Protein changes in post mortem sea bass (Dicentrarchus labrax) muscle monitored by one- and two-dimensional gel electrophoresis

This study was devoted to the identification of specific peptides and proteins which can be used as indicators of freshness in fish. The post mortem evolution of protein patterns in farmed sea bass muscle was monitored by Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional electrophoresis (2-DE) after 0, 2, 4, and 6 days cold storage. SDS-electrophoresis, of total proteins and proteins soluble in low-ionic-strength solutions, revealed the gradual disappearance of a protein band of 16 kDa immediately after fish death. 2-DE allowed the classification of fish samples according to post mortem time. Three spots of interest, which disappeared progressively, were identified on the 2-DE patterns. Further research is required to establish the identity of these polypeptides and to evaluate their expression and post mortem evolution in another fish species.     

H2O和N2的谱线碰撞增宽的理论计算

采用Ｔｅｊｗａｎｉ修正的Ａｎｄｅｒｓｏｎ模型和Ａｓｈｏｋ、Ｔｈｏｍｐｓｏｎ计算水的转动能级和波函数的最新程序，计算了水和Ｎ２碰撞谱线增宽，获得了较高量子数的半宽数据     

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 3. Calculation and parameterization of the potentials of mean force of pairs of identical hydrophobic side chains

The potentials of mean force of homodimers of the molecules modeling hydrophobic amino acid side chains (ethane (for alanine), propane (for proline), isobutane (for valine), isopentane (for leucine and isoleucine), ethylbenzene (for phenylalanine), and methyl propyl sulfide (for methionine)) were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation. Analytical expressions consisting of the Gay-Berne term to represent effective van der Waals interactions and the cavity term derived in paper 1 of this series were fitted to the potentials of mean force. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules, were well represented by the analytical expressions for all systems, which justifies use of such potentials in coarse-grain protein-folding simulations.     

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.     

Charge carrier mobility in poly[methyl(phenyl)silylene] studied by time-resolved terahertz spectroscopy and molecular modelling

Time-resolved terahertz spectroscopy and combination of quantum chemistry modeling and molecular dynamics simulations were used for the determination of charge carrier mobility in poly[methyl(phenyl)silylene]. Using time-resolved THz spectroscopy we established the on-chain charge carrier drift mobility in PMPSi as 0.02 cm(2) V(-1) s(-1). This value is low due to the formation of polarons: the hole is self-trapped in a potential formed by local chain distortion and the transient THz conductivity spectra show signatures of its oscillations within this potential well. This view is supported by the agreement between experimental and calculated values of the on-chain charge carrier mobility.     

Efficient synthesis of 3,6-dialkoxythieno[3,2-b]thiophenes as precursors of electrogenerated conjugated polymers

A series of 3,6-dialkoxythieno[3,2-b]thiophenes have been synthesized through three synthetic pathways. Symmetrical derivatives have been obtained from 3,6-dibromothieno[3,2-b]thiophene or by trans-etherification of 3,6-dimethoxythieno[3,2-b]thiophene while unsymmetrical derivatives have been easily prepared from the readily accessible dimethyl 3-hydroxythiophene-2,5-dicarboxylate. These compounds have been used as precursors for electropolymerisation and a first characterisation of the electronic properties of the resulting polymers is presented.     

Synthesis and biological properties of conjugates between fluoroquinolones and a N3'-functionalized pyochelin

Pyochelin is a siderophore common to Pseudomonas aeruginosa and several other pathogenic bacteria. A pyochelin functionalized at the N3' position with a propyl-amine extension was previously synthesized. In the present work we proved that this analog binds FptA, the pyochelin outer membrane receptor, and transports iron(III) efficiently into bacteria. This functionalized pyochelin seemed to be a good candidate for antibiotic vectorization in the framework of a Trojan horse prodrug strategy. In this context, conjugates between pyochelin and three fluoroquinolones (norfloxacin, ciprofloxacin and N-desmethyl-ofloxacin) were synthesized with a spacer arm that was either stable or hydrolyzable in vivo. Some pyochelin-fluoroquinolone conjugates had antibacterial activities in growth inhibition experiments on several P. aeruginosa strains. However, these activities were weaker than those of the antibiotic alone. These properties appeared to be related to both the solubility and bioavailability of conjugates and to the stability of the spacer arm used.     

Carbonyl-inserted organo-hybrids of a Dawson-type phosphovanadotungstate: scope and chemoselective oxidation catalysis

The Dawson-type polyoxometalate (POM) [P(2)V(3)W(15)O(62)](9-) is a prototype for inclusion of carbonyls of amides, ureas, carbamates, and thiocarbamates into polyoxometallic structures. The carbonyl-inserted POMs catalyze the oxidation of sulfides. Chemoselectivity depends primarily on the proton content of the POM, but it is also influenced by the organic substituent.     

Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures

Dynamical averages based on functionals of dynamical trajectories, such as time-correlation functions, play an important role in determining kinetic or transport properties of matter. At temperatures of interest, the expectations of these quantities are often dominated by contributions from rare events, making the precise calculation of these quantities by molecular dynamics simulation difficult. Here, we present a reweighting method for combining simulations from multiple temperatures (or from simulated or parallel tempering simulations) to compute an optimal estimate of the dynamical properties at the temperature of interest without the need to invoke an approximate kinetic model (such as the Arrhenius law). Continuous and differentiable estimates of these expectations at any temperature in the sampled range can also be computed, along with an assessment of the associated statistical uncertainty. For rare events, aggregating data from multiple temperatures can produce an estimate with the desired precision at greatly reduced computational cost compared with simulations conducted at a single temperature. Here, we describe use of the method for the canonical (NVT) ensemble using four common models of dynamics (canonical distribution of Hamiltonian trajectories, Andersen thermostatting, Langevin, and overdamped Langevin or Brownian dynamics), but it can be applied to any thermodynamic ensemble provided the ratio of path probabilities at different temperatures can be computed. To illustrate the method, we compute a time-correlation function for solvated terminally-blocked alanine peptide across a range of temperatures using trajectories harvested using a modified parallel tempering protocol.     

Effect of gamma irradiation on gas-ionic liquid and water-ionic liquid interfacial stability

The effect of γ-radiation on gas-ionic liquid (IL) and water-IL interfacial stability was investigated. Three phosphonium-based ILs, which vary considerably in their viscosity, conductivity and miscibility with water, were examined. The gas phase above the IL samples (headspace gas) was analyzed using gas chromatography with a mass spectrometer detector while the changes in the IL and aqueous phases were followed by conductivity measurements and Raman spectroscopy. For the gas-IL systems, the headspace samples showed trace amounts of the radiolytic decomposition products of the ILs that were small and volatile enough to become airborne. The type of cover gas, air or Ar, had no effect on the gas speciation. Negligible changes in the conductivity and the Raman spectra of the IL phase due to irradiation indicate that γ-irradiation induces negligible chemical changes in the IL phase when it is in contact with a gas phase. For the water-IL systems, the initially immiscible layers slowly developed an interfacial emulsion layer, even in the absence of radiation. This layer started at the water-IL interface and then grew downwards, eventually converting the entire IL phase to an emulsion. Gamma-irradiation accelerated the conversion of the IL phase to an emulsion. The development of the emulsion layer was accompanied by changes in the conductivity and the Raman spectra of both the IL and water phases. Based on these results, a mechanism involving the formation of micelles at, or near, the water-IL interface has been proposed to explain the development of an emulsion layer. We also suggest that radiolytic decomposition of ILs produces surfactants that can accumulate at the interface and, even at low concentrations, accelerate the emulsification process.