Geochemical investigation of alluvial sediments: validation of ICP-OES determination of heavy metals. A case study from the Utrata River Valley (central Poland)

The development and validation of a reliable analytical procedure for the determination of selected metals (Cd, Cr, Cu, Pb, Zn and Mn) in sediments accumulated in the Utrata River (Poland) is described. The aqua regia extraction followed by inductively coupled plasma optical emission spectrometry (ICP-OES) was used for this purpose. The optimized analytical procedure was validated, and adequate quality control actions were implemented in order to provide reliable data. The precision under’ within-laboratory’ reproducibility conditions was estimated from duplicate analysis. Certified reference material (CRM) was used in order to evaluate the accuracy of the results regarding the sewage sludge amended soil CRM 143R. The detection limits for all elements of interest were well-below their content in the investigated sediment samples. The obtained reliable data could be used for assessment of the relationship between human economic activity in the past and the geochemical features of the sediments.     

Determination of antioxidant activity using oxidative damage to plasmid DNA — pursuit of solvent optimization

Oxidative stress plays a key role in the pathophysiology of many diseases. Hydroxyl radical is the oxidative species most commonly causing damage to cells. The aim of this work was to optimize the method for antioxidant activity determination on a model lipophilic geranylated flavanone, diplacone. This method uses protection of plasmid DNA from oxidation by a hydroxyl radical generated by the Fenton reaction involving oxidation of metal ions using H₂O₂ and ascorbate. The method was optimized for lipophilic compounds using several solvents and co-solvents. It was found that (2-hydroxypropyl)-β-cyclodextrin (0.1 mass % aq. sol.) is the best co-solvent for our model lipophilic compound to measure the antioxidant activity by the method presented. Other solvents, namely dimethyl sulfoxide, Cremophor EL® (0.1 mass % aq. sol.), ethanol, and methanol, were not suitable for the determination of the antioxidant activity by the method described. Tween 80 (0.1 mass % aq. sol.) and a mixture of 10 vol. % ethanol and 9 mass % bovine serum albumin (aq. sol.) significantly decreased the antioxidant activity of the model lipophilic compound and thus were not suitable for this method.     

On homology modeling of the M2 muscarinic acetylcholine receptor subtype

Twelve homology models of the human M₂ muscarinic receptor using different sets of templates have been designed using the Prime program or the modeller program and compared to crystallographic structure (PDB:3UON). The best models were obtained using single template of the closest published structure, the M₃ muscarinic receptor (PDB:4DAJ). Adding more (structurally distant) templates led to worse models. Data document a key role of the template in homology modeling. The models differ substantially. The quality checks built into the programs do not correlate with the RMSDs to the crystallographic structure and cannot be used to select the best model. Re-docking of the antagonists present in crystallographic structure and relative binding energy estimation by calculating MM/GBSA in Prime and the binding energy function in YASARA suggested it could be possible to evaluate the quality of the orthosteric binding site based on the prediction of relative binding energies. Although estimation of relative binding energies distinguishes between relatively good and bad models it does not indicate the best one. On the other hand, visual inspection of the models for known features and knowledge-based analysis of the intramolecular interactions allows an experimenter to select overall best models manually.     

Unlocking the Hydrolytic Mechanism of GH92 α-1,2-Mannosidases: Computation Inspires the use of C-Glycosides as Michaelis Complex Mimics

The conformational changes in a sugar moiety along the hydrolytic pathway are key to understand the mechanism of glycoside hydrolases (GHs) and to design new inhibitors. The two predominant itineraries for mannosidases go via ^OS₂→B_2,5→¹S₅ and ³S₁→³H₄→¹C₄. For the CAZy family 92, the conformational itinerary was unknown. Published complexes of Bacteroides thetaiotaomicron GH92 catalyst with a S-glycoside and mannoimidazole indicate a ⁴C₁→⁴H₅/¹S₅→¹S₅ mechanism. However, as observed with the GH125 family, S-glycosides may not act always as good mimics of GH's natural substrate. Here we present a cooperative study between computations and experiments where our results predict the E₅→B_2,5/¹S₅→¹S₅ pathway for GH92 enzymes. Furthermore, we demonstrate the Michaelis complex mimicry of a new kind of C-disaccharides, whose biochemical applicability was still a chimera.     

Carbazole-Based Colorimetric Anion Sensors

Owing to their strong carbazole chromophore and fluorophore, as well as to their powerful and convergent hydrogen bond donors, 1,8-diaminocarbazoles are amongst the most attractive and synthetically versatile building blocks for the construction of anion receptors, sensors, and transporters. Aiming to develop carbazole-based colorimetric anion sensors, herein we describe the synthesis of 1,8-diaminocarbazoles substituted with strongly electron-withdrawing substituents, i.e., 3,6-dicyano and 3,6-dinitro. Both of these precursors were subsequently converted into model diamide receptors. Anion binding studies revealed that the new receptors exhibited significantly enhanced anion affinities, but also significantly increased acidities. We also found that rear substitution of 1,8-diamidocarbazole with two nitro groups shifted its absorption spectrum into the visible region and converted the receptor into a colorimetric anion sensor. The new sensor displayed vivid color and fluorescence changes upon addition of basic anions in wet dimethyl sulfoxide, but it was poorly selective; because of its enhanced acidity, the dominant receptor-anion interaction for most anions was proton transfer and, accordingly, similar changes in color were observed for all basic anions. The highly acidic and strongly binding receptors developed in this study may be applicable in organocatalysis or in pH-switchable anion transport through lipophilic membranes.     

Allosteric Modulation of the CB1 Cannabinoid Receptor by Cannabidiol—A Molecular Modeling Study of the N-Terminal Domain and the Allosteric-Orthosteric Coupling

The CB₁ cannabinoid receptor (CB₁R) contains one of the longest N termini among class A G protein-coupled receptors. Mutagenesis studies suggest that the allosteric binding site of cannabidiol (CBD) involves residues from the N terminal domain. In order to study the allosteric binding of CBD to CB₁R we modeled the whole N-terminus of this receptor using the replica exchange molecular dynamics with solute tempering (REST2) approach. Then, the obtained structures of CB₁R with the N terminus were used for ligand docking. A natural cannabinoid receptor agonist, Δ⁹-THC, was docked to the orthosteric site and a negative allosteric modulator, CBD, to the allosteric site positioned between extracellular ends of helices TM1 and TM2. The molecular dynamics simulations were then performed for CB₁R with ligands: (i) CBD together with THC, and (ii) THC-only. Analyses of the differences in the residue-residue interaction patterns between those two cases allowed us to elucidate the allosteric network responsible for the modulation of the CB₁R by CBD. In addition, we identified the changes in the orthosteric binding mode of Δ⁹-THC, as well as the changes in its binding energy, caused by the CBD allosteric binding. We have also found that the presence of a complete N-terminal domain is essential for a stable binding of CBD in the allosteric site of CB₁R as well as for the allosteric-orthosteric coupling mechanism.     

Asymptotically optimal neighbour sum distinguishing colourings of graphs

Consider a simple graph G = (V,E) and its proper edge colouring c with the elements of the set {1,2,…,k}. The colouring c is said to be neighbour sum distinguishing if for every pair of vertices u, v adjacent in G, the sum of colours of the edges incident with u is distinct from the corresponding sum for v. The smallest integer k for which such colouring exists is known as the neighbour sum distinguishing index of a graph and denoted by . The definition of this parameter, which makes sense for graphs containing no isolated edges, immediately implies that , where Δ is the maximum degree of G. On the other hand, it was conjectured by Flandrin et al. that for all those graphs, except for C₅. We prove this bound to be asymptotically correct by showing that . The main idea of our argument relays on a random assignment of the colours, where the choice for every edge is biased by so called attractors, randomly assigned to the vertices. © 2014 Wiley Periodicals, Inc. Random Struct. Alg., 47, 776–791, 2015     

Molecular Characterization of DNA Double Strand Breaks with Tip‐Enhanced Raman Scattering

DNA double strand breaks (DSBs) are deadly lesions that can lead to genetic defects and cell apoptosis. Techniques that directly detect DNA DSBs include scanning electron microscopy, atomic force microscopy (AFM), and fluorescence based approaches. While these techniques can be used to identify DSBs they provide no information on the molecular events occurring at the break. Tip‐enhanced Raman scattering (TERS) can provide molecular information from DNA at the nanoscale and in combination with AFM provides a new way to visualize and characterize the molecular structure of DSBs. DSBs result from cleavage at the 3’‐ and 5’‐bonds of deoxyribose upon exposure to UVC radiation based on the observation of P? O? H and methyl/methylene deformation modes enhanced in the TERS spectra. It is hypothesized that strand fragments are hydrogen‐terminated at the lesion, indicating the action of free radicals during photon exposure.     

Analytical protocol for investigation of zinc speciation in plant tissue

A specific procedure is proposed for investigating the chemical speciation of zinc (Zn) in plant tissues, viz., the extraction of Zn compounds from Plantago lanceolata L. followed by the chromatographic separation and inductively coupled plasma mass spectrometry (ICP-MS) identification of these compounds. In order to separate the Zn compounds, both size-exclusion (SEC) and ionexchange liquid chromatography (IC) were used in direct sequential and reverse sequential modes. In the direct sequential mode, the entire extract undergoes SEC separation and then the individual fractions are injected onto the ion-exchange column. The molecular size distribution is evaluated by SEC coupled on-line to the UV detector. In the reverse sequential mode, the entire extract undergoes the ion-exchange chromatographic separation and then the individual fractions are injected onto the size-exclusion column. The identification of Zn incorporated into the compounds is further performed using ICP-MS. This procedure is particularly useful in speciation studies when identification of the individual components of the element is problematic due to the lack of suitable standard substances, as is the case for Zn compounds. The proposed procedure facilitates assignment of the signals to the individual components of the fractions for both types of chromatography, thus rendering the chemical speciation of Zn possible when the lack of suitable standard substances impedes the identification of individual components.