Pyochelin enantiomers and their outer-membrane siderophore transporters in fluorescent pseudomonads: structural bases for unique enantiospecific recognition.

Pyochelin (Pch) and enantiopyochelin (EPch) are enantiomeric siderophores, with three chiral centers, produced under iron limitation conditions by Pseudomonas aeruginosa and Pseudomonas fluorescens , respectively. After iron chelation in the extracellular medium, Pch-Fe and EPch-Fe are recognized and transported by their specific outer-membrane transporters: FptA in P. aeruginosa and FetA in P. fluorescens . Structural analysis of FetA-EPch-Fe and FptA-Pch-Fe, combined with mutagenesis and docking studies revealed the structural basis of the stereospecific recognition of these enantiomers by their respective transporters. Whereas FetA and FptA have a low sequence identity but high structural homology, the Pch and EPch binding pockets do not share any structural homology, but display similar physicochemical properties. The stereospecific recognition of both enantiomers by their corresponding transporters is imposed by the configuration of the siderophore's C4'' and C2'' chiral centers. This recognition involves specific hydrogen bonds between the Arg91 guanidinium group and EPch-Fe for FetA and between the Leu117-Leu116 main chain and Pch-Fe for FptA. FetA and FptA are the first membrane receptors to be structurally described with opposite binding enantioselectivities for their ligands, giving insights into the structural basis of their enantiospecificity.

Structural prediction of peptides bound to MHC class I.

An ab initio structure prediction approach adapted to the peptide-major histocompatibility complex (MHC) class I system is presented. Based on structure comparisons of a large set of peptide-MHC class I complexes, a molecular dynamics protocol is proposed using simulated annealing (SA) cycles to sample the conformational space of the peptide in its fixed MHC environment. A set of 14 peptide-human leukocyte antigen (HLA) A0201 and 27 peptide-non-HLA A0201 complexes for which X-ray structures are available is used to test the accuracy of the prediction method. For each complex, 1000 peptide conformers are obtained from the SA sampling. A graph theory clustering algorithm based on heavy atom root-mean-square deviation (RMSD) values is applied to the sampled conformers. The clusters are ranked using cluster size, mean effective or conformational free energies, with solvation free energies computed using Generalized Born MV 2 (GB-MV2) and Poisson-Boltzmann (PB) continuum models. The final conformation is chosen as the center of the best-ranked cluster. With conformational free energies, the overall prediction success is 83% using a 1.00 Angstroms crystal RMSD criterion for main-chain atoms, and 76% using a 1.50 Angstroms RMSD criterion for heavy atoms. The prediction success is even higher for the set of 14 peptide-HLA A0201 complexes: 100% of the peptides have main-chain RMSD values < or =1.00 Angstroms and 93% of the peptides have heavy atom RMSD values < or =1.50 Angstroms. This structure prediction method can be applied to complexes of natural or modified antigenic peptides in their MHC environment with the aim to perform rational structure-based optimizations of tumor vaccines.

Permeability properties of ENaC selectivity filter mutants.

The epithelial Na(+) channel (ENaC), located in the apical membrane of tight epithelia, allows vectorial Na(+) absorption. The amiloride-sensitive ENaC is highly selective for Na(+) and Li(+) ions. There is growing evidence that the short stretch of amino acid residues (preM2) preceding the putative second transmembrane domain M2 forms the outer channel pore with the amiloride binding site and the narrow ion-selective region of the pore. We have shown previously that mutations of the alphaS589 residue in the preM2 segment change the ion selectivity, making the channel permeant to K(+) ions. To understand the molecular basis of this important change in ionic selectivity, we have substituted alphaS589 with amino acids of different sizes and physicochemical properties. Here, we show that the molecular cutoff of the channel pore for inorganic and organic cations increases with the size of the amino acid residue at position alpha589, indicating that alphaS589 mutations enlarge the pore at the selectivity filter. Mutants with an increased permeability to large cations show a decrease in the ENaC unitary conductance of small cations such as Na(+) and Li(+). These findings demonstrate the critical role of the pore size at the alphaS589 residue for the selectivity properties of ENaC. Our data are consistent with the main chain carbonyl oxygens of the alphaS589 residues lining the channel pore at the selectivity filter with their side chain pointing away from the pore lumen. We propose that the alphaS589 side chain is oriented toward the subunit-subunit interface and that substitution of alphaS589 by larger residues increases the pore diameter by adding extra volume at the subunit-subunit interface.

Poly(beta,L-malic acid)Doxorubicin ionic complex: A pH-dependent delivery system.

Poly(ß,L-malic acid) (PMLA) was made to interact with the cationic anticancer drug Doxorubicin (DOX) in aqueous solution to form ionic complexes with different compositions and an efficiency near to 100%. The PMLA/DOX complexes were characterized by spectroscopy, thermal analysis, and scanning electron microscopy. According to their composition, the PMLA/DOX complexes spontaneously self-assembled into spherical micro or nanoparticles with negative surface charge. Hydrolytic degradation of PMLA/DOX complexes took place by cleavage of the main chain ester bond and simultaneous release of the drug. In vitro drug release studies revealed that DOX delivery from the complexes was favored by acidic pH and high ionic strength

Science and technology of rubber reclamation with special attention to NR-based waste latex products

A comprehensive overview of reclamation of cured rubber with special emphasis on latex reclamation is depicted in this paper. The latex industry has expanded over the years to meet the world demands for gloves, condoms, latex thread, etc. Due to the strict specifications for the products and the unstable nature of the latex as high as 15% of the final latex products are rejected. As waste latex rubber (WLR) represents a source of high-quality rubber hydrocarbon, it is a potential candidate for generating reclaimed rubber of superior quality. The role of the different components in the reclamation recipe is explained and the reaction mechanism and chemistry during reclamation are discussed in detail. Different types of reclaiming processes are described with special reference to processes, which selectively cleave the cross links in the vulcanized rubber. The state-of-the-art techniques of reclamation with special attention on latex treatment are reviewed. An overview of the latest development concerning the fundamental studies in the field of rubber recycling by means of low-molecular weight compounds is described. A mathematical model description of main-chain and crosslink scission during devulcanization of a rubber vulcanizate is also given.

Theory of Breaking of a Potyrner Molecule under Tension

The thesis presents the dynamics of a polymer chain under tension. It includes existing theories of polymer fracture, important theories of reaction rates, the rate using multidimensional transition state theory and apply it to the case of polyethylene etc. The main findings of the study are; the life time of the bond is somewhat sensitive to the potential lead to rather different answers, for a given potential a rough estimate of the rate can be obtained by a simples approximation that considers the dynamics of only the bond that breaks and neglects the coupling to neighboring bonds. Dynamics of neighboring bonds would decrease the rate, but usually not more than by one order of magnitude, for the breaking of polyethylene, quantum effects are important only for temperatures below 150K, the lifetime strongly depends on the strain and as the strain varies over a narrow range, the life varies rapidly from 105 seconds to 10_5 seconds, if we change one unit of the polymer by a foreign atom, say by one sulphure atom, in the main chain itself, by a weaker bond, the rate is found to increase by orders of magnitude etc.

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favorability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB)versus Thr(HB)-Asn(nHB). Significantly (p < or = 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi1 rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi1 conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi1 and chi2 conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favorability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http://www.rubic.rdg.ac.uk/betapairprefsparallel/).

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB) versus Thr(HB)-Asn(nHB). Significantly (p <= 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi(1) rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi(1) conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi(1) and chi(2) conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http:// www.rubic.rdg.ac.uk/betapairprefsparallel/). (c) 2005 Elsevier Ltd. All rights reserved.

Pyrolysis of polymer-derived carbons in the formation of graphitizing carbons and nanoparticles of zirconia

Carbons have been prepared by the low-temperature pyrolysis, under argon, of a number of long-chain polymers. We have found that the resistivity (Omega cm(-1)) varies considerably with the temperature of pyrolysis; thus, for ammonium polyacrylate, the resistivity of that pyrolyzed at 600 degrees C is 9.7 x 10(4) Omega cm(-1) whereas that pyrolyzed at 1000 degrees C is ca. 3 Omega cm(-1). A similar situation arises for the other polymers studied (including radiolyzed cross-linked polyacrylamide). All those pyrolyzed at 600 degrees C had a resistivity of > 1 x 10(6) Omega cm(-1), whereas those pyrolyzed at 1000 degrees C had a resistivity of ca. 3-5 Omega cm(-1). A notable exception was that of unirradiated polyacrylamide, where the resistivity remained at > 1 x 10(6) Omega cm(-1) over the range of temperatures studied. The decrease of resistivity with increase of temperature of pyrolysis has been related to the formation of glassy carbon. Nanoparticles (4 nm) of tetragonal zirconia were formed when zirconium polyacrylate was pyrolyzed under similar conditions.

Double-gyroid morphology of a polystyrene-block-poly(ferrocenylethylmethylsilane) diblock copolymer: a route to ordered bicontinuous nanoscale architectures

A polystyrene-block-poly(ferrocenylethylmethylsilane) diblock copolymer, displaying a double-gyroid morphology when self-assembled in the solid state, has been prepared with a PFEMS volume fraction phi(PFMS)=0.39 and a total molecular weight of 64 000 Da by sequential living anionic polymerisation. A block copolymer with a metal-containing block with iron and silicon in the main chain was selected due to its plasma etch resistance compared to the organic block. Self-assembly of the diblock copolymer in the bulk showed a stable, double-gyroid morphology as characterised by TEM. SAXS confirmed that the structure belonged to the Ia3d space group.

Electro-optical properties of liquid crystal copolymers and their relationship to structural order

A range of side chain liquid crystal copolymers have been prepared using mesogenic and non-mesogenic units. It is found that high levels of the non-mesogenic moieties may be introduced without completely disrupting the organization of the liquid crystal phase. Incorporation of this comonomer causes a marked reduction in the glass transition temperature (Tg), presumably as a result of enhanced backbone mobility and a corresponding lowering of the nematic transition temperature, thereby restricting the temperature range for stability of the liquid crystal phase. The effect of the interactions between the various components of these side-chain polymers on their electro-optic responses is described. Infrared (i.r.) dichroism measurements have been made to determine the order parameters of the liquid crystalline side-chain polymers. By identifying a certain band (CN stretching) in the i.r. absorption spectrum, the order parameter of the mesogenic groups can be obtained. The temperature and composition dependence of the observed order parameter are related to the liquid crystal phase transitions and to the electro-optic response. It is found that the introduction of the non-mesogenic units into the polymer chain lowers the threshold voltage of the electro-optic response over and above that due to the reduction in the order parameter. The dynamic electro-optic responses are dominated by the temperature-dependent viscosity and evidence is presented for relaxation processes involving the polymer backbone which are on a time scale greater than that for the mesogenic side-chain units.

Large is fast, small is tight: determinants of speed and affinity in subunit capture by a periplasmic chaperone

The chaperone/usher pathway assembles surface virulence organelles of Gram-negative bacteria, consisting of fibers of linearly polymerized protein subunits. Fiber subunits are connected through 'donor strand complementation': each subunit completes the immunoglobulin (Ig)-like fold of the neighboring subunit by donating the seventh β-strand in trans. Whereas the folding of Ig domains is a fast first-order process, folding of Ig modules into the fiber conformation is a slow second-order process. Periplasmic chaperones separate this process in two parts by forming transient complexes with subunits. Interactions between chaperones and subunits are also based on the principle of donor strand complementation. In this study, we have performed mutagenesis of the binding motifs of the Caf1M chaperone and Caf1 capsular subunit from Yersinia pestis and analyzed the effect of the mutations on the structure, stability, and kinetics of Caf1M-Caf1 and Caf1-Caf1 interactions. The results suggest that a large hydrophobic effect combined with extensive main-chain hydrogen bonding enables Caf1M to rapidly bind an early folding intermediate of Caf1 and direct its partial folding. The switch from the Caf1M-Caf1 contact to the less hydrophobic, but considerably tighter and less dynamic Caf1-Caf1 contact occurs via the zip-out-zip-in donor strand exchange pathway with pocket 5 acting as the initiation site. Based on these findings, Caf1M was engineered to bind Caf1 faster, tighter, or both faster and tighter. To our knowledge, this is the first successful attempt to rationally design an assembly chaperone with improved chaperone function.

Ionizing radiation induced degradation of poly (2-methoxy-5-(2 '-ethyl-hexyloxy)-1,4-phenylene vinylene) in solution

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Three exopolysaccharides of the beta-(1 -> 6)-D-glucan type and a beta-(1 -> 3;1 -> 6)-D-glucan produced by strains of Botryosphaeria rhodina isolated from rotting tropical fruit

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Thermal characterization of the interaction of poly(3-hydroxybutyrate) with maleic anhydride

Poly(3-hydroxybutyrate), PHB, has been structurally modified with maleic anhydride, MA, in the presence of triethylamine, TEA. Glass transition, melting, and crystallization temperature, obtained from DSC curves, and thermal degradation temperatures obtained from TG ones, were employed to evaluate the influence of the MA proportion on the modification in the PHB chain. According to the results, most of chain modification reactions are the 80/20 and 90/10 proportions. Observations suggest that most chain modification reactions occur when the ratio of PHB/MA is 80/20 or 90/10. This suggests that modifications of PHB in the presence of MA involve main chain scission.