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

Indian Academy of Sciences (India)

Supply chain management; dynamic pricing; partner selection; supply chain planning; electronic marketplaces. Abstract. 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.

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

Science.gov (United States)

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.

Side Chain Engineering in Solution-Processable Conjugated Polymers

KAUST Repository

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.

Side Chain Engineering in Solution-Processable Conjugated Polymers

KAUST Repository

Mei, Jianguo; Bao, Zhenan

2014-01-01

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

Modelling antibody side chain conformations using heuristic database search.

Science.gov (United States)

Ritchie, D W; Kemp, G J

1997-01-01

We have developed a knowledge-based system which models the side chain conformations of residues in the variable domains of antibody Fv fragments. The system is written in Prolog and uses an object-oriented database of aligned antibody structures in conjunction with a side chain rotamer library. The antibody database provides 3-dimensional clusters of side chain conformations which can be copied en masse into the model structure. The object-oriented database architecture facilitates a navigational style of database access, necessary to assemble side chains clusters. Around 60% of the model is built using side chain clusters and this eliminates much of the combinatorial complexity associated with many other side chain placement algorithms. Construction and placement of side chain clusters is guided by a heuristic cost function based on a simple model of side chain packing interactions. Even with a simple model, we find that a large proportion of side chain conformations are modelled accurately. We expect our approach could be used with other homologous protein families, in addition to antibodies, both to improve the quality of model structures and to give a "smart start" to the side chain placement problem.

A protein-dependent side-chain rotamer library.

KAUST Repository

Bhuyan, M.S.; Gao, Xin

2011-01-01

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.

A protein-dependent side-chain rotamer library.

KAUST Repository

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.

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

International Nuclear Information System (INIS)

Anderson, Kurtis M.; Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani; Gorenstein, David G.; Iwahara, Junji

2015-01-01

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

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

DEFF Research Database (Denmark)

Pless, Stephan Alexander; Elstone, Fisal D; Niciforovic, Ana P

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......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.......4). The results show that the highly conserved aromatic side chain constituting the S2 HC makes distinct functional contributions in each of the four NaV domains. No obvious cation-pi interaction exists with nearby S4 charges in any domain, and natural and unnatural mutations at these aromatic sites produce...

SCit: web tools for protein side chain conformation analysis.

Science.gov (United States)

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.

Residue-Specific Side-Chain Polymorphisms via Particle Belief Propagation.

Science.gov (United States)

Ghoraie, Laleh Soltan; Burkowski, Forbes; Li, Shuai Cheng; Zhu, Mu

2014-01-01

Protein side chains populate diverse conformational ensembles in crystals. Despite much evidence that there is widespread conformational polymorphism in protein side chains, most of the X-ray crystallography data are modeled by single conformations in the Protein Data Bank. The ability to extract or to predict these conformational polymorphisms is of crucial importance, as it facilitates deeper understanding of protein dynamics and functionality. In this paper, we describe a computational strategy capable of predicting side-chain polymorphisms. Our approach extends a particular class of algorithms for side-chain prediction by modeling the side-chain dihedral angles more appropriately as continuous rather than discrete variables. Employing a new inferential technique known as particle belief propagation, we predict residue-specific distributions that encode information about side-chain polymorphisms. Our predicted polymorphisms are in relatively close agreement with results from a state-of-the-art approach based on X-ray crystallography data, which characterizes the conformational polymorphisms of side chains using electron density information, and has successfully discovered previously unmodeled conformations.

Exploring the impact of the side-chain length on peptide/RNA binding events.

Science.gov (United States)

Sbicca, Lola; González, Alejandro López; Gresika, Alexandra; Di Giorgio, Audrey; Closa, Jordi Teixido; Tejedor, Roger Estrada; Andréola, Marie-Line; Azoulay, Stéphane; Patino, Nadia

2017-07-19

The impact of the amino-acid side-chain length on peptide-RNA binding events has been investigated using HIV-1 Tat derived peptides as ligands and the HIV-1 TAR RNA element as an RNA model. Our studies demonstrate that increasing the length of all peptide side-chains improves unexpectedly the binding affinity (K D ) but reduces the degree of compactness of the peptide-RNA complex. Overall, the side-chain length appears to modulate in an unpredictable way the ability of the peptide to compete with the cognate TAR RNA partner. Beyond the establishment of non-intuitive fundamental relationships, our results open up new perspectives in the design of effective RNA ligand competitors, since a large number of them have already been identified but few studies report on the modulation of the biological activity by modifying in the same way the length of all chains connecting RNA recognition motives to the central scaffold of a ligand.

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

Science.gov (United States)

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.

Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides.

Science.gov (United States)

Liang, Yuxue; Neta, Pedatsur; Yang, Xiaoyu; Stein, Stephen E

2018-03-01

High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with three to six residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The abundance of losses from the side chains of other amino acids is estimated relative to that of threonine. While some amino acids lose the whole side chain, others lose only part of it, and some exhibit two or more different losses. Side-chain neutral losses are less abundant in the spectra of protonated peptides, being significant mainly for methionine and arginine. In addition to the neutral losses, many amino acid residues in deprotonated peptides produce specific negative ions after peptide bond cleavage. An expanded list of fragment ions from protonated peptides is also presented and compared with those of deprotonated peptides. Fragment ions are mostly different for these two cases. These lists of fragments are used to annotate peptide mass spectral libraries and to aid in the confirmation of specific amino acids in peptides. Graphical Abstract ᅟ.

A chemical approach for site-specific identification of NMR signals from protein side-chain NH{sub 3}{sup +} groups forming intermolecular ion pairs in protein–nucleic acid complexes

Energy Technology Data Exchange (ETDEWEB)

Anderson, Kurtis M. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States); Gorenstein, David G. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Iwahara, Junji, E-mail: 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.

Simultaneous in vivo truncation of pectic side chains

DEFF Research Database (Denmark)

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

Characterizing hydrophobicity of amino acid side chains in a protein environment via measuring contact angle of a water nanodroplet on planar peptide network.

Science.gov (United States)

Zhu, Chongqin; Gao, Yurui; Li, Hui; Meng, Sheng; Li, Lei; Francisco, Joseph S; Zeng, Xiao Cheng

2016-11-15

Hydrophobicity of macroscopic planar surface is conventionally characterized by the contact angle of water droplets. However, this engineering measurement cannot be directly extended to surfaces of proteins, due to the nanometer scale of amino acids and inherent nonplanar structures. To measure the hydrophobicity of side chains of proteins quantitatively, numerous parameters were developed to characterize behavior of hydrophobic solvation. However, consistency among these parameters is not always apparent. Herein, we demonstrate an alternative way of characterizing hydrophobicity of amino acid side chains in a protein environment by constructing a monolayer of amino acids (i.e., artificial planar peptide network) according to the primary and the β-sheet secondary structures of protein so that the conventional engineering measurement of the contact angle of a water droplet can be brought to bear. Using molecular dynamics simulations, contact angles θ of a water nanodroplet on the planar peptide network, together with excess chemical potentials of purely repulsive methane-sized Weeks-Chandler-Andersen solute, are computed. All of the 20 types of amino acids and the corresponding planar peptide networks are studied. Expectedly, all of the planar peptide networks with nonpolar amino acids are hydrophobic due to θ [Formula: see text] 90°, whereas all of the planar peptide networks of the polar and charged amino acids are hydrophilic due to θ [Formula: see text] 90°. Planar peptide networks of the charged amino acids exhibit complete-wetting behavior due to θ [Formula: see text] 0°. This computational approach for characterization of hydrophobicity can be extended to artificial planar networks of other soft matter.

Regioselectively nucleus and/or side-chain fluorinated 2-(Phenanthryl)propionic acids by an effective combination of radical and organometallic chemistry.

Science.gov (United States)

Ricci, Giacomo; Ruzziconi, Renzo

2005-01-21

Regioselectively nucleus and/or side-chain fluorinated 2-(phenanthr-1-yl)- and 2-(phenanthr-2-yl)propionic acids 1-5 were prepared using phenanthren-1(2H)-ones 6a-c as key intermediates. Thus, ethyl 2-(fluorophenanthryl)propionates 11 were obtained in good yields by Reformatsky reaction of 6a-c with ethyl 2-bromopropionate followed by dehydratation and DDQ-promoted aromatization of the resulting beta-hydroxyesters. Side-chain alkyl 2-hydroxy-2-(phenanthr-1-yl)propionates 14 were obtained by bromine/lithium permutation of dihydrophenanthryl bromides 12a-c with butyllithium followed by quenching of the lithiated intermediates with methyl pyruvate or ethyl 3,3,3-trifluoropyruvate and subsequent DDQ-promoted aromatization. The alkyl 2-hydroxy-2-(phenanthr-1-yl)propionates 25 were prepared by reacting 8-bromo-1,3-difluorophenanthrene 24 with butyllithium for 10 seconds at -110 degrees C and subsequent addition of the suitable pyruvate to the lithiated intermediates. Alkyl 2-hydroxy-2-(phenanthr-2-yl)propionates 26 and 29 were suitably obtained by site-selective metalation of 1,3-difluorophenanthrene 28 and the bromophenanthrene 24, respectively, with LDA followed by quenching of the metalated intermediates with the suitable alkyl pyruvate. Fluorination of the above alpha-hydroxypropionates with DAST, followed by the alkaline hydrolysis, allowed the expected 2-(phenanthryl)propionic acids 1-5 to be obtained in satisfactory overall yields.

SCit: web tools for protein side chain conformation analysis

OpenAIRE

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

2004-01-01

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...

Solvent Exchange Rates of Side-chain Amide Protons in Proteins

International Nuclear Information System (INIS)

Rajagopal, Ponni; Jones, Bryan E.; Klevit, Rachel E.

1998-01-01

Solvent exchange rates and temperature coefficients for Asn/Gln side-chain amide protons have been measured in Escherichia coli HPr. The protons of the eight side-chain amide groups (two Asn and six Gln) exhibit varying exchange rates which are slower than some of the fast exchanging backbone amide protons. Differences in exchange rates of the E and Z protons of the same side-chain amide group are obtained by measuring exchange rates at pH values > 8. An NOE between a side-chain amide proton and a bound water molecule was also observed

Alanine scan of the peptide antibiotic feglymycin: assessment of amino acid side chains contributing to antimicrobial activity.

Science.gov (United States)

Hänchen, Anne; Rausch, Saskia; Landmann, Benjamin; Toti, Luigi; Nusser, Antje; Süssmuth, Roderich D

2013-03-18

The antibiotic feglymycin is a linear 13-mer peptide synthesized by the bacterium Streptomyces sp. DSM 11171. It mainly consists of the nonproteinogenic amino acids 4-hydroxyphenylglycine and 3,5-dihydroxyphenylglycine. An alanine scan of feglymycin was performed by solution-phase peptide synthesis in order to assess the significance of individual amino acid side chains for biological activity. Hence, 13 peptides were synthesized from di- and tripeptide building blocks, and subsequently tested for antibacterial activity against Staphylococcus aureus strains. Furthermore we tested the inhibition of peptidoglycan biosynthesis enzymes MurA and MurC, which are inhibited by feglymycin. Whereas the antibacterial activity is significantly based on the three amino acids D-Hpg1, L-Hpg5, and L-Phe12, the inhibitory activity against MurA and MurC depends mainly on L-Asp13. The difference in the position dependence for antibacterial activity and enzyme inhibition suggests multiple molecular targets in the modes of action of feglymycin. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

DEFF Research Database (Denmark)

Headlam, Henrietta A; Davies, Michael Jonathan

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 cleav...

Incorporation of basic side chains into cryptolepine scaffold: structure-antimalarial activity relationships and mechanistic studies.

Science.gov (United States)

Lavrado, João; Cabal, Ghislain G; Prudêncio, Miguel; Mota, Maria M; Gut, Jiri; Rosenthal, Philip J; Díaz, Cecília; Guedes, Rita C; dos Santos, Daniel J V A; Bichenkova, Elena; Douglas, Kenneth T; Moreira, Rui; Paulo, Alexandra

2011-02-10

The synthesis of cryptolepine derivatives containing basic side-chains at the C-11 position and their evaluations for antiplasmodial and cytotoxicity properties are reported. Propyl, butyl, and cycloalkyl diamine side chains significantly increased activity against chloroquine-resistant Plasmodium falciparum strains while reducing cytotoxicity when compared with the parent compound. Localization studies inside parasite blood stages by fluorescence microscopy showed that these derivatives accumulate inside the nucleus, indicating that the incorporation of a basic side chain is not sufficient enough to promote selective accumulation in the acidic digestive vacuole of the parasite. Most of the compounds within this series showed the ability to bind to a double-stranded DNA duplex as well to monomeric hematin, suggesting that these are possible targets associated with the observed antimalarial activity. Overall, these novel cryptolepine analogues with substantially improved antiplasmodial activity and selectivity index provide a promising starting point for development of potent and highly selective agents against drug-resistant malaria parasites.

Effect of side chain position on solar cell performance in cyclopentadithiophene-based copolymers

International Nuclear Information System (INIS)

Lee, Sang Kyu; Seo, Jung Hwa; Cho, Nam Sung; Cho, Shinuk

2012-01-01

The photovoltaic properties of a series of low band-gap conjugated copolymers, in which alkyl side chains were substituted at various positions, were investigated using donor–acceptor (D–A) conjugated copolymers consisting of a cyclopentadithiophene derivative and dithienyl-benzothiadiazole. The base polymer, which has no alkyl side chains, yielded promising power conversion efficiency of 3.8%. Polymers with alkyl side chains, however, exhibited significantly decreased performance. In addition, the effects of processing additive became negligible. The results indicate that substituted side chains, which were introduced to improve solubility, critically affected the optical and electronic properties of D–A conjugated copolymers. Furthermore, the position of the side chain was also very important for controlling the morphological properties of the D–A conjugated copolymers. - Highlights: ► Effect of side chain position on solar cell performance was investigated. ► Polymer without alkyl chains yielded promising power conversion efficiency of 3.8%. ► Position of side chains critically affected the optical and electronic properties.

Observation of the side chain O-methylation of glutamic acid or aspartic acid containing model peptides by electrospray ionization-mass spectrometry.

Science.gov (United States)

Atik, A Emin; Guray, Melda Z; Yalcin, Talat

2017-03-15

O-methylation of the side chains of glutamic acid (E) and aspartic acid (D) residues is generally observed modification when an acidified methanol/water (MeOH/dH 2 O) mixture is used as a solvent system during sample preparation for proteomic research. This chemical modification may result misidentification with endogenous protein methylation; therefore, a special care should be taken during sample handling prior to mass spectrometric analysis. In the current study, we systematically examined the extent of E/D methylation and C-terminus carboxyl group of synthetic model peptides in terms of different incubation temperatures, storage times, and added acid types as well as its percentages. To monitor these effects, C-terminus amidated and free acid forms of synthetic model peptides comprised of E or D residue(s) have been analyzed by electrospray ionization-mass spectrometry (ESI-MS). Additionally, LC-MS/MS experiments were performed to confirm the formation of methylated peptide product. The results showed that the rate of methylation was increased as the temperature increases along with prolong incubation times. Moreover, the extent of methylation was remarkably high when formic acid (FA) used as a protonation agent instead of acetic acid (AA). In addition, it was found that the degree of methylation was significantly decreased by lowering acid percentages in ESI solution. More than one acidic residue containing model peptides have been also used to explore the extent of multiple methylation reaction. Lastly, the ethanol (EtOH) and isopropanol (iPrOH) have been substituted separately with MeOH in sample preparation step to investigate the extent of esterification reaction under the same experimental conditions. However, in the positive perspective of view, this method can be used as a simple, rapid and cheap method for methylation of acidic residues under normal laboratory conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Theoretical predictions for side-chain liquid-crystal polymers and comparison to experiment

International Nuclear Information System (INIS)

Dowell, F.

1988-01-01

This paper presents results from a new unique microscopic molecular theory for side-chain liquid-crystalline polymers (LCPs) in the nematic (N) and multiple smectic-A (SA) LC phases and the isotropic (I) liquid phase. There are no ad hoc or arbitrarily adjustable parameters in this theory. The agreement between the theoretical and experimental values for various properties (including transition temperatures and quadratic characteristic radii) is very good (relative deviations between 0% and less than 6.2%). The theoretical results also show--for the first time--that the N and I phases for these LCPs involve the packing of plate-like sections of backbones and side chains and that the local bilayer SA phase involves packing of side-chains within a plate-like section. This type of packing is predicted to be typical for side-chain LCPs. This theory can predict--for the first time--whether the side chains of a molecule pack on the same or alternating opposite sides of the backbone and whether side chains on different molecules interdigitate (overlap) with each other. 13 refs., 1 fig., 4 tabs

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

International Nuclear Information System (INIS)

Prakash, S.R.; Ellsworth, R.L.

1988-01-01

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)

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

KAUST Repository

Wang, Tonghui; Ravva, Mahesh Kumar; Bredas, Jean-Luc

2016-01-01

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

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

KAUST Repository

Wang, Tonghui

2016-06-20

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

Chain-modified radioiodinated fatty acids

International Nuclear Information System (INIS)

Otto, C.A.

1987-01-01

Several carbon chain manipulations have been studied in terms of their effects on myocardial activity levels and residence time. The manipulations examined included: chain length, chain branching, chain unsaturation, and carbon-iodine bond stabilization. It was found that chain length affects myocardial activity levels for both straight-chain alkyl acids and branched chain alkyl and aryl acids. Similar results have been reported for the straight-chain aryl acids. Generally, the longer chain lengths correlated with higher myocardial activity levels and longer residence times. This behavior is attributed to storage as triglycerides. Branched chain acids are designed to be anti-metabolites but only the aryl β-methyl acids possessed the expected time course of constant or very slowly decreasing activity levels. The alkyl β-methyl acids underwent rapid deiodination - a process apparently independent of β-oxidation. Inhibition of β-oxidation by incorporation of carbon-carbon double and triple bonds was studied. Deiodination of ω-iodo alkyl fatty acids prevented an assessment of suicide inhibition using an unsaturated alkynoic acid. Stabilization of the carbon-iodine bond by attachment of iodine to a vinylic or aryl carbon was studied. The low myocardial values and high blood values observed for an eleven carbon ω-iodo vinylic fatty acid were not encouraging but ω-iodo aryl fatty acids appear to avoid the problems of rapid deiodination. (Auth.)

Effect of alkyl side chain location and cyclicity on the aerobic biotransformation of naphthenic acids.

Science.gov (United States)

Misiti, Teresa M; Tezel, Ulas; Pavlostathis, Spyros G

2014-07-15

Aerobic biodegradation of naphthenic acids is of importance to the oil industry for the long-term management and environmental impact of process water and wastewater. The effect of structure, particularly the location of the alkyl side chain as well as cyclicity, on the aerobic biotransformation of 10 model naphthenic acids (NAs) was investigated. Using an aerobic, mixed culture, enriched with a commercial NA mixture (NA sodium salt; TCI Chemicals), batch biotransformation assays were conducted with individual model NAs, including eight 8-carbon isomers. It was shown that NAs with a quaternary carbon at the α- or β-position or a tertiary carbon at the β- and/or β'-position are recalcitrant or have limited biodegradability. In addition, branched NAs exhibited lag periods and lower degradation rates than nonbranched or simple cyclic NAs. Two NA isomers used in a closed bottle, aerobic biodegradation assay were mineralized, while 21 and 35% of the parent compound carbon was incorporated into the biomass. The NA biodegradation probability estimated by two widely used models (BIOWIN 2 and 6) and a recently developed model (OCHEM) was compared to the biodegradability of the 10 model NAs tested in this study as well as other related NAs. The biodegradation probability estimated by the OCHEM model agreed best with the experimental data and was best correlated with the measured NA biodegradation rate.

Amino Acid Functionalization of Doped Single-Walled Carbon Nanotubes: Effects of Dopants and Side Chains as Well as Zwitterionic Stabilizations.

Science.gov (United States)

Jiang, Lisha; Zhu, Chang; Fu, Yujie; Yang, Gang

2017-04-06

Functionalization of single-walled carbon nanotubes (SWCNTs) is necessitated in a number of conditions such as drug delivery, and here amino acid functionalization of SWCNTs is conducted within the framework of density functional theory. Functionalization efficiencies of Gly are largely determined by dopants, as a combined effect of atomic radius, electronic configuration, and distortion to SWCNTs. Different functionalization sites in Gly have divergent interaction strengths with M/SWCNTs that decline as O b > N > O a , and this trend seems almost independent of the identity of metallic dopants. B/SWCNT behaves distinctly and prefers to the N site. Dopants affect principally interaction strengths, while amino acids regulate significantly both functionalization configurations and interaction energies. Then focus is given to stabilization of zwitterionic amino acids due to enhanced interactions with the widely used zwitterionic drugs. All metallic dopants render zwitterionic Gly to be the most stable, and side chains in amino acids rather than dopants in M/SWCNTs cause more pronounced effects to zwitterionic stabilizations. Charge transfers between amino acids and M/SWCNTs are closely associated with zwitterionic stabilization effects, and different charge transfer mechanisms between M/SWCNTs and metal ions are interpreted. Thus, this work provides a comprehensive understanding of amino acid functionalization of M/SWCNTs.

Simulation study of the initial crystallization processes of poly(3-hexylthiophene) in solution: ordering dynamics of main chains and side chains.

Science.gov (United States)

Takizawa, Yuumi; Shimomura, Takeshi; Miura, Toshiaki

2013-05-23

We study the initial nucleation dynamics of poly(3-hexylthiophene) (P3HT) in solution, focusing on the relationship between the ordering process of main chains and that of side chains. We carried out Langevin dynamics simulation and found that the initial nucleation processes consist of three steps: the ordering of ring orientation, the ordering of main-chain vectors, and the ordering of side chains. At the start, the normal vectors of thiophene rings aligned in a very short time, followed by alignment of main-chain end-to-end vectors. The flexible side-chain ordering took almost 5 times longer than the rigid-main-chain ordering. The simulation results indicated that the ordering of side chains was induced after the formation of the regular stack structure of main chains. This slow ordering dynamics of flexible side chains is one of the factors that cause anisotropic nuclei growth, which would be closely related to the formation of nanofiber structures without external flow field. Our simulation results revealed how the combined structure of the planar and rigid-main-chain backbones and the sparse flexible side chains lead to specific ordering behaviors that are not observed in ordinary linear polymer crystallization processes.

Peptide Nucleic Acids Having Amino Acid Side Chains

DEFF Research Database (Denmark)

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...

Photoinduced electron transfer involving eosin-tryptophan conjugates. Long-lived radical pair states for systems incorporating aromatic amino acid side chains

Energy Technology Data Exchange (ETDEWEB)

Jones, G. II; Farahat, C.W.; Oh, C. (Boston Univ., MA (United States))

1994-07-14

The electron-transfer photochemistry of the covalent derivatives of the dye eosin, in which the xanthene dye is covalently attached to the amino acid L-tryptophan via the thiohydantoin derivative, the tryptophan dipeptide, and an ethyl ester derivative, has been investigated. The singlet excited state of the dye is significantly quenched on attachment of the aromatic amino acid residue. Dye triplet states are also intercepted through intramolecular interaction of excited dye and amino acid pendants. Flash photolysis experiments verify that this interaction involves electron transfer from the indole side chains of tryptophan. Rate constants for electron transfer are discussed in terms of the distance relationships for the eosin chromophore and aromatic redox sites on peptide derivatives, the pathway for [sigma]-[pi] through-bond interaction between redox sites, and the multiplicity and state of protonation for electron-transfer intermediates. Selected electron-transfer photoreactions were studied under conditions of binding of the peptide derivatives in a high molecular weight, water-soluble, globular polymer, poly(vinyl-2-pyrrolidinone). 28 refs., 4 figs., 1 tab.

Linear rheology and structure of molecular bottlebrushes with short side chains

International Nuclear Information System (INIS)

López-Barrón, Carlos R.; Brant, Patrick; Crowther, Donna J.; Eberle, Aaron P. R.

2015-01-01

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 w /M 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 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 SC ). Therefore, the glassy behavior of these polymers as well as their molecular friction and dynamic properties are influenced by their N SC values. The apparent flow activation energies are a decreasing function of N SC , and their values explain the differences in zero-shear viscosity measured at different temperatures

Liquid crystal polymers: evidence of hairpin defects in nematic main chains, comparison with side chain polymers

Science.gov (United States)

Li, M. H.; Brûlet, A.; Keller, P.; Cotton, J. P.

1996-09-01

This article describes the conformation of two species of liquid crystalline polymers as revealed by small angle neutron scattering. The results obtained with side chain polymers are recalled. The procedure used to analyze the scattering data of main chains in the nematic phase is reported in this paper. It permits a demonstration of the existence of hairpins. Comparison of both polymer species shows that in the isotropic phase, the two polymers adopt a random coil conformation. In the nematic phase, the conformations are very different; the side chains behave as a melt of penetrable random coils whereas the main chains behave as a nematic phase of non penetrable cylinders.

Side chain polysiloxanes with phthalocyanine moieties

Directory of Open Access Journals (Sweden)

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.

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

Directory of Open Access Journals (Sweden)

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.

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

KAUST Repository

Li, Huawei; Termine, Roberto; Godbert, Nicolas; Angiolini, Luigi; Giorgini, Loris; Golemme, Attilio

2011-01-01

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.

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

KAUST Repository

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.

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

KAUST Repository

Dyer-Smith, Clare; Howard, Ian A.; Cabanetos, Clement; El Labban, Abdulrahman; Beaujuge, Pierre; Laquai, Fré dé ric

2015-01-01

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

Positioning of the carboxamide side chain in 11-oxo-11H-indeno[1,2-b]quinolinecarboxamide anticancer agents: effects on cytotoxicity.

Science.gov (United States)

Deady, L W; Desneves, J; Kaye, A J; Finlay, G J; Baguley, B C; Denny, W A

2001-02-01

A series of 11-oxo-11H-indeno[1,2-b]quinolines bearing a carboxamide-linked cationic side chain at various positions on the chromophore was studied to determine structure-activity relationships between cytotoxicity and the position of the side chain. The compounds were prepared by Pfitzinger synthesis from an appropriate isatin and 1-indanone, followed by various oxidative steps, to generate the required carboxylic acids. The 4- and 6-carboxamides (with the side chain on a terminal ring, off the short axis of the chromophore) were effective cytotoxins. The dimeric 4- and 6-linked analogues were considerably more cytotoxic than the parent monomers, but had broadly similar activities. In contrast, analogues with side chains at the 8-position (on a terminal ring but off the long axis of the chromophore) or 10-position (off the short axis of the chromophore but in a central ring) were drastically less effective. The 4,10- and 6,10-biscarboxamides had activities between those of the corresponding parent monocarboxamides. The first of these showed good activity against advanced subcutaneous colon 38 tumours in mice.

Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins.

Science.gov (United States)

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

2015-03-01

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

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

DEFF Research Database (Denmark)

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...... in rich medium and growth in defined medium supplemented with 2-methylpropanoic acid lead to extensive alteration of the fatty acid composition in the cell membrane. In rich medium, a change from 51.7% to 17.1% anteiso-C15:0, and from 3.6% to 33.9% iso-C14:0 fatty acids as compared to the wild-type strain...... for 2-methylpropanoic acid production, revealing that the IlvE protein plays an important, but not essential role in the biosynthesis of branched-chain fatty acids and secondary metabolites in S. carnosus....

Structure and isotopic ratios of aliphatic side chains in the insoluble organic matter of the Murchison carbonaceous chondrite

Science.gov (United States)

Huang, Yongsong; Alexandre, Marcelo R.; Wang, Yi

2007-07-01

We report in this paper the first molecular and isotopic characterization of individual aliphatic side chains from the insoluble organic matter (IOM) in the Murchison carbonaceous chondrite using a novel combined approach of RuO 4 oxidation and solid phase microextraction (SPME). The aliphatic side chains in the IOM of Murchison were first released by oxidizing aromatic structures using RuO 4. Because the IOM of carbonaceous chondrites contains predominantly short (C 1 to C 9) aliphatic substitutions, the resulting low molecular weight monocarboxylic acids (MCAs) are highly volatile and water-soluble. The conventional aqueous extraction and derivatization procedures following RuO 4 oxidation are unable to recover MCAs for subsequent analyses. We overcame this problem by employing SPME to directly capture the MCAs from the aqueous solution. We selected a SPME fiber with greater affinity for longer chain monoacids to compensate for the exponential decline of monoacid concentrations with increasing carbon numbers in meteorite IOM, allowing more accurate identification and quantification for the less abundant monoacids. We also determined the carbon and hydrogen isotopic ratios of individual MCAs derived from Murchinson IOM. Our results reveal significant similarity in both molecular structures and hydrogen isotopic ratios between the IOM aliphatic side chains and water-soluble MCAs in Murchison, suggesting that these compounds had common precursors. Our combined new approach of RuO 4 oxidation-SPME provides a new way to probe the molecular and isotopic characteristics of aliphatic side chains in carbonaceous chondrites.

The Role of the Side Chain on the Performance of N-type Conjugated Polymers in Aqueous Electrolytes

KAUST Repository

Giovannitti, Alexander

2018-04-24

We report a design strategy that allows the preparation of solution processable n-type materials from low boiling point solvents for organic electrochemical transistors (OECTs). The polymer backbone is based on NDI-T2 copolymers where a branched alkyl side chain is gradually exchanged for a linear ethylene glycol-based side chain. A series of random copolymers was prepared with glycol side chain percentages of 0, 10, 25, 50, 75, 90, and 100 with respect to the alkyl side chains. These were characterized to study the influence of the polar side chains on interaction with aqueous electrolytes, their electrochemical redox reactions, and performance in OECTs when operated in aqueous electrolytes. We observed that glycol side chain percentages of >50% are required to achieve volumetric charging, while lower glycol chain percentages show a mixed operation with high required voltages to allow for bulk charging of the organic semiconductor. A strong dependence of the electron mobility on the fraction of glycol chains was found for copolymers based on NDI-T2, with a significant drop as alkyl side chains are replaced by glycol side chains.

The Role of the Side Chain on the Performance of N-type Conjugated Polymers in Aqueous Electrolytes

KAUST Repository

Giovannitti, Alexander; Maria, Iuliana P.; Hanifi, David; Donahue, Mary J.; Bryant, Daniel; Barth, Katrina J.; Makdah, Beatrice E.; Savva, Achilleas; Moia, Davide; Zetek, Matyá š; Barnes, Piers R.F.; Reid, Obadiah G.; Inal, Sahika; Rumbles, Garry; Malliaras, George G.; Nelson, Jenny; Rivnay, Jonathan; McCulloch, Iain

2018-01-01

We report a design strategy that allows the preparation of solution processable n-type materials from low boiling point solvents for organic electrochemical transistors (OECTs). The polymer backbone is based on NDI-T2 copolymers where a branched alkyl side chain is gradually exchanged for a linear ethylene glycol-based side chain. A series of random copolymers was prepared with glycol side chain percentages of 0, 10, 25, 50, 75, 90, and 100 with respect to the alkyl side chains. These were characterized to study the influence of the polar side chains on interaction with aqueous electrolytes, their electrochemical redox reactions, and performance in OECTs when operated in aqueous electrolytes. We observed that glycol side chain percentages of >50% are required to achieve volumetric charging, while lower glycol chain percentages show a mixed operation with high required voltages to allow for bulk charging of the organic semiconductor. A strong dependence of the electron mobility on the fraction of glycol chains was found for copolymers based on NDI-T2, with a significant drop as alkyl side chains are replaced by glycol side chains.

A possibility for generation of two species of charge carriers along main-chain and side-chains for a π-conjugated polymer

International Nuclear Information System (INIS)

Kudo, Yuki; Kawabata, Kohsuke; Goto, Hiromasa

2013-01-01

Iodide doping produces charge carriers in π-conjugated polymers. Solitons can be generated in the case of polyacetylene, and polarons in the case of aromatic-type conjugated polymers. We synthesized a conjugated main-chain/side-chain polymer, which consists of polyene in the main-chain and aromatic-type conjugated units in the side-chains. Based on the SSH (Su, Schrieffer, Heeger) theoretical model of solitons in one-dimensional conjugated polymers, we experimentally carried out chemical doping to the main-chain/side-chains conjugated polymer. Generation of the charge carriers was examined by electron spin resonance spectroscopy. This study may lead to realization of a dual doping system of solitons and polarons in π-conjugation expanded to two-dimensional directions in polymers.

An in-situ FTIR study of the side-chain alkylation of toluene with methanol

International Nuclear Information System (INIS)

King, S.T.; Garces, J.

1985-01-01

The side-chain alkylation of toluene with methanol to styrene and ethylbenzene can be an economically attractive industrial process if it has high enough conversion and selectivity. This process has been investigated by many others using zeolites or metal oxides as the catalyst. It has been generally accepted that high basicity in certain size pores in the catalyst is required for such side-chain alkylation. However, the actual reaction mechanism is still not understood. In this paper the results of an in-situ FT-IR study of the side-chain alkylation in Li, Na, K, Rb and Cs exchanged X zeolites is discussed. It was found that the KX, RbX and CsX zeolites, which are capable of side-chain alkylation, also form surface formate and a surface precursor of formate from methanol decomposition. While the surface formate itself is not the alkylation agent, the observed formate precursor may be the intermediate for side-chain alkylation

Modified melanocortin tetrapeptide Ac-His-dPhe-Arg-Trp-NH at the arginine side chain with ureas and thioureas.

Science.gov (United States)

Joseph, C G; Sorensen, N B; Wood, M S; Xiang, Z; Moore, M C; Haskell-Luevano, C

2005-11-01

The Ac-His-dPhe-Arg-Trp-NH2 tetrapeptide is a nonselective melanocortin agonist and replacement of Arg in the tetrapeptide with acidic, basic or neutral amino acids results in reduced potency at the melanocortin receptor (MCR) isoforms (MC1R and MC3-5R). To determine the importance of the positive charge and the guanidine moiety for melanocortin activity, a series of urea- and thiourea-substituted tetrapeptides were designed. Replacement of Arg with Lys or ornithine reduced agonist activity at the mouse mMC1 and mMC3-5 receptors, thus supporting the hypothesis that the guanidine moiety is important for receptor potency, particularly at the MC3-5 receptors. The Arg side chain-modified tetrapeptides examined in this study include substituted phenyl, naphthyl, and aliphatic urea and thiourea residues using a Lys side-chain template. These ligands elicit full-agonist pharmacology at the mouse MCRs examined in this study.

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

Science.gov (United States)

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

2013-10-09

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.

Synthesis and characterization of novel side-chain liquid crystalline polycarbonates, 5 - Mesophase characterization of side-chain liquid crystalline polycarbonates with tails of different lengths

NARCIS (Netherlands)

Jansen, J.C.; Addink, R.; Nijenhuis, K.T.; Mijs, W.J.

1999-01-01

The mesomorphic properties and thermal stability of side-chain LC polycarbonates with alkoxyphenyl benzoate side groups having a short spacer and alkoxy tails ranging from 1 to 8 carbon atoms were studied by DSC, X-ray diffraction and polarized light optical microscopy. All polymers have a smectic A

TROSY of side-chain amides in large proteins

Science.gov (United States)

Liu, Aizhuo; Yao, Lishan; Li, Yue; Yan, Honggao

2012-01-01

By using the mixed solvent of 50% H2O/50% D2O and employing deuterium decoupling, TROSY experiments exclusively detect NMR signals from semideuterated isotopomers of carboxamide groups with high sensitivities for proteins with molecular weights up to 80 kDa. This isotopomer-selective strategy extends TROSY experiments from exclusively detecting backbone to both backbone and side-chain amides, particularly in large proteins. Because of differences in both TROSY effect and dynamics between 15N–HE{DZ} and 15N–HZ{DE} isotopomers of the same carboxamide, the 15N transverse magnetization of the latter relaxes significantly faster than that of the former, which provides a direct and reliable stereospecific distinction between the two configurations. The TROSY effects on the 15N–HE{DZ} isotopomers of side-chain amides are as significant as on backbone amides. PMID:17347000

THE DEAD-END ELIMINATION THEOREM AND ITS USE IN PROTEIN SIDE-CHAIN POSITIONING

NARCIS (Netherlands)

DESMET, J; DEMAEYER, M; HAZES, B; LASTERS, [No Value

1992-01-01

THE prediction of a protein's tertiary structure is still a considerable problem because the huge amount of possible conformational space' makes it computationally difficult. With regard to side-chain modelling, a solution has been attempted by the grouping of side-chain conformations into

Highly conductive side chain block copolymer anion exchange membranes.

Science.gov (United States)

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.

Bis(thienothiophenyl) diketopyrrolopyrrole-based conjugated polymers with various branched alkyl side chains and their applications in thin-film transistors and polymer solar cells.

Science.gov (United States)

Shin, Jicheol; Park, Gi Eun; Lee, Dae Hee; Um, Hyun Ah; Lee, Tae Wan; Cho, Min Ju; Choi, Dong Hoon

2015-02-11

New thienothiophene-flanked diketopyrrolopyrrole and thiophene-containing π-extended conjugated polymers with various branched alkyl side-chains were successfully synthesized. 2-Octyldodecyl, 2-decyltetradecyl, 2-tetradecylhexadecyl, 2-hexadecyloctadecyl, and 2-octadecyldocosyl groups were selected as the side-chain moieties and were anchored to the N-positions of the thienothiophene-flanked diketopyrrolopyrrole unit. All five polymers were found to be soluble owing to the bulkiness of the side chains. The thin-film transistor based on the 2-tetradecylhexadecyl-substituted polymer showed the highest hole mobility of 1.92 cm2 V(-1) s(-1) due to it having the smallest π-π stacking distance between the polymer chains, which was determined by grazing incidence X-ray diffraction. Bulk heterojunction polymer solar cells incorporating [6,6]-phenyl-C71-butyric acid methyl ester as the n-type molecule and the additive 1,8-diiodooctane (1 vol %) were also constructed from the synthesized polymers without thermal annealing; the device containing the 2-octyldodecyl-substituted polymer exhibited the highest power conversion efficiency of 5.8%. Although all the polymers showed similar physical properties, their device performance was clearly influenced by the sizes of the branched alkyl side-chain groups.

Synthesis of porphyryl boronates with (un)saturated side-chains

OpenAIRE

SENGE, MATHIAS; SERGEEVA, NATALIA

2008-01-01

PUBLISHED Porphyrins with (un)saturated side?chains containing boron residues were developed as synthons for porphyrin functionalization. Porphyrins with mono and bis-substituted unsaturated boronyl residues were prepared in good yields (52?66 %) using a cross?metathesis approach in the presence of Grubbs I-generation catalysts. In all cases complete E?stereoselectivity (100 %) was observed. Furthermore, formal cross?metathesis products with ?,??unsaturated chains smoothly underwent additi...

Synthesis and characterization of novel side-chain liquid crystalline polycarbonates, 4 - Synthesis of side-chain liquid crystalline polycarbonates with mesogenic groups having tails of different lengths

NARCIS (Netherlands)

Jansen, J.C.; Addink, R.; Nijenhuis, K.T.; Mijs, W.J.

1999-01-01

Side-chain liquid crystalline polycarbonates with alkoxyphenylbenzoate side groups, having a short spacer and tails ranging from 1 to 8 C-atoms, were synthesized. The polymers were prepared by an organo-zinc catalysed copolymerization of carbon dioxide and mesogenic 4-alkoxyphenyl

Photoinduced Circular Anisotropy in Side-Chain Azobenzene Polyesters

DEFF Research Database (Denmark)

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...

Exploring backbone-cation alkyl spacers for multi-cation side chain anion exchange membranes

Science.gov (United States)

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

2018-01-01

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

Prediction of methyl-side Chain Dynamics in Proteins

International Nuclear Information System (INIS)

Ming Dengming; Brueschweiler, Rafael

2004-01-01

A simple analytical model is presented for the prediction of methyl-side chain dynamics in comparison with S 2 order parameters obtained by NMR relaxation spectroscopy. The model, which is an extension of the local contact model for backbone order parameter prediction, uses a static 3D protein structure as input. It expresses the methyl-group S 2 order parameters as a function of local contacts of the methyl carbon with respect to the neighboring atoms in combination with the number of consecutive mobile dihedral angles between the methyl group and the protein backbone. For six out of seven proteins the prediction results are good when compared with experimentally determined methyl-group S 2 values with an average correlation coefficient r-bar=0.65±0.14. For the unusually rigid cytochrome c 2 no significant correlation between prediction and experiment is found. The presented model provides independent support for the reliability of current side-chain relaxation methods along with their interpretation by the model-free formalism

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

International Nuclear Information System (INIS)

Akaike, Kouki; Kanai, Kaname; Ouchi, Yukio; Seki, Kazuhiko

2013-01-01

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 C 60 -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-C 61 -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

Synthesis and solution self-assembly of side-chain cobaltocenium-containing block copolymers.

Science.gov (United States)

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

2010-07-07

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

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

International Nuclear Information System (INIS)

Headlam, H.A.; Davies, M.J.; Mortimer, A.; Easton, C.J.

2000-01-01

Full text: Exposure of proteins to radicals in the presence of O 2 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 O 2 , 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

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

KAUST Repository

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.

Microphase Separation within a Comb Copolymer with Attractive Side Chains : A Computer Simulation Study

NARCIS (Netherlands)

Vasilevskaya, V.V.; Klochkov, A.A.; Khalatur, P.G.; Khokhlov, A.R.; Brinke, G. ten

2001-01-01

Computer simulation modelling of a flexible comb copolymer with attractive interactions between the monomer units of the side chains is performed. The conditions for the coil-globule transition, induced by the increase of attractive interaction, ε, between side chain monomer units, are analysed for

Asymmetric Alkyl Side-Chain Engineering of Naphthalene Diimide-Based n-Type Polymers for Efficient All-Polymer Solar Cells.

Science.gov (United States)

Jia, Tao; Li, Zhenye; Ying, Lei; Jia, Jianchao; Fan, Baobing; Zhong, Wenkai; Pan, Feilong; He, Penghui; Chen, Junwu; Huang, Fei; Cao, Yong

2018-02-13

The design and synthesis of three n-type conjugated polymers based on a naphthalene diimide-thiophene skeleton are presented. The control polymer, PNDI-2HD, has two identical 2-hexyldecyl side chains, and the other polymers have different alkyl side chains; PNDI-EHDT has a 2-ethylhexyl and a 2-decyltetradecyl side chain, and PNDI-BOOD has a 2-butyloctyl and a 2-octyldodecyl side chain. These copolymers with different alkyl side chains exhibit higher melting and crystallization temperatures, and stronger aggregation in solution, than the control copolymer PNDI-2HD that has the same side chain. Polymer solar cells based on the electron-donating copolymer PTB7-Th and these novel copolymers exhibit nearly the same open-circuit voltage of 0.77 V. Devices based on the copolymer PNDI-BOOD with different side chains have a power-conversion efficiency of up to 6.89%, which is much higher than the 4.30% obtained with the symmetric PNDI-2HD. This improvement can be attributed to the improved charge-carrier mobility and the formation of favorable film morphology. These observations suggest that the molecular design strategy of incorporating different side chains can provide a new and promising approach to developing n-type conjugated polymers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol.

Science.gov (United States)

Sun, Delin; Forsman, Jan; Woodward, Clifford E

2015-04-14

Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the Wimley-White interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was ∼25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol.

A targeted metabolomic protocol for short-chain fatty acids and branched-chain amino acids

OpenAIRE

Zheng, Xiaojiao; Qiu, Yunping; Zhong, Wei; Baxter, Sarah; Su, Mingming; Li, Qiong; Xie, Guoxiang; Ore, Brandon M.; Qiao, Shanlei; Spencer, Melanie D.; Zeisel, Steven H.; Zhou, Zhanxiang; Zhao, Aihua; Jia, Wei

2013-01-01

Research in obesity and metabolic disorders that involve intestinal microbiota demands reliable methods for the precise measurement of the short-chain fatty acids (SCFAs) and branched-chain amino acids (BCAAs) concentration. Here, we report a rapid method of simultaneously determining SCFAs and BCAAs in biological samples using propyl chloroformate (PCF) derivatization followed by gas chromatography mass spectrometry (GC-MS) analysis. A one-step derivatization using 100 µL of PCF in a reactio...

Side chain effect on electronic structure of spin-coated films of [6,6]-phenyl-C{sub 61}-butyric acid methyl ester and its bis-adduct

Energy Technology Data Exchange (ETDEWEB)

Akaike, Kouki, E-mail: akaike@riken.jp [Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Kanai, Kaname [Department of Physics, Faculty of Science and Technology, Tokyo University of Science, Yamazaki 2641, Noda 278-8510 (Japan); Ouchi, Yukio; Seki, Kazuhiko [Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan)

2013-03-29

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 C{sub 60}-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-C{sub 61}-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.

Abnormal viscoelastic behavior of side-chain liquid-crystal polymers

Science.gov (United States)

Gallani, J. L.; Hilliou, L.; Martinoty, P.; Keller, P.

1994-03-01

We show that, contrary to what is commonly believed, the isotropic phase of side-chain liquid-crystal polymers has viscoelastic properties which are totally different from those of ordinary flexible melt polymers. The results can be explained by the existence of a transient network created by the dynamic association of mesogenic groups belonging to different chains. The extremely high sensitivity of the compound to the state of the surfaces with which it is in contact offers us an unexpected method of studying surface states.

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

DEFF Research Database (Denmark)

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

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...... side-chain on the DPP-unit leads to an increase in thin-film order and charge-carrier mobility if a sufficiently solubilizing, branched, side chain is attached to the BTZ. We compare two different synthetic routes, direct arylation and Suzuki-polycondensation, by a direct comparison of polymers...

Semi-crystalline photovoltaic polymers with siloxane-terminated hybrid side-chains

Institute of Scientific and Technical Information of China (English)

Yuxiang Li; Seyeong Song; Song Yi Park; Jin Young Kim; Han Young Woo

2017-01-01

Three types of semi-cry stalline photovoltaic polymers were synthesized by incorporating a siloxane-terminated organic/inorganic hybrid side-chain and changing the number of fluorine substituents.A branch point away from a polymer main backbone in the siloxane-containing side-chains and the intra-and/or interchain noncovalent coulombic interactions enhance a chain planarity and facile interchain organization.The resulting polymers formed strongly agglomerated films with high roughness,suggesting strong intermolecular interactions.The optical band gap of ca.1.7 eV was measured for all polymers with a pronounced shoulder peak due to tight π-π stacking.With increasing the fluorine substituents,the frontier energy levels decreased and preferential face-on orientation was observed.The siloxane-terminated side-chains and fluorine substitution promoted the intermolecular packing,showing well resolved lamellar scatterings up to（300） for this series of polymers in the grazing incidence wide angle X-ray scattering measurements.The PPsiDTBT,PPsiDTFBT and PPsiDT2 FBT devices showed a power conversion efficiency of 3.16%,4.40%and 5.65%,respectively,by blending with PC71BM.Langevin-type bimolecular charge recombination was similar for three polymeric solar cells.The main loss in the photocurrent generation for PPsiDTBT:PC71BM was interpreted to originate from the trap assisted charge recombination by measuring light-intensity dependent short-circuit current density(JSC) and open-circuit voltage(VOc).Our results provide a new insight into the rational selection of solubilizing substituents for optimizing crystalline interchain packing with appropriate miscibility with PC71 BM for further optimizing polymer solar cells.

Semi-crystalline photovoltaic polymers with siloxane-terminated hybrid side-chains

Institute of Scientific and Technical Information of China (English)

Yuxiang Li; Seyeong Song; Song Yi Park; Jin Young Kim; Han Young Woo

2017-01-01

Three types of semi-crystalline photovoltaic polymers were synthesized by incorporating a siloxane-terminated organic/inorganic hybrid side-chain and changing the number of fluorine substituents.A branch point away from a polymer main backbone in the siloxane-containing side-chains and the intra-and/or interchain noncovalent coulombic interactions enhance a chain planarity and facile interchain organization.The resulting polymers formed strongly agglomerated films with high roughness,suggesting strong intermolecular interactions.The optical band gap of ca.1.7 eV was measured for all polymers with a pronounced shoulder peak due to tight π-π stacking.With increasing the fluorine substituents,the frontier energy levels decreased and preferential face-on orientation was observed.The siloxane-terminated side-chains and fluorine substitution promoted the intermolecular packing,showing well resolved lamellar scatterings up to (300) for this series of polymers in the grazing incidence wide angle X-ray scattering measurements.The PPsiDTBT,PPsiDTFBT and PPsiDT2FBT devices showed a power conversion efficiency of 3.16％,4.40％ and 5.65％,respectively,by blending with PC71BM.Langevin-type bimolecular charge recombination was similar for three polymeric solar cells.The main loss in the photocurrent generation for PPsiDTBT:PC71BM was interpreted to originate from the trap assisted charge recombination by measuring light-intensity dependent short-circuit current density (Jsc) and open-circuit voltage (Voc).Our results provide a new insight into the rational selection of solubilizing substituents for optimizing crystalline interchain packing with appropriate miscibility with PC71BM for further optimizing polymer solar cells.

White emission from liquid-crystalline copolymers containing oxadiazole moieties in the side chain

Science.gov (United States)

Kawamoto, Masuki; Tsukamoto, Takuji; Kinoshita, Motoi; Ikeda, Tomiki

2006-09-01

A liquid-crystalline polymer in the side chain was synthesized through copolymerization of a bipolar carrier-transporting monomer with a liquid-crystalline monomer containing oxadiazole moieties substituted with trifluoromethyl groups. A single-layer light-emitting diode of indium tin oxide (ITO)/copolymer/MgAg emitted white light with a maximum luminous efficiency of 0.1cd/A. The origin of the white emission in the copolymer is the electroplex between bipolar carrier-transporting moieties and strong electron-withdrawing moieties. Furthermore, a simple multilayer device with configuration of ITO/poly(3,4-ethylenedioxythiophene)/poly(styrenesulfonic acid)/copolymer/MgAg device showed white emission with CIE 1931 chromaticity coordinates (x,y): (0.30, 0.33).

Medium-chain fatty acid binding to albumin and transfer to phospholipid bilayers

International Nuclear Information System (INIS)

Hamilton, J.A.

1989-01-01

Temperature-dependent (5-42 degree C) 13 C NMR spectra of albumin complexes with 90% isotopically substituted [1- 13 C]octanoic or [1- 13 C]decanoic acids showed a single peak at >30 degree C but three peaks at lower temperatures. The chemical-shift differences result from different ionic and/or hydrogen-bonding interactions between amino acid side chains and the fatty acid carboxyl carbon. Rapid exchange of fatty acid among binding sites obscures these sites at temperatures >30 degree C. Rate constants for exchange at 33 degree C were 350 sec -1 for octanoate and 20 sec -1 for decanoate. Temperature-dependent data for octanoate showed an activation energy of 2 kcal/mol for exchange. Spectra of albumin complexes with the 12-carbon saturated fatty acid, lauric acid, had several narrow laurate carboxyl peaks at 35 degree C, indicating longer lifetimes in the different binding sites. Fatty acid exchange between albumin and model membranes (phosphatidylcholine bilayers) occurred on a time scale comparable to that for exchange among albumin binding sites, following the order octanoate > decanoate > laurate. The equilibrium distribution of fatty acid between lipid bilayers and protein was measured directly from NMR spectra. Decreasing pH increased the relative affinity of fatty acid for the lipid bilayer. The results predict that the relative affinity of octanoic acid for albumin and membranes will be similar to that of long-chain fatty acids, but the rate of equilibration will be ∼ 10 4 faster for octanoic acid

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

International Nuclear Information System (INIS)

Heinze, D.; Mang, Th.; Popescu, C.; Weichold, O.

2016-01-01

Highlights: • Thermal behaviour of telomerized polyvinyl esters is investigated. • Thermal stability relies mainly on the contribution of side chains. • At equal molecular weights thermal stability is dictated by length of side chain. • Increasing the length of side chains improves also the packing degree of polymer. - Abstract: Four members of a homologous series of chlorinated poly(vinyl ester) oligomers CCl_3–(CH_2CH (OCO(CH_2)_mCH_3))_n–Cl with degrees of polymerization of 10 and 20 were prepared by telomerisation using carbon tetrachloride. The number of side chain carbon atoms ranges from 2 (poly(vinyl acetate) to 18 (poly(vinyl stearate)). The effect of the n-alkyl side chain length and of the degree of polymerization on the thermal stability and crystallization behaviour of the synthesized compounds was investigated. All oligomers degrade in two major steps by first losing HCl and side chains with subsequent breakdown of the backbone. The members with short side chains, up to poly(vinyl octanoate), are amorphous and show internal plasticization, whereas those with high number of side chain carbon atoms are semi-crystalline due to side-chain crystallization. A better packing for poly(vinyl stearate) is also noticeable. The glass transition and melting temperatures as well as the onset temperature of decomposition are influenced to a larger extent by the side chain length than by the degree of polymerization. Thermal stability is improved if both the size and number of side chains increase, but only a long side chain causes a significant increase of the resistance to degradation. This results in a stabilization of PVAc so that oligomers from poly(vinyl octanoate) on are stable under atmospheric conditions. Thus, the way to design stable, chlorinated PVEs oligomers is to use a long n-alkyl side chain.

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-08-10

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

The power of hard-sphere models: explaining side-chain dihedral angle distributions of Thr and Val.

Science.gov (United States)

Zhou, Alice Qinhua; O'Hern, Corey S; Regan, Lynne

2012-05-16

The energy functions used to predict protein structures typically include both molecular-mechanics and knowledge-based terms. In contrast, our approach is to develop robust physics- and geometry-based methods. Here, we investigate to what extent simple hard-sphere models can be used to predict side-chain conformations. The distributions of the side-chain dihedral angle χ(1) of Val and Thr in proteins of known structure show distinctive features: Val side chains predominantly adopt χ(1) = 180°, whereas Thr side chains typically adopt χ(1) = 60° and 300° (i.e., χ(1) = ±60° or g- and g(+) configurations). Several hypotheses have been proposed to explain these differences, including interresidue steric clashes and hydrogen-bonding interactions. In contrast, we show that the observed side-chain dihedral angle distributions for both Val and Thr can be explained using only local steric interactions in a dipeptide mimetic. Our results emphasize the power of simple physical approaches and their importance for future advances in protein engineering and design. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

Energy Technology Data Exchange (ETDEWEB)

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.

Branched-chain amino acids for hepatic encephalopathy

DEFF Research Database (Denmark)

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....

Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

Science.gov (United States)

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

2017-10-01

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

Nanophase separation in side chain polymers: new evidence from structure and dynamics

International Nuclear Information System (INIS)

Hiller, S; Pascui, O; Budde, H; Kabisch, O; Reichert, D; Beiner, M

2004-01-01

New evidence for a nanophase separation of incompatible main and side chain parts in amorphous poly(n-alkyl methacrylates) with long alkyl groups are presented. Independent indications for the existence of alkyl nanodomains with a typical dimension in the 1 nm range from studies on dynamics and structure are reported. Results from nuclear magnetic resonance (NMR) experiments are compared with data from different relaxation spectroscopy methods on poly(n-decyl methacrylate). The NMR results in combination with relaxation spectroscopy data support the existence of an independent polyethylene-like glass transition, α PE , within the alkyl nanodomains in addition to the conventional glass transition a at higher temperatures. X-ray scattering data show that the situation in homopolymers is similar to that for random poly(n-alkyl methacrylate) copolymers with the same average length of the alkyl group in the side chains. Scattering data for a series of n-butyl methacrylate samples with polymerization degrees reaching from P=1 to 405 indicate that nanophase separation is chain-length independent above P=25, while the nanophase separation tends to disappear below P=6. Insensitivity of structural aspects in nanophase-separated poly(n-alkyl methacrylates) to changes in the molecular microstructure and consistency of NMR results with independent conclusions from relaxation spectroscopy underline the general importance of nanophase separation effects in a broad class of side chain polymers

Topological side-chain classification of beta-turns: ideal motifs for peptidomimetic development.

Science.gov (United States)

Tran, Tran Trung; McKie, Jim; Meutermans, Wim D F; Bourne, Gregory T; Andrews, Peter R; Smythe, Mark L

2005-08-01

Beta-turns are important topological motifs for biological recognition of proteins and peptides. Organic molecules that sample the side chain positions of beta-turns have shown broad binding capacity to multiple different receptors, for example benzodiazepines. Beta-turns have traditionally been classified into various types based on the backbone dihedral angles (phi2, psi2, phi3 and psi3). Indeed, 57-68% of beta-turns are currently classified into 8 different backbone families (Type I, Type II, Type I', Type II', Type VIII, Type VIa1, Type VIa2 and Type VIb and Type IV which represents unclassified beta-turns). Although this classification of beta-turns has been useful, the resulting beta-turn types are not ideal for the design of beta-turn mimetics as they do not reflect topological features of the recognition elements, the side chains. To overcome this, we have extracted beta-turns from a data set of non-homologous and high-resolution protein crystal structures. The side chain positions, as defined by C(alpha)-C(beta) vectors, of these turns have been clustered using the kth nearest neighbor clustering and filtered nearest centroid sorting algorithms. Nine clusters were obtained that cluster 90% of the data, and the average intra-cluster RMSD of the four C(alpha)-C(beta) vectors is 0.36. The nine clusters therefore represent the topology of the side chain scaffold architecture of the vast majority of beta-turns. The mean structures of the nine clusters are useful for the development of beta-turn mimetics and as biological descriptors for focusing combinatorial chemistry towards biologically relevant topological space.

Can understanding the packing of side chains improve the design of protein-protein interactions?

Science.gov (United States)

Zhou, Alice; O'Hern, Corey; Regan, Lynne

2011-03-01

With the long-term goal to improve the design of protein-protein interactions, we have begun extensive computational studies to understand how side-chains of key residues of binding partners geometrically fit together at protein-peptide interfaces, e.g. the tetratrico-peptide repeat protein and its cognate peptide). We describe simple atomic-scale models of hydrophobic dipeptides, which include hard-core repulsion, bond length and angle constraints, and Van der Waals attraction. By completely enumerating all minimal energy structures in these systems, we are able to reproduce important features of the probability distributions of side chain dihedral angles of hydrophic residues in the protein data bank. These results are the crucial first step in developing computational models that can predict the side chain conformations of residues at protein-peptide interfaces. CSO acknowledges support from NSF grant no. CMMT-1006527.

A Solid-State Deuterium NMR and SFG Study of the Side Chain Dynamics of Peptides Adsorbed onto Surfaces

Science.gov (United States)

Breen, Nicholas F.; Weidner, Tobias; Li, Kun; Castner, David G.; Drobny, Gary P.

2011-01-01

The artificial amphiphilic peptide LKα14 adopts a helical structure at interfaces, with opposite orientation of its leucine (L, hydrophobic) and lysine (K, hydrophilic) side chains. When adsorbed onto surfaces, different residue side chains necessarily have different proximities to the surface, depending on both their position in the helix and the composition of the surface itself. Deuterating the individual leucine residues (isopropyl-d7) permits the use of solid-state deuterium NMR as a site-specific probe of side chain dynamics. In conjunction with SFG as a probe of the peptide binding face, we demonstrate that the mobility of specific leucine side chains at the interface is quantifiable in terms of their surface proximity. PMID:19764755

Cylindrical polymer brushes with dendritic side chains by iterative anionic reactions

KAUST Repository

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.

Peramivir analogues bearing hydrophilic side chains exhibit higher activities against H275Y mutant than wild-type influenza virus.

Science.gov (United States)

Chiu, Din-Chi; Lin, Tzu-Chen; Huang, Wen-I; Cheng, Ting-Jen; Tsai, Keng-Chang; Fang, Jim-Min

2017-11-29

Peramivir is an effective anti-influenza drug in the clinical treatment of influenza, but its efficacy toward the H275Y mutant is reduced. The previously reported cocrystal structures of inhibitors in the mutant neuraminidase (NA) suggest that the hydrophobic side chain should be at the origin of reduced binding affinity. In contrast, zanamivir having a hydrophilic glycerol side chain still possesses high affinity toward the H275Y NA. We thus designed five peramivir analogues (5-9) carrying hydrophilic glycol or glycerol side chains, and evaluated their roles in anti-influenza activity, especially for the H275Y mutant. The synthetic sequence involves a key step of (3 + 2) cycloaddition reactions between alkenes and nitrile oxides to construct the scaffold of peramivir carrying the desired hydrophilic side chains and other appropriate functional groups. The molecular docking experiments reveal that the hydrophilic side chain can provide extra hydrogen bonding with the translocated Glu-276 residue in the H275Y NA active site. Thus, the H275Y mutant may be even more sensitive than wild-type virus toward the peramivir analogues bearing hydrophilic side chains. Notably, the peramivir analogue bearing a glycerol side chain inhibits the H275Y mutant with an IC 50 value of 35 nM, which is better than the WSN virus by 9 fold.

Cylindrical polymer brushes with dendritic side chains by iterative anionic reactions

KAUST Repository

Zhang, Hefeng; Qu, Chengke; He, Junpo

2015-01-01

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

UV resonance Raman finds peptide bond-Arg side chain electronic interactions.

Science.gov (United States)

Sharma, Bhavya; Asher, Sanford A

2011-05-12

We measured the UV resonance Raman excitation profiles and Raman depolarization ratios of the arginine (Arg) vibrations of the amino acid monomer as well as Arg in the 21-residue predominantly alanine peptide AAAAA(AAARA)(3)A (AP) between 194 and 218 nm. Excitation within the π → π* peptide bond electronic transitions result in UVRR spectra dominated by amide peptide bond vibrations. The Raman cross sections and excitation profiles indicate that the Arg side chain electronic transitions mix with the AP peptide bond electronic transitions. The Arg Raman bands in AP exhibit Raman excitation profiles similar to those of the amide bands in AP which are conformation specific. These Arg excitation profiles distinctly differ from the Arg monomer. The Raman depolarization ratios of Arg in monomeric solution are quite simple with ρ = 0.33 indicating enhancement by a single electronic transition. In contrast, we see very complex depolarization ratios of Arg in AP that indicate that the Arg residues are resonance enhanced by multiple electronic transitions.

The Influence of Side-Chain Position on the Optoelectronic Properties of a Red-Emitting Conjugated Polymer

NARCIS (Netherlands)

Lu, Li Ping; Finlayson, Chris E.; Kabra, Dinesh; Albert-Seifried, Sebastian; Song, Myoung Hoon; Havenith, Remco W. A.; Tu, Guoli; Huck, Wilhelm T. S.; Friend, Richard H.

2013-01-01

A study of the organic semiconductor F8TBT is presented, directly comparing a conventional form (F8TBT-out) with a form with varied alkyl side-chain position (F8TBT-in), in terms of optical properties and device performance in light-emitting-diodes (LEDs). Computational simulations of the side-chain

Synthesis and antimalarial activity of new chloroquine analogues carrying a multifunctional linear side chain

OpenAIRE

Iwaniuk, Daniel P.; Whetmore, Eric D.; Rosa, Nicholas; Ekoue-Kovi, Kekeli; Alumasa, John; de Dios, Angel C.; Roepe, Paul D.; Wolf, Christian

2009-01-01

We report the synthesis and in vitro antimalarial activity of several new 4-amino-and 4-alkoxy-7-chloroquinolines carrying a linear dibasic side chain. Many of these chloroquine analogues have submicromolar antimalarial activity versus HB3 (chloroquine sensitive) and Dd2 (chloroquine resistant strain of P. falciparum) and low resistance indices were obtained in most cases. Importantly, compounds 11–15 and 24 proved to be more potent against Dd2 than chloroquine. Branching of the side chain st...

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

KAUST Repository

Giovannitti, Alexander

2016-10-11

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

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

Science.gov (United States)

Giovannitti, Alexander; Sbircea, Dan-Tiberiu; Inal, Sahika; Nielsen, Christian B.; Bandiello, Enrico; Hanifi, David A.; Sessolo, Michele; Malliaras, George G.; McCulloch, Iain; Rivnay, Jonathan

2016-01-01

Electrolyte-gated organic transistors offer low bias operation facilitated by direct contact of the transistor channel with an electrolyte. Their operation mode is generally defined by the dimensionality of charge transport, where a field-effect transistor allows for electrostatic charge accumulation at the electrolyte/semiconductor interface, whereas an organic electrochemical transistor (OECT) facilitates penetration of ions into the bulk of the channel, considered a slow process, leading to volumetric doping and electronic transport. Conducting polymer OECTs allow for fast switching and high currents through incorporation of excess, hygroscopic ionic phases, but operate in depletion mode. Here, we show that the use of glycolated side chains on a thiophene backbone can result in accumulation mode OECTs with high currents, transconductance, and sharp subthreshold switching, while maintaining fast switching speeds. Compared with alkylated analogs of the same backbone, the triethylene glycol side chains shift the mode of operation of aqueous electrolyte-gated transistors from interfacial to bulk doping/transport and show complete and reversible electrochromism and high volumetric capacitance at low operating biases. We propose that the glycol side chains facilitate hydration and ion penetration, without compromising electronic mobility, and suggest that this synthetic approach can be used to guide the design of organic mixed conductors. PMID:27790983

Boosting the ambipolar performance of solution-processable polymer semiconductors via hybrid side-chain engineering.

Science.gov (United States)

Lee, Junghoon; Han, A-Reum; Yu, Hojeong; Shin, Tae Joo; Yang, Changduk; Oh, Joon Hak

2013-06-26

Ambipolar polymer semiconductors are highly suited for use in flexible, printable, and large-area electronics as they exhibit both n-type (electron-transporting) and p-type (hole-transporting) operations within a single layer. This allows for cost-effective fabrication of complementary circuits with high noise immunity and operational stability. Currently, the performance of ambipolar polymer semiconductors lags behind that of their unipolar counterparts. Here, we report on the side-chain engineering of conjugated, alternating electron donor-acceptor (D-A) polymers using diketopyrrolopyrrole-selenophene copolymers with hybrid siloxane-solubilizing groups (PTDPPSe-Si) to enhance ambipolar performance. The alkyl spacer length of the hybrid side chains was systematically tuned to boost ambipolar performance. The optimized three-dimensional (3-D) charge transport of PTDPPSe-Si with pentyl spacers yielded unprecedentedly high hole and electron mobilities of 8.84 and 4.34 cm(2) V(-1) s(-1), respectively. These results provide guidelines for the molecular design of semiconducting polymers with hybrid side chains.

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

DEFF Research Database (Denmark)

Hvilsted, Søren; Pedersen, M; Holme, NCR

1998-01-01

A flexible azobenzene side-chain liquid crystalline (SCLC) polyester architecture employed for reversible optical storage is described. The modular design allows four structural parameters to be individually modified. These parameters: i- the methylene side-chain spacer length, ii- the substituent......,000 are routinely obtained by melt transesterification of the novel diols and selected diacid precursors (parameter iii). Prominent storage features include no prealignment of thin SCLC polyester films prior to the writing process, and sensitivity in a broad laser wavelength window (415-532 nm). Additionally...... sign of fatigue. The non-destructive read out is performed with red light (600-750 nm). Finally, erasing the information can be achieved by heating the polyester film to 80 degrees C or irradiating it briefly with UV-light. In the latter case at least 10,000 write, read and erase cycles are possible...

Improved zeolite regeneration processes for preparing saturated branched-chain fatty acids

Science.gov (United States)

Ferrierite zeolite solid is an excellent catalyst for the skeletal isomerization of unsaturated linear-chain fatty acids (i.e., oleic acid) to unsaturated branched-chain fatty acids (i.e., iso-oleic acid) follow by hydrogenation to give saturated branched-chain fatty acids (i.e., isostearic acid). ...

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

DEFF Research Database (Denmark)

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

2003-01-01

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

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

Directory of Open Access Journals (Sweden)

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.

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

DEFF Research Database (Denmark)

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

2009-01-01

the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from N-15 backbone relaxation measurements. Compared to measurements of backbone nuclei, C-13(epsilon 1) dispersion provides a more direct method to monitor interchanging protonation states...... or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the C-13(epsilon 1) dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains...

Liquid-crystalline side chain block copolymers - synthesis, morphology and LC behavior

NARCIS (Netherlands)

Arnold, M.; Poser, S.; Fischer, H.R.; Frank, W.; Utschick, H.

1994-01-01

Side-chain liq.-cryst. 2-hydroxyethyl methacrylate-styrene diblock copolymer (I) was prepd. by polymn. of 2-(trimethylsiloxy)ethyl methacrylate with styrene with further treatment with cholesteryl chloroformate. Morphol. and phase behavior of I were investigated. [on SciFinder (R)

Direct observation of backbone planarization via side-chain alignment in single bulky-substituted polythiophenes

Science.gov (United States)

Raithel, Dominic; Simine, Lena; Pickel, Sebastian; Schötz, Konstantin; Panzer, Fabian; Baderschneider, Sebastian; Schiefer, Daniel; Lohwasser, Ruth; Köhler, Jürgen; Thelakkat, Mukundan; Sommer, Michael; Köhler, Anna; Rossky, Peter J.; Hildner, Richard

2018-03-01

The backbone conformation of conjugated polymers affects, to a large extent, their optical and electronic properties. The usually flexible substituents provide solubility and influence the packing behavior of conjugated polymers in films or in bad solvents. However, the role of the side chains in determining and potentially controlling the backbone conformation, and thus the optical and electronic properties on the single polymer level, is currently under debate. Here, we investigate directly the impact of the side chains by studying the bulky-substituted poly(3-(2,5-dioctylphenyl)thiophene) (PDOPT) and the common poly(3-hexylthiophene) (P3HT), both with a defined molecular weight and high regioregularity, using low-temperature single-chain photoluminescence (PL) spectroscopy and quantum-classical simulations. Surprisingly, the optical transition energy of PDOPT is significantly (˜2,000 cm‑1 or 0.25 eV) red-shifted relative to P3HT despite a higher static and dynamic disorder in the former. We ascribe this red shift to a side-chain induced backbone planarization in PDOPT, supported by temperature-dependent ensemble PL spectroscopy. Our atomistic simulations reveal that the bulkier 2,5-dioctylphenyl side chains of PDOPT adopt a clear secondary helical structural motif and thus protect conjugation, i.e., enforce backbone planarity, whereas, for P3HT, this is not the case. These different degrees of planarity in both thiophenes do not result in different conjugation lengths, which we found to be similar. It is rather the stronger electronic coupling between the repeating units in the more planar PDOPT which gives rise to the observed spectral red shift as well as to a reduced calculated electron‑hole polarization.

Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

Science.gov (United States)

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

2018-05-01

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

Synthesis and antimalarial activity of new chloroquine analogues carrying a multifunctional linear side chain.

Science.gov (United States)

Iwaniuk, Daniel P; Whetmore, Eric D; Rosa, Nicholas; Ekoue-Kovi, Kekeli; Alumasa, John; de Dios, Angel C; Roepe, Paul D; Wolf, Christian

2009-09-15

We report the synthesis and in vitro antimalarial activity of several new 4-amino- and 4-alkoxy-7-chloroquinolines carrying a linear dibasic side chain. Many of these chloroquine analogues have submicromolar antimalarial activity versus HB3 (chloroquine sensitive) and Dd2 (chloroquine resistant strain of Plasmodium falciparum) and low resistance indices were obtained in most cases. Importantly, compounds 11-15 and 24 proved to be more potent against Dd2 than chloroquine. Branching of the side chain structure proved detrimental to the activity against the CQR strain.

Side-chain liquid-crystalline polyesters for optical information storage

DEFF Research Database (Denmark)

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....

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

Institute of Scientific and Technical Information of China (English)

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.

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

DEFF Research Database (Denmark)

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...

Microscopic theory of light-induced deformation in amorphous side-chain azobenzene polymers.

Science.gov (United States)

Toshchevikov, V; Saphiannikova, M; Heinrich, G

2009-04-16

We propose a microscopic theory of light-induced deformation of side-chain azobenzene polymers taking into account the internal structure of polymer chains. Our theory is based on the fact that interaction of chromophores with the polarized light leads to the orientation anisotropy of azobenzene macromolecules which is accompanied by the appearance of mechanical stress. It is the first microscopic theory which provides the value of the light-induced stress larger than the yield stress. This result explains a possibility for the inscription of surface relief gratings in glassy side-chain azobenzene polymers. For some chemical architectures, elongation of a sample demonstrates a nonmonotonic behavior with the light intensity and can change its sign (a stretched sample starts to be uniaxially compressed), in agreement with experiments. Using a viscoplastic approach, we show that the irreversible strain of a sample, which remains after the light is switched off, decreases with increasing temperature and can disappear at certain temperature below the glass transition temperature. This theoretical prediction is also confirmed by recent experiments.

Substituted group and side chain effects for the porphyrin and zinc(II)–porphyrin derivatives: A DFT and TD-DFT study

International Nuclear Information System (INIS)

Tai, Chin-Kuen; Chuang, Wen-Hua; Wang, Bo-Cheng

2013-01-01

The DFT/B3LYP/LANL2DZ and TD-DFT calculations have been performed to generate the optimized structures, electronic and photo-physical properties for the porphyrin and zinc(II)–porphyrin (metalloporphyrin) derivatives. The substituted group and side chain effects for these derivatives are discussed in this study. According to the calculation results, the side chain moiety extends the π-delocalization length from the porphyrin core to the side chain moiety. The substituted group with a stronger electron-donating ability increases the energy level of highest occupied molecular orbital (E HOMO ). The side chain moiety with a lower resonance energy decreases E HOMO , the energy level of the lowest unoccupied molecular orbital (E LUMO ), and the energy gap (E g ) between HOMO and LUMO in the porphyrin and zinc(II)–porphyrin derivatives. The natural bonding orbital (NBO) analysis determines the possible electron transfer mechanism from the electron-donating to -withdrawing groups (the side chain moiety) in these porphyrin derivatives. The projected density of state (PDOS) analysis shows that the electron-donating group affects the electron density distribution in both HOMO and LUMO, and the side chain moiety influence the electron density distribution in LUMO. The calculated photo-physical properties (absorption wavelengths and the related oscillator strength, f) in dichloromethane environment for porphyrin and zinc(II)–porphyrin derivatives have been simulated by using the TD-DFT method within the Polarizable Continuum Model (PCM). The present of both of the substituted group and the side chain moiety in these derivatives results in a red shift and broadening of the range of the absorption peaks of the Q/Soret band as compared to porphin. -- Highlights: • Side chain moiety extends the π-delocalization for the porphyrins. • Substituted group increases the energy of highest occupied molecular orbital. • Side chain moiety influences the Q/Soret band of

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

Science.gov (United States)

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

2014-04-01

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

Effect of Non-fullerene Acceptors' Side Chains on the Morphology and Photovoltaic Performance of Organic Solar Cells.

Science.gov (United States)

Zhang, Cai'e; Feng, Shiyu; Liu, Yahui; Hou, Ran; Zhang, Zhe; Xu, Xinjun; Wu, Youzhi; Bo, Zhishan

2017-10-04

Three indacenodithieno[3,2-b]thiophene (IT) cored small molecular acceptors (ITIC-SC6, ITIC-SC8, and ITIC-SC2C6) were synthesized, and the influence of side chains on their performances in solar cells was systematically probed. Our investigations have demonstrated the variation of side chains greatly affects the charge dissociation, charge mobility, and morphology of the donor:acceptor blend films. ITIC-SC2C6 with four branched side chains showed improved solubility, which can ensure the polymer donor to form favorable fibrous nanostructure during the drying of the blend film. Consequently, devices based on PBDB-ST:ITIC-SC2C6 demonstrated higher charge mobility, more effective exciton dissociation, and the optimal power conversion efficiency up to 9.16% with an FF of 0.63, a J sc of 15.81 mA cm -2 , and a V oc of 0.92 V. These results reveal that the side chain engineering is a valid way of tuning the morphology of blend films and further improving PCE in polymer solar cells.

Importance of medium chain fatty acids in animal nutrition

Science.gov (United States)

Baltić, B.; Starčević, M.; Đorđević, J.; Mrdović, B.; Marković, R.

2017-09-01

Fats in animal and human nutrition are a common subject of research. These studies most often pay attention to particular fat groups (saturated, unsaturated, polyunsaturated fats or fats grouped by the length of their fatty acid chains into short, medium or long chain fatty acids). Medium chain fatty acids (MCFAs) have two main sources: milk and coconut oil. To date, research has shown these acids have positive effects on health, production, feed digestibility and lower body and muscle fats in broilers and swine. MCFAs possess antibacterial, anticoccidial and antiviral effects. Also, it has been proven that these acids act synergistically if they are used together with organic acids, essential oils, or probiotics. Nowadays, commercial MCFA products are available for use in animal nutrition as feed additives.

Effect of perfluorosulfonic acid membrane equivalent weight on degradation under accelerated stress conditions

International Nuclear Information System (INIS)

Rodgers, Marianne P.; Pearman, Benjamin P.; Mohajeri, Nahid; Bonville, Leonard J.; Slattery, Darlene K.

2013-01-01

The equivalent weight of proton exchange membranes has a large effect on their properties and can impact performance and durability in hydrogen fuel cells. For example, increasing the EW increases the crystallinity of perfluorosulfonic acid membranes, while water content and glass transition temperature decrease. The length of the sulfonic acid side chain also impacts membrane properties. Perfluorosulfonic acid membranes with shorter sulfonic acid side chains, though they exhibit similar gas permeability, have been shown to have higher crystallinity, higher glass transition temperature, slightly lower water content, and lower proton conductivity than membranes with longer sulfonic acid side chains for a given EW. Although many reports have investigated cell performance for membranes as a function of low EW and side chains length, their impact on cell durability is not well understood. Because side chain attack by radicals formed during fuel cell operation is a major source of membrane degradation, it is reasonable to hypothesize that membranes with lower EW and, therefore, more sulfonic acid side chains, would have lower durability. This study evaluates membrane degradation for cells containing PFSA membranes with 750 EW, 950 EW, and 1100 EW. The 750 EW membrane contained short sulfonic acid side-chains while the 950 EW and 1100 EW membranes were Nafion ® -based with long sulfonic acid side-chains. Membranes were tested in fuel cells for 100 h under open circuit voltage, at 90 °C and 30% relative humidity. Diagnostic tests conducted on the cells included hydrogen crossover, fluoride emission, catalyst electrochemical surface area, posttest membrane scanning electron microscopy/transmission electron microscopy evaluation, and defect identification in membranes. The 950 EW cell had the highest decay metrics including fluoride emission, voltage decay, loss in ECA, and loss in cell performance. In all cases, the 1100 EW cell showed the lowest degradation. This has

Biotransformation of cannabidiol in mice. Identification of new acid metabolites.

Science.gov (United States)

Martin, B R; Harvey, D J; Paton, W D

1977-01-01

The in vivo metabolism of cannabidiol (CBD) was investigated in mice. Following the ip administration of CBD to mice, livers were removed and metabolites were extracted with ethyl acetate prior to partial purification on Sephadex LH-20 columns. Fractions from the columns were converted into trimethylsilyl, d9-trimethylsilyl, and methylester-trimethylsilyl derivatives for analysis by gas-liquid chromatography-mass spectrometry. In addition, metabolites containing carboxylic acid and ketone functional groups were reduced to alcohols with lithium aluminum deuteride before trimethylsilation. A total of 22 metabolites were characterized, 14 of which had not been reported previously. The metabolites could be categorized as follows: monohydroxylated (N=2), dihydroxylated (N=3), CBD-7-oic acid, side chain hydroxy-GBD-7-oic acids (N=3), side-chain acids (N=3), 7-hydroxy-side-chain acids (N=4), 6-oxo-side-chain acids (N=3) and glucuronide conjugates (N=3). The most significant biotransformations were glucuronide conjugation and, to a lesser extent, formation of CBD-7-oic acid.

Access to Functionalized Steroid Side Chains via Modified Julia Olefination

Science.gov (United States)

Izgu, Enver Cagri; Burns, Aaron C.; Hoye, Thomas R.

2011-01-01

Various functionalized steroidal side chains were conveniently accessed by a modified Julia olefination strategy using a common sulfone donor and an appropriate α-branched aldehyde acceptor. For the coupling of these hindered classes of reaction partners (and in contrast to typically observed trends), the benzothiazolyl(BT)-sulfone anion gave superior outcomes compared to the phenyltetrazolyl(PT)-sulfone anion. PMID:21244047

Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment.

Science.gov (United States)

Stewart, Alex; Harrison, Joseph S; Regula, Lauren K; Lai, Jonathan R

2013-04-08

Analysis of factors contributing to high affinity antibody-protein interactions provides insight into natural antibody evolution, and guides the design of antibodies with new or enhanced function. We previously studied the interaction between antibody D5 and its target, a designed protein based on HIV-1 gp41 known as 5-Helix, as a model system [Da Silva, G. F.; Harrison, J. S.; Lai, J. R., Biochemistry, 2010, 49, 5464-5472]. Antibody D5 represents an interesting case study because it is derived from the VH1-69 germline segment; this germline segment is characterized by a hydrophobic second heavy chain complementarity determining region (HCDR2) that constitutes the major functional paratope in D5 and several antibodies derived from the same progenitor. Here we explore side chain requirements for affinity and specificity in D5 using phage display. Two D5-based libraries were prepared that contained diversity in all three light chain complementarity determining regions (LCDRs 1-3), and in the third HCDR (HCDR3). The first library allowed residues to vary among a restricted set of six amino acids (Tyr/Ala/Asp/Ser/His/Pro; D5-Lib-I). The second library was designed based on a survey of existing VH1-69 antibody structures (D5-Lib-II). Both libraries were subjected to multiple rounds of selection against 5-Helix, and individual clones characterized. We found that selectants from D5-Lib-I generally had moderate affinity and specificity, while many clones from D5-Lib-II exhibited D5-like properties. Additional analysis of the D5-Lib-II functional population revealed position-specific biases for particular amino acids, many that differed from the identity of those side chains in D5. Together these results suggest that there is some permissiveness for alternative side chains in the LCDRs and HCDR3 of D5, but that replacement with a minimal set of residues is not tolerated in this scaffold for 5-Helix recognition. This work provides novel information about this high

Backbone and sidechain 1H, 13C and 15N resonance assignments of the human brain-type fatty acid binding protein (FABP7) in its apo form and the holo forms binding to DHA, oleic acid, linoleic acid and elaidic acid

DEFF Research Database (Denmark)

Oeemig, Jesper S; Jørgensen, Mathilde L; Hansen, Mikka S

2009-01-01

In this manuscript, we present the backbone and side chain assignments of human brain-type fatty acid binding protein, also known as FABP7, in its apo form and in four different holo forms, bound to DHA, oleic acid, linoleic acid and elaidic acid.......In this manuscript, we present the backbone and side chain assignments of human brain-type fatty acid binding protein, also known as FABP7, in its apo form and in four different holo forms, bound to DHA, oleic acid, linoleic acid and elaidic acid....

Roles of head group architecture and side chain length on colorimetric response of polydiacetylene vesicles to temperature, ethanol and pH.

Science.gov (United States)

Charoenthai, Nipaphat; Pattanatornchai, Thanutpon; Wacharasindhu, Sumrit; Sukwattanasinitt, Mongkol; Traiphol, Rakchart

2011-08-15

In this contribution, we report the relationship between molecular structures of polydiacetylene (PDA) vesicles, fabricated by using three monomers, 10,12-tricosadiynoic acid (TCDA), 10,12-pentacosadiynoic acid (PCDA) and N-(2-aminoethyl)pentacosa-10,12-diynamide (AEPCDA), and their color-transition behaviors. The modification of side chain length and head group of the PDA vesicles strongly affects the colorimetric response to temperature, ethanol and pH. A shorter side chain of poly(TCDA) yields weaker inter- and intra-chain dispersion interactions in the bilayers compared to the system of poly(PCDA), which in turn results in a faster color transition upon exposure to all stimuli. A change of head group in poly(AEPCDA) slightly reduces the transition temperature. Interestingly, the colorimetric response of poly(AEPCDA) vesicles to the addition of ethanol is found to occur in a two-step fashion while the response of poly(PCDA) vesicles takes place in a one-step process. The amount of ethanol required for inducing complete color-transition of poly(AEPCDA) vesicles is also much higher, about 87% v/v. The increase of pH to ~9 and ~10 causes a color-transition of poly(TCDA) and poly(PCDA) vesicles, respectively. The poly(AEPCDA) vesicles, on the other hand, change color upon decreasing pH to ~0. The colorimetric response also occurs in a multi-step fashion. These discrepancies are attributed to the architecture of surface layers of poly(AEPCDA), constituting amine and amide groups separated by ethyl linkers. Copyright © 2011 Elsevier Inc. All rights reserved.

Side-chain liquid crystalline polyesters for optical information storage

DEFF Research Database (Denmark)

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

1996-01-01

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

Correlation between protein secondary structure, backbone bond angles, and side-chain orientations

Science.gov (United States)

Lundgren, Martin; Niemi, Antti J.

2012-08-01

We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central Cα carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the 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 Cβ carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the Cα-Cβ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage

Science.gov (United States)

Shih, I-hung; Been, Michael D.

2001-01-01

Ribozymes of hepatitis delta virus have been proposed to use an active-site cytosine as an acid-base catalyst in the self-cleavage reaction. In this study, we have examined the role of cytosine in more detail with the antigenomic ribozyme. Evidence that proton transfer in the rate-determining step involved cytosine 76 (C76) was obtained from examining cleavage activity of the wild-type and imidazole buffer-rescued C76-deleted (C76Δ) ribozymes in D2O and H2O. In both reactions, a similar kinetic isotope effect and shift in the apparent pKa indicate that the buffer is functionally substituting for the side chain in proton transfer. Proton inventory of the wild-type reaction supported a mechanism of a single proton transfer at the transition state. This proton transfer step was further characterized by exogenous base rescue of a C76Δ mutant with cytosine and imidazole analogues. For the imidazole analogues that rescued activity, the apparent pKa of the rescue reaction, measured under kcat/KM conditions, correlated with the pKa of the base. From these data a Brønsted coefficient (β) of 0.51 was determined for the base-rescued reaction of C76Δ. This value is consistent with that expected for proton transfer in the transition state. Together, these data provide strong support for a mechanism where an RNA side chain participates directly in general acid or general base catalysis of the wild-type ribozyme to facilitate RNA cleavage. PMID:11171978

Topochemical approach to efficiently produce main-chain poly(bile acid)s with high molecular weights.

Science.gov (United States)

Li, Weina; Li, Xuesong; Zhu, Wei; Li, Changxu; Xu, Dan; Ju, Yong; Li, Guangtao

2011-07-21

Based on a topochemical approach, a strategy for efficiently producing main-chain poly(bile acid)s in the solid state was developed. This strategy allows for facile and scalable synthesis of main-chain poly(bile acid)s not only with high molecular weights, but also with quantitative conversions and yields.

Systematic and efficient side chain optimization for molecular docking using a cheapest-path procedure.

Science.gov (United States)

Schumann, Marcel; Armen, Roger S

2013-05-30

Molecular docking of small-molecules is an important procedure for computer-aided drug design. Modeling receptor side chain flexibility is often important or even crucial, as it allows the receptor to adopt new conformations as induced by ligand binding. However, the accurate and efficient incorporation of receptor side chain flexibility has proven to be a challenge due to the huge computational complexity required to adequately address this problem. Here we describe a new docking approach with a very fast, graph-based optimization algorithm for assignment of the near-optimal set of residue rotamers. We extensively validate our approach using the 40 DUD target benchmarks commonly used to assess virtual screening performance and demonstrate a large improvement using the developed side chain optimization over rigid receptor docking (average ROC AUC of 0.693 vs. 0.623). Compared to numerous benchmarks, the overall performance is better than nearly all other commonly used procedures. Furthermore, we provide a detailed analysis of the level of receptor flexibility observed in docking results for different classes of residues and elucidate potential avenues for further improvement. Copyright © 2013 Wiley Periodicals, Inc.

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

Science.gov (United States)

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. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

DEFF Research Database (Denmark)

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......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...

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

Directory of Open Access Journals (Sweden)

Zied Gaieb

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

Side-chain degradation of ultrapure π-conjugated oligomers: implications for organic electronics

NARCIS (Netherlands)

Abbel, R.J.; Wolffs, M.; Bovee, R.A.A.; Dongen, van J.L.J.; Lou, X.W.; Henze, O.; Feast, W.J.; Meijer, E.W.; Schenning, A.P.H.J.

2009-01-01

The degrdn. of two defect-free pi-conjugated oligomers and the participation of their solubilizing side chains in the process are studied in unprecedented detail. The detected intermediate products reveal a mechanism of successive shortening of alkyl and oligo(ethylene glycol) substituents.

Effect of side chain length on the stability and structural properties of 3

African Journals Online (AJOL)

thiophene (DOOPT) and their dimers studied by Hartree-Fock (HF) and Density Functional Theory (DFT) methods. The DFT calculations suggest that dimers of the dialkoxyphenylthiophenes with longer side chains are thermodynamically more ...

Inhibition of gastrin-stimulated gastric acid secretion by medium-chain triglycerides and long-chain triglycerides in healthy young men.

NARCIS (Netherlands)

Maas, M.I.M.; Hopman, W.P.M.; Katan, M.B.; Jansen, J.B.M.J.

1996-01-01

Long-chain triglycerides inhibit gastric acid secretion, but the effect of medium-chain triglycerides in humans is unknown. We compared the effects of intraduodenally perfused saline, medium-chain and long-chain triglycerides on gastrin-stimulated gastric acid secretion and cholecystokinin release.

Investigating side chain mediated electroluminescence from carbazole-modified polyfluorene.

Science.gov (United States)

Liao, Jin-Long; Chen, Xiwen; Liu, Ching-Yang; Chen, Show-An; Su, Chiu-Huen; Su, An-Chung

2007-09-06

In molecular design of electroluminescent (EL) conjugated polymers, introducing a charge transport moiety on a side chain is found to be a promising method for balancing electron and hole fluxes in EL devices without changing the emitting color if there is no interaction between moiety and main chain. In the case of grafting a carbazole (Cz) moiety (hole transporting) on blue emitting polyfluorene, a green emission appears with intensity comparable to the blue emission, which was attributed to a possible interaction between main chain and Cz as previously reported by us. Here, a detailed study of its EL mechanism was carried out by means of time-resolved EL with the assistance of molecular simulation and thermally stimulated current measurements; exploration of how main chain segments interact with the transport moiety was performed. We found the Cz groups in Cz100PF play multiple roles: they act as (1) hole transporter to improve hole injection, (2) hole trapping site for efficient electron-hole recombination to yield blue-emitting excitons, and (3) source of green emission from electroplex formed via electric field-mediated interaction of the Cz/Cz radical cation with an electron in the nearby PF backbone. In combination, these observations suggest that integrated consideration for both intramolecular and intermolecular interactions provides a new route of molecular design of efficient EL polymers.

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

DEFF Research Database (Denmark)

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

1999-01-01

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

Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected ¹³C CPMG relaxation dispersion.

Science.gov (United States)

Weininger, Ulrich; Respondek, Michal; Akke, Mikael

2012-09-01

Protein dynamics on the millisecond time scale commonly reflect conformational transitions between distinct functional states. NMR relaxation dispersion experiments have provided important insights into biologically relevant dynamics with site-specific resolution, primarily targeting the protein backbone and methyl-bearing side chains. Aromatic side chains represent attractive probes of protein dynamics because they are over-represented in protein binding interfaces, play critical roles in enzyme catalysis, and form an important part of the core. Here we introduce a method to characterize millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimized CPMG relaxation dispersion. By monitoring (13)C relaxation in a spin-state selective manner, significant sensitivity enhancement can be achieved in terms of both signal intensity and the relative exchange contribution to transverse relaxation. Further signal enhancement results from optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-CPMG experiment by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined unfolding rate matches perfectly with previous results from stopped-flow kinetics. The CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained by urea-dependent chemical shift analysis. The present method enables characterization of conformational exchange involving aromatic side chains and should serve as a valuable complement to methods developed for other types of protein side chains.

Impact of Branched-Chain Amino Acid Catabolism on Fatty Acid and Alkene Biosynthesis in Micrococcus luteus.

Science.gov (United States)

Surger, Maximilian J; Angelov, Angel; Stier, Philipp; Übelacker, Maria; Liebl, Wolfgang

2018-01-01

Micrococcus luteus naturally produces alkenes, unsaturated aliphatic hydrocarbons, and represents a promising host to produce hydrocarbons as constituents of biofuels and lubricants. In this work, we identify the genes for key enzymes of the branched-chain amino acid catabolism in M. luteus , whose first metabolic steps lead also to the formation of primer molecules for branched-chain fatty acid and olefin biosynthesis, and demonstrate how these genes can be used to manipulate the production of specific olefins in this organism. We constructed mutants of several gene candidates involved in the branched-chain amino acid metabolism or its regulation and investigated the resulting changes in the cellular fatty acid and olefin profiles by GC/MS. The gene cluster encoding the components of the branched-chain α-keto acid dehydrogenase (BCKD) complex was identified by deletion and promoter exchange mutagenesis. Overexpression of the BCKD gene cluster resulted in about threefold increased olefin production whereas deletion of the cluster led to a drastic reduction in branched-chain fatty acid content and a complete loss of olefin production. The specificities of the acyl-CoA dehydrogenases of the branched amino acid degradation pathways were deduced from the fatty acid and olefin profiles of the respective deletion mutant strains. In addition, growth experiments with branched amino acids as the only nitrogen source were carried out with the mutants in order to confirm our annotations. Both the deletion mutant of the BCKD complex, responsible for the further degradation of all three branched-chain amino acids, as well as the deletion mutant of the proposed isovaleryl-CoA dehydrogenase (specific for leucine degradation) were not able to grow on leucine in contrast to the parental strain. In conclusion, our experiments allow the unambigous assignment of specific functions to the genes for key enzymes of the branched-chain amino acid metabolism of M. luteus . We also show how

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

KAUST Repository

Kim, Do Hwan

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.

Lipidization of Simple and di-Functional Amino Acids

International Nuclear Information System (INIS)

Zainab Idris; Mohd Wahid Samsudin; Salmiah Ahmad

2013-01-01

This paper discuss the modification of azelaic acid into its applicable form by attachment of both its carboxyl sites to N-terminal of amino acid ethyl ester forming amide linkages in anhydrous medium. Acylation of glycine ethyl ester hydrochloride with azelaic acid dichloride was best conducted in a 100 % anhydrous medium. L-amino acid ethyl ester bearing a primary hydroxyl group on its side chain gave mixtures of product and variation in composition depending on the mole ratio of reactants used. Reduction in purity was also observed for L-amino acid ethyl ester with primary -SH group on its side chain as compared to L-amino acid ethyl ester having -SCH 3 group on the L-amino acid side chain. The diamidoester of azelaic acid with L-alanine ethyl ester, L-valine ethyl ester, L-leucine ethyl ester and L-glutamic acid diethyl ester were in good yield when prepared through the modified Schotten-Baumann reaction conditions. (author)

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

DEFF Research Database (Denmark)

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

2016-01-01

The synthesis of linear- and (1→6)-branched-β-(1→4)-D-galactans, side chains of the pectic polysaccharide rhamnogalacturonan I is described. The strategy relies on iterative couplings of n-pentenyl disaccharides followed by a late stage glycosylation of a common hexasaccharide core. Reaction...

Revealing the Supramolecular Nature of Side-Chain Terpyridine-Functionalized Polymer Networks

Directory of Open Access Journals (Sweden)

Jérémy Brassinne

2015-01-01

Full Text Available Nowadays, finely controlling the mechanical properties of polymeric materials is possible by incorporating supramolecular motifs into their architecture. In this context, the synthesis of a side-chain terpyridine-functionalized poly(2-(dimethylaminoethyl methacrylate is reported via reversible addition-fragmentation chain transfer polymerization. By addition of transition metal ions, concentrated aqueous solutions of this polymer turn into metallo-supramolecular hydrogels whose dynamic mechanical properties are investigated by rotational rheometry. Hence, the possibility for the material to relax mechanical constrains via dissociation of transient cross-links is brought into light. In addition, the complex phenomena occurring under large oscillatory shear are interpreted in the context of transient networks.

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

DEFF Research Database (Denmark)

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

2017-01-01

Glutamate recognition by neurotransmitter receptors often relies on arginine (Arg) residues in the binding site, leading to the assumption that charge-charge interactions underlie ligand recognition. However, assessing the precise chemical contribution of Arg side chains to protein function......-gated chloride channel from the nematode Haemonchus contortus. Our data unveil a surprisingly small contribution of charge at a conserved arginine side chain previously suggested to form a salt bridge with the ligand, glutamate. Instead, our data show that Arg contributes crucially to ligand sensitivity via...

Inhibition of telomerase by linear-chain fatty acids: a structural analysis.

Science.gov (United States)

Oda, Masako; Ueno, Takamasa; Kasai, Nobuyuki; Takahashi, Hirotada; Yoshida, Hiromi; Sugawara, Fumio; Sakaguchi, Kengo; Hayashi, Hideya; Mizushina, Yoshiyuki

2002-01-01

In the present study, we have found that mono-unsaturated linear-chain fatty acids in the cis configuration with C(18) hydrocarbon chains (i.e. oleic acid) strongly inhibited the activity of human telomerase in a cell-free enzymic assay, with an IC(50) value of 8.6 microM. Interestingly, fatty acids with hydrocarbon chain lengths below 16 or above 20 carbons substantially decreased the potency of inhibition of telomerase. Moreover, the cis-mono-unsaturated C(18) linear-chain fatty acid oleic acid was the strongest inhibitor of all the fatty acids tested. A kinetic study revealed that oleic acid competitively inhibited the activity of telomerase ( K (i)=3.06 microM) with respect to the telomerase substrate primer. The energy-minimized three-dimensional structure of the linear-chain fatty acid was calculated and modelled. A molecule width of 11.53-14.26 A (where 1 A=0.1 nm) in the C(16) to C(20) fatty acid structure was suggested to be important for telomerase inhibition. The three-dimensional structure of the telomerase active site (i.e. the substrate primer-binding site) appears to have a pocket that could bind oleic acid, with the pocket being 8.50 A long and 12.80 A wide. PMID:12121150

Optimization of the alkyl side chain length of fluorine-18-labeled 7α-alkyl-fluoroestradiol

International Nuclear Information System (INIS)

Okamoto, Mayumi; Shibayama, Hiromitsu; Naka, Kyosuke; Kitagawa, Yuya; Ishiwata, Kiichi; Shimizu, Isao; Toyohara, Jun

2016-01-01

Introduction: Several lines of evidence suggest that 7α-substituted estradiol derivatives bind to the estrogen receptor (ER). In line with this hypothesis, we designed and synthesized 18 F-labeled 7α-fluoroalkylestradiol (Cn-7α-[ 18 F]FES) derivatives as molecular probes for visualizing ERs. Previously, we successfully synthesized 7α-(3-[ 18 F]fluoropropyl)estradiol (C3-7α-[ 18 F]FES) and showed promising results for quantification of ER density in vivo, although extensive metabolism was observed in rodents. Therefore, optimization of the alkyl side chain length is needed to obtain suitable radioligands based on Cn-7α-substituted estradiol pharmacophores. Methods: We synthesized fluoromethyl (23; C1-7α-[ 18 F]FES) to fluorohexyl (26; C6-7α-[ 18 F]FES) derivatives, except fluoropropyl (C3-7α-[ 18 F]FES) and fluoropentyl derivatives (C5-7α-[ 18 F]FES), which have been previously synthesized. In vitro binding to the α-subtype (ERα) isoform of ERs and in vivo biodistribution studies in mature female mice were carried out. Results: The in vitro IC 50 value of Cn-7α-FES tended to gradually decrease depending on the alkyl side chain length. C1-7α-[ 18 F]FES (23) showed the highest uptake in ER-rich tissues such as the uterus. Uterus uptake also gradually decreased depending on the alkyl side chain length. As a result, in vivo uterus uptake reflected the in vitro ERα affinity of each compound. Bone uptake, which indicates de-fluorination, was marked in 7α-(2-[ 18 F]fluoroethyl)estradiol (C2-7α-[ 18 F]FES) (24) and 7α-(4-[ 18 F]fluorobutyl)estradiol (C4-7α-[ 18 F]FES) (25) derivatives. However, C1-7α-[ 18 F]FES (23) and C6-7α-[ 18 F]FES (26) showed limited uptake in bone. As a result, in vivo bone uptake (de-fluorination) showed a bell-shaped pattern, depending on the alkyl side chain length. C1-7α-[ 18 F]FES (23) showed the same levels of uptake in uterus and bone compared with those of 16α-[ 18 F]fluoro-17β-estradiol. Conclusions: The optimal alkyl

Electron transport chains of lactic acid bacteria

NARCIS (Netherlands)

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

Improving proton conduction pathways in di- and triblock copolymer membranes: Branched versus linear side chains

Science.gov (United States)

Dorenbos, G.

2017-06-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2017-12-05

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

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

DEFF Research Database (Denmark)

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

2016-01-01

]thiazole (TzTz) acceptor units, were selected toward effective device scalability by roll-coating. The influence of the partial exchange (5% or 10%) of the solubilizing 2-hexyldecyloxy by alternative 2-phenylethoxy groups on efficiency and stability was investigated. With an increasing 2-phenylethoxy ratio...... studies under constant sun irradiance showed a diminishing initial degradation rate for the BT-based devices upon including the alternative side chains, whereas the (more stable) TzTz-based devices degraded at a faster rate from the start of the experiment upon partly exchanging the side chains. No clear......The stability of polymer solar cells (PSCs) can be influenced by the introduction of particular moieties on the conjugated polymer side chains. In this study, two series of donor-acceptor copolymers, based on bis(thienyl)dialkoxybenzene donor and benzo[c][1,2,5]thiadiazole (BT) or thiazolo[5,4-d...

Role of Side-Chain Molecular Features in Tuning Lower Critical Solution Temperatures (LCSTs) of Oligoethylene Glycol Modified Polypeptides.

Science.gov (United States)

Gharakhanian, Eric G; Deming, Timothy J

2016-07-07

A series of thermoresponsive polypeptides has been synthesized using a methodology that allowed facile adjustment of side-chain functional groups. The lower critical solution temperature (LCST) properties of these polymers in water were then evaluated relative to systematic molecular modifications in their side-chains. It was found that in addition to the number of ethylene glycol repeats in the side-chains, terminal and linker groups also have substantial and predictable effects on cloud point temperatures (Tcp). In particular, we found that the structure of these polypeptides allowed for inclusion of polar hydroxyl groups, which significantly increased their hydrophilicity and decreased the need to use long oligoethylene glycol repeats to obtain LCSTs. The thioether linkages in these polypeptides were found to provide an additional structural feature for reversible switching of both polypeptide conformation and thermoresponsive properties.

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

International Nuclear Information System (INIS)

Lee, Chang Ho; Ryu, Seung Hoon; Jang, Hee Dong; Oh, Se Young

2004-01-01

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

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

NARCIS (Netherlands)

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

2011-01-01

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

Medium-chain fatty acids undergo elongation before β-oxidation in fibroblasts

International Nuclear Information System (INIS)

Jones, Patricia M.; Butt, Yasmeen; Messmer, Bette; Boriak, Richard; Bennett, Michael J.

2006-01-01

Although mitochondrial fatty acid β-oxidation (FAO) is considered to be well understood, further elucidation of the pathway continues through evaluation of patients with FAO defects. The FAO pathway can be examined by measuring the 3-hydroxy-fatty acid (3-OHFA) intermediates. We present a unique finding in the study of this pathway: the addition of medium-chain fatty acids to the culture media of fibroblasts results in generation of 3-OHFAs which are two carbons longer than the precursor substrate. Cultured skin fibroblasts from normal and LCHAD-deficient individuals were grown in media supplemented with various chain-length fatty acids. The cell-free medium was analyzed for 3-OHFAs by stable-isotope dilution gas-chromatography/mass-spectrometry. Our finding suggests that a novel carbon chain-length elongation process precedes the oxidation of medium-chain fatty acids. This previously undescribed metabolic step may have important implications for the metabolism of medium-chain triglycerides, components in the dietary treatment of a number of disorders

Branched-Chain Amino Acids

Directory of Open Access Journals (Sweden)

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.

Effect of side chain length on charge transport, morphology, and photovoltaic performance of conjugated polymers in bulk heterojunction solar cells

NARCIS (Netherlands)

Duan, C.; Willems, R.E.M.; van Franeker, J.J.; Bruijnaers, B.J.; Wienk, M.M.; Janssen, R.A.J.

2016-01-01

The effect of side chain length on the photovoltaic properties of conjugated polymers is systematically investigated with two sets of polymers that bear different alkyl side chain lengths based on benzodithiophene and benzo[2,1,3]thiadiazole or 5,6-difluorobenzo[2,1,3]thiadiazole. Characterization

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

Directory of Open Access Journals (Sweden)

Martin Baumgarten

2013-06-01

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

Blocking of proteolytic processing and deletion of glycosaminoglycan side chain of mouse DMP1 by substituting critical amino acid residues.

Science.gov (United States)

Peng, Tao; Huang, Bingzhen; Sun, Yao; Lu, Yongbo; Bonewald, Lynda; Chen, Shuo; Butler, William T; Feng, Jerry Q; D'Souza, Rena N; Qin, Chunlin

2009-01-01

Dentin matrix protein 1 (DMP1) is present in the extracellular matrix (ECM) of dentin and bone as processed NH(2)- and COOH-terminal fragments, resulting from proteolytic cleavage at the NH(2) termini of 4 aspartic acid residues during rat DMP1 processing. One cleavage site residue, Asp(181) (corresponding to Asp(197) of mouse DMP1), and its flanking region are highly conserved across species. We speculate that cleavage at the NH(2) terminus of Asp(197) of mouse DMP1 represents an initial, first-step scission in the whole cascade of proteolytic processing. To test if Asp(197) is critical for initiating the proteolytic processing of mouse DMP1, we substituted Asp(197) with Ala(197) by mutating the corresponding nucleotides of mouse cDNA that encode this amino acid residue. This mutant DMP1 cDNA was cloned into a pcDNA3.1 vector. Data from transfection experiments indicated that this single substitution blocked the proteolytic processing of mouse DMP1 in HEK-293 cells, indicating that cleavage at the NH(2) terminus of Asp(197) is essential for exposing other cleavage sites for the conversion of DMP1 to its fragments. The NH(2)-terminal fragment of DMP1 occurs as a proteoglycan form (DMP1-PG) that contains a glycosaminoglycan (GAG) chain. Previously, we showed that a GAG chain is linked to Ser(74) in rat DMP1 (Ser(89) in mouse DMP1). To confirm that mouse DMP1-PG possesses a single GAG chain attached to Ser(89), we substituted Ser(89) by Gly(89). Data from transfection analysis indicated that this substitution completely prevented formation of the GAG-containing form, confirming that DMP1-PG contains a single GAG chain attached to Ser(89) in mouse DMP1. Copyright 2008 S. Karger AG, Basel.

PMMA-g-OEtOx Graft Copolymers: Influence of Grafting Degree and Side Chain Length on the Conformation in Aqueous Solution

Directory of Open Access Journals (Sweden)

Irina Muljajew

2018-03-01

Full Text Available Depending on the degree of grafting (DG and the side chain degree of polymerization (DP, graft copolymers may feature properties similar to statistical copolymers or to block copolymers. This issue is approached by studying aqueous solutions of PMMA-g-OEtOx graft copolymers comprising a hydrophobic poly(methyl methacrylate (PMMA backbone and hydrophilic oligo(2-ethyl-2-oxazoline (OEtOx side chains. The graft copolymers were synthesized via reversible addition-fragmentation chain transfer (RAFT copolymerization of methyl methacrylate (MMA and OEtOx-methacrylate macromonomers of varying DP. All aqueous solutions of PMMA-g-OEtOx (9% ≤ DG ≤ 34%; 5 ≤ side chain DP ≤ 24 revealed lower critical solution temperature behavior. The graft copolymer architecture significantly influenced the aggregation behavior, the conformation in aqueous solution and the coil to globule transition, as verified by means of turbidimetry, dynamic light scattering, nuclear magnetic resonance spectroscopy, and analytical ultracentrifugation. The aggregation behavior of graft copolymers with a side chain DP of 5 was significantly affected by small variations of the DG, occasionally forming mesoglobules above the cloud point temperature (Tcp, which was around human body temperature. On the other hand, PMMA-g-OEtOx with elongated side chains assembled into well-defined structures below the Tcp (apparent aggregation number (Nagg = 10 that were able to solubilize Disperse Orange 3. The thermoresponsive behavior of aqueous solutions thus resembled that of micelles comprising a poly(2-ethyl-2-oxazoline (PEtOx shell (Tcp > 60 °C.

The dominant role of side chains in supramolecular double helical organisation in synthetic tripeptides

Science.gov (United States)

Sharma, Ankita; Tiwari, Priyanka; Dutt Konar, Anita

2018-06-01

Peptide self-assembled nanostructures have attracted attention recently owing to their promising applications in diversified avenues. To validate the importance of sidechains in supramolecular architectural stabilization, herein this report describes the self-assembly propensities involving weak interactions in a series of model tripeptides Boc-Xaa-Aib-Yaa-OMe I-IV, (where Xaa = 4-F-Phe/NMeSer/Ile & Yaa = Tyr in peptide I-III respectively and Xaa = 4-F-Phe & Yaa = Ile in peptide IV) differing in terminal side chains. The solid state structural analysis reveals that tripeptide (I) displays supramolecular preference for double helical architecture. However, when slight modification has been introduced in the N-terminal side chains disfavour the double helical organisation (Peptide II and III). Indeed the peptides display sheet like ensemble within the framework. Besides replacement of C-terminal Tyr by Ile in peptide I even do not promote the architecture, emphasizing the dominant role of balance of side chains in stabilizing double helical organisation. The CD measurements, concentration dependant studies, NMR titrations and ROESY spectra are well in agreement with the solid state conformational investigation. Moreover the morphological experiments utilizing FE-SEM, support the heterogeneity present in the peptides. Thus this work may not only hold future promise in understanding the structure and function of neurodegenerative diseases but also assist in rational design of protein modification in biologically active peptides.

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

DEFF Research Database (Denmark)

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

2014-01-01

Polysulfones functionalized with highly phosphonated poly(pentafluorostyrene) side chains of different lengths were synthesized applying controlled polymerization and modification methods. The graft copolymers' thermal properties were evaluated by differential scanning calorimetry and thermal...... gravimetrical analyses. The proton conductivity of membrane prepared from the graft copolymer with the shortest phosphonated side chains was 134 mS cm(-1) at 100 degrees C under fully immersed conditions. The graft copolymer TEM image shows a nanophase separation of ion-rich segments within the polysulfone...

De novo fatty acid biosynthesis and elongation in very long-chain acyl-CoA dehydrogenase-deficient mice supplemented with odd or even medium-chain fatty acids.

Science.gov (United States)

Tucci, Sara; Behringer, Sidney; Spiekerkoetter, Ute

2015-11-01

An even medium-chain triglyceride (MCT)-based diet is the mainstay of treatment in very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency (VLCADD). Previous studies with magnetic resonance spectroscopy have shown an impact of MCT on the average fatty acid chain length in abdominal fat. We therefore assume that medium-chain fatty acids (MCFAs) are elongated and accumulate in tissue as long-chain fatty acids. In this study, we explored the hepatic effects of long-term supplementation with MCT or triheptanoin, an odd-chain C7-based triglyceride, in wild-type and VLCAD-deficient (VLCAD(-/-) ) mice after 1 year of supplementation as compared with a control diet. The de novo biosynthesis and elongation of fatty acids, and peroxisomal β-oxidation, were quantified by RT-PCR. This was followed by a comprehensive analysis of hepatic and cardiac fatty acid profiles by GC-MS. Long-term application of even and odd MCFAs strongly induced de novo biosynthesis and elongation of fatty acids in both wild-type and VLCAD(-/-) mice, leading to an alteration of the hepatic fatty acid profiles. We detected de novo-synthesized and elongated fatty acids, such as heptadecenoic acid (C17:1n9), eicosanoic acid (C20:1n9), erucic acid (C22:1n9), and mead acid (C20:3n9), that were otherwise completely absent in mice under control conditions. In parallel, the content of monounsaturated fatty acids was massively increased. Furthermore, we observed strong upregulation of peroxisomal β-oxidation in VLCAD(-/-) mice, especially when they were fed an MCT diet. Our data raise the question of whether long-term MCFA supplementation represents the most efficient treatment in the long term. Studies on the hepatic toxicity of triheptanoin are still ongoing. © 2015 FEBS.

Structural and kinetic mapping of side-chain exposure onto the protein energy landscape.

Science.gov (United States)

Bernstein, Rachel; Schmidt, Kierstin L; Harbury, Pehr B; Marqusee, Susan

2011-06-28

Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of Escherichia coli ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated.

Controlling the morphology and efficiency of hybrid ZnO: Polythiophene solar cells via side chain functionalization

NARCIS (Netherlands)

Oosterhout, S.D.; Koster, L.J.A.; Bavel, van S.S.; Loos, J.; Stenzel, O.; Thiedmann, R.; Schmidt, V.; Campo, B.J.; Cleij, T.J.; Lutzen, L.; Vanderzande, D.J.M.; Wienk, M.M.; Janssen, R.A.J.

2011-01-01

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

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

International Nuclear Information System (INIS)

Daley, Margaret E.; Sykes, Brian D.

2004-01-01

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

Accessing ns-μs side chain dynamics in ubiquitin with methyl RDCs

International Nuclear Information System (INIS)

Fares, Christophe; Lakomek, Nils-Alexander; Walter, Korvin F. A.; Frank, Benedikt T. C.; Meiler, Jens; Becker, Stefan; Griesinger, Christian

2009-01-01

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-τ 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 τ c . In fact, the average amplitude of motion expressed in terms of order parameters S 2 associated with the supra-τ 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

MgO encapsulated mesoporous zeolite for the side chain alkylation of toluene with methanol.

Science.gov (United States)

Jiang, Nanzhe; Jin, Hailian; Jeong, Eun-Young; Park, Sang-Eon

2010-01-01

Side chain alkylation of toluene with methanol was studied over mesoporous zeolite supported MgO catalysts. MgO were supported onto the carbon templated mesoporous silicalite-1 by direct synthesis route under microwave conditions. This direct synthesis route yields the majority of MgO highly dispersed into the mesopores of the silicalite-1 crystals. The vapor phase alkylation of toluene with methanol was performed over these catalysts under vapor phase conditions at atmospheric pressure. Mesoporous silicalite-1 supported MgO catalysts gave improved yields towards side chain alkylated products compared to the bulk MgO. The higher activity exhibited by 5% MgO supported on mesoporous silicalite compared to the one with 1% MgO can be attributed to the large number of weak basic sites observed from the CO2 TPD.

Zeolites relieves inhibitory stress from high concentrations of long chain fatty acids.

Science.gov (United States)

Nordell, Erik; Hansson, Anna B; Karlsson, Martin

2013-12-01

Protein and fat rich slaughterhouse waste is a very attractive waste stream for the production of biogas because of the high biochemical methane potential of the substrate. The material has however some drawbacks as the sole material for biogas production due to the production of several process disturbing metabolites such as ammonia, sulfides and long chain fatty acids. We can in this work present results that show that zeolites have the potential to relieve inhibitory stress from the presence of long chain fatty acids. Moreover, the results strongly indicate that it is mainly acetic acid consumers that are most negatively affected by long chain fatty acids and that the mechanism of stress relief is an adsorption of long chain fatty acids to the zeolites. In addition to this, it is shown that the effect is immediate and that only a small amount of zeolites is necessary to cancel the inhibitory effect of long chain fatty acids. Copyright © 2013 Elsevier Ltd. All rights reserved.

The C8 side chain is one of the key functional group of Garcinol for its anti-cancer effects.

Science.gov (United States)

Zhou, Xin-Ying; Cao, Jing; Han, Chao-Ming; Li, Shu-Wen; Zhang, Chen; Du, Yin-Duan; Zhou, Qian-Qian; Zhang, Xin-Yan; Chen, Xin

2017-04-01

Garcinol from the fruit rind of Garcinia indica shows anti-carcinogenic and anti-inflammatory properties, but its mechanism and key functional groups were still need to be identified. Our previous computer modeling suggested that the C8 side chain of Garcinol is so large that it may influence the bioactivity of the compound. 8-Me Garcinol, a derivative of Garcinol in which the bulky side chain at the C8 position of Garcinol is replaced with a much smaller methyl group, was synthesized through a 12-step procedure starting from 1,3-cyclohexanedione. The antitumor activity of Garcinol and 8-Me Garcinol was evaluated in vitro by MTT, cell cycle and cell apoptosis assays. The results showed that 8-Me Garcinol had weaker inhibitory activity on cells proliferation, and little effects on cell cycle and apoptosis in oral cancer cell line SCC15 cells when compared with Garcinol. All of the results indicated 8-Me Garcinol exerts weaker antitumor activity than Garcinol, and the C8 side chain might be an important active site in Garcinol. Changing the C8 side chain will affect the inhibitory effect of Garcinol. Copyright © 2017 Elsevier Inc. All rights reserved.

A stability study of polymer solar cells using conjugated polymers with different donor or acceptor side chain patterns

DEFF Research Database (Denmark)

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

2016-01-01

-phenylethyl group. It is shown that the exchange of the hexyl chain on the DTBT moiety has a negative impact on the stability of the polymer as well as on the performance of the resulting PSCs. On the other hand, partial exchange of the 2-hexyldecyl side chain of the BDT unit by a 2-hydroxyethyl group results......)benzo[c][1,2,5]thiadiazole (DTBT), specifically selected because of its suitability for roll-coating in the ambient environment, is investigated in terms of operational stability via partial exchange (5 or 10%) of the alkyl side chain on either the donor or the acceptor monomer with a 2-hydroxyethyl or 2...

Metal cation dependence of interactions with amino acids: bond dissociation energies of Rb(+) and Cs(+) to the acidic amino acids and their amide derivatives.

Science.gov (United States)

Armentrout, P B; Yang, Bo; Rodgers, M T

2014-04-24

Metal cation-amino acid interactions are key components controlling the secondary structure and biological function of proteins, enzymes, and macromolecular complexes comprising these species. Determination of pairwise interactions of alkali metal cations with amino acids provides a thermodynamic vocabulary that begins to quantify these fundamental processes. In the present work, we expand a systematic study of such interactions by examining rubidium and cesium cations binding with the acidic amino acids (AA), aspartic acid (Asp) and glutamic acid (Glu), and their amide derivatives, asparagine (Asn) and glutamine (Gln). These eight complexes are formed using electrospray ionization and their bond dissociation energies (BDEs) are determined experimentally using threshold collision-induced dissociation with xenon in a guided ion beam tandem mass spectrometer. Analyses of the energy-dependent cross sections include consideration of unimolecular decay rates, internal energy of the reactant ions, and multiple ion-neutral collisions. Quantum chemical calculations are conducted at the B3LYP, MP2(full), and M06 levels of theory using def2-TZVPPD basis sets, with results showing reasonable agreement with experiment. At 0 and 298 K, most levels of theory predict that the ground-state conformers for M(+)(Asp) and M(+)(Asn) involve tridentate binding of the metal cation to the backbone carbonyl, amino, and side-chain carbonyl groups, although tridentate binding to the carboxylic acid group and side-chain carbonyl is competitive for M(+)(Asn). For the two longer side-chain amino acids, Glu and Gln, multiple structures are competitive. A comparison of these results to those for the smaller alkali cations, Na(+) and K(+), provides insight into the trends in binding energies associated with the molecular polarizability and dipole moment of the side chain. For all four metal cations, the BDEs are inversely correlated with the size of the metal cation and follow the order Asp < Glu

Evolution of the biosynthesis of the branched-chain amino acids

Science.gov (United States)

Keefe, Anthony D.; Lazcano, Antonio; Miller, Stanley L.

1995-01-01

The origins of the biosynthetic pathways for the branched-chain amino acids cannot be understood in terms of the backwards development of the present acetolactate pathway because it contains unstable intermediates. We propose that the first biosynthesis of the branched-chain amino acids was by the reductive carboxylation of short branched chain fatty acids giving keto acids which were then transaminated. Similar reaction sequences mediated by nonspecific enzymes would produce serine and threomine from the abundant prebiotic compounds glycolic and lactic acids. The aromatic amino acids may also have first been synthesized in this way, e.g. tryptophan from indole acetic acid. The next step would have been the biosynthesis of leucine from alpha-ketoisovalerc acid. The acetolactate pathway developed subsequently. The first version of the Krebs cycle, which was used for amino acid biosynthesis, would have been assembled by making use fo the reductive carboxylation and leucine biosynthesis enzymes, and completed with the development of a single new enzyme, succinate dehydrogenase. This evolutionary scheme suggests that there may be limitations to inferring the origins of metabolism by a simple back extrapolation of current pathways.

Off-resonance rotating-frame relaxation dispersion experiment for 13C in aromatic side chains using L-optimized TROSY-selection

DEFF Research Database (Denmark)

Weininger, Ulrich; Brath, Ulrika; Modig, Kristofer

2014-01-01

Protein dynamics on the microsecond-millisecond time scales often play a critical role in biological function. NMR relaxation dispersion experiments are powerful approaches for investigating biologically relevant dynamics with site-specific resolution, as shown by a growing number of publications...... on enzyme catalysis, protein folding, ligand binding, and allostery. To date, the majority of studies has probed the backbone amides or side-chain methyl groups, while experiments targeting other sites have been used more sparingly. Aromatic side chains are useful probes of protein dynamics, because...... they are over-represented in protein binding interfaces, have important catalytic roles in enzymes, and form a sizable part of the protein interior. Here we present an off-resonance R 1ρ experiment for measuring microsecond to millisecond conformational exchange of aromatic side chains in selectively (13)C...

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

KAUST Repository

Li, Yongxin

2012-09-01

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

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

KAUST Repository

Li, Yongxin; Zhang, Fengying; Xu, Ying; Matsumura, Kiyotaka; Han, Zhuang; Liu, Lingli; Lin, Wenhan; Jia, Yanxing; Qian, Pei Yuan

2012-01-01

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

Effect of Side Chains on Molecular Conformation of Anthracene-Ethynylene-Phenylene-Vinylene Oligomers: A Comparative Density Functional Study With and Without Dispersion Interaction.

Science.gov (United States)

Dong, Chuanding; Hoppe, Harald; Beenken, Wichard J D

2016-06-02

Using density functional calculations with and without dispersion interaction, we studied the effects of linear octyl and branched 2-ethylhexyl side chains on the oligomer conformation of the conjugated copolymer poly(p-anthracene-ethynylene)-alt-poly(p-phenylene-vinylene). With dispersion included, the branched side chains can cause significant bending of the oligomer backbone, while without dispersion they induce mainly torsional disorder. The oligomers with mainly linear side chains keep good planarity when optimized with and without dispersion. Despite their dramatically different conformations, the calculated absorption spectra of the oligomers with various side chain combinations are very similar, indicating that the conformation of the copolymer is not the main reason for the experimentally observed different spectra of ordered and disordered phases.

Synthesis of side-chain polystyrenes for all organic solution processed OLEDs

OpenAIRE

Lorente Sánchez, Alejandro Jose (Dr.)

2017-01-01

In the present work side-chain polystyrenes were synthesized and characterized, in order to be applied in multilayer OLEDs fabricated by solution process techniques. Manufacture of optoelectronic devices by solution process techniques is meant to decrease significantly fabrication cost and allow large scale production of such devices. This dissertation focusses in three series, enveloped in two material classes. The two classes differ to each other in the type of charge transport exhibited...

Polymerase chain reaction system using magnetic beads for analyzing a sample that includes nucleic acid

Science.gov (United States)

Nasarabadi, Shanavaz [Livermore, CA

2011-01-11

A polymerase chain reaction system for analyzing a sample containing nucleic acid includes providing magnetic beads; providing a flow channel having a polymerase chain reaction chamber, a pre polymerase chain reaction magnet position adjacent the polymerase chain reaction chamber, and a post pre polymerase magnet position adjacent the polymerase chain reaction chamber. The nucleic acid is bound to the magnetic beads. The magnetic beads with the nucleic acid flow to the pre polymerase chain reaction magnet position in the flow channel. The magnetic beads and the nucleic acid are washed with ethanol. The nucleic acid in the polymerase chain reaction chamber is amplified. The magnetic beads and the nucleic acid are separated into a waste stream containing the magnetic beads and a post polymerase chain reaction mix containing the nucleic acid. The reaction mix containing the nucleic acid flows to an analysis unit in the channel for analysis.

Fine-tuning blend morphology via alkylthio side chain engineering towards high performance non-fullerene polymer solar cells

Science.gov (United States)

Li, Ling; Feng, Liuliu; Yuan, Jun; Peng, Hongjian; Zou, Yingping; Li, Yongfang

2018-03-01

Two medium bandgap polymers (ffQx-TS1, ffQx-TS2) were designed and synthesized to investigate the influence of different alkylthio side chain on the morphology and photovoltaic performance of non-fullerene polymer solar cells (PSCs). Both polymers exhibit similar molecular weights and comparable the highest occupied molecular orbital (HOMO) energy level. However, the polymer with straight alkylthio chain delivers a root-mean-square (RMS) of 0.86 nm, which is slightly lower than that with branched chain (1.40 nm). The lower RMS benefits the ohmic contact between the active lay and interface layer, thus enhanced short circuit current (Jsc) (from 13.54 mA cm-1 to 15.25 mA cm-1) could be obtained. Due to the enhancement of Jsc, better power conversion efficiency (PCE) of 7.69% for ffQx-TS2 could be realized. These results indicated that alkylthio side chain engineering is a promising method to improve photovoltaic performance.

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

Energy Technology Data Exchange (ETDEWEB)

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

2004-06-15

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

Growth-Environment Dependent Modulation of Staphylococcus aureus Branched-Chain to Straight-Chain Fatty Acid Ratio and Incorporation of Unsaturated Fatty Acids.

Science.gov (United States)

Sen, Suranjana; Sirobhushanam, Sirisha; Johnson, Seth R; Song, Yang; Tefft, Ryan; Gatto, Craig; Wilkinson, Brian J

2016-01-01

The fatty acid composition of membrane glycerolipids is a major determinant of Staphylococcus aureus membrane biophysical properties that impacts key factors in cell physiology including susceptibility to membrane active antimicrobials, pathogenesis, and response to environmental stress. The fatty acids of S. aureus are considered to be a mixture of branched-chain fatty acids (BCFAs), which increase membrane fluidity, and straight-chain fatty acids (SCFAs) that decrease it. The balance of BCFAs and SCFAs in USA300 strain JE2 and strain SH1000 was affected considerably by differences in the conventional laboratory medium in which the strains were grown with media such as Mueller-Hinton broth and Luria broth resulting in high BCFAs and low SCFAs, whereas growth in Tryptic Soy Broth and Brain-Heart Infusion broth led to reduction in BCFAs and an increase in SCFAs. Straight-chain unsaturated fatty acids (SCUFAs) were not detected. However, when S. aureus was grown ex vivo in serum, the fatty acid composition was radically different with SCUFAs, which increase membrane fluidity, making up a substantial proportion of the total (37%) and BCFAs (>36%) making up the rest. Staphyloxanthin, an additional major membrane lipid component unique to S. aureus, tended to be greater in content in cells with high BCFAs or SCUFAs. Cells with high staphyloxanthin content had a lower membrane fluidity that was attributed to increased production of staphyloxanthin. S. aureus saves energy and carbon by utilizing host fatty acids for part of its total fatty acids when growing in serum, which may impact biophysical properties and pathogenesis given the role of SCUFAs in virulence. The nutritional environment in which S. aureus is grown in vitro or in vivo in an infection is likely to be a major determinant of membrane fatty acid composition.

Straight and branched-chain fatty acids in preorbital glands of sika deer, Cervus nippon.

Science.gov (United States)

Wood, William F

2004-02-01

Using GC-MS analysis, 11 major volatile compounds were found in the preorbital gland secretion from a female sika deer, Cervus nippon. These compounds are the C14 through C18 straight-chain fatty acids, (ZZ)-9,12-octadecadienoic acid, 12-methyltridecanoic acid, 13-methyltetradecanoic acid, 14-methylpentadecanoic acid, 14-methylhexadecanoic acid, and 15-methylhexadecanoic acid. The five branched-chain acids make up over 29% of the volatiles in the gland. This is the first time branched-chain carboxylic acids have been reported from ungulate preorbital glands.

[Odd- and branched-chain fatty acids in milk fat--characteristic and health properties].

Science.gov (United States)

Adamska, Agata; Rutkowska, Jarosława

2014-08-22

This review analyzes the current state of knowledge on odd- and branched-chain fatty acids present in milk fat. Special attention is devoted to the characteristic, synthesis in ruminants, factors affecting their content in milk fat and pro-health properties of these compounds. The group of odd- and branched-chain fatty acids includes mainly saturated fatty acids with one or more methyl branches in the iso or anteiso position. These fatty acids are largely derived from ruminal bacteria and they have been transferred to ruminant tissue (milk and meat). For that reason they have been used as biomarkers of rumen fermentation. Odd- and branched-chain fatty acids are exogenous products for humans, and therefore have specific properties. The results of research from recent decades show that odd- and branched-chain fatty acids have anti-cancer activity. Branched-chain fatty acids may reduce the incidence of necrotizing enterocolitis. Additionally, these compounds have a beneficial effect on proper tissue function and on functioning and development of the infant gut, whereas odd-chain fatty acids are considered as biomarkers of milk fat intake by humans. So far, not all the mechanisms of activity of these compounds are known thoroughly. They should be more carefully studied for application of their biological effects in prevention and treatment.

Fused-Ring Acceptors with Asymmetric Side Chains for High-Performance Thick-Film Organic Solar Cells.

Science.gov (United States)

Feng, Shiyu; Zhang, Cai'e; Liu, Yahui; Bi, Zhaozhao; Zhang, Zhe; Xu, Xinjun; Ma, Wei; Bo, Zhishan

2017-11-01

A kind of new fused-ring electron acceptor, IDT-OB, bearing asymmetric side chains, is synthesized for high-efficiency thick-film organic solar cells. The introduction of asymmetric side chains can increase the solubility of acceptor molecules, enable the acceptor molecules to pack closely in a dislocated way, and form favorable phase separation when blended with PBDB-T. As expected, PBDB-T:IDT-OB-based devices exhibit high and balanced hole and electron mobility and give a high power conversion efficiency (PCE) of 10.12%. More importantly, the IDT-OB-based devices are not very sensitive to the film thickness, a PCE of 9.17% can still be obtained even the thickness of active layer is up to 210 nm. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Estimating side-chain order in methyl-protonated, perdeuterated proteins via multiple-quantum relaxation violated coherence transfer NMR spectroscopy

International Nuclear Information System (INIS)

Sun Hechao; Godoy-Ruiz, Raquel; Tugarinov, Vitali

2012-01-01

Relaxation violated coherence transfer NMR spectroscopy (Tugarinov et al. in J Am Chem Soc 129:1743–1750, 2007) is an established experimental tool for quantitative estimation of the amplitudes of side-chain motions in methyl-protonated, highly deuterated proteins. Relaxation violated coherence transfer experiments monitor the build-up of methyl proton multiple-quantum coherences that can be created in magnetically equivalent spin-systems as long as their transverse magnetization components relax with substantially different rates. The rate of this build-up is a reporter of the methyl-bearing side-chain mobility. Although the build-up of multiple-quantum 1 H coherences is monitored in these experiments, the decay of the methyl signal during relaxation delays occurs when methyl proton magnetization is in a single-quantum state. We describe a relaxation violated coherence transfer approach where the relaxation of multiple-quantum 1 H– 13 C methyl coherences during the relaxation delay period is quantified. The NMR experiment and the associated fitting procedure that models the time-dependence of the signal build-up, are applicable to the characterization of side-chain order in [ 13 CH 3 ]-methyl-labeled, highly deuterated protein systems up to ∼100 kDa in molecular weight. The feasibility of extracting reliable measures of side-chain order is experimentally verified on methyl-protonated, perdeuterated samples of an 8.5-kDa ubiquitin at 10°C and an 82-kDa Malate Synthase G at 37°C.

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

International Nuclear Information System (INIS)

Garrison, W.M.

1983-11-01

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

Amphiphilic polymer based on fluoroalkyl and PEG side chains for fouling release coating

Science.gov (United States)

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

2017-12-01

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

Interactions between Therapeutic Proteins and Acrylic Acid Leachable.

Science.gov (United States)

Liu, Dengfeng; Nashed-Samuel, Yasser; Bondarenko, Pavel V; Brems, David N; Ren, Da

2012-01-01

Leachables are chemical compounds that migrate from manufacturing equipment, primary containers and closure systems, and packaging components into biopharmaceutical and pharmaceutical products. Acrylic acid (at concentration around 5 μg/mL) was detected as leachable in syringes from one of the potential vendors (X syringes). In order to evaluate the potential impact of acrylic acid on therapeutic proteins, an IgG 2 molecule was filled into a sterilized X syringe and then incubated at 45 °C for 45 days in a pH 5 acetate buffer. We discovered that acrylic acid can interact with proteins at three different sites: (1) the lysine side chain, (2) the N-terminus, and (3) the histidine side chain, by the Michael reaction. In this report, the direct interactions between acrylic acid leachable and a biopharmaceutical product were demonstrated and the reaction mechanism was proposed. Even thought a small amount (from 0.02% to 0.3%) of protein was found to be modified by acrylic acid, the modified protein can potentially be harmful due to the toxicity of acrylic acid. After being modified by acrylic acid, the properties of the therapeutic protein may change due to charge and hydrophobicity variations. Acrylic acid was detected to migrate from syringes (Vendor X) into a therapeutic protein solution (at a concentration around 5 μg/mL). In this study, we discovered that acrylic acid can modify proteins at three different sites: (1) the lysine side chain, 2) the N-terminus, and 3) the histidine side chain, by the Michael reaction. In this report, the direct interactions between acrylic acid leachable and a biopharmaceutical product were demonstrated and the reaction mechanism was proposed.

Light scattering of thin azobenzene side-chain polyester layers

DEFF Research Database (Denmark)

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....

Influence of the side chain and substrate on polythiophene thin film surface, bulk, and buried interfacial structures.

Science.gov (United States)

Xiao, Minyu; Jasensky, Joshua; Zhang, Xiaoxian; Li, Yaoxin; Pichan, Cayla; Lu, Xiaolin; Chen, Zhan

2016-08-10

The molecular structures of organic semiconducting thin films mediate the performance of various devices composed of such materials. To fully understand how the structures of organic semiconductors alter on substrates due to different polymer side chains and different interfacial interactions, thin films of two kinds of polythiophene derivatives with different side-chains, poly(3-hexylthiophene) (P3HT) and poly(3-potassium-6-hexanoate thiophene) (P3KHT), were deposited and compared on various surfaces. A combination of analytical tools was applied in this research: contact angle goniometry and X-ray photoelectron spectroscopy (XPS) were used to characterize substrate dielectric surfaces with varied hydrophobicity for polymer film deposition; X-ray diffraction and UV-vis spectroscopy were used to examine the polythiophene film bulk structure; sum frequency generation (SFG) vibrational spectroscopy was utilized to probe the molecular structures of polymer film surfaces in air and buried solid/solid interfaces. Both side-chain hydrophobicity and substrate hydrophobicity were found to mediate the crystallinity of the polythiophene film, as well as the orientation of the thiophene ring within the polymer backbone at the buried polymer/substrate interface and the polymer thin film surface in air. For the same type of polythiophene film deposited on different substrates, a more hydrophobic substrate surface induced thiophene ring alignment with the surface normal at both the buried interface and on the surface in air. For different films (P3HT vs. P3KHT) deposited on the same dielectric substrate, a more hydrophobic polythiophene side chain caused the thiophene ring to align more towards the surface at the buried polymer/substrate interface and on the surface in air. We believe that the polythiophene surface, bulk, and buried interfacial molecular structures all influence the hole mobility within the polythiophene film. Successful characterization of an organic conducting

Influence of biopolymers on the solubility of branched-chain amino acids and stability of their solutions.

Science.gov (United States)

Hong, Chi Rac; Lee, Gyu Whan; Paik, Hyun-Dong; Chang, Pahn-Shick; Choi, Seung Jun

2018-01-15

This study confirmed the possibility of biopolymer-type stabilizers to increase the saturation concentration of branched-chain amino acids by preventing their crystallization/precipitation. Although microfluidization increased the initial solubility, it failed to increase the saturation concentration of the branched-chain amino acids. The saturation concentration of the branched-chain amino acids increased from 3.81% to 4.42% and 4.85% after the incorporation of food hydrocolloids and proteins, respectively. However, the branched-chain amino acids:stabilizer ratio did not affect the solubility. In the case of food hydrocolloid-based solutions, crystal formation and growth of branched-chain amino acids occurred during storage, resulting in the precipitation of branched-chain amino acid crystals. However, food proteins effectively increased the stability of the solubilized branched-chain amino acids. The improved solubility and stability of the solubilized branched-chain amino acids could be attributed to interactions between the functional groups (carboxyl, amine, sulfate, aliphatic, aromatic, etc.) of the stabilizer and the branched-chain amino acid molecules. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluating the role of acidic, basic, and polar amino acids and dipeptides on a molecular electrocatalyst for H ₂ oxidation

Energy Technology Data Exchange (ETDEWEB)

Boralugodage, Nilusha Priyadarshani; Arachchige, Rajith Jayasingha; Dutta, Arnab; Buchko, Garry W.; Shaw, Wendy J.

2017-01-01

Amino acids and peptides have been shown to have a significant influence on the H2 production and oxidation reactivity of Ni(P^R₂N^R’₂)₂, where P^R₂N^R’₂ = 1,5-diaza-3,7-diphosphacyclooctane, R is either phenyl (Ph) or cyclohexyl (Cy), and R’ is either an amino acid or peptide. Most recently, the Ni(P^Cy₂Naminoacid₂)₂ complexes (CyAA) have shown enhanced H₂ oxidation rates, water solubility, and in the case of arginine (CyArg) and phenylalanine (CyPhe), electrocatalytic reversibility. Both the backbone –COOH and side chain interactions were shown to be critical to catalytic performance. Here we further investigate the roles of the outer coordination sphere by evaluating amino acids with acidic, basic, and hydrophilic side chains, as well as dipeptides which combine multiple successful features from previous complexes. Six new complexes were prepared, three containing single amino acids: aspartic acid (CyAsp), lysine (CyLys), and serine (CySer) and three containing dipeptides: glycine-phenylalanine (Cy(GlyPhe)), phenylalanine-glycine (Cy(PheGly)), and aspartic acid-phenylananine (Cy(AspPhe)). The resulting catalytic performance demonstrates that complexes need both interactions between side chain and –COOH groups for fast, efficient catalysis. The fastest of all of the catalysts, Cy(AspPhe), had both of these features, while the other dipeptide complexes with an amide replacing the -COOH were both slower; however, the amide group was demonstrated to participate in the proton pathway when side chain interactions are present to position it. Both the hydrophilic and basic side chains, notably lacking in side chain interactions, significantly increased the overpotential, with only modest increases in TOF. Of all of the complexes, only CyAsp was reversible at room temperature, and only in water, the first of these

Mesogenic polybuthadiene diols with thiol side-chain units: synthesis and thermal behaviour

Czech Academy of Sciences Publication Activity Database

Bubnov, Alexej; Kašpar, Miroslav; Sedláková, Zdeňka

2010-01-01

Roč. 83, č. 1 (2010), 16-27 ISSN 0141-1594 R&D Projects: GA AV ČR IAA100100911; GA AV ČR(CZ) GA202/09/0047; GA MŠk OC 175 Institutional research plan: CEZ:AV0Z10100520; CEZ:AV0Z40500505 Keywords : mesogenic polymer * phase transition * polybutadiene diol * side -chain polymer Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.006, year: 2010

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

Science.gov (United States)

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.

Association between very long chain fatty acids in the meibomian gland and dry eye resulting from n-3 fatty acid deficiency.

Science.gov (United States)

Tanaka, Hideko; Harauma, Akiko; Takimoto, Mao; Moriguchi, Toru

2015-06-01

In our previously study, we reported lower tear volume in with an n-3 fatty acid deficient mice and that the docosahexaenoic acid and total n-3 fatty acid levels in these mice are significantly reduced in the meibomian gland, which secretes an oily tear product. Furthermore, we noted very long chain fatty acids (≥25 carbons) in the meibomian gland. To verify the detailed mechanism of the low tear volume in the n-3 fatty acid-deficient mice, we identified the very long chain fatty acids in the meibomian gland, measured the fatty acid composition in the tear product. Very long chain fatty acids were found to exist as monoesters. In particular, very long chain fatty acids with 25-29 carbons existed for the most part as iso or anteiso branched-chain fatty acids. n-3 fatty acid deficiency was decreased the amount of meibum secretion from meibomian gland without change of fatty acid composition. These results suggest that the n-3 fatty acid deficiency causes the enhancement of evaporation of tear film by reducing oily tear secretion along with the decrease of meibomian gland function. Copyright © 2015 Elsevier Ltd. All rights reserved.

New approaches towards the synthesis of the side-chain of mycolactones A and B

NARCIS (Netherlands)

van Summeren, RP; Feringa, BL; Minnaard, AJ; Summeren, Ruben P. van

2005-01-01

New approaches towards the synthesis of the C1' - C16' side-chain of mycolactones A and B from Mycobacterium ulcerans are reported. Chiral building block 4 ( Fig. 2) with the correct stereochemistry was obtained starting from naturally occurring monosaccharides, i.e. D-glucose or L-rhamnose. The

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

KAUST Repository

Yiu, Alan T.; Beaujuge, Pierre; Lee, Olivia P.; Woo, Claire; Toney, Michael F.; Frechet, Jean

2012-01-01

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

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

KAUST Repository

Yiu, Alan T.

2012-02-01

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

Improvement in carrier mobility and photovoltaic performance through random distribution of segments of linear and branched side chains

Energy Technology Data Exchange (ETDEWEB)

Egbe, Daniel A.M.; Adam, Getachew; Pivrikas, Almantas; Ulbricht, Christoph; Ramil, Alberto M.; Sariciftci, Niyazi Serdar [Johannes Kepler Univ., Linz (AT). Linz Inst. for Organic Solar Cells (LIOS); Hoppe, Harald [Technische Univ. Ilmenau (Germany). Inst. of Physics and Inst. of Micro- and Nanotechnologies; Rathgeber, Silke [Mainz Univ. (Germany). Inst. of Physics

2010-07-01

The random distribution of segments of linear octyloxy side chains and of branched 2-ethylhexyloxy side chains, on the backbone of anthracene containing poly(p-phenylene-ethynylene)-alt-poly(p-phenylene-vinylene) (PPE-PPV) has resulted in a side chain based statistical copolymer, denoted AnE-PVstat, showing optimized features as compared to the well defined homologues AnE-PVaa, -ab, -ba and -bb, whose constitutional units are incorporated into its backbone. WAXS studies on AnE-P's demonstrate the highest degree of order at the self-assembly state of AnE-PVstat, which is confirmed by its highly structured thin film absorption band. Electric field independent charge carrier mobility ({mu}{sub hole}) for AnE-PVstat was demonstrated by CELIV and OFET measurements, both methods resulting in similar {mu}{sub hole} values of up to 5.43 x 10{sup -4} cm{sup 2}/Vs. Upon comparison, our results show that charge carrier mobility as measured by CELIV technique is predominantly an intrachain process and less an interchain one, which is in line with past photoconductivity results from PPE-PPV based materials. The present side chain distribution favors efficient solar cell active layer phase separation. As a result, a smaller amount of PC{sub 60}BM is needed to achieve relatively high energy conversion efficiencies above 3 %. The efficiency of {eta}{sub AM1.5} {approx} 3.8 % obtained for AnE-PVstat:PC{sub 60}BM blend is presently the state-of-art value for PPV-based materials. (orig.)

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

Science.gov (United States)

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

2015-02-01

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

Dissociation of branched-chain alpha-keto acid dehydrogenase kinase (BDK) from branched-chain alpha-keto acid dehydrogenase complex (BCKDC) by BDK inhibitors.

Science.gov (United States)

Murakami, Taro; Matsuo, Masayuki; Shimizu, Ayako; Shimomura, Yoshiharu

2005-02-01

Branched-chain alpha-keto acid dehydrogenase kinase (BDK) phosphorylates and inactivates the branched-chain alpha-keto acid dehydrogenase complex (BCKDC), which is the rate-limiting enzyme in the branched-chain amino acid catabolism. BDK has been believed to be bound to the BCKDC. However, recent our studies demonstrated that protein-protein interaction between BDK and BCKDC is one of the factors to regulate BDK activity. Furthermore, only the bound form of BDK appears to have its activity. In the present study, we examined effects of BDK inhibitors on the amount of BDK bound to the BCKDC using rat liver extracts. The bound form of BDK in the extracts of liver from low protein diet-fed rats was measured by an immunoprecipitation pull down assay with or without BDK inhibitors. Among the BDK inhibitors. alpha-ketoisocaproate, alpha-chloroisocaproate, and a-ketoisovalerate released the BDK from the complex. Furthermore, the releasing effect of these inhibitors on the BDK appeared to depend on their inhibition constants. On the other hand, clofibric acid and thiamine pyrophosphate had no effect on the protein-protein interaction between two enzymes. These results suggest that the dissociation of the BDK from the BCKDC is one of the mechanisms responsible for the action of some inhibitors to BDK.

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

Directory of Open Access Journals (Sweden)

Yih-Dean Jan

2014-04-01

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

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

DEFF Research Database (Denmark)

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

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...

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

NARCIS (Netherlands)

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

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

DISTRIBUTION OF GBM HEPARAN-SULFATE PROTEOGLYCAN CORE PROTEIN AND SIDE-CHAINS IN HUMAN GLOMERULAR-DISEASES

NARCIS (Netherlands)

VANDENBORN, J; VANDENHEUVEL, LPWJ; BAKKER, MAH; VEERKAMP, JH; ASSMANN, KJM; WEENING, JJ; BERDEN, JHM

Using monoclonal antibodies (mAbs) recognizing either the core protein or the heparan sulfate (HS) side chain of human GBM heparan sulfate proteoglycan (HSPG), we investigated their glomerular distribution on cryostat sections of human kidney tissues. The study involved 95 biopsies comprising twelve

Odd- and branched-chain fatty acids in milk fat – characteristic and health properties

Directory of Open Access Journals (Sweden)

Agata Adamska

2014-08-01

Full Text Available This review analyzes the current state of knowledge on odd- and branched-chain fatty acids present in milk fat. Special attention is devoted to the characteristic, synthesis in ruminants, factors affecting their content in milk fat and pro-health properties of these compounds. The group of odd- and branched-chain fatty acids includes mainly saturated fatty acids with one or more methyl branches in the iso or anteiso position. These fatty acids are largely derived from ruminal bacteria and they have been transferred to ruminant tissue (milk and meat. For that reason they have been used as biomarkers of rumen fermentation. Odd- and branched-chain fatty acids are exogenous products for humans, and therefore have specific properties. The results of research from recent decades show that odd- and branched-chain fatty acids have anti-cancer activity. Branched-chain fatty acids may reduce the incidence of necrotizing enterocolitis. Additionally, these compounds have a beneficial effect on proper tissue function and on functioning and development of the infant gut, whereas odd-chain fatty acids are considered as biomarkers of milk fat intake by humans. So far, not all the mechanisms of activity of these compounds are known thoroughly. They should be more carefully studied for application of their biological effects in prevention and treatment.

Molecular origin of urea driven hydrophobic polymer collapse and unfolding depending on side chain chemistry.

Science.gov (United States)

Nayar, Divya; Folberth, Angelina; van der Vegt, Nico F A

2017-07-19

Osmolytes affect hydrophobic collapse and protein folding equilibria. The underlying mechanisms are, however, not well understood. We report large-scale conformational sampling of two hydrophobic polymers with secondary and tertiary amide side chains using extensive molecular dynamics simulations. The calculated free energy of unfolding increases with urea for the secondary amide, yet decreases for the tertiary amide, in agreement with experiment. The underlying mechanism is rooted in opposing entropic driving forces: while urea screens the hydrophobic macromolecular interface and drives unfolding of the tertiary amide, urea's concomitant loss in configurational entropy drives collapse of the secondary amide. Only at sufficiently high urea concentrations bivalent urea hydrogen bonding interactions with the secondary amide lead to further stabilisation of its collapsed state. The observations provide a new angle on the interplay between side chain chemistry, urea hydrogen bonding, and the role of urea in attenuating or strengthening the hydrophobic effect.

Aromatic Side Chain Water-to-Lipid Transfer Free Energies Show a Depth Dependence across the Membrane Normal.

Science.gov (United States)

McDonald, Sarah K; Fleming, Karen G

2016-06-29

Quantitating and understanding the physical forces responsible for the interactions of biomolecules are fundamental to the biological sciences. This is especially challenging for membrane proteins because they are embedded within cellular bilayers that provide a unique medium in which hydrophobic sequences must fold. Knowledge of the energetics of protein-lipid interactions is thus vital to understand cellular processes involving membrane proteins. Here we used a host-guest mutational strategy to calculate the Gibbs free energy changes of water-to-lipid transfer for the aromatic side chains Trp, Tyr, and Phe as a function of depth in the membrane. This work reveals an energetic gradient in the transfer free energies for Trp and Tyr, where transfer was most favorable to the membrane interfacial region and comparatively less favorable into the bilayer center. The transfer energetics follows the concentration gradient of polar atoms across the bilayer normal that naturally occurs in biological membranes. Additional measurements revealed nearest-neighbor coupling in the data set are influenced by a network of aromatic side chains in the host protein. Taken together, these results show that aromatic side chains contribute significantly to membrane protein stability through either aromatic-aromatic interactions or placement at the membrane interface.

Gas-phase salt bridge interactions between glutamic acid and arginine

NARCIS (Netherlands)

Jaeqx, S.; Oomens, J.; Rijs, A.M.

2013-01-01

The gas-phase side chain-side chain (SC-SC) interaction and possible proton transfer between glutamic acid (Glu) and arginine (Arg) residues are studied under low-temperature conditions in an overall neutral peptide. Conformation-specific IR spectra, obtained with the free electron laser FELIX, in

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

DEFF Research Database (Denmark)

Li, Xue; Zhao, Yang; Li, Weiwei

2017-01-01

In order to study the microstructure of the prepared potential proton exchange membrane (PEM), molecular dynamics (MD) simulations were used to lucubrate the transport behavior of water molecules and hydronium ions inside the hydrated sulfonated styrene grafted fluorinated ethylene propylene (FEP...... whereas larger water clusters formed. The results of the mean square displacements (MSDs) show that the proton conductivities of the membranes with the proposed side chain lengths were about three fifths of the experimental data, of which the membrane with side chain length of 7 sulfonic styrene units...... was supposed to exhibit the highest proton conductivity, that is 115.69 mS cm-1. All of the supposed membrane models presented good proton conductivity that could definitely meet the application requirements of the proton exchange membranes. The MD simulations can provide an insight to the chain structure...

Chemoselective O-acylation of hydroxyamino acids and amino alcohols under acidic reaction conditions: History, scope and applications

Directory of Open Access Journals (Sweden)

Tor E. Kristensen

2015-04-01

Full Text Available Amino acids, whether natural, semisynthetic or synthetic, are among the most important and useful chiral building blocks available for organic chemical synthesis. In principle, they can function as inexpensive, chiral and densely functionalized starting materials. On the other hand, the use of amino acid starting materials routinely necessitates protective group chemistry, and in reality, large-scale preparations of even the simplest side-chain derivatives of many amino acids often become annoyingly strenuous due to the necessity of employing protecting groups, on one or more of the amino acid functionalities, during the synthetic sequence. However, in the case of hydroxyamino acids such as hydroxyproline, serine, threonine, tyrosine and 3,4-dihydroxyphenylalanine (DOPA, many O-acyl side-chain derivatives are directly accessible via a particularly expedient and scalable method not commonly applied until recently. Direct acylation of unprotected hydroxyamino acids with acyl halides or carboxylic anhydrides under appropriately acidic reaction conditions renders possible chemoselective O-acylation, furnishing the corresponding side-chain esters directly, on multigram-scale, in a single step, and without chromatographic purification. Assuming a certain degree of stability under acidic reaction conditions, the method is also applicable for a number of related compounds, such as various amino alcohols and the thiol-functional amino acid cysteine. While the basic methodology underlying this approach has been known for decades, it has evolved through recent developments connected to amino acid-derived chiral organocatalysts to become a more widely recognized procedure for large-scale preparation of many useful side-chain derivatives of hydroxyamino acids and related compounds. Such derivatives are useful in peptide chemistry and drug development, as amino acid amphiphiles for asymmetric catalysis, and as amino acid acrylic precursors for preparation of

Chemoselective O-acylation of hydroxyamino acids and amino alcohols under acidic reaction conditions: History, scope and applications

Science.gov (United States)

2015-01-01

Summary Amino acids, whether natural, semisynthetic or synthetic, are among the most important and useful chiral building blocks available for organic chemical synthesis. In principle, they can function as inexpensive, chiral and densely functionalized starting materials. On the other hand, the use of amino acid starting materials routinely necessitates protective group chemistry, and in reality, large-scale preparations of even the simplest side-chain derivatives of many amino acids often become annoyingly strenuous due to the necessity of employing protecting groups, on one or more of the amino acid functionalities, during the synthetic sequence. However, in the case of hydroxyamino acids such as hydroxyproline, serine, threonine, tyrosine and 3,4-dihydroxyphenylalanine (DOPA), many O-acyl side-chain derivatives are directly accessible via a particularly expedient and scalable method not commonly applied until recently. Direct acylation of unprotected hydroxyamino acids with acyl halides or carboxylic anhydrides under appropriately acidic reaction conditions renders possible chemoselective O-acylation, furnishing the corresponding side-chain esters directly, on multigram-scale, in a single step, and without chromatographic purification. Assuming a certain degree of stability under acidic reaction conditions, the method is also applicable for a number of related compounds, such as various amino alcohols and the thiol-functional amino acid cysteine. While the basic methodology underlying this approach has been known for decades, it has evolved through recent developments connected to amino acid-derived chiral organocatalysts to become a more widely recognized procedure for large-scale preparation of many useful side-chain derivatives of hydroxyamino acids and related compounds. Such derivatives are useful in peptide chemistry and drug development, as amino acid amphiphiles for asymmetric catalysis, and as amino acid acrylic precursors for preparation of

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

DEFF Research Database (Denmark)

Han, Mina; Kidowaki, Masatoshi; Ichimura, Kunihiro

2001-01-01

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

Azide- and Alkyne-Functionalised α- and β3-Amino Acids

DEFF Research Database (Denmark)

Sminia, T.J.; Pedersen, Daniel Sejer

2012-01-01

The synthesis and full characterisation of bifunctional β -amino acids that have side chains functionalised with terminal azides (S)-4 and (R)-4 or acetylenes 5 and 6 is reported for the first time. The building blocks incorporate a turn-inducing β -segment and a side chain that can...... be functionalised further, for example, through copper-catalysed Huisgen cycloaddition. Moreover, the corresponding α-amino acids 1 and 3 have been synthesised and characterised. All amino acid building blocks were of high optical purity as demonstrated by derivatisation and subsequent NMR analysis....

Activity of 3-Ketosteroid 9α-Hydroxylase (KshAB) Indicates Cholesterol Side Chain and Ring Degradation Occur Simultaneously in Mycobacterium tuberculosis*

Science.gov (United States)

Capyk, Jenna K.; Casabon, Israël; Gruninger, Robert; Strynadka, Natalie C.; Eltis, Lindsay D.

2011-01-01

Mycobacterium tuberculosis (Mtb), a significant global pathogen, contains a cholesterol catabolic pathway. Although the precise role of cholesterol catabolism in Mtb remains unclear, the Rieske monooxygenase in this pathway, 3-ketosteroid 9α-hydroxylase (KshAB), has been identified as a virulence factor. To investigate the physiological substrate of KshAB, a rhodococcal acyl-CoA synthetase was used to produce the coenzyme A thioesters of two cholesterol derivatives: 3-oxo-23,24-bisnorchol-4-en-22-oic acid (forming 4-BNC-CoA) and 3-oxo-23,24-bisnorchola-1,4-dien-22-oic acid (forming 1,4-BNC-CoA). The apparent specificity constant (kcat/Km) of KshAB for the CoA thioester substrates was 20–30 times that for the corresponding 17-keto compounds previously proposed as physiological substrates. The apparent KmO2 was 90 ± 10 μm in the presence of 1,4-BNC-CoA, consistent with the value for two other cholesterol catabolic oxygenases. The Δ1 ketosteroid dehydrogenase KstD acted with KshAB to cleave steroid ring B with a specific activity eight times greater for a CoA thioester than the corresponding ketone. Finally, modeling 1,4-BNC-CoA into the KshA crystal structure suggested that the CoA moiety binds in a pocket at the mouth of the active site channel and could contribute to substrate specificity. These results indicate that the physiological substrates of KshAB are CoA thioester intermediates of cholesterol side chain degradation and that side chain and ring degradation occur concurrently in Mtb. This finding has implications for steroid metabolites potentially released by the pathogen during infection and for the design of inhibitors for cholesterol-degrading enzymes. The methodologies and rhodococcal enzymes used to generate thioesters will facilitate the further study of cholesterol catabolism. PMID:21987574

Activity of 3-ketosteroid 9α-hydroxylase (KshAB) indicates cholesterol side chain and ring degradation occur simultaneously in Mycobacterium tuberculosis.

Science.gov (United States)

Capyk, Jenna K; Casabon, Israël; Gruninger, Robert; Strynadka, Natalie C; Eltis, Lindsay D

2011-11-25

Mycobacterium tuberculosis (Mtb), a significant global pathogen, contains a cholesterol catabolic pathway. Although the precise role of cholesterol catabolism in Mtb remains unclear, the Rieske monooxygenase in this pathway, 3-ketosteroid 9α-hydroxylase (KshAB), has been identified as a virulence factor. To investigate the physiological substrate of KshAB, a rhodococcal acyl-CoA synthetase was used to produce the coenzyme A thioesters of two cholesterol derivatives: 3-oxo-23,24-bisnorchol-4-en-22-oic acid (forming 4-BNC-CoA) and 3-oxo-23,24-bisnorchola-1,4-dien-22-oic acid (forming 1,4-BNC-CoA). The apparent specificity constant (k(cat)/K(m)) of KshAB for the CoA thioester substrates was 20-30 times that for the corresponding 17-keto compounds previously proposed as physiological substrates. The apparent K(m)(O(2)) was 90 ± 10 μM in the presence of 1,4-BNC-CoA, consistent with the value for two other cholesterol catabolic oxygenases. The Δ(1) ketosteroid dehydrogenase KstD acted with KshAB to cleave steroid ring B with a specific activity eight times greater for a CoA thioester than the corresponding ketone. Finally, modeling 1,4-BNC-CoA into the KshA crystal structure suggested that the CoA moiety binds in a pocket at the mouth of the active site channel and could contribute to substrate specificity. These results indicate that the physiological substrates of KshAB are CoA thioester intermediates of cholesterol side chain degradation and that side chain and ring degradation occur concurrently in Mtb. This finding has implications for steroid metabolites potentially released by the pathogen during infection and for the design of inhibitors for cholesterol-degrading enzymes. The methodologies and rhodococcal enzymes used to generate thioesters will facilitate the further study of cholesterol catabolism.

Metabolism of Very Long-Chain Fatty Acids: Genes and Pathophysiology

OpenAIRE

Sassa, Takayuki; Kihara, Akio

2014-01-01

Fatty acids (FAs) are highly diverse in terms of carbon (C) chain-length and number of double bonds. FAs with C>20 are called very long-chain fatty acids (VLCFAs). VLCFAs are found not only as constituents of cellular lipids such as sphingolipids and glycerophospholipids but also as precursors of lipid mediators. Our understanding on the function of VLCFAs is growing in parallel with the identification of enzymes involved in VLCFA synthesis or degradation. A variety of inherited diseases, suc...

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

CSIR Research Space (South Africa)

Reddy, GSM

2013-05-01

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

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

KAUST Repository

El Labban, Abdulrahman; Warnan, Julien; Cabanetos, Clement; Ratel, Olivier; Tassone, Christopher J.; Toney, Michael F.; Beaujuge, Pierre

2014-01-01

-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

side chains

African Journals Online (AJOL)

USER

The effect of ionic exchange degree of aluminated mesoporous materials H(X)- ... zeolites catalysts in cumene conversion and observed distinct differences in the ... with HCl acid solution with varied concentration going from 0.01 N to 0.5 N by .... 14. 16. 18. 20. Number of pulse. Cu m en e co n v ersio n. (%. ) 673. 673. 623.

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

Science.gov (United States)

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

2016-03-09

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

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

Directory of Open Access Journals (Sweden)

Ilona M. Heckler

2016-03-01

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

Prenatal long-chain polyunsaturated fatty acid status : the importance of a balanced intake of docosahexaenoic acid and arachidonic acid

NARCIS (Netherlands)

Hadders-Algra, Mijna

2008-01-01

This review addresses the effect of prenatal long-chain polyunsaturated fatty acid (LCPUFA) status on neuro-developmental outcome. It focuses on the major LPCUFA doxosahexaenoic acid (DNA; 22:6 omega 3) and arachidonic acid (AA; 20:4 omega 6). Due to enzymatic competition high DHA intake results in

Whole-body nitrogen and tyrosine metabolism in surgical patients receiving branched-chain amino acid solutions

International Nuclear Information System (INIS)

Desai, S.P.; Bistrian, B.R.; Moldawer, L.L.; Blackburn, G.L.

1985-01-01

Fifteen patients undergoing gastric bypass surgery for morbid obesity received preoperatively a standard crystalline amino acid solution containing 15.6% branched-chain amino acids. During the first five postoperative days, the patients were randomized to receive one of three amino acid solutions of different branched-chain amino acid content. Whole-body amino acid appearance and oxidation were estimated using a continuous intravenous infusion of L-(U- 14 C)-tyrosine preoperatively and on the third postoperative day. This study suggests that an adequate nitrogen intake of a balanced amino acid mixture, as well as a solution enriched with branched-chain amino acids, maintains protein homeostasis and supports protein synthesis similarly in well-nourished patients following major abdominal surgery. A diet containing only branched-chain amino acids in isomolar ratios was as effective at maintaining protein retention and whole-body protein synthesis and albumin renewal postoperatively when compared with a standard amino acid formula

Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization.

Science.gov (United States)

Ran-Ressler, Rinat R; Lawrence, Peter; Brenna, J Thomas

2012-01-01

Saturated branched chain fatty acids (BCFA) are present as complex mixtures in numerous biological samples. The traditional method for structure elucidation, electron ionization (EI) mass spectrometry, sometimes does not unambiguously enable assignment of branching in isomeric BCFA. Zirrolli and Murphy (Zirrolli , J. A. , and R. A. Murphy. 1993. Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: a novel method for analysis of branched-chain fatty acids. J. Am. Soc. Mass Spectrom. 4: 223-229.) showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confirm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso-BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C₃H₇), corresponding to the terminal isopropyl moiety in the original iso-BCFAME. Anteiso-FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specific ions that enable highly confident structural identification and quantification of BCFAME.

Naphthalenetetracarboxylic diimide layer-based transistors with nanometer oxide and side chain dielectrics operating below one volt.

Science.gov (United States)

Jung, Byung Jun; Martinez Hardigree, Josue F; Dhar, Bal Mukund; Dawidczyk, Thomas J; Sun, Jia; See, Kevin Cua; Katz, Howard E

2011-04-26

We designed a new naphthalenetetracarboxylic diimide (NTCDI) semiconductor molecule with long fluoroalkylbenzyl side chains. The side chains, 1.2 nm long, not only aid in self-assembly and kinetically stabilize injected electrons but also act as part of the gate dielectric in field-effect transistors. On Si substrates coated only with the 2 nm thick native oxide, NTCDI semiconductor films were deposited with thicknesses from 17 to 120 nm. Top contact Au electrodes were deposited as sources and drains. The devices showed good transistor characteristics in air with 0.1-1 μA of drain current at 0.5 V of V(G) and V(DS) and W/L of 10-20, even though channel width (250 μm) is over 1000 times the distance (20 nm) between gate and drain electrodes. The extracted capacitance-times-mobility product, an expression of the sheet transconductance, can exceed 100 nS V(-1), 2 orders of magnitude higher than typical organic transistors. The vertical low-frequency capacitance with gate voltage applied in the accumulation regime reached as high as 650 nF/cm(2), matching the harmonic sum of capacitances of the native oxide and one side chain and indicating that some gate-induced carriers in such devices are distributed among all of the NTCDI core layers, although the preponderance of the carriers are still near the gate electrode. Besides demonstrating and analyzing thickness-dependent NTCDI-based transistor behavior, we also showed <1 V detection of dinitrotoluene vapor by such transistors.

Synthesis and anti-HIV activity of novel N-1 side chain-modified analogs of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT).

Science.gov (United States)

Pontikis, R; Benhida, R; Aubertin, A M; Grierson, D S; Monneret, C

1997-06-06

A series of 33 N-1 side chain-modified analogs of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (1, HEPT) were synthesized and evaluated for their anti-HIV-1 activity. In particular, the influence of substitution of the terminal hydroxy group of the acyclic structure of HEPT and the structural rigidity of this side chain were investigated. Halo (7, 8), azido (9), and amino (10-15) derivatives were synthesized from HEPT via the p-tosylate derivative 6. Acylation of the primary amine 15 afforded the amido analogs 16-20. The diaryl derivatives 26-29 were prepared by reaction of HEPT, or of the 6-(2-pyridylthio) analog 23, with diaryl disulfides in the presence of tri-n-butylphosphine. Compounds 39-41, in which the N-1 side chain is rigidified by incorporation of an E-configured double bond, were obtained by palladium(0)-catalyzed coupling of several different 6-(arylthio)uracil derivatives (37, 38) with allyl acetates 33. Compounds 13, 40a,c,d,f, and 41, incorporating an aromatic ring at the end of the acyclic side chain, were found to be more potent than the known diphenyl-substituted HEPT analog BPT (2), two of them, 40c,d, being 10-fold more active.

Effect of Difference in Fatty Acid Chain Lengths of Medium- Chain Lipids on Lipid/Surfactant/Water Phase Diagrams and Drug Solubility

Directory of Open Access Journals (Sweden)

Hetal N. Prajapati

2011-09-01

Full Text Available Lipids consisting of medium chain fatty acids are commonly used in the development of lipid-based selfemulsifying and self-microemulsifying drug delivery systems. However, no systematic approach to selecting one lipid over another has been reported in the literature. In this study, propylene glycol (PG monoester (PG monocaprylate, Capmul PG-8® and PG diester (PG dicaprylocaprate, Captex 200P® of C8-fatty acids were compared with PG monoester (PG monolaurate, Capmul PG-12® and PG diester (PG dilaurate, Capmul PG-2L® of C12-fatty acids with respect to their phase diagrams, and especially for their ability to form microemulsions in the presence of a common surfactant, Cremophor EL®, and water. The solubility of two model drugs, danazol and probucol, in the lipids and lipid/surfactant mixtures were also compared. The effect of the chain length of medium-chain fatty acids (C8 versus C12 on the phase diagrams of the lipids was minimal. Both shorter and longer chain lipids formed essentially similar microemulsion and emulsion regions in the presence of Cremophor EL® and water, although the C12-fatty acid esters formed larger gel regions in the phase diagrams than the C8-fatty acid esters. When monoesters were mixed with their respective diesters at 1:1 ratios, larger microemulsion regions with lower lipid particle sizes were observed compared to those obtained with individual lipids alone. While the solubility of both danazol and probucol increased greatly in all lipids studied, compared to their aqueous solubility, the solubility in C12-fatty acid esters was found to be lower than in C8-fatty acid esters when the lipids were used alone. This difference in solubility due to the difference in fatty acid chain length, practically disappeared when the lipids were combined with the surfactant.

Main chain acid-degradable polymers for the delivery of bioactive materials

Science.gov (United States)

Frechet, Jean M. J. [Oakland, CA; Standley, Stephany M [Evanston, IL; Jain, Rachna [Milpitas, CA; Lee, Cameron C [Cambridge, MA

2012-03-20

Novel main chain acid degradable polymer backbones and drug delivery systems comprised of materials capable of delivering bioactive materials to cells for use as vaccines or other therapeutic agents are described. The polymers are synthesized using monomers that contain acid-degradable linkages cleavable under mild acidic conditions. The main chain of the resulting polymers readily degrade into many small molecules at low pH, but remain relatively stable and intact at physiological pH. The new materials have the common characteristic of being able to degrade by acid hydrolysis under conditions commonly found within the endosomal or lysosomal compartments of cells thereby releasing their payload within the cell. The materials can also be used for the delivery of therapeutics to the acidic regions of tumors and other sites of inflammation.

the influence of aliphatic side chain of anacardic acid on molecular ...

African Journals Online (AJOL)

Mgina

synthesized and used as a functional monomer to prepare imprinted polymers for comparison with ... precipitation polymerization method. MATERIALS ... HCl. O. OH. O. O. 2. Scheme 1: Synthesis of SaMcr. Salicylic acid (2.49 g, 18 mmol) was.

Utilizing alkoxyphenyl substituents for side-chain engineering of efficient benzo[1,2-b:4,5-b ']dithiophene-based small molecule organic solar cells

DEFF Research Database (Denmark)

Du, Zhengkun; Chen, Weichao; Qiu, Meng

2015-01-01

-processed organic solar cells (OSCs) as an electron donor material, in which an alkoxyphenyl group was introduced as a weak electrondonating side chain of the BDT moiety. The DCA3TBDTP molecule exhibited good solubility, a deep highest occupied molecular orbital (HOMO) level (-5.25 eV), an appropriate optical band......-gap (1.82 eV) and a high decomposition temperature (362 degrees C). By applying the simple solution spin-coating fabrication process, the bulk heterojunction (BHJ) OSCs based on DCA3TBDTP and [6,6]-phenyl-C-61-butyric acid methyl ester (PC61BM) exhibited a good power conversion efficiency (PCE) of 4...

Oxidative cleavage of the octyl side chain of 1-(3,4-dichlorobenzyl)-5-octylbiguanide (OPB-2045) in rat and dog liver preparations.

Science.gov (United States)

Umehara, K; Kudo, S; Hirao, Y; Morita, S; Uchida, M; Odomi, M; Miyamoto, G

2000-08-01

The metabolism of 1-(3,4-dichlorobenzyl)-5-octylbiguanide (OPB-2045), a new potent biguanide antiseptic, was investigated using rat and dog liver preparations to elucidate the mechanism of OPB-2045 metabolite formation, in which the octyl side chain is reduced to four, five, or six carbon atoms. Chemical structures of metabolites were characterized by 1H NMR, fast atom bombardment/mass spectrometry, and liquid chromatography/electrospray ionization-tandem mass spectrometry. Three main metabolites were observed during incubation of OPB-2045 with rat liver S9: 2-octanol (M-1), 3-octanol (M-2), and 4-octanol (M-3). In the incubation of OPB-2045 with dog liver S9, eight metabolites were observed, seven of which being M-1, M-2, M-3, 2-octanone (M-4), threo-2,3-octandiol (M-5), erythro-2,3-octandiol (M-6), and 1,2-octandiol (M-7). M-5 and M-6 were further biotransformed to a ketol derivative and C-C bond cleavage metabolite (hexanoic acid derivative), an in vivo end product, in the incubation with dog liver microsomes. The reactions required NADPH as a cofactor and were significantly inhibited by the various inhibitors of cytochrome P450 (i.e., CO, n-octylamine, SKF 525-A, metyrapone, and alpha-naphthoflavone). The results indicate that the degraded products of OPB-2045 are produced by C-C bond cleavage after monohydroxylation, dihydroxylation, and ketol formation at the site of the octyl side chain with possible involvement of cytochrome P450 systems. This aliphatic C-C bond cleavage by sequential oxidative reactions may play an important role in the metabolism of other drugs or endogenous compounds that possess aliphatic chains.

CONTENT OF LONG CHAIN OMEGA-3 FATTY ACID COMPOSITION IN SOME IRANIAN CANNED FISH

Directory of Open Access Journals (Sweden)

Bahar Nazari

2010-12-01

Full Text Available Abstract    BACKGROUND: Ecological studies have found a negative correlation between the risk of developing heart disease and fish consumption because of their long chain omega-3 fatty acids. This study was undertaken to determine the amounts of the common fatty acid content of several commercial canned fish marketing in Iran, with particular attention to long chain omega-3 fatty acids.    METHODS: The most consumed available brands of canned fish were randomly selected seven times from products available in supermarkets. Total lipids were extracted by using the Folch method and prepared for fatty acid analysis. Individual fatty acids were quantified by gas chromatography (GC with 60 meter capillary column and flame ionization detector.    RESULTS: The most common saturated fatty acids (SFA in Iranian canned fish was palmitic acid (C16:0 followed by stearic acid (C18:0. The amount of all trans fatty acids (TFAs except elaidic acid (C18:1 9t was 0%. The highest amount of polyunsaturated fatty acids (PUFAs related to long chain omega-3 fatty acids include eicosapentaenoic acid (EPA and docosahexaenoic acid (DHA. The most abundant monounsaturated fatty acids (MUFAs were oleic acid (C18:1 9c.     CONCLUSION: This study showed higher contents of EPA and DHA in Iranian commercially available canned fish compared to the canned fish in other countries.      Keywords: Iranian canned fish, fatty acids, long chain omega-3 fatty acids, gas chromatography.  

A targeted metabolomic protocol for short-chain fatty acids and branched-chain amino acids.

Science.gov (United States)

Zheng, Xiaojiao; Qiu, Yunping; Zhong, Wei; Baxter, Sarah; Su, Mingming; Li, Qiong; Xie, Guoxiang; Ore, Brandon M; Qiao, Shanlei; Spencer, Melanie D; Zeisel, Steven H; Zhou, Zhanxiang; Zhao, Aihua; Jia, Wei

2013-08-01

Research in obesity and metabolic disorders that involve intestinal microbiota demands reliable methods for the precise measurement of the short-chain fatty acids (SCFAs) and branched-chain amino acids (BCAAs) concentration. Here, we report a rapid method of simultaneously determining SCFAs and BCAAs in biological samples using propyl chloroformate (PCF) derivatization followed by gas chromatography mass spectrometry (GC-MS) analysis. A one-step derivatization using 100 µL of PCF in a reaction system of water, propanol, and pyridine (v/v/v = 8:3:2) at pH 8 provided the optimal derivatization efficiency. The best extraction efficiency of the derivatized products was achieved by a two-step extraction with hexane. The method exhibited good derivatization efficiency and recovery for a wide range of concentrations with a low limit of detection for each compound. The relative standard deviations (RSDs) of all targeted compounds showed good intra- and inter-day (within 7 days) precision (< 10%), and good stability (< 20%) within 4 days at room temperature (23-25 °C), or 7 days when stored at -20 °C. We applied our method to measure SCFA and BCAA levels in fecal samples from rats administrated with different diet. Both univariate and multivariate statistics analysis of the concentrations of these target metabolites could differentiate three groups with ethanol intervention and different oils in diet. This method was also successfully employed to determine SCFA and BCAA in the feces, plasma and urine from normal humans, providing important baseline information of the concentrations of these metabolites. This novel metabolic profile study has great potential for translational research.

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

KAUST Repository

Kiefer, David; Giovannitti, Alexander; Sun, Hengda; Biskup, Till; Hofmann, Anna; Koopmans, Marten; Cendra, Camila; Weber, Stefan; Anton Koster, L. Jan; Olsson, Eva; Rivnay, Jonathan; Fabiano, Simone; McCulloch, Iain; Mü ller, Christian

2018-01-01

(gNDI-gT2) that carries oligoethylene glycol-based side chains and show that the polymer displays superior miscibility with the benzimidazole–dimethylbenzenamine-based n-dopant N-DMBI. The good compatibility of p(gNDI-gT2) and N-DMBI results in a relatively

A Strategy Combining Higher Energy C-Trap Dissociation with Neutral Loss- and Product Ion-Based MSn Acquisition for Global Profiling and Structure Annotation of Fatty Acids Conjugates.

Science.gov (United States)

Bi, Qi-Rui; Hou, Jin-Jun; Yang, Min; Shen, Yao; Qi, Peng; Feng, Rui-Hong; Dai, Zhuo; Yan, Bing-Peng; Wang, Jian-Wei; Shi, Xiao-Jian; Wu, Wan-Ying; Guo, De-An

2017-03-01

Fatty acids conjugates (FACs) are ubiquitous but found in trace amounts in the natural world. They are composed of multiple unknown substructures and side chains. Thus, FACs are difficult to be analyzed by traditional mass spectrometric methods. In this study, an integrated strategy was developed to global profiling and targeted structure annotation of FACs in complex matrix by LTQ Orbitrap. Dicarboxylic acid conjugated bufotoxins (DACBs) in Venenum bufonis (VB) were used as model compounds. The new strategy (abbreviated as HPNA) combined higher-energy C-trap dissociation (HCD) with product ion- (PI), neutral loss- (NL) based MS n (n ≥ 3) acquisition in both positive-ion mode and negative-ion mode. Several advantages are presented. First, various side chains were found under HCD in negative-ion mode, which included both known and unknown side chains. Second, DACBs with multiple side chains were simultaneously detected in one run. Compared with traditional quadrupole-based mass method, it greatly increased analysis throughput. Third, the fragment ions of side chain and steroids substructure could be obtained by PI- and NL-based MS n acquisition, respectively, which greatly increased the accuracy of the structure annotation of DACBs. In all, 78 DACBs have been discovered, of which 68 were new compounds; 25 types of substructure formulas and seven dicarboxylic acid side chains were found, especially five new side chains, including two saturated dicarboxylic acids [(azelaic acid (C 9 ) and sebacic acid (C 10 )] and three unsaturated dicarboxylic acids (u-C 8 , u-C 9 , and u-C 10 ). All these results greatly enriched the structures of DACBs in VB. Graphical Abstract ᅟ.

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

KAUST Repository

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.

A Tc-99m-labeled long chain fatty acid derivative for myocardial imaging.

Science.gov (United States)

Magata, Yasuhiro; Kawaguchi, Takayoshi; Ukon, Misa; Yamamura, Norio; Uehara, Tomoya; Ogawa, Kazuma; Arano, Yasushi; Temma, Takashi; Mukai, Takahiro; Tadamura, Eiji; Saji, Hideo

2004-01-01

C-11- and I-123-labeled long chain fatty acid derivatives have been reported as useful radiopharmaceuticals for the estimation of myocardial fatty acid metabolism. We have reported that Tc-99m-labeled N-[[[(2-mercaptoethyl)amino]carbonyl]methyl]-N-(2-mercaptoethyl)-6-aminohexanoic acid ([(99m)Tc]MAMA-HA), a medium chain fatty acid derivative, is metabolized by beta-oxidation in the liver and that the MAMA ligand is useful for attaching to the omega-position of fatty acid derivatives as a chelating group for Tc-99m. On the basis of these findings, we focused on developing a Tc-99m-labeled long chain fatty acid derivative that reflected fatty acid metabolism in the myocardium. In this study, we synthesized a dodecanoic acid derivative, MAMA-DA, and a hexadecanoic acid derivative, MAMA-HDA, and performed radiolabeling and biodistribution studies. [(99m)Tc]MAMA-DA and [(99m)Tc]MAMA-HDA were prepared using a ligand-exchange reaction. Biodistribution studies were carried out in normal mice and rats. Then, a high initial uptake of Tc-99m was observed, followed by a rapid clearance from the heart. The maximum heart/blood ratio was 3.6 at 2 min postinjection of [(99m)Tc]MAMA-HDA. These kinetics were similar to those with postinjection of p-[(125)I]iodophenylpentadecanoic acid. Metabolite analysis showed [(99m)Tc]MAMA-HDA was metabolized by beta-oxidation in the body. In conclusion, [(99m)Tc]MAMA-HDA is a promising compound as a long chain fatty acid analogue for estimating beta-oxidation of fatty acid in the heart.

Developmental changes in rat liver branched-chain 2-oxo acid dehydrogenase.

OpenAIRE

May, E E; May, M E; Aftring, R P; Buse, M G

1982-01-01

Branched-chain 2-oxo acid dehydrogenase catalyses the first irreversible step in the degradation of the branched-chain amino acids leucine, isoleucine and valine. With specifically labelled 4-methyl-2-oxo[1-14C]pentanoate as substrate, the enzyme's activity was measured in rat liver homogenates. Activity (per g wet wL of liver or per mg of protein) increased most rapidly during the perinatal period (2 days before to 1 day after birth), reaching approximately adult values by the time of weanin...

Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization[S

Science.gov (United States)

Ran-Ressler, Rinat R.; Lawrence, Peter; Brenna, J. Thomas

2012-01-01

Saturated branched chain fatty acids (BCFA) are present as complex mixtures in numerous biological samples. The traditional method for structure elucidation, electron ionization (EI) mass spectrometry, sometimes does not unambiguously enable assignment of branching in isomeric BCFA. Zirrolli and Murphy (Zirrolli , J. A. , and R. A. Murphy. 1993. Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: a novel method for analysis of branched-chain fatty acids. J. Am. Soc. Mass Spectrom. 4: 223–229.) showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confirm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso-BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C3H7), corresponding to the terminal isopropyl moiety in the original iso-BCFAME. Anteiso-FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specific ions that enable highly confident structural identification and quantification of BCFAME. PMID:22021637

Degradation of amino acids to short-chain fatty acids in humans. An in vitro study

DEFF Research Database (Denmark)

Rasmussen, H S; Holtug, K; Mortensen, P B

1988-01-01

Short-chain fatty acids (SCFA) originate mainly in the colon through bacterial fermentation of polysaccharides. To test the hypothesis that SCFA may originate from polypeptides as well, the production of these acids from albumin and specific amino acids was examined in a faecal incubation system....... Albumin was converted to all C2-C5-fatty acids, whereas amino acids generally were converted to specific SCFA, most often through the combination of a deamination and decarboxylation of the amino acids, although more complex processes also took place. This study indicates that a part of the intestinal...

[Overexpression of four fatty acid synthase genes elevated the efficiency of long-chain polyunsaturated fatty acids biosynthesis in mammalian cells].

Science.gov (United States)

Zhu, Guiming; Saleh, Abdulmomen Ali Mohammed; Bahwal, Said Ahmed; Wang, Kunfu; Wang, Mingfu; Wang, Didi; Ge, Tangdong; Sun, Jie

2014-09-01

Three long-chain polyunsaturated fatty acids, docosahexaenoic acid (DHA, 22:6n-3), eicosapentaenoic acid (EPA, 20:5n-3) and arachidonic acid (ARA, 20:4n-6), are the most biologically active polyunsaturated fatty acids in the body. They are important in developing and maintaining the brain function, and in preventing and treating many diseases such as cardiovascular disease, inflammation and cancer. Although mammals can biosynthesize these long-chain polyunsaturated fatty acids, the efficiency is very low and dietary intake is needed to meet the requirement. In this study, a multiple-genes expression vector carrying mammalian A6/A5 fatty acid desaturases and multiple-genes expression vector carrying mammalian Δ6/Δ5 fatty acid desaturases and Δ6/Δ5 fatty acid elongases coding genes was used to transfect HEK293T cells, then the overexpression of the target genes was detected. GC-MS analysis shows that the biosynthesis efficiency and level of DHA, EPA and ARA were significantly increased in cells transfected with the multiple-genes expression vector. Particularly, DHA level in these cells was 2.5 times higher than in the control cells. This study indicates mammal possess a certain mechanism for suppression of high level of biosynthesis of long chain polyunsaturated fatty acids, and the overexpression of Δ6/Δ5 fatty acid desaturases and Δ6/Δ5 fatty acid elongases broke this suppression mechanism so that the level of DHA, EPA and ARA was significantly increased. This study also provides a basis for potential applications of this gene construct in transgenic animal to produce high level of these long-chain polyunsaturated fatty acid.

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

KAUST Repository

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.

Gas chromatography/mass spectrometry analysis of very long chain fatty acids, docosahexaenoic acid, phytanic acid and plasmalogen for the screening of peroxisomal disorders

NARCIS (Netherlands)

Takemoto, Yasuhiko; Suzuki, Yasuyuki; Horibe, Ryoko; Shimozawa, Nobuyuki; Wanders, Ronald J. A.; Kondo, Naomi

2003-01-01

Very long chain fatty acids (VLCFAs) and docosahexaenoic acid (DHA), phytanic acid, and plasmalogens are usually measured individually. A novel method for the screening of peroxisomal disorders, using gas chromatography/mass spectrometry (GC/MS), was developed. Saturated and unsaturated fatty acids,

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

KAUST Repository

Zhou, Yan; Kurosawa, Tadanori; Ma, Wei; Guo, Yikun; Fang, Lei; Vandewal, Koen; Diao, Ying; Wang, Chenggong; Yan, Qifan; Reinspach, Julia; Mei, Jianguo; Appleton, Anthony Lucas; Koleilat, Ghada I.; Gao, Yongli; Mannsfeld, Stefan C. B.; Salleo, Alberto; Ade, Harald; Zhao, Dahui; Bao, Zhenan

2014-01-01

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.

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

KAUST Repository

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.

The Role of GPR84 in Medium-chain Saturated Fatty Acid Taste Transduction

OpenAIRE

Liu, Yan

2016-01-01

Previous research has shown the gustatory recognition of the long-chain unsaturated fatty acids. In this study, I showed for the first time that medium-chain saturated fatty acids (MCFAs) are effective taste stimuli at both the cellular and behavioral levels. The mechanisms of gustatory recognition of MCFAs in mice were also partially elucidated using pharmaceutical approaches. The inward currents induced by capric acid in mouse taste cells were significantly inhibited by the antagonists of G...

Two-stage medium chain fatty acid (MCFA) production from municipal solid waste and ethanol

NARCIS (Netherlands)

Grootscholten, T.I.M.; Strik, D.P.B.T.B.; Steinbusch, K.J.J.; Buisman, C.J.N.; Hamelers, B.

2014-01-01

Chain elongation is an anaerobic fermentation that produces medium chain fatty acids (MCFAs) from volatile fatty acids and ethanol. These MCFAs can be used as biochemical building blocks for fuel production and other chemical processes. Producing MCFAs from the organic fraction of municipal solid

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

Science.gov (United States)

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

2010-08-06

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

Branched-Chain Amino Acids.

Science.gov (United States)

Yamamoto, Keisuke; Tsuchisaka, Atsunari; Yukawa, Hideaki

Branched-chain amino acids (BCAAs), viz., L-isoleucine, L-leucine, and L-valine, are essential amino acids that cannot be synthesized in higher organisms and are important nutrition for humans as well as livestock. They are also valued as synthetic intermediates for pharmaceuticals. Therefore, the demand for BCAAs in the feed and pharmaceutical industries is increasing continuously. Traditional industrial fermentative production of BCAAs was performed using microorganisms isolated by random mutagenesis. A collection of these classical strains was also scientifically useful to clarify the details of the BCAA biosynthetic pathways, which are tightly regulated by feedback inhibition and transcriptional attenuation. Based on this understanding of the metabolism of BCAAs, it is now possible for us to pursue strains with higher BCAA productivity using rational design and advanced molecular biology techniques. Additionally, systems biology approaches using augmented omics information help us to optimize carbon flux toward BCAA production. Here, we describe the biosynthetic pathways of BCAAs and their regulation and then overview the microorganisms developed for BCAA production. Other chemicals, including isobutanol, i.e., a second-generation biofuel, can be synthesized by branching the BCAA biosynthetic pathways, which are also outlined.

Long-chain polyunsaturated fatty acids in maternal and infant nutrition

NARCIS (Netherlands)

Muskiet, Frits A. J.; van Goor, Saskia A.; Kuipers, Remko S.; Velzing-Aarts, Francien V.; Smit, Ella N.; Bouwstra, Hylco; Dijck-Brouwer, D. A. Janneke; Boersma, E. Rudy; Hadders-Algra, Mijna

Homo sapiens has evolved on a diet rich in alpha-linolenic acid and long chain polyunsaturated fatty acids (LCP). We have, however, gradually changed our diet from about 10,000 years ago and accelerated this change from about 100 to 200 years ago. The many dietary changes, including lower intake of

Interactions among the branched-chain amino acids and their effects on methionine utilization in growing pigs: effects on plasma amino- and keto-acid concentrations and branched-chain keto-acid dehydrogenase activity.

Science.gov (United States)

Langer, S; Scislowski, P W; Brown, D S; Dewey, P; Fuller, M F

2000-01-01

The present experiment was designed to elucidate the mechanism of the methionine-sparing effect of excess branched-chain amino acids (BCAA) reported in the previous paper (Langer & Fuller, 2000). Twelve growing gilts (30-35 kg) were prepared with arterial catheters. After recovery, they received for 7 d a semipurified diet with a balanced amino acid pattern. On the 7th day blood samples were taken before (16 h postabsorptive) and after the morning meal (4 h postprandial). The animals were then divided into three groups and received for a further 7 d a methionine-limiting diet (80% of requirement) (1) without any amino acid excess; (2) with excess leucine (50% over requirement); or (3) with excesses of all three BCAA (leucine, isoleucine, valine, each 50% over the requirement). On the 7th day blood samples were taken as in the first period, after which the animals were killed and liver and muscle samples taken. Plasma amino acid and branched-chain keto acid (BCKA) concentrations in the blood and branched-chain keto-acid dehydrogenase (BCKDH; EC 1.2.4.4) activity in liver and muscle homogenates were determined. Compared with those on the balanced diet, pigs fed on methionine-limiting diets had significantly lower (P < 0.05) plasma methionine concentrations in the postprandial but not in the postabsorptive state. There was no effect of either leucine or a mixture of all three BCAA fed in excess on plasma methionine concentrations. Excess dietary leucine reduced (P < 0.05) the plasma concentrations of isoleucine and valine in both the postprandial and postabsorptive states. Plasma concentrations of the BCKA reflected the changes in the corresponding amino acids. Basal BCKDH activity in the liver and total BCKDH activity in the biceps femoris muscle were significantly (P < 0.05) increased by excesses of leucine or all BCAA.

Contributions of a disulfide bond and a reduced cysteine side chain to the intrinsic activity of the high-density lipoprotein receptor SR-BI.

Science.gov (United States)

Yu, Miao; Lau, Thomas Y; Carr, Steven A; Krieger, Monty

2012-12-18

The high-density lipoprotein (HDL) receptor scavenger receptor class B, type I (SR-BI), binds HDL and mediates selective cholesteryl ester uptake. SR-BI's structure and mechanism are poorly understood. We used mass spectrometry to assign the two disulfide bonds in SR-BI that connect cysteines within the conserved Cys(321)-Pro(322)-Cys(323) (CPC) motif and connect Cys(280) to Cys(334). We used site-specific mutagenesis to evaluate the contributions of the CPC motif and the side chain of extracellular Cys(384) to HDL binding and lipid uptake. The effects of CPC mutations on activity were context-dependent. Full wild-type (WT) activity required Pro(322) and Cys(323) only when Cys(321) was present. Reduced intrinsic activities were observed for CXC and CPX, but not XXC, XPX, or XXX mutants (X ≠ WT residue). Apparently, a free thiol side chain at position 321 that cannot form an intra-CPC disulfide bond with Cys(323) is deleterious, perhaps because of aberrant disulfide bond formation. Pro(322) may stabilize an otherwise strained CPC disulfide bond, thus supporting WT activity, but this disulfide bond is not absolutely required for normal activity. C(384)X (X = S, T, L, Y, G, or A) mutants exhibited altered activities that varied with the side chain's size: larger side chains phenocopied WT SR-BI treated with its thiosemicarbazone inhibitor BLT-1 (enhanced binding, weakened uptake); smaller side chains produced almost inverse effects (increased uptake:binding ratio). C(384)X mutants were BLT-1-resistant, supporting the proposal that Cys(384)'s thiol interacts with BLT-1. We discuss the implications of our findings on the functions of the extracellular loop cysteines in SR-BI and compare our results to those presented by other laboratories.

Adsorption of amino acids by fullerenes and fullerene nanowhiskers

International Nuclear Information System (INIS)

Hashizume, Hideo; Hirata, Chika; Fujii, Kazuko; Miyazawa, Kun’ichi

2015-01-01

We have investigated the adsorption of some amino acids and an oligopeptide by fullerene (C 60 ) and fullerene nanowhiskers (FNWs). C 60 and FNWs hardly adsorbed amino acids. Most of the amino acids used have a hydrophobic side chain. Ala and Val, with an alkyl chain, were not adsorbed by the C 60 or FNWs. Trp, Phe and Pro, with a cyclic structure, were not adsorbed by them either. The aromatic group of C 60 did not interact with the side chain. The carboxyl or amino group, with the frame structure of an amino acid, has a positive or negative charge in solution. It is likely that the C 60 and FNWs would not prefer the charged carboxyl or amino group. Tri-Ala was adsorbed slightly by the C 60 and FNWs. The carboxyl or amino group is not close to the center of the methyl group of Tri-Ala. One of the methyl groups in Tri-Ala would interact with the aromatic structure of the C 60 and FNWs. We compared our results with the theoretical interaction of 20 bio-amino acids with C 60 . The theoretical simulations showed the bonding distance between C 60 and an amino acid and the dissociation energy. The dissociation energy was shown to increase in the order, Val < Phe < Pro < Asp < Ala < Trp < Tyr < Arg < Leu. However, the simulation was not consistent with our experimental results. The adsorption of albumin (a protein) by C 60 showed the effect on the side chains of Try and Trp. The structure of albumin was changed a little by C 60 . In our study Try and Tyr were hardly adsorbed by C 60 and FNWs. These amino acids did not show a different adsorption behavior compared with other amino acids. The adsorptive behavior of mono-amino acids might be different from that of polypeptides. (paper)

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

KAUST Repository

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.

Fatty acid biosynthesis VII. Substrate control of chain-length of products synthesised by rat liver fatty acid synthetase

DEFF Research Database (Denmark)

Hansen, Heinz Johs. Max; Carey, E.M.; Dils, R.

1970-01-01

- 1. Gas-liquid and paper chromatography have been used to determine the chain-lengths of fatty acids synthesised by purified rat liver fatty acid synthetase from [1-14C]acetyl-CoA, [1,3-14C2]malonyl-CoA and from [1-14C]acetyl-CoA plus partially purified rat liver acetyl-CoA carboxylase. - 2....... A wide range (C4:0–C18:0) of fatty acids was synthesised and the proportions were modified by substrate concentrations in the same manner as for purified rabbit mammary gland fatty acid synthetase. - 3. The relative amount of radioactivity incorporated from added acetyl-CoA and malonyl-CoA depended...... of long-chain fatty acids was synthesised from carboxylated acetyl-CoA than from added malonyl-CoA. - 5. It is suggested that acetyl-CoA carboxylase may carboxylate acetate bound to fatty acid synthetase....

An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides.

Science.gov (United States)

Plummer, Chelsea E; Stover, Michele L; Bokatzian, Samantha S; Davis, John T M; Dixon, David A; Cassady, Carolyn J

2015-07-30

Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.

Linear side chains in benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c] pyrrole-4,6-dione polymers direct self-assembly and solar cell performance

KAUST Repository

Cabanetos, Clement; El Labban, Abdulrahman; Bartelt, Jonathan A.; Douglas, Jessica D.; Mateker, William R.; Frechet, Jean; McGehee, Michael D.; Beaujuge, Pierre

2013-01-01

role that linear side-chain substituents play in poly(benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers for bulk heterojunction (BHJ) solar cell applications. We show that replacing branched side chains by linear ones

Amino acid metabolism during exercise in trained rats: the potential role of carnitine in the metabolic fate of branched-chain amino acids.

Science.gov (United States)

Ji, L L; Miller, R H; Nagle, F J; Lardy, H A; Stratman, F W

1987-08-01

The influence of endurance training and an acute bout of exercise on plasma concentrations of free amino acids and the intermediates of branched-chain amino acid (BCAA) metabolism were investigated in the rat. Training did not affect the plasma amino acid levels in the resting state. Plasma concentrations of alanine (Ala), aspartic acid (Asp), asparagine (Asn), arginine (Arg), histidine (His), isoleucine (Ile), leucine (Leu), lysine (Lys), methionine (Met), phenylalanine (Phe), proline (Pro), serine (Ser), threonine (Thr), and valine (Val) were significantly lower, whereas glutamate (Glu), glycine (Gly), ornithine (Orn), tryptophan (Trp), tyrosine (Tyr), creatinine, urea, and ammonia levels were unchanged, after one hour of treadmill running in the trained rats. Plasma concentration of glutamine (Glu), the branched-chain keto acids (BCKA) and short-chain acyl carnitines were elevated with exercise. Ratios of plasma BCAA/BCKA were dramatically lowered by exercise in the trained rats. A decrease in plasma-free carnitine levels was also observed. These data suggest that amino acid metabolism is enhanced by exercise even in the trained state. BCAA may only be partially metabolized within muscle and some of their carbon skeletons are released into the circulation in forms of BCKA and short-chain acyl carnitines.

4-N, 4-S & 4-O Chloroquine Analogues: Influence of Side Chain Length and Quinolyl Nitrogen pKa on Activity vs. Chloroquine Resistant Malaria+, #

OpenAIRE

Natarajan, Jayakumar K.; Alumasa, John; Yearick, Kimberly; Ekoue-Kovi, Kekeli A.; Casabianca, Leah B.; de Dios, Angel C.; Wolf, Christian; Roepe, Paul D.

2008-01-01

Using predictions from heme – quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure – function principles. We vary side chain length for both monoethyl and diethyl 4N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position, and vary side chain length for these analogues. We introduce an additio...

Can long chain n-3 fatty acids from feed be converted into very long chain n-3 fatty acids in fillets from farmed rainbow trout (Oncorhynchus mykiss)?

Science.gov (United States)

Lušnic Polak, M.; Demšar, L.; Luzar, U.; Polak, T.

2017-09-01

The link between the basic chemical and fatty acid composition of trout feed on one hand and trout (Oncorhynchus mykiss) meat (fillet) was investigated.. The content of 52 fatty acids from feed and trout meat lipids was determined by in-situ transesterification and capillary column gas-liquid chromatography. On average, 100 g of trout feed contained 7.4 g of moisture, 47.7 g of proteins, 6.09 g of ash, 21.4 g of fat, and as for fatty acid composition, 47.8 wt. % were monounsaturated, 34.0 wt. % were polyunsaturated and 18.1 wt. % were saturated fatty acids, with the PS ratio 1.88, n-6/n-3 ratio 1.74, 0.80 wt. % of trans and 3.28 wt. % of very long chain n-3 fatty acids. On average, 100 g of trout meat contained 76.1 g of moisture, 21.4 g of proteins, 1.34 g of ash, 2.52 g of fat, and in the fatty acid composition 42.1 wt. % were monounsaturated, 38.2 wt. % were polyunsaturated and 18.9 wt. % were saturated fatty acids, with the PS ratio 2.02, n-6/n-3 ratio 0.98, 0.95 wt. % of trans and 13.25 wt. % of very long chain n-3 fatty acids.

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

CERN Document Server

Choi, D H

2002-01-01

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

Minor amounts of plasma medium-chain fatty acids and no improved time trial performance after consuming lipids

DEFF Research Database (Denmark)

Vistisen, Bodil; Nybo, L.; Xu, Xuebing

2003-01-01

after consumption of specific structured triacylglycerol, consisting of a mixture of medium-chain fatty acids and long-chain fatty acids, to prevent the adverse effects observed by MCT (pure medium-chain fatty acids) regarding gastrointestinal distress. Seven well-trained subjects cycled 3 h at 55......% of maximum 02 uptake during which they ingested CHO or CHO plus specific structured triacylglycerols. Immediately after the constant-load cycling, the subjects performed a time trial of similar to50-min duration. Breath and blood samples were obtained regularly during the experiment. Fatty acid composition...... of plasma triacylglycerols, fatty acids, and phospholipids was determined. Performance was similar after administration of CHO plus specific structured triacylglycerol [medium-, long-, and medium-chain fatty acid (MLM)] compared with CHO (50.0 +/- 1.8 and 50.8 +/- 3.6 min, respectively). No plasma 8...

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

Directory of Open Access Journals (Sweden)

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.

Orphan drugs in development for long-chain fatty acid oxidation disorders: challenges and progress

Directory of Open Access Journals (Sweden)

Sun A

2015-04-01

Full Text Available Angela Sun, J Lawrence Merritt II Department of Pediatrics, University of Washington, Seattle, WA, USA Abstract: Fatty acid oxidation disorders are inborn errors of metabolism resulting in failure of ß-oxidation within or transport of fatty acids into the mitochondria. The long-chain fatty acid oxidation disorders are characterized by variable presentations ranging from newborn cardiomyopathy, to infantile hypoketotic hypoglycemia resulting from liver involvement, to skeletal myopathy often resulting in rhabdomyolysis in adolescents and adults. Treatments for these long-chain fatty acid oxidation disorders have typically focused upon avoidance of fasting with dietary fat restriction and medium-chain triglyceride supplementation. These treatments have resulted in only a partial response with improvements in hypoglycemia, reduction in frequency of rhabdomyolysis, and improvement in cardiomyopathy with early therapy, but significant risk remains. Recent advances in therapies for long-chain fatty acid oxidation disorders are reviewed in this article. These include sodium D,L-3-hydroxybutyrate, triheptanoin, gene therapy, and bezafibrates. Sodium D,L-3-hydroxybutyrate has shown clinical effect, with improvements in muscle tone, neurological abnormalities, and some cases of cardiomyopathy and leukodystrophy. Triheptanoin has been used as an alternative medium-chain triglyceride in a number of fatty acid oxidation disorders and has shown promising findings in the treatment of cardiomyopathy and hypoglycemia. However, it does not significantly reduce episodes of rhabdomyolysis. Gene therapy has been shown to improve acylcarnitine levels in very-long-chain acyl-coenzyme A dehydrogenase deficiency mouse models, with preservation of glucose levels. Bezafibrates have shown improvements in acylcarnitine concentrations in fibroblast studies, but clinical observations have not demonstrated consistent effects. Together, these treatments have shown some

Regulation of hepatic branched-chain alpha-keto acid dehydrogenase complex in rats fed a high-fat diet

Science.gov (United States)

Objective: Branched-chain alpha-keto acid dehydrogenase complex (BCKDC) regulates branched-chain amino acid (BCAA) metabolism at the level of branched chain alpha-ketoacid (BCKA) catabolism. It has been demonstrated that the activity of hepatic BCKDC is markedly decreased in type 2 diabetic animal...

Branched-chain amino acids for people with hepatic encephalopathy

DEFF Research Database (Denmark)

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...

Branched-chain amino acids for people with hepatic encephalopathy

DEFF Research Database (Denmark)

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

2017-01-01

-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...

Thermodynamic Interactions between Polystyrene and Long-Chain Poly(n-Alkyl Acrylates) Derived from Plant Oils.

Science.gov (United States)

Wang, Shu; Robertson, Megan L

2015-06-10

Vegetable oils and their fatty acids are promising sources for the derivation of polymers. Long-chain poly(n-alkyl acrylates) and poly(n-alkyl methacrylates) are readily derived from fatty acids through conversion of the carboxylic acid end-group to an acrylate or methacrylate group. The resulting polymers contain long alkyl side-chains with around 10-22 carbon atoms. Regardless of the monomer source, the presence of alkyl side-chains in poly(n-alkyl acrylates) and poly(n-alkyl methacrylates) provides a convenient mechanism for tuning their physical properties. The development of structured multicomponent materials, including block copolymers and blends, containing poly(n-alkyl acrylates) and poly(n-alkyl methacrylates) requires knowledge of the thermodynamic interactions governing their self-assembly, typically described by the Flory-Huggins interaction parameter χ. We have investigated the χ parameter between polystyrene and long-chain poly(n-alkyl acrylate) homopolymers and copolymers: specifically we have included poly(stearyl acrylate), poly(lauryl acrylate), and their random copolymers. Lauryl and stearyl acrylate were chosen as model alkyl acrylates derived from vegetable oils and have alkyl side-chain lengths of 12 and 18 carbon atoms, respectively. Polystyrene is included in this study as a model petroleum-sourced polymer, which has wide applicability in commercially relevant multicomponent polymeric materials. Two independent methods were employed to measure the χ parameter: cloud point measurements on binary blends and characterization of the order-disorder transition of triblock copolymers, which were in relatively good agreement with one another. The χ parameter was found to be independent of the alkyl side-chain length (n) for large values of n (i.e., n > 10). This behavior is in stark contrast to the n-dependence of the χ parameter predicted from solubility parameter theory. Our study complements prior work investigating the interactions between

Pregnancy duration and the ratio of long-chain n-3 fatty acids to arachidonic acid in erythrocytes from Faroese women

DEFF Research Database (Denmark)

Olsen, S.F.; Hansen, Harald S.; Jensen, B.

1989-01-01

of long-chain n-3 FA to arachidonic acid (the (3/6) ratio) was used as the most relevant single measure of exposure. In 18 women with certain gestational age and with spontaneous onset of delivery, gestational age was significantly associated with the (3/6) ratio quantified in PC (correlation coefficient......Dietary long-chain n-3 fatty acids (FA) may prolong gestation by inhibiting formation of prostaglandins from arachidonic acid. FA were quantified in phosphatidylcholine (PC), phosphatidylethanolamine (PE), and total lipids (TL) of red cells sampled during pregnancy from 29 Faroese women. The ratio...

Fatty acid profile and composition of milk protein fraction in dairy cows fed long-chain unsaturated fatty acids during the transition period

Directory of Open Access Journals (Sweden)

Francisco Palma Rennó

2013-11-01

Full Text Available The objective of this study was to evaluate the utilization of different sources of unsaturated long-chain fatty acids in diets for dairy cows during the transition period and early lactation on the milk fatty acid profile and composition of the protein fraction. Thirty-six Holstein cows were divided into three groups, fed the following diets: control (C; soybean oil (SO; and calcium salts of long-chain unsaturated fatty acids (CS. The milk samples utilized for analysis were obtained weekly from parturition to twelve weeks of lactation; each one of the samples originated from two daily milkings. Milk composition and total nitrogen, non-protein nitrogen and non-casein nitrogen levels were analyzed. The cows receiving the diet with calcium salts had lower concentrations of non-protein nitrogen (%CP in milk compared with the animals fed the diet with soybean oil. There was a decrease in concentration of medium-chain fatty acids C12-C16, and a concomitant increase in concentrations of long-chain fatty acids >C18 in milk fat for the animals fed the diets CS and SO when compared with diet C. Soybean oil and CS diets increased milk-fat concentrations of the acids C18: 1 trans-11, C18: 2 cis-9, trans-11 and C18: 2 trans-10 cis-12 in relation to diet C. The utilization of sources of long-chain fatty acids in the diet of dairy cows increases the biological value of milk in early lactation due to higher concentrations of specific fatty acids such as CLA C18: 2cis-9, trans-11.

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

DEFF Research Database (Denmark)

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...

Effects of medium-chain fatty acids and oleic acid on blood lipids, lipoproteins, glucose, insulin, and lipid transfer protein activities

DEFF Research Database (Denmark)

Tholstrup, T.; Ehnholm, C.; Jauhiainen, M.

2004-01-01

Background: Dietary medium-chain fatty acids (MCFAs) are of nutritional interest because they are more easily absorbed from dietary medium-chain triacylglycerols (MCTs) than are long-chain fatty acids from, for example, vegetable oils. It has generally been claimed that MCFAs do not increase plasma...... cholesterol, although this claim is poorly documented. Objective: We compared the effects of a diet rich in either MCFAs or oleic acid on fasting blood lipids, lipoproteins, glucose, insulin, and lipid transfer protein activities in healthy men. Design: In a study with a double-blind, randomized, crossover...... plasma total triacylglycerol (P = 0.0361), and higher plasma glucose (P = 0.033). Plasma HDL-cholesterol and insulin concentrations and activities of cholesterol ester transfer protein and phospholipid transfer protein did not differ significantly between the diets. Conclusions: Compared with fat high...

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

Directory of Open Access Journals (Sweden)

Norbert Haider

1998-01-01

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

Mean-field theory of photoinduced formation of surface reliefs in side-chain azobenzene polymers

DEFF Research Database (Denmark)

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

1998-01-01

A mean-field model of photoinduced surface reliefs in dye containing side-chain polymers is presented. It is demonstrated that photoinduced ordering of dye molecules subject to anisotropic intermolecular interactions leads to mass transport even when the intensity of the incident light is spatially...... uniform. Theoretical profiles are obtained using a simple variational method and excellent agreement with experimental surface reliefs recorded under various polarization configurations is found. The polarization dependence of both period and shape of the profiles is correctly reproduced by the model....

Mean-field theory of photoinduced molecular reorientation in azobenzene liquid crystalline side-chain polymers

DEFF Research Database (Denmark)

Pedersen, T.G.; Johansen, P.M.

1997-01-01

. The theory provides an explanation for the high long-term stability of the photoinduced anisotropy as well as a theoretical prediction of the temporal behavior of photoinduced birefringence. The theoretical results agree favorably with measurements in the entire range of writing intensities used......A novel mean-field theory of photoinduced reorientation and optical anisotropy in liquid crystalline side-chain polymers is presented and compared with experiments, The reorientation mechanism is based on photoinduced trans cis isomerization and a multidomain model of the material is introduced...

A 13C{31P} REDOR NMR Investigation of the Role of Glutamic Acid Residues in Statherin-Hydroxyapatite Recognition

Science.gov (United States)

Ndao, Moise; Ash, Jason T.; Breen, Nicholas F.; Goobes, Gil; Stayton, Patrick S.; Drobny, Gary P.

2011-01-01

The side chain carboxyl groups of acidic proteins found in the extra-cellular matrix (ECM) of mineralized tissues play a key role in promoting or inhibiting the growth of minerals such as hydroxyapatite (HAP), the principal mineral component of bone and teeth. Among the acidic proteins found in the saliva is statherin, a 43-residue tyrosine-rich peptide that is a potent lubricant in the salivary pellicle and an inhibitor of both HAP crystal nucleation and growth. Three acidic amino acids – D1, E4, and E5 – are located in the N-terminal 15 amino acid segment, with a fourth amino acid, E26, located outside the N-terminus. We have utilized 13C{31P} REDOR NMR to analyze the role played by acidic amino acids in the binding mechanism of statherin to the HAP surface by measuring the distance between the δ-carboxyl 13C spins of the three glutamic acid side chains of statherin (residues E4, E5, E26) and 31P spins of the phosphate groups at the HAP surface. 13C{31P} REDOR studies of glutamic-5-13C acid incorporated at positions E4 and E26 indicate a 13C–31P distance of more than 6.5 Å between the side chain carboxyl 13C spin of E4 and the closest 31P in the HAP surface. In contrast, the carboxyl 13C spin at E5 has a much shorter 13C–31P internuclear distance of 4.25±0.09 Å, indicating that the carboxyl group of this side chain interacts directly with the surface. 13C T1ρ and slow-spinning MAS studies indicate that the motions of the side chains of E4 and E5 are more restricted than that of E26. Together, these results provide further insight into the molecular interactions of statherin with HAP surfaces. PMID:19678690

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

DEFF Research Database (Denmark)

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

2005-01-01

to be abnormally low (-2.4), suggesting that these side chains may interact with each other. Mutation of Glu203 to alanine (E203A) completely eliminated the enzymatic activity and impaired the thermal stability (deltaT(m) = 6.4 degrees C) of the enzyme. Substrate binding ability was also affected by the Glu203...

Synthesis of deuterium-labeled plant sterols and analysis of their side-chain mobility by solid state deuterium NMR

International Nuclear Information System (INIS)

Marsan, M.P.; Muller, I.; Milon, A.

1996-01-01

Sitosterol and stigmasterol, plant sterols, were deuterated at specific positions. Orientation and mobility of the deuterated sitosterol and stigmasterol (and two of their diasteromers) on oriented lipid bilayers were analyzed by deuterium NMR spectroscopy. Orientation and mobility of the side chains was revealed by these studies

Stereospecific assignment of the NH2 resonances from the primary amides of asparagine and glutamine side chains in isotopically labeled proteins

International Nuclear Information System (INIS)

McIntosh, Lawrence P.; Brun, Emmanuel; Kay, Lewis E.

1997-01-01

An HMQC-based pulse scheme is presented for the stereospecific assignment of asparagine and glutamine side-chain amide protons. The approach makes use of the recently developed quantitative-J correlation spectroscopy [Bax, A. et al. (1994) Methods Enzymol., 239,79-105] to distinguish the E and Z primary amide protons and, as such, eliminates the need for assignments derived from more time-consuming and potentially ambiguous NOE methods. An application of this method to a uniformly 15N,13C-labeled cellulose-binding domain is presented. When used in combination with a NOESY-HSQC experiment, the predominant χ2 dihedral angles of two asparagine side chains in this protein can also be defined

4-N, 4-S & 4-O Chloroquine Analogues: Influence of Side Chain Length and Quinolyl Nitrogen pKa on Activity vs. Chloroquine Resistant Malaria+, #

Science.gov (United States)

Natarajan, Jayakumar K.; Alumasa, John; Yearick, Kimberly; Ekoue-Kovi, Kekeli A.; Casabianca, Leah B.; de Dios, Angel C.; Wolf, Christian; Roepe, Paul D.

2009-01-01

Using predictions from heme – quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure – function principles. We vary side chain length for both monoethyl and diethyl 4N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position, and vary side chain length for these analogues. We introduce an additional titratable amino group to the side chain of 4O analogues with promising CQR strain selectivity and increase activity while retaining selectivity. We solve atomic resolution structures for complexes formed between representative 4N, 4S and 4O derivatives vs. μ-oxo dimeric heme, measure binding constants for monomeric vs. dimeric heme, and quantify hemozoin (Hz) formation inhibition in vitro. The data provide additional insight for the design of CQ analogues with improved activity vs. CQR malaria. PMID:18512900

Trapping social wasps (Hymenoptera: Vespidae) with acetic acid and saturated short chain alcohols.

Science.gov (United States)

Landolt, P J; Smithhisler, C S; Reed, H C; McDonough, L M

2000-12-01

Nineteen compounds were evaluated in combination with a solution of acetic acid as baits for trapping the German yellowjacket, Vespula germanica (F.), the western yellowjacket Vespula pensylvanica (Sausssure), and the golden paper wasp Polistes aurifer Saussure. Compounds with three to six carbon chains or branched chains and with a hydroxy functional group were selected for testing based on their similarity to isobutanol. They were compared with isobutanol with acetic acid, which is a known wasp attractant. None of the compounds tested were superior to isobutanol when presented with acetic acid as a lure for these species of wasps. However, traps baited with either the S-(-)- or the racemic mixture of 2-methyl-1-butanol in combination with acetic acid captured similar numbers of both species of yellowjackets, compared with isobutanol with acetic acid. Polistes aurifer responded strongly to the S-(-)-enantiomer and to the racemic mixture of 2-methyl-1-butanol with acetic acid and not to the R-(+)-enantiomer with acetic acid.

Mechanism of long chain monoenoic fatty acids acting on the energy metabolism of heart

Energy Technology Data Exchange (ETDEWEB)

Buddecke, E; Filipovic, I; Wortberg, B; Seher, A

1975-01-01

The oxidation of 1-/sup 14/C-erucic (Csub(22:1)) and 1-/sup 14/C-nervonic (Csub(24:1)) acid was studied compared to 1-/sup 14/C-palmitic and -oleic acid in isolated rat and pig heart mitochondria. After mitochondrial incubation with the albumin-bound fatty acids only small amounts of /sup 14/CO/sub 2/ developed from the oxidation of the long chain monoenoic acids as compared to palmitic or oleic acid. The slow down of the oxidation rate was more pronounced in rat than in pig heart mitochondria. The oxidation of palmitic or oleic acid was not found to be inhibited by the C/sub 20/-C/sub 24/-monoeneic acids, whereas palmitic or oleic acid inhibited the oxidation of erucic acid competitively. From present findings an idea may be developed of the interference on fatty acid metabolism in heart muscle by erucic and other long chain monenoic acids.

Metabolism of very long-chain Fatty acids: genes and pathophysiology.

Science.gov (United States)

Sassa, Takayuki; Kihara, Akio

2014-02-01

Fatty acids (FAs) are highly diverse in terms of carbon (C) chain-length and number of double bonds. FAs with C>20 are called very long-chain fatty acids (VLCFAs). VLCFAs are found not only as constituents of cellular lipids such as sphingolipids and glycerophospholipids but also as precursors of lipid mediators. Our understanding on the function of VLCFAs is growing in parallel with the identification of enzymes involved in VLCFA synthesis or degradation. A variety of inherited diseases, such as ichthyosis, macular degeneration, myopathy, mental retardation, and demyelination, are caused by mutations in the genes encoding VLCFA metabolizing enzymes. In this review, we describe mammalian VLCFAs by highlighting their tissue distribution and metabolic pathways, and we discuss responsible genes and enzymes with reference to their roles in pathophysiology.

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

KAUST Repository

Mei, Jianguo; Kim, Do Hwan; Ayzner, Alexander L.; Toney, Michael F.; Bao, Zhenan

2011-01-01

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

Pronounced Side Chain Effects in Triple Bond-Conjugated Polymers Containing Naphthalene Diimides for n-Channel Organic Field-Effect Transistors

KAUST Repository

Nam, Sungho

2018-03-23

Three triple bond-conjugated naphthalene diimide (NDI) copolymers, poly{[N,N′-bis(2-R1)-naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-[(2,5-bis(2-R2)-1,4-phenylene)bis(ethyn-2,1-diyl)]} (PNDIR1-R2), were synthesized via Sonogashira coupling polymerization with varying alkyl side chains at the nitrogen atoms of the imide ring and 2,5-positions of the 1,4-diethynylbenzene moiety. Considering their identical polymer backbone structures, the side chains were found to have a strong influence on the surface morphology/nanostructure, thus playing a critical role in charge-transporting properties of the three NDI-based copolymers. Among the polymers, the one with an octyldodecyl (OD) chain at the nitrogen atoms of imide ring and a hexadecyloxy (HO) chain at the 2,5-positions of 1,4-diethynylbenzene, P(NDIOD-HO), exhibited the highest electron mobility of 0.016 cm2 V–1 s–1, as compared to NDI-based copolymers with an ethylhexyl chain at the 2,5-positions of 1,4-diethynylbenzene. The enhanced charge mobility in the P(NDIOD-HO) layers is attributed to the well-aligned nano-fiber-like surface morphology and highly ordered packing structure with a dominant edge-on orientation, thus enabling efficient in-plane charge transport. Our results on the molecular structure–charge transport property relationship in these materials may provide an insight into novel design of n-type conjugated polymers for applications in the organic electronics of the future.

Branched-chain amino acid metabolism in rat muscle: abnormal regulation in acidosis

International Nuclear Information System (INIS)

May, R.C.; Hara, Y.; Kelly, R.A.; Block, K.P.; Buse, M.G.; Mitch, W.E.

1987-01-01

Branched-chain amino acid (BCAA) metabolism is frequently abnormal in pathological conditions accompanied by chronic metabolic acidosis. To study how metabolic acidosis affects BCAA metabolism in muscle, rats were gavage fed a 14% protein diet with or without 4 mmol NH 4 Cl x 100 g body wt -1 x day -1 . Epitrochlearis muscles were incubated with L-[1- 14 C]-valine and L-[1- 14 C]leucine, and rates of decarboxylation, net transamination, and incorporation into muscle protein were measured. Plasma and muscle BCAA levels were lower in acidotic rats. Rates of valine and leucine decarboxylation and net transamination were higher in muscles from acidotic rats; these differences were associated with a 79% increase in the total activity of branched-chain α-keto acid dehydrogenase and a 146% increase in the activated form of the enzyme. They conclude that acidosis affects the regulation of BCAA metabolism by enhancing flux through the transaminase and by directly stimulating oxidative catabolism through activation of branched-chain α-keto acid dehydrogenase

Zinc absorption in experimental osmotic diarrhea: effect of long-chain fatty acids.

Science.gov (United States)

Lee, S Y; Wapnir, R A

1993-03-01

The effect of free fatty acids on zinc absorption was studied in a rat model of chronic osmotic diarrhea induced with magnesium citrate and phenolphthalein. In vivo rates of zinc removal from the lumen and analysis of tissue for zinc uptake and metallothionein alterations were monitored. One mmol/L stearate enhanced zinc absorption in rats with or without diarrhea, from 207 +/- 22 and 353 +/- 13 pmol/min x cm to 676 +/- 34 and 610 +/- 26 pmol/min x cm, respectively. Palmitate was only effective in normal rats. Zinc absorption inversely correlated with mucosal zinc content in the perfused intestinal segments, in both type of rats. Hepatic metallothionein was enhanced by zinc and even more by oleate plus zinc in both groups; kidney metallothionein in animals with diarrhea was normalized by either oleate or zinc. The data support previous reports on the effect of long-chain fatty acids on the enhancement of zinc absorption: saturation and a longer chain appear to be positive factors. A membrane modification role of long-chain fatty acids could have nutritional implications in the formulation of special diets.

Branched-chain amino acid metabolism in rat muscle: abnormal regulation in acidosis

Energy Technology Data Exchange (ETDEWEB)

May, R.C.; Hara, Y.; Kelly, R.A.; Block, K.P.; Buse, M.G.; Mitch, W.E.

1987-06-01

Branched-chain amino acid (BCAA) metabolism is frequently abnormal in pathological conditions accompanied by chronic metabolic acidosis. To study how metabolic acidosis affects BCAA metabolism in muscle, rats were gavage fed a 14% protein diet with or without 4 mmol NH/sub 4/Cl x 100 g body wt/sup -1/ x day/sup -1/. Epitrochlearis muscles were incubated with L-(1-/sup 14/C)-valine and L-(1-/sup 14/C)leucine, and rates of decarboxylation, net transamination, and incorporation into muscle protein were measured. Plasma and muscle BCAA levels were lower in acidotic rats. Rates of valine and leucine decarboxylation and net transamination were higher in muscles from acidotic rats; these differences were associated with a 79% increase in the total activity of branched-chain ..cap alpha..-keto acid dehydrogenase and a 146% increase in the activated form of the enzyme. They conclude that acidosis affects the regulation of BCAA metabolism by enhancing flux through the transaminase and by directly stimulating oxidative catabolism through activation of branched-chain ..cap alpha..-keto acid dehydrogenase.

Surface Propensity of Atmospherically Relevant Amino Acids Studied by XPS.

Science.gov (United States)

Mocellin, Alexandra; Gomes, Anderson Herbert de Abreu; Araújo, Oscar Cardoso; de Brito, Arnaldo Naves; Björneholm, Olle

2017-04-27

Amino acids constitute an important fraction of the water-soluble organic nitrogen (WSON) compounds in aerosols and are involved in many processes in the atmosphere. In this work, we applied X-ray photoelectron spectroscopy (XPS) to study aqueous solutions of four amino acids, glycine, alanine, valine, and methionine, in their zwitterionic forms. We found that amino acids with hydrophilic side chains and smaller size, GLY and ALA, tend to stay in the bulk of the liquid, while the hydrophobic and bigger amino acids, VAL and MET, are found to concentrate more on the surface. We found experimental evidence that the amino acids have preferential orientation relative to the surface, with the hydrophobic side chain being closer to the surface than the hydrophilic carboxylate group. The observed amino acid surface propensity has implications in atmospheric science as the surface interactions play a central role in cloud droplet formation, and they should be considered in climate models.

Probing the effects of the ester functional group, alkyl side chain length and anions on the bulk nanostructure of ionic liquids: a computational study.

Science.gov (United States)

Fakhraee, Mostafa; Gholami, Mohammad Reza

2016-04-14

The effects of ester addition on nanostructural properties of biodegradable ILs composed of 1-alkoxycarbonyl-3-alkyl-imidazolium cations ([C1COOCnC1im](+), n = 1, 2, 4) combined with [Br](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) were explored by using the molecular dynamics (MD) simulations and quantum theory of atoms in molecules (QTAIM) analysis at 400 K. Various thermodynamic properties of these ILs were extensively computed in our earlier work (Ind. Eng. Chem. Res., 2015, 54, 11678-11700). Nano-scale segregation analysis demonstrates the formation of a small spherical island-like hydrocarbon within the continuous ionic domain for ILs with short alkyl side chain ([C1COOC1C1im]), and a sponge-like nanostructure for the compound with long alkyl side chain ([C1COOC4C1im]). Ester-functionalized ILs with ethyl side chain ([C1COOC2C1im]) are the turning point between two different morphologies. Non-polar channels were observed for [C1COOC4C1im] ILs composed of smaller anions such as [Br] and [NO3], whereas clustering organization was found for the other anions. Formation of the spherical micelle-like nanostructure was seen for lengthened cations. Finally, the incorporation of an ester group into the alkyl side chain of the cation leads to stronger segregation between charged and uncharged networks, which consequently increased the possibility of self-assembly and micelle formation.

Plasma phospholipid long-chain n-3 polyunsaturated fatty acids and body weight change

DEFF Research Database (Denmark)

Jakobsen, Marianne Uhre; Dethlefsen, Claus; Due, Karen Margrete

2011-01-01

We investigated the association between the proportion of long-chain n-3 polyunsaturated fatty acids (PUFA) in plasma phospholipids from blood samples drawn at enrollment and subsequent change in body weight. Sex, age, and BMI were considered as potential effect modifiers.......We investigated the association between the proportion of long-chain n-3 polyunsaturated fatty acids (PUFA) in plasma phospholipids from blood samples drawn at enrollment and subsequent change in body weight. Sex, age, and BMI were considered as potential effect modifiers....

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

DEFF Research Database (Denmark)

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

2010-01-01

fluorescence data to show how Tg and chemical analogs of the compound with modified or removed side chains bind to isolated SERCA 1a membranes. This occurs by uptake via the membrane lipid followed by insertion into a resident intramembranous binding site with few adaptative changes. Our binding data indicate...... that a balanced hydrophobicity and accurate positioning of the side chains, provided by the central guaianolide ring structure, defines a pharmacophore of Tg that governs both high affinity and access to the protein-binding site. Tg analogs substituted with long linkers at O-8 extend from the binding site between...... transmembrane segments to the putative N-terminal Ca(2+) entry pathway. The long chain analogs provide a rational basis for the localization of the linker, the presence of which is necessary for enabling prostate-specific antigen to cleave peptide-conjugated prodrugs targeting SERCA of cancer cells (Denmeade, S...

Hydration of amino acids: FTIR spectra and molecular dynamics studies.

Science.gov (United States)

Panuszko, Aneta; Adamczak, Beata; Czub, Jacek; Gojło, Emilia; Stangret, Janusz

2015-11-01

The hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results, molecular dynamics simulations of amino acids were performed. The structural-energetic characteristic of these solute-affected water molecules shows that, on average, water affected by amino acids forms stronger and shorter H-bonds than those in pure water. Differences in the influence of amino acids on water structure have been noticed. The effect of the hydrophobic side chain of an amino acid on the solvent interactions seems to be enhanced because of the specific cooperative coupling of water strong H-bond chain, connecting the carboxyl and amino groups, with the clathrate-like H-bond network surrounding the hydrocarbon side chain. The parameter derived from the spectral data, which corresponds to the contributions of the population of weak hydrogen bonds of water molecules which have been substituted by the stronger ones in the hydration sphere of amino acids, correlated well with the amino acid hydrophobicity indexes.

Side Chain and Flexibility Contributions to the Raman Optical Activity Spectra of a Model Cyclic Hexapeptide

Czech Academy of Sciences Publication Activity Database

Hudecová, J.; Kapitán, Josef; Baumruk, V.; Hammer, R. P.; Keiderling, T. A.; Bouř, Petr

2010-01-01

Roč. 114, č. 28 (2010), s. 7642-7651 ISSN 1089-5639 R&D Projects: GA ČR GA203/06/0420; GA ČR GA202/07/0732; GA AV ČR IAA400550702 Grant - others:GA UK(CZ) 126310 Institutional research plan: CEZ:AV0Z40550506 Keywords : Raman optical activity * ab initio * side chain * flexibility * peptide Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.732, year: 2010

Acidic-Basic Properties of Three Alanine-Based Peptides Containing Acidic and Basic Side Chains: Comparison Between Theory and Experiment

OpenAIRE

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

2008-01-01

The purpose of this work was to evaluate the effect of the nature of the ionizable end groups, and the solvent, on their acid-base properties in alanine-based peptides. Hence, the acid-base properties of three alanine-based peptides: Ac-KK-(A)7-KK-NH2 (KAK), Ac-OO-(A)7-DD-NH2 (OAD), Ac-KK-(A)7-EE-NH2 (KAE), where A, D, E, K, and O denote alanine, aspartic acid, glutamic acid, lysine, and ornithine, respectively, were determined in water and in methanol by potentiometry. With the availability ...

Single-Step Access to Long-Chain α,ω-Dicarboxylic Acids by Isomerizing Hydroxycarbonylation of Unsaturated Fatty Acids

KAUST Repository

Goldbach, Verena

2016-11-09

Dicarboxylic acids are compounds of high value, but to date long-chain alpha,omega-dicarboxylic acids have been difficult to access in a direct way. Unsaturated fatty acids are ideal starting materials with their molecular structure of long methylene sequences and a carboxylate functionality, in addition to a double bond that offers itself for functionalization. Within this paper, we established a direct access to alpha,omega-dicarboxylic acids by combining isomerization and selective terminal carbonylation of the internal double bond with water as a nucleophile on unsaturated fatty acids. We identified the key elements of this reaction: a homogeneous reaction mixture ensuring sufficient contact between all reactants and a catalyst system allowing for activation of the Pd precursor under aqueous conditions. Experiments under pressure reactor conditions with [(dtbpx)Pd(OTf)(2)] as catalyst precursor revealed the importance of nucleophile and reactant concentrations and the addition of the diprotonated diphosphine ligand (dtbpxH(2))(OTf)(2) to achieve turnover numbers >120. A variety of unsaturated fatty acids, including a triglyceride, were converted to valuable long-chain dicarboxylic acids with high turnover numbers and selectivities for the linear product of >90%. We unraveled the activation pathway of the Pd-II precursor, which proceeds via a reductive elimination step forming a Pd species and oxidative addition of the diprotonated diphosphine ligand, resulting in the formation of the catalytically active Pd hydride species. Theoretical calculations identified the hydrolysis as the rate-determining step. A low nucleophile concentration in the reaction mixture in combination with this high energetic barrier limits the potential of this reaction. In conclusion, water can be utilized as a nucleophile in isomerizing functionalization reactions and gives access to long-chain dicarboxylic acids from a variety of unsaturated substrates. The activity of the catalytic

Genetic analysis of pathway regulation for enhancing branched-chain amino acid biosynthesis in plants

KAUST Repository

Chen, Hao; Saksa, Kristen; Zhao, Feiyi; Qiu, Joyce; Xiong, Liming

2010-01-01

The branched-chain amino acids (BCAAs) valine, leucine and isoleucine are essential amino acids that play critical roles in animal growth and development. Animals cannot synthesize these amino acids and must obtain them from their diet. Plants

Synthesis and characterisation of new types of side chain cholesteryl polymers.

Science.gov (United States)

Wang, Bin; Du, Haiyan; Zhang, Junhua

2011-01-01

A series of cholesterol derivatives have been synthesised via the alkylation reaction of the 3-hydroxyl group with the aliphatic bromide compounds with different chain lengths, namely 3β-alkyloxy-cholesterol. The double bond between the C5 and C6 positions in these cholesterol derivatives was oxidised into epoxy, followed by an epoxy-ring-opening reaction with the treatment with acrylic acid, resulting in a series of 3β-alkyloxy-5α-hydroxy-6β-acryloyloxycholesterol, C(n)OCh (n=1, 2, 4, 6, 8, 10, 12), The acrylate group is connected to the C6 position, which is confirmed by the single crystal structure analysis. The corresponding polymers, PC(n)OCh, were prepared via free radical polymerisation. The structure of monomers and the resulting polymers were characterised with nuclear magnetic resonance (NMR), Fourier transform infrared spectroscopy (FT-IR) and gel permeation chromatography (GPC). The thermal properties of PC(n)OCh were studied using differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). To determine the secondary structure of polymers, circular dichroism (CD) spectra were performed. It was found that not all monomers produce high-molecular-weight polymers because of steric hindrance. However, all polymers have a helical structure, which can be enhanced by increasing the alkoxy chain length. In addition, increasing the alkoxy chain length decreases the glass transition temperature and increases the decomposition temperature of the polymers. Copyright © 2010 Elsevier Inc. All rights reserved.

Production of hydrophobic amino acids from biobased resources

NARCIS (Netherlands)

Widyarani, W.; Sari, Yessie W.; Ratnaningsih, Enny; Sanders, Johan P.M.; Bruins, Marieke E.

2016-01-01

Protein hydrolysis enables production of peptides and free amino acids that are suitable for usage in food and feed or can be used as precursors for bulk chemicals. Several essential amino acids for food and feed have hydrophobic side chains; this property may also be exploited for subsequent

4-N-, 4-S-, and 4-O-chloroquine analogues: influence of side chain length and quinolyl nitrogen pKa on activity vs chloroquine resistant malaria.

Science.gov (United States)

Natarajan, Jayakumar K; Alumasa, John N; Yearick, Kimberly; Ekoue-Kovi, Kekeli A; Casabianca, Leah B; de Dios, Angel C; Wolf, Christian; Roepe, Paul D

2008-06-26

Using predictions from heme-quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure-function principles. We vary side chain length for both monoethyl and diethyl 4-N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position and vary side chain length for these analogues. We introduce an additional titratable amino group to the side chain of 4-O analogues with promising CQR strain selectivity and increase activity while retaining selectivity. We solve atomic resolution structures for complexes formed between representative 4-N, 4-S, and 4-O derivatives vs mu-oxo dimeric heme, measure binding constants for monomeric vs dimeric heme, and quantify hemozoin (Hz) formation inhibition in vitro. The data provide additional insight for the design of CQ analogues with improved activity vs CQR malaria.

Branched Chain Amino Acid Oxidation in Cultured Rat Skeletal Muscle Cells

Science.gov (United States)

Pardridge, William M.; Casanello-Ertl, Delia; Duducgian-Vartavarian, Luiza

1980-01-01

Leucine metabolism in skeletal muscle is linked to protein turnover. Since clofibrate is known both to cause myopathy and to decrease muscle protein content, the present investigations were designed to examine the effects of acute clofibrate treatment on leucine oxidation. Rat skeletal muscle cells in tissue culture were used in these studies because cultivated skeletal muscle cells, like muscle in vivo, have been shown to actively utilize branched chain amino acids and to produce alanine. The conversion of [1-14C]leucine to 14CO2 or to the [1-14C]keto-acid of leucine (α-keto-isocaproate) was linear for at least 2 h of incubation; the production of 14CO2 from [1-14C]leucine was saturable with a Km = 6.3 mM and a maximum oxidation rate (Vmax) = 31 nmol/mg protein per 120 min. Clofibric acid selectively inhibited the oxidation of [1-14C]leucine (Ki = 0.85 mM) and [U-14C]isoleucine, but had no effect on the oxidation of [U-14C]glutamate, -alanine, -lactate, or -palmitate. The inhibition of [1-14C]leucine oxidation by clofibrate was also observed in the rat quarter-diaphragm preparation. Clofibrate primarily inhibited the production of 14CO2 and had relatively little effect on the production of [1-14C]keto-acid of leucine. A physiological concentration—3.0 g/100 ml—of albumin, which actively binds clofibric acid, inhibited but did not abolish the effects of a 2-mM concentration of clofibric acid on leucine oxidation. Clofibrate treatment stimulated the net consumption of pyruvate, and inhibited the net production of alanine. The drug also increased the cytosolic NADH/NAD+ ratio as reflected by an increase in the lactate/pyruvate ratio, in association with a decrease in cell aspartate levels. The changes in pyruvate metabolism and cell redox state induced by the drug were delayed compared with the nearly immediate inhibition of leucine oxidation. These studies suggest that clofibric acid, in concentrations that approximate high therapeutic levels of the drug

Ethylmalonic aciduria is associated with an amino acid variant of short chain acyl-coenzyme A dehydrogenase

DEFF Research Database (Denmark)

Corydon, M J; Gregersen, N; Lehnert, W

1996-01-01

Ethylmalonic aciduria is a common biochemical finding in patients with inborn errors of short chain fatty acid beta-oxidation. The urinary excretion of ethylmalonic acid (EMA) may stem from decreased oxidation by short chain acyl-CoA dehydrogenase (SCAD) of butyryl-CoA, which is alternatively...

Homoserine as an Aspartic Acid Precursor for Synthesis of Proteoglycan Glycopeptide Containing Aspartic Acid and Sulfated Glycan Chain

OpenAIRE

Yang, Weizhun; Ramadan, Sherif; Yang, Bo; Yoshida, Keisuke; Huang, Xuefei

2016-01-01

Among many hurdles in synthesizing proteoglycan glycopeptides, one challenge is the incorporation of aspartic acid in the peptide backbone and acid sensitive O-sulfated glycan chains. To overcome this, a new strategy was developed utilizing homoserine as an aspartic acid precursor. The conversion of homoserine to aspartic acid in the glycopeptide was successfully accomplished by late stage oxidation using 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) and bis(acetoxy)iodobenzene (BAIB). This is...

Diversion of phagosome trafficking by pathogenic Rhodococcus equi depends on mycolic acid chain length.

Science.gov (United States)

Sydor, Tobias; von Bargen, Kristine; Hsu, Fong-Fu; Huth, Gitta; Holst, Otto; Wohlmann, Jens; Becken, Ulrike; Dykstra, Tobias; Söhl, Kristina; Lindner, Buko; Prescott, John F; Schaible, Ulrich E; Utermöhlen, Olaf; Haas, Albert

2013-03-01

Rhodococcus equi is a close relative of Mycobacterium spp. and a facultative intracellular pathogen which arrests phagosome maturation in macrophages before the late endocytic stage. We have screened a transposon mutant library of R. equi for mutants with decreased capability to prevent phagolysosome formation. This screen yielded a mutant in the gene for β-ketoacyl-(acyl carrier protein)-synthase A (KasA), a key enzyme of the long-chain mycolic acid synthesizing FAS-II system. The longest kasA mutant mycolic acid chains were 10 carbon units shorter than those of wild-type bacteria. Coating of non-pathogenic E. coli with purified wild-type trehalose dimycolate reduced phagolysosome formation substantially which was not the case with shorter kasA mutant-derived trehalose dimycolate. The mutant was moderately attenuated in macrophages and in a mouse infection model, but was fully cytotoxic.Whereas loss of KasA is lethal in mycobacteria, R. equi kasA mutant multiplication in broth was normal proving that long-chain mycolic acid compounds are not necessarily required for cellular integrity and viability of the bacteria that typically produce them. This study demonstrates a central role of mycolic acid chain length in diversion of trafficking by R. equi. © 2012 Blackwell Publishing Ltd.

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

Energy Technology Data Exchange (ETDEWEB)

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

2017-04-18

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

Self-assembly of long chain fatty acids: Effect of a methyl branch

DEFF Research Database (Denmark)

Liljeblad, Jonathan F. D.; Tyrode, Eric; Thormann, Esben

2014-01-01

chains of the straight chain fatty acids appear to be oriented perpendicular to the sample surface, based on an orientational analysis of VSFS data and the odd/even effect. In addition, the selection of the subphase (neat water or CdCl2 containing water buffered to pH 6.0) used for the LB-deposition has...

Acetic Acid Can Catalyze Succinimide Formation from Aspartic Acid Residues by a Concerted Bond Reorganization Mechanism: A Computational Study

Directory of Open Access Journals (Sweden)

Ohgi Takahashi

2015-01-01

Full Text Available Succinimide formation from aspartic acid (Asp residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe as a model compound, we propose the possibility that acetic acid (AA, which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

Acetic acid can catalyze succinimide formation from aspartic acid residues by a concerted bond reorganization mechanism: a computational study.

Science.gov (United States)

Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

2015-01-12

Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

The normally expressed kappa immunoglobulin light chain gene repertoire and somatic mutations studied by single-sided specific polymerase chain reaction (PCR); frequent occurrence of features often assigned to autoimmunity

DEFF Research Database (Denmark)

Juul, L; Hougs, L; Andersen, V

1997-01-01

The expressed human kappa light chain gene repertoire utilized by healthy individuals was studied by two different single-sided specific PCR techniques to avoid bias for certain V genes. A total of 103 rearranged kappa sequences from peripheral blood mononuclear cells from healthy individuals were...

Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures

Science.gov (United States)

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

2013-01-01

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

Clofibric acid stimulates branched-chain amino acid catabolism by three mechanisms.

Science.gov (United States)

Kobayashi, Rumi; Murakami, Taro; Obayashi, Mariko; Nakai, Naoya; Jaskiewicz, Jerzy; Fujiwara, Yoko; Shimomura, Yoshiharu; Harris, Robert A

2002-11-15

Clofibrate promotes catabolism of branched-chain amino acids by increasing the activity of the branched-chain alpha-keto acid dehydrogenase [BCKDH] complex. Depending upon the sex of the rats, nutritional state, and tissue being studied, clofibrate can affect BCKDH complex activity by three different mechanisms. First, by directly inhibiting BCKDH kinase activity, clofibrate can increase the proportion of the BCKDH complex in the active, dephosphorylated state. This occurs in situations in which the BCKDH complex is largely inactive due to phosphorylation, e.g., in the skeletal muscle of chow-fed rats or in the liver of female rats late in the light cycle. Second, by increasing the levels at which the enzyme components of the BCKDH complex are expressed, clofibrate can increase the total enzymatic activity of the BCKDH complex. This is readily demonstrated in livers of rats fed a low-protein diet, a nutritional condition that induces a decrease in the level of expression of the BCKDH complex. Third, by decreasing the amount of BCKDH kinase expressed and therefore its activity, clofibrate induces an increase in the percentage of the BCKDH complex in the active, dephosphorylated state. This occurs in the livers of rats fed a low-protein diet, a nutritional condition that causes inactivation of the BCKDH complex due to upregulation of the amount of BCKDH kinase. WY-14,643, which, like clofibric acid, is a ligand for the peroxisome-proliferator-activated receptor alpha [PPARalpha], does not directly inhibit BCKDH kinase but produces the same long-term effects as clofibrate on expression of the BCKDH complex and its kinase. Thus, clofibrate is unique in its capacity to stimulate BCAA oxidation through inhibition of BCKDH kinase activity, whereas PPARalpha activators in general promote BCAA oxidation by increasing expression of components of the BCKDH complex and decreasing expression of the BCKDH kinase.

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

DEFF Research Database (Denmark)

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

1996-01-01

Atomic force and scanning near-field optical microscopic investigations have been carried out on a polarization holographic grating recorded in an azobenzene side-chain Liquid crystalline polyester. It has been found that immediately following laser irradiation, a topographic surface grating...

Side chain and backbone contributions of Phe508 to CFTR folding

Energy Technology Data Exchange (ETDEWEB)

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

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.

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

Science.gov (United States)

Michalak, Karol; Wicha, Jerzy

2011-08-19

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

Resonant electron capture by aspartame and aspartic acid molecules.

Science.gov (United States)

Muftakhov, M V; Shchukin, P V

2016-12-30

The processes for dissociative electron capture are the key mechanisms for decomposition of biomolecules, proteins in particular, under interaction with low-energy electrons. Molecules of aspartic acid and aspartame, i.e. modified dipeptides, were studied herein to define the impact of the side functional groups on peptide chain decomposition in resonant electron-molecular reactions. The processes of formation and decomposition of negative ions of both aspartame and aspartic acid were studied by mass spectrometry of negative ions under resonant electron capture. The obtained mass spectra were interpreted under thermochemical analysis by quantum chemical calculations. Main channels of negative molecular ions fragmentation were found and characteristic fragment ions were identified. The СООН fragment of the side chain in aspartic acid is shown to play a key role like the carboxyl group in amino acids and aliphatic oligopeptides. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

The relationship between odd- and branched-chain fatty acids and microbial nucleic acid bases in rumen

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Keyuan Liu

2017-11-01

Full Text Available Objective This study aims to identify the relationship between odd- and branched-chain fatty acids (OBCFAs and microbial nucleic acid bases in the rumen, and to establish a model to accurately predict microbial protein flow by using OBCFA. Methods To develop the regression equations, data on the rumen contents of individual cows were obtained from 2 feeding experiments. In the first experiment, 3 rumen-fistulated dry dairy cows arranged in a 3×3 Latin square were fed diets of differing forage to concentration ratios (F:C. The second experiment consisted of 9 lactating Holstein dairy cows of similar body weights at the same stage of pregnancy. For each lactation stage, 3 cows with similar milk production were selected. The rumen contents were sampled at 4 time points of every two hours after morning feeding 6 h, and then to analyse the concentrations of OBCFA and microbial nucleic acid bases in the rumen samples. Results The ruminal bacteria nucleic acid bases were significantly influenced by feeding diets of differing forge to concentration ratios and lactation stages of dairy cows (p<0.05. The concentrations of OBCFAs, especially odd-chain fatty acids and C15:0 isomers, strongly correlated with the microbial nucleic acid bases in the rumen (p<0.05. The equations of ruminal microbial nucleic acid bases established by ruminal OBCFAs contents showed a good predictive capacity, as indicated by reasonably low standard errors and high R-squared values. Conclusion This finding suggests that the rumen OBCFA composition could be used as an internal marker of rumen microbial matter.

Characterization of citrus pectin samples extracted under different conditions: influence of acid type and pH of extraction

DEFF Research Database (Denmark)

Kaya, Merve; Sousa, Antonio G.; Crepeau, Marie-Jeanne

2014-01-01

on the chemical and macromolecular characteristics of pectin samples. Methods Citrus peel (orange, lemon, lime and grapefruit) from a commercial supplier was used as raw material. Pectin samples were obtained on a bulk plant scale (kilograms; harsh nitric acid, mild nitric acid and harsh oxalic acid extraction......) and on a laboratory scale (grams; mild oxalic acid extraction). Pectin composition (acidic and neutral sugars) and physicochemical properties (molar mass and intrinsic viscosity) were determined. Key Results Oxalic acid extraction allowed the recovery of pectin samples of high molecular weight. Mild oxalic acid......-extracted pectins were rich in long homogalacturonan stretches and contained rhamnogalacturonan I stretches with conserved side chains. Nitric acid-extracted pectins exhibited lower molecular weights and contained rhamnogalacturonan I stretches encompassing few and/or short side chains. Grapefruit pectin was found...

Effect of Supplementation of Branched Chain Fatty Acid on Colony of Ruminal Bacteria and Cell of Protozoa

Directory of Open Access Journals (Sweden)

W Suryapratama

2009-05-01

Full Text Available A study was conducted to evaluate the potential of branched-chain volatile fatty acids (isobutyric, α-methylbutyric and β-methylbutiric that supplemented into the diet on the colony of ruminal bacteria and the cell of protozoa population. Five progeny Friesian Holstein males with initial weight 348±29 kg were used in a 5x5 Latin square design (30-d periods. The basal diet composed of 55% forage and 45% concentrate containing 10.5 MJ ME/kg and 15% crude protein (CP. There were five dietary treatments where A: basal diet, B: A+139 mg urea/kg W0.75, C: B+28 mg CaSO4/kg W0.75, D: C+0.05 mM isobutyric acid+0.05 mM β-methylbutyric acid, and E: D+0.05 mM α-methylbutyric acid. Rearing period was 30 days, consists of feed adaptation period 20 days, then growth observation was done within the last 10 days. Collection of ruminal fluid was done within the last day of observation period, and took 3-4 h after the feeding. The results showed that supplementation branched chain volatile fatty acids did not significant affect on the number of colonies of bacteria and protozoa population, but the significant effect (P<0.05 on the concentration of branched chain volatile fatty acids in the rumen fluid. The supplementation of α-methylbutyric (P <0.05 decreased of concentration of isobutyric and isovaleric in rumen fluid than the other treatments. It is concluded that supplementation of branched chain volatile fatty acids not used by rumen bacteria for their growth but for the elongation of fatty acid synthesis. The supplementation of branched chain volatile fatty acids was 0.05 mM not enough strong influence on the growth of colony of rumen bacteria. (Animal Production 11(2: 129-134 (2009 Key Words: rumen fermentation, branched-chain fatty acid, ruminal bacteria, protozoa

Application of the Solid-Phase Julia–Lythgoe Olefination in Vitamin D Side-Chain Construction

Directory of Open Access Journals (Sweden)

Pierre J. De Clercq

2006-08-01

Full Text Available An example of the Julia–Lythgoe attachment of the vitamin D side chain to a solid-phase linked Inhoffen–Lythgoe diol derived CD-ring fragment is reported.

Effects of medium-chain triglycerides, long-chain triglycerides, or 2-monododecanoin on fatty acid composition in the portal vein, intestinal lymph, and systemic circulation in rats.

Science.gov (United States)

You, Yi-Qian Nancy; Ling, Pei-Ra; Qu, Jason Zhensheng; Bistrian, Bruce R

2008-01-01

Fatty acid absorption patterns can have a major impact on the fatty acid composition in the portal, intestinal lymph, and systemic circulation. This study sought to determine the effects of long-chain triglycerides (LCT), medium-chain triglycerides (MCT), and 2-monododecanoin (2mono) on intestinal fatty acid composition during continuous feeding over a brief period. The lipid sources were 100% LCT, 100% MCT, a 50:50 mixture of LCT and MCT (LCT/MCT), and a 50:50 mixture of LCT and 2mono (LCT/2mono). A total of 27 rats were randomly given 1 of the 4 diets at 200 kcal/kg/d, with 30% of total calories from lipids over 3 hours. MCT significantly increased each of the medium-chain fatty acids (C6:0, C8:0, and C10:0) as free fatty acids in the portal vein and about 10%/mol of C10:0 as triglycerides in the lymph compared with the other groups. There was significantly less C10:0 in lymphatic triglycerides with LCT/MCT than with MCT, but more than in the LCT and LCT/2mono diets. MCT also significantly increased the contents of C16:0, C18:0, C18:1, and C20:4 in the lymphatic triglycerides compared with all other groups including LCT/MCT. The amount of linoleic acid (C18:2) in lymphatic triglycerides followed the relative amounts of this fatty acid in the diet, with the greatest in LCT followed by LCT/MCT and LCT/2mono and least in MCT. A so-called structured lipid composed of the medium-chain fatty acid dodecanoic acid on the 2 position and long-chain fatty acids on the 1 and 3 positions appeared to be endogenously synthesized in response to the LCT/2mono diet. The original differences in MCT and LCT content in the diets were preserved in the fatty acid composition in the intestinal free fatty acids and triglycerides during feeding. In addition, the duration of lipid administration can play a role in altering fatty acid composition in the intestine.

Effects of Medium-Chain Triglycerides, Long-Chain Triglycerides, or 2-Monododecanoin on Fatty Acid Composition in the Portal Vein, Intestinal Lymph, and Systemic Circulation in Rats

Science.gov (United States)

Nancy You, Yi-Qian; Ling, Pei-Ra; Qu, Jason Zhensheng; Bistrian, Bruce R.

2011-01-01

Background Fatty acid absorption patterns can have a major impact on the fatty acid composition in the portal, intestinal lymph, and systemic circulation. This study sought to determine the effects of long-chain triglycerides (LCT), medium-chain triglycerides (MCT), and 2-monododecanoin (2mono) on intestinal fatty acid composition during continuous feeding over a brief period. Methods The lipid sources were 100% LCT, 100% MCT, a 50:50 mixture of LCT and MCT (LCT/MCT), and a 50:50 mixture of LCT and 2mono (LCT/2mono). A total of 27 rats were randomly given 1 of the 4 diets at 200 kcal/kg/d, with 30% of total calories from lipids over 3 hours. Results MCT significantly increased each of the medium-chain fatty acids (C6:0, C8:0, and C10:0) as free fatty acids in the portal vein and about 10%/mol of C10:0 as triglycerides in the lymph compared with the other groups. There was significantly less C10:0 in lymphatic triglycerides with LCT/MCT than with MCT, but more than in the LCT and LCT/2mono diets. MCT also significantly increased the contents of C16:0, C18:0, C18:1, and C20:4 in the lymphatic triglycerides compared with all other groups including LCT/MCT. The amount of linoleic acid (C18:2) in lymphatic triglycerides followed the relative amounts of this fatty acid in the diet, with the greatest in LCT followed by LCT/MCT and LCT/2mono and least in MCT. A so-called structured lipid composed of the medium-chain fatty acid dodecanoic acid on the 2 position and long-chain fatty acids on the 1 and 3 positions appeared to be endogenously synthesized in response to the LCT/2mono diet. Conclusions The original differences in MCT and LCT content in the diets were preserved in the fatty acid composition in the intestinal free fatty acids and triglycerides during feeding. In addition, the duration of lipid administration can play a role in altering fatty acid composition in the intestine. PMID:18407910

Branched-chain amino acids in metabolic signaling and insulin resistance

Science.gov (United States)

Branched-chain amino acids (BCAAs) are important directly- and indirectly-acting nutrient signals. Frequently, their actions have been reported to be anti-obesity in nature, especially in rodent models. Yet, circulating BCAAs tend to be elevated in obesity, and even associated with poorer metaboli...

On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins.

Science.gov (United States)

Habka, S; Sohn, W Y; Vaquero-Vara, V; Géléoc, M; Tardivel, B; Brenner, V; Gloaguen, E; Mons, M

2018-01-31

Asparagine (Asn) is a powerful turn-inducer residue, with a large propensity to occupy the second position in the central region of β-turns of proteins. The present work aims at investigating the role of a local anchoring between the Asn side chain and the main chain in this remarkable property. For this purpose, the H-bonding patterns of an asparagine residue in an isolated protein chain fragment forming a γ- or a β-turn have been determined using IR/UV double resonance gas phase spectroscopy on laser-desorbed, jet-cooled short models in conjunction with relevant quantum chemistry calculations. These gas phase data provide evidence for an original double anchoring linking the Asn primary amide side chain (SC), which adopts a gauche+ rotameric form, to its main chain (MC) local environment. From both IR spectroscopic evidence (H-bond induced red shifts) and quantum chemistry, Asn SC is found to behave as a stronger H-bond acceptor than donor, resulting in stronger MC→SC H-bonds than SC→MC ones. These gas phase structural data, relevant to a hydrophobic environment, have been used as a reference to assess the anchoring taking place in high resolution crystallized proteins of the Protein Data Bank. This approach reveals that, when the SC adopts a gauche+ orientation, the stronger MC→SC bonds are preserved in many cases whereas the SC→MC bonds are always disrupted, in qualitative agreement with the gas phase ranking of these interactions. Most interestingly, when Asn occupies the second position of central part of a β-turn (i.e., the very turn-inducer position), the MC→SC H-bonds are also disrupted and replaced by a water-mediated SC to MC anchoring. Owing to the specific features of the hydrated Asn side chain, we propose that it could be a turn precursor structure, able to facilitate turn formation in the early events of the folding process.

Effect of the Side Chains and Anode Material on Thermal Stability and Performance of Bulk-Heterojunction Solar Cells Using DPP(TBFu2 Derivatives as Donor Materials

Directory of Open Access Journals (Sweden)

Alexander Kovalenko

2015-01-01

Full Text Available An optimized fabrication of bulk-heterojunction solar cells (BHJ SCs based on previously reported diketopyrrolopyrrole donor, ethyl-hexylated DPP(TBFu2, as well as two new DPP(TBFu2 derivatives with ethyl-hexyl acetate and diethyl acetal solubilizing side-chains and PC60BM as an acceptor is demonstrated. Slow gradual annealing of the solar cell causing the effective donor-acceptor reorganization, and as a result higher power conversion efficiency (PCE, is described. By replacing a hole transporting layer PEDOT:PSS with MoO3 we obtained higher PCE values as well as higher thermal stability of the anode contact interface. DPP(TBFu2 derivative containing ethyl-hexyl acetate solubilizing side-chains possessed the best as-cast self-assembly and high crystallinity. However, the presence of ethyl-hexyl acetate and diethyl acetal electrophilic side-chains stabilizes HOMO energy of isolated DPP(TBFu2 donors with respect to the ethyl-hexylated one, according to cyclic voltammetry.

Moving Segmentation Up the Supply-Chain: Supply Chain Segmentation and Artificial Neural Networks

OpenAIRE

Erevelles, Sunil; Fukawa, Nobuyuki

2008-01-01

This paper explained the concept of supply-side segmentation and transvectional alignment, and applies these concepts in the artificial neural network (ANN). To the best of our knowledge, no research has applied ANN in explaining the heterogeneity of both the supply-side and demand-side of a market in forming relational entity that consists of firms at all levels of the supply chain and the demand chain. The ANN offers a way of operationalizing the concept of supply-side segmentation. In toda...

Significance of long chain polyunsaturated fatty acids in human health

Czech Academy of Sciences Publication Activity Database

Zárate, R.; El Jaber-Vazdekis, Nabil; Tejera, N.; Pérez, J.A.; Rodrígues, C.

2017-01-01

Roč. 6, JUL 27 (2017), s. 1-19, č. článku 25. ISSN 2001-1326 R&D Projects: GA MŠk(CZ) LO1416 Institutional support: RVO:61388971 Keywords : Lipidomics * Lipids * Long chain polyunsaturated fatty acids Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology

The influence of chirality in the amide side chain on the carbonyl orientation in rotational isomers of 3-carbamoylpyridinium halides

NARCIS (Netherlands)

Bastiaansen, L.A.M.; Vermeulen, T.J.M.; Buck, H.M.; Smeets, W.J.J.; Kanters, J.A.

1988-01-01

The direction of the carbonyl orientation in solid amide rotamers of 3-(N-methyl-N-a-methylbenzylcarbamoyl)-1,2,4-trimethylpyridinium iodide is governed by the (R)- or (S)-chirality in the amide side chain; X-ray structures and c.d. spectra are correlated.

Acinetobacter baumannii K13 and K73 capsular polysaccharides differ only in K-unit side branches of novel non-2-ulosonic acids: di-N-acetylated forms of either acinetaminic acid or 8-epiacinetaminic acid.

Science.gov (United States)

Kenyon, Johanna J; Kasimova, Anastasiya A; Notaro, Anna; Arbatsky, Nikolay P; Speciale, Immacolata; Shashkov, Alexander S; De Castro, Cristina; Hall, Ruth M; Knirel, Yuriy A

2017-11-27

Structures of capsular polysaccharides of Acinetobacter baumannii isolates carrying KL13 and KL73 gene clusters were established. The closely related KL73 and KL13 gene clusters differ only by one gene in the module responsible for synthesis of the non-2-ulosonic acids. The K13 and K73 polysaccharides differ only in a single side-chain sugar, which is either 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-altro- or -d-glycero-l-altro-non-2-ulosonic acid [di-N-acetylated forms of acinetaminic acid (Aci5Ac7Ac) or 8-epiacinetaminic acid (8eAci5Ac7Ac), respectively]. The KL13 also is closely related to the KL12 gene cluster, which contains a different wzy gene encoding the K unit polymerase. Accordingly, the otherwise near identical K units are linked differently via an α-d-FucpNAc-(1 → 4)-d-Galp linkage in K13 and K73 or an α-d-FucpNAc-(1 → 3)-d-GalpNAc linkage in K12. This finding confirms the predicted substrate of the ItrB3 initiating transferase as d-FucpNAc. Glycosyltransferases predicted to catalyse the linkage of d-Galp or d-GalpNAc to l-FucpNAc in the growing K13 and K73 or K12 units, respectively, differ by only two amino acids. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gut microbiota–derived short-chain fatty acids and kidney diseases

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Li L

2017-12-01

Full Text Available Lingzhi Li, Liang Ma, Ping Fu Kidney Research Institute, Department of Nephrology, West China Hospital of Sichuan University, Chengdu 610041, China Abstract: Gut microbiota and its metabolites play pivotal roles in host physiology and pathology. Short-chain fatty acids (SCFAs, as a group of metabolites, exert positive regulatory effects on energy metabolism, hormone secretion, immune inflammation, hypertension, and cancer. The functions of SCFAs are related to their activation of transmembrane G protein-coupled receptors and their inhibition of histone acetylation. Though controversial, growing evidence suggests that SCFAs, which regulate inflammation, oxidative stress, and fibrosis, have been involved in kidney disease through the activation of the gut–kidney axis; however, the molecular relationship among gut microbiota–derived metabolites, signaling pathways, and kidney disease remains to be elucidated. This review will provide an overview of the physiology and functions of SCFAs in kidney disease. Keywords: gut microbiome, short-chain fatty acids, kidney diseases, gut–kidney axis

Lipase-catalyzed esterification of lactic acid with straight-chain alcohols

DEFF Research Database (Denmark)

Rønne, Torben Harald; Xu, Xuebing; Tan, Tianwei

2005-01-01

Enzymatic synthesis of esters of lactic acid and straight-chain alcohols with different chain lengths (C6–C18) were investigated in batch reactions with hexadecanol (C16) as the model alcohol. Cyclohexane was the best solvent for higher ester yields, and the best biocatalyst was the immobilized...... Candida antarctica lipase B (Novozym 435) as well as the textile-immobilized Candida sp. lipase. A method was established to obtain ester yields in the range of 71 to 82% for the different alcohols, and the most favorable conditions for the esterification reaction using Novozym 435 were an equimolar ratio...... of lactic acid to alcohol, each at a concentration of 120 mM each; a 50°C reaction temperature; 190 rpm shaking speed; and the addition of 100 mg molecular sieves (4 Å) for drying. The ester yield increased with increasing lipase load, and a yield of 79.2% could be obtained after 24 h of reaction at 20 wt...

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

DEFF Research Database (Denmark)

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

2012-01-01

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 subst...

Analysis of long-chain fatty acid binding activity in vesicles of the outer membrane generated from Escherchia coli

International Nuclear Information System (INIS)

Black, P.N.

1987-01-01

Escherichia coli transports long-chain fatty acids across the dual membrane by a high affinity, saturable, energy-dependent process. The fadL gene codes for an outer membrane protein which appears to act specifically as a long-chain fatty acid binding protein when fatty acid utilization is blocked by mutation. In an effort to understand the function of the fadL gene product, FLP, membranes have been isolated from fadL + and fadL - strains following osmotic lysis. Following isolation, total membranes were separated into inner and outer membrane fractions and assayed for long-chain fatty acid binding activity. Outer membrane vesicles were incubated 2-5 min at 37 0 C with 3 H oleate (C/sub 18:1/), cooled to 0 0 C, and centrifuged through a Lipidex 100 column for 3 min to remove the unbound fatty acid. The level of fatty acid binding was quantitated by scintillation counting of the eluate. Outer membrane vesicles generated from a fadL + strain bind 325 pmol fatty acid/mg protein whereas vesicles generated for a mutant strain bind 175 pmol fatty acid/mg protein. These data suggest that FLP acts at least as a long-chain fatty acid binding protein on the surface of the cell

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

KAUST Repository

Fetsch, Corinna

2014-12-22

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

Effects of side-chain and electron exchange correlation on the band structure of perylene diimide liquid crystals: a density functional study.

Science.gov (United States)

Arantes, J T; Lima, M P; Fazzio, A; Xiang, H; Wei, Su-Huai; Dalpian, G M

2009-04-23

The structural and electronic properties of perylene diimide liquid crystal PPEEB are studied using ab initio methods based on the density functional theory (DFT). Using available experimental crystallographic data as a guide, we propose a detailed structural model for the packing of solid PPEEB. We find that due to the localized nature of the band edge wave function, theoretical approaches beyond the standard method, such as hybrid functional (PBE0), are required to correctly characterize the band structure of this material. Moreover, unlike previous assumptions, we observe the formation of hydrogen bonds between the side chains of different molecules, which leads to a dispersion of the energy levels. This result indicates that the side chains of the molecular crystal not only are responsible for its structural conformation but also can be used for tuning the electronic and optical properties of these materials.

Synthesis of waterborne polyurethane containing alkoxysilane side groups and the properties of the hybrid coating films

Energy Technology Data Exchange (ETDEWEB)

Li, Qi; Guo, Longhai [State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029 (China); Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029 (China); Qiu, Teng, E-mail: qiuteng@mail.buct.edu.cn [State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029 (China); Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029 (China); Xiao, Weidong; Du, Dianxing [State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029 (China); Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029 (China); Li, Xiaoyu, E-mail: lixy@mail.buct.edu.cn [State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029 (China); Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029 (China)

2016-07-30

Highlights: • A diol with side-chain trimethoxysilane (DEA-Si) was synthesized using 3-(methacryloxypropyl)trimethoxysilane (MAPTS) and diethanolamine (DEA). • The crosslinking structure could in situ formed within the WPU matrix through sol-gel process. • The Si tends to shift to the polymer-air interface due to the flexible long alkyl-ester side chain. • The incorporation of DEA-Si enhanced mechanical and surface hydrophobic properties of WPU films. - Abstract: A series of waterborne polyurethane (WPU) containing alkoxysilane side groups were synthesized by using the dihydroxy functionalized alkoxysilane. The diol with trimethoxysilane groups at the side chains was synthesized via Michael addition between 3-(methacryloxypropyl)trimethoxysilane (MAPTS) and diethanolamine (DEA). The silane diol was applied as the chain extender for the NCO-endcapped prepolymer of isophorone diisocyanate, polycarbonate diol, 2,2-bis(hydroxymethyl) butyric acid and 1,4-butanediol. The products with the silane content varied from 1.2 to 16.5 wt% were dispersed in water after neutralization. The effect of the silane diol on the particle size and morphology of the WPU dispersion was studied by dynamic light scattering (DLS) and transmission electron microscopy (TEM), respectively. X-ray photoelectron spectroscopy (XPS) characterization was carried out on the coating film of the WPU, revealing that the long flexible side chain is favorable for the silane components to emigrate toward the film surface and crosslink during the film formation process. As a result, both the surface contact angle to water and water adsorption of the WPU coating films increased with the silane content. Furthermore, the mechanical properties including the modulus and tensile strength of the films were also improved by the incorporation of silane diol.

Molecular Design for Preparation of Hexagonal-Ordered Porous Films Based on Side-chain Type Liquid-Crystalline Star Polymer.

Science.gov (United States)

Naka, Yumiko; Takayama, Hiromu; Koyama, Teruhisa; Le, Khoa V; Sasaki, Takeo

2018-05-02

Fabrication of regularly porous films by the breath-figure method has attracted much attention. The simple, low-cost technique uses the condensation of water droplets to produce these structures, but the phenomenon itself is complex, requiring control over many interacting parameters that change throughout the process. Developing a unified understanding for the molecular design of polymers to prepare ordered porous films is challenging, but required for further advancements. In this article, the effects of the chemical structure of polymers in the breath-figure technique were systematically explored using side-chain type liquid-crystalline (LC) star polymers. The formation of porous films was affected by the structure of the polymers. Although the entire film surface of poly(11-[4-(4-cyanobiphenyl)oxy]undecyl methacrylate) (P11CB) had a hexagonal ordered porous structure over a certain Mn value, regularly arranged holes did not easily form in poly(methyl methacrylate) (PMMA), even though the main chain of PMMA is similar to that of P11CB. Comparing P11CB and poly(11-[(1,1'-biphenyl)-4-yloxy]undecyl methacrylate) (P11B) (P11CB without cyano groups) showed that the local polar groups in hydrophobic polymers promoted the formation of ordered porous films. No holes formed in poly(4-cyanobiphenyl methacrylate) (P0CB) (P11CB without alkyl spacers) films due to its hydrophilicity. The introduction of alkyl chains in P0CB allowed the preparation of honeycomb-structured films by increasing the internal tension. However, alkyl chains in the side chain alone did not result in a porous structure, as in the case of poly(11-[(1,1'-biphenyl)-4-yloxy]undecyl methacrylate) (P11). Aromatic rings are also required to increase the Tg and improve film formability. In the present study, suitable molecular designs of polymers were found, specifically hydrophobic polymers with local polar groups, to form a regularly porous structure. Development of clear guidelines for the molecular

Medium-chain fatty acids as ligands for orphan G protein-coupled receptor GPR84.

Science.gov (United States)

Wang, Jinghong; Wu, Xiaosu; Simonavicius, Nicole; Tian, Hui; Ling, Lei

2006-11-10

Free fatty acids (FFAs) play important physiological roles in many tissues as an energy source and as signaling molecules in various cellular processes. Elevated levels of circulating FFAs are associated with obesity, dyslipidemia, and diabetes. Here we show that GPR84, a previously orphan G protein-coupled receptor, functions as a receptor for medium-chain FFAs with carbon chain lengths of 9-14. Medium-chain FFAs elicit calcium mobilization, inhibit 3',5'-cyclic AMP production, and stimulate [35S]guanosine 5'-O-(3-thiotriphosphate) binding in a GPR84-dependent manner. The activation of GPR84 by medium-chain FFAs couples primarily to a pertussis toxin-sensitive G(i/o) pathway. In addition, we show that GPR84 is selectively expressed in leukocytes and markedly induced in monocytes/macrophages upon activation by lipopolysaccharide. Furthermore, we demonstrate that medium-chain FFAs amplify lipopolysaccharide-stimulated production of the proinflammatory cytokine interleukin-12 p40 through GPR84. Our results indicate a role for GPR84 in directly linking fatty acid metabolism to immunological regulation.

Tuning Thermoresponsive Properties of Cationic Elastin-like Polypeptides by Varying Counterions and Side-Chains.

Science.gov (United States)

Petitdemange, Rosine; Garanger, Elisabeth; Bataille, Laure; Bathany, Katell; Garbay, Bertrand; Deming, Timothy J; Lecommandoux, Sébastien

2017-05-17

We report the synthesis of methionine-containing recombinant elastin-like polypeptides (ELPs) of different lengths that contain periodically spaced methionine residues. These ELPs were chemoselectively alkylated at all methionine residues to give polycationic derivatives. Some of these samples were found to possess solubility transitions in water, where the temperature of these transitions varied with ELP concentration, nature of the methionine alkylating group, and nature of the sulfonium counterions. These studies show that introduction and controlled spacing of methionine sulfonium residues into ELPs can be used as a means both to tune their solubility transition temperatures in water using a variety of different parameters and to introduce new side-chain functionality.

Synthesis of tritium-labelled isopenicillin N, penicillin N and 6-aminopenicillanic acid

International Nuclear Information System (INIS)

Usher, J.J.; Loder, B.; Abraham, E.P.

1975-01-01

1. Phenoxymethylpenicillin sulphoxide 4-methoxybenzyl ester was labelled with 3 H in its 2-β-methyl group. Its specific radioactivity was 362mCi/mmol. 2. Removal of the side chain of this compound yielded the corresponding ester of 6-aminopenicillanic acid sulphoxide and coupling of the latter with the appropriate protected α-aminoadipic acid gave 4-methoxybenzyloxycarbonylisopenicillin N sulphoxide di-4-methoxybenzyl ester or the corresponding derivative of penicillin N. 3. Removal of the protective groups by hydrogenolysis and reduction of the sulphoxide group yielded 3 H-labelled isopenicillin N or penicillin N. 4. 3 H-labelled phenoxymethylpenicillin sulphoxide was obtained by hydrogenolysis from its 4-methoxybenzyl ester. Reducton of its sulphoxide group and subsequent removal of the side chain gave 3 H-labelled 6-aminopenicillanic acid. (author)

Multi-functionalized side-chain supramolecular polymers: A methodology towards tunable functional materials

Science.gov (United States)

Nair, Kamlesh Prabhakaran

Even as we see a significant growth in the field of supramolecular polymers in the last ten years, multi-functionalized systems have been scarcely studied. Noncovalent multi-functionalization provides unique advantages such as rapid materials optimization via reversible functionalization as well as for the tuning of materials properties by exploiting the differences in the nature of these reversible interactions. This thesis involves the design principles, synthesis & methodology of supramolecular side-chain multi-functionalized polymers. The combination of a functionally tolerant & controlled polymerization technique such as ROMP with multiple noncovalent interactions such as hydrogen bonding, metal coordination and ionic interactions has been successfully used to synthesize these polymers. Furthermore, the orthogonality between the above interactions in block/random copolymers has been studied in detail. It has been found that the studied interactions were orthogonal to each other. To validate the viability of this methodology using multiple orthogonal interactions towards materials design noncovalent crosslinking of polymers has been used as a potential application. Three classes of networks have been studied: complementary multiple hydrogen bonded networks, metal crosslinked networks, & multi-functionalized hydrogen bonded and metal coordinated networks. The first room temperature decrosslinking by exclusive complementary hydrogen bonded interactions has been successfully achieved. Furthermore network properties have been successfully tuned by varying the network micro-structure which in turn was tuned by the hydrogen bonding motifs used for inter-chain crosslinking. By combining two different noncovalent interactions used for inter-chain crosslinking, it was possible to make multi-functionalized materials whose properties could be controlled by varying the crosslinking strategy. Hence by employing multi-functionalization methodology, important materials

Radiolysis of N-acetyl amino acids as model compounds for radiation degradation of polypeptides

International Nuclear Information System (INIS)

Garrett, R.W.; Hill, D.J.T.; Ho, S.Y.; O'Donnell, J.H.; O'Sullivan, P.W.; Pomery, P.J.

1982-01-01

Radiation chemical yields of (i) the volatile radiolysis products and (ii) the trapped free radicals from the γ-radiolysis of the N-acetyl derivatives of glycine, L-alanine, L-valine, L-phenylalanine and L-tyrosine in the polycrystalline state have been determined at room temperature (303 K). Carbon dioxide was found to be the major molecular product for all these compounds with G(CO 2 ) varying from 0.36 for N-acetyl-L-tyrosine to 8 for N-acetyl-L-valine. There was evidence for some scission of the N-Csub(α) bond, indicated by the production of acetamide and the corresponding aliphatic acid, but the deamination reaction was found to be of much lesser importance than the decarboxylation reaction. A protective effect of the aromatic ring in N-acetyl-L-phenylalanine and in N-acetyl-L-tyrosine was indicated by the lower yields of volatile products for these compounds. The yields of trapped free radicals were found to vary with the nature of the amino acid side chain, increasing with chain length and chain branching. The radical yields were decreased by incorporation of an aromatic moiety in the side chain, this effect being greater for the tyrosyl side chain than for the phenyl side chain. The G(R) values showed a good correlation with G(CO 2 ) indicating that a common reaction may be involved in radical production and carbon dioxide formation. (author)

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

KAUST Repository

Moia, Davide

2017-11-28

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

Microscale and nanoscale hierarchical structured mesh films with superhydrophobic and superoleophilic properties induced by long-chain fatty acids

International Nuclear Information System (INIS)

Wang Shutao; Song Yanlin; Jiang Lei

2007-01-01

Inspired by the lotus effect, we fabricate new microscale and nanoscale hierarchical structured copper mesh films by a simple electrochemical deposition. After modification of the long-chain fatty acid monolayer, these films show superhydrophobic and superoleophilic properties, which could be used for the effective separation of oil and water. The length of the fatty acid chain strongly influences the surface wettability of as-prepared films. It is confirmed that the cooperative effect of the hierarchical structure of the copper film and the nature of the long-chain fatty acid contribute to this unique surface wettability

A critical role for very long-chain fatty acid elongases in oleic acid-mediated Saccharomyces cerevisiae cytotoxicity.

Science.gov (United States)

Wang, Qiao; Du, Xiuxiu; Ma, Ke; Shi, Ping; Liu, Wenbin; Sun, Jing; Peng, Min; Huang, Zhiwei

2018-03-01

Elongases FEN1/ELO2 and SUR4/ELO3 are important enzymes involved in the elongation of long-chain fatty acids (LCFAs) to very long-chain fatty acids (VLCFAs) in Saccharomyces cerevisiae. The molecular mechanism of the involvement of these elongases in lipotoxicity is unclear. In the present study, we investigated the role of VLCFA elongases in oleic acid-mediated yeast cytotoxicity. The spot test showed that yeast strains with the deletion of ELO2 or ELO3 were strikingly sensitive to oleic acid, while there was no change on the growth of strain with deleted ELO1 which was involved in the elongation of C 14 fatty acid (FA) to C 16 FA. By using GC-MS, the unsaturation index was increased in elo2△ and elo3△ mutants after treatment with oleic acid (OLA). However, the proportion of VLCFAs was increased in response to OLA in the wild-type strain. The growth inhibition of elo2△ and elo3△ could be partially rescued by two commonly used antioxidant agents N-acetyl cysteine (NAC) and Ascorbic acid (VC). The further study showed that exposure to excess OLA led to an increase in the levels of reactive oxygen species (ROS) and thiobarbituric acid reactive substances (TBARS), and a decline in the quantity of reduced glutathione (GSH) in both the wild type and mutant strains. However, the antioxidant enzyme activities of superoxide dismutase (SOD) and catalase (CAT) were increased in the wild type and elo1△ strains, while they were significantly decreased in the mutants of elo2△ and elo3△ after treated with excess OLA. Thus, oxidative damage mainly contributed to the cell death induced by OLA in ole2△ and ole3△. Taken together, although disruption of ELO2 or ELO3 did not affect the cellular lipid unsaturation, they altered the distribution and propotion of cellular VLCFAs, leading to the cell membrane impairment, which augmented the ability of OLA to permeabilize the plasma membrane. The data suggest that the very long-chain fatty acids elongases ELO2 and ELO3

Metabolism of branched-chain amino acids in leg muscles from tail-cast suspended intact and adrenalectomized rats

Science.gov (United States)

Jaspers, Stephen R.; Henriksen, Erik; Jacob, Stephan; Tischler, Marc E.

1989-01-01

The effects of muscle unloading, adrenalectomy, and cortisol treatment on the metabolism of branched-chain amino acids in the soleus and extensor digitorum longus of tail-cast suspended rats were investigated using C-14-labeled lucine, isoleucine, and valine in incubation studies. It was found that, compared to not suspended controls, the degradation of branched-chain amino acids in hind limb muscles was accelerated in tail-cast suspended rats. Adrenalectomy was found to abolish the aminotransferase flux and to diminish the dehydrogenase flux in the soleus. The data also suggest that cortisol treatment increases the rate of metabolism of branched-chain amino acids at the dehydrogenase step.

Controlling the morphology of side chain liquid crystalline block copolymer thin films through variations in liquid crystalline content.

Science.gov (United States)

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

2008-10-01

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 anchoring of the LC mesophase relative to the substrate and the intermaterial dividing surface. By manipulating the strength of these interactions, the arrangement and ordering of the ultrathin film block copolymer nanostructures can be controlled, yielding a range of morphologies that includes perpendicular and parallel cylinders, as well as both perpendicular and parallel lamellae. Additionally, we demonstrate the utilization of selective etching to create a nanoporous liquid crystalline polymer thin film. The unique control over the orientation and order of the self-assembled morphologies with respect to the substrate will allow for the custom design of thin films for specific nanopatterning applications without manipulation of the surface chemistry or the application of external fields.

Diabetes and branched-chain amino acids: What is the link?

Science.gov (United States)

Bloomgarden, Zachary

2018-05-01

Branched-chain amino acids (BCAA) have increasingly been studied as playing a role in diabetes, with the PubMed search string "diabetes" AND "branched chain amino acids" showing particular growth in studies of the topic over the past decade (Fig. ). In the Young Finn's Study, BCAA and, to a lesser extent, the aromatic amino acids phenylalanine and tyrosine were associated with insulin resistance (IR) in men but not in women, whereas the gluconeogenic amino acids alanine, glutamine, or glycine, and several other amino acids (i.e. histidine, arginine, and tryptophan) did not show an association with IR. Obesity may track more strongly than metabolic syndrome and diabetes with elevated BCAA. In a study of 1302 people aged 40-79; higher levels of BCAA tracked with older age, male sex, and metabolic syndrome, as well as with obesity, cardiovascular risk, dyslipidemia, hypertension, and uric acid. Medium- and long-chain acylcarnitines, by-products of mitochondrial catabolism of BCAAs, as well as branched-chain keto acids and the BCAA themselves distinguished obese people having versus not having features of IR, and in a study of 898 patients with essential hypertension, the BCAA and tyrosine and phenylalanine were associated with metabolic syndrome and impaired fasting glucose. In a meta-analysis of three genome-wide association studies, elevations in BCAA and, to a lesser extent, in alanine tracked with IR, whereas higher levels of glutamine and glycine were associated with lesser likelihood of IR. Given these associations with IR, it is not surprising that a number of studies have shown higher BCAA levels in people with and prior to development of type 2 diabetes (T2D), although this has particularly been shown in Caucasian and Asian ethnic groups while not appearing to occur in African Americans. Similarly, higher BCAA levels track with cardiovascular disease. [Figure: see text] The metabolism of BCAA involves two processes: (i) a reversible process catalysed by a

Bioavailability of omega-3 long-chain polyunsaturated fatty acids from foods

DEFF Research Database (Denmark)

Mu, Huiling

2008-01-01

Increasing recognition of the importance of the omega-3 long chain polyunsaturated fatty acids (LCPUFA) has caused greater attention about dietary intake of these fatty acids. Fatty fish is the major dietary source of these fatty acids. Because of the low intake of fish at many places, foods...... enriched with omega-3 LCPUFA can be good alternatives to improve the intake of these fatty acids. Effects of lipid structures and food matrices on bioavailability of omega-3 LCPUFA have been investigated. Short term studies showed that both lipid structure and food matrix affect the bioavailability...... of these fatty acids, whereas diverse results have been reported from long-term studies. Therefore more studies are encouraged to clarify the long-term effects....

Homoserine as an Aspartic Acid Precursor for Synthesis of Proteoglycan Glycopeptide Containing Aspartic Acid and a Sulfated Glycan Chain.

Science.gov (United States)

Yang, Weizhun; Ramadan, Sherif; Yang, Bo; Yoshida, Keisuke; Huang, Xuefei

2016-12-02

Among many hurdles in synthesizing proteoglycan glycopeptides, one challenge is the incorporation of aspartic acid in the peptide backbone and acid sensitive O-sulfated glycan chains. To overcome this, a new strategy was developed utilizing homoserine as an aspartic acid precursor. The conversion of homoserine to aspartic acid in the glycopeptide was successfully accomplished by late stage oxidation using (2,2,6,6-tetramethyl-piperidin-1-yl)oxyl (TEMPO) and bis(acetoxy)iodobenzene (BAIB). This is the first time that a glycopeptide containing aspartic acid and an O-sulfated glycan was synthesized.

Effect of alternative pathway therapy on branched chain amino acid metabolism in urea cycle disorder patients.

Science.gov (United States)

Scaglia, Fernando; Carter, Susan; O'Brien, William E; Lee, Brendan

2004-04-01

Urea cycle disorders (UCDs) are a group of inborn errors of hepatic metabolism caused by the loss of enzymatic activities that mediate the transfer of nitrogen from ammonia to urea. These disorders often result in life-threatening hyperammonemia and hyperglutaminemia. A combination of sodium phenylbutyrate and sodium phenylacetate/benzoate is used in the clinical management of children with urea cycle defects as a glutamine trap, diverting nitrogen from urea synthesis to alternatives routes of excretion. We have observed that patients treated with these compounds have selective branched chain amino acid (BCAA) deficiency despite adequate dietary protein intake. However, the direct effect of alternative therapy on the steady state levels of plasma branched chain amino acids has not been well characterized. We have measured steady state plasma branched chain and other essential non-branched chain amino acids in control subjects, untreated ornithine transcarbamylase deficiency females and treated null activity urea cycle disorder patients in the fed steady state during the course of stable isotope studies. Steady-state leucine levels were noted to be significantly lower in treated urea cycle disorder patients when compared to either untreated ornithine transcarbamylase deficiency females or control subjects (Purea cycle disorder patients. These findings suggest that better titration of protein restriction could be achieved with branched chain amino acid supplementation in patients with UCDs who are on alternative route therapy.

Interaction of (n-3) and (n-6) fatty acids in desaturation and chain elongation of essential fatty acids in cultured glioma cells

International Nuclear Information System (INIS)

Cook, H.W.; Spence, M.W.

1987-01-01

Recent research in various biological systems has revived interest in interactions between the (n-6) and (n-3) essential fatty acids. We have utilized cultured glioma cells to show that linolenic acid, 18:3(n-3), is rapidly desaturated and chain elongated; 20:5(n-3) is the major product and accumulates almost exclusively in phospholipids. We examined effects of various (n-6), (n-3), (n-9) and (n-7) fatty acids at 40 microM concentration on desaturation and chain elongation processes using [1- 14 C]18:3(n-3) as substrate. In general, monoenoic fatty acids were without effect. The (n-6) fatty acids (18:2, 18:3, 20:3, 20:4 and 22:4) had little effect on total product formed. There was a shift of labeled product to triacylglycerol, and in phospholipids, slightly enhanced conversion of 20:5 to 22:5 was evident. In contrast, 22:6(n-3) was inhibitory, whereas 20:3(n-3) and 20:5(n-3) had much less effect. At concentrations less than 75 microM, all acids were inhibitory. Most products were esterified to phosphatidylcholine, but phosphatidylethanolamine also contained a major portion of 20:5 and 22:5. We provide a condensed overview of how the (n-6) and (n-3) fatty acids interact to modify relative rates of desaturation and chain elongation, depending on the essential fatty acid precursor. Thus, the balance between these dietary acids can markedly influence enzymes providing crucial membrane components and substrates for biologically active oxygenated derivatives

Mathematical Modeling of the Process for Microbial Production of Branched Chained Amino Acids

Directory of Open Access Journals (Sweden)

Todorov K.

2009-12-01

Full Text Available This article deals with modelling of branched chained amino acids production. One of important branched chained amino acid is L-valine. The aim of the article is synthesis of dynamic unstructured model of fed-batch fermentation process with intensive droppings for L-valine production. The presented approach of the investigation includes the following main procedures: description of the process by generalized stoichiometric equations; preliminary data processing and calculation of specific rates for main kinetic variables; identification of the specific rates takes into account the dissolved oxygen tension; establishment and optimisation of dynamic model of the process; simulation researches. MATLAB is used as a research environment.

Saturated very long chain fatty acids are required for the production of infectious human cytomegalovirus progeny.

Directory of Open Access Journals (Sweden)

Emre Koyuncu

Full Text Available Human cytomegalovirus hijacks host cell metabolism, increasing the flux of carbon from glucose to malonyl-CoA, the committed precursor to fatty acid synthesis and elongation. Inhibition of acetyl-CoA carboxylase blocks the production of progeny virus. To probe further the role of fatty acid metabolism during infection, we performed an siRNA screen to identify host cell metabolic enzymes needed for the production of infectious cytomegalovirus progeny. The screen predicted that multiple long chain acyl-CoA synthetases and fatty acid elongases are needed during infection, and the levels of RNAs encoding several of these enzymes were upregulated by the virus. Roles for acyl-CoA synthetases and elongases during infection were confirmed by using small molecule antagonists. Consistent with a role for these enzymes, mass spectrometry-based fatty acid analysis with ¹³C-labeling revealed that malonyl-CoA is consumed by elongases to produce very long chain fatty acids, generating an approximately 8-fold increase in C26-C34 fatty acid tails in infected cells. The virion envelope was yet further enriched in C26-C34 saturated fatty acids, and elongase inhibitors caused the production of virions with lower levels of these fatty acids and markedly reduced infectivity. These results reveal a dependence of cytomegalovirus on very long chain fatty acid metabolism.

Lipase-catalyzed acidolysis of canola oil with caprylic acid to produce medium-, long- and medium-chain-type structured lipids

DEFF Research Database (Denmark)

Wang, Yingyao; Xia, Luan; Xu, Xuebing

2012-01-01

Lipase-catalyzed acidolysis of canola oil with caprylic acid was performed to produce structured lipids (SLs) containing medium-chain fatty acid (M) at position sn-1,3 and long-chain fatty acid (L) at the sn-2 position in a solvent-free system. Six commercial lipases from different sources were...

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

DEFF Research Database (Denmark)

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......% and 45%, respectively). However, the recovery of exogenous 18:1 n-9 was higher after a single bolus of MLM compared with a bolus of LLL in rats on the MLM diet (40% and 24%, respectively, P = 0.009). The recovery of lymphatic 18:1 n-9 of the LLL bolus tended to depend on the diet triacylglycerol...... structure and composition (P = 0.07). This study demonstrated that with a diet containing specific structured triacylglycerol, the lymphatic recovery of 18:1 n-9 after a single bolus of fat was dependent on the triacylglycerol structure of the bolus. This indicates that the lymphatic recovery of long...

Metformin inhibits Branched Chain Amino Acid (BCAA) derived ketoacidosis and promotes metabolic homeostasis in MSUD.

Science.gov (United States)

S Sonnet, Davis; N O'Leary, Monique; A Gutierrez, Mark; M Nguyen, Steven; Mateen, Samiha; Hsu, Yuehmei; P Mitchell, Kylie; J Lopez, Antonio; Vockley, Jerry; K Kennedy, Brian; Ramanathan, Arvind

2016-07-04

Maple Syrup Urine Disease (MSUD) is an inherited disorder caused by the dysfunction in the branched chain keto-acid dehydrogenase (BCKDH) enzyme. This leads to buildup of branched-chain keto-acids (BCKA) and branched-chain amino acids (BCAA) in body fluids (e.g. keto-isocaproic acid from the BCAA leucine), leading to numerous clinical features including a less understood skeletal muscle dysfunction in patients. KIC is an inhibitor of mitochondrial function at disease relevant concentrations. A murine model of intermediate MSUD (iMSUD) shows significant skeletal muscle dysfunction as by judged decreased muscle fiber diameter. MSUD is an orphan disease with a need for novel drug interventions. Here using a 96-well plate (liquid chromatography- mass spectrometry (LC-MS) based drug-screening platform we show that Metformin, a widely used anti-diabetic drug, reduces levels of KIC in patient-derived fibroblasts by 20-50%. This Metformin-mediated effect was conserved in vivo; Metformin-treatment significantly reduced levels of KIC in the muscle (by 69%) and serum (by 56%) isolated from iMSUD mice, and restored levels of mitochondrial metabolites (e.g. AMP and other TCA). The drug also decreased the expression of mitochondrial branched chain amino transferase (BCAT) which produces KIC in skeletal muscle. This suggests that Metformin can restore skeletal muscle homeostasis in MSUD by decreasing mitochondrial KIC production.

Synthesis and evaluation of new long alkyl side chain acetamide, isoxazolidine and isoxazoline derivatives as corrosion inhibitors

International Nuclear Information System (INIS)

Yildirim, A.; Cetin, M.

2008-01-01

2-(Alkylsulfanyl)-N-(pyridin-2-yl) acetamide derivatives were synthesized via amidation reaction of acyl chlorides bearing S atom in the long chain with 2-aminopyridine. Derivatives of isoxazolidine and isoxazoline were synthesized through 1,3-dipolar cycloaddition reactions with three different long chain alkenes containing O or S as hetero atoms and C,N-diphenyl nitrone or benzonitrile-N-oxide, respectively. Synthesized compounds were characterized with their FT-IR, 1 H NMR spectra and then their physical properties and corrosion prevention efficiencies were investigated. All compounds were tested with steel coupons in acidic medium by gravimetric method, and also some of them were tested with steel stripe in paraffin based mineral oil medium via standard method. Acidic test was done with a medium concentration of 2 M HCl for 20 h at room temperature. Mineral oil was used and the test in this medium was done at 60 deg. C constant temperature but varying time from 42 to 63 h. The best inhibition was generally obtained at 50 ppm inhibitor concentration in the acidic medium. All tested inhibitors except two of them in oil medium also showed promising inhibition efficiencies

A pilot, short-term dietary manipulation of branched chain amino acids has modest influence on fasting levels of branched chain amino acids

OpenAIRE

Cavallaro, Nicole Landa; Garry, Jamie; Shi, Xu; Gerszten, Robert E.; Anderson, Ellen J.; Walford, Geoffrey A.

2016-01-01

Background: Elevated fasting levels of branched chain amino acids (BCAAs: valine, isoleucine, leucine) in venous blood are associated with a variety of metabolic impairments, including increased risk of type 2 diabetes (T2D). Fasting BCAA levels are influenced by non-dietary factors. However, it is unknown whether fasting BCAAs can be altered through manipulation of dietary intake alone.Objective: To test whether a specific dietary intervention, using differences in BCAA intake, alters fastin...

Lithiated short side chain perfluorinated sulfonic ionomeric membranes: Water content and conductivity

Science.gov (United States)

Navarrini, Walter; Scrosati, Bruno; Panero, Stefania; Ghielmi, Alessandro; Sanguineti, Aldo; Geniram, Giuliana

In view of possible applications as single-ion electrolyte for lithium batteries, some aspects of the lithium form of Hyflon Ion ionomer, a sulfonic short side chain (SSC) electrolyte, have been investigated. The synthesis of the ionomer and the successive membrane preparation is reported. An appropriate methodology for the direct salification of the ionomeric membrane from the SO 2F form to lithium salt, using lithium hydroxide in absence of organic solvent has been found. Utilizing these SSC lithium ionomer membranes and though a particular methodology for the dehydration of the lithium ion membrane in non-aqueous media, it has been possible to achieve an ionic conductivity of 10 -3 S cm -1 at room temperature [W. Navarrini, S. Panero, B. Scrosati, A. Sanguineti, European Patent 1,403,958 A1 (2003)]. Surprisingly it was observed that the membrane ionic conductivity depends on the dehydration methodologies adopted.

Efficient and Mild Microwave-Assisted Stepwise Functionalization of Naphthalenediimide with α-Amino Acids

NARCIS (Netherlands)

Pengo, Paolo; Pantoş, G. Dan; Otto, Sijbren; Sanders, Jeremy K.M.

2006-01-01

Microwave dielectric heating proved to be an efficient method for the one-pot and stepwise syntheses of symmetrical and unsymmetrical naphthalenediimide derivatives of α-amino acids. Acid-labile side chain protecting groups are stable under the reaction conditions; protection of the α-carboxylic

The activity state of the branched-chain 2-oxo acid dehydrogenase complex in rat tissues.

OpenAIRE

Wagenmakers, A J; Schepens, J T; Veldhuizen, J A; Veerkamp, J H

1984-01-01

An assay is described to define the proportion of the branched-chain 2-oxo acid dehydrogenase complex that is present in the active state in rat tissues. Activities are measured in homogenates in two ways: actual activities, present in tissues, by blocking both the kinase and phosphatase of the enzyme complex during homogenization, preincubation, and incubation with 1-14C-labelled branched-chain 2-oxo acid, and total activities by blocking only the kinase during the 5 min preincubation (neces...

Effects of clofibric acid on the activity and activity state of the hepatic branched-chain 2-oxo acid dehydrogenase complex.

Science.gov (United States)

Zhao, Y; Jaskiewicz, J; Harris, R A

1992-01-01

Feeding clofibric acid to rats caused little or no change in total activity of the liver branched-chain 2-oxo acid dehydrogenase complex (BCODC). No change in mass of liver BCODC was detected by immunoblot analysis in response to dietary clofibric acid. No changes in abundance of mRNAs for the BCODC E1 alpha, E1 beta and E2 subunits were detected by Northern-blot analysis. Likewise, dietary clofibric acid had no effect on the activity state of liver BCODC (percentage of enzyme in the dephosphorylated, active, form) of rats fed on a chow diet. However, dietary clofibric acid greatly increased the activity state of liver BCODC of rats fed on a diet deficient in protein. No stable change in liver BCODC kinase activity was found in response to clofibric acid in either chow-fed or low-protein-fed rats. Clofibric acid had a biphasic effect on flux through BCODC in hepatocytes prepared from low-protein-fed rats. Stimulation of BCODC flux at low concentrations was due to clofibric acid inhibition of BCODC kinase, which in turn allowed activation of BCODC by BCODC phosphatase. Inhibition of BCODC flux at high concentrations was due to direct inhibition of BCODC by clofibric acid. The results suggest that the effects of clofibric acid in vivo on branched-chain amino acid metabolism can be explained by the inhibitory effects of this drug on BCODC kinase. Images Fig. 2. Fig. 3. PMID:1637295

Histone Deacetylase Inhibition and Dietary Short-Chain Fatty Acids

OpenAIRE

Licciardi, Paul V.; Ververis, Katherine; Karagiannis, Tom C.

2011-01-01

Changes in diet can also have dramatic effects on the composition of gut microbiota. Commensal bacteria of the gastrointestinal tract are critical regulators of health and disease by protecting against pathogen encounter whilst also maintaining immune tolerance to certain allergens. Moreover, consumption of fibre and vegetables typical of a non-Western diet generates substantial quantities of short-chain fatty acids (SCFAs) which have potent anti-inflammatory properties. Dietary interventions...

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

DEFF Research Database (Denmark)

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...... model is proposed to explain the experimental results, making it possible to understand the influence of the different photoinduced effects. It is shown that at low intensity the polarization properties of the diffraction at these gratings are determined by the interaction of the linear and circular...... photobirefringences, and at larger intensity the influence of the surface relief dominates the effect of the circular anisotropy. Owing to the high recording efficiency of the polyesters, the +/-1-order diffracted waves change the polarization interference pattern during the holographic recording, resulting...

Purification and characterization of a branched-chain amino acid aminotransferase from Lactobacillus paracasei subsp paracasei CHCC 2115

DEFF Research Database (Denmark)

Thage, B.V.; Rattray, F.P.; Laustsen, M.W.

2004-01-01

Purification and characterization of an aminotransferase (AT) specific for the degradation of branched-chain amino acids from Lactobacillus paracasei subsp. paracasei CHCC 2115. Methods and Results: The purification protocol consisted of anion exchange chromatography, affinity chromatography...... of other metal ions, thiol- and carbonyl-binding agents. The N-terminal sequence of the enzyme was SVNIDWNNLGFDYMQLPYRYVAHXKDGVXD, and had at the amino acid level, 60 and 53% identity to a branched-chain amino acid AT of Lact. plantarum and Lactococcus lactis, respectively. Conclusions: The results suggest...

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

Energy Technology Data Exchange (ETDEWEB)

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

2011-12-31

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

Branched-chain amino acid supplementation and the immune response of long-distance athletes.

Science.gov (United States)

Bassit, Reinaldo A; Sawada, Letícia A; Bacurau, Reury F P; Navarro, Franciso; Martins, Eivor; Santos, Ronaldo V T; Caperuto, Erico C; Rogeri, Patrícia; Costa Rosa, Luís F B P

2002-05-01

Intense long-duration exercise has been associated with immunosuppression, which affects natural killer cells, lymphokine-activated killer cells, and lymphocytes. The mechanisms involved, however, are not fully determined and seem to be multifactorial, including endocrine changes and alteration of plasma glutamine concentration. Therefore, we evaluated the effect of branched-chain amino acid supplementation on the immune response of triathletes and long-distance runners. Peripheral blood was collected prior to and immediately after an Olympic Triathlon or a 30k run. Lymphocyte proliferation, cytokine production by cultured cells, and plasma glutamine were measured. After the exercise bout, athletes from the placebo group presented a decreased plasma glutamine concentration that was abolished by branched-chain amino acid supplementation and an increased proliferative response in their peripheral blood mononuclear cells. Those cells also produced, after exercise, less tumor necrosis factor, interleukins-1 and -4, and interferon and 48% more interleukin-2. Supplementation stimulated the production of interleukin-2 and interferon after exercise and a more pronounced decrease in the production of interleukin-4, indicating a diversion toward a Th1 type immune response. Our results indicate that branched-chain amino acid (BCAA) supplementation recovers the ability of peripheral blood mononuclear cells proliferate in response to mitogens after a long distance intense exercise, as well as plasma glutamine concentration. The amino acids also modify the pattern of cytokine production leading to a diversion of the immune response toward a Th1 type of immune response.

Abscisic acid-regulated protein degradation causes osmotic stress-induced accumulation of branched-chain amino acids in Arabidopsis thaliana.

Science.gov (United States)

Huang, Tengfang; Jander, Georg

2017-10-01

Whereas proline accumulates through de novo biosynthesis in plants subjected to osmotic stress, leucine, isoleucine, and valine accumulation in drought-stressed Arabidopsis thaliana is caused by abscisic acid-regulated protein degradation. In response to several kinds of abiotic stress, plants greatly increase their accumulation of free amino acids. Although stress-induced proline increases have been studied the most extensively, the fold-increase of other amino acids, in particular branched-chain amino acids (BCAAs; leucine, isoleucine, and valine), is often higher than that of proline. In Arabidopsis thaliana (Arabidopsis), BCAAs accumulate in response to drought, salt, mannitol, polyethylene glycol, herbicide treatment, and nitrogen starvation. Plants that are deficient in abscisic acid signaling accumulate lower amounts of BCAAs, but not proline and most other amino acids. Previous bioinformatic studies had suggested that amino acid synthesis, rather than protein degradation, is responsible for the observed BCAA increase in osmotically stressed Arabidopsis. However, whereas treatment with the protease inhibitor MG132 decreased drought-induced BCAA accumulation, inhibition of BCAA biosynthesis with the acetolactate synthase inhibitors chlorsulfuron and imazapyr did not. Additionally, overexpression of BRANCHED-CHAIN AMINO ACID TRANSFERASE2 (BCAT2), which is upregulated in response to osmotic stress and functions in BCAA degradation, decreased drought-induced BCAA accumulation. Together, these results demonstrate that BCAA accumulation in osmotically stressed Arabidopsis is primarily the result of protein degradation. After relief of the osmotic stress, BCAA homeostasis is restored over time by amino acid degradation involving BCAT2. Thus, drought-induced BCAA accumulation is different from that of proline, which is accumulated due to de novo synthesis in an abscisic acid-independent manner and remains elevated for a more prolonged period of time after removal of

Spectra-structure correlations of saturated and unsaturated medium-chain fatty acids. Near-infrared and anharmonic DFT study of hexanoic acid and sorbic acid.

Science.gov (United States)

Grabska, Justyna; Beć, Krzysztof B; Ishigaki, Mika; Wójcik, Marek J; Ozaki, Yukihiro

2017-10-05

Quantum chemical reproduction of entire NIR spectra is a new trend, enabled by contemporary advances in the anharmonic approaches. At the same time, recent increase of the importance of NIR spectroscopy of biological samples raises high demand for gaining deeper understanding of NIR spectra of biomolecules, i.e. fatty acids. In this work we investigate saturated and unsaturated medium-chain fatty acids, hexanoic acid and sorbic acid, in the near-infrared region. By employing fully anharmonic density functional theory (DFT) calculations we reproduce the experimental NIR spectra of these systems, including the highly specific spectral features corresponding to the dimerization of fatty acids. Broad range of concentration levels from 5·10 -4 M in CCl 4 to pure samples are investigated. The major role of cyclic dimers can be evidenced for the vast majority of these samples. A highly specific NIR feature of fatty acids, the elevation of spectral baseline around 6500-4000cm -1 , is being explained by the contributions of combination bands resulting from the vibrations of hydrogen-bonded OH groups in the cyclic dimers. Based on the high agreement between the calculated and experimental NIR spectra, a detailed NIR band assignments are proposed for hexanoic acid and sorbic acid. Subsequently, the correlations between the structure and NIR spectra are elucidated, emphasizing the regions in which clear and universal traces of specific bands corresponding to saturated and unsaturated alkyl chains can be established, thus demonstrating the wavenumber regions highly valuable for structural identifications. Copyright © 2017 Elsevier B.V. All rights reserved.

Production of Medium Chain Fatty Acids by Yarrowia lipolytica: Combining Molecular Design and TALEN to Engineer the Fatty Acid Synthase.

Science.gov (United States)

Rigouin, Coraline; Gueroult, Marc; Croux, Christian; Dubois, Gwendoline; Borsenberger, Vinciane; Barbe, Sophie; Marty, Alain; Daboussi, Fayza; André, Isabelle; Bordes, Florence

2017-10-20

Yarrowia lipolytica is a promising organism for the production of lipids of biotechnological interest and particularly for biofuel. In this study, we engineered the key enzyme involved in lipid biosynthesis, the giant multifunctional fatty acid synthase (FAS), to shorten chain length of the synthesized fatty acids. Taking as starting point that the ketoacyl synthase (KS) domain of Yarrowia lipolytica FAS is directly involved in chain length specificity, we used molecular modeling to investigate molecular recognition of palmitic acid (C16 fatty acid) by the KS. This enabled to point out the key role of an isoleucine residue, I1220, from the fatty acid binding site, which could be targeted by mutagenesis. To address this challenge, TALEN (transcription activator-like effector nucleases)-based genome editing technology was applied for the first time to Yarrowia lipolytica and proved to be very efficient for inducing targeted genome modifications. Among the generated FAS mutants, those having a bulky aromatic amino acid residue in place of the native isoleucine at position 1220 led to a significant increase of myristic acid (C14) production compared to parental wild-type KS. Particularly, the best performing mutant, I1220W, accumulates C14 at a level of 11.6% total fatty acids. Overall, this work illustrates how a combination of molecular modeling and genome-editing technology can offer novel opportunities to rationally engineer complex systems for synthetic biology.

Adsorption of amino acids by fullerenes and fullerene nanowhiskers

Science.gov (United States)

Hashizume, Hideo; Hirata, Chika; Fujii, Kazuko; Miyazawa, Kun'ichi

2015-12-01

We have investigated the adsorption of some amino acids and an oligopeptide by fullerene (C60) and fullerene nanowhiskers (FNWs). C60 and FNWs hardly adsorbed amino acids. Most of the amino acids used have a hydrophobic side chain. Ala and Val, with an alkyl chain, were not adsorbed by the C60 or FNWs. Trp, Phe and Pro, with a cyclic structure, were not adsorbed by them either. The aromatic group of C60 did not interact with the side chain. The carboxyl or amino group, with the frame structure of an amino acid, has a positive or negative charge in solution. It is likely that the C60 and FNWs would not prefer the charged carboxyl or amino group. Tri-Ala was adsorbed slightly by the C60 and FNWs. The carboxyl or amino group is not close to the center of the methyl group of Tri-Ala. One of the methyl groups in Tri-Ala would interact with the aromatic structure of the C60 and FNWs. We compared our results with the theoretical interaction of 20 bio-amino acids with C60. The theoretical simulations showed the bonding distance between C60 and an amino acid and the dissociation energy. The dissociation energy was shown to increase in the order, Val changed a little by C60. In our study Try and Tyr were hardly adsorbed by C60 and FNWs. These amino acids did not show a different adsorption behavior compared with other amino acids. The adsorptive behavior of mono-amino acids might be different from that of polypeptides.

Influence of the chain length on the biological behaviour of 131I fatty acids

International Nuclear Information System (INIS)

Riche, F.; Mathieu, J.P.; Comet, M.; Vidal, M.; Pernin, C.; Marti-Batlle, D.; Busquet, G.; Bardy, A.

1983-01-01

Saturated and acetylenic fatty acids labeled with 131 I in ω position, differing by their chain length (C8 to C20) and the number odd or even of their carbon atoms are injected in mice. The evolution of the activity in myocardium, blood, liver and kidney is measured until 10 minutes after injection. The myocardial activity increases with chain length from C8 to C16 then decreases for C18 and C20. The odd or even number of carbon atoms does not influence myocardial activity but in the liver, activity is inferior with the odd fatty acids. The presence of a triple bond accelerates the output of activity from the myocardium and these fatty acids are not well suited for the study of myocardial metabolism [fr

Improved power conversion efficiency of dye-sensitized solar cells using side chain liquid crystal polymer embedded in polymer electrolytes

Energy Technology Data Exchange (ETDEWEB)

Cho, Woosum [Department of Chemistry Education, and Department of Frontier Materials Chemistry, and Institute for Plastic Information and Energy Materials, Pusan National University, Busan 609-735 (Korea, Republic of); Lee, Jae Wook, E-mail: jlee@donga.ac.kr [Department of Chemistry, Dong-A University, Busan 604-714 (Korea, Republic of); Gal, Yeong-Soon [Polymer Chemistry Lab, College of General Education, Kyungil University, Hayang 712-701 (Korea, Republic of); Kim, Mi-Ra, E-mail: mrkim2@pusan.ac.kr [Department of Polymer Science and Engineering, Pusan National University, Busan 609-735 (Korea, Republic of); Jin, Sung Ho, E-mail: shjin@pusan.ac.kr [Department of Chemistry Education, and Department of Frontier Materials Chemistry, and Institute for Plastic Information and Energy Materials, Pusan National University, Busan 609-735 (Korea, Republic of)

2014-02-14

Side chain liquid crystal polymer (SCLCP) embedded in poly(vinylidenefluoride-co-hexafluoropropylene) (PVdF-co-HFP)-based polymer electrolytes (PVdF-co-HFP:side chain liquid crystal polymer (SCLCP)) was prepared for dye-sensitized solar cell (DSSC) application. The polymer electrolytes contained tetrabutylammonium iodide (TBAI), iodine (I{sub 2}), and 8 wt% PVdF-co-HFP in acetonitrile. DSSCs comprised of PVdF-co-HFP:SCLCP-based polymer electrolytes displayed enhanced redox couple reduction and reduced charge recombination in comparison to those of the conventional PVdF-co-HFP-based polymer electrolyte. The significantly increased short-circuit current density (J{sub sc}, 10.75 mA cm{sup −2}) of the DSSCs with PVdF-co-HFP:SCLCP-based polymer electrolytes afforded a high power conversion efficiency (PCE) of 5.32% and a fill factor (FF) of 0.64 under standard light intensity of 100 mW cm{sup −2} irradiation of AM 1.5 sunlight. - Highlights: • We developed the liquid crystal polymer embedded on polymer electrolyte for DSSCs. • We fabricated the highly efficient DSSCs using polymer electrolyte. • The best PCE achieved for P1 is 5.32% using polymer electrolyte.

Improved power conversion efficiency of dye-sensitized solar cells using side chain liquid crystal polymer embedded in polymer electrolytes

International Nuclear Information System (INIS)

Cho, Woosum; Lee, Jae Wook; Gal, Yeong-Soon; Kim, Mi-Ra; Jin, Sung Ho

2014-01-01

Side chain liquid crystal polymer (SCLCP) embedded in poly(vinylidenefluoride-co-hexafluoropropylene) (PVdF-co-HFP)-based polymer electrolytes (PVdF-co-HFP:side chain liquid crystal polymer (SCLCP)) was prepared for dye-sensitized solar cell (DSSC) application. The polymer electrolytes contained tetrabutylammonium iodide (TBAI), iodine (I 2 ), and 8 wt% PVdF-co-HFP in acetonitrile. DSSCs comprised of PVdF-co-HFP:SCLCP-based polymer electrolytes displayed enhanced redox couple reduction and reduced charge recombination in comparison to those of the conventional PVdF-co-HFP-based polymer electrolyte. The significantly increased short-circuit current density (J sc , 10.75 mA cm −2 ) of the DSSCs with PVdF-co-HFP:SCLCP-based polymer electrolytes afforded a high power conversion efficiency (PCE) of 5.32% and a fill factor (FF) of 0.64 under standard light intensity of 100 mW cm −2 irradiation of AM 1.5 sunlight. - Highlights: • We developed the liquid crystal polymer embedded on polymer electrolyte for DSSCs. • We fabricated the highly efficient DSSCs using polymer electrolyte. • The best PCE achieved for P1 is 5.32% using polymer electrolyte

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

NARCIS (Netherlands)

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

1995-01-01

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

Prenatal and early postnatal long-chain polyunsaturated fatty acid status : do they affect neurodevelopmental outcome in healthy term infants?

NARCIS (Netherlands)

Bouwstra, Hylco

2007-01-01

Long-chain metabolites of the parent essential fatty acids called long-chain polyunsaturated fatty acids (LCPUFAs) are major membrane components in the central nervous system. Dictary intake partly determines the availability of LCPUFAs as building btocks for neuronal structures. Fifty till sixty

Structural similarity between β(3)-peptides synthesized from β(3)-homo-amino acids and aspartic acid monomers.

Science.gov (United States)

Ahmed, Sahar; Sprules, Tara; Kaur, Kamaljit

2014-07-01

Formation of stable secondary structures by oligomers that mimic natural peptides is a key asset for enhanced biological response. Here we show that oligomeric β(3)-hexapeptides synthesized from L-aspartic acid monomers (β(3)-peptides 1, 5a, and 6) or homologated β(3)-amino acids (β(3)-peptide 2), fold into similar stable 14-helical secondary structures in solution, except that the former form right-handed 14-helix and the later form left-handed 14-helix. β(3)-Peptides from L-Asp monomers contain an additional amide bond in the side chains that provides opportunities for more hydrogen bonding. However, based on the NMR solution structures, we found that β(3)-peptide from L-Asp monomers (1) and from homologated amino acids (2) form similar structures with no additional side-chain interactions. These results suggest that the β(3)-peptides derived from L-Asp are promising peptide-mimetics that can be readily synthesized using L-Asp monomers as well as the right-handed 14-helical conformation of these β(3)-peptides (such as 1 and 6) may prove beneficial in the design of mimics for right-handed α-helix of α-peptides. © 2014 Wiley Periodicals, Inc.

Barrier properties of lipid bilayers composed of lecithins with odd chain fatty acids

NARCIS (Netherlands)

Salvati, S.; Serlupi-Crescenzi, G.; Gier, J. de

Lecithins with fatty acid chain length of 17 carbon atoms and different degrees of unsaturation were synthesized. The thermotropic behaviour and barrier function of derived liposomal bilayers were studied.

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

DEFF Research Database (Denmark)

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...... be reeorded if the UV irradiated films have been kept in darkness for several hours. In another set of experiments performed with the P6d4 polymer, irradiation with high intensity linearly polarised 488 nm light induces an initial increase of An and then it goes back to zero. Subsequent irradiation...

Randomised clinical study: inulin short-chain fatty acid esters for targeted delivery of short-chain fatty acids to the human colon.

Science.gov (United States)

Polyviou, T; MacDougall, K; Chambers, E S; Viardot, A; Psichas, A; Jawaid, S; Harris, H C; Edwards, C A; Simpson, L; Murphy, K G; Zac-Varghese, S E K; Blundell, J E; Dhillo, W S; Bloom, S R; Frost, G S; Preston, T; Tedford, M C; Morrison, D J

2016-10-01

Short-chain fatty acids (SCFA) produced through fermentation of nondigestible carbohydrates by the gut microbiota are associated with positive metabolic effects. However, well-controlled trials are limited in humans. To develop a methodology to deliver SCFA directly to the colon, and to optimise colonic propionate delivery in humans, to determine its role in appetite regulation and food intake. Inulin SCFA esters were developed and tested as site-specific delivery vehicles for SCFA to the proximal colon. Inulin propionate esters containing 0-61 wt% (IPE-0-IPE-61) propionate were assessed in vitro using batch faecal fermentations. In a randomised, controlled, crossover study, with inulin as control, ad libitum food intake (kcal) was compared after 7 days on IPE-27 or IPE-54 (10 g/day all treatments). Propionate release was determined using (13) C-labelled IPE variants. In vitro, IPE-27-IPE-54 wt% propionate resulted in a sevenfold increase in propionate production compared with inulin (P inulin (439.5 vs. 703.9 kcal, P = 0.025) and IPE-54 (439.5 vs. 659.3 kcal, P = 0.025), whereas IPE-54 was not significantly different from inulin control. IPE-27 significantly reduced food intake suggesting colonic propionate plays a role in appetite regulation. Inulin short-chain fatty acid esters provide a novel tool for probing the diet-gut microbiome-host metabolism axis in humans. © 2016 The Authors. Alimentary Pharmacology & Therapeutics Published by John Wiley & Sons Ltd.

Analysis of short-chain acids from anaerobic bacteria by high-performance liquid chromatography.

OpenAIRE

Guerrant, G O; Lambert, M A; Moss, C W

1982-01-01

A standard mixture of 25 short-chain fatty acids was resolved by high-performance liquid chromatography, using an Aminex HPX-87 column. The acids produced in culture media by anaerobic bacteria were analyzed by high-performance liquid chromatography after extraction with ether and reextraction into a small volume of 0.1 N NaOH. The presence of fumaric acid in culture extracts of Peptostreptococcus anaerobius was confirmed by gas chromatography-mass spectrometry analysis of the trapped eluent ...

Orphan drugs in development for long-chain fatty acid oxidation disorders: challenges and progress

OpenAIRE

Merritt II, J Lawrence; Sun,Angela

2015-01-01

Angela Sun, J Lawrence Merritt II Department of Pediatrics, University of Washington, Seattle, WA, USA Abstract: Fatty acid oxidation disorders are inborn errors of metabolism resulting in failure of ß-oxidation within or transport of fatty acids into the mitochondria. The long-chain fatty acid oxidation disorders are characterized by variable presentations ranging from newborn cardiomyopathy, to infantile hypoketotic hypoglycemia resulting from liver involvement, to skeletal myopa...

Side-chain dynamics of a detergent-solubilized membrane protein: Measurement of tryptophan and glutamine hydrogen-exchange rates in M13 coat protein by 1H NMR spectroscopy

International Nuclear Information System (INIS)

O'Neil, J.D.J.; Sykes, B.D.

1989-01-01

M13 coat protein is a small (50 amino acids) lipid-soluble protein that becomes an integral membrane protein during the infection stage of the life cycle of the M13 phage and is therefore used as a model membrane protein. To study side-chain dynamics in the protein, the authors have measured individual hydrogen-exchange rates for a primary amide in the side chain of glutamine-15 and for the indole amine of tryptophan-26. The protein was solubilized with the use of perdeuteriated sodium dodecyl sulfate (SDS), and hydrogen-exchange rates were measured by using 1 H nuclear magnetic resonance spectroscopy. The glutamine-15 syn proton exchanged at a rate identical with that in glutamine model peptides except that the pH corresponding to minimum exchange was elevated by about 1.5 pH units. The tryptophan-26 indole amine proton exchange was biphasic, suggesting that two populations of tryptophan-26 exist. It is suggested that the two populations may reflect protein dimerization or aggregation in the SDS micelles. The pH values of minimum exchange for tryptophan-26 in both environments were also elevated by 1.3-1.9 pH units. This phenomenon is reproduced when small tryptophan- and glutamine-containing hydrophobic peptides are dissolved in the presence of SDS micelles. The electrostatic nature of this phenomenon is proven by showing that the minimum pH for exchange can be reduced by dissolving the hydrophobic peptides in the positively charged detergent micelle dodecyltrimethylammonium bromide

Effects of rough handling on short chain fatty acid production and ...

African Journals Online (AJOL)

The influence of stress due to rough handling (RH) on gastrointestinal tract (GIT) environmental pH, concentration of short chain fatty acids (SCFAs) and modulatory roles of two Lactobacillus strains was investigated in broiler chickens. Equal number of chicks was randomly assigned to one of the following treatment groups; ...

A new viscosupplement based on partially hydrophobic hyaluronic acid: a comparative study.

Science.gov (United States)

Finelli, Ivana; Chiessi, Ester; Galesso, Devis; Renier, Davide; Paradossi, Gaio

2011-01-01

A novel partially hydrophobized derivative of hyaluronic acid (HYADD® 4), containing a low number of C16 side-chains per polysaccharide backbone, provides injectable hydrogels stabilized by side-chain hydrophobic interactions. The rheological properties of Hymovis®, a physical hydrogel based on the hyaluronic acid derivative HYADD® 4, were evaluated using as reference a solution of the parent natural polysaccharide, hyaluronic acid. The rheological measurements were performed both in flow and oscillation regimes at the physiological frequency values of the knee, typically spanning the range from 0.5 Hz (walking frequency) to 3 Hz (running frequency). Moreover, the viscoelastic features of Hymovis® were compared with the market-available viscosupplementation products in view of its use in joint diseases.The different behavior of the investigated materials in crossover frequency measurements and in structure recovery experiments can be explained on the basis of the structural and dynamic properties of the polymeric systems.

Physiological characterisation of Penicillium chrysogenum strains expressing the expandase gene from Streptomyces clavuligerus during batch cultivations. Growth and adipoyl-7- aminodeacetoxycephalosporanic acid production

DEFF Research Database (Denmark)

Robin, Jarno Jacky Christian; Jakobsen, M.; Beyer, M.

2001-01-01

The production of adipoyl-7-aminodeacetoxy-cephalosporanic acid (ad-7-ADCA) was studied, using two recombinant strains of Penicillium chrysogenum carrying the expandase gene from Streptomyces clavuligerus. The adipoyl-side chain of this compound may easily be removed using an amidase; and this pr......The production of adipoyl-7-aminodeacetoxy-cephalosporanic acid (ad-7-ADCA) was studied, using two recombinant strains of Penicillium chrysogenum carrying the expandase gene from Streptomyces clavuligerus. The adipoyl-side chain of this compound may easily be removed using an amidase...

Effect of hydrophilic additives on volumetric and viscosity properties of amino acids in aqueous solutions at T = (283.15 to 333.15) K

International Nuclear Information System (INIS)

Sastry, Nandhibatla V.; Valand, Pinakin H.; Macwan, Pradip M.

2012-01-01

Highlights: ► Densities and viscosities of amino acids in aqueous additive solutions at different temperatures. ► Side chain partial molar volumes, V ¯ 2,tr ∘ and transfer volumes ΔV tr ∘ were calculated. ► Temperature effect on volumetric functions and B-coefficients were analyzed. ► Hydrophobic side chains facilitate the solute–solute interactions and hydrophobic hydration. - Abstract: Apparent molar volumes and partial molar volumes at infinite dilution, V ¯ 2 ∘ for amino acids (glycine, L-valine, L-leucine, L-phenylalanine, and L-aspargine) aqueous solutions in sucrose (0.05 to 0.2 (w/w)), urea (0.05), 2,3-butane diol (0.05) and 2-butoxyethanol (0.05) as additives have been calculated from the experimental densities at T = (283.15 to 233.15) K. Limiting partial molar expansibilities, E 2 ∘ , side chain partial molar volumes, V ¯ 2,tr ∘ and transfer volumes (from water to aqueous additive environment), ΔV tr ∘ for both the amino acids and their side chains have also been calculated. Relative viscosities for same systems were also calculated over the same temperature range and were analyzed in terms of Jones–Dole equation to calculate B-coefficients. The analysis of volumetric functions and B-coefficients suggests that the solute–co-solute interactions are more favored at elevated temperatures and in presence of high concentration of sucrose. Otherwise the hydrophobic side chains facilitate the solute–solute interactions and also time induced hydrophobic hydration in the bulk water.