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.     

Adamantyl ferrocene derivatives: Antioxidant abilities and effects on model lipid membranes

A series of homoannularly and heteroannularly substituted adamantyl ferrocene derivatives has been synthesized and their effects on membrane fluidity were investigated using liposomes as the membrane models. The liposome formulations of adamantyl ferrocene derivatives were characterized by using dynamic light scattering, differential scanning calorimetry and fluorescence anisotropy measurements. It was demonstrated that adamantyl ferrocene derivatives incorporated into the liposome significantly affect the structure of the lipid bilayer. The results of the study have revealed that adamantyl ferrocene derivatives, compounds 9 – 12, partition into the hydrophobic/hydrophilic interface of the membrane, causing a significant decrease in membrane fluidity. The antioxidant potential of synthesized compounds was assessed with DPPH method and it was shown that the examined compounds possess certain antioxidant activity.     

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,...     

1′-Acetylferrocene amino acid esters and amides. A simple model for parallel β-helical peptides

In this study we present a synthesis and conformational analysis of 1′-acetylferrocene amino acid derivatives of type Ac–Fn–CO–AA–Y (Fn=ferrocene-1,1-diyl; AA=Gly, Ala or Val; Y=OMe or NHMe) as a simple model for parallel β-helical peptides. Derivatives with only one amino acid adopt a reduced number of total conformations and allow a more exact analysis of intramolecular hydrogen bonds (IHB) close to the ferrocene unit. Conformational analysis of these bioconjugates was performed by a combination of spectroscopic techniques (IR, NMR and CD) and corroborated by solution-phase DFT calculations. The investigation of ester conjugates 1–3 indicates the coexistence of non-bonded (an open forms) and hydrogen bonded NH_a group forming a 7-membered ring (γ-turn). The amide derivatives 4–6 with an additional NH_b hydrogen bond donor are mostly constituted of conformers with a 10-membered ring (β-turn) as a single IHB pattern or the β-turn accompanied by a 7-membered ring (γ-turn) containing NH_a group. The exchange of the amino acid side-chain does not significantly affect the conformational properties and IHB pattern of the studied conjugates 1–6.     

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...     

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.