Sodium-tolerant matrix for matrix-assisted laser desorption/ionization mass spectrometry and post-source decay of oligonucleotides

A mixture of 2',4',6'-trihydroxyacetophenone in acetonitrile and aqueous triammonium citrate solution in a 1:1 molar proportion (0.2 M concentration) was found to be a good matrix for the detection of synthetic oligodeoxynucleotide samples. A high proportion of volatile solvent as well as the high salt content ensure fast co-crystallization of the matrix, co-matrix and analyte molecules. Matrix-assisted laser desorption/ionization (MALDI) mass spectra obtained in negative ion reflectron mode from samples prepared with this protocol show deprotonated molecules [M - H](-), rather than sodium adducts, as the most abundant ions even when up to 50 mM of sodium chloride is present in the sample. The matrix is shown to be effective for low mass modified single nucleotides as well as for longer oligodeoxynucleotides (up to 18mer). Post-source decay (PSD) mass spectra can also be obtained by increasing the laser fluence. Simple sequence information such as the identity and localization of a deleted base or the 5'/3' orientation can then easily be obtained. The calibration method and mass accuracy required are discussed depending on the type of information required.     

Hepcidin in iron metabolism

Hepcidin, which has been recently identified both by biochemical and genomic approaches, is a 25 amino acid polypeptide synthesized mainly by hepatocytes and secreted into the plasma. Besides its potential activity in antimicrobial defense, hepcidin plays a major role in iron metabolism. It controls two key steps of iron bioavailability, likely through a hormonal action: digestive iron absorption by enterocytes and iron recycling by macrophages. In humans, this could explain that low levels of hepcidin found during juvenile haemochromatosis and HFE-1 genetic haemochromatosis are associated with an iron overload phenotype. Conversely, an increase of hepcidin expression is suspected to play a major role in the development of anemia of chronic inflammatory diseases. However, the regulatory mechanisms of hepcidin expression are multiple, including iron-related parameters, anemia, hypoxia, inflammation and hepatocyte function. Therefore, many physiological and pathological situations may modulate hepcidin expression and subsequently iron metabolism. A better knowledge of the biological effects of hepcidin and of its expression regulatory mechanisms will clarify the place of hepcidin in the diagnosis and treatment of iron-related diseases.     

Cyan fluorescent protein: molecular dynamics, simulations, and electronic absorption spectrum

The dynamics and electronic absorption spectrum of enhanced cyan fluorescent protein (ECFP), a mutant of green fluorescent protein (GFP), have been studied by means of a 1 ns molecular dynamics (MD) simulation. The two X-ray conformations A' and B' of ECFP were considered. The chromophore was assumed to be neutral, and all titratable residues were taken in their standard protonation state at neutral pH. The protein was embedded in a box of water molecules (and counterions). The first result is that the two conformations A' and B' are found to be stable all along the simulation. Then, an analysis of the hydrogen-bond networks shows strong differences between the two conformations in the surroundings of the nitrogen atom of the indolic part of the chromophore. This is partly due to the imperfection in the beta barrel near the His148 residue, which allows the access of one solvent molecule inside the protein in conformation A'. Finally, quantum mechanical calculations of the electronic transition energies of the chromophore in the charge cloud of the protein and solvent water molecules were performed using the TDDFT method on 160 snapshots extracted every 5 ps of the MD trajectories. It is found that conformations A' and B' exhibit very similar spectra despite different H-bond networks involving the chromophore. This similarity is related to the weak charge transfer involved in the electronic transition and the weak electrostatic field created by ECFP near the chromophore, within the hypotheses made in the present simulation.     

Total synthesis of mauritines A, B, C, and F: cyclopeptide alkaloids with a 14-membered paracyclophane unit

A unified strategy for the synthesis of mauritines A (5), B (6), C (7), and F (10) has been developed based on a key intramolecular nucleophilic aromatic substitution reaction (S(N)Ar) for the formation of the strained 14-membered paracyclophane. It was demonstrated that the outcome of the cycloetherification is independent of the stereochemistry of the peptide backbone and that both (1R)-16 and (1S)-16 cyclized smoothly to provide the corresponding macrocycle. On the other hand, dehydration of the secondary benzylic alcohol, via the phenylselenide intermediate, is configuration dependent. (1R)-25 underwent the two-step syn-elimination much more easily than (1S)-22. A modified reductive deamination procedure via the diazonium intermediate was developed. A complete assignment of proton and carbon NMR spectroscopy signals for these natural products is reported for the first time.     

Application de reactions d'hydroalumination en synthese organique: obtention d'α-alkyl α-hydroxyesters par addition enantioselective de tetraalkylaluminates AU phenylglyoxalate de (−) menthyle.

Using tetraalkylaluminates prepared via hydroalumination in THF of various vinyl compounds resulted in selective addition to the keto group of phenylglyoxylic acid (?) menthyl ester. Not only simple alkyl groups but also functionalized alkyl groups were added. By this way, a variety of α-substituted mandelic acid (?) menthyl esters were obtained with diastereomeric excesses close to 70%.     

An opened route to 1,3-dimethylenecyclobutanes via sequential ruthenium-catalyzed [2 + 2] cycloaddition of allenyl boronate and palladium Suzuki coupling

The regioselective head-to-head [2 + 2] cyclodimerization of allenyl boronate catalyzed by the ruthenium catalyst [Cp*RuCl(COD)] leads to a novel diboronated 1,3-dimethylenecyclobutane. Consecutive palladium-catalyzed C-C couplings open a route to novel disubstituted 1,3-dimethylenecyclobutane species. The X-ray crystalline structure of the phenyl-substituted 1,3-dimethylenecyclobutane is provided.     

Multicomponent Adsorption of Pesticides onto Activated Carbon Fibers

The adsorption equilibria of pesticides and metabolites (atrazine, deethylatrazine, deisopropylatrazine and simazine) are studied onto activated carbon fibers –ACF– with a broad pore size distribution (32% mesopore volume, 68% micropore volume). Mono-and multi-component isotherms have been determined for low concentrations, from 0.23×10⁻⁶ to 9.52×10⁻⁶ mol L⁻¹. Single solute isotherms, modeled by Freundlich and Langmuir models, tend to prove the influence of the adsorbate's solubility in the adsorption capacity of activated carbon fibers. Binary solute isotherms confirm the strong influence of pesticide solubility on the competitive adsorption mechanism: the competition is higher in the case of adsorbates of different solubilities (atrazine and DEA or DIA for example). Multicomponent experimental data were modeled by extended Langmuir-based equations and the Ideal Adsorbed Solution theory. Whereas the first ones failed to model accurately binary adsorption due to restrictive hypothesis, the IAS model showed a good agreement between experimental and predicted data. It emphasised also the difficulty in satisfying the hypothesis of the model in the case of highly adsorbed compounds. Finally, the simultaneous adsorption of atrazine and NOM (in a natural water, DOC = 18.2 mg L⁻¹) shows no adsorption competition effects between natural organic matter and atrazine. This is due to the presence of secondary micropores (0.8–2 nm) and mesopores in the ACF, which limit a pore blockage phenomenon by NOM.     

Diazonium-protein adducts for graphite electrode microarrays modification: direct and addressed electrochemical immobilization

Diazonium cation electrodeposition was investigated for the direct and electro-addressed immobilization of proteins. For the first time, this reaction was triggered directly onto diazonium-modified proteins. Screen-printed (SP) graphite electrode microarrays were studied as active support for this immobilization. A 10-microelectrode (eight working electrodes, 0.2 mm2 each; one reference; and one auxiliary) setup was used to study the addressing possibilities of the method. These electrode microarrays were shown to be able to covalently graft diazonium cations through electrochemical reduction. Cyclic voltammetry and X-ray photoelectron spectroscopy were used to characterize the electrochemical grafting onto our SP graphite surface and suggested that a diazonium monolayer was deposited. Rabbit and human immunoglobulins (IgGs) were then chemically coupled to an aniline derivative (4-carboxymethylaniline), followed by diazotation to form an aryl diazonium function available for the electrodeposition. These modified proteins were both successfully electro-addressed at the surface of the graphite electrodes without cross-talk or interference. The immuno-biochip obtained using this novel approach enabled the specific detection of anti-rabbit IgG antibodies with a detection limit of 50 fmol of protein. A promising strategy to immobilize markedly different biological entities was then presented, providing an excellent spatial specificity of the electro-addressing.     

A straightforward methodology to overcome solubility challenges for N-terminal cysteinyl peptide segments used in native chemical ligation

One of the main limitations encountered during the chemical synthesis of proteins through native chemical ligation (NCL) is the limited solubility of some of the peptide segments. The most commonly used solution to overcome this problem is to derivatize the segment with a temporary solubilizing tag. Conveniently, the tag can be introduced on the thioester segment in such a way that it is removed concomitantly with the NCL reaction. We herein describe a generalization of this approach to N-terminal cysteinyl segment counterparts, using a straightforward synthetic approach that can be easily automated from commercially available building blocks, and applied it to a well-known problematic target, SUMO-2.

We herein describe a straightforward approach for the introduction of a solubilizing tag on N-terminal cysteinyl segments used in native chemical ligation-based protein chemical synthesis. Conveniently, the tag is removed during the ligation.     

Multicatalytic processes using diverse transition metals for the synthesis of alkenes

A series of cascade processes for the synthesis of alkenes from alcohols is described. Each individual step is catalyzed with a specific transition metal complex. The oxidation-methylenation one-pot procedure took place in the presence of a palladium and a rhodium catalyst to produce the desired terminal alkenes in high yields. A methylenation-ring-closing metathesis allowed the synthesis of cyclic alkenes from carbonyl derivatives, using the second-generation metathesis catalyst. Finally, an oxidation-methylenation-RCM process that involves up to three different transition metal catalysts in the same vessel is presented.