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Sample records for complex side-chain structures

  1. 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.

  2. 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

  3. 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.

  4. 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...

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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/.

  10. 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.

  11. 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.

  12. 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.

  13. 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....

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  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. 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.

  4. 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.

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

    NARCIS (Netherlands)

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

    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

  6. 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.

  7. 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.

  8. 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.

  9. Alkane oxidation with porphyrins and metal complexes thereof having haloalkyl side chains

    Science.gov (United States)

    Wijesekera, Tilak; Lyons, James E.; Ellis, Jr., Paul E.; Bhinde, Manoj V.

    1998-01-01

    Transition metal complexes of meso-haloalkylporphyrins, wherein the haloalkyl groups contain 2 to 8 carbon atoms have been found to be highly effective catalysts for oxidation of alkanes and for the decomposition of hydroperoxides.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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

  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. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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...

  6. 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.

  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. 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.

  9. 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

  10. 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.

  11. 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.

  12. Poly(dendrimers) with phosphorescent iridium(III) complex-based side chains prepared via ring-opening metathesis polymerization

    NARCIS (Netherlands)

    Lai, W.-Y.; Balfour, M.N.; Levell, J.W.; Bansal, A.K.; Burn, P.L.; Lo, S.-C.; Samuel, I.D.W.

    2012-01-01

    Phosphorescent poly(dendrimers) with a norbornene-derived backbone have been synthesized using ring-opening metathesis polymerization with the Grubbs III catalyst. The dendrimers are comprised of a heteroleptic iridium(III) complex core with two 2-phenylpyridyl ligands and a phenyltriazolyl ligand,

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Potentiometric and spectroscopic studies on the copper(II) complexes of rat amylin fragments. The anchoring ability of specific non-coordinating side chains.

    Science.gov (United States)

    Dávid, Ágnes; Kállay, Csilla; Sanna, Daniele; Lihi, Norbert; Sóvágó, Imre; Várnagy, Katalin

    2015-10-21

    Copper(ii) complexes of peptides modelling the sequence of the 17-22 residues of rat amylin have been studied by potentiometric, UV-Vis, CD and ESR spectroscopic methods. The peptides were synthesized in N-terminally free forms, NH2-VRSSNN-NH2, NH2-VRSSAA-NH2, NH2-VRAANN-NH2, NH2-VRSS-NH2, NH2-SSNN-NH2, NH2-SSNA-NH2 and NH2-AANN-NH2, providing a possibility for the comparison of the metal binding abilities of the amino terminus and the -SSNN- domain. The amino terminus was the primary ligating site in all cases and the formation of only mononuclear complexes was obtained for the tetrapeptides. The thermodynamic stability of the (NH2, N(-), N(-)) coordinated complexes was, however, enhanced by the asparaginyl moiety in the case of NH2-SSNN-NH2, NH2-SSNA-NH2 and NH2-AANN-NH2. Among the hexapeptides the formation of dinuclear complexes was characteristic for NH2-VRSSNN-NH2 demonstrating the anchoring ability of the -SSNN- (SerSerAsnAsn) domain. The complexes of the heptapeptide NH2-GGHSSNN-NH2 were also studied and the data supported the above mentioned anchoring ability of the -SSNN- site.

  14. 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.

  15. 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.

  16. 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

  17. Structure-based design of selective inhibitors of dihydrofolate reductase: synthesis and antiparasitic activity of 2, 4-diaminopteridine analogues with a bridged diarylamine side chain.

    Science.gov (United States)

    Rosowsky, A; Cody, V; Galitsky, N; Fu, H; Papoulis, A T; Queener, S F

    1999-11-18

    As part of a larger search for potent as well as selective inhibitors of dihydrofolate reductase (DHFR) enzymes from opportunistic pathogens found in patients with AIDS and other immune disorders, N-[(2,4-diaminopteridin-6-yl)methyl]dibenz[b,f]azepine (4a) and the corresponding dihydrodibenz[b,f]azepine, dihydroacridine, phenoxazine, phenothiazine, carbazole, and diphenylamine analogues were synthesized from 2, 4-diamino-6-(bromomethyl)pteridine in 50-75% yield by reaction with the sodium salts of the amines in dry tetrahydrofuran at room temperature. The products were tested for the ability to inhibit DHFR from Pneumocystis carinii (pcDHFR), Toxoplasma gondii (tgDHFR), Mycobacterium avium (maDHFR), and rat liver (rlDHFR). The member of the series with the best combination of potency and species selectivity was 4a, with IC(50) values against the four enzymes of 0. 21, 0.043, 0.012, and 4.4 microM, respectively. The dihydroacridine, phenothiazine, and carbazole analogues were also potent, but nonselective. Of the compounds tested, 4a was the only one to successfully combine the potency of trimetrexate with the selectivity of trimethoprim. Molecular docking simulations using published 3D structural coordinates for the crystalline ternary complexes of pcDHFR and hDHFR suggested a possible structural interpretation for the binding selectivity of 4a and the lack of selectivity of the other compounds. According to this model, 4a is selective because of a unique propensity of the seven-membered ring in the dibenz[b,f]azepine moiety to adopt a puckered orientation that allows it to fit more comfortably into the active site of the P. carinii enzyme than into the active site of the human enzyme. Compound 4a was also evaluated for the ability to be taken up into, and retard the growth of, P. carinii and T. gondii in culture. The IC(50) of 4a against P. carinii trophozoites after 7 days of continuous drug treatment was 1.9 microM as compared with previously observed IC(50

  18. 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.

  19. 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....

  20. 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....

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Trans-α-xylosidase, a widespread enzyme activity in plants, introduces (1→4)-α-d-xylobiose side-chains into xyloglucan structures.

    Science.gov (United States)

    Franková, Lenka; Fry, Stephen C

    2012-06-01

    Angiosperms possess a retaining trans-α-xylosidase activity that catalyses the inter-molecular transfer of xylose residues between xyloglucan structures. To identify the linkage of the newly transferred α-xylose residue, we used [Xyl-(3)H]XXXG (xyloglucan heptasaccharide) as donor substrate and reductively-aminated xyloglucan oligosaccharides (XGO-NH(2)) as acceptor. Asparagus officinalis enzyme extracts generated cationic radioactive products ([(3)H]Xyl·XGO-NH(2)) that were Driselase-digestible to a neutral trisaccharide containing an α-[(3)H]xylose residue. After borohydride reduction, the trimer exhibited high molybdate-affinity, indicating xylobiosyl-(1→6)-glucitol rather than a di-xylosylated glucitol. Thus the trans-α-xylosidase had grafted an additional α-[(3)H]xylose residue onto the xylose of an isoprimeverose unit. The trisaccharide was rapidly acetolysed to an α-[(3)H]xylobiose, confirming the presence of an acetolysis-labile (1→6)-bond. The α-[(3)H]xylobiitol formed by reduction of this α-[(3)H]xylobiose had low molybdate-affinity, indicating a (1→2) or (1→4) linkage. In NaOH, the α-[(3)H]xylobiose underwent alkaline peeling at the moderate rate characteristic of a (1→4)-disaccharide. Finally, we synthesised eight non-radioactive xylobioses [α and β; (1↔1), (1→2), (1→3) and (1→4)] and found that the [(3)H]xylobiose co-chromatographed only with (1→4)-α-xylobiose. We conclude that Asparagus trans-α-xylosidase activity generates a novel xyloglucan building block, α-d-Xylp-(1→4)-α-d-Xylp-(1→6)-d-Glc (abbreviation: 'V'). Modifying xyloglucan structures in this way may alter oligosaccharin activities, or change their suitability as acceptor substrates for xyloglucan endotransglucosylase (XET) activity. Copyright © 2012 Elsevier Ltd. All rights reserved.

  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-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).

  8. 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.

  9. 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...

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. 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.

  1. 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...

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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...

  7. 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.

  8. 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.

  9. 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

  10. 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...

  11. 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.

  12. 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.

  13. Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c

    Energy Technology Data Exchange (ETDEWEB)

    Novacek, Jiri; Janda, Lubomir; Dopitova, Radka; Zidek, Lukas, E-mail: lzidek@chemi.muni.cz; Sklenar, Vladimir [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic)

    2013-08-15

    Microtubule-associated proteins (MAPs) are abundantly present in axons and dendrites, and have been shown to play crucial role during the neuronal morphogenesis. The period of main dendritic outgrowth and synaptogenesis coincides with high expression levels of one of MAPs, the MAP2c, in rats. The MAP2c is a 49.2 kDa intrinsically disordered protein. To achieve an atomic resolution characterization of such a large protein, we have developed a protocol based on the acquisition of two five-dimensional {sup 13}C-directly detected NMR experiments. Our previously published 5D CACONCACO experiment (Novacek et al. in J Biomol NMR 50(1):1-11, 2011) provides the sequential assignment of the backbone resonances, which is not interrupted by the presence of the proline residues in the amino acid sequence. A novel 5D HC(CC-TOCSY)CACON experiment facilitates the assignment of the aliphatic side chain resonances. To streamline the data analysis, we have developed a semi-automated procedure for signal assignments. The obtained data provides the first atomic resolution insight into the conformational state of MAP2c and constitutes a model for further functional studies of MAPs.

  14. 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...

  15. 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.

  16. 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...

  17. 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...

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. NMR study of non-structural proteins--part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV).

    Science.gov (United States)

    Melekis, Efstathios; Tsika, Aikaterini C; Lichière, Julie; Chasapis, Christos T; Margiolaki, Irene; Papageorgiou, Nicolas; Coutard, Bruno; Bentrop, Detlef; Spyroulias, Georgios A

    2015-04-01

    Macro domains are ADP-ribose-binding modules present in all eukaryotic organisms, bacteria and archaea. They are also found in non-structural proteins of several positive strand RNA viruses such as alphaviruses. Here, we report the high yield expression and preliminary structural analysis through solution NMR spectroscopy of the macro domain from New World Mayaro Alphavirus. The recombinant protein was well-folded and in a monomeric state. An almost complete sequence-specific assignment of its (1)H, (15)N and (13)C resonances was obtained and its secondary structure determined by TALOS+.

  6. 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(

  7. 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...

  8. 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...

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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....

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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...

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  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. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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)

  12. 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.

  13. 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.

  14. 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...

  15. STRUCTURE AND REDOX TRANSFORMATIONS OF IRON(III COMPLEXES WITH SOME BIOLOGICALLY IMPORTANT INDOLE-3-ALKANOIC ACIDS IN AQUEOUS SOLUTIONS

    Directory of Open Access Journals (Sweden)

    Krisztina Kovács

    2007-06-01

    Full Text Available Interactions of a series of indole-3-alkanoic acids (with n-alkanoic acid side-chains from C1 to C4 with iron(III in acidic aqueous solutions have been shown to comprise two parallel processes including complexation and redox transformations giving iron(II hexaaquo complexes. The structure and composition of the reaction products are discussed, as analysed using a combination of instrumental techniques including 57Fe Mössbauer, vibrational and HNMR spectroscopies.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  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. 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.

  7. 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 .

  8. 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...

  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. 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...

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. 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 ...

  20. 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

  1. 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

  2. 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.

  3. 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...

  4. 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...

  5. 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...

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. One-electron oxidation of 2-(4-methoxyphenyl)-2-methylpropanoic and 1-(4-methoxyphenyl)cyclopropanecarboxylic acids in aqueous solution. the involvement of radical cations and the influence of structural effects and pH on the side-chain fragmentation reactivity.

    Science.gov (United States)

    Bietti, Massimo; Capone, Alberto

    2008-01-18

    A product and time-resolved kinetic study on the one-electron oxidation of 2-(4-methoxyphenyl)-2-methylpropanoic acid (2), 1-(4-methoxyphenyl)cyclopropanecarboxylic acid (3), and of the corresponding methyl esters (substrates 4 and 5, respectively) has been carried out in aqueous solution. With 2, no direct evidence for the formation of an intermediate radical cation 2*+ but only of the decarboxylated 4-methoxycumyl radical has been obtained, indicating either that 2*+ is not formed or that its decarboxylation is too fast to allow detection under the experimental conditions employed (k > 1 x 10(7) s(-1)). With 3, oxidation leads to the formation of the corresponding radical cation 3*+ or radical zwitterion -3*+ depending on pH. At pH 1.0 and 6.7, 3*+ and -3*+ have been observed to undergo decarboxylation as the exclusive side-chain fragmentation pathway with rate constants k = 4.6 x 10(3) and 2.3 x 10(4) s(-1), respectively. With methyl esters 4 and 5, direct evidence for the formation of the corresponding radical cations 4*+ and 5*+ has been obtained. Both radical cations have been observed to display a very low reactivity and an upper limit for their decay rate constants has been determined as k or=10, with the latter process that becomes the major fragmentation pathway around pH 12.

  17. 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.

  18. Crystal structures of Leishmania mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors.

    Science.gov (United States)

    Hai, Yang; Christianson, David W

    2016-04-01

    Leishmania arginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiates de novo polyamine biosynthesis by catalyzing the hydrolysis of L-arginine to generate L-ornithine and urea. The product L-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis. Polyamines such as spermidine are essential for the growth and survival of the parasite, so inhibition of enzymes in the polyamine-biosynthetic pathway comprises an effective strategy for treating parasitic infections. To this end, two X-ray crystal structures of L. mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors based on the molecular scaffold of 2-(S)-amino-6-boronohexanoic acid are now reported. Structural comparisons with human and parasitic arginase complexes reveal interesting differences in the binding modes of the additional α-substituents, i.e. the D side chains, of these inhibitors. Subtle differences in the three-dimensional contours of the outer active-site rims among arginases from different species lead to different conformations of the D side chains and thus different inhibitor-affinity trends. The structures suggest that it is possible to maintain affinity while fine-tuning intermolecular interactions of the D side chain of α,α-disubstituted boronic amino-acid inhibitors in the search for isozyme-specific and species-specific arginase inhibitors.

  19. 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

  20. 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.

  1. 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.

  2. 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...

  3. 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...

  4. 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.

  5. 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.

  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. 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.

  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. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. Stable generalized complex structures

    CERN Document Server

    Cavalcanti, Gil R

    2015-01-01

    A stable generalized complex structure is one that is generically symplectic but degenerates along a real codimension two submanifold, where it defines a generalized Calabi-Yau structure. We introduce a Lie algebroid which allows us to view such structures as symplectic forms. This allows us to construct new examples of stable structures, and also to define period maps for their deformations in which the background three-form flux is either fixed or not, proving the unobstructedness of both deformation problems. We then use the same tools to establish local normal forms for the degeneracy locus and for Lagrangian branes. Applying our normal forms to the four-dimensional case, we prove that any compact stable generalized complex 4-manifold has a symplectic completion, in the sense that it can be modified near its degeneracy locus to produce a compact symplectic 4-manifold.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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...

  12. 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.

  13. 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

  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. 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....

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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....

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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...

  13. 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.

  14. Crystal structures of Leishmania mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Hai, Yang; Christianson, David W.

    2016-03-16

    Leishmaniaarginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiatesde novopolyamine biosynthesis by catalyzing the hydrolysis of L-arginine to generate L-ornithine and urea. The product L-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis. Polyamines such as spermidine are essential for the growth and survival of the parasite, so inhibition of enzymes in the polyamine-biosynthetic pathway comprises an effective strategy for treating parasitic infections. To this end, two X-ray crystal structures ofL. mexicanaarginase complexed with α,α-disubstituted boronic amino-acid inhibitors based on the molecular scaffold of 2-(S)-amino-6-boronohexanoic acid are now reported. Structural comparisons with human and parasitic arginase complexes reveal interesting differences in the binding modes of the additional α-substituents,i.e.the D side chains, of these inhibitors. Subtle differences in the three-dimensional contours of the outer active-site rims among arginases from different species lead to different conformations of the D side chains and thus different inhibitor-affinity trends. The structures suggest that it is possible to maintain affinity while fine-tuning intermolecular interactions of the D side chain of α,α-disubstituted boronic amino-acid inhibitors in the search for isozyme-specific and species-specific arginase inhibitors.

  15. Towards theory driven structure elucidation of complex natural products: mandelalides and coibamide A.

    Science.gov (United States)

    Snyder, Kevin M; Sikorska, Justyna; Ye, Tao; Fang, Lijing; Su, Wu; Carter, Rich G; McPhail, Kerry L; Cheong, Paul H-Y

    2016-06-28

    The effectiveness of computational tools in determining relative configurations of complex molecules is investigated, using natural products mandelalides A-D and coibamide A, towards a generalized recipe for the scientific community at large. Ultimately, continuing efforts in this vein will accelerate and strengthen relative structure elucidation of complex molecules, such as natural products. Molecular mechanics conformational search, quantum mechanical NMR chemical shift predictions, and DP4 analyses led to confirmation of the revised structures of mandelalides A-D and coibamide A. All chiral centers in the northern hemisphere of mandelalides A-D are inverted with respect to the originally proposed structures, in agreement with recent total syntheses of mandelalide A by Ye, Fürstner & Carter. In the case of coibamide A, it was found that Fang & Su's revision, in which both the macrocycle [MeAla(11)] and the side chain [HIV(2)] residues are inverted from l to d, was consistent with the authentic natural product and computations.

  16. Solution structure of the complex of VEK-30 and plasminogen kringle 2.

    Science.gov (United States)

    Wang, Min; Zajicek, Jaroslav; Geiger, James H; Prorok, Mary; Castellino, Francis J

    2010-03-01

    The solution structure of the complex containing the isolated kringle 2 domain of human plasminogen (K2(Pg)) and VEK-30, a 30-amino acid residue internal peptide from a streptococcal M-like plasminogen (Pg) binding protein (PAM), has been determined by multinuclear high-resolution NMR. Complete backbone and side-chain assignments were obtained from triple-resonance experiments, after which structure calculations were performed and ultimately refined by restrained molecular simulation in water. We find that, in contrast with the dimer of complexes observed in the asymmetric unit of the crystal, global correlation times and buoyant molecular weight determinations of the complex and its individual components showed the monomeric nature of all species in solution. The NMR-derived structure of K2(Pg) in complex with VEK-30 presents a folding pattern typical of other kringle domains, while bound VEK-30 forms an end-to-end alpha-helix (residues 6-27) in the complex. Most of the VEK-30/K2(Pg) interactions in solution occur between a single face of the alpha-helix of VEK-30 and the lysine binding site (LBS) of K2(Pg). The canonical LBS of K2(Pg), consisting of Asp54, Asp56, Trp60, Arg69, and Trp70 (kringle numbering), interacts with an internal pseudo-lysine of VEK-30, comprising side-chains of Arg17, His18, and Glu20. Site-specific mutagenesis analysis confirmed that the electrostatic field formed by the N-terminal anionic residues of the VEK-30 alpha-helix, viz., Asp7, and the non-conserved cationic residues of K2(Pg), viz., Lys43 and Arg55, play additional important roles in the docking of VEK-30 to K2(Pg). Structural analysis and kringle sequence alignments revealed several important features related to exosite binding that provide a structural rationale for the high specificity and affinity of VEK-30 for K2(Pg).

  17. 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.

  18. 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.

  19. 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...

  20. 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....

  1. 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...

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  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. 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.

  11. 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.

  12. Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype

    DEFF Research Database (Denmark)

    Roder, G; Blicher, Thomas; Justesen, Sune Frederik Lamdahl

    2006-01-01

    -Barr virus nuclear antigen-3A) was determined to 2.3 A resolution. The structure of HLA-B*1501 in complex with a peptide (ILGPPGSVY) derived from human ubiquitin-conjugating enzyme-E2 corresponding to positions 91-99 was solved to 1.8 A resolution. Mutual comparisons of these two structures with structures......-pocket in HLA-B*1501. The residues most important for the specificity of this pocket are Tyr74, Leu81, Leu95, Tyr123 and Trp147. These residues create a hydrophobic interior in the F-pocket and their spatial arrangement makes the pocket capable of containing large, bulky peptide side chains. Ser116 is located...

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. "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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Structural complexity of quantum networks

    Energy Technology Data Exchange (ETDEWEB)

    Siomau, Michael [Physics Department, Jazan University, P.O.Box 114, 45142 Jazan (Saudi Arabia); Network Dynamics, Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen (Germany)

    2016-06-10

    Quantum network is a set of nodes connected with channels, through which the nodes communicate photons and classical information. Classical structural complexity of a quantum network may be defined through its physical structure, i.e. mutual position of nodes and channels connecting them. We show here that the classical structural complexity of a quantum network does not restrict the structural complexity of entanglement graphs, which may be created in the quantum network with local operations and classical communication. We show, in particular, that 1D quantum network can simulate both simple entanglement graphs such as lattices and random graphs and complex small-world graphs.

  11. 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

  12. 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.

  13. 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

  14. 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 ...

  15. 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

  16. 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...

  17. 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.

  18. 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.

  19. Recovery and fine structure variability of RGII sub-domains in wine (Vitis vinifera Merlot).

    Science.gov (United States)

    Buffetto, F; Ropartz, D; Zhang, X J; Gilbert, H J; Guillon, F; Ralet, M-C

    2014-10-01

    Rhamnogalacturonan II (RGII) is a structurally complex pectic sub-domain composed of more than 12 different sugars and 20 different linkages distributed in five side chains along a homogalacturonan backbone. Although RGII has long been described as highly conserved over plant evolution, recent studies have revealed variations in the structure of the polysaccharide. This study examines the fine structure variability of RGII in wine, focusing on the side chains A and B obtained after sequential mild acid hydrolysis. Specifically, this study aims to differentiate intrinsic structural variations in these RGII side chains from structural variations due to acid hydrolysis. RGII from wine (Vitis vinifera Merlot) was sequentially hydrolysed with trifluoroacetic acid (TFA) and the hydrolysis products were separated by anion-exchange chromatography (AEC). AEC fractions or total hydrolysates were analysed by MALDI-TOF mass spectrometry. The optimal conditions to recover non-degraded side chain B, side chain A and RGII backbone were 0·1 m TFA at 40 °C for 16 h, 0·48 m TFA at 40 °C for 16 h (or 0·1 m TFA at 60 °C for 8 h) and 0·1 m TFA at 60 °C for 16 h, respectively. Side chain B was particularly prone to acid degradation. Side chain A and the RGII GalA backbone were partly degraded by 0·1 m TFA at 80 °C for 1-4 h. AEC allowed separation of side chain B, methyl-esterified side chain A and non-methyl-esterified side chain A. The structure of side chain A and the GalA backbone were highly variable. Several modifications to the RGII structure of wine were identified. The observed dearabinosylation and deacetylation were primarily the consequence of acidic treatment, while variation in methyl-esterification, methyl-ether linkages and oxidation reflect natural diversity. The physiological significance of this variability, however, remains to be determined. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. Three-Dimentional Structures of Autophosphorylation Complexes in Crystals of Protein Kinases

    KAUST Repository

    Dumbrack, Roland

    2016-01-26

    Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Several autophosphorylation complexes have been identified in crystals of protein kinases, with a known serine, threonine, or tyrosine autophosphorylation site of one kinase monomer sitting in the active site of another monomer of the same protein in the crystal. We utilized a structural bioinformatics method to identify all such autophosphorylation complexes in X-ray crystallographic structures in the Protein Data Bank (PDB) by generating all unique kinase/kinase interfaces within and between asymmetric units of each crystal and measuring the distance between the hydroxyl oxygen of potential autophosphorylation sites and the oxygen atoms of the active site aspartic acid residue side chain. We have identified 15 unique autophosphorylation complexes in the PDB, of which 5 complexes have not previously been described in the relevant publications on the crystal structures (N-terminal juxtamembrane regions of CSF1R and EPHA2, activation loop tyrosines of LCK and IGF1R, and a serine in a nuclear localization signal region of CLK2. Mutation of residues in the autophosphorylation complex interface of LCK either severely impaired autophosphorylation or increased it. Taking the autophosphorylation complexes as a whole and comparing them with peptide-substrate/kinase complexes, we observe a number of important features among them. The novel and previously observed autophosphorylation sites are conserved in many kinases, indicating that by homology we can extend the relevance of these complexes to many other clinically relevant drug targets.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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...

  14. 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....

  15. 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)

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. Molecular Mechanics of Chitin-Protein Interface: Terminus and Side Chain

    CERN Document Server

    Yu, Zechuan

    2016-01-01

    Chitin and protein are two main building blocks for many natural biomaterials. The interaction between chitin and protein critically determines the properties of the composite biological materials. As living organisms usually encounter complex ambient conditions like water, pH and ions are critical factors towards the structural integrity of biomaterials. It is therefore essential to study the chitin-protein interface under different environmental conditions. Here, an atomistic model consisting of a chitin substrate and a protein filament is constructed, which is regarded as a representative of the chitin-protein interface existing in many chitin-based biomaterials. Based on this model, the mechanical properties of chitin-protein interface under different moisture and pH values are investigated through molecular dynamics simulations. The results reveal a weakening effect of water towards the chitin-protein interface, as well as acidity, i.e. the protonated protein forms a stronger adhesion to chitin than that...

  5. The structure of a tunicate C-type lectin from Polyandrocarpa misakiensis complexed with D -galactose.

    Science.gov (United States)

    Poget, S F; Legge, G B; Proctor, M R; Butler, P J; Bycroft, M; Williams, R L

    1999-07-23

    C-type lectins are calcium-dependent carbohydrate-recognising proteins. Isothermal titration calorimetry of the C-type Polyandrocarpa lectin (TC14) from the tunicate Polyandrocarpa misakiensis revealed the presence of a single calcium atom per monomer with a dissociation constant of 2.6 microM, and confirmed the specificity of TC14 for D -galactose and related monosaccharides. We have determined the 2.2 A X-ray crystal structure of Polyandrocarpa lectin complexed with D -galactose. Analytical ultracentrifugation revealed that TC14 behaves as a dimer in solution. This is reflected by the presence of two molecules in the asymmetric unit with the dimeric interface formed by antiparallel pairing of the two N-terminal beta-strands and hydrophobic interactions. TC14 adopts a typical C-type lectin fold with differences in structure from other C-type lectins mainly in the diverse loop regions and in the second alpha-helix, which is involved in the formation of the dimeric interface. The D -galactose is bound through coordination of the 3 and 4-hydroxyl oxygen atoms with a bound calcium atom. Additional hydrogen bonds are formed directly between serine, aspartate and glutamate side-chains of the protein and the sugar 3 and 4-hydroxyl groups. Comparison of the galactose binding by TC14 with the mannose binding by rat mannose-binding protein reveals how monosaccharide specificity is achieved in this lectin. A tryptophan side-chain close to the binding site and the distribution of hydrogen-bond acceptors and donors around the 3 and 4-hydroxyl groups of the sugar are essential determinants of specificity. These elements are, however, arranged in a very different way than in an engineered galactose-specific mutant of MBPA. Possible biological functions can more easily be understood from the fact that TC14 is a dimer under physiological conditions. Copyright 1999 Academic Press.

  6. 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.

  7. 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.

  8. A structural model of the E. coli PhoB Dimer in the transcription initiation complex

    Directory of Open Access Journals (Sweden)

    Tung Chang-Shung

    2012-03-01

    Full Text Available Abstract Background There exist > 78,000 proteins and/or nucleic acids structures that were determined experimentally. Only a small portion of these structures corresponds to those of protein complexes. While homology modeling is able to exploit knowledge-based potentials of side-chain rotomers and backbone motifs to infer structures for new proteins, no such general method exists to extend our understanding of protein interaction motifs to novel protein complexes. Results We use a Motif Binding Geometries (MBG approach, to infer the structure of a protein complex from the database of complexes of homologous proteins taken from other contexts (such as the helix-turn-helix motif binding double stranded DNA, and demonstrate its utility on one of the more important regulatory complexes in biology, that of the RNA polymerase initiating transcription under conditions of phosphate starvation. The modeled PhoB/RNAP/σ-factor/DNA complex is stereo-chemically reasonable, has sufficient interfacial Solvent Excluded Surface Areas (SESAs to provide adequate binding strength, is physically meaningful for transcription regulation, and is consistent with a variety of known experimental constraints. Conclusions Based on a straightforward and easy to comprehend concept, "proteins and protein domains that fold similarly could interact similarly", a structural model of the PhoB dimer in the transcription initiation complex has been developed. This approach could be extended to enable structural modeling and prediction of other bio-molecular complexes. Just as models of individual proteins provide insight into molecular recognition, catalytic mechanism, and substrate specificity, models of protein complexes will provide understanding into the combinatorial rules of cellular regulation and signaling.

  9. 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.

  10. 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.

  11. The 1.4 Å Crystal Structure of the Class D [beta]-Lactamase OXA-1 Complexed with Doripenem

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Kyle D.; Karpen, Mary E.; Bonomo, Robert A.; Leonard, David A.; Powers, Rachel A.; (Grand Valley); (Case Western U.-Med)

    2010-01-12

    The clinical efficacy of carbapenem antibiotics depends on their resistance to the hydrolytic action of {beta}-lactamase enzymes. The structure of the class D {beta}-lactamase OXA-1 as an acyl complex with the carbapenem doripenem was determined to 1.4 {angstrom} resolution. Unlike most class A and class C carbapenem complexes, the acyl carbonyl oxygen in the OXA-1-doripenem complex is bound in the oxyanion hole. Interestingly, no water molecules were observed in the vicinity of the acyl linkage, providing an explanation for why carbapenems inhibit OXA-1. The side chain amine of K70 remains fully carboxylated in the acyl structure, and the resulting carbamate group forms a hydrogen bond to the alcohol of the 6{alpha}-hydroxyethyl moiety of doripenem. The carboxylate attached to the {beta}-lactam ring of doripenem is stabilized by a salt bridge to K212 and a hydrogen bond with T213, in lieu of the interaction with an arginine side chain found in most other {beta}-lactamase-{beta}-lactam complexes (e.g., R244 in the class A member TEM-1). This novel set of interactions with the carboxylate results in a major shift of the carbapenem's pyrroline ring compared to the structure of the same ring in meropenem bound to OXA-13. Additionally, bond angles of the pyrroline ring suggest that after acylation, doripenem adopts the {Delta}{sup 1} tautomer. These findings provide important insights into the role that carbapenems may have in the inactivation process of class D {beta}-lactamases.

  12. 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

  13. 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 ...

  14. 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.

  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. 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...

  17. 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]-.

  18. 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.

  19. Structural insights into transcription complexes

    NARCIS (Netherlands)

    Berger, I.; Blanco, A.G.; Boelens, R.; Cavarelli, J.; Coll, M.; Folkers, G.E.; Nie, Y.; Pogenberg, V.; Schultz, P.; Wilmanns, M.; Moras, D.; Poterszman, A.

    2011-01-01

    Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of

  20. Structural insights into transcription complexes.

    Science.gov (United States)

    Berger, Imre; Blanco, Alexandre G; Boelens, Rolf; Cavarelli, Jean; Coll, Miquel; Folkers, Gert E; Nie, Yan; Pogenberg, Vivian; Schultz, Patrick; Wilmanns, Matthias; Moras, Dino; Poterszman, Arnaud

    2011-08-01

    Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of structural proteomics on our understanding of the molecular basis of gene expression. While most atomic structures were obtained by X-ray crystallography, the impact of solution NMR and cryo-electron microscopy is far from being negligible. Here, we summarize some highlights and illustrate the importance of specific technologies on the structural biology of protein-protein or protein/DNA transcription complexes: structure/function analysis of components the eukaryotic basal and activated transcription machinery with focus on the TFIID and TFIIH multi-subunit complexes as well as transcription regulators such as members of the nuclear hormone receptor families. We also discuss molecular aspects of promoter recognition and epigenetic control of gene expression. Copyright © 2011 Elsevier Inc. All rights reserved.

  1. Complex DNA structures and structures of DNA complexes

    Energy Technology Data Exchange (ETDEWEB)

    Chazin, W.J.; Carlstroem, G.; Shiow-Meei Chen; Miick, S.; Gomez-Paloma, L.; Smith, J.; Rydzewski, J. [Scripps Research Institute, La Jolla, CA (United States)

    1994-12-01

    Complex DNA structures (for example, triplexes, quadruplexes, junctions) and DNA-ligand complexes are more difficult to study by NMR than standard DNA duplexes are because they have high molecular weights, show nonstandard or distorted local conformations, and exhibit large resonance linewidths and severe {sup 1}H spectral overlap. These systems also tend to have limited solubility and may require specialized solution conditions to maintain favorable spectral characteristics, which adds to the spectroscopic difficulties. Furthermore, with more atoms in the system, both assignment and structure calculation become more challenging. In this article, we focus on demonstrating the current status of NMR studies of such systems and the limitations to further progress; we also indicate in what ways isotopic enrichment can be useful.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Structures of trihydroxynaphthalene reductase-fungicide complexes: implications for structure-based design and catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Liao, D.-I.; Basarab, G.S.; Gatenby, A.A.; Valent, B.; Jordan, D.B. (DuPont)

    2010-03-08

    Trihydroxynaphthalene reductase catalyzes two intermediate steps in the fungal melanin biosynthetic pathway. The enzyme, a typical short-chain dehydrogenase, is the biochemical target of three commercial fungicides. The fungicides bind preferentially to the NADPH form of the enzyme. Three X-ray structures of the Magnaporthe grisea enzyme complexed with NADPH and two commercial and one experimental fungicide were determined at 1.7 {angstrom} (pyroquilon), 2.0 {angstrom} (2,3-dihydro-4-nitro-1H-inden-1-one, 1), and 2.1 {angstrom} (phthalide) resolutions. The chemically distinct inhibitors occupy similar space within the enzyme's active site. The three inhibitors share hydrogen bonds with the side chain hydroxyls of Ser-164 and Tyr-178 via a carbonyl oxygen (pyroquilon and 1) or via a carbonyl oxygen and a ring oxygen (phthalide). Active site residues occupy similar positions among the three structures. A buried water molecule that is hydrogen bonded to the NZ nitrogen of Lys-182 in each of the three structures likely serves to stabilize the cationic form of the residue for participation in catalysis. The pro S hydrogen of NADPH (which is transferred as a hydride to the enzyme's naphthol substrates) is directed toward the carbonyl carbon of the inhibitors that mimic an intermediate along the reaction coordinate. Modeling tetrahydroxynaphthalene and trihydroxynaphthalene in the active site shows steric and electrostatic repulsion between the extra hydroxyl oxygen of the former substrate and the sulfur atom of Met-283 (the C-terminal residue), which accounts, in part, for the 4-fold greater substrate specificity for trihydroxynaphthalene over tetrahydroxynaphthalene.

  9. Structural Analysis of Complex Networks

    CERN Document Server

    Dehmer, Matthias

    2011-01-01

    Filling a gap in literature, this self-contained book presents theoretical and application-oriented results that allow for a structural exploration of complex networks. The work focuses not only on classical graph-theoretic methods, but also demonstrates the usefulness of structural graph theory as a tool for solving interdisciplinary problems. Applications to biology, chemistry, linguistics, and data analysis are emphasized. The book is suitable for a broad, interdisciplinary readership of researchers, practitioners, and graduate students in discrete mathematics, statistics, computer science,

  10. Tuning the photoluminescence of condensed-phase cyclic trinuclear Au(I) complexes through control of their aggregated structures by external stimuli

    Science.gov (United States)

    Fujisawa, Kaori; Yamada, Shigeyuki; Yanagi, Yukihiro; Yoshioka, Yasunori; Kiyohara, Ayumi; Tsutsumi, Osamu

    2015-01-01

    A series of new cyclic trinuclear Au(I) complexes with alkoxy side chains of various lengths were synthesized as photoluminescence materials. None of the complexes emitted luminescence in solution; however, some showed photoluminescence in the crystalline phase. Single crystal X-ray structural analyses revealed that an intermolecular interaction between two Au atoms (aurophilic interaction) existed only in the emissive complexes, which formed molecular aggregates in the crystal. Because isolated molecules show no luminescence in the present system, we conclude that only molecules aggregated via aurophilic interactions can luminesce. We demonstrated that luminescence properties, such as colour and intensity, were very sensitive to the aggregated structure of the molecules. We also found that such luminescence properties can be controlled by a change in the aggregated structure induced by external stimuli, such as heat, solvent, and mechanical stress. PMID:25879782

  11. Tuning the photoluminescence of condensed-phase cyclic trinuclear Au(I) complexes through control of their aggregated structures by external stimuli

    Science.gov (United States)

    Fujisawa, Kaori; Yamada, Shigeyuki; Yanagi, Yukihiro; Yoshioka, Yasunori; Kiyohara, Ayumi; Tsutsumi, Osamu

    2015-03-01

    A series of new cyclic trinuclear Au(I) complexes with alkoxy side chains of various lengths were synthesized as photoluminescence materials. None of the complexes emitted luminescence in solution; however, some showed photoluminescence in the crystalline phase. Single crystal X-ray structural analyses revealed that an intermolecular interaction between two Au atoms (aurophilic interaction) existed only in the emissive complexes, which formed molecular aggregates in the crystal. Because isolated molecules show no luminescence in the present system, we conclude that only molecules aggregated via aurophilic interactions can luminesce. We demonstrated that luminescence properties, such as colour and intensity, were very sensitive to the aggregated structure of the molecules. We also found that such luminescence properties can be controlled by a change in the aggregated structure induced by external stimuli, such as heat, solvent, and mechanical stress.

  12. Structural Complexity of DNA Sequence

    Directory of Open Access Journals (Sweden)

    Cheng-Yuan Liou

    2013-01-01

    Full Text Available In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results.

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

    Indian Academy of Sciences (India)

    Kumarasamy Gayathri; Subramanian Balamurugan; Palaninathan Kannan

    2011-05-01

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

  14. Structures of the acyl-enzyme complexes of the Staphylococcus aureus beta-lactamase mutant Glu166Asp:Asn170Gln with benzylpenicillin and cephaloridine.

    Science.gov (United States)

    Chen, C C; Herzberg, O

    2001-02-27

    The serine-beta-lactamases hydrolyze beta-lactam antibiotics in a reaction that proceeds via an acyl-enzyme intermediate. The double mutation, E166D:N170Q, of the class A enzyme from Staphylococcus aureus results in a protein incapable of deacylation. The crystal structure of this beta-lactamase, determined at 2.3 A resolution, shows that except for the mutation sites, the structure is very similar to that of the native protein. The crystal structures of two acyl-enzyme adducts, one with benzylpenicillin and the other with cephaloridine, have been determined at 1.76 and 1.86 A resolution, respectively. Both acyl-enzymes show similar key features, with the carbonyl carbon atom of the cleaved beta-lactam bond covalently bound to the side chain of the active site Ser70, and the carbonyl oxygen atom in an oxyanion hole. The thiadolizine ring of the cleaved penicillin is located in a slightly different position than the dihydrothiazine ring of cephaloridine. Consequently, the carboxylate moieties attached to the rings form different sets of interactions. The carboxylate group of benzylpenicillin interacts with the side chain of Gln237. The carboxylate group of cephaloridine is located between Arg244 and Lys234 side chains and also interacts with Ser235 hydroxyl group. The interactions of the cephaloridine resemble those seen in the structure of the acyl-enzyme of beta-lactamase from Escherichia coli with benzylpenicillin. The side chains attached to the cleaved beta-lactam rings of benzylpenicillin and cephaloridine are located in a similar position, which is different than the position observed in the E. coli benzylpenicillin acyl-enzyme complex. The three modes of binding do not show a trend that explains the preference for benzylpenicillin over cephaloridine in the class A beta-lactamases. Rather, the conformational variation arises because cleavage of the beta-lactam bond provides additional flexibility not available when the fused rings are intact. The structural

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

    NARCIS (Netherlands)

    Cankar, K.; Kortstee, A.J.; Toonen, M.A.J.; Wolters-Arts, M.; Houbein, R.; Mariani, C.; Ulvskov, P.; Jorgensen, B.; Schols, H.A.; Visser, R.G.F.; Trindade, L.M.

    2014-01-01

    Pectin is a complex polysaccharide and an integral part of the primary plant cell wall and middle lamella, contributing to cell wall mechanical strength and cell adhesion. To understand the structure–function relationships of pectin in the cell wall, a set of transgenic potato lines with altered pec

  16. Structural Characterisation of Fenchone and its Complexes with Ethanol by Broadband Rotational Spectroscopy

    Science.gov (United States)

    Loru, Donatella; Sanz, M. Eugenia

    2016-06-01

    Although significant advances in understanding the human olfactory system have taken place over the last two decades, detailed information on how the interactions between odorants and olfactory receptors occur at the molecular level is still lacking. To achieve a better understanding on the molecular mechanisms involved in olfaction, we are investigating several odorants and their interactions with mimics of amino acid residues in olfactory receptors. We present here the structural characterisation of fenchone (C10H16O) and its complexes with ethanol (to mimic the side chain of serine) using a 2-8 GHz chirped-pulse Fourier transform microwave spectrometer built at King's College London. The rotational spectrum of the parent species and all the 13C and 18O isotopologues of fenchone was observed, and from the experimental rotational constants the substitution (r0) and effective (rs) structures of fenchone were determined. The rotational spectrum of fenchone-ethanol was observed by adding ethanol to the carrier gas and passing the mixture through a receptacle with fenchone. Several 1:1 complexes of fenchone-ethanol have been identified in the rotational spectrum. In all the complexes the ethanol molecule binds to the carbonyl group through an O-H· · · O hydrogen bond.

  17. 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.

  18. 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.

  19. Efficient Analysis of Complex Structures

    Science.gov (United States)

    Kapania, Rakesh K.

    2000-01-01

    Last various accomplishments achieved during this project are : (1) A Survey of Neural Network (NN) applications using MATLAB NN Toolbox on structural engineering especially on equivalent continuum models (Appendix A). (2) Application of NN and GAs to simulate and synthesize substructures: 1-D and 2-D beam problems (Appendix B). (3) Development of an equivalent plate-model analysis method (EPA) for static and vibration analysis of general trapezoidal built-up wing structures composed of skins, spars and ribs. Calculation of all sorts of test cases and comparison with measurements or FEA results. (Appendix C). (4) Basic work on using second order sensitivities on simulating wing modal response, discussion of sensitivity evaluation approaches, and some results (Appendix D). (5) Establishing a general methodology of simulating the modal responses by direct application of NN and by sensitivity techniques, in a design space composed of a number of design points. Comparison is made through examples using these two methods (Appendix E). (6) Establishing a general methodology of efficient analysis of complex wing structures by indirect application of NN: the NN-aided Equivalent Plate Analysis. Training of the Neural Networks for this purpose in several cases of design spaces, which can be applicable for actual design of complex wings (Appendix F).

  20. 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.

  1. Determination of Leu Side-Chain Conformations in Excited Protein States by NMR Relaxation Dispersion

    NARCIS (Netherlands)

    Hansen, D. Flemming; Neudecker, Philipp; Vallurupalli, Pramodh; Mulder, Frans A. A.; Kay, Lewis E.

    2010-01-01

    Fits of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion profiles allow extraction of the kinetics and thermodynamics of exchange reactions that interconvert highly populated, ground state and low Populated, excited state conformers. Structural information is also available in the form of chem

  2. Effect of the Asn side chain on the dissociation of deprotonated peptides elucidated by IRMPD spectroscopy

    NARCIS (Netherlands)

    J. Grzetic; J. Oomens

    2013-01-01

    Infrared ion spectroscopy using the free electron laser FELIX was applied to identify the structure of b-type peptide fragments generated by collision and IR multiple-photon induced dissociation from singly deprotonated peptides containing an asparagine residue, in particular AlaAsnAla (ANA) and Ala

  3. 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.

  4. Crystal structure of an enzyme-substrate complex provides insight into the interaction between human arylsulfatase A and its substrates during catalysis.

    Science.gov (United States)

    von Bülow, R; Schmidt, B; Dierks, T; von Figura, K; Usón, I

    2001-01-12

    Arylsulfatase A (ASA) belongs to the sulfatase family whose members carry a C(alpha)-formylglycine that is post-translationally generated by oxidation of a conserved cysteine or serine residue. The crystal structures of two arylsulfatases, ASA and ASB, and kinetic studies on ASA mutants led to different proposals for the catalytic mechanism in the hydrolysis of sulfate esters. The structures of two ASA mutants that lack the functional C(alpha)-formylglycine residue 69, in complex with a synthetic substrate, have been determined in order to unravel the reaction mechanism. The crystal structure of the inactive mutant C69A-ASA in complex with p-nitrocatechol sulfate (pNCS) mimics a reaction intermediate during sulfate ester hydrolysis by the active enzyme, without the covalent bond to the key side-chain FGly69. The structure shows that the side-chains of lysine 123, lysine 302, serine 150, histidine 229, the main-chain of the key residue 69 and the divalent cation in the active center are involved in sulfate binding. It is proposed that histidine 229 protonates the leaving alcoholate after hydrolysis.C69S-ASA is able to bind covalently to the substrate and hydrolyze it, but is unable to release the resulting sulfate. Nevertheless, the resulting sulfation is low. The structure of C69S-ASA shows the serine side-chain in a single conformation, turned away from the position a substrate occupies in the complex. This suggests that the double conformation observed in the structure of wild-type ASA is more likely to correspond to a formylglycine hydrate than to a twofold disordered aldehyde oxo group, and accounts for the relative inertness of the C69S-ASA mutant. In the C69S-ASA-pNCS complex, the substrate occupies the same position as in the C69A-ASA-pNCS complex, which corresponds to the non-covalently bonded substrate. Based on the structural data, a detailed mechanism for sulfate ester cleavage is proposed, involving an aldehyde hydrate as the functional group. Copyright

  5. 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.

  6. 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.

  7. 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.

  8. 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....

  9. 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.

  10. 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....

  11. 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.

  12. 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.).

  13. 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.

  14. 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.

  15. 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.

  16. [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

  17. 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

  18. Structure of the carboxypeptidase B complex with N-sulfamoyl-L-phenylalanine - a transition state analog of non-specific substrate.

    Science.gov (United States)

    Akparov, Valery; Timofeev, Vladimir; Khaliullin, Ilyas; Švedas, Vytas; Kuranova, Inna

    2017-04-11

    Carboxypeptidase B (EC 3.4.17.2) (CPB) is commonly used in the industrial insulin production and as a template for drug design. However, its ability to discriminate substrates with hydrophobic, hydrophilic, and charged side chains is not well understood. We report structure of CPB complex with a transition state analog N-sulfamoyl-L-phenylalanine solved at 1.74Å. The study provided an insight into structural basis of CPB substrate specificity. Ligand binding is affected by structure-depended conformational changes of Asp255 in S1'-subsite, interactions with Asn144 and Arg145 in C-terminal binding subsite, and Glu270 in the catalytic center. Side chain of the non-specific substrate analog SPhe in comparison with that of specific substrate analog SArg (reported earlier) not only loses favorable electrostatic interactions and two hydrogen bonds with Asp255 and three fixed water molecules, but is forced to be in the unfavorable hydrophilic environment. Thus, Ser207, Gly253, Tyr248, and Asp255 residues play major role in the substrate recognition by S1'-subsite.

  19. Liquid Crystalline Side-Chain Polysiloxanes with 4-Amino-4’-Stilbene- Carboxylic Ester Mesogens

    Science.gov (United States)

    1993-12-09

    hydromevthyl)siloxane.- aebsdo odrXrydfrcto Wplrzn pia irsoS (dimethyl)siloxane in dry toluene Was catalyzed by chloroplatinic acid are based paon...Structures of monomners. homopolysiloxanes, and copolysiloxanes. ntheses Monomers, I and 2, were synthesized by transesterification of the I Phase...C 112 (0.27) SB 182 (1.04) SA 220WhanoI. (JPC analyses of the molecular weights based on polystyrene HPS-2 C 110(0.15) S9 c 192 (1.0) N 2314tidards

  20. Metal complexes of chiral pentaazacrowns as conformational templates for β-turn recognition

    Science.gov (United States)

    Reaka, Andrea J. H.; Ho, Chris M. W.; Marshall, Garland R.

    2002-08-01

    Examples of reverse turns as recognition motifs in biological systems can be found in high-resolution crystal structures of antibody-peptide complexes. Development of peptidomimetics is often based on replacing the amide backbone of peptides by sugar rings, steroids, benzodiazepines, or other hetero- and carbocycles. In this approach, the chemical scaffold of the peptide backbone can be replaced while retaining activity as long as the pharmacophoric groups of the peptide side chains stay in relatively the same place; in other words, similar functional groups must overlap in space for interaction with critical receptor sites. This study evaluates the potential of metal complexes of chiral pentaazacrowns (PAC) derived by reduction of cyclic pentapeptides as β-turn mimetics. Due to the limited flexibility of the pendant chiral side groups in these metal complexes, one can potentially elicit information about the receptor-bound conformation from their binding affinities. 11 PAC crystal structures with different substitution patterns complexed with 3 different metals (Mn, Fe, Cd) as a prototypical database of potential side-chain orientations. Complexation with different metals induces subtle differences in the conformations of a particular azacrown scaffold. The lack of parameterization of transition metals for force field calculations precludes a thorough theoretical study. Thus, this study utilizes a simple geometrical comparison between the experimental data for crystalline PAC complexes and the side-chain orientations seen in classic β-turns. The FOUNDATION program was used to overlap the Cα-Cβ vectors of the corresponding ideal β-turn side-chains to all possible leaving groups of the PAC complexes. When comparing the relative orientations of the chiral side chains, a strong overlap of the bonds (between about 0.1 Å to about 0.5 Å RMS for 3 residues and up to about 1 Å RMS for 4 residues) was observed for many of the molecules. Such metal complexes may lack

  1. Metal complexes of chiral pentaazacrowns as conformational templates for beta-turn recognition.

    Science.gov (United States)

    Reaka, Andrea J H; Ho, Chris M W; Marshall, Garland R

    2002-01-01

    Examples of reverse turns as recognition motifs in biological systems can be found in high-resolution crystal structures of antibody-peptide complexes. Development of peptidomimetics is often based on replacing the amide backbone of peptides by sugar rings, steroids, benzodiazepines, or other hetero- and carbocycles. In this approach, the chemical scaffold of the peptide backbone can be replaced while retaining activity as long as the pharmacophoric groups of the peptide side chains stay in relatively the same place; in other words, similar functional groups must overlap in space for interaction with critical receptor sites. This study evaluates the potential of metal complexes of chiral pentaazacrowns (PAC) derived by reduction of cyclic pentapeptides as beta-turn mimetics. Due to the limited flexibility of the pendant chiral side groups in these metal complexes, one can potentially elicit information about the receptor-bound conformation from their binding affinities. 11 PAC crystal structures with different substitution patterns complexed with 3 different metals (Mn, Fe, Cd) as a prototypical database of potential side-chain orientations. Complexation with different metals induces subtle differences in the conformations of a particular azacrown scaffold. The lack of parameterization of transition metals for force field calculations precludes a thorough theoretical study. Thus, this study utilizes a simple geometrical comparison between the experimental data for crystalline PAC complexes and the side-chain orientations seen in classic beta-turns. The FOUNDATION program was used to overlap the Calpha-Cbeta vectors of the corresponding ideal beta-turn side-chains to all possible leaving groups of the PAC complexes. When comparing the relative orientations of the chiral side chains, a strong overlap of the bonds (between about 0.1 A to about 0.5 A RMS for 3 residues and up to about 1 A RMS for 4 residues) was observed for many of the molecules. Such metal complexes

  2. 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.

  3. Rapid Optimization of Mcl-1 Inhibitors using Stapled Peptide Libraries Including Non-Natural Side Chains.

    Science.gov (United States)

    Rezaei Araghi, Raheleh; Ryan, Jeremy A; Letai, Anthony; Keating, Amy E

    2016-05-20

    Alpha helices form a critical part of the binding interface for many protein-protein interactions, and chemically stabilized synthetic helical peptides can be effective inhibitors of such helix-mediated complexes. In particular, hydrocarbon stapling of peptides to generate constrained helices can improve binding affinity and other peptide properties, but determining the best stapled peptide variant often requires laborious trial and error. Here, we describe the rapid discovery and optimization of a stapled-helix peptide that binds to Mcl-1, an antiapoptotic protein that is overexpressed in many chemoresistant cancers. To accelerate discovery, we developed a peptide library synthesis and screening scheme capable of identifying subtle affinity differences among Mcl-1-binding stapled peptides. We used our method to sample combinations of non-natural amino-acid substitutions that we introduced into Mcl-1 inhibitors in the context of a fixed helix-stabilizing hydrocarbon staple that increased peptide helical content and reduced proteolysis. Peptides discovered in our screen contained surprising substitutions at sites that are conserved in natural binding partners. Library-identified peptide M3d is the most potent molecule yet tested for selectively triggering mitochondrial permeabilization in Mcl-1 dependent cell lines. Our library approach for optimizing helical peptide inhibitors can be readily applied to the study of other biomedically important targets.

  4. Structures of Mycobacterium Tuberculosis Folylpolyglutamate Synthase Complexed With ADP And AMPPCD

    Energy Technology Data Exchange (ETDEWEB)

    Young, P.G.; Smith, C.A.; Metcalf, P.; Baker, E.N.

    2009-05-28

    Folate derivatives are essential vitamins for cell growth and replication, primarily because of their central role in reactions of one-carbon metabolism. Folates require polyglutamation to be efficiently retained within the cell and folate-dependent enzymes have a higher affinity for the polyglutamylated forms of this cofactor. Polyglutamylation is dependent on the enzyme folylpolyglutamate synthetase (FPGS), which catalyzes the sequential addition of several glutamates to folate. FPGS is essential for the growth and survival of important bacterial species, including Mycobacterium tuberculosis, and is a potential drug target. Here, the crystal structures of M. tuberculosis FPGS in complex with ADP and AMPPCP are reported at 2.0 and 2.3 angstroms resolution, respectively. The structures reveal a deeply buried nucleotide-binding site, as in the Escherichia coli and Lactobacillus casei FPGS structures, and a long extended groove for the binding of folate substrates. Differences from the E. coli and L. casei FPGS structures are seen in the binding of a key divalent cation, the carbamylation state of an essential lysine side chain and the adoption of an 'open' position by the active-site beta5-alpha6 loop. These changes point to coordinated events that are associated with dihydropteroate/folate binding and the catalysis of the new amide bond with an incoming glutamate residue.

  5. FlexAID: Revisiting Docking on Non-Native-Complex Structures.

    Science.gov (United States)

    Gaudreault, Francis; Najmanovich, Rafael J

    2015-07-27

    Small-molecule protein docking is an essential tool in drug design and to understand molecular recognition. In the present work we introduce FlexAID, a small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specific geometric criteria, based on surface complementarity. The pairwise energy parameters were derived from a large dataset of true positive poses and negative decoys from the PDBbind database through an iterative process using Monte Carlo simulations. The prediction of binding poses is tested using the widely used Astex dataset as well as the HAP2 dataset, while performance in virtual screening is evaluated using a subset of the DUD dataset. We compare FlexAID to AutoDock Vina, FlexX, and rDock in an extensive number of scenarios to understand the strengths and limitations of the different programs as well as to reported results for Glide, GOLD, and DOCK6 where applicable. The most relevant among these scenarios is that of docking on flexible non-native-complex structures where as is the case in reality, the target conformation in the bound form is not known a priori. We demonstrate that FlexAID, unlike other programs, is robust against increasing structural variability. FlexAID obtains equivalent sampling success as GOLD and performs better than AutoDock Vina or FlexX in all scenarios against non-native-complex structures. FlexAID is better than rDock when there is at least one critical side-chain movement required upon ligand binding. In virtual screening, FlexAID results are lower on average than those of AutoDock Vina and rDock. The higher accuracy in flexible targets where critical movements are required, intuitive PyMOL-integrated graphical user interface and free source code as well as precompiled executables for Windows, Linux, and Mac OS make FlexAID a welcome addition to the arsenal of existing small-molecule protein docking methods.

  6. Synthesis and Characterization of Polycarbonate Copolymers Containing Benzoyl Groups on the Side Chain for Scratch Resistance

    Directory of Open Access Journals (Sweden)

    Hohyoun Jang

    2016-01-01

    Full Text Available The purpose of this study was to enhance the scratch resistance of polycarbonate copolymer by using 3,3′-dibenzoyl-4,4′-dihydroxybiphenyl (DBHP monomer, containing benzoyl moieties on the ortho positions. DBHP monomer was synthesized from 4,4′-dihydroxybiphenyl and benzoyl chloride, followed by the Friedel-Craft rearrangement reaction with AlCl3. The polymerizations were conducted following the low-temperature procedure, which is carried out in methylene chloride by using triphosgene, triethylamine, bisphenol-A, and DBHP. The chemical structures of the polycarbonate copolymers were confirmed by 1H-NMR. The thermal properties of copolymers were investigated by thermogravimetric analysis and differential scanning calorimetry, and also surface morphologies were assessed by atomic force microscopy. The scratch resistance of homopolymer film (100 μm changed from 6B to 1B, and the contact angle of a sessile water drop onto the homopolymer film also increased.

  7. New poly(p-phenylenevinylene derivatives containing isosorbide unit in the side-chain

    Directory of Open Access Journals (Sweden)

    H. Zrida

    2014-10-01

    Full Text Available New conjugated PPV derivatives containing the chiral isosorbide group (P1-3 have been synthesized via the Gilch reaction. The polymers are optically active, soluble in common organic solvents and show good film-forming abilities. High number-average molecular weights were determined by size exclusion chromatography (SEC (16•103–21•103 g•mol–1. The molecular structures of the polymers were confirmed by nuclear magnetic resonance (NMR and Fourier transform infrared (FTIR spectroscopies. Thermogravimetric analysis of the polymers showed good thermal stability up to 320°C. The optical properties of these π-conjugated materials were investigated by UV-vis absorption and photoluminescence (PL spectroscopies. The polymers show a yellow fluorescence in dilute solution, and an orange emission is observed in thin films. The introduction of the polar isosorbide groups improved the PL intensity, and quantum yields between 50 and 73% were obtained. The HOMO-LUMO energy levels were estimated by cyclic voltammetry, and the electrochemical gaps were 1.81, 1.83 and 2.48 eV for P1, P2 and P3, respectively. Single-layer diode devices were fabricated and show relatively low turn-on voltages between 3.1 and 3.4 V.

  8. The Crystal Structure of Cytochrome P450 4B1 (CYP4B1) Monoxygenase Complexed with Octane Discloses Several Structural Adaptations for ω-Hydroxylation.

    Science.gov (United States)

    Hsu, Mei-Hui; Baer, Brian R; Rettie, Allan E; Johnson, Eric F

    2017-02-06

    P450 family 4 fatty acid ω-hydroxylases preferentially oxygenate primary C-H bonds over adjacent, energetically favored secondary C-H bonds, but the mechanism explaining this intriguing preference is unclear. To this end, the structure of rabbit P450 4B1 complexed with its substrate octane was determined by X-ray crystallography to define features of the active site that contribute to a preference for ω-hydroxylation. The structure indicated that octane is bound in a narrow active site cavity that limits access of the secondary C-H bond to the reactive intermediate. A highly conserved sequence motif on helix I contributes to positioning the terminal carbon of octane for ω-hydroxylation. Glu-310 of this motif auto-catalytically forms an ester bond with the heme 5-methyl, and the immobilized E310 contributes to substrate positioning. The preference for ω-hydroxylation was decreased in a E310A mutant having a shorter side-chain, but overall rates of metabolism were retained. E310D and E310Q substitutions having longer side-chains exhibit lower overall rates, likely due to higher conformational entropy for these residues, but they retained high preferences for octane ω-hydroxylation. Sequence comparisons indicated that active-site residues constraining octane for ω-hydroxylation are conserved in family 4 P450s. Moreover, the heme 7-propionate is positioned in the active site and provides additional restraints on substrate binding. In conclusion, P450 4B1 exhibits structural adaptations for ω-hydroxylation that include changes in the conformation of the heme and changes in a highly conserved helix I motif that is associated with selective oxygenation of un-activated primary C-H bonds.

  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. 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...

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

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

    Science.gov (United States)

    Bi, Qi-rui; Hou, Jin-jun; Yang, Min; Shen, Yao; Qi, Peng; Feng, Rui-hong; Dai, Zhuo; Yan, Bing-peng; Wang, Jian-wei; Shi, Xiao-jian; Wu, Wan-ying; Guo, De-an

    2016-12-01

    Fatty acids conjugates (FACs) are ubiquitous but found in trace amounts in the natural world. They are composed of multiple unknown substructures and side chains. Thus, FACs are difficult to be analyzed by traditional mass spectrometric methods. In this study, an integrated strategy was developed to global profiling and targeted structure annotation of FACs in complex matrix by LTQ Orbitrap. Dicarboxylic acid conjugated bufotoxins (DACBs) in Venenum bufonis (VB) were used as model compounds. The new strategy (abbreviated as HPNA) combined higher-energy C-trap dissociation (HCD) with product ion- (PI), neutral loss- (NL) based MSn (n ≥ 3) acquisition in both positive-ion mode and negative-ion mode. Several advantages are presented. First, various side chains were found under HCD in negative-ion mode, which included both known and unknown side chains. Second, DACBs with multiple side chains were simultaneously detected in one run. Compared with traditional quadrupole-based mass method, it greatly increased analysis throughput. Third, the fragment ions of side chain and steroids substructure could be obtained by PI- and NL-based MSn acquisition, respectively, which greatly increased the accuracy of the structure annotation of DACBs. In all, 78 DACBs have been discovered, of which 68 were new compounds; 25 types of substructure formulas and seven dicarboxylic acid side chains were found, especially five new side chains, including two saturated dicarboxylic acids [(azelaic acid (C9) and sebacic acid (C10)] and three unsaturated dicarboxylic acids (u-C8, u-C9, and u-C10). All these results greatly enriched the structures of DACBs in VB.

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

    Science.gov (United States)

    Bi, Qi-rui; Hou, Jin-jun; Yang, Min; Shen, Yao; Qi, Peng; Feng, Rui-hong; Dai, Zhuo; Yan, Bing-peng; Wang, Jian-wei; Shi, Xiao-jian; Wu, Wan-ying; Guo, De-an

    2017-03-01

    Fatty acids conjugates (FACs) are ubiquitous but found in trace amounts in the natural world. They are composed of multiple unknown substructures and side chains. Thus, FACs are difficult to be analyzed by traditional mass spectrometric methods. In this study, an integrated strategy was developed to global profiling and targeted structure annotation of FACs in complex matrix by LTQ Orbitrap. Dicarboxylic acid conjugated bufotoxins (DACBs) in Venenum bufonis (VB) were used as model compounds. The new strategy (abbreviated as HPNA) combined higher-energy C-trap dissociation (HCD) with product ion- (PI), neutral loss- (NL) based MSn (n ≥ 3) acquisition in both positive-ion mode and negative-ion mode. Several advantages are presented. First, various side chains were found under HCD in negative-ion mode, which included both known and unknown side chains. Second, DACBs with multiple side chains were simultaneously detected in one run. Compared with traditional quadrupole-based mass method, it greatly increased analysis throughput. Third, the fragment ions of side chain and steroids substructure could be obtained by PI- and NL-based MSn acquisition, respectively, which greatly increased the accuracy of the structure annotation of DACBs. In all, 78 DACBs have been discovered, of which 68 were new compounds; 25 types of substructure formulas and seven dicarboxylic acid side chains were found, especially five new side chains, including two saturated dicarboxylic acids [(azelaic acid (C9) and sebacic acid (C10)] and three unsaturated dicarboxylic acids (u-C8, u-C9, and u-C10). All these results greatly enriched the structures of DACBs in VB.

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

    Science.gov (United States)

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

    2017-03-01

    Fatty acids conjugates (FACs) are ubiquitous but found in trace amounts in the natural world. They are composed of multiple unknown substructures and side chains. Thus, FACs are difficult to be analyzed by traditional mass spectrometric methods. In this study, an integrated strategy was developed to global profiling and targeted structure annotation of FACs in complex matrix by LTQ Orbitrap. Dicarboxylic acid conjugated bufotoxins (DACBs) in Venenum bufonis (VB) were used as model compounds. The new strategy (abbreviated as HPNA) combined higher-energy C-trap dissociation (HCD) with product ion- (PI), neutral loss- (NL) based MS(n) (n ≥ 3) acquisition in both positive-ion mode and negative-ion mode. Several advantages are presented. First, various side chains were found under HCD in negative-ion mode, which included both known and unknown side chains. Second, DACBs with multiple side chains were simultaneously detected in one run. Compared with traditional quadrupole-based mass method, it greatly increased analysis throughput. Third, the fragment ions of side chain and steroids substructure could be obtained by PI- and NL-based MS(n) acquisition, respectively, which greatly increased the accuracy of the structure annotation of DACBs. In all, 78 DACBs have been discovered, of which 68 were new compounds; 25 types of substructure formulas and seven dicarboxylic acid side chains were found, especially five new side chains, including two saturated dicarboxylic acids [(azelaic acid (C9) and sebacic acid (C10)] and three unsaturated dicarboxylic acids (u-C8, u-C9, and u-C10). All these results greatly enriched the structures of DACBs in VB. Graphical Abstract ᅟ.

  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. 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.

  1. 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.

  2. 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.

  3. UV–Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 2: selected applications

    OpenAIRE

    Antosiewicz, Jan M.; Shugar, David

    2016-01-01

    In Part 2 we discuss application of several different types of UV–Vis spectroscopy, such as normal, difference, and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, of the side-chain of tyrosine residues in different molecular environments. We review the ways these spectroscopies can be used to probe complex protein structures.

  4. UV-Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 2: selected applications.

    Science.gov (United States)

    Antosiewicz, Jan M; Shugar, David

    2016-06-01

    In Part 2 we discuss application of several different types of UV-Vis spectroscopy, such as normal, difference, and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, of the side-chain of tyrosine residues in different molecular environments. We review the ways these spectroscopies can be used to probe complex protein structures.

  5. UV-Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 2: selected applications.

    Science.gov (United States)

    Antosiewicz, Jan M; Shugar, David

    In Part 2 we discuss application of several different types of UV-Vis spectroscopy, such as normal, difference, and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, of the side-chain of tyrosine residues in different molecular environments. We review the ways these spectroscopies can be used to probe complex protein structures.

  6. 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....

  7. 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...

  8. 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.

  9. 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.

  10. 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.

  11. 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...

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. Structures of some surfactant–polyelectrolyte complexes

    Indian Academy of Sciences (India)

    Rema Krishnaswamy; V A Raghunathan; A K Sood

    2003-08-01

    Structures of complexes formed in aqueous solutions by some anionic polyelectrolytes (double and single stranded (ds and ss) DNA, poly(vinyl sulfonate) (PVS), and poly(styrene sulfonate) (PSS)) with a cationic surfactant system consisting of cetyltrimethylammonium bromide (CTAB) and sodium 3-hydroxy-2-naphthoate (SHN) have been determined using small angle X-ray diffraction. All complexes are found to have a two-dimensional (2-D) hexagonal structure at low SHN concentrations. Analysis of the diffraction data shows that the ds DNA–CTAB complex has an intercalated structure, with each DNA strand surrounded by three cylindrical micelles. On increasing SHN concentration, DNA–CTAB–SHN complexes exhibit a hexagonal-to-lamellar transition, whereas PVS complexes show a hexagonal → centered rectangular → lamellar transition. PSS complexes show yet another sequence of structures. These results indicate the significant influence of the chemical nature of the polyelectrolyte on the structure of the complexes.

  17. Computational Simulation of Complex Structure Fancy Yarns

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A study is reported for mathematical model and simulation of complex structure fancy yarns. The investigated complex structure fancy yarns have a multithread structure composed of three components -core, effect, and binder yams. In current research the precondition was accepted that the cross-sections of the both two yarns of the effect intermediate product in the complex structure fancy yarn remain the circles shaped, and this shape does not change during manufacturing of the fancy yarn. Mathematical model of complex structure fancy yarn is established based on parameter equation of space helix line and computer simulation is further carried out using the computational mathematical tool Matlab 6.5. Theoretical structure of fancy yarn is compared with an experimental sample. The simulation system would help for further the set ofinformation in designing of new assortment of the complex structure fancy yarns and prediction of visual effects of fancy yarns in end-use fabrics.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 3D complex: a structural classification of protein complexes.

    Directory of Open Access Journals (Sweden)

    Emmanuel D Levy

    2006-11-01

    Full Text Available Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

  4. High performance films of cellulose butyral derivative having a necklace-like annular structure in the side chains

    OpenAIRE

    2014-01-01

    We fabricated high performance films using cellulose butyral (CB) synthesized from native cellulose. Two-step reactions were adopted to produce the derivative CB, including etherification of cellulose with glycidol in NaOH/urea aqueous solution to yield O-(2, 3-dihydroxypropyl) cellulose (DHPC), and butyralization of DHPC. Both DHPC and CB products were easily processed into a thin film by hot-press molding. The butyral modifier significantly improved the tenacity of highly ductile DHPC, by v...

  5. Crystal Structure of Hyp-1, a Hypericum perforatum PR-10 Protein, in Complex with Melatonin.

    Science.gov (United States)

    Sliwiak, Joanna; Dauter, Zbigniew; Jaskolski, Mariusz

    2016-01-01

    Hyp-1, a PR-10-fold protein from Hypericum perforatum, was crystallized in complex with melatonin (MEL). The structure confirms the conserved protein fold and the presence of three unusual ligand binding sites, two of which are internal chambers (1,2), while the third one (3) is formed as an invagination of the protein surface. The MEL ligand in site 1 is well defined while that in site 3 seems to be rotating between the side chains of Lys33 and Tyr150 that act as a molecular vise. The patch of electron density in site 2 does not allow unambiguous modeling of a melatonin molecule but suggests a possible presence of its degradation product. This pattern of ligand occupation is reproducible in repeated crystallization/structure determination experiments. Although the binding of melatonin by Hyp-1 does not appear to be very strong (for example, MEL cannot displace the artificial fluorescence probe ANS), it is strong enough to suggest a physiological role of this interaction. For example, trans-zeatin, which is a common ligand of PR-10 proteins, does not overcompete melatonin for binding to Hyp-1 as it does not affect the crystallization process of the Hyp-1/MEL complex, and among a number of potential natural mediators tested, melatonin was the only one to form a crystalline complex with Hyp-1 with the use of standard crystallization screens. Hyp-1 is the second protein in the Protein Data Bank for which melatonin binding has been demonstrated crystallographically, the first one being human quinone reductase.

  6. Crystal structure of Hyp-1, a Hypericum perforatum PR-10 protein, in complex with melatonin

    Directory of Open Access Journals (Sweden)

    Joanna eSliwiak

    2016-05-01

    Full Text Available Hyp-1, a PR-10-fold protein from H. perforatum, was crystallized in complex with melatonin (MEL. The structure confirms the conserved protein fold and the presence of three unusual ligand binding sites, two of which are internal chambers (1, 2, while the third one (3 is formed as an invagination of the protein surface. The MEL ligand in site 1 is well defined while that in site 3 seems to be rotating between the side chains of Lys33 and Tyr150 that act as a molecular vise. The patch of electron density in site 2 does not allow unambiguous modeling of a melatonin molecule but suggests a possible presence of its degradation product. This pattern of ligand occupation is reproducible in repeated crystallization/structure determination experiments. Although the binding of melatonin by Hyp-1 does not appear to be very strong (for example, MEL cannot displace the artificial fluorescence probe ANS, it is strong enough to suggest a physiological role of this interaction. For example, trans-zeatin, which is a common ligand of PR-10 proteins, does not overcompete melatonin for binding to Hyp-1 as it does not affect the crystallization process of the Hyp-1/MEL complex, and among a number of potential natural mediators tested, melatonin was the only one to form a crystalline complex with Hyp-1 with the use of standard crystallization screens. Hyp-1 is the second protein in the Protein Data Bank (PDB for which melatonin binding has been demonstrated crystallographically, the first one being human quinone reductase.

  7. Predicting complex mineral structures using genetic algorithms.

    Science.gov (United States)

    Mohn, Chris E; Kob, Walter

    2015-10-28

    We show that symmetry-adapted genetic algorithms are capable of finding the ground state of a range of complex crystalline phases including layered- and incommensurate super-structures. This opens the way for the atomistic prediction of complex crystal structures of functional materials and mineral phases.

  8. Active impedance matching of complex structural systems

    Science.gov (United States)

    Macmartin, Douglas G.; Miller, David W.; Hall, Steven R.

    1991-01-01

    Viewgraphs on active impedance matching of complex structural systems are presented. Topics covered include: traveling wave model; dereverberated mobility model; computation of dereverberated mobility; control problem: optimal impedance matching; H2 optimal solution; statistical energy analysis (SEA) solution; experimental transfer functions; interferometer actuator and sensor locations; active strut configurations; power dual variables; dereverberation of complex structure; dereverberated transfer function; compensators; and relative power flow.

  9. Structure of the complex of carboxypeptidase B and N-sulfamoyl-L-arginine.

    Science.gov (United States)

    Akparov, Valery; Sokolenko, Nikolay; Timofeev, Vladimir; Kuranova, Inna

    2015-10-01

    Porcine pancreatic carboxypeptidase B (EC 3.4.23.6) was complexed with a stable transition-state analogue, N-sulfamoyl-L-arginine, in which an S atom imitates the sp(3)-hybridized carbon in the scissile-bond surrogate. Crystals were grown in a form belonging to the same space group, P41212, as the uncomplexed enzyme. X-ray data were collected to a resolution of 1.25 Å. The molecule was refined and the positions of non-H atoms of the inhibitor and water molecules were defined using difference Fourier maps. The enzyme-inhibitor complex and 329 water molecules were further refined to a crystallographic R factor of 0.159. The differences in conformation between the complexed and uncomplexed forms of carboxypeptidase B are shown. The inhibitor is bound in a curved conformation in the active-site cleft, and the sulfamide group is bound to the Zn ion in an asymmetric bidentate fashion. The complex is stabilized by hydrogen bonds between the N1/N2 guanidine group of the inhibitor and the Asp255 carboxyl of the enzyme. The side-chain CH2 groups of the inhibitor are in van der Waals contact with Leu203 and Ile247 in the enzyme. This study provides useful clues concerning how the transition state of arginine may bind to carboxypeptidase B and therefore provides an insight into the structural basis of carboxypeptidase B selectivity, which is useful for the rational design of a carboxypeptidase with improved selectivity for industrial recombinant pro-insulin processing.

  10. TASI lectures on complex structures

    CERN Document Server

    Denef, Frederik

    2011-01-01

    These lecture notes give an introduction to a number of ideas and methods that have been useful in the study of complex systems ranging from spin glasses to D-branes on Calabi-Yau manifolds. Topics include the replica formalism, Parisi's solution of the Sherrington-Kirkpatrick model, overlap order parameters, supersymmetric quantum mechanics, D-brane landscapes and their black hole duals.

  11. TASI Lectures on Complex Structures

    Science.gov (United States)

    Denef, Frederik

    2012-11-01

    These lecture notes give an introduction to a number of ideas and methods that have been useful in the study of complex systems ranging from spin glasses to D-branes on Calabi-Yau manifolds. Topics include the replica formalism, Parisi's solution of the Sherrington-Kirkpatrick model, overlap order parameters, supersymmetric quantum mechanics, D-brane landscapes and their black hole duals.

  12. Argument structure frames: a lexical complexity metric?

    Science.gov (United States)

    Schmauder, A R

    1991-01-01

    The number of semantic argument structure frames associated with a verb has been reported to influence ease of processing during language comprehension. The present experiments tested the generality of the argument structure complexity effect with three dependent measures: eye-fixation times, naming latencies, and lexical decision latencies. Two eye-movement experiments and two experiments using cross-modal tasks failed to provide evidence supporting the argument structure complexity effect. The present experiments indicated that results reflecting verbs' argument structure complexity are not generalizable.

  13. Computational Complexity in Electronic Structure

    CERN Document Server

    Whitfield, James D; Aspuru-Guzik, Alan

    2012-01-01

    In quantum chemistry, the price paid by all known efficient model chemistries is either the truncation of the Hilbert space or uncontrolled approximations. Theoretical computer science suggests that these restrictions are not mere shortcomings of the algorithm designers and programmers but could stem from the inherent difficulty of simulating quantum systems. Extensions of computer science and information processing exploiting quantum mechanics has led to new ways of understanding the ultimate limitations of computational power. Interestingly, this perspective helps us understand widely used model chemistries in a new light. In this article, the fundamentals of computational complexity will be reviewed and motivated from the vantage point of chemistry. Then recent results from the computational complexity literature regarding common model chemistries including Hartree-Fock and density functional theory are discussed.

  14. Structures of photosynthetic membrane complexes

    OpenAIRE

    Semchonok, Dmitry Alexandrovich

    2016-01-01

    Photosynthesis is essential to all life on Earth. It is the biological process that captures energy of sunlight and converts it into chemical compounds usable by any living organism. The processes occurring within photosynthesis can be divided into the light-dependent reactions and the light-independent reactions. In my PhD thesis several integral membrane protein complexes were investigated that catalyze the light dependent reactions. Primarily the photosystem I and II that are taking part i...

  15. Structure-based characterization of multiprotein complexes.

    Science.gov (United States)

    Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

    2014-07-08

    Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies.

  16. The structure of complex Lie groups

    CERN Document Server

    Lee, Dong Hoon

    2001-01-01

    Complex Lie groups have often been used as auxiliaries in the study of real Lie groups in areas such as differential geometry and representation theory. To date, however, no book has fully explored and developed their structural aspects.The Structure of Complex Lie Groups addresses this need. Self-contained, it begins with general concepts introduced via an almost complex structure on a real Lie group. It then moves to the theory of representative functions of Lie groups- used as a primary tool in subsequent chapters-and discusses the extension problem of representations that is essential for studying the structure of complex Lie groups. This is followed by a discourse on complex analytic groups that carry the structure of affine algebraic groups compatible with their analytic group structure. The author then uses the results of his earlier discussions to determine the observability of subgroups of complex Lie groups.The differences between complex algebraic groups and complex Lie groups are sometimes subtle ...

  17. Crystal Structure of the Complex of Human FasL and Its Decoy Receptor DcR3.

    Science.gov (United States)

    Liu, Weifeng; Ramagopal, Udupi; Cheng, Huiyong; Bonanno, Jeffrey B; Toro, Rafael; Bhosle, Rahul; Zhan, Chenyang; Almo, Steven C

    2016-11-01

    The apoptotic effect of FasL:Fas signaling is disrupted by DcR3, a unique secreted member of the tumor necrosis factor receptor superfamily, which also binds and neutralizes TL1A and LIGHT. DcR3 is highly elevated in patients with various tumors and contributes to mechanisms by which tumor cells to evade host immune surveillance. Here we report the crystal structure of FasL in complex with DcR3. Comparison of FasL:DcR3 structure with our earlier TL1A:DcR3 and LIGHT:DcR3 structures supports a paradigm involving the recognition of invariant main-chain and conserved side-chain functionalities, which is responsible for the recognition of multiple TNF ligands exhibited by DcR3. The FasL:DcR3 structure also provides insight into the FasL:Fas recognition surface. We demonstrate that the ability of recombinant FasL to induce Jurkat cell apoptosis is significantly enhanced by native glycosylation or by structure-inspired mutations, both of which result in reduced tendency to aggregate. All of these activities are efficiently inhibited by recombinant DcR3.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Structures of D-amino-acid amidase complexed with L-phenylalanine and with L-phenylalanine amide: insight into the D-stereospecificity of D-amino-acid amidase from Ochrobactrum anthropi SV3.

    Science.gov (United States)

    Okazaki, Seiji; Suzuki, Atsuo; Mizushima, Tsunehiro; Komeda, Hidenobu; Asano, Yasuhisa; Yamane, Takashi

    2008-03-01

    The crystal structures of D-amino-acid amidase (DAA) from Ochrobactrum anthropi SV3 in complex with L-phenylalanine and with L-phenylalanine amide were determined at 2.3 and 2.2 A resolution, respectively. Comparison of the L-phenylalanine amide complex with the D-phenylalanine complex reveals that the D-stereospecificity of DAA might be achieved as a consequence of three structural factors: (i) the hydrophobic cavity in the region in which the hydrophobic side chain of the substrate is held, (ii) the spatial arrangement of Gln310 O and Glu114 O epsilon2 that fixes the amino N atom of the substrate and (iii) the existence of two cavities that keep the carboxyl/amide group of the substrate near or apart from Ser60 O gamma.

  3. 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.

  4. 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.

  5. 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.

  6. Crystal packing and hydrogen bonding in platinum(II) nucleotide complexes: X-ray crystal structure of [Pt(MeSCH(2)CH(2)SMe)(5'-GMP-N7)(2)].6H(2)O.

    Science.gov (United States)

    Djuran, Milos I; Milinkovic, Snezana U; Habtemariam, Abraha; Parsons, Simon; Sadler, Peter J

    2002-02-01

    We have synthesised the complex [Pt(CH(3)SCH(2)CH(2)SCH(3))(5'-GMP-N7)(2)].6H(2)O (1), where 5'-GMP is 5'-guanosine monophosphate, and determined its X-ray crystal structure. Pt(II) adopts a square-planar geometry in which the bases are coordinated head-to-tail (HT) in the Delta configuration. The nucleotide conformation in this complex is almost identical to that in the previously reported complex [Pt(en)(5'-GMP-N7)(2)].9H(2)O (2), in which there is outer sphere macrochelation via intramolecular H-bonding between the monoanionic phosphate groups and the coordinated ethylenediamine (en) NH. It is therefore apparent that intermolecular interactions rather than intramolecular H-bonding determines the orientation of the sugar-phosphate side-chain in these Pt(II) bisnucleotide complexes in the solid state.

  7. Structure of Complex Verb Forms in Meiteilon

    Directory of Open Access Journals (Sweden)

    Lourembam Surjit Singh

    2016-12-01

    Full Text Available This piece of work proposes to descriptively investigate the structures of complex verbs in Meiteilon. The categorization of such verbs is based on the nature of semantic and syntactic functions of a lexeme or verbal lexeme. A lexeme or verbal lexeme in Meiteilon may have multifunctional properties in the nature of occurrence. Such lexical items can be co-occurred together in a phrase as single functional word. Specifically, in the co-occurrences of two lexical items, the first component of lexical items has different semantic and syntactic functions in comparison to semantic and syntactic functions of the second component of lexical items. Such co-occurrences of two lexical items are the forms of complex verb that are covered with the term complex predicate in this work. The investigation in constructing complex predicate is thoroughly presenting in this work. Keywords: Structures, complex verb, conjunct verb, compound verb, complex predicate

  8. Crystal structure of GAP50, the anchor of the invasion machinery in the inner membrane complex of Plasmodium falciparum.

    Science.gov (United States)

    Bosch, Jürgen; Paige, Matthew H; Vaidya, Akhil B; Bergman, Lawrence W; Hol, Wim G J

    2012-04-01

    The glideosome associated protein GAP50 is an essential protein in apicomplexan parasites such as Plasmodium, Toxoplasma and Cryptosporidium, several species of which are important human pathogens. The 44.6kDa protein is part of a multi-protein complex known as the invasion machinery or glideosome, which is required for cell invasion and substrate gliding motility empowered by an actin-myosin motor. GAP50 is anchored through its C-terminal transmembrane helix into the inner membrane complex and interacts via a short six residue C-terminal tail with other proteins of the invasion machinery in the pellicle of the parasite. In this paper we describe the 1.7Å resolution crystal structure of the soluble GAP50 domain from the malaria parasite Plasmodium falciparum. The structure shows an αßßα fold with overall similarity to purple acid phosphatases with, however, little homology regarding the nature of the residues in the active site region of the latter enzyme. While purple acid phosphatases contain a phosphate bridged binuclear Fe-site coordinated by seven side chains with the Fe-ions 3.2Å apart, GAP50 in our crystals contains two cobalt ions each with one protein ligand and a distance between the Co(2+) ions of 18Å. Copyright © 2012 Elsevier Inc. All rights reserved.

  9. Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode.

    Science.gov (United States)

    Shimada, Satoru; Shinzawa-Itoh, Kyoko; Baba, Junpei; Aoe, Shimpei; Shimada, Atsuhiro; Yamashita, Eiki; Kang, Jiyoung; Tateno, Masaru; Yoshikawa, Shinya; Tsukihara, Tomitake

    2017-02-01

    Mitochondrial cytochrome c oxidase (CcO) transfers electrons from cytochrome c (Cyt.c) to O2 to generate H2O, a process coupled to proton pumping. To elucidate the mechanism of electron transfer, we determined the structure of the mammalian Cyt.c-CcO complex at 2.0-Å resolution and identified an electron transfer pathway from Cyt.c to CcO. The specific interaction between Cyt.c and CcO is stabilized by a few electrostatic interactions between side chains within a small contact surface area. Between the two proteins are three water layers with a long inter-molecular span, one of which lies between the other two layers without significant direct interaction with either protein. Cyt.c undergoes large structural fluctuations, using the interacting regions with CcO as a fulcrum. These features of the protein-protein interaction at the docking interface represent the first known example of a new class of protein-protein interaction, which we term "soft and specific". This interaction is likely to contribute to the rapid association/dissociation of the Cyt.c-CcO complex, which facilitates the sequential supply of four electrons for the O2 reduction reaction.

  10. Alpha complexes in protein structure prediction

    DEFF Research Database (Denmark)

    Winter, Pawel; Fonseca, Rasmus

    2015-01-01

    Reducing the computational effort and increasing the accuracy of potential energy functions is of utmost importance in modeling biological systems, for instance in protein structure prediction, docking or design. Evaluating interactions between nonbonded atoms is the bottleneck of such computations......-complexes and kinetic a-complexes in protein related problems (e.g., protein structure prediction and protein-ligand docking) deserves furhter investigation.)...

  11. Modern structure of marketing communications complex

    Directory of Open Access Journals (Sweden)

    Hrebenyukova Elena

    2015-08-01

    Full Text Available The article presents the results of the desk research, in which the current structure of the marketing communications complex was analyzed. According to the results of the content analysis of scientific and educational literature in marketing it was proved that there is a certain structural asymmetry in today's complex of marketing communication: the rejection of impersonal tools and actualization of those which make possible personalized communication with the consumer.

  12. Crystal structure of dimeric heme oxygenase-2 from Synechocystis sp. PCC 6803 in complex with heme.

    Science.gov (United States)

    Sugishima, Masakazu; Hagiwara, Yoshinori; Zhang, Xuhong; Yoshida, Tadashi; Migita, Catharina T; Fukuyama, Keiichi

    2005-03-22

    Phycobiliproteins, light-harvesting proteins in cyanobacteria, red algae, and cryptophytes, contain phycobilin pigments. Phycobilins are synthesized from biliverdin, which is produced by the oxidative cleavage of the heme porphyrin ring catalyzed by heme oxygenase (HO). Two paralogs of ho (ho1 and ho2) have been identified in the genome of the cyanobacterium, Synechocystis sp. PCC 6803. The recombinant proteins of both paralogs (Syn HO-1 and Syn HO-2) possess in vitro heme degradation activity. We have determined the crystal structures of Syn HO-2 in complex with heme (heme-Syn HO-2) and its reduced and NO bound forms. The heme-Syn HO-2 crystal was a nonmerohedral twin, and detwinned diffraction data were used to refine the structure. Although heme-Syn HO-2 shares common folding with other HOs, the C-terminal segment is ordered and turns back to the heme-binding side. Gel-filtration chromatography analysis and molecular packing in the crystal indicate that heme-Syn HO-2 forms a homodimer, in which the C-terminal ordered segments interact with each other. Because Syn HO-2 is a monomer in the apo state, the dimeric interaction may aid in the selection of the reducing partner but likely does not interfere with heme binding. The heme iron is coordinated by a water molecule in the ferric form, but the distal water is absent in the ferrous form. In all of the Syn HO-2 structures, several water molecules form a hydrogen-bond network at the distal hemepocket, which is involved in HO activity. Upon NO binding, the side-chain conformation of Tyr 156 changes. Tyr 156 is located at the hydrophobic cluster, which interrupts the possible H(+) pathway from the molecular surface to the hemepocket. Thus, Tyr 156 may function as a H(+) shuttle by changing conformation.

  13. Structural Dissection for Controlling Complex Networks

    CERN Document Server

    Wang, Wen-Xu; Zhao, Chen; Liu, Yang-Yu; Lai, Ying-Cheng

    2015-01-01

    Controlling complex networked systems has been a central goal in different fields and understanding controllability of complex networks has been at the forefront of contemporary science. Despite the recent progress in the development of controllability theories for complex networks, we continue to lack efficient tools to fully understand the effect of network topology and interaction strengths among nodes on controllability. Here we establish a framework to discern the significance of links and nodes for controlling general complex networks in a simple way based on local information. A dissection process is offered by the framework to probe and classify nodes and links completely, giving rise to a criterion for strong structural controllability. Analytical results indicate phase transitions associated with link and node categories, and strong structural controllability. Applying the tools to real networks demonstrate that real technological networks are strong structurally controllable, whereas most of real s...

  14. Complex II from a structural perspective.

    Science.gov (United States)

    Horsefield, Rob; Iwata, So; Byrne, Bernadette

    2004-04-01

    The super-macromolecular complex, succinate:quinone oxidoreductase (SQR, Complex II, succinate dehydrogenase) couples the oxidation of succinate in the matrix / cytoplasm to the reduction of quinone in the membrane. This function directly connects the Krebs cycle and the aerobic respiratory chain. Until the recent first report of the structure of SQR from Escherichia coli (E. coli) the structure-function relationships in SQR have been inferred from the structures of the homologous QFR, which catalyses the same reaction in the opposite direction. The structure of SQR from E. coli, analogous to the mitochondrial respiratory Complex II, has provided new insight into SQR's molecular design and mechanism, revealing the electron transport pathway through the enzyme. Comparison of the structures of SQR, QFR and other related flavoproteins shows how common amino acid residues at the interface of two domains facilitate the inter-conversion of succinate and fumarate. Additionally, the structure has provided a possible explanation as to why certain organisms utilise both SQR and QFR despite the fact that both can catalyse the inter-conversion of succinate and fumarate, in vitro and in vivo. Here we review how this structure has advanced our knowledge of this important enzyme and compare the structural information to other members of the Complex II superfamily and related flavoproteins.

  15. Synthesis, Structure and Noncovalent Interactions of Palladium(Ⅱ) Complexes with N-Benzoyl-β-phenylalaninate Dianion and Aromatic Diimine

    Institute of Scientific and Technical Information of China (English)

    CHEN,Yao-Feng(陈耀峰); GONG,Yu-Qiu(龚钰秋); ZHANG,Hua-Song(张华松)

    2002-01-01

    Two palladiun(Ⅱ) complexes, [Pd(bipy)(BzPhe-N,O) ] and [Pd(phen) (BzPhe-N,O) ] @4H2O were synthesized by reactions between Pd(bipy)Cl2 and BzPheH2 ( N-benzoyl- β-phenylalanine), Pd(phen) Cla and BzPheH2 in water at pH ~ 9, with their structrues determined by X-ray diffraction analysis. The Pd atom is coordinated by two nitrogen atoms of bipy (or phen), the deprotonated amido type nitrogen atom and one of the carboxylic oxygens of BzPhe (BzPhe = N-benzoyl-β-phenylalaninate dianion). In the complex [Pd(phen)(BzPhe-N,O)]@ 4H2O, the side chain of phenvlalanine is located above and approximately parallels to the coordination plane. Both the aromic-aromatic stacking interaction between the phenyl ring of phenylalanine and phen, and the metal ion-aromatic interaction between the phenyi ring of phenylalanine and Pd(Ⅱ) were observed. [Pd(bipy)(BzPhe-N,O) ] has the phenylalanyl side chain oriented outwards from the coordination plane, which is mainly due to the interaction between the carbonyl oxygen atom of the amido group and the phenyl ring of phenylalanine. The reason for the different orientation of phenylalanyl side chain in the complexes was suggested.

  16. Probing complex RNA structures by mechanical force

    CERN Document Server

    Harlepp, S; Robert, J; Leger, J F; Xayaphoummine, A; Isambert, H; Chatenay, D

    2003-01-01

    RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induced, long-lived intermediates including non-native helices. This is first shown for a set of generic structural motifs found in larger RNA structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA, which exhibits a surprisingly well-structured and reproducible unfolding pathway under mechanical stretching. Using out-of-equilibrium stochastic simulations, we demonstrate that these experimental results reflect the slow relaxation of RNA structural rearrangements. Hence, micromanipulations of single RNA molecules probe both their native structures and long-lived intermediates, so-called "kinetic traps",...

  17. Structural and Topology Optimization of Complex Civil Engineering Structures

    DEFF Research Database (Denmark)

    Hald, Frederik; Kirkegaard, Poul Henning; Andersen, Lars Vabbersgaard

    2013-01-01

    will be optimized using the commercial code Abaqus CAE. The structures are: a bucket foundation for an off-shore submarine structure for a wind turbine, and a pedestrian footbridge over a freeway. The topology optimization method used is the SIMP method, based on minimizing the structures' compliance. Complex load...

  18. Structures of the Class D Carbapenemase OXA-24 from Acinetobacter baumannii in Complex with Doripenem

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Kyle D.; Ortega, Caleb J.; Renck, Nicholas A.; Bonomo, Robert A.; Powers, Rachel A.; Leonard, David A. (Case Western); (Grand Valley)

    2012-02-08

    The emergence of class D {beta}-lactamases with carbapenemase activity presents an enormous challenge to health practitioners, particularly with regard to the treatment of infections caused by Gram-negative pathogens such as Acinetobacter baumannii. Unfortunately, class D {beta}-lactamases with carbapenemase activity are resistant to {beta}-lactamase inhibitors. To better understand the details of the how these enzymes bind and hydrolyze carbapenems, we have determined the structures of two deacylation-deficient variants (K84D and V130D) of the class D carbapenemase OXA-24 with doripenem bound as a covalent acyl-enzyme intermediate. Doripenem adopts essentially the same configuration in both OXA-24 variant structures, but varies significantly when compared to the non-carbapenemase class D member OXA-1/doripenem complex. The alcohol of the 6a hydroxyethyl moiety is directed away from the general base carboxy-K84, with implications for activation of the deacylating water. The tunnel formed by the Y112/M223 bridge in the apo form of OXA-24 is largely unchanged by the binding of doripenem. The presence of this bridge, however, causes the distal pyrrolidine/sulfonamide group to bind in a drastically different conformation compared to doripenem bound to OXA-1. The resulting difference in the position of the side-chain bridge sulfur of doripenem is consistent with the hypothesis that the tautomeric state of the pyrroline ring contributes to the different carbapenem hydrolysis rates of OXA-1 and OXA-24. These findings represent a snapshot of a key step in the catalytic mechanism of an important class D enzyme, and might be useful for the design of novel inhibitors.

  19. Structural Features of Caspase-Activating Complexes

    Directory of Open Access Journals (Sweden)

    Hyun Ho Park

    2012-04-01

    Full Text Available Apoptosis, also called programmed cell death, is an orderly cellular suicide program that is critical for the development, immune regulation and homeostasis of a multi-cellular organism. Failure to control this process can lead to serious human diseases, including many types of cancer, neurodegenerative diseases, and autoimmununity. The process of apoptosis is mediated by the sequential activation of caspases, which are cysteine proteases. Initiator caspases, such as caspase-2, -8, -9, and -10, are activated by formation of caspase-activating complexes, which function as a platform to recruit caspases, providing proximity for self-activation. Well-known initiator caspase-activating complexes include (1 DISC (Death Inducing Signaling Complex, which activates caspases-8 and 10; (2 Apoptosome, which activates caspase-9; and (3 PIDDosome, which activates caspase-2. Because of the fundamental biological importance of capases, many structural and biochemical studies to understand the molecular basis of assembly mechanism of caspase-activating complexes have been performed. In this review, we summarize previous studies that have examined the structural and biochemical features of caspase-activating complexes. By analyzing the structural basis for the assembly mechanism of the caspase-activating complex, we hope to provide a comprehensive understanding of caspase activation by these important oligomeric complexes.

  20. Preparation and Property of Acrylic Acid Rare Earth Complex and Its Hydrosilylation

    Institute of Scientific and Technical Information of China (English)

    Zhang Ming; Chen Haiyan; Chen Xiaosong; Dai Shaojun; Inoue Shinich; Okamoto Hiroshi

    2004-01-01

    Acrylic acid rare earth complex was prepared. Its chemical composition was determined by chemical and elemental analysis, and its structure as well as properties was characterized using IR, Fluorescence and UV spectrum, and its solubility was also investigated. Meanwhile a kind of elastic functional polymer with rare earth units in the side chains was produced. It is confirmed by IR spectrum that the Si-H bonds really react with acrylic acid rare earth.

  1. Detecting highly cyclic structure with complex eigenpairs

    CERN Document Server

    Klymko, Christine

    2016-01-01

    Many large, real-world complex networks have rich community structure that a network scientist seeks to understand. These communities may overlap or have intricate internal structure. Extracting communities with particular topological structure, even when they overlap with other communities, is a powerful capability that would provide novel avenues of focusing in on structure of interest. In this work we consider extracting highly-cyclic regions of directed graphs (digraphs). We demonstrate that embeddings derived from complex-valued eigenvectors associated with stochastic propagator eigenvalues near roots of unity are well-suited for this purpose. We prove several fundamental theoretic results demonstrating the connection between these eigenpairs and the presence of highly-cyclic structure and we demonstrate the use of these vectors on a few real-world examples.

  2. Introduction of Peripheral Carboxylates to Decrease the Charge on Tm(3+) DOTAM-Alkyl Complexes: Implications for Detection Sensitivity and in Vivo Toxicity of PARACEST MRI Contrast Agents.

    Science.gov (United States)

    Suchý, Mojmír; Milne, Mark; Elmehriki, Adam A H; McVicar, Nevin; Li, Alex X; Bartha, Robert; Hudson, Robert H E

    2015-08-27

    A series of structurally modified Tm(3+) DOTAM-alkyl complexes as potential PARACEST MRI contrast agents has been synthesized with the aim to decrease the overall positive charge associated with these molecules and increase their biocompatibility. Two types of structural modification have been performed, an introduction of terminal carboxylate arms to the alkyl side chains and a conjugation of one of the alkyl side chains with aspartic acid. Detailed evaluation of the magnetic resonance imaging chemical exchange contrast associated with the structurally modified contrast agents has been performed. In contrast to the acutely toxic Tm(3+) DOTAM-alkyl complexes, the structurally modified compounds were found to be tolerated well during in vivo MRI studies in mice; however, only the aspartic acid modified chelates produced an amide proton-based PARACEST signal.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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%.

  9. 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...

  10. 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.

  11. Modelling the structure of complex networks

    DEFF Research Database (Denmark)

    Herlau, Tue

    networks has been independently studied as mathematical objects in their own right. As such, there has been both an increased demand for statistical methods for complex networks as well as a quickly growing mathematical literature on the subject. In this dissertation we explore aspects of modelling complex....... The next chapters will treat some of the various symmetries, representer theorems and probabilistic structures often deployed in the modelling complex networks, the construction of sampling methods and various network models. The introductory chapters will serve to provide context for the included written...

  12. Structure of a copper-isoniazid complex.

    Science.gov (United States)

    Hanson, J C; Camerman, N; Camerman, A

    1981-11-01

    It is well-known that complex formation with copper ions increases the in vitro mycobactericidal action of the antituberculosis agent isoniazid. We report here the preparation and structure of a copper(II)-isoniazid complex. Unit cell parameters are a = 9.575, b = 14.855, and c = 7.056 A and space group P2(1)2(1)2(1). Copper bonding geometry is square planar with the isoniazid carbonyl oxygen and hydrazide amino nitrogen atoms and two chlorines occupying coordination positions. Complexing with copper(II) does not significantly alter the isoniazid molecular conformation.

  13. The Electronic Structure of Heavy Element Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Bursten, Bruce E.

    2000-07-25

    The area of study is the bonding in heavy element complexes, and the application of more sophisticated electronic structure theories. Progress is recounted in several areas: (a) technological advances and current methodologies - Relativistic effects are extremely important in gaining an understanding of the electronic structure of compounds of the actinides, transactinides, and other heavy elements. Therefore, a major part of the continual benchmarking was the proper inclusion of the appropriate relativistic effects for the properties under study. (b) specific applications - These include organoactinide sandwich complexes, CO activation by actinide atoms, and theoretical studies of molecules of the transactinide elements. Finally, specific directions in proposed research are described.

  14. Crystal structure of swine major histocompatibility complex class I SLA-1 0401 and identification of 2009 pandemic swine-origin influenza A H1N1 virus cytotoxic T lymphocyte epitope peptides.

    Science.gov (United States)

    Zhang, Nianzhi; Qi, Jianxun; Feng, Sijia; Gao, Feng; Liu, Jun; Pan, Xiaocheng; Chen, Rong; Li, Qirun; Chen, Zhaosan; Li, Xiaoying; Xia, Chun; Gao, George F

    2011-11-01

    The presentation of viral epitopes to cytotoxic T lymphocytes (CTLs) by swine leukocyte antigen class I (SLA I) is crucial for swine immunity. To illustrate the structural basis of swine CTL epitope presentation, the first SLA crystal structures, SLA-1 0401, complexed with peptides derived from either 2009 pandemic H1N1 (pH1N1) swine-origin influenza A virus (S-OIV(NW9); NSDTVGWSW) or Ebola virus (Ebola(AY9); ATAAATEAY) were determined in this study. The overall peptide-SLA-1 0401 structures resemble, as expected, the general conformations of other structure-solved peptide major histocompatibility complexes (pMHC). The major distinction of SLA-1 0401 is that Arg(156) has a "one-ballot veto" function in peptide binding, due to its flexible side chain. S-OIV(NW9) and Ebola(AY9) bind SLA-1 0401 with similar conformations but employ different water molecules to stabilize their binding. The side chain of P7 residues in both peptides is exposed, indicating that the epitopes are "featured" peptides presented by this SLA. Further analyses showed that SLA-1 0401 and human leukocyte antigen (HLA) class I HLA-A 0101 can present the same peptides, but in different conformations, demonstrating cross-species epitope presentation. CTL epitope peptides derived from 2009 pandemic S-OIV were screened and evaluated by the in vitro refolding method. Three peptides were identified as potential cross-species influenza virus (IV) CTL epitopes. The binding motif of SLA-1 0401 was proposed, and thermostabilities of key peptide-SLA-1 0401 complexes were analyzed by circular dichroism spectra. Our results not only provide the structural basis of peptide presentation by SLA I but also identify some IV CTL epitope peptides. These results will benefit both vaccine development and swine organ-based xenotransplantation.

  15. Crystal Structure of Swine Major Histocompatibility Complex Class I SLA-1*0401 and Identification of 2009 Pandemic Swine-Origin Influenza A H1N1 Virus Cytotoxic T Lymphocyte Epitope Peptides ▿

    Science.gov (United States)

    Zhang, Nianzhi; Qi, Jianxun; Feng, Sijia; Gao, Feng; Liu, Jun; Pan, Xiaocheng; Chen, Rong; Li, Qirun; Chen, Zhaosan; Li, Xiaoying; Xia, Chun; Gao, George F.

    2011-01-01

    The presentation of viral epitopes to cytotoxic T lymphocytes (CTLs) by swine leukocyte antigen class I (SLA I) is crucial for swine immunity. To illustrate the structural basis of swine CTL epitope presentation, the first SLA crystal structures, SLA-1*0401, complexed with peptides derived from either 2009 pandemic H1N1 (pH1N1) swine-origin influenza A virus (S-OIVNW9; NSDTVGWSW) or Ebola virus (EbolaAY9; ATAAATEAY) were determined in this study. The overall peptide–SLA-1*0401 structures resemble, as expected, the general conformations of other structure-solved peptide major histocompatibility complexes (pMHC). The major distinction of SLA-1*0401 is that Arg156 has a “one-ballot veto” function in peptide binding, due to its flexible side chain. S-OIVNW9 and EbolaAY9 bind SLA-1*0401 with similar conformations but employ different water molecules to stabilize their binding. The side chain of P7 residues in both peptides is exposed, indicating that the epitopes are “featured” peptides presented by this SLA. Further analyses showed that SLA-1*0401 and human leukocyte antigen (HLA) class I HLA-A*0101 can present the same peptides, but in different conformations, demonstrating cross-species epitope presentation. CTL epitope peptides derived from 2009 pandemic S-OIV were screened and evaluated by the in vitro refolding method. Three peptides were identified as potential cross-species influenza virus (IV) CTL epitopes. The binding motif of SLA-1*0401 was proposed, and thermostabilities of key peptide–SLA-1*0401 complexes were analyzed by circular dichroism spectra. Our results not only provide the structural basis of peptide presentation by SLA I but also identify some IV CTL epitope peptides. These results will benefit both vaccine development and swine organ-based xenotransplantation. PMID:21900158

  16. Effect of structural parameters on the electron capture dissociation and collision-induced dissociation pathways of copper(II)-peptide complexes.

    Science.gov (United States)

    Chen, Xiangfeng; Wang, Ze; Li, Wan; Wong, Y L Elaine; Chan, T-W Dominic

    2015-01-01

    The gas-phase dissociation pathways of proteins/peptides are usually affected by the nature of the charge carrier and the sequence of amino acid residues. The effects of peptide structural parameters, including peptide composition, chain length and amide hydrogen, on the gas-phase dissociation of Cu(II)-model peptide complexes were explored in this study. Polyglycine peptides with flexible frames were used as probes to reduce the complexity of the system and illustrate the mechanism. Results revealed that the types of fragment ions generated in the electron capture dissociation (ECD) of Cu(II)-adducted peptides changed according to the basic amino acid residue composition. Charged or neutral tryptophan side-chain losses were observed in the collision-induced dissociation (CID) of Cu(II)-peptide complexes. Internal electron transfer between tryptophan and metal ion within the complex occurred during the CID reaction, leaving the charge-reduced Cu(+) as a closed d-shell stable electron configuration. The choice of the reaction channel was then determined by the gas-phase basicity of the peptide. Amide hydrogen was critical in the formation of metalated b-/y-ions in the ECD process as determined through mutation of the backbone amide group. Increasing the chain length suppressed the ECD of Cu-metalated peptide species. Our results indicate that the structural parameters of peptides play important roles in the gas-phase dissociation processes of Cu-peptide complexes.

  17. Structural and Topology Optimization of Complex Civil Engineering Structures

    DEFF Research Database (Denmark)

    Hald, Frederik; Kirkegaard, Poul Henning; Andersen, Lars Vabbersgaard

    2013-01-01

    This paper shows the use of topology optimization for finding an optimized form for civil engineering structures. Today topology optimization and shape optimization have been integrated in several commercial finite element codes. Here, the topology of two complex civil engineering structures...

  18. NMR solution structure of the bicoid homeodomain bound to DNA and molecular dynamics simulations of the homeodomain/DNA complex

    Science.gov (United States)

    Baird-Titus, Jamie M.

    The homeodomain is a common DNA recognition motif consisting of three helices and an N-terminal arm that serves as a valuable model for exploring the basis of specific DNA recognition by proteins. Recognition of specific DNA sites, loosely defined by a TAAT core, is dependent on the side-chains of key amino acids in the N-terminal arm and the third "recognition" helix of the homeodomain. While much is known about homeodomain/DNA recognition, key questions concerning the role of individual amino acids and the extent of side-chain, DNA, and water dynamics during recognition remain, often focusing on the dynamic role of position 50 during recognition of the two bases immediately 3' to the 5'-TAAT-3'/3'-ATTA-5' core (ATTANN). The Bicoid homeodomain provides an interesting model system for addressing these and other questions, serving as the only known homeodomain that has a dual role in both transcriptional (DNA-binding) and translational (RNA-binding) control, discriminating between these two functions by a single amino acid, arginine 54. To add to the understanding of both general protein/DNA recognition and to the specific function of the Bicoid transcription factor homeodomain, we have determined the solution structure of the Bicoid homeodomain bound to the consensus duplex B-DNA binding site 5'-TAATCC-3'/3'-ATTAGG-5'. Our structure indicates that the Bicoid homeodomain exhibits variation from other homeodomain structures at the end of helix I, and NMR resonance line broadening of the K50 and R54 side-chains, consistent with side-chain motion and supportive of the adaptive-recognition theory of protein/DNA interactions.

  19. Designing complex systems - a structured activity

    NARCIS (Netherlands)

    van der Veer, Gerrit C.; van Vliet, Johannes C.; Lenting, Bert; Olson, Gary M.; Schuon, Sue

    1995-01-01

    This paper concerns the development of complex systems from the point of view of design as a structure of activities, related both to the clients and the users. Several modeling approaches will be adopted for different aspects of design, and several views on design will be integrated. The proposed

  20. Designing complex systems - a structured activity

    NARCIS (Netherlands)

    van der Veer, Gerrit C.; van Vliet, Johannes C.; Lenting, Bert; Olson, Gary M.; Schuon, Sue

    1995-01-01

    This paper concerns the development of complex systems from the point of view of design as a structure of activities, related both to the clients and the users. Several modeling approaches will be adopted for different aspects of design, and several views on design will be integrated. The proposed a