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Sample records for acid side chains

  1. Peptide Nucleic Acids Having Amino Acid Side Chains

    1998-01-01

    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...

  2. In Vitro Enzymatic Synthesis of New Penicillins Containing Keto Acids as Side Chains

    Ferrero, Miguel A.; Reglero, Angel; Martínez-Blanco, Honorina; Fernández-Valverde, Martiniano; Luengo, Jose M.

    1991-01-01

    Seven different penicillins containing α-ketobutyric, β-ketobutyric, γ-ketovaleric, α-ketohexanoic, δ-ketohexanoic, ε-ketoheptanoic, and α-ketooctanoic acids as side chains have been synthesized in vitro by incubating the enzymes phenylacetyl coenzyme A (CoA) ligase from Pseudomonas putida and acyl-CoA:6-aminopenicillanic acid acyltransferase from Penicillium chrysogenum with CoA, ATP, Mg2+, dithiothreitol, 6-aminopenicillanic acid, and the corresponding side chain precursor.

  3. Pyrrolidinobenzoic Acid Inhibitors of Influenza Virus Neuraminidase: the Hydrophobic Side Chain Influences Type A Subtype Selectivity

    Li, Yanwu; Silamkoti, Arundutt; Kolavi, Gundurao; Mou, Liyuan; Gulati, Shelly; Air, Gillian M; Brouillette, Wayne J.

    2012-01-01

    Neuraminidase (NA) plays a critical role in the life cycle of influenza virus and is a target for new therapeutic agents. A series of influenza neuraminidase inhibitors with the pyrrolidinobenzoic acid scaffold containing lipophilic side chains at the C3 position have been synthesized and evaluated for influenza neuraminidase inhibitory activity. The size and geometry of the C3 side chains have been modified in order to investigate structure-activity relationships. The results indicated that ...

  4. Asymmetric functional contributions of acidic and aromatic side chains in sodium channel voltage-sensor domains

    Pless, Stephan Alexander; Elstone, Fisal D; Niciforovic, Ana P; Galpin, Jason D; Yang, Runying; Kurata, Harley T; Ahern, Christopher A

    2014-01-01

    largely enigmatic. To this end, natural and unnatural side chain substitutions were made in the S2 hydrophobic core (HC), the extracellular negative charge cluster (ENC), and the intracellular negative charge cluster (INC) of the four VSDs of the skeletal muscle sodium channel isoform (NaV1.4). The......Voltage-gated sodium (NaV) channels mediate electrical excitability in animals. Despite strong sequence conservation among the voltage-sensor domains (VSDs) of closely related voltage-gated potassium (KV) and NaV channels, the functional contributions of individual side chains in Nav VSDs remain...... functional phenotypes that are different from those observed previously in Kv VSDs. In contrast, and similar to results obtained with Kv channels, individually neutralizing acidic side chains with synthetic derivatives and with natural amino acid substitutions in the INC had little or no effect on the...

  5. Pyrrolidinobenzoic acid inhibitors of influenza virus neuraminidase: the hydrophobic side chain influences type A subtype selectivity.

    Li, Yanwu; Silamkoti, Arundutt; Kolavi, Gundurao; Mou, Liyuan; Gulati, Shelly; Air, Gillian M; Brouillette, Wayne J

    2012-07-15

    Neuraminidase (NA) plays a critical role in the life cycle of influenza virus and is a target for new therapeutic agents. A series of influenza neuraminidase inhibitors with the pyrrolidinobenzoic acid scaffold containing lipophilic side chains at the C3 position have been synthesized and evaluated for influenza neuraminidase inhibitory activity. The size and geometry of the C3 side chains have been modified in order to investigate structure-activity relationships. The results indicated that size and geometry of the C3-side chain are important for selectivity of inhibition against N1 versus N2 NA, important type A influenza variants that infect man, including the highly lethal avian influenza. PMID:22677529

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

    Vaitheeswaran, S

    2014-01-01

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

    Carl Henrik Görbitz

    2016-09-01

    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.

  8. DNA-Templated Polymerization of Side-Chain-Functionalized Peptide Nucleic Acid Aldehydes

    Kleiner, Ralph E.; Brudno, Yevgeny; Birnbaum, Michael E.; Liu, David R.

    2008-01-01

    The DNA-templated polymerization of synthetic building blocks provides a potential route to the laboratory evolution of sequence-defined polymers with structures and properties not necessarily limited to those of natural biopolymers. We previously reported the efficient and sequence-specific DNA-templated polymerization of peptide nucleic acid (PNA) aldehydes. Here, we report the enzyme-free, DNA-templated polymerization of side-chain-functionalized PNA tetramer and pentamer aldehydes. We obs...

  9. The impact of amino acid side chain mutations in conformational design of peptides and proteins

    Laufer, B.; Frank, A.O.; Chatterjee, J; Neubauer, T; Mas Moruno, Carlos; Kummerlöwe, G.; Kessler, H.

    2010-01-01

    Local energetic effects of amino acid replacements are often considered to have only a moderate influence on the backbone conformation of proteins or peptides. As these effects are difficult to determine experimentally, no comparison has yet been performed. However, knowledge of the influence of side chain mutations is essential in protein homology modeling and in optimizing biologically active peptide ligands in medicinal chemistry. Furthermore, the tool of N-methylation of peptides is of in...

  10. Synthesis and Quantitative Structure-Property Relationships of Side Chain-Modified Hyodeoxycholic Acid Derivatives

    Antimo Gioiello

    2013-08-01

    Full Text Available Bile acids have emerged as versatile signalling compounds of a complex network of nuclear and membrane receptors regulating various endocrine and paracrine functions. The elucidation of the interconnection between the biological pathways under the bile acid control and manifestations of hepatic and metabolic diseases have extended the scope of this class of steroids for in vivo investigations. In this framework, the design and synthesis of novel biliary derivatives able to modulate a specific receptor requires a deep understanding of both structure-activity and structure-property relationships of bile acids. In this paper, we report the preparation and the critical micellization concentration evaluation of a series of hyodeoxycholic acid derivatives characterized by a diverse side chain length and by the presence of a methyl group at the alpha position with respect to the terminal carboxylic acid moiety. The data collected are instrumental to extend on a quantitative basis, the knowledge of the current structure-property relationships of bile acids and will be fruitful, in combination with models of receptor activity, to design and prioritize the synthesis of novel pharmacokinetically suitable ligands useful in the validation of bile acid-responsive receptors as therapeutic targets.

  11. Investigation of side chain liquid crystal polymers bearing cholesterol and bile acid derivatives

    Zhang Junhua; Stephen Freiberg; Francois Brisse; C.Géraldine Bazuin; Zhu Xiaoxia

    2004-01-01

    Cholic acid (or 3a,7a,12a-trihydoxyl-5a-cholan-24-oic acid) and lithocholic acid (or 3a-hydroxyl-5a-cholanic-24-oic acid) are commonly occurring bile acids synthesized from cholesterol in the liver in mammals. They all possess a steroid skeleton containing four rings, three with six carbons and one with five carbons. The transformation of cholesterol to cholic acid results in two major structural changes that affect the steroid skeleton. The first is the hydrogenation of the double bond between C5 and C6 and the second is a conformational flip of ring A from the 5a-position to the 5a-position. In addition, one or more hydroxyl groups are added to the steroid skeleton. Outside of the ring system, C24 is converted from a saturated alkyl to a carboxylic acid group.Side chain polymers based on cholesterol moiety have been made as reported in the literature.Since bile acids and cholesterol are all in the family of steroid molecules, it is of interest to investigate whether bile acids may also act as mesogenic groups.Therefore, flexible spacer groups with 10 carbons are introduced between bile acid skeleton and the poymerizable double bonds. The monomers and polymers are compared with cholesterol and dihydrocholesterol monomers and polymers with the same spacers. Dihydrocholesterol is chosen to investigate the influence of the double bond in the formation of LC, given that both cholesterol and dihydrocholesterol have a planar structure but there is no double bond in the latter. These monomers and their corresponding polymers were characterized for their liquid crystalline (LC) properties by differential scanning calorimetry (DSC), polarizing optical microscopy (POM) and X-ray diffraction.It was found that only the compounds bearing the planar cholesterol moieties possess LC phases. It is concluded that the 5a-configuration between the first and second cycles on the steroid skeleton of bile acids does not favor proper alignment of the rigid part of the bile acid moieties

  12. Extension of microwave-accelerated residue-specific acid cleavage to proteins with carbohydrate side chains and disulfide linkages

    Li, Jinxi; Shefcheck, Kevin; Callahan, John; Fenselau, Catherine

    2008-12-01

    This laboratory has introduced a chemical method for residue-specific protein cleavage and has provided a preliminary assessment of the suitability of microwave-accelerated acid cleavage as a proteomic tool. This report is a continuing assessment of the fate of common protein modifications in microwave-accelerated acid cleavage. We have examined the cleavage of ribonuclease A and the related N-linked glycoprotein ribonuclease B, and the O-linked glycoprotein alpha crystallin A chain, using MALDI-TOF and LC-ESI-MS to identify the peptide products. RNase A and B each contains four disulfide bonds, and the addition of a reducing reagent, such as dithiothreitol, was found to be required to achieve efficient acidic proteolysis. The linkage of the glycosidic group to the asparagine side chain in ribonuclease B was found not to be cleaved by brief microwave treatment in 12.5% acetic acid. The distribution of the heterogeneous carbohydrate side chain in the glycopeptide products of acid cleavage was compared to that of the glycopeptide products of tryptic digestion. Hydrolysis within the carbohydrate chain itself is minimal under the conditions used. The O-linked side chain on alpha crystalline A was found to be cleaved during acid cleavage of the protein.

  13. Local softness, softness dipole and polarizabilities of functional groups: application to the side chains of the twenty amino acids

    Krishta, Alisa; Van Alsenoy, Christian; 10.1063/1.3185349

    2010-01-01

    The values of molecular polarizabilities and softnesses of the twenty amino acids were computed ab initio (MP2). By using the iterative Hirshfeld scheme to partition the molecular electronic properties, we demonstrate that the values of the softness of the side chain of the twenty amino acid are clustered in groups reflecting their biochemical classification, namely: aliphatic, basic, acidic, sulfur containing, and aromatic amino acids . The present findings are in agreement with previous results using different approximations and partitioning schemes [P. Senet and F. Aparicio, J. Chem. Phys. 126,145105 (2007)]. In addition, we show that the polarizability of the side chain of an amino acid depends mainly on its number of electrons (reflecting its size) and consequently cannot be used to cluster the amino acids in different biochemical groups, in contrast to the local softness. Our results also demonstrate that the global softness is not simply proportional to the global polarizability in disagreement with th...

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

    Pattison, D I; Davies, Michael Jonathan

    2001-01-01

    , 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....... 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...

  15. Synthesis of a new β-amino acid with a 3-deoxy-L-ara furnaoside side chain: the influence of the side chain on the conformation of α/β-peptides.

    Sharma, Gangavaram V M; Anjaiah, Gonuguntla; Kanakaraju, Marumudi; Sudhakar, Bommeda; Chatterjee, Deepak; Kunwar, Ajit C

    2016-01-14

    The important role of side chains in the stabilization of helical folds in peptidic foldamers containing C-linked carbo-β-amino acids (β-Caa), an interesting class of β-amino acids, with carbohydrate side chains has been extensively elaborated. As a pragmatic approach to alleviate the interference of substituents in the side chains on the folding propensities of the peptides, they are often modified or removed. The present study reports the synthesis of a new β-Caa with a 3-deoxy-L-ara furanoside side chain, [(R)-β-Caa(da)], from D-glucose, and its use in the synthesis of α/β-peptides in 1 : 1 alternation with D-Ala. The synthesis of peptides using (R)-β-Caa(da), was facile unlike those from (R)-β-Caa(a) having the L-ara furanoside side chain. The detailed NMR, molecular dynamics (MD) and CD studies on the new α/β-peptides showed the presence of robust left-handed 11/9-mixed helices. The study demonstrates that the new (R)-β-Caa(da), behaves differently compared to the other two related monomers, (R)-β-Caa(x) with the D-xylo furanoside side chain and (R)-β-Caa(a). PMID:26489370

  16. Characterization of novel perylene diimides containing aromatic amino acid side chains

    Farooqi, Mohammed J.; Penick, Mark A.; Burch, Jessica; Negrete, George R.; Brancaleon, Lorenzo

    2016-01-01

    Perylene diimide derivatives have attracted initial interest as industrial dyes. Recently, much attention has been focused on their strong π- π stacks resulting from the large PDI aromatic core. These PDI stacks have distinct optical properties, and provide informative models that could mimic light-harvesting systems and initial charge transfer typical of photosynthetic systems. The absorption property of PDI derivatives may be tuned from visible to near-infrared region by peripheral substitution. We have studied a new class of PDI derivatives with aryl substituents derived from the side chains of aromatic aminoacids (Tyrosine, Tryptophan and Phenylalanine). We have investigated their absorption and the fluorescence properties in a set of organic solvents and established their different tendencies to aggregate in solution despite their solubility. Most aggregation appears to be unordered. One PDI analogue (the one formed from Tyr) in Methanol, however, appears to form J-type aggregates. Based on our results the compounds appear to be promising for future investigations regarding the interaction of these dyes with biomolecules.

  17. Solvation free energies in [bmim]-based ionic liquids: Anion effect toward solvation of amino acid side chain analogues

    Latif, Muhammad Alif Mohammad; Micaêlo, Nuno; Abdul Rahman, Mohd Basyaruddin

    2014-11-01

    Stochastic molecular dynamics simulations were performed to investigate the solvation free energy of 15 neutral amino acid side chain analogues in aqueous and five, 1-butyl-3-methylimidazolium ([BMIM])-based ionic liquids. The results in aqueous were found highly correlated with previous experimental and simulation data. Meanwhile, [BMIM]-based RTILs showed better solvation thermodynamics than water to an extent that they were capable of solvating molecules immiscible in water. Non-polar analogues showed stronger solvation in hydrophobic RTIL anions such as [PF6]- and [Tf2N]- while polar analogues showed stronger solvation in the more hydrophilic RTIL anions such as [Cl]-, [TfO]- and [BF4]-.

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

    Werner Tegge

    2010-01-01

    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.

  19. Peptide Nucleic Acid with a Lysine Side Chain at the β-Position: Synthesis and Application for DNA Cleavage.

    Sugiyama, Toru; Kuwata, Keiko; Imamura, Yasutada; Demizu, Yosuke; Kurihara, Masaaki; Takano, Masashi; Kittaka, Atsushi

    2016-01-01

    This paper reports the synthesis of new β-Lys peptide nucleic acid (PNA) monomers and their incorporation into a 10-residue PNA sequence. PNA containing β-Lys PNA units formed a stable hybrid duplex with DNA. However, incorporation of β-Lys PNA units caused destabilization of PNA-DNA duplexes to some extent. Electrostatic attractions between β-PNA and DNA could reduce this destabilization effect. Subsequently, bipyridine-conjugated β-Lys PNA was prepared and exhibited sequence selective cleavage of DNA. Based on the structures of the cleavage products and molecular modeling, we reasoned that bipyridine moiety locates within the minor groove of the PNA-DNA duplexes. The lysine side chain of β-PNA is a versatile handle for attaching various functional molecules. PMID:27373637

  20. Synthesis and Quantitative Structure-Property Relationships of Side Chain-Modified Hyodeoxycholic Acid Derivatives

    Antimo Gioiello; Antonio Macchiarulo; Roberto Pellicciari; Roberto Nuti; Roccaldo Sardella; Benedetto Natalini; Paola Sabbatini; Paolo Filipponi

    2013-01-01

    Bile acids have emerged as versatile signalling compounds of a complex network of nuclear and membrane receptors regulating various endocrine and paracrine functions. The elucidation of the interconnection between the biological pathways under the bile acid control and manifestations of hepatic and metabolic diseases have extended the scope of this class of steroids for in vivo investigations. In this framework, the design and synthesis of novel biliary derivatives able to modulate a specific...

  1. Low-temperature side-chain cleavage and decarboxylation of polythiophene esters by acid catalysis

    Søndergaard, Roar; Norrman, Kion; Krebs, Frederik C

    2012-01-01

    substituents have been examined by TGA‐MS using different sulphonic acids. A substantial lowering of the cleavage temperature is observed, and the ester cleavage can even be performed in situ on roll‐to‐roll‐coated films on polyethylene terephthalate (PET). © 2011 Wiley Periodicals, Inc. J Polym Sci Part A......Solubility switching of polymers is very useful in thin layer processing of conjugated polymers, as it allows for multilayer processing and increases the stability of the polymer. Acid catalyzed thermocleavage of ester groups from thiophene polymers carrying primary, secondary, and tertiary......: Polym Chem, 2012...

  2. Self-assembly of azobenzene based side-chain liquid crystalline polymer and -alkyloxybenzoic acids

    Kumarasamy Gayathri; Subramanian Balamurugan; Palaninathan Kannan

    2011-05-01

    Liquid crystalline pendant polymeric complexes have been obtained by supramolecular assembly of two mesogenic components namely, poly[4-(10-acryloyloxydecyloxy)-4'- phenylazobenzonitrile] (P10) and 4-alkyloxybenzoic acids (A7-A12). Hydrogen bond formed between carboxylic acid and cyano moiety served as molecular bridge. The polymeric complexes acquitted as undivided liquid crystalline properties exhibited stable and enantiotropic mesophases. The precursor, monomer and polymer were analysed by 1H-NMR and 13C-NMR spectroscopy. The hydrogen bonding interaction in polymer complexes (P10-A7 to P10-A12) was investigated by FT-IR spectroscopy. The thermal behaviours and textural analysis were studied by differential scanning calorimetry and polarized optical microscopy respectively.

  3. Side chain modified peptide nucleic acids (PNA for knock-down of six3 in medaka embryos

    Dorn Sebastian

    2012-08-01

    Full Text Available Abstract Background Synthetic antisense molecules have an enormous potential for therapeutic applications in humans. The major aim of such strategies is to specifically interfere with gene function, thus modulating cellular pathways according to the therapeutic demands. Among the molecules which can block mRNA function in a sequence specific manner are peptide nucleic acids (PNA. They are highly stable and efficiently and selectively interact with RNA. However, some properties of non-modified aminoethyl glycine PNAs (aegPNA hamper their in vivo applications. Results We generated new backbone modifications of PNAs, which exhibit more hydrophilic properties. When we examined the activity and specificity of these novel phosphonic ester PNAs (pePNA molecules in medaka (Oryzias latipes embryos, high solubility and selective binding to mRNA was observed. In particular, mixing of the novel components with aegPNA components resulted in mixed PNAs with superior properties. Injection of mixed PNAs directed against the medaka six3 gene, which is important for eye and brain development, resulted in specific six3 phenotypes. Conclusions PNAs are well established as powerful antisense molecules. Modification of the backbone with phosphonic ester side chains further improves their properties and allows the efficient knock down of a single gene in fish embryos.

  4. Role of Side Chains in β-Sheet Self-Assembly into Peptide Fibrils. IR and VCD Spectroscopic Studies of Glutamic Acid-Containing Peptides.

    Tobias, Fernando; Keiderling, Timothy A

    2016-05-10

    Poly(glutamic acid) at low pH self-assembles after incubation at higher temperature into fibrils composed of antiparallel sheets that are stacked in a β2-type structure whose amide carbonyls have bifurcated H-bonds involving the side chains from the next sheet. Oligomers of Glu can also form such structures, and isotope labeling has provided insight into their out-of-register antiparallel structure [ Biomacromolecules 2013 , 14 , 3880 - 3891 ]. In this paper we report IR and VCD spectra and transmission electron micrograph (TEM) images for a series of alternately sequenced oligomers, Lys-(Aaa-Glu)5-Lys-NH2, where Aaa was varied over a variety of polar, aliphatic, or aromatic residues. Their spectral and TEM data show that these oligopeptides self-assemble into different structures, both local and morphological, that are dependent on both the nature of the Aaa side chains and growth conditions employed. Such alternate peptides substituted with small or polar residues, Ala and Thr, do not yield fibrils; but with β-branched aliphatic residues, Val and Ile, that could potentially pack with Glu side chains, these oligopeptides do show evidence of β2-stacking. By contrast, for Leu, with longer side chains, only β1-stacking is seen while with even larger Phe side chains, either β-form can be detected separately, depending on preparation conditions. These structures are dependent on high temperature incubation after reducing the pH and in some cases after sonication of initial fibril forms and reincubation. Some of these fibrillar peptides, but not all, show enhanced VCD, which can offer evidence for formation of long, multistrand, often twisted structures. Substitution of Glu with residues having selected side chains yields a variety of morphologies, leading to both β1- and β2-structures, that overall suggests two different packing modes for the hydrophobic side chains depending on size and type. PMID:27099990

  5. Identification of Oxygenated Fatty Acid as a Side Chain of Lipo-Alkaloids in Aconitum carmichaelii by UHPLC-Q-TOF-MS and a Database

    Ying Liang

    2016-03-01

    Full Text Available Lipo-alkaloid is a kind of C19-norditerpenoid alkaloid usually found in Aconitum species. Structurally, they contain an aconitane skeleton and one or two fatty acid moieties of 3–25 carbon chains with 1–6 unsaturated degrees. Analysis of the lipo-alkaloids in roots of Aconitum carmichaelii resulted in the isolation of six known pure lipo-alkaloids (A1–A6 and a lipo-alkaloid mixture (A7. The mixture shared the same aconitane skeleton of 14-benzoylmesaconine, but their side chains were determined to be 9-hydroxy-octadecadienoic acid, 13-hydroxy-octadecadienoic acid and 10-hydroxy-octadecadienoic acid, respectively, by MS/MS analysis after alkaline hydrolysis. To our knowledge, this is the first time of the reporting of the oxygenated fatty acids as the side chains in naturally-occurring lipo-alkaloids. In order to identify more lipo-alkaloids, a compound database was established based on various combinations between the aconitane skeleton and the fatty acid chain, and then, the identification of lipo-alkaloids was conducted using the database, UHPLC-Q-TOF-MS and MS/MS. Finally, 148 lipo-alkaloids were identified from A. carmichaelii after intensive MS/MS analysis, including 93 potential new compounds and 38 compounds with oxygenated fatty acid moieties.

  6. Extension of microwave-accelerated residue-specific acid cleavage to proteins with carbohydrate side chains and disulfide linkages

    Li, Jinxi; Shefcheck, Kevin; Callahan, John; Fenselau, Catherine

    2008-01-01

    This laboratory has introduced a chemical method for residue-specific protein cleavage and has provided a preliminary assessment of the suitability of microwave accelerated acid cleavage as a proteomic tool. This report is a continuing assessment of the fate of common protein modifications in microwave-accelerated acid cleavage. We have examined the cleavage of ribonuclease A and the related N-linked glycoprotein ribonuclease B, and the O-linked glycoprotein alpha crystallin A chain, using MA...

  7. Primary structure of peptides and ion channels. Role of amino acid side chains in voltage gating of melittin channels.

    Tosteson, M T; Alvarez, O; Hubbell, W; Bieganski, R M; Attenbach, C; Caporales, L H; Levy, J J; Nutt, R F; Rosenblatt, M.; Tosteson, D. C.

    1990-01-01

    Melittin produces a voltage-dependent increase in the conductance of planar lipid bilayers. The conductance increases when the side of the membrane to which melittin has been added (cis-side) is made positive. This paper reports observations on the effect of modifying two positively charged amino acid residues within the NH2-terminal region of the molecule: lysine at position 7 (K7), and the NH2-terminal glycine (G1). We have synthesized melittin analogues in which K7 is replaced by asparagin...

  8. Mouse Siglec-1 Mediates trans-Infection of Surface-bound Murine Leukemia Virus in a Sialic Acid N-Acyl Side Chain-dependent Manner.

    Erikson, Elina; Wratil, Paul R; Frank, Martin; Ambiel, Ina; Pahnke, Katharina; Pino, Maria; Azadi, Parastoo; Izquierdo-Useros, Nuria; Martinez-Picado, Javier; Meier, Chris; Schnaar, Ronald L; Crocker, Paul R; Reutter, Werner; Keppler, Oliver T

    2015-11-01

    Siglec-1 (sialoadhesin, CD169) is a surface receptor on human cells that mediates trans-enhancement of HIV-1 infection through recognition of sialic acid moieties in virus membrane gangliosides. Here, we demonstrate that mouse Siglec-1, expressed on the surface of primary macrophages in an interferon-α-responsive manner, captures murine leukemia virus (MLV) particles and mediates their transfer to proliferating lymphocytes. The MLV infection of primary B-cells was markedly more efficient than that of primary T-cells. The major structural protein of MLV particles, Gag, frequently co-localized with Siglec-1, and trans-infection, primarily of surface-bound MLV particles, efficiently occurred. To explore the role of sialic acid for MLV trans-infection at a submolecular level, we analyzed the potential of six sialic acid precursor analogs to modulate the sialylated ganglioside-dependent interaction of MLV particles with Siglec-1. Biosynthetically engineered sialic acids were detected in both the glycolipid and glycoprotein fractions of MLV producer cells. MLV released from cells carrying N-acyl-modified sialic acids displayed strikingly different capacities for Siglec-1-mediated capture and trans-infection; N-butanoyl, N-isobutanoyl, N-glycolyl, or N-pentanoyl side chain modifications resulted in up to 92 and 80% reduction of virus particle capture and trans-infection, respectively, whereas N-propanoyl or N-cyclopropylcarbamyl side chains had no effect. In agreement with these functional analyses, molecular modeling indicated reduced binding affinities for non-functional N-acyl modifications. Thus, Siglec-1 is a key receptor for macrophage/lymphocyte trans-infection of surface-bound virions, and the N-acyl side chain of sialic acid is a critical determinant for the Siglec-1/MLV interaction. PMID:26370074

  9. Side chain and backbone ordering in a polypeptide

    Wei, Y; Hansmann, U H E

    2006-01-01

    We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of the two transitions vary between the peptide in gas phase and in an implicit solvent, our results indicate that, independent of the specific surroundings, upon continuously lowering the temperature side-chain ordering occurs only after the backbone topology is completely formed.

  10. Side chain effect on electronic structure of spin-coated films of [6,6]-phenyl-C61-butyric acid methyl ester and its bis-adduct

    Highlights: ► Electronic structure of spin-coated films of PCBM and bis-PCBM was investigated. ► Ionization energy and electron affinity of bis-PCBM are smaller than those of PCBM. ► Electron donation from the side chain to C60-backbone raises the HOMO and LUMO. ► Open circuit voltages of PCBM-based solar cells relates to electron affinities. - Abstract: We investigated the electronic structure of spin-coated films of two soluble fullerenes; [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and its bis-adduct (bis-PCBM) using ultraviolet photoelectron spectroscopy, inverse photoemission spectroscopy and molecular orbital calculations. The ionization energy and electron affinity of spin-coated films of bis-PCBM were determined to be 6.01 eV and 3.4 eV, respectively. Analysis of electron density suggested the stronger electron donation from the two side chains to fullerene-backbone in a bis-PCBM molecule, compared with PCBM. The electron donation raises the energies of the frontier orbitals of bis-PCBM, which mainly consist of π-orbitals of fullerene-backbone. As a result, the ionization energy and electron affinity of bis-PCBM are smaller than those of PCBM. Moreover, we also concluded that the larger open circuit voltage observed for bis-PCBM based organic photovoltaics was explained by the higher-lying unoccupied molecular orbital of bis-PCBM

  11. PEM steam electrolysis at 130 °C using a phosphoric acid doped short side chain PFSA membrane

    Hansen, Martin Kalmar; Aili, David; Christensen, Erik;

    2012-01-01

    Steam electrolysis test with a phosphoric acid doped Aquivion™ membrane was successfully conducted and current densities up to 775 mA cm-2 at 1.8 V was reached at 130 ºC and ambient pressure. A new composite membrane system using a perfluorosulfonic acid membrane (Aquivion™) as matrix and phospho......Steam electrolysis test with a phosphoric acid doped Aquivion™ membrane was successfully conducted and current densities up to 775 mA cm-2 at 1.8 V was reached at 130 ºC and ambient pressure. A new composite membrane system using a perfluorosulfonic acid membrane (Aquivion™) as matrix...... and phosphoric acid as proton conducting electrolyte was developed. Traditional perfluorosulfonic acid membranes do not possess sufficient dimensional stability and proton conductivity to be used at elevated temperatures and ambient pressures. The elevated temperature, high potentials and acidic conditions...

  12. Differential DNA and RNA sequence discrimination by PNA having charged side chains.

    De Costa, N Tilani S; Heemstra, Jennifer M

    2014-05-15

    PNA sequences modified with charged side chains were evaluated for base-pairing sequence selectivity under physiological conditions. PNA having negatively charged aspartic acid side chains shows higher selectivity with RNA, while PNA having positively charged lysine side chains shows higher selectivity with DNA. These observations provide insight into the binding selectivity of modified PNA in antisense and antigene applications. PMID:24731279

  13. Side-chain dynamics of two aromatic amino acids in pancreatic phospholipase A2 as studied by deuterium nuclear magnetic resonance

    The flexibility of individual amino acid side chains of pancreatic phospholipase A2 in aqueous and micellar solutions was studied with deuterium nuclear magnetic resonance (2H NMR). Bovine pancreatic phospholipase A2 was selectively deuterated at the aromatic ring systems of Trp-3 and Phe-5 and porcine pancreatic phospholipase A2 at Trp-3 only. Solid-state 2H NMR spectra of the lyophilized enzymes exhibited quadrupole splittings on the order of 130 kHz, indicating almost complete immobilization of the aromatic ring systems. Exposure to a water-saturated atmosphere did not remove these steric constraints. However, side-chain mobility could be induced for the tryptophyl residue of the bovine enzyme by dissolving this enzyme in aqueous buffer or micellar solution whereas the phenyl ring always remained immobile and served as a probe for the protein's overall rotation. Typical correlation times for the tryptophyl and phenyl aromatic ring systems in aqueous solution were 7 ps and 13 ns (at 20 degrees C), respectively. The correlation time of the phenyl ring was longer than expected for the monomeric protein (approximately 6 ns), suggesting some aggregation of the protein at the high concentrations used for the NMR measurements. Addition of a micellar solution of oleoylphosphocholine had no influence on the motional freedom of the tryptophyl residue but approximately doubled the correlation time of the phenyl ring, indicating an increase of the effective volume of the tumbling particle due to lipid-protein interaction. A different behavior was observed for the Trp-3 residue of porcine phospholipase A2

  14. Side chain polysiloxanes with phthalocyanine moieties

    T. Ganicz

    2012-05-01

    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.

  15. INCLUSION COMPLEX FORMATION BETWEEN α-CYCLODEXTRIN AND BIODEGRADABLE COMBLIKE COPOLYMERS WITH POLY(α,β-MALIC ACID) BACKBONES AND mPEG SIDE CHAINS

    Jing Zeng; Yuan Li; Jia-jing Li; Rui Wang; Bin He; Yu Nie; Xiang-lin Luo; Zhi-rong Zhang; Zhong-wei Gua

    2009-01-01

    Inclusion complexes(ICs)composed of ocyclodextrins(α-CD)and biodegradable comblike copolymers with poly(α,β-malic acid)(PMA)backbones and methylated poly(ethylene glycol)(mPEG)side chains were prepared by the host-guest reaction.Two series of ICs with mPEG750 and mPEG2000 were prepared.The stoichiometry(EG/CD)of all the ICs in mPEG2000 series was 3.1,no matter what the graft degree was.While in mPEG750 series,the stoichiometry(EG/CD)was very different;it increased with the amount of mPEG decreasing.The decomposition temperatures of the fragments in ICs were closely related to graft degrees.The stack of α-CDs in ICs was a channel-type structure.The crystal of ICs was lamellar,and it could be reorganized to well-defined supermolecular structure.

  16. A chemical approach for site-specific identification of NMR signals from protein side-chain NH3+ groups forming intermolecular ion pairs in protein–nucleic acid complexes

    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 NH3+ groups forming the intermolecular ion pairs. A characteristic change in their 1H and 15N 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 15N and DNA phosphorodithiaote 31P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to protein–RNA complexes as well

  17. 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

    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: juiwahar@utmb.edu, E-mail: j.iwahara@utmb.edu [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States)

    2015-05-15

    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.

  18. Side Chain Engineering in Solution-Processable Conjugated Polymers

    Mei, Jianguo

    2014-01-14

    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.

  19. SCit: web tools for protein side chain conformation analysis.

    Gautier, R; Camproux, A-C; Tufféry, P

    2004-07-01

    SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit. PMID:15215438

  20. Selective cleavage enhanced by acetylating the side chain of lysine.

    Fu, Leixiaomeng; Chen, Tingting; Xue, Gaiqing; Zu, Lily; Fang, Weihai

    2013-01-01

    Selective cleavage is of great interest in mass spectrometry studies as it can help sequence identification by promoting simple fragmentation pattern of peptides and proteins. In this work, the collision-induced dissociation of peptides containing internal lysine and acetylated lysine residues were studied. The experimental and computational results revealed that multiple fragmentation pathways coexisted when the lysine residue was two amino acid residues away from N-terminal of the peptide. After acetylation of the lysine side-chain, b(n)+ ions were the most abundant primary fragment products and the Lys(Ac)-Gly amide bond became the dominant cleavage site via an oxazolone pathway. Acetylating the side-chain of lysine promoted the selective cleavage of Lys-Xxx amide bond and generated much more information of the peptide backbone sequence. The results re-evaluate the selective cleavage due to the lysine basic side-chain and provide information for studying the post-translational modification of proteins and other bio-molecules containing Lys residues. PMID:23303756

  1. Simultaneous in vivo truncation of pectic side chains

    Øbro, Jens; Borkhardt, Bernhard; Harholt, Jesper;

    2009-01-01

    . These modifications often prevent gelation, which has been a major functional requirement of commercial pectins until recently. We have previously shown that modification of pectin is possible through heterologous expression of pectin degrading enzymes in planta. To test the effect of simultaneous...... modification of the two main neutral pectic side chains in pectic rhamnogalacturonan I (RGI), we constitutively expressed two different enzymes in Arabidopsis thaliana that would either modify the galactan or the arabinan side chains, or both side chains simultaneously. Our analysis showed that the...... simultaneous truncation of arabinan and galactan side chains is achievable and does not severely affect the growth of Arabidopsis thaliana....

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

    Headlam, Henrietta A; Davies, Michael Jonathan

    2002-01-01

    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 for...

  3. Transport properties of a random binary side-coupled chain

    Hu Dong-Sheng; Lu Xiu-Juan; Zhang Yong-Mei; Zhu Chen-Ping

    2009-01-01

    We investigate the transport properties of a random binary side-coupled chain by using the transfer-matrix technique. It is found that there are resonant states in the systems with short-range correlations between the host chain atoms and the side-coupled atoms. The analytic expressions for the extended states are also presented in the systems with the side couplings between like atoms and between unlike atoms.

  4. Supramolecular routes towards liquid crystalline side-chain polymers

    Hammond, Matthew R.; Mezzenga, Raffaele

    2008-01-01

    Supramolecular attachment of mesogenic or non-mesogenic side chains to polymer backbones can result in the formation of liquid crystalline morphologies. The various parameters that can be tuned in order to achieve these morphologies, such as the type of non-covalent bonding chemistry (hydrogen bonding, ionic bonding, metal coordination, π–π interactions), the polymeric template architecture, and the side chain structure and properties, are reviewed in what follows, with emphasis placed on the...

  5. Holographic Gratings in Azobenzene Side-Chain Polymethacrylates

    Andruzzi, Luisa; Altomare, Angelina; Ciardelli, Francesco; Solaro, Roberto; Hvilsted, Søren; Ramanujam, P.S.

    1999-01-01

    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'-cyanoazoben......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...

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

    Bhuyan, M.S.

    2011-12-14

    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.

  7. Protein–ligand docking with multiple flexible side chains

    Zhao, Yong; Sanner, Michel F.

    2007-01-01

    In this work, we validate and analyze the results of previously published cross docking experiments and classify failed dockings based on the conformational changes observed in the receptors. We show that a majority of failed experiments (i.e. 25 out of 33, involving four different receptors: cAPK, CDK2, Ricin and HIVp) are due to conformational changes in side chains near the active site. For these cases, we identify the side chains to be made flexible during docking calculation by superimpo...

  8. Mesomorphic structure of poly(styrene)-block-poly(4-vinylpyridine) with oligo(ethylene oxide)sulfonic acid side chains as a model for molecularly reinforced polymer electrolyte

    Kosonen, H; Valkama, S; Hartikainen, J; Eerikainen, H; Torkkeli, M; Jokela, K; Serimaa, R; Sundholm, F; ten Brinke, G; Ikkala, O; Eerikäinen, Hannele

    2002-01-01

    We report self-organized polymer electrolytes based on poly(styrene)-block-poly(4-vinylpyridine) (PS-block-P4VP). Liquidlike ethylene oxide (EO) oligomers with sulfonic acid end groups are bonded to the P4VP block, leading to comb-shaped supramolecules with the PS-block-P4VP backbone. Lithium perchl

  9. SDRL: a sequence-dependent protein side-chain rotamer library.

    Taghizadeh, Mohammad; Goliaei, Bahram; Madadkar-Sobhani, Armin

    2015-07-01

    Since the introduction of the first protein side-chain rotamer library (RL) almost half a century ago, RLs have been components of many programs and algorithms in structural bioinformatics. Based on the dependence of side-chain dihedral angles on the local backbone, three types of RLs have been identified: backbone-independent, secondary-structure-dependent and backbone-dependent. In all previous studies, the effect of sequence specificity on side-chain conformational preferences was neglected. In the effort to develop a new class of RLs, we considered that the side-chain conformation of the central residue in each triplet on a protein backbone depends on the sequence of the triplet; therefore, we developed a sequence-dependent rotamer library (SDRL). To accomplish this, 400 possible triplet sequences for 18 natural amino acids as the central residue, which corresponds to 7200 triplet sequences in total, were considered. Searching the set of 11 546 selected PDB entries for the 7200 triplet sequences resulted in 2 364 541 instances occurring for 18 amino acids. Our results show that Leu and Val experience minimal impact from the adjacent residues in adopting side-chain conformations. Cys, Ile, Trp, His, Asp, Met, Glu, Gln, Arg and Lys, on the other hand, adopt their side-chain conformations mostly based on the adjacent residues on the backbone. The remaining residue types were moderately dependent on the adjacent residues. Using the new library, side-chain repacking algorithms can find preferred conformations of each residue more easily than with other backbone-independent RLs. PMID:25953624

  10. Synthesis of Bisphenols Carrying Long Hydrocarbon Side Chains

    XU Jing-zhe; JIANG Nan-zhe; ZHANG Jian; JIANG Ri-shan

    2005-01-01

    Bisphenols containing long aliphatic hydrocarbon side chains were synthesized by the condensation of phenol with aldehyde or ketone in the presence of heteropolyacid. Their structures were characterized by IR, 1H NMR, 13C NMR and element analysis. The experiment results show that when heteropolyacid was used as a catalyst, these bisphenols were obtained in high selectivity and high yields.

  11. Photoinduced Circular Anisotropy in Side-Chain Azobenzene Polyesters

    Nikolova, L.; Todorov, T.; Ivanov, M.;

    1997-01-01

    We report for the first time the inducing of large circular anisotropy in previously unoriented films of side-chain azobenzene polyesters on illumination with circularly polarized light at a wavelength of 488 nm. The circular dichroism and optical activity are measured simultaneously in real time...

  12. Functional Identification of Close Proximity Amino Acid Side Chains within the Transmembrane-Spanning Helixes of the P2X2 Receptor

    Liang, Xin; Xu, Huijuan; Li, Caiyue; Yin, Shikui; Xu, Tingting; Liu, Jinsong; Li, Zhiyuan

    2013-01-01

    The transition from the closed to open state greatly alters the intra- and inter-subunit interactions of the P2X receptor (P2XR). The interactions that occur in the transmembrane domain of the P2X2R remain unclear. We used substituted cysteine mutagenesis disulfide mapping to identify pairs of residues that are in close proximity within the transmembrane domain of rP2X2R and compared our results to the predicted positions of these amino acids obtained from a rat P2X2R homology model of the av...

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

    Roshan Gaonkar; N Viswanadham

    2005-04-01

    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 components from suppliers through a component marketplace and sells its manufactured sub-assemblies to original equipment manufacturers (OEMs), through a sub-assembly marketplace. In these web-enabled supply chains, embedded with upstream and downstream electronic marketplaces, we need methods for online supply-chain partner selection based on pricing and delivery schedules. In this paper, we develop and present such a model that selects partners, synchronizes supply chain activities and optimizes the profit through optimal revenue pricing and cost minimization.

  14. Arginine side chain interactions and the role of arginine as a gating charge carrier in voltage sensitive ion channels

    Armstrong, Craig T.; Mason, Philip E.; Anderson, J. L. Ross; Dempsey, Christopher E.

    2016-02-01

    Gating charges in voltage-sensing domains (VSD) of voltage-sensitive ion channels and enzymes are carried on arginine side chains rather than lysine. This arginine preference may result from the unique hydration properties of the side chain guanidinium group which facilitates its movement through a hydrophobic plug that seals the center of the VSD, as suggested by molecular dynamics simulations. To test for side chain interactions implicit in this model we inspected interactions of the side chains of arginine and lysine with each of the 19 non-glycine amino acids in proteins in the protein data bank. The arginine guanidinium interacts with non-polar aromatic and aliphatic side chains above and below the guanidinium plane while hydrogen bonding with polar side chains is restricted to in-plane positions. In contrast, non-polar side chains interact largely with the aliphatic part of the lysine side chain. The hydration properties of arginine and lysine are strongly reflected in their respective interactions with non-polar and polar side chains as observed in protein structures and in molecular dynamics simulations, and likely underlie the preference for arginine as a mobile charge carrier in VSD.

  15. A set of engineered Escherichia coli expression strains for selective isotope and reactivity labeling of amino acid side chains and flavin cofactors.

    Jennifer Mehlhorn

    Full Text Available Biological reactions are facilitated by delicate molecular interactions between proteins, cofactors and substrates. To study and understand their dynamic interactions researchers have to take great care not to influence or distort the object of study. As a non-invasive alternative to a site-directed mutagenesis approach, selective isotope labeling in combination with vibrational spectroscopy may be employed to directly identify structural transitions in wild type proteins. Here we present a set of customized Escherichia coli expression strains, suitable for replacing both the flavin cofactor and/or selective amino acids with isotope enriched or chemically modified substrates. For flavin labeling we report optimized auxotrophic strains with significantly enhanced flavin uptake properties. Labeled protein biosynthesis using these strains was achieved in optimized cultivation procedures using high cell density fermentation. Finally, we demonstrate how this approach is used for a clear assignment of vibrational spectroscopic difference signals of apoprotein and cofactor of a flavin containing photoreceptor of the BLUF (Blue Light receptors Using FAD family.

  16. Functional identification of close proximity amino acid side chains within the transmembrane-spanning helixes of the P2X2 receptor.

    Xin Liang

    Full Text Available The transition from the closed to open state greatly alters the intra- and inter-subunit interactions of the P2X receptor (P2XR. The interactions that occur in the transmembrane domain of the P2X2R remain unclear. We used substituted cysteine mutagenesis disulfide mapping to identify pairs of residues that are in close proximity within the transmembrane domain of rP2X2R and compared our results to the predicted positions of these amino acids obtained from a rat P2X2R homology model of the available open and closed zebrafish P2X4R structures. Alternations in channel function were measured as a change in the ATP-gated current before and after exposure to dithiothreitol. Thirty-six pairs of double mutants of rP2X2R expressed in HEK293 cells produced normal functioning channels. Thirty-five pairs of these mutants did not exhibit a functionally detectable disulfide bond. The double mutant H33C/S345C formed redox-dependent cross-links in the absence of ATP. Dithiothreitol ruptured the disulfide bond of H33C/S345C and induced a 2 to 3-fold increase in current. The EC50 for H33C/S345C before dithiothreitol treatment was ~2-fold higher than that after dithiothreitol treatment. Dithiothreitol reduced the EC50 to wild-type levels. Furthermore, expression of trimeric concatamer receptors with Cys mutations at some but not all six positions showed that the more disulfide bond formation sites within the concatamer, the greater current potentiation after dithiothreitol incubation. Immunoblot analysis of H33C/S345C revealed one monomer band under nonreducing conditions strongly suggesting that disulfide bonds are formed within single subunits (intra-subunit and not between two subunits (inter-subunit. Taken together, these data indicate that His33 and Ser345 are proximal to each other across an intra-subunit interface. The relative movement between the first transmembrane and the second transmembrane in the intra-subunit is likely important for transmitting the

  17. Carbon-14 methylation of the 2-methylbutyryl side chain of mevinolin and its analogs

    A one step procedure for the preparation of three labeled mevinolin analogs possessing the 2,2-dimethylbutyryloxy side chain is described. Three lactones were converted into potassium salts of their corresponding di or trihydroxy carboxylic acids from which anionic ester enolates were generated and alkylated with [14]methyl iodide. Workup and purification by reverse phase HPLC provided the three radiochemically pure mevinolin analogs. The labeled lactones were converted into ammonium salts of their corresponding di or trihydroxy acids. (author)

  18. An Exact Algorithm for Side-Chain Placement in Protein Design

    Canzar, Stefan; Klau, Gunnar W

    2011-01-01

    Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial side-chain placement problem consists of choosing a side-chain placement for each residue position such that the resulting overall energy is minimum. The choice of the side-chain then also determines the amino acid for this position. Many algorithms for this NP-hard problem have been proposed in the context of homology modeling, which, however, reach their limits when faced with large protein design instances. In this paper, we propose a new exact method for the side-chain placement problem that works well even for large instance sizes as they appear in protein design. Our main contribution is a dedicated branch-and-bound algorithm that combines tight upper and lower bounds resulting from a novel Lagrangian relaxation approach for side-chain placement. Our experimental results show...

  19. Holographic Gratings in Azobenzene Side-Chain Polymethacrylates

    Andruzzi, Luisa; Altomare, Angelina; Ciardelli, Francesco;

    1999-01-01

    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'-cyanoazoben......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...... polarizing optical microscopy. Atomic force microscopy investigations have been carried out on the polarization holographic gratings recorded in the polymethacrylate films. A surface relief grating has been found to appear in all films after irradiation. The copolymers with 50-75% dye content exhibit the...

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

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

    1996-01-01

    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 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....

  1. Highly conductive side chain block copolymer anion exchange membranes.

    Wang, Lizhu; Hickner, Michael A

    2016-06-28

    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. PMID:27216558

  2. Branched-Chain Amino Acids

    Matteo Ghiringhelli

    2015-07-01

    Full Text Available Our study is focused on evaluation and use of the most effective and correct nutrients. In particular, our attention is directed to the role of certain amino acids in cachectic patients.During parenteral nutrition in humans, physician already associates in the PN-bags different formulations including amino acids, lipids and glucose solutions or essential amino acids solution alone or exclusively branched-chain amino acids (BCAA. Studies investigated the effects of dietary BCAA ingestion on different diseases and conditions such as obesity and metabolic disorders, liver disease, muscle atrophy, cancer, impaired immunity or injuries (surgery, trauma, burns, and sepsis. BCAAs have been shown to affect gene expression, protein metabolism, apoptosis and regeneration of hepatocytes, and insulin resistance. They have also been shown to inhibit the proliferation of liver cancer cells in vitro, and are essential for lymphocyte proliferation and dendritic cell maturation. Oral or parenteral administration of these three amino acids will allow us to evaluate the real efficacy of these compounds during a therapy to treat malnutrition in subjects unable to feed themselves.

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

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

    2010-03-05

    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

  4. Development of metallocomplex amino acids synthons for the asymmetric preparation of α-amino acids by stereoselective introduction of a side chain. Evaluation of the model asymmetric preparation of alanine and β-13C monolabelled α-aminoisobutyric acid

    In this communication the evaluation of eleven new metallocomplex alanine synthons bearing C2-symmetric benzyl groups with electron-donating and electron-withdrawing substituents is described. α-Methylated glycine synthons (alanine complexes) were evaluated alongside alanine synthons in order to obtain a deeper understanding of the relationship between their structures and stereochemistry of monoalkylated products and to choose several candidates for their further tests for stereospecific preparation of 6-[18F]FDOPA. Glycine-derived analogues of the complexes 3-5 are the best candidates for the development of a 6-[18F]FDOPA preparation procedure. In the model epimerisation reaction they demonstrated the best performance, much better compared to the previously described compound 2. Complexes 3, 5 and 8 are the best in asymmetric preparation of β-13C monolabelled α-aminoisobutyric acid. They have to be tested in the preparation of ?-methyl amino acids like 6-[18F]-α-methylDOPA and 2-[18F]-α-methyltyrosine. (author)

  5. Simultaneous NMR assignment of backbone and side chain amides in large proteins with IS-TROSY

    A new strategy for the simultaneous NMR assignment of both backbone and side chain amides in large proteins with isotopomer-selective transverse-relaxation-optimized spectroscopy (IS-TROSY) is reported. The method considers aspects of both the NMR sample preparation and the experimental design. First, the protein is dissolved in a buffer with 50%H2O/50%D2O in order to promote the population of semideuterated NHD isotopomers in side chain amides of Asn/Gln residues. Second, a 13C'-coupled 2D 15N-1H IS-TROSY spectrum provides a stereospecific distinction between the geminal protons in the E and Z configurations of the carboxyamide group. Third, a suite of IS-TROSY-based triple-resonance NMR experiments, e.g. 3D IS-TROSY-HNCA and 3D IS-TROSY-HNCACB, are designed to correlate aliphatic carbon atoms with backbone amides and, for Asn/Gln residues, at the same time with side chain amides. The NMR assignment procedure is similar to that for small proteins using conventional 3D HNCA/3D HNCACB spectra, in which, however, signals from NH2 groups are often very weak or even missing due to the use of broad-band proton decoupling schemes and NOE data have to be used as a remedy. For large proteins, the use of conventional TROSY experiments makes resonances of side chain amides not observable at all. The application of IS-TROSY experiments to the 35-kDa yeast cytosine deaminase has established a complete resonance assignment for the backbone and stereospecific assignment for side chain amides, which otherwise could not be achieved with existing NMR experiments. Thus, the development of IS-TROSY-based method provides new opportunities for the NMR study of important structural and biological roles of carboxyamides and side chain moieties of arginine and lysine residues in large proteins as well as amino moieties in nucleic acids

  6. Purification and characterization of corticosteroid side chain isomerase

    Corticosteroid side chain isomerase of rat liver catalyzes the interconversion of the ketol (20-oxo-21-ol) and (20-hydroxy-21-al) forms of the corticosteroid side chain. The enzyme has now been purified to apparent homogeneity from rat liver cytosol by sequential chromatography on anionic, hydroxylapatite, and gel filtration columns. Ketol-aldol isomerization is followed by measuring the exchange of tritium from 21-tritiated steroids with water. The native enzyme is a dimer of MW 44,000. The isoelectric point is 4.8 ± 0.1 pH units. The purified enzyme is stimulated by Co3+ or Ni2+. The enzyme utilizes 11-deoxycorticosterone, corticosterone, and 17-deoxycortisol as substrate but not cortisol, tetrahydrocortisol, and prednisolone. Tritium-water exchange of (21S)-[21-3H]DOC is a pseudo-first-order reaction; 21-3H exchange from the 21R isomer proceeds with first-order kinetics only after a lag associated with its epimerization to the 21S form

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

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

    2002-01-01

    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 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....

  8. Novel Fluorinated Polymers Containing Short Perfluorobutyl Side Chains and Their Super Wetting Performance on Diverse Substrates.

    Jiang, Jingxian; Zhang, Guangfa; Wang, Qiongyan; Zhang, Qinghua; Zhan, Xiaoli; Chen, Fengqiu

    2016-04-27

    Because the emission of perfluorooctanoic acid (PFOA) was completely prohibited in 2015, the widely used poly- and perfluoroalkyl substances with long perfluoroalkyl groups must be substituted by environmentally friendly alternatives. In this study, one kind of potential alternative (i.e., fluorinated polymers with short perfluorobutyl side chains) has been synthesized from the prepared monomers {i.e., (perfluorobutyl)ethyl acrylate (C4A), (perfluorobutyl)ethyl methacrylate (C4MA), 2-[[[[2-(perfluorobutyl)]sulfonyl]methyl]amino]ethyl acrylate (C4SA), and methacrylate (C4SMA)}, and the microstructure, super wetting performance, and applications of the synthesized fluorinated polymers were systematically investigated. The thermal and crystallization behaviors of the fluoropolymer films were characterized by differential scanning calorimetry and wide-angle X-ray diffraction analysis, respectively. Dynamic water-repellent models were constructed. The stable low surface energy and dynamic water- and oil-repellent properties of these synthesized fluorinated polymers with short perfluorobutyl side chains were attributed to the synergetic effect of amorphous fluorinated side chains in perfluoroalkyl acrylate and crystalline hydrocarbon pendant groups in stearyl acrylate. Outstanding water- and oil-repellent properties of fabrics and any other substrates could be achieved by a facile dip-coating treatment using a fluorinated copolymer dispersion. As a result, we believe that our prepared fluorinated copolymers are potential candidates to replace the fluoroalkylated polymers with long perfluorinated chains in nonstick and self-cleaning applications in our daily life. PMID:27052113

  9. A new model for ligand release. Role of side chain in gating the enediyne antibiotic.

    Hariharan, Parameswaran; Liang, Wenchuan; Chou, Shan-Ho; Chin, Der-Hang

    2006-06-01

    Antitumor antibiotic chromoproteins such as neocarzinostatin involve a labile toxin that is tightly bound by a protective protein with very high affinity but must also be freed to exert its function. Contrary to the prevalent concept of ligand release, we established that toxin release from neocarzinostatin requires no major backbone conformational changes. We report, herein, that subtle changes in the side chains of specific amino acid residues are adequate to gate the release of chromophore. A recombinant wild type aponeocarzinostatin and its variants mutated around the opening of the chromophore binding cleft are employed to identify specific side chains likely to affect chromophore release. Preliminary, biophysical characterization of mutant apoproteins by circular dichroism and thermal denaturation indicate that the fundamental structural characteristics of wild type protein are conserved in these mutants. The chromophore reconstitution studies further show that all mutants are able to bind chromophore efficiently with similar complex structures. NMR studies on 15N-labeled mutants also suggest the intactness of binding pocket structure. Kinetic studies of chromophore release monitored by time course fluorescence and quantitative high pressure liquid chromatography analyses show that the ligand release rate is significantly enhanced only in Phe78 mutants. The extent of DNA cleavage in vitro corresponds well to the rate of chromophore release. The results provide the first clear-cut indication of how toxin release can be controlled by a specific side chain of a carrier protein. PMID:16567802

  10. Quantitative Profiling of Feruloylated Arabinoxylan Side-Chains from Graminaceous Cell Walls

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

    2016-01-01

    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. PMID:26834763

  11. Effects of Side Chains with Similar Lengths and Different Structures of Polyimides on Liquid Crystal Alignment Behavior

    Jia-hao Xia; Ying Jiang; Shi-ming Gong; Zhen Sun; Ying-han Wang

    2014-01-01

    Polyimides (PI) with different side chains in structure were synthesized by copolycondensation of pyromelliticmdianhydride (PMDA) with 3,5-diamino-(4'-methane acid hexyl ester) phenyl-benzamide (C6-PDA),(4-butoxybiphenol)-3',5'-diaminobenzoate (C4-BBDA) and 3,5-diamino-benzoic acid decyl ester (C 10-DA) named PI-PDA,PI-C4,PI-DA,respectively.The lengths of side chains of PI-PDA and PI-DA are as similar as that of PI-C4.Through the pretilt angle tests it is demonstrated that neither the structure of side chains nor the rubbing process could make an obvious difference on vertical alignment property when the lengths of the side chains are similar,standing at around 1.6 nm.The measurement of surface energy of PI surfaces further proved this result.The result of the X-ray photo-electron spectroscope measurement indicated that the side chains of PIs stretched out from the polymer bulk phase and accumulated on the surface.

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

    Arlette A. Santiago

    2012-01-01

    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.

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

    Boryana Trusheva

    2016-01-01

    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.

  14. Copoly(γ,DL-glutamate)s containing octadecyl and dodecyl side chains: Synthesis and characterization

    Oh, Sejin

    2012-01-01

    Copoly(-alkyl γ,DL-glutamate)s containing octadecyl and dodecyl side chains in a wide range of compositions (coPAAG-18,12) were synthesized from microbial racemic poly(γ,DL-glutamic acid) (PGGA). Feed ratios of 1-octadecanol to 1-dodecanol were 100:0, 75:25, 50:50, 25:75, and 0:100. The procedure of synthesis consisted of two-steps: Poly(-ethyl γ,DL-glutamate) (PAAG-2) was prepared by esterification of PGGA and then transesterified with 1-octadecanol or/and 1-dodecanol to obt...

  15. Selective side-chain oxidation of alkyl aromatic compounds catalyzed by cerium modified silver catalysts

    Beier, Matthias Josef; Schimmoeller, Bjoern; Hansen, Thomas Willum; Andersen, Jens Enevold Thaulov; Pratsinis, Sotiris E.; Grunwaldt, Jan-Dierk

    2010-01-01

    Silver supported on silica effectively catalyzes the aerobic side-chain oxidation of alkyl aromatic compounds under solvent-free conditions. Toluene, p-xylene, ethylbenzene and cumene were investigated as model substrates. Typically, the reaction was performed at ambient pressure; only for toluene...... an elevated pressure was required. Carboxylic acids, such as benzoic acid or p-toluic acid, additionally increased the reaction rate while CeO2 could act both as a promoter and an inhibitor depending on the substrate and the reaction conditions. Silver catalysts were prepared both by standard...... catalysis. In addition, flame-made catalysts were more stable against silver leaching compared to the impregnated catalysts. The structure of the silver catalysts was studied in detail both by X-ray absorption spectroscopy and transmission electron microscopy suggesting metallic silver to be required for...

  16. Branched-Chain Amino Acids

    Pátek, Miroslav

    Berlin : Springer-Verlag Berlin Heidelberg, 2007, s. 129-162. ISBN 978-3-540-48595-7 Institutional research plan: CEZ:AV0Z50200510 Keywords : amino acids * homologous reactions Subject RIV: EE - Microbiology, Virology

  17. Switching effect of the side chain on quantum walks on triple graphs

    Du, Yi-Mu; Lu, Li-Hua; Li, You-Quan

    2015-07-01

    We consider a continuous-time quantum walk on a triple graph and investigate the influence of the side chain on propagation in the main chain. Calculating the interchange of the probabilities between the two parts of the main chain, we find that a switching effect appears if there is an odd number of points in the side chain when concrete conditions between the length of the main chain and the position of the side chain are satisfied. However, such an effect does not occur if there is an even number of points in the side chain. We also suggest two proposals for experiments to demonstrate this effect, which may be employed to design a new type of switching device.

  18. Variation of the net charge, lipophilicity and side chain flexibility in Dmt1-DALDA: effect on opioid activity and biodistribution

    Novoa, Alexandre; Van Dorpe, Sylvia; Wynendaele, Evelien; Spetea, Mariana; Bracke, Nathalie; Stalmans, Sofie; Betti, Cecilia; Chung, Nga N.; Lemieux, Carole; Zuegg, Johannes; Cooper, Matthew A.; Tourwé, Dirk; De Spiegeleer, Bart; Schiller, Peter W.; Ballet, Steven

    2012-01-01

    The influence of the side chain charges of the second and fourth amino acid residues in the peptidic μ opioid lead agonist Dmt-D-Arg-Phe-Lys-NH2 ([Dmt1]-DALDA) was examined. Additionally, to increase the overall lipophilicity of [Dmt1]-DALDA and to investigate the Phe3 side chain flexibility, the final amide bond was N-methylated and Phe3 was replaced by a constrained aminobenzazepine analogue. The in vitro receptor binding and activity of the peptides, as well as their in vivo transport (bra...

  19. Electron transport chains of lactic acid bacteria

    Brooijmans, R.J.W.

    2008-01-01

    Lactic acid bacteria are generally considered facultative anaerobic obligate fermentative bacteria. They are unable to synthesize heme. Some lactic acid bacteria are unable to form menaquinone as well. Both these components are cofactors of respiratory (electron transport) chains of prokaryotic bacteria. Lactococcus lactis, and several other lactic acid bacteria, however respond to the addition of heme in aerobic growth conditions. This response includes increased biomass and robustness. In t...

  20. Macromolecular recognition: Recognition of polymer side chains by cyclodextrin

    Hashidzume, Akihito; Harada, Akira

    2015-12-01

    The interaction of cyclodextrins (CD) with water soluble polymers possessing guest residues has been investigated as model systems in biological molecular recognition. The selectivity of interaction of CD with polymer-carrying guest residues is controlled by polymer chains, i.e., the steric effect of polymer main chain, the conformational effect of polymer main chain, and multi-site interaction. Macroscopic assemblies have been also realized based on molecular recognition using polyacrylamide-based gels possessing CD and guest residues.

  1. Inosine Nucleobase Acts as Guanine in Interactions with Protein Side Chains.

    Hajnic, Matea; Ruiter, Anita de; Polyansky, Anton A; Zagrovic, Bojan

    2016-05-01

    A central intermediate in purine catabolism, the inosine nucleobase hypoxanthine is also one of the most abundant modified nucleobases in RNA and plays key roles in the regulation of gene expression and determination of cell fate. It is known that hypoxanthine acts as guanine when interacting with other nucleobases and base pairs most favorably with cytosine. However, its preferences when it comes to interactions with amino acids remain unknown. Here we present for the first time the absolute binding free energies and the associated interaction modes between hypoxanthine and all standard, non-glycyl/non-prolyl amino acid side chain analogs as derived from molecular dynamics simulations and umbrella sampling in high- and low-dielectric environments. We illustrate the biological relevance of the derived affinities by providing a quantitative explanation for the specificity of hypoxanthine-guanine phosphoribosyltransferase, a key enzyme in the purine salvage pathway. Our results demonstrate that in its affinities for protein side chains, hypoxanthine closely matches guanine, much more so than its precursor adenine. PMID:27093234

  2. Synthesis and Properties of a Novel Polyimide with Side Chain Containing Biphenyl Unit

    WANG Xu; CHANG Tong-xin; ZHANG Peng; CHEN Yi; LIU Xiang-yang

    2012-01-01

    A novel biphenyl side-chained diamine with alkyloxy spacer and alkyloxy tail,4'-butoxy-4-(3,5-diami-nobenzoyloxy)hexyloxybiphenyl(C6BBC4),was synthesized and characterized by FTIR and 1H NMR.A series of polyimide(PI)films with different side chain contents was synthesized from biphenyltetracarboxylicdianhydride (BPDA),4,4'-oxydianiline(ODA)and C6BBC4,and their thermal properties,optical transparency and liquid crystal alignment property,and so on,were investigated by thermogravimetric analysis(TGA),differential scanning calorimetry(DSC),crystal rotation method,polarizing microscopy and UV-Vis spectra.With the content of side chained diamine increasing from 0 to 100%,the ηinh of poly(amide acid)(PAA)decreased rapidly from 3.0 to 0.51,the glass transition temperature(Tg)of polyimides(PIs)decreased from 274 ℃ to 203 ℃ and the Vis-light transmittance of alignment films substantially increased.As for the alignment properties,the pretilt angle of PI alignment films without rubbing could reach 90° when the content of C6BBC4 was 60% or more.At the same time,the alignment stability could meet the industrial requirements.It was considered that the alkoxy spacer,the biphenyl unit and the alkoxy tail may all play important roles in achieving a large pretilt angle even up to 90°,and the introduction of only the alkoxy spacer or alkoxy tail can also improve the pretilt angle,but not by much.

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

    Li, Huawei

    2011-07-01

    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.

  4. Electronic absorption spectroscopy probed side-chain movement in chromic transitions of polydiacetylene vesicles.

    Potisatityuenyong, Anupat; Rojanathanes, Rojrit; Tumcharern, Gamolwan; Sukwattanasinitt, Mongkol

    2008-05-01

    Thermochromism, solvatochromism, and alkalinochromism of a poly-10,12-pentacosadiynoic acid (poly(PCDA)) vesicle solution are studied by electronic absorption spectroscopy. The spectroscopic profiles reveal different sequences of side-chain movement during the chromic transitions. The gradual hypsochromic shift and reversibility of the purple solution at low temperature in the thermochromic transition indicates that the transition starts with reversible conformational alteration of methylene side chains leading to metastable purple vesicles. Further heating to 80 degrees C or higher eventually causes the hydrogen bonds at the carboxylic head groups to break and turns the vesicle solution to red. The irreversibility of the red vesicles indicates that it is the most thermodynamically stable form. In the ethanolochromism and alkalinochromism, the processes are however induced at the vesicle-media interface, directly bringing about the hydrogen bond breaking. The purple solutions observed in the ethanolochromism and alkalinochromism cannot reverse back to the blue one. The absorption spectra clearly demonstrate that they are mixtures of the blue and red vesicles. PMID:18366237

  5. MORPHOLOGICAL STUDIES OF A THERMOTROPIC SIDE-CHAIN LIQUID CRYSTALLINE POLYMER DURING MESOPHASE TRANSITIONS

    Chi-bing Tan; Quan-ling Zhang; Shu-fan Zhang; Xia-yu Wang; Mao Xu

    1999-01-01

    The morphological features of a side-chain liquid crystalline polymer during the mesophase transitions were investigated by using the DSC technique. The polymer used was polyacrylate with mesogens of three benzene rings attached to the main chain through a flexible spacer. A special two-phase texture was observed in the transition temperature range. Similar to main-chain liquid crystalline polymers the transition process of the side-chain liquid crystalline polymer was composed of an initiation of the new phase at local places of the old phase matrix and a growth process of the new phase domains.

  6. Dual mesomorphic assemblage of chitin normal acylates and rapid enthalpy relaxation of their side chains.

    Teramoto, Yoshikuni; Miyata, Tomoya; Nishio, Yoshiyuki

    2006-01-01

    Chitin derivatives having normalacyl groups (C(n)H(2n-1)O-; n = 4-20) were synthesized with pyridine, p-toluenesulfonyl chloride, and normal alkanoic acid in an N,N-dimethylacetamide-lithium chloride homogeneous system. The products (C(n)-ACs; degree of acyl substitution, DS = 1.7-1.9) showed an n-dependent thermal transition behavior: no evident transition (n = 4-10), a glass transition (n = 12 and 14), and a pseudo-first-order phase transition (n = 16-20), the latter two occurring usually below room temperature when examined by differential scanning calorimetry. Wide-angle X-ray diffractometry (WAXD) at 20 degrees C displayed a sharp diffraction peak (2theta = 2 degrees -7 degrees ) and a diffuse halo (2theta approximately 20 degrees ) for the respective C(n)-ACs. The former d-spacing (1.5-3.6 nm) increased with an increase in n to yield two stages of mutually different increasing rates, which reflects a systematic n-dependence of the period of a layered structure of the main chains. The molecular assembly of C(n)-ACs exhibited "dual mesomorphy"; nematic ordering for the semirigid carbohydrate trunk and smectic one for the flexible side chains. On the other hand, WAXD profiles of C(n)-ACs (n = 14-18) indicated almost no temperature dependence from -150 to +220 degrees C. Therefore, it was reasonably assumed that the pseudo-first-order transition observed in thermograms of C(n)-ACs (n = 16-20) was due to the enthalpy relaxation of the side-chain assemblage. An insight was provided into the kinetics of the characteristic aging behavior as a liquid-crystalline glass, in comparison with the corresponding data for other noncrystalline macromolecules. PMID:16398515

  7. Cholesterol Analogs with Degradation-resistant Alkyl Side Chains Are Effective Mycobacterium tuberculosis Growth Inhibitors.

    Frank, Daniel J; Zhao, Yan; Wong, Siew Hoon; Basudhar, Debashree; De Voss, James J; Ortiz de Montellano, Paul R

    2016-04-01

    Cholest-4-en-3-one, whether added exogenously or generated intracellularly from cholesterol, inhibits the growth ofMycobacterium tuberculosiswhen CYP125A1 and CYP142A1, the cytochrome P450 enzymes that initiate degradation of the sterol side chain, are disabled. Here we demonstrate that a 16-hydroxy derivative of cholesterol, which was previously reported to inhibit growth ofM. tuberculosis, acts by preventing the oxidation of the sterol side chain even in the presence of the relevant cytochrome P450 enzymes. The finding that (25R)-cholest-5-en-3β,16β,26-triol (1) (and its 3-keto metabolite) inhibit growth suggests that cholesterol analogs with non-degradable side chains represent a novel class of anti-mycobacterial agents. In accord with this, two cholesterol analogs with truncated, fluorinated side chains have been synthesized and shown to similarly block the growth in culture ofM. tuberculosis. PMID:26833565

  8. Beyond rotamers: a generative, probabilistic model of side chains in proteins

    Harder, Tim; Boomsma, Wouter; Paluszewski, Martin; Frellsen, Jes; Johansson, Kristoffer Enøe; Hamelryck, Thomas

    2010-01-01

    collections of side chain conformations derived from experimentally determined protein structures. The discretization can be exploited to efficiently search the conformational space. However, discretizing this naturally continuous space comes at the cost of losing detailed information that is crucial for...

  9. Studies on the Model Synthesis of the Brassinolide and Dolicholide Side Chains

    Li Zeng PENG; Feng Zhi ZHANG; Tian Sheng MEI; Yu Lin LI

    2003-01-01

    A stereoselective synthesis of brassinolide and dolicholide, which involves constructionof the side chain enantiomers by a highly stereoselective aldol reaction of aldehyde 5 with theanion of α-silyloxy ketone 6 is described.

  10. iTreePack: Protein Complex Side-Chain Packing by Dual Decomposition

    Peng, Jian; Hosur, Raghavendra; Berger, Bonnie; Xu, Jinbo

    2015-01-01

    Protein side-chain packing is a critical component in obtaining the 3D coordinates of a structure and drug discovery. Single-domain protein side-chain packing has been thoroughly studied. A major challenge in generalizing these methods to protein complexes is that they, unlike monomers, often have very large treewidth, and thus algorithms such as TreePack cannot be directly applied. To address this issue, SCWRL4 treats the complex effectively as a monomer, heuristically excluding weak interac...

  11. Surface relief measurements in side-chain azobenzene polyesters with different substituents

    Helgert, M.; Wenke, L.; Hvilsted, Søren;

    2001-01-01

    Light-induced surface modification of a series of liquid-crystalline side-chain azobenzene polyesters which have the same main- and side-chain structure but eleven different substituents on the azobenzene is investigated. Using a transmission mask as well as single focused beams we show that the...... azobenzene polyester was included in the study for comparison. The results point to a mechanism of the surface relief phenomenon, in which the architecture of the polyesters plays a crucial role....

  12. Conformational gel analysis and graphics: Measurement of side chain rotational isomer populations by NMR and molecular mechanics

    Haydock, Christopher

    2007-01-01

    Conformational gel analysis and graphics systematically identifies and evaluates plausible alternatives to the side chain conformations found by conventional peptide or protein structure determination methods. The proposed analysis determines the populations of side chain rotational isomers and the probability distribution of these populations. The following steps are repeated for each side chain of a peptide or protein: first, extract the local molecular mechanics of side chain rotational is...

  13. ZnO hybrid photovoltaics with variable side-chain lengths of thienothiophene polymer

    The effect of the side-chain length of poly(3,6-dialkylthieno[3,2-b]thiophene-co-bithiophene) (pATBT) on the performance of hybrid polymer-metal oxide photovoltaics (PVs) utilizing zinc oxide (ZnO) acceptor is investigated. The pATBT attached with a dodecyl side chain (pATBT-C12) in hybrid photovoltaics with ZnO was compared to pATBT with a hexadecyl side chain (pATBT-C16). Atomic force microscopic analysis reveals a smoother surface for the pATBT-C16 photoactive layer compared to the pATBT-C12. For hybrid PVs using pATBT-C16, the relative intensity of the external quantum efficiency (EQE) increased particularly in wavelength region associated with the ZnO. Furthermore, the EQE spectrum shows a red shift for pATBT-C16 indicating better structural ordering compared to hybrid PVs with pATBT-C12. As a result, the hybrid PV utilizing pATBT-C16:ZnO blend layer is observed to display a better performance with a power conversion efficiency of 1.02% compared to 0.672% of pATBT-C12:ZnO PV. - Highlights: • The effect of polymer side-chain length on hybrid photovoltaics is investigated. • Longer side chains positively influence structural and optical properties of hybrid films. • Longer side-chain length leads to better photovoltaic performance

  14. Searching for low percolation thresholds within amphiphilic polymer membranes: The effect of side chain branching

    Dorenbos, G.

    2015-06-01

    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.

  15. Searching for low percolation thresholds within amphiphilic polymer membranes: The effect of side chain branching

    Dorenbos, G., E-mail: dorenbos@ny.thn.ne.jp [Sano 1107-2, Belle Crea 502, Susono 410-1118 (Japan)

    2015-06-14

    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.

  16. Searching for low percolation thresholds within amphiphilic polymer membranes: The effect of side chain branching

    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

  17. Alternating copolymers containing side-chain liquid crystal groups

    The copolymerisation of N-ethyl maleimide (NEM) with ethyl vinyl ether (EVE) in benzene (Bz) was investigated. The copolymerisation displays a tendency towards alternation but is not alternating and propagation involves the formation of a 1:1 NEM/EVE charge-transfer complex. This complex and the monomer/solvent complexes were investigated by 1H NMR spectroscopic methods. The equilibria were combined mathematically to model the NEM/EVE/Bz system. The copolymerisations of functionalized N-substituted maleimides, N-4-[6-(4'-methoxy-4-azobenzoxy) hexoxycarbonyl] phenylmaleimide (NMeAz6PM) and N-4-[6-(4'-nitro-4-azobenzoxy) hexoxycarbonyl] phenylmaleimide (NNitAz6PM), with styrene (St), 4-vinyl pyridine (4VP), or EVE as the comonomer were studied and the reactivity ratios calculated. The monomer pairs NMeAz6PM/St, NMeAz6PM/4VP and NNitAz6PM/St produce alternating copolymers but NMeAz6PM/EVE does not. The absence of liquid crystallinity in these materials was attributed to the rigidity of the polymer backbone coupled with the low mesogen content arising from the alternating backbone. Blends of amorphous maleimide based copolymers with 6-(4-methoxy-4'-azobenzoxy)hexanoic acid, 4.2, were investigated. The copolymers chosen were believed to be alternating and are the product of the copolymerisation of N-phenyl, N-(4-methoxy) phenyl, or N(4-hydroxy) phenyl maleimide with St or 4VP. 4.2 is essentially immiscible with the St based copolymers. However, 4.2 is miscible with the 4VP based copolymers and liquid crystallinity is induced. This behaviour is attributed to the formation of hydrogen bonds between 4.2 and the pyridyl units of the copolymer backbone. Blends of 4.2 or 6-(4-nitro-4'-azobenzoxy)hexanoic acid, 5.2, with copoly(NMeAz6PM-alt-St) or copoly(NMeAz6PM-alt-4VP) were investigated. The limited miscibility and liquid crystalline behaviour of the acid/styrene copolymer blends was attributed to interactions between the mesogens on the copolymer and the acid. However, the

  18. Linear rheology and structure of molecular bottlebrushes with short side chains

    López-Barrón, Carlos R., E-mail: carlos.r.lopez-barron@exxonmobil.com; Brant, Patrick; Crowther, Donna J. [ExxonMobil Chemical Company, Baytown, Texas 77520 (United States); Eberle, Aaron P. R. [ExxonMobil Research and Engineering Company, Annandale, New Jersey 08801 (United States)

    2015-05-15

    We investigate the microstructure and linear viscoelasticity of model molecular bottlebrushes (BBs) using rheological and small-angle X-ray and neutron scattering measurements. Our polymers have short atactic polypropylene (aPP) side chains of molecular weight ranging from 119 g/mol to 259 g/mol and narrow molecular weight distribution (M{sub w}/M{sub n} 1.02–1.05). The side chain molecular weights are a small fraction of the entanglement molecular weight of the corresponding linear polymer (M{sub e,aPP}= 7.05 kg/mol), and as such, they are unentangled. The morphology of the aPP BBs is characterized as semiflexible thick chains with small side chain interdigitation. Their dynamic master curves, obtained by time-temperature superposition, reveal two sequential relaxation processes corresponding to the segmental relaxation and the relaxation of the BB backbone. Due to the short length of the side chains, their fast relaxation could not be distinguished from the glassy relaxation. The fractional free volume is an increasing function of the side chain length (N{sub SC}). Therefore, the glassy behavior of these polymers as well as their molecular friction and dynamic properties are influenced by their N{sub SC} values. The apparent flow activation energies are a decreasing function of N{sub SC}, and their values explain the differences in zero-shear viscosity measured at different temperatures.

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

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

    2011-01-01

    shifts can in principle report the conformations of aliphatic side chains in disordered proteins and in order to examine this two model systems were chosen: the acid denatured state of acyl-CoA binding protein (ACBP) and the intrinsically disordered activation domain of the activator for thyroid hormone...... allow a quantitative analysis of the ensemble of ¿(2)-angles of especially leucine residues in disordered proteins. The changes in the rotamer distributions upon denaturation correlate to the changes upon helix induction by the co-solvent trifluoroethanol, suggesting that the side chain conformers are......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...

  20. Branched-chain fatty acid biosynthesis in a branched-chain amino acid aminotransferase mutant of Staphylococcus carnosus

    Beck, Hans Christian

    2005-01-01

    Fatty acid biosynthesis by a mutant strain of Staphylococcus carnosus deficient in branched-chain amino acid aminotransferase (IlvE) activity was analysed. This mutant was unable to produce the appropriate branched-chain alpha-ketoacid precursors for branched-chain fatty acid biosynthesis from th...

  1. Assessment of Protein Side-Chain Conformation Prediction Methods in Different Residue Environments

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

    2016-01-01

    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

  2. Structure–property relationships of electroluminescent polythiophenes: role of nitrogen-based heterocycles as side chains

    S Radhakrishnan; S J Ananthakrishnan; N Somanathan

    2011-07-01

    A series of conjugated polythiophenes containing nitrogen-containing heterocycles as side chain, with differing substituent nature and linkage have been studied using quantum-chemical calculations. The optical properties of synthesized polymers were compared with that of model compounds with intricate structural variations. The theoretically predicted optical characteristics are correlated with the experimentally determined parameters. Experimentally determined band gap and absorption maxima found to follow the predicted trends. Single emissive layer polymeric light emitting diodes are fabricated and the structural influence on photo- and electro-emission was studied in detail. The study shows that the nature of side chain substituent such as number/position of nitrogen atoms and mode of linking of side chain plays a crucial role in deciding the geometry which in turn controls the voltage response of the electroluminescence.

  3. Bottlebrush Copolymer Morphology Transition: Influence of Side Chain Length and Block Volume Fraction

    Gai, Yue; Song, Dong-Po; Watkins, James

    Brush block copolymers synthesized via living ring-opening metathesis polymerization (ROMP) offer unique advantages as templates for functional hybrid materials. Unlike linear block copolymer, the bottlebrush polymer phase transition not only depends on volume fractions of the two blocks but also on side chain length. Here we report the morphology transitions of PS-b-PEO bottlebrush copolymer (BBCP) as a function of PEO side chain length and block volume fraction. For the BBCPs with similar side chain lengths, highly ordered lamellar morphologies were observed with PEO volume fractions in a wide range from 32 vol% to 72 vol%, which is significantly different from that of traditional linear block copolymers. This study will lay the groundwork for nanostructure fabrications using the BBCPs and provides new insights into the phase behavior of the new type of materials. This work was supported by NSF center for Hierarchical Manufacturing at the University of Massachusetts, Amherst.

  4. Record high hole mobility in polymer semiconductors via side-chain engineering.

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

    2013-10-01

    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. PMID:24053786

  5. Ultrafast energy transfer from rigid, branched side-chains into a conjugated, alternating copolymer

    Griffin, Graham B.; Rolczynski, Brian S.; Linkin, Alexander; McGillicuddy, Ryan D.; Engel, Gregory S., E-mail: gsengel@uchicago.edu [Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637 (United States); Lundin, Pamela M. [Department of Chemical Engineering, Stanford University, Stauffer III, 381 North-South Mall, Stanford, California 94305 (United States); A. R. Smith Department of Chemistry, Appalachian State University, 417 CAP Building, 525 Rivers Street, Boone, North Carolina 28608 (United States); Bao, Zhenan [Department of Chemical Engineering, Stanford University, Stauffer III, 381 North-South Mall, Stanford, California 94305 (United States)

    2014-01-21

    We present the synthesis and characterization of a benzodithiophene/thiophene alternating copolymer decorated with rigid, singly branched pendant side chains. We characterize exciton migration and recombination dynamics in these molecules in tetrahydrofuran solution, using a combination of static and time-resolved spectroscopies. As control experiments, we also measure electronic relaxation dynamics in isolated molecular analogues of both the side chain and polymer moieties. We employ semi-empirical and time-dependent density functional theory calculations to show that photoexcitation of the decorated copolymer using 395 nm laser pulses results in excited states primarily localized on the pendant side chains. We use ultrafast transient absorption spectroscopy to show that excitations are transferred to the polymer backbone faster than the instrumental response function, ∼250 fs.

  6. ZnO hybrid photovoltaics with variable side-chain lengths of thienothiophene polymer

    Han, SeungJin [Advanced Technology Institute, Department of Electronic Engineering, University of Surrey, Guildford GU2 7XH (United Kingdom); Fei, Zhuping [Department of Chemistry and Centre for Plastic Electronics, Imperial College London, South Kensington SW7 2AZ (United Kingdom); Jayawardena, K.D.G.I.; Beliatis, Michail J. [Advanced Technology Institute, Department of Electronic Engineering, University of Surrey, Guildford GU2 7XH (United Kingdom); Hahn, Yoon-Bong [School of Chemical Engineering, Chonbuk National University, Jeon-ju, Jeonbuk 561-756 (Korea, Republic of); Adikaari, A.A.D.T. [Advanced Technology Institute, Department of Electronic Engineering, University of Surrey, Guildford GU2 7XH (United Kingdom); Heeney, Martin J. [Department of Chemistry and Centre for Plastic Electronics, Imperial College London, South Kensington SW7 2AZ (United Kingdom); Silva, S. Ravi P., E-mail: s.silva@surrey.ac.uk [Advanced Technology Institute, Department of Electronic Engineering, University of Surrey, Guildford GU2 7XH (United Kingdom)

    2015-02-02

    The effect of the side-chain length of poly(3,6-dialkylthieno[3,2-b]thiophene-co-bithiophene) (pATBT) on the performance of hybrid polymer-metal oxide photovoltaics (PVs) utilizing zinc oxide (ZnO) acceptor is investigated. The pATBT attached with a dodecyl side chain (pATBT-C{sub 12}) in hybrid photovoltaics with ZnO was compared to pATBT with a hexadecyl side chain (pATBT-C{sub 16}). Atomic force microscopic analysis reveals a smoother surface for the pATBT-C{sub 16} photoactive layer compared to the pATBT-C{sub 12}. For hybrid PVs using pATBT-C{sub 16}, the relative intensity of the external quantum efficiency (EQE) increased particularly in wavelength region associated with the ZnO. Furthermore, the EQE spectrum shows a red shift for pATBT-C{sub 16} indicating better structural ordering compared to hybrid PVs with pATBT-C{sub 12}. As a result, the hybrid PV utilizing pATBT-C{sub 16}:ZnO blend layer is observed to display a better performance with a power conversion efficiency of 1.02% compared to 0.672% of pATBT-C{sub 12}:ZnO PV. - Highlights: • The effect of polymer side-chain length on hybrid photovoltaics is investigated. • Longer side chains positively influence structural and optical properties of hybrid films. • Longer side-chain length leads to better photovoltaic performance.

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

    Bublitz, D.; Fleck, B.; Wenke, L.; Ramanujam, P. S.; Ramanujam, P.S.; Hvilsted, Søren

    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...... sophisticated time resolving measuring equipment. The time resolution is in the order 10 ps and is comparable with the laser pulse duration. The response time of the azobenzene side-chain polyester E1aP has determined to be about 40 ps. (C) 2000 Elsevier Science B.V. All rights reserved....

  8. Naphthalene Tetracarboxydiimide-Based n-Type Polymers with Removable Solubility via Thermally Cleavable Side Chains.

    Hillebrandt, Sabina; Adermann, Torben; Alt, Milan; Schinke, Janusz; Glaser, Tobias; Mankel, Eric; Hernandez-Sosa, Gerardo; Jaegermann, Wolfram; Lemmer, Uli; Pucci, Annemarie; Kowalsky, Wolfgang; Müllen, Klaus; Lovrincic, Robert; Hamburger, Manuel

    2016-02-01

    Multilayer solution-processed devices in organic electronics show the tendency of intermixing of subsequently deposited layers. Here, we synthesize naphthalene tetracarboxydiimide (NDI)-based n-type semiconducting polymers with thermally cleavable side chains which upon removal render the polymer insoluble. Infrared and photoelectron spectroscopy were performed to investigate the pyrolysis process. Characterization of organic field-effect transistors provides insight into charge transport. After the pyrolysis homogeneous films could be produced which are insoluble in the primary solvent. By varying curing temperature and time we show that these process parameters govern the amount of side chains in the film and influence the device performance. PMID:26829619

  9. SYNTHESIS AND CHARACTERIZATION OF PALLADIUM COORDINATING IMINE SIDE CHAIN LIQUID CRYSTALLINE POLYSILOXANES

    CHEN Gang; ZHANG Rongben

    1991-01-01

    New thermotropic chloro-bridged dinuclear palladium coordinating imine side chain liquid crystalline polysiloxanes have been synthesized. Their mesomorphic properties have been investigated by DSC, X-ray diffraction and polarizing microscopy. The polymeric complexes show nematicdiscotic (Nd) mesophase. It is found that the temperature range of liquid crystalline state of chloro-bridged polymeric complexes is much wider than that of acetato-bridged ones and imine side chain polysiloxane. This indicates that the disc-like chloro-bridged palladium complexing units play a role as mesogen in mesophase.

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

    Dyer-Smith, Clare

    2015-05-01

    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.

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

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

    1992-01-01

    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...

  12. Theoretical model of photoinduced anisotropy in liquid-crystalline azobenzene side-chain polyesters

    Pedersen, Thomas Garm; Johansen, Per Michael; Holme, N.C.R.;

    1998-01-01

    A theoretical framework for the temporal behavior of photoinduced anisotropy in liquid-crystalline azobenzene side-chain polyesters is constructed. The domain structure of the material is taken into account and inter molecular interactions are included through a mean-field description. Photoinduced...

  13. Diffraction from polarization holographic gratings with surface relief in side-chain azobenzene polyesters

    Naydenova, I; Nikolova, L; Todorov, T;

    1998-01-01

    We investigate the polarization properties of holographic gratings in side-chain azobenzene polyesters in which an anisotropic grating that is due to photoinduced linear and circular birefringence is recorded in the volume of the material and a relief grating appears on the surface. A theoretical...

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

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

    2000-01-01

    sophisticated time resolving measuring equipment. The time resolution is in the order 10 ps and is comparable with the laser pulse duration. The response time of the azobenzene side-chain polyester E1aP has determined to be about 40 ps. (C) 2000 Elsevier Science B.V. All rights reserved....

  15. Improved Side Chain Dynamics in MARTINI Simulations of Protein-Lipid Interfaces.

    Herzog, Florian A; Braun, Lukas; Schoen, Ingmar; Vogel, Viola

    2016-05-10

    Specific interactions of protein side chains and lipid membranes regulate the localization, orientation, and activity of many peripheral proteins. Here, we introduce a modification of the coarse-grained MARTINI protein model, called 'side chain fix' (scFix), that was necessary and sufficient to correctly sample the side chain dynamics of β-strands in several globular proteins. When compared to μs long atomistic simulations or previous experimental findings, scFix MARTINI simulations reproduced all key interactions between the well-studied PLC-δ1 pleckstrin homology domain and a phosphatidylinositol-4,5-bisphosphate (PIP2) containing lipid membrane. Moreover, the extended runtime and higher sampling speed enabled the systematic mapping of the protein's rolling motion at the membrane, the identification of short-lived and stable binding orientations, as well as the verification and prediction of already known and of novel transient PIP2 binding sites. scFix also showed promise to maintain proper side chain orientation in other secondary structural motifs of the α-spectrin SH3 domain, the B1 domain of protein G, and the villin headpiece. This suggests that scFix improves on the predictive power of MARTINI simulations regarding protein-lipid and protein-ligand interactions. PMID:27042944

  16. Photoinduced anisotropy measurements in liquid-crystalline azobenzene side-chain polyesters

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

    1996-01-01

    Reversible photoinduced anisotropy in a series of Liquid-crystalline azobenzene side-chain polyesters is investigated as a function of intensity of the write beam and the sample temperature. Measurements reveal that the erasing takes place at a temperature much higher than the glass transition...... temperature. induced anisotropy can be erased by heating the polyesters to approximately 80 degrees C....

  17. CD and UV Resonance Raman Indicate Little arg-glu Side Chain α-helix Peptide Stabilization

    Hong, Zhenmin; Ahmed, Zeeshan; Asher, Sanford A.

    2011-01-01

    Electrostatic interactions between side chains can control the conformation and folding of peptides and proteins. We used CD and UV resonance Raman spectroscopy (UVRR) to examine the impact of side chain charge on the conformations of two 21 residue mainly polyala peptides with a few arg and glu residues. We expected that attractions between arg-10 and glu-14 side chains would stabilize the α-helix conformation compared to a peptide with an arg-14. Surprisingly, CD suggests that the peptide w...

  18. Self-assembly and adsorption properties of Fmoc-substituted short peptide bearing charged side chains

    Nakayama, Toru; Sakuraba, Taro; Yamamoto, Yohei

    2015-12-01

    Charge-separated peptide β-sheet with a positive charge on one side and a negative charge on the other side adsorbed on a mica surface with well-ordered geometry along the crystallographic direction of the mica surface. In MeOH and MeOH/H2O mixed solvent, the peptides do not form β-sheet structure. During the evaporation process of the solvent on a mica substrate, the peptides self-assembled to form β-sheet and adsorb on the surface via electrostatic interaction between negative charge of the mica surface and positive charge of the lysine side chain on one side of the β-sheet.

  19. Branched-chain amino acids for hepatic encephalopathy

    Als-Nielsen, B; Koretz, R L; Kjaergard, L L;

    2003-01-01

    Hepatic encephalopathy may be caused by a decreased plasma ratio of branched-chain amino acids (BCAA) to aromatic amino acids. Treatment with BCAA may therefore have a beneficial effect on patients with hepatic encephalopathy.......Hepatic encephalopathy may be caused by a decreased plasma ratio of branched-chain amino acids (BCAA) to aromatic amino acids. Treatment with BCAA may therefore have a beneficial effect on patients with hepatic encephalopathy....

  20. Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data

    Zeng Jianyang [Duke University, Department of Computer Science (United States); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)

    2011-08-15

    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

  1. Responsive behavior of 4-(N-maleimido)azobenzene in polymers with aromatic main chain and side chain linked units

    Airinei, Anton; Rusu, Elena; Barboiu, Virgil, E-mail: airineia@icmpp.r [Romanian Academy, Iasi (Romania). Petru Poni Institute of Macromolecular Chemistry

    2010-07-01

    Polymer matrices with aromatic main chain and side chain linked units (polystyrene, polysulfone) were employed to construct thin films containing maleimidoazobenzene molecules in order to develop new materials with responsive properties. The photochromic behavior of the active compound was studied both in the solid and solution state for comparison. The thermal cis-trans isomerization of azobenzene chromophores in polymer films follows two different kinetic pathways. A double-exponential relaxation process (fast and slow) took place in polystyrene matrix under 70 deg C while the thermal isomerization at 70 deg C and higher follows a first-order kinetics. The cis isomer content corresponding to the photostationary state was found to be lower in polymer films than in solution. (author)

  2. Equilibrium and shear-induced conformations of a side-chain liquid crystal polymer

    Castelletto, V.; Noirez, L.; Vigoureux, P.

    2000-11-01

    These studies delineate the conformations adopted by a side-chain liquid-crystalline polymer subjected to a steady-state shear flow as well as the corresponding me so pha se director orientations. Two distinct director orientations are identified in the nematic phase, giving evidence of a shear-induced transition from a flow-aligning to a non flow-aligning behavior. This transition coincides, at rest, with a subtle change from prolate to oblate polymer main-chain conformation. In the smectic phase, the layers form multilayer cylinders oriented along the velocity axis.

  3. Two-photon Pumped Up-conversion Lasing Properties of A Series of Organic Salts with Different Side-chains

    2001-01-01

    The synthesis and upconverted fluorescent properties of a series of organic compounds with the structure: donor/bridge/acceptor, and different side-chains are reported. The results show that the compounds with different side-chains exhibit different two-photon induced fluorescent properties, although they have the same main donor/bridge/acceptor structure.

  4. Effect of side-chain asymmetry on the intermolecular structure and order-disorder transition in alkyl-substituted polyfluorenes

    Knaapila, Matti; Stepanyan, R.; Torkkeli, M.;

    2016-01-01

    or below the average grafting distance). Calorimetry and x-ray scattering indicate the condition TODT(PF6)∼TODTbi(PF1−8) following the low grafting prediction. PF6 side chains coming from the alternating backbone layers appear as two separate layers with thickness H(PF6), whereas PF1-8 side chains...

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

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

    2014-01-01

    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...

  6. On correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    Lundgren, Martin

    2012-01-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to analyze high resolution X-ray structures in Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse grained energy function to describe the ensuing side-chain geometry in terms of the C$_\\beta$ carbon orientations. The energy function can model the side-chain geometry with a sub-atomic precision. As an example we construct the C$_\\alpha$-C$_\\beta$ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 \\.A in root-mean-square distance from the experimental X-ray structure.

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

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

    2009-01-01

    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...... Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for C-13(epsilon 1) nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from...... 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...

  8. Optical probe for the cytochrome P-450 cholesterol side chain cleavage enzyme

    Marrone, Babetta L.; Simpson, Daniel J.; Unkefer, Clifford J.; Whaley, Thomas W.

    1992-01-01

    An optical probe enables the study of enzyme activity by absorbance spectroscopy or by sensitive fluorescence methods. In particular, the probe provides the ability to monitor the activity of cytochrome P-450.sub.scc enzyme, the rate limiting enzyme for steroid biosynthesis. Located on the inner mitochondrial membrane, P-450.sub.scc catalyzes the conversion of cholesterol to pregnenolone and isocapraldehyde by sequential oxidations of the cholesterol side chain. The fluorogenic probe includes a cholesterol-like steroid linked to a chromophore through a linking group. The chromophore is selected to have little optical response when linked to the steroid substrate and an enhanced optical response when cleaved from the substrate and linking group. Thus, a fluorescent anion that can be optically detected is generated by the side-chain cleavage reaction during steroidogenesis.

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

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

    1992-01-01

    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 record...... recording of holograms. The holograms can be erased by heating them to approximately 80-degrees-C for approximately 2 min and are available for rerecording....

  10. Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state.

    Nicolas, A; Egmond, M; Verrips, C T; de Vlieg, J; Longhi, S; Cambillau, C; Martinez, C

    1996-01-16

    Cutinase from the fungus Fusarium solani pisi is a lipolytic enzyme able to hydrolyze both aggregated and soluble substrates. It therefore provides a powerful tool for probing the mechanisms underlying lipid hydrolysis. Lipolytic enzymes have a catalytic machinery similar to those present in serine proteinases. It is characterized by the triad Ser, His, and Asp (Glu) residues, by an oxyanion binding site that stabilizes the transition state via hydrogen bonds with two main chain amide groups, and possibly by other determinants. It has been suggested on the basis of a covalently bond inhibitor that the cutinase oxyanion hole may consist not only of two main chain amide groups but also of the Ser42 O gamma side chain. Among the esterases and the serine and the cysteine proteases, only Streptomyces scabies esterase, subtilisin, and papain, respectively, have a side chain residue which is involved in the oxyanion hole formation. The position of the cutinase Ser42 side chain is structurally conserved in Rhizomucor miehei lipase with Ser82 O gamma, in Rhizopus delemar lipase with Thr83 O gamma 1, and in Candida antartica B lipase with Thr40 O gamma 1. To evaluate the increase in the tetrahedral intermediate stability provided by Ser42 O gamma, we mutated Ser42 into Ala. Furthermore, since the proper orientation of Ser42 O gamma is directed by Asn84, we mutated Asn84 into Ala, Leu, Asp, and Trp, respectively, to investigate the contribution of this indirect interaction to the stabilization of the oxyanion hole. The S42A mutation resulted in a drastic decrease in the activity (450-fold) without significantly perturbing the three-dimensional structure. The N84A and N84L mutations had milder kinetic effects and did not disrupt the structure of the active site, whereas the N84W and N84D mutations abolished the enzymatic activity due to drastic steric and electrostatic effects, respectively. PMID:8555209

  11. Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach.

    Dukka Bahadur, K C; Tomita, Etsuji; Suzuki, Jun'ichi; Akutsu, Tatsuya

    2005-02-01

    "Protein Side-chain Packing" has an ever-increasing application in the field of bio-informatics, dating from the early methods of homology modeling to protein design and to the protein docking. However, this problem is computationally known to be NP-hard. In this regard, we have developed a novel approach to solve this problem using the notion of a maximum edge-weight clique. Our approach is based on efficient reduction of protein side-chain packing problem to a graph and then solving the reduced graph to find the maximum clique by applying an efficient clique finding algorithm developed by our co-authors. Since our approach is based on deterministic algorithms in contrast to the various existing algorithms based on heuristic approaches, our algorithm guarantees of finding an optimal solution. We have tested this approach to predict the side-chain conformations of a set of proteins and have compared the results with other existing methods. We have found that our results are favorably comparable or better than the results produced by the existing methods. As our test set contains a protein of 494 residues, we have obtained considerable improvement in terms of size of the proteins and in terms of the efficiency and the accuracy of prediction. PMID:15751115

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

    Zhang, Hefeng

    2015-05-01

    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. Trans fatty acids may impair biosynthesis of long-chain polyunsaturates and growth in man.

    Koletzko, B

    1992-04-01

    Human diet contains large amounts of trans fatty acids originating primarily from hydrogenated fats. Consumption of trans fatty acids is considered safe for man, but side effects, including impaired biosynthesis of long-chain polyunsaturated fatty acids with 20 and 22 carbon atoms and reduced growth have been observed in animals. We studied whether or not there are indications of untoward effects of trans fatty acids in 29 premature infants (birth weight 1700 +/- 127 g, gestational age 33.6 +/- 1.4 weeks, mean +/- SD). Plasma samples obtained on day 4 of life were analysed for fatty acid composition. Trans octadecenoic acid and total trans fatty acids in plasma lipid fractions (% wt/wt) were not related to the precursor essential fatty acids linoleic and alpha-linolenic acids but correlated inversely to n - 3 and n - 6 long-chain polyunsaturated fatty acids and to the product/substrate ratios of long-chain polyunsaturate biosynthesis. Trans fatty acids were also inversely correlated to birth weight but not to gestational age. These data indicate a potential impairment of essential fatty acid metabolism and early growth by trans isomers in man, and question the safety of high dietary trans isomer intakes during pregnancy and the perinatal period. PMID:1606388

  14. Effect of cationic side-chains on intracellular delivery and cytotoxicity of pH sensitive polymer-doxorubicin nanocarriers

    Fang, Chen; Kievit, Forrest M.; Cho, Yong-Chan; Mok, Hyejung; Press, Oliver W.; Zhang, Miqin

    2012-10-01

    Fine-tuning the design of polymer-doxorubicin conjugates permits optimization of an efficient nanocarrier to greatly increase intracellular uptake and cytotoxicity. Here, we report synthesis of a family of self-assembled polymer-doxorubicin nanoparticles and an evaluation of the effects of various types of side-chains on intracellular uptake and cytotoxicity of the nanocarriers for lymphoma cells. Monomers with three different cationic side-chains (CA) and pKa's, i.e., a guanidinium group (Ag), an imidazole group (Im), and a tertiary amine group (Dm), were comparatively investigated. The cationic monomer, poly(ethylene glycol) (PEG), and doxorubicin (Dox) were reacted with 1,4-(butanediol) diacrylate (BUDA) to prepare a poly(β-amino ester) (PBAE) polymer via Michael addition. All three polymer-Dox conjugates spontaneously formed nanoparticles (NP) through hydrophobic interactions between doxorubicin in aqueous solution, resulting in NP-Im/Dox, NP-Ag/Dox, and NP-Dm/Dox, with hydrodynamic sizes below 80 nm. Doxorubicin was linked to all 3 types of NPs with a hydrazone bond to assure selective release of doxorubicin only at acidic pH, as it occurs in the tumor microenvironment. Both NP-Im/Dox and NP-Ag/Dox exhibited much higher intracellular uptake by Ramos cells (Burkitt's lymphoma) than NP-Dm/Dox, suggesting that the type of side chain in the NPs determines the extent of intracellular uptake. As a result, NP-Im/Dox and NP-Ag/Dox showed cytotoxicity that was comparable to free Dox in vitro. Our findings suggest that the nature of surface cationic group on nanocarriers may profoundly influence their intracellular trafficking and resulting therapeutic efficacy. Thus, it is a crucial factor to be considered in the design of novel carriers for intracellular drug delivery.

  15. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

    Noah Ollikainen

    Full Text Available Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein-ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i prediction of enzyme specificity altering mutations and (ii prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art "fixed backbone" design methods perform poorly on these tests, we develop a new "coupled moves" design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein-ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.

  16. Synthesis and characterization of poly(vinylchloride type macrophotoinitiator comprising side-chain thioxanthone via click chemistry

    2011-04-01

    Full Text Available Nowadays, the use of macromolecular photoinitiators provides for a good compatibility of the initiator in the formulation. Moreover, the migration of the initiator to the surface of the material is prevented, which results in low-odor and non-toxic coatings. In the present study, it has been demonstrated that polyvinylchloride macrophotoinitiator (PVC-TX containing side chain thioxanthone (2% moieties were successfully prepared by 'click chemistry'. For this purpose, propargyl thioxanthone and polyvinylchloride with side chain azide moieties were reacted in N,N-dimethylformamide for 24 hours at 25°C in order to give corresponding macrophotoinitiator. The synthesized polymer was characterized by 1H-NMR (nuclear magnetic resonance, UV (ultraviolet and fluorescence spectroscopies and water based gel permeation chromatography. Obtained macrophotoinitiator has similar absorption characteristics compared to parent thioxanthone. Its capabilities to act as initiator for the photopolymerization of methacrylic acid, methyl methacrylate, N-vinyl pyrrolidone and styrene in various solvents in the absence and presence of triethylamine media were also examined.

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

    El Labban, Abdulrahman

    2014-11-26

    (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.

  18. Effect of the side chain length on the optical and electrical properties of soluble PPV derivatives

    2-Alkoxy-5-methoxy poly(1,4-phenylenevinylene) derivatives with different lengths of the alkoxy side chain have been synthesized via a modified Gilch polymerization. Their number-average molecular weights are in the range of 10,000-14,000. 1H NMR, 13C NMR, FT-IR spectroscopies have shown that the polymer structures are the expected ones and were free from defects. The polymers are amorphous and show good thermal stability up to 300 deg. C. The optical absorption band of MB-PPV, MH-PPV, MO-PPV and MDD-PPV thin films are at 496 nm, 496 nm, 494 nm and 507 nm, respectively. Photoluminescence emission maxima of the above polymers appear at 624 nm, 582 nm, 629 nm and 578 nm, respectively. A composite photoluminescence response is observed at the exception of MO-PPV showing a single PL maximum. Light-emitting diodes (LEDs) based on these polymers were fabricated and characterized by current-voltage measurements. The comparison of the optical and electrical properties of these different polymers showed a small influence of the length of the side alkoxy chain and/or to the length of the main polymeric chain

  19. Theory of microphase separation on side-chain liquid-crystalline polymers with flexible spacers.

    Hernández-Jiménez, M; Westfahl, H

    2007-05-01

    We model a melt of monodisperse side-chain liquid-crystalline polymers as a melt of comb copolymers in which the side groups are rod-coil diblock copolymers. We consider both excluded-volume and Maier-Saupe interactions. The first acts among any pair of segments while the latter acts only between rods. Using a free-energy functional calculated from this microscopic model, we study the spinodal stability of the isotropic phase against density and orientational fluctuations. The phase diagram obtained in this way predicts nematic and smectic instabilities as well as the existence of microphases or phases with modulated wave vector but without nematic ordering. Such microphases are the result of the competition between the incompatibility among the blocks and the connectivity constraints imposed by the spacer and the backbone. Also the effects of the polymerization degree and structural conformation of the monomeric units on the phase behavior of the side-chain liquid-crystalline polymers are studied. PMID:17541501

  20. 26 kDa endochitinase from barley seeds: an interaction of the ionizable side chains essential for catalysis

    Ohnishi, Tsuneo; Juffer, André H; Tamoi, Masahiro;

    2005-01-01

    To explore the structure essential for the catalysis in 26 kDa endochitinase from barley seeds, we calculated theoretical pKa values of the ionizable groups based on the crystal structure, and then the roles of ionizable side chains located near the catalytic residue were examined by site...... coli expression system. The transition temperature of thermal unfolding (T(m)) of R215A was lower than that of the wild type protein by about 6.2 degrees C. In the crystal structure, the Arg215 side chain is in close proximity to the Glu203 side chain, whose theoretical pKa value was found to be...

  1. Accessing ns-{mu}s side chain dynamics in ubiquitin with methyl RDCs

    Fares, Christophe [University of Toronto, University Health Network, Max Bell Research Center (Canada); Lakomek, Nils-Alexander [National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Walter, Korvin F. A.; Frank, Benedikt T. C. [Max-Planck Institute for Biophysical Chemistry, Department of NMR-based Structural Biology (Germany); Meiler, Jens [Vanderbilt University, Department of Chemistry, Center of Structural Biology (United States); Becker, Stefan; Griesinger, Christian [Max-Planck Institute for Biophysical Chemistry, Department of NMR-based Structural Biology (Germany)], E-mail: cigr@nmr.mpibpc.mpg.de

    2009-09-15

    This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-{tau}{sub c} dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time {tau}{sub c}. In fact, the average amplitude of motion expressed in terms of order parameters S{sup 2} associated with the supra-{tau}{sub c} window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959-8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471-1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains.

  2. Solubility control of regioregular 3-substituted polythiophenes bearing 2-phenylnaphthalene side chain by copolymerisation

    Watanabe, Mari; Kijima, Masashi

    2014-03-01

    Two types of 2,5-dibromothiophene monomers having a dodecyl chain and a 2-phenylnaphthalene one were randomly copolymerised in different feed molar ratio by Ni-catalysed chain-growth polymerisation method. Regioregularity of all polymers were sufficiently high (88-97%). Absorption λmax due to π-π* transition of polythiophene backbones in solutions were observed at 444-451 nm for all polymers, which were almost similar to each other and typical of the optical characteristics of regioregular poly(3-alkylthiophene)s. The homopolymer of the latter monomer that had the phenylnaphthalene side group showed poor solubility to common organic solvents, i.e., it was insoluble in chloroform at room temperature and could dissolve only in hot solvents above 100 °C. The copolymers, which had higher number average molecular weights (Mn), had better solubility than that of the homopolymer.

  3. Synthesis of novel aromatic polyimides containing bulky side chain for vertical alignment liquid crystals

    Jian Wang; Ying Han Wang

    2008-01-01

    In this study, a novel 4-(4-octyloxybenzoyloxy)biphenyl-3',5'-diaminobenzoate and polyimides based on it were synthesized. The polyimide with mesogenic unit side chain exhibited excellent vertical alignment for nematic liquid crystal (LC). The pretilt angles of LCs above 89° were kept after the rubbing process with 220 mm rubbing strength. The polyimide films as the alignment layer were baked at 120℃ for 12 h, the vertical alignment of LCs was still uniform and stable. Meanwhile, the UV-vis spectra of the novel polyimide films showed the high transparency in a visible wave length.

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

    Ileana Dragutan

    2015-12-01

    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.

  5. Unusual Photo-Induced Behaviour in a Side Chain Liquid Crystalline Azo-Polyester

    López, D; Rodríguez, F.J.; Sánchez, C.;

    2006-01-01

    An unusual behaviour has been observed in the photo-indueed response of an azobenzene side chain liquid erystalline polyester (P6d4). Room temperature irradiation with linearly polarised 488 nm light does not induce any birefringence (An) in films of this polymer that have been quenehed from...... the isotropie state. However, using the same irradiation conditions An is indueed in quenehed films that have been kept in darkness for a few minutes. Besides, no photo-induced An is observed in films irradiated with 488 nm light that have been previously irradiated with UV light. In this ease, An can...

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

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

    2003-04-01

    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.

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

    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

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

    Norbert Haider; Günther Fülep

    1998-01-01

    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]...

  9. The Frozen State in the Liquid Phase of Side-Chain Liquid-Crystal Polymers

    Quenched isotropic melts of side-chain liquid-crystal polymers reveal surprisingly an anisotropic polymer conformation. This small-angle neutron-scattering (SANS) result is consistent with the identification of a macroscopic, solidlike response in the isotropic phase. Both experiments (rheology and SANS) indicate that the polymer system appears frozen on millimeter length scales and at the time scales of the observation. This result implies that the flow behavior is not the terminal behavior and that cross-links or entanglements are not a necessary condition to provide elasticity in melts

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

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

    1993-01-01

    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...... molecules. We believe that this technique would have a great potential in the recording of thousands of holograms in a two-dimensional plane, as for instance in text retrieval systems and in the fabrication of high density interconnects in optical neural networks....

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

    Dragutan, Ileana; Dragutan, Valerian; Simionescu, Bogdan C; Demonceau, Albert; Fischer, Helmut

    2015-01-01

    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. PMID:26877797

  12. Development of a sufficiently reactive thioalkylester involving the side-chain thiol of cysteine applicable for kinetically controlled ligation.

    Tsuda, Shugo; Mochizuki, Masayoshi; Nishio, Hideki; Yoshiya, Taku; Nishiuchi, Yuji

    2016-11-01

    N(α) -Trifluoroacetyl-Cys-Leu-NH2 (TfaC-Leu-NH2 ) was incorporated into thioesters through its side-chain thiol group to develop a more reactive peptide-thioester than the commonly used peptide-3-mercaptopropionic acid (MPA)-thioester. The TfaC-thioester could be readily synthesized by solid-phase peptide synthesis (SPPS) with Boc chemistry using in situ neutralization protocols in sufficient yield without any side reaction associated with the use of TfaC. This thioester proved to display a much higher reactivity in the thiol-free native chemical ligation (NCL) reaction than the MPA-thioester and to be comparable to the thioarylester, such as the 4-mercaptophenylacetic acid (MPAA)-thioester, in terms of the ligation rate. We were able to demonstrate the usefulness of the TfaC-thioester by using it to synthesize neuromedin S via a one-pot sequential NCL approach followed by desulfurization. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 503-511, 2016. PMID:26583564

  13. Conformational gel analysis and graphics: Measurement of side chain rotational isomer populations by NMR and molecular mechanics

    Haydock, Christopher

    2007-01-01

    Conformational gel analysis and graphics systematically identifies and evaluates plausible alternatives to the side chain conformations found by conventional peptide or protein structure determination methods. The proposed analysis determines the populations of side chain rotational isomers and the probability distribution of these populations. The following steps are repeated for each side chain of a peptide or protein: first, extract the local molecular mechanics of side chain rotational isomerization from a single representative global conformation; second, expand the predominant set of rotational isomers to include all probable rotational isomers down to those that constitute just a small percentage of the population; and third, evaluate the constraints vicinal coupling constants and NOESY cross relaxation rates place on rotational isomer populations. In this article we apply conformational gel analysis to the cobalt glycyl-leucine dipeptide and detail the steps necessary to generalize the analysis to oth...

  14. Highly sensitive and selective ratiometric fluorescent copper sensors: Different binding affinities modulated by three separate side chains of naphthalimide

    XU YuFang; LU Feng; XU ZhaoChao; CHENG TanYu; QIAN XuHong

    2009-01-01

    A series of compounds 1 --11 with different side chains of naphthalimide as fluorescent copper sensors were designed and synthesized. Compounds 1, 9, 10 and 11 presented a high selectivity to Cu2+ in a neutral aqueous environment. Here 1, 9 and 10 showed selectivity and affinity to Cu2+ with an association constant of about ~106. It gave somewhat response to Ag+, Co2+, Ni2+ and Fe2+ while 1 detected copper. 9 and 10 displayed better selectivity by changing their hydrophobic side chains to the hydrophilic ones on imide moieties. 11, with one flexible side chain, showed high selectivity and an association constant (Ka = 2.2 × 108), which were much higher than those of 1, 9 and 10. These results indicated that the selectivity and affinity could be improved by changing side chains of naphthalimide. That might provide a novel strategy or method for the development of fluorescent sensors.

  15. Side chain engineering of poly-thiophene and its impact on crystalline silicon based hybrid solar cells

    The influence of ether groups in the side chain of spin coated regioregular polythiophene derivatives on the polymer layer formation and the hybrid solar cell properties was investigated using electrical, optical, and X-ray diffraction experiments. The polymer layers are of high crystallinity but the polymer with 3 ether groups in the side chain (P3TOT) did not show any vibrational fine structure in the UV-Vis spectrum. The presence of ether groups in the side chains leads to better adhesion resulting in thinner and more homogeneous polymer layers. This, in turn, enhances the electronic properties of the planar c-Si/poly-thiophene hybrid solar cell. We find that the power conversion efficiency increases with the number of ether groups in the side chains, and a maximum power conversion efficiency of η = 9.6% is achieved even in simple planar structures

  16. Effect of side-chain asymmetry on the intermolecular structure and order-disorder transition in alkyl-substituted polyfluorenes

    Knaapila, M.; Stepanyan, R.; Torkkeli, M.; Haase, D.; Fröhlich, N.; Helfer, A.; Forster, M.; Scherf, U.

    2016-04-01

    We study relations among the side-chain asymmetry, structure, and order-disorder transition (ODT) in hairy-rod-type poly(9,9-dihexylfluorene) (PF6) with two identical side chains and atactic poly(9-octyl-9-methyl-fluorene) (PF1-8) with two different side chains per repeat. PF6 and PF1-8 organize into alternating side-chain and backbone layers that transform into an isotropic phase at TODT(PF 6 ) and TbiODT(PF 1 -8 ) . We interpret polymers in terms of monodisperse and bidisperse brushes and predict scenarios TODTstructurally possible but not certain for PF6 and confirmed for PF1-8.

  17. Side chain engineering of poly-thiophene and its impact on crystalline silicon based hybrid solar cells

    Zellmeier, M.; Rappich, J.; Nickel, N. H. [Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Silicon Photovoltaics, Kekuléstr. 5, 12489 Berlin (Germany); Klaus, M.; Genzel, Ch. [Department of Microstructure and Residual Stress Analysis, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Straße 15, 12489 Berlin (Germany); Janietz, S. [Department of Polymer Electronics, Fraunhofer Institute for Applied Polymer Research, Geiselbergstr. 69, 14476 Potsdam (Germany); Frisch, J.; Koch, N. [Humboldt Universität zu Berlin, Brook-Taylor-Straße 6, 12489 Berlin (Germany)

    2015-11-16

    The influence of ether groups in the side chain of spin coated regioregular polythiophene derivatives on the polymer layer formation and the hybrid solar cell properties was investigated using electrical, optical, and X-ray diffraction experiments. The polymer layers are of high crystallinity but the polymer with 3 ether groups in the side chain (P3TOT) did not show any vibrational fine structure in the UV-Vis spectrum. The presence of ether groups in the side chains leads to better adhesion resulting in thinner and more homogeneous polymer layers. This, in turn, enhances the electronic properties of the planar c-Si/poly-thiophene hybrid solar cell. We find that the power conversion efficiency increases with the number of ether groups in the side chains, and a maximum power conversion efficiency of η = 9.6% is achieved even in simple planar structures.

  18. Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins II reactions at side-chain loci in model systems

    The major emphasis in radiation biology at the molecular level has been on the nucleic acid component of the nucleic acid-protein complex because of its primary genetic importance. But there is increasing evidence that radiation damage to the protein component also has important biological implications. Damage to capsid protein now appears to be a major factor in the radiation inactivation of phage and other viruses. And, there is increasing evidence that radiation-chemical change in the protein component of chromation leads to changes in the stability of the repressor-operator complexes involved in gene expression. Knowledge of the radiation chemistry of protein is also of importance in other fields such as the application of radiation sterilization to foods and drugs. Recent findings that a class of compounds, the α,α'-diaminodicarboxylic acids, not normally present in food proteins, are formed in protein radiolysis is of particular significance since certain of their peptide derivatives have been showing to exhibit immunological activity. The purpose of this review is to bring together and to correlate our present knowledge of products and mechanisms in the radiolysis of peptides, polypeptides and proteins both aqueous and solid-state. In part 1 we presented a discussion of the radiation-induced reactions of the peptide main-chain in model peptide and polypeptide systems. Here in part 2 the emphasis is on the competing radiation chemistry at side-chain loci of peptide derivatives of aliphatic, aromatic-unsaturated and sulfur-containing amino acids in similar systems. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis, and ESR spectroscopy are included

  19. Measurability of side chain rotational isomer populations: NMR and molecular mechanics of cobalt glycyl-leucine dipeptide model system

    Haydock, Christopher; Juranić, Nenad; Prendergast, Franklyn G.; Macura, Slobodan; Likić, Vladimir A

    1999-01-01

    The cobalt glycyl-leucine dipeptide is a model system for studying the effects of Karplus equation calibration, molecular mechanics accuracy, backbone conformation, and thermal motions on the measurability of side chain rotational isomer populations. We analyze measurements of 8 vicinal coupling constants about the alpha to beta-carbon and beta to gamma-carbon bonds of the leucine side chain and of 10 NOESY cross relaxation rates across these bonds. Molecular mechanics and peptide and protein...

  20. Controlling the Morphology of Side Chain Liquid Crystalline Block Copolymer Thin Films through Variations in Liquid Crystalline Content

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

    2008-01-01

    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...

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

    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-C61-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/cm2. - 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

  2. Methanol to olefin Conversion on HSAPO-34 zeolite from periodic density functional theory calculations: a complete cycle of side chain hydrocarbon pool mechanism

    Wang, C.M.; Wang, Y.D.; Xie, Z.K.; Liu, Z.P. [SINOPEC, Shanghai (China)

    2009-03-15

    For its unique position in the coal chemical industry, the methanol to olefin (MTO) reaction has been a hot topic in zeolite catalysis. Due to the complexities of catalyst structure and reaction networks, many questions such as how the olefin chain is built from methanol remain elusive. On the basis of periodic density functional theory calculations, this work establishes the first complete catalytic cycle for MTO reaction via hexamethylbenzene (HMB) trapped in HSAPO-34 zeolite based on the so-called side chain hydrocarbon pool mechanism. The cycle starts from the methylation of HMB that leads to heptamethylbenzenium ion (heptaMB{sup +}) intermediate. This is then followed by the growth of side chain via repeated deprotonation of benzenium ions and methylation of the exocyclic double bond. Ethene and propene can finally be released from the side ethyl and isopropyl groups of benzenium ions by deprotonation and subsequent protonation steps. We demonstrate that (i) HMB/HSAPO-34 only yields propene as the primary product based on the side chain hydrocarbon pool mechanism and (ii) an indirect proton-shift step mediated by water that is always available in the system is energetically more favorable than the traditionally regarded internal hydrogen-shift step. Finally, the implications of our results toward understanding the effect of acidity of zeolite on MTO activity are also discussed.

  3. Cyclic side-chain-linked opioid analogs utilizing cis- and trans-4-aminocyclohexyl-D-alanine.

    Piekielna, Justyna; Gentilucci, Luca; De Marco, Rossella; Perlikowska, Renata; Adamska, Anna; Olczak, Jacek; Mazur, Marzena; Artali, Roberto; Modranka, Jakub; Janecki, Tomasz; Tömböly, Csaba; Janecka, Anna

    2014-12-01

    Cyclization of linear sequences is a well recognized tool in opioid peptide chemistry for generating analogs with improved bioactivities. Cyclization can be achieved through various bridging bonds between peptide ends or side-chains. In our earlier paper we have reported the synthesis and biological activity of a cyclic peptide, Tyr-c[D-Lys-Phe-Phe-Asp]NH2 (1), which can be viewed as an analog of endomorphin-2 (EM-2, Tyr-Pro-Phe-Phe-NH2). Cyclization was achieved through an amide bond between side-chains of D-Lys and Asp residues. Here, to increase rigidity of the cyclic structure, we replaced d-Lys with cis- or trans-4-aminocyclohexyl-D-alanine (D-ACAla). Two sets of analogs incorporating either Tyr or Dmt (2',6'-dimethyltyrosine) residues in position 1 were synthesized. In the binding studies the analog incorporating Dmt and trans-D-ACAla showed high affinity for both, μ- and δ-opioid receptors (MOR and DOR, respectively) and moderate affinity for the κ-opioid receptor (KOR), while analog with Dmt and cis-D-ACAla was exceptionally MOR-selective. Conformational analyses by NMR and molecular docking studies have been performed to investigate the molecular structural features responsible for the noteworthy MOR selectivity. PMID:25456075

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

    The use of 13C 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 13C labeled histidine residues in plastocyanin (PCu) from Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for 13Cε1 nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from 15N backbone relaxation measurements. Compared to measurements of backbone nuclei, 13Cε1 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 13Cε1 dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains are discussed

  5. Histidine side-chain dynamics and protonation monitored by {sup 13}C CPMG NMR relaxation dispersion

    Hass, Mathias A. S. [Leiden University, Institute of Chemistry (Netherlands); Yilmaz, Ali [University of Copenhagen, Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences (Denmark); Christensen, Hans E. M. [Technical University of Denmark, Department of Chemistry (Denmark); Led, Jens J. [University of Copenhagen, Department of Chemistry (Denmark)], E-mail: led@kiku.dk

    2009-08-15

    The use of {sup 13}C 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 {sup 13}C labeled histidine residues in plastocyanin (PCu) from Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for {sup 13}C{sup {epsilon}}{sup 1} nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from {sup 15}N backbone relaxation measurements. Compared to measurements of backbone nuclei, {sup 13}C{sup {epsilon}}{sup 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 {sup 13}C{sup {epsilon}}{sup 1} dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains are discussed.

  6. Proton spin-lattice relaxation in silkworm cocoons: physisorbed water and serine side-chain motions.

    Geppi, Marco; Mollica, Giulia; Borsacchi, Silvia; Cappellozza, Silvia

    2010-03-01

    The molecular dynamic behavior of silkworm cocoons produced by a single Bombyx mori strain was investigated by means of high- and low-resolution solid-state NMR experiments. Cocoons with different moisture content were prepared to study the effects of physisorbed water on their molecular dynamics in the MHz regime, which was probed through the measurement of (1)H T(1) relaxation times at 25 MHz in the 25-95 degrees C temperature range. The water content of the different samples was determined from the analysis of (1)H free-induction decays. In addition to the rotation of methyl groups, mostly from alanine, and to the reorientation of physisorbed water molecules, already identified in previous works as relaxation sinks, the reorientation of serine side-chains was here found to contribute to (1)H T(1) above room temperature. The analysis of the trends of (1)H T(1) versus temperature was carried out in terms of semiempirical models describing the three main motional processes, and indicated that methyl rotation, water reorientation and serine side-chain motions are the most efficient relaxation mechanisms below 0 degrees C, between 0 and 60 degrees C, and above 60 degrees C, respectively. The activation energies were found to decrease passing from serine to water to methyl motions. PMID:20136080

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

    X. Liu

    2015-11-01

    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.

  8. Branched-chain 2-keto acid decarboxylases derived from Psychrobacter.

    Wei, Jiashi; Timler, Jacobe G; Knutson, Carolann M; Barney, Brett M

    2013-09-01

    The conversion of branched-chain amino acids to branched-chain acids or alcohols is an important aspect of flavor in the food industry and is dependent on the Ehrlich pathway found in certain lactic acid bacteria. A key enzyme in the pathway, the 2-keto acid decarboxylase (KDC), is also of interest in biotechnology applications to produce small branched-chain alcohols that might serve as improved biofuels or other commodity feedstocks. This enzyme has been extensively studied in the model bacterium Lactococcus lactis, but is also found in other bacteria and higher organisms. In this report, distinct homologs of the L. lactis KDC originally annotated as pyruvate decarboxylases from Psychrobacter cryohalolentis K5 and P. arcticus 273-4 were cloned and characterized, confirming a related activity toward specific branched-chain 2-keto acids derived from branched-chain amino acids. Further, KDC activity was confirmed in intact cells and cell-free extracts of P. cryohalolentis K5 grown on both rich and defined media, indicating that the Ehrlich pathway may also be utilized in some psychrotrophs and psychrophiles. A comparison of the similarities and differences in the P. cryohalolentis K5 and P. arcticus 273-4 KDC activities to other bacterial KDCs is presented. PMID:23826991

  9. Uptake of Branched-Chain Amino Acids by Streptococcus thermophilus

    Akpemado, K. M.; Bracquart, P. A.

    1983-01-01

    The transport of branched-chain amino acids in Streptococcus thermophilus was energy dependent. The metabolic inhibitors of glycolysis and ATPase enzymes were active, but the proton-conducting uncouplers were not. Transport was optimal at temperatures of between 30 and 45°C and at pH 7.0 for the three amino acids leucine, valine, and isoleucine; a second peak existed at pH 5.0 with valine and isoleucine. By competition and kinetics studies, the branched-chain amino acids were found to share a...

  10. Ultra-thin films based on random copolymers containing perfluoropolyether side chains

    Random copolymers were synthesised by copolymerizing methylmethacrylate and perfluoropolyetherurethanemethacrylate monomers, differing for the structural unit of the fluorinated chain, its end group and its molecular weight. The copolymers obtained had similar molecular weight and polydispersity, with a fluorine content between 5 and 10% wt/wt; they showed remarkable features such as biphasicity with coexistence of soft domains made of the perfluoropolyether chains and hard domains due to the methylmethacrylate backbone: the glass transition temperature Tg of the soft and hard phases was Tg1 g2 ≅ 110 °C respectively. All the copolymers were highly hydrophobic: water contact angle was always higher than 105°. The copolymers were used for the preparation of ultra thin films by spin coatings: by atomic force microscopy and X-ray reflectivity the thickness was found in the range of 20–400 Å depending on the spinning conditions, in particular the concentration of the spun solutions. The films were also highly smooth, with a roughness lower than 5 Å. - Highlights: ► We describe random methacrylic copolymers with perfluoropolyether side chain. ► The copolymers had a fluorine content of 5–10% wt/wt. ► The copolymers were spin coated and formed hydrophobic films. ► The film thickness was in the range of 20–400 Å. ► The coatings' roughness was always lower than 5 Å.

  11. Acid-base actuation of [c2]daisy chains.

    Fang, Lei; Hmadeh, Mohamad; Wu, Jishan; Olson, Mark A; Spruell, Jason M; Trabolsi, Ali; Yang, Ying-Wei; Elhabiri, Mourad; Albrecht-Gary, Anne-Marie; Stoddart, J Fraser

    2009-05-27

    A versatile synthetic strategy, which was conceived and employed to prepare doubly threaded, bistable [c2]daisy chain compounds, is described. Propargyl and 1-pentenyl groups have been grafted onto the stoppers of [c2]daisy chain molecules obtained using a template-directed synthetic protocol. Such [c2]daisy chain molecules undergo reversible extension and contraction upon treatment with acid and base, respectively. The dialkyne-functionalized [c2]daisy chain (AA) was subjected to an [AA+BB] type polymerization with an appropriate diazide (BB) to afford a linear, mechanically interlocked, main-chain polymer. The macromolecular properties of this polymer were characterized by chronocoulometry, size exclusion chromatography, and static light-scattering analysis. The acid-base switching properties of both the monomers and the polymer have been studied in solution, using (1)H NMR spectroscopy, UV/vis absorption spectroscopy, and cyclic voltammetry. The experimental results demonstrate that the functionalized [c2]daisy chains, along with their polymeric derivatives, undergo quantitative, efficient, and fully reversible switching processes in solution. Kinetics measurements demonstrate that the acid/base-promoted extension/contraction movements of the polymeric [c2]daisy chain are actually faster than those of its monomeric counterpart. These observations open the door to correlated molecular motions and to changes in material properties. PMID:19419175

  12. Effect of Long-Chain Fatty Acids on Anaerobic Digestion

    Qian, Cheng

    2013-01-01

    An investigation was carried out to study whether long-chain fatty acids (LCFAs) have an effect on digestion of waste sludge under anaerobic conditions. Four different kinds of LCFAs were used in this study. The 18 carbon series with 0, 1, 2 and 3 double bonds were studied to evaluate the degree of saturation on fatty acid degradation. Due to their molecular structure, unsaturated LCFAs are more soluble than saturated LCFAs. Oleic, linoleic, linolenic acid with an ascending number of double b...

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

    Zhou, Yan

    2014-03-24

    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.

  14. SYNTHESIS AND PROPERTIES OF METAL COMPLEXES OF β-DIKETONE BASED SIDE CHAIN LIQUID CRYSTAL POLYSILOXANE

    WU Fuzhou; ZHANG Rongben; JIANG Yingyan

    1991-01-01

    A new type of metal coordinated liquid crystalline polymers has been synthesized by complexation of metal ions with β-diketone based side chain liquid crystal polysiloxane (DKLCP).The complexation of copper ions with DKLCP greatly increases the phase transition temperature Tk from crystalline state to liquid crystalline state and Tcl from LC to isotropic state and makes the range of phase transition △T(△T= Tcl- Tk ) widened. These complexes are soluble in common organic solvents. However, the incorporation of europium ions into DKLCP molecules gives rise to reduction in liquid crystallinity and crosslinking in some cases. The DKLCP coordinated with suitable amount of Eu ions can show good liquid crystallinity and fluorescent property.

  15. SYNTHESIS AND CHARACTERIZATION OF SIDE CHAIN LIQUID CRYSTALLINE POLYSILOXANES CONTAINING BENZYL ETHER LINKING UNITS

    1998-01-01

    Side chain liquid crystalline polysiloxanes containing benzyl ether linking units were synthesized by the hydrosilylation of poly(methylhydrosiloxane) with a series of 4-(4-alkoxybenzyloxy)-4'-allyloxybiphenyl monomers [4-(4-methoxybenzyloxy)-4'-allyloxybiphenyl (M1), 4-(4-ethoxybenzyloxy)-4'-allyloxybiphenyl (M2), 4-(4-propoxybenzyloxy)-4'-allyloxybiphenyl (M3), 4-(4-butoxybenzyloxy)-4'-allyloxybiphenyl (M4), 4-(4-pentoxybenzyloxy)-4'-allyloxybiphenyl (Ms), 4-benzyloxy-4'-allyloxybiphenyl (M6)]. The phase behavior of monomeric and polymeric liquid crystals was characterized by differential scanning calorimetry and optical polarization microscopy where the groups are ranged from methoxy to pentoxy. Both the monomeric and polymeric liquid crystals exhibit liquid crystal behaviors.

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

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

    2010-12-07

    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.

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

    Hvilsted, Søren; Andruzzi, Fulvio; Kulinna, Chrisian;

    1995-01-01

    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...... have molecular masses in the range 5000-89 000. Solution C-13 NMR spectroscopy has been employed to identify carbons of polyester repeat units and of both types of end groups. Polyester phases and phase transitions have been investigated in detail by polarizing optical microscopy and differential...... scanning calorimetry for the hexamethylene spacer architecture with different molecular masses. Using FTIR polarization spectroscopy, the segmental orientation in unoriented polyester films induced by argon ion laser irradiation has been followed and an irradiation-dependent order parameter for the...

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

    Inbar Yuval

    2010-07-01

    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 http://bioinfo.weizmann.ac.il/hunter/ 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.

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

    Junnila, Susanna

    2012-03-27

    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.

  20. Ultra-thin films based on random copolymers containing perfluoropolyether side chains

    Bongiovanni, Roberta, E-mail: roberta.bongiovanni@polito.it [Department of Materials Science and Technology, Politecnico di Torino, C. Duca Degli Abruzzi 24, 10129 Torino (Italy); Nelson, Andrew [Bragg Institute, Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Menai, Sydney (Australia); Vitale, Alessandra [Department of Materials Science and Technology, Politecnico di Torino, C. Duca Degli Abruzzi 24, 10129 Torino (Italy); Bernardi, Ettore [I.N.RI.M. Istituto Nazionale di Ricerca Metrologica, Strada delle Cacce 91, 10135 Torino (Italy)

    2012-06-30

    Random copolymers were synthesised by copolymerizing methylmethacrylate and perfluoropolyetherurethanemethacrylate monomers, differing for the structural unit of the fluorinated chain, its end group and its molecular weight. The copolymers obtained had similar molecular weight and polydispersity, with a fluorine content between 5 and 10% wt/wt; they showed remarkable features such as biphasicity with coexistence of soft domains made of the perfluoropolyether chains and hard domains due to the methylmethacrylate backbone: the glass transition temperature T{sub g} of the soft and hard phases was T{sub g1} < 90 Degree-Sign C and T{sub g2} {approx_equal} 110 Degree-Sign C respectively. All the copolymers were highly hydrophobic: water contact angle was always higher than 105 Degree-Sign . The copolymers were used for the preparation of ultra thin films by spin coatings: by atomic force microscopy and X-ray reflectivity the thickness was found in the range of 20-400 Angstrom-Sign depending on the spinning conditions, in particular the concentration of the spun solutions. The films were also highly smooth, with a roughness lower than 5 A. - Highlights: Black-Right-Pointing-Pointer We describe random methacrylic copolymers with perfluoropolyether side chain. Black-Right-Pointing-Pointer The copolymers had a fluorine content of 5-10% wt/wt. Black-Right-Pointing-Pointer The copolymers were spin coated and formed hydrophobic films. Black-Right-Pointing-Pointer The film thickness was in the range of 20-400 A. Black-Right-Pointing-Pointer The coatings' roughness was always lower than 5 Angstrom-Sign .

  1. Towards a Mathematical Foundation of Immunology and Amino Acid Chains

    Shen, Wen-Jun; Xiao, Quan-Wu; Guo, Xin; Smale, Stephen

    2012-01-01

    We attempt to set a mathematical foundation of immunology and amino acid chains. To measure the similarities of these chains, a kernel on strings is defined using only the sequence of the chains and a good amino acid substitution matrix (e.g. BLOSUM62). The kernel is used in learning machines to predict binding affinities of peptides to human leukocyte antigens DR (HLA-DR) molecules. On both fixed allele (Nielsen and Lund 2009) and pan-allele (Nielsen et.al. 2010) benchmark databases, our algorithm achieves the state-of-the-art performance. The kernel is also used to define a distance on an HLA-DR allele set based on which a clustering analysis precisely recovers the serotype classifications assigned by WHO (Nielsen and Lund 2009, and Marsh et.al. 2010). These results suggest that our kernel relates well the chain structure of both peptides and HLA-DR molecules to their biological functions, and that it offers a simple, powerful and promising methodology to immunology and amino acid chain studies.

  2. Synthesis, Structural Studies and Antitumoral Evaluation of C-6 Alkyl and Alkenyl Side Chain Pyrimidine Derivatives S

    Marijeta Kralj

    2009-11-01

    Full Text Available The synthetic route for introduction of fluorophenylalkyl (compounds 5, 7, 14 and 15 and fluorophenylalkenyl (compounds 4E and 13 side chains at C-6 of the pyrimidine nucleus involved the lithiation of the pyrimidine derivatives 1, 2 and 11 and subsequent nucleophilic addition or substitution reactions of the organolithium intermediate thus obtained with 2-fluorophenylacetone, 4-fluoroacetophenone or ethyl 4-fluorobenzoate as electrophiles. The structures of novel compounds were confirmed by 1H-, 19F- and 13C-NMR and MS. Compounds 8 and 10 containing unsaturated fluorophenylalkyl side chains showed better inhibitory effect than their saturated fluorophenylalkylated pyrimidine counterparts 7 and 9. A conformational study based on NOE enhancements showed the importance of the double bond and substitution in the side chain for the conformational preferences in relation to inhibitory activity. Among all tested compounds, C-5 furyl (12 and phenyl (13 and 15 substituted pyrimidine derivatives showed significant cytostatic activities against all tested tumor cell lines.

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

    Although carbon 13 nuclear magnetic resonance spectroscopy (13C-NMR) is widely used in lignin structural studies, serious difficulties are encountered in the assignments of 13C 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 13C-enriched precursors of lignin biosynthesis, coniferin-[side chain-β-13C] and coniferin-[side chain-γ-13C], 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

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

    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.

  5. Structural effects of a light emitting copolymer having perylene moieties in the side chain on the electroluminescent characteristics

    We have synthesized a novel side chain light emitting copolymer. The side chain light emitting copolymer has a perylene moiety as an emitting unit and methylmethacrylate (MMA) as a spacer to decrease the concentration quenching of light emitting site in the polymer intrachain. These polymers are very soluble in most organic solvents such as monochlorobenzene, tetrahydrofuran, chloroform and benzene. The single-layered electroluminescent (EL) device consisting of ITO/carrier transporting copolymer and light emitting copolymer/Al was manufactured. The carrier transporting copolymer has triphenylamine moiety as a hole transporting unit and triazine moiety as an electron transporting unit in the polymer side chain. This device exhibits maximum external quantum efficiency when the MMA contents of light emitting copolymer is 30 wt.%. In particular, the device emits more blue light as MMA contents increase

  6. Measurability of side chain rotational isomer populations NMR and molecular mechanics of cobalt glycyl-leucine dipeptide model system

    Haydock, C; Likic, V A; Prendergast, F G; Macura, S; Haydock, Christopher; Juranic, Nenad; Likic, Vladimir A.; Prendergast, Franklyn G.; Macura, Slobodan

    1999-01-01

    The cobalt glycyl-leucine dipeptide is a model system for studying the effects of Karplus equation calibration, molecular mechanics accuracy, backbone conformation, and thermal motions on the measurability of side chain rotational isomer populations. We analyze measurements of 8 vicinal coupling constants about the alpha to beta-carbon and beta to gamma-carbon bonds of the leucine side chain and of 10 NOESY cross relaxation rates across these bonds. Molecular mechanics and peptide and protein crystallographic databases are an essential part of this analysis because they independently suggest that the trans gauche-plus and gauche-minus trans rotational isomers of the leucine side chain predominate. They also both suggest that puckering of the cobalt dipeptide ring system reduces the gauche-plus gauche-plus rotational isomer population to less than about 10%. At the present +/- 1 Hz calibration accuracy of Karplus equations for vicinal coupling constants, the predominant trans gauche-plus and gauche-minus trans...

  7. Radiolytic chain oxidation of dithiothreitol in aerated acidic solutions

    In the radiolysis of dithiothreitol (DTT or HS-D-SH) in air saturated acidic and neutral solutions sulphur centered radicals are formed. In the presence of oxygen the final products are ox - DTT and H2O2 via certain complex reactions. G(ox - DTT) and G(H2O2) are dependent upon DTT and acid concentrations and dose rate. The chain is predominant only at low pH. The HO2 radical carries the chain by abstracting an H atom from DTT (k = 120 dm3mol-1s-1). The chain is continued when the DTT radicals react with oxygen to give an unstable peroxyl radical finally yielding ox - DTT and HO2. (author)

  8. Thermochromism and structural change in polydiacetylenes including carboxy and 4-carboxyphenyl groups as the intermolecular hydrogen bond linkages in the side chain.

    Tanioku, Chiaki; Matsukawa, Kimihiro; Matsumoto, Akikazu

    2013-02-01

    We investigated the thermochromic behavior of polydiacetylenes including the carboxy and 4-carboxyphenyl groups as the side-chain substituents adjacent to the conjugated main chain, and then, the thermal stability and the thermochromism reversibility of the polymers were related to changes in the polymer conformations monitored by IR and Raman spectroscopies and powder X-ray diffractions. The polydiacetylenes with no or a phenylene spacer between the main chain and the carboxylic acid moiety were revealed to exhibit a thermal resistance for maintaining reversible thermochromism in a high temperature range, rather than polydiacetylenes with a conventional structure with a flexible alkylene spacer. The molecular stacking structures of the diacetylenes and the corresponding polymers in the crystals were discussed based on the results of an X-ray single-crystal structure analysis as well as the powder X-ray diffraction measurements. PMID:23276165

  9. Branched-chain amino acids for people with hepatic encephalopathy

    Gluud, Lise Lotte; Dam, Gitte; Les, Iñigo;

    2015-01-01

    -chain amino acids (BCAA) versus control interventions has evaluated if BCAA may benefit people with hepatic encephalopathy. OBJECTIVES: To evaluate the beneficial and harmful effects of BCAA versus any control intervention for people with hepatic encephalopathy. SEARCH METHODS: We identified trials through...

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

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

    2001-01-01

    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...... have been reproducibly recorded in a thin film of the polyester. These observations are consistent with the fact that at low intensities peaks are produced evolving into formation of trenches at high intensities in the case of amorphous side-chain azobenzene polyesters. This may find applications in...

  11. gamma-linolenic acid does not augment long-chain polyunsaturated fatty acid omega-3 status

    Brouwer, DAJ; Hettema, Y; van Doormaal, JJ; Muskiet, FAJ

    1998-01-01

    Augmentation of long chain polyunsaturated omega 3 fatty acid (LCPUFA omega 3) status can be reached by consumption of fish oil or by improvement of the conversion of a-linolenic acid (ALA) to LCPUFA omega 3. Since gamma-linolenic acid (GLA) might activate the rate-limiting Delta-6 desaturation, we

  12. Structural Origins of Nitroxide Side Chain Dynamics on Membrane Protein [alpha]-Helical Sites

    Kroncke, Brett M.; Horanyi, Peter S.; Columbus, Linda (UV)

    2010-12-07

    Understanding the structure and dynamics of membrane proteins in their native, hydrophobic environment is important to understanding how these proteins function. EPR spectroscopy in combination with site-directed spin labeling (SDSL) can measure dynamics and structure of membrane proteins in their native lipid environment; however, until now the dynamics measured have been qualitative due to limited knowledge of the nitroxide spin label's intramolecular motion in the hydrophobic environment. Although several studies have elucidated the structural origins of EPR line shapes of water-soluble proteins, EPR spectra of nitroxide spin-labeled proteins in detergents or lipids have characteristic differences from their water-soluble counterparts, suggesting significant differences in the underlying molecular motion of the spin label between the two environments. To elucidate these differences, membrane-exposed {alpha}-helical sites of the leucine transporter, LeuT, from Aquifex aeolicus, were investigated using X-ray crystallography, mutational analysis, nitroxide side chain derivatives, and spectral simulations in order to obtain a motional model of the nitroxide. For each crystal structure, the nitroxide ring of a disulfide-linked spin label side chain (R1) is resolved and makes contacts with hydrophobic residues on the protein surface. The spin label at site I204 on LeuT makes a nontraditional hydrogen bond with the ortho-hydrogen on its nearest neighbor F208, whereas the spin label at site F177 makes multiple van der Waals contacts with a hydrophobic pocket formed with an adjacent helix. These results coupled with the spectral effect of mutating the i {+-} 3, 4 residues suggest that the spin label has a greater affinity for its local protein environment in the low dielectric than on a water-soluble protein surface. The simulations of the EPR spectra presented here suggest the spin label oscillates about the terminal bond nearest the ring while maintaining weak

  13. Shear Flow Induced Transition from Liquid-Crystalline to Polymer Behavior in Side-Chain Liquid Crystal Polymers

    Noirez, L.; Lapp, A.

    1997-01-01

    We determine the structure and conformation of side-chain liquid-crystalline polymers subjected to shear flow in the vicinity of the smectic phase by neutron scattering on the velocity gradient plane. Below the nematic-smectic transition we observe a typical liquid-crystal behavior; the smectic layers slide, leading to a main-chain elongation parallel to the velocity direction. In contrast, a shear applied above the transition induces a tilted main-chain conformation which is typical for polymer behavior.

  14. Anti-Biofouling Properties of Comblike Block Copolymers with Amphiphilic Side Chains

    Surfaces of novel block copolymers with amphiphilic side chains were studied for their ability to influence the adhesion of marine organisms. The surface-active polymer, obtained by grafting fluorinated molecules with hydrophobic and hydrophilic blocks to a block copolymer precursor, showed interesting bioadhesion properties. Two different algal species, one of which adhered strongly to hydrophobic surfaces, and the other, to hydrophilic surfaces, showed notably weak adhesion to the amphiphilic surfaces. Both organisms are known to secrete adhesive macromolecules, with apparently different wetting characteristics, to attach to underwater surfaces. The ability of the amphiphilic surface to undergo an environment-dependent transformation in surface chemistry when in contact with the extracellular polymeric substances is a possible reason for its antifouling nature. Near-edge X-ray absorption fine structure spectroscopy (NEXAFS) was used, in a new approach based on angle-resolved X-ray photoelectron spectroscopy (XPS), to determine the variation in chemical composition within the top few nanometers of the surface and also to study the surface segregation of the amphiphilic block. A mathematical model to extract depth-profile information from the normalized NEXAFS partial electron yield is developed

  15. Synthesis and Antiplasmodial Activity of Novel Chloroquine Analogues with Bulky Basic Side Chains.

    Tasso, Bruno; Novelli, Federica; Tonelli, Michele; Barteselli, Anna; Basilico, Nicoletta; Parapini, Silvia; Taramelli, Donatella; Sparatore, Anna; Sparatore, Fabio

    2015-09-01

    Chloroquine is commonly used in the treatment and prevention of malaria, but Plasmodium falciparum, the main species responsible for malaria-related deaths, has developed resistance against this drug. Twenty-seven novel chloroquine (CQ) analogues characterized by a side chain terminated with a bulky basic head group, i.e., octahydro-2H-quinolizine and 1,2,3,4,5,6-hexahydro-1,5-methano-8H-pyrido[1,2-a][1,5]diazocin-8-one, were synthesized and tested for activity against D-10 (CQ-susceptible) and W-2 (CQ-resistant) strains of P. falciparum. Most compounds were found to be active against both strains with nanomolar or sub-micromolar IC50 values. Eleven compounds were found to be 2.7- to 13.4-fold more potent than CQ against the W-2 strain; among them, four cytisine derivatives appear to be of particular interest, as they combine high potency with low cytotoxicity against two human cell lines (HMEC-1 and HepG2) along with easier synthetic accessibility. Replacement of the 4-NH group with a sulfur bridge maintained antiplasmodial activity at a lower level, but produced an improvement in the resistance factor. These compounds warrant further investigation as potential drugs for use in the fight against malaria. PMID:26213237

  16. Poly(Amido Amine)s Containing Agmatine and Butanol Side Chains as Efficient Gene Carriers.

    Won, Young-Wook; Ankoné, Marc; Engbersen, Johan F J; Feijen, Jan; Kim, Sung Wan

    2016-04-01

    A new type of bioreducible poly(amido amine) copolymer is synthesized by the Michael addition polymerization of cystamine bisacrylamide (CBA) with 4-aminobutylguanidine (agmatine, AGM) and 4-aminobutanol (ABOL). Since the positively charged guanidinium groups of AGM and the hydroxybutyl groups of ABOL in the side chains have shown to improve the overall transfection efficiency of poly(amido amine)s, it is hypothesized that poly(CBA-ABOL/AGM) synthesized at the optimal ratio of both components would result in high transfection efficiency and minimal toxicity. In this study, a series of the poly(CBA-ABOL/AGM) copolymers is synthesized as gene carriers. The polymers are characterized and luciferase transfection efficiencies of the polymers in various cell lines are investigated to select the ideal ratio between AGM and ABOL. The poly(CBA-ABOL/AGM) containing 80% AGM and 20% ABOL has shown the best transfection efficiency with the lowest cytotoxicity, indicating that this polymer is very promising as a potent and nontoxic gene carrier. PMID:26663734

  17. Composition of the epicuticular waxes coating the adaxial side of Phyllostachys aurea leaves: Identification of very-long-chain primary amides.

    Racovita, Radu C; Jetter, Reinhard

    2016-10-01

    The present study presents comprehensive chemical analyses of cuticular wax mixtures of the bamboo Phyllostachys aurea. The epicuticular and intracuticular waxes were sampled selectively from the adaxial side of leaves on young and old plants and investigated by gas chromatography-mass spectrometry and flame ionization detection. The epi- and intracuticular layers on young and old leaves had wax loads ranging from 1.7 μg/cm(2) to 1.9 μg/cm(2). Typical very-long-chain aliphatic wax constituents were found with characteristic chain length patterns, including alkyl esters (primarily C48), alkanes (primarily C29), fatty acids (primarily C28 and C16), primary alcohols (primarily C28) and aldehydes (primarily C30). Alicyclic wax components were identified as tocopherols and triterpenoids, including substantial amounts of triterpenoid esters. Alkyl esters, alkanes, fatty acids and aldehydes were found in greater amounts in the epicuticular layer, while primary alcohols and most terpenoids accumulated more in the intracuticular wax. Alkyl esters occurred as mixtures of metamers, combining C20 alcohol with various acids into shorter ester homologs (C36C40), and a wide range of alcohols with C22 and C24 acids into longer esters (C42C52). Primary amides were identified, with a characteristic chain length profile peaking at C30. The amides were present exclusively in the epicuticular layer and thus at or near the surface, where they may affect plant-herbivore or plant-pathogen interactions. PMID:27402630

  18. Protein loops, solitons and side-chain visualization with applications to the left-handed helix region

    Lundgren, Martin; Sha, Fan

    2012-01-01

    Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha-helices and beta-strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two-sphere. Unlike the more conventional approaches that only describea given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C-alpha atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-han...

  19. Role of Side-Chains in Forming Peptide Aggregates and Fibrils. IR and VCD Spectroscopic Studies. Theory and Experiment

    Chi, H.; Tobias, F.; Kessler, Jiří; Kubelka, J.; Bouř, Petr; Keiderling, T. A.

    Cambridge : Cell press, 2014. Roč. 108, Suppl 1 (2015), 523A. ISSN 0006-3495. [Annual Meeting of the Biophysical Society /59./. 07.02.2015-11.02.2015, Baltimore] Institutional support: RVO:61388963 Keywords : side chains * peptide aggregates * Glu * IR * VCD Subject RIV: CF - Physical ; Theoretical Chemistry

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

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

    2015-01-01

    In this article we discuss the synthesis of four new low band-gap co-polymers based on the diketopyrrolopyrrole (DPP) and benzotriazole (BTZ) monomer unit. We demonstrate that the BTZ unit allows for additional solubilizing side-chains on the co-monomer and show that the introduction of a linear ...

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

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

    2012-01-01

    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...

  2. Modulation of the kinetics of cholesterol side-chain cleavage by an activator and by an inhibitor isolated from the cytosol of the cortex of bovine adrenals.

    Warne, P A; Greenfield, N J; Lieberman, S.

    1983-01-01

    Two modulators of sterol side-chain cleavage activity have been detected in the cytosol from the cortex of bovine adrenals. One is an inhibitor of side-chain cleavage which increases the Km of a purified and reconstituted mitochondrial side-chain cleavage system for both cholesterol and cholesterol sulfate. It also lowers the Vmax of cleavage when cholesterol sulfate is the substrate. The other modulator is a low molecular weight protein which in the reconstituted system increases the Vmax of...

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

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

    2010-01-01

    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.

  4. Structural relaxation accompanied by photo-induced chromatic phase transition of polydiacetylenes with butylene-N-difluorophenyl carbamate side chains

    Maekawa, Yuuki; Sakamoto, Naoya; Kokado, Ryousuke; Kajimoto, Naoshi; Izumi, Yuuichiro [Department of Materials Science and Chemistry, Wakayama University, 930 Sakaedani, Wakayama (Japan); Itoh, Chihiro, E-mail: citoh@sys.wakayama-u.ac.jp [Department of Materials Science and Chemistry, Wakayama University, 930 Sakaedani, Wakayama (Japan)

    2013-01-15

    We have studied the phase transition of poly-5,7-dodecadiyne-1,12-diol bis[2,4-difluorophenyl carbamate] (PDA-2,4-DFPC) and poly-5,7-dodecadiyne-1,12-diol bis[3,4-difluorophenyl carbamate] (PDA-3,4-DFPC) by visible reflection spectroscopy and mid-infrared absorption spectroscopy. Both PDA-2,4-DFPC and PDA-3,4-DFPC show the reflection spectra characterized by a sharp peak at around 1.9 eV at room temperature. While PDA-3,4-DFPC shows thermochromic phase transition to the phase showing the reflection spectrum with a peak around 2.2 eV above 120 Degree-Sign C, PDA-2,4-DFPC shows no abrupt change of the reflection spectrum. However, PDA-2,4-DFPC shows drastic change of the reflection spectrum under 532-nm CW-laser excitation. Based on these results, we can draw the following two conclusions. First, the phase transition behavior of PDA can be controlled by modifying the side-chain structure. Second, we demonstrate that thermally inaccessible phase of PDA is induced by the photo-excitation. By measuring mid-infrared absorption of PDAs, we elucidated that conformational change of side chains is accompanied with the phase transition. Based on the results, we discussed the role of the side chain in the phase transition. - Highlights: Black-Right-Pointing-Pointer We have synthesized polydiacetylene (PDA) with difluorophenyl carbamate side chain. Black-Right-Pointing-Pointer PDAs show distinct phase transition (PT) depending on the side-chain structure. Black-Right-Pointing-Pointer PDA with 3,4-difluorophenyl carbamate shows PT by thermal stimulation. Black-Right-Pointing-Pointer However, PDA with 2,4-difluorophenyl carbamate shows PT only under photo-excitation.

  5. Shear mechanical anisotropy of side chain liquid-crystal elastomers: Influence of sample preparation

    Rogez, D.; Francius, G.; Finkelmann, H.; Martinoty, P.

    2006-08-01

    We study the mechanical anisotropy of a series of uniaxial side chain nematic elastomers prepared with the same chemical composition but with different preparation protocols. For all the compounds, the experiments performed as a function of temperature show no discontinuity in both G'// and G'⊥ (the labels // and ⊥ stand for the director parallel, respectively perpendicular to the shear displacement) around the nematic-isotropic (N-I) phase transition temperature determined by DSC. They also all show a small decrease in G'// starting at temperatures well above this temperature (from ˜ 4°C to ˜ 20°C depending on the compound studied) and leading to a small hydrodynamic value of the G'⊥/G'// ratio. The measurements taken as a function of frequency show that the second plateau in G'// and the associated dip in G//” expected from dynamic semi-soft elasticity are not observed. These results can be described by the de Gennes model, which predicts small elastic anisotropy in the hydrodynamic and linear regimes. They correspond to the behavior expected for compounds beyond the mechanical critical point, which is consistent with the NMR and specific heat measurements taken on similar compounds. We also show that a reduction in the cross-linking density does not change the non-soft character of the mechanical response. From the measurements taken as a function of frequency at several temperatures we deduce that the time-temperature superposition method does not apply. From these measurements, we also determine the temperature dependence of the longest relaxation time τE of the network for the situations where the director is either parallel or perpendicular to the shear velocity. Finally, we discuss the influence on the measurements of the mechanical constraint associated with the fact that the samples cannot change their shape around the pseudo phase transition, because of their strong adherence on the sample-bearing glass slides.

  6. Polymer gels with associating side chains and their interaction with surfactants.

    Gordievskaya, Yulia D; Rumyantsev, Artem M; Kramarenko, Elena Yu

    2016-05-14

    Conformational behaviour of hydrophobically modified (HM) polymer gels in solutions of nonionic surfactants is studied theoretically. A HM gel contains hydrophobic side chains (stickers) grafted to its subchains. Hydrophobic stickers are capable to aggregate into joint micelles with surfactant molecules. Micelles containing more than one sticker serve as additional physical cross-links of the network, and their formation causes gel shrinking. In the proposed theoretical model, the interior of the gel/surfactant complex is treated as an array of densely packed spherical polymer brushes consisting of gel subchains tethered to the surface of the spherical sticker/surfactant micelles. Effect of stickers length and grafting density, surfactant concentration and hydrophobicity on gel swelling as well as on hydrophobic association inside it is analyzed. It is shown that increasing surfactant concentration can result in a gel collapse, which is caused by surfactant-induced hydrophobic aggregation of stickers, and a successive gel reswelling. The latter should be attributed to a growing fraction of surfactants in joint aggregates and, hence, increasing number of micelles containing only one sticker and not participating in gel physical cross-linking. In polyelectrolyte (PE) gels hydrophobic aggregation is opposed by osmotic pressure of mobile counterions, so that at some critical ionization degree hydrophobic association is completely suppressed. Hydrophobic modification of polymers is shown to open new ways for controlling gel responsiveness. In particular, it is discussed that incorporation of photosensitive groups into gel subchains and/or surfactant tail could give a possibility to vary the gel volume by light. Since hydrophobic aggregation regularities in gels and solutions are common, we hope our findings will be useful for design of polymer based self-healing materials as well. PMID:27179504

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

    Alexey G. Gerbst

    2015-02-01

    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.

  8. Heterologous Expression of Hen Egg White Lysozyme and Resonance Assignment of Tryptophan Side Chains in its Non-native States

    A new protocol is described for the isotope (15N and 13C,15N) enrichment of hen egg white lysozyme. Hen egg white lysozyme and an all-Ala-mutant of this protein have been expressed in E. coli. They formed inclusion bodies from which mg quantities of the proteins were purified and prepared for NMR spectroscopic investigations. 1H,13C and 15N main chain resonances of disulfide reduced and S-methylated lysozyme were assigned and its residual structure in water pH 2 was characterized by chemical shift perturbation analysis. A new NMR experiment has been developed to assign tryptophan side chain indole resonances by correlation of side chain and backbone NH resonances with the Cγ resonances of these residues. Assignment of tryptophan side chains enables further residue specific investigations on structural and dynamical properties, which are of significant interest for the understanding of non-natives states of lysozyme stabilized by hydrophobic interactions between clusters of tryptophan residues

  9. Lymphatic recovery of exogenous oleic acid in rats on long chain or specific structured triacylglycerol diets

    Vistisen, Bodil; Mu, Huiling; Høy, Carl-Erik

    2006-01-01

    Specific structured triacylglycerols, MLM (M = medium-chain fatty acid, L = long-chain fatty acid), rapidly deliver energy and long-chain fatty acids to the body and are used for longer periods in human enteral feeding. In the present study rats were fed diets of 10 wt% MLM or LLL (L = oleic acid......-chain fatty acids from a single meal depends on the overall long-chain fatty acid composition of the habitual diet. This could have implications for enteral feeding for longer periods....

  10. Catabolism of Branched Chain Amino Acids Contributes Significantly to Synthesis of Odd-Chain and Even-Chain Fatty Acids in 3T3-L1 Adipocytes.

    Scott B Crown

    Full Text Available The branched chain amino acids (BCAA valine, leucine and isoleucine have been implicated in a number of diseases including obesity, insulin resistance, and type 2 diabetes mellitus, although the mechanisms are still poorly understood. Adipose tissue plays an important role in BCAA homeostasis by actively metabolizing circulating BCAA. In this work, we have investigated the link between BCAA catabolism and fatty acid synthesis in 3T3-L1 adipocytes using parallel 13C-labeling experiments, mass spectrometry and model-based isotopomer data analysis. Specifically, we performed parallel labeling experiments with four fully 13C-labeled tracers, [U-13C]valine, [U-13C]leucine, [U-13C]isoleucine and [U-13C]glutamine. We measured mass isotopomer distributions of fatty acids and intracellular metabolites by GC-MS and analyzed the data using the isotopomer spectral analysis (ISA framework. We demonstrate that 3T3-L1 adipocytes accumulate significant amounts of even chain length (C14:0, C16:0 and C18:0 and odd chain length (C15:0 and C17:0 fatty acids under standard cell culture conditions. Using a novel GC-MS method, we demonstrate that propionyl-CoA acts as the primer on fatty acid synthase for the production of odd chain fatty acids. BCAA contributed significantly to the production of all fatty acids. Leucine and isoleucine contributed at least 25% to lipogenic acetyl-CoA pool, and valine and isoleucine contributed 100% to lipogenic propionyl-CoA pool. Our results further suggest that low activity of methylmalonyl-CoA mutase and mass action kinetics of propionyl-CoA on fatty acid synthase result in high rates of odd chain fatty acid synthesis in 3T3-L1 cells. Overall, this work provides important new insights into the connection between BCAA catabolism and fatty acid synthesis in adipocytes and underscores the high capacity of adipocytes for metabolizing BCAA.

  11. Polyunsaturated fatty acids in the food chain in Europe.

    Sanders, T A

    2000-01-01

    Intakes of partially hydrogenated fish oil and animal fats have declined and those of palm, soybean, sunflower, and rapeseed oils have increased in northern Europe in the past 30 y. Soybean and rapeseed oils are currently the most plentiful liquid vegetable oils and both have desirable ratios of n-6 to n-3 fatty acids. However, soybean and rapeseed oils are commonly partially hydrogenated for use in commercial frying to decrease susceptibility to oxidative degradation. This process leads to selective losses of alpha-linolenic acid (18:3n-3). Intake of linoleic acid (18:2n-6) has risen in many northern European countries. In the United Kingdom, intakes have increased from approximately 10 g/d in the late 1970s to approximately 15 g/d in the 1990s. The intake of alpha-linolenic acid is estimated to be approximately 1-2 g/d but varies with the type of culinary oil used. There are few reliable estimates of the intake of long-chain n-3 fatty acids, but those are generally approximately 0.1-0.5 g/d. The increased use of intensive, cereal-based livestock production systems has resulted in a lower proportion of n-3 fatty acids in meat compared with traditional extensive production systems. Overall, there has been a shift in the balance between n-6 and n-3 fatty acids over the past 30 y. This shift is reflected in the declining concentrations of docosahexaenoic acid and rising concentrations of linoleic acid in breast milk. PMID:10617968

  12. Absolute Side-chain Structure at Position 13 Is Required for the Inhibitory Activity of Bromein*

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

    2008-01-01

    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 construct...

  13. Control of the anchoring behavior of polymer-dispersed liquid crystals: effect of branching in the side chains of polyacrylates.

    Zhou, Jian; Collard, David M; Park, Jung O; Srinivasarao, Mohan

    2002-08-28

    A temperature-driven anchoring transition in a polymer/nematic fluid composite that is far from the bulk nematic-isotropic transition temperature is reported. A series of poly(methylheptyl acrylates) were studied to probe the subtle effects of the side chain structure of the polymer on control of the anchoring. A polymer-dispersed liquid crystal film made from TL205 and 1-methylheptyl acrylate shows only planar anchoring over the temperature range studied, while the films made from TL205 and each of the other methylheptyl acrylates or n-heptyl acrylate show the homeotropic-to-planar anchoring transition at temperatures between 70 and 78 degrees C. An interfacial model is proposed in which the different conformation of the side chains is suggested as the cause for the dramatic difference in the observed anchoring behavior. PMID:12188649

  14. Photoinduced changes of surface order in coumarin side-chain polymer films used for liquid crystal photoalignment

    Specular x-ray reflectivity probes morphological changes in a crosslinkable coumarin photoalignment polymer film resulting from ultraviolet irradiation. An ordered surface layer with density oscillations compatible with planar side-chain alignment is obtained before irradiation. The ordering is enhanced in the early stages of crosslinking. This is attributed to the photoinduced increase of mobility of the side-chains resulting from the creation of free volume by the crosslinking process. The expansion of the thin film confirms that free volume is created. The surface ordering decreases with prolonged ultraviolet irradiation because of increased material viscosity resulting from a high crosslinked density. The implications of surface ordering on liquid crystal photoalignment are discussed

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

    Mei, Jianguo

    2011-12-21

    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.

  16. Design and synthesis of side-chain conformationally restricted phenylalanines and their use for structure-activity studies on tachykinin NK-1 receptor.

    Josien, H; Lavielle, S; Brunissen, A; Saffroy, M; Torrens, Y; Beaujouan, J C; Glowinski, J; Chassaing, G

    1994-05-27

    Constrained analogues of phenylalanine have been conceptually designed for analyzing the binding pockets of Phe7 (S7) and Phe8 (S8), two aromatic residues important for the pharmacological properties of SP, i.e., L-tetrahydroisoquinoleic acid, L-diphenylalanine, L-9-fluorenylglycine (Flg), 2-indanylglycine, the diastereomers of L-1-indanylglycine (Ing) and L-1-benz[f]indanylglycine (Bfi), and the Z and E isomers of dehydrophenylalanine (delta ZPhe, delta EPhe). Binding studies were performed with appropriate ligands and tissue preparations allowing the discrimination of the three tachykinin binding sites, NK-1, NK-2, and NK-3. The potencies of these agonists were evaluated in the guinea pig ileum bioassay. According to the binding data, we can conclude that the S7 subsite is small, only the gauche (-) probe [(2S,3S)-Ing7]SP presents a high affinity for specific NK-1 binding sites. Surprisingly, the [delta EPhe7]SP analogue, which projects the aromatic ring toward the trans orientation, is over 40-fold more potent than the Z isomer, [delta ZPhe7]SP. A plausible explanation of these conflictual results is that either the binding protein quenches the minor trans rotamer of [(2S,3S)-Ing7]SP in solution or this constrained amino acid side chain rotates when inserted in the protein. In position 8, the high binding affinities of [Flg8]SP and [(2S,3S)-Bfi8]SP suggest that the S8 subsite is large enough to accept two aromatic rings in the gauche (-) and one aromatic ring in the trans direction. Peptides bearing two conformational probes in positions 7, 8, or 9 led to postulate that S7, S8, and S9 subsites are independent from each other. The volumes available for side chains 7 and 8 can be estimated to be close to 110 and 240 A3, respectively. The large volume of the S8 subsite raises question on the localization of the SP-binding site in the NK-1 receptor. If SP were to bind in the transmembrane domains, the cleft defined by the seven transmembrane segments must rearrange

  17. A simple strategy to the side chain functionalization on the quinoxaline unit for efficient polymer solar cells.

    Yuan, Jun; Qiu, Lixia; Zhang, Zhiguo; Li, Yongfang; He, Yuehui; Jiang, Lihui; Zou, Yingping

    2016-05-25

    A new tetrafluoridequinoxaline electron accepting block from a quinoxaline core, which is substituted with a fluorine atom onto its backbone and side chains, was designed. A new copolymer (PBDTT-ffQx) was synthesized from tetrafluoridequinoxaline and benzodithiophene. The copolymer was characterized in detail. The photovoltaic properties were well investigated. A high PCE of 8.6% based on the single junction device was obtained. PMID:27025274

  18. The synthesis and characterization of organometallic copolymers with Mn-Re binuclear transition-metal group in the side chain

    XU Zhi; FENG Gang; BAI Zhifeng; MA Yongqiang; CHANG Weixing; LI Jing

    2006-01-01

    Novel organometallic copolymers with Mn-Re binuclear transition-metal groups in the side chain are synthesized and characterized. The structure and properties of the copolymers are characterized by GPC, DSC, TG, NMR, FT-IR, UV-Vis spectra and elemental analysis. The glass transition temperature and UV-Vis spectra properties of these three organometallic copolymers are found to be different from the normal polystyrene. New synthetic strategy for the synthesis of organometallic copolymer is developed.

  19. Synthesis and properties of aromatic polyethers containing poly(ethylene oxide) side chains as polymer electrolytes for lithium ion batteries

    Polymer electrolytes consisting of polar pyridine units in the backbone and poly(ethylene oxide) (PEO) side chains are designed for possible application in lithium ion batteries. In particular, aromatic polyethers bearing PEO side chains with varying length are synthesized either by copolymerization of the corresponding PEO based diols with different arylfluorides or by modification of dihydroxyl functionalized precursor polymers with poly(ethylene oxide) methyl ether tosylate. The formation of free standing films is dependent on the PEO content, polymers' composition as well as on the different monomers used. The mechanical properties study shows that the glass transition temperature can be controlled by varying the PEO content. Thermal stability is also influenced by the PEO length: the shorter the PEO side chain, the higher the stability. XRD analysis gives information about the desired amorphous character of these polymers, which is independent of the PEO content. Solid polymer electrolytes prepared by blending the PEO-based polymers with lithium salt and PEO 2000 (used as plasticizer) show ambient temperature conductivities in the range of 10−6 S/cm. To further improve conductivity doping of PEO-based polymers in liquid electrolyte (1 M LiPF6 in EC/DMC 1/1) in some cases results in high conductivities in the range of 10−3 S cm−1 at 80 °C. - Highlights: • Polymer electrolytes bearing PEO side chains of varying lengths were designed. • DMA and TGA show that Tg and Td can be controlled by varying the PEO content. • XRD confirms polymers amorphous character, independent of the PEO content. • Membranes doped in liquid electrolyte have high conductivities (10−3 S cm−1, 80 °C)

  20. 2D IR Spectroscopy of Histidine: Probing Side-Chain Structure and Dynamics via Backbone Amide Vibrations

    Ghosh, Ayanjeet; Tucker, Matthew J.; Gai, Feng

    2014-01-01

    It is well known that histidine is involved in many biological functions due to the structural versatility of its side chain. However, probing the conformational transitions of histidine in proteins, especially those occurring on an ultrafast time scale, is difficult. Herein we show, using a histidine dipeptide as a model, that it is possible to probe the tautomer and protonation status of a histidine residue by measuring the two-dimensional infrared (2D IR) spectrum of its amide I vibrationa...

  1. Study of Class I and Class III Polyhydroxyalkanoate (PHA) Synthases with Substrates Containing a Modified Side Chain.

    Jia, Kaimin; Cao, Ruikai; Hua, Duy H; Li, Ping

    2016-04-11

    Polyhydroxyalkanoates (PHAs) are carbon and energy storage polymers produced by a variety of microbial organisms under nutrient-limited conditions. They have been considered as an environmentally friendly alternative to oil-based plastics due to their renewability, versatility, and biodegradability. PHA synthase (PhaC) plays a central role in PHA biosynthesis, in which its activity and substrate specificity are major factors in determining the productivity and properties of the produced polymers. However, the effects of modifying the substrate side chain are not well understood because of the difficulty to accessing the desired analogues. In this report, a series of 3-(R)-hydroxyacyl coenzyme A (HACoA) analogues were synthesized and tested with class I synthases from Chromobacterium sp. USM2 (PhaCCs and A479S-PhaCCs) and Caulobacter crescentus (PhaCCc) as well as class III synthase from Allochromatium vinosum (PhaECAv). It was found that, while different PHA synthases displayed distinct preference with regard to the length of the alkyl side chains, they could withstand moderate side chain modifications such as terminal unsaturated bonds and the azide group. Specifically, the specific activity of PhaCCs toward propynyl analogue (HHxyCoA) was only 5-fold less than that toward the classical substrate HBCoA. The catalytic efficiency (kcat/Km) of PhaECAv toward azide analogue (HABCoA) was determined to be 2.86 × 10(5) M(-1) s(-1), which was 6.2% of the value of HBCoA (4.62 × 10(6) M(-1) s(-1)) measured in the presence of bovine serum albumin (BSA). These side chain modifications may be employed to introduce new material functions to PHAs as well as to study PHA biogenesis via click-chemistry, in which the latter remains unknown and is important for metabolic engineering to produce PHAs economically. PMID:26974339

  2. Beta-scission of alkoxyl radicals on peptides and proteins can give rise to backbone cleavage and loss of side-chains

    Full text: Exposure of proteins to radicals in the presence of O2 brings about multiple changes including side-chain oxidation, backbone fragmentation, cross-linking, unfolding, changes in hydrophobicity and conformation, altered susceptibility to proteolytic enzymes and formation of new reactive groups (e.g. hydroperoxides and 3,4-dihydroxyphenylalanine). All of these processes can result in loss of structural or enzymatic activity. The mechanisms that give rise to backbone cleavage are only partly understood. Whilst it is known that direct hydrogen atom abstraction at a-carbon sites gives backbone cleavages it has also been proposed that initial attack at side-chain sites might also give rise to backbone cleavage. In this study we have examined whether initial attack at the β- (C-3) position can give rise to α-carbon radicals (and hence backbone cleavage) via the formation, and subsequent β- scission, of C-3 alkoxyl radicals. This process has been observed previously with protected amino acids in organic solvents (J. Chem. Soc. Perkin Trans. 2, 1997, 503-507) but the occurrence of such reactions with proteins in aqueous solution has not been explored. Alkoxyl radicals were generated at the C-3 position of a variety of protected amino acids and small peptides by two methods: metal-ion catalysed decomposition of hydroperoxides formed as a result of γ-radiolysis in the presence of O2, and UV photolysis of nitrate esters. In most cases radicals have been detected by EPR spectroscopy using nitroso and nitrone spin traps, which can be assigned by comparison with literature data to α-carbon radicals; in some case assignments were confirmed by the generation of the putative species by other routes. With Ala peptide hydroperoxides and nitrate esters, and MNP as the spin trap, the major radical detected in each case has been assigned to the adduct of an α-carbon radical with partial structure - NH-.CH-C(O) - consistent with the rapid occurrence of the above reaction

  3. Regulation of Inflammation by Short Chain Fatty Acids

    Renato T. Nachbar

    2011-10-01

    Full Text Available The short chain fatty acids (SCFAs acetate (C2, propionate (C3 and butyrate (C4 are the main metabolic products of anaerobic bacteria fermentation in the intestine. In addition to their important role as fuel for intestinal epithelial cells, SCFAs modulate different processes in the gastrointestinal (GI tract such as electrolyte and water absorption. These fatty acids have been recognized as potential mediators involved in the effects of gut microbiota on intestinal immune function. SCFAs act on leukocytes and endothelial cells through at least two mechanisms: activation of GPCRs (GPR41 and GPR43 and inhibiton of histone deacetylase (HDAC. SCFAs regulate several leukocyte functions including production of cytokines (TNF-α, IL-2, IL-6 and IL-10, eicosanoids and chemokines (e.g., MCP-1 and CINC-2. The ability of leukocytes to migrate to the foci of inflammation and to destroy microbial pathogens also seems to be affected by the SCFAs. In this review, the latest research that describes how SCFAs regulate the inflammatory process is presented. The effects of these fatty acids on isolated cells (leukocytes, endothelial and intestinal epithelial cells and, particularly, on the recruitment and activation of leukocytes are discussed. Therapeutic application of these fatty acids for the treatment of inflammatory pathologies is also highlighted.

  4. 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

    Zhang, Ning

    2012-04-17

    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.

  5. Fungicidal Activity of a Medium-chain Fatty Acids Mixture Comprising Caprylic, Pelargonic and Capric Acids

    Xiaojin Liu

    2014-01-01

    Full Text Available This study examines the fungicidal activity of a medium-chain fatty acids mixture comprising caprylic acid (C8:0, pelargonic acid (C9:0 and capric acid (C10:0, against Rhizoctonia solani, Phytophthora infestans, Colletotrichum gloeosporioides, Botrytis cinerea, Fusarium oxysporum and Sphaerotheca cucurbitae. The mixture of caprylic, pelargonic and capric acids (2/5/3, w/w/w is prepared into a micro-emulsion concentrate and tested for its inhibitory effect on fungal growth using disc diffusion method except for S. cucurbitae using pot bioassay method. Results show that the fatty acids mixture is self-stabilized under either 4°C during a seven-day-storage or 54°C during fortnight. The doses of the mixed fatty acids completely inhibiting the mycelial growth are 100 ppm for P. infestans and 125 ppm C. gloeosporioides after three days and 200 ppm for B. cinerea after 4 days. A dose of 100 ppm reduces the mycelial growth in R. solani by 93.7% after 4 days and that in F. oxysporum by 92.9% after 3 days. For S. cucurbitae, a dose of 250 ppm results in a control effect of 81.0% in the pot bioassay. Our study provides so far the first report of the fungicidal activity of medium-chain saturated fatty acids mixture at relative low dosage rates.

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

    Kim, Do Hwan

    2013-02-12

    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.

  7. 保护的预酯化紫杉醇侧链的合成%Synthesis of the Protected Esterification-ready Paclitaxel Side Chain

    胡章; 李思东

    2008-01-01

    以市场可购得的(2R,3S)-苯基异丝氨酸盐酸盐为起始原料,通过在甲醇的氯化亚砜溶液中进行酯化反应,及随后对氨基进行苯甲酰化,氨基羟基的环化保护,最后对其酯进行水解,合成得到保护的预酯化的紫杉醇侧链.整个过程无需柱层析操作,适于工业化生产.为制备保护的预酯化紫杉醇侧链提供了一种有效而又实用的合成方法.%Starting from the commercially available (2R,3S)-phenylisoserine hydrochloride, the protected, esterification-ready paclitaxel side chain acid was obtained by esterification of (2R,3S)-phenylisoserine hydrochloride with sulfurous dichloride in methanol, following benzoylation, cyclic N,O-acetalization and hydrolysis.The whole process was purified without column chromatography and suitable for large scale production.A practical and efficient synthesis of the protected, esterification-ready paclitaxel side chain was established.

  8. On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters.

    O'Brien, Evan S; Wand, A Joshua; Sharp, Kim A

    2016-06-01

    Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify MD force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or nuclear magnetic resonance (NMR) chemical shifts and residual dipolar couplings. NMR derived Lipari-Szabo squared generalized order parameter (O(2) ) values of amide NH bond vectors of the polypeptide chain were also often employed for refinement and validation. However, with a few exceptions, side chain methyl symmetry axis order parameters have not been incorporated into experimental reference sets. Using a test set of five diverse proteins, the performance of several force fields implemented in the NAMDD simulation package was examined. It was found that simulations employing explicit water implemented using the TIP3 model generally performed significantly better than those using implicit water in reproducing experimental methyl symmetry axis O(2) values. Overall the CHARMM27 force field performs nominally better than two implementations of the Amber force field. It appeared that recent quantum mechanics modifications to side chain torsional angles of leucine and isoleucine in the Amber force field have significantly hindered proper motional modeling for these residues. There remained significant room for improvement as even the best correlations of experimental and simulated methyl group Lipari-Szabo generalized order parameters fall below an R(2) of 0.8. PMID:26990788

  9. Effects of side chain isomerism on the physical and photovoltaic properties of indacenodithieno[3,2-b]thiophene–quinoxaline copolymers: toward a side chain design for enhanced photovoltaic performance

    Xu, Xiaofeng; Li, Zhaojun; Bäcke, Olof; Bini, Kim; James, David; Olsson, Eva; Andersson, Mats R.; Wang, Ergang

    2014-01-01

    Four new D–A polymers PIDTT-Q-p, PIDTT-Q-m, PIDTT-QF-p and PIDTT-QF-m, using indacenodithieno[3,2-b]thiophene (IDTT) as an electron-rich unit and quinoxaline (Q) as an electron-deficient unit, were synthesized via a Pd-catalyzed Stille polymerization. The side chains on the pendant phenyl rings of IDTT were varied from the para- to the meta-position, and the effect of the inclusion of fluorine on the quinoxaline unit was simultaneously investigated. The influence on the optical and electroche...

  10. Branched chain amino acid profile in early chronic kidney disease

    M Anil Kumar

    2012-01-01

    Full Text Available The nutritional status in chronic kidney disease (CKD patients is a predictor of prognosis during the first period of dialysis. Serum albumin is the most commonly used nutritional marker. Another index is plasma amino acid profile. Of these, the plasma levels of branched chain amino acids (BCAA, especially valine and leucine, correlate well with nutritional status. Plasma BCAAs were evaluated along with albumin and C-reactive protein in 15 patients of early stages of CKD and 15 age- and sex-matched healthy controls. A significant decrease in plasma valine, leucine and albumin levels was observed in CKD patients when compared with the controls (P <0.05. No significant difference in C-reactive protein (CRP levels was observed between the two groups. Malnutrition seen in our CKD patients in the form of hypoalbuminemia and decreased concentrations of BCAA points to the need to evaluate the nutritional status in the early stages itself. Simple measures in the form of amino acid supplementation should be instituted early to decrease the morbidity and mortality before start of dialysis in these patients.

  11. Modification of eucalyptus pulp fiber using silane coupling agents with aliphatic side chains of different length

    The objective of this work was to evaluate the effect of three silane coupling agents with different aliphatic chain lengths on the hydrophobicity of eucalyptus pulp fiber. The three silanes coupling agents used (isobutyltrimethoxysilane, methyltrimethoxysilane, and n-octyltriethoxysilane [OTES]) we...

  12. Catabolism of leucine to branched-chain fatty acids in Staphylococcus xylosus

    Beck, Hans Christian; Hansen, A M; Lauritsen, F R

    2004-01-01

    Staphylococcus xylosus is an important starter culture in the production of flavours from the branched-chain amino acids leucine, valine and isoleucine in fermented meat products. The sensorially most important flavour compounds are the branched-chain aldehydes and acids derived from the correspo...... corresponding amino acids and this paper intends to perspectivate these flavour compounds in the context of leucine metabolism....

  13. Evaluating the effect of ionic strength on duplex stability for PNA having negatively or positively charged side chains.

    N Tilani S De Costa

    Full Text Available The enhanced thermodynamic stability of PNA:DNA and PNA:RNA duplexes compared with DNA:DNA and DNA:RNA duplexes has been attributed in part to the lack of electrostatic repulsion between the uncharged PNA backbone and negatively charged DNA or RNA backbone. However, there are no previously reported studies that systematically evaluate the effect of ionic strength on duplex stability for PNA having a charged backbone. Here we investigate the role of charge repulsion in PNA binding by synthesizing PNA strands having negatively or positively charged side chains, then measuring their duplex stability with DNA or RNA at varying salt concentrations. At low salt concentrations, positively charged PNA binds more strongly to DNA and RNA than does negatively charged PNA. However, at medium to high salt concentrations, this trend is reversed, and negatively charged PNA shows higher affinity for DNA and RNA than does positively charged PNA. These results show that charge screening by counterions in solution enables negatively charged side chains to be incorporated into the PNA backbone without reducing duplex stability with DNA and RNA. This research provides new insight into the role of electrostatics in PNA binding, and demonstrates that introduction of negatively charged side chains is not significantly detrimental to PNA binding affinity at physiological ionic strength. The ability to incorporate negative charge without sacrificing binding affinity is anticipated to enable the development of PNA therapeutics that take advantage of both the inherent benefits of PNA and the multitude of charge-based delivery technologies currently being developed for DNA and RNA.

  14. Evaluating the effect of ionic strength on duplex stability for PNA having negatively or positively charged side chains.

    De Costa, N Tilani S; Heemstra, Jennifer M

    2013-01-01

    The enhanced thermodynamic stability of PNA:DNA and PNA:RNA duplexes compared with DNA:DNA and DNA:RNA duplexes has been attributed in part to the lack of electrostatic repulsion between the uncharged PNA backbone and negatively charged DNA or RNA backbone. However, there are no previously reported studies that systematically evaluate the effect of ionic strength on duplex stability for PNA having a charged backbone. Here we investigate the role of charge repulsion in PNA binding by synthesizing PNA strands having negatively or positively charged side chains, then measuring their duplex stability with DNA or RNA at varying salt concentrations. At low salt concentrations, positively charged PNA binds more strongly to DNA and RNA than does negatively charged PNA. However, at medium to high salt concentrations, this trend is reversed, and negatively charged PNA shows higher affinity for DNA and RNA than does positively charged PNA. These results show that charge screening by counterions in solution enables negatively charged side chains to be incorporated into the PNA backbone without reducing duplex stability with DNA and RNA. This research provides new insight into the role of electrostatics in PNA binding, and demonstrates that introduction of negatively charged side chains is not significantly detrimental to PNA binding affinity at physiological ionic strength. The ability to incorporate negative charge without sacrificing binding affinity is anticipated to enable the development of PNA therapeutics that take advantage of both the inherent benefits of PNA and the multitude of charge-based delivery technologies currently being developed for DNA and RNA. PMID:23484047

  15. Engineering Yarrowia lipolytica for production of medium-chain fatty acids.

    Rutter, Charles D; Zhang, Shuyan; Rao, Christopher V

    2015-09-01

    Lipids are naturally derived products that offer an attractive, renewable alternative to petroleum-based hydrocarbons. While naturally produced long-chain fatty acids can replace some petroleum analogs, medium-chain fatty acid would more closely match the desired physical and chemical properties of currently employed petroleum products. In this study, we engineered Yarrowia lipolytica, an oleaginous yeast that naturally produces lipids at high titers, to produce medium-chain fatty acids. Five different acyl-acyl carrier protein (ACP) thioesterases with specificity for medium-chain acyl-ACP molecules were expressed in Y. lipolytica, resulting in formation of either decanoic or octanoic acid. These novel fatty acid products were found to comprise up to 40 % of the total cell lipids. Furthermore, the reduction in chain length resulted in a twofold increase in specific lipid productivity in these engineered strains. The medium-chain fatty acids were found to be incorporated into all lipid classes. PMID:26129951

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

    Mondal, Rajib

    2011-01-01

    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.

  17. STUDY ON MAGNETIC FIELD-INDUCED ORIENTATION OF A CHIRAL SIDE-CHAIN LIQUID CRYSTAL POLYACRYLATE USING INFRARED DICHROISM

    HE Liu; JIN Shunzi; ZHANG Shufan; QI Zongneng; WANG Fosong

    1996-01-01

    Magnetic field-induced orientation of a chiral side chain liquid crystalline polyacrylate (P-11) was studied by using IR dichroism. For the investigated P-11, it has been shown that the magnetic alignment takes place over the entire temperature range between its melting point and clearing point and the orientation level is strongly temperature-dependent, the development with time of the magnetic orientation follows an exponential-type relation,and the smectic phase state influences the thermal relaxation process in the absence of the magnetic field.

  18. X-ray scattering by edge-dislocations in the SA phase of mesomorphic side chain polyacrylates

    Davidson, P.; Pansu, B.; Levelut, A.; Strzelecki, L.

    1991-01-01

    The X-ray diffraction patterns of mesomorphic side chain polymers in the SA phase present diffuse streaks in shape of “butterfly wings”. We show that this diffuse scattering may be due to the presence of edge dislocations. On the basis of a previous description of edge dislocations within the framework of the elastic continuum theory of the SA phase given by De Gennes, we have calculated the Fourier transform of the deformation field. Optical diffraction experiments on sketches of defects hav...

  19. Structure-property optimizations in donor polymers via electronics, substituents, and side chains toward high efficiency solar cells.

    Uy, Rycel L; Price, Samuel C; You, Wei

    2012-07-26

    Many advances in organic photovoltaic efficiency are not yet fully understood and new insight into structure-property relationships is required to push this technology into broad commercial use. The aim of this article is not to comprehensively review recent work, but to provide commentary on recent successes and forecast where researchers should look to enhance the efficiency of photovoltaics. By lowering the LUMO level, utilizing electron-withdrawing substituents advantageously, and employing appropriate side chains on donor polymers, researchers can elucidate further aspects of polymer-PCBM interactions while ultimately developing materials that will push past 10% efficiency. PMID:22588903

  20. Synthesis and characterization of fluorinated copolyetherimides with -CH2-C6F13 side chains based on the ULTEM structure

    Kaba, Meriyam; Romero, Ricardo Escarcena; Essamri, Azzouz; MAS, Andre

    2005-01-01

    International audience Step polymn. of bisphenol A diphthalic anhydride (BAPA) with various mixts. from m-phenylene diamine (m-PDA) and 2-(perfluorohexylmethyl)butan-1,4-diamine (TFD) led to hydrophobic copolyetherimides bearing RF = CH2C6F13 side chains that were characterized by NMR, element anal., DSC, TGA and surface energy anal. By increasing the TFD unit %, the glass transition temp. (Tg) decreases according to the Fox equation from 217° (m-PDA 100% and TFD 0% like in ULTEM 1000) to ...

  1. An Aromatic Side Chain Is Required at Residue 8 of SU for Fusion of Ecotropic Murine Leukemia Virus

    Qian, Zhaohui; Albritton, Lorraine M.

    2004-01-01

    The surface glycoprotein (SU) of most gammaretroviruses contains a conserved histidine at its amino terminus. In ecotropic murine leukemia virus SU, replacement of histidine 8 with arginine (H8R) or deletion of H8 (H8del) abolishes infection and cell-cell fusion but has no effect on binding to the cellular receptor. We report here that an aromatic ring side chain is essential to the function of residue 8. The size of the aromatic ring appears to be important, as does its ability to form a hyd...

  2. Metallo-supramolecular hydrogels based on copolymers bearing terpyridine side-chain ligands

    Jochum, Florian Daniel; Brassinne, Jérémy; Fustin, Charles-André; Gohy, Jean-François

    2013-01-01

    A well-defined amphiphilic poly(triethyleneglycol methylether methacrylate)-block-polystyrene (PTEGMAb-PS) block copolymer with terpyridine groups randomly distributed within the water-soluble block has been sequentially synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization. Its self-assembly into micellar structures was analyzed in dilute aqueous solution by dynamic light scattering measurements (DLS). Metallo-supramolecular hydrogels were obtained after the a...

  3. Probing the Carboxyester Side Chain in Controlled Deactivation (−)-Δ8-Tetrahydrocannabinols

    Nikas, Spyros P.; Sharma, Rishi; Paronis, Carol A.; Kulkarni, Shashank; Thakur, Ganesh A.; Hurst, Dow; Wood, JodiAnne T.; Gifford, Roger S.; Rajarshi, Girija; Liu, Yingpeng; Raghav, Jimit Girish; Guo, Jason Jianxin; Järbe, Torbjörn U.C.; Reggio, Patricia H.; Bergman, Jack

    2014-01-01

    We recently reported on a controlled deactivation/detoxification approach for obtaining cannabinoids with improved druggability. Our design incorporates a metabolically labile ester group at strategic positions within the THC structure. We have now synthesized a series of (−)-Δ8-THC analogues encompassing a carboxyester group within the 3-alkyl chain in an effort to explore this novel cannabinergic chemotype for CB receptor binding affinity, in vitro and in vivo potency and efficacy, as well ...

  4. Probing alkali metal–π interactions with the side chain residue of tryptophan

    Hu, Jiaxin; Barbour, Leonard J.; Gokel, George W.

    2002-01-01

    Feeble forces play a significant role in the organization of proteins. These include hydrogen bonding, hydrophobic interactions, salt bridge formation, and steric interactions. The alkali metal cation-π interaction is a force of potentially profound importance but its consideration in biology has been limited by the lack of experimental evidence. Our previous studies of cation–π interactions with Na+ and K+ involved the side arms of tryptophan (indole), tyrosine (phenol),...

  5. Catabolism of Branched Chain Amino Acids Supports Respiration but Not Volatile Synthesis in Tomato Fruits

    Andrej Kochevenko; Wagner L.Araújo; Gregory S.Maloney; Denise M.Tieman; Phuc Thi Do; Mark G.Taylor; Harry J.Klee; Alisdair R.Fernie

    2012-01-01

    The branched-chain amino acid transaminases (BCATs) have a crucial role in metabolism of the branched-chain amino acids leucine,isoleucine,and valine.These enzymes catalyze the last step of synthesis and the initial step of degradation of these amino acids.Although the biosynthetic pathways of branched chain amino acids in plants have been extensively investigated and a number of genes have been characterized,their catabolism in plants is not yet completely understood.We previously characterized the branched chain amino acid transaminase gene family in tomato,revealing both the subcellular localization and kinetic properties of the enzymes encoded by six genes.Here,we examined possible functions of the enzymes during fruit development.We further characterized transgenic plants differing in the expression of branched chain amino acid transaminases 1 and 3,evaluating the rates of respiration in fruits deficient in BCAT1 and the levels of volatiles in lines overexpressing either BCAT1 or BCAT3.We quantitatively tested,via precursor and isotope feeding experiments,the importance of the branched chain amino acids and their corresponding keto acids in the formation of fruit volatiles.Our results not only demonstrate for the first time the importance of branched chain amino acids in fruit respiration,but also reveal that keto acids,rather than amino acids,are the likely precursors for the branched chain flavor volatiles.

  6. Short-chain fatty acids produced by intestinal bacteria.

    Topping, D L

    1996-03-01

    The colon is the major site of bacterial colonisation in the human gut and the resident species are predominantly anaerobes. They include potential pathogens but the greater proportion appear to be organisms which salvage energy through the metabolism of undigested carbohydrates and gut secretions. The major products of carbohydrate metabolism are the short chain fatty acids (SCFA), acetate, propionate and butyrate. In addition to general effects (such as lowering of pH) individual acids exert specific effects. All of the major SCFA appear to promote the flow of blood through the colonic vasculature while propionate enhances muscular activity and epithelial cell proliferation. Butyrate appears to promote a normal cell phenotype as well as being a major fuel for colonocytes. Important substrates for bacterial fermentation include non-starch polysaccharides (major components of dietary fibre) but it seems that starch which has escaped digestion in the small intestine (resistant starch) is the major contributor. Oligosaccharides are utilised by probiotic organisms and in the diet, act as prebiotics in promoting their numbers in faeces. High amylose starch is a form of RS and it appears to act as a prebiotic also. Although there is evidence that probiotics such as Bifidobacteria metabolise oligosaccharides and other carbohydrates, there appears to be little evidence to support a change in faecal SCFA excretion. It seems that any health benefits of probiotics are exerted through means other than SCFA. PMID:24394459

  7. Structural properties of the active layer of discotic hexabenzocoronene/perylene diimide bulk hetero junction photovoltaic devices: The role of alkyl side chain length

    We investigate thin blend films of phenyl-substituted hexa-peri-hexabenzocoronenes (HBC) with various alkyl side chain lengths ((CH2)n, n = 6, 8, 12 and 16)/perylenediimide (PDI). These blends constitute the active layers in bulk-hetero junction organic solar cells we studied recently [1]. Their structural properties are studied by both scanning electron microscopy and X-ray diffraction measurements. The results support the evidence for the formation of HBC donor-PDI acceptor complexes in all blends regardless of the side chain length of the HBC molecule. These complexes are packed into a layered structure parallel to the substrate for short side chain HBC molecules (n = 6 and 8). The layered structure is disrupted by increasing the side chain length of the HBC molecule and eventually a disordered structure is formed for long side chains (n > 12). We attribute this behavior to the size difference between the aromatic parts of the HBC and PDI molecules. For short side chains, the size difference results in a room for the side chains of the two molecules to fill in the space around the aromatic cores. For long side chains (n > 12), the empty space will not be enough to accommodate this increase, leading to the disruption of the layered structure and a rather disordered structure is formed. Our results highlight the importance of the donor-acceptor interaction in a bulk heterojunction active layer as well as the geometry of the two molecules and their role in determining the structure of the active layer and thus their photovoltaic performance.

  8. Asparagine and glutamine side-chain conformation in solution and crystal: A comparison for hen egg-white lysozyme using residual dipolar ouplings

    Experimental 15N-1H and 1H-1H residual dipolar couplings (RDCs) for the asparagine (Asn) and glutamine (Gln) side chains of hen egg-white lysozyme are measured and analysed in conjunction with 1N relaxation data, information about χ1 torsion angles in solution and molecular dynamics simulations. The RDCs are compared to values predicted from 16 high-resolution crystal structures. Two distinct groups of Asn and Gln side chains are identified. The first contains residues whose side chains show a fixed, relatively rigid, conformation in solution. For these residues there is good agreement between the experimental and predicted RDCs. This agreement improves when the experimental order parameter, S, is included in the calculation of the RDCs from the crystal structures. The comparison of the experimental RDCs with values calculated from the X-ray structures shows that the similarity between the oxygen and nitrogen electron densities is a limitation to the correct assignment of the Asn and Gln side-chain orientation in X-ray structures. In the majority of X-ray structures a 180 deg. rotation about χ2 or χ3, leading to the swapping of Nδε2 and Oδε1, is necessary for at least one Asn or Gln residue in order to achieve good agreement between experimental and predicted RDCs. The second group contains residues whose side chains do not adopt a single, well-defined, conformation in solution. These residues do not show a correlation between the experimental and predicted RDCs. In many cases the family of crystal structures shows a range of orientations for these side chains, but in others the crystal structures show a well-defined side-chain position. In the latter case, this is found to arise from crystallographic contacts and does not represent the behaviour of the side chain in solution

  9. Branched-chain amino acids and brain function.

    Fernstrom, John D

    2005-06-01

    Branched-chain amino acids (BCAAs) influence brain function by modifying large, neutral amino acid (LNAA) transport at the blood-brain barrier. Transport is shared by several LNAAs, notably the BCAAs and the aromatic amino acids (ArAAs), and is competitive. Consequently, when plasma BCAA concentrations rise, which can occur in response to food ingestion or BCAA administration, or with the onset of certain metabolic diseases (e.g., uncontrolled diabetes), brain BCAA concentrations rise, and ArAA concentrations decline. Such effects occur acutely and chronically. Such reductions in brain ArAA concentrations have functional consequences: biochemically, they reduce the synthesis and the release of neurotransmitters derived from ArAAs, notably serotonin (from tryptophan) and catecholamines (from tyrosine and phenylalanine). The functional effects of such neurochemical changes include altered hormonal function, blood pressure, and affective state. Although the BCAAs thus have biochemical and functional effects in the brain, few attempts have been made to characterize time-course or dose-response relations for such effects. And, no studies have attempted to identify levels of BCAA intake that might produce adverse effects on the brain. The only "model" of very high BCAA exposure is a very rare genetic disorder, maple syrup urine disease, a feature of which is substantial brain dysfunction but that probably cannot serve as a useful model for excessive BCAA intake by normal individuals. Given the known biochemical and functional effects of the BCAAs, it should be a straightforward exercise to design studies to assess dose-response relations for biochemical and functional effects and, in this context, to explore for adverse effect thresholds. PMID:15930466

  10. Synthesis and characterization of new biodegradable thermosensitive polyphosphazenes with lactic acid ester and methoxyethoxyethoxy side groups

    2010-01-01

    Two novel biodegradable thermosensitive polyphosphazenes with lactic acid ester and methoxyethoxyethoxy side groups were synthesized via the macromolecular substitution reactions of poly(dichlorophosphazene) with the sodium salt of lactic acid ester and sodium methoxyethoxyethoxide.Their structures were confirmed by ~(31)p NMR,~1H NMR,~(13)C NMR,IR,DSC,and elemental analysis.The lower critical solution temperature(LCST) behavior in water and in vitro degradation property of the polymers was investigated....