Mapping phosphorylation sites: a new strategy based on the use of isotopically labelled DTT and mass spectrometry

Phosphoproteomics, nowadays, represents a front line in functional proteomics as testified by the number of papers recently appearing in the literature. In an attempt to improve and simplify the methods so far suggested we have set up a simple isotope-coded approach to label and quantitate phospho-Ser/-Thr residues in protein mixtures. First of all, after appropriate oxidation of cysteine/cystine residues followed by tryptic hydrolysis, we have optimised and simplified the beta-elimination reaction to get the corresponding alkene moiety from the phosphate esters. This was achieved by (a) separating the elimination reaction from the addition reaction, (b) the use of Ba(OH)(2) as alkali reagent and (c) its further elimination by the simple addition of solid CO(2) to the peptide mixture. The Michael reaction was then performed, after the removal of BaCO(3) by centrifugation, by adding dithiothreitol (DTT) to the peptide mixture. Finally, the direct purification of the modified phosphopeptides was performed on a thiol-sepharose column. The availability of fully deuterated DTT, introducing a 6 Da difference with respect to the non-deuterated species, allows quantitation of the differential extent of signalling modification when analysed by matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) and liquid chromatography/mass spectrometry. The entire procedure has been set up by using bovine alpha-casein, and resulted in the identification of all the phosphorylated tryptic peptides, including the tetraphosphorylated peptides, which escaped all previously reported procedures     

Structural studies on Ba(II) adducts of the cytosine nucleobase and its derivative 1-Methylcytosine*

Abstract

The use of the cytosine nucleobase or its 1-Methylcytosine derivative as ligands toward barium(II) cations led to the formation of three compounds, {[Ba(1-Mecyt)(H₂O)X₂]}_n [X=Cl (1), Br (2)], and {[Ba(cyt)₂(H₂O)(ClO₄)₂]}_n (3). Depending on the ligand and the counterion employed, 1–3 exhibit different architectures, which serve as a playground to study how the methyl substitution, together with the nature of the counterion are both significant in the self-assembling process of such species. The effect of the nature and size of the alkaline-earth metal ion on the final structural motif is also evident when comparing these structures with parent complexes of the Ca(II) ion.     

Free radical-scavenging activity of indolic compounds in aqueous and ethanolic media

Indolic compounds are a broad family of substances present in microorganisms, plants and animals. They are mainly related with tryptophan metabolism, and present particularities that depend on their respective chemical structures. The most important members of the family are the plant hormone, indole-3-acetic acid, and the animal hormone, melatonin. An important characteristic of some indolic compounds is that they may be useful as chemical preventive agents against diseases such as cancer, oxidative stress, etc. For this reason, the possible antioxidant activities (free radical-scavenging activity) of several indoles were studied. The2,2'-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid /H(2)O(2)/HRP decoloration method was applied to determine both hydrophilic (in buffered media) and lipophilic (in organic media) antioxidant properties of the indolic compounds. Also, a study of the hydrophilic antioxidant activities of indoles at different pH values (between 4.5 and 8.5) was made. Finally, their possible role as diet plant antioxidants is discussed.     

New phosphorylating reagents for deoxyribonucleosides and oligonucleotides

New phosphorylating reagents 1 and 2 were prepared in three steps from 4-hydroxybenzaldehyde. They showed good efficiency in the solid phase synthesis of 5′-phosphate monoester nucleosides. End-phosphate DNA sequence synthesis demonstrated the efficiency of the new reagents (1 and 2) according to the general procedure of automated DNA synthesis. The oxidation of P(III) to P(V) and the removal of benzyl protecting groups were achieved in a single step by treatment with a 0.02 M I₂/pyridine/H₂O solution. Due to this one-pot treatment, it is possible to use the phosphorylating reagents (1 and 2) for the synthesis of base-sensitive ODNs. The reagents 1 and 2 are unique among phosphorylating reagents.     

Derivatives of 2,3‐dihydroimidazo[1,5,4‐ef][1,2,5]‐benzothiadiazepin‐6(4h,7h)‐thione 1,1‐dioxide,a new heterocyclic system related to tibo

The synthesis of derivatives of 2,3‐dihydroimidazo[1,5,4‐ef][1,2,5]benzothiadiazepin‐6(4H,7H)‐thione 1,1‐dioxide is reported starting from N‐substituted ethyl 2‐(5‐chloro‐2‐nitrobenzenesulfonamido)‐2‐alkyl‐acetates. Fundamental steps of the synthetic pathway were: i) intramolecular cyclization of N‐substituted 2‐(2‐amino‐5‐chlorobenzenesulfonamido)‐2‐alkylacetic acids in the presence of N‐(3‐dimethyl‐aminopropyl)‐N′‐ethyl carbodiimide hydrochloride‐N,N‐dimethylaminopyridine complex; ii) building of imidazole ring from 2‐alkyl‐8‐chloro‐2,3‐dihydro‐3‐methyl‐1,2,5‐benzothiadiazepin‐4(5H)‐one 1,1‐dioxide to achieve 2‐alkyl‐9‐chloro‐2,3‐dihydro‐3‐methylimidazo[1,5,4‐ef][1,2,5]benzothiadiazepin‐6(4H,7H)‐one 1,1‐dioxide; iii) preparation of thiocarbonyl derivative by treatment with Lawesson's reagent. Introduction of a 3‐methyl‐2‐butenyl chain at position 2 of above imidazobenzothiadiazepinone required protection at the 7 position with thermally removable tert‐butoxycarbonyl moiety, due to the fact that alkylation of unprotected structure proved to be regioselective for the 7 position.     

Determination of maize and grain herbicides and their transformation products in soil by use of soil column extraction then liquid chromatography with tandem mass spectrometry

Summary A multiresidue method has been developed for identification and quantitation of the herbicides most commonly used in cultivation of maize and grain, and of their transformation products, in soil samples. The analytes were isolated by soil column extraction (SCE) and the extracts were purified by use of a Carbograph-1 cartridge. Analysis was performed by liquid chromatography coupled with tandem mass spectrometric detection (LC-TISP-MS-MS) in negative-ion mode. To optimize the extraction conditions affecting the performance of SCE, e.g. the extracting solvent used, temperature, extracting volume, and solvent flow rate, were studied. To evaluate the matrix effect in SCE, recovery experiments were performed on soil samples, with different physical and chemical characteristics, fortified with the 100 ng g⁻¹ of the target compounds. Recovery data were satisfactory and the method detection limits were between 3 and 100 ng g⁻¹, depending on the compound.     

Perthamides C-F, potent human antipsoriatic cyclopeptides

Two new cyclopeptides, perthamides E and F were isolated from the polar extracts of the sponge Theonella swinhoei. The new structures, featuring an unprecedented β-amino acid unit (AHMOA), were determined by interpretation of NMR and MS data. The absolute configuration of the AHMOA residue was proposed on the basis of quantum chemical calculation of NMR chemical shifts. Perthamides were proved to inhibit TNF-α and IL-8 release in primary human keratinocytes cells and therefore could represent potentially leads for the treatment of psoriasis.     

Conformational studies by dynamic NMR. 86. Structure, stereodynamics, and cryogenic enantioseparation of the stereolabile isomers of o-dinaphthylphenyl derivatives

Static and dynamic stereochemistry of the hydrocarbon comprising a phenyl ring bearing two alpha-naphthyl substituents in the ortho positions, i.e., 1,2-di-(4-methyl-naphth-1-yl)-benzene 1, has been studied by a combination of variable temperature NMR, cryogenic HPLC, and MM calculations. Whereas in solution both syn (meso) and anti (chiral) forms were observed and the corresponding interconversion barrier was determined (Delta G(++) = 19.5 kcal mol(-1)), only the diastereoisomer anti was found to be present in the crystalline state (X-ray diffraction). When the molecule is rendered asymmetric by introduction of a nitro group in the phenyl ring as in 1,2-di-(4-methyl-naphth-1-yl)-4-nitrobenzene 2, the chiral syn and anti diastereoisomers are simultaneously present both in solution and in the solid state, albeit in different proportions. Cryogenic chromatography on a HPLC chiral stationary phase at 20 degrees C allowed the stereolabile diastereoisomers and the corresponding enantiomers to be separated.     

Allylation of exocyclic N-Acyliminium ions generated from chiral N-[1-(phenylsulfonyl)alkyl]oxazolidin-2-ones

N-[1-(Phenylsulfonyl)alkyl]oxazolidin-2-ones are successfully prepared by condensation of the corresponding optically active oxazolidin-2-ones with aldehydes and benzenesulfinic acid. At low temperature, in the presence of titanium tetrachloride, these sulfones are converted into N-acyliminium ions, which react with allyltrimethylsilane with a variable degree of stereoselectivity. The best results are obtained with (R)-5,5-dimethyl-4-phenyloxazolidin-2-one as a chiral auxiliary. Cleavage of the oxazolidin-2-one ring with lithium/ammonia affords the corresponding homoallylamines, which reveal an absolute configuration opposite that expected on the basis of the usual steric effects. A complexation of the Lewis acid with the N-acyliminium ion may be responsible of this rather unusual stereochemical outcome.     

Interaction of Cu(+) and Cu(2+) ions with alpha-alanine. A density functional study

The Cu(+) and Cu(2+) preferred binding sites on alpha-alanine and their affinity values for this amino acid were determined at the density functional level using three different hybrid exchange correlation potentials and the 6-311++G** basis set. The results demonstrated that the two ions both give stable complexes with alpha-alanine but the stability order of the metalated species and the coordination sites are different depending on the nature of the cation. In particular, the Cu(+)-alpha-alanine ground-state structure is characterized by an eta(2)-N,O coordination with the nitrogen and oxygen atoms belonging to the amino and carbonyl groups, respectively. In contrast, the most stable complex of the Cu(2+)-alpha-alanine system has an eta(2)-O,O coordination with the cation bonded to the -CO(2) (-) moiety of the zwitterionic form of the amino acid. Comparison with the Cu(+) and Cu(2+) affinity values for glycine, computed at the same levels of theory, demonstrated that the relative values do not change significantly as different hybrid functionals are used, although the absolute affinities are strongly influenced by the choice of the hybrid potential.