Bio-orthogonal affinity purification of direct kinase substrates

Protein phosphorylation is a major mechanism of post-translational protein modification used to control cellular signaling. A challenge in phosphoproteomics is to identify the direct substrates of each protein kinase. Herein, we describe a chemical strategy for delivery of a bio-orthogonal affinity tag to the substrates of an individual protein kinase. The kinase of interest is engineered to transfer a phosphorothioate moiety to phosphoacceptor hydroxyl groups on direct substrates. In a second nonenzymatic step, the introduced phosphorothioate is alkylated with p-nitrobenzylmesylate (PNBM). Antibodies directed against the alkylated phosphorothioate epitope recognize these labeled substrates, but not alkylation products of other cellular nucleophiles. This strategy is demonstrated with Cdk1/cyclinB substrates using ELISA, western blotting, and immunoprecipitation in the context of whole cell lysates.     

Delphinidin–Aluminum(III) Complexes in Aqueous and Non-Aqueous Media: Spectroscopic Characterization and Theoretical Study

Summary. The study of delphinidin complexation with trivalent aluminum in acidic aqueous buffered (pH 3.0 and 3.8) and methanolic solutions was performed utilizing electronic absorption spectroscopy and quantum chemical calculations. In its structure delphinidin possesses several chelating sites in competition towards aluminum(III). Molar ratio plots denoted the formation of only one aluminum(III):delphinidin complex of stoichiometry of 1:1 in both investigated media. Semiempirical calculations, performed at the restricted HF AM1 level, enabled the determination of the structural features of free delphinidin and structural modifications caused by chelation of aluminum(III). Considering the pigment molecular structure and the results of the theoretical calculations it is possible to equally implicate C3′–C4′ and C4′–C5′ hydroxyl groups as those with the predominant chelating power.     

The effects of eluent mixing on TLS detection in gradient elution HPLC

The effects of changing solvent composition on the LOD of TLS detection in gradient elution HPLC have been studied from the perspective of thermo-optical properties of the solvent. Hyphenated gradient high-performance liquid chromatography (HPLC)-thermal lens spectrometry (TLS), was used to separate and detect 13 carotenoid compounds and two chlorophylls. Utilization of mixing coils into the system reduces the inhomogeneities during eluent changes and therefore enables the application of thermal lens detection in the gradient HPLC method. For gradient chromatographic conditions in which the thermo-optical properties and related enhancement factor change as much as 50% over 10 min, the LODs for the TLS detector were enhanced by as much as three times in comparison with UV-Vis detection. For the isocratic part of the chromatogram, up to a tenfold improvement of LODs was achieved with TLS detection.     

Modeling anhydrous and aqua copper(II) amino acid complexes: a new molecular mechanics force field parametrization based on quantum chemical studies and experimental crystal data

This paper presents the vacuum structures of aquacopper(II) bis(amino acid) complexes with glycine, sarcosine, N,N-dimethylglycine, and N-tert-butyl-N-methylglycine estimated using the B3LYP method. The differences between the B3LYP vacuum structures and experimental crystal structures suggested considerable influence of crystal lattice packing effects on the changes in the complexes' geometries. A previously developed molecular mechanics force field for modeling anhydrous copper(II) amino acidates was reoptimized to simulate these changes and predict the properties of both trans and cis anhydrous and aqua copper(II) amino acid complexes. The modeling included experimental molecular and crystal structures of 13 anhydrous and 10 aqua copper(II) amino acidates with the same atom types (Cu(II), C, H, N, and O) but various copper(II) coordination polyhedron geometries, crystal symmetries, and intermolecular interactions. The empirical parameters of the selected potential energy functions were optimized on the B3LYP vacuum copper(II) coordination geometries of three anhydrous copper(II) amino acidates and on experimental crystalline internal coordinates and unit cell dimensions of six anhydrous and six aqua copper(II) amino acid complexes. The respective equilibrium structures were calculated in vacuo and in simulated crystalline environment. The efficacy of the final force field, FFW, was examined. The total root-mean-square deviations between the experimental and theoretical crystal values were 0.018 A in the bond lengths, 2.2 degrees in the valence angles, 5.5 degrees in the torsion angles, and 0.395 A in the unit cell lengths. FFW reproduced the unit cell volumes in the range from -8.1 to 9.6%. The means of Cu to axial water oxygen distances were 2.4 +/- 0.1 A (experiment) and 2.6 +/- 0.1 A (FFW). This paper describes the ability of the molecular mechanics model and FFW force field to simulate the flexibility of the metal coordination polyhedron. The new force field proved effective in predicting the most stable molecular conformation of copper(II) amino acidato systems in vacuo.     

Pomegranate peel waste biomass modified with H3PO4 as a promising sorbent for uranium(VI) removal

Journal of Radioanalytical and Nuclear Chemistry - Modified pomegranate peel was utilized as a sorbent for the biosorption of uranium(VI) from the aqueous solution. The biosorbent was characterized...     

Characterization analysis of raw and pyrolyzed plane tree seed (Platanus orientalis L.) samples for its application in carbon capture and storage (CCS) technology

Journal of Thermal Analysis and Calorimetry - Raw and pyrolyzed samples of the plane tree seeds (PTS) were tested by various advanced analytical techniques including simultaneous TG-DSC technique,...     

Photoinduced charge separation reactions of J-aggregates coated on silver nanoparticles

The photochemistry of cyanine J-aggregates on the surface of colloidal Ag nanoparticles is reported. The photochemistry is initiated through ultrafast photoexcitation of the plasmon band in Ag nanoparticles, producing an enhanced near-field that interacts with the J-aggregate monolayer. Through transient absorption spectroscopy, we show that photoexcitation of the plasmon in Ag nanoparticles leads to exciton dynamics that differ strongly from J-aggregates alone or for J-aggregate monolayers on bulk metal surfaces. Specifically, charge-separated states with a lifetime of approximately 300 ps between the J-aggregate and Ag colloid are formed. The reduction of the Ag nanoparticles is shown to be a multielectron process.     

Tritium in organic matter around Krško Nuclear Power Plant

The aim of the research was to obtain first results of tritium in the organic matter of environmental samples in the vicinity of Kr?ko NPP. The emphasis was on the layout of suitable sampling network of crops and fruits in nearby agricultural area. Method for determination of tritium in organic matter in the form of Tissue Free Water Tritium (TFWT) and Organically Bound Tritium (OBT) has been implemented. Capabilities of the methods were tested on real environmental samples and its findings were compared to modeled activities of tritium from atmospheric releases and literature based results of TFWT and OBT.     

Antibacterial effects of the essential oils of commonly consumed medicinal herbs using an in vitro model

The chemical composition and antibacterial activity of essential oils from 10 commonly consumed herbs: Citrus aurantium, C. limon, Lavandula angustifolia, Matricaria chamomilla, Mentha piperita, M. spicata, Ocimum basilicum, Origanum vulgare, Thymus vulgaris and Salvia officinalis have been determined. The antibacterial activity of these oils and their main components; i.e. camphor, carvacrol, 1,8-cineole, linalool, linalyl acetate, limonene, menthol, a-pinene, b-pinene, and thymol were assayed against the human pathogenic bacteria Bacillus subtilis, Enterobacter cloacae, Escherichia coli O157:H7, Micrococcus flavus, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella enteritidis, S. epidermidis, S. typhimurium, and Staphylococcus aureus. The highest and broadest activity was shown by O. vulgare oil. Carvacrol had the highest antibacterial activity among the tested components.     

Mechanistic pathways for the reaction of quercetin with hydroperoxy radical

The extensive theoretical study of the interaction of one of the most abundant and reactive flavonols, quercetin, with hydroperoxy radical (HOO·), using the M052X/6-31 + Gd, p level of theory, was performed. Results indicating that quercetin is not a planar molecule are in accord with the X-ray analysis. The applied method successfully reproduces the bond dissociation enthalpy, and reveals that the reaction of quercetin with the hydroperoxy radical is governed by a hydrogen atom transfer mechanism. It is confirmed that the 3′OH and 4′OH are the most reactive sites, and that the reaction in the 3′OH position is faster than that in the 4′OH position.