High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

Coarse‐grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full‐atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log‐likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full‐atom models using Rosetta which has implications for multiscale protein modeling using coarse‐grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/ . © 2013 Wiley Periodicals, Inc.     

New 1,2,4‐ and 1,3,4‐oxadiazole materials: synthesis,and mesomorphic and luminescence properties

The synthesis and liquid crystalline properties of new series of 1,2,4‐ and 1,3,4‐oxadiazole derivatives (2a–f and 5a–f respectively) are reported. These compounds contain only one terminal flexible alkoxy chain, the other terminal substituent is a protecting benzyl group. All compounds of series 2 exhibit an enantiotropic nematic phase. The homologue with the longest chain (2f) displays an enantiotropic dimorphism smectic A– nematic. None of the compounds of series 5 shows mesomorphism and only crystal–isotropic transitions were observed. The liquid crystalline properties were investigated by differential scanning calorimetry, polarizing optical microscopy and X‐ray measurements. Luminescence properties, in chloroform solution, of 2f and the series 5 compounds were evaluated. Good photoluminescence quantum yields for compounds of series 5 were observed. Compound 2f, incorporating the 1,2,4‐oxadiazole ring shows a very strong reduction in emissive properties.     

Columnar liquid crystalline benzenetrisamides with pendant 1,3,4-oxadiazole groups

Novel liquid crystal materials based on 1,3,5-benzenetrisamide derivatives with three pendant 2-phenyl-5-(mono-, di-, and/or tri-n-alkoxyphenyl)-1,3,4-oxadiazole arms (Ia–c, IIa–c) were prepared. The mesomorphic properties of these compounds were characterised and studied by differential scanning calorimetry, polarising optical microscopy and X-ray diffraction. The formation of a columnar mesophase was found to be dependent on the number of alkoxy side chains. The compounds Ib and IIb, with a total of six alkoxy chains, and compounds Ic and IIc, with nine alkoxy chains, exhibited an enantiotropic hexagonal columnar (Col_h ) phase with high isotropisation temperatures; however, compounds Ia and IIa with a total of three alkoxy chains formed a crystalline phase. Compounds IIb and c were room temperature liquid crystals.     

Sandwich Techniques in flow injection analysis : Part 1. Continuous recalibration techniques for process control

Flow injection methodology based on sample insertion between two different standard solutions used as carrier streams is described. This approach provides a simple system for continuous recalibration in process control; spectrophotometric and ion-selective electrode procedures are outlined.     

Ionic Liquid Crystalline Calixarene with Photo-Switchable Proton Conduction

We have developed a new strategy for the preparation of a light-responsive ionic liquid crystal (LC) that shows photo-switchable proton conduction. The ionic LC consists of a bowl-shaped calix[4]arene core ionically functionalized with azobenzene moieties. The non-covalent architectures were obtained by the formation of ionic salts between the carboxylic acid group of an azo-derivative and the terminal amine groups of a calixarene core. The presence of ionic salts results in a hierarchical self-assembly process that extends to the formation of a nanostructured lamellar LC arrangement (smectic A phase). In this LC phase, the ionic LC calixarene is able to display proton conductive properties, since the ionic nanosegregated areas (formed by the ionic pairs) generate the continuous channels that favor proton transport. The optical and photo-responsive properties were studied by UV-Vis spectroscopy, demonstrating that the azobenzene moieties of the ionic LC undergo reversible (E)-to-(Z) isomerization by irradiation with UV light. Interestingly, this (E)-to-(Z) photoisomerization results in a decrease of the proton conductivity values since the bent-shaped (Z)-isomer disrupts the lamellar LC phase. This isomerization process is totally reversible and leads to an ionic LC material with unique photo-switchable proton conductive properties.     

Designing liquid-crystalline dendronised hexa-adducts of [60]fullerene via click chemistry

ABSTRACT

Liquid-crystalline [60]fullerodendrimers were constructed via click chemistry based on the reaction between hexa-adducts of [60]fullerene (C₆₀) bearing 12 azide groups and alkyne-terminated cyanobiphenyl dendrons of first- and second-generation. The structure of all the new compounds was confirmed by IR, UV, ¹H and ¹³C NMR spectroscopies and mass spectrometry. The mesomorphic properties were studied by polarised optical microscopy, differential scanning calorimetry and small-angle X-ray scattering. The hexa-adduct of C₆₀ functionalised with the first-generation dendrons gave rise to the formation of a smectic A phase and a rectangular columnar phase (c2mm symmetry) while the hexa-adduct of C₆₀ decorated with the second-generation dendrons displayed only a rectangular columnar phase (c2mm symmetry). Our results show that the hexa-adduct of C₆₀ is a unique synthetic platform for the design of fullerodendrimers and dendronised materials.     

High-performance liquid chromatographic determination of tocopherols in infant formulas

A method for the simultaneous determination of alpha-tocopherol acetate and alpha-, delta-, and gamma-tocopherols by normal-phase high-performance liquid chromatography (HPLC) with a fluorescent detector in infant formula is proposed. The values obtained in the determination of the analytical parameters: linearity, precision, limit of detection and accuracy (analysis of a standard reference material, SRM 1846), confirm the quality of the method. The proposed method is useful for the determination of alpha-, delta-, and gamma-tocopherols and alpha-tocopherol acetate in infant formulas at a low cost and in a total time of 2 h.