Advantages and drawbacks of nanospray for studying noncovalent protein-DNA complexes by mass spectrometry

The noncovalent complexes between the BlaI protein dimer (wild-type and GM2 mutant) and its double-stranded DNA operator were studied by nanospray mass spectrometry and tandem mass spectrometry (MS/MS). Reproducibility problems in the nanospray single-stage mass spectra are emphasized. The relative intensities depend greatly on the shape of the capillary tip and on the capillary-cone distance. This results in difficulties in assessing the relative stabilities of the complexes simply from MS(1) spectra of protein-DNA mixtures. Competition experiments using MS/MS are a better approach to determine relative binding affinities. A competition between histidine-tagged BlaIWT (BlaIWTHis) and the GM2 mutant revealed that the two proteins have similar affinities for the DNA operator, and that they co-dimerize to form heterocomplexes. The low sample consumption of nanospray allows MS/MS spectra to be recorded at different collision energies for different charge states with 1 microL of sample. The MS/MS experiments on the dimers reveal that the GM2 dimer is more kinetically stable in the gas phase than the wild-type dimer. The MS/MS experiments on the complexes shows that the two proteins require the same collision energy to dissociate from the complex. This indicates that the rate-limiting step in the monomer loss from the protein-DNA complex arises from the breaking of the protein-DNA interface rather than the protein-protein interface. The dissociation of the protein-DNA complex proceeds by the loss of a highly charged monomer (carrying about two-thirds of the total charge and one-third of the total mass). MS/MS experiments on a heterocomplex also show that the two proteins BlaIWTHis and BlaIGM2 have slightly different charge distributions in the fragments. This emphasizes the need for better understanding the dissociation mechanisms of biomolecular complexes.     

Analysis of t-Butyldimethylsilyl Derivatives of Chlorophenols in the Atmosphere of Urban and Rural Areas in East of France

A method using GC-MS and derivatization with N-(t-butyldimethylsilyl)-N-ethyltrifluoroacetamide (MTBSTFA) was developed for the analysis of 19 chlorophenols compounds in atmospheric samples (gas and particles). Air sampling was carried out using a Hi-Vol sampler with glass fibre filter and XAD-2 resin at a flow rate of 60 m³ h⁻¹. The particle and gas phases were collected separately over a period of 4 h. Samples were Soxhlet extracted, evaporated to dryness under nitrogen and refilled with acetonitrile. 100 mL of these extracts were derivatized with 100 μL of MTBSTFA at 80 °C for 1 h under strong stirring. Sylylated chlorophenols were injected into a GC-MS in splitless mode and quantified as their TBDMS derivatives in the SIM mode. Mass spectral analysis of the derivatives of the 19 compounds studied indicates that the spectra are highly specific showing an ion at [M - 57]⁺ which is useful for structure confirmation or analysis at low levels using selected ion monitoring. Quantification limits varied between 5 μg L⁻¹ and 10 μg L⁻¹ which correspond to 20 pg m⁻³ and 40 pg m⁻³ for 250 m³ of air sampled. This method was successfully applied to atmospheric samples collected simultaneously in winter 2004 in an urban (Strasbourg) and rural (Erstein) areas in east of France.     

Synthesis of original benzo[g]quinoxaline‐5,10‐diones by bis‐SRN1 methodology

A new heterocyclic bioreductive bis‐alkylating agent, 2,3‐bis(chloromethyl)benzo[g]quinoxaline‐5,10‐dione, was prepared in a four‐steps synthesis. It was shown to react under electron transfer conditions with 2‐nitropropane anion by an bis‐S_RN1 mechanism to give three C‐alkylation products in excellent yields. Extension of this bis‐S_RN1 reaction to various nitronate or malonate anions and S‐centered anions led to a new class of potentially active benzo[g]quinoxaline‐5,10‐dione derivatives.     

Application of relaxation periods during electrodialysis of a casein solution: Impact on anion-exchange membrane fouling

Electrodialysis (ED) is a membrane process used on a large scale. However, one of the common problems is fouling of ion-exchange membranes stacked in the cell. The use of pulsed power, consisting in applying a constant current density during a fixed time of application (T_on) followed by a pause duration (T_off), was demonstrated recently as an effective fouling mitigation method for electrodialysis. Up until now, no work has investigated the potential of electrodialysis using pulsed electric field on protein fouling. The aim of the present work was to study the influence of pulsed electric field (PEF) with a low frequency square shaped periodic signal (T_on = 10 s–T_off = 10 s, T_on = 10 s–T_off = 40 s) in comparison with dc current during electrodialysis of a casein solution at different current densities (10, 20 and 30 mA/cm²) on membrane fouling. It appeared from these results that PEF, under certain conditions of pulse, would avoid fouling on anion-exchange membranes. For 10 s–40 s pulsed electric field conditions, no fouling was observed with any density, while for 10 s–10 s PEF conditions, fouling appeared only at current density over 10 mA/cm². dc current, whatever the current density conditions, led to a fouling on the diluate side of the AEM. Furthermore, when fouling occurred, magnitude layer thickness and dry weight increased with the applied current density. The nature of the fouling was identified as 97% protein. The protein fouling would be due to the dissociation of water molecules and/or heat increase at the anion-exchange membrane interface. The relaxation time of the pulse would limit both phenomena on the membrane.     

One-pot preparation of 2-(alkyl)arylbenzoselenazoles from the corresponding N-(acetyl)benzoyl-2-iodoanilines via a microwave-assisted methodology

We report here the first example of a one-pot synthesis of 2-(alkyl)arylbenzoselenazoles from N-(acetyl)benzoyl-2-iodoanilines. The reaction was carried out in the presence of Woollins’ reagent under microwave irradiation and resulted in moderate to good yields.     

Automated DBS Extraction Prior to Hilic/RP LC–MS/MS Target Screening of Drugs

This article describes a rapid LC–MS/MS target screening method based on an automated extraction of 5 μL dried blood spots (DBS), two 5 min chromatographic runs on orthogonal phase columns (RP and Hilic) and a data dependent acquisition (DDA) of product ions spectra for the reliable identification of the detected compounds. The extraction step was performed in 2 min by using the LC autosampler itself in 96-well plates. This procedure was evaluated using 22 model compounds frequently encountered in forensic investigations, i.e., cocaine, benzodiazepines, amphetamines, opioids, antidepressants and antipsychotics. These investigations showed that even if the extraction step was reduced to a minimum, the extraction recoveries were satisfactory (median value of 40 %) and allowed for the detection of the model compounds in their therapeutic ranges, with the exception of morphine. Moreover, the use of two different chromatographic columns broadened the number of screening targets to those that behaved poorly under RP conditions, such as amphetamines or glucuronides, while keeping chromatographic gradients very short. This procedure was applied to 34 authentic post-mortem cases. It allowed the detection of 89 % of the compounds that were quantified in the routine procedures and the formal identification of 77 % of the compounds using their product ions spectra. These results were considered more than satisfactory compared to routine screening alone (GC–MS and LC-DAD, 55 % compound identification). The method described in this article is therefore a powerful approach for a fast, reliable and efficient target screening of drugs in forensic and clinical investigations.     

Discrete filter operators for large‐eddy simulation using high‐order spectral difference methods

The combination of a high‐order unstructured spectral difference (SD) spatial discretization scheme with sub‐grid scale (SGS) modeling for large‐eddy simulation is investigated with particular focus on the consistent implementation of a structural mixed model based on the scale similarity hypothesis. The difficult task of deriving a consistent formulation for the discrete filter within the SD element of arbitrary order led to the development of a new class of three‐dimensional constrained discrete filters. The discrete filters satisfy a set of selected criteria and are completely local within the SD element. Their weights can be automatically computed at run time from the number of solution points within each element and the expected filter cutoff length scale. The novel discrete filters can be applied to any SGS model involving explicit filtering and to a broad class of high‐order discontinuous finite element numerical schemes. The code is applied to the computation of turbulent channel flows at three Reynolds numbers, namely Re_τ = 180, 395, and 590 (based on the friction velocity u_τ and channel half‐width δ). Results from computations with and without the SGS model are compared against results from direct numerical simulation. The numerical experiments suggest that the results are sensitive to the use of the SGS model, even when a high‐order numerical scheme is used, especially when the grid resolution is kept relatively low and mostly in terms of resolved Reynolds stresses. Results obtained using existing filters based on the projection of the solution over lower‐order polynomial bases are also shown and demonstrate that these filters are inadequate for SGS modeling purposes, mostly because of their inability to enforce the selected cutoff length scale with sufficient accuracy. The use of the similarity mixed formulation proved to be particularly accurate in reproducing SGS interactions, confirming that its well‐known potential can be realized in conjunction with state‐of‐the‐art high‐order numerical schemes.Copyright © 2012 John Wiley & Sons, Ltd.     

Unravelling the Time Scale of Conformational Plasticity and Allostery in Glycan Recognition by Human Galectin-1

The interaction of human galectin-1 with a variety of oligosaccharides, from di-(N-acetyllactosamine) to tetra-saccharides (blood B type-II antigen) has been scrutinized by using a combined approach of different NMR experiments, molecular dynamics (MD) simulations, and isothermal titration calorimetry. Ligand- and receptor-based NMR experiments assisted by computational methods allowed proposing three-dimensional structures for the different complexes, which explained the lack of enthalpy gain when increasing the chemical complexity of the glycan. Interestingly, and independently of the glycan ligand, the entropy term does not oppose the binding event, a rather unusual feature for protein-sugar interactions. CLEANEX-PM and relaxation dispersion experiments revealed that sugar binding affected residues far from the binding site and described significant changes in the dynamics of the protein. In particular, motions in the microsecond-millisecond timescale in residues at the protein dimer interface were identified in the presence of high affinity ligands. The dynamic process was further explored by extensive MD simulations, which provided additional support for the existence of allostery in glycan recognition by human galectin-1.     

Two-Photon Absorption and Cell Imaging of Fluorene-Functionalized Epicocconone Analogues

Epicocconone 1 is a natural chromophore isolated from the fungus Epicoccum nigrum that has shown applications in proteomics and fluorescent microscopy thanks to its unique pro-fluorescence properties. The modification of the skeleton of the natural product by replacing the triene side chain by a fluorenyl scaffold can noticeably increase the fluorophore's absorption coefficient. The synthesis of the analogues of the natural product has been made possible by the use of a palladium-catalyzed carbonylation reaction, allowing the construction of the β-keto-dioxinone key intermediate. Two-photon absorption cross-section measurements of the fluorenyl epicocconone analogues show a structure dependency with values ranging from 60 to 280 GM and live cell imaging show intense staining of intracellular vesicle-like structures around the nucleus.