Effect of CyDye minimum labeling in differential gel electrophoresis on the reliability of protein identification

Differential 2-DE (DIGE) is a widely applied tool for the quantitative analysis of differentially represented proteins. The method involves covalent minimal labeling of proteins prior to their electrophoretic separation using CyDye DIGE Fluor minimal dyes. This methodology creates two different species per protein, the labeled (approx. 1-2%) and unlabeled (approx. 98-99%) ones, which differ in their molecular masses by 434-464 Da, depending on the attached dye. DIGE followed by automated spot picking according to the CyDye coordinates misses in many instances the exact positions where the maximum amounts of the considered proteins are located. This fact leads to a loss in sensitivity of the subsequent MALDI-MS analyses and results in a reduced reliability of protein identification and sequence coverage. In this paper, the migration differences of labeled and unlabeled species are quantified together with the impact of this effect on the certainty of protein identification and sequence coverage investigating proteins up to 90 kDa.     

Synthesis of novel 5H‐Pyrimido[5,4‐b]mdole‐(1H,3H)2,4‐diones as potential ligands for the cloned α1‐adrenoceptor subtypes

A new series of 3‐[ω‐[4‐(4‐substituted phenyl)piperazin‐1‐yl]alkyl]‐5H‐pyrimido[5,4‐b]indole‐(1H,3H)‐2,4‐diones ( 3–10 and 12–13 ) were synthesized from the N‐(2‐chloroethyl)‐N'‐[3‐(2‐ethoxycarbonyl)indolyl] urea ( 1 ) or the N‐(3‐chloropropyl)‐N'‐[3‐(2‐ethoxycarbonyl)indolyl] urea ( 2 ) and a number of 1‐(4‐substi‐tuted‐phenyl)piperazines. 3‐[2‐[4‐(4‐Aminophenyl)piperazin‐1‐yl]ethyl]‐5H‐pyrimido[5,4‐b]indole‐(1H,3H)2,4‐dione ( 14 ) was obtained by reduction of the parent nitro compound 8 . The obtained 5H‐pyrimido[5,4‐b]indole‐(1H,3H)2,4‐dione derivatives were tested towards cloned α_1A, α_1B and α_1D adrenergic receptors subtypes in binding assays. Some compounds showed good affinity and selectivity for the α_1D‐adrenoceptor subtype.     

Performance studies of a full-length prototype for the CASTOR forward calorimeter at the CMS experiment

The Time-Of-Flight detector (TOF) of the ALICE experiment at the CERN LHC is based on Multi-gap Resistive Plate Chambers (MRPCs). The TOF detector consists of 152928 readout channels covering a total area of 141 m². In this paper the results of the calibration with cosmic-ray data collected during 2009 are presented.     

Carboxylate-bridged copper(II)-lanthanide(III) complexes [(Cu(3)Ln(2)(oda)(6)(H(2)O)(6)).12H(2)O](n)(Ln = Dy,Ho, Er,Y; oda = oxydiacetate)

The hydrothermal reaction of Ln(2)O(3) (Ln = Dy and Ho), Cu(OAc)(2).2H(2)O, and oxydiacetic acid in the approximate mole ratio of 1:3:8 resulted in the formation of two new members of the isostructural series of polymers formulated as [(Cu(3)Ln(2)(oda)(6)(H(2)O)(6)).12H(2)O](n), crystallizing in the hexagonal crystal system, space group P6/mcc (No. 192). Temperature-dependent magnetic susceptibilities and EPR spectra are reported for the heterometallic compounds Cu-Dy 1, Cu-Ho 2, Cu-Er 3, and Cu-Y 4. The results are discussed in terms of the structure of the compounds, the electronic properties of the lanthanide ions, and the exchange interactions between the magnetic ions.     

Characterization of antithrombin III from human plasma by two-dimensional gel electrophoresis and capillary electrophoretic methods

The isoforms distribution of the glycoprotein antithrombin III (ATIII) derived from human plasma was investigated by means of isoelectric focusing (IEF) in polyacrylamide gels with immobilized pH gradients (IPG) and two-dimensional gel electrophoresis (2-DE) as well as capillary electrophoretic methods. It turned out that the presence of high concentrations of chaotropics (urea, thiourea) and zwitterionic detergents (3-[(3-cholamidepropyl)dimethylammonio]-1-propanesulfonate (CHAPS)) was decisive for attaining good resolution of the protein isoforms. Resolution by IPG-IEF was obtained with excellent reproducibility and pI differences down to 0.01 pH units could be distinguished. ATIII-alpha and ATIII-beta-fractions preseparated by heparin affinity chromatography showed an analogous but shifted spot pattern consisting each of one major and three minor isoforms. The main isoforms of ATIII-alpha and ATIII-beta exhibit pI values of 5.18 and 5.32, respectively, both values determined in the presence of high concentrations of urea. The pI difference of 0.14 pH units correspond to the effect of two sialic acids absent in ATIII-beta. The formation and occurrence of ATIII dimers and trimers turned out to be dependent on the sample preparation. The results obtained by 2-DE were compared with those of capillary zone electrophoresis (CZE) and capillary IEF (CIEF). Quantitative analysis regarding the CZE separated isoforms of plasma derived ATIII yielded a content of about 70% ATIII-alpha main isoform and about 6.6% of ATIII-beta. The pI values of ATIII determined by CIEF with internal calibration were in fair agreement with the pI values of the main isoforms achieved with 2-DE.     

An Improved Synthesis of 2′-Hydroxy-3′,4′,6′-trimethoxyacylophenones

A wide variety of 2′-hydroxypolymethoxyacetophenones and propiophenones, e.g. 1a and 1b are used in the synthesis of flavone and ehromone natural products.¹ Repeated attempts to prepare 1a and 1b by reacting 1,2,3,5-tetramethoxybenzene 2 with acetyl or propionyl chlorides and AlCl₃ in ether² gave products which were difficult to purify.³ We traced the problem to ring-ethoxy contaminants which were isolated and tentatively identified as 3a and 3b.     

Conformational and photophysical studies on porphyrin-containing donor-bridge-acceptor compounds. Charge separation in micellar nanoreactors

Photophysical studies with semi-rigid, 1, and flexible, 2, donor-bridge-acceptor (D-b-A2+) molecules with D a porphyrin and A2+ a methyl viologen moiety, were performed in neat polar solvents as well as included in surfactant (DTAB) aqueous and in reverse AOT/n-alkane micelles. The micelles acted as nanoreactors for the photoinduced electron transfer reaction upon laser excitation. In spite of the longer lifetime of the charge separated (CS) state in the semi-rigid tetrad 1(ca. 200 ns vs. ca. 100 ns for the flexible dyad 2), the CS formation quantum yield, for example in acetonitrile, was lower for the former (phi(CS) = 0.13) than for the latter (0.58). Comparison of the time-resolved fluorescence data in neat solvent and in the micelles yielded the phi(CS) values in the dilute micellar solutions. Application of laser-induced optoacoustic spectroscopy at various temperatures to 1 dissolved in a polar organic solvent (benzonitrile, BZN) included in aqueous DTAB nanoreactors afforded structural volume changes for the production in hundreds of ps of the CS state upon excitation of a polar molecule. The contraction during CS formation upon excitation of the collapsed conformer in BZN is attributed to the entering of solvent into the open molecular cavity. The opening upon formation of the CS state due to photoinduced electron transfer in the 1 collapsed conformation arises from the repulsion of the two positively charged ends in this state, as previously calculated. Inclusion of 1 in reverse AOT micelles in various n-alkanes also led to a contraction upon excitation, but the data had much more error due to the limited range of variability of the ratio of thermoelastic parameters. The data obtained with the more flexible "supermolecule" 2 showed the predicted large conformation flexibility of these molecules.     

Single crystal EPR study of the dinuclear Cu(II) complex [Cu(tda)(phen)](2)·H(2)tda (tda = thiodiacetate, phen = phenanthroline): influence of weak interdimeric magnetic interactions

We report powder and single crystal EPR measurements of [Cu(tda)(phen)](2)·H(2)tda (tda = thiodiacetate, phen = phenanthroline) at 9.7 GHz. This compound consists of centrosymmetric copper(II) ion dimers, weakly ferromagnetically exchange-coupled (J = +3.2 cm(-1)), in which the dimeric units are linked by hydrophobic chemical paths involving the phen molecules. EPR revealed that the triplet spectra are collapsed by interdimeric exchange interactions mediated by that chemical path. Analysis and simulation of the single crystal EPR spectra were performed using Anderson's exchange narrowing model, together with statistical arguments. This approach allowed us to interpret the spectra modulated by the interdimeric interactions in situations of weak, intermediate, and strong exchange. We evaluated an interdimeric exchange constant J' = 0.0070(3) cm(-1), indicating that hydrophobic paths can transmit weak exchange interactions between centers at relatively long distances of the order of ～10 ?.     

A Unique Tryptophan C‐Prenyltransferase from the Kawaguchipeptin Biosynthetic Pathway

Cyanobactins are a rapidly growing family of linear and cyclic peptides produced by cyanobacteria. Kawaguchipeptins A and B, two macrocyclic undecapeptides reported earlier from Microcystis aeruginosa NIES‐88, are shown to be products of the cyanobactin biosynthetic pathway. The 9 kb kawaguchipeptin (kgp) gene cluster was identified in a 5.26 Mb draft genome of Microcystis aeruginosa NIES‐88. We verified that this gene cluster is responsible for the production of the kawaguchipeptins through heterologous expression of the kgp gene cluster in Escherichia coli. The KgpF prenyltransferase was overexpressed and was shown to prenylate C‐3 of Trp residues in both linear and cyclic peptides in vitro. Our findings serve to further enhance the structural diversity of cyanobactins to include tryptophan‐prenylated cyclic peptides.     

Full-fledged proteomic analysis of bioactive wheat amylase inhibitors by a 3-D analytical technique: Identification of new heterodimeric aggregation states

Wheat proteinaceous alpha-amylase inhibitors (alpha-AIs) are increasingly investigated for their agronomical role as natural defence molecules of plants against the attack of insects and pests, but also for their effects on human health. The wheat genomes code for several bioactive alpha-AIs that share sequence homology, but differ in their specificity against alpha-amylases from different species and for their aggregation states. Wheat alpha-AIs are traditionally classified as belonging to the three classes of tetrameric, homodimeric and monomeric forms, each class being constituted by a number of polypeptides that display different electrophoretic mobilities. Here we describe a proteomic approach for the identification of bioactive alpha-AIs from wheat and, in particular, a 3-D technique that allows to best identify and characterize the dimeric fraction. The technique takes advantage of the thermal resistance of alpha-AIs (resistant to T > 70 degrees C) and consists in the separation of protein mixtures by 2-D polyacrylamide/starch electrophoresis under nondissociating PAGE (ND-PAGE, first dimension) and dissociating (urea-PAGE or U-PAGE second dimension) conditions, followed by in-gel spontaneous reaggregation of protein complexes and identification of the alpha-amylase inhibitory activity (antizymogram, third dimension) using enzymes from human salivary glands and from the larvae of Tenebrio molitor coleopter (yellow mealworm). Dimeric alpha-AIs from Triticum aestivum (bread wheat) were observed to exist as heterodimers. The formation of heterodimeric complexes was also confirmed by in vitro reaggregation assays carried out on RP-HPLC purified wheat dimeric alpha-AIs, and their bioactivity assayed by antizymogram analysis. The present 3-D analytical technique can be exploited for fast, full-fledged identification and characterization of wheat alpha-AIs.