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.     

Structure and stereochemistry of a new cytotoxic polychlorinated sulfolipid from Adriatic shellfish

A detailed analysis of the causative toxins contained in the hepatopancreas of toxic mussels from the northern Adriatic sea has been carried out. Along with some DSP (diarrhetic shellfish poisoning) type toxins, such as okadaic acid, yessotoxin, and their derivatives, which are involved in a number of human intoxications throughout the world, we have now isolated a new cytotoxin, a polychlorinated sulfolipid 1, whose gross structure has been elucidated by spectral analysis, including various 2D NMR techniques. The relative stereochemistry of 1 was elucidated by successful application of the J-based configuration analysis developed for acyclic compounds using carbon-proton spin-coupling constants ((2,3)J(C,H)) and proton-proton spin-coupling constants ((3)J(H,H)); its absolute stereochemistry was established by the Mosher method. Compound 1 possesses in vitro cytotoxicity against WEHI 164 and RAW 264.7 cells.     

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.     

Time shift correction in second-order liquid chromatographic data with iterative target transformation factor analysis

When the generalized rank annihilation method (GRAM) is applied to liquid chromatographic data with diode-array detection, an important problem is the time shift of the peak of the analyte in the test sample. This problem leads to erroneous predictions. This time shift can be corrected if a time window is selected so that the chromatographic profile of the analyte in the test sample is trilinear with the peak of the analyte in the calibration sample. In this paper we present a new method to determine when this condition is met. This method is based on the curve resolution with iterative target transformation factor analysis (ITTFA). The calibration and test matrices are independently decomposed into profiles and spectra, and aligned before GRAM is applied. Here we study two situations: first, when the calibration matrix has one analyte and second, when it has two analytes. When the calibration matrix has two analytes, we selectively determine the time window for the analyte to be quantified. There were considerably fewer prediction errors after correction.     

The direct detection of a hydrogen bond in the solid state by NMR through the observation of a hydrogen-bond mediated (15)N [bond] (15)N J coupling

A new method for detecting hydrogen bonds in the solid state is presented. Using two-dimensional NMR correlation experiments, it is shown that a hydrogen-bond mediated J coupling can be observed in a powder under magic-angle spinning conditions, even though the J coupling is 2 orders of magnitude smaller than the dominant anisotropic interactions encountered in solid-state NMR. Specifically, the observation of a pair of peaks in a two-dimensional 15N-15N solid-state INADEQUATE experiment due to two nitrogens that have no covalent connectivity is attributed to the presence of a J coupling across a linking hydrogen bond.     

Stereoselective synthesis of novel types of cyclopropyl carbocyclic nucleosides containing quaternary stereogenic centers

Versatile and stereocontrolled synthetic entries to novel types of cyclopropyl carbocyclic nucleosides are described. The target products have been synthesized from suitable cyclopropane precursors obtained, in turn, from olefinic compounds derived from D-glyceraldehyde as a chiral precursor. Selective manipulation of the functional groups has allowed the preparation of enantiopure nucleosides, some of them displaying opposite chirality. All these molecules contain a quaternary stereogenic carbon at C-1 or C-3 of the cyclopropane ring and bear an amino, a hydroxymethyl, or a methyl group as an additional substituent. In one instance, thymine is directly linked to the cyclopropane. A methylene unit serves as the spacer in the other synthesized nucleosides.     

A New Ent-Kaurane from the Roots of Lasianthaea aurea

Chemistry of Natural Compounds - A known kaurenoic acid (1), together with a new kaurane derivative named 3α-isobutyryloxykaurenoic acid (2), was isolated from the roots of Lasianthaea aurea,...     

Gas chromatography–triple-quadrupole mass spectrometry for analysis of selected polyhalogenated pollutants in plants. Comparison of extraction methods

Different extraction methods, followed by gas chromatography coupled to triple quadrupole mass spectrometry, were evaluated for simultaneous extraction of seven polychlorinated biphenyls (PCBs) and six polybrominated diphenyl ethers (PBDEs) from common weeds. Pressurized liquid extraction (PLE) with in-cell clean-up, ultrasound-assisted extraction (UAE) with in-column clean-up, and UAE with dispersive solid-phase extraction (dSPE) clean-up were evaluated and compared. In-cell clean-up with 4 g Florisil and 0.5 g graphitized carbon black (GCB) and two extraction cycles of 10 min with n-hexane–ethyl acetate 80:20 (v/v) at 60 °C were used for the PLE procedure. UAE with in-column clean-up was conducted under conditions similar to those reported for the PLE method whereas in UAE with dSPE clean-up purification of the extract was performed after extraction using primary and secondary amine sorbent (PSA) and GCB. Recovery from 82 to 104 % was obtained for all the compounds by PLE whereas, in general, lower extraction efficiency was obtained by UAE with in-column clean-up (especially for BDE-17 and BDE-183, for which recovery was 70 and 41 %, respectively) and by UAE with dSPE clean-up, for which the main drawback is that BDE-183 cannot be extracted. Finally, PLE was used for analysis of PCBs and PBDEs in different plants (Lolium rigidum, Lactuca serriola, Malva sylvestris, and Verbascum thapsus) collected from residential and/or rural areas of Madrid (Spain). Several of the analyzed compounds were detected at low levels in these plants, but only PCB-153 could be quantified.

Intermolecular spin–spin coupling constants between P atoms

This paper reports the study by NMR spectroscopy and ab initio methods of the structure of 3,4-dimethyl-1-cyanophosphole and its dimer. The dimer presents a P···P interaction of the pnictogen type due to the presence of σ-holes. NMR of the monomer was recorded in CDCl₃ solution while NMR of the dimer corresponds to the solid state (CPMAS) experiments. The ^2pJ_PP spin–spin coupling constant has not been measured, but calculated at the B3LYP level. AIM, NBO and ELF methodologies have been used to describe the electronic structure of the dimer.