WorldWideScience

Sample records for lysine side chain

  1. Snorkeling of lysine side chains in transmembrane helices: how easy can it get?

    Science.gov (United States)

    Strandberg, Erik; Killian, J Antoinette

    2003-06-05

    Transmembrane segments of proteins are often flanked by lysine residues. The side chains of these residues may snorkel, i.e. they may bury themselves with their aliphatic part in the hydrophobic region of the lipid bilayer, while positioning the charged amino group in the more polar interface. Here we estimate the free energy cost of snorkeling from thermodynamical calculations based on studies with synthetic transmembrane peptides [Strandberg et al. (2002) Biochemistry 41, 7190-7198]. The value is estimated to be between 0.07 and 0.7 kcal mol(-1) for a lysine side chain. This very low value indicates that snorkeling may be a common process, which should be taken into consideration both in experimental and in theoretical studies on protein-lipid interactions.

  2. Ion pair formation of phosphorylated amino acids and lysine and arginine side chains : A theoretical study

    NARCIS (Netherlands)

    Mavri, J; Vogel, HJ

    Protein phosphorylation is one of the major signal transduction mechanisms for controlling and regulating intracellular processes, Phosphorylation of specific hydroxylated amino acid side chains (Ser, Thr, Tyr) by protein kinases can activate numerous enzymes; this effect can be reversed by the

  3. Investigation of nonfouling polypeptides of poly(glutamic acid) with lysine side chains synthesized by EDC·HCl/HOBt chemistry.

    Science.gov (United States)

    Yang, Qinghua; Li, Wenchen; Wang, Longgang; Wang, Guangzhi; Wang, Zhen; Liu, Lingyun; Chen, Shengfu

    2014-01-01

    Nonfouling polypeptides with homogenous alternating charges draw peoples' attentions for their potential capability in biodegradation. Homogenous glutamic acid (E) and lysine (K) polypeptides were proposed and synthesized before. In this work, a new polypeptide formed by poly(glutamic acid) with lysine side chains (poly(E)-K) was synthesized by facile EDC·HCl/HOBt chemistry and investigated. Results show that these polypeptides also have good nonspecific protein resistance determined by enzyme-linked immunosorbent assay. The lowest nonspecific adsorption of the model proteins, anti-IgG and fibrinogen (Fg), on the self-assembling monolayers (SAMs) surface of poly(E)-K was only 3.3 ± 1.8 and 4.4 ± 1.6%, respectively, when protein adsorption on tissue culture polystyrene surface was set as 100%. And, the relative nonspecific protein adsorption increases when the polypeptide molecular weight increases due to the repression of low density polymer brushes. Moreover, almost no obvious cytotoxicity and hemolytic activity in vitro were detected. This work suggests that polypeptides with various formats of homogenous balanced charges could achieve excellent nonspecific protein resistance, which might be the intrinsic reason for the coexistence of high concentration serum proteins in blood.

  4. Nuclear Magnetic Resonance Observation of α-Synuclein Membrane Interaction by Monitoring the Acetylation Reactivity of Its Lysine Side Chains.

    Science.gov (United States)

    Lee, Jung Ho; Ying, Jinfa; Bax, Ad

    2016-09-06

    The interaction between α-synuclein (αS) protein and lipid membranes is key to its role in synaptic vesicle homeostasis and plays a role in initiating fibril formation, which is implicated in Parkinson's disease. The natural state of αS inside the cell is generally believed to be intrinsically disordered, but chemical cross-linking experiments provided evidence of a tetrameric arrangement, which was reported to be rich in α-helical secondary structure based on circular dichroism (CD). Cross-linking relies on chemical modification of the protein's Lys C(ε) amino groups, commonly by glutaraldehyde, or by disuccinimidyl glutarate (DSG), with the latter agent preferred for cellular assays. We used ultra-high-resolution homonuclear decoupled nuclear magnetic resonance experiments to probe the reactivity of the 15 αS Lys residues toward N-succinimidyl acetate, effectively half the DSG cross-linker, which results in acetylation of Lys. The intensities of both side chain and backbone amide signals of acetylated Lys residues provide direct information about the reactivity, showing a difference of a factor of 2.5 between the most reactive (K6) and the least reactive (K102) residue. The presence of phospholipid vesicles decreases reactivity of most Lys residues by up to an order of magnitude at high lipid:protein stoichiometries (500:1), but only weakly at low ratios. The decrease in Lys reactivity is found to be impacted by lipid composition, even for vesicles that yield similar αS CD signatures. Our data provide new insight into the αS-bilayer interaction, including the pivotal state in which the available lipid surface is limited. Protection of Lys C(ε) amino groups by αS-bilayer interaction will strongly impact quantitative interpretation of DSG cross-linking experiments.

  5. Expansion of the Lysine Acylation Landscape

    DEFF Research Database (Denmark)

    Olsen, Christian A.

    2012-01-01

    Leaving marks: The number of known posttranslational modifications for lysine has been expanded considerably. In addition to acetylation of side-chain amino functionalities of lysine residues in proteins, crotonylation, succinylation, and malonylation have now been identified as posttranslational...

  6. 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.

  7. Side Chain Cyclized Aromatic Amino Acids

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  8. Side-Chain-Induced Rigid Backbone Organization of Polymer Semiconductors through Semifluoroalkyl Side Chains.

    Science.gov (United States)

    Kang, Boseok; Kim, Ran; Lee, Seon Baek; Kwon, Soon-Ki; Kim, Yun-Hi; Cho, Kilwon

    2016-03-23

    While high-mobility p-type conjugated polymers have been widely reported, high-mobility n-type conjugated polymers are still rare. In the present work, we designed semifluorinated alkyl side chains and introduced them into naphthalene diimide-based polymers (PNDIF-T2 and PNDIF-TVT). We found that the strong self-organization of these side chains induced a high degree of order in the attached polymer backbones by forming a superstructure composed of "backbone crystals" and "side-chain crystals". This phenomenon was shown to greatly enhance the ordering along the backbone direction, and the resulting polymers thus exhibited unipolar n-channel transport in field-effect transistors with remarkably high electron mobility values of up to 6.50 cm(2) V(-1) s(-1) and with a high on-off current ratio of 10(5).

  9. 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.

  10. Rational Design of Coordination Polymers with Flexible Oxyethylene Side Chains

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Eun Young; Gao, Chunji; Lee, Suck Hyun; Kwon, O Pil [Ajou University, Suwon (Korea, Republic of)

    2012-04-15

    We rationally designed and synthesized metallopolymers with organic 1,4-benzenedicarboxylic acid (BDC) linkers with different lengths of oxyethylene side chains in order to examine the influence of side chains on the coordination characteristics. While in a previous report the BDC linkers with alkyl side chains were found to form three-dimensional (3D) isoreticular metal-organic framework (IRMOF) structures or one-dimensional (1D) coordination polymeric structures with short -O(CH{sub 2}){sub 6}CH{sub 3} or long -O(CH{sub 2}){sub 9}CH{sub 3} side chains, respectively, new BDC linkers with oxyethylene side chains of the same lengths, -(OCH{sub 2}CH{sub 2}){sub 2}CH{sub 3} and -(OCH{sub 2}CH{sub 2}){sub 3}CH{sub 3}, form only 3D IRMOF structures. This result is attributed to the higher flexibility and smaller volume of oxyethylene side chains compared to alkyl side chains

  11. Holographic Gratings in Azobenzene Side-Chain Polymethacrylates

    DEFF Research Database (Denmark)

    Andruzzi, Luisa; Altomare, Angelina; Ciardelli, Francesco

    1999-01-01

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

  12. Weakening of a Polyethylene Chain by Methyl Side Groups

    NARCIS (Netherlands)

    Hageman, J.C.L.; Wijs, G.A. de; Groot, R.A. de; Meier, Robert J.

    2003-01-01

    The effect of methyl side groups on the strength of a single polyethylene chain is calculated with Density Functional Theory. Using transition state theory, the scission rate is calculated as function of stress for bonds next to a methyl side group. The increase in the scission rate due to the prese

  13. Weakening of a Polyethylene Chain by Methyl Side Groups

    NARCIS (Netherlands)

    Hageman, J.C.L.; Wijs, G.A. de; Groot, R.A. de; Meier, Robert J.

    2003-01-01

    The effect of methyl side groups on the strength of a single polyethylene chain is calculated with Density Functional Theory. Using transition state theory, the scission rate is calculated as function of stress for bonds next to a methyl side group. The increase in the scission rate due to the prese

  14. 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.

  15. A protein-dependent side-chain rotamer library

    Directory of Open Access Journals (Sweden)

    Bhuyan Md Shariful

    2011-12-01

    Full Text Available Abstract Background 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. Methods 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. Results 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.

  16. A protein-dependent side-chain rotamer library

    Science.gov (United States)

    2011-01-01

    Background 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. Methods 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. Results 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. PMID:22373394

  17. Arginine side chains as a dispersant for individual single-wall carbon nanotubes.

    Science.gov (United States)

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

    2014-04-22

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

  18. Interstrand side chain--side chain interactions in a designed beta-hairpin: significance of both lateral and diagonal pairings.

    Science.gov (United States)

    Syud, F A; Stanger, H E; Gellman, S H

    2001-09-12

    The contributions of interstrand side chain-side chain contacts to beta-sheet stability have been examined with an autonomously folding beta-hairpin model system. RYVEV(D)PGOKILQ-NH2 ((D)P = D-proline, O = ornithine) has previously been shown to adopt a beta-hairpin conformation in aqueous solution, with a two-residue loop at D-Pro-Gly. In the present study, side chains that display interstrand NOEs (Tyr-2, Lys-9, and Leu-11) are mutated to alanine or serine, and the conformational impact of the mutations is assessed. In the beta-hairpin conformation Tyr-2 and Leu-11 are directly across from one another (non-hydrogen bonded pair). This "lateral" juxtaposition of two hydrophobic side chains appears to contribute to beta-hairpin conformational stability, which is consistent with results from other beta-sheet model studies and with statistical analyses of interstrand residue contacts in protein crystal structures. Interaction between the side chains of Tyr-2 and Lys-9 also stabilizes the beta-hairpin conformation. Tyr-2/Lys-9 is a "diagonal" interstrand juxtaposition because these residues are not directly across from one another in terms of the hydrogen bonding registry between the strands. This diagonal interaction arises from the right-handed twist that is commonly observed among beta-sheets. Evidence of diagonal side chain-side chain contacts has been observed in other autonomously folding beta-sheet model systems, but we are not aware of other efforts to determine whether a diagonal interaction contributes to beta-sheet stability.

  19. Improved packing of protein side chains with parallel ant colonies.

    Science.gov (United States)

    Quan, Lijun; Lü, Qiang; Li, Haiou; Xia, Xiaoyan; Wu, Hongjie

    2014-01-01

    The accurate packing of protein side chains is important for many computational biology problems, such as ab initio protein structure prediction, homology modelling, and protein design and ligand docking applications. Many of existing solutions are modelled as a computational optimisation problem. As well as the design of search algorithms, most solutions suffer from an inaccurate energy function for judging whether a prediction is good or bad. Even if the search has found the lowest energy, there is no certainty of obtaining the protein structures with correct side chains. We present a side-chain modelling method, pacoPacker, which uses a parallel ant colony optimisation strategy based on sharing a single pheromone matrix. This parallel approach combines different sources of energy functions and generates protein side-chain conformations with the lowest energies jointly determined by the various energy functions. We further optimised the selected rotamers to construct subrotamer by rotamer minimisation, which reasonably improved the discreteness of the rotamer library. We focused on improving the accuracy of side-chain conformation prediction. For a testing set of 442 proteins, 87.19% of X1 and 77.11% of X12 angles were predicted correctly within 40° of the X-ray positions. We compared the accuracy of pacoPacker with state-of-the-art methods, such as CIS-RR and SCWRL4. We analysed the results from different perspectives, in terms of protein chain and individual residues. In this comprehensive benchmark testing, 51.5% of proteins within a length of 400 amino acids predicted by pacoPacker were superior to the results of CIS-RR and SCWRL4 simultaneously. Finally, we also showed the advantage of using the subrotamers strategy. All results confirmed that our parallel approach is competitive to state-of-the-art solutions for packing side chains. This parallel approach combines various sources of searching intelligence and energy functions to pack protein side chains

  20. Frustration-induced quantum phases in mixed spin chain with frustrated side chains

    Science.gov (United States)

    Hida, Kazuo; Takano, Ken'Ichi

    2008-08-01

    A mixed Heisenberg spin chain with frustrated side chains is investigated by numerical and perturbational calculations. A frustration-induced quantum partially polarized ferrimagnetic phase and a nonmagnetic spin quadrupolar phase are found adjacent to the conventional Lieb-Mattis-type ferrimagnetic phase or the nonmagnetic singlet cluster solid phases. The partially polarized ferrimagnetic phase has an incommensurate spin structure. Similar structures are commonly found in other frustration-induced partially polarized ferrimagnetic phases. Numerical results also suggest a series of almost critical nonmagnetic ground states in a highly frustrated regime if the side chain spins weakly couple to the main chain.

  1. Synthesis of macrocyclic lactones with methoxysulfonyl side chain

    Institute of Scientific and Technical Information of China (English)

    Chuan Jin Hou; Xiao Mei Liang; Jing Ping Wu; Dao Quan Wang

    2008-01-01

    Two representative macrocyclic lactones with methoxysulfonyl side chain (5a and 5b) were synthesized employing Michael addition with acrolein and ring enlargement as the key steps,starting from potassium a-oxocycloalkylsulfonates (1) in total yields of 45 and 57%,respectively.

  2. 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...

  3. Synthesis of Bisphenols Carrying Long Hydrocarbon Side Chains

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  4. Simultaneous in vivo truncation of pectic side chains

    DEFF Research Database (Denmark)

    Øbro, Jens; Borkhardt, Bernhard; Harholt, Jesper

    2009-01-01

    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...

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

    Indian Academy of Sciences (India)

    Roshan Gaonkar; N Viswanadham

    2005-04-01

    In this paper we develop a quadratic programming model for partner selection and planning in integrated supply chain networks embedded with both sell-side and buy-side electronic marketplaces. Such a scenario arises in several practical applications. In particular, we consider a contract manufacturer who procures components from suppliers through a component marketplace and sells its manufactured sub-assemblies to original equipment manufacturers (OEMs), through a sub-assembly marketplace. In these web-enabled supply chains, embedded with upstream and downstream electronic marketplaces, we need methods for online supply-chain partner selection based on pricing and delivery schedules. In this paper, we develop and present such a model that selects partners, synchronizes supply chain activities and optimizes the profit through optimal revenue pricing and cost minimization.

  6. 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.

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

    DEFF Research Database (Denmark)

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

    1996-01-01

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

  8. An experimental and theoretical study of the amino acid side chain Raman bands in proteins

    Science.gov (United States)

    Sjöberg, Béatrice; Foley, Sarah; Cardey, Bruno; Enescu, Mironel

    2014-07-01

    The Raman spectra of a series of tripeptides with the basic formula GlyAAGly where the central amino acid (AA) was tryptophan, tyrosine, phenylalanine, glycine, methionine, histidine, lysine and leucine were measured in H2O. The theoretical Raman spectra obtained using density functional theory (DFT) calculations at the B3LYP/6-311+G(2df,2pd) level of theory allows a precise attribution of the vibrational bands. The experimental results show that there is a blue shift in the frequencies of several bands of the amino acid side chains in tripeptides compared to free amino acids, especially in the case of AAs containing aromatic rings. On the other hand, a very good agreement was found between the Raman bands of AA residues in tripeptides and those measured on three model proteins: bovine serum albumin, β-lactoglobulin and lysozyme. The present analysis contributes to an unambiguous interpretation of the protein Raman spectra that is useful in monitoring the biological reactions involving AA side chains alteration.

  9. Side chain conformational averaging in human dihydrofolate reductase.

    Science.gov (United States)

    Tuttle, Lisa M; Dyson, H Jane; Wright, Peter E

    2014-02-25

    The three-dimensional structures of the dihydrofolate reductase enzymes from Escherichia coli (ecDHFR or ecE) and Homo sapiens (hDHFR or hE) are very similar, despite a rather low level of sequence identity. Whereas the active site loops of ecDHFR undergo major conformational rearrangements during progression through the reaction cycle, hDHFR remains fixed in a closed loop conformation in all of its catalytic intermediates. To elucidate the structural and dynamic differences between the human and E. coli enzymes, we conducted a comprehensive analysis of side chain flexibility and dynamics in complexes of hDHFR that represent intermediates in the major catalytic cycle. Nuclear magnetic resonance relaxation dispersion experiments show that, in marked contrast to the functionally important motions that feature prominently in the catalytic intermediates of ecDHFR, millisecond time scale fluctuations cannot be detected for hDHFR side chains. Ligand flux in hDHFR is thought to be mediated by conformational changes between a hinge-open state when the substrate/product-binding pocket is vacant and a hinge-closed state when this pocket is occupied. Comparison of X-ray structures of hinge-open and hinge-closed states shows that helix αF changes position by sliding between the two states. Analysis of χ1 rotamer populations derived from measurements of (3)JCγCO and (3)JCγN couplings indicates that many of the side chains that contact helix αF exhibit rotamer averaging that may facilitate the conformational change. The χ1 rotamer adopted by the Phe31 side chain depends upon whether the active site contains the substrate or product. In the holoenzyme (the binary complex of hDHFR with reduced nicotinamide adenine dinucleotide phosphate), a combination of hinge opening and a change in the Phe31 χ1 rotamer opens the active site to facilitate entry of the substrate. Overall, the data suggest that, unlike ecDHFR, hDHFR requires minimal backbone conformational rearrangement as

  10. The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: a side-chain prediction algorithm based on side-chain backbone interactions.

    Science.gov (United States)

    Spassov, Velin Z; Yan, Lisa; Flook, Paul K

    2007-03-01

    The basic differences between the 20 natural amino acid residues are due to differences in their side-chain structures. This characteristic design of protein building blocks implies that side-chain-side-chain interactions play an important, even dominant role in 3D-structural realization of amino acid codes. Here we present the results of a comparative analysis of the contributions of side-chain-side-chain (s-s) and side-chain-backbone (s-b) interactions to the stabilization of folded protein structures within the framework of the CHARMm molecular data model. Contrary to intuition, our results suggest that side-chain-backbone interactions play the major role in side-chain packing, in stabilizing the folded structures, and in differentiating the folded structures from the unfolded or misfolded structures, while the interactions between side chains have a secondary effect. An additional analysis of electrostatic energies suggests that combinatorial dominance of the interactions between opposite charges makes the electrostatic interactions act as an unspecific folding force that stabilizes not only native structure, but also compact random conformations. This observation is in agreement with experimental findings that, in the denatured state, the charge-charge interactions stabilize more compact conformations. Taking advantage of the dominant role of side-chain-backbone interactions in side-chain packing to reduce the combinatorial problem, we developed a new algorithm, ChiRotor, for rapid prediction of side-chain conformations. We present the results of a validation study of the method based on a set of high resolution X-ray structures.

  11. Disordered ground states in a quantum frustrated spin chain with side chains

    Science.gov (United States)

    Takano, Ken'Ichi; Hida, Kazuo

    2008-04-01

    We study a frustrated mixed spin chain with side chains, where the spin species and the exchange interactions are spatially varied. A nonlinear σ model method is formulated for this model, and a phase diagram with two disordered spin-gap phases is obtained for typical cases. Among them, we examine the case with a main chain, which consists of an alternating array of spin-1 and spin- (1)/(2) sites, and side chains, each of which consists of a single spin- (1)/(2) site, in great detail. Based on numerical, perturbational, and variational approaches, we propose a singlet cluster solid picture for each phase, where the ground state is expressed as a tensor product of local singlet states.

  12. Quantification of Nε-(2-Furoylmethyl)-L-lysine (furosine), Nε-(Carboxymethyl)-L-lysine (CML), Nε-(Carboxyethyl)-L-lysine (CEL) and total lysine through stable isotope dilution assay and tandem mass spectrometry

    NARCIS (Netherlands)

    Troise, A.D.; Fiore, A.; Wiltafsky, M.; Fogliano, V.

    2015-01-01

    The control of Maillard reaction (MR) is a key point to ensure processed foods quality. Due to the presence of a primary amino group on its side chain, lysine is particularly prone to chemical modifications with the formation of Amadori products (AP), Nε-(Carboxymethyl)-L-lysine (CML),

  13. Comb-type prepolymers consisting of a polyacrylamide backbone and poly(L-lysine) graft chains for multivalent ligands.

    Science.gov (United States)

    Asayama, S; Maruyama, A; Akaike, T

    1999-01-01

    The comb-type copolymers consisting of a polyacrylamide (PAAm) backbone and poly(L-lysine) (PLL) graft chains have been prepared as the "prepolymer" for designing multivalent ligands. To regulate the length and density of the clusters of primary amino groups, the Nalpha-carboxyanhydride of Nepsilon-carbobenzoxy (CBZ)-L-lysine was first polymerized using p-vinylbenzylamine as an initiator. The resulting poly(CBZ-L-lysine) macromonomer was then radically copolymerized with AAm, followed by the deprotection of amino groups. For the model study, the reactive clusters of primary amino groups were completely converted into anion clusters by the reaction with succinic anhydride. The model multivalent ligands having the biotin label on the PAAm backbone were prepared by the terpolymerization of the macromonomer, AAm, and the biotin derivative having a vinyl group. The enzyme-linked immunosorbent assay showed that the biotin with no spacer on the PAAm backbone was recognized by the avidin-peroxidase conjugate specifically. Therefore, the highly sensitive detection of the interaction between cells and various model multivalent ligands was possible. The selective labeling onto the PAAm backbone revealed that the converted anion clusters of graft chains interacted exclusively with the cell and that the backbone was inert to the interaction with the cell. These results indicate that the various PAAm-graft-PLL comb-type copolymers with the defined length and density of the PLL-grafts are the potential prepolymers to investigate and to optimize the affinity of the multivalent ligands for receptors.

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

    OpenAIRE

    2012-01-01

    Novel soluble polyimides having long-chain alkyl groups on their side chain were synthesized via polymer reaction with the polyimides having phenolic OH groups and 3,4,5-tris(dodecyloxy)benzoic acid (12GA) using N,N′-dicyclohexylcarbodiimide (DCC) as a dehydration reagent. The polyimides having phenolic OH groups were synthesized from the tetracarboxylic dianhydrides such as 5-(2,5-dioxotetrahydrofuryl)-3-methyl-3-cyclohexene-1,2-dicarboxylic anhydride (cyclohexene-DA), 4,4′-hexafluoroisoprop...

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

    DEFF Research Database (Denmark)

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

    2002-01-01

    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.......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...

  16. 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...

  17. Water and side-chain embedded π-turns.

    Science.gov (United States)

    Dasgupta, Bhaskar; Dey, Sucharita; Chakrabarti, Pinak

    2014-05-01

    Elucidating protein function from its structure is central to the understanding of cellular mechanisms. This involves deciphering the dependence of local structural motifs on sequence. These structural motifs may be stabilized by direct or water-mediated hydrogen bonding among the constituent residues. π-Turns, defined by interactions between (i) and (i + 5) positions, are large enough to contain a central space that can embed a water molecule (or a protein moiety) to form a stable structure. This work is an analysis of such embedded π-turns using a nonredundant dataset of protein structures. A total of 2965 embedded π-turns have been identified, as also 281 embedded Schellman motif, a type of π-turn which occurs at the C-termini of α-helices. Embedded π-turns and Schellman motifs have been classified on the basis of the protein atoms of the terminal turn residues that are linked by the embedded moiety, conformation, residue composition, and compared with the turns that have terminal residues connected by direct hydrogen bonds. Geometrically, the turns have been fitted to a circle and the position of the linker relative to its center analyzed. The hydroxyl group of Ser and Thr, located at (i + 3) position, is the most prominent linker for the side-chain mediated π-turns. Consideration of residue conservation among homologous sequences indicates the terminal and the linker positions to be the most conserved. The embedded π-turn as a binding site (for the linker) is discussed in the context of "nest," a concave depression that is formed in protein structures with adjacent residues having enantiomeric main-chain conformations.

  18. Electrostatic Self-Assembled Multilayers from Side Chain Azo Polyelectrolytes

    Institute of Scientific and Technical Information of China (English)

    庹新林; 陈峥; 邓永红; 王晓工; 刘德山

    2002-01-01

    Photoresponsive behavior and self-assembly properties of three side chain azo polyelectrolytes, poly (2-(4-phenylazophenoxy) ethanol-co-acrylic acid) (PPAPE), poly (2-(4-(4′-nitrophenylazo) phenoxy) ethanol-co-acrylic acid) (PNAPE), and poly (2-(4-(4′-ethoxyphenylazo) phenoxy) ethanol-co-acrylic acid) (PEAPE), were studied. These polyelectrolytes with different degrees of functionalization of azo chromophores were fabricated into nano-composite multilayers using two types of dipping solutions through a layer-by-layer electrostatic self-assembling process. Results show that the ratio between tetrahydrofuran (THF) and H2O significantly influences the photoresponsive behavior of PNAPE in THF-H2O mixture. The THF-H2O dipping solution, used in this work for self-assembly of hydrophobic polyelectrolytes, is proved to be as applicable as aqueous dipping solution for normal self-assembly of hydrophobic polyelectrolytes. However, significant differences in the multilayer growth between the two systems were also observed, which resulted from the remarkable difference of the existing forms of the polyelectrolytes in these two dipping solutions.

  19. Synthesis, surface characterization, and biointeraction studies of low-surface energy side-chain polyetherurethanes

    Science.gov (United States)

    Porter, Stephen Christopher

    1999-10-01

    New segmented polyetherurethanes (PEUs) with low surface energy hydrocarbon and fluorocarbon side-chains attached to the polymer hard segments were synthesized. The surface chemistry of solvent cast polymer films was studied using X-ray photoelectron spectroscopy, time-of-flight secondary ion mass spectrometry, and dynamic contact angle (DCA) measurements. Increases in the overall density and length of the alkyl side-chains within the PEUs resulted in greater side-chain concentrations at the polymer surface. PEUs bearing long alkyl (> C10 ) and perfluorocarbon side-chains were found to posses surfaces with highly enriched side-chain concentrations relative to the bulk polymer. In PEUs with significant side-chain surface enrichment, the relatively polar hard segment blocks were shown to reside in high concentrations just below the side-chain enriched surface layer. Furthermore, DCA measurements demonstrated that the surface of the alkyl side-chain PEUs did not undergo significant rearrangement when placed into an aqueous environment, whereas the surface of a hard segment model polymer bearing C18 sidechains (PEU-C18-HS) did. Hydrogen bonding within the PEUs was examined using FTIR and was shown to be disrupted by the addition of side-chains; an effect dependent on the density but not on the length of the side-chains. Heteropolymer blends comprised of mixtures of high side-chain density and side-chain free PEUs were compared with homopolymers having the same overall side-chain concentration as the blends. Significantly more surface enrichment of side-chains was found in the heteropolymer blends whereas hydrogen bonding nearly the same as in the homopolymers. Adsorption of native and delipidized human serum albumin (HSA) from pure solution and blood plasma; the elutabilty of adsorbed HSA; and static platelet adhesion to plasma preadsorbed surfaces, were all examined on alkyl side-chain PEUs. Several polymers with high C18 side-chain densities displayed increased

  20. Arginyltransferase ATE1 catalyzes mid-chain arginylation of proteins at side chain carboxylates in vivo

    Science.gov (United States)

    Wang, Junling; Han, Xuemei; Wong, Catherine C.L.; Cheng, Hong; Aslanian, Aaron; Xu, Tao; Leavis, Paul; Roder, Heinrich; Hedstrom, Lizbeth; Yates, John R.; Kashina, Anna

    2014-01-01

    Summary Arginylation is an emerging posttranslational modification mediated by Arg-tRNA-protein-transferase (ATE1). It is believed that ATE1 links Arg solely to the N-terminus of proteins, requiring prior proteolysis or action by Met-aminopeptidases to expose the arginylated site. Here, we tested the possibility of Arg linkage to mid-chain sites within intact protein targets and found that many proteins in vivo are modified on the side chains of Asp and Glu by a novel chemistry that targets the carboxy rather than the amino groups at the target sites. Such arginylation appears to be functionally regulated, and it can be directly mediated by ATE1, in addition to the more conventional Ate1-mediated linkage of Arg to the N-terminal alpha amino group. This new type of arginylation implies an unconventional mechanism of ATE1 action that likely facilitates its major biological role. PMID:24529990

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

    Directory of Open Access Journals (Sweden)

    Yusuke Tsuda

    2012-01-01

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

  2. Effects of Alkylthio and Alkoxy Side Chains in Polymer Donor Materials for Organic Solar Cells.

    Science.gov (United States)

    Cui, Chaohua; Wong, Wai-Yeung

    2016-02-01

    Side chains play a considerable role not only in improving the solubility of polymers for solution-processed device fabrication, but also in affecting the molecular packing, electron affinity and thus the device performance. In particular, electron-donating side chains show unique properties when employed to tune the electronic character of conjugated polymers in many cases. Therefore, rational electron-donating side chain engineering can improve the photovoltaic properties of the resulting polymer donors to some extent. Here, a survey of some representative examples which use electron-donating alkylthio and alkoxy side chains in conjugated organic polymers for polymer solar cell applications will be presented. It is envisioned that an analysis of the effect of such electron-donating side chains in polymer donors would contribute to a better understanding of this kind of side chain behavior in solution-processed conjugated organic polymers for polymer solar cells.

  3. Dispersion of Co-poly Carboxylate Superplasticizer Containing Polyether Side Chain

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Free radical co-polymerization was employed to synthesize co-poly carboxylate (PC) superplasticizers with different amount of carboxyl and methyl polyethylene glycol (MPEG) side chain.Dispersion ability and retention of PC were compared with one another. The results show that increase of side chain is advantageous to dispersion, but it decreases when amount of MPEG is beyond a certain value which is different with the proportion of carboxyl. If the amount of carboxyl increases, the influence of side chain in copolymer on dispersion diminishes. Polyether side chain is advantageous to retention. And the author explained the mechanism of PC using the theory of steric repulsive force.

  4. Gamma scintigraphy of {sup 111}In-labelled branched chain polypeptides (BCP) with a poly(L-lysine) backbone in mice with mammary carcinoma. Effect of charge on biodistribution and tumour imaging potential

    Energy Technology Data Exchange (ETDEWEB)

    Pimm, M.V.; Gribben, S.J. [University of Nottingham (United Kingdom); Perkins, A.C.; Mezo, G.; Gaal, D.; Hudecz, F.

    1995-11-01

    Radiolabelled synthetic branched chain polypeptides (BCP) represent a new and novel range of materials with potential as radiopharmaceuticals. Preliminary imaging studies have been undertaken with {sup 111}In-labelled BCP in mice with subcutaneously transplanted mammary carcinoma. Four polypeptides each with a poly(L-lysine) backbone and side chains of DL-alanine residues were studied. These were AK, which is polycationic, EAK which is amphoteric, having additional glutamic acid residues at the end of the side chains, and AcEAK (anionic) and SucEAK (highly polyanionic) where the terminal glutamic acid amino groups were acetylated or succinylated respectively. Radiolabelling was achieved by previous conjugation with DTPA. Serial images up to 48 hours showed marked retention of {sup 111}In-labelled polycationic AK and polyanionic SucEAK in the liver and spleen, with renal uptake also being visible in the case of AK. {sup 111}In-labelled EAK and AcEAK showed longer blood survival with some liver uptake, but tumour uptake was also visualized by 24 hours with both of these polypeptides. These studies demonstrate the feasibility of using {sup 111}In-labelled synthetic branched chain polypeptides as radiopharmaceuticals for gamma scintigraphy and the visualization of tumours by modification of the side chain structure. These materials warrant further study. (author).

  5. Modification of the side chain of micromolide, an anti-tuberculosis natural product.

    Science.gov (United States)

    Yuan, Hai; He, Rong; Wan, Baojie; Wang, Yuehong; Pauli, Guido F; Franzblau, Scott G; Kozikowski, Alan P

    2008-10-01

    This paper describes a series of modifications of the side chain of micromolide, an anti-tuberculosis natural product. Most of the synthesized compounds showed significantly decreased activities, which suggests that the long aliphatic side chain of micromolide and its double bond are essential to its activity.

  6. Conformational Studies of ε- CBz- L- Lysine and L- Valine Block Copolypeptides

    Directory of Open Access Journals (Sweden)

    Ajay Kumar

    2010-01-01

    Full Text Available Conformational studies of ε-CBz-L-lysine and L-valine block copoylpeptides using x- ray diffraction and CD spectra are described. The block copolypeptides contain valine block in the center and on both side of the valine are ε-CBz-L-lysine blocks. The conformation of the copolypeptides changes with increases in the chain length of ε- CBz-L- lysine blocks. When length of ε- CBZ- L- lysine blocks is 9, the block copolypeptide has exclusive beta sheet structure. With the increase in chain length of ε-CBz-L-lysine blocks from 9 to 14, the block copolypeptide shows presence of both alpha helix and beta sheet components. With further increase in chain length of ε- CBz- L- lysine blocks, the beta sheet component disappears and block copolypeptides exhibits exclusive α -helix conformation.

  7. The impact of side-chain packing on protein docking refinement.

    Science.gov (United States)

    Moghadasi, Mohammad; Mirzaei, Hanieh; Mamonov, Artem; Vakili, Pirooz; Vajda, Sandor; Paschalidis, Ioannis Ch; Kozakov, Dima

    2015-04-27

    We study the impact of optimizing the side-chain positions in the interface region between two proteins during the process of binding. Mathematically, the problem is similar to side-chain prediction, which has been extensively explored in the process of protein structure prediction. The protein-protein docking application, however, has a number of characteristics that necessitate different algorithmic and implementation choices. In this work, we implement a distributed approximate algorithm that can be implemented on multiprocessor architectures and enables a trade-off between accuracy and running speed. We report computational results on benchmarks of enzyme-inhibitor and other types of complexes, establishing that the side-chain flexibility our algorithm introduces substantially improves the performance of docking protocols. Furthermore, we establish that the inclusion of unbound side-chain conformers in the side-chain positioning problem is critical in these performance improvements. The code is available to the community under open source license.

  8. Diketopyrrolopyrrole-based Conjugated Polymers Bearing Branched Oligo(Ethylene Glycol) Side Chains for Photovoltaic Devices.

    Science.gov (United States)

    Chen, Xingxing; Zhang, Zijian; Ding, Zicheng; Liu, Jun; Wang, Lixiang

    2016-08-22

    Conjugated polymers are essential for solution-processable organic opto-electronic devices. In contrast to the great efforts on developing new conjugated polymer backbones, research on developing side chains is rare. Herein, we report branched oligo(ethylene glycol) (OEG) as side chains of conjugated polymers. Compared with typical alkyl side chains, branched OEG side chains endowed the resulting conjugated polymers with a smaller π-π stacking distance, higher hole mobility, smaller optical band gap, higher dielectric constant, and larger surface energy. Moreover, the conjugated polymers with branched OEG side chains exhibited outstanding photovoltaic performance in polymer solar cells. A power conversion efficiency of 5.37 % with near-infrared photoresponse was demonstrated and the device performance could be insensitive to the active layer thickness.

  9. Maximum-likelihood, self-consistent side chain free energies with applications to protein molecular dynamics

    CERN Document Server

    Jumper, John M; Sosnick, Tobin R

    2016-01-01

    To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a new methodology that computes a self-consistent approximation of the side chain free energy at every integration step. In analogy with the adiabatic Born-Oppenheimer approximation in which the nuclear dynamics are governed by the energy of the instantaneously-equilibrated electronic degrees of freedom, the protein backbone dynamics are simulated as preceding according to the dictates of the free energy of an instantaneously-equilibrated side chain potential. The side chain free energy is computed on the fly; hence, the protein backbone dynamics traverse a greatly smoothed energetic landscape, resulting in extremely rapid equilibration and sampling of the Boltzmann distribution. Because our method employs a reduced model involving single-bead side chains, we also provide a novel, maximum-likelihood type method to parameterize the side chain model using...

  10. 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.

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

    Institute of Scientific and Technical Information of China (English)

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

    1999-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Pedro M. Rocha

    2004-04-01

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

  13. From labdanes to drimanes. Degradation of the side chain of dihydrozamoranic acid.

    Science.gov (United States)

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

    2004-04-30

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

  14. 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.

  15. Electronic properties of amino acid side chains: quantum mechanics calculation of substituent effects

    Directory of Open Access Journals (Sweden)

    Dwyer Donard S

    2005-08-01

    Full Text Available Abstract Background Electronic properties of amino acid side chains such as inductive and field effects have not been characterized in any detail. Quantum mechanics (QM calculations and fundamental equations that account for substituent effects may provide insight into these important properties. PM3 analysis of electron distribution and polarizability was used to derive quantitative scales that describe steric factors, inductive effects, resonance effects, and field effects of amino acid side chains. Results These studies revealed that: (1 different semiempirical QM methods yield similar results for the electronic effects of side chain groups, (2 polarizability, which reflects molecular deformability, represents steric factors in electronic terms, and (3 inductive effects contribute to the propensity of an amino acid for α-helices. Conclusion The data provide initial characterization of the substituent effects of amino acid side chains and suggest that these properties affect electron density along the peptide backbone.

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

    Science.gov (United States)

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

    2016-04-01

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

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

    DEFF Research Database (Denmark)

    Harder, Tim; Boomsma, Wouter; Paluszewski, Martin;

    2010-01-01

    Background: Accurately covering the conformational space of amino acid side chains is essential for important applications such as protein design, docking and high resolution structure prediction. Today, the most common way to capture this conformational space is through rotamer libraries discrete...... for certain applications. For example, rigorously combining rotamers with physical force fields is associated with numerous problems. Results: In this work we present BASILISK: a generative, probabilistic model of the conformational space of side chains that makes it possible to sample in continuous space...... model of side chain conformational space. We also illustrate how the model can be used for rigorous, unbiased sampling with a physical force field, and how it improves side chain prediction when used as a pseudo-energy term. In conclusion, BASILISK is an important step forward on the way to a rigorous...

  18. 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.

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

    Science.gov (United States)

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

    2014-05-01

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

  20. A Semiautomated Assignment Protocol for Methyl Group Side Chains in Large Proteins.

    Science.gov (United States)

    Kim, Jonggul; Wang, Yingjie; Li, Geoffrey; Veglia, Gianluigi

    2016-01-01

    The developments of biosynthetic specific labeling strategies for side-chain methyl groups have allowed structural and dynamic characterization of very large proteins and protein complexes. However, the assignment of the methyl-group resonances remains an Achilles' heel for NMR, as the experiments designed to correlate side chains to the protein backbone become rather insensitive with the increase of the transverse relaxation rates. In this chapter, we outline a semiempirical approach to assign the resonances of methyl-group side chains in large proteins. This method requires a crystal structure or an NMR ensemble of conformers as an input, together with NMR data sets such as nuclear Overhauser effects (NOEs) and paramagnetic relaxation enhancements (PREs), to be implemented in a computational protocol that provides a probabilistic assignment of methyl-group resonances. As an example, we report the protocol used in our laboratory to assign the side chains of the 42-kDa catalytic subunit of the cAMP-dependent protein kinase A. Although we emphasize the labeling of isoleucine, leucine, and valine residues, this method is applicable to other methyl group side chains such as those of alanine, methionine, and threonine, as well as reductively methylated cysteine side chains.

  1. Side-chain modification and "grafting onto" via olefin cross-metathesis.

    Science.gov (United States)

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

    2012-12-13

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-15

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

  3. Effects of alkyl side chains on properties of aliphatic amino acids probed using quantum chemical calculations.

    Science.gov (United States)

    Ganesan, Aravindhan; Wang, Feng; Brunger, Michael; Prince, Kevin

    2011-09-01

    Effects of alkyl side chains (R-) on the electronic structural properties of aliphatic amino acids are investigated using quantum mechanical approaches. The carbon (C 1s) binding energy spectra of the aliphatic amino acids are derived from the C 1s spectrum of glycine (the parent spectrum) by the addition of spectral peaks, depending on the alkyl side chains, appearing in the lower energy region IP aliphatic amino acids owing to perturbations depending on the size and structure of the alkyl chains. The pattern of the N 1s and O 1s spectra in glycine is retained in the spectra of the other amino acids with small shifts to lower energy, again depending on the alkyl side chain. The Hirshfeld charge analyses confirm the observations. The alkyl effects on the valence binding energy spectra of the amino acids are concentrated in the middle valence energy region of 12-16 eV, and hence this energy region of 12-16 eV is considered as the `fingerprint' of the alkyl side chains. Selected valence orbitals, either inside or outside of the alkyl fingerprint region, are presented using both density distributions and orbital momentum distributions, in order to understand the chemical bonding of the amino acids. It is also observed that the HOMO-LUMO energy gaps of the aliphatic amino acids are reduced with the growth of the alkyl side chain.

  4. 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.

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

    CERN Document Server

    Canzar, Stefan; Klau, Gunnar W

    2011-01-01

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

  6. Influence of the sterol aliphatic side chain on membrane properties: a molecular dynamics study.

    Science.gov (United States)

    Robalo, João R; Ramalho, J P Prates; Huster, Daniel; Loura, Luís M S

    2015-09-21

    Following a recent experimental investigation of the effect of the length of the alkyl side chain in a series of cholesterol analogues (Angew. Chem., Int. Ed., 2013, 52, 12848-12851), we report here an atomistic molecular dynamics characterization of the behaviour of methyl-branched side chain sterols (iso series) in POPC bilayers. The studied sterols included androstenol (i-C0-sterol) and cholesterol (i-C8-sterol), as well as four other derivatives (i-C5, i-C10, i-C12 and i-C14-sterol). For each sterol, both subtle local effects and more substantial differential alterations of membrane properties along the iso series were investigated. The location and orientation of the tetracyclic ring system is almost identical in all compounds. Among all the studied sterols, cholesterol is the sterol that presents the best matching with the hydrophobic length of POPC acyl chains, whereas longer-chained sterols interdigitate into the opposing membrane leaflet. In accordance with the experimental observations, a maximal ordering effect is observed for intermediate sterol chain length (i-C5, cholesterol, i-C10). Only for these sterols a preferential interaction with the saturated sn-1 chain of POPC (compared to the unsaturated sn-2 chain) was observed, but not for either shorter or longer-chained derivatives. This work highlights the importance of the sterol alkyl chain in the modulation of membrane properties and lateral organization in biological membranes.

  7. 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

    functional phenotypes that are different from those observed previously in Kv VSDs. In contrast, and similar to results obtained with Kv channels, individually neutralizing acidic side chains with synthetic derivatives and with natural amino acid substitutions in the INC had little or no effect......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...... 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...

  8. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-01-21

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

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

    CERN Document Server

    Vaitheeswaran, S

    2014-01-01

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

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

    Indian Academy of Sciences (India)

    S Radhakrishnan; S J Ananthakrishnan; N Somanathan

    2011-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-02-02

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

  13. Using quantum mechanics to improve estimates of amino acid side chain rotamer energies.

    Science.gov (United States)

    Renfrew, P Douglas; Butterfoss, Glenn L; Kuhlman, Brian

    2008-06-01

    Amino acid side chains adopt a discrete set of favorable conformations typically referred to as rotamers. The relative energies of rotamers partially determine which side chain conformations are more often observed in protein structures and accurate estimates of these energies are important for predicting protein structure and designing new proteins. Protein modelers typically calculate side chain rotamer energies by using molecular mechanics (MM) potentials or by converting rotamer probabilities from the protein database (PDB) into relative free energies. One limitation of the knowledge-based energies is that rotamer preferences observed in the PDB can reflect internal side chain energies as well as longer-range interactions with the rest of the protein. Here, we test an alternative approach for calculating rotamer energies. We use three different quantum mechanics (QM) methods (second order Møller-Plesset (MP2), density functional theory (DFT) energy calculation using the B3LYP functional, and Hartree-Fock) to calculate the energy of amino acid rotamers in a dipeptide model system, and then use these pre-calculated values in side chain placement simulations. Energies were calculated for over 36,000 different conformations of leucine, isoleucine, and valine dipeptides with backbone torsion angles from the helical and strand regions of the Ramachandran plot. In a subset of cases these energies differ significantly from those calculated with standard molecular mechanics potentials or those derived from PDB statistics. We find that in these cases the energies from the QM methods result in more accurate placement of amino acid side chains in structure prediction tests.

  14. Transport Properties in a One-Dimensional Chain with Randomly Side-Coupled Impurities

    Institute of Scientific and Technical Information of China (English)

    胡冬生; 张桂平; 熊诗杰

    2002-01-01

    We investigate the transport properties of a one-dimensional (1D) chain with randomly side-coupled impurities.By using the transfer matrix technique, we present numerical results of the transmission coefficient as a function of the electron energy. It is found that an extended state will be shown in such a random 1D system if the impurities are side-coupled to the chain with not only the nearest-neighbour bonds but also the next-nearest-neighbour bonds. We present an analytical expression for the energy of this extended state, which is determined by the strength of the nearest and next-nearest couplings between the impurities and the chain. The obtained results can be used to explain the transport properties of DNA chains and other quasi-lD organic structures.

  15. Synthesis and Characterization of a New Network Polymer Electrolyte Containing Polyether in the Main Chains and Side Chains

    Institute of Scientific and Technical Information of China (English)

    Wang; Cheng-chien; Chen; Chuh-yung

    2007-01-01

    1 Results A new network polymer electrolyte matrix with polyether in the side chains and main chains was synthesized by the azo-macroinitiator method and urethane reaction.The macroinitiator,polymer and network polymer were confirmed by Fourier-transform infrared (FT-IR) spectroscopy and 1H NMR.FT-IR was also used to study the environment of lithium ions doped in these network polymer electrolytes.Three important groups are considered: N-H,carbonyl,and ether groups.The thermal properties of the polymer ...

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

    Institute of Scientific and Technical Information of China (English)

    CHEN Gang; ZHANG Rongben

    1991-01-01

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

  17. Preparation of Novel Side-chain Pseudopolyrotaxanes Consisting of Cucurbituril[6] and Polyamine Salts

    Institute of Scientific and Technical Information of China (English)

    Zhao Sheng HOU; Ye Bang TAN; Kimoon KIM; Qi Feng ZHOU

    2005-01-01

    Pseudorotaxane monomer (VBCB) containing cucurbitutil[6] (CB[6]) and N1-(4-vinylbenzyl)-1,4-diaminobutane dihydrochloride (VBDADC) is obtained by self-assembly of cucurbituril[6] with VBDADC in water and then polymerized using potassium persulfate (KPS) as initiator to give novel water-soluble side-chain cucurbituril[6]-based pseudopolyr1o taxane (PVBCB). The chemical structures of PVBCB, VBCB and VBDADC are confirmed by H NMR,13C NMR spectra and elemental analysis. In VBCB, CB[6] is localized aliphatic group of the side chain and the molar ratio of CB[6] to VBDAC is 1:1.

  18. Covalent docking using autodock: Two-point attractor and flexible side chain methods.

    Science.gov (United States)

    Bianco, Giulia; Forli, Stefano; Goodsell, David S; Olson, Arthur J

    2016-01-01

    We describe two methods of automated covalent docking using Autodock4: the two-point attractor method and the flexible side chain method. Both methods were applied to a training set of 20 diverse protein-ligand covalent complexes, evaluating their reliability in predicting the crystallographic pose of the ligands. The flexible side chain method performed best, recovering the pose in 75% of cases, with failures for the largest inhibitors tested. Both methods are freely available at the AutoDock website (http://autodock.scripps.edu). © 2015 The Protein Society.

  19. Peptide release, side-chain deprotection, work-up, and isolation

    DEFF Research Database (Denmark)

    Pedersen, Søren Ljungberg; Jensen, Knud Jørgen

    2013-01-01

    After having successfully synthesized a peptide, it has to be released from the solid support, unless it is being used for on-resin display. The linker and, in some cases, the cleavage mixture determine the C-terminal functionality of the released peptide. In most cases, the peptide is released...... with concomitant removal of side-chain protecting groups. However, some combinations of linkers and side-chain protecting groups enable a two-stage procedure, either using orthogonal chemistry or graduated labilities. Herein, we describe protocols for the release of peptides from the most commonly used linker...

  20. Degradable terpolymers with alkyl side chains demonstrate enhanced gene delivery potency and nanoparticle stability.

    Science.gov (United States)

    Eltoukhy, Ahmed A; Chen, Delai; Alabi, Christopher A; Langer, Robert; Anderson, Daniel G

    2013-03-13

    Degradable, cationic poly(β-amino ester)s (PBAEs) with alkyl side chains are developed for non-viral gene delivery. Nanoparticles formed from these PBAE terpolymers exhibit significantly enhanced DNA transfection potency and resistance to aggregation. These hydrophobic PBAE terpolymers, but not PBAEs lacking alkyl side chains, support interaction with PEG-lipid conjugates, facilitating their functionalization with shielding and targeting moieties and accelerating the in vivo translation of these materials. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. side chains

    African Journals Online (AJOL)

    USER

    KEY WORDS: Metropolis Monte Carlo simulation, Hydration structure, Fe(III) and Co(III) ions, ... ions have a similar importance in many chemical and biological processes. ..... simulation method, quantum mechanical/molecular mechanical.

  2. MORPHOLOGICAL AND KINETIC STUDIES OF PHASE TRANSITIONS OF A SIDE-CHAIN LIQUID CRYSTALLINE POLYMER

    Institute of Scientific and Technical Information of China (English)

    Chi-bing Tan; Shu-fan Zhang; Mao Xu

    1999-01-01

    The morphological changes of a side-chain liquid-crystalline polymethacrylate during isotropization and liquid-crystallization transitions were studied by means of polarizing microscopy. These transitions were found to be composed of the initiation of a new phase at local places of the old phase matrix and the growth of the new phase domains. The kinetics of the liquid-crystallization of the polymer from an isotropic melt to a smectic mesophase was also investigated. The isothermal process of the transition can be described by the Avrami equation. The values of the Avrami exponent were found to be around 2.6. which is lower than the value usually obtained for crystallization transition of polymers, but larger than that reported for liquid-crystallization transition of main-chain polymers. These results may indicate the difference in growth geometry of new phase during transition between crystallization and liquid-crystallization in general and between liquid-crystallization of main-chain and side-chain polymers. It was found that the liquidcrystallization of the used side-chain polymethacrylate may occur at small undercoolings with high transformation rate similar to that of main-chain polymers and small-molecule liquid crystals, while the crystallization of polymers can only proceed at large undercoolings. These phenomena can be explained by the idea that the surface free energy of nucleus during liquid-crystallization transition is less than that for crystallization, and evidence was obtained from analysis of the temperature dependence of the transformation rate.

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

    DEFF Research Database (Denmark)

    Kulinna, Christian; Hvilsted, Søren; Hendann, Claudia;

    1998-01-01

    Two sets of specifically deuterated cyanoazobenzene side-chain polyadipates and polytetrade-canedioates have been prepared by transesterification in the melt. Combinations of three different, selectively deuterium labeled 2-[6-[4-[(4-cyanophenyl)azo]phenoxy]hexyl]-1,3-propanediols or the non-deut...

  4. 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 ...

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

    NARCIS (Netherlands)

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

    2001-01-01

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

  6. A Concise Access to C2-Symmetric Chiral 4-Pyrrolidinopyridine Catalysts with Dual Functional Side Chains.

    Science.gov (United States)

    Mishiro, Kenji; Takeuchi, Hironori; Furuta, Takumi; Kawabata, Takeo

    2016-07-01

    A practical method was developed for the preparation of a diastereomeric library of C2-symmetric chiral 4-pyrrolidinopyridine catalysts with dual amide side chains. Use of a racemic precursor is the key to the concise production of catalysts with diverse stereochemisty.

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. Alternating Side-Chain Liquid-Crystalline Copolymers with Polar Moieties in the Backbone

    NARCIS (Netherlands)

    Nieuwhof, R.P.

    1999-01-01

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

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

    NARCIS (Netherlands)

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

    2005-01-01

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

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

    DEFF Research Database (Denmark)

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

    1998-01-01

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

  14. On the Role of Aromatic Side Chains in the Photoactivation of BLUF Domains

    NARCIS (Netherlands)

    Gauden, M.; Grinstead, J.S.; Laan, W.; Stokkum, I.H.M.; Avila-Perez, M.; Toh, K.C.; Boelens, R.; Kaptein, R.; van Grondelle, R.; Hellingwerf, K.J.; Kennis, J.T.M.

    2007-01-01

    BLUF (blue-light sensing using FAD) domain proteins are a novel group of blue-light sensing receptors found in many microorganisms. The role of the aromatic side chains Y21 and W104, which are in close vicinity to the FAD cofactor in the AppA BLUF domain from Rhodobacter sphaeroides, is investigated

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-03-05

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

  16. 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.

  17. Preparation of quinolinium salts differing in the length of the alkyl side chain.

    Science.gov (United States)

    Marek, Jan; Buchta, Vladimir; Soukup, Ondrej; Stodulka, Petr; Cabal, Jiri; Ghosh, Kallol K; Musilek, Kamil; Kuca, Kamil

    2012-05-25

    Quaternary quinolinium salts differing in alkyl chain length are members of a widespread group of cationic surfactants. These compounds have numerous applications in various branches of industry and research. In this work, the preparation of quinoline-derived cationic surface active agents differing in the length of the side alkyl chains (from C₈ to C₂₀) is described. An HPLC method was successfully developed for distinction of all members of the series of prepared long-chain quinolinium derivatives. In conclusion, some possibilities of intended tests or usage have been summarized. In vitro testing using a microdilution broth method showed good activity of a substance with a C12 chain length against Gram-positive cocci and Candida species.

  18. Too packed to change: side-chain packing and site-specific substitution rates in protein evolution

    Directory of Open Access Journals (Sweden)

    María Laura Marcos

    2015-04-01

    Full Text Available In protein evolution, due to functional and biophysical constraints, the rates of amino acid substitution differ from site to site. Among the best predictors of site-specific rates are solvent accessibility and packing density. The packing density measure that best correlates with rates is the weighted contact number (WCN, the sum of inverse square distances between a site’s Cα and the Cα of the other sites. According to a mechanistic stress model proposed recently, rates are determined by packing because mutating packed sites stresses and destabilizes the protein’s active conformation. While WCN is a measure of Cα packing, mutations replace side chains. Here, we consider whether a site’s evolutionary divergence is constrained by main-chain packing or side-chain packing. To address this issue, we extended the stress theory to model side chains explicitly. The theory predicts that rates should depend solely on side-chain contact density. We tested this prediction on a data set of structurally and functionally diverse monomeric enzymes. We compared side-chain contact density with main-chain contact density measures and with relative solvent accessibility (RSA. We found that side-chain contact density is the best predictor of rate variation among sites (it explains 39.2% of the variation. Moreover, the independent contribution of main-chain contact density measures and RSA are negligible. Thus, as predicted by the stress theory, site-specific evolutionary rates are determined by side-chain packing.

  19. Too packed to change: side-chain packing and site-specific substitution rates in protein evolution.

    Science.gov (United States)

    Marcos, María Laura; Echave, Julian

    2015-01-01

    In protein evolution, due to functional and biophysical constraints, the rates of amino acid substitution differ from site to site. Among the best predictors of site-specific rates are solvent accessibility and packing density. The packing density measure that best correlates with rates is the weighted contact number (WCN), the sum of inverse square distances between a site's C α and the C α of the other sites. According to a mechanistic stress model proposed recently, rates are determined by packing because mutating packed sites stresses and destabilizes the protein's active conformation. While WCN is a measure of C α packing, mutations replace side chains. Here, we consider whether a site's evolutionary divergence is constrained by main-chain packing or side-chain packing. To address this issue, we extended the stress theory to model side chains explicitly. The theory predicts that rates should depend solely on side-chain contact density. We tested this prediction on a data set of structurally and functionally diverse monomeric enzymes. We compared side-chain contact density with main-chain contact density measures and with relative solvent accessibility (RSA). We found that side-chain contact density is the best predictor of rate variation among sites (it explains 39.2% of the variation). Moreover, the independent contribution of main-chain contact density measures and RSA are negligible. Thus, as predicted by the stress theory, site-specific evolutionary rates are determined by side-chain packing.

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

    Science.gov (United States)

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

    2011-08-01

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

  1. DNA binding property and antitumor evaluation of xanthone with dimethylamine side chain.

    Science.gov (United States)

    Shen, Rui; Wang, Weihua; Yang, Gengliang

    2014-05-01

    In this work, a xanthone derivative was obtained by cationic modification of the free hydroxyl group of xanthone with dimethylamine group of high pKa value. The interactions of xanthones with DNA were investigated by spectroscopic methods, electrophoretic migration assay and polymerase chain reaction test. Results indicate that xanthones can intercalate into the DNA base pairs by the hydrophobic plane and the xanthone with dimethylamine side chain may also bind the DNA phosphate framework by the basic amine alkyl chain, thus showing a better DNA binding ability than the xanthone. Furthermore, inhibition on tumor cells (ECA109, SGC7901, GLC-82) proliferation of xanthones were evaluated by MTT method. Analysis results show that the xanthone with dimethylamine side chain exhibits more effective inhibition activity against three cancer cells than the xanthone. The effects on the inhibition of tumor cells in vitro agree with the studies of DNA binding. It means that the amine alkyl chain would play an important role in its antitumor activity and DNA binding property.

  2. Synthetic studies on maitotoxin. 1. Stereoselective synthesis of the C'D'E'F'-ring system having a side chain.

    Science.gov (United States)

    Morita, Masayuki; Ishiyama, Seishi; Koshino, Hiroyuki; Nakata, Tadashi

    2008-05-01

    The stereoselective synthesis of the maitotoxin C'D'E'F'-ring system having a side chain has been accomplished through a convergent strategy. The key reactions include Horner-Wadsworth-Emmons coupling of the C'D'E'-ring and the side chain and subsequent construction of the F'-ring by silane reduction of dihydropyran.

  3. 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 use of C-13 NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically C-13 labeled histidine residues in plastocyanin (PCu) from...... Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for C-13(epsilon 1) nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from...... 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...

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

    CERN Document Server

    Lundgren, Martin

    2012-01-01

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

  5. Side Chain Hydrophobicity Modulates Therapeutic Activity and Membrane Selectivity of Antimicrobial Peptide Mastoparan-X

    DEFF Research Database (Denmark)

    Henriksen, Jonas Rosager; Etzerodt, Thomas Povl; Gjetting, Torben;

    2014-01-01

    The discovery of new anti-infective compounds is stagnating and multi-resistant bacteria continue to emerge, threatening to end the "antibiotic era''. Antimicrobial peptides (AMPs) and lipo-peptides such as daptomycin offer themselves as a new potential class of antibiotics; however, further...... optimization is needed if AMPs are to find broad use as antibiotics. In the present work, eight analogues of mastoparan-X (MPX) were investigated, having side chain modifications in position 1, 8 and 14 to modulate peptide hydrophobicity. The self-association properties of the peptides were characterized...... in target selectivity correlated to biophysical parameters showing an increased effective charge and reduction in the partitioning coefficient for membrane insertion. Introduction of an unnatural amino acid, with an octyl side chain by amino acid substitution, at positions 1, 8 and 14 resulted in increased...

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

    Energy Technology Data Exchange (ETDEWEB)

    Marrone, Babetta L. (Los Alamos, NM); Simpson, Daniel J. (Los Alamos, NM); Unkefer, Clifford J. (Los Alamos, NM); Whaley, Thomas W. (Santa Fe, NM)

    1993-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Marrone, B.L.; Simpson, D.J.; Unkefer, C.J.; Whaley, T.W.

    1993-05-04

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Marrone, Babetta L. (Los Alamos, NM); Simpson, Daniel J. (Los Alamos, NM); Unkefer, Clifford J. (Los Alamos, NM); Whaley, Thomas W. (Santa Fe, NM)

    1992-01-01

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

  9. SYNTHESIS AND PROPERTIES OF A NEW AZOBENZENE SIDE-CHAIN POLYMER CONTAINING A TEMPO RADICAL

    Institute of Scientific and Technical Information of China (English)

    Yong Zhang; Ze-da Xu; Xing-he Fan; Xiao-fang Chen; Xin-hua Wan; Qi-feng Zhou

    2002-01-01

    To allow anisotropies of optical properties in a magnetic field, nitroxide radical is introduced into the ortho-position of the phenylene ring in the side chain. A new azobenzene side-chain polymer (TEMPO-PAZ) containing TEMPOradical was synthesized. The polymer has a good solubility in organic solvents. The ESR spectrum of the polymer indicatedthree absorption lines characteristic of TEMPO radical. The optical phase conjugated responses (I4) of the polymer filmswere investigated by degenerate four-wave mixing (DFWM). The experimental results showed that optical phase conjugatedresponse of the TEMPO-PAZ could be easily controlled by choosing the appropriate direction of magnetic field presumablydue to the nitroxide radical in the TEMPO-PAZ molecular structure. For the polymer investigated here, the nitroxide radicalwas introduced to increase optical phase conjugated response intensity in a magnetic field, aiming originally at searching fora new photo-active organic magnetic multifunctional materials.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    transgenes were not transmitted to the next generation when these lines were used as a pollen donor, suggesting male sterility. Viability of mature pollen was severely decreased in potato lines with reduced pectic arabinan, but not in lines with altered galactan side chains. Anthers and pollen of different...... developmental stages were microscopically examined to study the phenotype in more detail. Scanning electron microscopy of flowers showed collapsed pollen grains in mature anthers and in earlier stages cytoplasmic protrusions at the site of the of kin pore, eventually leading to bursting of the pollen grain...... and leaking of the cytoplasm. This phenomenon is only observed after the microspores are released and the tapetum starts to degenerate. Timing of the phenotype indicates a role for pectic arabinan side chains during remodelling of the cell wall when the pollen grain is maturing and dehydrating....

  11. 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.

  12. Synthesis and characterization of alternating fluorene–thiophene copolymers bearing ethylene glycol side-chains

    OpenAIRE

    Ziegler, Elisabeth; Pein, Andreas; Fischereder, Achim; Trimmel, Gregor

    2011-01-01

    Abstract New alternating fluorene–thiophene copolymers are introduced bearing polar ethylene glycol-carboxylate functionalities on the thiophene ring to achieve enhanced solubility in polar solvents. Suzuki polycondensation was applied to synthesize a set of three polymers with differing lengths of the ethylene glycol side-chains. The polymers are thermally stable up to temperatures of 300 °C. Solutions of the polymers in CHCl3 show an absorption maximum at approximately 397 nm and a luminesc...

  13. Synthesis and antibacterial activity of pleuromutilin derivatives with novel C(14) side chain

    Institute of Scientific and Technical Information of China (English)

    Li Qiang Fu; Chen Yu Ling; Xing Sheng Guo; Hui Li He; Yu She Yang

    2012-01-01

    In order to find novel antibacterial agents with superior antibacterial activity and overcoming multidrug resistance,a series of pleuromutilin derivatives with novel C(14) side chain were synthesized and evaluated for their in vitro antibacterial activities.The results of antibacterial acticities indicated that most of the derivatives showed potent activities against Gram-positive organisms.In particular,compound 10d exhibited the most potent inhibitory activity compared with pleuromutilin and linezoid,emerged as potential molecule for further investigation.

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

    Directory of Open Access Journals (Sweden)

    Karen Catalán Marín

    2007-03-01

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

  15. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    Science.gov (United States)

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

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

    Science.gov (United States)

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

    2017-09-27

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

  17. Interactions of protein side chains with RNA defined with REDOR solid state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Huang Wei; Varani, Gabriele; Drobny, Gary P., E-mail: drobny@chem.washington.edu [University of Washington, Department of Chemistry (United States)

    2011-11-15

    Formation of the complex between human immunodeficiency virus type-1 Tat protein and the transactivation response region (TAR) RNA is vital for transcriptional elongation, yet the structure of the Tat-TAR complex remains to be established. The NMR structures of free TAR, and TAR bound to Tat-derived peptides have been obtained by solution NMR, but only a small number of intermolecular NOEs could be identified unambiguously, preventing the determination of a complete structure. Here we show that a combination of multiple solid state NMR REDOR experiments can be used to obtain multiple distance constraints from {sup 15}N to {sup 13}C spins within the backbone and side chain guanidinium groups of arginine in a Tat-derived peptide, using {sup 19}F spins incorporated into the base of U23 in TAR and {sup 31}P spins in the P22 and P23 phosphate groups. Distances between the side chain of Arg52 and the base and phosphodiester backbone near U23 measured by REDOR NMR are comparable to distances observed in solution NMR-derived structural models, indicating that interactions of TAR RNA with key amino acid side chains in Tat are the same in the amorphous solid state as in solution. This method is generally applicable to other protein-RNA complexes where crystallization or solution NMR has failed to provide high resolution structural information.

  18. 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.

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

    Science.gov (United States)

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

    2014-05-01

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

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

    Science.gov (United States)

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

    2005-02-01

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

  1. High-Performance Electron Acceptor with Thienyl Side Chains for Organic Photovoltaics.

    Science.gov (United States)

    Lin, Yuze; Zhao, Fuwen; He, Qiao; Huo, Lijun; Wu, Yang; Parker, Timothy C; Ma, Wei; Sun, Yanming; Wang, Chunru; Zhu, Daoben; Heeger, Alan J; Marder, Seth R; Zhan, Xiaowei

    2016-04-13

    We develop an efficient fused-ring electron acceptor (ITIC-Th) based on indacenodithieno[3,2-b]thiophene core and thienyl side-chains for organic solar cells (OSCs). Relative to its counterpart with phenyl side-chains (ITIC), ITIC-Th shows lower energy levels (ITIC-Th: HOMO = -5.66 eV, LUMO = -3.93 eV; ITIC: HOMO = -5.48 eV, LUMO = -3.83 eV) due to the σ-inductive effect of thienyl side-chains, which can match with high-performance narrow-band-gap polymer donors and wide-band-gap polymer donors. ITIC-Th has higher electron mobility (6.1 × 10(-4) cm(2) V(-1) s(-1)) than ITIC (2.6 × 10(-4) cm(2) V(-1) s(-1)) due to enhanced intermolecular interaction induced by sulfur-sulfur interaction. We fabricate OSCs by blending ITIC-Th acceptor with two different low-band-gap and wide-band-gap polymer donors. In one case, a power conversion efficiency of 9.6% was observed, which rivals some of the highest efficiencies for single junction OSCs based on fullerene acceptors.

  2. Role of side chains in collagen triple helix stabilization and partner recognition.

    Science.gov (United States)

    Berisio, Rita; De Simone, Alfonso; Ruggiero, Alessia; Improta, Roberto; Vitagliano, Luigi

    2009-03-01

    Collagen is a widespread protein family involved in a variety of biological processes. The complexity of collagen and its fibrous nature prevent detailed investigations on the full-length protein. Reductionist approaches conducted by dissecting the protein complexity through the use of model peptides have proved to be quite effective. There are, however, several issues regarding structure-stability relationships, aggregation in higher-order assemblies, and partner recognition that are still extensively investigated. In this review, we discuss the role that side chains play in triple helix stabilization and in partner recognition. On the basis of recent literature data, we show that collagen triple helix stability is the result of the interplay of different factors. As a general trend, interactions established by amino/imino acid side chains within the triple helix scaffold effectively modulate the intrinsic residue propensity for this common structural motif. The use of peptide models has also highlighted the role that side chains play in collagen self-association and in its interactions with receptors. Valuable examples in these fields are illustrated. Finally, future actions required to obtain more detailed information on the structure and the function of this complex protein are also delineated.

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

    Directory of Open Access Journals (Sweden)

    Jonas R Henriksen

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

  4. Predicting side-chain conformations of methionine using a hard-sphere model with stereochemical constraints

    Science.gov (United States)

    Virrueta, A.; Gaines, J.; O'Hern, C. S.; Regan, L.

    2015-03-01

    Current research in the O'Hern and Regan laboratories focuses on the development of hard-sphere models with stereochemical constraints for protein structure prediction as an alternative to molecular dynamics methods that utilize knowledge-based corrections in their force-fields. Beginning with simple hydrophobic dipeptides like valine, leucine, and isoleucine, we have shown that our model is able to reproduce the side-chain dihedral angle distributions derived from sets of high-resolution protein crystal structures. However, methionine remains an exception - our model yields a chi-3 side-chain dihedral angle distribution that is relatively uniform from 60 to 300 degrees, while the observed distribution displays peaks at 60, 180, and 300 degrees. Our goal is to resolve this discrepancy by considering clashes with neighboring residues, and averaging the reduced distribution of allowable methionine structures taken from a set of crystallized proteins. We will also re-evaluate the electron density maps from which these protein structures are derived to ensure that the methionines and their local environments are correctly modeled. This work will ultimately serve as a tool for computing side-chain entropy and protein stability. A. V. is supported by an NSF Graduate Research Fellowship and a Ford Foundation Fellowship. J. G. is supported by NIH training Grant NIH-5T15LM007056-28.

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

    Directory of Open Access Journals (Sweden)

    Carl Henrik Görbitz

    2016-09-01

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

  6. Nascent peptide side chains induce rearrangements in distinct locations of the ribosomal tunnel.

    Science.gov (United States)

    Lu, Jianli; Hua, Zhengmao; Kobertz, William R; Deutsch, Carol

    2011-08-12

    Although we have numerous structures of ribosomes, none disclose side-chain rearrangements of the nascent peptide during chain elongation. This study reports for the first time that rearrangement of the peptide and/or tunnel occurs in distinct regions of the tunnel and is directed by the unique primary sequence of each nascent peptide. In the tunnel mid-region, the accessibility of an introduced cysteine to a series of novel hydrophilic maleimide reagents increases with increasing volume of the adjacent chain residue, a sensitivity not manifest at the constriction and exit port. This surprising result reveals molecular movements not yet resolvable from structural studies. These findings map solvent-accessible volumes along the tunnel and provide novel insights critical to our understanding of allosteric communication within the ribosomal tunnel, translational arrest, chaperone interaction, folding, and rates of elongation.

  7. 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.

  8. Actinobacterial acyl coenzyme A synthetases involved in steroid side-chain catabolism.

    Science.gov (United States)

    Casabon, Israël; Swain, Kendra; Crowe, Adam M; Eltis, Lindsay D; Mohn, William W

    2014-02-01

    Bacterial steroid catabolism is an important component of the global carbon cycle and has applications in drug synthesis. Pathways for this catabolism involve multiple acyl coenzyme A (CoA) synthetases, which activate alkanoate substituents for β-oxidation. The functions of these synthetases are poorly understood. We enzymatically characterized four distinct acyl-CoA synthetases from the cholate catabolic pathway of Rhodococcus jostii RHA1 and the cholesterol catabolic pathway of Mycobacterium tuberculosis. Phylogenetic analysis of 70 acyl-CoA synthetases predicted to be involved in steroid metabolism revealed that the characterized synthetases each represent an orthologous class with a distinct function in steroid side-chain degradation. The synthetases were specific for the length of alkanoate substituent. FadD19 from M. tuberculosis H37Rv (FadD19Mtb) transformed 3-oxo-4-cholesten-26-oate (kcat/Km = 0.33 × 10(5) ± 0.03 × 10(5) M(-1) s(-1)) and represents orthologs that activate the C8 side chain of cholesterol. Both CasGRHA1 and FadD17Mtb are steroid-24-oyl-CoA synthetases. CasG and its orthologs activate the C5 side chain of cholate, while FadD17 and its orthologs appear to activate the C5 side chain of one or more cholesterol metabolites. CasIRHA1 is a steroid-22-oyl-CoA synthetase, representing orthologs that activate metabolites with a C3 side chain, which accumulate during cholate catabolism. CasI had similar apparent specificities for substrates with intact or extensively degraded steroid nuclei, exemplified by 3-oxo-23,24-bisnorchol-4-en-22-oate and 1β(2'-propanoate)-3aα-H-4α(3″-propanoate)-7aβ-methylhexahydro-5-indanone (kcat/Km = 2.4 × 10(5) ± 0.1 × 10(5) M(-1) s(-1) and 3.2 × 10(5) ± 0.3 × 10(5) M(-1) s(-1), respectively). Acyl-CoA synthetase classes involved in cholate catabolism were found in both Actinobacteria and Proteobacteria. Overall, this study provides insight into the physiological roles of acyl-CoA synthetases in steroid

  9. Biotransformation of linear alkylbenzene sulfonate (LAS) by Phanerochaete chrysosporium: oxidation of alkyl side-chain.

    Science.gov (United States)

    Yadav, J S; Lawrence, D L; Nuck, B A; Federle, T W; Reddy, C A

    2001-01-01

    The white rot fungus Phanerochaete chrysosporium, which generally mineralizes substituted aromatics to CO2, transformed linear alkylbenzene sulfonate (LAS) surfactants mainly at their alkyl side chain. Degradation of LAS was evidenced by a zone of clearing on LAS-containing agar plates and colorimetric analysis of liquid cultures. Disappearance of LAS was virtually complete within 10 days in low nitrogen (2.4 mM N), high nitrogen (24 mM N) and malt extract (ME) liquid media. After 5 days of incubation in ME medium, transformation of LAS was complete at concentrations < or = 4 mg l(-1), but decreased at higher concentrations. The LAS degradation was not dependent on lignin peroxidases (LiPs) and manganese-dependent peroxidases (MnPs). Mineralization of 14C-ring-LAS to 14CO2 by P. chrysosporium was < 1% regardless of the culture conditions used. Thin layer chromatography and mass spectral analyses indicated that P. chrysosporium transformed LAS to sulfophenyl carboxylates (SPCs) through oxidative shortening of the alkyl side-chains. While LAS disappearance in the cultures was not dependent on LiPs and MnPs, transformation of the parent LAS moieties to SPCs was more extensive in low N medium that favors expression of these enzymes. The SPCs produced in LN cultures were shorter in chain- length than those produced in ME cultures. Also there was a notable shift in the relative abundance of odd and even chain length metabolites compared to the starting LAS particularly in the low N cultures suggesting the possible involvement of processes other than or in addition to beta-oxidation in the chain-shortening process.

  10. Molecular dynamics studies of side chain effect on the beta-1,3-D-glucan triple helix in aqueous solution.

    Science.gov (United States)

    Okobira, Tadashi; Miyoshi, Kentaro; Uezu, Kazuya; Sakurai, Kazuo; Shinkai, Seiji

    2008-03-01

    beta-1,3-D-glucans have been isolated from fungi as right-handed 6(1) triple helices. They are categorized by the side chains bound to the main triple helix through beta-(1-->6)-D-glycosyl linkage. Indeed, since a glucose-based side chain is water soluble, the presence and frequency of glucose-based side chains give rise to significant variation in the physical properties of the glucan family. Curdlan has no side chains and self-assembles to form an water-insoluble triple helical structure, while schizophyllan, which has a 1,6-D-glucose side chain on every third glucose unit along the main chain, is completely water soluble. A thermal fluctuation in the optical rotatory dispersion is observed for the side chain, indicating probable co-operative interaction between the side chains and water molecules. This paper documents molecular dynamics simulations in aqueous solution for three models of the beta-1,3-D-glucan series: curdlan (no side chain), schizophyllan (a beta-(1-->6)-D-glycosyl side-chain at every third position), and a hypothetical triple helix with a side chain at every sixth main-chain glucose unit. A decrease was observed in the helical pitch as the population of the side chain increased. Two types of hydrogen bonding via water molecules, the side chain/main chain and the side chain/side chain hydrogen bonding, play an important role in determination of the triple helix conformation. The formation of a one-dimensional cavity of diameter about 3.5 A was observed in the schizophyllan triple helix, while curdlan showed no such cavity. The side chain/side chain hydrogen bonding in schizophyllan and the hypothetical beta-1,3-D-glucan triple helix could cause the tilt of the main-chain glucose residues to the helix.

  11. Lattice and off-lattice side chain models of protein folding: linear time structure prediction better than 86% of optimal.

    Science.gov (United States)

    Hart, W E; Istrail, S

    1997-01-01

    This paper considers the protein energy minimization problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. We consider two side chain models: a lattice model that generalizes the HP model (Dill, 1985) to explicitly represent side chains on the cubic lattice and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. We describe algorithms with mathematically guaranteed error bounds for both of these models. In particular, we describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 86% of optimal in a face-centered cubic lattice, and we demonstrate how this provides a better than 70% performance guarantee for the HP-TSSC model. Our analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Ngo et al. (1994) concerning the complexity of protein folding models that include side chains.

  12. 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.

  13. 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.

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

    Science.gov (United States)

    El Labban, Abdulrahman; Warnan, Julien; Cabanetos, Clément; Ratel, Olivier; Tassone, Christopher; Toney, Michael F; Beaujuge, Pierre M

    2014-11-26

    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.

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    We study relations among the side-chain asymmetry, structure, and order-disorder transition (ODT) in hairy-rod-type poly(9,9-dihexylfluorene) (PF6) with two identical side chains and atactic poly(9-octyl-9-methyl-fluorene) (PF1-8) with two different side chains per repeat. PF6 and PF1-8 organize...... as an indistinguishable bilayer with a half thickness Hbilayer(PF1−8)/2≈H(PF6). The low grafting density region is structurally possible but not certain for PF6 and confirmed for PF1-8....

  16. 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

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

  17. Glucal-conjugated sterols as novel vascular leakage blocker: structure-activity relationship focusing on the C17-side chain.

    Science.gov (United States)

    Kim, Kyeojin; Maharjan, Sony; Lim, Changjin; Kim, Nam-Jung; Agrawal, Vijayendra; Han, Young Taek; Lee, Sujin; An, Hongchan; Yun, Hwayoung; Choi, Hyun-Jung; Kwon, Young-Guen; Suh, Young-Ger

    2014-03-21

    A series of glucal-conjugated sterols as novel vascular leakage blocker were identified through design, synthesis and biologically evaluation. In addition, the structure-activity relationship (SAR) of the glucal-conjugated sterols focusing on the C17-side chain was also established. The sterol analogs linked with the rigid C17-side chain side chains exhibited potent cell survival activities. In particular, analog 21l, which possesses a cyclopentyl oxime moiety, was shown to have excellent pharmacological effects on retinal vascular leakage in a diabetic mouse model. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  18. The Involvement of Amino Acid Side Chains in Shielding the Nickel Coordination Site: An NMR Study

    Directory of Open Access Journals (Sweden)

    Serenella Medici

    2013-10-01

    Full Text Available Coordination of proteins and peptides to metal ions is known to affect their properties, often by a change in their structural organization. Side chains of the residues directly involved in metal binding or very close to the coordination centre may arrange themselves around it, in such a way that they can, for instance, disrupt the protein functions or stabilize a metal complex by shielding it from the attack of water or other small molecules. The conformation of these side chains may be crucial to different biological or toxic processes. In our research we have encountered such behaviour in several cases, leading to interesting results for our purposes. Here we give an overview on the structural changes involving peptide side chains induced by Ni(II coordination. In this paper we deal with a number of peptides, deriving from proteins containing one or more metal coordinating sites, which have been studied through a series of NMR experiments in their structural changes caused by Ni(II complexation. Several peptides have been included in the study: short sequences from serum albumin (HSA, Des-Angiotensinogen, the 30-amino acid tail of histone H4, some fragments from histone H2A and H2B, the initial fragment of human protamine HP2 and selected fragments from prion and Cap43 proteins. NMR was the election technique for gathering structural information. Experiments performed for this purpose included 1D 1H and 13C, and 2D HSQC, COSY, TOCSY, NOESY and ROESY acquisitions, which allowed the calculation of the Ni(II complexes structural models.

  19. Effect of side chain length on intrahelical interactions between carboxylate- and guanidinium-containing amino acids.

    Science.gov (United States)

    Kuo, Hsiou-Ting; Yang, Po-An; Wang, Wei-Ren; Hsu, Hao-Chun; Wu, Cheng-Hsun; Ting, Yu-Te; Weng, Ming-Huei; Kuo, Li-Hung; Cheng, Richard P

    2014-08-01

    The charge-containing hydrophilic functionalities of encoded charged amino acids are linked to the backbone via different numbers of hydrophobic methylenes, despite the apparent electrostatic nature of protein ion pairing interactions. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on ion pairing interactions, α-helical peptides containing Zbb-Xaa (i, i + 3), (i, i + 4) and (i, i + 5) (Zbb = carboxylate-containing residues Aad, Glu, Asp in decreasing length; Xaa = guanidinium residues Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by circular dichroism spectroscopy (CD). The helicity of Aad- and Glu-containing peptides was similar and mostly pH independent, whereas the helicity of Asp-containing peptides was mostly pH dependent. Furthermore, the Arg-containing peptides consistently exhibited higher helicity compared to the corresponding Agp-, Agb-, and Agh-containing peptides. Side chain conformational analysis by molecular mechanics calculations showed that the Zbb-Xaa (i, i + 3) and (i, i + 4) interactions mainly involved the χ 1 dihedral combinations (g+, g+) and (g-, g+), respectively. These low energy conformations were also observed in intrahelical Asp-Arg and Glu-Arg salt bridges of natural proteins. Accordingly, Asp and Glu provides variation in helix characteristics associated with Arg, but Aad does not provide features beyond those already delivered by Glu. Importantly, nature may have chosen the side chain length of Arg to support helical conformations through inherent high helix propensity coupled with stabilizing intrahelical ion pairing interactions with the carboxylate-containing residues.

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

    Energy Technology Data Exchange (ETDEWEB)

    Alnervik, M.

    1996-12-31

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

  1. 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.

  2. 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.

  3. 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....

  4. Effects of Laser-Induced Heating on the Photoinduced Birefringence in Azobenzene-Side-Chain Copolymer

    Institute of Scientific and Technical Information of China (English)

    杨军; 明海; 章江英; 王沛; 郎建英; 鲁拥华; 刘剑; 张其锦

    2003-01-01

    The photoinduced birefringence was observed in the polymer poly[2-(4-(4-cyanophenyl) diazenyl phenyloxy) ethoxyl methacrylatel with a cw 532nm laser. The azobenzene polymer character has been studied under the conditions of various illuminating time and light intensities. By analysing the processes of reorientation, the effect of laser-induced heating has been introduced to the buildup of photoinduced birefringence in azobenzene-side-chain copolymer. The curves for the buildup of birefringence were fitted with a modified function, i.e., biexponential curves and Gaussian curves. The relationship among all the parameters has also been presented. With the modified fitting function, we obtain a better fitting result.

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

    Directory of Open Access Journals (Sweden)

    Boryana Trusheva

    2016-01-01

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

  6. Third-order nonlinear optical characterization of side-chain copolymers

    Science.gov (United States)

    Norwood, Robert A.; Sounik, James R.; Popolo, J.; Holcomb, Douglas P.

    1991-12-01

    Third order nonlinear optical properties of side-chain methacrylate copolymers incorporating 4-amino-4'-nitrostilbene, 4-oxy-4'nitrostilbene, and functionalized silicon phthalocyanine chromophores are measured by picosecond degenerate four wave mixing at 598 nm. The nonresonant stilbene system exhibits a pulse limited ultrafast response, while the resonant phthalocyanine system has a large excited state nonlinearity. Comparison of silicon phthalocyanine copolymers with solubilized guest/host systems dispersed in polymethylmethacrylate illustrate the importance of aggregation and phthalocyanine ring interaction in determining the linear optical properties and the magnitude and speed of the nonlinear optical response.

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

    Institute of Scientific and Technical Information of China (English)

    Jian Wang; Ying Han Wang

    2008-01-01

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

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

    Directory of Open Access Journals (Sweden)

    María Cristina Chamy

    2007-12-01

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

  9. SYNTHESIS AND CHARACTERIZATION OF β-DIKETONE BASED SIDE CHAIN LIQUID CRYSTALLINE POLYSILOXANES

    Institute of Scientific and Technical Information of China (English)

    WU Fuzhou; ZHANG Rongben; JIANG Yingyan

    1990-01-01

    A new type of β-diketone based side chain liquid crystalline polysiloxanes (DKLCP) with different length of flexible spacers and end groups have been synthesized by hydrosilation reaction. This is liquid crystal polymers (LCP) using coordinating β-diketone ligand as mesogens. The phase behaviour of DKLCP polymers was studied by differential scanning calorimetry and polarizing microscopy.X-ray diffraction investigations demonstrated that the polysiloxanes with sufficiently long flexible spacers were smectic liquid crystal polymers, while those with much shorter spacers were nematic ones.

  10. 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...... 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...... in the appearance of a surface relief with doubled frequency....

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

    CERN Document Server

    Haydock, Christopher

    2007-01-01

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

  12. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-16

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

  14. Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3

    Science.gov (United States)

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

    2011-01-01

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

  15. Side chain effects in reactions of the potassium-tyrosine charge transfer complex

    Science.gov (United States)

    da Silva, F. Ferreira; Meneses, G.; Ingólfsson, O.; Limão-Vieira, P.

    2016-10-01

    Fragmentation of transient negative ions of tyrosine formed through electron transfer in collisions with neutral potassium atoms is presented in the collision energy range from 30 to 75 eV. At low collision energies the dominating side chain channel observed corresponds to the cleavage of the bond from the para-position of the phenyl ring to the β-C of the remaining moiety, but cleavage of the Cαsbnd Cβ bond is also observed. Further fragments are formed through cleavage of the Cα bond to the carbonyl group, through decomposition of the carboxyl group or through significant decomposition of the backbone. The dehydrogenated molecular anion is also observed with appreciable intensity. These results are discussed in the context of earlier studies on dissociative electron attachment to tyrosine and other amino acids, as well as within the role of the side chain in electron induced decomposition of this aromatic amino acid. Stabilization of the temporary molecular anion in the transient collision complex is discussed and we argue that this may have significant influence on the branching ratios observed.

  16. Proton exchange membranes based on the short-side-chain perfluorinated ionomer

    Science.gov (United States)

    Ghielmi, A.; Vaccarono, P.; Troglia, C.; Arcella, V.

    Due to the renovated availability of the base monomer for the synthesis of the short-side-chain (SSC) perfluorinated ionomer, fuel cell membrane development is being pursued using this well known ionomer structure, which was originally developed by Dow in the 1980s. The new membranes under development have the trade name Hyflon Ion. After briefly reviewing the literature on the Dow ionomer, new characterization data are reported on extruded Hyflon Ion membranes. The data are compared to those available in the literature on the Dow SSC ionomer and membranes. Comparison is made also with data obtained in this work or available in the literature on the long-side-chain (LSC) perfluorinated ionomer (Nafion). Thermal, visco-elastic, water absorption and mechanical properties of Hyflon Ion are studied. While the general behavior is similar to that shown in the past by the Dow membranes, slight differences are evident in the hydration behavior at equivalent weight (EW) glass transition temperature compared to Nafion, which makes it a more promising material for high temperature proton exchange membrane (PEM) fuel cell operation ( T > 100 °C). Beginning of life fuel cell performance has also been confirmed to be higher than that given by a Nafion membrane of equal thickness.

  17. Enzyme directed formation of un-natural side-chains for covalent surface attachment of proteins.

    Science.gov (United States)

    Cho, Hwayoung; Jaworski, Justyn

    2014-10-01

    The covalent immobilization of proteins onto surfaces is an essential aspect of several fields of research, including proteomics, sensing, heterogeneous biocatalysis, and more broadly biotechnology. Site-specific, covalent attachment of proteins has been achieved in recent years by the use of expanded genetic codes to produce proteins with controlled placement of un-natural amino acids bearing bio-orthogonal functional groups. Unfortunately, the complexity of developing such systems is impractical for most laboratories; hence, a less complicated approach to generating un-natural amino acid side-chains has been employed. Utilizing a straightforward reaction with formylglycine generating enzyme, we use the site-specific modification of engineered proteins to yield un-natural amino acid side-chains for protein immobilization. Using this approach, we demonstrate the controlled immobilization of various enzymes onto a variety of amine coated surfaces. Our results reveal reusability of the immobilized enzymes via this strategy, and furthermore, we find the activity of the immobilized enzymes to remain even after a month of use indicating significant stability of the linkage.

  18. Characterization and Diagnostic Value of Amino Acid Side Chain Neutral Losses Following Electron-Transfer Dissociation

    Science.gov (United States)

    Xia, Qiangwei; Lee, M. Violet; Rose, Christopher M.; Marsh, Alyce J.; Hubler, Shane L.; Wenger, Craig D.; Coon, Joshua J.

    2011-02-01

    Using a large set of high mass accuracy and resolution ETD tandem mass spectra, we characterized ETD-induced neutral losses. From these data we deduced the chemical formula for 20 of these losses. Many of them have been previously observed in electron-capture dissociation (ECD) spectra, such as losses of the side chains of arginine, aspartic acid, glutamic acid, glutamine, asparagine, leucine, histidine, and carbamidomethylated cysteine residues. With this information, we examined the diagnostic value of these amino acid-specific losses. Among 1285 peptide-spectrum matches, 92.5% have agreement between neutral loss-derived peptide amino acid composition and the peptide sequences. Moreover, we show that peptides can be uniquely identified by using only the accurate precursor mass and amino acid composition based on neutral losses; the median number of sequence candidates from an accurate mass query is reduced from 21 to 8 by adding side chain loss information. Besides increasing confidence in peptide identification, our findings suggest the potential use of these diagnostic losses in ETD spectra to improve false discovery rate estimation and to enhance the performance of scoring functions in database search algorithms.

  19. Subcritical Water Hydrolysis of Peptides: Amino Acid Side-Chain Modifications

    Science.gov (United States)

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

    2017-09-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-08-15

    The use of {sup 13}C NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically {sup 13}C labeled histidine residues in plastocyanin (PCu) from Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for {sup 13}C{sup {epsilon}}{sup 1} nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from {sup 15}N backbone relaxation measurements. Compared to measurements of backbone nuclei, {sup 13}C{sup {epsilon}}{sup 1} dispersion provides a more direct method to monitor interchanging protonation states or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the {sup 13}C{sup {epsilon}}{sup 1} dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains are discussed.

  1. 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.

  2. A Major Role for Side-Chain Polyglutamine Hydrogen Bonding in Irreversible Ataxin-3 Aggregation

    Science.gov (United States)

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

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Antonino Natalello

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

  4. 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 ch

  5. Control of the PEO chain conformation on nanoparticles by adsorption of PEO-block-poly(L-lysine) copolymers and its significance on colloidal stability and protein repellency.

    Science.gov (United States)

    Louguet, Stéphanie; Kumar, Anitha C; Guidolin, Nicolas; Sigaud, Gilles; Duguet, Etienne; Lecommandoux, Sébastien; Schatz, Christophe

    2011-11-01

    The physical adsorption of PEO(n)-b-PLL(m) copolymers onto silica nanoparticles and the related properties of poly(ethylene oxide) (PEO)-coated particles were studied as a function of the block copolymer composition. Copolymers adopt an anchor-buoy conformation at the particle surface owing to a preferential affinity of poly(L-lysine) (PLL) blocks with the silica surface over PEO blocks when a large excess of copolymer is used. The interdistance between PEO chains at particle surface is highly dependent on the size of PLL segments; a dense brush of PEO is obtained for short PLL blocks (DP = 10), whereas PEO chains adopt a so-called interacting "mushroom" conformation for large PLL blocks (DP = 270). The size of the PEO blocks does not really influence the copolymer surface density, but it has a strong effect on the PEO layer thickness as expected. Salt and protein stability studies led to similar conclusions about the effectiveness of a PEO layer with a dense brush conformation to prevent colloidal aggregation and protein adsorption. Besides, a minimal PEO length is required to get full stabilization properties; as a matter of fact, both PEO(45)-b-PLL(10) and PEO(113)-b-PLL(10) give rise to a PEO brush conformation but only the latter copolymer efficiently stabilizes the particles in the presence of salt or proteins.

  6. Contribution of main chain and side chain atoms and their locations to the stability of thermophilic proteins.

    Science.gov (United States)

    Tompa, Dharma Rao; Gromiha, M Michael; Saraboji, K

    2016-03-01

    Proteins belonging to the same class, having similar structures thus performing the same function are known to have different thermal stabilities depending on the source- thermophile or mesophile. The variation in thermo-stability has not been attributed to any unified factor yet and understanding this phenomenon is critically needed in several areas, particularly in protein engineering to design stable variants of the proteins. Toward this motive, the present study focuses on the sequence and structural investigation of a dataset of 373 pairs of proteins; a thermophilic protein and its mesophilic structural analog in each pair, from the perspectives of hydrophobic free energy, hydrogen bonds, physico-chemical properties of amino acids and residue-residue contacts. Our results showed that the hydrophobic free energy due to carbon, charged nitrogen and charged oxygen atoms was stronger in 65% of thermophilic proteins. The number of hydrogen bonds which bridges the buried and exposed regions of proteins was also greater in case of thermophiles. Amino acids of extended shape, volume and molecular weight along with more medium and long range contacts were observed in many of the thermophilic proteins. These results highlight the preference of thermophiles toward the amino acids with larger side chain and charged to make up greater free energy, better packing of residues and increase the overall compactness.

  7. Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal

    Energy Technology Data Exchange (ETDEWEB)

    Hart, W.E.; Istrail, S. [Sandia National Labs., Albuquerque, NM (United States). Algorithms and Discrete Mathematics Dept.

    1996-08-09

    This paper considers the protein structure prediction problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven extremely useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. The authors consider two side chain models: a lattice model that generalizes the HP model (Dill 85) to explicitly represent side chains on the cubic lattice, and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. They describe algorithms for both of these models with mathematically guaranteed error bounds. In particular, the authors describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 865 of optimal in a face centered cubic lattice, and they demonstrate how this provides a 70% performance guarantee for the HP-TSSC model. This is the first algorithm in the literature for off-lattice protein structure prediction that has a rigorous performance guarantee. The analysis of the HP-TSSC model builds off of the work of Dancik and Hannenhalli who have developed a 16/30 approximation algorithm for the HP model on the hexagonal close packed lattice. Further, the analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Karplus et al. concerning the complexity of protein folding models that include side chains.

  8. Vacuum-Ultraviolet Circular Dichroism Spectra of Escherichia coli Dihydrofolate Reductase and Its Mutants: Contributions of Phenylalanine and Tyrosine Side Chains and Exciton Coupling of Two Tryptophan Side Chains.

    Science.gov (United States)

    Ohmae, Eiji; Tanaka, Suguru; Miyashita, Yurina; Katayanagi, Katsuo; Matsuo, Koichi

    2015-10-15

    Vacuum-ultraviolet (VUV) circular dichroism (CD) spectroscopy has recently been used for secondary structure analysis of proteins; however, the contribution of aromatic side chains to protein VUV CD spectra is unresolved. In this report, VUV CD spectra of 10 Escherichia coli dihydrofolate reductase (DHFR) mutants, in which each phenylalanine or tyrosine residue was mutated to leucine, were measured down to 175 nm at 25 °C and pH 8.0 to elucidate the contributions of these aromatic side chains to the high-energy transitions of peptide bonds. The VUV CD spectra of these mutants were different from the spectrum of the wild-type protein, indicating that the contribution of the phenylalanine and tyrosine side chains of DHFR extends to the VUV region. Furthermore, the VUV CD spectrum and the folate- or NADP(+)-induced spectral change of F103L mutant DHFR indicated a modification and regeneration of exciton coupling between the Trp47 and Trp74 side chains, respectively, suggesting that exciton coupling may also contribute to the CD spectrum of DHFR in the VUV region. These results should be useful for theoretically characterizing the contribution of aromatic side chains to protein CD spectra, leading to the improvement of protein secondary-structure analysis by VUV CD spectroscopy.

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

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

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

  10. Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.

    Science.gov (United States)

    Ostermeir, Katja; Zacharias, Martin

    2014-01-15

    A Hamiltonian Replica-Exchange Molecular Dynamics (REMD) simulation method has been developed that employs a two-dimensional backbone and one-dimensional side chain biasing potential specifically to promote conformational transitions in peptides. To exploit the replica framework optimally, the level of the biasing potential in each replica was appropriately adapted during the simulations. This resulted in both high exchange rates between neighboring replicas and improved occupancy/flow of all conformers in each replica. The performance of the approach was tested on several peptide and protein systems and compared with regular MD simulations and previous REMD studies. Improved sampling of relevant conformational states was observed for unrestrained protein and peptide folding simulations as well as for refinement of a loop structure with restricted mobility of loop flanking protein regions.

  11. 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.

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

    DEFF Research Database (Denmark)

    Beier, Matthias Josef; Schimmoeller, Bjoern; Hansen, Thomas Willum

    2010-01-01

    an elevated pressure was required. Carboxylic acids, such as benzoic acid or p-toluic acid, additionally increased the reaction rate while CeO2 could act both as a promoter and an inhibitor depending on the substrate and the reaction conditions. Silver catalysts were prepared both by standard impregnation......Silver supported on silica effectively catalyzes the aerobic side-chain oxidation of alkyl aromatic compounds under solvent-free conditions. Toluene, p-xylene, ethylbenzene and cumene were investigated as model substrates. Typically, the reaction was performed at ambient pressure; only for toluene...... and flame spray pyrolysis. Addition of a Ce precursor to the FSP catalyst resulted in significantly smaller silver particles. Ce-doped FSP catalysts in general exhibited a superior catalytic performance with TONs up to 2000 except for cumene oxidation that appeared to proceed mainly by homogeneous catalysis...

  13. Polarization holographic gratings in side-chain azobenzene polyesters with linear and circular photoanisotropy

    DEFF Research Database (Denmark)

    Nikolova, Ludmila; Todorov, T.; Ivanov, Mario Tonev

    1996-01-01

    We investigate thin phase polarization holographic gratings recorded with two waves with orthogonal linear polarizations in materials in which illumination with linearly/circularly polarized light gives rise to linear/circular birefringence. The theoretical analysis shows that the presence...... of circular photoanisotropy changes significantly the diffraction characteristics of the gratings. The intensities of the waves diffracted in the +1 and -1 orders of diffraction and their ratio depend substantially on the reconstructing-wave polarization. Experiments with films of side-chain liquid......-crystalline azobenzene polyester that is a photoanisotropic material of the considered type confirm the unusual polarization properties. It is shown that polarization holography may be used for real-time simultaneous measurement of photoinduced linear and circular birefringence....

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

    DEFF Research Database (Denmark)

    Pattison, D I; Davies, Michael Jonathan

    2001-01-01

    , absolute second-order rate constants for the reactions of HOCl with protein side chains, model compounds, and backbone amide (peptide) bonds have been determined at physiological pH values. The reactivity of HOCl with potential reactive sites in proteins is summarized by the series: Met (3.8 x 10(7) M(-1......) x s(-1)) > backbone amides (10-10(-3) M(-1) x s(-1)) > Gln(0.03 M(-1) x s(-1)) approximately Asn (0.03 M(-1) x s(-1)). The rate constants for reaction of HOCl with backbone amides (peptide bonds) vary by 4 orders of magnitude with uncharged peptide bonds reacting more readily with HOCl than those...

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

    Institute of Scientific and Technical Information of China (English)

    WU Fuzhou; ZHANG Rongben; JIANG Yingyan

    1991-01-01

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

  16. Optical probe for the cytochrom P-450 cholesterol side chain cleavage enzyme

    Energy Technology Data Exchange (ETDEWEB)

    Marrone, B.L.; Simpson, D.J.; Unkefer, C.J.; Whaley, T.W.

    1992-05-05

    This patent describes a method for quantifying the activity of the P-450[sub scc] enzyme in the conversion of cholesterol to pregnenolone in steroidogenesis, forming a fluorogenic probe having a cholesterol-based steroid connected through a linking group at the C-22 position with a chromophore effective to have a low optical response when attached to the steroid and a high optical response as an anion, incorporating the probe in a process for the conversion of cholesterol to pregnenolone; reacting the probe with the P-450[sub scc] enzyme to cleave the side-chain from the probe and form the anion having the high optical response from the chromophore; and exciting the anion to obtain the high optical response; and optically detecting the response as a measure of the P-450[sub scc] enzyme activity.

  17. Non-innocent side-chains with dipole moments in organic solar cells improve charge separation.

    Science.gov (United States)

    de Gier, Hilde D; Broer, Ria; Havenith, Remco W A

    2014-06-28

    Providing sustainable energy is one of the biggest challenges nowadays. An attractive answer is the use of organic solar cells to capture solar energy. Recently a promising route to increase their efficiency has been suggested: developing new organic materials with a high dielectric constant. This solution focuses on lowering the coulomb attraction between electrons and holes, thereby increasing the yield of free charges. In here, we demonstrate from a theoretical point of view that incorporation of dipole moments in organic materials indeed lowers the coulomb attraction. A combination of molecular dynamics simulations for modelling the blend and ab initio quantum chemical calculations to study specific regions was performed. This approach gives predictive insight in the suitability of new materials for application in organic solar cells. In addition to all requirements that make conjugated polymers suitable for application in organic solar cells, this study demonstrates the importance of large dipole moments in polymer side-chains.

  18. Arginyltransferase ATE1 catalyzes midchain arginylation of proteins at side chain carboxylates in vivo.

    Science.gov (United States)

    Wang, Junling; Han, Xuemei; Wong, Catherine C L; Cheng, Hong; Aslanian, Aaron; Xu, Tao; Leavis, Paul; Roder, Heinrich; Hedstrom, Lizbeth; Yates, John R; Kashina, Anna

    2014-03-20

    Arginylation is an emerging posttranslational modification mediated by Arg-tRNA-protein-transferase (ATE1). It is believed that ATE1 links Arg solely to the N terminus of proteins, requiring prior proteolysis or action by Met-aminopeptidases to expose the arginylated site. Here, we tested the possibility of Arg linkage to midchain sites within intact protein targets and found that many proteins in vivo are modified on the side chains of Asp and Glu by unconventional chemistry that targets the carboxy rather than the amino groups at the target sites. Such arginylation appears to be functionally regulated, and it can be directly mediated by ATE1, in addition to the more conventional ATE1-mediated linkage of Arg to the N-terminal alpha amino group. This midchain arginylation implies an unconventional mechanism of ATE1 action that likely facilitates its major biological role.

  19. Shape-Selectivity with Liquid Crystal and Side-Chain Liquid Crystalline Polymer SAW Sensor Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    FRYE-MASON,GREGORY CHARLES; OBORNY,MICHAEL C.; PUGH,COLEEN; RICCO,ANTONIO; THOMAS,ROSS C.; ZELLERS,EDWARD T.; ZHANG,GUO-ZHENG

    1999-09-23

    A liquid crystal (LC) and a side-chain liquid crystalline polymer (SCLCP) were tested as surface acoustic wave (SAW) vapor sensor coatings for discriminating between pairs of isomeric organic vapors. Both exhibit room temperature smectic mesophases. Temperature, electric-field, and pretreatment with self-assembled monolayers comprising either a methyl-terminated or carboxylic acid-terminated alkane thiol anchored to a gold layer in the delay path of the sensor were explored as means of affecting the alignment and selectivity of the LC and SCLCP films. Results for the LC were mixed, while those for the SCLCP showed a consistent preference for the more rod-like isomer of each isomer pair examined.

  20. 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.

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

    Directory of Open Access Journals (Sweden)

    Inbar Yuval

    2010-07-01

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

  2. Ozonolysis of surface adsorbed methoxyphenols: kinetics of aromatic ring cleavage vs. alkene side-chain oxidation

    Directory of Open Access Journals (Sweden)

    E. M. O'Neill

    2013-07-01

    Full Text Available Lignin pyrolysis products, which include a variety of substituted methoxyphenols, constitute a major component of organics released by biomass combustion and may play a central role in the formation of atmospheric brown carbon. Understanding the atmospheric fate of these compounds upon exposure to trace gases is therefore critical to predicting the chemical and physical properties of biomass burning aerosol. We used diffuse reflectance infrared spectroscopy to monitor the heterogeneous ozonolysis of 4-propylguaiacol, eugenol, and isoeugenol adsorbed on NaCl and α-Al2O3 substrates. Adsorption of gaseous methoxyphenols onto these substrates produced near monolayer surface concentrations of 3 × 1018 molecules m-2. The subsequent dark heterogeneous ozonolysis of adsorbed 4-propylguaiacol cleaved the aromatic ring between the methoxy and phenol groups with the product conclusively identified by GC-MS and 1H-NMR. Kinetic analysis of eugenol and isoeugenol dark ozonolysis also suggested the formation of ring-cleaved products, although ozonolysis of the unsaturated substituent groups forming carboxylic acids and aldehydes was an order of magnitude faster. Average uptake coefficients for NaCl-adsorbed methoxyphenols were γ = 2.3 (±0.8 × 10-7 and 2 (±1 × 10-6 for ozonolysis of the aromatic ring and the unsaturated side chain, respectively, and reactions on α-Al2O3 were approximately two times slower. UV-visible radiation (λ>300 nm enhanced eugenol ozonolysis of the aromatic ring by a factor of 4(±1 but had no effect on ozonolysis of the alkene side-chain.

  3. Engineering the residual side chains of HAP phytases to improve their pepsin resistance and catalytic efficiency

    Science.gov (United States)

    Niu, Canfang; Yang, Peilong; Luo, Huiying; Huang, Huoqing; Wang, Yaru; Yao, Bin

    2017-01-01

    Strong resistance to proteolytic attack is important for feed enzymes. Here, we selected three predicted pepsin cleavage sites, L99, L162, and E230 (numbering from the initiator M of premature proteins), in pepsin-sensitive HAP phytases YkAPPA from Yersinia kristensenii and YeAPPA from Y. enterocolitica, which corresponded to L99, V162, and D230 in pepsin-resistant YrAPPA from Y. rohdei. We constructed mutants with different side chain structures at these sites using site-directed mutagenesis and produced all enzymes in Escherichia coli for catalytic and biochemical characterization. The substitutions E230G/A/P/R/S/T/D, L162G/A/V, L99A, L99A/L162G, and L99A/L162G/E230G improved the pepsin resistance. Moreover, E230G/A and L162G/V conferred enhanced pepsin resistance on YkAPPA and YeAPPA, increased their catalytic efficiency 1.3–2.4-fold, improved their stability at 60 °C and pH 1.0–2.0 and alleviated inhibition by metal ions. In addition, E230G increased the ability of YkAPPA and YeAPPA to hydrolyze phytate from corn meal at a high pepsin concentration and low pH, which indicated that optimization of the pepsin cleavage site side chains may enhance the pepsin resistance, improve the stability at acidic pH, and increase the catalytic activity. This study proposes an efficient approach to improve enzyme performance in monogastric animals fed feed with a high phytate content. PMID:28186144

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

    Institute of Scientific and Technical Information of China (English)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2011-09-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Weininger, Ulrich; Respondek, Michal; Akke, Mikael, E-mail: mikael.akke@bpc.lu.se [Center for Molecular Protein Science, Lund University, Department of Biophysical Chemistry (Sweden)

    2012-09-15

    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 {sup 13}C labeled proteins by means of longitudinal- and transverse-relaxation optimized CPMG relaxation dispersion. By monitoring {sup 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 {sup 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.

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

    Directory of Open Access Journals (Sweden)

    Nobutaka Endo

    2016-08-01

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

  8. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

    Science.gov (United States)

    Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C

    2015-03-01

    The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding.

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

    Energy Technology Data Exchange (ETDEWEB)

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

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

  10. 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.

  11. "Bicontinuous cubic" liquid crystalline materials from discotic molecules: a special effect of paraffinic side chains with ionic liquid pendants.

    Science.gov (United States)

    Alam, Md Akhtarul; Motoyanagi, Jin; Yamamoto, Yohei; Fukushima, Takanori; Kim, Jungeun; Kato, Kenichi; Takata, Masaki; Saeki, Akinori; Seki, Shu; Tagawa, Seiichi; Aida, Takuzo

    2009-12-16

    Triphenylene (TP) derivatives bearing appropriate paraffinic side chains with imidazolium ion-based ionic liquid (IL) pendants were unveiled to display a phase diagram with liquid crystalline (LC) mesophases of bicontinuous cubic (Cub(bi)) and hexagonal columnar (Col(h)) geometries. While their phase transition behaviors are highly dependent on the length of the side chains and the size of the ionic liquid pendants, TPs with hexadecyl side chains exclusively form a Cub(bi) LC assembly over an extremely wide temperature range of approximately 200 degrees C from room temperature when the anions of the IL pendants are relatively small. Wide-angle X-ray diffraction analysis suggested that the Cub(bi) LC mesophase contains pi-stacked columnar TP arrays with a plane-to-plane separation of approximately 3.5 A. Consistently, upon laser flash photolysis, it showed a transient microwave conductivity comparable to that of a Col(h) LC reference.

  12. Monoquaternary pyridinium salts with modified side chain-synthesis and evaluation on model of tabun- and paraoxon-inhibited acetylcholinesterase.

    Science.gov (United States)

    Musilek, Kamil; Kucera, Jiri; Jun, Daniel; Dohnal, Vlastimil; Opletalova, Veronika; Kuca, Kamil

    2008-09-01

    Acetylcholinesterase reactivators are crucial antidotes for the treatment of organophosphate intoxication. Eighteen monoquaternary reactivators of acetylcholinesterase with modified side chain were developed in an effort to extend the properties of pralidoxime. The known reactivators (pralidoxime, HI-6, obidoxime, trimedoxime, methoxime) and the prepared compounds were tested in vitro on a model of tabun- and paraoxon-inhibited AChE. Monoquaternary reactivators were not able to exceed the best known compounds for tabun poisoning, but some of them did show reactivation better or comparable with pralidoxime for paraoxon poisoning. However, extensive differences were found by a SAR study for various side chains on the non-oxime part of the reactivator molecule.

  13. Genes involved in cell wall localization and side chain formation of rhamnose-glucose polysaccharide in Streptococcus mutans.

    Science.gov (United States)

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

    1998-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-12-07

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

  15. Influence of LC Content on the Phase Structures of Side-Chain Liquid

    Energy Technology Data Exchange (ETDEWEB)

    Tenneti, K.; Chen, X; Li, C; Shen, Z; Wan, X; Fan, X; Zhou, Q; Rong, L; Hsiao, B

    2009-01-01

    We report the phase structures of a series of poly(styrene-block-{l_brace}3'-[4-(4-n-dodecyloxybenzoyloxy)benzoyloxy]-4-(12-methacryloyloxydodecyloxy)benzoyloxybiphenyl{r_brace}) (PS-b-PMAC) side-chain liquid crystalline block copolymers (SC LCBCP). The SC liquid crystalline polymer was formed by side attaching a bent-core mesogen to the polymer backbone using a 12-carbon spacer. The phase structure of the high and low fPMAC samples were investigated using differential scanning calorimetry, small-angle and wide-angle X-ray scattering, and transmission electron microscopy techniques. The PS coil block and PMAC LC block phase separate into a lamellar morphology in all of the samples investigated (volume fraction of PMAC fPMAC 0.31-0.65). However, both the LC phase and the orientation of the hierarchical structure under mechanical shear showed strong dependence on the LC content. Samples having a high fPMAC (0.5-0.65) showed a SmC2 LC phase (Smectic C denotes the LC molecules are tilted with respect to the layer normal, and 2 represents a bilayered structure), similar to that observed in PMAC homopolymers. Upon mechanical shear, these smectic layers oriented parallel to the shear plane and the BCP lamellae oriented perpendicular to the shear plane with the layer normal parallel to the vorticity direction. In samples having a lower fPMAC, the BCP lamellae laid parallel to the shear plane and the LC phase structure in these samples was columnar rectangular. A detailed structural and morphological study will be reported.

  16. Preparation of main-chain-type and side-chain-type sulfonated poly(ether ether ketone) membranes for direct methanol fuel cell applications

    Science.gov (United States)

    Tsai, Jie-Cheng; Lin, Chien-Kung

    Novel main-chain-type and side-chain-type sulphonated poly(ether ether ketone)s (MS-SPEEKs) are synthesised by reacting the sulphonic acid groups of pristine SPEEKs with 2-aminoethanesulphonic acid to improve the nano-phase separated morphology of the material. 1H NMR and FT-IR spectroscopy are employed to determine the structure and composition of main-chain-type and side-chain-type sulphonated polymers. Flexible and tough membranes with reasonable thermal properties are obtained. The MS-SPEEKs show good hydrolytic stability, and water uptake values ranging from 15% to 30% are observed. Compared to Nafion 117 ®, the methanol permeability of the MS-SPEEKs is dramatically reduced to 8.83 × 10 -8 cm 2 s -1 to 3.31 × 10 -7 cm 2 s -1. The proton conductivity increases with increasing temperature, reaching 0.013-0.182 S cm -1. A maximum power density and open circuit voltage of 115 mW cm -2 and 0.830 V are obtained at 80 °C, respectively, which is significantly greater than the values generated with Nafion 117 ®. The introduction of pendent side-chain-type sulphonic acid groups increases the single-cell performance by more than approximately 20%; thus, the lower water diffusivity, methanol permeability, electro-osmotic drag coefficient and high cell performance indicated that MS-SPEEK is a promising candidate for DMFC applications.

  17. 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.

  18. Structure-activity study on the Phe side chain arrangement of endomorphins using conformationally constrained analogues.

    Science.gov (United States)

    Tömböly, Csaba; Kövér, Katalin E; Péter, Antal; Tourwé, Dirk; Biyashev, Dauren; Benyhe, Sándor; Borsodi, Anna; Al-Khrasani, Mahmoud; Rónai, András Z; Tóth, Géza

    2004-01-29

    Endomorphins-1 and -2 were substituted with all the beta-MePhe stereoisomers in their Phe residues to generate a conformationally constrained peptide set. This series of molecules was subjected to biological assays, and for beta-MePhe(4)-endomorphins-2, a conformational analysis was performed. Incorporation of (2S,3S)-beta-MePhe(4) resulted in the most potent analogues of both endomorphins with enhanced enzymatic stability. Their micro opioid affinities were 4-times higher than the parent peptides, they stimulated [(35)S]GTPgammaS binding, and they were found to be full agonists. NMR experiments revealed that C-terminal (2S,3S)-beta-MePhe in endomorphin-2 strongly favored the gauche (-) spatial orientation which implies the presence of the chi(1) = -60 degrees rotamer of Phe(4) in the binding conformer of endomorphins. Our results emphasize that the appropriate orientation of the C-terminal aromatic side chain of endomorphins is substantial for binding to the micro opioid receptor.

  19. The effect of intermolecular interactions on photoluminescence of a porphyrin side-chain polymer

    Institute of Scientific and Technical Information of China (English)

    Wang Hui; Zhang Wei; Yu Han-Cheng; Huang Jin-Wang; Lin Wei-Zhu; Ji Liang-Nian

    2006-01-01

    Photoluminescence properties and exciton decay dynamics in a porphyrin side-chain polymer, poly[porphyrin acrylate- acrylonitrile (abbreviated p[(por)A-AN]), have been investigated by femtosecond time-resolved photoluminescence spectroscopy. All the luminescences of p[(por)A-AN] films are due to the emissive decay of the photoexcited singlet excitons in the porphyrins. The luminescence efficiencies and lifetimes are increased for samples from pure films to dilute blend films. However, they are increased as the intrachain concentration of the porphyrin sidechain groups is decreased. The intrachain rotation motions of porphyrin sidechain groups result in the initial ultrafast luminescence decays, which are much faster than those due to the interchain interactions. All the samples show no significant red-shift and broadening of the transient luminescence spectra. The interchain and intrachain nonradiative exciton relaxation processes may play an important role in the luminescence dynamics in the p[(por)A-AN] films. The possible origin of different intrachain and interchain dynamic behaviours in p[(por)A-AN] films is discussed.

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

    Science.gov (United States)

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

    2002-08-01

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

  1. Backbone, side chain and heme resonance assignments of cytochrome OmcF from Geobacter sulfurreducens.

    Science.gov (United States)

    Dantas, Joana M; Silva E Sousa, Marta; Salgueiro, Carlos A; Bruix, Marta

    2015-10-01

    Gene knockout studies on Geobacter sulfurreducens (Gs) cells showed that the outer membrane cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) citrate and U(VI) oxide. In addition, microarray analysis of OmcF-deficient mutant versus the wild-type strain revealed that many of the genes with decreased transcript level were those whose expression is upregulated in cells grown with a graphite electrode as electron acceptor. This suggests that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electrical current production by Gs in microbial fuel cells. Extracellular electron transfer processes (EET) constitute nowadays the foundations to develop biotechnological applications in biofuel production, bioremediation and bioenergy. Therefore, the structural characterization of OmcF is a fundamental step to understand the mechanisms underlying EET. Here, we report the complete assignment of the heme proton signals together with (1)H, (13)C and (15)N backbone and side chain assignments of the OmcF, excluding the hydrophobic residues of the N-terminal predicted lipid anchor.

  2. Nucleic acid chemistry in the organic phase: from functionalized oligonucleotides to DNA side chain polymers.

    Science.gov (United States)

    Liu, Kai; Zheng, Lifei; Liu, Qing; de Vries, Jan Willem; Gerasimov, Jennifer Y; Herrmann, Andreas

    2014-10-08

    DNA-incorporating hydrophobic moieties can be synthesized by either solid-phase or solution-phase coupling. On a solid support the DNA is protected, and hydrophobic units are usually attached employing phosphoramidite chemistry involving a DNA synthesizer. On the other hand, solution coupling in aqueous medium results in low yields due to the solvent incompatibility of DNA and hydrophobic compounds. Hence, the development of a general coupling method for producing amphiphilic DNA conjugates with high yield in solution remains a major challenge. Here, we report an organic-phase coupling strategy for nucleic acid modification and polymerization by introducing a hydrophobic DNA-surfactant complex as a reactive scaffold. A remarkable range of amphiphile-DNA structures (DNA-pyrene, DNA-triphenylphosphine, DNA-hydrocarbon, and DNA block copolymers) and a series of new brush-type DNA side-chain homopolymers with high DNA grafting density are produced efficiently. We believe that this method is an important breakthrough in developing a generalized approach to synthesizing functional DNA molecules for self-assembly and related technological applications.

  3. Synthesis and quantitative structure-property relationships of side chain-modified hyodeoxycholic acid derivatives.

    Science.gov (United States)

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

    2013-08-30

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

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

    Directory of Open Access Journals (Sweden)

    Antimo Gioiello

    2013-08-01

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

  5. OPUS-Rota: a fast and accurate method for side-chain modeling.

    Science.gov (United States)

    Lu, Mingyang; Dousis, Athanasios D; Ma, Jianpeng

    2008-09-01

    In this paper, we introduce a fast and accurate side-chain modeling method, named OPUS-Rota. In a benchmark comparison with the methods SCWRL, NCN, LGA, SPRUCE, Rosetta, and SCAP, OPUS-Rota is shown to be much faster than all the methods except SCWRL, which is comparably fast. In terms of overall chi (1) and chi (1+2) accuracies, however, OPUS-Rota is 5.4 and 8.8 percentage points better, respectively, than SCWRL. Compared with NCN, which has the best accuracy in the literature, OPUS-Rota is 1.6 percentage points better for overall chi (1+2) but 0.3 percentage points weaker for overall chi (1). Hence, our algorithm is much more accurate than SCWRL with similar execution speed, and it has accuracy comparable to or better than the most accurate methods in the literature, but with a runtime that is one or two orders of magnitude shorter. In addition, OPUS-Rota consistently outperforms SCWRL on the Wallner and Elofsson homology-modeling benchmark set when the sequence identity is greater than 40%. We hope that OPUS-Rota will contribute to high-accuracy structure refinement, and the computer program is freely available for academic users.

  6. Synthesis, characterisation and drug release properties of microspheres of polystyrene with aliphatic polyester side-chains.

    Science.gov (United States)

    Kukut, Manolya; Karal-Yilmaz, Oksan; Yagci, Yusuf

    2014-01-01

    A series of graft copolymers consisting of polystyrene backbone with biocompatible side chains based on (co)polymers of l-lactic acid and glycolic acid were synthesised by combination two controlled polymerisations, namely, nitroxide mediated radical polymerisation (NMRP) and ring opening polymerisation (ROP) with "Click" chemistry. The main goal of this work was to design new biodegradable microspheres using obtained graft copolymers for long-term sustained release of imatinib mesylate (IMM) as a model drug. The IMM loaded microspheres of the graft copolymers, polystyrene-g-poly(lactide-co-glycolide) (PS-g-PLLGA), polystyrene-g-poly(lactic acid) (PS-g-PLLA) and poly(lactic-coglycolic acid) (PLLGA) were then prepared by a modified water-in-oil-in-water (w1/o/w2) double emulsion/solvent evaporation technique. The optimised microspheres were characterised by particle size, encapsulation efficiency, and surface morphology also; their degradation and release properties were studied in vitro. The degradation studies of three different types of microspheres showed that the PS backbone of the graft copolymers slows down the degradation rate compared to PLLGA.

  7. O-feruloylated, O-acetylated oligosaccharides as side-chains of grass xylans.

    Science.gov (United States)

    Wende, G; Fry, S C

    1997-03-01

    Partial acid hydrolysis of cell wall material from Festuca arundinacea cell cultures yielded a novel O-feruloylated trisaccharide (3). Treatment of 3 with Driselase, which contains beta- but not alpha-D-xylosidase, released xylose plus the known compound, beta-D-xylopyranosyl-(1-->2)-(5-O-feruloyl)-L-arabinose. Since 3 contained one NaIO4-resistant xylose residue, it was concluded to be beta-D-xylopyranosyl-(1-->3)-beta-D-xylopyranosyl-(1--> 2)-(5-O-feruloyl)-L-arabinose. Partial acid hydrolysis of Festuca cell walls also yielded several higher-M(r) feruloylated oligosaccharides, including a feruloylated pentasaccharide, 4 (sugar composition: Ara + Xyl2 + two non-pentose residues) and a feruloylated heptasaccharide, 5 (Ara + Xyl3 + three non-pentose residues). Compounds 4 and 5 were endogenously O-acetylated but 3 was not. Similar or identical compounds were found in hydrolysates of 20 additional species of the Gramineae. These products represent a series of complex side-chains which, in vivo, are attached via Araf residues to the parent xylan. Their possible biological roles are discussed.

  8. Digestion by fungal glycanases of arabinoxylans with different feruloylated side-chains.

    Science.gov (United States)

    Wende, G; Fry, S C

    1997-07-01

    Alcohol-insoluble residues (AIRs) from Festuca and Zea cell cultures contained 7.4 and 35 nmol esterified ferulate mg-1, respectively. Driselase solubilised 79% of the feruloylated material from both AIRs. Of the feruloyl esters solubilised from Festuca and Zea AIRs, 72 and 56% respectively were small enough to be mobile on paper chromatography. The major feruloylated product of Zea AIR was the known 5-O-feruloyl-alpha-L-Araf-(1-->3)-beta-D-Xylp-(1-->4)- D-Xyl (Fer-Ara-Xyl-Xyl). In contrast, the smallest major feruloylated product of Festuca AIR was a feruloyl pentasaccharide (3) containing 3 Xyl, 1 Ara and 1 non-pentose residue (NPR). The Ara and two of the three Xyl groups of 3 were resistant to NaIO4. Mild acid hydrolysis of 3 gave xylobiose, a feruloyl trisaccharide and beta-D-Xylp-(1-->2)-(5-O-feruloyl)-L-Ara. Compound 3 was therefore NPR-(1-->3)-beta-D-Xylp-(1-->2)-(5-O-feruloyl)-alpha-L-Ar af-(1-->3)-beta-D-Xylp-(1-->4)-D-Xyl. We conclude that the complex feruloyl oligosaccharide side-chains of Festuca arabinoxylan do not protect the polysaccharide against hydrolysis by the fungal glycanases present in Driselase.

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

    Science.gov (United States)

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

    2016-01-01

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

  10. Evaluations of Mesogen Orientation in Thin Films of Polyacrylate with Cyanobiphenyl Side Chain.

    Science.gov (United States)

    Tanaka, Daisuke; Mizuno, Tasuku; Hara, Mitsuo; Nagano, Shusaku; Saito, Itsuki; Yamamoto, Katsuhiro; Seki, Takahiro

    2016-04-19

    The orientation behavior of mesogens in a polyacrylate with cyanobiphenyl (CB) side chain in thin films was investigated in detail by UV-vis absorption spectroscopy and grazing incidence small-angle X-ray scattering (GI-SAXS) measurements using both high-energy X-rays of Cu Kα line (λ = 0.154 nm) and low-energy synchrotron X-rays (λ = 0.539 nm). By changing the film thickness ranging 7-200 nm, it is concluded that the planar orientation is predominant for thin films with thickness below 10-15 nm. This planar mesogen orientation near the substrate surface coexists with the homeotropically aligned CB mesogens in films thicker than 30 nm. For the thinnest 7 nm film, the planar orientation is unexpectedly lost, which is in consort with a disordering of smectic layer structure. Peculiar orienting characteristics of CB mesogen are suggested, which probably stem from the tendency to form an antiparallel arrangement of mesogens due to the strong dipole moment of the terminal cyano group.

  11. Azapeptide Synthesis Methods for Expanding Side-Chain Diversity for Biomedical Applications.

    Science.gov (United States)

    Chingle, Ramesh; Proulx, Caroline; Lubell, William D

    2017-07-18

    Mimicry of bioactive conformations is critical for peptide-based medicinal chemistry because such peptidomimetics may augment stability, enhance affinity, and increase specificity. Azapeptides are peptidomimetics in which the α-carbon(s) of one or more amino acid residues are substituted by nitrogen. The resulting semicarbazide analogues have been shown to reinforce β-turn conformation through the combination of lone pair-lone pair repulsion of the adjacent hydrazine nitrogen and urea planarity. Substitution of a semicarbazide for an amino amide residue in a peptide may retain biological activity and add benefits such as improved metabolic stability. The applications of azapeptides include receptor ligands, enzyme inhibitors, prodrugs, probes, and imaging agents. Moreover, azapeptides have proven therapeutic utility. For example, the aza-glycinamide analogue of the luteinizing hormone-releasing hormone analogue Zoladex is a potent long-acting agonist currently used in the clinic for the treatment of prostate and breast cancer. However, the use of azapeptides was hampered by tedious solution-phase synthetic routes for selective hydrazine functionalization. A remarkable stride to overcome this bottleneck was made in 2009 through the introduction of the submonomer procedure for azapeptide synthesis, which enabled addition of diverse side chains onto a common semicarbazone intermediate, providing a means to construct azapeptide libraries by solution- and solid-phase chemistry. In brief, aza residues are introduced into the peptide chain using the submonomer strategy by semicarbazone incorporation, deprotonation, N-alkylation, and orthogonal deprotection. Amino acylation of the resulting semicarbazide and elongation gives the desired azapeptide. Since the initial report, a number of chemical transformations have taken advantage of the orthogonal chemistry of semicarbazone residues (e.g., Michael additions and N-arylations). In addition, libraries have been synthesized

  12. Side-chain engineering of benzodithiophene-fluorinated quinoxaline low-band-gap co-polymers for high-performance polymer solar cells.

    Science.gov (United States)

    Xu, Xiaopeng; Wu, Yulei; Fang, Junfeng; Li, Zuojia; Wang, Zhenguo; Li, Ying; Peng, Qiang

    2014-10-06

    A new series of donor-acceptor co-polymers based on benzodithiophene and quinoxaline with various side chains have been developed for polymer solar cells. The effect of the degree of branching and dimensionality of the side chains were systematically investigated on the thermal stability, optical absorption, energy levels, molecular packing, and photovoltaic performance of the resulting co-polymers. The results indicated that the linear and 2D conjugated side chains improved the thermal stabilities and optical absorptions. The introduction of alkylthienyl side chains could efficiently lower the energy levels compared with the alkoxyl-substituted analogues, and the branched alkoxyl side chains could deepen the HOMO levels relative to the linear alkoxyl chains. The branched alkoxyl groups induced better lamellar-like ordering, but poorer face-to-face packing behavior. The 2D conjugated side chains had a negative influence on the crystalline properties of the co-polymers. The performance of the devices indicated that the branched alkoxyl side chains improved the Voc, but decreased the Jsc and fill factor (FF). However, the 2D conjugated side chains would increase the Voc, Jsc, and FF simultaneously. For the first time, our work provides insight into molecular design strategies through side-chain engineering to achieve efficient polymer solar cells by considering both the degree of branching and dimensionality. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Quantifying millisecond time-scale exchange in proteins by CPMG relaxation dispersion NMR spectroscopy of side-chain carbonyl groups

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, Alexandar L.; Kay, Lewis E., E-mail: kay@pound.med.utoronto.ca [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)

    2011-08-15

    A new pulse sequence is presented for the measurement of relaxation dispersion profiles quantifying millisecond time-scale exchange dynamics of side-chain carbonyl groups in uniformly {sup 13}C labeled proteins. The methodology has been tested using the 87-residue colicin E7 immunity protein, Im7, which is known to fold via a partially structured low populated intermediate that interconverts with the folded, ground state on the millisecond time-scale. Comparison of exchange parameters extracted for this folding 'reaction' using the present methodology with those obtained from more 'traditional' {sup 15}N and backbone carbonyl probes establishes the utility of the approach. The extracted excited state side-chain carbonyl chemical shifts indicate that the Asx/Glx side-chains are predominantly unstructured in the Im7 folding intermediate. However, several crucial salt-bridges that exist in the native structure appear to be already formed in the excited state, either in part or in full. This information, in concert with that obtained from existing backbone and side-chain methyl relaxation dispersion experiments, will ultimately facilitate a detailed description of the structure of the Im7 folding intermediate.

  14. Attenuating HIV Tat/TAR-mediated protein expression by exploring the side chain length of positively charged residues.

    Science.gov (United States)

    Wu, Cheng-Hsun; Chen, Yi-Ping; Liu, Shing-Lung; Chien, Fan-Ching; Mou, Chung-Yuan; Cheng, Richard P

    2015-12-07

    RNA is a drug target involved in diverse cellular functions and viral processes. Molecules that inhibit the HIV TAR RNA-Tat protein interaction may attenuate Tat/TAR-dependent protein expression and potentially serve as anti-HIV therapeutics. By incorporating positively charged residues with mixed side chain lengths, we designed peptides that bind TAR RNA with enhanced intracellular activity. Tat-derived peptides that were individually substituted with positively charged residues with varying side chain lengths were evaluated for TAR RNA binding. Positively charged residues with different side chain lengths were incorporated at each Arg and Lys position in the Tat-derived peptide to enhance TAR RNA binding. The resulting peptides showed enhanced TAR RNA binding affinity, cellular uptake, nuclear localization, proteolytic resistance, and inhibition of intracellular Tat/TAR-dependent protein expression compared to the parent Tat-derived peptide with no cytotoxicity. Apparently, the enhanced inhibition of protein expression by these peptides was not determined by RNA binding affinity, but by proteolytic resistance. Despite the high TAR binding affinity, a higher binding specificity would be necessary for practical purposes. Importantly, altering the positively charged residue side chain length should be a viable strategy to generate potentially useful RNA-targeting bioactive molecules.

  15. Mixed mono- and multilayers of poly(isocyanide)s with non-linear optically active side chains

    NARCIS (Netherlands)

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

    1994-01-01

    The properties and structure of Langmuir-Blodgett mono- and multilayers of several poly(isocyanide)s with non-linear optically active side-chains were studied. These polymers formed very rigid layers or layers which appeared to be unstable. To circumvent this problem they were mixed with other poly(

  16. Predicting the side-chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models.

    Science.gov (United States)

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

    2014-10-01

    The side-chain dihedral angle distributions of all amino acids have been measured from myriad high-resolution protein crystal structures. However, we do not yet know the dominant interactions that determine these distributions. Here, we explore to what extent the defining features of the side-chain dihedral angle distributions of different amino acids can be captured by a simple physical model. We find that a hard-sphere model for a dipeptide mimetic that includes only steric interactions plus stereochemical constraints is able to recapitulate the key features of the back-bone dependent observed amino acid side-chain dihedral angle distributions of Ser, Cys, Thr, Val, Ile, Leu, Phe, Tyr, and Trp. We find that for certain amino acids, performing the calculations with the amino acid of interest in the central position of a short α-helical segment improves the match between the predicted and observed distributions. We also identify the atomic interactions that give rise to the differences between the predicted distributions for the hard-sphere model of the dipeptide and that of the α-helical segment. Finally, we point out a case where the hard-sphere plus stereochemical constraint model is insufficient to recapitulate the observed side-chain dihedral angle distribution, namely the distribution P(χ₃) for Met.

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

    NARCIS (Netherlands)

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

    1993-01-01

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

  18. 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

    1993-01-01

    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

  19. 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 ...

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

    NARCIS (Netherlands)

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

    2009-01-01

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

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

    Science.gov (United States)

    Westereng, Bjorge; Coenen, Gerd Jan; Michaelsen, Terje Einar; Voragen, Alphons G J; Samuelsen, Anne Berit; Schols, Henk A; Knutsen, Svein Halvor

    2009-06-01

    A mixture of single side chains from white cabbage pectin were obtained by anion exchange chromatography after applying mild chemical conditions promoting beta-elimination. These pectin fragments were characterized by their molecular weight distribution, sugar composition, 13C-NMR, and MALDI-TOF-MS analysis. These analyses revealed that the large oligosaccharides released by beta-eliminative treatment were composed of alpha-1,5 linked arabinosyl residues with 2- and 3-linked alpha-arabinosyl side chains, and, or beta-1,4 linked galactosyl side chains. Fractions were tested for complement-fixing activity in order to determine their interaction with the complement system. These results strongly indicated that there was a minimal unit size responsible for the complement-fixing activity. Neutral pectin fragments (8 kDa) obtained from beta-elimination were inactive in the complement system, although they contained a sugar composition previously shown to be highly active. Larger pectin fragments (17 kDa) retained some activity, but much lower than polymers containing rhamnogalacturonan type 1 (RGI) structures isolated from the same source. This implied that structural elements containing multiple side chains is necessary for efficient complement-fixing activity.

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

    DEFF Research Database (Denmark)

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

    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 n...

  3. A protocol for CABS-dock protein-peptide docking driven by side-chain contact information.

    Science.gov (United States)

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

    2017-08-18

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

  4. The isotridecanyl side chain of plusbacin-A3 is essential for the transglycosylase inhibition of peptidoglycan biosynthesis.

    Science.gov (United States)

    Kim, Sung Joon; Singh, Manmilan; Wohlrab, Aaron; Yu, Tsyr-Yan; Patti, Gary J; O'Connor, Robert D; VanNieuwenhze, Michael; Schaefer, Jacob

    2013-03-19

    Plusbacin-A3 (pb-A3) is a cyclic lipodepsipeptide that exhibits antibacterial activity against multidrug-resistant Gram-positive pathogens. Plusbacin-A3 is thought not to enter the cell cytoplasm, and its lipophilic isotridecanyl side chain is presumed to insert into the membrane bilayer, thereby facilitating either lipid II binding or some form of membrane disruption. Analogues of pb-A3, [(2)H]pb-A3 and deslipo-pb-A3, were synthesized to test membrane insertion as a key to the mode of action. [(2)H]pb-A3 has an isotopically (2)H-labeled isopropyl subunit of the lipid side chain, and deslipo-pb-A3 is missing the isotridecanyl side chain. Both analogues have the pb-A3 core structure. The loss of antimicrobial activity in deslipo-pb-A3 showed that the isotridecanyl side chain is crucial for the mode of action of the drug. However, rotational-echo double-resonance nuclear magnetic resonance characterization of [(2)H]pb-A3 bound to [1-(13)C]glycine-labeled whole cells of Staphylococcus aureus showed that the isotridecanyl side chain does not insert into the lipid membrane but instead is found in the staphylococcal cell wall, positioned near the pentaglycyl cross-bridge of the cell-wall peptidoglycan. Addition of [(2)H]pb-A3 during the growth of S. aureus resulted in the accumulation of Park's nucleotide, consistent with the inhibition of the transglycosylation step of peptidoglycan biosynthesis.

  5. Amphiphilic surface active triblock copolymers with mixed hydrophobic and hydrophilic side chains for tuned marine fouling-release properties.

    Science.gov (United States)

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

    2010-06-15

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

  6. Protein side-chain packing problem: is there still room for improvement?

    Science.gov (United States)

    Colbes, José; Corona, Rosario I; Lezcano, Christian; Rodríguez, David; Brizuela, Carlos A

    2016-08-26

    The protein side-chain packing problem (PSCPP) is an important subproblem of both protein structure prediction and protein design. During the past two decades, a large number of methods have been proposed to tackle this problem. These methods consist of three main components: a rotamer library, a scoring function and a search strategy. The average overall accuracy level obtained by these methods is approximately 87%. Whether a better accuracy level could be achieved remains to be answered. To address this question, we calculated the maximum accuracy level attainable using a simple rotamer library, independently of the energy function or the search method. Using 2883 different structures from the Protein Data Bank, we compared this accuracy level with the accuracy level of five state-of-the-art methods. These comparisons indicated that, for buried residues in the protein, we are already close to the best possible accuracy results. In addition, for exposed residues, we found that a significant gap exists between the possible improvement and the maximum accuracy level achievable with current methods. After determining that an improvement is possible, the next step is to understand what limitations are preventing us from obtaining such an improvement. Previous works on protein structure prediction and protein design have shown that scoring function inaccuracies may represent the main obstacle to achieving better results for these problems. To show that the same is true for the PSCPP, we evaluated the quality of two scoring functions used by some state-of-the-art algorithms. Our results indicate that neither of these scoring functions can guide the search method correctly, thereby reinforcing the idea that efforts to solve the PSCPP must also focus on developing better scoring functions. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2002-08-15

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

  8. Hydrophobic side chain dynamics of a glutamate receptor ligand binding domain.

    Science.gov (United States)

    Maltsev, Alexander S; Oswald, Robert E

    2010-03-26

    Ionotropic glutamate receptors are ligand-gated ion channels that mediate much of the fast excitatory neurotransmission in the central nervous system. The extracellular ligand binding core (S1S2) of the GluR2 subtype of ionotropic glutamate receptors can be produced as a soluble protein with properties essentially identical to the corresponding domain in the intact, membrane-bound protein. Using a variety of biophysical techniques, much has been learned about the structure and dynamics of S1S2 and the relationship between its ligand-induced conformational changes and the function of the receptor. It is clear that dynamic processes are essential to the function of ionotropic glutamate receptors. We have isotopically labeled side chain methyls of GluR2 S1S2 and used NMR spectroscopy to study their dynamics on the ps-ns and mus-ms time scales. Increased disorder is seen in regions that are part of the key dimer interface in the intact protein. When glutamate is bound, the degree of ps-ns motion is less than that observed with other ligands, suggesting that the physiological agonist binds to a preformed binding site. At the slower time scales, the degree of S1S2 flexibility induced by ligand binding is greatest for willardiine partial agonists, least for antagonists, and intermediate for full agonists. Notable differences among bound ligands are in the region of the protein that forms a hinge between two lobes that close upon agonist binding, and along the beta-sheet in Lobe 2. These motions provide clues as to the functional properties of partial agonists and to the conformational changes associated with lobe closure and channel activation.

  9. Enhancing the Performance of Polymer Solar Cells by Using Donor Polymers Carrying Discretely Distributed Side Chains.

    Science.gov (United States)

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

    2017-07-19

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

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

    Science.gov (United States)

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

    2016-05-01

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

  11. OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.

    Science.gov (United States)

    Lu, Mingyang; Dousis, Athanasios D; Ma, Jianpeng

    2008-02-08

    Here we report an orientation-dependent statistical all-atom potential derived from side-chain packing, named OPUS-PSP. It features a basis set of 19 rigid-body blocks extracted from the chemical structures of all 20 amino acid residues. The potential is generated from the orientation-specific packing statistics of pairs of those blocks in a non-redundant structural database. The purpose of such an approach is to capture the essential elements of orientation dependence in molecular packing interactions. Tests of OPUS-PSP on commonly used decoy sets demonstrate that it significantly outperforms most of the existing knowledge-based potentials in terms of both its ability to recognize native structures and consistency in achieving high Z-scores across decoy sets. As OPUS-PSP excludes interactions among main-chain atoms, its success highlights the crucial importance of side-chain packing in forming native protein structures. Moreover, OPUS-PSP does not explicitly include solvation terms, and thus the potential should perform well when the solvation effect is difficult to determine, such as in membrane proteins. Overall, OPUS-PSP is a generally applicable potential for protein structure modeling, especially for handling side-chain conformations, one of the most difficult steps in high-accuracy protein structure prediction and refinement.

  12. When function follows form: effects of donor copolymer side chains on film morphology and BHJ solar cell performance

    Energy Technology Data Exchange (ETDEWEB)

    Szarko, Jodi M.; Rolczynski, Brian S.; Chen, Lin X. [Department of Chemistry, Northwestern University, Evanston, Illinois 60208 (United States); Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 (United States); Guo, Jianchang [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 (United States); Department of Chemistry and The James Franck Institute, The University of Chicago, 929 E 57th Street, Chicago, IL 60637 (United States); Liang, Yongye; Xu, Tao; Yu, Luping [Department of Chemistry and The James Franck Institute, The University of Chicago, 929 E 57th Street, Chicago, IL 60637 (United States); Lee, Byeongdu; Strzalka, Joseph [X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 (United States); Loser, Stephen; Marks, Tobin J. [Department of Chemistry, Northwestern University, Evanston, Illinois 60208 (United States); Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 (United States)

    2010-12-21

    Detailed structural organization in organic films are investigated using grazing incidence X-ray scattering (GIXS) methods. The key structural features are revealed and the influence of specific side chain positions and shapes are characterized. A correlation between the fill factor (FF) of the corresponding device and the tightness of the polymer chain stacking inspires a new set of structural parameters for design of materials to optimize device efficiency. (Copyright copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  13. Structure control for fine tuning fluorescence emission from side-chain azobenzene polymers.

    Science.gov (United States)

    Smitha, P; Asha, S K

    2007-06-14

    New fluorescent azobenzene dyes and side-chain polymers have been synthesized and characterized and their photophysical properties studied. A series of azobenzene dyes having different fluorophores such as phenol (S1), phenylphenol (S2) and naphthol (S3) incorporated in them were synthesized. S2 had unusually high fluorescence with a quantum yield of phi f = 0.2 recorded in dichloromethane (DCM), whereas S1 and S3 were found to be weakly fluorescent. The azobenzene dyes were converted into methacrylate monomers having short ethyleneoxy spacers and then free radically polymerized. Phenylphenol-based azobenzene polymer (P2) continued to show fluorescence, whereas fluorescence was completely quenched in the case of phenol (P1)- and naphthol (P3)-based polymers. Phenylphenol, though twisted in the ground state is known to have a more planar geometry in the excited state--a factor that enables it to retain its fluorescence behavior even when it is incorporated as part of an azobenzene unit. In contrast, naphthol, which is a better fluorophore compared to phenylphenol, loses much of its emissive behavior upon coupling to the azobenzene unit. The extent of trans to cis photoisomerization in solution was very low (approximately 17%) for P2 after 30 min of continuous irradiation using 365 nm light, in contrast to approximately 40% for P1 under identical conditions. This is attributed to the steric repulsion brought about by the bulky phenylphenol units that restrict rotation. A 2-fold enhancement in fluorescence emission was observed for P2 upon irradiation by UV light at 360 nm, which relaxed to the original intensity in about 7 day's time. The higher emission of the cis azobenzenes is generally attributed to an inhibition of photoinduced electron transfer (PET) mechanism. The emission of P2 showed a concentration dependence which increased initially and then decreased in intensity with the formation of a new red-shifted peak at higher concentration due to aggregation

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

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

  15. Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids.

    Science.gov (United States)

    Öjemalm, Karin; Higuchi, Takashi; Lara, Patricia; Lindahl, Erik; Suga, Hiroaki; von Heijne, Gunnar

    2016-09-20

    Cotranslational translocon-mediated insertion of membrane proteins into the endoplasmic reticulum is a key process in membrane protein biogenesis. Although the mechanism is understood in outline, quantitative data on the energetics of the process is scarce. Here, we have measured the effect on membrane integration efficiency of nonproteinogenic analogs of the positively charged amino acids arginine and lysine incorporated into model transmembrane segments. We provide estimates of the influence on the apparent free energy of membrane integration (ΔGapp) of "snorkeling" of charged amino acids toward the lipid-water interface, and of charge neutralization. We further determine the effect of fluorine atoms and backbone hydrogen bonds (H-bonds) on ΔGapp These results help establish a quantitative basis for our understanding of membrane protein assembly in eukaryotic cells.

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

    OpenAIRE

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

    2012-01-01

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

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

    OpenAIRE

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

    2012-01-01

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

  18. Purification and side chain selective chemical modifications of glutamate dehydrogenase from Bacillus subtilis natto.

    Science.gov (United States)

    Ni, Yinyun; Wang, Jiale; Qian, Bingjun; Song, Guangyan; Yao, Xiaomin; Zhang, Jian-hua

    2014-04-01

    Glutamate dehydrogenase (GDH) from Bacillus subtilis natto was purified to apparent homogeneity by ammonium sulfate precipitation, ion-exchange chromatography, size exclusion chromatography, and hydroxyapatite (HA) affinity chromatography. The GDH was purified 34-fold, with a yield of 41 % of total activity and a specific activity of 34.29 U/mg proteins. The molecular weight (Mr) of was measured at 47 kDa with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and 264 kDa with high-performance liquid chromatography (HPLC). The optimum pH and temperature for the deammoniation reaction were measured to be 7.5 and 30 °C, respectively. The active-site amino acid residues of GDH were investigated by chemical modification. The compounds 2,4,6-trinitrobenzenesulfonic acid (TNBS), phenylglyoxal (PG), and phenylmethanesulfonyl fluoride (PMSF) were used to modify lysine, arginine, and serine active site residues, respectively. After treatment with modifying reagents at concentrations of 1 mM, GDH activity fell to 10.7 % with TNBS, 83.3 % with PG, and 12.8 % with PMSF. However, with substrate protection, there was almost no loss in GDH activity following treatment with any modifying reagent. The kinetic parameters K m and V max were determined in each case. K m values for native GDH, 50 % TNBS-inactivated GDH, and 50 % PMSF-inactivated GDH were 0.037, 0.104, and 0.017 mM, respectively. V max values were 0.048, 0.022, and 0.031 mM/s, respectively. These results suggest that the active site contains one or more lysine residues that play a role in substrate binding and one or more serine residues that may maintain the enzyme conformation. However, arginine residues played less of a role in the activity of GDH.

  19. Specific Interactions of Neutral Side Chains of an Adsorbed Protein with the Surface of α-Quartz and Silica Gel.

    Science.gov (United States)

    Odinokov, Alexey V; Bagaturyants, Alexander A

    2015-07-16

    Many key features of the protein adsorption on the silica surfaces still remain unraveled. One of the open questions is the interaction of nonpolar side chains with siloxane cavities. Here, we use nonequilibrium molecular dynamics simulations for the detailed investigation of the binding of several hydrophobic and amphiphilic protein side chains with silica surface. These interactions were found to be a possible driving force for protein adsorption. The free energy gain was larger for the disordered surface of amorphous silica gel as compared to α-quartz, but the impact depended on the type of amino acid. The dependence was analyzed from the structural point of view. For every amino acid an enthalpy-entropy compensation behavior was observed. These results confirm a hypothesis of an essential role of hydrophobic interactions in protein unfolding and irreversible adsorption on the silica surface.

  20. 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.

  1. Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for Aromatic-Aromatic Side Chain Interactions in Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Valdes, Haydee; Pluhackova, Kristyna; Hobza, Pavel

    2009-09-08

    The performance of a wide range of quantum chemical calculations for the ab initio study of realistic model systems of aromatic-aromatic side chain interactions in proteins (in particular those π-π interactions occurring between adjacent residues along the protein sequence) is here assessed on the phenylalanyl-glycyl-phenylalanine (FGF) tripeptide. Energies and geometries obtained at different levels of theory are compared with CCSD(T)/CBS benchmark energies and RI-MP2/cc-pVTZ benchmark geometries, respectively. Consequently, a protocol of calculation alternative to the very expensive CCSD(T)/CBS is proposed. In addition to this, the preferred orientation of the Phe aromatic side chains is discussed and compared with previous results on the topic.

  2. Triazine-Based Sequence-Defined Polymers with Side-Chain Diversity and Backbone-Backbone Interaction Motifs.

    Science.gov (United States)

    Grate, Jay W; Mo, Kai-For; Daily, Michael D

    2016-03-14

    Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone-backbone interactions, including H-bonding motifs and pi-pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone-backbone hydrogen-bonding motifs, and will thus enable new macromolecules and materials with useful functions.

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

    CERN Document Server

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

    2010-01-01

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

  4. Tuning structural and mechanical properties of two-dimensional molecular crystals: the roles of carbon side chains.

    Science.gov (United States)

    Cun, Huanyao; Wang, Yeliang; Du, Shixuan; Zhang, Lei; Zhang, Lizhi; Yang, Bing; He, Xiaobo; Wang, Yue; Zhu, Xueyan; Yuan, Quanzi; Zhao, Ya-Pu; Ouyang, Min; Hofer, Werner A; Pennycook, Stephen J; Gao, Hong-jun

    2012-03-14

    A key requirement for the future applicability of molecular electronics devices is a resilience of their properties to mechanical deformation. At present, however, there is no fundamental understanding of the origins of mechanical properties of molecular films. Here we use quinacridone, which possesses flexible carbon side chains, as a model molecular system to address this issue. Eight molecular configurations with different molecular coverage are identified by scanning tunneling microscopy. Theoretical calculations reveal quantitatively the roles of different molecule-molecule and molecule-substrate interactions and predict the observed sequence of configurations. Remarkably, we find that a single Young's modulus applies for all configurations, the magnitude of which is controlled by side chain length, suggesting a versatile avenue for tuning not only the physical and chemical properties of molecular films but also their elastic properties.

  5. 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.

  6. 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 explore the structure essential for the catalysis in 26 kDa endochitinase from barley seeds, we calculated theoretical pKa values of the ionizable groups based on the crystal structure, and then the roles of ionizable side chains located near the catalytic residue were examined by site......-25640]; hence, this type of interaction seems to be at least partly conserved in the catalytic cleft of other glycosyl hydrolases....

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    used short peptides as a model system for intrinsically disordered proteins. Linear free-energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate...... governed by their association rate constants. Instead, we observe the opposite for peptide-PDZ interactions, namely that changes in Kd correlate with changes in koff....

  8. One-sided time constraints routing problem in supply chain management- An Ant colony optimization based heuristic

    OpenAIRE

    2013-01-01

    Transportation costs constitute a significant fraction of total logistics cost in Supply Chain Management (SCM). To reduce transportation costs, improve customer service and to achieve maximum customer satisfaction, the optimal selection of the vehicle route is a frequent decision problem and this is commonly known as vehicle routing problem. Vehicle routing problem with one-sided time constraint, where the delivery of products from depots to distribution centers has to take place within the ...

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

    Energy Technology Data Exchange (ETDEWEB)

    Vöge, Andrea, E-mail: andreavoege@online.de [Department of Chemistry, University of Patras, 26500 Patras (Greece); Deimede, Valadoula, E-mail: deimede@upatras.gr [Department of Chemistry, University of Patras, 26500 Patras (Greece); Paloukis, Fotis; Neophytides, Stylianos G. [Foundation of Research and Technology – Hellas, Institute of Chemical Engineering Sciences (FORTH/ICE-HT), Patras 26504 (Greece); Kallitsis, Joannis K. [Department of Chemistry, University of Patras, 26500 Patras (Greece)

    2014-11-14

    Polymer electrolytes consisting of polar pyridine units in the backbone and poly(ethylene oxide) (PEO) side chains are designed for possible application in lithium ion batteries. In particular, aromatic polyethers bearing PEO side chains with varying length are synthesized either by copolymerization of the corresponding PEO based diols with different arylfluorides or by modification of dihydroxyl functionalized precursor polymers with poly(ethylene oxide) methyl ether tosylate. The formation of free standing films is dependent on the PEO content, polymers' composition as well as on the different monomers used. The mechanical properties study shows that the glass transition temperature can be controlled by varying the PEO content. Thermal stability is also influenced by the PEO length: the shorter the PEO side chain, the higher the stability. XRD analysis gives information about the desired amorphous character of these polymers, which is independent of the PEO content. Solid polymer electrolytes prepared by blending the PEO-based polymers with lithium salt and PEO 2000 (used as plasticizer) show ambient temperature conductivities in the range of 10{sup −6} S/cm. To further improve conductivity doping of PEO-based polymers in liquid electrolyte (1 M LiPF{sub 6} in EC/DMC 1/1) in some cases results in high conductivities in the range of 10{sup −3} S cm{sup −1} at 80 °C. - Highlights: • Polymer electrolytes bearing PEO side chains of varying lengths were designed. • DMA and TGA show that T{sub g} and T{sub d} can be controlled by varying the PEO content. • XRD confirms polymers amorphous character, independent of the PEO content. • Membranes doped in liquid electrolyte have high conductivities (10{sup −3} S cm{sup −1}, 80 °C)

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

    Science.gov (United States)

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

    2016-05-25

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2006-01-01

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

  12. The influence of poly(phenyleneethynylene) side chain structure on single-walled carbon nanotubes hybrid photovoltaic cells.

    Science.gov (United States)

    Mao, Jie; Liu, Qian; Wang, Shujing; Lv, Xin; Huang, Yi; Ma, Yanfeng; Chen, Yongsheng; Yin, Shougen

    2008-07-01

    A novel poly(phenyleneethynylene)/single walled carbon nanotubes (SWNTs) donor-acceptor nanohybrid system was constructed based on the bulk heterojunction concept, and their photovoltaic (PV) properties were studied. Comparing with that of the pristine polymer poly(phenyleneethynylene) (PPE) device, the PV performance of the SWNTs/PPE hybrid is dramatically improved. The origin of open-circuit voltage (V(oc)) of the pristine polymer PPE device and SWNTs/PPE device was explained by metal-insulator-metal (MIM) diode model and pinning mechanism, respectively. Furthermore, incorporation of sensitizing groups to the side chain of PPE has great effect on the photovoltaic cell performance based on these hybrid materials and both the short-circuit current density (I(sc)) and power conversion efficiency are significantly enhanced. It is proposed that the main reason for the increase of short circuit current is due to efficient transfer of holes by sensitizer to PPE backbone and the transfer of electrons to the SWNTs. The power conversion efficiency is enhanced by approximately 1 order magnitude to 0.031% for the device based on the PPE3 with anthracene sensitizer group on the side chain compared with that (4.2 x 10(-3)% for SWNTs/PPE1 and 6.2 x 10(-3)% for SWNTs/PPE2) of the device without anthracene sensitizer on the side chain.

  13. Molecular structure of an alkyl-side-chain polymer-water interface: origins of contact angle hysteresis.

    Science.gov (United States)

    Rangwalla, Hasnain; Schwab, Alexander D; Yurdumakan, Betül; Yablon, Dalia G; Yeganeh, Mohsen S; Dhinojwala, Ali

    2004-09-28

    A new and direct approach to verify surface heterogeneity as the microscopic origin of contact-angle hysteresis is demonstrated. IR-visible sum-frequency-generation spectroscopy (SFG) was used to selectively probe the molecules at the interface of an alkyl-side-chain polymer [poly(vinyl n-octadecyl carbamate-co-vinyl acetate)] with water. The spectra indicate that in contact with water, the polymer surface is heterogeneous (having areas of differing surface energies). This evidence of surface heterogeneity supports the hysteresis observed in the advancing and receding contact angles of the polymer surface with water. The same measurements made for the chemically and structurally similar surface of an octadecyltrichlorosilane self-assembled monolayer indicates a homogeneous surface at the water interface. In this case, contact-angle hysteresis measurements implicate surface roughness as the cause of hysteresis. Atomic force microscopy measurements of roughness for these surfaces further support our conclusions. The polymer-water interface was probed using SFG at above-ambient temperatures, and an order-to-disorder transition (ODT) of alkyl side chains at the interface was observed, which closely follows the melting of crystalline side chains in the bulk. This transition explains the increased wettability of the polymer, by water, when the temperature is raised above the bulk melting temperature. Furthermore, the irreversibility of this ODT suggests that the disordered polymer-water interface is the thermodynamic equilibrium state, whereas the before-heating structure of this interface is a kinetically hindered metastable state.

  14. Water, proton, and oxygen transport in high IEC, short side chain PFSA ionomer membranes: consequences of a frustrated network.

    Science.gov (United States)

    Luo, Xiaoyan; Holdcroft, Steven; Mani, Ana; Zhang, Yongming; Shi, Zhiqing

    2011-10-28

    The effect of ion exchange capacity (IEC) on the water sorption properties of high IEC, short side chain (SSC) PFSA ionomer membranes, and the relationships between water content, proton conductivity, proton mobility, water permeation, oxygen diffusion, and oxygen permeation are investigated. SSC PFSA ionomer membranes possessing 1.3, 1.4, and 1.5 mmol g(-1) IEC are compared to a series of long side chain (LSC) PFSA ionomer membranes ranging in IEC from 0.9 to 1.13 mmol g(-1). At 25 °C, fully-hydrated SSC ionomer membranes are characterized as possessing higher water contents (56-75 vol%), moderate λ values (15-18), high analytical acid concentrations (2-2.8 M), and moderate conductivity (88-115 mS/cm); but lower than anticipated effective proton mobility. Complementary measurements of water permeability, oxygen diffusion, and oxygen permeability also yield lower than expected values given their much higher water contents. Potential benefits afforded by reducing the side chain length of PFSA ionomer membranes, such as increased crystallinity, higher IEC, and high hydrated acid concentration are offset by a less-developed, frustrated hydrophilic percolation network, which provides a motivation for future improvements of transport properties for this class of material. This journal is © the Owner Societies 2011

  15. 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.

  16. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1980-06-01

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

  18. Differences in lysine pKa values may be used to improve NMR signal dispersion in reductively methylated proteins

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, Sherwin J. [University of Illinois at Chicago, Department of Biochemistry and Molecular Genetics (United States); Kobayashi, Tomoyoshi; John Solaro, R. [University of Illinois at Chicago, Department of Physiology and Biophysics, Center for Cardiovascular Research (United States); Gaponenko, Vadim [University of Illinois at Chicago, Department of Biochemistry and Molecular Genetics (United States)], E-mail: vadimg@uic.edu

    2009-04-15

    Reductive methylation of lysine residues in proteins offers a way to introduce {sup 13}C methyl groups into otherwise unlabeled molecules. The {sup 13}C methyl groups on lysines possess favorable relaxation properties that allow highly sensitive NMR signal detection. One of the major limitations in the use of reductive methylation in NMR is the signal overlap of {sup 13}C methyl groups in NMR spectra. Here we show that the uniform influence of the solvent on chemical shifts of exposed lysine methyl groups could be overcome by adjusting the pH of the buffering solution closer to the pKa of lysine side chains. Under these conditions, due to variable pKa values of individual lysine side chains in the protein of interest different levels of lysine protonation are observed. These differences are reflected in the chemical shift differences of methyl groups in reductively methylated lysines. We show that this approach is successful in four different proteins including Ca{sup 2+}-bound Calmodulin, Lysozyme, Ca{sup 2+}-bound Troponin C, and Glutathione S-Transferase. In all cases significant improvement in NMR spectral resolution of methyl signals in reductively methylated proteins was obtained. The increased spectral resolution helps with more precise characterization of protein structural rearrangements caused by ligand binding as shown by studying binding of Calmodulin antagonist trifluoperazine to Calmodulin. Thus, this approach may be used to increase resolution in NMR spectra of {sup 13}C methyl groups on lysine residues in reductively methylated proteins that enhances the accuracy of protein structural assessment.

  19. Characterization of the deoxyguanosine-lysine cross-link of methylglyoxal.

    Science.gov (United States)

    Petrova, Katya V; Millsap, Amy D; Stec, Donald F; Rizzo, Carmelo J

    2014-06-16

    Methylglyoxal is a mutagenic bis-electrophile that is produced endogenously from carbohydrate precursors. Methylglyoxal has been reported to induce DNA-protein cross-links (DPCs) in vitro and in cultured cells. Previous work suggests that these cross-links are formed between guanine and either lysine or cysteine side chains. However, the chemical nature of the methylglyoxal induced DPC have not been determined. We have examined the reaction of methylglyoxal, deoxyguanosine (dGuo), and Nα-acetyllysine (AcLys) and determined the structure of the cross-link to be the N2-ethyl-1-carboxamide with the lysine side chain amino group (1). The cross-link was identified by mass spectrometry and the structure confirmed by comparison to a synthetic sample. Further, the cross-link between methylglyoxal, dGuo, and a peptide (AcAVAGKAGAR) was also characterized. The mechanism of cross-link formation is likely to involve an Amadori rearrangement.

  20. 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

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

    KAUST Repository

    Zhang, Ning

    2012-04-17

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

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

    Science.gov (United States)

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

    2013-07-16

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

  3. Job Vacancy Chains and Local Employment Creation; the Case of Supply-Side Restrictions

    OpenAIRE

    Felsenstein, Daniel; Persky, Joseph

    2006-01-01

    The job-chains model of local labor market change is a demand-driven analytic device for estimating the effects of new job creation. This paper explores the effects of restricting supply, i.e. limiting job access, on the model’s primary outcomes: vacancy chain multipliers, welfare effects and distributional impacts. Major sources of labor supply are the local unemployed, out of the labor force and in-migrants. Three simulations are reported relating to 1) restricting new jobs to current loc...

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

    Science.gov (United States)

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

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

    DEFF Research Database (Denmark)

    Hvilsted, Søren; Pedersen, M; Holme, NCR

    1998-01-01

    on azobenzene, iii- the methylene main-chain segment length, and iv-the polyester molecular mass, all influence the optical storage properties. A general synthetic route to novel mesogenic azobenzene diols comprising parameters i and ii is outlined. Polyesters with molecular masses (parameter iv) up to 100...

  6. Decomposition of total solvation energy into core, side-chains and water contributions: Role of cross correlations and protein conformational fluctuations in dynamics of hydration layer

    Science.gov (United States)

    Mondal, Sayantan; Mukherjee, Saumyak; Bagchi, Biman

    2017-09-01

    Dynamical coupling between water and amino acid side-chain residues in solvation dynamics is investigated by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on protein surface. Such differently placed residues are found to exhibit different timescales of relaxation. The total solvation response measured by the probe is decomposed in terms of its interactions with (i) protein core, (ii) side-chain and (iii) water. Significant anti cross-correlation among these contributions are observed. When the motion of the protein side-chains is quenched, solvation either becomes faster or slower depending on the location of the probe.

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

    Science.gov (United States)

    Lundgren, Martin; Niemi, Antti J; Sha, Fan

    2012-06-01

    Folded proteins have a modular assembly. They are constructed from regular secondary structures like α helices and β strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two sphere. Unlike the more conventional approaches that describe only a given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C_{α} atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-handed helix region of nonglycyl amino acids. This region corresponds to an isolated and highly localized residue independent sector in the direction of the C_{β} carbons on the two-sphere. We show that the residue independent localization extends to C_{γ} and C_{δ} carbons and to side-chain oxygen and nitrogen atoms in the case of asparagine and aspartic acid. When we extend the analysis to the side-chain atoms of the neighboring residues, we observe that left-handed β turns display a regular and largely amino acid independent structure that can extend to seven consecutive residues. This collective pattern is due to the presence of a backbone soliton. We show how one can use our visualization techniques to analyze and classify the different solitons in terms of selection rules that we describe in detail.

  8. Theoretical study on the charge transport properties of triphenylene discogens with a phenylpropionyloxy or 3-phenylpropenoyloxy side chain

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Charge transport is one of the most important properties in organic materials.Charge transport properties of triphenylene discogens with a phenylpropionyloxy or 3-phenylpropenoyloxy side chain have been investigated computationally on the basis of semi-classical Marcus theory.The results show that three triphenylene derivatives have high charge mobility.Title compounds have much better electronic mobility than the triphenylene.The triphenylenes containing 3-phenylpropenoyloxy have better hole mobility,but smaller electronic mobility than the triphenylenes with phenylpropionyloxy.For the triphenylene discogens with a phenylpropionyloxy,the longer the alkloxy chains,the better the positive charge transfer rate,but the smaller the negative charge transfer rate.

  9. SYNTHESIS AND CHARACTERIZATION OF AMPHIPHILIC GRAFT COPOLYMER CONTAINING MICROPHASE SEPARATED AND LONG POLY(ETHYLENE OXIDE ) SIDE CHAIN STRUCTURES

    Institute of Scientific and Technical Information of China (English)

    QIU Yongxing; YU Xiaojie; FENG Linxian; YANG Shilin

    1993-01-01

    Acryloyl terminated Poly (ethyleneoxide)macromonomers(PEO-A) with different PEO chain lengths have been prepared by deactivation of PEO alkoxide with acryloyl chloride. A new kind of amphiphilic polystyrene-g-poly (ethylene oxide)graft copolymer containing both microphase separated and PEO side chain structures has been synthesized from radical copolymerization of PEO-A macromonomer with styrene. After careful purification by a newly-developed method called "selective dissolution", the well-defined structure of the purified copolymers was confirmed by IR, 1H-NMR and GPC. Various experimental parameters controlling the copolymerization were studied in detail. The results indicated that the feed ratio of styrene to macromonomer(S/M) was the most important determining factor for the composition of the copolymers. A detailed "comb-model" was proposed to describe the molecular structure of the graft copolymers. Finally, this amphiphilic graft copolymers may readily form microphase separated structures as clearly indicated by transmission electron microscopy.

  10. The softer and more hydrophobic the better: influence of the side chain of polymethacrylate nanoparticles for cellular uptake.

    Science.gov (United States)

    Lorenz, Steffen; Hauser, Christoph P; Autenrieth, Benjamin; Weiss, Clemens K; Landfester, Katharina; Mailänder, Volker

    2010-09-09

    Intracellular uptake of nanoparticles is highly interesting for labeling of cells, drug delivery, or non-viral gene delivery. In this study we have synthesized a wide variety of poly(alkyl methacrylate) nanoparticles with the same size and investigated their uptake into cells. The nanoparticles were prepared from alkylmethacrylates with different linear and branched ester chains as well as from benzylmethacrylate using the miniemulsion polymerizaiton technique. By adding a fluorescent dye as a marker, the internalization of the nanoparticles could be investigated quantitatively with flow cytometry and qualitatively with confocal laser scanning microscopy. With increasing side chain of the ester and therefore increasing hydrophobicity and at glass transition temperature (T(g)), below the incubation temperature of 37 degrees C the uptake of the nanoparticles into cells is favored.

  11. Structure-guided optimization of estrogen receptor binding affinity and antagonist potency of pyrazolopyrimidines with basic side chains.

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, H.; Sheng, S.; Compton, D.; Kim, Y.; Joachimiak, A.; Sharma, S.; Carlson, K.; Katzenellenbogen, B.; Nettles, K.; Greene, G.; Katzenellenbogen, J.; Biosciences Division; Univ. of Illinois; Univ. of Chicago; The Scripps Research Inst.

    2007-01-01

    2,3-Diarylpyrazolo[1,5-a]pyrimidines are estrogen receptor (ER) antagonists of modest potency that we have described previously. Guided by the crystal structure of an ER-ligand complex that we have obtained with one of these compounds, we prepared analogs that contain a basic side chain at the 2- or 3-aryl group and quickly found one that, according to the structure-based prediction, shows an increase in binding affinity and antagonist potency and a loss of residual agonist activity.

  12. Proton clouds to measure long-range contacts between nonexchangeable side chain protons in solid-state NMR.

    Science.gov (United States)

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

    2014-03-26

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

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

    KAUST Repository

    Mondal, Rajib

    2011-01-01

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

  14. Point matching under non-uniform distortions and protein side chain packing based on an efficient maximum clique algorithm.

    Science.gov (United States)

    Dukka, Bahadur K C; Akutsu, Tatsuya; Tomita, Etsuji; Seki, Tomokazu; Fujiyama, Asao

    2002-01-01

    We developed maximum clique-based algorithms for spot matching for two-dimensional gel electrophoresis images, protein structure alignment and protein side-chain packing, where these problems are known to be NP-hard. Algorithms based on direct reductions to the maximum clique can find optimal solutions for instances of size (the number of points or residues) up to 50-150 using a standard PC. We also developed pre-processing techniques to reduce the sizes of graphs. Combined with some heuristics, many realistic instances can be solved approximately.

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

    OpenAIRE

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

    1998-01-01

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

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

    OpenAIRE

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

    2005-01-01

    International audience; Step polymn. of bisphenol A diphthalic anhydride (BAPA) with various mixts. from m-phenylene diamine (m-PDA) and 2-(perfluorohexylmethyl)butan-1,4-diamine (TFD) led to hydrophobic copolyetherimides bearing RF = CH2C6F13 side chains that were characterized by NMR, element anal., DSC, TGA and surface energy anal. By increasing the TFD unit %, the glass transition temp. (Tg) decreases according to the Fox equation from 217° (m-PDA 100% and TFD 0% like in ULTEM 1000) to 11...

  17. Influence of the side chain next to C-terminal benzimidazole in opioid pseudopeptides containing the Dmt-Tic pharmacophore.

    Science.gov (United States)

    Balboni, Gianfranco; Trapella, Claudio; Sasaki, Yusuke; Ambo, Akihiro; Marczak, Ewa D; Lazarus, Lawrence H; Salvadori, Severo

    2009-09-10

    To improve the structure-activity studies of the lead delta opioid agonist H-Dmt-Tic-Asp*-Bid, we synthesized and pharmacologically characterized a series of analogues in which the side chain next to 1H-benzimidazole-2-yl (Bid) was substituted by those endowed with different chemical properties. Interesting results were obtained: (1) only Gly, Ala, and Asp resulted in delta agonism, (2) Phe yielded delta antagonism, (3) and all other residues except Glu (devoid of any activity) gave mu agonism.

  18. 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

    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......, 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...

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

    Science.gov (United States)

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

    2014-11-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    1996-01-01

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

  1. 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.

  2. Amphiphilic Polyphosphazene with Poly(ethylene oxide) Side Chains Prepared through the Decker-Forster Reaction

    Institute of Scientific and Technical Information of China (English)

    LIU Chengmei; HU Fuzhen; QIU Jinjun; LEI Guofu; BAO Rui

    2006-01-01

    Poly(4-methylphenoxyphosphazene)-graft-poly(ethylene oxide) (PPZ-g-PEO), a novel amphiphilic grafting polymer was prepared via the Decker-Forster reaction. It is found that the graft efficiency increased with extension of reaction time. Low molecular weight of poly(ethylene oxide) favored the grafting reaction. The grafted polymer has two different glass transition temperatures(Tg) with those of pure poly(4-methylphenoxy-phopsphazene) and PEO. The emulsifying ability of grafted polymer was studied with benzene-water mixture. The emulsifying volumes increased with the decreasing of PEO's molecular weight. The contact angle of film forming from grafted polymer decreased after introduction of PEO grafting chain.

  3. Oligo(ethylene glycol)-incorporated hybrid linear alkyl side chains for n-channel polymer semiconductors and their effect on the thin-film crystalline structure.

    Science.gov (United States)

    Kim, Ran; Kang, Boseok; Sin, Dong Hun; Choi, Hyun Ho; Kwon, Soon-Ki; Kim, Yun-Hi; Cho, Kilwon

    2015-01-28

    Oligo(ethylene glycol)-incorporated hybrid linear alkyl side chains, serving as solubilizing groups, are designed and introduced into naphthalene-diimide-based n-channel copolymers. The synthesized polymers exhibit unipolar n-type operation with an electron mobility of up to 1.64 cm(2) V(-1) s(-1), which demonstrates the usefulness of the hybrid side chains in polymer electronics applications.

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

    Energy Technology Data Exchange (ETDEWEB)

    Al-Hussein, M., E-mail: m.alhussein@ju.edu.jo [Department of Physics, University of Jordan, Amman 11942 (Jordan); Hesse, H.C.; Weickert, J. [Ludwig-Maximilians-University Munich, Department of Physics and Center for NanoScience(CeNS), Amalienstr.54, 80799 Munich (Germany); Doessel, L.; Feng, X.; Muellen, K. [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany); Schmidt-Mende, L. [Ludwig-Maximilians-University Munich, Department of Physics and Center for NanoScience(CeNS), Amalienstr.54, 80799 Munich (Germany)

    2011-10-31

    We investigate thin blend films of phenyl-substituted hexa-peri-hexabenzocoronenes (HBC) with various alkyl side chain lengths ((CH{sub 2})n, n = 6, 8, 12 and 16)/perylenediimide (PDI). These blends constitute the active layers in bulk-hetero junction organic solar cells we studied recently [1]. Their structural properties are studied by both scanning electron microscopy and X-ray diffraction measurements. The results support the evidence for the formation of HBC donor-PDI acceptor complexes in all blends regardless of the side chain length of the HBC molecule. These complexes are packed into a layered structure parallel to the substrate for short side chain HBC molecules (n = 6 and 8). The layered structure is disrupted by increasing the side chain length of the HBC molecule and eventually a disordered structure is formed for long side chains (n > 12). We attribute this behavior to the size difference between the aromatic parts of the HBC and PDI molecules. For short side chains, the size difference results in a room for the side chains of the two molecules to fill in the space around the aromatic cores. For long side chains (n > 12), the empty space will not be enough to accommodate this increase, leading to the disruption of the layered structure and a rather disordered structure is formed. Our results highlight the importance of the donor-acceptor interaction in a bulk heterojunction active layer as well as the geometry of the two molecules and their role in determining the structure of the active layer and thus their photovoltaic performance.

  5. Aromatic substituents for prohibiting side-chain packing and π-π stacking in tin-cored tetrahedral stilbenoids

    Science.gov (United States)

    Kim, Cheolmin; Yoon, Min-Ju; Hong, Seok Hee; Park, Minjoon; Park, Kwangyong; Kim, Soo Young

    2016-05-01

    Tetrahedral structures comprising Sn-cored materials with five different types of substituents were synthesized. For the substituents, we employed methyl and tert-butyl as aliphatic groups, and naphthyl and phenyl as aromatic groups. The bandgap is in the range of 3.28 - 3.56 eV. The All the compounds with substituents showed bathochromical photoluminescence characteristics and exhibited aggregation-induced emission characteristics. Specifically, the compounds with aromatic substituents prohibited side-chain packing and π-π stacking. The energy levels of the highest occupied and lowest unoccupied molecular orbitals were measured to be 5.5 - 5.75 and 2.0 - 2.37 eV, respectively. The maximum luminance efficiencies and power efficiencies of the Sn-cored compound-based organic light-emitting diodes (OLEDs) were 0.38 - 0.71 cd/A and 0.15 - 0.28 lm/W. Therefore, it is expected that Sn-cored compounds with a tetrahedral structure, especially those containing aromatic substituents, can be used as an active material in blue OLEDs for prohibiting side-chain packing and π-π stacking. [Figure not available: see fulltext.

  6. Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution.

    Science.gov (United States)

    Grahnen, Johan A; Kubelka, Jan; Liberles, David A

    2011-08-01

    For high-throughput structural genomic and evolutionary bioinformatics approaches, there is a clear need for fast methods to evaluate substitutions structurally. Coarse-grained methods are both powerful and fast, and a coarse-grained approach to position the substituted side chains is presented. Through the application of a coarse-grained method, a speed-up on the single- residue replacement, of at least sevenfold is achieved compared with modern all-atom approaches. At the same time, this approach maintains a small median RMSD from the leading all-atom approach (as measured in coarse-grained space), and predicts the conformation of point mutants with similar accuracy and generates biologically realistic side chain angles. This method is also substantially more predictable in its run time, making it useful for high-throughput studies of protein structural evolution. To demonstrate the utility of this method, it has been implemented in a forward simulation of sequences threaded through the SH2 domains, with selective pressures to fold and bind specifically. The relative substitution rates across the protein structure and at the binding interface are reflective of those observed in SH2 domain evolution. The algorithm has been implemented in C++, with the source code and binaries (currently supported for Linux systems) freely available as SARA at http://www.wyomingbioinformatics.org/LiberlesGroup/SARA .

  7. 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.

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

    Science.gov (United States)

    Ollikainen, Noah; de Jong, René M.; Kortemme, Tanja

    2015-01-01

    Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein–ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art “fixed backbone” design methods perform poorly on these tests, we develop a new “coupled moves” design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein – ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution. PMID:26397464

  9. Exploring the effect of side-chain substitutions upon the secondary structure preferences of β-peptides.

    Science.gov (United States)

    Lin, Zhixiong; van Gunsteren, Wilfred F

    2011-11-10

    The ability to design well-folding β-peptides with a specific biological activity requires detailed insight into the relationship between the β-amino acid sequence and the dominant three-dimensional structure of such a peptide. To this end, secondary structure preferences of two sets of 16 β-peptides were investigated by means of one-step perturbation using molecular dynamics (MD) simulations. For each set of peptides, two reference-state simulations and one perturbed-state simulation were carried out to predict the secondary structure preferences for the other 15 peptides. The results show that the substitution of a methyl group in the third or fourth residue stabilizes the left-handed 3(14)-helix over the right-handed 2.7(10/12)-helix for the set of hexapeptides A; for the set of heptapeptides B, having methyl substitutions at both β- and α-carbon positions of the fourth or fifth residue stabilizes the left-handed 3(14)-helix over the right-handed 2.5(12)-helix. Not only the side-chain substitution pattern but also the side-chain composition affects the relative stability of different secondary structures. The approach described here may be of use in peptide design with an eye to obtaining peptides with particular folds and biological activities.

  10. 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.

  11. Selective flexibility of side-chain residues improves VEGFR-2 docking score using AutoDock Vina.

    Science.gov (United States)

    Abreu, Rui M V; Froufe, Hugo J C; Queiroz, Maria-João R P; Ferreira, Isabel C F R

    2012-04-01

    Selective side-chain residue flexibility is an option available on AutoDock Vina docking software. This approach is promising as it attempts to provide a more realistic ligand-protein interaction environment without an unmanageable increase in computer processing time. However, studies validating this approach are still scarce. VEGFR-2 (vascular endothelial growth factor receptor 2), a known protein target for anti-angiogenic agents, was used in this study. Four residues located in the VEGFR-2 kinase site were selected and made flexible: Lys868, Glu885, Cys919, and Asp1046. The docking scores for all possible combinations of flexible residues were compared to the docking scores using a rigid conformation. The best overall docking scores were obtained using the Glu885 flexible conformation, with Pearson and Spearman rank correlation values of 0.568 and 0.543, respectively, and a 51% increase in processing time. Using different VEGFR-2 crystal structures, a similar trend was observed with the Glu885 flexible conformation presenting best scores. This study demonstrates that careful use of selective side-chain residue flexibility can improve AutoDock Vina docking score accuracy, without a significant increase in processing time. This methodology can be a valuable tool in drug design projects using VEGFR-2 but will also probably be useful if applied to other protein targets. © 2011 John Wiley & Sons A/S.

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

    Science.gov (United States)

    Li, Pengfei; Jackson, Glen P.

    2017-01-01

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

  13. Z-Selective olefin metathesis on peptides: investigation of side-chain influence, preorganization, and guidelines in substrate selection.

    Science.gov (United States)

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

    2014-09-01

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

  14. Z-Selective Olefin Metathesis on Peptides: Investigation of Side-Chain Influence, Preorganization, and Guidelines in Substrate Selection

    Science.gov (United States)

    2015-01-01

    Olefin metathesis has emerged as a promising strategy for modulating the stability and activity of biologically relevant compounds; however, the ability to control olefin geometry in the product remains a challenge. Recent advances in the design of cyclometalated ruthenium catalysts has led to new strategies for achieving such control with high fidelity and Z selectivity, but the scope and limitations of these catalysts on substrates bearing multiple functionalities, including peptides, remained unexplored. Herein, we report an assessment of various factors that contribute to both productive and nonproductive Z-selective metathesis on peptides. The influence of sterics, side-chain identity, and preorganization through peptide secondary structure are explored by homodimerization, cross metathesis, and ring-closing metathesis. Our results indicate that the amino acid side chain and identity of the olefin profoundly influence the activity of cyclometalated ruthenium catalysts in Z-selective metathesis. The criteria set forth for achieving high conversion and Z selectivity are highlighted by cross metathesis and ring-closing metathesis on diverse peptide substrates. The principles outlined in this report are important not only for expanding the scope of Z-selective olefin metathesis to peptides but also for applying stereoselective olefin metathesis in general synthetic endeavors. PMID:25102124

  15. 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.

  16. Variation of the net charge, lipophilicity, and side chain flexibility in Dmt(1)-DALDA: Effect on Opioid Activity and Biodistribution.

    Science.gov (United States)

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

    2012-11-26

    The influence of the side chain charges of the second and fourth amino acid residues in the peptidic μ opioid lead agonist Dmt-d-Arg-Phe-Lys-NH(2) ([Dmt(1)]-DALDA) was examined. Additionally, to increase the overall lipophilicity of [Dmt(1)]-DALDA and to investigate the Phe(3) side chain flexibility, the final amide bond was N-methylated and Phe(3) was replaced by a constrained aminobenzazepine analogue. The in vitro receptor binding and activity of the peptides, as well as their in vivo transport (brain in- and efflux and tissue biodistribution) and antinociceptive properties after peripheral administration (ip and sc) in mice were determined. The structural modifications result in significant shifts of receptor binding, activity, and transport properties. Strikingly, while [Dmt(1)]-DALDA and its N-methyl analogue, Dmt-d-Arg-Phe-NMeLys-NH(2), showed a long-lasting antinociceptive effect (>7 h), the peptides with d-Cit(2) generate potent antinociception more rapidly (maximal effect at 1h postinjection) but also lose their analgesic activity faster when compared to [Dmt(1)]-DALDA and [Dmt(1),NMeLys(4)]-DALDA.

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

    Directory of Open Access Journals (Sweden)

    2011-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Noah Ollikainen

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

  19. Probing China's Lysine Market

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ The lysine sector in China developed further in 2006. Both the capacity and the output hit new highs and China had a major impact on the global lysine market. The import amount of lysine satisfied only a very small portion of the domestic market's demand.

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

    Directory of Open Access Journals (Sweden)

    Douglas W Lowman

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

  1. Rubbing-Induced Molecular Reorientation on an Alignment Surface of an Aromatic Polyimide Containing Cyanobiphenyl Side Chains

    Science.gov (United States)

    Cheng, S. Z. D.; Ge, Jason J.; Li, Christopher Y.; Harris, Frank W.; Hong, Seok-Cheol; Zhuang, Xiaowei; Shen, Y. R.

    2002-03-01

    Surface lamellar decoration (SLD), surface enhanced Raman scattering (SERS) and optical second harmonic generation (SHG) experiments have been utilized to study the molecular orientation and conformation changes at a rubbed polyimide alignment layer surface. This aromatic polyimide containing pendent cyanobiphenyl mesogens was synthesized via a polycondensation, and abbreviated as 6FDA-6CBBP. Uniform alignment layers, possessing high pretilt angles ranging from 39^o to 43^o, have been achieved after mechanical rubbing of the polyimide thin film surface at room temperature and subsequent annealing. This is the first time that high pretilt angles have been detected to possess a negative angle [θ(c)] with respect to the rubbing direction (i.e., opposite to the rubbing direction), considerably different from the conventional pretilt angle [θc)] observed along the rubbing direction. Combined polyethylene (PE) SLD and atomic force microscopy experiments reveal that the azimuthal orientation distribution of the long axis of the edge-on PE lamellar crystals is oriented normal to the rubbing direction, indicating that the PE chains are aligned parallel to the rubbing direction. The SERS results show that mechanical rubbing causes not only tilting of the backbone moieties, but also significant conformational rearrangements of the pendent side chains at the surfaces. The molecular mechanism of this unusual alignment is due to the fact that the pendent cyanobiphenyls forms a uniformly tilted conformation on the rubbed surface, and the polar cyano groups point down towards the layer surface deduced from SHG phase measurements. This conformational rearrangement of the side chains results in the formation of fold-like bent structures on the surface, which directly leads to the long axis of cyanobiphenyls having the [θc)] pretilt angle with respect to the rubbing direction.

  2. Preparation, curing kinetic and properties of a novel amine with flexible polyoxypropylene side chain curing agent for epoxy resin

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Guiyou, E-mail: guiyouwang@ecust.edu.cn; Jiang, Guanlan; Zhang, Jie

    2014-08-10

    Highlights: • Novel amines with different length of flexible polyoxypropylene side chain (AFPE) were synthesized. • The non-isothermal curing kinetics of DGEBA/AFPEs were studied in detail. • Structure, morphology and physical properties of AFPEs modified diethylenetriamine/DGEBA systems were studied, and results showed that AFPE was a novel and effective toughening agent for epoxy resins. - Abstract: A novel amine with flexible polyoxypropylene side chain (AFPE) was synthesized and characterized with FT-IR and NMR. Then, AFPEs with different molecular weight were used as a curing agent for diglycidyl ether of bisphenol A (DGEBA), and non-isothermal reaction was detected with DSC. The kinetic parameters of the curing process were determined by Málek method. A two-parameter (m, n) autocatalytic model (Šesták–Berggren equation) was found to be adequate to describe the reaction-controlled kinetics of the studied epoxy resins, yet was insufficient in depicting the diffusion-controlled kinetics of the epoxy resins. The values of E{sub a} depended on the molecular weight of AFPEs, and increased with longer polyoxypropylene chain length in the AFPE. Dynamic mechanical analysis of AFPEs modified DGEBA/diethylenetriamine systems found that with the increasing molecular weight of AFPEs, α relaxation temperature, β relaxation temperature and crosslinking density decreased, while impact strength and elongation at break improved. From scanning electron microscope, tensile surfaces were rougher and sizes of cavities in the surface became larger with the increasing molecular weight of AFPEs. Our study showed that AFPE was a novel and effective toughening agent for epoxy resins.

  3. Synthesis, pharmacokinetics, and biological use of lysine-modified single-walled carbon nanotubes.

    Science.gov (United States)

    Mulvey, J Justin; Feinberg, Evan N; Alidori, Simone; McDevitt, Michael R; Heller, Daniel A; Scheinberg, David A

    2014-01-01

    We aimed to create a more robust and more accessible standard for amine-modifying single-walled carbon nanotubes (SWCNTs). A 1,3-cycloaddition was developed using an azomethine ylide, generated by reacting paraformaldehyde and a side-chain-Boc (tert-Butyloxycarbonyl)-protected, lysine-derived alpha-amino acid, H-Lys(Boc)-OH, with purified SWCNT or C60. This cycloaddition and its lysine adduct provides the benefits of dense, covalent modification, ease of purification, commercial availability of reagents, and pH-dependent solubility of the product. Subsequently, SWCNTs functionalized with lysine amine handles were covalently conjugated to a radiometalated chelator, 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA). The (111)In-labeled construct showed rapid renal clearance in a murine model and a favorable biodistribution, permitting utility in biomedical applications. Functionalized SWCNTs strongly wrapped small interfering RNA (siRNA). In the first disclosed deployment of thermophoresis with carbon nanotubes, the lysine-modified tubes showed a desirable, weak SWCNT-albumin binding constant. Thus, lysine-modified nanotubes are a favorable candidate for medicinal work.

  4. Multifunctional conjugated polymers with main-chain donors and side-chain acceptors for dye sensitized solar cells (DSSCs) and organic photovoltaic cells (OPVs).

    Science.gov (United States)

    Chang, Dong Wook; Ko, Seo-Jin; Kim, Jin Young; Park, Su-Moon; Lee, Hyo Joong; Dai, Liming; Baek, Jong-Beom

    2011-11-15

    A novel multifunctional conjugated polymer (RCP-1) composed of an electron-donating backbone (carbazole) and an electron-accepting side chain (cyanoacetic acid) connected through conjugated vinylene and terthiophene has been synthesized and tested as a photosensitizer in two major molecule-based solar cells, namely dye sensitized solar cells (DSSCs) and organic photovoltaic cells (OPVs). Promising initial results on overall power conversion efficiencies of 4.11% and 1.04% are obtained from the basic structure of DSSCs and OPVs based on RCP-1, respectively. The well-defined donor (D)-acceptor (A) structure of RCP-1 has made it possible, for the first time, to reach over 4% of power conversion efficiency in DSSCs with an organic polymer sensitizer and good operation stability.

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

    Directory of Open Access Journals (Sweden)

    L. Weng

    2015-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Alexey G. Gerbst

    2015-02-01

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

  7. Effects of side-chain orientation on the {sup 13}C chemical shifts of antiparallel {beta}-sheet model peptides

    Energy Technology Data Exchange (ETDEWEB)

    Villegas, Myriam E.; Vila, Jorge A. [Facultad de Ciencias Fisico Matematicas y Naturales, Instituto de Matematica Aplicada San Luis, Universidad Nacional de San Luis, CONICET (Argentina); Scheraga, Harold A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)], E-mail: has5@cornell.edu

    2007-02-15

    The dependence of the {sup 13}C chemical shift on side-chain orientation was investigated at the density functional level for a two-strand antiparallel {beta}-sheet model peptide represented by the amino acid sequence Ac-(Ala){sub 3}-X-(Ala){sub 12}-NH{sub 2} where X represents any of the 17 naturally occurring amino acids, i.e., not including alanine, glycine and proline. The dihedral angles adopted for the backbone were taken from, and fixed at, observed experimental values of an antiparallel {beta}-sheet. We carried out a cluster analysis of the ensembles of conformations generated by considering the side-chain dihedral angles for each residue X as variables, and use them to compute the {sup 13}C chemical shifts at the density functional theory level. It is shown that the adoption of the locally-dense basis set approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 17 naturally occurring amino acids in an antiparallel {beta}-sheet, there is (i) good agreement between computed and observed {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts, with correlation coefficients of 0.95 and 0.99, respectively; (ii) significant variability of the computed {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts as a function of {chi}{sup 1} for all amino acid residues except Ser; and (iii) a smaller, although significant, dependence of the computed {sup 13}C{sup {alpha}} chemical shifts on {chi}{sup {xi}} (with {xi} {>=} 2) compared to {chi}{sup 1} for eleven out of seventeen residues. Our results suggest that predicted {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts, based only on backbone ({phi},{psi}) dihedral angles from high-resolution X-ray structure data or from NMR-derived models, may differ significantly from those observed in solution if the dihedral-angle preferences for the side chains are not taken into

  8. Structure-activity relationships of nonisomerizable derivatives of tamoxifen: importance of hydroxyl group and side chain positioning for biological activity.

    Science.gov (United States)

    Murphy, C S; Parker, C J; McCague, R; Jordan, V C

    1991-03-01

    The antiestrogen tamoxifen [(Z)-1(p-beta-dimethylaminoethoxy-phenyl)-1,2-diphenylbut-1-ene] is an effective anticancer agent against estrogen receptor (ER)-positive breast cancer. The alkylaminoethane side chain is essential for antiestrogenic activity, but the potency of the antiestrogen can be increased by para hydroxylation of the phenyl ring on carbon 1 of but-1-ene. This compound, 4-hydroxytamoxifen, is a metabolite of tamoxifen and has a very high binding affinity for ER [J. Endocrinol. 75:305-316 (1977)] because the hydroxyl is located in the equivalent position as the 3-phenolic hydroxyl of 17 beta-estradiol. In this study, we have examined the relationship between the relative positions of the hydroxyl and the alkyl-aminoethane side chain and the pharmacological activity of the ligand. A fixed seven-membered ring derivative of the triphenylethylene was used to prevent isomerization. All compounds were tested, with and without 17 beta-estradiol, for their effects on the growth of estrogen-responsive T47D and MCF-7 human breast cancer cells in vitro. The growth of MDA-MB-231 ER-negative breast cancer cells was not affected by any of the compounds tested, at a concentration (1 microM) that had a profound estrogenic or antiestrogenic action in ER-positive cell lines. The relative binding affinity of the compounds was determined using rat uterine ER and was found to be consistent with the observed potencies in vitro. The compounds found to be antiestrogens in vitro were antiestrogenic against estradiol (0.08 micrograms daily) in the 3-day immature rat uterine weight test. All compounds were partial agonists in vivo. In general, the estrogenic and antiestrogenic results obtained in vivo were consistent with the potency estimates obtained with the breast cancer cells in vitro. The results of this extensive structure-activity relationship study demonstrate that the substitution for 4-hydroxytamoxifen appears to be optimal to produce a potent antiestrogen; all

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

    Directory of Open Access Journals (Sweden)

    Werner Tegge

    2010-01-01

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

  10. Unraveling the interplay of backbone rigidity and electron rich side-chains on electron transfer in peptides: the realization of tunable molecular wires.

    Science.gov (United States)

    Horsley, John R; Yu, Jingxian; Moore, Katherine E; Shapter, Joe G; Abell, Andrew D

    2014-09-03

    Electrochemical studies are reported on a series of peptides constrained into either a 310-helix (1-6) or β-strand (7-9) conformation, with variable numbers of electron rich alkene containing side chains. Peptides (1 and 2) and (7 and 8) are further constrained into these geometries with a suitable side chain tether introduced by ring closing metathesis (RCM). Peptides 1, 4 and 5, each containing a single alkene side chain reveal a direct link between backbone rigidity and electron transfer, in isolation from any effects due to the electronic properties of the electron rich side-chains. Further studies on the linear peptides 3-6 confirm the ability of the alkene to facilitate electron transfer through the peptide. A comparison of the electrochemical data for the unsaturated tethered peptides (1 and 7) and saturated tethered peptides (2 and 8) reveals an interplay between backbone rigidity and effects arising from the electron rich alkene side-chains on electron transfer. Theoretical calculations on β-strand models analogous to 7, 8 and 9 provide further insights into the relative roles of backbone rigidity and electron rich side-chains on intramolecular electron transfer. Furthermore, electron population analysis confirms the role of the alkene as a "stepping stone" for electron transfer. These findings provide a new approach for fine-tuning the electronic properties of peptides by controlling backbone rigidity, and through the inclusion of electron rich side-chains. This allows for manipulation of energy barriers and hence conductance in peptides, a crucial step in the design and fabrication of molecular-based electronic devices.

  11. The Synthesis of Rosuvastatin Side Chain%瑞舒伐他汀侧链的合成

    Institute of Scientific and Technical Information of China (English)

    孔叶青

    2014-01-01

    以3-叔丁基二甲硅氧基戊二酸酐和(S)2-羟基-2苯基乙酸苄酯为原料,经过缩合、还原、酯交换、酯化和酯交换制得瑞舒伐他汀侧链(3R)叔丁基二甲硅氧基-6-二甲氧基磷酰基-5-氧代己酸叔丁酯。%Rosuvastatin side chains-(3R) t-butyldimethylsilyloxy-6-dimethoxy-naphthalene acyl-5-ox-o-hexanoic acid tert-butyl ester was synthesized through condensation, reduction, transesterification, esterifi-cation and transesterification using 3-tert-butyldimethylsilyloxy glutaric anhydride and (S) 2-hydroxy-2-phenyl-acetic acid benzyl ester as raw materials.

  12. Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues.

    Science.gov (United States)

    Li, Xinbi; Ponomarev, Sergei Y; Sa, Qina; Sigalovsky, Daniel L; Kaminski, George A

    2013-05-30

    A previously introduced polarizable simulations with second-order interaction model (POSSIM) force field has been extended to include parameters for small molecules serving as models for peptide and protein side-chains. Parameters have been fitted to permit reproducing many-body energies, gas-phase dimerization energies, and geometries and liquid-phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second-order approximation of the full-scale induced point dipole polarization formalism. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters are currently being used in further development of the POSSIM fast polarizable force field for proteins.

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

    Science.gov (United States)

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

    2012-07-26

    Many advances in organic photovoltaic efficiency are not yet fully understood and new insight into structure-property relationships is required to push this technology into broad commercial use. The aim of this article is not to comprehensively review recent work, but to provide commentary on recent successes and forecast where researchers should look to enhance the efficiency of photovoltaics. By lowering the LUMO level, utilizing electron-withdrawing substituents advantageously, and employing appropriate side chains on donor polymers, researchers can elucidate further aspects of polymer-PCBM interactions while ultimately developing materials that will push past 10% efficiency. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. 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

    Improvement of the power conversion efficiency and long term stability remains to be of crucial importance for the further development of polymer solar cells (PSCs). Herein, a donor-acceptor copolymer based on 4,8-di(thiophene-2′-yl)benzo[1,2-b:4,5-b′]dithiophene (DTBDT) and 4,7-di(thiophene-2′-y...... in an improved photochemical stability of the polymer film and a higher efficiency of 5.6% for the spin-coated PSC. The stability of roll-coated devices also slightly increases with the incorporation of 10% of either the 2-hydroxyethyl or 2-phenylethyl side chain....

  15. SYNTHESIS AND MESOMORPHIC PROPERTIES OF PALLADIUM CHELATES OF LIQUID CRYSTAL POLYSILOXANE WITH β-DIKETONE-BASED SIDE CHAINS

    Institute of Scientific and Technical Information of China (English)

    ZHOU Zhaohui; DAI Daorong; ZHANG Rongben

    1992-01-01

    A new type of palladium chelate of β-diketone-based side chain liquid crystal polysiloxane(Pd-DKLCP) has been synthesized by chelation reaction of palladium dichloride with polymeric ligand, β-diketone polysiloxane (DKLCP), using THF as solvent at R .T.. The Pd-chelation results in greatly increasing the phase transition temperature TK and the enthalpy change AHK from crystal to liquid crystal state and making the temperature range of LC state AT (A T=Tc1- TK) widened.All these chelates Pd-DKLCP's do not show TCl until decomposition at 205 ℃. It is noteworthy that the Pd-chelation can exert more positive effect on the mesomorphic behaviour of the polymer ligand than the counterpart Cu-DKLCP does. It is probable due to the bigger size of disc-like mesogen formed from β-diketone and Pd +2 ion with 4d orbital.

  16. Catalytic Kinetics of the Schiff Base Metal Complexes Bearing Side Chain of Cyclic morpholine in Carboxylic Ester Hydrolysis

    Institute of Scientific and Technical Information of China (English)

    ZHANG,Shu-Lin; LI,Min-Jiao; OU,Zhong-Wen; CHEN,Guo-Xu; LIU,Fu-An; XIE,Jia-Qing

    2007-01-01

    It has been reported that two Schiff base transition metal complexes bearing the side chain of the morpholine ring were synthesized and characterized, and two complexes with the same base agent but different metal ions were used as a simulant hydrolase in the catalytic hydrolysis of p-nitrophenyl picolinate in this paper. The mechanism of PNPP catalytic hydrolysis is proposed and supported by the results of the spectral analysis and the kinetic calculation. A kinetic mathematical model, applied to the calculation of the kinetic and thermodynamics parameters of PNPP catalytic hydrolysis, has been established on the foundation of the mechanism proposed. The result of the study shows that the two complexes have a good catalytic activity in PNPP catalytic hydrolysis, and the rate of the PNPP catalytic hydrolysis was increased with the increase of the pH values in the buffer solution and affected by the polarization effect of metal ion of the complexes.

  17. 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

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

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

    Science.gov (United States)

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

    2014-07-23

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

  19. LITHIUM ION CONDUCTING POLYMER ELECTROLYTES BASED ON ALTERNATING MALEIC ANHYDRIDE COPOLYMER WITH OLIGO-OXYETHYLENE SIDE CHAINS

    Institute of Scientific and Technical Information of China (English)

    DING Liming

    1996-01-01

    A comb polymer with oligo-oxyethylene side chains of the type -(CH2CH2O)12CH3 was prepared from methyl vinyl ether/maleic anhydride copolymer and poly (ethylene glycol) methyl ether. The polymer can dissolve LiClO4 salt to form homogeneous amorphous polymer electrolyte. The ac ion conduction was measured using the complex impedance method, and conductivities were investigated as functions of temperatures and salt concentration. The complexes were first found to have two classes of glass transition which increase with increasing salt content. The optimum conductivity attained at 25℃ is in the order of 5.50 × 10-6Scm-1. IR spectroscopy was used to study the cation-polymer interaction.

  20. Effect of side-chain length on rectification and photovoltaic characteristics of poly(3-alkylthiophene) Schottky barriers

    Energy Technology Data Exchange (ETDEWEB)

    Fang Yih; Chen Showan (Dept. of Chemical Engineering, National Tsing-Hua Univ., Hsinchu (Taiwan)); Chu, M.L. (Inst. of Electro-Optical Engineering, National Chiao-Tung Univ., Hsinchu (Taiwan))

    1992-10-15

    Schottky diodes of aluminium/poly(3-alkylthiophene) (P3AT)/indium-tin oxide (ITO) with large area (0.15-0.5 cm[sup 2]) are prepared using the proposed new casting technique. The P3ATs investigated involve poly(3-butylthiophene) (P3BT), poly(3-octylthiophene) (P3OT) and poly(3-dodecylthiophene) (P3DDT), which are prepared using the chemical method. The diodes, in which P3AT behaves as a p-type semiconductor, exhibit a moderate rectifying behaviour and low leakage current. Photovoltaic measurements show a power conversion efficiency of about 10[sup -2]-10[sup -3]% at a light intensity of 0.5-5 mW/cm[sup 2], which decreases with increasing light intensity. The longer alkyl side-chain length of P3ATs can cause a lower rectifying effect, barrier height, depletion region width and photovoltaic conversion efficiency. (orig.).

  1. Pressure dependence of side chain (13)C 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

    2017-09-14

    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-NH2 (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.

  2. Hydrogen bond switching among flavin and amino acid side chains in the BLUF photoreceptor observed by ultrafast infrared spectroscopy.

    Science.gov (United States)

    Bonetti, Cosimo; Mathes, Tilo; van Stokkum, Ivo H M; Mullen, Katharine M; Groot, Marie-Louise; van Grondelle, Rienk; Hegemann, Peter; Kennis, John T M

    2008-11-15

    BLUF domains constitute a recently discovered class of photoreceptor proteins found in bacteria and eukaryotic algae. BLUF domains are blue-light sensitive through a FAD cofactor that is involved in an extensive hydrogen-bond network with nearby amino acid side chains, including a highly conserved tyrosine and glutamine. The participation of particular amino acid side chains in the ultrafast hydrogen-bond switching reaction with FAD that underlies photoactivation of BLUF domains is assessed by means of ultrafast infrared spectroscopy. Blue-light absorption by FAD results in formation of FAD(*-) and a bleach of the tyrosine ring vibrational mode on a picosecond timescale, showing that electron transfer from tyrosine to FAD constitutes the primary photochemistry. This interpretation is supported by the absence of a kinetic isotope effect on the fluorescence decay on H/D exchange. Subsequent protonation of FAD(*-) to result in FADH(*) on a picosecond timescale is evidenced by the appearance of a N-H bending mode at the FAD N5 protonation site and of a FADH(*) C=N stretch marker mode, with tyrosine as the likely proton donor. FADH(*) is reoxidized in 67 ps (180 ps in D(2)O) to result in a long-lived hydrogen-bond switched network around FAD. This hydrogen-bond switch shows infrared signatures from the C-OH stretch of tyrosine and the FAD C4=O and C=N stretches, which indicate increased hydrogen-bond strength at all these sites. The results support a previously hypothesized rotation of glutamine by approximately 180 degrees through a light-driven radical-pair mechanism as the determinant of the hydrogen-bond switch.

  3. Exploiting Supramolecular Interactions for the Intramolecular Folding of Side-Chain Functionalized Polymers and Assembly of Anisotropic Colloids

    Science.gov (United States)

    Romulus, Joy

    The overarching goal presented in this thesis is the self-assembly of synthetic systems into higher ordered structures utilizing supramolecular chemistry. Noncovalent interactions including charge-transfer and hydrogen bonding as well as DNA hybridization are exploited to induce the assembly of polymers and colloids into well-defined architectures. This strategy provides a tunable handle on materials bulk properties that can be adjusted by simply changing variables such as temperature and solvent. A brief overview of design principles for the supramolecular assembly of side-chain functionalized polymers is presented. The polymerization technique selected was living ring-opening metathesis polymerization (ROMP), thus affording control over molecular weight and molecular weight distributions. ROMP also allowed for the incorporation of functional groups that were used to assemble the polymers into ordered structures. Charge-transfer motifs were exploited and shown to drive the assembly of random and alternating copolymers via intramolecular side-chain interactions. Incorporation of complementary hydrogen bonding motifs was shown to guide the single-chain folding of a multifunctional triblock copolymer into sheet-like structures. Precision over the size, shape, and monomer sequence were identified as key elements for efficient self-assembly. The self-assembly of colloids using DNA hybridization was also investigated. Previously, the majority of colloid-based research relied upon the self-assembly of spherical isotropic particles into closed-packed arrangements. In contrast, anisotropic particles may allow for the realization of open structures. By expanding upon a method to permanently cross-link DNA strands incubated on a colloidal surface, a new strategy to engineer patchy particles is described. These functional DNA-coated patches are demonstrated to direct particle assembly. The self-assembly of polymer and colloidal systems utilizing noncovalent interactions

  4. Quantum transport through a multi-quantum-dot-pair chain side-coupled with Majorana bound states

    Science.gov (United States)

    Zhao-Tan, Jiang; Cheng-Cheng, Zhong

    2016-06-01

    We investigate the quantum transport properties through a special kind of quantum dot (QD) system composed of a serially coupled multi-QD-pair (multi-QDP) chain and side-coupled Majorana bound states (MBSs) by using the Green functions method, where the conductance can be classified into two kinds: the electron tunneling (ET) conductance and the Andreev reflection (AR) one. First we find that for the nonzero MBS-QDP coupling a sharp AR-induced zero-bias conductance peak with the height of e 2/h is present (or absent) when the MBS is coupled to the far left (or the other) QDP. Moreover, the MBS-QDP coupling can suppress the ET conductance and strengthen the AR one, and further split into two sub-peaks each of the total conductance peaks of the isolated multi-QDPs, indicating that the MBS will make obvious influences on the competition between the ET and AR processes. Then we find that the tunneling rate Γ L is able to affect the conductances of leads L and R in different ways, demonstrating that there exists a Γ L-related competition between the AR and ET processes. Finally we consider the effect of the inter-MBS coupling on the conductances of the multi-QDP chains and it is shown that the inter-MBS coupling will split the zero-bias conductance peak with the height of e 2/h into two sub-peaks. As the inter-MBS coupling becomes stronger, the two sub-peaks are pushed away from each other and simultaneously become lower, which is opposite to that of the single QDP chain where the two sub-peaks with the height of about e 2/2h become higher. Also, the decay of the conductance sub-peaks with the increase of the MBS-QDP coupling becomes slower as the number of the QDPs becomes larger. This research should be an important extension in studying the transport properties in the kind of QD systems coupled with the side MBSs, which is helpful for understanding the nature of the MBSs, as well as the MBS-related QD transport properties. Project supported by the National Natural

  5. Design and construction of novel molecular conjugates for signal amplification (I): conjugation of multiple horseradish peroxidase molecules to immunoglobulin via primary amines on lysine peptide chains.

    Science.gov (United States)

    Dhawan, Subhash

    2002-12-01

    Immunoconjugates are widely used for indirect detection of analytes (such as antibodies or antigens) in a variety of immunoassays. However, the availability of functional groups such as primary amines or free sulfhydryls in an immunoglobulin molecule is the limiting factor for optimal conjugation and, therefore, determines the sensitivity of an assay. In the present study, an N-terminal bromoacetylated 20 amino acid peptide containing 20 lysine residues was conjugated to N-succinimidyl-S-acetylthioacetate (SATA)-modified IgG or free sulfhydryl groups on 2-mercaptoethylamine (2-MEA)-reduced IgG molecules via a thioether (S[bond]CH(2)CONH) linkage to introduce multiple reactive primary amines per IgG. These primary amines were then covalently coupled with maleimide-activated horseradish peroxidase (HRP). The poly-HRP-antibody conjugates thus generated demonstrated greater than 15-fold signal amplification upon reaction with orthophenyldiamine substrate. The poly-HRP-antibody conjugates efficiently detected human immunodeficiency virus (HIV)-1 antibodies in plasma specimens with significantly higher sensitivity than conventionally prepared HRP-antibody conjugates in an HIV-1 solid-phase enzyme immunoassay and Western blot analysis. The signal amplification techniques reported here could have the potential for development of highly sensitive immunodiagnostic assay systems.

  6. The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70.

    Science.gov (United States)

    Bhowmick, Asmit; Sharma, Sudhir C; Honma, Hallie; Head-Gordon, Teresa

    2016-07-28

    Side chain entropy and mutual entropy information between residue pairs have been calculated for two de novo designed Kemp eliminase enzymes, KE07 and KE70, and for their most improved versions at the end of laboratory directed evolution (LDE). We find that entropy, not just enthalpy, helped to destabilize the preference for the reactant state complex of the designed enzyme as well as favoring stabilization of the transition state complex for the best LDE enzymes. Furthermore, residues with the highest side chain couplings as measured by mutual information, when experimentally mutated, were found to diminish or annihilate catalytic activity, some of which were far from the active site. In summary, our findings demonstrate how side chain fluctuations and their coupling can be an important design feature for de novo enzymes, and furthermore could be utilized in the computational steps in lieu of or in addition to the LDE steps in future enzyme design projects.

  7. 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

    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...... exchange to transverse relaxation; additional signal enhancement is achieved by optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-selected R 1ρ experiment by measuring exchange parameters for Y23 in bovine pancreatic trypsin inhibitor...

  8. Synthesis of new opioid derivatives with a propellane skeleton and their pharmacology. Part 2: Propellane derivatives with an amide side chain.

    Science.gov (United States)

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

    2012-04-15

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

  9. SELF-ASSEMBLED MICRO-DOMAINS ON THE UPPERMOST SURFACE OF FLUORINATED POLY(CARBONATE URETHANE)S WITH FLUORINATED SIDE CHAIN ATTACHED ON HARD SEGMENTS

    Institute of Scientific and Technical Information of China (English)

    Hong Tan; Min Guo; Jie-hua Li; Xing-yi Xie; Yin-ping Zhong; Qiang Fu

    2004-01-01

    The surface phase separated structure of polyurethanes is always desired due to the advantage of better biocompatibility, compared with the homogeneous one. The key issue is how to control and characterize the surface morphology. In this work, we report the uppermost surface morphology of fluorinated poly(carbonate urethane)s with fluorinated side chains attached to hard segments as studied by AFM, XPS and contact angle measurement. A self-assembled micro-domain with the fluorinated side chain standing up on the uppermost surface has been proposed for polyurethane with higher fluorinated content, based on the result obtained.

  10. Synthesis of new opioid derivatives with a propellane skeleton and their pharmacologies: Part 5, novel pentacyclic propellane derivatives with a 6-amide side chain.

    Science.gov (United States)

    Nakajima, Ryo; Yamamoto, Naoshi; Hirayama, Shigeto; Iwai, Takashi; Saitoh, Akiyoshi; Nagumo, Yasuyuki; Fujii, Hideaki; Nagase, Hiroshi

    2015-10-01

    We designed and synthesized pentacyclic propellane derivatives with a 6-amide side chain to afford compounds with higher MOR/KOR ratio and lower sedative effects than nalfurafine. The obtained etheno-bridged derivative with a β-amide side chain, YNT-854, showed a higher MOR/KOR ratio than nalfurafine. YNT-854 also exhibited a higher dose ratio between the sedative effect and the analgesic effect than observed with nalfurafine, which may guide the future design of useful analgesics with a weaker sedative effect than nalfurafine.

  11. 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.

  12. 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...

  13. 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.

  14. SYNTHESIS OF SIDE-CHAIN LIQUID CRYSTALLINE POLYSILOXANE CONTAINING SCHIFF'S BASE MESOGENS WITH NO2-END GROUP AND ITS BEHAVIOR IN A DC ELECTRIC FIELD

    Institute of Scientific and Technical Information of China (English)

    XIE Ping; SUN Limin; ZHANG Rongben

    1993-01-01

    A side chain liquid crystalline copolysiloxane, which would show electro-optic effects as known from low mass liquid crystal, was synthesized by hydrosilylation reaction, and the two homologous monomers with different length spacers containing Schiff's base mesogen with -NO2 terminated group were grafted to a polysiloxane main chain. Residual monomer in crude product is effective in reinforcing the response to an electric field over that of pure polymeric liquid crystal.

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

    Energy Technology Data Exchange (ETDEWEB)

    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 ..cap alpha..,..cap alpha..'-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.

  16. Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants.

    Directory of Open Access Journals (Sweden)

    Hsin-Mao Wu

    Full Text Available Lysine racemase, a pyridoxal 5'-phosphate (PLP-dependent amino acid racemase that catalyzes the interconversion of lysine enantiomers, is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants. Here, we have determined the first crystal structure of a lysine racemase (Lyr from Proteus mirabilis BCRC10725, which shows the highest activity toward lysine and weaker activity towards arginine. In addition, we establish the first broad-specificity amino acid racemase (Bar structure from Pseudomonas putida DSM84, which presents not only the highest activity toward lysine but also remarkably broad substrate specificity. A complex structure of Bar-lysine is also established here. These structures demonstrate the similar fold of alanine racemase, which is a head-to-tail homodimer with each protomer containing an N-terminal (α/β(8 barrel and a C-terminal β-stranded domain. The active-site residues are located at the protomer interface that is a funnel-like cavity with two catalytic bases, one from each protomer, and the PLP binding site is at the bottom of this cavity. Structural comparisons, site-directed mutagenesis, kinetic, and modeling studies identify a conserved arginine and an adjacent conserved asparagine that fix the orientation of the PLP O3 atom in both structures and assist in the enzyme activity. Furthermore, side chains of two residues in α-helix 10 have been discovered to point toward the cavity and define the substrate specificity. Our results provide a structural foundation for the design of racemases with pre-determined substrate specificity and for the development of the non-antibiotic selection system in transgenic plants.

  17. Characterization of Kbot21 Reveals Novel Side Chain Interactions of Scorpion Toxins Inhibiting Voltage-Gated Potassium Channels.

    Science.gov (United States)

    ElFessi-Magouri, Rym; Peigneur, Steve; Othman, Houcemeddine; Srairi-Abid, Najet; ElAyeb, Mohamed; Tytgat, Jan; Kharrat, Riadh

    2015-01-01

    Scorpion toxins are important pharmacological tools for probing the physiological roles of ion channels which are involved in many physiological processes and as such have significant therapeutic potential. The discovery of new scorpion toxins with different specificities and affinities is needed to further characterize the physiology of ion channels. In this regard, a new short polypeptide called Kbot21 has been purified to homogeneity from the venom of Buthus occitanus tunetanus scorpion. Kbot21 is structurally related to BmBKTx1 from the venom of the Asian scorpion Buthus martensii Karsch. These two toxins differ by only two residues at position 13 (R /V) and 24 (D/N).Despite their very similar sequences, Kbot21 and BmBKTx1 differ in their electrophysiological activities. Kbot21 targets KV channel subtypes whereas BmBKTx1 is active on both big conductance (BK) and small conductance (SK) Ca2+-activated K+ channel subtypes, but has no effects on Kv channel subtypes. The docking model of Kbot21 with the Kv1.2 channel shows that the D24 and R13 side-chain of Kbot21 are critical for its interaction with KV channels.

  18. 2D IR spectroscopy of histidine: probing side-chain structure and dynamics via backbone amide vibrations.

    Science.gov (United States)

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

    2014-07-17

    It is well known that histidine is involved in many biological functions due to the structural versatility of its side chain. However, probing the conformational transitions of histidine in proteins, especially those occurring on an ultrafast time scale, is difficult. Herein we show, using a histidine dipeptide as a model, that it is possible to probe the tautomer and protonation status of a histidine residue by measuring the two-dimensional infrared (2D IR) spectrum of its amide I vibrational transition. Specifically, for the histidine dipeptide studied, the amide unit of the histidine gives rise to three spectrally resolvable amide I features at approximately 1630, 1644, and 1656 cm(-1), respectively, which, based on measurements at different pH values and frequency calculations, are assigned to a τ tautomer (1630 cm(-1) component) and a π tautomer with a hydrated (1644 cm(-1) component) or dehydrated (1656 cm(-1) component) amide. Because of the intrinsic ultrafast time resolution of 2D IR spectroscopy, we believe that the current approach, when combined with the isotope editing techniques, will be useful in revealing the structural dynamics of key histidine residues in proteins that are important for function.

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

    KAUST Repository

    Miller, Nichole Cates

    2012-08-22

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

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

    CERN Document Server

    Lundgren, Martin; Sha, Fan

    2012-01-01

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

  1. Preparation and Characterization of Polyurethanes with Cross-Linked Siloxane in the Side Chain by Sol-Gel Reactions

    Science.gov (United States)

    Zhao, Hui; Hao, Tong-Hui; Hu, Guo-Hua; Shi, Dean; Huang, Da; Jiang, Tao; Zhang, Qun-Chao

    2017-01-01

    A series of novel polyurethanes containing cross-linked siloxane in the side chain (SPU) were successfully synthesized through a sol-gel process. The SPU was composed of 0%–20% N-(n-butyl)-3-aminopropyltriethoxysilane (HDI-T) modified hexamethylene diisocynate homopolymer. The effects of HDI-T content on both the structure and properties of SPU were investigated by Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), mechanical properties tests, gel content test, water contact angle measurement and water absorption test. FT-IR, XPS and XRD results confirmed the successful incorporation of HDI-T onto polyurethanes and the formation of Si–O–Si. The surface roughness and the Si content of SPU enhanced with the increase of HDI-T content. Both crystallization and melting temperature shifted to a lower point after the incorporation of HDI-T. The hydrophobicity, tensile strength, Young’s modulus and pencil hardness overall increased with the increasing of HDI-T content, whereas the thermal stability and the elongation at break of SPU slightly decreased. PMID:28772607

  2. Restricted mobility of side chains on concave surfaces of solenoid proteins may impart heightened potential for intermolecular interactions.

    Science.gov (United States)

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

    2015-09-01

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

  3. Influence of {alpha}-methyl group on molecular aggregation structure and surface physicochemical properties of fluoroalkyl side chain polymers

    Energy Technology Data Exchange (ETDEWEB)

    Honda, K; Yamaguchi, H; Takahara, A [Graduate School of Engineering, Kyushu University, Motooka, Nishi-ku, Fukuoka, 819-0395 (Japan); Sakata, O; Sasaki, S; Takata, M [Japan Synchrotron Radiation Research Institute (JASRI) / SPring-8, Hyogo 679-5198 (Japan); Morita, M, E-mail: takahara@cstfkyushu-u.ac.j [Chemical Division, Daikin Industries, Ltd., 1-1 Nishi Hitotsuya, Settsu-shi, Osaka 566-8585 (Japan)

    2009-08-01

    Influence of {alpha}-methyl group on molecular aggregation states and surface physicochemical properties of poly(fluoroalkyl acrylate)s [PFA-C{sub y}, where y is fluoromethylene number in R{sub f} group] and poly(fluoroalkykl methacrylate)s [PFMA-C{sub y}] thin films were systematically investigated. Spin-coated PFA-C{sub y} and PFMA-C{sub y} thin films were characterized by dynamic contact angle measurements and grazing-incidence wide-angle X-ray diffraction (GIWAXD) measurements. GIWAXD data revealed that fluoroalkyl side chains of PFA-C{sub y} and PFMA-C{sub y} with y{>=}8 formed regular structures in the surface region as well as bulk one. However, the degree of orientation and ordering of the R{sub f} groups of PFMA-C{sub 8} thin films was low. Also, the receding contact angle ({theta}{sub r}) of PFMA-C{sub 8} thin films was lower than that of PFA-C{sub 8} ones. By annealing treatment, the {theta}{sub r} of PFMA-C{sub 8} was increased. These results suggest that the R{sub f} groups of PFMA-C{sub 8} were disordered due to presence of the {alpha}-methyl group. The R{sub f} groups became ordered to pack closely each other by annealing treatment, so that the water repellency was increased.

  4. Characterization of Kbot21 Reveals Novel Side Chain Interactions of Scorpion Toxins Inhibiting Voltage-Gated Potassium Channels.

    Directory of Open Access Journals (Sweden)

    Rym ElFessi-Magouri

    Full Text Available Scorpion toxins are important pharmacological tools for probing the physiological roles of ion channels which are involved in many physiological processes and as such have significant therapeutic potential. The discovery of new scorpion toxins with different specificities and affinities is needed to further characterize the physiology of ion channels. In this regard, a new short polypeptide called Kbot21 has been purified to homogeneity from the venom of Buthus occitanus tunetanus scorpion. Kbot21 is structurally related to BmBKTx1 from the venom of the Asian scorpion Buthus martensii Karsch. These two toxins differ by only two residues at position 13 (R /V and 24 (D/N.Despite their very similar sequences, Kbot21 and BmBKTx1 differ in their electrophysiological activities. Kbot21 targets KV channel subtypes whereas BmBKTx1 is active on both big conductance (BK and small conductance (SK Ca2+-activated K+ channel subtypes, but has no effects on Kv channel subtypes. The docking model of Kbot21 with the Kv1.2 channel shows that the D24 and R13 side-chain of Kbot21 are critical for its interaction with KV channels.

  5. Investigation on ultrafast third-order nonlinear optical properties of benzothiadiazole copolymer with triphenylamine derivative side chain

    Science.gov (United States)

    Gong, Weixiang; Yang, Junyi; Qin, Yuan-cheng; Wu, Xing-zhi; Jin, Xiao; Song, Yinglin

    2016-10-01

    The third-order nonlinear optical properties of benzothiadiazole copolymer with triphenylamine derivative side chain (BCT) dissolved in chloroform are investigated by top-hat Z-scan and time-resolved pump-probe techniques with a picoseconds pulses laser at wavelength of 532nm. Organic polymers of triphenylamine have been widely applied to optoelectronic devices owing to its outstanding physics and chemistry characteristic. So its nonlinear optical characteristic is worth studying. The sample's excited-state dynamics can be detected by the pump-probe with phase object device with/without an aperture in the far field. We can determine the sample's nonlinear absorptive and refractive coefficient by the top-hot Z-scan device with/without an aperture in the far field. The experimental results show that the BCT has a good reverse saturation absorption and negative refraction. At the same time, the BCT showed up long excited-state lifetimes. By means of a five-level model and analyzing the experimental curves, all nonlinear optical parameters are obtained. With the proper lifetime and intersystem crossing time, this sample can be a candidate for optical limiting.

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

    Science.gov (United States)

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

    2015-01-21

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

  7. Tuning backbones and side-chains of cationic conjugated polymers for optical signal amplification of fluorescent DNA detection.

    Science.gov (United States)

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

    2009-06-15

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

  8. Interaction of charged amino-acid side chains with ions: an optimization strategy for classical force fields.

    Science.gov (United States)

    Kahlen, Jens; Salimi, Leila; Sulpizi, Marialore; Peter, Christine; Donadio, Davide

    2014-04-10

    Many well-established classical biomolecular force fields, fitted on the solvation properties of single ions, do not necessarily describe all the details of ion pairing accurately, especially for complex polyatomic ions. Depending on the target application, it might not be sufficient to reproduce the thermodynamics of ion pairing, but it may also be necessary to correctly capture structural details, such as the coordination mode. In this work, we analyzed how classical force fields can be optimized to yield a realistic description of these different aspects of ion pairing. Given the prominent role of the interactions of negatively charged amino-acid side chains and divalent cations in many biomolecular systems, we chose calcium acetate as a benchmark system to devise a general optimization strategy that we applied to two popular force fields, namely, GROMOS and OPLS-AA. Using experimental association constants and first-principles molecular dynamics simulations as a reference, we found that small modifications of the van der Waals ion-ion interaction parameters allow a systematic improvement of the essential thermodynamic and structural properties of ion pairing.

  9. Elucidating the effects of arginine and lysine on a monoclonal antibody C-terminal lysine variation in CHO cell cultures.

    Science.gov (United States)

    Zhang, Xintao; Tang, Hongping; Sun, Ya-Ting; Liu, Xuping; Tan, Wen-Song; Fan, Li

    2015-08-01

    C-terminal lysine variants are commonly observed in monoclonal antibodies (mAbs) and found sensitive to process conditions, especially specific components in culture medium. The potential roles of media arginine (Arg) and lysine (Lys) in mAb heavy chain C-terminal lysine processing were investigated by monitoring the lysine variant levels under various Arg and Lys concentrations. Both Arg and Lys were found to significantly affect lysine variant level. Specifically, lysine variant level increased from 18.7 to 31.8 % when Arg and Lys concentrations were increased from 2 to 10 mM. Since heterogeneity of C-terminal lysine residues is due to the varying degree of proteolysis by basic carboxypeptidases (Cps), enzyme (basic Cps) level, pH conditions, and product (Arg and Lys) inhibition, which potentially affect the enzymatic reaction, were investigated under various Arg and Lys conditions. Enzyme level and pH conditions were found not to account for the different lysine variant levels, which was evident from the minimal variation in transcription level and intracellular pH. On the other hand, product inhibition effect of Arg and Lys on basic Cps was evident from the notable intracellular and extracellular Arg and Lys concentrations comparable with Ki values (inhibition constant) of basic Cps and further confirmed by cell-free assays. Additionally, a kinetic study of lysine variant level during the cell culture process enabled further characterization of the C-terminal lysine processing.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    backbone for polymer solar cells. All the polymers were roll slot die coated under ambient conditions on flexible ITO-free plastic substrates to give inverted polymer solar cell devices with an upscaled active area of 1 cm2. The best characteristics were found for the polymer carrying alkoxy side chains......-scale fabrication of polymer solar cells....

  11. 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...

  12. 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.

  13. Compounds having aromatic rings and side-chain amide-functionality and a method for transporting monovalent anions across biological membranes using the same

    Science.gov (United States)

    Davis, Jeffery T.; Sidorov, Vladimir; Kotch, Frank W.

    2008-04-08

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

  14. 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.

  15. 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...

  16. Pressure-dependent helix inversion of poly(quinoxaline-2,3-diyl)s containing chiral side chains in non-aqueous solvents.

    Science.gov (United States)

    Nagata, Yuuya; Takeda, Ryohei; Suginome, Michinori

    2015-06-30

    Poly(quinoxaline-2,3-diyl)s with chiral (S)-2-butoxymethyl side chains dissolved in 1,2-dichloroethane experience a reversible pressure-dependent helix inversion from P- to M-helical structures between 0.1 MPa and 200 MPa.

  17. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Bin, E-mail: xtuzb@163.com [College of Chemistry and Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Xiangtan University, Xiangtan 411105 (China); Key Laboratory of Advanced Functional Polymeric Materials of College of Hunan Province, Xiangtan University, Xiangtan 411105 (China); Li, Xinwei; Tang, Peng; Cao, Zhencai; Huang, Hongyan; Shen, Ping [College of Chemistry and Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Xiangtan University, Xiangtan 411105 (China); Tan, Songting [College of Chemistry and Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Xiangtan University, Xiangtan 411105 (China); Key Laboratory of Advanced Functional Polymeric Materials of College of Hunan Province, Xiangtan University, Xiangtan 411105 (China)

    2013-07-31

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

  19. The stereoselective construction of E- and Z-Δ-Ile from E-dehydroamino acid ester: the synthesis of the phomopsin A tripeptide side chain.

    Science.gov (United States)

    Yasuno, Yoko; Nishimura, Akito; Yasukawa, Yoshifumi; Karita, Yuma; Ohfune, Yasufumi; Shinada, Tetsuro

    2016-01-25

    The stereoselective synthesis of the phomopsin A tripeptide side chain was achieved by using methyl 2-(((benzyloxy)carbonyl)amino)-2-(diphenoxyphosphoryl)acetate as a common synthetic precursor for the synthesis of E-Δ-dehydroisoleucine and E-Δ-aspartate.

  20. FadD19 of Rhodococcus rhodochrous DSM43269, a Steroid-Coenzyme A Ligase Essential for Degradation of C-24 Branched Sterol Side Chains

    NARCIS (Netherlands)

    Wilbrink, M. H.; Petrusma, M.; Dijkhuizen, L.; van der Geize, R.

    The actinobacterial cholesterol catabolic gene cluster contains a subset of genes that encode beta-oxidation enzymes with a putative role in sterol side chain degradation. We investigated the physiological roles of several genes, i.e., fadD17, fadD19, fadE26, fadE27, and ro04690(DSM43269), by gene

  1. Effect of dietary lysine on hepatic lysine catabolism in broilers

    Science.gov (United States)

    Lysine is frequently a first- or second-limiting amino acid in poultry diets. Improving the efficiency of lysine use for protein synthesis would effectively lower the lysine requirement and decrease feed costs. Understanding how lysine is degraded and how the degradation is regulated would identif...

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    Alisdair M Boag

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

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

    Science.gov (United States)

    Boag, Alisdair M; Christie, Michael R; McLaughlin, Kerry A; Syme, Harriet M; Graham, Peter; Catchpole, Brian

    2015-01-01

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

  5. Sequence-specific, nanomolar peptide binding via cucurbit[8]uril-induced folding and inclusion of neighboring side chains.

    Science.gov (United States)

    Smith, Lauren C; Leach, David G; Blaylock, Brittney E; Ali, Omar A; Urbach, Adam R

    2015-03-18

    This paper describes the molecular recognition of the tripeptide Tyr-Leu-Ala by the synthetic receptor cucurbit[8]uril (Q8) in aqueous buffer with nanomolar affinity and exceptional specificity. This combination of characteristics, which also applies to antibodies, is desirable for applications in biochemistry and biotechnology but has eluded supramolecular chemists for decades. Building on prior knowledge that Q8 binds to peptides with N-terminal aromatic residues, a library screen of 105 peptides was designed to test the effects of residues adjacent to N-terminal Trp, Phe, or Tyr. The screen used tetramethylbenzobis(imidazolium) (MBBI) as a fluorescent indicator and resulted in the unexpected discovery that MBBI can serve not only as a turn-off sensor via the simultaneous inclusion of a Trp residue but also as a turn-on sensor via the competitive displacement of MBBI upon binding of Phe- or Tyr-terminated peptides. The unusual fluorescence response of the Tyr series prompted further investigation by (1)H NMR spectroscopy, electrospray ionization mass spectrometry, and isothermal titration calorimetry. From these studies, a novel binding motif was discovered in which only 1 equiv of peptide binds to Q8, and the side chains of both the N-terminal Tyr residue and its immediate neighbor bind within the Q8 cavity. For the peptide Tyr-Leu-Ala, the equilibrium dissociation constant value is 7.2 nM, whereas that of its sequence isomer Tyr-Ala-Leu is 34 μM. The high stability, recyclability, and low cost of Q8 combined with the straightforward incorporation of Tyr-Leu-Ala into recombinant proteins should make this system attractive for the development of biological applications.

  6. Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents

    Directory of Open Access Journals (Sweden)

    John C Rohloff

    2014-01-01

    Full Text Available Limited chemical diversity of nucleic acid libraries has long been suspected to be a major constraining factor in the overall success of SELEX (Systematic Evolution of Ligands by EXponential enrichment. Despite this constraint, SELEX has enjoyed considerable success over the past quarter of a century as a result of the enormous size of starting libraries and conformational richness of nucleic acids. With judicious introduction of functional groups absent in natural nucleic acids, the “diversity gap” between nucleic acid–based ligands and protein-based ligands can be substantially bridged, to generate a new class of ligands that represent the best of both worlds. We have explored the effect of various functional groups at the 5-position of uracil and found that hydrophobic aromatic side chains have the most profound influence on the success rate of SELEX and allow the identification of ligands with very low dissociation rate constants (named Slow Off-rate Modified Aptamers or SOMAmers. Such modified nucleotides create unique intramolecular motifs and make direct contacts with proteins. Importantly, SOMAmers engage their protein targets with surfaces that have significantly more hydrophobic character compared with conventional aptamers, thereby increasing the range of epitopes that are available for binding. These improvements have enabled us to build a collection of SOMAmers to over 3,000 human proteins encompassing major families such as growth factors, cytokines, enzymes, hormones, and receptors, with additional SOMAmers aimed at pathogen and rodent proteins. Such a large and growing collection of exquisite affinity reagents expands the scope of possible applications in diagnostics and therapeutics.

  7. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification.

    Science.gov (United States)

    Eudes, Aymerick; George, Anthe; Mukerjee, Purba; Kim, Jin S; Pollet, Brigitte; Benke, Peter I; Yang, Fan; Mitra, Prajakta; Sun, Lan; Cetinkol, Ozgül P; Chabout, Salem; Mouille, Grégory; Soubigou-Taconnat, Ludivine; Balzergue, Sandrine; Singh, Seema; Holmes, Bradley M; Mukhopadhyay, Aindrila; Keasling, Jay D; Simmons, Blake A; Lapierre, Catherine; Ralph, John; Loqué, Dominique

    2012-06-01

    Lignocellulosic biomass is utilized as a renewable feedstock in various agro-industrial activities. Lignin is an aromatic, hydrophobic and mildly branched polymer integrally associated with polysaccharides within the biomass, which negatively affects their extraction and hydrolysis during industrial processing. Engineering the monomer composition of lignins offers an attractive option towards new lignins with reduced recalcitrance. The presented work describes a new strategy developed in Arabidopsis for the overproduction of rare lignin monomers to reduce lignin polymerization degree (DP). Biosynthesis of these 'DP reducers' is achieved by expressing a bacterial hydroxycinnamoyl-CoA hydratase-lyase (HCHL) in lignifying tissues of Arabidopsis inflorescence stems. HCHL cleaves the propanoid side-chain of hydroxycinnamoyl-CoA lignin precursors to produce the corresponding hydroxybenzaldehydes so that plant stems expressing HCHL accumulate in their cell wall higher amounts of hydroxybenzaldehyde and hydroxybenzoate derivatives. Engineered plants with intermediate HCHL activity levels show no reduction in total lignin, sugar content or biomass yield compared with wild-type plants. However, cell wall characterization of extract-free stems by thioacidolysis and by 2D-NMR revealed an increased amount of unusual C₆C₁ lignin monomers most likely linked with lignin as end-groups. Moreover the analysis of lignin isolated from these plants using size-exclusion chromatography revealed a reduced molecular weight. Furthermore, these engineered lines show saccharification improvement of pretreated stem cell walls. Therefore, we conclude that enhancing the biosynthesis and incorporation of C₆C₁ monomers ('DP reducers') into lignin polymers represents a promising strategy to reduce lignin DP and to decrease cell wall recalcitrance to enzymatic hydrolysis. © 2012 The Authors. Plant Biotechnology Journal © 2012 Society for Experimental Biology, Association of Applied

  8. Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C.

    Science.gov (United States)

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

    2008-02-12

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

  9. 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...

  10. High-performance all-polymer solar cells via side-chain engineering of the polymer acceptor: the importance of the polymer packing structure and the nanoscale blend morphology.

    Science.gov (United States)

    Lee, Changyeon; Kang, Hyunbum; Lee, Wonho; Kim, Taesu; Kim, Ki-Hyun; Woo, Han Young; Wang, Cheng; Kim, Bumjoon J

    2015-04-17

    The effectiveness of side-chain engineering is demonstrated to produce highly efficient all-polymer solar cells (efficiency of 5.96%) using a series of naphthalene diimide-based polymer acceptors with controlled side chains. The dramatic changes in the polymer packing, blend morphology, and electron mobility of all-polymer solar cells elucidate clear trends in the photovoltaic performances.

  11. Effects of Side-Chain and Electron Exchange Correlation on the Band Structure of Perylene Diimide Liquid Crystals: A Density Functional Study

    Energy Technology Data Exchange (ETDEWEB)

    Arantes, J. T.; Lima, M. P.; Fazzio, A.; Xiang, H.; Wei, S. H.; Dalpian, G. M.

    2009-04-01

    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.

  12. Side-chain Engineering of Benzo[1,2-b:4,5-b’]dithiophene Core-structured Small Molecules for High-Performance Organic Solar Cells

    Science.gov (United States)

    Yin, Xinxing; An, Qiaoshi; Yu, Jiangsheng; Guo, Fengning; Geng, Yongliang; Bian, Linyi; Xu, Zhongsheng; Zhou, Baojing; Xie, Linghai; Zhang, Fujun; Tang, Weihua

    2016-05-01

    Three novel small molecules have been developed by side-chain engineering on benzo[1,2-b:4,5-b’]dithiophene (BDT) core. The typical acceptor-donor-acceptor (A-D-A) structure is adopted with 4,8-functionalized BDT moieties as core, dioctylterthiophene as π bridge and 3-ethylrhodanine as electron-withdrawing end group. Side-chain engineering on BDT core exhibits small but measurable effect on the optoelectronic properties of small molecules. Theoretical simulation and X-ray diffraction study reveal the subtle tuning of interchain distance between conjugated backbones has large effect on the charge transport and thus the photovoltaic performance of these molecules. Bulk-heterojunction solar cells fabricated with a configuration of ITO/PEDOT:PSS/SM:PC71BM/PFN/Al exhibit a highest power conversion efficiency (PCE) of 6.99% after solvent vapor annealing.

  13. Synthesis, pharmacokinetics, and biological use of lysine-modified single-walled carbon nanotubes

    Directory of Open Access Journals (Sweden)

    Mulvey JJ

    2014-09-01

    Full Text Available J Justin Mulvey,1,2 Evan N Feinberg,1,3 Simone Alidori,1 Michael R McDevitt,4,5 Daniel A Heller,1,6 David A Scheinberg1,5,6 1Molecular Pharmacology and Chemistry Program, Sloan Kettering Institute, New York, NY, USA; 2Tri-Institutional MD-PhD Program, New York, NY, USA; 3Department of Applied Physics, Yale University, New Haven, CT USA; 4Department of Radiology and 5Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; 6Weill Cornell Medical College, New York, NY, USA Abstract: We aimed to create a more robust and more accessible standard for amine-modifying single-walled carbon nanotubes (SWCNTs. A 1,3-cycloaddition was developed using an azomethine ylide, generated by reacting paraformaldehyde and a side-chain-Boc (tert-Butyloxycarbonyl-protected, lysine-derived alpha-amino acid, H-Lys(Boc-OH, with purified SWCNT or C60. This cycloaddition and its lysine adduct provides the benefits of dense, covalent modification, ease of purification, commercial availability of reagents, and pH-dependent solubility of the product. Subsequently, SWCNTs functionalized with lysine amine handles were covalently conjugated to a radiometalated chelator, 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA. The 111In-labeled construct showed rapid renal clearance in a murine model and a favorable biodistribution, permitting utility in biomedical applications. Functionalized SWCNTs strongly wrapped small interfering RNA (siRNA. In the first disclosed deployment of thermophoresis with carbon nanotubes, the lysine-modified tubes showed a desirable, weak SWCNT-albumin binding constant. Thus, lysine-modified nanotubes are a favorable candidate for medicinal work. Keywords: fullerene, cycloaddition, azomethine, DOTA, thermophoresis, 111In

  14. Influence of molecular weight on the phase behavior and structure formation of branched side-chain hairy-rod polyfluorene in bulk phase.

    NARCIS (Netherlands)

    Knaapila, M.; Stepanyan, R.; Torkkeli, M.; Lyons, B.P.; Ikonen, T.P.; Almasy, L.; Foreman, J.P.; Serimaa, R.; Guntner, R; Scherf, U.; Monkman, A.P.

    2005-01-01

    We report on an experimental study of the self-organization and phase behavior of hairy-rod π -conjugated branched side-chain polyfluorene, poly[9,9-bis(2-ethylhexyl)-fluorene-2,7-diyl]—i.e., poly[2,7–(9,9–bis(2–ethylhexyl)fluorene] (PF2∕6) —as a function of molecular weight (Mn) . The results have

  15. Modular synthesis of polyene side chain analogues of the potent macrolide antibiotic etnangien by a flexible coupling strategy based on hetero-bis-metallated alkenes.

    Science.gov (United States)

    Altendorfer, Mario; Raja, Aruna; Sasse, Florenz; Irschik, Herbert; Menche, Dirk

    2013-04-07

    An efficient procedure for the concise synthesis of hetero-bis-metallated alkenes as useful building blocks for the modular access to highly elaborate polyenes and stabilized analogues is reported. By applying these bifunctional olefins in convergent Stille/Suzuki-Miyaura couplings, novel, carefully selected side chain analogues of the potent RNA polymerase inhibitor etnangien were synthesized by a modular late stage coupling strategy and evaluated for antibacterial and antiproliferative activities.

  16. Side Chain Conformational Distributions of a Small Protein Derived from Model-Free Analysis of a Large Set of Residual Dipolar Couplings.

    Science.gov (United States)

    Li, Fang; Grishaev, Alexander; Ying, Jinfa; Bax, Ad

    2015-11-25

    Accurate quantitative measurement of structural dispersion in proteins remains a prime challenge to both X-ray crystallography and NMR spectroscopy. Here we use a model-free approach based on measurement of many residual dipolar couplings (RDCs) in differentially orienting aqueous liquid crystalline solutions to obtain the side chain χ1 distribution sampled by each residue in solution. Applied to the small well-ordered model protein GB3, our approach reveals that the RDC data are compatible with a single narrow distribution of side chain χ1 angles for only about 40% of the residues. For more than half of the residues, populations greater than 10% for a second rotamer are observed, and four residues require sampling of three rotameric states to fit the RDC data. In virtually all cases, sampled χ1 values are found to center closely around ideal g(-), g(+) and t rotameric angles, even though no rotamer restraint is used when deriving the sampled angles. The root-mean-square difference between experimental (3)JHαHβ couplings and those predicted by the Haasnoot-parametrized, motion-adjusted Karplus equation reduces from 2.05 to 0.75 Hz when using the new rotamer analysis instead of the 1.1-Å X-ray structure as input for the dihedral angles. A comparison between observed and predicted (3)JHαHβ values suggests that the root-mean-square amplitude of χ1 angle fluctuations within a given rotamer well is ca. 20°. The quantitatively defined side chain rotamer equilibria obtained from our study set new benchmarks for evaluating improved molecular dynamics force fields, and also will enable further development of quantitative relations between side chain chemical shift and structure.

  17. Pyroacm Resin: An Acetamidomethyl Derived Resin for Solid Phase Synthesis of Peptides through Side Chain Anchoring of C-Terminal Cysteine Residues.

    Science.gov (United States)

    Juvekar, Vinayak; Gong, Young Dae

    2016-02-19

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

  18. NETWORK CROWN ETHER POLYMERS WITH CENTRIC FUNCTIONAL GROUPS.Ⅱ.SYNTHESIS OF NETROWK CROWN ETHER POLYMER WITH PENDANT SULFIDE SIDE CHAIN AND ITS PLATINUM COMPLEX

    Institute of Scientific and Technical Information of China (English)

    CHENYuanyin; MENGLingzhi; 等

    1995-01-01

    Network crown ether polymer with pendant sulfide side chain in the network structure units has been synthesized via ring-opening copolymerization of β-ethylthioethyl glycidyl ether and diethylene glycol bisglycidyl ether.A kind of active catalyst suitable for this reaction was suggested.The title polymer was found to be a good ligand for platinous chloride,and the platinous complex could catalyze the hydrosilylation of ole fins with triethoxysilane efficiently.

  19. Time-Resolved EPR Study of Electron-Hole Dissociations Influenced by Alkyl Side Chains at the Photovoltaic Polyalkylthiophene:PCBM Interface.

    Science.gov (United States)

    Miura, Taku; Aikawa, Motoko; Kobori, Yasuhiro

    2014-01-02

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

  20. 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.

  1. Exploration on natural product anibamine side chain modification toward development of novel CCR5 antagonists and potential anti-prostate cancer agents.

    Science.gov (United States)

    Xu, Guoyan G; Zaidi, Saheem A; Zhang, Feng; Singh, Shilpa; Raborg, Thomas J; Yuan, Yunyun; Zhang, Yan

    2015-09-01

    Prostate cancer is one of the leading causes of death among males in the world. Prostate cancer cells have been shown to express upregulated chemokine receptor CCR5, a G protein-coupled receptor (GPCR) that relates to the inflammation process. Anibamine, a natural product containing a pyridine ring and two aliphatic side chains, was shown to carry a binding affinity of 1 μM at CCR5 as an antagonist with potential anti-cancer activity. However, it is not drug-like according to the Lipinski's rule of five mainly due to its two long aliphatic side chains. In our effort to improve its drug-like property, a series of anibamine derivatives were designed and synthesized by placement of aromatic side chains through an amide linkage to the pyridine ring. The newly synthesized compounds were tested for their CCR5 affinity and antagonism, and potential anti-proliferation activity against prostate cancer cell lines. Basal cytotoxicity was finally studied for compounds showing potent anti-proliferation activity. It was found that compounds with hydrophobic substitutions on the aromatic systems seemed to carry more promising CCR5 binding and prostate cancer cell proliferation inhibition activities.

  2. Control over phase behavior and solution structure of hairy-rod polyfluorene by means of side-chain length and branching

    Science.gov (United States)

    Knaapila, M.; Stepanyan, R.; Torkkeli, M.; Garamus, V. M.; Galbrecht, F.; Nehls, B. S.; Preis, E.; Scherf, U.; Monkman, A. P.

    2008-05-01

    We present guidelines on how the solution structure of π -conjugated hairy-rod polyfluorenes is controlled by the side-chain length and branching. First, the semiquantitative mean-field theory is formulated to predict the phase behavior of the system as a function of side-chain beads (N) . The phase transition at N=N∗ separates a lyotropic phase with solvent coexistence (NN∗) . The membrane phase transforms into the isotropic phase of dissolved rodlike polymers at the temperature Tmem∗(N) , which decreases both with N and with the degree of side-chain branching. This picture is complemented by polymer demixing with the transition temperature TIN∗(N) , which decreases with N . For NN∗ , stable membranes are predicted for TIN∗N∗ . Tmem∗(N) decreases from 340 K to 280 K for N≥8 . For copolymers, the membrane phase is found when the fraction of F8 units is at least 90%, Tmem∗ decreasing with this fraction. The membrane phase contains three material types: loose sheets of two polymer layers, a better packed β phase, and dissolved polymer. For N≥7 and T

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

    Science.gov (United States)

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

    2011-04-18

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

  4. 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.

  5. 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; Liu, Zitong; Cai, Zheng-Xu; Dyson, Matthew J.; Stingelin, Natalie; Chen, Wei; Ju, Hua-Jun; Zhang, Guan-Xin; Zhang, De-Qing

    2017-08-01

    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.

  6. Amphiphilic block copolymers bearing six-membered ortho ester ring in side chains as potential drug carriers: synthesis, characterization, and in vivo toxicity evaluation.

    Science.gov (United States)

    Luo, Shi; Tao, Yangyang; Tang, Rupei; Wang, Rui; Ji, Weihang; Wang, Chun; Zhao, Youliang

    2014-07-01

    A new type of amphiphilic block copolymers, poly(ethylene glycol)-block-poly(2-methyl-acrylicacid 2-methoxy-5-methyl-[1,3]dioxin-5-ylmethyl ester) (PEG-b-PMME), bearing acid-labile six-membered ortho ester rings in side chains was synthesized by reversible addition-fragmentation chain-transfer polymerization, and the influence of chain length of the hydrophobic PMME block on micelle properties was investigated. The PEG-b-PMME micelles were stable in aqueous buffer at physiological pH with a low critical micelle concentration. Nile Red as a model drug was encapsulated into the micelles to explore the release profiles. The Nile Red-loaded polymeric micelles showed rapid release of Nile Red in weakly acidic environments (pH 5) but slow release under physiological condition (pH 7.4), due to different hydrolysis rate of ortho ester side chains of PEG-b-PMME. The Paclitaxel (PTX)-loaded micelles retained potency in killing lung cancer cells (A549), compared with the free PTX. No obvious toxicity was found in vitro and in vivo after intraperitoneal injection of the micelles, which confirms that the PEG-b-PMME micelles with unique acid-labile characteristic have great potential as nano-scaled carriers for drug delivery.

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

    Science.gov (United States)

    Liang, Ying; Wu, Jian-Lin; Leung, Elaine Lai-Han; Zhou, Hua; Liu, Zhongqiu; Yan, Guanyu; Liu, Ying; Liu, Liang; Li, Na

    2016-03-31

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

  8. Lysine methylation: beyond histones

    Institute of Scientific and Technical Information of China (English)

    Xi Zhang; Hong Wen; Xiaobing Shi

    2012-01-01

    Posttranslational modifications (PTMs) of histone proteins,such as acetylation,methylation,phosphorylation,and ubiquitylation,play essential roles in regulating chromatin dynamics.Combinations of different modifications on the histone proteins,termed 'histone code' in many cases,extend the information potential of the genetic code by regulating DNA at the epigenetic level.Many PTMs occur on non-histone proteins as well as histones,regulating protein-protein interactions,stability,localization,and/or enzymatic activities of proteins involved in diverse cellular processes.Although protein phosphorylation,ubiquitylation,and acetylation have been extensively studied,only a few proteins other than histones have been reported that can be modified by lysine methylation.This review summarizes the current progress on lysine methylation of nonhistone proteins,and we propose that lysine methylation,like phosphorylation and acetylation,is a common PTM that regulates proteins in diverse cellular processes.

  9. NMR determination of lysine pKa values in the Pol lambda lyase domain: mechanistic implications.

    Science.gov (United States)

    Gao, Guanghua; DeRose, Eugene F; Kirby, Thomas W; London, Robert E

    2006-02-14

    The base excision repair (BER) process requires removal of an abasic deoxyribose-5-phosphate group, a catalytic activity that has been demonstrated for the N-terminal 8 kDa domain of DNA polymerase beta (Pol beta), and for the homologous domain of DNA polymerase lambda (Pol lambda). Previous studies have demonstrated that this activity results from formation of a Schiff base adduct of the abasic deoxyribose C-1' with a lysine residue (K312 in the case of Pol lambda), followed by a beta-elimination reaction. To better understand the underlying chemistry, we have determined pKa values for the lysine residues in the Pol lambda lyase domain labeled with [epsilon-13C]lysine. At neutral pH, the H(epsilon) protons on 3 of the 10 lysine residues in this domain, K287, K291, and K312, exhibit chemical shift inequivalence that results from immobilization of the lysyl side chains. For K287 and K291, this results from the K287-E261 and K291-E298 salt bridge interactions, while for K312, immobilization apparently results from steric and hydrogen-bonding interactions that constrain the position of the lysine side chain. The pKa value of K312 is depressed to 9.58, a value indicating that at physiological pH K312 will exist predominantly in the protonated form. Titration of the domain with hairpin DNA containing a 5'-tetrahydrofuran terminus to model the abasic site produced shifts of the labeled lysine resonances that were in fast exchange but appeared to be complete at a stoichiometry of approximately 1:1.3, consistent with a dissociation constant of approximately 1 microM. The epsilon-proton shifts of K273 were the most sensitive to the addition of the DNA, apparently due to changes in the relative orientation between K273 and W274 in the DNA complex. The average pKa values increased by 0.55, consistent with the formation of some DNA-lysine salt bridges and with the general pH increase expected to result from a reduction in the net positive charge of the complex. A general

  10. Intra-residue interactions in proteins: interplay between serine or cysteine side chains and backbone conformations, revealed by laser spectroscopy of isolated model peptides.

    Science.gov (United States)

    Alauddin, Mohammad; Biswal, Himansu S; Gloaguen, Eric; Mons, Michel

    2015-01-21

    Intra-residue interactions play an important role in proteins by influencing local folding of the backbone. Taking advantage of the capability of gas phase experiments to provide relevant information on the intrinsic H-bonding pattern of isolated peptide chains, the intra-residue interactions of serine and cysteine residues, i.e., OH/SH···OC(i) C6 and NH(i···)O/S C5 interactions in Ser/Cys residues, are probed by laser spectroscopy of isolated peptides. The strength of these local side chain-main chain interactions, elegantly documented from their IR spectral features for well-defined conformations of the main chain, demonstrates that a subtle competition exists between the two types of intra-residue bond: the C6 H-bond is the major interaction with Ser, in contrast to Cys where C5 interaction takes over. The restricted number of conformers observed in the gas phase experiment with Ser compared to Cys (where both extended and folded forms are observed) also suggests a significant mediation role of these intra-residue interactions on the competition between the several main chain folding patterns.

  11. Correlation between polymer architecture, mesoscale structure and photovoltaic performance in side-chain-modified PAE-PAV:fullerene bulk-heterojunction solar cells

    Science.gov (United States)

    Rathgeber, S.; Kuehnlenz, F.; Hoppe, H.; Egbe, D. A. M.; Tuerk, S.; Perlich, J.; Gehrke, R.

    2012-02-01

    A poly(arylene-ethynylene)-alt-poly(arylene-vinylene) statistical copolymer carrying linear and branched alkoxy side chains along the conjugated backbone in a random manner, yields, compared to its regular substituted counterparts, an improved performance in polymer:fullerene bulk-heterojunction solar cells. Results obtained from GiWAXS experiments show that the improved performance of the statistical copolymer may be attributed to the following structural characteristics: 1) Well, ordered stacked domains that promote backbone planarization and thus improve the ππ-overlap. 2) Partly face-on alignment of domains relative to the electrodes for an improved active layer electrode charge transfer. Branched side chains seem to promote face-on domain orientation. Most likely they can minimize their unfavorable contact with the interface by just bringing the CH3 groups of the branches into direct contact with the surface so that favorable phenylene-substrate interaction can promote face-on orientation. 3) A more isotropic domain orientation throughout the active layer to ensure that the backbone alignment direction has components perpendicular and parallel to the electrodes in order to compromise between light absorption and efficient intra-chain charge transport.

  12. Imidazolium-Functionalized Poly(arylene ether sulfone) Anion-Exchange Membranes Densely Grafted with Flexible Side Chains for Fuel Cells.

    Science.gov (United States)

    Guo, Dong; Lai, Ao Nan; Lin, Chen Xiao; Zhang, Qiu Gen; Zhu, Ai Mei; Liu, Qing Lin

    2016-09-28

    With the intention of optimizing the performance of anion-exchange membranes (AEMs), a set of imidazolium-functionalized poly(arylene ether sulfone)s with densely distributed long flexible aliphatic side chains were synthesized. The membranes made from the as-synthesized polymers are robust, transparent, and endowed with microphase segregation capability. The ionic exchange capacity (IEC), hydroxide conductivity, water uptake, thermal stability, and alkaline resistance of the AEMs were evaluated in detail for fuel cell applications. Morphological observation with the use of atomic force microscopy and small-angle X-ray scattering reveals that the combination of high-local-density-type and side-chain-type architectures induces distinguished nanophase separation in the AEMs. The as-prepared membranes have advantages in effective water management and ionic conductivity over traditional main-chain polymers. Typically, the conductivity and IEC were in the ranges of 57.3-112.5 mS cm(-1) and 1.35-1.84 mequiv g(-1) at 80 °C, respectively. Furthermore, the membranes exhibit good thermal and alkaline stability and achieve a peak power density of 114.5 mW cm(-2) at a current density of 250.1 mA cm(-2). Therefore, the present polymers containing clustered flexible pendent aliphatic imidazolium promise to be attractive AEM materials for fuel cells.

  13. Site-specific protonation kinetics of acidic side chains in proteins determined by pH-dependent carboxyl (13)C NMR relaxation.

    Science.gov (United States)

    Wallerstein, Johan; Weininger, Ulrich; Khan, M Ashhar I; Linse, Sara; Akke, Mikael

    2015-03-04

    Proton-transfer dynamics plays a critical role in many biochemical processes, such as proton pumping across membranes and enzyme catalysis. The large majority of enzymes utilize acid-base catalysis and proton-transfer mechanisms, where the rates of proton transfer can be rate limiting for the overall reaction. However, measurement of proton-exchange kinetics for individual side-chain carboxyl groups in proteins has been achieved in only a handful of cases, which typically have involved comparative analysis of mutant proteins in the context of reaction network modeling. Here we describe an approach to determine site-specific protonation and deprotonation rate constants (kon and koff, respectively) of carboxyl side chains, based on (13)C NMR relaxation measurements as a function of pH. We validated the method using an extensively studied model system, the B1 domain of protein G, for which we measured rate constants koff in the range (0.1-3) × 10(6) s(-1) and kon in the range (0.6-300) × 10(9) M(-1) s(-1), which correspond to acid-base equilibrium dissociation constants (Ka) in excellent agreement with previous results determined by chemical shift titrations. Our results further reveal a linear free-energy relationship between log kon and pKa, which provides information on the free-energy landscape of the protonation reaction, showing that the variability among residues in these parameters arises primarily from the extent of charge stabilization of the deprotonated state by the protein environment. We find that side-chain carboxyls with extreme values of koff or kon are involved in hydrogen bonding, thus providing a mechanistic explanation for the observed stabilization of the protonated or deprotonated state.

  14. Role of amino acid side chains in region 17-31 of parathyroid hormone (PTH) in binding to the PTH receptor.

    Science.gov (United States)

    Dean, Thomas; Khatri, Ashok; Potetinova, Zhanna; Willick, Gordon E; Gardella, Thomas J

    2006-10-27

    The principal receptor-binding domain (Ser(17)-Val(31)) of parathyroid hormone (PTH) is predicted to form an amphiphilic alpha-helix and to interact primarily with the N-terminal extracellular domain (N domain) of the PTH receptor (PTHR). We explored these hypotheses by introducing a variety of substitutions in region 17-31 of PTH-(1-31) and assessing, via competition assays, their effects on binding to the wild-type PTHR and to PTHR-delNt, which lacks most of the N domain. Substitutions at Arg(20) reduced affinity for the intact PTHR by 200-fold or more, but altered affinity for PTHR-delNt by 4-fold or less. Similar effects were observed for Glu substitutions at Trp(23), Leu(24), and Leu(28), which together form the hydrophobic face of the predicted amphiphilic alpha-helix. Glu substitutions at Arg(25), Lys(26), and Lys(27) (which forms the hydrophilic face of the helix) caused 4-10-fold reductions in affinity for both receptors. Thus, the side chains of Arg(20), together with those composing the hydrophobic face of the ligand's putative amphiphilic alpha-helix, contribute strongly to PTHR-binding affinity by interacting specifically with the N domain of the receptor. The side chains projecting from the opposite helical face contribute weakly to binding affinity by different mechanisms, possibly involving interactions with the extracellular loop/transmembrane domain region of the receptor. The data help define the roles that side chains in the binding domain of PTH play in the PTH-PTHR interaction process and provide new clues for understanding the overall topology of the bimolecular complex.

  15. Precise Side-Chain Engineering of Thienylenevinylene-Benzotriazole-Based Conjugated Polymers with Coplanar Backbone for Organic Field Effect Transistors and CMOS-like Inverters.

    Science.gov (United States)

    Lee, Min-Hye; Kim, Juhwan; Kang, Minji; Kim, Jihong; Kang, Boseok; Hwang, Hansu; Cho, Kilwon; Kim, Dong-Yu

    2017-01-25

    Two donor-acceptor (D-A) alternating conjugated polymers based on thienylenevinylene-benzotriazole (TV-BTz), PTV6B with a linear side chain and PTVEhB with a branched side chain, were synthesized and characterized for organic field effect transistors (OFETs) and complementary metal-oxide-semiconductor (CMOS)-like inverters. According to density functional theory (DFT), polymers based on TV-BTz exhibit a coplanar and rigid structure with no significant twists, which could cause to an increase in charge-carrier mobility in OFETs. Alternating alkyl side chains of the polymers impacted neither the band gap nor the energy level. However, it significantly affected the morphology and crystallinity when the polymer films were thermally annealed. To investigate the effect of thermal annealing on the morphology and crystallinity, we characterized the polymer films using atomic force microscopy (AFM) and 2D-grazing incidence X-ray diffraction (2D-GIWAXD). Fibrillary morphologies with larger domains and increased crystallinity were observed in the polymer films after thermal annealing. These polymers exhibited improved charge-carrier mobilities in annealed films at 200 °C and demonstrated optimal OFET device performance with p-type transport characteristics with charge-carrier mobilities of 1.51 cm(2)/(V s) (PTV6B) and 2.58 cm(2)/(V s) (PTVEhB). Furthermore, CMOS-like inorganic (ZnO)-organic (PTVEhB) hybrid bilayer inverter showed that the inverting voltage (Vinv) was positioned near the ideal switching point at half (1/2) of supplied voltage (VDD) due to fairly balanced p- and n-channels.

  16. Synthesis and characterization of homopolymers bearing acid-cleavable cationic side-chains for pH-modulated release of DNA.

    Science.gov (United States)

    Xu, Zhangyan; Lai, Junping; Tang, Rupei; Ji, Weihang; Wang, Rui; Wang, Jun; Wang, Chun

    2014-07-01

    A new type of homopolymers, PMAOE, bearing acid-cleavable cationic side-chains is synthesized and characterized. PMAOE is obtained via free radical polymerization, and they could efficiently bind and condense plasmid DNA at neutral pH. The strength of DNA binding is dependent on the length of PMAOE chains. NMR analysis reveals that hydrolysis of the ortho ester group of PMAOE follows an exocyclic mechanism and the rate of hydrolysis is much accelerated at mildly acidic pH, leading to accelerated disruption of polyplexes and release of DNA in mildly acidic environment. PMAOE is not toxic to cultured NIH 3T3 and COS-7 cells measured by MTT. This study demonstrates a unique mechanism of achieving pH-modulated binding and release of DNA from polymers with potential applications for gene delivery.

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

    Science.gov (United States)

    Huck, Lena; González, Juan F; de la Cuesta, Elena

    2016-01-01

    Summary A sequential three-component process is described, starting from 3-arylmethylene-2,5-piperazinediones and involving a one-pot sequence of reactions achieving regioselective opening of the 2,5-diketopiperazine ring and diastereoselective generation of an aziridine ring. This method allows the preparation of N-unprotected, trisubstituted aziridines bearing a peptide side chain under mild conditions. Their transformation into β-trifluoroacetamido-α-ketoamide and α,β-diketoamide frameworks was also achieved in a single step. PMID:27559422

  18. A new approach to the side chain formation of 24-alkyl-22-hydroxy steroids: application to the preparation of early brassinolide biosynthetic precursors.

    Science.gov (United States)

    Hurski, Alaksiej L; Zhabinskii, Vladimir N; Khripach, Vladimir A

    2012-06-01

    A new synthetic route to 22S-hydroxy-24R-methyl steroids has been developed and applied for the preparation of cathasterone, (22S)-hydroxycampesterol, and 6-deoxocathasterone, which are precursors in the early stages of the biosynthesis of brassinolide. The construction of the steroid side chain with the correct stereochemistry at C-24 is based on the use of Claisen rearrangement. The introduction of the 22-hydroxyl group has been achieved by epoxidation of the Δ(22)-double bond, nucleophilic opening of the intermediate mesyl epoxide with sodium sulfide, and desulfurization of the formed tetrahydrothiophenes with Raney nickel.

  19. Synthesis of peptides containing C-terminal methyl esters using trityl side-chain anchoring: application to the synthesis of a-factor and a-factor analogs.

    Science.gov (United States)

    Diaz-Rodriguez, Veronica; Mullen, Daniel G; Ganusova, Elena; Becker, Jeffrey M; Distefano, Mark D

    2012-11-16

    A new cysteine anchoring method was developed for the synthesis of peptides containing C-terminal cysteine methyl esters. This method consists of attachment of Fmoc-Cys-OCH(3) to either 2-ClTrt-Cl or Trt-Cl resins (via the side-chain thiol) followed by preparation of the desired peptide using Fmoc-based SPPS. We applied this method to the synthesis of the mating pheromone a-factor and a 5-FAM labeled a-factor analog. The peptides were obtained with high yield and purity and were shown to be bioactive in a growth arrest assay.

  20. 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.

  1. Ultrasonic pretreatment of liquid NaK metal catalyst for side-chain alkenylation of o-xylene with 1,3-butadiene.

    Science.gov (United States)

    Wang, Leizheng; Zheng, Jiaming

    2006-04-01

    The effects of sonochemical treatment of a NaK eutectic mixture as catalyst on the side-chain alkenylation of o-xylene with 1,3-butadiene were studied. The parameters studied include ultrasound frequency, insonation time, sonication power as well as the reaction temperature. In addition, the effect of N,N,N',N'-tetramethylethylenediamine (TMEDA) on the reaction was also studied. The results showed that sonochemical treatment of this NaK eutectic mixture catalyst resulted in excellent conversion (up to 83.16%) under mild conditions. The introduction of TMEDA further increased the conversion to 89.4%.

  2. Antidotes to anthrax lethal factor intoxication. Part 3: Evaluation of core structures and further modifications to the C2-side chain.

    Science.gov (United States)

    Jiao, Guan-Sheng; Kim, Seongjin; Moayeri, Mahtab; Crown, Devorah; Thai, April; Cregar-Hernandez, Lynne; McKasson, Linda; Sankaran, Banumathi; Lehrer, Axel; Wong, Teri; Johns, Lisa; Margosiak, Stephen A; Leppla, Stephen H; Johnson, Alan T

    2012-03-15

    Four core structures capable of providing sub-nanomolar inhibitors of anthrax lethal factor (LF) were evaluated by comparing the potential for toxicity, physicochemical properties, in vitro ADME profiles, and relative efficacy in a rat lethal toxin (LT) model of LF intoxication. Poor efficacy in the rat LT model exhibited by the phenoxyacetic acid series (3) correlated with low rat microsome and plasma stability. Specific molecular interactions contributing to the high affinity of inhibitors with a secondary amine in the C2-side chain were revealed by X-ray crystallography.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the ¿-gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation...... of ¿-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow...

  4. 1H, 13C and 15N backbone and side-chain chemical shift assignment of the Fyn SH2 domain and its complex with a phosphotyrosine peptide.

    Science.gov (United States)

    Huculeci, Radu; Buts, Lieven; Lenaerts, Tom; van Nuland, Nico A J

    2011-10-01

    SH2 domains are interaction modules uniquely dedicated to recognize phosphotyrosine sites, playing a central role in for instance the activation of tyrosine kinases or phosphatases. Here we report the (1)H, (15)N and (13)C backbone and side-chain chemical shift assignments of the SH2 domain of the human protein tyrosine kinase Fyn, both in its free state and bound to a high-affinity phosphotyrosine peptide corresponding to a specific sequence in the hamster middle-T antigen. The BMRB accession numbers are 17,368 and 17,369, respectively.

  5. Application of palladium-catalyzed carboxyl anhydride-boronic acid cross coupling in the synthesis of novel bile acids analogs with modified side chains.

    Science.gov (United States)

    Mayorquín-Torres, Martha C; Flores-Álamo, Marcos; Iglesias-Arteaga, Martin A

    2015-09-01

    Palladium-catalyzed cross coupling of 4-methoxycarbonyl phenyboronic acid with acetylated bile acids in which the carboxyl functions was activated by formation of a mixed anhydride with pivalic anhydride afforded the cross coupled compounds, which were converted in novel side chain modified bile acids by one pot carbonyl reduction/removal of the protecting acetyl groups by Wolff-Kishner reduction. Unambiguous assignments of the NMR signals and crystal characterization of the heretofore unknown compounds are provided. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Residual dipolar couplings in short peptidic foldamers: combined analyses of backbone and side-chain conformations and evaluation of structure coordinates of rigid unnatural amino acids.

    Science.gov (United States)

    Schmid, Markus B; Fleischmann, Matthias; D'Elia, Valerio; Reiser, Oliver; Gronwald, Wolfram; Gschwind, Ruth M

    2009-02-13

    A flexible tool for rigid systems. Residual dipolar couplings (RDCs) have proven to be valuable NMR structural parameters that provide insights into the backbone conformations of short linear peptidic foldamers, as illustrated here. This study demonstrates that RDCs at natural abundance can provide essential structural information even in the case of short linear peptides with unnatural amino acids. In addition, they allow for the detection of proline side-chain conformations and are used as a quality check for the parameterizations of rigid unnatural amino acids.

  7. 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....... V genes from the Jkappa-proximal duplication unit of the kappa locus were almost exclusively used. A total of 65% of the sequences could be assigned to four or five genes: A27 (humkv325), L6 (Vg), L2 (humkv328), and A3 and/or A19. N additions and P nucleotides were quite common and found in 32...

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

    Science.gov (United States)

    Kirikoshi, Ryota; Manabe, Noriyoshi; Takahashi, Ohgi

    2017-02-16

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Goebel, Carsten, E-mail: goebel.c.1@pg.com [The Procter and Gamble Co., Central Product Safety and Communications, Darmstadt (Germany); Troutman, John [The Procter and Gamble Co., Central Product Safety, Cincinnati, OH (United States); Hennen, Jenny [Dept. of Environmental Toxicology, Trier University, Trier (Germany); Rothe, Helga; Schlatter, Harald [The Procter and Gamble Co., Central Product Safety and Communications, Darmstadt (Germany); Gerberick, G. Frank [The Procter and Gamble Co., Central Product Safety, Cincinnati, OH (United States); Blömeke, Brunhilde [Dept. of Environmental Toxicology, Trier University, Trier (Germany)

    2014-02-01

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

  10. Synthesis and biological evaluation of quinazolin-4(3H)-one derivatives bearing dithiocarbamate side chain at C2-position as potential antitumor agents.

    Science.gov (United States)

    Ding, Pan-Pan; Gao, Man; Mao, Bei-Bei; Cao, Sheng-Li; Liu, Cui-Huan; Yang, Chao-Rui; Li, Zhong-Feng; Liao, Ji; Zhao, Hongchang; Li, Zheng; Li, Jing; Wang, Hailong; Xu, Xingzhi

    2016-01-27

    A series of quinazolin-4(3H)-one derivatives bearing dithiocarbamate side chain at the C2-position were synthesized and evaluated for their antiproliferative activities against A549, MCF-7, HeLa, HT29 and HCT-116 cell lines. Most of the synthesized compounds exhibited broad spectrum antitproliferative activity against five cell lines, of which 5c was the most potent against HT29 cell line with an IC50 value of 5.53 μM, inducing a G2/M phase arrest in HT29 cells. Treatment of HT29 cells with 5c resulted in BubR1 phosphorylation and an increase of mitotic index in a time-dependent manner. Furthermore, 5c promoted tubulin polymerization in vitro. These results demonstrate that quinazolin-4(3H)-one derivatives bearing dithiocarbamate side chain at C2-position may be potentially novel antitumor agents targeting tubulin to activate the spindle assembly checkpoint.

  11. Arylsulfanyl groups - Suitable side chains for 5-substituted 1,10-phenanthroline and nickel complexes as G4 ligands and telomerase inhibitors.

    Science.gov (United States)

    Liu, Wanbo; Wang, Siwen; Dotsenko, Irina A; Samoshin, Vyacheslav V; Xue, Liang

    2017-08-01

    Guanine-rich DNA sequences can undergo self-assembly into unique G-quadruplex structures that interfere with the binding of proteins to the same DNA region. The formation of DNA G-quadruplexes requires monovalent cations (Na(+) and K(+)) or small molecules known as G-quadruplex (G4) ligands. Phenanthroline is a type of G4 ligand scaffold known for its coordination with metal ions to form complexes with a large aromatic surface area, which aptly stack with G-quartets. In this report, we have investigated the side chain effect on G-quadruplex recognition by evaluating a series of 5-substituted phenanthroline-based metal complexes (Phen-Ni) binding to telomeric G-quadruplex DNA. Results from biophysical methods including fluorescence and circular dichroism (CD) thermal denaturation, CD titration, and the fluorescent intercalator displacement (FID) assay suggest that several Phen-Ni complexes bind to G-quadruplex DNA with submicromolar (G4)DC50 values. Arylsulfanyl groups at the 5 position of 1,10-phenanthroline are the best side chains regarding binding affinity and selectivity towards G-quadruplex DNA. Most of the G-quadruplex binding Phen-Ni complexes can inhibit telomerase activity in vitro as indicated by the telomeric repeat amplification protocol (TRAP) assay and such inhibition is clearly concentration dependent. Our results here provide a guidance of utilizing 5-substituted phenanthroline derivatives as a viable and facile approach to design novel G4 ligands. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Ryota Kirikoshi

    2017-02-01

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

  13. In vivo cough suppressive activity of pectic polysaccharide with arabinogalactan type II side chains of Piper nigrum fruits and its synergistic effect with piperine.

    Science.gov (United States)

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

    2017-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-05-15

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

  15. Poly(ethylene glycol)-block-poly(glycidyl methacrylate) with oligoamine side chains as efficient gene vectors.

    Science.gov (United States)

    Ma, Ming; Li, Feng; Chen, Fu-jie; Cheng, Si-xue; Zhuo, Ren-xi

    2010-02-11

    Well-defined diblock copolymers, poly(ethylene glycol)-block-poly(glycidyl methacrylate)s (PEG-b-PGMAs), with different poly(glycidyl methacrylate) (PGMA) chains, were prepared via atom transfer radical polymerization (ATRP) from the same macromolecular initiator 2-bromoisobutyryl-terminated poly(ethylene glycol) (PEG). Ethyldiamine (EDA), diethylenetriamine (DETA), triethylenetetramine (TETA), and polyethyleneimine (PEI) with an M(W) of 400 (PEI(400)) were used to decorate PEG-b-PGMAs to get the cationic polymers PEG-b-PGMA- oligoamines. These cationic polymers possessed high buffer capability and could condense plasmid DNA (pDNA) into nanoscaled complexes of 125-530 nm. These complexes showed the positive zeta potential of 20-35 mV at N/P ratios of 10-50. Most of them exhibited very low cytotoxicity and good transfection efficiency in 293T cells. The presence of the serum medium did not decrease the transfection efficiency due to the steric stabilization of the PEG chains.

  16. Richness of Side-Chain Liquid-Crystal Polymers: From Isotropic Phase towards the Identification of Neglected Solid-Like Properties in Liquids

    Directory of Open Access Journals (Sweden)

    Joachim H. Wendorff

    2012-04-01

    Full Text Available Very few studies concern the isotropic phase of Side-Chain Liquid-Crystalline Polymers (SCLCPs. However, the interest for the isotropic phase appears particularly obvious in flow experiments. Unforeseen shear-induced nematic phases are revealed away from the N-I transition temperature. The non-equilibrium nematic phase in the isotropic phase of SCLCP melts challenges the conventional timescales described in theoretical approaches and reveal very long timescales, neglected until now. This spectacular behavior is the starter of the present survey that reveals long range solid-like interactions up to the sub-millimetre scale. We address the question of the origin of this solid-like property by probing more particularly the non-equilibrium behavior of a polyacrylate substituted by a nitrobiphenyl group (PANO2. The comparison with a polybutylacrylate chain of the same degree of polymerization evidences that the solid-like response is exacerbated in SCLCPs. We conclude that the liquid crystal moieties interplay as efficient elastic connectors. Finally, we show that the “solid” character can be evidenced away from the glass transition temperature in glass formers and for the first time, in purely alkane chains above their crystallization temperature. We thus have probed collective elastic effects contained not only in the isotropic phase of SCLCPs, but also more generically in the liquid state of ordinary melts and of ordinary liquids.

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

    Science.gov (United States)

    Cai, Lu; Dai, Li; Yuan, Yanhua; Liu, Anqi; Zhanxiong, Li

    2016-05-01

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

  18. Effects of Odd–Even Side Chain Length of Alkyl-Substituted Diphenylbithiophenes on First Monolayer Thin Film Packing Structure

    KAUST Repository

    Akkerman, Hylke B.

    2013-07-31

    Because of their preferential two-dimensional layer-by-layer growth in thin films, 5,5′bis(4-alkylphenyl)-2,2′-bithiophenes (P2TPs) are model compounds for studying the effects of systematic chemical structure variations on thin-film structure and morphology, which in turn, impact the charge transport in organic field-effect transistors. For the first time, we observed, by grazing incidence X-ray diffraction (GIXD), a strong change in molecular tilt angle in a monolayer of P2TP, depending on whether the alkyl chain on the P2TP molecules was of odd or even length. The monolayers were deposited on densely packed ultrasmooth self-assembled alkane silane modified SiO2 surfaces. Our work shows that a subtle change in molecular structure can have a significant impact on the molecular packing structure in thin film, which in turn, will have a strong impact on charge transport of organic semiconductors. This was verified by quantum-chemical calculations that predict a corresponding odd-even effect in the strength of the intermolecular electronic coupling. © 2013 American Chemical Society.

  19. Significant Improvement of Semiconducting Performance of the Diketopyrrolopyrrole-Quaterthiophene Conjugated Polymer through Side-Chain Engineering via Hydrogen-Bonding.

    Science.gov (United States)

    Yao, Jingjing; Yu, Chenmin; Liu, Zitong; Luo, Hewei; Yang, Yang; Zhang, Guanxin; Zhang, Deqing

    2016-01-13

    Three diketopyrrolopyrrole (DPP)-quaterthiophene conjugated polymers, pDPP4T-1, pDPP4T-2, and pDPP4T-3, in which the molar ratios of the urea-containing alkyl chains vs branching alkyl chains are 1:30, 1:20, and 1:10, respectively, were prepared and investigated. In comparison with pDPP4T without urea groups in the alkyl side chains and pDPP4T-A, pDPP4T-B, and pDPP4T-C containing both linear and branched alkyl chains, thin films of pDPP4T-1, pDPP4T-2, and pDPP4T-3 exhibit higher hole mobilities; thin-film mobility increases in the order pDPP4T-1 thin film of pDPP4T-3 can reach 13.1 cm(2) V(-1) s(-1) after thermal annealing at just 100 °C. The incorporation of urea groups in the alkyl side chains also has an interesting effect on the photovoltaic performances of DPP-quaterthiophene conjugated polymers after blending with PC71BM. Blended thin films of pDPP4T-1:PC71BM, pDPP4T-2:PC71BM, and pDPP4T-3:PC71BM exhibit higher power conversion efficiencies (PCEs) than pDPP4T:PC71BM, pDPP4T-A:PC71BM, pDPP4T-B:PC71BM, and pDPP4T-C:PC71BM. The PCE of pDPP4T-1:PC71BM reaches 6.8%. Thin films of pDPP4T-1, pDPP4T-2, and pDPP4T-3 and corresponding thin films with PC71BM were characterized with AFM, GIXRD, and STEM. The results reveal that the lamellar packing order of the alkyl chains is obviously enhanced for thin films of pDPP4T-1, pDPP4T-2, and pDPP4T-3; after thermal annealing, slight inter-chain π-π stacking emerges for pDPP4T-2 and pDPP4T-3. Blends of pDPP4T-1, pDPP4T-2, and pDPP4T-3 with PC71BM show a more pronounced micro-phase separation. These observations suggest that the presence of urea groups may further facilitate the assemblies of these conjugated polymers into nanofibers and ordered aggregation of PC71BM.

  20. Biochemical engineering of the N-acyl side chain of sialic acids alters the kinetics of a glycosylated potassium channel Kv3.1.

    Science.gov (United States)

    Hall, M Kristen; Reutter, Werner; Lindhorst, Thisbe; Schwalbe, Ruth A

    2011-10-20

    The sialic acid of complex N-glycans can be biochemically engineered by substituting the physiological precursor N-acetylmannosamine with non-natural N-acylmannosamines. The Kv3.1 glycoprotein, a neuronal voltage-gated potassium channel, contains sialic acid. Western blots of the Kv3.1 glycoprotein isolated from transfected B35 neuroblastoma cells incubated with N-acylmannosamines verified sialylated N-glycans attached to the Kv3.1 glycoprotein. Outward ionic currents of Kv3.1 transfected B35 cells treated with N-pentanoylmannosamine or N-propanoylmannosamine had slower activation and inactivation rates than those of untreated cells. Therefore, the N-acyl side chain of sialic acid is intimately connected with the activation and inactivation rates of this glycosylated potassium channel.

  1. Discovery of 2-azetidinone and 1H-pyrrole-2,5-dione derivatives containing sulfonamide group at the side chain as potential cholesterol absorption inhibitors.

    Science.gov (United States)

    Yuan, Xinrui; Lu, Peng; Xue, Xiaojian; Qin, Hui; Fan, Chen; Wang, Yubin; Zhang, Qi

    2016-02-01

    Cholesterol absorption inhibitor (CAI) targeting Niemann-Pick C1-like1 protein was developed for the treatment of hyperlipidaemia and only ezetimibe was approved so far. For developing novel CAIs, we synthesized sixteen 2-azetidinone derivatives and thirteen 1H-pyrrole-2,5-dione derivatives containing sulfonamide group at the side chain, and their inhibitory activity of cholesterol absorption was evaluated in Caco-2 cell line in vitro. Furthermore, top six compounds were measured by cytotoxicity and partition coefficient, and 2-azetidinone analogue 9e was selected for in vivo study. Finally, 9e considerably reduced total cholesterol, LDL-C, FFA and triglyceride in the serum and increased the rate of HDL-C to total cholesterol, suggesting it could regulate the lipid metabolism and act as a potent CAI.

  2. Benzimidazole inhibitors of the protein kinase CHK2: Clarification of the binding mode by flexible side chain docking and protein–ligand crystallography

    Science.gov (United States)

    Matijssen, Cornelis; Silva-Santisteban, M. Cris; Westwood, Isaac M.; Siddique, Samerene; Choi, Vanessa; Sheldrake, Peter; van Montfort, Rob L.M.; Blagg, Julian

    2012-01-01

    Two closely related binding modes have previously been proposed for the ATP-competitive benzimidazole class of checkpoint kinase 2 (CHK2) inhibitors; however, neither binding mode is entirely consistent with the reported SAR. Unconstrained rigid docking of benzimidazole ligands into representative CHK2 protein crystal structures reveals an alternative binding mode involving a water-mediated interaction with the hinge region; docking which incorporates protein side chain flexibility for selected residues in the ATP binding site resulted in a refinement of the water-mediated hinge binding mode that is consistent with observed SAR. The flexible docking results are in good agreement with the crystal structures of four exemplar benzimidazole ligands bound to CHK2 which unambiguously confirmed the binding mode of these inhibitors, including the water-mediated interaction with the hinge region, and which is significantly different from binding modes previously postulated in the literature. PMID:23058106

  3. Synthesis of Macrocyclic Hexaoxazole (6OTD Dimers, Containing Guanidine and Amine Functionalized Side Chains, and an Evaluation of Their Telomeric G4 Stabilizing Properties

    Directory of Open Access Journals (Sweden)

    Keisuke Iida

    2010-01-01

    Full Text Available Structure-activity relationship studies were carried out on macrocyclic hexaoxazole (6OTD dimers, whose core structure stabilizes telomeric G-quadruplexes (G4. Two new 6OTD dimers having side chain amine and guanidine functional groups were synthesized and evaluated for their stabilizing ability against a telomeric G4 DNA sequence. The results show that the 6OTD dimers interact with the DNA to form 1:1 complexes and stabilize the antiparallel G4 structure of DNA in the presence of potassium cation. The guanidine functionalized dimer displays a potent stabilizing ability of the G4 structure, as determined by using a FRET melting assay (ΔTm=14 °C.

  4. Cytotoxicity towards CCO cells of imidazolium ionic liquids with functionalized side chains: preliminary QSTR modeling using regression and classification based approaches.

    Science.gov (United States)

    Bubalo, Marina Cvjetko; Radošević, Kristina; Srček, Višnja Gaurina; Das, Rudra Narayan; Popelier, Paul; Roy, Kunal

    2015-02-01

    Within this work we evaluated the cytotoxicity towards the Channel Catfish Ovary (CCO) cell line of some imidazolium-based ionic liquids containing different functionalized and unsaturated side chains. The toxic effects were measured by the reduction of the WST-1 dye after 72 h exposure resulting in dose- and structure-dependent toxicities. The obtained data on cytotoxic effects of 14 different imidazolium ionic liquids in CCO cells, expressed as EC50 values, were used in a preliminary quantitative structure-toxicity relationship (QSTR) study employing regression- and classification-based approaches. The toxicity of ILs towards CCO was chiefly related to the shape and hydrophobicity parameters of cations. A significant influence of the quantum topological molecular similarity descriptor ellipticity (ε) of the imine bond was also observed.

  5. A tailor-made specific anion-binding motif in the side chain transforms a tetrapeptide into an efficient vector for gene delivery.

    Science.gov (United States)

    Li, Mao; Schlesiger, Stefanie; Knauer, Shirley K; Schmuck, Carsten

    2015-03-02

    Arginine-rich cell-penetrating peptides are widely utilized as vectors for gene delivery. However, their transfection efficacy still needs to be optimized. To accomplish this, guanidinocarbonylpyrrole groups, which are tailor-made anion binding sites, were introduced into the side chains of tetralysine to obtain the peptide analogue 1. In contrast to the common strategy of adding a lipophilic tail to peptide vectors, this novel method most likely enhances transfection efficacy through more specific interactions between the binding motifs and DNA or the cell membrane. Tetrapeptide analogue 1 is thus the smallest peptidic transfection vector that has been reported to date. The transfection efficacy of 1, which on average has less than two positive charges under physiological conditions, is even better than that of polyethylenimine (PEI). Furthermore, 1 exhibits only negligible cytotoxicity, which makes it an interesting candidate for further development.

  6. Foldamers to nanotubes: influence of amino acid side chains in the hierarchical assembly of α,γ(4)-hybrid peptide helices.

    Science.gov (United States)

    Jadhav, Sandip V; Misra, Rajkumar; Gopi, Hosahudya N

    2014-12-08

    Supramolecular assembly of various artificially folded 12-helical architectures composed of γ(4) -Val, γ(4) -Leu and γ(4) -Phe residues is investigated. In contrast to the 12-helices composed of γ(4) -Val and γ(4) -Leu residues, the helices with γ(4) -Phe residues displayed unique elongated nanotubular architectures. The elongated nanotube assembly was further explored as a template for biomineralization of silver ions to silver nanowires. A comparative study using an analogous α-peptide helix reveals the importance of the spatial arrangement of aromatic side chains along the helical cylinder in a 12-helix. These results suggested that the proteolytically and structurally stable α,γ(4) -hybrid peptide 12-helices may serve as a new generation of potential templates in the design of functional biomaterials.

  7. A novel branched side-chain-type sulfonated polyimide membrane with flexible sulfoalkyl pendants and trifluoromethyl groups for vanadium redox flow batteries

    Science.gov (United States)

    Li, Jinchao; Liu, Suqin; He, Zhen; Zhou, Zhi

    2017-04-01

    A novel branched side-chain-type sulfonated polyimide (6F-s-bSPI) membrane with accessible branching agents of melamine, hydrophobic trifluoromethyl groups (sbnd CF3), and flexible sulfoalkyl pendants is prepared by a high-temperature polycondensation and post-sulfonation method for use in vanadium redox flow batteries (VRFBs). The chemical structure of the 6F-s-bSPI membrane is confirmed by ATR-FTIR and 1H NMR spectra. The physico-chemical properties of the as-prepared 6F-s-bSPI membrane are systematically investigated and found to be strongly related to the specially designed structure. The 6F-s-bSPI membrane offers a reduced cost and possesses a significantly lowered vanadium ion permeability (1.18 × 10-7 cm2 min-1) compared to the linear SPI (2.25 × 10-7 cm2 min-1) and commercial Nafion 115 (1.36 × 10-6 cm2 min-1) membranes, prolonging the self-discharge duration of the VRFBs. In addition, the VRFB assembled with a 6F-s-bSPI membrane shows higher coulombic (98.3%-99.7%) and energy efficiencies (88.4%-66.12%) than that with a SPI or Nafion 115 membrane under current densities ranging from 20 to 100 mA cm-2. Moreover, the VRFB with a 6F-s-bSPI membrane delivers a stable cycling performance over 100 cycles with no decline in coulombic and energy efficiencies. These results show that the branched side-chain-type structure is a promising design to prepare excellent proton conductive membranes.

  8. 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.

  9. Side-Chain Isomerization on an n-type Organic Semiconductor ITIC Acceptor Makes 11.77% High Efficiency Polymer Solar Cells.

    Science.gov (United States)

    Yang, Yankang; Zhang, Zhi-Guo; Bin, Haijun; Chen, Shanshan; Gao, Liang; Xue, Lingwei; Yang, Changduk; Li, Yongfang

    2016-11-16

    Low bandgap n-type organic semiconductor (n-OS) ITIC has attracted great attention for the application as an acceptor with medium bandgap p-type conjugated polymer as donor in nonfullerene polymer solar cells (PSCs) because of its attractive photovoltaic performance. Here we report a modification on the molecular structure of ITIC by side-chain isomerization with meta-alkyl-phenyl substitution, m-ITIC, to further improve its photovoltaic performance. In a comparison with its isomeric counterpart ITIC with para-alkyl-phenyl substitution, m-ITIC shows a higher film absorption coefficient, a larger crystalline coherence, and higher electron mobility. These inherent advantages of m-ITIC resulted in a higher power conversion efficiency (PCE) of 11.77% for the nonfullerene PSCs with m-ITIC as acceptor and a medium bandgap polymer J61 as donor, which is significantly improved over that (10.57%) of the corresponding devices with ITIC as acceptor. To the best of our knowledge, the PCE of 11.77% is one of the highest values reported in the literature to date for nonfullerene PSCs. More importantly, the m-ITIC-based device shows less thickness-dependent photovoltaic behavior than ITIC-based devices in the active-layer thickness range of 80-360 nm, which is beneficial for large area device fabrication. These results indicate that m-ITIC is a promising low bandgap n-OS for the application as an acceptor in PSCs, and the side-chain isomerization could be an easy and convenient way to further improve the photovoltaic performance of the donor and acceptor materials for high efficiency PSCs.

  10. Catalytic roles of lysines (K9, K27, K31) in the N-terminal domain in human adenylate kinase by random site-directed mutagenesis.

    Science.gov (United States)

    Ayabe, T; Park, S K; Takenaka, H; Sumida, M; Uesugi, S; Takenaka, O; Hamada, M

    1996-11-01

    To elucidate lysine residues in the N-terminal domain of human cytosolic adenylate kinase (hAK1, EC 2.7.4.3), random site-directed mutagenesis of K9, K27, and K31 residues was performed, and six mutants were analyzed by steady-state kinetics. K9 residue may play an important role in catalysis by interacting with AMP2-. K27 and K31 residues appear to play a functional role in catalysis by interacting with MgATP2-. In human AK, the epsilon-amino group in the side chain of these lysine residues would be essential for phosphoryl transfer between MgATP2- and AMP2- during transition state.

  11. 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.

  12. Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines

    DEFF Research Database (Denmark)

    Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;

    2011-01-01

    Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation....... This method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously and can directly calculate the geometrical difference induced by H/D isotope effects. The calculations show that the one-bond deuterium isotope effects on 15N nuclear shielding, 1Δ15N......(D), in ammonium and amines decrease as a counterion or water molecule moves closer to the nitrogen. 1Δ15N(D) and 2Δ1H(D) of the NH3+ groups of lysine residues in the B1 domain of protein G have been calculated using truncated side chains and also determined experimentally by NMR. Comparisons show...

  13. [Optimization of alkaline hydrolysis based on the side chain of diethyl ester 4-amino-N(5)-formyl-N(8), N(10)-dideazatetrahydrofolic acid].

    Science.gov (United States)

    Yuan, M M; Wang, M; Liu, J Y; Zhang, Z L

    2017-08-18

    To optimize and establish the best hydrolysis method of diethyl ester 4-amino-N(5)-formyl-N(8), N(10)-dideazatetrahydrofolate through the optimization of simple compound of diethyl N-(4-aminobenzoyl)-L-glutamate. To increase the low yield of hydrolysis reaction of diethyl ester 4-amino-N(5)-formyl-N(8), N(10)-dideazatetrahydrofolate due to the by-products and difficult purification, we studied the effect of NaOH and KOH, two kinds of alkalis, three concentrations between 0.175-1 mol/L and five types of reaction time involved in 20, 30, 60, 120 and 180 min on the common side chain diethyl N-(4-aminobenzoyl)-L-glutamate. A high performance liquid chromatography was established for measuring the target product and the by-products in reaction liquid in different reaction conditions. Finally, on the basis of the best hydrolysis method of diethyl ester 4-amino-N(5)-formyl-N(8), N(10)-dideazatetrahydrofolate, we completed the optimization of the hydrolysis reaction conditions of diethyl ester 4-amino-N(5)-formyl-N(8), N(10)-dideazatetrahydrofolate. We developed the best reaction condition for the hydrolysis of diethyl ester 4-amino-N(5)-formyl-N(8), N(10)-dideazatetrahydrofolate, which could be carried out easily and efficiently. The results indicated that treated with the optimized condition of 0.3 mol/L KOH in 60 min at the room temperature, diethyl ester 4-amino-N(5)-formyl-N(8), N(10)-dideazatetrahydrofolate was converted into its diacid derivative in 95.6 % yield, which turned to be a better reaction condition compared with the previous reaction condition. The structures of those compounds were identified to be correct by 1H nuclear magnetic resonance(1H NMR), 13C nuclear magnetic resonance(13C NMR) and electrospray ionization time of flight mass spectrometry (ESI-MS). The purity of the diacid derivative of the compound was determined to be 96% by high performance liquid chromatography(HPLC).The new hydrolysis reaction condition could not only avoid the formation of

  14. Vibrational analysis of amino acids and short peptides in hydrated media. VIII. Amino acids with aromatic side chains: L-phenylalanine, L-tyrosine, and L-tryptophan.

    Science.gov (United States)

    Hernández, Belén; Pflüger, Fernando; Adenier, Alain; Kruglik, Sergei G; Ghomi, Mahmoud

    2010-11-25

    Four out of the 20 natural α-amino acids (α-AAs) contain aromatic rings in their side chains. In a recent paper (J. Phys. Chem. B 2010, 114, 9072-9083), we have analyzed the structural and vibrational features of l-histidine, one of the potent elements of this series. Here, we report on the three remaining members of this family, i.e., l-phenylalanine, l-tyrosine, and l-tryptophan. Their solution (H(2)O and D(2)O) Raman scattering and Fourier transform infrared absorption attenuated total reflection (FT-IR ATR) spectra were measured at room temperature from the species corresponding to those existing at physiological conditions. Because of the very low water solubility of tyrosine, special attention was paid to avoid any artifact concerning the report of the vibrational spectra corresponding to nondissolved powder of this AA in aqueous solution. Finally, we could obtain for the first time the Raman and FT-IR spectra of tyrosine at very low concentration (2.3 mM) upon long accumulation time. To clarify this point, those vibrational spectra of tyrosine recorded either in the solid phase or in a heterogeneous state, where dissolved and nondissolved species of this AA coexist in aqueous solution, are also provided as Supporting Information . To carry out a discussion on the general geometrical and vibrational behavior of these AAs, we resorted to quantum mechanical calculations at the DFT/B3LYP/6-31++G* level, allowing (i) determination of potential energy surfaces of these AAs in a continuum solvent as a function of the torsion angles χ(1) and χ(2), defining the conformation of each aromatic side chain around C(α)-C(β) and C(β)-C(γ) bonds, respectively; (ii) analysis of geometrical features of the AAs surrounded by clusters of n explicit (n = 5-7) water molecules interacting with the backbone and aromatic rings; and (iii) assignment of the observed vibrational modes by means of the theoretical data provided by the lowest energy conformers of explicitly

  15. Preparation of side-chain-type sulfonated polysulfone and preliminary exploration the effect of side chain length on properties of proton exchange membrane%侧链型磺化聚砜的制备及侧链链长对质子交换膜性能影响的研究

    Institute of Scientific and Technical Information of China (English)

    乔宗文; 高保娇; 陈涛

    2015-01-01

    以氯乙酰氯和氯丁酰氯为亲电试剂,通过Friedel-Crafts酰基化反应,在聚砜( PSF)主链引入了含氯的且碳原子数目不同的(分别为2和4)柔性侧链,然后以对羟基苯磺酸钠(HBSS)为试剂,通过亲核取代反应制备了侧链型磺化聚砜2PSF-BSS和4PSF-BSS。采用佛尔哈德分析法、红外光谱(FT-IR)以及核磁氢谱(1H-NMR)对侧链型磺化聚砜的化学结构和性能进行了表征,重点考察主要因素对Friedel-Crafts酰基化和亲核取代反应的影响,实验结果表明:以无水AlCl3为催化剂,CH2 Cl2为反应溶剂,反应温度50℃,CAPSF和CBPSF中氯含量分别达到2.03mmol/g和2.07mmol/g,第2步亲核取代反应遵循SN1机理,在强极性溶剂DMSO中磺酸基键合量分别为1.48mmol/g和1.46mmol/g。同时初步探索侧链链长对质子交换膜的质子传导率的影响,随着侧链长度的增长,侧链的柔性增强,亲水微区与疏水微区微相分离的程度增强,导致交换膜的质子传导率增大。%With chloroacetyl chloride and chlorobutyryl chloride as electrophilic reagents, a flexible side chain with exchangeable chlorine was bonded on the backbone of polysulfone ( PSF ) via Friedel-Crafts acylation reaction. Subsequently, with sodium 4-hydroxybenzenesulfonate(HBSS)as reagent,two kinds of sulfonated polysulfones with side-chain-type(2PSF-BSS and 4PSF-BSS) were obtained via nucleophilic substitution. The chemical structure and properties of the target polymer PSF-sas were characterized by Vilhard methods,FT-IR and 1 H-NMR. The effects of various factors on the Friedel-Crafts acylation reaction and nucleophilic sub-stitution reaction were mainly investigated. The experimental results show that the degree of chloride ( DC ) of CAPSF and CBPSF could reach to 2. 03mmol/g and 2. 07mmol/g at 50℃ with AlCl3(0. 90 g)as catalyst and CH2Cl2as solvent,respectively. The sec-ond step is a unimolecular nucleophilic substitution reaction,i. e. SN1. CAPSF-sas with a

  16. Backbone and side chain NMR assignments of Geobacillus stearothermophilus ZapA allow identification of residues that mediate the interaction of ZapA with FtsZ.

    Science.gov (United States)

    Nogueira, Maria Luiza C; Sforça, Mauricio Luis; Chin, Yanni K-Y; Mobli, Mehdi; Handler, Aaron; Gorbatyuk, Vitaliy Y; Robson, Scott A; King, Glenn F; Gueiros-Filho, Frederico J; Zeri, Ana Carolina de Mattos

    2015-10-01

    Bacterial division begins with the formation of a contractile protein ring at midcell, which constricts the bacterial envelope to generate two daughter cells. The central component of the division ring is FtsZ, a tubulin-like protein capable of self-assembling into filaments which further associate into a higher order structure known as the Z ring. Proteins that bind to FtsZ play a crucial role in the formation and regulation of the Z ring. One such protein is ZapA, a widely conserved 21 kDa homodimeric protein that associates with FtsZ filaments and promotes their bundling. Although ZapA was discovered more than a decade ago, the structural details of its interaction with FtsZ remain unknown. In this work, backbone and side chain NMR assignments for the Geobacillus stearothermophilus ZapA homodimer are described. We titrated FtsZ into (15)N(2)H-ZapA and mapped ZapA residues whose resonances are perturbed upon FtsZ binding. This information provides a structural understanding of the interaction between FtsZ and ZapA.

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

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

  18. Supramolecular Phase-Selective Gelation by Peptides Bearing Side-Chain Azobenzenes: Effect of Ultrasound and Potential for Dye Removal and Oil Spill Remediation

    Directory of Open Access Journals (Sweden)

    Jürgen Bachl

    2015-05-01

    Full Text Available Phase selective gelation (PSG of organic phases from their non-miscible mixtures with water was achieved using tetrapeptides bearing a side-chain azobenzene moiety. The presence of the chromophore allowed PSG at the same concentration as the minimum gelation concentration (MGC necessary to obtain the gels in pure organic phases. Remarkably, the presence of the water phase during PSG did not impact the thermal, mechanical, and morphological properties of the corresponding organogels. In the case of miscible oil/water mixtures, the entire mixture was gelled, resulting in the formation of quasi-hydrogels. Importantly, PSG could be triggered at room temperature by ultrasound treatment of the mixture or by adding ultrasound-aided concentrated solution of the peptide in an oil-phase to a mixture of the same oil and water. Moreover, the PSG was not affected by the presence of salts or impurities existing in water from natural sources. The process could be scaled-up, and the oil phases (e.g., aromatic solvents, gasoline, diesel fuel recovered almost quantitatively after a simple distillation process, which also allowed the recovery and reuse of the gelator. Finally, these peptidic gelators could be used to quantitatively remove toxic dyes from aqueous solutions.

  19. Supramolecular Phase-Selective Gelation by Peptides Bearing Side-Chain Azobenzenes: Effect of Ultrasound and Potential for Dye Removal and Oil Spill Remediation

    Science.gov (United States)

    Bachl, Jürgen; Oehm, Stefan; Mayr, Judith; Cativiela, Carlos; Marrero-Tellado, José Juan; Díaz Díaz, David

    2015-01-01

    Phase selective gelation (PSG) of organic phases from their non-miscible mixtures with water was achieved using tetrapeptides bearing a side-chain azobenzene moiety. The presence of the chromophore allowed PSG at the same concentration as the minimum gelation concentration (MGC) necessary to obtain the gels in pure organic phases. Remarkably, the presence of the water phase during PSG did not impact the thermal, mechanical, and morphological properties of the corresponding organogels. In the case of miscible oil/water mixtures, the entire mixture was gelled, resulting in the formation of quasi-hydrogels. Importantly, PSG could be triggered at room temperature by ultrasound treatment of the mixture or by adding ultrasound-aided concentrated solution of the peptide in an oil-phase to a mixture of the same oil and water. Moreover, the PSG was not affected by the presence of salts or impurities existing in water from natural sources. The process could be scaled-up, and the oil phases (e.g., aromatic solvents, gasoline, diesel fuel) recovered almost quantitatively after a simple distillation process, which also allowed the recovery and reuse of the gelator. Finally, these peptidic gelators could be used to quantitatively remove toxic dyes from aqueous solutions. PMID:26006247

  20. Supramolecular phase-selective gelation by peptides bearing side-chain azobenzenes: effect of ultrasound and potential for dye removal and oil spill remediation.

    Science.gov (United States)

    Bachl, Jürgen; Oehm, Stefan; Mayr, Judith; Cativiela, Carlos; Marrero-Tellado, José Juan; Díaz, David Díaz

    2015-05-22

    Phase selective gelation (PSG) of organic phases from their non-miscible mixtures with water was achieved using tetrapeptides bearing a side-chain azobenzene moiety. The presence of the chromophore allowed PSG at the same concentration as the minimum gelation concentration (MGC) necessary to obtain the gels in pure organic phases. Remarkably, the presence of the water phase during PSG did not impact the thermal, mechanical, and morphological properties of the corresponding organogels. In the case of miscible oil/water mixtures, the entire mixture was gelled, resulting in the formation of quasi-hydrogels. Importantly, PSG could be triggered at room temperature by ultrasound treatment of the mixture or by adding ultrasound-aided concentrated solution of the peptide in an oil-phase to a mixture of the same oil and water. Moreover, the PSG was not affected by the presence of salts or impurities existing in water from natural sources. The process could be scaled-up, and the oil phases (e.g., aromatic solvents, gasoline, diesel fuel) recovered almost quantitatively after a simple distillation process, which also allowed the recovery and reuse of the gelator. Finally, these peptidic gelators could be used to quantitatively remove toxic dyes from aqueous solutions.

  1. Sterol Side Chain Reductase 2 Is a Key Enzyme in the Biosynthesis of Cholesterol, the Common Precursor of Toxic Steroidal Glycoalkaloids in Potato[W][OPEN

    Science.gov (United States)

    Sawai, Satoru; Ohyama, Kiyoshi; Yasumoto, Shuhei; Seki, Hikaru; Sakuma, Tetsushi; Yamamoto, Takashi; Takebayashi, Yumiko; Kojima, Mikiko; Sakakibara, Hitoshi; Aoki, Toshio; Muranaka, Toshiya; Saito, Kazuki; Umemoto, Naoyuki

    2014-01-01

    Potatoes (Solanum tuberosum) contain α-solanine and α-chaconine, two well-known toxic steroidal glycoalkaloids (SGAs). Sprouts and green tubers accumulate especially high levels of SGAs. Although SGAs were proposed to be biosynthesized from cholesterol, the biosynthetic pathway for plant cholesterol is poorly understood. Here, we identify sterol side chain reductase 2 (SSR2) from potato as a key enzyme in the biosynthesis of cholesterol and related SGAs. Using in vitro enzyme activity assays, we determined that potato SSR2 (St SSR2) reduces desmosterol and cycloartenol to cholesterol and cycloartanol, respectively. These reduction steps are branch points in the biosynthetic pathways between C-24 alkylsterols and cholesterol in potato. Similar enzymatic results were also obtained from tomato SSR2. St SSR2-silenced potatoes or St SSR2-disrupted potato generated by targeted genome editing had significantly lower levels of cholesterol and SGAs without affecting plant growth. Our results suggest that St SSR2 is a promising target gene for breeding potatoes with low SGA levels. PMID:25217510

  2. SOMO (SOlution MOdeler) differences between X-Ray- and NMR-derived bead models suggest a role for side chain flexibility in protein hydrodynamics.

    Science.gov (United States)

    Rai, Nithin; Nöllmann, Marcelo; Spotorno, Bruno; Tassara, Giovanni; Byron, Olwyn; Rocco, Mattia

    2005-05-01

    Reduced numbers of frictional/scattering centers are essential for tractable hydrodynamic and small-angle scattering data modeling. We present a method for generating medium-resolution models from the atomic coordinates of proteins, basically by using two nonoverlapping spheres of differing radii per residue. The computed rigid-body hydrodynamic parameters of BPTI, RNase A, and lysozyme models were compared with a large database of critically assessed experimental values. Overall, very good results were obtained, but significant discrepancies between X-ray- and NMR-derived models were found. Interestingly, they could be accounted for by properly considering the extent to which highly mobile surface side chains differently affect translational/rotational properties. Models of larger structures, such as fibrinogen fragment D and citrate synthase, also produced consistent results. Foremost among this method's potential applications is the overall conformation and dynamics of modular/multidomain proteins and of supramolecular complexes. The possibility of merging data from high- and low-resolution structures greatly expands its scope.

  3. Photoinduced dichroism and optical anisotropy in a liquid-crystalline azobenzene side chain polymer caused by anisotropic angular distribution of trans and cis isomers

    Science.gov (United States)

    Blinov, Lev M.; Kozlovsky, Mikhail V.; Ozaki, Masanori; Skarp, Kent; Yoshino, Katsumi

    1998-10-01

    Photochromism has been studied for two comb-like liquid-crystalline copolymers (I) and (II) containing azobenzene chromophores in their side chains. In a smectic glass phase of both copolymers, upon short-time irradiation by UV light, long-living cis isomers are observed. Both copolymers manifest the photoinduced anisotropy, the physical mechanisms of which seem to be quite different. In spin-coated films of polymer (II), the origin of the anisotropy is a strong stable dichroism, which is due to an enrichment and depletion of the chosen angular direction, correspondingly, with trans and cis isomers of the azobenzene chromophores. Polymer (I) manifests no dichroism at all, and its induced optical anisotropy may be accounted for by a rather slow chromophore reorientation. In copolymer (II) a considerable reorientation of the mesogenic groups also occurs as a secondary phenomenon at the stage of the cis isomer formation only. This observation shed more light on the general process of the light-induced molecular reorientation in polymers, liquid crystals, and Langmuir-Blodgett films, which is of great importance for holographic information recording.

  4. Theoretical studies on interactions between low energy electrons and protein-DNA fragments: valence anions of AT-amino acids side chain complexes.

    Science.gov (United States)

    Szyperska, Anna; Gajewicz, Agnieszka; Mazurkiewicz, Kamil; Leszczynski, Jerzy; Rak, Janusz

    2011-11-21

    Electron attachment to trimeric complexes that mimic most frequent hydrogen bonding interactions between an amino acid side chain (AASC) and the Watson-Crick (WC) 9-methyladenine-1-methylthymine (MAMT) base pair has been studied at the B3LYP/6-31++G(d,p) level of theory. Although the neutral trimers will not occur in the gas phase due to unfavorable free energy of stabilization (G(stab)) they should form a protein-DNA complex where entropy changes related to formation of such a complex will more than balance its disadvantageous G(stab). The most stable neutrals possess an identical pattern of hydrogen bonds (HBs). In addition, the proton-acceptor (N7) and proton-donor (N10) atoms of adenine involved in those HBs are located in the main groove of DNA. All neutral structures support the adiabatically stable valence anions in which the excess electron is localized on a π* orbital of thymine. The vertical detachment energies (VDEs) of anions corresponding to the most stable neutrals are substantially smaller than that of the isolated WC MAMT base pair. Hence, electron transfer from the anionic thymine to the phosphate group and as a consequence formation of a single strand break (SSB) should proceed more efficiently in a protein-dsDNA complex than in the naked dsDNA as far as electron attachment to thymine is concerned. This journal is © the Owner Societies 2011

  5. Stable polyglutamine dimers can contain β-hairpins with interdigitated side chains-but not α-helices, β-nanotubes, β-pseudohelices, or steric zippers.

    Science.gov (United States)

    Miettinen, Markus S; Monticelli, Luca; Nedumpully-Govindan, Praveen; Knecht, Volker; Ignatova, Zoya

    2014-04-15

    A common thread connecting nine fatal neurodegenerative protein aggregation diseases is an abnormally expanded polyglutamine tract found in the respective proteins. Although the structure of this tract in the large mature aggregates is increasingly well described, its structure in the small early aggregates remains largely unknown. As experimental evidence suggests that the most toxic species along the aggregation pathway are the small early ones, developing strategies to alleviate disease pathology calls for understanding the structure of polyglutamine peptides in the early stages of aggregation. Here, we present a criterion, grounded in available experimental data, that allows for using kinetic stability of dimers to assess whether a given polyglutamine conformer can be on the aggregation path. We then demonstrate that this criterion can be assessed using present-day molecular dynamics simulations. We find that although the α-helical conformer of polyglutamine is very stable, dimers of α-helices lack the kinetic stability necessary to support further oligomerization. Dimers of steric zipper, β-nanotube, and β-pseudohelix conformers are also too short-lived to initiate aggregation. The β-hairpin-containing conformers, instead, invariably form very stable dimers when their side chains are interdigitated. Combining these findings with the implications of recent solid-state NMR data on mature fibrils, we propose a possible pathway for the initial stages of polyglutamine aggregation, in which β-hairpin-containing conformers act as templates for fibril formation.

  6. Is buffer a good proxy for a crowded cell-like environment? A comparative NMR study of calmodulin side-chain dynamics in buffer and E. coli lysate.

    Directory of Open Access Journals (Sweden)

    Michael P Latham

    Full Text Available Biophysical studies of protein structure and dynamics are typically performed in a highly controlled manner involving only the protein(s of interest. Comparatively fewer such studies have been carried out in the context of a cellular environment that typically involves many biomolecules, ions and metabolites. Recently, solution NMR spectroscopy, focusing primarily on backbone amide groups as reporters, has emerged as a powerful technique for investigating protein structure and dynamics in vivo and in crowded "cell-like" environments. Here we extend these studies through a comparative analysis of Ile, Leu, Val and Met methyl side-chain motions in apo, Ca(2+-bound and Ca(2+, peptide-bound calmodulin dissolved in aqueous buffer or in E. coli lysate. Deuterium spin relaxation experiments, sensitive to pico- to nano-second time-scale processes and Carr-Purcell-Meiboom-Gill relaxation dispersion experiments, reporting on millisecond dynamics, have been recorded. Both similarities and differences in motional properties are noted for calmodulin dissolved in buffer or in lysate. These results emphasize that while significant insights can be obtained through detailed "test-tube" studies, experiments performed under conditions that are "cell-like" are critical for obtaining a comprehensive understanding of protein motion in vivo and therefore for elucidating the relation between motion and function.

  7. Vasoactive intestinal peptide-induced expression of cytochrome P450 cholesterol side-chain cleavage and 17 alpha-hydroxylase enzyme activity in hen granulosa cells.

    Science.gov (United States)

    Johnson, A L; Li, Z; Gibney, J A; Malamed, S

    1994-08-01

    Experiments were conducted to determine whether vasoactive intestinal peptide (VIP) can regulate expression of cytochrome P450 side-chain cleavage (P450scc) and P450 17 alpha-hydroxylase (P450 17 alpha-OH) mRNA levels and enzyme activity in granulosa cells from nonhierarchal (6-8-mm) follicles. Initial studies demonstrated that immunoreactive VIP is localized within the theca (but not granulosa) layer of both resting (< 0.5-mm follicles) and 6-8-mm follicles, thus providing a potential paracrine mechanism of action for VIP. While short-term (3 h) incubation of granulosa cells with VIP (0.001-1.0 microM) failed to stimulate progesterone production from 6-8-mm follicle granulosa cells, a 4-h culture period in the presence of VIP resulted in increased cyclic AMP (cAMP) accumulation, and a 24-h culture period resulted in progesterone synthesis and increased P450scc mRNA levels; control levels of each endpoint measurement were not altered within the period observed. By contrast, culture with the growth factor transforming growth factor alpha (TGF alpha) in the presence of VIP (1 microM) prevented increases in P450scc mRNA levels and progesterone production. Similar effects of VIP and TGF alpha in the presence of VIP were demonstrated for P450 17 alpha-OH mRNA levels and enzyme activity. Finally, there was an additive effect of VIP (0.1 microM) plus recombinant human (rh) FSH (100 mIU) on the initiation of progesterone production in cultured 6-8-mm follicle granulosa cells compared to the addition of VIP or rhFSH alone.(ABSTRACT TRUNCATED AT 250 WORDS)

  8. Transmembrane Segment 6 of the Glut1 Glucose Transporter Is an Outer Helix and Contains Amino Acid Side Chains Essential for Transport Activity*

    Science.gov (United States)

    Mueckler, Mike; Makepeace, Carol

    2008-01-01

    Experimental data and homology modeling suggest a structure for the exofacial configuration of the Glut1 glucose transporter in which 8 transmembrane helices form an aqueous cavity in the bilayer that is stabilized by four outer helices. The role of transmembrane segment 6, predicted to be an outer helix in this model, was examined by cysteine-scanning mutagenesis and the substituted cysteine accessibility method using the membrane-impermeant, sulfhydryl-specific reagent, p-chloromercuribenzene-sulfonate (pCMBS). A fully functional Glut1 molecule lacking all 6 native cysteine residues was used as a template to produce a series of 21 Glut1 point mutants in which each residue along helix 6 was individually changed to cysteine. These mutants were expressed in Xenopus oocytes, and their expression levels, functional activities, and sensitivities to inhibition by pCMBS were determined. Cysteine substitutions at Leu204 and Pro205 abolished transport activity, whereas substitutions at Ile192, Pro196, Gln200, and Gly201 resulted in inhibition of activity that ranged from ∼35 to ∼80%. Cysteine substitutions at Leu188, Ser191, and Leu199 moderately augmented specific transport activity relative to the control. These results were dramatically different from those previously reported for helix 12, the structural cognate of helix 6 in the pseudo-symmetrical structural model, for which none of the 21 single-cysteine mutants exhibited reduced activity. Only the substitution at Leu188 conferred inhibition by pCMBS, suggesting that most of helix 6 is not exposed to the external solvent, consistent with its proposed role as an outer helix. These data suggest that helix 6 contains amino acid side chains that are critical for transport activity and that structurally analogous outer helices may play distinct roles in the function of membrane transporters. PMID:18245775

  9. Side chain flexibility and coupling between the S4-S5 linker and the TRP domain in thermo-sensitive TRP channels: Insights from protein modeling.

    Science.gov (United States)

    Romero-Romero, Sergio; Gomez Lagunas, Froylan; Balleza, Daniel

    2017-04-01

    The transient receptor potential (TRP) superfamily is subdivided into several subfamilies on the basis of sequence similarity, which is highly heterogeneous but shows a molecular architecture that resembles the one present in members of the Kv channel superfamily. Because of this diversity, they produce a large variety of channels with different gating and permeability properties. Elucidation of these particular features necessarily requires comparative studies based on structural and functional data. The present study aims to compilate, analyze, and determine, in a coherent way, the relationship between intrinsic side-chain flexibility and the allosteric coupling in members of the TRPV, TRPM, and TRPC families. Based on the recently determined structures of TRPV1 and TRPV2, we have generated protein models for single subunits of TRPV5, TRPM8, and TRPC5 channels. With these models, we focused our attention on the apparently crucial role of the GP dipeptide at the center of the S4-S5 linker and discussed its role in the interaction with the TRP domain, specifically with the highly-conserved Trp during this coupling. Our analysis suggests an important role of the S4-S5L flexibility in the thermosensitivity, where heat-activated channels possess rigid S4-S5 linkers, whereas cold-activated channels have flexible ones. Finally, we also present evidence of the key interaction between the conserved Trp residue of the TRP box and of several residues in the S4-S5L, importantly the central Pro. Proteins 2017; 85:630-646. © 2016 Wiley Periodicals, Inc.

  10. Hydrogen exchange study on the hydroxyl groups of serine and threonine residues in proteins and structure refinement using NOE restraints with polar side-chain groups.

    Science.gov (United States)

    Takeda, Mitsuhiro; Jee, JunGoo; Ono, Akira M; Terauchi, Tsutomu; Kainosho, Masatsune

    2011-11-02

    We recently developed new NMR methods for monitoring the hydrogen exchange rates of tyrosine hydroxyl (Tyr-OH) and cysteine sulfhydryl (Cys-SH) groups in proteins. These methods facilitate the identification of slowly exchanging polar side-chain protons in proteins, which serve as sources of NOE restraints for protein structure refinement. Here, we have extended the methods for monitoring the hydrogen exchange rates of the OH groups of serine (Ser) and threonine (Thr) residues in an 18.2 kDa protein, EPPIb, and thus demonstrated the usefulness of NOE restraints with slowly exchanging OH protons for refining the protein structure. The slowly exchanging Ser/Thr-OH groups were readily identified by monitoring the (13)C(β)-NMR signals in an H(2)O/D(2)O (1:1) mixture, for the protein containing Ser/Thr residues with (13)C, (2)H-double labels at their β carbons. Under these circumstances, the OH groups exist in equilibrium between the protonated and deuterated isotopomers, and the (13)C(β) peaks of the two species are resolved when their exchange rate is slower than the time scale of the isotope shift effect. In the case of EPPIb dissolved in 50 mM sodium phosphate buffer (pH 7.5) at 40 °C, one Ser and four Thr residues were found to have slowly exchanging hydroxyl groups (k(ex) OH groups in hand, we could collect additional NOE restraints for EPPIb, thereby making a unique and important contribution toward defining the spatial positions of the OH protons, and thus the hydrogen-bonding acceptor atoms.

  11. A novel GH43 α-l-arabinofuranosidase of Penicillium chrysogenum that preferentially degrades single-substituted arabinosyl side chains in arabinan.

    Science.gov (United States)

    Shinozaki, Ayaka; Kawakami, Takuya; Hosokawa, Sachiko; Sakamoto, Tatsuji

    2014-05-10

    We previously described three α-l-arabinofuranosidases (ABFs) secreted by Penicillium chrysogenum 31B. Here, we purified a fourth ABF, termed PcABF43A, from the culture filtrate. The molecular mass of the enzyme was estimated to be 31kDa. PcABF43A had the highest activity at 35°C and at around pH 5. The enzyme activity was strong on sugar beet l-arabinan but weak on debranched arabinan and arabinoxylan. Low molecular-mass substrates such as p-nitrophenyl α-l-arabinofuranoside, α-1,5-l-arabinooligosaccharides, and branched arabinotriose were highly resistant to the action of PcABF43A. (1)H-NMR analysis revealed that PcABF43A hydrolyzed arabinosyl side chains linked to C-2 or C-3 of single-substituted arabinose residues in l-arabinan. Reports concerning enzymes specific for l-arabinan are quite limited. Pcabf43A cDNA encoding PcABF43A was isolated by in vitro cloning. The deduced amino acid sequence of the enzyme shows high similarities with the sequences of other fungal uncharacterized proteins. Semi-quantitative RT-PCR analysis indicated that the Pcabf43A gene was constitutively expressed in P. chrysogenum 31B at a low level, although the expression was induced with pectic components such as l-arabinose, l-rhamnose, and d-galacturonic acid. Analysis of enzymatic characteristics of PcABF43A, GH51 ABF (AFQ1), and GH54 ABF (AFS1) from P. chrysogenum suggested that PcABF43A and AFS1 function as debranching enzymes and AFQ1 plays a role of saccharification in the degradation of l-arabinan by this fungus.

  12. The constant electric field effect on the dipole moment of a comb-like polymer with chromophore groups in side chains

    Directory of Open Access Journals (Sweden)

    Tamara P. Stepanova

    2015-03-01

    Full Text Available The study of conformational properties and tendency to association for chromophore-containing comb-like copolymer of β-(3,4-dicyanophenylazobenzenethyazole methacrylate (A and amylmethacrylate (B (1:1 has been carried out. The copolymer AB is of particular interest because of non-linear optical properties of its films. Dielectric permittivity and dipole moment temperature dependences in dilute cyclohexanone solutions in the temperature range from 20 to 70 °С, in the electric field E ≤ 104 V/cm were investigated by means of static dielectric polarization. It was shown that temperature and concentration dependences of dielectric permittivity for the solvent, copolymer AB, monomer A and polymer B were linear indicating low molecular interactions at temperatures and fields used. The invariable stoichiometry of components in solution for concentration lower than 10–3 mol/mol was proved. The values of dielectric permittivity were extrapolated to infinite dilution and increments α=(Δɛ12/Δx2x2=0 were calculated. The solvent dipole moments were calculated in terms of the Onsager theory whereas dipole moments of AB, A and B were calculated in terms of the Backingham statistical theory of dielectric polarization. Intramacromolecular conformational transition was found to be at ∼40 °C. Dipole moment of A was shown to increase with both temperature and electric field strength. Copolymer side chains trans-location takes place due to intramacromolecular association resulting in the compensation of dipole moments and Kirkwood factor g ≈ 0.6. The association of A units increases in the electric field reducing the dipole moment per monomer unit significantly and g values approximately twice.

  13. Aromatic side-chain cluster of biotin binding site of avidin allows circular dichroism spectroscopic investigation of its ligand binding properties.

    Science.gov (United States)

    Zsila, Ferenc

    2011-01-01

    Promiscuous ligand binding by hen egg-white avidin has been demonstrated and studied by using circular dichroism (CD) spectroscopy complemented by molecular docking calculations. It has been shown that the biotin-binding pocket of avidin is able to accommodate a wide variety of chemical compounds including therapeutic drugs (e.g., thalidomide, NSAIDs, antihistamines), natural compounds (bilirubin, myristic acid), and synthetic agents (xanthenone dyes). The cluster of aromatic residues located at the biotin-binding pocket renders the intrinsic CD spectrum of avidin sensitive to ligand binding that results in the increase of the vibronic components of the (1) L(b) transition of the Trp residues. Extrinsic (induced) CD bands measured with chemically diverse avidin ligands are generated by intramolecular coupled oscillator (e.g., bilirubin) or by intermolecular ligand-Trp exciton coupling mechanism [e.g., 2-(4'-hydroxyazobenzene)-benzoic acid (HABA)]. Among the compounds of which avidin-binding affinity constants have been calculated, two novel high-affinity ligands, flufenamic acid and an enzyme inhibitor thiazole derivative have been identified (K(d) ≈ 1 μM). Avidin binding mode of the ligand molecules has been discussed in the light of docking results. The induced CD profile of the thiazole derivative has been correlated with the stereochemistry of its docked conformation. The important role in the ligand binding of a polar side-chain cluster at the bottom of the biotin-binding cavity as well as the analogous avidin-binding mode of HABA and fenamic acid type NSAIDs have been proposed. Copyright © 2011 John Wiley & Sons, Ltd.

  14. 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/dH2O) mixture is used as a solvent system during sample preparation for proteomic research. This chemical modification may result misidentification with endogenous protein methylation; therefore, a special care should be taken during sample handling prior to mass spectrometric analysis. In the current study, we systematically examined the extent of E/D methylation and C-terminus carboxyl group of synthetic model peptides in terms of different incubation temperatures, storage times, and added acid types as well as its percentages. To monitor these effects, C-terminus amidated and free acid forms of synthetic model peptides comprised of E or D residue(s) have been analyzed by electrospray ionization-mass spectrometry (ESI-MS). Additionally, LC-MS/MS experiments were performed to confirm the formation of methylated peptide product. The results showed that the rate of methylation was increased as the temperature increases along with prolong incubation times. Moreover, the extent of methylation was remarkably high when formic acid (FA) used as a protonation agent instead of acetic acid (AA). In addition, it was found that the degree of methylation was significantly decreased by lowering acid percentages in ESI solution. More than one acidic residue containing model peptides have been also used to explore the extent of multiple methylation reaction. Lastly, the ethanol (EtOH) and isopropanol (iPrOH) have been substituted separately with MeOH in sample preparation step to investigate the extent of esterification reaction under the same experimental conditions. However, in the positive perspective of view, this method can be used as a simple, rapid and cheap method for methylation of acidic residues under normal laboratory conditions.

  15. In vivo exposure of young adult male rats to methoxychlor reduces serum testosterone levels and ex vivo Leydig cell testosterone formation and cholesterol side-chain cleavage activity.

    Science.gov (United States)

    Murono, Eisuke P; Derk, Raymond C; Akgul, Yucel

    2006-02-01

    Methoxychlor (MC) was developed as a replacement for the banned pesticide DDT. After in vivo administration, it is metabolized in the liver to 2,2-bis(p-hydroxyphenyl)-1,1,1-trichloroethane (HPTE), which is proposed to be the active agent. Both MC and HPTE have been shown to exhibit weak estrogenic and antiandrogenic activities, and they are thought to exert their effects through estrogen and androgen receptors, respectively. Although in vitro studies using cultured rat Leydig cells have reported that HPTE inhibits both basal and hCG-stimulated testosterone formation, the response of circulating testosterone levels to in vivo MC has been more variable. Therefore, the current studies evaluated whether the daily in vivo administration of MC (0, 5, 40 and 200 mg/kg body weight) for a short duration (days 54-60 of age) by gavage altered serum testosterone levels and ex vivo Leydig cell testosterone formation in young adult male rats. These results demonstrate that both fluid-retained and fluid-expressed seminal vesicle weights declined to 44 and 60% of control, respectively, in the 200 mg/kg MC-exposed animals. Similarly, serum testosterone and dehydroepiandrosterone levels declined to 41 and 45% of control, respectively, in the 200 mg/kg MC-exposed animals; however, serum LH and FSH levels were unaffected. Ex vivo Leydig cell basal testosterone formation over 4h declined to 49% of control in animals exposed to 200 mg/kg MC, and ex vivo Leydig cell P450 cholesterol side-chain cleavage activity declined to 79 and 50% of control in animals exposed to 40 and 200 mg/kg of MC, respectively, supporting previous in vitro studies which demonstrated the sensitivity of this step to MC.

  16. Solubility of n-butane and 2-methylpropane (isobutane) in 1-alkyl-3-methylimidazolium-based ionic liquids with linear and branched alkyl side-chains.

    Science.gov (United States)

    Pison, Laure; Shimizu, Karina; Tamas, George; Lopes, José Nuno Canongia; Quitevis, Edward L; Gomes, Margarida F Costa

    2015-11-11

    The solubility of n-butane and 2-methylpropane (isobutane) in three ionic liquids - 1-(2-methylpropyl)-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [(2mC3)C1im][Ntf2], 1-(3-methylbutyl)-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [(3mC4)C1im][Ntf2] and 1-methyl-3-pentylimidazolium bis(trifluoromethylsulfonyl)imide [C5C1im][Ntf2] - has been measured at atmospheric pressure from 303 to 343 K. Isobutane is less soluble than n-butane in all the ionic liquids. Henry's constant values range from 13.8 × 10(5) Pa for n-butane in [C5C1im][Ntf2] at 303 K to 64.5 × 10(5) Pa for isobutane in [(2mC3)C1im][Ntf2] at 343 K. The difference in solubility between the two gases can be explained by a more negative enthalpy of solvation for n-butane. A structural analysis of the pure solvents and of the solutions of the gases, probed by molecular dynamics simulations, could explain the differences found in the systems: (i) the nonpolar domains of the ionic liquids accommodate better the long and more flexible n-butane solute; (ii) the small differences in solubility of each gas in the ionic liquids with the same number of carbon atoms in the alkyl side-chains are explained by the absence of large structural differences in the pure solvents. In all cases, the structural analysis of the four ionic liquids confirms that the studied gases can act as probes of the molecular structure of the ionic liquids, the simulations being always compatible with the experimental solubility data.

  17. Benchmark Database on Isolated Small Peptides Containing an Aromatic Side Chain: Comparison Between Wave Function and Density Functional Theory Methods and Empirical Force Field

    Energy Technology Data Exchange (ETDEWEB)

    Valdes, Haydee; Pluhackova, Kristyna; Pitonak, Michal; Rezac, Jan; Hobza, Pavel

    2008-03-13

    A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A)—where F and W are of aromatic character—is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone–aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a ‘-D’ symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals—not covering this energy—fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.

  18. Digestible lysine requirements of broilers

    Directory of Open Access Journals (Sweden)

    LEP Bernal

    2014-03-01

    Full Text Available Modern broilers have been submitted to continuous genetic improvement, and therefore, their nutritional requirements must be constantly updated to ensure their performance. Two experiments were carried out to evaluate different digestible lysine levels for starter (1021 days and grower (22-35 days phases. The experiments were carried out with male and female Cobb 500 broilers, distributed according to a randomized block experimental design in a 5x2 factorial arrangement (5 increasing digestible lysine levels x 2 sexes, totaling 10 treatments, with 8 replicates of 22 and 20 birds during the starter and grower phase, respectively. Digestible lysine levels of 1.06, 1.12, 1.18, 1.24, and 1.30 were used in the starter diets (10-21 days and 0.9, 0.98, 1.04, 1.10, and 1.16% in the grower diets (22-35 days. Based on the statistical analyses of the evaluated performance parameters, digestible lysine requirements for maximum performance were determined as 1.22% for males and 1.24% for females in the starter phase, and 1.16% for both sexes in the grower phase. Carcass and performance results indicate that digestible lysine requirements vary with sex and evaluated production parameter. Considering the most relevant broiler production parameters, in 22- to 35-d-old males, digestible lysine requirement for breast meat yield (1.16% was higher than those for feed conversion ratio (1.07% and weight gain (1.05%.

  19. Hypochlorite-induced damage to proteins: formation of nitrogen-centred radicals from lysine residues and their role in protein fragmentation.

    Science.gov (United States)

    Hawkins, C L; Davies, M J

    1998-01-01

    Stimulated monocytes and neutrophils generate hypochlorite (HOCl) via the release of the enzyme myeloperoxidase and hydrogen peroxide. HOCl damages proteins by reaction with amino acid side-chains or backbone cleavage. Little information is available about the mechanisms and intermediates involved in these reactions. EPR spin trapping has been employed to identify radicals on proteins, peptides and amino acids after treatment with HOCl. Reaction with HOCl gives both high- and low-molecular-mass nitrogen-centred, protein-derived radicals; the yield of the latter increases with both higher HOCl:protein ratios and enzymic digestion. These radicals, which arise from lysine side-chain amino groups, react with ascorbate, glutathione and Trolox. Reaction of HOCl-treated proteins with excess methionine eliminates radical formation, which is consistent with lysine-derived chloramines (via homolysis of N-Cl bonds) being the radical source. Incubation of HOCl-treated proteins, after removal of excess oxidant, gives rise to both nitrogen-centred radicals, over a period of hours, and time-dependent fragmentation of the protein. Treatment with excess methionine or antioxidants (Trolox, ascorbate, glutathione) protects against fragmentation; urate and bilirubin do not. Chloramine formation and nitrogen-centred radicals are therefore key species in HOCl-induced protein fragmentation. PMID:9620862

  20. The methoxychlor metabolite, HPTE, directly inhibits the catalytic activity of cholesterol side-chain cleavage (P450scc) in cultured rat ovarian cells.

    Science.gov (United States)

    Akgul, Yucel; Derk, Raymond C; Meighan, Terence; Rao, K Murali Krishna; Murono, Eisuke P

    2008-01-01

    Exposure to the pesticide methoxychlor in rodents is linked to impaired steroid production, ovarian atrophy and reduced fertility. Following in vivo administration, it is rapidly converted by the liver to 2,2-bis-(p-hydroxyphenyl)-1,1,1-trichloroethane (HPTE), the reported active metabolite. Both methoxychlor and HPTE have weak estrogenic and antiandrogenic activities, and these effects are thought to be mediated through the estrogen and androgen receptors, respectively. Previous in vivo studies on methoxychlor exposure to female animals have demonstrated decreased progesterone production but no change in serum estrogen levels. We recently showed that HPTE specifically inhibits the P450 cholesterol side-chain cleavage (P450scc, CYP11A1) step resulting in decreased androgen production by cultured rat testicular Leydig cells. The current studies examined the mechanism of action of HPTE on progesterone production by cultured ovarian cells (granulosa and theca-interstitial) from pregnant mare serum gonadotropin-primed immature rats. In addition, we evaluated whether the effects of HPTE on rat ovarian cell progesterone biosynthesis were mediated through the estrogen or androgen receptors. Exposure to HPTE (0, 10, 50 or 100nM) alone progressively inhibited progesterone formation in cultured theca-interstitial and granulosa cells and the P450scc catalytic activity in theca-interstitial cells in a dose-dependent manner with significant declines starting at 50nM. However, HPTE did not change mRNA levels of the P450scc system (P450scc, adrenodoxin reductase and adrenodoxin) as well as P450scc protein levels. Of interest, estradiol, xenoestrogens (bisphenol-A or 4-tert-octylphenol), a pure antiestrogen (ICI 182,780), or antiandrogens (4-hydroxyflutamide or the vinclozolin metabolite M-2), had no effect on progesterone production even at 1000nM. Co-treatment of HPTE with ICI 182,780 did not block the effect of HPTE on progesterone formation. These studies suggest that the

  1. Phenolic compounds reduce formation of N(ε)-(carboxymethyl)lysine and pyrazines formed by Maillard reactions in a model bread system.

    Science.gov (United States)

    Mildner-Szkudlarz, Sylwia; Siger, Aleksander; Szwengiel, Artur; Przygoński, Krzysztof; Wojtowicz, Elżbieta; Zawirska-Wojtasiak, Renata

    2017-09-15

    This study had the objective of determining the antiglycation activity of phenolic compounds (PCs) ((+)-catechin, quercetin, gallic, ferulic, and caffeic acids) added to a model bread with regards to the inhibition of N(ε)-(carboxymethyl)lysine (CML) formation. PCs were found to significantly reduce CML (31.77%-87.56%), even at the lowest concentration, with the exception of ferulic acid (FA). The strongest inhibitory effect of FA (∼62%) appeared when concentration was increased to 1.0g/100g of flour. The available lysine losses (0.00%-90.51%) showed a significant correlation (0.853-0.990) with effectiveness of CML inhibition, except in the case of samples with FA. (+)-Catechin reduced CML levels the most, probably due to its structure-antioxidant activity relationship, its thermal stability (∼51% loss), and its reactivity with ε-lysine side chains (∼40.77% loss). Although the bread supplemented with PCs contained low levels of CML, this process may adversely affect bread flavor, reducing the formation of pyrazines (1.10%-80.77%). Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Steroids excreted in urine by neonates with 21-hydroxylase deficiency: characterization, using GC-MS and GC-MS/MS, of the D-ring and side chain structure of pregnanes and pregnenes.

    Science.gov (United States)

    Christakoudi, Sofia; Cowan, David A; Taylor, Norman F

    2010-01-01

    Steroid metabolites in urine from neonates with 21-hydroxylase deficiency are predominantly polyhydroxylated 17-hydroxyprogesterone and androgen metabolites, and most have incompletely defined structure. This study forms part of a comprehensive project to characterize and identify these in order to enhance diagnosis and to further elucidate neonatal types of steroid metabolism. Steroids were analyzed, after extraction and enzymatic conjugate hydrolysis, as methyloxime-trimethylsilyl ether derivatives on gas-chromatographs coupled to quadrupole and ion-trap mass-spectrometers. GC-MS and GC-MS/MS spectra, obtained with constant excitation conditions, were used together to determine the structure of the D-ring and the side chain of 20-oxo and 20-hydroxy pregnane(ene)s without oxo groups on the A-, B-, and C-ring. All possible combinations of D-ring and side chain configuration were considered. Most fragmentations could be interpreted as partial or complete D-ring cleavages with loss of the side chain, aided by comparison with spectra of deuterated derivatives and of borohydride reduced metabolites. Possible rearrangement ions are also discussed. More than 140 endogenous metabolites were characterized. GC-MS/MS was especially beneficial for characterization of compounds with 16,17-dihydroxy-20-oxo structure, interpreted as markers of intra-uterine enzyme induction. It also assisted the differentiation of 16-hydroxy-20-oxo metabolites, present in urine of non-affected neonates, from the diagnostic 17-hydroxy-20-oxosteroids and enabled the detection of 15,17-dihydroxy-20-oxo compounds in low concentrations. The presence of 17,21-dihydroxylated pregnane(ene)s despite the deficit in CYP21A2 is discussed. We conclude that GC-MS combined with GC-MS/MS allows reliable identification of the structure of the D-ring and side chain of pregnane(ene)s without prior isolation, even when in low concentrations in urine.

  3. Nano-mole scale side-chain signal assignment by 1H-detected protein solid-state NMR by ultra-fast magic-angle spinning and stereo-array isotope labeling.

    Directory of Open Access Journals (Sweden)

    Songlin Wang

    Full Text Available We present a general approach in 1H-detected 13C solid-state NMR (SSNMR for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS at ~80 kHz, and stereo-array-isotope-labeled (SAIL proteins [Kainosho M. et al., Nature 440, 52-57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg that was SAIL-labeled at seven isoleucine (Ile residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.

  4. Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling

    KAUST Repository

    Wang, Songlin

    2015-04-09

    We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52–57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.

  5. 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

    2013-03-27

    While varying the size and branching of solubilizing side chains in π-conjugated polymers impacts their self-assembling properties in thin-film devices, these structural changes remain difficult to anticipate. This report emphasizes the determining role that linear side-chain substituents play in poly(benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers for bulk heterojunction (BHJ) solar cell applications. We show that replacing branched side chains by linear ones in the BDT motifs induces a critical change in polymer self-assembly and backbone orientation in thin films that correlates with a dramatic drop in solar cell efficiency. In contrast, we show that for polymers with branched alkyl-substituted BDT motifs, controlling the number of aliphatic carbons in the linear N-alkyl-substituted TPD motifs is a major contributor to improved material performance. With this approach, PBDTTPD polymers were found to reach power conversion efficiencies of 8.5% and open-circuit voltages of 0.97 V in BHJ devices with PC71BM, making PBDTTPD one of the best polymer donors for use in the high-band-gap cell of tandem solar cells. © 2013 American Chemical Society.

  6. Site-specific protein backbone and side-chain NMR chemical shift and relaxation analysis of human vinexin SH3 domain using a genetically encoded {sup 15}N/{sup 19}F-labeled unnatural amino acid

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Pan [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xi, Zhaoyong; Wang, Hu [School of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026 (China); Shi, Chaowei [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2010-11-19

    Research highlights: {yields} Chemical synthesis of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine. {yields} Site-specific incorporation of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine to SH3. {yields} Site-specific backbone and side chain chemical shift and relaxation analysis. {yields} Different internal motions at different sites of SH3 domain upon ligand binding. -- Abstract: SH3 is a ubiquitous domain mediating protein-protein interactions. Recent solution NMR structural studies have shown that a proline-rich peptide is capable of binding to the human vinexin SH3 domain. Here, an orthogonal amber tRNA/tRNA synthetase pair for {sup 15}N/{sup 19}F-trifluoromethyl-phenylalanine ({sup 15}N/{sup 19}F-tfmF) has been applied to achieve site-specific labeling of SH3 at three different sites. One-dimensional solution NMR spectra of backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F were obtained for SH3 with three different site-specific labels. Site-specific backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F chemical shift and relaxation analysis of SH3 in the absence or presence of a peptide ligand demonstrated different internal motions upon ligand binding at the three different sites. This site-specific NMR analysis might be very useful for studying large-sized proteins or protein complexes.

  7. Available lysine in canned fish

    OpenAIRE

    Rao, D. Ramananda; Gadre, Ujjwala V.

    1984-01-01

    Otolithus argenteus was canned in brine by heat processing at two different steam pressures either at 0.70 kg/cm super(2) or 1.05 kg/cm super(2) for 25 minutes. The nutritive value of canned fish as evaluated by the total nitrogen and available lysine did not alter much either during heat processing or during storage over a period of nine months at 28 degree plus or minus 5 degree C.

  8. Effect of bacteriophage lysin on lysogens

    Institute of Scientific and Technical Information of China (English)

    Balaji Subramanyam; Vanaja Kumar

    2011-01-01

    Objective: To study the effect of phage lysin on the growth of lysogens. Methods: Sputum specimens processed by modified Petroff's method were respectively treated with phagebiotics in combination with lysin and lysin alone. The specimens were incubated at 37℃ for 4 days. At the end of day 1, 2, 3 and day 4, the specimens were streaked on blood agar plates and incubated at 37℃ for 18-24 hours. The growth of normal flora observed after day 1 was considered as lysogens.Results:When specimens treated with lysin alone, lysogen formation was avoided and normal flora was controlled. Conclusions: Lysin may have no effect on the growth of lysogens. Sputum specimens treated with phagebiotics-lysin showed the growth of lysogens.

  9. Inversion of the Side-Chain Stereochemistry of Indvidual Thr or Ile Residues in a Protein Molecule: Impact on the Folding, Stability, and Structure of the ShK Toxin.

    Science.gov (United States)

    Dang, Bobo; Shen, Rong; Kubota, Tomoya; Mandal, Kalyaneswar; Bezanilla, Francisco; Roux, Benoit; Kent, Stephen B H

    2017-03-13

    ShK toxin is a cysteine-rich 35-residue protein ion-channel ligand isolated from the sea anemone Stichodactyla helianthus. In this work, we studied the effect of inverting the side chain stereochemistry of individual Thr or Ile residues on the properties of the ShK protein. Molecular dynamics simulations were used to calculate the free energy cost of inverting the side-chain stereochemistry of individual Thr or Ile residues. Guided by the computational results, we used chemical protein synthesis to prepare three ShK polypeptide chain analogues, each containing either an allo-Thr or an allo-Ile residue. The three allo-Thr or allo-Ile-containing ShK polypeptides were able to fold into defined protein products, but with different folding propensities. Their relative thermal stabilities were measured and were consistent with the MD simulation data. Structures of the three ShK analogue proteins were determined by quasi-racemic X-ray crystallography and were similar to wild-type ShK. All three ShK analogues retained ion-channel blocking activity.

  10. Hemoglobin Labeled by Radioactive Lysine

    Science.gov (United States)

    Bale, W. F.; Yuile, C. L.; DeLaVergne, L.; Miller, L. L.; Whipple, G. H.

    1949-12-08

    This paper reports on the utilization of tagged epsilon carbon of DL-lysine by a dog both anemic and hypoproteinemic due to repeated bleeding plus a diet low in protein. The experiment extended over period of 234 days, a time sufficient to indicate an erythrocyte life span of at least 115 days based upon the rate of replacement of labeled red cell proteins. The proteins of broken down red cells seem not to be used with any great preference for the synthesis of new hemoglobin.

  11. Low-band-gap conjugated polymers of dithieno[2,3-b:7,6-b]carbazole and diketopyrrolopyrrole: effect of the alkyl side chain on photovoltaic properties.

    Science.gov (United States)

    Deng, Yunfeng; Chen, Yagang; Liu, Jian; Liu, Lihui; Tian, Hongkun; Xie, Zhiyuan; Geng, Yanhou; Wang, Fosong

    2013-06-26

    Four donor–acceptor (D–A) conjugated polymers of dithieno[2,3-b;7,6-b]carbazole (DTC) and diketopyrrolopyrrole, which have different alkyls on the nitrogen atom in the DTC unit and are named as P-C8C8, P-C5C5, P-C12, and P-C10, respectively, have been synthesized for studying the effect of the alkyl side chains on the optoelectronic properties of the polymers. All polymers are soluble in various organic solvents and exhibit identical optical band gaps (E(g)(opt)) of ~1.3 eV and highest occupied molecular orbital energy levels of ~−5.1 eV. Organic thin-film transistors and bulk heterojunction polymer solar cells (BHJ PSCs) with phenyl-C(71)-butyric acid methyl ester (PC(71)BM) as the electron-accepting material were fabricated via solution spin-casting. Compared to the polymers substituted by branched alkyl chains, the polymers with straight alkyl chains show higher hole mobility. Of these polymers, P-C10 exhibits the highest field effect mobility up to 0.011 cm(2)/V·s. The alkyl chain on the DTC unit has a strong impact on the film morphology of polymer:PC(71)BM blends. Severe phase separation was found for polymers containing branched alkyl chains, and those with straight alkyl chains formed uniform films featuring fine phase separation. An open-circuit voltage (V(oc)) of 0.72 V, a short-circuit current density (J(sc)) of 13.4 mA/cm(2), a fill factor (FF) of 62%, and a power conversion efficiency (PCE) of 5.9% were demonstrated for BHJ PSCs based on the P-C10:PC(71)BM [1:3 (w/w)] blend film.

  12. Integrated low-carbon location-routing method for the demand side of a product distribution supply chain: a DoE-guided MOPSO optimiser-based solution approach

    OpenAIRE

    Validi, Sahar; Bhattacharya, Arijit; Byrne, P J

    2014-01-01

    This article contributes to location-routing literature on three inter-linked aspects viz., formulation of a novel integrated low-carbon/green location-routing model for the demand side of a Supply Chain (SC) with a single product and multiple consumers, i.e., Drop-off Points (DoPs), a novel and robust solution approach through a Design of Experiment (DoE)-guided Multiple-Objective Particle Swarm Optimisation (MOPSO) optimiser and exhaustive analysis of the location-routing solutions (i.e., p...

  13. Property-based design and synthesis of new chloroquine hybrids via simple incorporation of 2-imino-thiazolidine-4-one or 1h-pyrrol-2, 5-dione fragments on the 4-amino-7-chloroquinoline side chain

    Energy Technology Data Exchange (ETDEWEB)

    Rojas, Fernando A.; Kouznetsov, Vladimir V., E-mail: kouznet@uis.edu.co [Laboratorio de Quimica Organica y Biomolecular, Escuela de Quimica, Universidad Industrial de Santander, Bucaramanga (Colombia)

    2011-09-15

    In the present work, the syntheses of new 4-amino-7-chloroquinoline N-derivatives were performed by selective modification of the side chain amino group of N-(7-chloroquinoline-4-yl) alkyldiamines, basis framework of chloroquine (CQ) drug through the incorporation of heterocyclic 2-imino-thiazolidine-4-one and {sup 1}H-pyrrol-2,5-dione systems. These potential activity modulators were selected thanks to their characteristic properties, and evaluated by virtual screening employing the OSIRIS and Molinspirations platforms. Designed and synthesized quinolinic derivatives could increase the antimalarial activity of CQ analogues without affecting the lipophilicity as described in literature, suggesting them as candidates for further biological assessments. (author)

  14. PENILAIAN PENGARUH PENAMBAHAN LYSINE PADA NASI

    Directory of Open Access Journals (Sweden)

    Ignatius Tarwotjo

    2012-11-01

    Full Text Available Pengaruh penambahan lysine pada mutu protein nasi dilakukan pada tikus putih dengan mengukur Protein Efficiency Ratio. Nasi dan Nasi dengan sayur beserta laukpauk, seperti dikonsumsi oleh kebanyakan keluarga di Indonesia, yang berasnya lebih dulu ditambahi butiran premix berisi lysine, thiamine dan riboflavin ternaya menghasilkan Protein Efficiency Ratio lebih tinggi dari pada yang tidak ditambahi.

  15. 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

    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....... R., Jakobsen, C. M., Janssen, S., Khan, S. R., Garrett, E. S., Lilja, H., Christensen, S. B., and Isaacs, J. T. (2003) J. Natl. Cancer Inst. 95, 990-1000). Our study demonstrates the usefulness of a simple in vitro system to test and direct development toward the formulation of new Tg derivatives...

  16. Design of Side Payment Incentive Scheme in Tourism Service Supply Chain%旅游服务供应链中旁支付激励机制的设计

    Institute of Scientific and Technical Information of China (English)

    鲁芳; 牛文举

    2012-01-01

    旅游服务供应链中,如何促使导游提高服务努力水平是旅行社面临的实际问题。针对这一问题提出了旁支付激励机制,利用博弈论等分析了旁支付激励机制实施前后各博弈方的最优策略及期望收益,证明了旁支付激励机制不仅能促使导游提高服务努力水平,而且还能增加旅行社的期望收益并使旅游服务供应链的运作效率得到提升。%A practical problem that the travel agency faces is to promote tour guides to improve their service effort level in the tourism service supply chain.A side payment incentive scheme is presented to solve this problem.Analyzed the game players’optimal strategies and expected profits before and after the implementation of the side payment incentive scheme by means of game theory,and proved that this incentive scheme not only could motivate tour guides to enhance their service effort level,but also could increase the travel agency’s expected returns and improve the operational efficiency of the tourism service supply chain.

  17. Engineering a Lysine-ON Riboswitch for Metabolic Control of Lysine Production in Corynebacterium glutamicum.

    Science.gov (United States)

    Zhou, Li-Bang; Zeng, An-Ping

    2015-12-18

    Riboswitches are natural RNA elements that regulate gene expression by binding a ligand. Here, we demonstrate the possibility of altering a natural lysine-OFF riboswitch from Eschericia coli (ECRS) to a synthetic lysine-ON riboswitch and using it for metabolic control. To this end, a lysine-ON riboswitch library was constructed using tetA-based dual genetic selection. After screening the library, the functionality of the selected lysine-ON riboswitches was examined using a report gene, lacZ. Selected lysine-ON riboswitches were introduced into the lysE gene (encoding a lysine transport protein) of Corynebacterium glutamicum and used to achieve dynamic control of lysine transport in a recombinant lysine-producing strain, C. glutamicum LPECRS, which bears a deregulated aspartokinase and a lysine-OFF riboswitch for dynamic control of the enzyme citrate synthase. Batch fermentation results of the strains showed that the C. glutamicum LPECRS strain with an additional lysine-ON riboswitch for the control of lysE achieved a 21% increase in the yield of lysine compared to that of the C. glutamicum LPECRS strain and even a 89% increase in yield compared to that of the strain with deregulated aspartokinase. This work provides a useful approach to generate lysine-ON riboswitches for C. glutamicum metabolic engineering and demonstrates for the first time a synergetic effect of lysine-ON and -OFF riboswitches for improving lysine production in this industrially important microorganism. The approach can be used to dynamically control other genes and can be applied to other microorganisms.

  18. Molecular and crystalline structures of three (S)-4-alkoxycarbonyl-2-azetidinones containing long alkyl side chains from synchrotron X-ray powder diffraction data.

    Science.gov (United States)

    Seijas, Luis E; Mora, Asiloé J; Delgado, Gerzon E; López-Carrasquero, Francisco; Báez, María E; Brunelli, Michela; Fitch, Andrew N

    2009-12-01

    The (S)-4-alkoxo-2-azetidinecarboxylic acids are optically active beta-lactam derivatives of aspartic acid, which are used as precursors of carbapenem-type antibiotics and poly-beta-aspartates. The crystal structures of three (S)-4-alkoxo-2-azetidinecarboxylic acids with alkyl chains with 10, 12 and 16 C atoms were solved using parallel tempering and refined against the X-ray powder diffraction data using the Rietveld method. The azetidinone rings in the three compounds display a pattern of asymmetrical bond distances and an almost planar conformation; these characteristics are compared with periodic solid-state, gas-phase density-functional theory (DFT) calculations and MOGUL average bond distances and angles from the CSD. The compounds pack along [001] as corrugated sheets separated by approximately 4.40 A and connected by hydrogen bonds of the type N-H...O.

  19. Structural definition of early lysine and histidine adduction chemistry of 4-hydroxynonenal.

    Science.gov (United States)

    Nadkarni, D V; Sayre, L M

    1995-03-01

    The lipid peroxidation product trans-4-hydroxy-2-nonenal (HNE) has been implicated in the covalent modification of low-density lipoproteins (LDL) thought to contribute to the over-accumulation of LDL in the arterial wall in the initial stages of atherosclerosis. Proposals for the exact structures of "early" protein side-chain modifications until now have been based on indirect evidence. In this paper, the structures of first-formed His- and Lys-based adducts were elucidated by correlating NMR spectral properties with those obtained on models with reduced chiral center content, in some cases following hydride reduction. In this manner, we could confirm unambiguously the structure of a HNE-His imidazole(N tau) Michael adduct, stabilized as a cyclic hemiacetal and isolated from a neutral aqueous 1:1 stoichiometry reaction mixture. In the case of Lys/amine reactivity, where an excess of amine is needed to avert HNE aldol condensation, the predominance of a 1:1 Michael adduct in homogeneous aqueous solution and a 1:2 Michael-Schiff base adduct under two-phase aqueous-organic conditions could be verified by isolation of the respective borohydride-reduced forms. The 1:2 adduct, shown to exist as the cyclic hemiaminal, could represent a stable lysine-based cross-link in certain protein microenvironments.

  20. Lysine-Tryptophan-Crosslinked Peptides Produced by Radical SAM Enzymes in Pathogenic Streptococci.

    Science.gov (United States)

    Schramma, Kelsey R; Seyedsayamdost, Mohammad R

    2017-04-21

    Macrocycles represent a common structural framework in many naturally occurring peptides. Several strategies exist for macrocyclization, and the enzymes that incorporate them are of great interest, as they enhance our repertoire for creating complex molecules. We recently discovered a new peptide cyclization reaction involving a crosslink between the side chains of lysine and tryptophan that is installed by a radical SAM enzyme. Herein, we characterize relatives of this metalloenzyme from the pathogens Streptococcus agalactiae and Streptococcus suis. Our results show that the corresponding enzymes, which we call AgaB and SuiB, contain multiple [4Fe-4S] clusters and catalyze Lys-Trp crosslink formation in their respective substrates. Subsequent high-resolution-MS and 2D-NMR analyses located the site of macrocyclization. Moreover, we report that AgaB can accept modified substrates containing natural or unnatural amino acids. Aside from providing insights into the mechanism of this unusual modification, the substrate promiscuity of AgaB may be exploited to create diverse macrocyclic peptides.

  1. Carboxypeptidase D is the only enzyme responsible for antibody C-terminal lysine cleavage in Chinese hamster ovary (CHO) cells.

    Science.gov (United States)

    Hu, Zhilan; Zhang, Henry; Haley, Benjamin; Macchi, Frank; Yang, Feng; Misaghi, Shahram; Elich, Joseph; Yang, Renee; Tang, Yun; Joly, John C; Snedecor, Bradley R; Shen, Amy

    2016-10-01

    Heterogeneity of C-terminal lysine levels often observed in therapeutic monoclonal antibodies is believed to result from the proteolysis by endogenous carboxypeptidase(s) during cell culture production. Identifying the responsible carboxypeptidase(s) for C-terminal lysine cleavage in CHO cells would provide valuable insights for antibody production cell culture processes development and optimization. In this study, five carboxypeptidases, CpD, CpM, CpN, CpB, and CpE, were studied for message RNA (mRNA) expression by qRT-PCR analysis in two most commonly used blank hosts (DUXB-11 derived DHFR-deficient DP12 host and DHFR-positive CHOK1 host), used for therapeutic antibody production, as well an antibody-expressing cell line derived from each host. Our results showed that CpD had the highest mRNA expression. When CpD mRNA levels were reduced by RNAi (RNA interference) technology, C-terminal lysine levels increased, whereas there was no obvious change in C-terminal lysine levels when a different carboxypeptidase mRNA level was knocked down suggesting that carboxypeptidase D is the main contributor for C-terminal lysine processing. Most importantly, when CpD expression was knocked out by CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology, C-terminal lysine cleavage was completely abolished in CpD knockout cells based on mass spectrometry analysis, demonstrating that CpD is the only endogenous carboxypeptidase that cleaves antibody heavy chain C-terminal lysine in CHO cells. Hence, our work showed for the first time that the cleavage of antibody heavy chain C-terminal lysine is solely mediated by the carboxypeptidase D in CHO cells and our finding provides one solution to eliminating C-terminal lysine heterogeneity for therapeutic antibody production by knocking out CpD gene expression. Biotechnol. Bioeng. 2016;113: 2100-2106. © 2016 Wiley Periodicals, Inc.

  2. 双方不完全信息下政府引导的逆向供应链协调研究%Study on the Coordinating with Incomplete Information of Both Sides and Government Guidance in Reverse Supply Chain

    Institute of Scientific and Technical Information of China (English)

    贡文伟; 葛翠翠

    2012-01-01

    In this paper, we discusses the coordinating problem of a reverse supply chain consisted of one manufacturer and two retailers with incomplete information of both sides and government guidance. We use signal screening and principal-agent theory to get coordinated strategies from three aspects of government does not participate in the chain, government incentives retailers and government incentives manufacturers. The studies show that:the contract pricing can be effective to avoid adverse selection, to achieve the reverse supply chain coordination; retailer of low cost and with high market demand to obtain higher profit; the reasonable reward enterprise, especially rewards for retailers can promote reverse supply chain coordination,and increase profitability.%讨论双方不完全信息下政府引导一个制造商和两个零售商组成的逆向供应链的协调问题.运用信号甄别和委托代理理论,分别从政府不参与、政府奖励零售商和政府奖励制造商三个方面得到零售商和制造商的协调策略.研究表明:定价合同可有效避免逆向选择,实现逆向供应链协调;高市场需求状态下低成本零售商获得收益较高;政府对企业的合理奖励,尤其是对零售商的奖励,可以促进逆向供应链协调,提高收益.

  3. Synthesis and Anchoring of Antineoplastic Ferrocene and Phthalocyanine Derivatives on Water-Soluble Polymeric Drug Carriers Derived from Lysine and Aspartic Acid

    Science.gov (United States)

    Maree, M. David; Neuse, Eberhard W.; Erasmus, Elizabeth; Swarts, Jannie C.

    2008-01-01

    The general synthetic strategy towards water-soluble biodegradable drug carriers and the properties that they must have are discussed. The syntheses of water-soluble biodegradable copolymers of lysine and aspartic acid as potential drug-delivering devices, having amine-functionalised side chains are then described. Covalent anchoring of carboxylic acid derivatives of the antineoplastic ferrocene and photodynamically active phthalocyanine moieties to the amine-containing drug carrier copolymers under mild coupling conditions has been achieved utilising the coupling reagent O-benzotriazolyl-N,N,N′,N′-tetramethyluronium hexafluorophosphate to promote formation of the biodegradable amide bond. Even though the parent antineoplastic ferrocene and phthalocyanine derivatives are themselves insoluble in water at pH < 7, the new carrier-drug conjugates that were obtained are well water-soluble. PMID:18288243

  4. A highly productive, whole-cell DERA chemoenzymatic process for production of key lactonized side-chain intermediates in statin synthesis.

    Directory of Open Access Journals (Sweden)

    Matej Ošlaj

    Full Text Available Employing DERA (2-deoxyribose-5-phosphate aldolase, we developed the first whole-cell biotransformation process for production of chiral lactol intermediates useful for synthesis of optically pure super-statins such as rosuvastatin and pitavastatin. Herein, we report the development of a fed-batch, high-density fermentation with Escherichia coli BL21 (DE3 overexpressing the native E. coli deoC gene. High activity of this biomass allows direct utilization of the fermentation broth as a whole-cell DERA biocatalyst. We further show a highly productive bioconversion processes with this biocatalyst for conversion of 2-substituted acetaldehydes to the corresponding lactols. The process is evaluated in detail for conversion of acetyloxy-acetaldehyde with the first insight into the dynamics of reaction intermediates, side products and enzyme activity, allowing optimization of the feeding strategy of the aldehyde substrates for improved productivities, yields and purities. The resulting process for production of ((2S,4R-4,6-dihydroxytetrahydro-2H-pyran-2-ylmethyl acetate (acetyloxymethylene-lactol has a volumetric productivity exceeding 40 g L(-1 h(-1 (up to 50 g L(-1 h(-1 with >80% yield and >80% chromatographic purity with titers reaching 100 g L(-1. Stereochemical selectivity of DERA allows excellent enantiomeric purities (ee >99.9%, which were demonstrated on downstream advanced intermediates. The presented process is highly cost effective and environmentally friendly. To our knowledge, this is the first asymmetric aldol condensation process achieved with whole-cell DERA catalysis and it simplifies and extends previously developed DERA-catalyzed approaches based on the isolated enzyme. Finally, applicability of the presented process is demonstrated by efficient preparation of a key lactol precursor, which fits directly into the lactone pathway to optically pure super-statins.

  5. Reactive lysine content in commercially available pet foods

    NARCIS (Netherlands)

    Rooijen, van C.; Bosch, G.; Poel, van der A.F.B.; Wierenga, P.A.; Alexander, L.; Hendriks, W.H.

    2014-01-01

    The Maillard reaction can occur during processing of pet foods. During this reaction, the e-amino group of lysine reacts with reducing sugars to become unavailable for metabolism. The aim of the present study was to determine the reactive lysine (RL; the remaining available lysine) to total lysine (

  6. SPOTing Acetyl-Lysine Dependent Interactions

    Directory of Open Access Journals (Sweden)

    Sarah Picaud

    2015-08-01

    Full Text Available Post translational modifications have been recognized as chemical signals that create docking sites for evolutionary conserved effector modules, allowing for signal integration within large networks of interactions. Lysine acetylation in particular has attracted attention as a regulatory modification, affecting chromatin structure and linking to transcriptional activation. Advances in peptide array technologies have facilitated the study of acetyl-lysine-containing linear motifs interacting with the evolutionary conserved bromodomain module, which specifically recognizes and binds to acetylated sequences in histones and other proteins. Here we summarize recent work employing SPOT peptide technology to identify acetyl-lysine dependent interactions and document the protocols adapted in our lab, as well as our efforts to characterize such bromodomain-histone interactions. Our results highlight the versatility of SPOT methods and establish an affordable tool for rapid access to potential protein/modified-peptide interactions involving lysine acetylation.

  7. Oligo(L-lysine)-induced titanium dioxide: Effects of consecutive lysine on precipitation

    Science.gov (United States)

    Ahn, Sungjun; Park, Sangwoo; Lee, Sang-Yup

    2011-11-01

    Biomineralization of metal oxide utilizes biomolecular substances, such as peptides and proteins, to induce mineralization of metal precursors in a mild aqueous solution. In this study, we investigated biomineralization of an abiological substance, titanium dioxide (TiO 2), by oligo(L-lysine). Specifically, we systemically studied the influence of the number of consecutive lysine on TiO 2 precipitation. Oligo(L-lysine) was chosen as a homopeptide lysine source whose lysine quantity was adjusted. When oligo(L-lysine) contains more than three consecutive lysine, it induces notably fast precipitation, while single and dilysine do not readily form TiO 2 precipitates. Precipitation of TiO 2 was promoted with the length of oligo(L-lysine). The oligo(L-lysine) was associated with TiO 2 precipitate, which was confirmed by spectroscopic and thermogravitational analyses. The outcomes of this research provide a plausible rationale for explaining precipitation of the Ti precursor that is highly dependent on peptide sequences.

  8. (1)H, (13)C, (15)N backbone and side-chain resonance assignment of Nostoc sp. C139A variant of the heme-nitric oxide/oxygen binding (H-NOX) domain.

    Science.gov (United States)

    Alexandropoulos, Ioannis I; Argyriou, Aikaterini I; Marousis, Kostas D; Topouzis, Stavros; Papapetropoulos, Andreas; Spyroulias, Georgios A

    2016-10-01

    The H-NOX (Heme-nitric oxide/oxygen binding) domain is conserved across eukaryotes and bacteria. In human soluble guanylyl cyclase (sGC) the H-NOX domain functions as a sensor for the gaseous signaling agent nitric oxide (NO). sGC contains the heme-binding H-NOX domain at its N-terminus, which regulates the catalytic site contained within the C-terminal end of the enzyme catalyzing the conversion of GTP (guanosine 5'-triphosphate) to GMP (guanylyl monophosphate). Here, we present the backbone and side-chain assignments of the (1)H, (13)C and (15)N resonances of the 183-residue H-NOX domain from Nostoc sp. through solution NMR.

  9. HIV-1 p17 matrix protein interacts with heparan sulfate side chain of CD44v3, syndecan-2, and syndecan-4 proteoglycans expressed on human activated CD4+ T cells affecting tumor necrosis factor alpha and interleukin 2 production.

    Science.gov (United States)

    De Francesco, Maria A; Baronio, Manuela; Poiesi, Claudio

    2011-06-01

    HIV-1 p17 contains C- and N-terminal sequences with positively charged residues and a consensus cluster for heparin binding. We have previously demonstrated by affinity chromatography that HIV-1 p17 binds strongly to heparin-agarose at physiological pH and to human activated CD4(+) T cells. In this study we demonstrated that the viral protein binds to heparan sulfate side chains of syndecan-2, syndecan-4, and CD44v3 purified from HeLa cells and that these heparan sulfate proteoglycans (HSPGs) co-localize with HIV-1 p17 on activated human CD4(+) T cells by confocal fluorescence analysis. Moreover, we observed a stimulatory or inhibitory activity when CD4(+) T cells were activated with mitogens together with nanomolar or micromolar concentrations of the matrix protein.

  10. Insight into the collagen assembly in the presence of lysine and glutamic acid: An in vitro study.

    Science.gov (United States)

    Liu, Xinhua; Dan, Nianhua; Dan, Weihua

    2017-01-01

    The aim of this study is to evaluate the effects of two different charged amino acids in collagen chains, lysine and glutamic acid, on the fibrillogenesis process of collagen molecules. The turbidity, zeta potential, and fiber diameter analysis suggest that introducing the positively charged lysine into collagen might improve the sizes or amounts of the self-assembled collagen fibrils significantly. Conversely, the negatively charged glutamic acid might restrict the self-assembly of collagen building blocks into a higher order structure. Meanwhile, the optimal fibrillogenesis condition is achieved when the concentration of lysine reaches to 1mM. Both scanning electron microscopy (SEM) and atomic force microscope (AFM) analysis indicates that compared to pure collagen fibrils, the reconstructed collagen-lysine co-fibrils exhibit a higher degree of inter-fiber entanglements with more straight and longer fibrils. Noted that the specific D-period patterns of the reconstructed collagen fibrils could be clearly discernible and the width of D-banding increases steadily after introducing lysine. Besides, the kinetic and thermodynamic collagen self-assembly analysis confirms that the rate constants of both the first and second assembly phase decrease after introducing lysine, and lysine could promote the process of collagen fibrillogenesis obeying the laws of thermodynamics. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. CYLD, a deubiquitinase specific for lysine63-linked polyubiquitins, accumulates at the postsynaptic density in an activity-dependent manner

    Energy Technology Data Exchange (ETDEWEB)

    Dosemeci, Ayse, E-mail: dosemeca@mail.nih.gov [Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 (United States); Thein, Soe; Yang, Yijung; Reese, Thomas S. [Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 (United States); Tao-Cheng, Jung-Hwa [EM Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 (United States)

    2013-01-04

    Highlights: Black-Right-Pointing-Pointer CYLD is a deubiquitinase specific for lysine63-linked polyubiquitins. Black-Right-Pointing-Pointer Presence of CYLD in PSDs is established by biochemistry and immunoEM. Black-Right-Pointing-Pointer CYLD accumulates on PSDs upon depolarization of neurons. Black-Right-Pointing-Pointer Accumulation of CYLD at PSDs may regulate trafficking/degradation of synaptic proteins. -- Abstract: Polyubiquitin chains on proteins flag them for distinct fates depending on the type of polyubiquitin linkage. While lysine48-linked polyubiquitination directs proteins to proteasomal degradation, lysine63-linked polyubiquitination promotes different protein trafficking and is involved in autophagy. Here we show that postsynaptic density (PSD) fractions from adult rat brain contain deubiquitinase activity that targets both lysine48 and lysine63-linked polyubiquitins. Comparison of PSD fractions with parent subcellular fractions by Western immunoblotting reveals that CYLD, a deubiquitinase specific for lysine63-linked polyubiquitins, is highly enriched in the PSD fraction. Electron microscopic examination of hippocampal neurons in culture under basal conditions shows immunogold label for CYLD at the PSD complex in approximately one in four synapses. Following depolarization by exposure to high K+, the proportion of CYLD-labeled PSDs as well as the labeling intensity of CYLD at the PSD increased by more than eighty percent, indicating that neuronal activity promotes accumulation of CYLD at the PSD. An increase in postsynaptic CYLD following activity would promote removal of lysine63-polyubiquitins from PSD proteins and thus could regulate their trafficking and prevent their autophagic degradation.

  12. Lysine requirement of growing male Pekin ducks.

    Science.gov (United States)

    Bons, A; Timmler, R; Jeroch, H

    2002-12-01

    1. One growth experiment and one balance test were conducted to study the response to increasing levels of dietary lysine supplementation in male Pekin ducks with special reference to the growth periods from 1 to 3 weeks and 4 to 7 weeks of age. 2. Two different low-lysine diets were used as basal diets in both periods. The basal lysine levels were 7.6 g/kg (d 1 to 21) and 6.2 g/kg (d 22 to 49) and the ranges in lysine concentration were 7.6 to 12.6 g/kg (d 1 to 21) and 6.2 to 11.2 g/kg (d 22 to 49). 3. Growth performance, feed conversion efficiency and meat yield increased (P < 0.05) with increasing lysine concentration (requirement defined as 95% of the asymptote). 4. It is concluded that the dietary lysine concentration should be 0.93 g/MJ nitrogen corrected apparent metabolisable energy (AMEN) (11.7 g/kg) for the starter period (until d 21) and 0.75 g/MJ AMEN (10.0 g/kg) for the grower period (from d 22 onwards).

  13. Bioavailability of free lysine and protein-bound lysine from casein and fishmeal in juvenile turbot (Psetta maxima).

    Science.gov (United States)

    Kroeckel, Saskia; Dietz, Carsten; Schulz, Carsten; Susenbeth, Andreas

    2015-03-14

    In the present study, a linear regression analysis between lysine intake and lysine retention was conducted to investigate the efficiency of lysine utilisation (k(Lys)) at marginal lysine intake of either protein-bound or free lysine sources in juvenile turbot (Psetta maxima). For this purpose, nine isonitrogenous and isoenergetic diets were formulated to contain 2·25-4·12 g lysine/100 g crude protein (CP) to ensure that lysine was the first-limiting amino acid in all diets. The basal diet contained 2·25 g lysine/100 g CP. Graded levels of casein (Cas), fishmeal (FM) and L-lysine HCl (Lys) were added to the experimental diets to achieve stepwise lysine increments. A total of 240 fish (initial weight 50·1 g) were hand-fed all the experimental diets once daily until apparent satiation over a period of 56 d. Feed intake was significantly affected by dietary lysine concentration rather than by dietary lysine source. Specific growth rate increased significantly at higher lysine concentrations (PCas, Lys or FM were 0·833, 0·857 and 0·684, respectively. The bioavailability of lysine from the respective lysine sources was determined by a slope-ratio approach. The bioavailability of lysine (relative to the reference lysine source Cas) from FM and Lys was 82·1 and 103 %, respectively. Nutrient requirement for maintenance was in the range of 16·7-23·4 mg/kg(0·8) per d, and did not differ between the treatments. There were no significant differences in lysine utilisation efficiency or bioavailability of protein-bound or crystalline lysine from the respective sources observed when lysine was confirmed to be the first-limiting nutrient.

  14. Lysine-Rich Proteins in High-Lysine Hordeum Vulgare Grain

    DEFF Research Database (Denmark)

    Ingversen, J.; Køie, B.

    1973-01-01

    The salt-soluble proteins in barley grain selected for high-lysine content (Hiproly, CI 7115 and the mutants 29 and 86) and of a control (Carlsberg II) with normal lysine content, contain identical major proteins as determined by MW and electrophoretic mobility. The concentration of a protein group...

  15. 新型侧链型聚酰亚胺膜的制备及其渗透汽化分离性能%Synthesis of novel membranes of polyimide with side-chains and their pervaporation performance

    Institute of Scientific and Technical Information of China (English)

    秦琳; 李继定; 郑冬菊; 王涛

    2013-01-01

    Two novel aromatic diamines 3,5-diaminobenzophenone (PDA) and 4-(trifluoromethyl) phenyl 3,5-diaminobenzoate (FPDA) were mixed separately with 4, 4'-diaminodiphenyl ether (ODA) and 3,5-diaminebenzoic acid (DABA) with different ratios, and then copolymerized separately with 4, 4'-oxydiphthalic anhydride (ODPA), 3,3' ,4,4'-benzophenonetetracarboxylic dianhydride (BTDA) and 4,4'-(hexafluoroisopropylidene) diphthalic anhydride (6FDA) to give poly(amic acid)s, which were converted into cross-linked polyimides (Pis) with ethylene glycol (EG) by thermal imidization. The structures of these series of Pis were characterized by FT-IR, NMR and GPC. The effect of side-chain content on the thermal stability was investigated by DSC and TGA. The effects of the fluorine group on the properties and separation performance of side-chain polyimides were investigated. The membranes of polyimide obtained were employed in pervaporation separation of benzene/cyclohexane mixtures. The two side-chain polyimide membranes containing 6FDA have an optimal separation efficiency in terms of both flux and separation factor. The cross-linked 6FDA-FPDA/ODA/DABA (1 : 7 : 2) membranes show the most promising separation performance with a flux of 9. 84 kg · μm · m-2 · h-1 and separation factor of 6. 1 for benzene/cyclo-hexane (50/50, mass ratio) at 50℃.%针对苯/环己烷混合物体系的特点,采用两种新型侧链二胺3,5-二氨基苯甲酸苯酯(PDA)和3,5-二氨基苯甲酸-4-三氟甲基苯酯(FPDA),制备了一系列由不同二酐与二胺单体如4,4'-二氨基二苯醚(ODA)和3,5-二氨基苯甲酸(DABA)聚合而成的用于渗透汽化分离苯/环己烷的聚酰亚胺膜,对其结构和各项性质进行了表征,并对膜材料的微观结构与宏观分离性能之间的关系进行了较为深入的研究.随着侧链二胺的引入,聚酰亚胺膜的分离效率随之持续增大,分离能力得以改善.渗透汽化实验结果表明,以6FDA为二酐单体的两类聚酰亚

  16. Analyzing sites of OH radical attack (ring vs. side chain) in oxidation of substituted benzenes via dual stable isotope analysis (δ{sup 13}C and δ{sup 2}H)

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ning [Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig (Germany); Geronimo, Inacrist; Paneth, Piotr [Institute of Applied Radiation Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź (Poland); Schindelka, Janine; Schaefer, Thomas; Herrmann, Hartmut [Department of Chemistry, Leibniz Institute for Tropospheric Research (TROPOS), Permoserstraße 15, 04318 Leipzig (Germany); Vogt, Carsten [Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig (Germany); Richnow, Hans H., E-mail: hans.richnow@ufz.de [Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig (Germany)

    2016-01-15

    OH radicals generated by the photolysis of H{sub 2}O{sub 2} can degrade aromatic contaminants by either attacking the aromatic ring to form phenolic products or oxidizing the substituent. We characterized these competing pathways by analyzing the carbon and hydrogen isotope fractionation (ε{sub C} and ε{sub H}) of various substituted benzenes. For benzene and halobenzenes that only undergo ring addition, low values of ε{sub C} (− 0.7‰ to − 1.0‰) were observed compared with theoretical values (− 7.2‰ to − 8‰), possibly owing to masking effect caused by pre-equilibrium between the substrate and OH radical preceding the rate-limiting step. In contrast, the addition of OH radicals to nitrobenzene ring showed a higher ε{sub C} (− 3.9‰), probably due to the lower reactivity. Xylene isomers, anisole, aniline, N,N-dimethylaniline, and benzonitrile yielded normal ε{sub H} values (− 2.8‰ to − 29‰) indicating the occurrence of side-chain reactions, in contrast to the inverse ε{sub H} (11.7‰ to 30‰) observed for ring addition due to an sp{sup 2} to sp{sup 3} hybridization change at the reacting carbon. Inverse ε{sub H} values for toluene (14‰) and ethylbenzene (30‰) were observed despite the formation of side-chain oxidation products, suggesting that ring addition has a larger contribution to isotope fractionation. Dual element isotope slopes (∆ δ{sup 2}H/∆δ{sup 13}C) therefore allow identification of significant degradation pathways of aromatic compounds by photochemically induced OH radicals. Issues that should be addressed in future studies include quantitative determination of the contribution of each competing pathway to the observed isotope fractionation and characterization of physical processes preceding the reaction that could affect isotope fractionation. - Highlights: • Isotope fractionation to investigate photoreaction pathways of substituted benzenes • Normal {sup 13}C AKIE and inverse {sup 2}H AKIE for

  17. Novel Side-Chain Liquid Cyrstalline Polymers

    Science.gov (United States)

    1989-01-01

    4’- biphenyl)oxyjhexyl vinyl ether). EXEBIMENTA 4- Phenylphenol (98%), 1,10-phenanthroline (anhydrous, 99%), palladium (11) diacetate (all from...monomeric structural unit of poly{8-[4(cyano-4’- biphenyl)oxyloctyl vinyl ether). EX ,RMENTA. MaeiLS 4- Phenylphenol (98%), 1,10-phenanthroline...monomeric structural unit of poly{ll-[(4- cyano-4’-biphenyl)oxy]undecanyl vinyl ether). Mateials 4- Phenylphenol (98%), 1,10-phenanthroline (anhydrous, 99

  18. Site-Specific Conjugation to Native and Engineered Lysines in Human Immunoglobulins by Microbial Transglutaminase.

    Science.gov (United States)

    Spidel, Jared L; Vaessen, Benjamin; Albone, Earl F; Cheng, Xin; Verdi, Arielle; Kline, J Bradford

    2017-09-20

    The use of microbial transglutaminase (MTG) to produce site-specific antibody-drug conjugates (ADCs) has thus far focused on the transamidation of engineered acyl donor glutamine residues in an antibody based on the hypothesis that the lower specificity of MTG for acyl acceptor lysines may result in the transamidation of multiple native lysine residues, thereby yielding heterogeneous products. We investigated the utilization of native IgG lysines as acyl acceptor sites for glutamine-based acyl donor substrates. Of the approximately 80 lysines in multiple recombinant IgG monoclonal antibodies (mAbs), none were transamidated. Because recombinant mAbs lack the C-terminal Lys447 due to cleavage by carboxypeptidase B in the production cell host, we explored whether blocking the cleavage of Lys447 by the addition of a C-terminal amino acid could result in transamidation of Lys447 by a variety of acyl donor substrates. MTG efficiently transamidated Lys447 in the presence of any nonacidic, nonproline amino acid residue at position 448. Lysine scanning mutagenesis throughout the antibody further revealed several transamidation sites in both the heavy- and light-chain constant regions. Additionally, scanning mutagenesis of the hinge region in a Fab' fragment revealed sites of transamidation that were not reactive in the context of the full-length mAb. Here, we demonstrate the utility of single lysine substitutions and the C-terminal Lys447 for engineering efficient acyl acceptor sites suitable for site-specific conjugation to a range of glutamine-based acyl donor substrates.

  19. Optimal Poly(l-lysine) Grafting Density in Hydrogels for Promoting Neural Progenitor Cell Functions

    OpenAIRE

    Cai, Lei; Lu, Jie; Sheen, Volney; Wang, Shanfeng

    2012-01-01

    Recently we have developed a photo-polymerizable poly(l-lysine) (PLL) that can be covalently incorporated into poly(ethylene glycol) diacrylate (PEGDA) hydrogels to improve their bioactivity by providing positive charges. To explore the potential of these PLL-grafted PEGDA hydrogels as a cell delivery vehicle and luminal filler in nerve guidance conduits for peripheral and central nerve regeneration, we varied the amount of pendent PLL chains in the hydrogels by photo-crosslinking PEGDA with ...

  20. Synthesis and characterization of methacryloyl monomers containing short perfluorocarbon side chains and aromatic rings%含短氟碳侧链及芳香环的甲基丙烯酰类单体的合成与表征

    Institute of Scientific and Technical Information of China (English)

    冯泽峰; 谭业邦; 邢卫国; 袁培林; 王明刚

    2012-01-01

    以全氟己基碘烷为原料通过一锅法制备了3-(全氟正已基)环氧丙烷,总收率达79.6%.从该环氧丙烷出发合成分离出了5种含短氟碳侧链及芳香环侧基的甲基丙烯酰类单体,并探讨了中间体含氟醇的最佳合成条件;通过1 HNMR、13CNMR、19FNMR对合成单体进行了表征.%Perfluorohexyl iodide has been used as a raw material in preparing 3-perfluorohexyl-l, 2-epoxypropane ( PFOP) by one-pot reaction. The total yield reached 79. 6% . Starting from 3-perfluorohexyl-l ,2-epoxypropane,five novel methacryloyl monomers containing aromatic rings and short perfluorocarbon side chains were obtained;and the optimal conditions of the intermediates were discussed. The monomers were confirmed by 1HNMR,13CNMR and 19FNMR.