Tagless extraction-retentate chromatography: a new global protein digestion strategy for monitoring differential protein expression

A new global protein digestion and selective peptide extraction strategy for the purpose of monitoring differential protein expression, coined as tagless extraction-retentate chromatography, is introduced. Target protein populations are firstly digested under reduced and alkylated conditions, and resultant peptides selectively extracted via covalent attachment to methionine residues by bromoacetyl reactive groups tethered to the surface of glass beads packed in small reaction vessels. After conjugation, reactive beads are stringently washed to remove nonspecifically bound peptides and then later treated with beta-mercaptoethanol to release captured methionine peptides in their nascent state, without complicating affinity tags. Recovered methionine containing peptides are profiled using the surface-enhanced laser desorption/ionization (SELDI) retentate chromatography mass spectrometry (RCMS) method. Selected peptides are further studied employing ProteinChip tandem mass spectrometry (MS/MS) analysis to identify their parent proteins. This approach has been applied to an Escherichia coli lysate model system and has demonstrated facility in reducing global digest complexity, sensitivity to low protein expression levels, and significant quantitative capability. It is envisioned that tagless extraction-RCMS will evolve to be a valuable approach for both basic research and clinical proteomics endeavors.     

Aroma composition of red wines by different extraction methods and Gas Chromatography-SIM/MASS spectrometry analysis

One hundred and one volatile compounds, reported in literature as powerful odorants of wine, were quantified by Gas Chromatography-Selective Ion Monitoring/Mass Spectrometry (GC-SIM/MS) in Primitivo, Aglianico, Merlot and Cabernet Sauvignon red wines. Wine samples were extracted by 3 different extraction methods: 1) separation of the alcoholic fraction from the aqueous phase by salting-out and subsequent extraction by liquid-liquid micro-extraction with 1,1,2-trichlorotrifluoroethane (Freon 113); 2) extraction by liquid-liquid micro-extraction with dichloromethane; 3) solid phase extraction (SPE cartridge: 800 mg of LiChrolut EN resin) with pentane-dichloromethane (20:1) and dichloromethane. The selection of the ion fragments used for quantification was directly performed on a red wine sample. For each compound the area of the corresponding peak was normalized respect to the peak of the internal standard and then interpolated in a calibration curve obtained analysing a model wine solution (water, ethanol, tartaric acid and known amounts of analytes and of internal standard). The methods showed a good linearity: r2>0.990, except for farnesol (isomer a and c), octanal, decanal, furaneol and phenylacetic acid with 0.966 < or = r2 < or = 0.990. The 7 most powerful odorants were: beta-damascenone, acetaldehyde, maltol, ethyl 2-methylbutanoate, ethyl 3-methylbutanoate, 3-methylbutanoic acid and acetal; 7 other slightly less important were: ethyl hexanoate, ethyl acetate, 1-octen-3-ol, butanoic acid, rose oxide, furaneol and sotolon. The Aglianico wines were characterised by the major fermentation compounds (esters, fatty acids and 2-phenylethanol), beta-damascenone, beta-ionone and linalool. The Primitivo wines were characterized by furaneol, methoxypyrazine, gamma-nonalactone and acetaldehyde, while Cabernet Sauvignon and Merlot wines principally by cask derivates (vanillin, (Z) 3-methyl-gamma-octalactone [(Z) wiskylactone], maltol and eugenol), some aldehydes and 3-isopropyl-2-methoxypyrazine.     

Methyl groups as probes for proteins and complexes in in-cell NMR experiments

Studying protein components of large intracellular complexes by in-cell NMR has so far been impossible because the backbone resonances are unobservable due to their slow tumbling rates. We describe a methodology that overcomes this difficulty through selective labeling of methyl groups, which possess more favorable relaxation behavior. Comparison of different in-cell labeling schemes with three different proteins, calmodulin, NmerA, and FKBP, shows that selective labeling with [(13)C]methyl groups on methionine and alanine provides excellent sensitivity with low background levels at very low costs.     

(+)- and (-)-2-aminocyclobutane-1-carboxylic acids and their incorporation into highly rigid beta-peptides: stereoselective synthesis and a structural study

[Chemical reaction: See text] Several derivatives of (+)- and (-)-2-aminocyclobutane-1-carboxylic acid, 1, have been prepared through enantiodivergent synthetic sequences. The stereoselective synthesis of free amino acid (+)-1 has been achieved, and this product has been fully characterized for the first time. Stereocontrolled alternative synthetic methodologies have been developed for the preparation of bis(cyclobutane) beta-dipeptides in high yields. Among them, enantio and diastereomers have been synthesized. beta,beta- and beta,delta-Dimers resulting from the coupling of a cyclobutane residue and a linear amino acid have also been prepared. The ability of the cyclobutane ring as a structure-promoting unit both in the monomers and in the dimers has been manifested. The NMR structural study and DFT theoretical calculations evidence the formation of strong intramolecular hydrogen bonds giving rise to cis-fused [4.2.0]octane structural units that confer high rigidity on these molecules both in solution and in the gas phase. The contribution of a cis-trans conformational equilibrium derived from the rotation around the carbamate N-C(O) bond has also been observed, the trans form being the major conformer. In the solid state, this equilibrium does not exist, and moreover, intermolecular hydrogen bonds are present.     

Using second-order calibration to identify and quantify aromatic sulfonates in water by high-performance liquid chromatography in the presence of coeluting interferences

We used the Generalized Rank Annihilation Method (GRAM), a second-order calibration method, to quantify aromatic sulfonates in water with high-performance liquid chromatography (HPLC) when interferences coeluted with the analytes of interest. With GRAM, we can quantify in only two chromatographic analyses, one for a calibration sample and one for the unknown sample. The calculated concentrations were not statistically different to those obtained when the chromatographic separation of the unknown sample was modified in order to completely separate the analyte from the interferences before univariate calibration. With GRAM, the concentrations are determined much more quickly because a complete resolution is not required.     

Extraction and exchange behavior of metal species in therapeutically applied peat

The binding and availability of metals (Al, Ca, Cd, Co, Cr, Cu, Fe, Mg, Mn, Ni, Pb, Zn) in therapeutically applied peat (Grosses Gifhorner Moor, Sassenburg/North Germany) was characterized by means of a versatile extraction approach. Aqueous extracts of peat were obtained by a standardized batch equilibrium procedure using high-purity water (pH 4.5 and 5.0), 0.01 mol l(-1) calcium chloride solution, 0.01 mol l(-1) ethylenediaminetetraacetic acid (EDTA) and 0.01 mol l(-1) diethylenetriamine pentaacetic acid (DTPA) solution as metal extractants. In addition, the availability of peat-bound metal species was kinetically studied by collecting aliquots of extracts after different periods of extraction time (5, 10, 15, 30, 60 and 120 min). Metal determinations were performed by atomic spectrometry methods (AAS, ICP-OES) and dissolved organic matter (DOM) was characterized by UV/Vis measurements at 254 and 436 nm, respectively. Of the extractants studied Ca, Mg and Mn were the most available metals, in contrast to peat-bound Fe and Al. The relative standard deviation s(r) of the developed extraction procedures was mostly in the range of 4 to 20%, depending on the metal and its concentration in peat. A pH increase favored the extraction of metals and DOM from peat revealing complex extraction kinetics. Moreover, a competitive exchange between peat-bound metal species and added Cu(II) ions showed that >100 mg of Cu(II) per 50 g wet peat was necessary to exchange the maximum of bound metals (e.g. 21.8% of Al, 3.9% of Fe, 79.0% of Mn, 81.9% of Sr, related to their total content).     

Study on resolution capacity and secondary mechanisms of three different TSK gels for organic SEC

A comparative study on the elution behavior in size-exclusion chromatography (SEC) of three polymeric TSK gel packings, named H, H(HR), and H(XL) types, is performed. The deviations of the universal calibration (u.c.) curves of seven solvent-polymer systems show evidence that the existence of secondary effects accompanying the main SEC mechanism. These secondary mechanisms are a consequence of the binary enthalpic interactions between the different components of the chromatographic system, such as polymer-solvent, polymer-gel and solvent-gel. However, in the present case, the observed deviations from a unique u.c. curve can mainly be attributed to adsorption of polymeric solutes (analytes) onto the residual moieties of the gel surfaces, (i.e., to polymer-gel interactions). These enthalpic interactions can be quantitated by the values of the distribution coefficient, Kp, which follows the order: Kp (gel H(XL)) > Kp (gel H(HR)) > Kp (gel H). Moreover, the specific resolution of the three types of packings is also estimated, and its comparison yields that Rsp (gel H(HR)) > Rsp (gel H(XL)) > Rsp (gel H), in good agreement with their increasing particle size and decreasing crosslinking degrees. Finally, the errors and inaccuracies committed on the estimation of the sample average molar masses from their respective calibration curves serves the assessment that the packing with lesser secondary mechanisms is the H-type.     

Densities and excess molar volumes for binary mixtures of N,N-dimethylformamide+ 1,2-dimethoxyethane

Densities are reported for N,N-dimethylformamide and 1,2-dimethoxyethane binary mixtures at different mole fractions covering the whole miscibility range and at 19 temperatures ranging from –10 to 80°C. The experimental density data have been fitted by empirical relations and the excess volumes by a Redlich-Kister equation. The 11 N,N-dimethylformamide and 1,2-dimethoxyethane adduct appears to be stable throughout the temperature range. A comparison with other DMF containing mixtures is made.     

Derivatives of carbohydrazide, thiocarbohydrazide and diaminoguanidine as photometric analytical reagents-I 1,3-bis[(2-pyridyl)methyleneamino]thiourea and 1,3-bis[(2-pyridyl)methyleneamino]guanidine

1,3-Bis[(2-pyridyl)methyleneamino]thiourea (PMAT) and 1,3-bis[(2-pyridyl)methyleneamino]-guanidine (PMAG) have been prepared. They have been examined and characterized by infrared and ultraviolet spectroscopy. A spectrophotometric method has been used for determination of the protonation constants of the reagents. Finally, a spectrophotometric survey has been made of the reactions of various cations with PMAT and PMAG.     

Solid state coordination chemistry of copper(II)/α-hydroxycarboxylato/2,2′-bipyridine systems

Four new two-ligand complexes of copper(II) with 2,2′-bipyridine and one of three different α-hydroxycarboxylic acids (lactic, H₂LACO; 2-methyllactic, H₂MLACO; and mandelic, H₂MANO) were prepared. Complexes 1–3 of general formula [Cu(HL)₂(bipy)]·nH₂O (HL=monodeprotonated acid), were characterized by elemental analysis, IR, electronic and EPR spectroscopy, magnetic measurements and thermogravimetric analysis. Complexes 1 (HL=HLACO, n=2), 2 (HL=HMLACO, n=1) and 3a (the result of attempted recrystallization of 3, of formula [Cu(HMANO)(bipy)₂](HMANO)·H₂MANO·CH₃CN were studied by X-ray diffractometry. The copper atom is in an elongated, tetragonally distorted octahedral environment in 1 and 2 and in 3a has a coordination polyhedron intermediate between a square pyramid and a trigonal bipyramid, as evaluated in terms of the parameter τ. In 1 and 2 the α-hydroxycarboxylato ligand is bidentate and monoanionic but in 3a there are three forms: a monodentate monoanion, a monoanionic counterion, and a neutral molecule.