Quantitative validation of different protein precipitation methods in proteome analysis of blood platelets

For the preparation of proteins for proteome analysis, precipitation is frequently used to concentrate proteins and to remove interfering compounds. Various methods for protein precipitation are applied, which rely on different chemical principles. This study compares the changes in the protein composition of human blood platelet extracts after precipitation with ethanol (EtOH) or trichloroacetic acid (TCA). Both methods yielded the same amount of proteins from the platelet preparations. However, the EtOH-precipitated samples had to be dialyzed because of the considerable salt content. To characterize single platelet proteins, samples were analyzed by two-dimensional fluorescence differential gel electrophoresis. More than 90% of all the spots were equally present in the EtOH- and TCA-precipitated samples. However, both precipitation methods showed a smaller correlation with nonprecipitated samples (EtOH 74.9%, TCA 79.2%). Several proteins were either reduced or relatively enriched in the precipitated samples. The proteins varied randomly in molecular weight and isoelectric point. This study shows that protein precipitation leads to specific changes in the protein composition of proteomics samples. This depends more on the specific structure of the protein than on the precipitating agent used in the experiment.     

Electrode processes in the oxidation of tetrahydroisoquinoline derivatives

The electrochemical oxidation of the alkaloid laudanosine (Ia) to O-methylflavinantine (II) has been studied in acetonitrile solvent. Using cyclic voltammetry, rotating disc voltammetry and preparative electrolyses on several alkaloids, simple aliphatic amines and aromatic compounds, some aspects of the mechanism of this coupling reaction are elucidated. The first anodic wave for laudanosine at platinum has E_p=0.55 V vs. Ag/Ag⁺. The electrode rapidly becomes partially passivated at potentials above 0.5 V. This is due to a film which “dissolves” below 0.5 V, at a rate independent of the potential. It is shown that the reaction (Ia)→(II) proceeds at 0.5 V by initial oxidation of the amine moiety. If acids such as sodium bicarbonate are added to the anolyte the amine is protonated causing the first wave to disappear. Oxidation at 1.1 V under these acidic conditions produces the same product, but more rapidly and in significantly higher yield because electrode filming and side reactions resulting from the amine oxidation are abrogated.     

Eliminative deoxygenation: the facile formation of α-trimethylsilyl vinyl sulfides from sulfoxides

Synthetically useful α-trimethylsilyl vinyl sulfides are generated in high yields by deoxygenation of the corresponding sulfoxides in the presence of excess LDA and trimethylsilyl chloride.     

Eliminative deoxygenation: A facile synthesis of α-cyano and α-carboalkoxy substituted vinyl sulfides

The faciIe eliminative deoxygenation of α-cyano and carboalkoxy sulfoxides by trimethylsilyl triflate under mildly basic conditions results in the formation of α-thiophenyl substituted α,β-unsaturated nitriles and esters in high yields.     

Adamantane-like cluster complexes of mixed-valent copper-copper and nickel-copper thiolates

Square-planar copper(II) and nickel(II) derivatives of the cis-dithiolate N(2)S(2) ligand bis(N,N'-2-mercapto-2-methylpropyl)-1,5-diazocyclooctane, (bme*daco)M, nucleate four Cu(I)Cl moieties, forming M(II)(2)Cu(I)(4)S(4) clusters with unusual triply bridging thiolates, mu(3)-SR, in the topological form of adamantane. As determined by X-ray crystallography, the (bme*daco)M (M = Cu or Ni) metallothiolate serves as a bidentate ligand that bridges four Cu(I) ions, utilizing all lone pairs on sulfurs. Further characterization by electrochemical and electronic spectral measurements suggests greater electron delocalization in the all-copper complex as compared to the NiCu heterometallic complex. Mass spectral data imply that the mixed-metal Ni(II)(2)Cu(I)(4)S(4) is more stable toward CuCl loss than Cu(II)(2)Cu(I)(4)S(4), a result that is corroborated by extraction of Cu(I) by 1,2-bis(diphenylphosphino)ethane in the latter but not the former.     

Impact of prefractionation using Gradiflow on two-dimensional gel electrophoresis and protein identification by matrix assisted laser desorption/ionization-time of flight-mass spectrometry

Prefractionation of protein samples prior to two-dimensional electrophoresis (2-DE) has the potential to increase the dynamic detection range for proteomic analysis. We evaluated a membrane-based electrophoretic separation technique (Gradiflow) for its ability to fractionate an exoproteome sample from the filamentous fungus Trichoderma reesei. The sample was separated on the basis of size and charge. Buffer optimization was found to be necessary for successful size fractionation. Fractionation by charge was used to resolve the sample into four fractions that were subjected to analysis by two-dimensional electrophoresis (2-DE). Enhanced detection of low-abundance proteins with selective removal of high-abundance species was achieved. Fractionated and unfractionated samples were examined for differences in the ability to identify proteins following 2-DE using trypsin in-gel digestion followed by peptide mass fingerprinting using matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). Fractionated samples showed marked improvement in protein identification ability and sequence coverage. This study demonstrates the utility of the Gradiflow for fractionation, resulting in an enhancement of resolution and characterization of a moderately complex proteome.     

Stability of a fluid-fluid interface in a biconical pore segment

Pore networks that include biconical pore segments are frequently used to model two-phase flow. In this work, we describe in detail the displacement of a fluid-fluid interface in such a pore segment. We assume sharp edges in the throat, inlet, and outlet of the pore segment to be the limiting cases of round edges, the radii of which vanish. We account for interfacial and lineal tensions that cause nonconstant contact angles. For zero lineal tension, we provide analytical solutions for flow induced by changing infinitesimally slowly either capillary pressure or the volume of one fluid. In diverging and converging cones, the common line among the two fluids and the solid phase slides while it is pinned in the throat, inlet, and outlet. We observe hysteresis within the pore segment, and drainage entry pressures deviate from prior work.     

First and second derivative matrix elements for the stretching,bending, and torsional energy

Matrix elements for the first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for stretching, linear, nonlinear, and out-of-plane bending and torsional motion. Derivatives of the energy with respect to the Cartesian coordinates are calculated with the chain rule. Derivatives of the energy with respect to the internal coordinates are straightforward, but the calculation of the derivatives of the internal coordinates with respect to the Cartesian coordinates can be simplified by the following two steps outlined in this article. First, the number of terms in the analytical functions can be reduced or will vanish when the derivatives of the bond length, bond angle, and torsion angle are reported in a local coordinate system in which one bond lies on an axis and an adjacent bond lies in the plane of two axes or is projected onto perpendicular planes for linear and out-of-plane bending motion. Second, a simple rotation transforms these derivatives to the appropriate orientation in the space-fixed molecular coordinate system. Functions of the internal coordinates are invariant with respect to translation and rotation. The translational invariance and the symmetry of the second derivatives for a system with L atoms are used to select L-1- and L(L-1)/2-independent first and second derivatives, respectively, of which approximately half of the latter vanish in the local coordinate system. The rotational invariance permits the transformation of the simplified derivatives in the local coordinate system to any orientation in space. The approach outlined in this article simplifies the formulas by expressing them in a local coordinate system, identifies the most convenient independent elements to compute, from which the dependent ones are calculated, and defines a transformation to the space-fixed molecular coordinate system.     

Optical sensor for sulfur dioxide based on fluorescence quenching

A series of potential indicator dyes is evaluated for use in the development of optical sensors for measuring sulfur dioxide in gaseous samples. Rhodamine B isothiocyanate is selected on the basis of relative sensitivity to dynamic quenching by sulfur dioxide and oxygen. A solid-state fluorometer is described for monitoring the sulfur dioxide induced fluorescence quenching of sensing membranes composed of silicone and rhodamine B isothiocyanate. A modulated blue LED is coupled with the lock-in detection of a photodiode detector to provide high signal-to-noise ratios. The limit of detection is 0.114+/-0.009% for sulfur dioxide in a carrier stream of nitrogen gas. Selectivity measurements indicate no interference from several common gases (HCl, NH(3), NO, and CO(2)). Oxygen alters the sensor response when comparing signals for sulfur dioxide in 0, 20 and 100% oxygen environments.     

Development and validation of a stability-indicating HPLC method for the determination of degradation products in dipyridamole injection

Summary The development and subsequent validation of an isocratic high-performance liquid chromatographic (HPLC) procedure employing ultraviolet (UV) detection for the determination of degradation products in Dipyridamole Injection is reported. The development of this assay involved the evaluation of several factors including buffer type, ionic strength, pH, organic composition, and column type. The described method is simple, reproducible, accurate, and selective. The precision, relative standard deviation (RSD), amongst five sample preparations for total degradation products was not more than (NMT) 10.2 %, while the individual degradation products were NMT 12.1%. Intermediate precision, as determined from fifteen sample preparations, generated by two Analysts on different HPLC systems over three days, exhibited an RSD for total and individual degradation products of 8.2 % and NMT 27.5 %, respectively. The mean absolute recovery of dipyridamole using the described method is 102.1±1. 9%, (mean±SD, n=12) over the concentration range of 0.03 % to 5.0 % of its label claim of 5 mg mL⁻¹. The limit of detection and limit of quantitation were 0.1 and 0.3 μg mL⁻¹, respectively. The linearity of the peak response was verified with respect to dipyridamole concentration over a range of 0.3 and 50 μg mL⁻¹ (0.03 % to 5.0 % label claim). The Standard and Assay Preparations are stable for up to 48 hours at room temperature. The selectivity was evaluated by subjecting the finished product (Dipyridamole Injection) to thermal, acidic, basic, oxidative and fluorescent radiation stress conditions. No interference in the analysis of degradation products was observed, showing the method is stability-indicating.