine [1-(3,4-dichlorobenzyl)-5-octylbiguanide], a new potent biguanide antiseptic, was characterized in dog liver microsomes. 2. Olanexidine was initially biotransformed to a monohydroxylated metabolite, 8-[5-(3,4-dichlorobenzyl)-1-biguanidino]-2-octanol (DM-215), and DM-215 was subsequently oxidized to the diol derivative, 8-[5-(3,4-dichlorobenzyl)-1-biguanidino]-1,2-octandiol (DM-220). DM-220 was further biotransformed to 2-hydroxy aldehyde derivative, 2-hydroxy carboxylic acid derivative, and an oxidative C-1-C-2 bond cleavage metabolite, 7-[5-(3,4-dichlorobenzyl)-1-biguanidino] heptanoic acid [DM-223 (C7), a seven-carbon chain derivative], after incubation with dog liver microsomes. 3. DM-223 formation required NADPH as a cofactor and was inhibited by quinidine and quinine, relatively selective inhibitors of CYP2D subfamilies in dogs. 4. The results suggest that the one-carbon fragment of the octyl side chain of olanexidine could be removed by the oxidative C-C bond cleavage with the possible involvement of cytochrome P450 systems such as CYP2D subfamily. This oxidative C-C bond cleavage reaction by cytochrome P450s could play an important role in the removal of one-carbon fragment of other drugs or endogenous compounds containing aliphatic chains.

  10. Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL.

    Directory of Open Access Journals (Sweden)

    Josef Houser

    Full Text Available Protein-carbohydrate interactions are very often mediated by the stacking CH-π interactions involving the side chains of aromatic amino acids such as tryptophan (Trp, tyrosine (Tyr or phenylalanine (Phe. Especially suitable for stacking is the Trp residue. Analysis of the PDB database shows Trp stacking for 265 carbohydrate or carbohydrate like ligands in 5 208 Trp containing motives. An appropriate model system to study such an interaction is the AAL lectin family where the stacking interactions play a crucial role and are thought to be a driving force for carbohydrate binding. In this study we present data showing a novel finding in the stacking interaction of the AAL Trp side chain with the carbohydrate. High resolution X-ray structure of the AAL lectin from Aleuria aurantia with α-methyl-l-fucoside ligand shows two possible Trp side chain conformations with the same occupation in electron density. The in silico data shows that the conformation of the Trp side chain does not influence the interaction energy despite the fact that each conformation creates interactions with different carbohydrate CH groups. Moreover, the PDB data search shows that the conformations are almost equally distributed across all Trp-carbohydrate complexes, which would suggest no substantial preference for one conformation over another.

  11. Thermoresponsive Poly(2-oxazoline) Molecular Brushes by Living Ionic Polymerization: Kinetic Investigations of Pendant Chain Grafting and Cloud Point Modulation by Backbone and Side Chain Length Variation

    KAUST Repository

    Zhang, Ning


    Molecular brushes of poly(2-oxazoline)s were prepared by living anionic polymerization of 2-iso-propenyl-2-oxazoline to form the backbone and subsequent living cationic ring-opening polymerization of 2-n- or 2-iso-propyl-2-oxazoline for pendant chain grafting. In situ kinetic studies indicate that the initiation efficiency and polymerization rates are independent from the number of initiator functions per initiator molecule. This was attributed to the high efficiency of oxazolinium salt and the stretched conformation of the backbone, which is caused by the electrostatic repulsion of the oxazolinium moieties along the macroinitiator. The resulting molecular brushes showed thermoresponsive properties, that is, having a defined cloud point (CP). The dependence of the CP as a function of backbone and side chain length as well as concentration was studied. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Inversion of the stereochemistry around the sulfur atom of the axial methionine side chain through alteration of amino acid side chain packing in Hydrogenobacter thermophilus cytochrome C552 and its functional consequences. (United States)

    Tai, Hulin; Tonegawa, Ken; Shibata, Tomokazu; Hemmi, Hikaru; Kobayashi, Nagao; Yamamoto, Yasuhiko


    In cytochrome c, the coordination of the axial Met Sδ atom to the heme Fe atom occurs in one of two distinctly different stereochemical manners, i.e., R and S configurations, depending upon which of the two lone pairs of the Sδ atom is involved in the bond; hence, the Fe-coordinated Sδ atom becomes a chiral center. In this study, we demonstrated that an alteration of amino acid side chain packing induced by the mutation of a single amino acid residue, i.e., the A73V mutation, in Hydrogenobacter thermophilus cytochrome c552 (HT) forces the inversion of the stereochemistry around the Sδ atom from the R configuration [Travaglini-Allocatelli, C., et al. (2005) J. Biol. Chem. 280, 25729-25734] to the S configuration. Functional comparison between the wild-type HT and the A73V mutant possessing the R and S configurations as to the stereochemistry around the Sδ atom, respectively, demonstrated that the redox potential (Em) of the mutant at pH 6.00 and 25 °C exhibited a positive shift of ∼20 mV relative to that of the wild-type HT, i.e., 245 mV, in an entropic manner. Because these two proteins have similar enthalpically stabilizing interactions, the difference in the entropic contribution to the Em value between them is likely to be due to the effect of the conformational alteration of the axial Met side chain associated with the inversion of the stereochemistry around the Sδ atom due to the effect of mutation on the internal mobility of the loop bearing the axial Met. Thus, the present study demonstrated that the internal mobility of the loop bearing the axial Met, relevant to entropic control of the redox function of the protein, is affected quite sensitively by the contextual stereochemical packing of amino acid side chains in the proximity of the axial Met.

  13. Side-chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains

    DEFF Research Database (Denmark)

    Haq, S Raza; Chi, Celestine N; Bach, Anders


    used short peptides as a model system for intrinsically disordered proteins. Linear free-energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate......-limiting barrier for binding, in a cooperative fashion. This finding suggests that these disordered peptides first form a weak encounter complex with non-native interactions. The data do not support the recent notion that the affinities of intrinsically disordered proteins towards their targets are generally...

  14. Side chain engineering of fused aromatic thienopyrazine based low band-gap polymers for enhanced charge carrier mobility

    KAUST Repository

    Mondal, Rajib


    A strategic side-chain engineering approach leads to the two orders of magnitude enhancement of charge carrier mobility in phenanthrene based fused aromatic thienopyrazine polymers. Hole carrier mobility up to 0.012 cm 2/Vs can be obtained in thin film transistor devices. Polymers were also utilized to fabricate bulk heterojunction photovoltaic devices and the maximum PCE obtained in these OPV\\'s was 1.15%. Most importantly, performances of the devices were correlated with thin morphological analysis performed by atomic force microscopy and grazing incidence X-ray scattering. © 2011 The Royal Society of Chemistry.

  15. Proton conducting graft copolymers with tunable length and density of phosphonated side chains for fuel cell membranes

    DEFF Research Database (Denmark)

    Dimitrov, Ivaylo; Takamuku, Shogo; Jankova Atanasova, Katja


    matrix. increasing the ionic groups content in the graft copolymers led to extensive membrane swelling. To improve the dimensional stability the graft copolymers were blended with pyridine-modified polysulfone. The blend membranes were transparent with formation of nano-phase domains as revealed from TEM...... gravimetrical analyses. The proton conductivity of membrane prepared from the graft copolymer with the shortest phosphonated side chains was 134 mS cm(-1) at 100 degrees C under fully immersed conditions. The graft copolymer TEM image shows a nanophase separation of ion-rich segments within the polysulfone...

  16. Phase behaviors, molecular and supramolecular structures in polymers containing rigid-rod backbones with cyanobiphenyl side chains (United States)

    Ruan, Jrjeng

    One of the most important and challenging topics in materials chemistry involves designing nano-structures in synthetic materials via self-assembly for various highly technical applications. A specially designed combined liquid crystalline polymer containing a polyester backbone with cyanobiphenyl side chains has been studied in aspects of phase behaviors and crystal structures. The triclinic crystal phases identified in this series of polymer are all found to be constricted by 4-monomer unit cells. This discovery of 4-monomer triclinic unit cells motivates a search for the existence of supramolecular phases and understanding the possible molecular packing. A series of newly designed polyimides, which are composed of aromatic polyimide backbones with 4-cyanobiphenyl mesogens on the side chains has been synthesized. This series of polymers possesses a lesser degree of coupling between the backbones and side chains, which indicates the possibility of microphase separation between them. The representative polyimides of BPDA-7CBBP and BPDA-11CBBP in this series, in which 4-cyanobiphenyl side chains are connected onto the backbones through seven and eleven methylene units respectively have systematically studied in this research. Two crystal forms were recognized in BPDA-11CBBA, and one of them possesses six repeating units in one monoclinic unit cell. Moreover, the existence of a supramolecular phase has been proposed based on 2D WAXD fiber patterns. In the case of BPDA-7CBBP, three crystal forms were identified: two of them are constructed by triclinic lattices with large unit cells. The numbers of repeating units in those unit cells are seven and eight, respectively. Complicated phase behaviors including a second-order transition between the supramolecular phase and a high-order liquid crystal phase have been explored. The fact that large unit cells in both polymers with the numbers of repeating units in unit cells being 6, 7, and 8 leads to an important issue for

  17. Proton clouds to measure long-range contacts between nonexchangeable side chain protons in solid-state NMR. (United States)

    Sinnige, Tessa; Daniëls, Mark; Baldus, Marc; Weingarth, Markus


    We show that selective labeling of proteins with protonated amino acids embedded in a perdeuterated matrix, dubbed 'proton clouds', provides general access to long-range contacts between nonexchangeable side chain protons in proton-detected solid-state NMR, which is important to study protein tertiary structure. Proton-cloud labeling significantly improves spectral resolution by simultaneously reducing proton line width and spectral crowding despite a high local proton density in clouds. The approach is amenable to almost all canonical amino acids. Our method is demonstrated on ubiquitin and the β-barrel membrane protein BamA.

  18. Genes Involved in Cell Wall Localization and Side Chain Formation of Rhamnose-Glucose Polysaccharide in Streptococcus mutans


    Yamashita, Yoshihisa; Tsukioka, Yuichi; Tomihisa, Kiyotaka; Nakano, Yoshio; Koga, Toshihiko


    We identified in Streptococcus mutans six new genes (rgpA through rgpF), whose disruption results in a loss of serotype-specific antigenicity, specified by the glucose side chains of rhamnose-glucose polysaccharide from the cell wall. Rhamnose and glucose content of the cell wall decreased drastically in all these disruption mutants, except that in the rgpE mutant only the glucose content decreased. RgpC and RgpD are homologous to ATP-binding cassette transporter components and may be involve...

  19. Total synthesis of a CD-ring: side-chain building block for preparing 17-epi-calcitriol derivatives from the Hajos-Parrish dione. (United States)

    Michalak, Karol; Wicha, Jerzy


    An efficient synthesis of the key building block for 17-epi-calctriol from the Hajos-Parrish dione involving a sequence of diastereoselective transformation of the azulene core and the side-chain construction is presented.

  20. Charge Transfer Dissociation (CTD) Mass Spectrometry of Peptide Cations: Study of Charge State Effects and Side-Chain Losses (United States)

    Li, Pengfei; Jackson, Glen P.


    1+, 2+, and 3+ precursors of substance P and bradykinin were subjected to helium cation irradiation in a 3D ion trap mass spectrometer. Charge exchange with the helium cations produces a variety of fragment ions, the number and type of which are dependent on the charge state of the precursor ions. For 1+ peptide precursors, fragmentation is generally restricted to C-CO backbone bonds ( a and x ions), whereas for 2+ and 3+ peptide precursors, all three backbone bonds (C-CO, C-N, and N-Cα) are cleaved. The type of backbone bond cleavage is indicative of possible dissociation channels involved in CTD process, including high-energy, kinetic-based, and ETD-like pathways. In addition to backbone cleavages, amino acid side-chain cleavages are observed in CTD, which are consistent with other high-energy and radical-mediated techniques. The unique dissociation pattern and supplementary information available from side-chain cleavages make CTD a potentially useful activation method for the structural study of gas-phase biomolecules.

  1. Z-Selective olefin metathesis on peptides: investigation of side-chain influence, preorganization, and guidelines in substrate selection. (United States)

    Mangold, Shane L; O'Leary, Daniel J; Grubbs, Robert H


    Olefin metathesis has emerged as a promising strategy for modulating the stability and activity of biologically relevant compounds; however, the ability to control olefin geometry in the product remains a challenge. Recent advances in the design of cyclometalated ruthenium catalysts has led to new strategies for achieving such control with high fidelity and Z selectivity, but the scope and limitations of these catalysts on substrates bearing multiple functionalities, including peptides, remained unexplored. Herein, we report an assessment of various factors that contribute to both productive and nonproductive Z-selective metathesis on peptides. The influence of sterics, side-chain identity, and preorganization through peptide secondary structure are explored by homodimerization, cross metathesis, and ring-closing metathesis. Our results indicate that the amino acid side chain and identity of the olefin profoundly influence the activity of cyclometalated ruthenium catalysts in Z-selective metathesis. The criteria set forth for achieving high conversion and Z selectivity are highlighted by cross metathesis and ring-closing metathesis on diverse peptide substrates. The principles outlined in this report are important not only for expanding the scope of Z-selective olefin metathesis to peptides but also for applying stereoselective olefin metathesis in general synthetic endeavors.

  2. A salt water battery with high stability and charging rates made from solution processed conjugated polymers with polar side chains

    KAUST Repository

    Moia, Davide


    We report a neutral salt water based battery which uses p-type and n-type solution processed polymer films as the cathode and the anode of the cell. The specific capacity of the electrodes (approximately 30 mAh cm-3) is achieved via formation of bipolarons in both the p-type and n-type polymers. By engineering ethylene glycol and zwitterion based side chains attached to the polymer backbone we facilitate rapid ion transport through the non-porous polymer films. This, combined with efficient transport of electronic charge via the conjugated polymer backbones, allowed the films to maintain constant capacity at high charge and discharge rates (>1000 C-rate). The electrodes also show good stability during electrochemical cycling (less than 30% decrease in capacity over >1000 cycles) and an output voltage up to 1.4 V. The performance of these semiconducting polymers with polar side-chains demonstrates the potential of this material class for fast-charging, water based electrochemical energy storage devices.

  3. Triblock Copolymers with Grafted Fluorine-Free Amphiphilic Non-Ionic Side Chains for Antifouling and Fouling-Release Applications

    Energy Technology Data Exchange (ETDEWEB)

    Y Cho; H Sundaram; C Weinman; M Paik; M Dimitriou; J Finlay; M Callow; J Callow; E Kramer; C Ober


    Fluorine-free, amphiphilic, nonionic surface active block copolymers (SABCs) were synthesized through chemical modification of a polystyrene-block-poly(ethylene-ran-butylene)-block-polyisoprene triblock copolymer precursor with selected amphiphilic nonionic Brij and other surfactants. Amphiphilicity was imparted by a hydrophobic aliphatic group combined with a hydrophilic poly(ethylene glycol) (PEG) group-containing moiety. The surfaces were characterized by dynamic water contact angle, atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and near edge X-ray absorption fine structure (NEXAFS) analysis. In biofouling assays, settlement (attachment) of both spores of the green alga Ulva and cells of the diatom Navicula on SABCs modified with Brij nonionic side chains was significantly reduced relative to a PDMS standard, with a nonionic surfactant combining a PEG group and an aliphatic moiety demonstrating the best performance. Additionally, a fouling-release assay using sporelings (young plants) of Ulva and Navicula suggested that the SABC derived from nonionic Brij side chains also out-performed PDMS as a fouling-release material. Good antifouling and fouling-release properties were not demonstrated for the other two amphiphilic surfaces derived from silicone and aromatic group containing nonionic surfactants included in this study. The results suggest that small differences in chemical surface functionality impart more significant changes with respect to the antifouling settlement and fouling-release performance of materials than overall wettability behavior.

  4. Synthesis and Photophysical Properties of Soluble Low-Bandgap Thienothiophene Polymers with Various Alkyl Side-Chain Lengths

    Energy Technology Data Exchange (ETDEWEB)

    Bae, W. J.; Scilla, C.; Duzhko, V. V.; Jo, Jang; Coughlin, E. B.


    We report the facile synthesis and characterization of a class of thienothiophene polymers with various lengths of alkyl side chains. A series of 2-alkylthieno[3,4-b]thiophene monomers (Ttx) have been synthesized in a two-step protocol in an overall yield of 28–37%. Poly(2-alkylthieno[3,4-b]thiophenes) (PTtx, alkyl: pentyl, hexyl, heptyl, octyl, and tridecyl) were synthesized by oxidative polymerization with FeCl₃ or via Grignard metathesis (GRIM) polymerization methods. The polymers are readily soluble in common organic solvents. The polymers synthesized by GRIM polymerization method (PTtx-G) have narrower molecular weight distribution (Ð) with lower molecular weight (Mn) than those synthesized by oxidative polymerization (PTtx-O). The band structures of the polymers with various lengths of alkyl side chains were investigated by UV–vis spectroscopy, cyclic voltammetry, and ultraviolet photoelectron spectroscopy. These low-bandgap polymers are good candidates for organic transistors, organic light-emitting diodes, and organic photovoltaic cells.

  5. Amide side chain amphiphilic polymers disrupt surface established bacterial bio-films and protect mice from chronic Acinetobacter baumannii infection. (United States)

    Uppu, Divakara S S M; Samaddar, Sandip; Ghosh, Chandradhish; Paramanandham, Krishnamoorthy; Shome, Bibek R; Haldar, Jayanta


    Bacterial biofilms represent the root-cause of chronic or persistent infections in humans. Gram-negative bacterial infections due to nosocomial and opportunistic pathogens such as Acinetobacter baumannii are more difficult to treat because of their inherent and rapidly acquiring resistance to antibiotics. Due to biofilm formation, A. baumannii has been noted for its apparent ability to survive on artificial surfaces for an extended period of time, therefore allowing it to persist in the hospital environment. Here we report, maleic anhydride based novel cationic polymers appended with amide side chains that disrupt surface established multi-drug resistant A. baumannii biofilms. More importantly, these polymers significantly (p polymers also show potent antibacterial efficacy against methicillin resistant Staphylococcus aureus (MRSA), vancomycin resistant Enterococci (VRE) and multi-drug resistant clinical isolates of A. baumannii with minimal toxicity to mammalian cells. We observe that optimal hydrophobicity dependent on the side chain chemical structure of these polymers dictate the selective toxicity to bacteria. Polymers interact with the bacterial cell membranes by causing membrane depolarization, permeabilization and energy depletion. Bacteria develop rapid resistance to erythromycin and colistin whereas no detectable development of resistance occurs against these polymers even after several passages. These results suggest the potential use of these polymeric biomaterials in disinfecting biomedical device surfaces after the infection has become established and also for the topical treatment of chronic bacterial infections. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Modulation of the transglycosylation activity of plant family GH18 chitinase by removing or introducing a tryptophan side chain. (United States)

    Umemoto, Naoyuki; Ohnuma, Takayuki; Osawa, Takuo; Numata, Tomoyuki; Fukamizo, Tamo


    Transglycosylation (TG) activity of a family GH18 chitinase from the cycad, Cycas revoluta, (CrChiA) was modulated by removing or introducing a tryptophan side chain. The removal from subsite +3 through mutation of Trp168 to alanine suppressed TG activity, while introduction into subsite +1 through mutation of Gly77 to tryptophan (CrChiA-G77W) enhanced TG activity. The crystal structures of an inactive double mutant of CrChiA (CrChiA-G77W/E119Q) with one or two N-acetylglucosamine residues occupying subsites +1 or +1/+2, respectively, revealed that the Trp77 side chain was oriented toward +1 GlcNAc to be stacked with it face-to-face, but rotated away from subsite +1 in the absence of GlcNAc at the subsite. Aromatic residues in the aglycon-binding site are key determinants of TG activity of GH18 chitinases. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  7. Controlling the morphology of side chain liquid crystalline block copolymer thin films through variations in liquid crystalline content. (United States)

    Verploegen, Eric; Zhang, Tejia; Jung, Yeon Sik; Ross, Caroline; Hammond, Paula T


    In this paper, we describe methods for manipulating the morphology of side-chain liquid crystalline block copolymers through variations in the liquid crystalline content. By systematically controlling the covalent attachment of side chain liquid crystals to a block copolymer (BCP) backbone, the morphology of both the liquid crystalline (LC) mesophase and the phase-segregated BCP microstructures can be precisely manipulated. Increases in LC functionalization lead to stronger preferences for the anchoring of the LC mesophase relative to the substrate and the intermaterial dividing surface. By manipulating the strength of these interactions, the arrangement and ordering of the ultrathin film block copolymer nanostructures can be controlled, yielding a range of morphologies that includes perpendicular and parallel cylinders, as well as both perpendicular and parallel lamellae. Additionally, we demonstrate the utilization of selective etching to create a nanoporous liquid crystalline polymer thin film. The unique control over the orientation and order of the self-assembled morphologies with respect to the substrate will allow for the custom design of thin films for specific nanopatterning applications without manipulation of the surface chemistry or the application of external fields.

  8. Length increase of the side chain of idoxifene does not improve its antagonistic potency in breast-cancer cell lines. (United States)

    Jin, L; Legros, N; Leclercq, G; Hardcastle, I R; Jarman, M


    Linkage of specific residues onto steroidal estrogens through a long aliphatic side chain leads to "pure antiestrogens" devoid of residual estrogenic activity. Therefore, we assessed whether an increase in the length of the side chain of the triphenylethylenic antiestrogen idoxifene might increase its antagonistic potency. Culture of MCF-7 and tamoxifen-resistant variant RTX6 cells in the presence of CB 7675, a (CH2)8 derivative of idoxifene [(CH2)2], ruled out this possibility. This compound partly blocked MCF-7 cell growth only at 10(-6) M to almost the same extent as tamoxifen and failed to inhibit the growth of RTX6 cells, whereas the pure antiestrogen RU 58 668 was effective on both cell lines at much lower concentration. This absence of improvement was reflected in the observation of an efficiency for down-regulating progesterone receptor no better than that of tamoxifen. Pure antiestrogens are known to down-regulate the estrogen receptor, whereas triphenylethylenic antiestrogens up-regulate the receptor; CB 7675 behaves as the latter in agreement with its lack of strong antagonistic activity.

  9. Self-Assembly of Amphiphilic Block Copolypeptoids with C 2 -C 5 Side Chains in Aqueous Solution

    KAUST Repository

    Fetsch, Corinna


    © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Nowadays, amphiphilic molecules play an important role in our life. In medical applications, amphiphilic block copolymers have attracted much attention as excipients in drug delivery systems. Here, the polymers are used as emulsifiers, micelles, or polymersomes with a hydrophilic corona block and a hydrophobic core or membrane. The aggregation behavior in aqueous solutions of a series of different amphiphilic block copolypeptoids comprising polysarcosine as a hydrophilic part is here reported. The formation of aggregates is investigated with 1H NMR spectroscopy and dynamic light scattering, and the determination of the critical micelle concentration (cmc) is performed using pyrene fluorescence spectroscopy. For the different block copolypeptoids cmc values ranging from 0.6 × 10-6 M to 0.1 × 10-3 M are found. The tendency to form micelles increases with increasing hydrophobicity at the nitrogen side chain in the hydrophobic moiety. Furthermore, in the case of the same hydrophobic side chain, a decreasing hydrophilic/lipophilic balance leads to the formation of larger aggregates. The aggregates formed in the buffer are able to solubilize the hydrophobic model compounds Reichardt\\'s dye and pyrene, and exhibit versatile microenvironments. Final investigations about the cytotoxicity reveal that the block copolypeptoids are well tolerated by mammalian cells up to high concentrations.

  10. Novel Random PBS-Based Copolymers Containing Aliphatic Side Chains for Sustainable Flexible Food Packaging

    Directory of Open Access Journals (Sweden)

    Giulia Guidotti


    Full Text Available In the last decade, there has been an increased interest from the food packaging industry toward the development and application of biodegradable and biobased plastics, to contribute to the sustainable economy and to reduce the huge environmental problem afflicting the planet. In this framework, the present paper describes the synthesis of novel PBS (poly(butylene succinate-based random copolymers with different composition containing glycol sub-units characterized by alkyl pendant groups of different length. The prepared samples were subjected to molecular, thermal, diffractometric and mechanical characterization. The barrier performances to O2, CO2 and N2 gases were also evaluated, envisioning for these new materials an application in food packaging. The presence of the side alkyl groups did not alter the thermal stability, whereas it significantly reduced the sample crystallinity degree, making these materials more flexible. The barrier properties were found to be worse than PBS; however, some of them were comparable to, or even better than, those of Low Density Polyethylene (LDPE, widely employed for flexible food packaging. The entity of variations in the final properties due to copolymerization were more modest in the case of the co-unit with short side methyl groups, which, when included in the PBS crystal lattice, causes a more modest decrement of crystallinity degree.

  11. New insights into the structure of (1→3,1→6-β-D-glucan side chains in the Candida glabrata cell wall.

    Directory of Open Access Journals (Sweden)

    Douglas W Lowman

    Full Text Available β-Glucan is a (1→3-β-linked glucose polymer with (1→6-β-linked side chains and a major component of fungal cell walls. β-Glucans provide structural integrity to the fungal cell wall. The nature of the (1-6-β-linked side chain structure of fungal (1→3,1→6-β-D-glucans has been very difficult to elucidate. Herein, we report the first detailed structural characterization of the (1→6-β-linked side chains of Candida glabrata using high-field NMR. The (1→6-β-linked side chains have an average length of 4 to 5 repeat units spaced every 21 repeat units along the (1→3-linked polymer backbone. Computer modeling suggests that the side chains have a bent curve structure that allows for a flexible interconnection with parallel (1→3-β-D-glucan polymers, and/or as a point of attachment for proteins. Based on these observations we propose new approaches to how (1→6-β-linked side chains interconnect with neighboring glucan polymers in a manner that maximizes fungal cell wall strength, while also allowing for flexibility, or plasticity.

  12. Combined main-chain/side-chain ionic liquid crystalline polymer based on ‘jacketing’ effect: Design, synthesis, supra-molecular self-assembly and photophysical properties

    Directory of Open Access Journals (Sweden)

    L. Weng


    Full Text Available Reasonably fabricating ordered structures of ionic polymers is very important for the development of novel functional materials. By combining the ions and liquid cry stalline polymer, we successfully designed and synthesized a series of novel combined main-chain/side-chain ionic liquid crystalline polymer (MCSC-ILCPs containing imidazolium groups and different counter-anions, poly (2,5-bis{[6-(4-butoxy-4'-imidazolium biphenylhexyl]oxycarbonyl}styrene salts poly(BImBHCS-X with the following types of counter-anions (Br¯, BF4¯, PF6¯ and TFSI¯. Combined technologies confirmed the chemical structures of the monomers and polymers with imidazolium cation and different counter-anions. Differential scanning calorimetry (DSC, polarized light microscopy (PLM and one- and two-dimensional wide-angle X-ray diffraction (1D and 2D WAXD results illustrated that the LC structures and the transitions of ordered structures depended on the nature of the counter-anion employed. The polymers with Br¯ and BF4¯ counter-anions exhibited smectic A (SmA LC behavior below the isotropic temperature. The another one, poly(BImBHCS–TFSI with the large volume of the TFSI¯ anion destroyed the packing of the LC ordered structure resulting in an amorphous structure. The photophysical properties of the polymers prepared can be adjusted by tuning the ionic interaction of the polymers by switching the counter-anion.

  13. Conformational Analysis of the Oligosaccharides Related to Side Chains of Holothurian Fucosylated Chondroitin Sulfates

    Directory of Open Access Journals (Sweden)

    Alexey G. Gerbst


    Full Text Available Anionic polysaccharides fucosylated chondroitin sulfates (FCS from holothurian species were shown to affect various biological processes, such as metastasis, angiogenesis, clot formation, thrombosis, inflammation, and some others. To understand the mechanism of FCSs action, knowledge about their spatial arrangement is required. We have started the systematic synthesis, conformational analysis, and study of biological activity of the oligosaccharides related to various fragments of these types of natural polysaccharides. In this communication, five molecules representing distinct structural fragments of chondroitin sulfate have been studied by means of molecular modeling and NMR. These are three disaccharides and two trisaccharides containing fucose and glucuronic acid residues with one sulfate group per each fucose residue or without it. Long-range C–H coupling constants were used for the verification of the theoretical models. The presence of two conformers for both linkage types was revealed. For the Fuc–GlA linkage, the dominant conformer was the same as described previously in a literature as the molecular dynamics (MD average in a dodechasaccharide FCS fragment representing the backbone chain of the polysaccharide including GalNAc residues. This shows that the studied oligosaccharides, in addition to larger ones, may be considered as reliable models for Quantitative Structure-Activity Relationship (QSAR studies to reveal pharmacophore fragments of FCS.

  14. 5-Ethynyl-2'-deoxycytidine: a DNA building block with a 'clickable' side chain. (United States)

    Seela, Frank; Mei, Hui; Xiong, Hai; Budow, Simone; Eickmeier, Henning; Reuter, Hans


    The title compound [systematic name: 4-amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-5-ethynylpyrimidin-2(1H)-one], C(11)H(13)N(3)O(4), shows two conformations in the crystalline state. The N-glycosylic bonds of both conformers adopt similar conformations, with χ = -149.2 (1)° for conformer (I-1) and -151.4 (1)° for conformer (I-2), both in the anti range. The sugar residue of (I-1) shows a C2'-endo envelope conformation ((2)E, S-type), with P = 164.7 (1)° and τ(m) = 36.9 (1)°, while (I-2) shows a major C3'-exo sugar pucker (C3'-exo-C2'-endo, (3)T(2), S-type), with P = 189.2 (1)° and τ(m) = 33.3 (1)°. Both conformers participate in the formation of a layered three-dimensional crystal structure with a chain-like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.

  15. Effect of different forage species supplemented with two carbohydrate sources on short and medium chain fatty acids in sheep milk

    Directory of Open Access Journals (Sweden)

    G. Piredda


    Full Text Available Sixty four Sarda dairy sheep fed with diets based on fresh forage were allocated to eight groups to evaluate the effect of corn or beet pulp based supplementation on milk fatty acid composition. Four forage species were compared: annual ryegrass (RY, Lolium rigidum Gaudin, sulla (SU, Hedysarum coronarium L., burr medic (BM, Medicago polymorpha L., and garland, a daisy forb, (CH, Chrysanthemum coronarium L.. The supplements were iso-nitrogenous but differed in carbohydrate composition consisting either of 60% (DM of corn (concentrate C or 40% sugar beet pulp (concentrate BP. The supplementation was iso-energetic (500 and 530 g/d, respectively. Overall during winter period (growing stage of the forages SU and RY groups showed higher levels of atherogenicity index and C16:0. In winter period BP outperformed C for palmitic acid. In spring AI showed a trend similar to that of winter. Moreover C concentrate gave a better level of AI and myristic acid than BP. This study confirms that forage species and, to a lesser extent, carbohydrate source in the supplement markedly affect mediumchain FA profile and hence atherogenicity index in sheep milk.

  16. Effect of Anion and Alkyl Side Chain on Structural and Dynamic Features of Ester Functionalized Ionic Liquids: Confirming Nanoscale Organization. (United States)

    Fakhraee, Mostafa; Gholami, Mohammad Reza


    The effects of ester addition on structural and dynamic properties of biodegradable ILs composed of the 1-(alkoxycarbonyl)-3-alkylimidazolium cation ([C 1 COOC n C 1 im] + , n = 1, 2, 4) coupled with [Br] - , [NO 3 ] - , [BF 4 ] - , [PF 6 ] - , [TfO] - , and [Tf 2 N] - are explored using the molecular dynamics (MD) simulations and quantum theory of atoms in molecules (QTAIM) at 400 K. Formation of the intramolecular H bonds between O atoms of the ester group and H atoms of the imidazolium ring as well as the nearest H atom of the alkyl chain to the ester group are disclosed from reduced density gradient (RDG) results. Nanoscale organization that leads to aggregation of the alkyl chain into the uncharged domains and formation of different morphologies can be clearly found by the results of site-site static partial structure factors of cations. Despite the fact that H atoms of the imidazolium ring are more acidic than the nearest H atoms of the alkyl side chain to the ester group, the cation-cation spatial distribution functions (SDFs) and the velocity SDFs demonstrate a reverse trend. This corresponds to the long-range organization of cations and nanoscale arrangement. Transport properties were calculated using the Green-Kubo and Einstein relations. Cations totally diffuse faster than anions and their discrepancies gradually vanish with elongation of the alkyl side chain. The translational motion of the terminal carbon atoms of the ester-functionalized cations decrease when the alkyl group is elongated, whereas the reverse trend is reported for common imidazolium-based ILs. The dynamic heterogeneity of selected ILs is comprehensively investigated by the computing vibrational density of states, van Hove function, and non-Gaussian parameter. Non-Gaussian parameters are finite over the entire time scale for ILs composed of bulkier cations and diverge from zero, verifying the long-lived cage effect. Nanoscale ordering is believed to be responsible for these observations

  17. Synthesis of Peptides from α- and β-Tubulin Containing Glutamic Acid Side-Chain Linked Oligo-Glu with Defined Length

    Directory of Open Access Journals (Sweden)

    Werner Tegge


    Full Text Available Side-chain oligo- and polyglutamylation represents an important posttranslational modification in tubulin physiology. The particular number of glutamate units is related to specific regulatory functions. In this work, we present a method for the synthesis of building blocks for the Fmoc synthesis of peptides containing main chain glutamic acid residues that carry side-chain branching with oligo-glutamic acid. The two model peptide sequences CYEEVGVDSVEGEG-E(E-EEGEEY and CQDATADEQG-E(E-FEEEEGEDEA from the C-termini of mammalian α1- and β1-tubulin, respectively, containing oligo-glutamic acid side-chain branching with lengths of 1 to 5 amino acids were assembled in good yield and purity. The products may lead to the generation of specific antibodies which should be important tools for a more detailed investigation of polyglutamylation processes.

  18. Controlled ring-opening polymerization of substituted episulfides for side-chain functional polysulfide-based amphiphiles. (United States)

    Kuhlmann, Matthias; Singh, Smriti; Groll, Jürgen


    We used initiation solutions of DBU and different thiols for the controlled ring-opening homo- and copolymerization of ethoxy ethyl thio glycidyl ether (EETGE) and allyl thio glycidyl ether (ATGE) to side-chain multifunctional polysulfides. Optimized preparation conditions allow the syntheses of monomodal homopolysulfides and monomodal polysulfide-block-mPEG copolymers. Furthermore, copolymers of EETGE and mPEG are firstly synthesized, characterized, and finally deprotected to yield intact poly(thio glycidol)-block-poly(ethylene glycol) copolymers. These amphiphiles are suitable to form particles in aqueous solutions as confirmed by DLS and cryo-SEM measurements. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Beta-adrenergic blocking agents: substituted phenylalkanolamines. Effect of side-chain length on beta-blocking potency in vitro. (United States)

    Fuhrer, W; Ostermayer, F; Zimmermann, M; Meier, M; Müller, H


    The synthesis of a group of potential beta-blockers bearing a new 5-ethoxysalicylamide substituent on nitrogen is described. These compounds were tested for beta-adrenergic blocking potency in vitro and compared with analogous compounds bearing a tert-butyl group on nitrogen. The new N-substituent increased the beta-blocking potency substantially. In a series of five homologous compounds of the type Ar(CH2)nCHOHCH2NHR (R = 5-ethoxysalicylamide; n = 0-4), two maxima of beta-blocking potency were found for n = 0 and 2. Moreover, the carbon isostere of the corresponding (aryloxy)propanolamine still proved to be a very potent beta-blocker. The ether oxygen in the side chain is therefore not an absolute requirement for activity. Structure-activity relationships are discussed.

  20. Design, synthesis and structure-activity relationships of new triazole derivatives containing N-substituted phenoxypropylamino side chains. (United States)

    Wang, Shengzheng; Jin, Gang; Wang, Wenya; Zhu, Lingjian; Zhang, Yongqiang; Dong, Guoqiang; Liu, Yang; Zhuang, Chunlin; Miao, Zhenyuan; Yao, Jianzhong; Zhang, Wannian; Sheng, Chunquan


    The incidence of invasive fungal infections and resistance to antifungal agents is increasing dramatically. It is highly desirable to develop novel azoles with improved biological profiles. The structure-activity relationship (SAR) of the N-substitutions was investigated in this study. In vitro antifungal activities revealed that sterically large groups were not favored for the N-substitutions. The removal of the N-substitutions had little effect on the antifungal activity. Two compounds with free amine group (i.e.9a and 10a) showed excellent activity with broad antifungal spectrum. The SAR results were supported by molecular docking and the N-substitutions were found to be important for the conformation of the side chains. The SAR and binding mode of the azoles are useful for further lead optimization. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  1. Design, synthesis and antifungal activity of novel triazole derivatives containing substituted 1,2,3-triazole-piperdine side chains. (United States)

    Jiang, Zhigan; Gu, Julin; Wang, Chen; Wang, Shengzheng; Liu, Na; Jiang, Yan; Dong, Guoqiang; Wang, Yan; Liu, Yang; Yao, Jianzhong; Miao, Zhenyuan; Zhang, Wannian; Sheng, Chunquan


    Due to increasing incidence of invasive fungal infections and severe drug resistance to triazole antifungal agents, a series of novel antifungal triazoles with substituted triazole-piperidine side chains were designed and synthesized. Most of the target compounds showed good inhibitory activity against a variety of clinically important fungal pathogens. In particular, compounds 8t and 8v were highly active against Candida albicans and Cryptococcus neoformans with MIC values in the range of 0.125 μg/mL to 0.0125 μg/mL. They represent promising leads for the development of new generation of triazole antifungal agents. Molecular docking studies revealed that the target compounds interacted with CACYP51 mainly through hydrophobic and Van der Waals interactions. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  2. Improved specificity of serum phosphatidylcholine detection based on side-chain losses during negative electrospray ionization tandem mass spectrometry. (United States)

    Ritchie, Shawn A; Jayasinge, Dushmanthi; Wang, Li; Goodenowe, Dayan B


    Many current tandem mass spectrometry (MS) methods for measuring phosphatidylcholines (PtdChos) rely only on precursor ion scanning of the common 184 m/z phosphocholine fragment with positive electrospray ionization (+ESI), and thus measure pools of PtdChos rather than specific isoforms. In this paper, we developed and compared an isotope dilution, tandem MS method capable of quantifying PtdChos based on specific fatty acid side-chains to the traditional 184 m/z method. The method is based on the detection of PtdCho ammonium formate (AmF) adduct as parent ions and fatty acid fragment daughter ions under negative electrospray ionization (-ESI). Accuracy, imprecision, and recovery were below 15 %, with acceptable linearity (R 2 > 0.99) up to 5 μg/mL. We used the method to analyze the distributions of PtdChos with common side-chain combinations among 60 subjects and showed that it was possible for two individuals to have the same PtdCho pool concentration based on detection of the 184 m/z fragment, but up to a fourfold difference in the levels of specific isoforms comprising the pool based on our method. We then compared the results of both methods across 572 patients with mild cognitive impairment (MCI), Alzheimer's disease (AD), or no impairment (NI), which showed that statistically significant associations between specific PtdCho isoforms and AD were masked with the 184 m/z method. Our findings demonstrate the importance of isoform specificity for quantifying PtdChos, and suggest caution when interpreting analytical data based on pools of biomarkers.

  3. Pressure dependence of side chain13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2. (United States)

    Beck Erlach, Markus; Koehler, Joerg; Crusca, Edson; Munte, Claudia E; Kainosho, Masatsune; Kremer, Werner; Kalbitzer, Hans Robert


    For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13 C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH 2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For H N , N and C α the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13 C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.

  4. Multistimuli-responsive supramolecular organogels formed by low-molecular-weight peptides bearing side-chain azobenzene moieties. (United States)

    Fatás, Paola; Bachl, Jürgen; Oehm, Stefan; Jiménez, Ana I; Cativiela, Carlos; Díaz Díaz, David


    This work demonstrates that the incorporation of azobenzene residues into the side chain of low-molecular-weight peptides can modulate their self-assembly process in organic solvents leading to the formation of stimuli responsive physical organogels. The major driving forces for the gelation process are hydrogen bonding and π-π interactions, which can be triggered either by thermal or ultrasound external stimuli, affording materials having virtually the same properties. In addition, a predictive model for gelation of polar protic solvent was developed by using Kamlet-Taft solvent parameters and experimental data. The obtained viscoelastic materials exhibited interconnected multistimuli responsive behaviors including thermal-, photo-, chemo- and mechanical responses. All of them displayed thermoreversability with gel-to-sol transition temperatures established between 33-80 °C and gelation times from minutes to several hours. Structure-property relationship studies of a designed peptide library have demonstrated that the presence and position of the azobenzene residue can be operated as a versatile regulator to reduce the critical gelation concentration and enhance both the thermal stability and mechanical strength of the gels, as demonstrated by comparative dynamic rheology. The presence of N-Boc protecting group in the peptides showed also a remarkable effect on the formation and properties of the gels. Despite numerous examples of peptide-based gelators known in the literature, this is the first time in which low-molecular-weight peptides bearing side chain azobenzene units are used for the synthesis of "intelligent" supramolecular organogels. Compared with other approaches, this strategy is advantageous in terms of structural flexibility since it is compatible with a free, unprotected amino terminus and allows placement of the chromophore at any position of the peptide sequence. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Selective side-chain modification of cysteine and arginine residues blocks pathogenic activity of HIV-1-Tat functional peptides. (United States)

    Devadas, Krishnakumar; Boykins, Robert A; Hardegen, Neil J; Philp, Deborah; Kleinman, Hynda K; Osa, Etin-Osa; Wang, Jiun; Clouse, Kathleen A; Wahl, Larry M; Hewlett, Indira K; Rappaport, Jay; Yamada, Kenneth M; Dhawan, Subhash


    Extracellular Tat protein of HIV-1 activates virus replication in HIV-infected cells and induces a variety of host factors in the uninfected cells, some of which play a critical role in the progression of HIV infection. The cysteine-rich and arginine-rich basic domains represent key components of the HIV-Tat protein for pathogenic effects of the full-length Tat protein and, therefore, could be ideal candidates for the development of a therapeutic AIDS vaccine. The present study describes selective modifications of the side-chain functional groups of cysteine and arginine amino acids of these HIV-Tat peptides to minimize the pathogenic effects of these peptides while maintaining natural peptide linkages. Modification of cysteine by introducing either a methyl or t-butyl group in the free sulfhydryl group and replacing the guanidine group with a urea linkage in the side chain of arginine in the cysteine-rich and arginine-rich Tat peptide sequences completely blocked the ability of these peptides to induce HIV replication, chemokine receptor CCR-5 expression, and NF-kappaB activity in monocytes. Such modifications also inhibited angiogenesis and migration of Kaposi's sarcoma cells normally induced by Tat peptides. Such chemical modifications of the cysteine-rich and arginine-rich peptides did not affect their reactivity with antibodies against the full-length Tat protein. With an estimated 40 million HIV-positive individuals worldwide and approximately 4 million new infections emerging every year, a synthetic subunit HIV-Tat vaccine comprised of functionally inactive Tat domains could provide a safe, effective, and economical therapeutic vaccine to reduce the progression of HIV disease.

  6. The Effects of Adding Whey Protein and Branched-chain Amino Acid to Carbohydrate Beverages on Indices of Muscle Damage after Eccentric Resistance Exercise in Untrained Young Males

    Directory of Open Access Journals (Sweden)

    Foad Asjodi


    Full Text Available Abstract Background: The aim of this study was to evaluate the effects of supplementation of Branched-Chain Amino Acids (BCAAs plus carbohydrate (CHO and whey protein plus CHO on muscle damage indices after eccentric resistant exercise. Materials and Methods: Twenty four untrained healthy males participated in this study. They were randomly divided into three groups, BCAA +glucose (0.1+0.1g/kg supplement group (n=8, Whey+glucose (0.1+0.1g/kg supplement group (n=8, and placebo (malto dextrin 0.2g/kg group (n=8. Each subject consumed a carbohydrate beverage with addition of whey protein or branched-chain amino acid or placebo 30 minutes before exercise in a randomized,double-blind fashion. Serum levels of Creatine Kinase (CK, Lactate dehydrogenase (LDH, and muscle pain were measured before, 24, 48, 72 h after exercise. Follow-up analyses included 1-way repeated measures ANOVAs, and Bonferroni post hoc comparisons. Results: 24 h after test, serum levels of CK, LDH and muscle pain in both supplement groups were increased less than placebo group (0.015, 0.001 and 0.001, respectively. Also, the levels of CK and LDH showed significant changes in both intervention groups compared to placebo group at 24 h (0.001, 0. 015, respectively. Similarly, significant differences in the levels of CK and LDH between groups were observed. Conclusion: These data indicate that muscle damage and pain after resistant exercise were reduced by an ingestion of either BCAA drink or whey protein drink.

  7. Effects of the molecular weight and the side-chain length on the photovoltaic performance of dithienosilole/thienopyrrolodione copolymers

    Energy Technology Data Exchange (ETDEWEB)

    Chu, Ta-Ya; Lu, Jianping; Zhang, Yanguang; Zhou, Jiayun; Tao, Ye [Institute for Microstructural Sciences (IMS), National Research Council of Canada (NRC), Ottawa, ON, K1A 0R6 (Canada); Beaupre, Serge; Pouliot, Jean-Remi; Najari, Ahmed; Leclerc, Mario [Departement de Chimie, Universite Laval, Quebec City, QC, G1V 0A6 (Canada)


    A series of low-bandgap alternating copolymers of dithienosilole and thienopyrrolodione (PDTSTPDs) are prepared to investigate the effects of the polymer molecular weight and the alkyl chain length of the thienopyrrole-4,6-dione (TPD) unit on the photovoltaic performance. High-molecular-weight PDTSTPD leads to a higher hole mobility, lower device series resistance, a larger fill factor, and a higher photocurrent in PDTSTPD:[6,6]-phenyl C{sub 71} butyric acid methyl ester (PC{sub 71}BM) bulk-heterojunction solar cells. Different side-chain lengths show a significant impact on the interchain packing between polymers and affect the blend film morphology due to different solubilities. A high power conversion efficiency of 7.5% is achieved for a solar cell with a 1.0 cm{sup 2} active area, along with a maximum external quantum efficiency (EQE) of 63% in the red region. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  8. Counting carbohydrates (United States)

    Carb counting; Carbohydrate-controlled diet; Diabetic diet; Diabetes-counting carbohydrates ... Many foods contain carbohydrates (carbs), including: Fruit and fruit juice Cereal, bread, pasta, and rice Milk and milk products, soy milk Beans, legumes, ...

  9. Understanding Carbohydrates (United States)

    ... Size: A A A Listen En Español Understanding Carbohydrates How much and what type of carbohydrate foods ... glucose levels in your target range. Explore: Understanding Carbohydrates Glycemic Index and Diabetes Learn about the glycemic ...

  10. Design and synthesis of novel opioid ligands with an azabicyclo[2.2.2]octane skeleton having a 7-amide side chain and their pharmacologies. (United States)

    Watanabe, Yoshikazu; Kitazawa, Shota; Nemoto, Toru; Hirayama, Shigeto; Iwai, Takashi; Fujii, Hideaki; Nagase, Hiroshi


    Several derivatives with an azabicyclo[2.2.2]octane skeleton having a 7-amide side chain were synthesized. Compounds that had an electron-donating group exhibited high affinity for the μ opioid receptor while those with a bulky substituent at the 8-nitrogen atom had low affinities for all receptor types. High affinities and selectivities for the κ receptor resulted from the introduction of the longer amide side chain at the 7α-position. Our studies indicate that the orientation of the amide side chain at the 7-position within the azabicyclo[2.2.2]octane skeleton is related to selectivity for the κ receptor. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Synthesis of new opioid derivatives with a propellane skeleton and their pharmacology. Part 2: Propellane derivatives with an amide side chain. (United States)

    Nagase, Hiroshi; Akiyama, Junko; Nakajima, Ryo; Hirayama, Shigeto; Nemoto, Toru; Gouda, Hiroaki; Hirono, Shuichi; Fujii, Hideaki


    We designed and synthesized propellane derivatives with a 6- or 7-amide side chain on the basis of the active conformation of the κ selective agonist nalfurafine. The 6-amides showed high affinities for the κ receptor, and one of the 6β-amides showed higher κ selectivity than nalfurafine. On the other hand, although the affinities of the 7-amides decreased compared to the 6-amides, some 7α-amides showed the highest selectivities for the κ receptor among the tested compounds. The affinities of 7β-isomers were extremely low, which was postulated to result from the shielding effect of the 7β-amide side chain against the lone electron pair on the 17-nitrogen. This is the first conformational information about the 7-amide side chain in propellane derivatives. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Human urokinase contains GalNAcβ(1-4)[Fucα(1-3)]GlcNAcα(1-2) as a novel terminal element in N-linked carbohydrate chains

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Bergwerff, A.A.; Thomas-Oates, J.E.; Oostrum, J. van; Kamerling, J.P.


    Structural analysis of enzymically released N-linked carbohydrate chains of human urokinase (urinary-type plasminogen activator) by 1H NMR spectroscopy and FAB-MS demonstrated that the N-linked oligosaccharides on the only N-glycosylation site contain diantennary structures with the novel Ga1NAc

  13. Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors

    Directory of Open Access Journals (Sweden)

    Zied Gaieb


    Full Text Available Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach designed to reduce the large MD simulation spatiotemporal datasets into a manageable set in order to guide our understanding of how protein mechanics emerge from side chain organization and dynamic reorganization. We focus on the detection of side chain interactions that undergo rearrangements mediating global domain motions and vice versa. Side chain rearrangements are extracted from side chain interactions that undergo well-defined abrupt and persistent changes in distance time series using Gaussian mixture models, whereas global domain motions are detected using dynamic cross-correlation. Both side chain rearrangements and global domain motions represent the dynamic components of the protein MD simulation, and are both mapped into a network where they are connected based on their degree of coupling. This method allows for the study of allosteric communication in proteins by mapping out the protein dynamics into an intramolecular network to reduce the large simulation data into a manageable set of communities composed of coupled side chain rearrangements and global domain motions. This computational framework is suitable for the study of tightly packed proteins, such as G protein-coupled receptors, and we present an application on a seven microseconds MD trajectory of CC chemokine receptor 7 (CCR7 bound to its ligand CCL21.

  14. Optical anisotropy of polyimide and polymethacrylate containing photocrosslinkable chalcone group in the side chain under irradiation of a linearly polarized UV light

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Dong Hoon; Cha, Young Kwan [Kyunghee Univ., Yongin (Korea, Republic of)


    Photocrosslinkable soluble polyimide and polymethacrylate compound were synthesized for studying the optically induced anisotropy of the thin films. Chalcone group was introduced into the side chain unit of two polymers. We observed a photodimerization behavior between the double bonds in the chalcone group and an optical anisotropy of these materials by irradiation of a linearly polarized UV light (LPL). Optical anisotropy of the thin film was also investigated by using polarized UV absorption spectroscopy.The dynamic property of optical anisotropy in photoreactive polyimide was compared to that in polymethacrylate containing chalcone group in the side chain.

  15. Optical anisotropy of polyimide and polymethacrylate containing photocrosslinkable chalcone group in the side chain under irradiation of a linearly polarized UV light

    CERN Document Server

    Choi, D H


    Photocrosslinkable soluble polyimide and polymethacrylate compound were synthesized for studying the optically induced anisotropy of the thin films. Chalcone group was introduced into the side chain unit of two polymers. We observed a photodimerization behavior between the double bonds in the chalcone group and an optical anisotropy of these materials by irradiation of a linearly polarized UV light (LPL). Optical anisotropy of the thin film was also investigated by using polarized UV absorption spectroscopy.The dynamic property of optical anisotropy in photoreactive polyimide was compared to that in polymethacrylate containing chalcone group in the side chain.

  16. Microbial degradation of whole-grain complex carbohydrates and impact on short-chain fatty acids and health

    DEFF Research Database (Denmark)

    Knudsen, Knud Erik Bach


    Whole-grain cereals have a complex dietary fiber (DF) composition consisting of oligosaccharides (mostly fructans), resistant starch, and nonstarch polysaccharides (NSPs); the most important are arabinoxylans, mixed-linkage β(1,3; 1,4)-d-glucan (β-glucan), and cellulose and the noncarbohydrate...... to the intake of DF. The type and composition of cereal DF can consequently be used to modulate the microbial composition and activity as well as the production and molar ratios of short-chain fatty acids (SCFAs). Arabinoxylans and β-glucan in whole-grain cereals and cereal ingredients have been shown...... on the concentration in peripheral blood was less because the majority of propionate and butyrate is cleared in the liver. Active microbial fermentation with increased SCFA production reduced the exposure of potentially toxic compounds to the epithelium, potentially stimulating anorectic hormones and acting...

  17. Effect of Side Chain Functional Group on Interactions in Ionic Liquid Systems: Insights from Infinite Dilution Thermodynamic Data. (United States)

    Paduszyński, Kamil; Królikowska, Marta


    Measurements of infinite dilution activity coefficients of 48 molecular solutes (including alkanes, alkenes, alkynes, aromatics, ethers, alcohols, water, ketones, pyridine, thiophene, acetonitrile, and 1-nitropropane) in two ionic liquids (ILs), namely, 1-(2-hydroxyethyl)-3-methylimidazolium dicyanamide and 1-(2-chloroethyl)-3-methylimidazolium dicyanamide, are reported in the temperature range from T = 308.15 to 358.15 K. Comparative analysis of an effect of OH/Cl substitution of terminal carbon in side chains of imidazolium cations is presented and discussed in terms of different types of intermolecular forces acting between ILs and solutes. The new data also are confronted to those published previously for a "plain" counterpart of the studied ILs, namely, 1-ethyl-3-methylimidazolium dicyanamide. Infinite dilution capacity and selectivity of the studied ILs are presented to evaluate them as separating agents in extraction of aromatics from alkanes and sulfur compounds from alkanes. Three modeling approaches, namely, linear solvation energy relationship (LSER), regular solution theory, and conductor-like screening model for real solvents (COSMO-RS), are tested for their capabilities of capturing the substitution effects detected experimentally.

  18. Neutral Pectin side chains of Amaranth (Amaranthus hypochondriacus) contain long, partially branched Arabinans and short galactans, both with terminal arabinopyranoses. (United States)

    Wefers, Daniel; Tyl, Catrin E; Bunzel, Mirko


    Amaranth is a pseudocereal of high nutritional value, including a high dietary fiber content. Amaranth dietary fiber was suggested to contain large amounts of neutral rhamnogalacturonan I side chains. In this study, endo-arabinanase and endo-galactanase were used to liberate arabinan and galactan oligosaccharides from amaranth fiber. The liberated oligosaccharides were identified by high-performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD) and HPLC-MS(n) using standard compounds, which were isolated from amaranth, sugar beet, potato, and red clover sprouts and characterized by one- and two-dimensional NMR spectroscopy. It was demonstrated that insoluble amaranth arabinans have linear and branched areas, with the O-3 position being the dominant branching point. Minor amounts of branches at position O-2 and double substitution were also found. Amaranth arabinans were also demonstrated to contain terminal α-(1→5)-linked l-arabinopyranose units. In addition, it was evidenced that galactans from amaranth seeds are composed of β-(1→4)-linked d-galactopyranose units, which can also be terminated with l-arabinopyranose units. In direct comparison to structural elucidation of amaranth fiber by using methylation analysis, the advantage of the enzymatic approach over methylation analysis was demonstrated.

  19. Microbial side-chain cleavage of phytosterols by mycobacteria in vegetable oil/aqueous two-phase system. (United States)

    Xu, Yang-Guang; Guan, Yi-Xin; Wang, Hai-Qing; Yao, Shan-Jing


    Microbial side-chain cleavage of natural sterols to 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD) by Mycobacteria has received much attention in pharmaceutical industry, while low yield of the reaction owing to the strong hydrophobicity of sterols is a tough problem to be solved urgently. Eight kinds of vegetable oils, i.e., sunflower, peanut, corn, olive, linseed, walnut, grape seed, and rice oil, were used to construct oil/aqueous biphasic systems in the biotransformation of phytosterols by Mycobacterium sp. MB 3683 cells. The results indicated that vegetable oils are suitable for phytosterol biotransformation. Specially, the yield of AD carried out in sunflower biphasic system (phase ratio of 1:9, oil to aqueous) was greatly increased to 84.8 % with 10 g/L feeding concentration after 120-h transformation at 30 °C and 200 rpm. Distribution coefficients of AD in different oil/aqueous systems were also determined. Because vegetable oils are of low cost and because of their eco-friendly characters, there is a great potential for the application of oil/aqueous two-phase systems in bacteria whole cell biocatalysis.

  20. Factors Governing Intercalation of Fullerenes and Other Small Molecules Between the Side Chains of Semiconducting Polymers Used in Solar Cells

    KAUST Repository

    Miller, Nichole Cates


    While recent reports have established signifi cant miscibility in polymer:fullerene blends used in organic solar cells, little is actually known about why polymers and fullerenes mix and how their mixing can be controlled. Here, X-ray diffraction (XRD), differential scanning calorimetry (DSC), and molecular simulations are used to study mixing in a variety of polymer:molecule blends by systematically varying the polymer and smallmolecule properties. It is found that a variety of polymer:fullerene blends mix by forming bimolecular crystals provided there is suffi cient space between the polymer side chains to accommodate a fullerene. Polymer:tetrafl uoro-tetracyanoquinodimethane (F4-TCNQ) bimolecular crystals were also observed, although bimolecular crystals did not form in the other studied polymer:nonfullerene blends, including those with both conjugated and non-conjugated small molecules. DSC and molecular simulations demonstrate that strong polymer-fullerene interactions can exist, and the calculations point to van der Waals interactions as a signifi cant driving force for molecular mixing. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Tuning backbones and side-chains of cationic conjugated polymers for optical signal amplification of fluorescent DNA detection. (United States)

    Huang, Yan-Qin; Liu, Xing-Fen; Fan, Qu-Li; Wang, Lihua; Song, Shiping; Wang, Lian-Hui; Fan, Chunhai; Huang, Wei


    Three cationic conjugated polymers (CCPs) exhibiting different backbone geometries and charge densities were used to investigate how their conjugated backbone and side chain properties, together with the transitions of DNA amphiphilic properties, interplay in the CCP/DNA-C* (DNA-C*: fluorophore-labeled DNA) complexes to influence the optical signal amplification of fluorescent DNA detection based on Förster resonance energy transfer (FRET). By examining the FRET efficiencies to dsDNA-C* (dsDNA: double-stranded DNA) and ssDNA-C* (ssDNA: single-stranded DNA) for each CCP, twisted conjugated backbones and higher charge densities were proved to facilitate electrostatic attraction in CCP/dsDNA-C* complexes, and induced improved sensitivity to DNA hybridization. Especially, by using the CCP with twisted conjugated backbone and the highest charge density, a more than 7-fold higher efficiency of FRET to dsDNA-C* was found than to ssDNA-C*, indicating a high signal amplification for discriminating between dsDNA and ssDNA. By contrast, linear conjugated backbones and lower charge density were demonstrated to favor hydrophobic interactions in CCP/ssDNA-C* complexes. These findings provided guidelines for the design of novel sensitive CCP, which can be useful to recognize many other important DNA activities involving transitions of DNA amphiphilic properties like DNA hybridization, such as specific DNA binding with ions, some secondary or tertiary structural changes of DNA, and so forth.

  2. Tunable solubility parameter of poly(3-hexyl thiophene) with hydrophobic side-chains to achieve rubbery conjugated films. (United States)

    Lee, Seulyi; Jeon, Hyeonyeol; Jang, Mi; Baek, Kyung-Youl; Yang, Hoichang


    A highly π-conjugated nanofibrillar network of poly(3-hexyl thiophene) (P3HT) embedded in polydimethylsiloxane (PDMS) elastomer films on SiO2 dielectrics was facilely developed via solution-blending of an ultrasound-assisted dilute P3HT solution with a PDMS precursor followed by spin-casting and curing. In contrast, simple blending without ultrasonication against the dilute P3HT solution yielded large agglomerates in cast films owing to a great difference in solubility parameter (δ) values (P3HT = 9.5 cal(1/2) cm(-3/2), PDMS = 7.3 cal(1/2) cm(-3/2)). In the ultrasound-assisted 0.1 vol % P3HT solutions, the π-conjugated polymer could develop crystalline nanofibrils surrounded by nonpolar hexyl side chains with the same δ value as that of PDMS, yielding homogeneously dispersed 10 wt % loaded P3HT/PDMS blend films. Spun-cast P3HT/PDMS blend films could yield high electrical properties in organic field-effect transistor, including mobilities of up to 0.045 cm(2) V(-1) s(-1) and on/off current ratios of >5 × 10(5), as well as excellent environmental stability owing to the outer PDMS layer.

  3. o-Boronato- and o-Trifluoroborato-Phosphonium Salts Supported by L-α-Amino Acid Side Chain. (United States)

    Bernard, Julie; Malacea-Kabbara, Raluca; Clemente, Gonçalo S; Burke, Benjamin P; Eymin, Marie-Joëlle; Archibald, Stephen J; Jugé, Sylvain


    The synthesis of o-boronato- and o-trifluoroborato-phosphonium salts supported by the L-amino acid side chain is described. The synthesis of these new class of amino acid derivatives was achieved by stereoselective quaternization of o-(pinacolato)boronatophenylphosphine with β- or γ-iodo amino acid derivatives which are prepared from L-serine or L-aspartic acid, respectively. The quaternization of the phosphine was performed using either iodo amino ester or carboxylic acid derivatives. In addition, free carboxylic acid and amine derivatives were obtained by saponification or HCl acidolysis of o-boronato-phosphonium amino esters, respectively. The usefulness of these compounds in peptide coupling was demonstrated by coupling an o-boronato-phosphonium amino ester with an aspartic acid moiety. When the o-boronato-phosphonium amino acid or dipeptide derivatives were mixed with fluoride, the corresponding o-trifluoroborated products were cleanly and rapidly obtained in high isolated yields. The hydrolysis of these compounds at room temperature using a phosphate buffer pH 7/CD3CN mixture has shown only traces of free fluoride F(-) after several days. Finally, a preliminary radiolabeling essay has proven the facile [(18)F]-fluoride incorporation and high stability of the radiolabeled product in aqueous conditions. Indeed, this new class of boron-phosphonium amino acid derivatives shows promising properties for their applications in synthesis and labeling of peptides.

  4. Restricted mobility of side chains on concave surfaces of solenoid proteins may impart heightened potential for intermolecular interactions. (United States)

    Ramya, L; Gautham, N; Chaloin, Laurent; Kajava, Andrey V


    Significant progress has been made in the determination of the protein structures with their number today passing over a hundred thousand structures. The next challenge is the understanding and prediction of protein-protein and protein-ligand interactions. In this work we address this problem by analyzing curved solenoid proteins. Many of these proteins are considered as "hub molecules" for their high potential to interact with many different molecules and to be a scaffold for multisubunit protein machineries. Our analysis of these structures through molecular dynamics simulations reveals that the mobility of the side-chains on the concave surfaces of the solenoids is lower than on the convex ones. This result provides an explanation to the observed preferential binding of the ligands, including small and flexible ligands, to the concave surface of the curved solenoid proteins. The relationship between the landscapes and dynamic properties of the protein surfaces can be further generalized to the other types of protein structures and eventually used in the computer algorithms, allowing prediction of protein-ligand interactions by analysis of protein surfaces. © 2015 Wiley Periodicals, Inc.

  5. ABC triblock surface active block copolymer with grafted ethoxylated fluoroalkyl amphiphilic side chains for marine antifouling/fouling-release applications. (United States)

    Weinman, Craig J; Finlay, John A; Park, Daewon; Paik, Marvin Y; Krishnan, Sitaraman; Sundaram, Harihara S; Dimitriou, Michael; Sohn, Karen E; Callow, Maureen E; Callow, James A; Handlin, Dale L; Willis, Carl L; Kramer, Edward J; Ober, Christopher K


    An amphiphilic triblock surface-active block copolymer (SABC) possessing ethoxylated fluoroalkyl side chains was synthesized through the chemical modification of a polystyrene-block-poly(ethylene-ran-butylene)-block-polyisoprene polymer precursor. Bilayer coatings on glass slides consisting of a thin layer of the amphiphilic SABC spray coated on a thick layer of a polystyrene-block-poly(ethylene-ran-butylene)-block-polystyrene (SEBS) thermoplastic elastomer were prepared for biofouling assays with the green alga Ulva and the diatom Navicula. Dynamic water contact angle analysis and X-ray photoelectron spectroscopy (XPS) were used to characterize the surfaces. Additionally, the effect of the Young's modulus of the coating on the release properties of sporelings (young plants) of the green alga Ulva was examined through the use of two different SEBS thermoplastic elastomers possessing modulus values of an order of magnitude in difference. The amphiphilic SABC was found to reduce the settlement density of zoospores of Ulva as well as the strength of attachment of sporelings. The attachment strength of the sporelings was further reduced for the amphiphilic SABC on the "low"-modulus SEBS base layer. The weaker adhesion of diatoms, relative to a PDMS standard, further highlights the antifouling potential of this amphiphilic triblock hybrid copolymer.

  6. Enhanced n-Doping Efficiency of a Naphthalenediimide-Based Copolymer through Polar Side Chains for Organic Thermoelectrics

    KAUST Repository

    Kiefer, David


    N-doping of conjugated polymers either requires a high dopant fraction or yields a low electrical conductivity because of their poor compatibility with molecular dopants. We explore n-doping of the polar naphthalenediimide–bithiophene copolymer p(gNDI-gT2) that carries oligoethylene glycol-based side chains and show that the polymer displays superior miscibility with the benzimidazole–dimethylbenzenamine-based n-dopant N-DMBI. The good compatibility of p(gNDI-gT2) and N-DMBI results in a relatively high doping efficiency of 13% for n-dopants, which leads to a high electrical conductivity of more than 10–1 S cm–1 for a dopant concentration of only 10 mol % when measured in an inert atmosphere. We find that the doped polymer is able to maintain its electrical conductivity for about 20 min when exposed to air and recovers rapidly when returned to a nitrogen atmosphere. Overall, solution coprocessing of p(gNDI-gT2) and N-DMBI results in a larger thermoelectric power factor of up to 0.4 μW K–2 m–1 compared to other NDI-based polymers.

  7. Structural optimization and evaluation of butenolides as potent antifouling agents: modification of the side chain affects the biological activities of compounds

    KAUST Repository

    Li, Yongxin


    A recent global ban on the use of organotin compounds as antifouling agents has increased the need for safe and effective antifouling compounds. In this study, a series of new butenolide derivatives with various amine side chains was synthesized and evaluated for their anti-larval settlement activities in the barnacle, Balanus amphitrite. Side chain modification of butenolide resulted in butenolides 3c-3d, which possessed desirable physico-chemical properties and demonstrated highly effective non-toxic anti-larval settlement efficacy. A structure-activity relationship analysis revealed that varying the alkyl side chain had a notable effect on anti-larval settlement activity and that seven to eight carbon alkyl side chains with a tert-butyloxycarbonyl (Boc) substituent on an amine terminal were optimal in terms of bioactivity. Analysis of the physico-chemical profile of butenolide analogues indicated that lipophilicity is a very important physico-chemical parameter contributing to bioactivity. © 2012 Copyright Taylor and Francis Group, LLC.

  8. Alternating side-chain liquid-crystalline copolymers with polar moieties in the backbone = Alternerende zijketen vloeibaar-kristallijne copolymeren met polaire groepen in de hoofdketen

    NARCIS (Netherlands)

    Nieuwhof, R.P.


    Side-chain liquid-crystalline polymers (SCLCPs) obtained via the alternating copolymeri-zation of maleic anhydride (MA) and mesogenic 1-alkenes are an interesting class of polymers that may show good adhesion towards metal surfaces and form ordered layered structures. If these polymers

  9. Introduction of a tryptophan side chain into subsite +1 enhances transglycosylation activity of a GH-18 chitinase from Arabidopsis thaliana, AtChiC

    DEFF Research Database (Denmark)

    Umemoto, Naoyuki; Ohnuma, Takayuki; Mizuhara, Mamiko


    . The introduced tryptophan side chain might protect the oxazolinium ion intermediate from attack by a nucleophilic water molecule. The enhancement of transglycosylation activity was much more distinct in G75W-AtChiC than in G74W-NtChiV. Nuclear magnetic resonance titration experiments using the inactive double...

  10. Synthesis and Catalytic Properties of Non-Cross-Linked and Cross-Linked Poly(alkylmethyldiallylammonium bromides) Having Decyl, Octyl, and Hexyl Side Chains

    NARCIS (Netherlands)

    Wang, G.J; Engberts, J.B.F.N.


    A family of non-cross-linked and cross-linked copolymers containing decyl, octyl, and hexyl groups as side chains ((CL)-CopolC1-10, (CL)-CopolC1-8, and (CL)-CopolC1-6, respectively) were synthesized by radical-initiated cyclocopolymerization of alkylmethyldiallylammonium bromide monomers without and

  11. Synthesis and photovoltaic properties of the polymers base on thiophene derivatives with electron-deficient 3-nitro-1,2,4-triazole side chains

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Bin, E-mail: [College of Chemistry and Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Xiangtan University, Xiangtan 411105 (China); Key Laboratory of Advanced Functional Polymeric Materials of College of Hunan Province, Xiangtan University, Xiangtan 411105 (China); Li, Xinwei; Tang, Peng; Cao, Zhencai; Huang, Hongyan; Shen, Ping [College of Chemistry and Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Xiangtan University, Xiangtan 411105 (China); Tan, Songting [College of Chemistry and Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Xiangtan University, Xiangtan 411105 (China); Key Laboratory of Advanced Functional Polymeric Materials of College of Hunan Province, Xiangtan University, Xiangtan 411105 (China)


    Three soluble alternating conjugated copolymers PT-TZN, PF-TZN, and PBDT-TZN, composed of thiophene, fluorene, benzo[1,2-b:4,5-b′]dithiophene and thiophene derivatives with 3-nitro-1,2,4-triazole side chains, were synthesized via the palladium-catalyzed Suzuki coupling reaction and Stille coupling reaction. The effects of 3-nitro-1,2,4-triazole on the thermal, photophysical, electrochemical and photovoltaic properties were investigated. The introduction of the 3-nitro-1,2,4-triazole side chains is beneficial for lowering the bandgaps of the polymers. The bulk-heterojunction polymer solar cells were fabricated based on the blend of the as-synthesized polymers and the fullerene acceptor [6, 6]-phenyl-C{sub 61}-butyric acid methyl ester. The maximum power conversion efficiency (1.13%) was obtained with PBDT-TZN as the electron donor under the illumination of Air Mass 1.5, 100 mW/cm{sup 2}. - Highlights: • Three conjugated polymers with 3-nitro-1,2,4-triazole side chains were synthesized. • The introduction of the side chains favors lowering the bandgaps of the polymers. • The strong electron-withdrawing nitro group likely promotes excimer quenching.

  12. Side-chain liquid-crystalline poly(ketone)s : effect of spacer length, mesogen type and mesogen density on mesomorphic behavior

    NARCIS (Netherlands)

    Nieuwhof, R.P.; Marcelis, A.T.M.; Sudhölter, E.J.R.; Wursche, R.; Rieger, B.


    Novel side-chain liquid-crystalline copolymers (SCLCPs) were synthesized via the Pd(II) catalyzed alternating copolymerization of mesogenic 1-alkenes and carbon monoxide. For methoxybiphenyl mesogens, these copolymers exhibited highly ordered smectic E mesophases and high glass transition

  13. Critical roles of hydrophobicity and orientation of side chains for inactivation of sarcoplasmic reticulum Ca2+-ATPase with thapsigargin and thapsigargin analogs

    DEFF Research Database (Denmark)

    Winther, Anne-Marie Lund; Liu, Huizhen; Sonntag, Yonathan


    fluorescence data to show how Tg and chemical analogs of the compound with modified or removed side chains bind to isolated SERCA 1a membranes. This occurs by uptake via the membrane lipid followed by insertion into a resident intramembranous binding site with few adaptative changes. Our binding data indicate...

  14. Impact of constitution of the terthiophene-vinylene conjugated side chain on the optical and photovoltaic properties of two-dimensional polythiophenes. (United States)

    Hsiow, Chuen-Yo; Raja, Rathinam; Wang, Chun-Yao; Lin, Yu-Hsiang; Yang, Yu-Wen; Hsieh, Yen-Ju; Rwei, Syang-Peng; Chiu, Wen-Yen; Huang, Ching-I; Wang, Leeyih


    The effects of the spatial arrangement of the conjugated side chains of two-dimensional polymers on their optical, electrochemical, molecular-packing, and photovoltaic characteristics were investigated. Accordingly, novel polythiophenes with horizontally (PBTTTV-h) and vertically (PBTTTV-v) grafted terthiophene–vinylene (TTV) conjugated side chains were synthesized that display two and one UV-vis peaks, respectively; the difference is due to the different constitutions of the conjugated side-chains. Because the spatial arrangement affects the molecular self-assembly, PBTTTV-h shows stronger crystallinity than PBTTTV-v, which enhances the charge mobility in devices. Moreover, PBTTTV-h has a lower HOMO energy level (−5.49 eV) than PBTTTV-v (−5.40 eV). Bulk heterojunction solar cells fabricated from PBTTTV-h/PC71BM and PBTTTV-v/PC71BM exhibit power conversion efficiencies of 4.75% and 4.00%, respectively, and Voc values of 800 and 730 mV, respectively, under AM1.5G illumination (100 mW cm(−2)). Thus, the architecture of the TTV conjugated side chains affects the optical, electrochemical, and photovoltaic properties; this study provides more ideas for improving 2-D conjugated polymers for semiconductor devices.

  15. Compounds having aromatic rings and side-chain amide-functionality and a method for transporting monovalent anions across biological membranes using the same (United States)

    Davis, Jeffery T [College Park, MD; Sidorov, Vladimir [Richmond, VA; Kotch, Frank W [New Phila., PA


    A compound containing at least two aromatic rings covalently bonded together, with each aromatic ring containing at least one oxyacetamide-based side chain, the compound being capable of forming a chloride ion channel across a lipid bilayer, and transporting chloride ion across the lipid bilayer.

  16. Residue-specific pK(a) determination of lysine and arginine side chains by indirect N-15 and C-13 NMR spectroscopy : Application to apo calmodulin

    NARCIS (Netherlands)

    Andre, Ingemar; Linse, Sara; Mulder, Frans A. A.


    Electrostatic interactions in proteins can be probed experimentally through determination of residue-specific acidity constants, We describe here triple-resonance NMR techniques for direct determination of lysine and arginine side-chain protonation states in proteins. The experiments are based on

  17. Effect of side chain length on the stability and structural properties of 3-(2’,5’-dialkoxy-phenylthiophenes: a theoretical study

    Directory of Open Access Journals (Sweden)

    Taye Beyene Demissie


    Full Text Available We report on the effect of the alkoxy chain length on the thermodynamic properties of neutral and the corresponding radical cations of 3-(2’,5’-dibutyloxyphenylthiophene (DBOPT, 3-(2’,5’-diheptyloxyphenylthiophene (DHOPT, and 3-(2’,5’-dioctyloxyphenylthiophene (DOOPT and their dimers studied by Hartree-Fock (HF and Density Functional Theory (DFT methods. The DFT calculations suggest that dimers of the dialkoxyphenylthiophenes with longer side chains are thermodynamically more stable by about 61.39 kJ/mol than the ones with shorter side chains at the radical cation state. The results correlate well with the experimental observations made during the electrochemical synthesis of these polymers from their monomers.

  18. Interrogation of side chain biases for oligomannose recognition by antibody 2G12 via structure-guided phage display libraries. (United States)

    Lin, Tsung-Yi; Lai, Jonathan R


    Monoclonal antibodies (mAbs) are essential reagents for deciphering gene or protein function and have been a fruitful source of therapeutic and diagnostic agents. However, developing anticarbohydrate antibodies to target glycans for those purposes has been less successful because the molecular basis for glycan-mAb interactions is poorly understood relative to protein- or peptide-binding mAbs. Here, we report our investigation on glycan-mAb interactions by using the unique architectural scaffold of 2G12, an antibody that targets oligomannoses on the HIV-1 glycoprotein gp120, as the template for engineering highly specific mAbs to target glycans. We first analyzed 24 different X-ray structures of antiglycan mAbs from the Protein Data Bank to determine side chain amino acid distributions in of glycan-mAb interactions. We identified Tyr, Arg, Asn, Ser, Asp, and His as the six most prevalent residues in the glycan-mAb contacts. We then utilized this information to construct two phage display libraries ("Lib1" and "Lib2") in which positions on the heavy chain variable domains of 2G12 were allowed to vary in restricted manner among Tyr, Asp, Ser, His, Asn, Thr, Ala and Pro to interrogate the minimal physicochemical requirements for oligomannose recognition. We analyzed the sequences of 39 variants from Lib1 and 14 variants from Lib2 following selection against gp120, the results showed that there is a high degree of malleability within the 2G12 for glycan recognitions. We further characterized five unique phage clones from both libraries that exhibited a gp120-specific binding profile. Expression of two of these variants as soluble mAbs indicated that, while specificity of gp120-binding was retained, the affinity of these mutants was significantly reduced relative to WT 2G12. Nonetheless, the results indicate these is some malleability in the identity of contact residues and provide a novel insight into the nature of glycan-antibody interactions and how they may differ

  19. Influencing the size and anion selectivity of dimeric Ln(3+)[15-metallacrown-5] compartments through systematic variation of the host side chains and central metal. (United States)

    Jankolovits, Joseph; Lim, Choong-Sun; Mezei, Gellert; Kampf, Jeff W; Pecoraro, Vincent L


    Dimeric Ln(3+)[15-metallacrown-5] compartments selectively recognize carboxylates through guest binding to host metal ions and intermolecular interactions with the phenyl side chains. A systematic study is presented on how the size, selectivity, and number of encapsulated guests in the dimeric containers is influenced by the Ln(3+)[15-metallacrown(Cu(II))-5] ligand side chain and central metal. Compartments of varying heights were assembled from metallacrowns with S-phenylglycine hydroxamic acid (pgHA), S-phenylalanine hydroxamic acid (pheHA), and S-homophenylalanine hydroxamic acid (hpheHA) ligands. Guests that were examined include the fully deprotonated forms of terephthalic acid, isonicotinic acid, and bithiophene dicarboxylic acid (btDC). X-ray crystallography reveals that the side-chain length constrains the maximum and minimum length guest that can be encapsulated in the compartment. Compartments with heights ranging from 9.7 to 15.2 Å are formed with different phenyl side chains that complex 4.3-9.2 Å long guests. Up to five guests are accommodated in Ln(3+)[15-metallacrown(Cu(II))-5] compartments depending on steric effects from the host side chains. The nine-coordinate La(3+) central metal promotes the encapsulation of multiple guests, while the eight-coordinate Gd(3+) typically binds only one dicarboxylate. Electrospray ionization mass spectrometry reveals that the dimerization phenomenon occurs beyond the solid state, suggesting that these containers can be utilized in solid-state and solution applications. © 2012 American Chemical Society

  20. Solid-State Organization and Ambipolar Field-Effect Transistors of Benzothiadiazole-Cyclopentadithiophene Copolymer with Long Branched Alkyl Side Chains

    Directory of Open Access Journals (Sweden)

    Martin Baumgarten


    Full Text Available The solid-state organization of a benzothiadiazole-cyclopentadithiophene copolymer with long, branched decyl-tetradecyl side chains (CDT-BTZ-C14,10 is investigated. The C14,10 substituents are sterically demanding and increase the π-stacking distance to 0.40 nm from 0.37 nm for the same polymer with linear hexadecyls (C16. Despite the bulkiness, the C14,10 side chains tend to crystallize, leading to a small chain-to-chain distance between lamellae stacks and to a crystal-like microstructure in the thin film. Interestingly, field-effect transistors based on solution processed layers of CDT-BTZ-C14,10 show ambipolar behavior in contrast to CDT-BTZ-C16 with linear side chains, for which hole transport was previously observed. Due to the increased π-stacking distance, the mobilities are only 6 × 10−4 cm²/Vs for electrons and 6 × 10−5 cm²/Vs for holes, while CDT-BTZ-C16 leads to values up to 5.5 cm²/Vs. The ambipolarity is attributed to a lateral shift between stacked backbones provoked by the bulky C14,10 side chains. This reorganization is supposed to change the transfer integrals between the C16 and C14,10 substituted polymers. This work shows that the electronic behavior in devices of one single conjugated polymer (in this case CDT-BTZ can be controlled by the right choice of the substituents to place the backbones in the desired packing.

  1. Autoantibodies against Cytochrome P450 Side-Chain Cleavage Enzyme in Dogs (Canis lupus familiaris Affected with Hypoadrenocorticism (Addison's Disease.

    Directory of Open Access Journals (Sweden)

    Alisdair M Boag

    Full Text Available Canine hypoadrenocorticism likely arises from immune-mediated destruction of adrenocortical tissue, leading to glucocorticoid and mineralocorticoid deficiency. In humans with autoimmune Addison's disease (AAD or autoimmune polyendocrine syndrome (APS, circulating autoantibodies have been demonstrated against enzymes associated with adrenal steroid synthesis. The current study investigates autoantibodies against steroid synthesis enzymes in dogs with spontaneous hypoadrenocorticism. Coding regions of canine CYP21A2 (21-hydroxylase; 21-OH, CYP17A1 (17-hydroxylase; 17-OH, CYP11A1 (P450 side-chain cleavage enzyme; P450scc and HSD3B2 (3β hydroxysteroid dehydrogenase; 3βHSD were amplified, cloned and expressed as 35S-methionine radiolabelled recombinant protein. In a pilot study, serum samples from 20 dogs with hypoadrenocorticism and four unaffected control dogs were screened by radio-immunoprecipitation assay. There was no evidence of reactivity against 21-OH, 17-OH or 3βHSD, but five dogs with hypoadrenocorticism showed immunoreactivity to P450scc compared with controls. Serum samples were subsequently obtained from 213 dogs diagnosed with hypoadrenocorticism and 110 dogs from a hospital control population. Thirty control dogs were randomly selected to establish a threshold for antibody positivity (mean + 3 × standard deviation. Dogs with hypoadrenocorticism were more likely to be P450scc autoantibody positive than hospital controls (24% vs. 1.2%, respectively; p = 0.0016. Sex was significantly associated with the presence of P450scc autoantibodies in the case population, with 30% of females testing positive compared with 17% of males (p = 0.037. Significant associations with breed (p = 0.015 and DLA-type (DQA1*006:01 allele; p = 0.017 were also found. This cross-sectional study indicates that P450scc autoantibodies are present in a proportion of dogs affected with hypoadrenocorticism.

  2. Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C. (United States)

    Brown, Nathan J; Wu, Cindy W; Seurynck-Servoss, Shannon L; Barron, Annelise E


    The hydrophobic proteins of lung surfactant (LS), SP-B and SP-C, are critical constituents of an effective surfactant replacement therapy for the treatment of respiratory distress syndrome. Because of concerns and difficulties associated with animal-derived surfactants, recent investigations have focused on the creation of synthetic analogues of the LS proteins. However, creating an accurate mimic of SP-C that retains its biophysical surface activity is extraordinarily challenging given the lipopeptide's extreme hydrophobicity and propensity to misfold and aggregate. One successful approach that overcomes these difficulties is the use of poly-N-substituted glycines, or peptoids, to mimic SP-C. To develop a non-natural, bioactive mimic of SP-C and to investigate the effects of side chain chemistry and length of the helical hydrophobic region, we synthesized, purified, and performed in vitro testing of two classes of peptoid SP-C mimics: those having a rigid alpha-chiral aromatic helix and those having a biomimetic alpha-chiral aliphatic helix. The length of the two classes of mimics was also systematically altered. Circular dichroism spectroscopy gave evidence that all of the peptoid-based mimics studied here emulated SP-C's secondary structure, forming stable helical structures in solution. Langmuir-Wilhelmy surface balance, fluorescence microscopy, and pulsating bubble surfactometry experiments provide evidence that the aromatic-based SP-C peptoid mimics, in conjunction with a synthetic lipid mixture, have superior surface activity and biomimetic film morphology in comparison to the aliphatic-based mimics and that there is an increase in surface activity corresponding to increasing helical length.

  3. Modulated protonation of side chain aminoethylene repeats in N-substituted polyaspartamides promotes mRNA transfection. (United States)

    Uchida, Hirokuni; Itaka, Keiji; Nomoto, Takahiro; Ishii, Takehiko; Suma, Tomoya; Ikegami, Masaru; Miyata, Kanjiro; Oba, Makoto; Nishiyama, Nobuhiro; Kataoka, Kazunori


    Fine-tuning of chemical structures of polycation-based carriers (polyplexes) is an attractive strategy for safe and efficient mRNA transfaction. Here, mRNA polyplexes comprising N-substituted polyaspartamides with varied numbers of side chain aminoethylene repeats were constructed, and their transfection ability against human hepatoma cells was examined. Transfection efficacy clearly correlated with the number of aminoethylene repeats: polyplexes with odd number repeats (PA-Os) produced sustained increases in mRNA expression compared with those with even number repeats (PA-Es). This predominant efficacy of PA-Os over PA-Es was contradictory to our previous findings for pDNA polyplexes prepared from the same N-substituted polyaspartamides, that is, PA-Es revealed superior transfection efficacy of pDNA than PA-Os. Intracellular FRET analysis using flow cytometry and polyplex tracking under confocal laser scanning microscopy revealed that overall transfection efficacy was determined through the balance between endosomal escaping capability and stability of translocated mRNA in cytoplasm. PA-Es efficiently transported mRNA into the cytoplasm. However, their poor cytoplasmic stability led to facile degradation of mRNA, resulting in a less durable pattern of transfection. Alternatively, PA-Os with limited capability of endosomal escape eventually protect mRNA in the cytoplasm to induce sustainable mRNA expression. Higher cytoplasmic stability of pDNA compared to mRNA may shift the limiting step in transfection from cytoplasmic stability to endosomal escape capacity, thereby giving an opposite odd-even effect in transfection efficacy. Endosomal escaping capability and nuclease stability of polyplexes are correlated with the modulated protonation behavior in aminoethylene repeats responding to pH, appealing the substantial importance of chemistry to design polycation structures for promoted mRNA transfection.

  4. Poly(quinoxaline-2,3-diyl)s bearing (S)-3-octyloxymethyl side chains as an efficient amplifier of alkane solvent effect leading to switch of main-chain helical chirality. (United States)

    Nagata, Yuuya; Nishikawa, Tsuyoshi; Suginome, Michinori


    Poly(quinoxaline-2,3-diyl) containing (S)-3-octyloxymethyl side chains was synthesized to investigate the induction of a single-handed helical sense to the main chain in various alkane solvents. The polymer showed an efficient solvent dependent helix inversion between n-octane (M-helix) and cyclooctane (P-helix). After a screening of alkane solvents, it was found that linear alkanes having large molecular aspect ratios induced M-helical structure, and branched or cyclic alkanes having small molecular aspect ratios induced P-helical structure. A polymer ligand containing (S)-3-octyloxymethyl side chains and diphenylphosphino pendants also exhibited solvent-dependent helical inversion between n-octane and cyclooctane, leading to the highly enantioselective production of the both enantiomeric product in a palladium-catalyzed asymmetric hydrosilylation reaction of styrene (R-product 94% ee in n-octane and S-product 90% ee in cyclooctane).

  5. Carbohydrate Microarray on Glass: a Tool for Carbohydrate-Lectin Interactions

    NARCIS (Netherlands)

    Tetala, K.K.R.; Giesbers, M.; Visser, G.M.; Sudhölter, E.J.R.; Beek, van T.A.


    A simple method to immobilize carbohydrates on a glass surface to obtain a carbohydrate microarray is described. The array was used to study carbohydrate-lectin interactions. The glass surface was modified with aldehyde terminated linker groups of various chain lengths. Coupling of carbohydrates

  6. Post-exercise branched chain amino acid supplementation does not affect recovery markers following three consecutive high intensity resistance training bouts compared to carbohydrate supplementation. (United States)

    Kephart, Wesley C; Mumford, Petey W; McCloskey, Anna E; Holland, A Maleah; Shake, Joshua J; Mobley, C Brooks; Jagodinsky, Adam E; Weimar, Wendi H; Oliver, Gretchen D; Young, Kaelin C; Moon, Jordan R; Roberts, Michael D


    Amino acid supplementation has been shown to potentially reduced exercise-induced muscle soreness. Thus, the purpose of this study was to examine if branched chain amino acid and carbohydrate (BCAACHO) versus carbohydrate-only sports drink (CHO) supplementation attenuated markers of muscle damage while preserving performance markers following 3 days of intense weight training. Healthy resistance-trained males (n = 30) performed preliminary testing (T1) whereby they: 1) donated a baseline blood draw, 2) performed knee extensor dynamometry to obtain peak quadriceps isometric and isokinetic torque as well as electromyography (EMG) activity at 60°/s and 120°/s, and 3) performed a one repetition maximum (1RM) barbell back squat. The following week participants performed 10 sets x 5 repetitions at 80 % of their 1RM barbell back squat for 3 consecutive days and 48 h following the third lifting bout participants returned for (T2) testing whereby they repeated the T1 battery. Immediately following and 24 h after the three lifting bouts, participants were randomly assigned to consume one of two commercial products in 600 mL of tap water: 1) BCAAs and CHO (3 g/d L-leucine, 1 g/d L-isoleucine and 2 g/d L-valine with 2 g of CHO; n = 15), or 2) 42 g of CHO only (n = 15). Additionally, venous blood was drawn 24 h following the first and second lifting bouts and 48 h following the third bout to assess serum myoglobin concentrations, and a visual analog scale was utilized prior, during, and after the 3-d protocol to measure subjective perceptions of muscular soreness. There were similar decrements in 1RM squat strength and isokinetic peak torque measures in the BCAA-CHO and CHO groups. Serum myoglobin concentrations (p = 0.027) and perceived muscle soreness (p < 0.001) increased over the intervention regardless of supplementation. A group*time interaction was observed for monocyte percentages (p = 0.01) whereby BCAA-CHO supplementation

  7. carbohydrate complexes

    Indian Academy of Sciences (India)

    ferrocene-carbohydrate conjugates38,39 have lead to the design and study of the cytotoxic activity of metal com- plexes containing carbohydrate ligands. Hence, here we present the detailed synthesis and characteriza- tion of the carbohydrate triazole ligands and their Pd- complexes together with the crystal structures of ...

  8. Exploring amino acid side chain decomposition using enzymatic digestion and HPLC-MS: combined lysine transformations in chlorinated waters. (United States)

    Walse, Spencer S; Plewa, Michael J; Mitch, William A


    Characterizing the transformations of polypeptides is important across a broad range of scientific disciplines. As polypeptides are an important constituent of dissolved organic matter within seawater and freshwater, it is important to understand their (bio)geochemical fate. Oxidants, formed in blood as part of the immunological response or applied to waters for disinfection, react with polypeptides to form transformation products that may exert toxicity. An analytical method was developed to characterize and quantify modifications to the side chains of amino acid residues within polypeptides. Enzymatic digestion of polypeptides using Pronase E, a protease cocktail, proved preferable to common strong acid digestion techniques, because the circumneutral pH conditions employed during enzymatic digestion prevent artifacts arising from extreme pH conditions. Lysine nitrile, one of the predicted transformation products of lysine residues within polypeptides, was destroyed during strong acid digestion but not enzymatic digestion. Due to the potential variability in enzymatic digestion efficiencies, the liberation of a mass-labeled leucine monomer from an octapeptide spiked standard was employed as a measure of complete digestion efficiency for each sample and enabled quantification of modified amino acid residues within polypeptides. A multivariate statistical analysis was conducted to evaluate the influence on digestion efficiency of Pronase E loadings, salinity, natural organic matter concentration, and pH across the range of conditions relevant to blood, seawater, and concentrated freshwaters and disinfected drinking/recreational waters. At Pronase E loadings of 10 mg, the analysis indicated that digestion efficiencies ranged from 25 to 55% over the range of conditions expected for typical drinking waters concentrated from 1 L to 10 mL. The analytical method was applied to triplicate 1 L samples of a chlorinated tap water and a chlorinated indoor pool water. For the

  9. A Computational and Experimental Study of the Conformers of Pyrrolidinium Ionic Liquid Cations Containing an Ethoxy Group in the Alkyl Side Chain

    Directory of Open Access Journals (Sweden)

    Francesco Trequattrini


    Full Text Available We investigate the conformers of the N-methoxyethyl-N-methylpyrrolidinium (PYR1(2O1 and N-ethoxyethyl-N-methylpyrrolidinium (PYR1(2O2 ionic liquid cations by means of DFT calculations at the B3LYP/6-31G⁎⁎ level and we calculate their infrared vibration frequencies. The comparison with the absorbance spectra of two ionic liquids containing these ions indicates good performance of such a combination of theory and basis set. The lowest energy conformer of each pyrrolidinium cation displays equatorial-envelope geometry; however, in contrast with the prototypical PYR14, the main alkyl side chain is not in an all-trans configuration, but it tends to be bent. Moreover, calculations indicate that the LUMO orbital extends more along the alkyl side chain in PYR1(2O1 and PYR1(2O2 than in the parent ion 1-butyl-1-methylpyrrolidinium (PYR14.

  10. The probability distribution of side-chain conformations in [Leu] and [Met]enkephalin determines the potency and selectivity to mu and delta opiate receptors

    DEFF Research Database (Denmark)

    Nielsen, Bjørn Gilbert; Jensen, Morten Østergaard; Bohr, Henrik


    The structure of enkephalin, a small neuropeptide with five amino acids, has been simulated on computers using molecular dynamics. Such simulations exhibit a few stable conformations, which also have been identified experimentally. The simulations provide the possibility to perform cluster analysis...... in the space defined by potentially pharmacophoric measures such as dihedral angles, side-chain orientation, etc. By analyzing the statistics of the resulting clusters, the probability distribution of the side-chain conformations may be determined. These probabilities allow us to predict the selectivity...... of [Leu]enkephalin and [Met]enkephalin to the known mu- and delta-type opiate receptors to which they bind as agonists. Other plausible consequences of these probability distributions are discussed in relation to the way in which they may influence the dynamics of the synapse....

  11. C35 Hopanoid Side Chain Biosynthesis: Reduction of Ribosylhopane into Bacteriohopanetetrol by a Cell-Free System Derived from Methylobacterium organophilum. (United States)

    Bodlenner, Anne; Liu, Wenjun; Hirsch, Guillaume; Schaeffer, Philippe; Blumenberg, Martin; Lendt, Ralf; Tritsch, Denis; Michaelis, Walter; Rohmer, Michel


    The major bacterial triterpenoids of the hopane series each consist of a C30 triterpene hopane moiety and an additional nonterpene C5 side chain derived from D-ribose and linked through its C-5 carbon atom to the hopane side chain. Bacteriohopanetetrol and aminobacteriohopanetriol are the most common representatives of this natural product series, adenosylhopane and ribosylhopane being putative precursors. Deuterium-labelled ribosylhopane was obtained by hemisynthesis and converted into deuterium-labelled bacteriohopanetetrol in the presence of NADPH, thus giving evidence of this as yet unknown precursor-to-product relationship in the bacterial hopanoid metabolic pathway. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Synthesis of novel vitamin K derivatives with alkylated phenyl groups introduced at the ω-terminal side chain and evaluation of their neural differentiation activities. (United States)

    Sakane, Rie; Kimura, Kimito; Hirota, Yoshihisa; Ishizawa, Michiyasu; Takagi, Yuta; Wada, Akimori; Kuwahara, Shigefumi; Makishima, Makoto; Suhara, Yoshitomo


    Vitamin K is an essential cofactor of γ-glutamylcarboxylase as related to blood coagulation and bone formation. Menaquinone-4, one of the vitamin K homologues, is biosynthesized in the body and has various biological activities such as being a ligand for steroid and xenobiotic receptors, protection of neuronal cells from oxidative stress, and so on. From this background, we focused on the role of menaquinone in the differentiation activity of progenitor cells into neuronal cells and we synthesized novel vitamin K derivatives with modification of the ω-terminal side chain. We report here new vitamin K analogues, which introduced an alkylated phenyl group at the ω-terminal side chain. These compounds exhibited potent differentiation activity as compared to control. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  13. Synthesis and structure-activity relationship study of FD-891: importance of the side chain and C8-C9 epoxide for cytotoxic activity against cancer cells. (United States)

    Itagaki, Tomohiro; Kawamata, Ayano; Takeuchi, Miho; Hamada, Keisuke; Iwabuchi, Yoshiharu; Eguchi, Tadashi; Kudo, Fumitaka; Usui, Takeo; Kanoh, Naoki


    Unified synthesis of FD-891 analogs and their structure-activity relationship are described. By using stereoselective allylation/crotylation and Evans aldol chemistry, six side-chain fragments having different length and terminus were synthesized. These fragments were coupled with a macrolactone fragment, improved synthesis of which was also developed here, to generate FD-891 and five truncated analogs. These synthetic compounds as well as three analogs obtained from fermentation of gene-disrupted Streptomyces graminofaciens mutants were tested for in vitro cytotoxic activity against HeLa cells. As a result, coexistence of the C8-C9 epoxide and side-chain terminus was found to be critical for the cytotoxic activity.

  14. Influence of Side Chain Position on the Electrical Properties of Organic Solar Cells Based on Dithienylbenzothiadiazole-alt-phenylene Conjugated Polymers

    DEFF Research Database (Denmark)

    Livi, Francesco; Zawacka, Natalia Klaudia; Angmo, Dechan


    backbone for polymer solar cells. All the polymers were roll slot die coated under ambient conditions on flexible ITO-free plastic substrates to give inverted polymer solar cell devices with an upscaled active area of 1 cm2. The best characteristics were found for the polymer carrying alkoxy side chains...... on the benzene ring where power conversion efficiencies of up to 3.6% were achieved. All studied materials were prepared with an objective of low-cost starting materials, simple synthesis, and simple processing conditions which was most successful for the polymer P5. The polymer P7 containing fluorine atoms...... results were corroborated with full optical and morphological characterization of the conjugated polymers. We conclude that the determination of the best anchoring position for the side chains is the most rational starting point for the optimization of a polymer with a potential for large...

  15. Pyroacm Resin: An Acetamidomethyl Derived Resin for Solid Phase Synthesis of Peptides through Side Chain Anchoring of C-Terminal Cysteine Residues. (United States)

    Juvekar, Vinayak; Gong, Young Dae


    The design, synthesis and utilization of an efficient acetamidomethyl derived resin for the peptide synthesis is presented using established Fmoc and Boc protocols via side chain anchoring. Cleavage of the target peptide from the resin is performed using carboxymethylsulfenyl chloride under mild conditions which gave in situ thiol-sulfenyl protection of the cysteine residues. The utility of the resin is successfully demonstrated through applications to the syntheses of model peptides and natural products Riparin 1.1 and Riparin 1.2.

  16. Three-component synthesis of highly functionalized aziridines containing a peptide side chain and their one-step transformation into β-functionalized α-ketoamides. (United States)

    Huck, Lena; González, Juan F; de la Cuesta, Elena; Menéndez, J Carlos


    A sequential three-component process is described, starting from 3-arylmethylene-2,5-piperazinediones and involving a one-pot sequence of reactions achieving regioselective opening of the 2,5-diketopiperazine ring and diastereoselective generation of an aziridine ring. This method allows the preparation of N-unprotected, trisubstituted aziridines bearing a peptide side chain under mild conditions. Their transformation into β-trifluoroacetamido-α-ketoamide and α,β-diketoamide frameworks was also achieved in a single step.

  17. Atomic force and optical near-field microscopic investigations of polarization holographic gratings in a liquid crystalline azobenzene side-chain polyester

    DEFF Research Database (Denmark)

    Ramanujam, P.S.; Holme, N.C.R.; Hvilsted, S.


    Atomic force and scanning near-field optical microscopic investigations have been carried out on a polarization holographic grating recorded in an azobenzene side-chain Liquid crystalline polyester. It has been found that immediately following laser irradiation, a topographic surface grating......-field optical microscopic scanning of the grating reveals, however, that the bulk of the film remains optically anisotropic. (C) 1996 American Institute of Physics....

  18. Formation of a Three-Electron Sulfur-Sulfur Bond as a Probe for Interaction between Side Chains of Methionine Residues. (United States)

    Filipiak, Piotr; Bobrowski, Krzysztof; Hug, Gordon L; Pogocki, Dariusz; Schöneich, Christian; Marciniak, Bronislaw


    The mechanism of oxidation processes of l-Met-(Pro)n-l-Met peptides that contain two Met residues located on the N- and C-terminal and separated by a defined number (n = 0-4) of proline residues was investigated in aqueous solutions using pulse radiolysis. The use of such peptides allowed for distance control between the sulfur atoms located in the side chains of the Met residues. The formation of a contact between the side chains of the Met residues was probed by the observation of transients with σ*-type 2c-3e S∴S and S∴O bonds as well as of α-(alkylthio)alkyl radicals (αS). This approach enabled the monitoring, in real time, of the efficiency and kinetics of interactions between methionine side chains. Such knowledge is important, inter alia, for long-distance electron transfer processes because methionine side chains can serve as relay stations and also for many aspects of protein folding when the formation of a contact between two amino acid residues in an unfolded polypeptide chain plays a central role in protein-folding mechanisms. The yields of these transients (measured as G-values) were found to be dependent on the number of Pro residues; however, they were not dependent in a simple way on the average distance ⟨rS-S⟩ between the sulfur atoms in Met residues. A decrease in the yield of the (S∴S)(+) species with an increase in the number of Pro residues in the bridge occurred at the expense of an increase in the yields of the intramolecular three-electron-bonded (S∴O)(+) radical cations and αS radicals. A detailed understanding of these trends in the chemical yields was developed by modeling the underlying chemical kinetics with Langevin dynamical simulations of the various oligoproline peptide chains and combining them with a simple statistical mechanical theory on the end-to-end contact rates for polymer chains. This analysis showed that the formation of a contact between terminal Met residues in the peptides with 0-2 Pro residues was

  19. Side-chain amino-acid-based pH-responsive self-assembled block copolymers for drug delivery and gene transfer. (United States)

    Kumar, Sonu; Acharya, Rituparna; Chatterji, Urmi; De, Priyadarsi


    Developing safe and effective nanocarriers for multitype of delivery system is advantageous for several kinds of successful biomedicinal therapy with the same carrier. In the present study, we have designed amino acid biomolecules derived hybrid block copolymers which can act as a promising vehicle for both drug delivery and gene transfer. Two representative natural chiral amino acid-containing (l-phenylalanine and l-alanine) vinyl monomers were polymerized via reversible addition-fragmentation chain transfer (RAFT) process in the presence of monomethoxy poly(ethylene glycol) based macro-chain transfer agents (mPEGn-CTA) for the synthesis of well-defined side-chain amino-acid-based amphiphilic block copolymers, monomethoxy poly(ethylene glycol)-b-poly(Boc-amino acid methacryloyloxyethyl ester) (mPEGn-b-P(Boc-AA-EMA)). The self-assembled micellar aggregation of these amphiphilic block copolymers were studied by fluorescence spectroscopy, atomic force microscopy (AFM) and scanning electron microscopy (SEM). Potential applications of these hybrid polymers as drug carrier have been demonstrated in vitro by encapsulation of nile red dye or doxorubicin drug into the core of the micellar nanoaggregates. Deprotection of side-chain Boc- groups in the amphiphilic block copolymers subsequently transformed them into double hydrophilic pH-responsive cationic block copolymers having primary amino groups in the side-chain terminal. The DNA binding ability of these cationic block copolymers were further investigated by using agarose gel retardation assay and AFM. The in vitro cytotoxicity assay demonstrated their biocompatible nature and these polymers can serve as "smart" materials for promising bioapplications.

  20. Diketopyrrolopyrrole-Based Conjugated Polymer Entailing Triethylene Glycols as Side Chains with High Thin-Film Charge Mobility without Post-Treatments

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Si-Fen [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; University of Chinese Academy of Sciences, Beijing 100049 P. R. China; Liu, Zi-Tong [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; Cai, Zheng-Xu [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; Dyson, Matthew J. [Department of Materials and Centre for Plastic Electronics, Imperial College London, London SW72AZ UK; Stingelin, Natalie [Department of Materials and Centre for Plastic Electronics, Imperial College London, London SW72AZ UK; Chen, Wei [Materials Science Division, Argonne National Laboratory, 9700 Cass Avenue Lemont IL 60439 USA; Institute for Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue Chicago IL 60637 USA; Ju, Hua-Jun [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; Zhang, Guan-Xin [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; Zhang, De-Qing [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; University of Chinese Academy of Sciences, Beijing 100049 P. R. China


    Side chain engineering of conjugated donor-acceptor polymers is a new way to manipulate their optoelectronic properties. Two new diketopyrrolopyrrole (DPP)-terthiophene-based conjugated polymers PDPP3T-1 and PDPP3T-2, with both hydrophilic triethylene glycol (TEG) and hydrophobic alkyl chains, are reported. It is demonstrated that the incorporation of TEG chains has a significant effect on the interchain packing and thin-film morphology with noticeable effect on charge transport. Polymer chains of PDPP3T-1 in which TEG chains are uniformly distributed can self-assemble spontaneously into a more ordered thin film. As a result, the thin film of PDPP3T-1 exhibits high saturated hole mobility up to 2.6 cm(2) V-1 s(-1) without any post-treatment. This is superior to those of PDPP3T with just alkyl chains and PDPP3T-2. Moreover, the respective field effect transistors made of PDPP3T-1 can be utilized for sensing ethanol vapor with high sensitivity (down to 100 ppb) and good selectivity.

  1. Time-Resolved EPR Study of Electron-Hole Dissociations Influenced by Alkyl Side Chains at the Photovoltaic Polyalkylthiophene:PCBM Interface. (United States)

    Miura, Taku; Aikawa, Motoko; Kobori, Yasuhiro


    Nanosecond time-resolved electron paramagnetic resonance (TREPR) spectroscopy has been utilized at T = 77 K to characterize alkyl side-chain effects on geometries and on the electronic couplings (VCR) of transient charge-separated (CS) states in the photoactive layers fabricated by the spin-coating of mixed solutions of regioregular polyalkylthiophenes (RR-P3AT) and [6,6]-C61-butyric acid methyl ester (PCBM). By increasing the alkyl side-chain number from 6 to 12 in P3AT, a highly distant and long-lived CS state has been obtained. This result is explained by a coupling of the hole dissociation to the polymer librations by the side-chains. From an exponential decay of VCR with respect to the CS distance, the attenuation factor (βe) has been determined to be βe = 0.2 Å(-1). Such a long-range tunneling feature is explained by the generations of the shallowly trapped, delocalized electron-hole pairs by the dissociation of the hole toward π-stacking directions at the organic photovoltaic interface.

  2. Superiority of branched side chains in spontaneous nanowire formation: exemplified by poly(3-2-methylbutylthiophene) for high-performance solar cells. (United States)

    Chen, Hsieh-Chih; Wu, I-Che; Hung, Jui-Hsiang; Chen, Fu-Je; Chen, I-Wen P; Peng, Yung-Kang; Lin, Chao-Sung; Chen, Chun-Hsien; Sheng, Yu-Jane; Tsao, Heng-Kwong; Chou, Pi-Tai


    One-dimensional nanostructures containing heterojunctions by conjugated polymers, such as nanowires, are expected to greatly facilitate efficient charge transfer in bulk-heterojunction (BHJ) solar cells. Thus, a combined theoretical and experimental approach is pursued to explore spontaneous nanowire formation. A dissipative particle dynamics simulation is first performed to study the morphologies formed by rodlike polymers with various side-chain structures. The results surprisingly predict that conjugated polymers with branched side chains are well suited to form thermodynamically stable nanowires. Proof of this concept is provided via the design and synthesis of a branched polymer of regioregular poly(3-2-methylbutylthiophene) (P3MBT), which successfully demonstrates highly dense nanowire formation free from any stringent conditions and stratagies. In BHJ solar cells fabricated using a blend of P3MBT and [6,6]-phenyl-C71-butyric acid methyl ester (PC(71) BM), P3MBT polymers are self-organized into highly crystalline nanowires with a d(100) spacing of 13.30 Å. The hole mobility of the P3MBT:PC(71) BM (1:0.5 by weight) blend film reaches 3.83 × 10(-4) cm(2) V(-1) s(-1) , and the maximum incident photon-to-current efficiency reaches 68%. The results unambiguously prove the spontaneous formation of nanowires using solution-processable conjugated polymers with branched alkyl side chains in BHJ solar cells. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Side-chain tunability of furan-containing low-band-gap polymers provides control of structural order in efficient solar cells

    KAUST Repository

    Yiu, Alan T.


    The solution-processability of conjugated polymers in organic solvents has classically been achieved by modulating the size and branching of alkyl substituents appended to the backbone. However, these substituents impact structural order and charge transport properties in thin-film devices. As a result, a trade-off must be found between material solubility and insulating alkyl content. It was recently shown that the substitution of furan for thiophene in the backbone of the polymer PDPP2FT significantly improves polymer solubility, allowing for the use of shorter branched side chains while maintaining high device efficiency. In this report, we use PDPP2FT to demonstrate that linear alkyl side chains can be used to promote thin-film nanostructural order. In particular, linear side chains are shown to shorten π-π stacking distances between backbones and increase the correlation lengths of both π-π stacking and lamellar spacing, leading to a substantial increase in the efficiency of bulk heterojunction solar cells. © 2011 American Chemical Society.

  4. Temperature dependence of internal motions of protein side-chain NH3(+) groups: insight into energy barriers for transient breakage of hydrogen bonds. (United States)

    Zandarashvili, Levani; Iwahara, Junji


    Although charged side chains play important roles in protein function, their dynamic properties are not well understood. Nuclear magnetic resonance methods for investigating the dynamics of lysine side-chain NH3(+) groups were established recently. Using this methodology, we have studied the temperature dependence of the internal motions of the lysine side-chain NH3(+) groups that form ion pairs with DNA phosphate groups in the HoxD9 homeodomain-DNA complex. For these NH3(+) groups, we determined order parameters and correlation times for bond rotations and reorientations at 15, 22, 28, and 35 °C. The order parameters were found to be virtually constant in this temperature range. In contrast, the bond-rotation correlation times of the NH3(+) groups were found to depend strongly on temperature. On the basis of transition state theory, the energy barriers for NH3(+) rotations were analyzed and compared to those for CH3 rotations. Enthalpies of activation for NH3(+) rotations were found to be significantly higher than those for CH3 rotations, which can be attributed to the requirement of hydrogen bond breakage. However, entropies of activation substantially reduce the overall free energies of activation for NH3(+) rotations to a level comparable to those for CH3 rotations. This entropic reduction in energy barriers may accelerate molecular processes requiring hydrogen bond breakage and play a kinetically important role in protein function.

  5. Photo-aligned blend films of azobenzene-containing polyimides with and without side-chains for inducing inclined alignment of liquid crystal molecules (United States)

    Usami, Kiyoaki; Sakamoto, Kenji


    We have succeeded in controlling the pretilt angle of liquid crystal (LC) molecules over the whole range of 0 to 90° by using photo-aligned blend films of two azobenzene-containing polyimides (Azo-PIs) with and without side-chains. The Azo-PIs were synthesized from pyromellitic dianhydride and a mixture of 4,4'-diaminoazobenzene and 4-(4'-propylbi(cyclohexan)-4-yl)phenyl 3,5-diaminobenzoate (PBCP-DABA). PBCP-DABA is a diamine to introduce a side-chain structure into the polyimide. Defect-free uniform LC alignment was obtained in the pretilt angle (θp) ranges of θp ≤ 11° and θp ≥ 78°. Previously, we reported that the pretilt angle can be controlled using pure photo-aligned films of Azo-PIs with different molar fractions of PBCP-DABA. For the pure photo-aligned films, the defect-free pretilt angle ranges were θp < 5° and θp ≥ 85°. These results suggest that the azimuthal anchoring strength of the blend Azo-PI film is stronger than that of the pure films of Azo-PIs with side-chains, at least for the pretilt angle range from 5 to 11°. We found that the defect-free pretilt angle range can be extended by using the blend Azo-PI films instead of the pure Azo-PI films.

  6. Carbohydrate Analysis (United States)

    Bemiller, James N.

    Carbohydrates are important in foods as a major source of energy, to impart crucial textural properties, and as dietary fiber which influences physiological processes. Digestible carbohydrates, which are converted into monosaccharides, which are absorbed, provide metabolic energy. Worldwide, carbohydrates account for more than 70% of the caloric value of the human diet. It is recommended that all persons should limit calories from fat (the other significant source) to not more than 30% and that most of the carbohydrate calories should come from starch. Nondigestible polysaccharides (all those other than starch) comprise the major portion of dietary fiber (Sect. 10.5). Carbohydrates also contribute other attributes, including bulk, body, viscosity, stability to emulsions and foams, water-holding capacity, freeze-thaw stability, browning, flavors, aromas, and a range of desirable textures (from crispness to smooth, soft gels). They also provide satiety. Basic carbohydrate structures, chemistry, and terminology can be found in references (1, 2).

  7. Side chain structure determines unique physiologic and therapeutic properties of norursodeoxycholic acid in Mdr2−/− mice

    National Research Council Canada - National Science Library

    Halilbasic, Emina; Fiorotto, Romina; Fickert, Peter; Marschall, Hanns‐Ulrich; Moustafa, Tarek; Spirli, Carlo; Fuchsbichler, Andrea; Gumhold, Judith; Silbert, Dagmar; Zatloukal, Kurt; Langner, Cord; Maitra, Uday; Denk, Helmut; Hofmann, Alan F; Strazzabosco, Mario; Trauner, Michael


    24‐ nor ursodeoxycholic acid ( nor UDCA), a side chain–modified ursodeoxycholic acid derivative, has dramatic therapeutic effects in experimental cholestasis and may be a promising agent for the treatment of cholestatic liver diseases...

  8. Carbohydrate Loading. (United States)

    Csernus, Marilyn

    Carbohydrate loading is a frequently used technique to improve performance by altering an athlete's diet. The objective is to increase glycogen stored in muscles for use in prolonged strenuous exercise. For two to three days, the athlete consumes a diet that is low in carbohydrates and high in fat and protein while continuing to exercise and…

  9. Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: comparison between theory and experiment. (United States)

    Makowska, Joanna; Bagińska, Katarzyna; Liwo, Adam; Chmurzyński, Lech; Scheraga, Harold A


    The purpose of this work was to evaluate the effect of the nature of the ionizable end groups, and the solvent, on their acid-base properties in alanine-based peptides. Hence, the acid-base properties of three alanine-based peptides: Ac-KK-(A)(7)-KK-NH(2) (KAK), Ac-OO-(A)(7)-DD-NH(2) (OAD), Ac-KK-(A)(7)-EE-NH(2) (KAE), where A, D, E, K, and O denote alanine, aspartic acid, glutamic acid, lysine, and ornithine, respectively, were determined in water and in methanol by potentiometry. With the availability of these data, the ability of two theoretical methods to simulate pH-metric titration of those peptides was assessed: (i) the electrostatically driven Monte Carlo method with the ECEPP/3 force field and the Poisson-Boltzmann approach to compute solvation energy (EDMC/PB/pH), and (ii) the molecular dynamics method with the AMBER force field and the Generalized Born model (MD/GB/pH). For OAD and KAE, pK(a1) and pK(a2) correspond to the acidic side chains. For all three compounds in both solvents, the pK(a1) value is remarkably lower than the pK(a) of a compound modeling the respective isolated side chain, which can be explained by the influence of the electrostatic field from positively charged ornithine or lysine side chains. The experimental titration curves are reproduced well by the MD/GB/pH approach, the agreement being better if restraints derived from NMR measurements are incorporated in the conformational search. Poorer agreement is achieved by the EDMC/PB/pH method.

  10. Estimating the pKa values of basic and acidic side chains in ion channels using electrophysiological recordings: a robust approach to an elusive problem. (United States)

    Cymes, Gisela D; Grosman, Claudio


    As a step toward gaining a better understanding of the physicochemical bases of pK(a)-value shifts in ion channels, we have previously proposed a method for estimating the proton affinities of systematically engineered ionizable side chains from the kinetic analysis of single-channel current recordings. We reported that the open-channel current flowing through mutants of the (cation-selective) muscle nicotinic acetylcholine receptor (AChR) engineered to bear single basic residues in the transmembrane portion of the pore domain fluctuates between two levels of conductance. Our observations were consistent with the idea that these fluctuations track directly the alternate protonation-deprotonation of basic side chains: protonation of the introduced basic group would attenuate the single-channel conductance, whereas its deprotonation would restore the wild-type-like level. Thus, analysis of the kinetics of these transitions was interpreted to yield the pK(a) values of the substituted side chains. However, other mechanisms can be postulated that would also be consistent with some of our findings but according to which the kinetic analysis of the fluctuations would not yield true pK(a)s. Such mechanisms include the pH-dependent interconversion between two conformations of the channel that, while both ion permeable, would support different cation-conduction rates. In this article, we present experimental evidence for the notion that the fluctuations of the open-channel current observed for the muscle AChR result from the electrostatic interaction between fixed charges and the passing cations rather than from a change in conformation. Hence, we conclude that bona fide pK(a) values can be obtained from single-channel recordings. Copyright © 2011 Wiley-Liss, Inc.

  11. Chemoenzymatic synthesis of statine side chain building blocks and application in the total synthesis of the cholesterol-lowering compound solistatin. (United States)

    Rieder, Oliver; Wolberg, Michael; Foegen, Silke E; Müller, Michael


    The synthesis and enzymatic reduction of several 6-substituted dioxohexanoates are presented. Two-step syntheses of tert-butyl 6-bromo-3,5-dioxohexanoate and the corresponding 6-hydroxy compound have been achieved in 89% and 59% yield, respectively. Regio- and enantioselective reduction of these diketones and of the 6-chloro derivative with alcohol dehydrogenase from Lactobacillus brevis (LBADH) gave the (5S)-5-hydroxy-3-oxo products with enantiomeric excesses of 91%, 98.4%, and >99.5%, respectively. Chain elongation of the reduction products by one carbon via cyanide addition, and by more than one carbon by Julia-Kocienski olefination, gave access to well-established statine side-chain building blocks. Application in the synthesis of the cholesterol-lowering natural compound solistatin is given. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Rapid assessment of oxidation via middle-down LCMS correlates with methionine side-chain solvent-accessible surface area for 121 clinical stage monoclonal antibodies. (United States)

    Yang, Rong; Jain, Tushar; Lynaugh, Heather; Nobrega, R Paul; Lu, Xiaojun; Boland, Todd; Burnina, Irina; Sun, Tingwan; Caffry, Isabelle; Brown, Michael; Zhi, Xiaoyong; Lilov, Asparouh; Xu, Yingda

    Susceptibility of methionine to oxidation is an important concern for chemical stability during the development of a monoclonal antibody (mAb) therapeutic. To minimize downstream risks, leading candidates are usually screened under forced oxidation conditions to identify oxidation-labile molecules. Here we report results of forced oxidation on a large set of in-house expressed and purified mAbs with variable region sequences corresponding to 121 clinical stage mAbs. These mAb samples were treated with 0.1% H2O2 for 24 hours before enzymatic cleavage below the hinge, followed by reduction of inter-chain disulfide bonds for the detection of the light chain, Fab portion of heavy chain (Fd) and Fc by liquid chromatography-mass spectrometry. This high-throughput, middle-down approach allows detection of oxidation site(s) at the resolution of 3 distinct segments. The experimental oxidation data correlates well with theoretical predictions based on the solvent-accessible surface area of the methionine side-chains within these segments. These results validate the use of upstream computational modeling to predict mAb oxidation susceptibility at the sequence level.

  13. Comparison of the Photovoltaic Characteristics and Nanostructure of Fullerenes Blended with Conjugated Polymers with Siloxane-Terminated and Branched Aliphatic Side Chains

    KAUST Repository

    Kim, Do Hwan


    All-organic bulk heterojunction solar cells based on blends of conjugated polymers with fullerenes have recently surpassed the 8% efficiency mark and are well on their way to the industrially relevant ∼15% threshold. Using a low band-gap conjugated polymer, we have recently shown that polymer side chain engineering can lead to dramatic improvement in the in-plane charge carrier mobility. In this article, we investigate the effectiveness of siloxy side chain derivatization in controlling the photovoltaic performance of polymer:[6,6]-phenyl-C[71]-butyric acid methyl ester (PC71BM) blends and hence its influence on charge transport in the out-of-plane direction relevant for organic solar cells. We find that, in neat blends, the photocurrent of the polymer with siloxy side chains (PII2T-Si) is 4 times greater than that in blends using the polymer with branched aliphatic side chains (PII2T-ref). This difference is due to a larger out-of-plane hole mobility for PII2T-Si brought about by a largely face-on crystallite orientation as well as more optimal nanoscale polymer:PC71BM mixing. However, upon incorporating a common processing additive, 1,8-diiodooctane (DIO), into the spin-casting blend solution and following optimization, the PII2T-ref:PC71BM OPV device performance undergoes a large improvement and becomes the better-performing device, almost independent of DIO concentration (>1%). We find that the precise amount of DIO plays a larger role in determining the efficiency of PII2T-Si:PC71BM, and even at its maximum, the device performance lags behind optimized PII2T-ref:PC71BM blends. Using a combination of atomic force microscopy and small- and wide-angle X-ray scattering, we are able to elucidate the morphological modifications associated with the DIO-induced changes in both the nanoscale morphology and the molecular packing in blend films. © 2012 American Chemical Society.

  14. Three-component synthesis of highly functionalized aziridines containing a peptide side chain and their one-step transformation into β-functionalized α-ketoamides

    Directory of Open Access Journals (Sweden)

    Lena Huck


    Full Text Available A sequential three-component process is described, starting from 3-arylmethylene-2,5-piperazinediones and involving a one-pot sequence of reactions achieving regioselective opening of the 2,5-diketopiperazine ring and diastereoselective generation of an aziridine ring. This method allows the preparation of N-unprotected, trisubstituted aziridines bearing a peptide side chain under mild conditions. Their transformation into β-trifluoroacetamido-α-ketoamide and α,β-diketoamide frameworks was also achieved in a single step.

  15. Rapid and scalable synthesis of innovative unnatural α,β or γ-amino acids functionalized with tertiary amines on their side-chains. (United States)

    Schneider, Séverine; Ftouni, Hussein; Niu, Songlin; Schmitt, Martine; Simonin, Frédéric; Bihel, Frédéric


    We report a selective ruthenium catalyzed reduction of tertiary amides on the side chain of Fmoc-Gln-OtBu derivatives, leading to innovative unnatural α,β or γ-amino acids functionalized with tertiary amines. Rapid and scalable, this process allowed us to build a library of basic unnatural amino acids at the gram-scale and directly usable for liquid- or solid-phase peptide synthesis. The diversity of available tertiary amines allows us to modulate the physicochemical properties of the resulting amino acids, such as basicity or hydrophobicity.

  16. Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations. (United States)

    Sieradzan, Adam K; Krupa, Paweł; Scheraga, Harold A; Liwo, Adam; Czaplewski, Cezary


    The UNited RESidue (UNRES) model of polypeptide chains is a coarse-grained model in which each amino-acid residue is reduced to two interaction sites, namely, a united peptide group (p) located halfway between the two neighboring α-carbon atoms (Cαs), which serve only as geometrical points, and a united side chain (SC) attached to the respective Cα. Owing to this simplification, millisecond molecular dynamics simulations of large systems can be performed. While UNRES predicts overall folds well, it reproduces the details of local chain conformation with lower accuracy. Recently, we implemented new knowledge-based torsional potentials (Krupa et al. J. Chem. Theory Comput. 2013, 9, 4620–4632) that depend on the virtual-bond dihedral angles involving side chains: Cα···Cα···Cα···SC (τ(1)), SC···Cα···Cα···Cα (τ(2)), and SC···Cα···Cα···SC (τ(3)) in the UNRES force field. These potentials resulted in significant improvement of the simulated structures, especially in the loop regions. In this work, we introduce the physics-based counterparts of these potentials, which we derived from the all-atom energy surfaces of terminally blocked amino-acid residues by Boltzmann integration over the angles λ(1) and λ(2) for rotation about the Cα···Cα virtual-bond angles and over the side-chain angles χ. The energy surfaces were, in turn, calculated by using the semiempirical AM1 method of molecular quantum mechanics. Entropy contribution was evaluated with use of the harmonic approximation from Hessian matrices. One-dimensional Fourier series in the respective virtual-bond-dihedral angles were fitted to the calculated potentials, and these expressions have been implemented in the UNRES force field. Basic calibration of the UNRES force field with the new potentials was carried out with eight training proteins, by selecting the optimal weight of the new energy terms and reducing the weight of the regular torsional terms. The force field

  17. Engineered, highly productive biosynthesis of artificial, lactonized statin side-chain building blocks: The hidden potential of Escherichia coli unleashed. (United States)

    Vajdič, Tadeja; Ošlaj, Matej; Kopitar, Gregor; Mrak, Peter


    We have recently reported the development of an efficient, whole-cell process for chemoenzymatic production of key chiral intermediates in statin synthesis by employing high-density Escherichia coli culture with the overexpressed deoxyribose-5-phosphate aldolase (DERA). The optically pure, 6-substituted cyclic hemiacetals can be used for the synthesis of atorvastatin, rosuvastatin and pitavastatin using further chemical steps. All of the synthetic routes established to date begin with a regiospecific oxidation of these lactol intermediates into the corresponding lactones, followed by several steps yielding 6-substituted, open-chain or lactonized derivatives which can be coupled by various approaches with the heterocyclic part of the statin molecule. Here we report for the first time the use of PQQ-dependent glucose dehydrogenases for a highly efficient, regioselective oxidation of artificial, derivatized aldohexoses, more specifically, the statin lactol intermediates. First, PQQ-dependent dehydrogenases of both soluble and membrane-bound type were characterized for their activity toward various DERA-derived lactols. Further, we describe a highly productive whole-cell system for oxidation of these 2,4-dideoxyaldopyranoses using a PQQ-dependent glucose dehydrogenase (Gcd) overexpressed in E. coli while taking advantage of the respiratory chain as the mediator of the electron transfer to oxygen. Finally, a two-step artificial biosynthetic pathway was developed by unleashing the intrinsic genetic potential of E. coli. The combined overexpression of the endogenous DERA and the membrane-bound, PQQ-dependent glucose dehydrogenase, the latter being coupled to the respiratory chain, allows direct biosynthesis of 6-substituted lactones in a highly productive, high-yield, cost-effective and industrially scalable process. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Carbohydrate microarrays. (United States)

    Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Ola; Shin, Injae


    In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray-based technology has been widely employed for rapid analysis of the glycan binding properties of lectins and antibodies, the quantitative measurements of glycan-protein interactions, detection of cells and pathogens, identification of disease-related anti-glycan antibodies for diagnosis, and fast assessment of substrate specificities of glycosyltransferases. This review covers the construction of carbohydrate microarrays, detection methods of carbohydrate microarrays and their applications in biological and biomedical research.

  19. Carbohydrate microarrays

    DEFF Research Database (Denmark)

    Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Klas Ola


    In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray-based technol......In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray......-based technology has been widely employed for rapid analysis of the glycan binding properties of lectins and antibodies, the quantitative measurements of glycan-protein interactions, detection of cells and pathogens, identification of disease-related anti-glycan antibodies for diagnosis, and fast assessment...

  20. Characterization of the primary structure and the microheterogeneity of the carbohydrate chains of porcine blood-group H substance by 500-MHz 1H-NMR spectroscopy

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Halbeek, H. van; Dorland, L.; Kochetkov, N.K.; Arbatsky, N.P.; Derevitskaya, V.A.


    In blood-group H substance from pig stomach cell linings, carbohydrate structures are known to occur which are O-glycosidically linked via GalNAc to Ser or Thr of the polypeptide backbone. They have in common the Gal(beta1->3)GalNAc core unit, which bears one or more N-acetyllactosamine branches.

  1. Molecular dynamics simulation of radiation grafted FEP films as proton exchange membranes: Effects of the side chain length

    DEFF Research Database (Denmark)

    Li, Xue; Zhao, Yang; Li, Weiwei


    In order to study the microstructure of the prepared potential proton exchange membrane (PEM), molecular dynamics (MD) simulations were used to lucubrate the transport behavior of water molecules and hydronium ions inside the hydrated sulfonated styrene grafted fluorinated ethylene propylene (FEP...... was supposed to exhibit the highest proton conductivity, that is 115.69 mS cm-1. All of the supposed membrane models presented good proton conductivity that could definitely meet the application requirements of the proton exchange membranes. The MD simulations can provide an insight to the chain structure...

  2. In vivo cough suppressive activity of pectic polysaccharide with arabinogalactan type II side chains of Piper nigrum fruits and its synergistic effect with piperine. (United States)

    Khawas, Sadhana; Nosáľová, Gabriela; Majee, Sujay Kumar; Ghosh, Kanika; Raja, Washim; Sivová, Veronika; Ray, Bimalendu


    Piper nigrum L. fruits are not only a prized spice, but also highly valued therapeutic agent that heals many ailments including asthma, cold and respiratory problems. Herein, we have investigated structural features and in vivo antitussive activity of three fractions isolated from Piper nigrum fruits. The water extract (PN-WE) upon fractionation with EtOH yielded two fractions: a soluble fraction (PN-eSf) and a precipitated (PN-ePf) one. The existence of a pectic polysaccharide with arabinogalactan type II side chains (147kDa) in PN-ePf and piperine in PN-eSf were revealed. Moreover, oligosaccharides providing fine structural details of side chains were generated from PN-ePf and then characterized. The parental water extract (PN-WE) that contained both pectic polysaccharide and piperine, after oral administration (50mgkg-1 body weight) to guinea pigs, showed antitussive activity comparable to codeine phosphate (10mgkg-1 body weight). The EtOH precipitated fraction (PN-ePf) containing pectic polysaccharide showed comparatively higher antitussive activity than EtOH soluble fraction (PN-eSf) that contained piperine, but their potencies are lower than the parental water extract. Significantly, the specific airway smooth muscle reactivity of all three fractions remained unchanged. Finally, pectic polysaccharide-piperine combination in parental extract synergistically enhances antitussive effect in guinea pigs. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Succinimide Formation from an NGR-Containing Cyclic Peptide: Computational Evidence for Catalytic Roles of Phosphate Buffer and the Arginine Side Chain

    Directory of Open Access Journals (Sweden)

    Ryota Kirikoshi


    Full Text Available The Asn-Gly-Arg (NGR motif and its deamidation product isoAsp-Gly-Arg (isoDGR have recently attracted considerable attention as tumor-targeting ligands. Because an NGR-containing peptide and the corresponding isoDGR-containing peptide target different receptors, the spontaneous NGR deamidation can be used in dual targeting strategies. It is well known that the Asn deamidation proceeds via a succinimide derivative. In the present study, we computationally investigated the mechanism of succinimide formation from a cyclic peptide, c[CH2CO-NGRC]-NH2, which has recently been shown to undergo rapid deamidation in a phosphate buffer. An H2PO4− ion was explicitly included in the calculations. We employed the density functional theory using the B3LYP functional. While geometry optimizations were performed in the gas phase, hydration Gibbs energies were calculated by the SM8 (solvation model 8 continuum model. We have found a pathway leading to the five-membered ring tetrahedral intermediate in which both the H2PO4− ion and the Arg side chain act as catalyst. This intermediate, once protonated at the NH2 group on the five-membered ring, was shown to easily undergo NH3 elimination leading to the succinimide formation. This study is the first to propose a possible catalytic role for the Arg side chain in the NGR deamidation.

  4. Introduction of a methoxymethyl side chain into p-phenylenediamine attenuates its sensitizing potency and reduces the risk of allergy induction

    Energy Technology Data Exchange (ETDEWEB)

    Goebel, Carsten, E-mail: [The Procter and Gamble Co., Central Product Safety and Communications, Darmstadt (Germany); Troutman, John [The Procter and Gamble Co., Central Product Safety, Cincinnati, OH (United States); Hennen, Jenny [Dept. of Environmental Toxicology, Trier University, Trier (Germany); Rothe, Helga; Schlatter, Harald [The Procter and Gamble Co., Central Product Safety and Communications, Darmstadt (Germany); Gerberick, G. Frank [The Procter and Gamble Co., Central Product Safety, Cincinnati, OH (United States); Blömeke, Brunhilde [Dept. of Environmental Toxicology, Trier University, Trier (Germany)


    The strong sensitizing potencies of the most important primary intermediates of oxidative hair dyes, p-phenylenediamine (PPD) and p-toluylenediamine (PTD, i.e. 2-methyl-PPD) are well established. They are considered as the key sensitizers in hair dye allergic contact dermatitis. While modification of their molecular structure is expected to alter their sensitizing properties, it may also impair their color performance. With introduction of a methoxymethyl side chain we found the primary intermediate 2-methoxymethyl-p-phenylenediamine (ME-PPD) with excellent hair coloring performance but significantly reduced sensitizing properties compared to PPD and PTD: In vitro, ME-PPD showed an attenuated innate immune response when analyzed for its protein reactivity and dendritic cell activation potential. In vivo, the effective concentration of ME-PPD necessary to induce an immune response 3-fold above vehicle control (EC3 value) in the local lymph node assay (LLNA) was 4.3%, indicating a moderate skin sensitizing potency compared to values of 0.1 and 0.17% for PPD and PTD, respectively. Finally, assessing the skin sensitizing potency of ME-PPD under consumer hair dye usage conditions through a quantitative risk assessment (QRA) indicated an allergy induction risk negligible compared to PPD or PTD. - Highlights: • Methoxymethyl side chain in p-phenylenediamine reduces its strong skin sensitizing properties. • Reduced protein reactivity and dendritic cell activation. • Reduced skin sensitizing potency in local lymph node assay (LLNA). • Negligible allergy induction risk under hair dye usage conditions.

  5. Design of the influenza virus inhibitors targeting the PA endonuclease using 3D-QSAR modeling, side-chain hopping, and docking. (United States)

    Yan, Zhihui; Zhang, Lijie; Fu, Haiyang; Wang, Zhonghua; Lin, Jianping


    With the emergence of drug resistance and the structural determination of the PA N-terminal domain (PAN), influenza endonucleases have become an attractive target for antiviral therapies for influenza infection. Here, we combined 3D-QSAR with side-chain hopping and molecular docking to produce novel structures as endonuclease inhibitors. First, a new molecular library was generated with side-chain hopping on an existing template molecule, L-742001, using an in-house fragment library that targets bivalent-cation-binding proteins. Then, the best 3D-QSAR model (AAAHR.500), with q(2)=0.76 and r(2)=0.97 from phase modeling, was constructed from 23 endonuclease inhibitors and validated with 17 test compounds. The AAAHR.500 model was then used to select effective candidates from the new molecular library. Combining 3D-QSAR with docking using Glide and Autodock, 13 compounds were considered the most likely candidate inhibitors. Docking studies showed that the binding modes of these compounds were consistent with the crystal structures of known inhibitors. These compounds could serve as potential endonuclease inhibitors for further biological activity tests. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Characterizing methyl-bearing side chain contacts and dynamics mediating amyloid β protofibril interactions using ¹³C(methyl)-DEST and lifetime line broadening. (United States)

    Fawzi, Nicolas L; Libich, David S; Ying, Jinfa; Tugarinov, Vitali; Clore, G Marius


    Many details pertaining to the formation and interactions of protein aggregates associated with neurodegenerative diseases are invisible to conventional biophysical techniques. We recently introduced (15)N dark-state exchange saturation transfer (DEST) and (15)N lifetime line-broadening to study solution backbone dynamics and position-specific binding probabilities for amyloid β (Aβ) monomers in exchange with large (2-80 MDa) protofibrillar Aβ aggregates. Here we use (13)C(methyl)DEST and lifetime line-broadening to probe the interactions and dynamics of methyl-bearing side chains in the Aβ-protofibril-bound state. We show that all methyl groups of Aβ40 populate direct-contact bound states with a very fast effective transverse relaxation rate, indicative of side-chain-mediated direct binding to the protofibril surface. The data are consistent with position-specific enhancements of (13)C(methyl)-R₂(tethered) values in tethered states, providing further insights into the structural ensemble of the protofibril-bound state. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Symmetry Breaking in Side Chains Leading to Mixed Orientations and Improved Charge Transport in Isoindigo- alt -Bithiophene Based Polymer Thin Films

    Energy Technology Data Exchange (ETDEWEB)

    Xue, Guobiao [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; MOE Key; Zhao, Xikang [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; Qu, Ge [Department of Chemical & amp, Biomolecular; Xu, Tianbai [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; College; amp, Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China; Gumyusenge, Aristide [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; Zhang, Zhuorui [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China; Zhao, Yan [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; Diao, Ying [Department of Chemical & amp, Biomolecular; Li, Hanying [MOE Key; Mei, Jianguo [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; Birck Nanotechnology Center, Purdue University, 1205 West State Street, West Lafayette, Indiana 47906, United States


    The selection of side chains is important in design of conjugated polymers. It not only affects their intrinsic physical properties, but also has an impact on thin film morphologies. Recent reports suggested that a face-on/edge-on bimodal orientation observed in polymer thin films may be responsible for a three-dimensional (3D) charge transport and leads to dramatically improved mobility in donor–acceptor based conjugated polymers. To achieve a bimodal orientation in thin films has been seldom explored from the aspect of molecular design. Here, we demonstrate a design strategy involving the use of asymmetric side chains that enables an isoindigo-based polymer to adopt a distinct bimodal orientation, confirmed by the grazing incidence X-ray diffraction. As a result, the polymer presents an average high mobility of 3.8 ± 0.7 cm2 V–1 s–1 with a maximum value of 5.1 cm2 V–1 s–1, in comparison with 0.47 and 0.51 cm2 V–1 s–1 obtained from the two reference polymers. This study exemplifies a new strategy to develop the next generation polymers through understanding the property-structure relationship.

  8. Pretilt angle control of liquid crystal molecules by photoaligned films of azobenzene-containing polyimide with a different content of side-chain (United States)

    Usami, Kiyoaki; Sakamoto, Kenji; Yokota, Junichiro; Uehara, Yoichi; Ushioda, Sukekatsu


    We have investigated the pretilt angle of liquid crystal (LC) molecules induced by photoaligned films of a series of polyimides. The polyimides were random copolymers synthesized from pyromellitic dianhydride and a mixture of 4,4'-diaminoazobenzene and 4-[4'-propylbi(cyclohexan)-4-yl]phenyl 3,5-diaminobenzoate (PBCP-DABA). PBCP-DABA is a diamine to introduce a side-chain structure into polyimide. We found that the pretilt angle of LC molecules can be controlled from 0° to 90° by varying the molar fraction (x) of PBCP-DABA from 0 to 0.5. Defect-free uniform LC alignment was observed for x ≤0.125 and x ≥0.3, but threadlike textures appeared for 0.15≤x≤0.25. Since the interaction between the polyimide backbone structure and the LC molecule may be blocked by relatively dense side-chains, the appearance of threadlike texture is tentatively attributed to weak azimuthal anchoring strength of the photoaligned polyimide films with x ≥0.15.

  9. Synthesis of novel polymethacrylates with siloxyl bridging perfluoroalkyl side-chains for hydrophobic application on cotton fabrics

    Energy Technology Data Exchange (ETDEWEB)

    Cai, Lu; Dai, Li; Yuan, Yanhua; Liu, Anqi [College of Textile and Clothing Engineering, Soochow University, Suzhou 215021 (China); National Engineering Laboratory for Modern Silk, Suzhou 215123 (China); Zhanxiong, Li, E-mail: [College of Textile and Clothing Engineering, Soochow University, Suzhou 215021 (China); National Engineering Laboratory for Modern Silk, Suzhou 215123 (China)


    Highlights: • Novel polymethacrylates with multi-perfluoroalkyl groups were reported. • TFSMA monomer in the polymer contributed much to the lower surface free energy. • PSD and TEM showed a broader size distribution with the increasing fluorine content. • EDS and XPS revealed migration of perfluoroalkyl chains under high temperature. - Abstract: Three novel fluorinated methacrylate monomers with siloxyl bridging perfluoroalkyl groups were synthesized and characterized. Afterwards, the corresponding polymethacrylate latexes, namely monofluoroalkylsiloxyl polymethacrylate (PMFSMA), bisfluoroalkylsiloxyl polymethacrylate (PBFSMA) and trisfluoroalkylsiloxyl polymethacrylate (PTFSMA), were prepared and coated onto cotton fabrics to make them water-repellent. Particle size, particle size distribution, zeta potential and high-resolution transmission electron microscope (TEM) were tested to assess the emulsion stability and particle morphology. Thermal properties of PTFSMA were evaluated by thermal-gravimetric analysis (TGA). Surface properties of the coated cotton fabrics were characterized by Fourier transform infrared spectroscopy (FT-IR), scanning electron microscope (SEM), water contact angle (WCA), adhesive force and X-ray photoelectron spectroscopy (XPS). It was found that the incorporation of more perfluoroalkyl chains and the annealing process could decrease the surface free energy of polymer film to 13.7 mN/m. Furthermore, the EDS spectra of PTFSMA film after annealing showed an enrichment of fluorine in the film-air interface.

  10. Carbohydrate-Loading Diet (United States)

    ... of your calories from carbohydrates. The role of carbohydrates Carbohydrates, also known as starches and sugars, are ... to consume some energy sources during your event. Carbohydrate loading Carbohydrate loading is done the week before ...

  11. [Carbohydrates in clinical nutrition]. (United States)

    Lysikov, Iu A


    The article presents data on role of carbohydrate in clinical nutrition. The review described carbohydrate metabolism, hormonal regulation of carbohydrate, carbohydrate energy source role, carbohydrate requirements in critical study.

  12. Natural-abundance 13C-NMR spectroscopy of two glyco-asparagines derived from the core of N-glycosidic carbohydrate chains

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Dijkstra, B.W.; Strecker, G.; Montreuil, J.


    13C-NMR spectroscopic studies were carried out on Manalpha(1->6)Man beta(1->4)GlcNAc beta(1->4)GlcNAc beta(1->N)-Asn and Man alpha(1->6)Man beta(1->4)GlcNAc beta(1->4)[Fuc alpha(1->6)]GlcNAc beta(1->N)Asn, which are part of the invariant core of N-glycosidically linked carbohydrates of

  13. Side-chain anchoring strategy for solid-phase synthesis of peptide acids with C-terminal cysteine. (United States)

    Barany, George; Han, Yongxin; Hargittai, Balazs; Liu, Rong-Qiang; Varkey, Jaya T


    Many naturally occurring peptide acids, e.g., somatostatins, conotoxins, and defensins, contain a cysteine residue at the C-terminus. Furthermore, installation of C-terminal cysteine onto epitopic peptide sequences as a preliminary to conjugating such structures to carrier proteins is a valuable tactic for antibody preparation. Anchoring of N(alpha)-Fmoc, S-protected C-terminal cysteine as an ester onto the support for solid-phase peptide synthesis is known to sometimes occur in low yields, has attendant risks of racemization, and may also result in conversion to a C-terminal 3-(1-piperidinyl)alanine residue as the peptide chain grows by Fmoc chemistry. These problems are documented for several current strategies, but can be circumvented by the title anchoring strategy, which features the following: (a). conversion of the eventual C-terminal cysteine residue, with Fmoc for N(alpha)-amino protection and tert-butyl for C(alpha)-carboxyl protection, to a corresponding S-xanthenyl ((2)XAL(4)) preformed handle derivative; and (b). attachment of the resultant preformed handle to amino-containing supports. This approach uses key intermediates that are similar to previously reported Fmoc-XAL handles, and builds on earlier experience with Xan and related protection for cysteine. Implementation of this strategy is documented here with syntheses of three small model peptides, as well as the tetradecapeptide somatostatin. Anchoring occurs without racemization, and the absence of 3-(1-piperidinyl)alanine formation is inferred by retention of chains on the support throughout the cycles of Fmoc chemistry. Fully deprotected peptides, including free sulfhydryl peptides, are released from the support in excellent yield by using cocktails containing a high concentration (i.e., 80-90%) of TFA plus appropriate thiols or silanes as scavengers. High-yield release of partially protected peptides is achieved by treatment with cocktails containing a low concentration (i.e., 1-5%) of TFA. In

  14. [Biological function of cancer-associated carbohydrate antigens]. (United States)

    Kannagi, R


    An important outcome of the monoclonal antibody approach for cancer-associated antigens is that cell-surface carbohydrates have been shown to be very important cancer-associated antigens. These antigens are currently classified into several groups. The first group has the sugar determinant carried by so-called type 1 chain carbohydrates, with a backbone structure composed of the Gal beta 1-->3GlcNAc beta repeating unit. The antigens in this group are utilized mainly for the diagnosis of cancers in the pancreas, biliary tract and other digestive organs. This group includes the well-known serum tumor marker, the 2 -->3 sialyl Le(a) antigen, which is detected by N19-9 and other antibodies. This group also includes DU-PAN-2, which was recently confirmed to be the sialyl Lec. The second group has the polysaccharide determinant carried by so-called type 2 chain carbohydrates, the characteristic feature of which is a backbone structure composed of the Gal beta1 -->4GlcNAc beta repeating unit. This group includes the tumor markers, sialyl SSEA-1, CSLEX-1 or sialyl Lewis X, and is used for the diagnosis of cancers originating in the lung, ovary and digestive organs. The third group has the antigenic determinant carried by the innermost core structures in O-linked carbohydrate side chains. The example of this group is the sialyl Tn antigen, which is detected in ovarian cancers. This group also includes the recently described carbohydrate determinant called Fl alpha antigen, which is frequently expressed in gastric cancer cells. Some of the antigens in the first and second groups such as sialyl Le(a) and sialyl Le(x), serve as ligands for E-selectin, a cell adhesion molecule expressed on activated human endothelial cells, and play significant roles in hematogenous metastasis of cancer.

  15. Dietary non-digestible carbohydrates and the resistance to intestinal infections

    NARCIS (Netherlands)

    Bruggencate, ten S.J.M.


    Keywords: Non-digestible carbohydrates, prebiotics, inulin, FOS, calcium, microflora, short-chain fatty acids, mucin, intestinal permeability, salmonella, infection, rat, humanDietary non-digestible carbohydrates and the resistance to intestinal infectionsNon-digestible carbohydrates (NDC) stimulate

  16. Effects of Odd–Even Side Chain Length of Alkyl-Substituted Diphenylbithiophenes on First Monolayer Thin Film Packing Structure

    KAUST Repository

    Akkerman, Hylke B.


    Because of their preferential two-dimensional layer-by-layer growth in thin films, 5,5′bis(4-alkylphenyl)-2,2′-bithiophenes (P2TPs) are model compounds for studying the effects of systematic chemical structure variations on thin-film structure and morphology, which in turn, impact the charge transport in organic field-effect transistors. For the first time, we observed, by grazing incidence X-ray diffraction (GIXD), a strong change in molecular tilt angle in a monolayer of P2TP, depending on whether the alkyl chain on the P2TP molecules was of odd or even length. The monolayers were deposited on densely packed ultrasmooth self-assembled alkane silane modified SiO2 surfaces. Our work shows that a subtle change in molecular structure can have a significant impact on the molecular packing structure in thin film, which in turn, will have a strong impact on charge transport of organic semiconductors. This was verified by quantum-chemical calculations that predict a corresponding odd-even effect in the strength of the intermolecular electronic coupling. © 2013 American Chemical Society.

  17. A novel α-galactosidase from Fusarium oxysporum and its application in determining the structure of the gum arabic side chain. (United States)

    Maruta, Akiho; Yamane, Mirei; Matsubara, Midori; Suzuki, Shiho; Nakazawa, Masami; Ueda, Mitsuhiro; Sakamoto, Tatsuji


    We previously reported that Fusarium oxysporum 12S produces two bifunctional proteins, FoAP1 and FoAP2, with α-d-galactopyranosidase (GPase) and β-l-arabinopyranosidase (APase) activities. The aim of this paper was to purify a third GPase, FoGP1, from culture supernatant of F. oxysporum 12S, to characterize it, and to determine its mode of action towards gum arabic. A cDNA encoding FoGP1 was cloned and the protein was overexpressed in Escherichia coli. Module sequence analysis revealed the presence of a GH27 domain in FoGP1. The recombinant enzyme (rFoGP1) showed a GPase/APase activity ratio of 330, which was quite different from that of FoAP1 (1.7) and FoAP2 (0.2). Among the natural substrates tested, rFoGP1 showed the highest activity towards gum arabic. In contrast to other well-characterized GPases, rFoGP1 released a small amount of galactose from α-galactosyl oligosaccharides such as raffinose and exhibited no activity toward galactomannans, which are highly substituted with α-galactosyl side chains. This indicated that FoGP1 is an unusual type of GPase. rFoGP1 released 30% of the total galactose from gum arabic, suggesting the existence of a large number of α-galactosyl residues at the non-reducing ends of gum arabic side chains. Together, rFoGP1 and α-l-arabinofuranosidase released four times more arabinose than α-l-arabinofuranosidase acting alone. This suggested that a large number of α-l-arabinofuranosyl residues is capped by α-galactosyl residues. 1H NMR experiments revealed that rFoGP1 hydrolyzed the α-1,3-galactosidic linkage within the side chain structure of [α-d-Galp-(1→3)-α-l-Araf-(1→] in gum arabic. In conclusion, rFoGP1 is highly active toward α-1,3-galactosyl linkages but negligibly or not active toward α-1,6-galactosyl linkages. The novel FoGP1 might be used to modify the physical properties of gum arabic, which is an industrially important polysaccharide used as an emulsion stabilizer and coating agent. Copyright © 2017

  18. Significant Improvement of Semiconducting Performance of the Diketopyrrolopyrrole-Quaterthiophene Conjugated Polymer through Side-Chain Engineering via Hydrogen-Bonding. (United States)

    Yao, Jingjing; Yu, Chenmin; Liu, Zitong; Luo, Hewei; Yang, Yang; Zhang, Guanxin; Zhang, Deqing


    Three diketopyrrolopyrrole (DPP)-quaterthiophene conjugated polymers, pDPP4T-1, pDPP4T-2, and pDPP4T-3, in which the molar ratios of the urea-containing alkyl chains vs branching alkyl chains are 1:30, 1:20, and 1:10, respectively, were prepared and investigated. In comparison with pDPP4T without urea groups in the alkyl side chains and pDPP4T-A, pDPP4T-B, and pDPP4T-C containing both linear and branched alkyl chains, thin films of pDPP4T-1, pDPP4T-2, and pDPP4T-3 exhibit higher hole mobilities; thin-film mobility increases in the order pDPP4T-1 thin film of pDPP4T-3 can reach 13.1 cm(2) V(-1) s(-1) after thermal annealing at just 100 °C. The incorporation of urea groups in the alkyl side chains also has an interesting effect on the photovoltaic performances of DPP-quaterthiophene conjugated polymers after blending with PC71BM. Blended thin films of pDPP4T-1:PC71BM, pDPP4T-2:PC71BM, and pDPP4T-3:PC71BM exhibit higher power conversion efficiencies (PCEs) than pDPP4T:PC71BM, pDPP4T-A:PC71BM, pDPP4T-B:PC71BM, and pDPP4T-C:PC71BM. The PCE of pDPP4T-1:PC71BM reaches 6.8%. Thin films of pDPP4T-1, pDPP4T-2, and pDPP4T-3 and corresponding thin films with PC71BM were characterized with AFM, GIXRD, and STEM. The results reveal that the lamellar packing order of the alkyl chains is obviously enhanced for thin films of pDPP4T-1, pDPP4T-2, and pDPP4T-3; after thermal annealing, slight inter-chain π-π stacking emerges for pDPP4T-2 and pDPP4T-3. Blends of pDPP4T-1, pDPP4T-2, and pDPP4T-3 with PC71BM show a more pronounced micro-phase separation. These observations suggest that the presence of urea groups may further facilitate the assemblies of these conjugated polymers into nanofibers and ordered aggregation of PC71BM.

  19. Synthesis and crystallochromy of 1,4,7,10-tetraalkyltetracenes: tuning of solid-state optical properties of tetracenes by alkyl side-chain length. (United States)

    Kitamura, Chitoshi; Abe, Yasushi; Ohara, Takuya; Yoneda, Akio; Kawase, Takeshi; Kobayashi, Takashi; Naito, Hiroyoshi; Komatsu, Toshiki


    We synthesized a series of 1,4,7,10-tetraalkyltetracenes using a new 2,6-naphthodiyne precursor and 2,5-dialkylfurans as starting materials (alkyl=methyl to hexyl). Surprisingly, the solid-state color of the tetracenes ranges through yellow, orange, and red. Both yellow and red solids are obtained for the butyl derivative. Optical properties in solution show no marked differences; however, those in the solid state show characteristics that vary with alkyl side-chain length: methyl, propyl, and pentyl derivatives are orange; ethyl and butyl derivatives are yellow; and another butyl and hexyl derivative are red. X-ray analyses reveal that the molecular structures are planar, semi-chair, or chair forms; the chair form takes a herringbone-like arrangement and the other forms take slipped parallel arrangements. The mechanism of crystallochromy is discussed in terms of molecular structure, crystal packing, and calculations that take account of exciton coupling.

  20. Circulating N-Linked Glycoprotein Side-Chain Biomarker, Rosuvastatin Therapy, and Incident Cardiovascular Disease: An Analysis From the JUPITER Trial. (United States)

    Akinkuolie, Akintunde O; Glynn, Robert J; Padmanabhan, Latha; Ridker, Paul M; Mora, Samia


    GlycA, a novel protein glycan biomarker of N-acetyl side chains of acute-phase proteins, was recently associated with incident cardiovascular disease (CVD) in healthy women. Whether GlycA predicts CVD events in the setting of statin therapy in men and women without CVD but with evidence of chronic inflammation is unknown. In the Justfication for the Use of Statins in Prevention: an Intervention Trial Evaluating Rosuvastatin (JUPITER) trial (NCT00239681), participants with low-density lipoprotein cholesterol 0.20). In the JUPITER trial, increased levels of GlycA were associated with an increased risk of CVD events independent of traditional risk factors and hsCRP. URL: Unique identifier: NCT00239681. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

  1. Analysis of amino acid-water interactions by partitioning in aqueous two-phase systems. I--amino acids with non-polar side-chains. (United States)

    Madeira, Pedro P; Bessa, Ana; Álvares-Ribeiro, Luís; Aires-Barros, M Raquel; Rodrigues, Alírio E; Zaslavsky, Boris Y


    Partition ratios of 10 L-amino acids with non-polar side chains (Gly, Ala, Val, nor-Val, Ile, Leu, nor-Leu, Phe, Trp and Pro) were measured in ten different polymer/polymer aqueous two-phase systems (ATPS) containing 0.15 M NaCl in 0.01 M phosphate buffer, pH 7.4. The solute-specific coefficients representing the solute dipole-dipole, hydrogen bonding and electrostatic interactions with aqueous environment for the compounds examined were determined by the multiple linear regression analysis using the modified linear solvation energy relationship equation. It is shown that linear combinations of these coefficients are correlated with the amino acid lipophilicity/hydrophobicity scales reported in the literature. The results obtained imply that the solute-specific coefficients may be used as solute descriptors for quantitative structure-property relationship (QSPR) analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Synthesis of steroid-biaryl ether hybrid macrocycles with high skeletal and side chain variability by multiple multicomponent macrocyclization including bifunctional building blocks. (United States)

    Wessjohann, Ludger A; Rivera, Daniel G; Coll, Francisco


    Utilizing the multiple multicomponent macrocyclization including bifunctional building blocks (MiB) strategy, a library of nonracemic, nonrepetitive peptoid-containing steroid-biaryl ether hybrid macrocycles was built. Up to 16 new bonds, including those of the macrocyclization, can be formed in one pot simultaneously while introducing varied elements of diversity. Functional diversity is generated primarily by choosing Ugi-reactive functional building blocks, bearing the respective recognition or catalytic motifs. These appear attached to the peptoid backbone of the macrocyclic cavity, similar to side chains of amino acids found in enzyme active sites. Likewise, skeletal diversity is based on the variation of defined bifunctional building blocks which allow the parallel formation of macrocyclic cavities that are highly diverse in shape and size and thus perspectively in function. This straightforward approach is suitable to generate multifunctional macrocycles for applications in catalysis, supramolecular, or biological chemistry.

  3. Food carbohydrate chemistry

    National Research Council Canada - National Science Library

    Wrolstad, R. E


    .... Now in Food Carbohydrate Chemistry, author Wrolstad emphasizes the application of carbohydrate chemistry to understanding the chemistry, physical and functional properties of food carbohydrates...

  4. Side-Chain Isomerization on an n-type Organic Semiconductor ITIC Acceptor Makes 11.77% High Efficiency Polymer Solar Cells. (United States)

    Yang, Yankang; Zhang, Zhi-Guo; Bin, Haijun; Chen, Shanshan; Gao, Liang; Xue, Lingwei; Yang, Changduk; Li, Yongfang


    Low bandgap n-type organic semiconductor (n-OS) ITIC has attracted great attention for the application as an acceptor with medium bandgap p-type conjugated polymer as donor in nonfullerene polymer solar cells (PSCs) because of its attractive photovoltaic performance. Here we report a modification on the molecular structure of ITIC by side-chain isomerization with meta-alkyl-phenyl substitution, m-ITIC, to further improve its photovoltaic performance. In a comparison with its isomeric counterpart ITIC with para-alkyl-phenyl substitution, m-ITIC shows a higher film absorption coefficient, a larger crystalline coherence, and higher electron mobility. These inherent advantages of m-ITIC resulted in a higher power conversion efficiency (PCE) of 11.77% for the nonfullerene PSCs with m-ITIC as acceptor and a medium bandgap polymer J61 as donor, which is significantly improved over that (10.57%) of the corresponding devices with ITIC as acceptor. To the best of our knowledge, the PCE of 11.77% is one of the highest values reported in the literature to date for nonfullerene PSCs. More importantly, the m-ITIC-based device shows less thickness-dependent photovoltaic behavior than ITIC-based devices in the active-layer thickness range of 80-360 nm, which is beneficial for large area device fabrication. These results indicate that m-ITIC is a promising low bandgap n-OS for the application as an acceptor in PSCs, and the side-chain isomerization could be an easy and convenient way to further improve the photovoltaic performance of the donor and acceptor materials for high efficiency PSCs.

  5. Side-chain fluorinated polymer surfactants in aquatic sediment and biosolid-augmented agricultural soil from the Great Lakes basin of North America. (United States)

    Chu, Shaogang; Letcher, Robert J


    Side-chain fluorinated polymer surfactants are the main components of fabric protector sprays and used extensively on furniture and textiles. The composition of these commercial protector products has changed, but there is currently a total dearth of information on these novel fluorinated polymers in the environment. Using a developed analytical approach, two complementary studies examined the distribution of Scotchgard™ fabric protector components in aquatic sediment and in agricultural soils where wastewater treatment plant (WWTP) sourced biosolid application occurred, and in samples from sites in the Laurentian Great Lakes basin of North America. The main components in the pre- and post-2002 Scotchgard™ fabric protectors were identified by MS/MS and Q-TOF-MS to contain a perfluorooctane sulfonamide (S1) and perfluorobutane sulfonamide (S2) based side-chain, respectively, and bonded to a polymer backbone. In fifteen sediment samples collected in 2012-2013 from western Lake Erie and Saginaw Bay (Lake Huron), S1 was in all sediment samples (0.18 to 461.59ng/g dry weight (d.w.)); S2 was in 80% of the sediment samples (agricultural sites (mean 236.36ng/g d.w.; range 41.87 to 622.46ng/g d.w.), and at concentrations much greater than in the aquatic sediment samples. The concentration of S1 and S2 in soil and sediment samples were also much greater than the total concentration of other per-and poly-fluoroalkyl substances (PFASs) that were measured. The ratio of S1 concentration versus ∑22PFAS concentration was up to 1616 in sediment samples from Lake Erie. This results helps to explain why known PFASs account for low percentages of the total extractable organic fluorine (EOF) content in sediment. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  6. Role of aromatic amino acids in carbohydrate binding of plant lectins : Laser photo chemically induced dynamic nuclear polarization study of hevein domain-containing lectins

    NARCIS (Netherlands)

    Siebert, HC; vonderLieth, CW; Kaptein, R; Beintema, JJ; Dijkstra, K; vanNuland, N; Soedjanaatmadja, UMS; Rice, A; Vliegenthart, JFG; Wright, CS; Gabius, HJ

    Carbohydrate recognition by lectins often involves the side chains of tyrosine, tryptophan, and histidine residues. These moieties are able to produce chemically induced dynamic nuclear polarization (CIDNP) signals after laser irradiation in the presence of a suitable radical pair-generating dye.

  7. Healthy carbohydrates (United States)

    Functional foods include dietary fiber consisting of health-promoting carbohydrates. We have produced novel prebiotics from orange peel and observed that they extend the shelf life of probiotic bacteria in synbiotics. Some pectic-oligosaccharides and xyloglucan-oligosaccharides also have anti-adhesi...

  8. Isolation of the putative cDNA encoding cholesterol side chain cleavage cytochrome P450 (CYP11A) of the southern stingray (Dasyatis americana). (United States)

    Nunez, S; Trant, J M


    Cholesterol side chain cleavage cytochrome P450 (P450scc; CYP11A) catalyzes the first step in the production of steroid hormones. By utilizing degenerate oligonucleotide primers in a reverse transcriptase-coupled polymerase chain reaction (RT-PCR), a specific 252 bp fragment of the putative P450scc was amplified from RNA of interrenal tissue (the adrenal cortex homolog) from the southern stingray (Dasyatis americana), blacktip shark (Carcharhinus limbatus), and the spiny dogfish shark (Squalus acanthias). The amino-acid sequences predicted by these PCR products were 73-90% identical to each other. Using the homologous PCR-generated probe, five positive clones were isolated from a cDNA library constructed from interrenal mRNA of the southern stingray. The longest clone (4619 bp) contained the 3'-untranslated region, including four putative polyadenylation signals. Northern blot analysis of stingray interrenal RNA revealed a single transcript of 4.2 kb in length. The incomplete amino-acid sequence predicted by the open reading frame of the cDNA (514 residues in length) is 48% homologous to the trout form and 39-40% homologous to mammalian forms. Even though the stingray P450scc contains an amino terminus longer than the other forms of P450scc, no translation initiation signal (ATG) was evident within the open reading frame. This report presents the first sequence of cytochrome P450scc from this evolutionary unique taxon of vertebrates.

  9. Arginine Residues on the Opposite Side of the Active Site Stimulate the Catalysis of Ribosome Depurination by Ricin A Chain by Interacting with the P-protein Stalk* (United States)

    Li, Xiao-Ping; Kahn, Peter C.; Kahn, Jennifer Nielsen; Grela, Przemysław; Tumer, Nilgun E.


    Ricin inhibits protein synthesis by depurinating the α-sarcin/ricin loop (SRL). Ricin holotoxin does not inhibit translation unless the disulfide bond between the A (RTA) and B (RTB) subunits is reduced. Ricin holotoxin did not bind ribosomes or depurinate them but could depurinate free RNA. When RTA is separated from RTB, arginine residues located at the interface are exposed to the solvent. Because this positively charged region, but not the active site, is blocked by RTB, we mutated arginine residues at or near the interface of RTB to determine if they are critical for ribosome binding. These variants were structurally similar to wild type RTA but could not bind ribosomes. Their Km values and catalytic rates (kcat) for an SRL mimic RNA were similar to those of wild type, indicating that their activity was not altered. However, they showed an up to 5-fold increase in Km and up to 38-fold decrease in kcat toward ribosomes. These results suggest that the stalk binding stimulates the catalysis of ribosome depurination by RTA. The mutated arginines have side chains behind the active site cleft, indicating that the ribosome binding surface of RTA is on the opposite side of the surface that interacts with the SRL. We propose that stalk binding stimulates the catalysis of ribosome depurination by orienting the active site of RTA toward the SRL and thereby allows docking of the target adenine into the active site. This model may apply to the translation factors that interact with the stalk. PMID:24003229

  10. The normally expressed kappa immunoglobulin light chain gene repertoire and somatic mutations studied by single-sided specific polymerase chain reaction (PCR); frequent occurrence of features often assigned to autoimmunity

    DEFF Research Database (Denmark)

    Juul, L; Hougs, L; Andersen, V


    The expressed human kappa light chain gene repertoire utilized by healthy individuals was studied by two different single-sided specific PCR techniques to avoid bias for certain V genes. A total of 103 rearranged kappa sequences from peripheral blood mononuclear cells from healthy individuals were...... cloned from cDNA and assigned to the Vkappa and Jkappa germ-line genes with the closest overall homology. The use of cDNA rather than genomic DNA focused the analysis on activated B cells rich in mRNA. Accordingly, the sequences represented the applied repertoire and almost all were somatically mutated......% and 21% of the sequences, respectively. Extended CDR3s more than nine residues in length were found in 18% of the sequences, and in 71% of cases this was due to insertion of an extra proline residue. This proline was usually explained from the germ-line sequences involved. These results are in good...

  11. Learning about Carbohydrates (United States)

    ... Videos for Educators Search English Español Learning About Carbohydrates KidsHealth / For Kids / Learning About Carbohydrates Print en ... source of energy for the body. What Are Carbohydrates? There are two major types of carbohydrates (or ...

  12. A chemical approach for site-specific identification of NMR signals from protein side-chain NH{sub 3}{sup +} groups forming intermolecular ion pairs in protein–nucleic acid complexes

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Kurtis M. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States); Gorenstein, David G. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Iwahara, Junji, E-mail:, E-mail: [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States)


    Protein–nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein–DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH{sub 3}{sup +} groups forming the intermolecular ion pairs. A characteristic change in their {sup 1}H and {sup 15}N resonances upon this modification (i.e., substitution of phosphate to phosphorodithioate) can represent a signature of an intermolecular ion pair. Hydrogen-bond scalar coupling between protein side-chain {sup 15}N and DNA phosphorodithiaote {sup 31}P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to protein–RNA complexes as well.

  13. Influence of the type of indigestible carbohydrate on plasma and urine short-chain fatty acid profiles in healthy human volunteers

    NARCIS (Netherlands)

    Verbeke, K.; Ferchaud-Roucher, V.; Preston, T.; Small, A. C.; Henckaerts, L.; Krempf, M.; Wang, H.; Vonk, R. J.; Priebe, M. G.

    Background/Objectives: Health effects of whole grain foods are becoming more evident. In this study, we analysed the short-chain fatty acid profiles in urine and serum derived from the colonic fermentation process of C-13-barley meals, prepared from barley grown under (CO2)-C-13 atmosphere.

  14. Disturbed hepatic carbohydrate management during high metabolic demand in medium-chain acyl-CoA dehydrogenase (MCAD)-deficient mice

    NARCIS (Netherlands)

    Herrema, Hillechien; Derks, Terry; van Dijk, Theo H.; Bloks, Vincent W.; Gerding, Albert; Havinga, Rick; Tietge, Uwe J. F.; Müller, Michael; Smit, G. Peter A.; Kuipers, Folkert; Reijngoud, Dirk-Jan

    Medium-chain acyl-coenzyme A (CoA) dehydrogenase (MCAD) catalyzes crucial steps in mitochondrial fatty acid oxidation, a process that is of key relevance for maintenance of energy homeostasis, especially during high metabolic demand. To gain insight into the metabolic consequences of MCAD deficiency

  15. Disturbed hepatic carbohydrate management during high metabolic demand in medium-chain acyl-CoA dehydrogenase (MCAD)-deficient mice

    NARCIS (Netherlands)

    Herrema, H.J.; Derks, T.G.; Dijk, van T.H.; Bloks, V.W.; Gerding, A.; Havinga, R.; Tietge, U.J.; Müller, M.R.; Smit, G.P.; Kuipers, F.; Reijngoud, D.J.


    Medium-chain acyl-coenzyme A (CoA) dehydrogenase (MCAD) catalyzes crucial steps in mitochondrial fatty acid oxidation, a process that is of key relevance for maintenance of energy homeostasis, especially during high metabolic demand. To gain insight into the metabolic consequences of MCAD deficiency

  16. Roles of aromatic side chains and template effects of the hydrophobic cavity of a self-assembled peptide nanoarchitecture for anisotropic growth of gold nanocrystals. (United States)

    Tomizaki, Kin-ya; Kishioka, Kohei; Kobayashi, Hiroki; Kobayashi, Akitsugu; Yamada, Naoki; Kataoka, Shunsuke; Imai, Takahito; Kasuno, Megumi


    Gold nanocrystals are promising as catalysts and for use in sensing/imaging systems, photonic/plasmonic devices, electronics, drug delivery systems, and for photothermal therapy due to their unique physical, chemical, and biocompatible properties. The use of various organic templates allows control of the size, shape, structure, surface modification and topology of gold nanocrystals; in particular, currently the synthesis of gold nanorods requires a cytotoxic surfactant to control morphology. To control the shape of gold nanocrystals, we previously demonstrated the de novo design and synthesis of a β-sheet-forming nonapeptide (RU006: Ac-AIAKAXKIA-NH2, X=L-2-naphthylalanine, Nal) and the fabrication of gold nanocrystals by mixing RU006 and HAuCl4 in water. The reaction afforded ultrathin gold nanoribbons 50-100 nm wide, several nanometers high, and microns long. To understand the mechanism underlying gold nanoribbon formation by the RU006 system, we here report (i) the effects of replacement of the Nal aromatic side chain in the RU006 sequence with other aromatic moieties, (ii) the electrochemical properties of aromatic side chains in the de novo designed template peptides to estimate the redox potential and number of electrons participating in the gold crystallization process, and (iii) the stoichiometry of the RU006 system for gold nanoribbon synthesis. Interestingly, RU006 bearing a naphthalene moiety (oxidation peak potential of 1.50 V vs Ag/Ag(+)) and an analog [Ant(6)]-RU006 bearing a bulky anthracene moiety (oxidation peak potential of 1.05 V vs Ag/Ag(+)) allowed the growth of anisotropic (ribbon-like) and isotropic (round) gold nanocrystals, respectively. This trend in morphology of gold nanocrystals was attributed to spatially-arranged hydrophobic cavities sufficiently large to accommodate the gold precursor and to allow directed crystal growth driven by cross-linking reactions among the naphthalene rings. Support for this mechanism was obtained by

  17. In vitro characterization of the oxidative cleavage of the octyl side chain of olanexidine, a novel antimicrobial agent, in dog liver microsomes. (United States)

    Umehara, K; Kudo, S; Hirao, Y; Morita, S; Ohtani, T; Uchida, M; Miyamoto, G


    The metabolism of olanexidine [1-(3,4-dichlorobenzyl)-5-octylbiguanide], a new potent biguanide antiseptic, was investigated in dog liver microsomes to characterize the enzyme(s) catalyzing the biotransformation of olanexidine to C-C bond cleavage metabolites. Olanexidine was initially biotransformed to monohydroxylated metabolite 2-octanol (DM-215), and DM-215 was subsequently oxidized to diol derivatives threo-2,3-octandiol (DM-221) and erythro-2,3-octandiol (DM-222). Diols were further biotransformed to a ketol derivative and C-C bond cleavage metabolite (DM-210, hexanoic acid derivative), an in vivo end product, in the incubation with dog liver microsomes. The formations of DM-215, DM-221, DM-222, and DM-210 followed Michaelis-Menten kinetics, and Eadie-Hofstee analysis of the metabolite formation activity confirmed single-enzyme Michaelis-Menten kinetics. The K(m) and V(max) values for the formation of DM-210 appeared to be 2.42 microM and 26.6 pmol/min/mg in the oxidation of DM-221 and 2.48 microM and 30.2 pmol/min/mg in the oxidation of DM-222. The intrinsic clearance (V(max)/K(m)) of the C-C bond cleavage reactions was essentially the same with either DM-221 or DM-222 as substrate. These oxidative reactions were significantly inhibited by quinidine, a selective inhibitor of CYP2D subfamilies, indicating the metabolic C-C bond cleavage of the octyl side chain of olanexidine to likely be mediated via the CYP2D subfamily in dog liver microsomes. This aliphatic C-C bond cleavage by cytochrome P450s may play an important role in the metabolism of other drugs or endogenous compounds possessing aliphatic chains.

  18. Arginine residues on the opposite side of the active site stimulate the catalysis of ribosome depurination by ricin A chain by interacting with the P-protein stalk. (United States)

    Li, Xiao-Ping; Kahn, Peter C; Kahn, Jennifer Nielsen; Grela, Przemyslaw; Tumer, Nilgun E


    Ricin inhibits protein synthesis by depurinating the α-sarcin/ricin loop (SRL). Ricin holotoxin does not inhibit translation unless the disulfide bond between the A (RTA) and B (RTB) subunits is reduced. Ricin holotoxin did not bind ribosomes or depurinate them but could depurinate free RNA. When RTA is separated from RTB, arginine residues located at the interface are exposed to the solvent. Because this positively charged region, but not the active site, is blocked by RTB, we mutated arginine residues at or near the interface of RTB to determine if they are critical for ribosome binding. These variants were structurally similar to wild type RTA but could not bind ribosomes. Their K(m) values and catalytic rates (k(cat)) for an SRL mimic RNA were similar to those of wild type, indicating that their activity was not altered. However, they showed an up to 5-fold increase in K(m) and up to 38-fold decrease in kcat toward ribosomes. These results suggest that the stalk binding stimulates the catalysis of ribosome depurination by RTA. The mutated arginines have side chains behind the active site cleft, indicating that the ribosome binding surface of RTA is on the opposite side of the surface that interacts with the SRL. We propose that stalk binding stimulates the catalysis of ribosome depurination by orienting the active site of RTA toward the SRL and thereby allows docking of the target adenine into the active site. This model may apply to the translation factors that interact with the stalk.

  19. The Multiple DSF-family QS Signals are Synthesized from Carbohydrate and Branched-chain Amino Acids via the FAS Elongation Cycle (United States)

    Zhou, Lian; Yu, Yonghong; Chen, Xiping; Diab, Abdelgader Abdeen; Ruan, Lifang; He, Jin; Wang, Haihong; He, Ya-Wen


    Members of the diffusible signal factor (DSF) family are a novel class of quorum sensing (QS) signals in diverse Gram-negative bacteria. Although previous studies have identified RpfF as a key enzyme for the biosynthesis of DSF family signals, many questions in their biosynthesis remain to be addressed. In this study with the phytopathogen Xanthomonas campestris pv. campestris (Xcc), we show that Xcc produces four DSF-family signals (DSF, BDSF, CDSF and IDSF) during cell culture, and that IDSF is a new functional signal characterized as cis-10-methyl-2-dodecenoic acid. Using a range of defined media, we further demonstrate that Xcc mainly produces BDSF in the presence of carbohydrates; leucine and valine are the primary precursor for DSF biosynthesis; isoleucine is the primary precursor for IDSF biosynthesis. Furthermore, our biochemical analyses show that the key DSF synthase RpfF has both thioesterase and dehydratase activities, and uses 3-hydroxydedecanoyl-ACP as a substrate to produce BDSF. Finally, our results show that the classic fatty acid synthesis elongation cycle is required for the biosynthesis of DSF-family signals. Taken all together, these findings establish a general biosynthetic pathway for the DSF-family quorum sensing signals. PMID:26289160

  20. Therapeutic effect of Semecarpus anacardium Linn. nut milk extract on carbohydrate metabolizing and mitochondrial TCA cycle and respiratory chain enzymes in mammary carcinoma rats. (United States)

    Arathi, G; Sachdanandam, P


    Semecarpus anacardium Linn. of the family Anacardiaceae has many applications in the Ayurvedic and Siddha systems of medicine. We have evaluated the effect of S. anacardium nut milk extract on carbohydrate metabolizing enzymes and mitochondrial tricarboxylic acid cycle and respiratory enzymes in liver and kidney mitochondria of dimethyl benzanthracene-induced mammary carcinoma in Sprague-Dawley rats. Mammary carcinoma-bearing rats showed a significant rise in glycolytic enzymes (hexokinase, phosphoglucoisomerase and aldolase) and a simultaneous fall in gluconeogenic enzymes (glucose-6-phosphatase and fructose 1,6-diphosphatase). The activities of mitochondrial enzymes isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase, succinate dehydrogenase, malate dehydrogenase, NADH-dehydrogenase and cytochrome C oxidase were significantly lowered in mammary carcinoma-bearing rats when compared with control rats. S. anacardium nut extract administration to tumour-induced animals significantly lowered the glycolytic enzyme activities (hexokinase, phosphoglucoisomerase and aldolase) and there was a rise in gluconeogenic enzymes (glucose-6-phosphatase and fructose 1,6-diphosphatase), which indicated an antitumour and anticancer effect. Comparison of normal control rats and rats administered S. anacardium only as drug control animals showed no significant variations in enzyme activities. S. anacardium nut extract administration to dimethyl benzanthracene-tumour-induced animals significantly increased the activities of mitochondrial enzymes, thereby suggesting its role in mitochondrial energy production.

  1. Carbohydrate microarrays: key developments in glycobiology. (United States)

    Liu, Yan; Palma, Angelina S; Feizi, Ten


    Carbohydrate chains of glycoproteins, glycolipids, proteoglycans, and polysaccharides mediate processes of biological and medical importance through their interactions with complementary proteins. The unraveling of these interactions is therefore a priority in biomedical sciences. Carbohydrate microarray technology is a new development at the frontier of glycomics that is revolutionizing the study of carbohydrate-protein interactions and the elucidation of their specificities in endogenous biological processes, microbe-host interactions, and immune defense mechanisms. In this review, we briefly refer to the principles of numerous platforms since the introduction of carbohydrate microarrays in 2002, and we highlight platforms that are beyond proof-of-concept and have provided new biological information.

  2. Supramolecular Phase-Selective Gelation by Peptides Bearing Side-Chain Azobenzenes: Effect of Ultrasound and Potential for Dye Removal and Oil Spill Remediation (United States)

    Bachl, Jürgen; Oehm, Stefan; Mayr, Judith; Cativiela, Carlos; Marrero-Tellado, José Juan; Díaz Díaz, David


    Phase selective gelation (PSG) of organic phases from their non-miscible mixtures with water was achieved using tetrapeptides bearing a side-chain azobenzene moiety. The presence of the chromophore allowed PSG at the same concentration as the minimum gelation concentration (MGC) necessary to obtain the gels in pure organic phases. Remarkably, the presence of the water phase during PSG did not impact the thermal, mechanical, and morphological properties of the corresponding organogels. In the case of miscible oil/water mixtures, the entire mixture was gelled, resulting in the formation of quasi-hydrogels. Importantly, PSG could be triggered at room temperature by ultrasound treatment of the mixture or by adding ultrasound-aided concentrated solution of the peptide in an oil-phase to a mixture of the same oil and water. Moreover, the PSG was not affected by the presence of salts or impurities existing in water from natural sources. The process could be scaled-up, and the oil phases (e.g., aromatic solvents, gasoline, diesel fuel) recovered almost quantitatively after a simple distillation process, which also allowed the recovery and reuse of the gelator. Finally, these peptidic gelators could be used to quantitatively remove toxic dyes from aqueous solutions. PMID:26006247

  3. Is buffer a good proxy for a crowded cell-like environment? A comparative NMR study of calmodulin side-chain dynamics in buffer and E. coli lysate.

    Directory of Open Access Journals (Sweden)

    Michael P Latham

    Full Text Available Biophysical studies of protein structure and dynamics are typically performed in a highly controlled manner involving only the protein(s of interest. Comparatively fewer such studies have been carried out in the context of a cellular environment that typically involves many biomolecules, ions and metabolites. Recently, solution NMR spectroscopy, focusing primarily on backbone amide groups as reporters, has emerged as a powerful technique for investigating protein structure and dynamics in vivo and in crowded "cell-like" environments. Here we extend these studies through a comparative analysis of Ile, Leu, Val and Met methyl side-chain motions in apo, Ca(2+-bound and Ca(2+, peptide-bound calmodulin dissolved in aqueous buffer or in E. coli lysate. Deuterium spin relaxation experiments, sensitive to pico- to nano-second time-scale processes and Carr-Purcell-Meiboom-Gill relaxation dispersion experiments, reporting on millisecond dynamics, have been recorded. Both similarities and differences in motional properties are noted for calmodulin dissolved in buffer or in lysate. These results emphasize that while significant insights can be obtained through detailed "test-tube" studies, experiments performed under conditions that are "cell-like" are critical for obtaining a comprehensive understanding of protein motion in vivo and therefore for elucidating the relation between motion and function.

  4. Sterol Side Chain Reductase 2 Is a Key Enzyme in the Biosynthesis of Cholesterol, the Common Precursor of Toxic Steroidal Glycoalkaloids in Potato[W][OPEN (United States)

    Sawai, Satoru; Ohyama, Kiyoshi; Yasumoto, Shuhei; Seki, Hikaru; Sakuma, Tetsushi; Yamamoto, Takashi; Takebayashi, Yumiko; Kojima, Mikiko; Sakakibara, Hitoshi; Aoki, Toshio; Muranaka, Toshiya; Saito, Kazuki; Umemoto, Naoyuki


    Potatoes (Solanum tuberosum) contain α-solanine and α-chaconine, two well-known toxic steroidal glycoalkaloids (SGAs). Sprouts and green tubers accumulate especially high levels of SGAs. Although SGAs were proposed to be biosynthesized from cholesterol, the biosynthetic pathway for plant cholesterol is poorly understood. Here, we identify sterol side chain reductase 2 (SSR2) from potato as a key enzyme in the biosynthesis of cholesterol and related SGAs. Using in vitro enzyme activity assays, we determined that potato SSR2 (St SSR2) reduces desmosterol and cycloartenol to cholesterol and cycloartanol, respectively. These reduction steps are branch points in the biosynthetic pathways between C-24 alkylsterols and cholesterol in potato. Similar enzymatic results were also obtained from tomato SSR2. St SSR2-silenced potatoes or St SSR2-disrupted potato generated by targeted genome editing had significantly lower levels of cholesterol and SGAs without affecting plant growth. Our results suggest that St SSR2 is a promising target gene for breeding potatoes with low SGA levels. PMID:25217510

  5. Effect of semiconductor polymer backbone structures and side-chain parameters on the facile separation of semiconducting single-walled carbon nanotubes from as-synthesized mixtures (United States)

    Lee, Dennis T.; Chung, Jong Won; Park, Geonhee; Kim, Yun-Tae; Lee, Chang Young; Cho, Yeonchoo; Yoo, Pil J.; Han, Jae-Hee; Shin, Hyeon-Jin; Kim, Woo-Jae


    Semiconducting single-walled carbon nanotubes (SWNTs) show promise as core materials for next-generation solar cells and nanoelectronic devices. However, most commercial SWNT production methods generate mixtures of metallic SWNTs (m-SWNTs) and semiconducting SWNT (sc-SWNTs). Therefore, sc-SWNTs must be separated from their original mixtures before use. In this study, we investigated a polymer-based, noncovalent sc-SWNT separation approach, which is simple to perform and does not disrupt the electrical properties of the SWNTs, thus improving the performance of the corresponding sc-SWNT-based applications. By systematically investigating the effect that different structural features of the semiconductor polymer have on the separation of sc-SWNTs, we discovered that the length and configuration of the alkyl side chains and the rigidity of the backbone structure exert significant effects on the efficiency of sc-SWNT separation. We also found that electron transfer between the semiconductor polymers and sc-SWNTs is strongly affected by their energy-level alignment, which can be tailored by controlling the donor-acceptor configuration in the polymer backbone structures. Among the polymers investigated, the highly planar P8T2Z-C12 semiconductor polymer showed the best sc-SWNT separation efficiency and unprecedentedly strong electronic interaction with the sc-SWNTs, which is important for improving their performance in applications.

  6. Supramolecular Phase-Selective Gelation by Peptides Bearing Side-Chain Azobenzenes: Effect of Ultrasound and Potential for Dye Removal and Oil Spill Remediation

    Directory of Open Access Journals (Sweden)

    Jürgen Bachl


    Full Text Available Phase selective gelation (PSG of organic phases from their non-miscible mixtures with water was achieved using tetrapeptides bearing a side-chain azobenzene moiety. The presence of the chromophore allowed PSG at the same concentration as the minimum gelation concentration (MGC necessary to obtain the gels in pure organic phases. Remarkably, the presence of the water phase during PSG did not impact the thermal, mechanical, and morphological properties of the corresponding organogels. In the case of miscible oil/water mixtures, the entire mixture was gelled, resulting in the formation of quasi-hydrogels. Importantly, PSG could be triggered at room temperature by ultrasound treatment of the mixture or by adding ultrasound-aided concentrated solution of the peptide in an oil-phase to a mixture of the same oil and water. Moreover, the PSG was not affected by the presence of salts or impurities existing in water from natural sources. The process could be scaled-up, and the oil phases (e.g., aromatic solvents, gasoline, diesel fuel recovered almost quantitatively after a simple distillation process, which also allowed the recovery and reuse of the gelator. Finally, these peptidic gelators could be used to quantitatively remove toxic dyes from aqueous solutions.

  7. Fluorescence spectroscopic study of the aggregation behavior of non-cross-linked and cross-linked poly(alkylmethyldiallylammonium bromides) having decyl, octyl, and hexyl side chains in aqueous solution

    NARCIS (Netherlands)

    Wang, G.J; Engberts, J.B.F.N.


    The conformational state of a series of non-cross-linked and cross-linked poly(alkylmethyldiallylammonium bromides) bearing decyl, octyl, and hexyl side chains ((CL)-CopolC1-10, (CL)-CopolC1-8, and (CL)-CopolC1-6, respectively) in aqueous solutions were investigated by fluorescence spectroscopy

  8. Novel multi-targeting anthra[2,3-b]thiophene-5,10-diones with guanidine-containing side chains: interaction with telomeric G-quadruplex, inhibition of telomerase and topoisomerase I and cytotoxic properties. (United States)

    Ilyinsky, Nikolay S; Shchyolkina, Anna K; Borisova, Olga F; Mamaeva, Olga K; Zvereva, Maria I; Azhibek, Dulat M; Livshits, Mikhail A; Mitkevich, Vladimir A; Balzarini, Jan; Sinkevich, Yuri B; Luzikov, Yuri N; Dezhenkova, Lybov G; Kolotova, Ekaterina S; Shtil, Alexander A; Shchekotikhin, Andrey E; Kaluzhny, Dmitry N


    Novel generations of antitumor anthraquinones are expected to be advantageous over the conventional chemotherapeutic agents. Previous structure-activity relationship studies demonstrated an importance of the positively charged side chains conjugated to anthra[2,3-b]thiophene-5,10-dione scaffolds. Exploring a role of individual side chain moieties in binding to the duplex and G-quadruplex DNA, modulation of telomerase and topoisomerase I activities, intracellular accumulation and cytostatic potency, we herein analyzed a series of reported and newly synthesized guanidine-containing derivatives of anthra[2,3-b]thiophene-5,10-dione. We found that the number of cationic side chains (namely, two) is critical for a tight interaction with human telomeric G-quadruplex (TelQ). Along with a larger drug-TelQ association constant, the telomerase attenuation by anthrathiophenediones with two basic groups in the side chains was more pronounced than by the analogs bearing one basic group. For mono-guanidinated compounds the substituent with the amino group in the side chain provided better TelQ affinity than the methylamine residue. The intracellular uptake of the mono-guanidino derivative with two side chains was >2-fold higher than the respective value for the bis(guanidino) derivative. This difference can explain a lower antiproliferative potency of bis(guanidine) containing compounds. Thus, the modifications of side chains of anthra[2,3-b]thiophene-5,10-dione differently modulated drug-target interactions and cellular effects. Nevertheless, the selected compound 11-(3-aminopropylamino)-4-(2-guanidinoethylamino)anthra[2,3-b]thiophene-5,10-dione 13 demonstrated a high affinity to TelQ and the ability to stabilize the quadruplex structure. These properties were paralleled by reasonable potency of 13 as a telomerase/topoisomerase I inhibitor and an antiproliferative agent. These results indicate that the structural elements of anthra[2,3-b]thiophene-5,10-dione derivatives can be

  9. Complex carbohydrates (image) (United States)

    ... foods such as peas, beans, whole grains, and vegetables. Both simple and complex carbohydrates are turned to ... majority of carbohydrates should come from complex carbohydrates (starches) and naturally occurring sugars, rather than processed or ...

  10. A systematic study of chemogenomics of carbohydrates. (United States)

    Gu, Jiangyong; Luo, Fang; Chen, Lirong; Yuan, Gu; Xu, Xiaojie


    Chemogenomics focuses on the interactions between biologically active molecules and protein targets for drug discovery. Carbohydrates are the most abundant compounds in natural products. Compared with other drugs, the carbohydrate drugs show weaker side effects. Searching for multi-target carbohydrate drugs can be regarded as a solution to improve therapeutic efficacy and safety. In this work, we collected 60 344 carbohydrates from the Universal Natural Products Database (UNPD) and explored the chemical space of carbohydrates by principal component analysis. We found that there is a large quantity of potential lead compounds among carbohydrates. Then we explored the potential of carbohydrates in drug discovery by using a network-based multi-target computational approach. All carbohydrates were docked to 2389 target proteins. The most potential carbohydrates for drug discovery and their indications were predicted based on a docking score-weighted prediction model. We also explored the interactions between carbohydrates and target proteins to find the pathological networks, potential drug candidates and new indications.

  11. The constant electric field effect on the dipole moment of a comb-like polymer with chromophore groups in side chains

    Directory of Open Access Journals (Sweden)

    Tamara P. Stepanova


    Full Text Available The study of conformational properties and tendency to association for chromophore-containing comb-like copolymer of β-(3,4-dicyanophenylazobenzenethyazole methacrylate (A and amylmethacrylate (B (1:1 has been carried out. The copolymer AB is of particular interest because of non-linear optical properties of its films. Dielectric permittivity and dipole moment temperature dependences in dilute cyclohexanone solutions in the temperature range from 20 to 70 °С, in the electric field E ≤ 104 V/cm were investigated by means of static dielectric polarization. It was shown that temperature and concentration dependences of dielectric permittivity for the solvent, copolymer AB, monomer A and polymer B were linear indicating low molecular interactions at temperatures and fields used. The invariable stoichiometry of components in solution for concentration lower than 10–3 mol/mol was proved. The values of dielectric permittivity were extrapolated to infinite dilution and increments α=(Δɛ12/Δx2x2=0 were calculated. The solvent dipole moments were calculated in terms of the Onsager theory whereas dipole moments of AB, A and B were calculated in terms of the Backingham statistical theory of dielectric polarization. Intramacromolecular conformational transition was found to be at ∼40 °C. Dipole moment of A was shown to increase with both temperature and electric field strength. Copolymer side chains trans-location takes place due to intramacromolecular association resulting in the compensation of dipole moments and Kirkwood factor g ≈ 0.6. The association of A units increases in the electric field reducing the dipole moment per monomer unit significantly and g values approximately twice.

  12. Observation of the side chain O-methylation of glutamic acid or aspartic acid containing model peptides by electrospray ionization-mass spectrometry. (United States)

    Atik, A Emin; Guray, Melda Z; Yalcin, Talat


    O-methylation of the side chains of glutamic acid (E) and aspartic acid (D) residues is generally observed modification when an acidified methanol/water (MeOH/dH2O) mixture is used as a solvent system during sample preparation for proteomic research. This chemical modification may result misidentification with endogenous protein methylation; therefore, a special care should be taken during sample handling prior to mass spectrometric analysis. In the current study, we systematically examined the extent of E/D methylation and C-terminus carboxyl group of synthetic model peptides in terms of different incubation temperatures, storage times, and added acid types as well as its percentages. To monitor these effects, C-terminus amidated and free acid forms of synthetic model peptides comprised of E or D residue(s) have been analyzed by electrospray ionization-mass spectrometry (ESI-MS). Additionally, LC-MS/MS experiments were performed to confirm the formation of methylated peptide product. The results showed that the rate of methylation was increased as the temperature increases along with prolong incubation times. Moreover, the extent of methylation was remarkably high when formic acid (FA) used as a protonation agent instead of acetic acid (AA). In addition, it was found that the degree of methylation was significantly decreased by lowering acid percentages in ESI solution. More than one acidic residue containing model peptides have been also used to explore the extent of multiple methylation reaction. Lastly, the ethanol (EtOH) and isopropanol (iPrOH) have been substituted separately with MeOH in sample preparation step to investigate the extent of esterification reaction under the same experimental conditions. However, in the positive perspective of view, this method can be used as a simple, rapid and cheap method for methylation of acidic residues under normal laboratory conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Benchmark Database on Isolated Small Peptides Containing an Aromatic Side Chain: Comparison Between Wave Function and Density Functional Theory Methods and Empirical Force Field

    Energy Technology Data Exchange (ETDEWEB)

    Valdes, Haydee; Pluhackova, Kristyna; Pitonak, Michal; Rezac, Jan; Hobza, Pavel


    A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A)—where F and W are of aromatic character—is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone–aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a ‘-D’ symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals—not covering this energy—fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.

  14. Vasoactive intestinal peptide-induced expression of cytochrome P450 cholesterol side-chain cleavage and 17 alpha-hydroxylase enzyme activity in hen granulosa cells. (United States)

    Johnson, A L; Li, Z; Gibney, J A; Malamed, S


    Experiments were conducted to determine whether vasoactive intestinal peptide (VIP) can regulate expression of cytochrome P450 side-chain cleavage (P450scc) and P450 17 alpha-hydroxylase (P450 17 alpha-OH) mRNA levels and enzyme activity in granulosa cells from nonhierarchal (6-8-mm) follicles. Initial studies demonstrated that immunoreactive VIP is localized within the theca (but not granulosa) layer of both resting (< 0.5-mm follicles) and 6-8-mm follicles, thus providing a potential paracrine mechanism of action for VIP. While short-term (3 h) incubation of granulosa cells with VIP (0.001-1.0 microM) failed to stimulate progesterone production from 6-8-mm follicle granulosa cells, a 4-h culture period in the presence of VIP resulted in increased cyclic AMP (cAMP) accumulation, and a 24-h culture period resulted in progesterone synthesis and increased P450scc mRNA levels; control levels of each endpoint measurement were not altered within the period observed. By contrast, culture with the growth factor transforming growth factor alpha (TGF alpha) in the presence of VIP (1 microM) prevented increases in P450scc mRNA levels and progesterone production. Similar effects of VIP and TGF alpha in the presence of VIP were demonstrated for P450 17 alpha-OH mRNA levels and enzyme activity. Finally, there was an additive effect of VIP (0.1 microM) plus recombinant human (rh) FSH (100 mIU) on the initiation of progesterone production in cultured 6-8-mm follicle granulosa cells compared to the addition of VIP or rhFSH alone.(ABSTRACT TRUNCATED AT 250 WORDS)

  15. Influence of imide-substituents on the H-type aggregates of perylene diimides bearing cetyloxy side-chains at bay positions. (United States)

    Raj, Michael Ruby; Margabandu, Rajamani; Mangalaraja, Ramalinga Viswanathan; Anandan, Sambandam


    A series of perylene-3,4:9,10-tetracarboxylic acid diimides (PDIs, namely TYR-PDI, AEP-PDI, CET-PDI, ANP-PDI and KOD-PDI), comprising long linear cetyloxy side-chains functionalized at the 1,7-bay positions and the different substituents (i.e., hydrophobic/hydrophilic segments) symmetrically linked at the two imide-positions of the perylene core were synthesized to investigate the influence of imide-substituent patterns on the aggregation behaviours of PDIs. The photophysical properties of these PDIs were studied by UV-Vis absorption, fluorescence and time-resolved photoluminescence spectroscopy. The differences in the photophysical properties of the PDIs indicate (i) blue-shifted and broadening absorption properties in both solution and thin-films, (ii) red-shifted and broadening fluorescence behavior at their emission maximum in solution, however, blue-shifted fluorescence behavior in thin-films, and (iii) obviously longer fluorescence life-times corresponding to the existence of rotationally displaced H-type aggregates. The formation of short-range ordered rod-like microstructures through face-to-face alignment of columnar rectangular H-type PDI aggregates was rationalized by scanning electron microscopy. The X-ray diffraction study revealed that the formation of well-defined columnar rectangular (Colrp) H-type PDI aggregates indicated a nearly constant intracolumnar stacking distance of ∼3.9 Å for all PDIs. All of these findings were consistent with the formation of hydrophobic/hydrophilic interactions between the imide-substituents in addition to the strong hydrophobic π-π stacking interactions between the conjugated perylene cores, which were enforced in the H-type PDI aggregates that spontaneously self-organized into Colrp structures.

  16. Effect of side-chain shortening on the physiologic properties of bile acids: hepatic transport and effect on biliary secretion of 23-nor-ursodeoxycholate in rodents. (United States)

    Yoon, Y B; Hagey, L R; Hofmann, A F; Gurantz, D; Michelotti, E L; Steinbach, J H


    To define whether side-chain length influences the physiologic properties of bile acids, nor-ursodeoxycholate (nor-UDC), the C23-nor derivative of ursodeoxycholate (UDC), was synthesized in both nonradioactive and radioactive forms (23-14C). Its hepatic translocation, hepatic biotransformation, and effect on bile flow, biliary bicarbonate, and biliary lipid secretion were compared with that of UDC and those of their respective glycine and taurine conjugates in anesthetized biliary fistula hamsters, rats, and guinea pigs, as well as the isolated perfused hamster liver. Hepatic uptake and biliary output of nor-UDC was slower than that of UDC or cholyltaurine in the isolated perfused hamster liver. In biliary fistula animals, nor-UDC was secreted only in bile. Biliary recovery of nor-UDC as compared to that of UDC was prolonged in the rat and hamster, although not in the guinea pig. Hepatic biotransformation, assessed by chromatography of bile, showed that conjugation of nor-UDC was inefficient, as unconjugated nor-UDC was present in bile; there was little amidation with glycine or taurine in any species, but sulfates and glucuronides, as well as other metabolites, were formed, with the pattern of biotransformation varying among species. When infused over a dosage range of 0.2-30 mumol/kg X min, nor-UDC induced a striking choleresis of canalicular origin. The bile acid-dependent flow was increased threefold in hamsters, ninefold in rats, and nearly twofold in guinea pigs when compared to that induced by UDC. The choleresis was associated with a linear increase in bicarbonate output and concentration in bile, and little phospholipid or cholesterol secretion was induced. A competition experiment in the bile fistula hamster indicated that nor-UDC or its metabolites, or both, appeared to compete for canalicular transport of ursocholyltaurine (a cholyltaurine epimer) when the latter was secreted under its Vmax conditions. Conjugates of nor-UDC and UDC were promptly and

  17. Property Enhancement Effects of Side-Chain-Type Naphthalene-Based Sulfonated Poly(arylene ether ketone) on Nafion Composite Membranes for Direct Methanol Fuel Cells. (United States)

    Wang, Baolong; Hong, Lihua; Li, Yunfeng; Zhao, Liang; Zhao, Chengji; Na, Hui


    Nafion/SNPAEK-x composite membranes were prepared by blending raw Nafion and synthesized side-chain-type naphthalene-based sulfonated poly(arylene ether ketone) with a sulfonation degree of 1.35 (SNPAEK-1.35). The incorporation of SNPAEK-1.35 polymer with ion exchange capacity (IEC) of 2.01 mequiv·g -1 into a Nafion matrix has the property enhancement effects, such as increasing IECs, improving proton conductivity, enhancing mechanical properties, reducing methanol crossover, and improving single cell performance of Nafion. Morphology studies show that Nafion/SNPAEK-x composite membranes exhibit a well-defined microphase separation structure depending on the contents of SNPAEK-1.35 polymer. Among them, Nafion/SNPAEK-7.5% with a bicontinuous morphology exhibits the best comprehensive properties. For example, it shows the highest proton conductivities of 0.092 S cm -1 at 25 °C and 0.163 S cm -1 at 80 °C, which are higher than those of recast Nafion with 0.073 S cm -1 at 25 °C and 0.133 S cm -1 at 80 °C, respectively. Nafion/SNPAEK-5.0% and Nafion/SNPAEK-7.5% membranes display an open circuit voltage of 0.77 V and a maximum power density of 47 mW cm -2 at 80 °C, which are much higher than those of recast Nafion of 0.63 V and 24 mW cm -2 under the same conditions. Nafion/SNPAEK-5.0% membrane also has comparable tensile strength (12.7 MPa) to recast Nafion (13.7 MPa), and higher Young's modulus (330 MPa) than that of recast Nafion (240 MPa). By combining their high proton conductivities, comparable mechanical properties, and good single cell performance, Nafion/SNPAEK-x composite membranes have the potential to be polymer electrolyte materials for direct methanol fuel cell applications.

  18. Allosteric tuning of the intra-cavity binding properties of a calix[6]arene through external binding to a ZnII center coordinated to amino side chains. (United States)

    Darbost, Ulrich; Sénèque, Olivier; Li, Yun; Bertho, Gildas; Marrot, Jérôme; Rager, Marie-Noëlle; Reinaud, Olivia; Jabin, Ivan


    Molecular recognition by calix[6]arene-based receptors bearing three primary alkylamino side chain arms (1) is described. Complexation of Zn(II) ion provides the dinuclear mu-hydroxo complex 2G(OH), XRD characterization of which, together with solution studies, provided evidence of its hosting of neutral polar organic guests G. Treatment of this complex with a carboxylic acid or a sulfonamide (XH) results in the formation of mononuclear species 3G(X), one of which (X = Cl) has been characterized by XRD. A dicationic complex 3G(RNH2) is obtained upon treatment of 2G(OH) with a mixture of an alkylamine and a strong acid. Each of these Zn(II) complexes features a tetrahedral metal ion bound to the three amino arms of ligand 1 and to an exogenous ligand (either HO-, X-, or RNH2) sitting outside of the cavity. As a result, the metal ion structures the calixarene core, constraining it in a cone conformation suitable for guest hosting. The receptor properties of these compounds have been explored in detail and are compared with those of the trisammonium receptor 1G(3H+), based on the same calixarene core, as well as those of the trisimidazole-based dicationic Zn funnel complexes. This study reveals very different host properties, in spite of the common hydrophobic, pi-basic, and hydrogen-bonding acceptor properties of the calixarene cores. A harder external ligand produces a less polarized receptor that is consequently particularly sensitive to the hydrogen-bonding ability of its guest. The less electron-rich the apical ligand, and a fortiori the trisammonium host, the more sensitive the receptor to the dipole moment of the guest. All this stands in contrast with the funnel Zn complexes, in which the coordination link plays a dominant role. It is also shown that the asymmetry of an exo-coordinated enantiopure amino ligand is sensed by the guest. This supramolecular system nicely illustrates how the receptor properties of a hydrophobic cavity can be allosterically tuned by

  19. The mycotoxin patulin induces intra- and intermolecular protein crosslinks in vitro involving cysteine, lysine, and histidine side chains, and alpha-amino groups. (United States)

    Fliege, R; Metzler, M


    As previous studies have indicated a multiple electrophilic reactivity of patulin (PAT) towards simple thiol nucleophiles, we have methodically investigated the ability of PAT to covalently crosslink proteins in vitro. By means of sodium dodecylsulphate polyacrylamide gel electrophoresis, the formation of PAT-induced intermolecular protein-protein crosslinks was clearly demonstrated for bovine serum albumin containing one thiol group per molecule, but also for the thiol-free hen egg lysozyme. Characterization of the crosslink sites was carried out by (1) modulation of the thiol groups with N-ethylimaleimide and 2-iminothiolane; (2) comparison with various known crosslinking agents, i.e. phenylenedimaleimide, glutardialdehyde, and dimethylsuberimidate, and (3) fluorescence incorporation studies using dansyl-labeled amino acids and a fluorescent glutathione derivative. The thiol group of cysteine was preferred for PAT-mediated crosslink reactions, but the side chains of lysine and histidine, and alpha-amino groups also exhibited reactivity. PAT can act both as a homobifunctional as well as a heterobifunctional crosslinking agent. The initial formation of a monoadduct with a thiol group appears to activate PAT for the subsequent reaction with an amino group, but also leads to rapid loss of further electrophilic properties when no second nucleophile for crosslink completion is available. Studies using microtubule proteins as a protein with experimentally controllable quarternary structure and a proposed cellular target for PAT toxicity emphasized the influence of specific sterical conditions on crosslink formation at low protein concentrations. Non-polymerized microtubule proteins, i.e. tubulin alpha,beta-dimers, formed a defined product with PAT consisting of an intramolecularly crosslinked beta-tubulin, whereas guanosine triphosphate- or paclitaxel-induced polymerization to microtubule-like quarternary structures prior to treatment with PAT gave rise to

  20. Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling

    KAUST Repository

    Wang, Songlin


    We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52–57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.

  1. Linear side chains in benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c] pyrrole-4,6-dione polymers direct self-assembly and solar cell performance

    KAUST Repository

    Cabanetos, Clement


    While varying the size and branching of solubilizing side chains in π-conjugated polymers impacts their self-assembling properties in thin-film devices, these structural changes remain difficult to anticipate. This report emphasizes the determining role that linear side-chain substituents play in poly(benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers for bulk heterojunction (BHJ) solar cell applications. We show that replacing branched side chains by linear ones in the BDT motifs induces a critical change in polymer self-assembly and backbone orientation in thin films that correlates with a dramatic drop in solar cell efficiency. In contrast, we show that for polymers with branched alkyl-substituted BDT motifs, controlling the number of aliphatic carbons in the linear N-alkyl-substituted TPD motifs is a major contributor to improved material performance. With this approach, PBDTTPD polymers were found to reach power conversion efficiencies of 8.5% and open-circuit voltages of 0.97 V in BHJ devices with PC71BM, making PBDTTPD one of the best polymer donors for use in the high-band-gap cell of tandem solar cells. © 2013 American Chemical Society.

  2. Cell surface carbohydrates as prognostic markers in human carcinomas

    DEFF Research Database (Denmark)

    Dabelsteen, Erik


    Tumour development is usually associated with changes in cell surface carbohydrates. These are often divided into changes related to terminal carbohydrate structures, which include incomplete synthesis and modification of normally existing carbohydrates, and changes in the carbohydrate core...... structure. The latter includes chain elongation of both glycolipids and proteins, increased branching of carbohydrates in N-linked glycoproteins, and blocked synthesis of carbohydrates in O-linked mucin-like glycoproteins. In mature organisms, expression of distinct carbohydrates is restricted to specific...... cell types; within a given tissue, variation in expression may be related to cell maturation. Tumour-associated carbohydrate structures often reflect a certain stage of cellular development; most of these moieties are structures normally found in other adult or embryonic tissues. There is no unique...

  3. Carbohydrate Metabolism Disorders (United States)

    ... you eat. Food is made up of proteins, carbohydrates, and fats. Chemicals in your digestive system (enzymes) ... metabolic disorder, something goes wrong with this process. Carbohydrate metabolism disorders are a group of metabolic disorders. ...

  4. Carbohydrates and Diabetes (United States)

    ... exactly are carbohydrates and how do they affect your blood sugar? The foods we eat contain nutrients that provide energy and other things the body needs, and one of these is carbohydrates . The two main forms of carbohydrates are: sugars such as ...

  5. Molecular architecture with carbohydrate functionalized β-peptides adopting 314-helical conformation

    Directory of Open Access Journals (Sweden)

    Nitin J. Pawar


    Full Text Available Carbohydrate recognition is essential in cellular interactions and biological processes. It is characterized by structural diversity, multivalency and cooperative effects. To evaluate carbohydrate interaction and recognition, the structurally defined attachment of sugar units to a rigid template is highly desired. β-Peptide helices offer conformationally stable templates for the linear presentation of sugar units in defined distances. The synthesis and β-peptide incorporation of sugar-β-amino acids are described providing the saccharide units as amino acid side chain. The respective sugar-β-amino acids are accessible by Michael addition of ammonia to sugar units derivatized as α,β-unsaturated esters. Three sugar units were incorporated in β-peptide oligomers varying the sugar (glucose, galactose, xylose and sugar protecting groups. The influence of sugar units and the configuration of sugar-β-amino acids on β-peptide secondary structure were investigated by CD spectroscopy.

  6. Low-band-gap conjugated polymers of dithieno[2,3-b:7,6-b]carbazole and diketopyrrolopyrrole: effect of the alkyl side chain on photovoltaic properties. (United States)

    Deng, Yunfeng; Chen, Yagang; Liu, Jian; Liu, Lihui; Tian, Hongkun; Xie, Zhiyuan; Geng, Yanhou; Wang, Fosong


    Four donor–acceptor (D–A) conjugated polymers of dithieno[2,3-b;7,6-b]carbazole (DTC) and diketopyrrolopyrrole, which have different alkyls on the nitrogen atom in the DTC unit and are named as P-C8C8, P-C5C5, P-C12, and P-C10, respectively, have been synthesized for studying the effect of the alkyl side chains on the optoelectronic properties of the polymers. All polymers are soluble in various organic solvents and exhibit identical optical band gaps (E(g)(opt)) of ~1.3 eV and highest occupied molecular orbital energy levels of ~−5.1 eV. Organic thin-film transistors and bulk heterojunction polymer solar cells (BHJ PSCs) with phenyl-C(71)-butyric acid methyl ester (PC(71)BM) as the electron-accepting material were fabricated via solution spin-casting. Compared to the polymers substituted by branched alkyl chains, the polymers with straight alkyl chains show higher hole mobility. Of these polymers, P-C10 exhibits the highest field effect mobility up to 0.011 cm(2)/V·s. The alkyl chain on the DTC unit has a strong impact on the film morphology of polymer:PC(71)BM blends. Severe phase separation was found for polymers containing branched alkyl chains, and those with straight alkyl chains formed uniform films featuring fine phase separation. An open-circuit voltage (V(oc)) of 0.72 V, a short-circuit current density (J(sc)) of 13.4 mA/cm(2), a fill factor (FF) of 62%, and a power conversion efficiency (PCE) of 5.9% were demonstrated for BHJ PSCs based on the P-C10:PC(71)BM [1:3 (w/w)] blend film.

  7. Side Effects (United States)

    Side effects are problems that occur when cancer treatment affects healthy tissues or organs. Learn about side effects caused by cancer treatment. Know what signs and symptoms to call your doctor about. Learn about treatments for side effects.

  8. Methylobacterium extorquens AM1 produces a novel type of acyl-homoserine lactone with a double unsaturated side chain under methylotrophic growth conditions. (United States)

    Nieto Penalver, Carlos G; Morin, Danièle; Cantet, Franck; Saurel, Olivier; Milon, Alain; Vorholt, Julia A


    Acyl-homoserine lactones (acyl-HSLs) have emerged as important regulatory molecules for many gram-negative bacteria. We have found that Methylobacterium extorquens AM1, a member of the pink-pigmented facultative methylotrophs commonly present on plant surfaces, produces several acyl-HSLs depending upon the carbon source. A novel HSL was discovered with a double unsaturated carbon chain (N-(tetradecenoyl)) (C14:2) and characterized by MS and proton NMR. This long-chain acyl-HSL is synthesized by MlaI that also directs synthesis of C14:1-HSL. The Alphaproteobacterium also produces N-hexanoyl-HSL (C6-HSL) and N-octanoyl-HSL (C8-HSL) via MsaI.

  9. Property-based design and synthesis of new chloroquine hybrids via simple incorporation of 2-imino-thiazolidine-4-one or 1h-pyrrol-2, 5-dione fragments on the 4-amino-7-chloroquinoline side chain

    Energy Technology Data Exchange (ETDEWEB)

    Rojas, Fernando A.; Kouznetsov, Vladimir V., E-mail: [Laboratorio de Quimica Organica y Biomolecular, Escuela de Quimica, Universidad Industrial de Santander, Bucaramanga (Colombia)


    In the present work, the syntheses of new 4-amino-7-chloroquinoline N-derivatives were performed by selective modification of the side chain amino group of N-(7-chloroquinoline-4-yl) alkyldiamines, basis framework of chloroquine (CQ) drug through the incorporation of heterocyclic 2-imino-thiazolidine-4-one and {sup 1}H-pyrrol-2,5-dione systems. These potential activity modulators were selected thanks to their characteristic properties, and evaluated by virtual screening employing the OSIRIS and Molinspirations platforms. Designed and synthesized quinolinic derivatives could increase the antimalarial activity of CQ analogues without affecting the lipophilicity as described in literature, suggesting them as candidates for further biological assessments. (author)

  10. Accomplishment of Multifunctional π-Conjugated Polymers by Regulating the Degree of Side-Chain Fluorination for Efficient Dopant-Free Ambient-Stable Perovskite Solar Cells and Organic Solar Cells. (United States)

    Kranthiraja, Kakaraparthi; Park, Sang Ho; Kim, Hyunji; Gunasekar, Kumarasamy; Han, Gibok; Kim, Bumjoon J; Kim, Chang Su; Kim, Soohyun; Lee, Hyunjung; Nishikubo, Ryosuke; Saeki, Akinori; Jin, Sung-Ho; Song, Myungkwan


    We present an efficient approach to develop a series of multifunctional π-conjugated polymers (P1-P3) by controlling the degree of fluorination (0F, 2F, and 4F) on the side chain linked to the benzodithiophene unit of the π-conjugated polymer. The most promising changes were noticed in optical, electrochemical, and morphological properties upon varying the degree of fluorine atoms on the side chain. The properly aligned energy levels with respect to the perovskite and PCBM prompted us to use them in perovskite solar cells (PSCs) as hole-transporting materials (HTMs) and in bulk heterojunction organic solar cells (BHJ OSCs) as photoactive donors. Interestingly, P2 (2F) and P3 (4F) showed an enhanced power conversion efficiency (PCE) of 14.94%, 10.35% compared to P1 (0F) (9.80%) in dopant-free PSCs. Similarly, P2 (2F) and P3 (4F) also showed improved PCE of 7.93% and 7.43%, respectively, compared to P1 (0F) (PCE of 4.35%) in BHJ OSCs. The high photvoltaic performance of the P2 and P3 based photovotaic devices over P1 are well correlated with their energy level alignment, charge transporting, morphological and packing properties, and hole transfer yields. In addition, the P1-P3 based dopant-free PSCs and BHJ OSCs showed an excellent ambient stability up to 30 days without a significant drop in their initial performance.

  11. Carbohydrates in Supramolecular Chemistry. (United States)

    Delbianco, Martina; Bharate, Priya; Varela-Aramburu, Silvia; Seeberger, Peter H


    Carbohydrates are involved in a variety of biological processes. The ability of sugars to form a large number of hydrogen bonds has made them important components for supramolecular chemistry. We discuss recent advances in the use of carbohydrates in supramolecular chemistry and reveal that carbohydrates are useful building blocks for the stabilization of complex architectures. Systems are presented according to the scaffold that supports the glyco-conjugate: organic macrocycles, dendrimers, nanomaterials, and polymers are considered. Glyco-conjugates can form host-guest complexes, and can self-assemble by using carbohydrate-carbohydrate interactions and other weak interactions such as π-π interactions. Finally, complex supramolecular architectures based on carbohydrate-protein interactions are discussed.

  12. Aliphatic side chains of proteins as potential geomarkers of NOM liberated from the melting permafrost and discharged to the Arctic Ocean by the Kolyma River run off (United States)

    Dubinenkov, I. V.; Perminova, I.; Kononikhin, A.; Nikolaev, E.; Hertkorn, N.; Bulygina, E. B.; Holmes, R. M.


    The Arctic ecosystem is highly sensitive to climate change. Global warming might have considerable effects on regional carbon cycling due to permafrost melting. Permafrost in the Arctic region represents an extremely large organic carbon reservoir mostly stored in the permafrost. Mobilization of just a small portion of carbon stored in Arctic soils will have considerable impacts on the flux of organic carbon from land to the Arctic Ocean, which can affect the Arctic environment. The Kolyma River watershed is one of the Arctic Ocean's largest. It is dominated by continuous permafrost which is underlain with rich organic soils susceptible to increased fluvial transport. The goal of the work was to analyze the structure of isolated natural organic matter from different fresh water environments of the Kolyma river basin. NOM was isolated from the Kolyma River main stream, its tributaries, a thermokarst lake, a floodplain stream and the permafrost. Solid phase extraction technique was used with Bond Elute PPL cartridges. Nuclear magnetic resonance spectroscopy (NMR) and Fourier Transform Ion Cyclotron Resonance Mass Spectroscopy (FTICRMS) was used for structural studies because of unsurpassed molecular level structural information provided by these high resolution magnetic resonance techniques. The NOM samples from the Kolyma River showed high contents of non-substituted aliphatic structures with a low content of aromatics and carbohydrates. Aliphatic nature may indicate a microbial source of NOM in the form of degraded terpenoids and hopanols. It was shown that almost all NOM samples from the rivers had similar molecular composition enriched with aliphatic units. The samples from permafrost mud streams were significantly different and contained sharp peptide signatures. In general, permafrost NOM contained much less degraded peptide residuest as compared to riverine samples. Identification of these residues showed the presence of branched amino acids (valine, alanine

  13. SET-RAFT Polymerization of Progargyl Methacrylate and a One-Pot/One-Step Preparation of Side-chain Functionalized Polymers via Combination of SET-RAFT and Click Chemistry. (United States)

    Zhang, Weidong; Zhang, Wei; Zhang, Zhengbiao; Zhu, Jian; Zhu, Xiulin


    A clickable alkyne monomer, PgMA, was successfully polymerized in a well-controlled manner via single electron transfer initiation and propagation through the radical addition fragmentation chain transfer (SET-RAFT) method. The living nature of the polymerization was confirmed by the first-order kinetic plots, the linear relationships between molecular weights and the monomer conversions while keeping relatively narrow $\\overline M _{\\rm w} /\\overline M _{\\rm n}$ (≤1.55), and the successful chain-extension with MMA. The better controllability of SET-RAFT than other CRP methods is attributed to the less competitive termination in view of the presence of the CTA as well as the Cu(II) that is generated in situ. Moreover, a one-pot/one-step technique combining SET-RAFT and "click chemistry" methods has been successfully employed to prepare the side-chain functionalized polymers. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Macrocyclic Pyridyl Polyoxazoles: Structure-Activity Studies of the Aminoalkyl Side-Chain on G-Quadruplex Stabilization and Cytotoxic Activity

    Directory of Open Access Journals (Sweden)

    Joseph E. Rice


    Full Text Available Pyridyl polyoxazoles are 24-membered macrocyclic lactams comprised of a pyridine, four oxazoles and a phenyl ring. A derivative having a 2-(dimethylaminoethyl chain attached to the 5-position of the phenyl ring was recently identified as a selective G-quadruplex stabilizer with excellent cytotoxic activity, and good in vivo anticancer activity against a human breast cancer xenograft in mice. Here we detail the synthesis of eight new dimethylamino-substituted pyridyl polyoxazoles in which the point of attachment to the macrocycle, as well as the distance between the amine and the macrocycle are varied. Each compound was evaluated for selective G-quadruplex stabilization and cytotoxic activity. The more active analogs have the amine either directly attached to, or separated from the phenyl ring by two methylene groups. There is a correlation between those macrocycles that are effective ligands for the stabilization of G-quadruplex DNA (DTtran 15.5–24.6 °C and cytotoxicity as observed in the human tumor cell lines, RPMI 8402 (IC50 0.06–0.50 μM and KB3-1 (IC50 0.03–0.07 μM. These are highly selective G-quadruplex stabilizers, which should prove especially useful for evaluating both in vitro and in vivo mechanism(s of biological activity associated with G-quaqdruplex ligands.

  15. Tuning Surface Properties of Poly(methyl methacrylate) Film Using Poly(perfluoromethyl methacrylate)s with Short Perfluorinated Side Chains. (United States)

    Sohn, Eun-Ho; Ha, Jong-Wook; Lee, Soo-Bok; Park, In Jun


    To control the surface properties of a commonly used polymer, poly(methyl methacrylate) (PMMA), poly(perfluoromethyl methacrylate)s (PFMMAs) with short perfluorinated side groups (i.e., -CF3, -CF2CF3, -(CF3)2, -CF2CF2CF3) were used as blend components because of their good solubility in organic solvents, low surface energies, and high optical transmittance. The surface energies of the blend films of PFMMA with the -CF3 group and PMMA increased continuously with increasing PMMA contents from 17.6 to 26.0 mN/m, whereas those of the other polymer blend films remained at very low levels (10.2-12.6 mN/m), similar to those of pure PFMMAs, even when the blends contained 90 wt %PMMA. Surface morphology and composition measurements revealed that this result originated from the different blend structures, such as lateral and vertical phase separations. We expect that these PFMMAs will be useful in widening the applicable window of PMMA.

  16. Phase transitions in the crystals of L- and DL-cysteine on cooling: intermolecular hydrogen bonds distortions and the side-chain motions of thiol-groups. 1. L-cysteine. (United States)

    Kolesov, Boris A; Minkov, Vasil S; Boldyreva, Elena V; Drebushchak, Tatyana N


    The role of the distortion of the hydrogen bond network and of the motions of the -CH 2SH side chains in the phase transition in the orthorhombic L-cysteine ( (+)NH 3-CH(CH 2SH)-COO (-)) on cooling and the reverse transformation on heating is discussed. The extended character of the phase transition, which was recently discovered by adiabatic calorimetry [ J. Phys. Chem. B 2007, 111, 9186 ], and its very high sensitivity to the thermal prehistory of the sample could be interpreted based on the changes in the polarized Raman spectra measured for the single-crystals in several orientations in the temperature range 3-300 K and precise diffraction data on the changes in intramolecular conformations and intermolecular hydrogen bonding. In the low-temperature phase the SH...S hydrogen bonds dominate as compared to the weaker SH...O contacts, and at ambient temperature the situation is inverse. The transition from one phase to another goes via a series of states differing in conformations of the cysteine zwitterions and the intermolecular contacts of the thiol-group. Motions of different molecular fragments (NH 3 (+), CH 2, CH, SH) are activated at different temperatures. Structural strain on cooling involves several dynamic processes, such as a rigid rotation of the molecule in the lattice, a rigid rotation of the NH 3 group with respect to NH 3-CH bond, and the rotation of the thiol side chain resulting in the switching of S-H hydrogen bonding from one type to another. Different NH...O hydrogen bonds forming the framework in the L-cysteine crystal structure are distorted to a different extent, and this provokes the rotation of the -CH 2SH side chains within the cavities of this framework resulting in a change in the coordination from SH...O to SH...S at low temperatures. The results are interesting for understanding the polymorphism of molecular crystals and the factors determining their dynamics and structural instability, and also for biophysical chemistry, since the

  17. Automated amino acid side-chain NMR assignment of proteins using {sup 13}C- and {sup 15}N-resolved 3D [{sup 1}H,{sup 1}H]-NOESY

    Energy Technology Data Exchange (ETDEWEB)

    Fiorito, Francesco [Institut fuer Molekularbiologie und Biophysik, ETH Zuerich (Switzerland); Herrmann, Torsten [Universite de Lyon, CNRS/ENS Lyon/UCB Lyon-1, Centre Europeen de RMN a Tres Hauts Champs de Lyon (France); Damberger, Fred F.; Wuethrich, Kurt [Institut fuer Molekularbiologie und Biophysik, ETH Zuerich (Switzerland)], E-mail:


    ASCAN is a new algorithm for automatic sequence-specific NMR assignment of amino acid side-chains in proteins, which uses as input the primary structure of the protein, chemical shift lists of {sup 1}H{sup N}, {sup 15}N, {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}} and possibly {sup 1}H{sup {alpha}} from the previous polypeptide backbone assignment, and one or several 3D {sup 13}C- or {sup 15}N-resolved [{sup 1}H,{sup 1}H]-NOESY spectra. ASCAN has also been laid out for the use of TOCSY-type data sets as supplementary input. The program assigns new resonances based on comparison of the NMR signals expected from the chemical structure with the experimentally observed NOESY peak patterns. The core parts of the algorithm are a procedure for generating expected peak positions, which is based on variable combinations of assigned and unassigned resonances that arise for the different amino acid types during the assignment procedure, and a corresponding set of acceptance criteria for assignments based on the NMR experiments used. Expected patterns of NOESY cross peaks involving unassigned resonances are generated using the list of previously assigned resonances, and tentative chemical shift values for the unassigned signals taken from the BMRB statistics for globular proteins. Use of this approach with the 101-amino acid residue protein FimD(25-125) resulted in 84% of the hydrogen atoms and their covalently bound heavy atoms being assigned with a correctness rate of 90%. Use of these side-chain assignments as input for automated NOE assignment and structure calculation with the ATNOS/CANDID/DYANA program suite yielded structure bundles of comparable quality, in terms of precision and accuracy of the atomic coordinates, as those of a reference structure determined with interactive assignment procedures. A rationale for the high quality of the ASCAN-based structure determination results from an analysis of the distribution of the assigned side chains, which revealed near

  18. Dietary carbohydrates for diabetics. (United States)

    Rivellese, Angela A; Giacco, Rosalba; Costabile, Giuseppina


    The literature on the impact of dietary carbohydrates in the regulation of blood glucose levels and other metabolic abnormalities in diabetic patients over the last 3 years is reviewed. We try to differentiate the metabolic effects due to the amount of carbohydrates from those due to their different types. The review comprises a part dealing with the effects of diets having low or high carbohydrate content on body weight reduction, and a part in which the amount and the quality of carbohydrates are discussed in relation to isoenergetic diets. Overall, the data accumulated in the period considered seem to confirm that the decrease in energy intake is more important than the qualitative composition of the diet to reduce body weight, but that both the amount and the quality of carbohydrates are important in modulating blood glucose levels and other cardiovascular risk factors in both the fasting and the postprandial phases in diabetic individuals.

  19. Carbohydrates and Diabetes (For Parents) (United States)

    ... Staying Safe Videos for Educators Search English Español Carbohydrates and Diabetes KidsHealth / For Parents / Carbohydrates and Diabetes ... many kids with diabetes take to stay healthy. Carbohydrates and Blood Sugar The two main forms of ...

  20. (1)H, (13)C, (15)N backbone and side-chain resonance assignment of Nostoc sp. C139A variant of the heme-nitric oxide/oxygen binding (H-NOX) domain. (United States)

    Alexandropoulos, Ioannis I; Argyriou, Aikaterini I; Marousis, Kostas D; Topouzis, Stavros; Papapetropoulos, Andreas; Spyroulias, Georgios A


    The H-NOX (Heme-nitric oxide/oxygen binding) domain is conserved across eukaryotes and bacteria. In human soluble guanylyl cyclase (sGC) the H-NOX domain functions as a sensor for the gaseous signaling agent nitric oxide (NO). sGC contains the heme-binding H-NOX domain at its N-terminus, which regulates the catalytic site contained within the C-terminal end of the enzyme catalyzing the conversion of GTP (guanosine 5'-triphosphate) to GMP (guanylyl monophosphate). Here, we present the backbone and side-chain assignments of the (1)H, (13)C and (15)N resonances of the 183-residue H-NOX domain from Nostoc sp. through solution NMR.

  1. (1)H, (13)C, (15)N backbone and side chain NMR resonance assignments for E73 from Sulfolobus spindle-shaped virus ragged hills, a hyperthermophilic crenarchaeal virus from Yellowstone National Park. (United States)

    Schlenker, Casey; Menon, Smita; Lawrence, C Martin; Copié, Valérie


    Crenarchaeal viruses are commonly found in hyperthermal acidic environments such as those of Yellowstone National Park. These remarkable viruses not only exhibit unusual morphologies, but also display extreme genetic diversity. However, little is known about crenarchaeal viral life cycles, virus-host interactions, and their adaptation to hyperthermophilic environments. In an effort to better understand the functions of crenarchaeal viruses and the proteins encoded by their genomes, we have undertaken detailed structural and functional studies of gene products encoded in the open reading frames of Sulfolobus spindle-shaped virus ragged hills. Herein, we report ((15)N, (13)C, (1)H) resonance assignments of backbone and side chain atoms of a 19.1 kDa homodimeric E73 protein of SSVRH.

  2. Carbohydrate antigen microarrays. (United States)

    Wang, Denong


    This chapter describes one of my laboratory's working protocols for carbohydrate-based microarrays. Using a standard microarray spotter, we print carbohydrate antigens directly on the nitrocellulose-coated bioarray substrates. Because these substrates support noncovalent immobilization of many spotted antigens, in general no chemical modification of the antigen is needed for microarray production. Thus, this bioarray platform is technically simple and applicable for high-throughput construction of carbohydrate antigen microarrays. A number of nitrocellulose-coated glass slides with different technical characteristics are commercially available. Given the structural diversity of carbohydrate antigens, examining each antigen preparation to determine the efficacy of its immobilization in a given type of substrate and the surface display of the desired glycoepitopes in a microarray assay is essential.

  3. Carbohydrate mediated bacterial adhesion. (United States)

    Pieters, Roland J


    In the process of adhesion, bacteria often carry proteins on their surface, adhesins, that bind to specific components of tissue cells or the extracellular matrix. In many cases these components are carbohydrate structures. The carbohydrate binding specificities of many bacteria have been uncovered over the years. The design and synthesis of inhibitors of bacterial adhesion has the potential to create new therapeutics for the prevention and possibly treatment of bacterial infections. Unfortunately, the carbohydrate structures often bind only weakly to the adhesion proteins, although drug design approaches can improve the situation. Furthermore, in some cases linking carbohydrates covalently together, to create so-called multivalent systems, can also significantly enhance the inhibitory potency. Besides adhesion inhibition as a potential therapeutic strategy, the adhesion proteins can also be used for detection. Novel methods to do this are being developed. These include the use of microarrays and glyconanoparticles. New developments in these areas are discussed.

  4. Carbohydrates and Depression. (United States)

    Wurtman, Richard J.; Wurtman, Judith J.


    Describes the symptoms, such as appetite change and mood fluctuation, basic mechanisms, and some treatments of Seasonal Affective Disorder (SAD), Carbohydrate-Craving Obesity (CCO) and Premenstrual Syndrome (PMS). Provides several tables and diagrams, and three reading references. (YP)

  5. Comparing Demand Side Management approaches

    NARCIS (Netherlands)

    Molderink, Albert; Bakker, Vincent; Hurink, Johann L.; Smit, Gerardus Johannes Maria


    Due to increasing energy prices and the greenhouse effect, a more efficient energy supply is desirable, preferably based on renewable sources. To cope with the decrease of flexibility due to the introduction of renewables in production side of the supply chain, a more flexible consumer side is

  6. Carbohydrates, Sugar, and Your Child (United States)

    ... Staying Safe Videos for Educators Search English Español Carbohydrates and Sugar KidsHealth / For Parents / Carbohydrates and Sugar ... carbohidratos, el azúcar y su hijo What Are Carbohydrates? Carbohydrates are the body's most important and readily ...

  7. Analyzing sites of OH radical attack (ring vs. side chain) in oxidation of substituted benzenes via dual stable isotope analysis (δ{sup 13}C and δ{sup 2}H)

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ning [Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig (Germany); Geronimo, Inacrist; Paneth, Piotr [Institute of Applied Radiation Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź (Poland); Schindelka, Janine; Schaefer, Thomas; Herrmann, Hartmut [Department of Chemistry, Leibniz Institute for Tropospheric Research (TROPOS), Permoserstraße 15, 04318 Leipzig (Germany); Vogt, Carsten [Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig (Germany); Richnow, Hans H., E-mail: [Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig (Germany)


    OH radicals generated by the photolysis of H{sub 2}O{sub 2} can degrade aromatic contaminants by either attacking the aromatic ring to form phenolic products or oxidizing the substituent. We characterized these competing pathways by analyzing the carbon and hydrogen isotope fractionation (ε{sub C} and ε{sub H}) of various substituted benzenes. For benzene and halobenzenes that only undergo ring addition, low values of ε{sub C} (− 0.7‰ to − 1.0‰) were observed compared with theoretical values (− 7.2‰ to − 8‰), possibly owing to masking effect caused by pre-equilibrium between the substrate and OH radical preceding the rate-limiting step. In contrast, the addition of OH radicals to nitrobenzene ring showed a higher ε{sub C} (− 3.9‰), probably due to the lower reactivity. Xylene isomers, anisole, aniline, N,N-dimethylaniline, and benzonitrile yielded normal ε{sub H} values (− 2.8‰ to − 29‰) indicating the occurrence of side-chain reactions, in contrast to the inverse ε{sub H} (11.7‰ to 30‰) observed for ring addition due to an sp{sup 2} to sp{sup 3} hybridization change at the reacting carbon. Inverse ε{sub H} values for toluene (14‰) and ethylbenzene (30‰) were observed despite the formation of side-chain oxidation products, suggesting that ring addition has a larger contribution to isotope fractionation. Dual element isotope slopes (∆ δ{sup 2}H/∆δ{sup 13}C) therefore allow identification of significant degradation pathways of aromatic compounds by photochemically induced OH radicals. Issues that should be addressed in future studies include quantitative determination of the contribution of each competing pathway to the observed isotope fractionation and characterization of physical processes preceding the reaction that could affect isotope fractionation. - Highlights: • Isotope fractionation to investigate photoreaction pathways of substituted benzenes • Normal {sup 13}C AKIE and inverse {sup 2}H AKIE for

  8. Novel Side-Chain Liquid Cyrstalline Polymers (United States)


    Reserve University Cleveland, OH 44106-2699 and M. Ebert and J. H. Wendorff Deutches Kunststoff -lnstitut, D-6100 Darmstadt, FRG Accepted for Publication...44106, USA M. Ebert and J.H. Wendorff Deutsches Kunststoff -Institut, D-6100 Darmstadt, FRG Part 7 in this series: Reference 8 To whom all

  9. Method for improving separation of carbohydrates from wood pulping and wood or biomass hydrolysis liquors (United States)

    Griffith, William Louis; Compere, Alicia Lucille; Leitten, Jr., Carl Frederick


    A method for separating carbohydrates from pulping liquors includes the steps of providing a wood pulping or wood or biomass hydrolysis pulping liquor having lignin therein, and mixing the liquor with an acid or a gas which forms an acid upon contact with water to initiate precipitation of carbohydrate to begin formation of a precipitate. During precipitation, at least one long chain carboxylated carbohydrate and at least one cationic polymer, such as a polyamine or polyimine are added, wherein the precipitate aggregates into larger precipitate structures. Carbohydrate gel precipitates are then selectively removed from the larger precipitate structures. The method process yields both a carbohydrate precipitate and a high purity lignin.

  10. Who is the carbohydrate?

    Directory of Open Access Journals (Sweden)

    Paulo Enrique Cuevas Mestanza


    Full Text Available Biochemistry is a complex science that studies biomolecules and their interactions in metabolic pathways in living beings. Due to the large amount of contents against the short period to apply them, only expositive classes are not enough to arouse the interest of students and solve questions. In this perspective, is very important to develop new educational tools to improve the understanding of these contents. “Who is the carbohydrate?” It is a didactic game created to review the structural and functional relationship of carbohydrates. Based on the classic “Guess who?” The objective of the player or group is to first find out the opponent's carbohydrate name.

  11. Carbohydrate and exercise performance: the role of multiple transportable carbohydrates. (United States)

    Jeukendrup, Asker E


    Carbohydrate feeding has been shown to be ergogenic, but recently substantial advances have been made in optimizing the guidelines for carbohydrate intake during prolonged exercise. It was found that limitations to carbohydrate oxidation were in the absorptive process most likely because of a saturation of carbohydrate transporters. By using a combination of carbohydrates that use different intestinal transporters for absorption it was shown that carbohydrate delivery and oxidation could be increased. Studies demonstrated increases in exogenous carbohydrate oxidation rates of up to 65% of glucose: fructose compared with glucose only. Exogenous carbohydrate oxidation rates reach values of 1.75 g/min whereas previously it was thought that 1 g/min was the absolute maximum. The increased carbohydrate oxidation with multiple transportable carbohydrates was accompanied by increased fluid delivery and improved oxidation efficiency, and thus the likelihood of gastrointestinal distress may be diminished. Studies also demonstrated reduced fatigue and improved exercise performance with multiple transportable carbohydrates compared with a single carbohydrate. Multiple transportable carbohydrates, ingested at high rates, can be beneficial during endurance sports in which the duration of exercise is 3 h or more.

  12. Analogues of tamoxifen: the role of the basic side-chain. Applications of a whole-cell oestrogen-receptor binding assay to N-oxides and quaternary salts. (United States)

    Jarman, M; Leung, O T; Leclercq, G; Devleeschouwer, N; Stoessel, S; Coombes, R C; Skilton, R A


    Derivatives of tamoxifen (1) and 4-hydroxy-2-methyltamoxifen (2) in which the basic side chain has been modified by N-oxidation or by quaternization have been investigated with respect to the effects on affinity for the oestrogen receptor and on cytostatic activity towards the MCF-7 cell line in vitro. In addition to the conventional cytosol assay for receptor binding affinity (RBA) a recently developed whole-cell assay was employed. N-oxidation (e.g. 2----3) produced no significant alteration in RBA value either in cytosol or in whole cells, nor in activity towards the MCF-7 line. Quaternization with methyl iodide (1----4, 2----6) or ethyl bromide (1----5, 2----7b: the cis isomer 7a also formed) did not alter receptor binding in the cytosol assay but almost abolished binding in the whole cell and cytostatic activity. The whole-cell RBA values for 2 (0.45) and 3 (0.5) were lower than those for 4-hydroxytamoxifen (2.9), suggested to be due to the lower oestrogenicity of the 2-methyl derivatives since activity against MCF-7 cells was unimpaired. The even lower values of whole-cell RBA (0.01-0.02) for the quaternary ethyl bromide derivatives 7a and 7b were ascribed to poor penetration into the cell since these compounds had minimal cytostatic activity.

  13. Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c

    Energy Technology Data Exchange (ETDEWEB)

    Novacek, Jiri; Janda, Lubomir; Dopitova, Radka; Zidek, Lukas, E-mail:; Sklenar, Vladimir [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic)


    Microtubule-associated proteins (MAPs) are abundantly present in axons and dendrites, and have been shown to play crucial role during the neuronal morphogenesis. The period of main dendritic outgrowth and synaptogenesis coincides with high expression levels of one of MAPs, the MAP2c, in rats. The MAP2c is a 49.2 kDa intrinsically disordered protein. To achieve an atomic resolution characterization of such a large protein, we have developed a protocol based on the acquisition of two five-dimensional {sup 13}C-directly detected NMR experiments. Our previously published 5D CACONCACO experiment (Novacek et al. in J Biomol NMR 50(1):1-11, 2011) provides the sequential assignment of the backbone resonances, which is not interrupted by the presence of the proline residues in the amino acid sequence. A novel 5D HC(CC-TOCSY)CACON experiment facilitates the assignment of the aliphatic side chain resonances. To streamline the data analysis, we have developed a semi-automated procedure for signal assignments. The obtained data provides the first atomic resolution insight into the conformational state of MAP2c and constitutes a model for further functional studies of MAPs.

  14. Analogues of chloramphenicol as mechanism-based inactivators of rat liver cytochrome P-450: modifications of the propanediol side chain, the p-nitro group, and the dichloromethyl moiety. (United States)

    Miller, N E; Halpert, J


    The importance of the p-nitro group, the propanediol side chain, and the dichloromethyl moiety of chloramphenicol in regulating its effectiveness and selectivity as a mechanism-based inactivator of rat liver cytochromes P-450 has been examined. 1-p-Nitrophenyl-2-dichloroacetamidoethane, 1-p-nitrophenyl-2-dibromoacetamidoethane, and 1-phenyl-2-dichloroacetamidoethane were as effective as chloramphenicol at inactivating the major phenobarbital-inducible isozyme of rat liver cytochrome P-450, whereas 1-p-nitrophenyl-2-difluoroacetamidoethane caused no enzyme inactivation. Unlike chloramphenicol, 1-p-nitrophenyl-2-dichloroacetamidoethane and 1-phenyl-2-dichloroacetamidoethane also inactivated the major beta-naphthoflavone-inducible isozyme of rat liver cytochrome P-450. Alkaline hydrolysis of the adducts formed upon in vitro incubation of liver microsomes from phenobarbital- and beta-naphthoflavone-induced rats with [14C]-1-p-nitrophenyl-2-dichloroacetamidoethane resulted in the release of 4-nitro-1-phenethyl-1,2-dicarboxylic acid amide and oxalic acid. Enzymatic digests of the radio-labeled protein produced by incubation of a reconstituted system containing the major isozymes induced by beta-naphthoflavone or phenobarbital with [14C]-1-p-nitrophenyl-2-dichloroacetamidoethane led to the release of 4-nitro-1-phenethyl-1,2-dicarboxylic acid amide and 4-nitro-1-phenethyl oxamyl lysine. These results suggest that a single oxamyl chloride intermediate is responsible for the covalent modification and, hence, inactivation of both isozymes by 1-p-nitrophenyl-2-dichloroacetamidoethane.

  15. Bioresolution Production of (2R,3S-Ethyl-3-phenylglycidate for Chemoenzymatic Synthesis of the Taxol C-13 Side Chain by Galactomyces geotrichum ZJUTZQ200, a New Epoxide-Hydrolase-Producing Strain

    Directory of Open Access Journals (Sweden)

    Chun Wei


    Full Text Available A newly isolated Galactomyces geotrichum ZJUTZQ200 strain containing an epoxide hydrolase was used to resolve racemic ethyl 3-phenylglycidate (rac-EPG for producing (2R,3S-ethyl-3-phenylglycidate ((2R,3S-EPG. G. geotrichum ZJUTZQ200 was verified to be able to afford high enantioselectivity in whole cell catalyzed synthesis of this chiral phenylglycidate synthon. After the optimization of the enzymatic production and bioresolution conditions, (2R,3S-EPG was afforded with high enantioselectivity (e.e.S > 99%, E > 49 after a 8 h reaction. The co-solvents, pH buffer solutions and substrate/cell ratio were found to have significant influences on the bioresolution properties of G. geotrichum ZJUTZQ200. Based on the bioresolution product (2R,3S-EPG, taxol’s side chain ethyl (2R,3S-3-benzoylamino-2-hydroxy-3-phenylpropionate was successfully synthesized by a chemoenzymatic route with high enantioselectivity (e.e.S > 95%.

  16. Bioresolution production of (2R,3S)-ethyl-3-phenylglycidate for chemoenzymatic synthesis of the taxol C-13 side chain by Galactomyces geotrichum ZJUTZQ200, a new epoxide-hydrolase-producing strain. (United States)

    Wei, Chun; Ling, Jinlong; Shen, Honglei; Zhu, Qing


    A newly isolated Galactomyces geotrichum ZJUTZQ200 strain containing an epoxide hydrolase was used to resolve racemic ethyl 3-phenylglycidate (rac-EPG) for producing (2R,3S)-ethyl-3-phenylglycidate ((2R,3S)-EPG). G. geotrichum ZJUTZQ200 was verified to be able to afford high enantioselectivity in whole cell catalyzed synthesis of this chiral phenylglycidate synthon. After the optimization of the enzymatic production and bioresolution conditions, (2R,3S)-EPG was afforded with high enantioselectivity (e.e.S > 99%, E > 49) after a 8 h reaction. The co-solvents, pH buffer solutions and substrate/cell ratio were found to have significant influences on the bioresolution properties of G. geotrichum ZJUTZQ200. Based on the bioresolution product (2R,3S)-EPG, taxol's side chain ethyl (2R,3S)-3-benzoylamino-2-hydroxy-3-phenylpropionate was successfully synthesized by a chemoenzymatic route with high enantioselectivity (e.e.S > 95%).

  17. The long underestimated carbonyl function of carbohydrates – an organocatalyzed shot into carbohydrate chemistry. (United States)

    Mahrwald, R


    The aggressive and strong development of organocatalysis provides several protocols for the convenient utilization of the carbonyl function of unprotected carbohydrates in C-C-bond formation processes. These amine-catalyzed mechanisms enable multiple cascade-protocols for the synthesis of a wide range of carbohydrate-derived compound classes. Several, only slightly different protocols, have been developed for the application of 1,3-dicarbonyl compounds in the stereoselective chain-elongation of unprotected carbohydrates and the synthesis of highly functionalized C-glycosides of defined configuration. In addition, C-glycosides can also be accessed by amine-catalyzed reactions with methyl ketones. By a one-pot cascade reaction of isocyanides with unprotected aldoses and amino acids access to defined configured glycopeptide mimetics is achieved. Depending on the reaction conditions different origins to control the installation of configuration during the bond-formation process were observed.

  18. Catalytic Conversion of Carbohydrates

    DEFF Research Database (Denmark)

    Osmundsen, Christian Mårup

    with the production of commodity chemicals from the most abundantly available renewable source of carbon, carbohydrates. The production of alkyl lactates by the Lewis acid catalyzed conversion of hexoses is an interesting alternative to current fermentation based processes. A range of stannosilicates were....... The synthesis of these by the cycloaddition of ethylene to furanic compounds, followed by dehydrative aromatization, was demonstrated in good yields, using a strong Brønsted acidic catalyst, WOx/ZrO2. As both ethylene and furanics can be derived from carbohydrates by known processes, this constitutes...

  19. Carbohydrate composition of immunoglobulins from diverse species of verterbrates

    Energy Technology Data Exchange (ETDEWEB)

    Acton, R.T.; Niedermeier, W.; Weinheimer, P.F.; Clem, L.W.; Leslie, G.A.; Bennett, J.C.


    Immunoglobulins and their respective heavy (H) and light (L) polypeptide chains from species representing the major classes of vertebrates were analyzed for their carbohydrate composition by gas chromatography of the alditol acetate derivatives of the monosaccharides released by acid hydrolysis. Mannose, galactose, glucosamine and sialic acid were present in the immunoglobulins from all the species investigated. Most of the carbohydrate was found associated with the H chains. Whereas species representative of the mammals and birds had mannose to galactose ratios greater than one, the ratio to these sugars to each other in the immunoglobulins from animals below the birds was on the order of one.

  20. Effects of Carbohydrate Consumption Case Study: carbohydrates in Bread


    Neacsu N.A.


    Carbohydrates perform numerous roles in living organisms; they are an important source of energy. The body uses carbohydrates to make glucose which is the fuel that gives it energy and helps keep everything going. However, excess carbohydrate consumption has negative health effects. Bread is a basic product in our nutrition and it also is a product with a high content of carbohydrates. So, it is important to find out more information on bread and on the recommended bread type best for con...

  1. Carbohydrate intake and obesity

    NARCIS (Netherlands)

    van Dam, R M; Seidell, J C


    The prevalence of obesity has increased rapidly worldwide and the importance of considering the role of diet in the prevention and treatment of obesity is widely acknowledged. This paper reviews data on the effects of dietary carbohydrates on body fatness. Does the composition of the diet as related

  2. Dietary carbohydrate restriction as the first approach in diabetes management

    DEFF Research Database (Denmark)

    Feinman, Richard D; Pogozelski, Wendy K; Astrup, Arne


    The inability of current recommendations to control the epidemic of diabetes, the specific failure of the prevailing low-fat diets to improve obesity, cardiovascular risk, or general health and the persistent reports of some serious side effects of commonly prescribed diabetic medications......, in combination with the continued success of low-carbohydrate diets in the treatment of diabetes and metabolic syndrome without significant side effects, point to the need for a reappraisal of dietary guidelines. The benefits of carbohydrate restriction in diabetes are immediate and well documented. Concerns...

  3. Role of carbohydrate metabolism in grass tetany

    Energy Technology Data Exchange (ETDEWEB)

    Miller, J.K.; Madsen, F.C.; Lentz, D.E.; Hansard, S.L.


    Clinical hypomagnesemia is confined primarily to beef cattle in the United States but also occurs in dairy cattle in other countries, probably due to different management practices. During periods when grass tetany is likely, early vegetative temperate zone grasses are usually low in total readily available carbohydrates and magnesium but high in potassium and nitrogen. The tetany syndrome may include hypoglycemia and ketosis, suggesting an imbalance in intermediary energy metabolism. Many enzyme systems critical to cellular metabolism, including those which hydrolyze and transfer phosphate groups, are activated by Mg. Thus, by inference, Mg is required for normal glucose utilization, fat, protein, nucleic acid and coenzyme synthesis, muscle contraction, methyl group transfer, and sulfate, acetate, and formate activation. Numerous clinical and experimental studies suggest an intimate relationship between metabolism of Mg and that of carbohydrate, glucagon, and insulin. The objective is to review this literature and suggest ways in which these relationships might contribute to a chain of events leading to grass tetany.

  4. [Spontaneous changes in carbohydrate tolerance and insulin secretion in persons with indications of disturbed carbohydrate tolerance. Preliminary results and follow-up observations for 7 years]. (United States)

    Ratzmann, K P; Schulz, B; Witt, S; Heinke, P; Michaelis, D


    115 patients with normal weight and 15 adipose persons with suspicion of a disturbance of the carbohydrate metabolism were characterized by means of a glucose infusion test lasting two hours concerning the carbohydrate tolerance and insulin secretion. Longitudinal analyses of the spontaneous behaviour of the carbohydrate tolerance and insulin secretion depending on the degree of the carbohydrate tolerance up to duration of the observation of 7 years. A deterioration of the carbohydrate tolerance was to be proved in 21% of 87 persons with normal carbohydrate tolerance within two years. With normal carbohydrate tolerance within two years. With an increase of the duration of the observation up to 7 years the frequency of disturbances of the carbohydrate tolerance increases to 30%. This development cannot be coordinated to a certain type of insulin secretion. In the individual case a deterioration of the carbohydrate tolerance may be associated with an increase or reduction of the glucose stimulated insuline secretion. An improvement of the carbohydrate tolerance was observed in 15 (54%) of 28 patients with disturbed carbohydrate tolerance within 2 years. In a group with pathological carbohydrate tolerance this development was associated with a significant reduction of the basic and glucose stimulated insulin secretion. In all patients with improved carbohydrate tolerance on the side of the insulin secretion primarily the type of "normal response" was present. The lacking relation between changes of the B-cell function and the carbohydrate tolerance emphasizes the importance of other factors, such as a peripheral insulin resistance, for the development of disturbances in the carbohydrate metabolism.

  5. Overexpression of the steroidogenic enzyme cytochrome P450 side chain cleavage in the ventral tegmental area increases 3α,5α-THP and reduces long-term operant ethanol self-administration. (United States)

    Cook, Jason B; Werner, David F; Maldonado-Devincci, Antoniette M; Leonard, Maggie N; Fisher, Kristen R; O'Buckley, Todd K; Porcu, Patrizia; McCown, Thomas J; Besheer, Joyce; Hodge, Clyde W; Morrow, A Leslie


    Neuroactive steroids are endogenous neuromodulators capable of altering neuronal activity and behavior. In rodents, systemic administration of endogenous or synthetic neuroactive steroids reduces ethanol self-administration. We hypothesized this effect arises from actions within mesolimbic brain regions that we targeted by viral gene delivery. Cytochrome P450 side chain cleavage (P450scc) converts cholesterol to pregnenolone, the rate-limiting enzymatic reaction in neurosteroidogenesis. Therefore, we constructed a recombinant adeno-associated serotype 2 viral vector (rAAV2), which drives P450scc expression and neuroactive steroid synthesis. The P450scc-expressing vector (rAAV2-P450scc) or control GFP-expressing vector (rAAV2-GFP) were injected bilaterally into the ventral tegmental area (VTA) or nucleus accumbens (NAc) of alcohol preferring (P) rats trained to self-administer ethanol. P450scc overexpression in the VTA significantly reduced ethanol self-administration by 20% over the 3 week test period. P450scc overexpression in the NAc, however, did not alter ethanol self-administration. Locomotor activity was unaltered by vector administration to either region. P450scc overexpression produced a 36% increase in (3α,5α)-3-hydroxypregnan-20-one (3α,5α-THP, allopregnanolone)-positive cells in the VTA, but did not increase 3α,5α-THP immunoreactivity in NAc. These results suggest that P450scc overexpression and the resultant increase of 3α,5α-THP-positive cells in the VTA reduces ethanol reinforcement. 3α,5α-THP is localized to neurons in the VTA, including tyrosine hydroxylase neurons, but not astrocytes. Overall, the results demonstrate that using gene delivery to modulate neuroactive steroids shows promise for examining the neuronal mechanisms of moderate ethanol drinking, which could be extended to other behavioral paradigms and neuropsychiatric pathology.

  6. β-thalassemia minor, carbohydrate malabsorption and histamine intolerance. (United States)

    Schnedl, Wolfgang J; Schenk, Michael; Lackner, Sonja; Holasek, Sandra J; Mangge, Harald


    Background: β-thalassemia minor is characterized by reduced β-haemoglobin chain synthesis and sometimes mild anaemia, although carriers of β-thalassemia minorare usually clinically asymptomatic.Nonspecific abdominal complaints may be caused by gastrointestinal carbohydrate malabsorption (lactose and fructose) and/or malabsorption of biogenic amines (histamine), or proteins (gluten). Objectives: We report on two patients with β-thalassemia minor suffering nonspecific abdominal symptoms due to a carbohydrate and histamine malabsorption. Design/methods: The diagnosis of β-thalassemia minorwas done with peripheral blood smear and cellulose acetate electrophoresis. Carbohydrate malabsorption was diagnosed with hydrogen breath tests and, histamine intolerance (HIT) with a serum diamine oxidase value diet free of symptom causing carbohydrates and histamine.

  7. The center for plant and microbial complex carbohydrates at the University of Georgia Complex Carbohydrate Research Center

    Energy Technology Data Exchange (ETDEWEB)

    Albersheim, P.; Darvill, A.


    Research from the Complex Carbohydrates Research Center at the University of Georgia is presented. Topics include: Structural determination of soybean isoflavones which specifically induce Bradyrhizobium japonicum nodD1 but not the nodYABCSUIJ operon; structural analysis of the lipopolysaccharides (LPSs) from symbiotic mutants of Bradyrhizobium japonicum; structural characterization of lipooligosaccharides from Bradyrhizobium japonicum that are required for the specific nodulation of soybean; structural characterization of the LPSs from R. Leguminosarum biovar phaseoli, the symbiont of bean; characterization of bacteroid-specific LPS epitopes in R. leguminosarum biovar viciae; analysis of the surface polysaccharides of Rhizobium meliloti mutants whose lipopolysaccharides and extracellular polysaccharides can have the same function in symbiosis; characterization of a polysaccharide produced by certain Bradyrhizobium japonicum strains within soybean nodules; structural analysis of a streptococcal adhesin polysaccharide receptor; conformational studies of xyloglucan, the role of the fucosylated side chain in surface-specific cellulose-xyloglucan interactions; the structure of an acylated glucosamine oligosaccharide signal molecule (nod factor) involved in the symbiosis of Rhizobium leguminosarum biovar viciae with its host Vicia sativa; investigating membrane responses induced by oligogalacturonides in cultured cells; the polygalacturonase inhibitor protein; characterization of the self-incompatability glycoproteins from Petunia hybrida; investigation of the cell wall polysaccharide structures of Arabidopsis thaliana; and the glucan inhibition of virus infection of tabacco.

  8. [Carbohydrates and fiber]. (United States)

    Lajolo, F M; de Menezes, E W; Filisetti-Cozzi, T M


    Dietary carbohydrates comprise two fractions that may be classified as digestible, and which are useful as energy sources (simple and complex carbohydrates) and fiber, which is presumed to be of no use to the human body. There are insufficient epidemiologic data on the metabolic effects of simple carbohydrates and it is not advisable to make quantitative recommendations of intake. It is questionable to recommend in developing countries that a fixed proportion of dietary energy be derived from simple sugars, due to the high prevalence of deficient energy intake, cultural habits, and regional differences in food intake and physical activity. In relation to recommendations of complex carbohydrates, it should be considered that their absorption is influenced by many factors inherent to the individual and to the foods. Fiber is defined as a series of different substances derived from tissue structures, cellular residues and undigested chemical substances that may be partially utilized after intestinal bacteria have acted on them. There is not a clear definition of the chemical composition of fiber, but it consists mainly of polysaccharides (such as cellulose, hemicellulose and pectins), lignin and end products of the interactions of various food components. The effects of fiber, such as control of food intake, regulation of gastrointestinal transit, post-prandial blood concentrations of cholesterol, glucose and insulin, flatulence and alterations in nutrient bioavailability are due to various physical properties inherent to its chemical components. Impairment of nutrient absorption may be harmful, mainly among populations whose food intake is lower than their energy needs, and with a high fiber content. This may be particularly important in pregnant women, growing children and the elderly, and should be considered when making nutrient recommendations. A precise knowledge of fiber is also important to calculate the real energy value of foods, mainly for two reasons: 1

  9. NMR Isotope Tracking Reveals Cascade Steps in Carbohydrate Conversion by Sn-Beta

    DEFF Research Database (Denmark)

    Elliot, Samuel Gilbert; Taarning, Esben; Madsen, Robert


    position to the C3 position of methyl lactate resembles enzymatic glycolysis. Likewise, the majority of retro-aldol cleavage occurs from the carbohydrate in the ketose form, again resembling biological glycolysis. In addition, various side-activities are detected in Sn-Beta catalyzed carbohydrate...

  10. Cell surface carbohydrate changes during embryonic and fetal skin development

    DEFF Research Database (Denmark)

    Dabelsteen, Erik; Holbrook, K; Clausen, H


    Monoclonal antibodies to four type 2 chain carbohydrate antigens were used for immunohistochemical studies of embryonic and fetal skin. The antibodies detected N-acetyllactosamine and 3 fucosyl substitutes of this, blood group antigen H, Lex, and Ley. Periderm consistently stained for N...

  11. Effects of Carbohydrate Consumption Case Study: carbohydrates in Bread

    Directory of Open Access Journals (Sweden)

    Neacsu N.A.


    Full Text Available Carbohydrates perform numerous roles in living organisms; they are an important source of energy. The body uses carbohydrates to make glucose which is the fuel that gives it energy and helps keep everything going. However, excess carbohydrate consumption has negative health effects. Bread is a basic product in our nutrition and it also is a product with a high content of carbohydrates. So, it is important to find out more information on bread and on the recommended bread type best for consumption.

  12. Heat capacity changes in carbohydrates and protein-carbohydrate complexes. (United States)

    Chavelas, Eneas A; García-Hernández, Enrique


    Carbohydrates are crucial for living cells, playing myriads of functional roles that range from being structural or energy-storage devices to molecular labels that, through non-covalent interaction with proteins, impart exquisite selectivity in processes such as molecular trafficking and cellular recognition. The molecular bases that govern the recognition between carbohydrates and proteins have not been fully understood yet. In the present study, we have obtained a surface-area-based model for the formation heat capacity of protein-carbohydrate complexes, which includes separate terms for the contributions of the two molecular types. The carbohydrate model, which was calibrated using carbohydrate dissolution data, indicates that the heat capacity contribution of a given group surface depends on its position in the saccharide molecule, a picture that is consistent with previous experimental and theoretical studies showing that the high abundance of hydroxy groups in carbohydrates yields particular solvation properties. This model was used to estimate the carbohydrate's contribution in the formation of a protein-carbohydrate complex, which in turn was used to obtain the heat capacity change associated with the protein's binding site. The model is able to account for protein-carbohydrate complexes that cannot be explained using a previous model that only considered the overall contribution of polar and apolar groups, while allowing a more detailed dissection of the elementary contributions that give rise to the formation heat capacity effects of these adducts.

  13. Investigating the prebiotic and gas-generating effects of selected carbohydrates on the human colonic microflora. (United States)

    Probert, H M; Gibson, G R


    To compare the fermentation of dietary carbohydrates with reference to their prebiotic and gas-generating capacity. Static anaerobic batch culture fermentations were carried out measuring gas generation and the prebiotic effect of five selected substrates (including various fructo-oligosaccharides, levan and maltodextrin). The largest gas producer was levan, whilst those showing no significant difference to Actilight included oligofructose and maltodextrin. Gas composition data showed that hydrogen and carbon dioxide were the two most quantitatively important gases. The substrate that appeared to have the best prebiotic effect in vitro was branched chain fructo-oligosaccharide (FOS), followed by oligofructose, Actilight and maltodextrin which each exerted a similar effect. The substrate with the least bifidogenic effect was levan. The composition and total gas generation data showed that there was much variation between and within donor inocula. Generally, the lower gas producers had a more selective fermentation whilst larger gas producers were less specific. The study of these three parameters enabled a more complete picture of carbohydrate breakdown to be drawn and hence highlighted the need for potential prebiotics to be more extensively evaluated in order to reduce negative side-effects such as gas distension.

  14. Carbohydrate microarrays by microcontact printing. (United States)

    Wendeln, Christian; Heile, Andreas; Arlinghaus, Heinrich F; Ravoo, Bart Jan


    This Article describes the preparation of carbohydrate microarrays by the immobilization of carbohydrates via microcontact printing (microCP) on glass and silicon substrates. To this end, diene-modified carbohydrates (galactose, glucose, mannose, lactose, and maltose) were printed on maleimide-terminated self-assembled monolayers (SAMs). A Diels-Alder reaction occurred exclusively in the contact area between stamp and substrate and resulted in a carbohydrate pattern on the substrate. It was found that cyclopentadiene-functionalized carbohydrates could be printed within minutes at room temperature, whereas furan-functionalized carbohydrates required long printing times and high temperatures. By successive printing, microstructured arrays of up to three different carbohydrates could be produced. Immobilization and patterning of the carbohydrates on the surfaces was investigated with contact angle measurements, X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (TOF-SIMS), and fluorescence microscopy. Furthermore, the lectins concanavalin A (ConA) and peanut agglutinin (PNA) bind to the microarrays, and the printed carbohydrates retain their characteristic selectivity toward these proteins.

  15. Carbohydrate composition of compost during composting and mycelium growth of Agaricus bisporus. (United States)

    Jurak, Edita; Kabel, Mirjam A; Gruppen, Harry


    Changes of plant cell wall carbohydrate structures occurring during the process to make suitable compost for growth of Agaricus bisporus are unknown. In this paper, composition and carbohydrate structures in compost samples collected during composting and mycelium growth were analyzed. Furthermore, different extracts of compost samples were prepared with water, 1M and 4M alkali and analyzed. At the beginning of composting, 34% and after 16 days of mycelium growth 27% of dry matter was carbohydrates. Carbohydrate composition analysis showed that mainly cellulose and poorly substituted xylan chains with similar amounts and ratios of xylan building blocks were present in all phases studied. Nevertheless, xylan solubility increased 20% over the period of mycelium growth indicating partial degradation of xylan backbone. Apparently, degradation of carbohydrates occurred over the process studied by both bacteria and fungi, mainly having an effect on xylan-chain length and solubility. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Regional variations of cell surface carbohydrates in human oral stratified epithelium

    DEFF Research Database (Denmark)

    Vedtofte, P; Dabelsteen, Erik; Hakomori, S


    The distribution of blood group carbohydrate chains with antigen A, B, H type 2 chain (A and B precursor), and N-acetyllactosamine (H type 2 precursor) specificity was studied in human oral epithelium from different anatomical regions. These represented various epithelial differentiation patterns...... epithelium from nine blood group A, two blood group B, and nine blood group O individuals. The blood group carbohydrate chains were examined in tissue sections by immunofluorescence microscopy. The A and B blood group antigens were detected by human blood group sera, and antigen H type 2 chains and N...... antigen H type 2 chains in metaplastically keratinized buccal epithelium was found to differ significantly from that seen in normal non-keratinized buccal epithelium. The regional variations demonstrated in cell surface carbohydrates are suggested to reflect differences in tissue differentiation....

  17. Impact of Dietary Carbohydrate and Protein Levels on Carbohydrate Metabolism (United States)

    Lasker, Denise Ann


    The goal of this dissertation was to investigate the impact of changing dietary carbohydrate (CARB) intakes within recommended dietary guidelines on metabolic outcomes specifically associated with glycemic regulations and carbohydrate metabolism. This research utilized both human and animal studies to examine changes in metabolism across a wide…

  18. (1)H, (13)C, and (15)N backbone and side-chain chemical shift assignments for the 36 proline-containing, full length 29 kDa human chimera-type galectin-3. (United States)

    Ippel, Hans; Miller, Michelle C; Berbís, Manuel Alvaro; Suylen, Dennis; André, Sabine; Hackeng, Tilman M; Cañada, F Javier; Weber, Christian; Gabius, Hans-Joachim; Jiménez-Barbero, Jesús; Mayo, Kevin H


    Galectin-3, an adhesion/growth regulatory lectin, has a unique trimodular design consisting of the canonical carbohydrate recognition domain, a collagen-like tandem-repeat section, and an N-terminal peptide with two sites for Ser phosphorylation. Structural characterization of the full length protein with its non-lectin part (115 of 250 residues total) will help understand the multi functionality of this potent cellular effector. Here, we report (1)H, (13)C, and (15)N chemical shift assignments as determined by heteronuclear NMR spectroscopy .

  19. Carbohydrates of human immunodeficiency virus

    DEFF Research Database (Denmark)

    Hansen, J E


    therapy with glycosylation enzyme inhibitors will, however, require the development of more specific and less toxic compounds. If carbohydrate antigens can elicit a neutralizing immune response in vivo, the possibility exists that carbohydrate neoantigens can be utilized in the construction of a vaccine...

  20. Evaluation of lignins from side-streams generated in an olive tree pruning-based biorefinery: Bioethanol production and alkaline pulping. (United States)

    Santos, José I; Fillat, Úrsula; Martín-Sampedro, Raquel; Eugenio, María E; Negro, María J; Ballesteros, Ignacio; Rodríguez, Alejandro; Ibarra, David


    In modern lignocellulosic-based biorefineries, carbohydrates can be transformed into biofuels and pulp and paper, whereas lignin is burned to obtain energy. However, a part of lignin could be converted into value-added products including bio-based aromatic chemicals, as well as building blocks for materials. Then, a good knowledge of lignin is necessary to define its valorisation procedure. This study characterized different lignins from side-streams produced from olive tree pruning bioethanol production (lignins collected from steam explosion pretreatment with water or phosphoric acid as catalysts, followed by simultaneous saccharification and fermentation process) and alkaline pulping (lignins recovered from kraft and soda-AQ black liquors). Together with the chemical composition, the structure of lignins was investigated by FTIR, (13)C NMR, and 2D NMR. Bioethanol lignins had clearly distinct characteristics compared to pulping lignins; a certain number of side-chain linkages (mostly alkyl-aryl ether and resinol) accompanied with lower phenolic hydroxyls content. Bioethanol lignins also showed a significant amount of carbohydrates, mainly glucose and protein impurities. By contrast, pulping lignins revealed xylose together with a dramatical reduction of side-chains (some resinol linkages survive) and thereby higher phenol content, indicating rather severe lignin degradation during alkaline pulping processes. All lignins showed a predominance of syringyl units. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Fabrication of carbohydrate microarrays through boronate formation. (United States)

    Hsiao, Hsuan-Yi; Chen, Mu-Lin; Wu, Huan-Ting; Huang, Li-De; Chien, Wei-Ting; Yu, Ching-Ching; Jan, Fan-Dan; Sahabuddin, Sk; Chang, Tsung-Che; Lin, Chun-Cheng


    A straightforward method for fabricating a stable and covalent carbohydrate microarray based on boronate formation between the hydroxyl groups of carbohydrate and boronic acid (BA) on the glass surface was used to identify carbohydrate-protein interactions.

  2. Synthesis of carbohydrate-based surfactants (United States)

    Pemberton, Jeanne E.; Polt, Robin L.; Maier, Raina M.


    The present invention provides carbohydrate-based surfactants and methods for producing the same. Methods for producing carbohydrate-based surfactants include using a glycosylation promoter to link a carbohydrate or its derivative to a hydrophobic compound.

  3. Methodological challenges in carbohydrate analyses

    Directory of Open Access Journals (Sweden)

    Mary Beth Hall


    Full Text Available Carbohydrates can provide up to 80% of the dry matter in animal diets, yet their specific evaluation for research and diet formulation is only now becoming a focus in the animal sciences. Partitioning of dietary carbohydrates for nutritional purposes should reflect differences in digestion and fermentation characteristics and effects on animal performance. Key challenges to designating nutritionally important carbohydrate fractions include classifying the carbohydrates in terms of nutritional characteristics, and selecting analytical methods that describe the desired fraction. The relative lack of information on digestion characteristics of various carbohydrates and their interactions with other fractions in diets means that fractions will not soon be perfectly established. Developing a system of carbohydrate analysis that could be used across animal species could enhance the utility of analyses and amount of data we can obtain on dietary effects of carbohydrates. Based on quantities present in diets and apparent effects on animal performance, some nutritionally important classes of carbohydrates that may be valuable to measure include sugars, starch, fructans, insoluble fiber, and soluble fiber. Essential to selection of methods for these fractions is agreement on precisely what carbohydrates should be included in each. Each of these fractions has analyses that could potentially be used to measure them, but most of the available methods have weaknesses that must be evaluated to see if they are fatal and the assay is unusable, or if the assay still may be made workable. Factors we must consider as we seek to analyze carbohydrates to describe diets: Does the assay accurately measure the desired fraction? Is the assay for research, regulatory, or field use (affects considerations of acceptable costs and throughput? What are acceptable accuracy and variability of measures? Is the assay robust (enhances accuracy of values? For some carbohydrates, we

  4. Carbohydrate polymers in amorphous states: an integrated thermodynamic and nanostructural investigation. (United States)

    Kilburn, Duncan; Claude, Johanna; Schweizer, Thomas; Alam, Ashraf; Ubbink, Job


    The effect of water on the structure and physical properties of amorphous polysaccharide matrices is investigated by combining a thermodynamic approach including pressure- and temperature-dependent dilatometry with a nanoscale analysis of the size of intermolecular voids using positron annihilation lifetime spectroscopy. Amorphous polysaccharides are of interest because of a number of unusual properties which are likely to be related to the extensive hydrogen bonding between the carbohydrate chains. Uptake of water by the carbohydrate matrices leads to a strong increase in the size of the holes between the polymer chains in both the glassy and rubbery states while at the same time leading to an increase in matrix free volume. Thermodynamic clustering theory indicates that, in low-moisture carbohydrate matrices, water molecules are closely associated with the carbohydrate chains. Based on these observations, we propose a novel model of plasticization of carbohydrate polymers by water in which the water dynamically disrupts chains the hydrogen bonding between the carbohydrates, leading to an expansion of the matrix originating at the nanolevel and increasing the number of degrees of freedom of the carbohydrate chains. Consequently, even in the glassy state, the uptake of water leads to increased rates of matrix relaxation and mobility of small permeants. In contrast, low-molecular weight sugars plasticize the carbohydrate matrix without appreciably changing the structure and density of the rubbery state, and their role as plasticizer is most likely related to a reduction of the number of molecular entanglements. The improved molecular packing in glassy matrices containing low molecular weight sugars leads to a higher matrix density, explaining, despite the lower glass transition temperature, the reduced mobility of small permeants in such matrices.

  5. Facultative thermogenesis induced by carbohydrate

    DEFF Research Database (Denmark)

    Astrup, A; Bülow, J; Christensen, N J


    In addition to the obligatory thermogenesis due to processing and storage, carbohydrate ingestion is accompanied by a facultative thermogenesis mediated by catecholamines via beta-adrenoceptors. The anatomical origin of facultative thermogenesis has hitherto not been determined. The possible...

  6. Carbohydrate microarrays in plant science. (United States)

    Fangel, Jonatan U; Pedersen, Henriette L; Vidal-Melgosa, Silvia; Ahl, Louise I; Salmean, Armando Asuncion; Egelund, Jack; Rydahl, Maja Gro; Clausen, Mads H; Willats, William G T


    Almost all plant cells are surrounded by glycan-rich cell walls, which form much of the plant body and collectively are the largest source of biomass on earth. Plants use polysaccharides for support, defense, signaling, cell adhesion, and as energy storage, and many plant glycans are also important industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high-throughput analysis of nucleotides, proteins, and increasingly carbohydrates. Using microarrays, the abundance of and interactions between hundreds and thousands of molecules can be assessed simultaneously using very small amounts of analytes. Here we show that carbohydrate microarrays are multifunctional tools for plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities.

  7. Carbohydrates of human immunodeficiency virus

    DEFF Research Database (Denmark)

    Hansen, J E


    Elucidation of the mechanism by which viral infection induces the appearance of carbohydrate neoantigens is highly important. Results from such studies could be expected to be significant for a general understanding of the regulation of glycosylation, and perhaps especially important for the unde......Elucidation of the mechanism by which viral infection induces the appearance of carbohydrate neoantigens is highly important. Results from such studies could be expected to be significant for a general understanding of the regulation of glycosylation, and perhaps especially important...... therapy with glycosylation enzyme inhibitors will, however, require the development of more specific and less toxic compounds. If carbohydrate antigens can elicit a neutralizing immune response in vivo, the possibility exists that carbohydrate neoantigens can be utilized in the construction of a vaccine...

  8. Racemic carbohydrates - fact or fiction?

    DEFF Research Database (Denmark)

    Senning, Alexander Erich Eugen


    Chemical Abstracts Service has developed unsound practices in the naming and handling of simple carbohydrates such as aldopentoses 1, aldohexoses 2, and ketohexoses 3. Typically, the common name glucose is sometimes, inappropriately, interpreted as meaning DL-glucose DL-2d. Thus, a considerable...... number of CA names and registry numbers have been created for non-existing racemic carbohydrates and linked to irrelevant references which, moreover, in many cases cannot be retrieved by the SciFinder Scholar program....

  9. Preparation of water-soluble glycoconjugated poly(acrylamide) for NMR analyses of carbohydrate-carbohydrate interactions (United States)

    Xuan, Trinh Anh; Trung, Phan Nghia; Dinh, Bui Long; Yamaguchi, Takumi; Kato, Koichi


    Oligosaccharide chains of glycoconjugates are important biopolymers not only as carriers of information in cell-cell interactions but also as markers of cellular differentiation, aging, and malignant alteration. Molecular interactions where carbohydrates are involved are usually considered as weak interactions, so the study and evaluation of these interactions is still in its infancy. The evidences and studies of carbohydrate-carbohydrate interactions (CCI) will be confirming the importance of this mechanism for specific cell adhesion and communication. Their development will go hand in hand with the development of new and more sensitive techniques to study weak interactions. Recently, synthetic glycopolymers with functions similar to those of such natural carbohydrates and with specific pendant saccharide moieties were used as a solution for enhancement CCI when forming polyvalent interactions. Carbohydrates are ubiquitous components of cell wall membranes and occur as glycolipids, glycoproteins, proteoglycans, and capsular polysaccharides. As such they can participate in forefront intramolecular and intracellular events. Apart from their recognized roles in the physicochemical properties of glycolipids and glycoproteins. In this study, we designed trisaccharide monomers for free radical polymerization. Subsequently, the trisaccharide unit for chemical conjugation was synthesized from galactosamine in good yield. For further NMR analyses of CCI, glycopolymers composed of these sugar derivatives will be provided.

  10. Carbohydrate microarrays by microcontact "click" chemistry. (United States)

    Michel, Olaf; Ravoo, Bart Jan


    Carbohydrate microarrays can be prepared by microcontact printing of carbohydrate alkyne conjugates on azide self-assembled monolayers (SAMs). The carbohydrates are immobilized by a "click" reaction in the contact area between the stamp and the substrate. The immobilized carbohydrates retain their characteristic selectivity toward lectins.

  11. Expression of mucin type carbohydrates may supplement histologic diagnosis in oral premalignant lesions. (United States)

    Bryne, M; Reibel, J; Mandel, U; Dabelsteen, E


    Recent studies have shown that changes within membrane bound carbohydrates may be essential for cellular differentiation and malignant transformation. We have therefore, by means of immunohistochemistry, studied the expression of T/Tn related (Thomsen-Friedenrich) carbohydrates in 13 oral lesions with squamous cell dysplasia. The epithelial grade of dysplasia was graded as mild, moderate or severe. The following carbohydrate structures were studied: Tn, T, mucintype 3 chain H, and the sialylated derivates, sialosyl-Tn and sialosyl-T. In general, short structures were detected on the basal cells and longer structures on the more mature spinous cells. In many cases, this sequential expression was more disturbed with increasing grade of epithelial dysplasia. However, our results also showed that some lesions with the same grade of epithelial dysplasia showed different carbohydrate expression. These findings indicate that expression of carbohydrates may supplement histologic diagnosis in the evaluation of the prognosis of premalignant lesions.

  12. Gender Differences in Carbohydrate Metabolism and Carbohydrate Loading

    Directory of Open Access Journals (Sweden)

    Willoughby Darryn


    Full Text Available Abstract Prior to endurance competition, many endurance athletes participate in a carbohydrate loading regimen in order to help delay the onset of fatigue. The "classic" regimen generally includes an intense glycogen depleting training period of approximately two days followed by a glycogen loading period for 3–4 days, ingesting approximately 60–70% of total energy intake as carbohydrates, while the newer method does not consist of an intense glycogen depletion protocol. However, recent evidence has indicated that glycogen loading does not occur in the same manner for males and females, thus affecting performance. The scope of this literature review will include a brief description of the role of estradiol in relation to metabolism and gender differences seen in carbohydrate metabolism and loading.

  13. Overall carbohydrate-binding properties of Castanea crenata agglutinin (CCA). (United States)

    Nomura, Keiichi; Takahashi, Nobuyuki; Hirose, Masaaki; Nakamura, Sachiko; Yagi, Fumio


    The carbohydrate-binding properties of Castanea crenata agglutinin (CCA) were investigated by an enzyme-linked lectin absorbent assay. The binding ability of each carbohydrate was compared using IC(50) values. CCA exhibited mannose/glucose specificity, as observed with many mannose-binding jacalin-related lectins. For oligosaccharides containing glucose, it has been shown that the degree of polymerization and the linkage mode of glucose residues have no effect on CCA-carbohydrate interaction; thus, only the non-reducing end glucose unit in glucooligosaccharides may be involved in the interaction with CCA. Among mannooligosaccharides, CCA strongly recognized alpha-(1-->3)-D-Man-[alpha-D-Man-(1-->6)]-D-Man, which is a core in N-linked carbohydrate chains. By considering the results with glycoproteins, it is likely that CCA binds preferentially to mono- or non-sialylated biantennary carbohydrate chains. We also obtained K(d) values by analysis of the dependency of the IC(50) on CCA concentration, based on the hypothesis that CCA has a single binding site or two equivalent binding sites. The estimated K(d) values for mannose, glucose and alpha-(1-->3)-D-Man-[alpha-D-Man-(1-->6)]-D-Man were 2.39, 7.19 and 0.483 mM, respectively. The relative binding abilities showed good agreement with the relative inhibition intensities. Isothermal calorimetric titration was carried out to directly estimate the dissociation constants of CCA for mannose and for alpha-D-Man-(1-->3)-D-Man. The values were 2.34 mM for mannose and 0.507 mM alpha-D-Man-(1-->3)-D-Man. These results suggest that the relative inhibition intensity represents the ratio of K(d) values and that CCA has a single or two equivalent binding sites.

  14. Carbohydrates Through Animation: Preliminary Step

    Directory of Open Access Journals (Sweden)

    J.K. Sugai


    Full Text Available Methods of education are changing, so the educational tools must change too. The developmentof the systems of information and communication gave the opportunity to bring new technology tothe learning process. Modern education needs interactive programs that may be available to theacademic community, in order to ease the learning process and sharing of the knowledge. Then,an educational software on Carbohydrates is being developed using concept maps and FLASH-MXanimations program, and approached through six modules. The introduction of Carbohydrates wasmade by the module Carbohydrates on Nature, which shows the animations gures of a teacher andstudents, visiting a farm, identifying the carbohydrates found in vegetables, animals, and microor-ganisms, integrated by links containing short texts to help understanding the structure and functionof carbohydrates. This module was presented, as pilot experiment, to teachers and students, whichdemonstrated satisfaction, and high receptivity, by using animation and interactivitys program asstrategy to biochemistrys education. The present work is part of the project Biochemistry throughanimation, which is having continuity.

  15. Aminooxylated Carbohydrates: Synthesis and Applications. (United States)

    Pifferi, Carlo; Daskhan, Gour Chand; Fiore, Michele; Shiao, Tze Chieh; Roy, René; Renaudet, Olivier


    Among other classes of biomolecules, carbohydrates and glycoconjugates are widely involved in numerous biological functions. In addition to addressing the related synthetic challenges, glycochemists have invested intense efforts in providing access to structures that can be used to study, activate, or inhibit these biological processes. Over the past few decades, aminooxylated carbohydrates have been found to be key building blocks for achieving these goals. This review provides the first in-depth overview covering several aspects related to the syntheses and applications of aminooxylated carbohydrates. After a brief introduction to oxime bonds and their relative stabilities compared to related C═N functions, synthetic aspects of oxime ligation and methodologies for introducing the aminooxy functionality onto both glycofuranosyls and glycopyranosyls are described. The subsequent section focuses on biological applications involving aminooxylated carbohydrates as components for the construcion of diverse architectures. Mimetics of natural structures represent useful tools for better understanding the features that drive carbohydrate-receptor interaction, their biological output and they also represent interesting structures with improved stability and tunable properties. In the next section, multivalent structures such as glycoclusters and glycodendrimers obtained through oxime ligation are described in terms of synthetic design and their biological applications such as immunomodulators. The second-to-last section discusses miscellaneous applications of oxime-based glycoconjugates, such as enantioselective catalysis and glycosylated oligonucleotides, and conclusions and perspectives are provided in the last section.

  16. The center for plant and microbial complex carbohydrates at the University of Georgia Complex Carbohydrate Research Center. Annual report, September 15, 1990--December 31, 1991

    Energy Technology Data Exchange (ETDEWEB)

    Albersheim, P.; Darvill, A.


    Research from the Complex Carbohydrates Research Center at the University of Georgia is presented. Topics include: Structural determination of soybean isoflavones which specifically induce Bradyrhizobium japonicum nodD1 but not the nodYABCSUIJ operon; structural analysis of the lipopolysaccharides (LPSs) from symbiotic mutants of Bradyrhizobium japonicum; structural characterization of lipooligosaccharides from Bradyrhizobium japonicum that are required for the specific nodulation of soybean; structural characterization of the LPSs from R. Leguminosarum biovar phaseoli, the symbiont of bean; characterization of bacteroid-specific LPS epitopes in R. leguminosarum biovar viciae; analysis of the surface polysaccharides of Rhizobium meliloti mutants whose lipopolysaccharides and extracellular polysaccharides can have the same function in symbiosis; characterization of a polysaccharide produced by certain Bradyrhizobium japonicum strains within soybean nodules; structural analysis of a streptococcal adhesin polysaccharide receptor; conformational studies of xyloglucan, the role of the fucosylated side chain in surface-specific cellulose-xyloglucan interactions; the structure of an acylated glucosamine oligosaccharide signal molecule (nod factor) involved in the symbiosis of Rhizobium leguminosarum biovar viciae with its host Vicia sativa; investigating membrane responses induced by oligogalacturonides in cultured cells; the polygalacturonase inhibitor protein; characterization of the self-incompatability glycoproteins from Petunia hybrida; investigation of the cell wall polysaccharide structures of Arabidopsis thaliana; and the glucan inhibition of virus infection of tabacco.

  17. Low-carbohydrate diets: what are the potential short- and long-term health implications? (United States)

    Bilsborough, Shane A; Crowe, Timothy C


    Low-carbohydrate diets for weight loss are receiving a lot of attention of late. Reasons for this interest include a plethora of low-carbohydrate diet books, the over-sensationalism of these diets in the media and by celebrities, and the promotion of these diets in fitness centres and health clubs. The re-emergence of low-carbohydrate diets into the spotlight has lead many people in the general public to question whether carbohydrates are inherently 'bad' and should be limited in the diet. Although low-carbohydrate diets were popular in the 1970s they have resurged again yet little scientific fact into the true nature of how these diets work or, more importantly, any potential for serious long-term health risks in adopting this dieting practice appear to have reached the mainstream literature. Evidence abounds that low-carbohydrate diets present no significant advantage over more traditional energy-restricted, nutritionally balanced diets both in terms of weight loss and weight maintenance. Studies examining the efficacy of using low-carbohydrate diets for long-term weight loss are few in number, however few positive benefits exist to promote the adoption of carbohydrate restriction as a realistic, and more importantly, safe means of dieting. While short-term carbohydrate restriction over a period of a week can result in a significant loss of weight (albeit mostly from water and glycogen stores), of serious concern is what potential exists for the following of this type of eating plan for longer periods of months to years. Complications such as heart arrhythmias, cardiac contractile function impairment, sudden death, osteoporosis, kidney damage, increased cancer risk, impairment of physical activity and lipid abnormalities can all be linked to long-term restriction of carbohydrates in the diet. The need to further explore and communicate the untoward side-effects of low-carbohydrate diets should be an important public health message from nutrition professionals.

  18. Carbohydrate chips for studying high-throughput carbohydrate-protein interactions. (United States)

    Park, Sungjin; Lee, Myung-ryul; Pyo, Soon-Jin; Shin, Injae


    Carbohydrate-protein interactions play important biological roles in living organisms. For the most part, biophysical and biochemical methods have been used for studying these biomolecular interactions. Less attention has been given to the development of high-throughput methods to elucidate recognition events between carbohydrates and proteins. In the current effort to develop a novel high-throughput tool for monitoring carbohydrate-protein interactions, we prepared carbohydrate microarrays by immobilizing maleimide-linked carbohydrates on thiol-derivatized glass slides and carried out lectin binding experiments by using these microarrays. The results showed that carbohydrates with different structural features selectively bound to the corresponding lectins with relative binding affinities that correlated with those obtained from solution-based assays. In addition, binding affinities of lectins to carbohydrates were also quantitatively analyzed by determining IC(50) values of soluble carbohydrates with the carbohydrate microarrays. To fabricate carbohydrate chips that contained more diverse carbohydrate probes, solution-phase parallel and enzymatic glycosylations were performed. Three model disaccharides were in parallel synthesized in solution-phase and used as carbohydrate probes for the fabrication of carbohydrate chips. Three enzymatic glycosylations on glass slides were consecutively performed to generate carbohydrate microarrays that contained the complex oligosaccharide, sialyl Le(x). Overall, these works demonstrated that carbohydrate chips could be efficiently prepared by covalent immobilization of maleimide-linked carbohydrates on the thiol-coated glass slides and applied for the high-throughput analyses of carbohydrate-protein interactions.

  19. Carbohydrates of human immunodeficiency virus

    DEFF Research Database (Denmark)

    Hansen, J E


    Elucidation of the mechanism by which viral infection induces the appearance of carbohydrate neoantigens is highly important. Results from such studies could be expected to be significant for a general understanding of the regulation of glycosylation, and perhaps especially important for the unde...

  20. Heavy Chain Diseases (United States)

    ... heavy chain produced: Alpha Gamma Mu Alpha Heavy Chain Disease Alpha heavy chain disease (IgA heavy chain ... disease or lead to a remission. Gamma Heavy Chain Disease Gamma heavy chain disease (IgG heavy chain ...

  1. Carbohydrate Chemistry from Fischer to Now

    Indian Academy of Sciences (India)

    , even to lay- men, are the carbohydrates, produced by plants. Green leaves ...... bacterial, viral and parasitic infections including meningitis,. HIV and malaria. The structure of a malaria vaccine contains a carbohydrate derivative of structure.

  2. Low-digestible carbohydrates in practice. (United States)

    Grabitske, Hollie A; Slavin, Joanne L


    Low-digestible carbohydrates are carbohydrates that are incompletely or not absorbed in the small intestine but are at least partly fermented by bacteria in the large intestine. Fiber, resistant starch, and sugar alcohols are types of low-digestible carbohydrates. Given potential health benefits (including a reduced caloric content, reduced or no effect on blood glucose levels, non-cariogenic effect), the prevalence of low-digestible carbohydrates in processed foods is increasing. Low-digestible carbohydrate fermentation in the gut causes gastrointestinal effects, especially at higher intakes. We review the wide range of low-digestible carbohydrates in food products, offer advice on identifying low-digestible carbohydrates in foods and beverages, and make suggestions for intakes of low-digestible carbohydrates.

  3. Carbohydrate-based immune adjuvants (United States)

    Petrovsky, Nikolai; Cooper, Peter D


    The role for adjuvants in human vaccines has been a matter of vigorous scientific debate, with the field hindered by the fact that for over 80 years, aluminum salts were the only adjuvants approved for human use. To this day, alum-based adjuvants, alone or combined with additional immune activators, remain the only adjuvants approved for use in the USA. This situation has not been helped by the fact that the mechanism of action of most adjuvants has been poorly understood. A relative lack of resources and funding for adjuvant development has only helped to maintain alum’s relative monopoly. To seriously challenge alum’s supremacy a new adjuvant has many major hurdles to overcome, not least being alum’s simplicity, tolerability, safety record and minimal cost. Carbohydrate structures play critical roles in immune system function and carbohydrates also have the virtue of a strong safety and tolerability record. A number of carbohydrate compounds from plant, bacterial, yeast and synthetic sources have emerged as promising vaccine adjuvant candidates. Carbohydrates are readily biodegradable and therefore unlikely to cause problems of long-term tissue deposits seen with alum adjuvants. Above all, the Holy Grail of human adjuvant development is to identify a compound that combines potent vaccine enhancement with maximum tolerability and safety. This has proved to be a tough challenge for many adjuvant contenders. Nevertheless, carbohydrate-based compounds have many favorable properties that could place them in a unique position to challenge alum’s monopoly over human vaccine usage. PMID:21506649

  4. Death by side rail. (United States)

    Brown, Sarah; Whitbread, Luana


    This study determined the prevalence of side rail use in chronic care units and the reduction of side rail use following education. An audit conducted in 2005 and repeated in 2007 looked at the number of side rails that were used and the reasons for this use. An educational presentation titled "Death by Side Rail" was provided for nurses and healthcare aides. Side rail use decreased by 60% from a prevalence of 90% of the population with side rails up on their beds. The primary reason for side rail use by nurses was determined to be "habit." Nurses no longer put up side rails out of habit, and they now assess the situation prior to the consideration of side rail use.

  5. Markov chains

    CERN Document Server

    Revuz, D


    This is the revised and augmented edition of a now classic book which is an introduction to sub-Markovian kernels on general measurable spaces and their associated homogeneous Markov chains. The first part, an expository text on the foundations of the subject, is intended for post-graduate students. A study of potential theory, the basic classification of chains according to their asymptotic behaviour and the celebrated Chacon-Ornstein theorem are examined in detail. The second part of the book is at a more advanced level and includes a treatment of random walks on general locally compact abelian groups. Further chapters develop renewal theory, an introduction to Martin boundary and the study of chains recurrent in the Harris sense. Finally, the last chapter deals with the construction of chains starting from a kernel satisfying some kind of maximum principle.


    Directory of Open Access Journals (Sweden)

    E. R. Meskina


    Full Text Available Background: Enteric viruses (mainly rotaviruses are the most common cause of infectious diarrhea in infants. One  of the  pathophysiologic mechanisms in rotaviral gastroenteritis is the  reduction of the  surface  activity of enterocyte disaccharidases  and  osmotic  diarrhea. Aim: To determine the clinical significance of metabolic activity of intestinal microbiota in the formation of the osmotic component of viral diarrhea in children of various ages. Materials and methods: The study involved 139 children aged  from 1 month  to 14 years admitted to the hospital in the first 24 to 72 hours of moderate-degree  viral gastroenteritis.  Rotaviral infection was the most prevalent  (90%. Viral etiology was confirmed  by the  reaction  of indirect hemagglutination and multiplex real-time PCR (in feces. Total carbohydrate content in the feces was measured and fecal microflora was investigated by two methods: bacteriological and gas liquid chromatography with the determination of short-chain fatty acids. Results: The mean carbohydrate content in the feces of children below 1.5 years of age was higher than  that  in older children (p = 0.014. There was an inverse correlation between the concentration of rotaviral antigens  and carbohydrate   contents (r = -0,43, p < 0.05 and the production of acetic and propionic acids (R = -0,35, p < 0.01. The carbohydrate content in acute stage of the disease was linearly associated with time to normalization of the stool (r = +0,47, p < 0.01. Previous acute  respiratory or intestinal  infections within 2 months (odds ratio [OR], 14.10; 95% confidence interval [CI] 3.86–51.53, previous  hospitalizations  (OR = 14.17; 95% CI 2.74–74.32 and  past  history of intestinal dysfunction (OR 5.68; 95% CI 1.67–19.76 were predictive of severe  carbohydrate malabsorption in children below 1.5 years of age. Conclusion: The lack of microbiota functional activity (assessed by production of short-chain

  7. Photo-Generation of Carbohydrate Microarrays (United States)

    Carroll, Gregory T.; Wang, Denong; Turro, Nicholas J.; Koberstein, Jeffrey T.

    The unparalleled structural diversity of carbohydrates among biological molecules has been recognized for decades. Recent studies have highlighted carbohydrate signaling roles in many important biological processes, such as fertilization, embryonic development, cell differentiation and cellȁ4cell communication, blood coagulation, inflammation, chemotaxis, as well as host recognition and immune responses to microbial pathogens. In this chapter, we summarize recent progress in the establishment of carbohydrate-based microarrays and the application of these technologies in exploring the biological information content in carbohydrates. A newly established photochemical platform of carbohydrate microarrays serves as a model for a focused discussion.

  8. Fluorous-based carbohydrate microarrays. (United States)

    Ko, Kwang-Seuk; Jaipuri, Firoz A; Pohl, Nicola L


    The success of microarrays, such as DNA chips, for biosample screening with minimal sample usage has led to a variety of technologies for assays on glass slides. Unfortunately, for small molecules, such as carbohydrates, these methods usually rely on covalent bond formation, which requires unique functional handles and multiple chemical steps. A new simpler concept in microarray formation is based on noncovalent fluorous-based interactions. A fluorous tail is designed not only to aid in saccharide purification but also to allow direct formation of carbohydrate microarrays on fluorous-derivatized glass slides for biological screening with lectins, such as concanavalin A. The noncovalent interactions in the fluorous-based array are even strong enough to withstand the detergents used in assays with the Erythrina crystagalli lectin. Additionally, the utility of benzyl carbonate protecting groups on fucose building blocks for the formation of alpha-linkages is demonstrated.

  9. Carbohydrate Microarrays in Plant Science

    DEFF Research Database (Denmark)

    Fangel, Jonatan Ulrik; Pedersen, H.L.; Vidal-Melgosa, S.


    industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high......Almost all plant cells are surrounded by glycan-rich cell walls, which form much of the plant body and collectively are the largest source of biomass on earth. Plants use polysaccharides for support, defense, signaling, cell adhesion, and as energy storage, and many plant glycans are also important...... for plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities....

  10. Carbohydrate cluster microarrays fabricated on three-dimensional dendrimeric platforms for functional glycomics exploration. (United States)

    Zhou, Xichun; Turchi, Craig; Wang, Denong


    We reported here a novel, ready-to-use bioarray platform and methodology for construction of sensitive carbohydrate cluster microarrays. This technology utilizes a three-dimensional (3-D) poly(amidoamine) starburst dendrimer monolayer assembled on glass surface, which is functionalized with terminal aminooxy and hydrazide groups for site-specific coupling of carbohydrates. A wide range of saccharides, including monosaccharides, oligosaccharides and polysaccharides of diverse structures, are applicable for the 3-D bioarray platform without prior chemical derivatization. The process of carbohydrate coupling is effectively accelerated by microwave radiation energy. The carbohydrate concentration required for microarray fabrication is substantially reduced using this technology. Importantly, this bioarray platform presents sugar chains in defined orientation and cluster configurations. It is, thus, uniquely useful for exploration of the structural and conformational diversities of glyco-epitope and their functional properties.

  11. Carbohydrate Cluster Microarrays Fabricated on 3-Dimensional Dendrimeric Platforms for Functional Glycomics Exploration (United States)

    Zhou, Xichun; Turchi, Craig; Wang, Denong


    We reported here a novel, ready-to-use bioarray platform and methodology for construction of sensitive carbohydrate cluster microarrays. This technology utilizes a 3-dimensional (3-D) poly(amidoamine) starburst dendrimer monolayer assembled on glass surface, which is functionalized with terminal aminooxy and hydrazide groups for site-specific coupling of carbohydrates. A wide range of saccharides, including monosaccharides, oligosaccharides and polysaccharides of diverse structures, are applicable for the 3-D bioarray platform without prior chemical derivatization. The process of carbohydrate coupling is effectively accelerated by microwave radiation energy. The carbohydrate concentration required for microarray fabrication is substantially reduced using this technology. Importantly, this bioarray platform presents sugar chains in defined orientation and cluster configurations. It is, thus, uniquely useful for exploration of the structural and conformational diversities of glyco-epitope and their functional properties. PMID:19791771

  12. Carbohydrates Through Animation: Preliminary Step


    J.K. Sugai; M.S.R. Figueiredo; R.V. Antônio; Oliveira,P.M.; V.A Cardoso; Ricardo, J.; Merino, E; Figueiredo, L. F.; D.N. Heidrich


    Methods of education are changing, so the educational tools must change too. The developmentof the systems of information and communication gave the opportunity to bring new technology tothe learning process. Modern education needs interactive programs that may be available to theacademic community, in order to ease the learning process and sharing of the knowledge. Then,an educational software on Carbohydrates is being developed using concept maps and FLASH-MXanimations program, and approach...

  13. Transition metals in carbohydrate chemistry

    DEFF Research Database (Denmark)

    Madsen, Robert


    This review describes the application of transition metal mediated reactions in carbohydrate synthesis. The different metal mediated transformations are divided into reaction types and illustrated by various examples on monosaccharide derivatives. Carbon-carbon bond forming reactions are further...... divided into cyclization reactions to carbocycles and branching reactions at terminal and non-terminal positions. In addition, carbon-oxygen and carbon-hydrogen bond forming reactions are illustrated by various oxidation and reduction procedures...

  14. Influence of various carbohydrate sources on postprandial glucose, insulin and NEFA concentrations in obese cats. (United States)

    Mori, A; Ueda, K; Lee, P; Oda, H; Ishioka, K; Sako, T


    Carbohydrate is an important source of energy, which can significantly affect postprandial blood glucose and insulin levels in cats. In healthy animals, this is not a big concern; however, in obese and diabetic animals, this is an important detail. In the present study, the impact of four different carbohydrate sources (glucose, maltose, corn starch, and trehalose) on short-term post-prandial serum glucose, insulin, and non-esterified fatty acid (NEFA) concentrations was investigated with four obese cats. Each of the carbohydrate sources was added to a commercial wet food diet for feeding the animals. A significant difference was observed in postprandial glucose, insulin, and NEFA area under the curve (AUC) values between each carbohydrate source in obese cats. Furthermore, glucose and maltose induced the highest postprandial glucose and insulin AUC values, whereas trehalose induced the lowest postprandial glucose and insulin AUC value amongst all carbohydrate sources, respectively, in obese cats. However, trehalose has a higher risk of inducing side effects, such as diarrhea, as compared to other carbohydrate sources. As such, different carbohydrate sources appear to have a very significant impact on post-prandial glycemia and subsequent insulin requirement levels in obese cats. These results might be useful when selecting a prescription diet for obese or diabetic cats. In addition, maltose appears to be capable of inducing experimentally evoked postprandial hyperglycemia in obese cats, which may serve as a good tool for use to check the impact and effectiveness of newly developed oral hypoglycemic drugs or supplements for cats in future experiments.

  15. Carbohydrate as covalent crosslink in human inter-alpha-trypsin inhibitor

    DEFF Research Database (Denmark)

    Jessen, T E; Faarvang, K L; Ploug, M


    The primary structure of inter-alpha-trypsin inhibitor is partially elucidated, but controversy about the construction of the polypeptide backbone still exists. We present evidence suggesting that inter-alpha-trypsin inhibitor represents a novel plasma protein structure with two separate polypept...... polypeptide chains covalently crosslinked only by carbohydrate (chondroitin sulphate)....

  16. Fabrication of carbohydrate chips and their use to probe protein-carbohydrate interactions. (United States)

    Park, Sungjin; Lee, Myung-Ryul; Shin, Injae


    Carbohydrate microarrays have received considerable attention as an advanced technology for the rapid analysis of carbohydrate-protein interactions. This protocol provides detailed procedures for the preparation of carbohydrate microarrays by immobilizing hydrazide-conjugated carbohydrates on epoxide-derivatized glass slides. In addition, we describe the use we make of these microarrays in glycomics research. Unlike other techniques that require large amounts of samples and long assay times, carbohydrate microarrays are used to carry out the rapid assessment of a number of carbohydrate-recognition events with tiny amounts of carbohydrate samples. Furthermore, the microarray technology is also utilized for the rapid assay of enzyme activities. We are able to routinely prepare carbohydrate microarrays within 12 h by using hydrazide-conjugated carbohydrates and apply these microarrays for the studies of glycan-protein interactions within 8 h.

  17. Photochemical micropatterning of carbohydrates on a surface. (United States)

    Carroll, Gregory T; Wang, Denong; Turro, Nicholas J; Koberstein, Jeffrey T


    In this report, we demonstrate a versatile method for the immobilization and patterning of unmodified carbohydrates onto glass substrates. The method employs a novel self-assembled monolayer to present photoactive phthalimide chromophores at the air-monolayer interface. Upon exposure to UV radiation, the phthalimide end-groups graft to surface-adsorbed carbohydrates, presumably by a hydrogen abstraction mechanism followed by radical recombination to form a covalent bond. Immobilized carbohydrate thin films are evidenced by fluorescence, ellipsometry and contact-angle measurements. Surface micropatterns of mono-, oligo-, and polysaccharides are generated by exposure through a contact photomask and are visualized by condensing water onto the surface. The efficiency of covalent coupling is dependent on the thermodynamic state of the surface. The amount of surface-grafted carbohydrate is enhanced when carbohydrate surface interactions are increased by the incorporation of amine-terminated molecules into the monolayer. Glass substrates modified with mixed monolayers of this nature are used to construct carbohydrate microarrays by spotting the carbohydrates with a robot and subsequently illuminating them with UV light to covalently link the carbohydrates. Surface-immobilized polysaccharides display well-defined antigenic determinants for antibody recognition. We demonstrate, therefore, that this novel technology combines the ability to create carbohydrate microarrays using the current state-of-the-art technology of robotic microspotting and the ability to control the shape of immobilized carbohydrate patterns with a spatial resolution defined by the UV wavelength and a shape defined by a photomask.

  18. Carbohydrates (United States)

    ... so you stay regular. Soluble fiber helps lower cholesterol levels and can help improve blood glucose control. ... fat milk or 8 ounces (225 grams) plain yogurt The food guide plate recommends filling half of ...

  19. Carbohydrates (United States)

    ... and refined grains. Whole grains are foods like whole wheat bread, brown rice, whole cornmeal, and oatmeal. They offer lots of nutrients ... items listed. Keep in mind that "multigrain," "100% wheat," and brown-looking bread are not necessarily whole grain breads. Refined grains mean that the food ...

  20. Aspergillus oryzae–Saccharomyces cerevisiae Consortium Allows Bio-Hybrid Fuel Cell to Run on Complex Carbohydrates


    Justin P. Jahnke; Thomas Hoyt; Hannah M. LeFors; James J. Sumner; David M. Mackie


    Consortia of Aspergillus oryzae and Saccharomyces cerevisiae are examined for their abilities to turn complex carbohydrates into ethanol. To understand the interactions between microorganisms in consortia, Fourier-transform infrared spectroscopy is used to follow the concentrations of various metabolites such as sugars (e.g., glucose, maltose), longer chain carbohydrates, and ethanol to optimize consortia conditions for the production of ethanol. It is shown that with proper design A. oryzae ...

  1. Surface characterization of carbohydrate microarrays. (United States)

    Scurr, David J; Horlacher, Tim; Oberli, Matthias A; Werz, Daniel B; Kroeck, Lenz; Bufali, Simone; Seeberger, Peter H; Shard, Alexander G; Alexander, Morgan R


    Carbohydrate microarrays are essential tools to determine the biological function of glycans. Here, we analyze a glycan array by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to gain a better understanding of the physicochemical properties of the individual spots and to improve carbohydrate microarray quality. The carbohydrate microarray is prepared by piezo printing of thiol-terminated sugars onto a maleimide functionalized glass slide. The hyperspectral ToF-SIMS imaging data are analyzed by multivariate curve resolution (MCR) to discern secondary ions from regions of the array containing saccharide, linker, salts from the printing buffer, and the background linker chemistry. Analysis of secondary ions from the linker common to all of the sugar molecules employed reveals a relatively uniform distribution of the sugars within the spots formed from solutions with saccharide concentration of 0.4 mM and less, whereas a doughnut shape is often formed at higher-concentration solutions. A detailed analysis of individual spots reveals that in the larger spots the phosphate buffered saline (PBS) salts are heterogeneously distributed, apparently resulting in saccharide concentrated at the rim of the spots. A model of spot formation from the evaporating sessile drop is proposed to explain these observations. Saccharide spot diameters increase with saccharide concentration due to a reduction in surface tension of the saccharide solution compared to PBS. The multivariate analytical partial least squares (PLS) technique identifies ions from the sugars that in the complex ToF-SIMS spectra correlate with the binding of galectin proteins.

  2. Carbohydrate microarrays as tools in HIV glycobiology. (United States)

    Ratner, Daniel M; Seeberger, Peter H


    Progress in carbohydrate microarray technology has positioned the glycochip among the expanding set of biophysical tools available to researchers. Synthetically-derived glycochips unite established microarray techniques with the versatility and structural precision of synthetic carbohydrate chemistry. A comprehensive demonstration of carbohydrate microarrays is illustrated by the chip-based study of protein/carbohydrate and protein/glycoprotein interactions as they relate to HIV glycobiology. Composed of a series of high-mannose oligosaccharides, carbohydrate microarrays were prepared utilizing a covalent linking strategy to immobilize synthetically-defined glycans in a uniform orientation. In concert with a simple glycoprotein array, these microarrays were used to establish the individual and competitive binding profiles of five gp120 binding proteins--DC-SIGN, CD4, 2G12 cyanovirin-N, and scytovirin--and established the carbohydrate structural requirements for these interactions.

  3. Microwave-assisted method for fabrication of carbohydrate cluster microarrays on 3-dimensional hydrazide-dendrimer substrate. (United States)

    Zhou, Xichun; Zhang, Jian; Wang, Denong


    We present here a method for construction of carbohydrate cluster microarrays. This technology utilizes a 3-dimensional poly(amidoamine) starburst dendrimer monolayer assembled on glass surface, which is functionalized with terminal hydrazide groups for site-specific coupling of carbohydrates without prior chemical derivatization. Microwave radiation energy is applied to accelerate carbohydrate coupling on chips. Since this bioarray platform is designed to present sugar chains in defined orientation and cluster configurations, it is particularly suitable for exploration of the structural and conformational diversities of glycoepitopes and their functional properties.

  4. Exercise and Regulation of Carbohydrate Metabolism


    Mul, Joram D.; Stanford, Kristin I.; Hirshman, Michael F.; Goodyear, Laurie J.


    Carbohydrates are the preferred substrate for contracting skeletal muscles during high-intensity exercise and are also readily utilized during moderate intensity exercise. This use of carbohydrates during physical activity likely played an important role during the survival of early Homo sapiens, and genes and traits regulating physical activity, carbohydrate metabolism, and energy storage have undoubtedly been selected throughout evolution. In contrast to the life of early H. sapiens, modern...

  5. Carbohydrate microarrays for assaying galactosyltransferase activity. (United States)

    Park, Sungjin; Shin, Injae


    [reaction: see text] Carbohydrate microarrays have been used recently for the rapid analysis of glycan-protein or glycan-cell interactions and for the detection of pathogens. As a demonstration of its significance and versatility, the microarray technology has been applied in this effort to assay glycosyltransferase activities. In addition, carbohydrate microarray based methods have been employed to quantitatively determine binding affinities between lectins and carbohydrates.

  6. Fabrication of Carbohydrate Microarrays by Boronate Formation. (United States)

    Adak, Avijit K; Lin, Ting-Wei; Li, Ben-Yuan; Lin, Chun-Cheng


    The interactions between soluble carbohydrates and/or surface displayed glycans and protein receptors are essential to many biological processes and cellular recognition events. Carbohydrate microarrays provide opportunities for high-throughput quantitative analysis of carbohydrate-protein interactions. Over the past decade, various techniques have been implemented for immobilizing glycans on solid surfaces in a microarray format. Herein, we describe a detailed protocol for fabricating carbohydrate microarrays that capitalizes on the intrinsic reactivity of boronic acid toward carbohydrates to form stable boronate diesters. A large variety of unprotected carbohydrates ranging in structure from simple disaccharides and trisaccharides to considerably more complex human milk and blood group (oligo)saccharides have been covalently immobilized in a single step on glass slides, which were derivatized with high-affinity boronic acid ligands. The immobilized ligands in these microarrays maintain the receptor-binding activities including those of lectins and antibodies according to the structures of their pendant carbohydrates for rapid analysis of a number of carbohydrate-recognition events within 30 h. This method facilitates the direct construction of otherwise difficult to obtain carbohydrate microarrays from underivatized glycans.

  7. Carbohydrate clearance receptors in transfusion medicine

    DEFF Research Database (Denmark)

    Sørensen, Anne Louise Tølbøll; Clausen, Henrik; Wandall, Hans H


    are especially important to enhance size and reduce glomerular filtration loss. Carbohydrates are, however, also ligands for a large number of carbohydrate-binding lectins exposed to the circulatory system that serve as scavenger receptors for the innate immune system, or have more specific roles in targeting......Complex carbohydrates play important functions for circulation of proteins and cells. They provide protective shields and refraction from non-specific interactions with negative charges from sialic acids to enhance circulatory half-life. For recombinant protein therapeutics carbohydrates...

  8. The effects of carbohydrate variation in isocaloric diets on glycogenolysis and gluconeogenesis in healthy men

    NARCIS (Netherlands)

    Bisschop, P. H.; Pereira Arias, A. M.; Ackermans, M. T.; Endert, E.; Pijl, H.; Kuipers, F.; Meijer, A. J.; Sauerwein, H. P.; Romijn, J. A.


    To evaluate the effect of dietary carbohydrate content on postabsorptive glucose metabolism, we quantified gluconeogenesis and glycogenolysis after 11 days of high carbohydrate (85% carbohydrate), control (44% carbohydrate), and very low carbohydrate (2% carbohydrate) diets in six healthy men. Diets

  9. The effects of carbohydrate variation in isocaloric diets on glycogenolysis and gluconeogenesis in healthy men

    NARCIS (Netherlands)

    Bisschop, PH; Arias, AMP; Ackermans, MT; Endert, E; Pijl, H; Kuipers, F; Meijer, AJ; Sauerwein, HP; Romijn, JA

    To evaluate the effect of dietary carbohydrate content on postabsorptive glucose metabolism, we quantified gluconeogenesis and glycogenolysis after 11 days of high carbohydrate (85% carbohydrate), control (44% carbohydrate), and very low carbohydrate (2% carbohydrate) diets in six healthy men. Diets

  10. Photogenerated Carbohydrate Microarrays to Study Carbohydrate-Protein Interactions using Surface Plasmon Resonance Imaging


    Tyagi, Anuradha; Wang, Xin; Deng, Lingquan; Ramström, Olof; Yan, Mingdi


    A photochemical strategy to generate carbohydrate microarrays on flat sensor surfaces, and to study the protein-binding effects of these arrays by surface plasmon resonance imaging is described. The approach was validated using a panel of carbohydrate-binding proteins. The coupling agents, thiol-functionalized perfluorophenyl azides, allow the covalent attachment of underivatized carbohydrates to gold surfaces by a fast photochemical reaction. Carbohydrate microarrays composed of 3,6-di-O-(α-...

  11. Hardwood siding performance. (United States)

    Glenn A. Cooper


    A 6-year exposure test of three styles of siding made from nine hardwoods and given three treatments showed that full-length yellow-poplar vertical tongue-and-groove siding dip-treated in a water-repellent preservative performed best.

  12. Single-sided NMR

    CERN Document Server

    Casanova, Federico; Blümich, Bernhard


    Single-Sided NMR describes the design of the first functioning single-sided tomograph, the related measurement methods, and a number of applications. One of the key advantages to this method is the speed at which the images are obtained.

  13. Distinct regulation in inflorescence carbohydrate metabolism according to grapevine cultivars during floral development. (United States)

    Sawicki, Mélodie; Jacquens, Lucile; Baillieul, Fabienne; Clément, Christophe; Vaillant-Gaveau, Nathalie; Jacquard, Cédric


    Carbohydrate metabolism is important in plant sexual reproduction because sugar contents are determining factors for both flower initiation and floral organ development. In woody plants, flowering represents the most energy-consuming step crucial to reproductive success. Nevertheless, in these species, the photosynthesis performed by flowers supplies the carbon required for reproduction. In grapevine (Vitis vinifera), the inflorescence has a specific status because this organ imports carbohydrates at the same time as it exports photoassimilates. In this study, fluctuations in carbohydrate metabolism were monitored by analyzing gas exchanges, photosynthetic electron transport capacity, carbohydrate contents and some activities of carbohydrate metabolism enzymes, in the inflorescences of Pinot noir and Gewurztraminer, two cultivars with a different sensitivity to coulure phenomenon. Our results showed that photosynthetic activity and carbohydrate metabolism are clearly different and differently regulated during the floral development in the two cultivars. Indeed, the regulation of the linear electron flow and the cyclic electron flow is not similar. Moreover, the regulation of PSII activity, with a higher Y(NPQ)/Y(NO) ratio in Gewurztraminer, can be correlated with the higher protection of the photosynthetic chain and consequently with the higher yield under optimal conditions of this cultivar. At least, our results showed a higher photosynthetic activity and a better protection of PSI in Pinot noir during the floral development. © 2015 Scandinavian Plant Physiology Society.

  14. Controllable construction of carbohydrate microarrays by site-directed grafting on self-organized porous films. (United States)

    Ke, Bei-Bei; Wan, Ling-Shu; Xu, Zhi-Kang


    Carbohydrate-protein interactions are critical in many biological processes. However, the interactions between individual carbohydrates and proteins are often of low affinity and difficult to study. Recent development of carbohydrate microarrays provides an effective tool to explore the interaction. In this work, carbohydrate microarrays were controllably constructed by grafting of a carbohydrate-containing monomer on self-organized honeycomb-patterned films. The films were prepared from an amphiphilic block copolymer, poly(styrene-block-(2-hydroxyethyl methacrylate)), by a breath figure method. Three-dimensional fluorescence results demonstrate that the hydroxyl groups aggregate mainly inside the pores, which afford a chance of site-directed surface modification. 2-(2,3,4,6-Tetra-O-acetyl-beta-D-glucosyloxy)ethyl methacrylate was selectively grafted in the pores by a surface-initiated atom transfer radical polymerization. Characterization by attenuated total reflectance Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, scanning electron microscopy, atomic force microscopy, and contact angle measurements confirms the site-directed growth of the glycopolymer chains. Further specific recognition of the carbohydrate microarrays to lectin (concanavalin A) leads to an organized microarray of protein, and hence this approach also opens a new route to fabricating other functional microarrays such as protein-patterned surfaces.

  15. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    20.6. 23.4. Zone of inhibition (mm); concentration used: 1 mg /1 mL of DMSO). Bull. Chem. Soc. Ethiop. 2006, 20(1) ... separated, washed with saturated brine, dried and concentrated. The crude compound was purified by thick ... washed with 10 % sodium hydroxide (2 x 60 mL). The basic solution was extracted with ether,.

  16. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    Recent findings by the Nigerian Geological Surveys in Kaduna, Nigeria reported the presence of ... classical methods in order to determine their respective major elements on interest that were hitherto not accounted for .... Vogel, A.I. A Textbook of Quantitative Inorganic Analysis including Elementary. Instrumental Analysis.

  17. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    2002 Chemical Society of Ethiopia. PICRANITINE, A NEW INDOLE ALKALOID FROM. PICRALIMA NITIDA (APOCYNACEAE). Pierre Tane1*, Mathieu Tene1 and Olov Sterner2. 1Department of Chemistry, University of Dschang, Box 67, Dschang, Cameroon. 2Division of Organic Chemistry 2, Lund Institute of Technology, ...

  18. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    The reactions were monitored by measuring the absorbance of ... ingestion. Much consideration is given to reduce pollution caused by organophosphate esters that are resistant ... formation of large amounts of organic waste is unacceptable.

  19. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    the total signal amplitude, becomes negligible as it approaches pH 7, so that the kinetics eventually becomes biphasic. The pH ... structure of guinea pig haemoglobin near the H3[125]β position shows that there is a lysine residue, LysA5[8]β, which is only 4 Χ ... ammonia forms of the resin in that order. The column was then ...

  20. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    heptyl- isocoumarin) (1), a metabolite of natural lichens, has been described. Reaction of 3,5- dimethoxyhomophthalic anhydride (2) with octanoyl chloride in the presence of 1,1,3,3- tetramethylguanidine (TMG) and triethyl amine afforded the 6 ...

  1. Propargyloxycarbonyl as a protecting group for the side chains of ...

    Indian Academy of Sciences (India)


    FTIR (neat): 3303, 2982,. 2131, 1777; δH (300 MHz, CDCl3): 2⋅6 (t, J = 2⋅4 Hz,. 1H), 4⋅7 (d, J = 2⋅4 Hz, 2H); δC (75 MHz, CDCl3):. 150⋅2, 77⋅6, 74⋅9, 58⋅3. 2.4 General procedure for the synthesis of O-Poc derivatives of serine, threonine and tyrosine. Serine, threonine or tyrosine, with the amino and carboxyl groups ...

  2. Propargyloxycarbonyl as a protecting group for the side chains of ...

    Indian Academy of Sciences (India)

    Propargyloxycarbonyl group is used as a protecting group for the hydroxyl groups of serine, threonine and tyrosine. The propargyloxycarbonyl derivatives of these hydroxy amino acids are stable to acidic and basic reagents commonly employed in peptide synthesis. The deprotection of the -Poc derivatives using ...

  3. Novel Polymers Containing Metal Ligands in the Side Chain (United States)


    great promise. In addition, interest in magnetic materials for giant- magnetoresistance devices, magnetic sensors, and more are highly sought after. (a...nanoparticles within the phase-separated domains were responsible for the RTF properties of the nanostructured BCPs. Monomer Synthesis. The same strained

  4. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    studied in attempt to mimic the potent inhibitor properties of DNA synthesis [1, 2]. H2L. (salicylaldehyde benzoylhydrazone) has been found to possess a bacterial activity [3]. The copper(II) complex of H2L was shown to be more potent than the free ligand, suggesting that the metal center was the biologically active site.

  5. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    materials with improved properties such as wide tunability of emission wavelength and high photoluminescence and ..... The oil was purified by vacuum distillation and the material that boiled at ... mixture was stirred under N2 atmosphere and the temperature was allowed to gradually rise to rt. After 29 h the mixture was ...

  6. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    A voucher specimen documenting the collection was identified at the Botanic Department of University of Douala by Dr Ndongo Din and was deposited there. Extraction and isolation. The air dried powdered seeds of S. zenkeri Harms (2.8 kg) were extracted with methanol at room temperature and the extract concentrated to ...

  7. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    2Department of Chemistry, University of Port Elizabeth, P.O. Box 1600, 6000 Port ... of these latter two ligands was authenticated by the X-ray crystal structure of .... the rotavaporator, and the green residue dissolved in 25 cm3 of acetone.

  8. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    About 50 million cars are produced every year, and over 700 million cars are used worldwide. Thus, the ... absolutely necessary and indispensable in every vehicle. Catalysts are composed of several .... hydrogen flow was stopped and the system was purged with argon (40 mL/min). The samples were heated to 973 K at a ...

  9. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    Considerable attention has been given over the past few years to the use of propargyltrimethylsilane magnesium bromide as a synthetic reagent, such as: (a) in the study of the methylisosartotuate synthesis [1]; (b) in the reaction with carbonyl derivatives [2-4] for the preparation of 4-(trimethylsilyl)but-2-ynol, ...

  10. Role of carboxylate side chains in the cation Hofmeister series. (United States)

    Kherb, Jaibir; Flores, Sarah C; Cremer, Paul S


    Thermodynamic and surface-specific spectroscopic investigations were carried with an elastin-like polypeptide (ELP) containing 16 aspartic acid residues. The goal was to explore the role of the carboxylate moieties in hydrophobic collapse and related Hofmeister effects. Experiments were conducted with a series of monovalent and divalent metal chloride salts. Both phase transition temperature and spectroscopic data demonstrated that the divalent cations showed relatively strong association to the carboxylate sites on the biopolymer with K(d) values in the range of 1 to 10 mM. The ordering of the divalent series was: Zn(2+) > Ca(2+) > Ba(2+) > Sr(2+) > Mg(2+). Monovalent cations displayed weaker binding which ranged from 78 mM for NH(4)(+) to 345 mM for Cs(+). The order for this series was: NH(4)(+) > Li(+) > Na(+) > NMe(4)(+) > K(+) > Rb(+) ≥ Cs(+). These results are in general agreement with the notion that strongly hydrated cations bind more tightly to carboxylate groups than do weakly hydrated cations. Moreover, the data for the monovalent series was partially consistent with the law of matching water affinity, although Li(+) and NH(4)(+) did not follow the model. The series for the divalent cations did not appear to obey the law of matching water affinity at all.

  11. Lignin-carbohydrate complexes from sisal (Agave sisalana) and abaca (Musa textilis): chemical composition and structural modifications during the isolation process. (United States)

    Del Río, José C; Prinsen, Pepijn; Cadena, Edith M; Martínez, Ángel T; Gutiérrez, Ana; Rencoret, Jorge


    Two types of lignins occurred in different lignin-carbohydrate fractions, a lignin enriched in syringyl units, less condensed, preferentially associated with xylans, and a lignin with more guaiacyl units, more condensed, associated with glucans. Lignin-carbohydrate complexes (LCC) were isolated from the fibers of sisal (Agave sisalana) and abaca (Musa textilis) according to a plant biomass fractionation procedure recently developed and which was termed as "universally" applicable to any type of lignocellulosic material. Two LCC fractions, namely glucan-lignin (GL) and xylan-lignin (XL), were isolated and differed in the content and composition of carbohydrates and lignin. In both cases, GL fractions were enriched in glucans and comparatively depleted in lignin, whereas XL fractions were depleted in glucans, but enriched in xylans and lignin. Analysis by two-dimensional Nuclear Magnetic Resonance (2D-NMR) and Derivatization Followed by Reductive Cleavage (DFRC) indicated that the XL fractions were enriched in syringyl (S)-lignin units and β-O-4' alkyl-aryl ether linkages, whereas GL fractions have more guaiacyl (G)-lignin units and less β-O-4' alkyl-aryl ether linkages per lignin unit. The data suggest that the structural characteristics of the lignin polymers are not homogeneously distributed within the same plant and that two different lignin polymers with different composition and structure might be present. The analyses also suggested that acetates from hemicelluloses and the acyl groups (acetates and p-coumarates) attached to the γ-OH of the lignin side chains were extensively hydrolyzed and removed during the LCC fractionation process. Therefore, caution must be paid when using this fractionation approach for the structural characterization of plants with acylated hemicelluloses and lignins. Finally, several chemical linkages (phenylglycosides and benzyl ethers) could be observed to occur between lignin and xylans in these plants.

  12. Gut feedback mechanisms and food intake: a physiological approach to slow carbohydrate bioavailability. (United States)

    Zhang, Genyi; Hasek, Like Y; Lee, Byung-Hoo; Hamaker, Bruce R


    Glycemic carbohydrates in foods are an important macronutrient providing the biological fuel of glucose for a variety of physiological processes. A classification of glycemic carbohydrates into rapidly digestible carbohydrate (RDC) and slowly digestible carbohydrate (SDC) has been used to specify their nutritional quality related to glucose homeostasis that is essential to normal functioning of the brain and critical to life. Although there have been many studies and reviews on slowly digestible starch (SDS) and SDC, the mechanisms of their slow digestion and absorption were mostly investigated from the material side without considering the physiological processes of their in vivo digestion, absorption, and most importantly interactions with other food components and the gastrointestinal tract. In this article, the physiological processes modulating the bioavailability of carbohydrates, specifically the rate and extent of their digestion and absorption as well as the related locations, in a whole food context, will be discussed by focusing on the activities of the gastrointestinal tract including glycolytic enzymes and glucose release, sugar sensing, gut hormones, and neurohormonal negative feedback mechanisms. It is hoped that a deep understanding of these physiological processes will facilitate the development of innovative dietary approaches to achieve desired carbohydrate or glucose bioavailability for improved health.

  13. Mastering ectomycorrhizal symbiosis: the impact of carbohydrates. (United States)

    Nehls, Uwe


    Mycorrhiza formation is the consequence of a mutualistic interaction between certain soil fungi and plant roots that helps to overcome nutritional limitations faced by the respective partners. In symbiosis, fungi contribute to tree nutrition by means of mineral weathering and mobilization of nutrients from organic matter, and obtain plant-derived carbohydrates as a response. Support with easily degradable carbohydrates seems to be the driving force for fungi to undergo this type of interaction. As a consequence, the fungal hexose uptake capacity is strongly increased in Hartig net hyphae of the model fungi Amanita muscaria and Laccaria bicolor. Next to fast carbohydrate uptake and metabolism, storage carbohydrates are of special interest. In functional A. muscaria ectomycorrhizas, expression and activity of proteins involved in trehalose biosynthesis is mainly localized in hyphae of the Hartig net, indicating an important function of trehalose in generation of a strong carbon sink by fungal hyphae. In symbiosis, fungal partners receive up to approximately 19 times more carbohydrates from their hosts than normal leakage of the root system would cause, resulting in a strong carbohydrate demand of infected roots and, as a consequence, a more efficient plant photosynthesis. To avoid fungal parasitism, the plant seems to have developed mechanisms to control carbohydrate drain towards the fungal partner and link it to the fungus-derived mineral nutrition. In this contribution, current knowledge on fungal strategies to obtain carbohydrates from its host and plant strategies to enable, but also to control and restrict (under certain conditions), carbon transfer are summarized.

  14. Hydropriming effects on carbohydrate metabolism, antioxidant ...

    African Journals Online (AJOL)



    Feb 21, 2012 ... Key words: Priming, seed vigor, carbohydrate metabolism, antioxidant enzymes. INTRODUCTION. Maize (Zea mays L.) is an .... al., 1995), changes in soluble carbohydrates (Bernal-. Lugo and Leopold, 1992, 1995) and ..... to a good seed storability (Bernal-Lugo and Leopold,. 1995), but loss of wheat grain ...

  15. Qualitative Carbohydrate Analysis using Alkaline Potassium ...

    Indian Academy of Sciences (India)

    IAS Admin

    Carbohydrates form a distinct class of organic compounds often identified by their characteristic behaviour towards a host of reagents [1–4]. Based on a kinetic study on the oxidation of carbohydrates with alkaline potassium ferricyanide [5], we had reported, in the April 2007 issue of Resonance, an unambiguous.

  16. Wood adhesives containing proteins and carbohydrates (United States)

    In recent years there has been resurgent interest in using biopolymers as sustainable and environmentally friendly ingredients in wood adhesive formulations. Among them, proteins and carbohydrates are the most commonly used. In this chapter, an overview is given of protein-based and carbohydrate-...

  17. Characterization of carbohydrate fractions and fermentation quality ...

    African Journals Online (AJOL)



    Aug 29, 2011 ... This experiment was carried out to evaluate the effects of adding fast-sile (FS), previous fermented juice (PFJ), sucrose (S) or fast-sile + sucrose (FS + S) on the fermentation characteristics and carbohydrates fractions of alfalfa silages by the Cornell net carbohydrates and proteins systems. (CNCPS).

  18. Characterization of carbohydrate fractions and fermentation quality ...

    African Journals Online (AJOL)

    This experiment was carried out to evaluate the effects of adding fast-sile (FS), previous fermented juice (PFJ), sucrose (S) or fast-sile + sucrose (FS + S) on the fermentation characteristics and carbohydrates fractions of alfalfa silages by the Cornell net carbohydrates and proteins systems (CNCPS). Silages quality were well ...

  19. Conversion of carbohydrates to levulinic acid esters

    DEFF Research Database (Denmark)


    The present invention relates to the field of converting carbohydrates into levulinic acid, a platform chemical for many chemical end products. More specifically the invention relates to a method for converting carbohydrates such as mono-, di- or polysaccharides, obtained from for example biomass...

  20. Total dissolved carbohydrate in Mahi river estuary

    Digital Repository Service at National Institute of Oceanography (India)

    Bhosle, N.B.; Rokade, M.A.; Zingde, M.D.

    Total dissolved carbohydrate varied from 4.37-15 mg l-1 and 3.71-15.95 mg l-1 in the surface and bottom samples respectively. Highest concentration of carbohydrate was observed at station 1 which decreased downward upto Station 6 which showed...