Dynamic Light Scattering and NMR Studies of Napin

We analyze the structure of napin (BngNAP1), a storage protein (m.w. 14.5 kDa) from Brassica napus. On the basis of the results of ¹H NMR spectroscopy and dynamic light scattering (DLS) studies, the overall shape and secondary structure of the molecule are estimated.     

On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adeninecdots, three dots, centeredthymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller-Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G(*)) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges-density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.     

Does Nitrogen Fertilization Affect the Secondary Structures of Gliadin Proteins in Hypoallergenic Wheat?

One of the macronutrients indispensable for plant growth and development is nitrogen (N). It is responsible for starch and storage protein (gliadins and glutenins) biosynthesis and, in consequence, influences kernels’ quality and yields. However, applying N-fertilizers increases gluten content in wheat, and it may intensify the risk of developing allergy symptoms in gluten-sensitive individuals. The purpose of our research was to analyse whether and how the elimination of N-fertilizers during the cultivation of wasko.gl− wheat (modified genotype lacking ω-gliadins) changes the secondary structures of gliadin proteins. To this aim, using the FT-Raman technique, we examined flour and gliadin protein extracts obtained from kernels of two winter wheat lines: wasko.gl+ (with a full set of gliadin proteins) and wasko.gl− (without ω-gliadin fraction) cultivated on two different N-fertilization levels—0 and 120 kg N·ha⁻¹. On the basis of the obtained results, we proved that nitrogen fertilization does not have a major impact on the stability of the secondary structures of gliadin proteins for wasko.gl− wheat line with reduced allergenic properties. Furthermore, the results presented herein suggest the possibility of increasing the stability of glutenin structures as a result of the N-fertilization of wasko.gl− wheat line, which gives hope for its use in the production of wheat articles devoted to people suffering from diseases related to gluten sensitivity.     

Antibody–Ferrocene Conjugates as a Platform for Electro-Chemical Detection of Low-Density Lipoprotein

Low-density lipoprotein (LDL) is a cardiac biomarker identified in the pathology of cardiovascular disease (CVD). Typically, the level of LDL is calculated using the Friedewald relationship based on measured values of total cholesterol, high-density lipoproteins (HDL), and triglycerides. Unfortunately, this approach leads to some errors in calculation. Therefore, direct methods that can be used for fast and accurate detection of LDL are needed. The purpose of this study was to develop an electrochemical platform for the detection of LDL based on an antibody–ferrocene conjugate. An anti-apolipoprotein B-100 antibody labeled with ferrocene was covalently immobilized on the layer of 4-aminothiophenol (4-ATP) on the surface of gold electrodes. Upon interaction between LDL and the antibody–ferrocene conjugate, a decrease in the ferrocene redox signal registered by square wave voltammetry was observed, which depends linearly on the concentration from 0.01 ng/mL to 1.0 ng/mL. The obtained limit of detection was equal to 0.53 ng/mL. Moreover, the satisfied selectivity toward human serum albumin (HSA), HDL, and malondialdehyde-modified low-density lipoprotein (MDA-LDL) was observed. In addition, the acceptable recovery rates of LDL in human serum samples indicate the possible application of immunosensors presented in clinical diagnostics.     

Cornelian Cherry (Cornus mas L.) Extracts Exert Cytotoxicity in Two Selected Melanoma Cell Lines—A Factorial Analysis of Time-Dependent Alterations in Values Obtained with SRB and MTT Assays

Despite the fact that phytochemicals of Cornaceae species have long been discussed as possible auxiliary agents in contemporary treatment, the insights on their properties remain relatively scarce. This study focuses on Cornus mas L. (Cornelian cherry), the extracts of which are reported to exert a pleiotropic effect shown in both in vivo and in vitro studies. This study aimed to explore the cytotoxic effect of extracts from fruits of red (Cornus mas L. ‘Podolski’) and yellow (Cornus mas L. ‘Yantarnyi’ and ‘Flava’) Cornelian cherries on two melanoma cell lines (A375 and MeWo). The extracts were characterized in the context of the concentration of bioactive compounds of antioxidative properties. Cytotoxicity was investigated with the use of the following two assays: SRB and MTT. An additional, alternative protocol for the SRB assay was used in this study so as to account for possible bias. Cytotoxicity was assessed as a difference in the whole time series of cell viability, instead of analyzing differences in raw values (often found in the literature). Both extracts from Cornus mas L. induced cytotoxicity in both A375 and MeWo cell lines, although the response of these cells was different. Moreover, based on this study, there is no evidence for claiming a different magnitude of cytotoxicity between these two extracts.     

Effectiveness of the Oxygenation over Classical Protonolysis Reactions: A Case of Alkylzinc Complexes Incorporating an Aminoalcoholate Ligand

Alkylzinc aminoalcoholates have emerged as powerful catalysts in organic synthesis and polymerization processes. Despite extensive research, difficulties in the rational design of these catalytic systems and in-depth understanding of their modes of action have hitherto been encountered. Most of the major obstacles stem largely from the relatively limited knowledge of the structure-activity relationship of zinc catalysts. In fact, the key active species are often generated in situ via the protonolysis of the alkylzinc precursors, which precludes their isolation and detailed characterization. Herein, the effectiveness of the oxygenation over the classical protonolysis in the synthesis of zinc alkylperoxides stabilized by an aminoalcoholate ligand is demonstrated. The controlled oxygenation of a tert-butylzinc complex incorporating a pridinolum (prinol) ligand leads to well-defined a dinuclear adduct of a (prinol)ZnOOtBu moiety with the parent tBuZn(prinol) complex and a novel dimer [tBuOOZn(prinol)]₂ with terminal alkylperoxide groups. The observed reaction outcomes strongly depend on the reaction conditions. Although sparse examples of heteroleptic adducts of the [RZn(L)]_x[ROOZn(L)]_y-type are known, the herein reported homoleptic [ROOZn(L)]_x aggregate is unprecedented. Strikingly, comparative studies involving reactions between tBuZn(prinol) and tert-butylhydroperoxide or ethanol revealed that the respective seemingly simple zinc alkylperoxides, or zinc alkoxides, respectively, are not accessible via the classical alcoholysis. We believe that these game-changing results concerning multifaceted chemistry of organozinc aminoalcoholates should pave the way for more rational development of various Zn-based catalytic systems.     

Unravelling Structural Mysteries of Simple Organozinc Alkoxides

Simple RZnOR’ alkoxides are among the first known organozinc compounds, and widespread interest in their multifaced chemistry has been driven by their fundamental significance and potential applications including various catalytic reactions. Nevertheless, their chemistry in solution and in the solid state remains both relatively poorly understood and a subject of constant debate. Herein, the synthesis and structural characterization of long-sought structural forms, a roof-like trimer [(tBuZn)₃(μ-OC(H)Ph₂)₂(μ₃-OC(H)Ph₂)] and a ladder-type tetramer [(PhZn)₄(μ-OC(H)Ph₂)₂(μ₃-OC(H)Ph₂)₂], incorporating diphenylmethanolate as a model alkoxide ligand, are reported. Both novel aggregates are robust in the solid state and resistant towards mechanical force. By using ¹H NMR and diffusion-order spectroscopy, it is demonstrated that new RZnOR’ alkoxides are kinetically labile in solution and readily undergo ligand scrambling, such as in the case of Schlenk equilibrium. The elucidated key structural issues, which have remained undiscovered for decades, significantly advance the chemistry of RZnOR’ alkoxides and should support the rational design of zinc alkoxide-based applications.     

Interaction with glycine increases stability of a mutagenic tautomer of uracil. A density functional theory study

The most stable structures for the gas-phase complexes of minor tautomers of uracil (U) with glycine (G) were characterized at the density functional B3LYP/6-31++G level of theory. These are cyclic structures stabilized by two hydrogen bonds. The relative stability of isolated tautomers of uracil was rationalized by using thermodynamic and structural arguments. The stabilization energies for complexes between the tautomers of U and G result from interplay between the stabilizing two-body interaction energies and destabilizing one-body terms. The latter are related to the energies of (i) tautomerization of the unperturbed moieties and (ii) distortions of the resulting rare tautomers in the complex. The two-body term describes the interaction energy between distorted tautomers. The two-body interaction energy term correlates with perturbations of length of the proton-donor bonds as well as with deprotonation enthalpies and proton affinities of the appropriate monomer sites. It was demonstrated that the relative instability of rare tautomers of uracil is diminished due to their interactions with glycine. In particular, the instability of the third most stable tautomer (U(III)) is decreased from 11.9 kcal/mol for non-interacting uracil to 6.7 kcal/mol for uracil in a complex with the zwitterionic tautomer of glycine. A decrease of instability by 5.2 kcal/mol could result in an increase of concentration of U(III) by almost 5 orders of magnitude. This is the tautomer with proton donor and acceptor sites matching guanine rather than adenine. Moreover, kinetic characteristics obtained for the glycine-assisted conversion of the most stable tautomer of uracil (U(I)) to U(III) indicate that the U(I)<-->U(III) thermodynamic equilibrium could be easily attained at room temperature. The resulting concentration of this tautomer falls in a mutationally significant range.     

Crystal structure of m-nitrobenzoic anhydride

The title compound (C₁₄H₈N₂O₇,M _r =306.2) crystallizes in the orthorhombic space group Pbca witha=6.962(1).b=24.688(1), andc=15.890(1)Å,V=2731.0 ų,D _x =1.489 g·cm^–3 forZ=8,=0.98 mm^–1,F(000)=1296,T=293 K. FinalR=0.053 for 1873 observed reflections. The structure was solved by direct methods. Approximately planar molecules lie perpendicular to the [100] direction and show partial stacking. The structure is the first example of a symmetric anhydride which does not retain the symmetry in the crystal state. The two independent nitro groups twist out of the ring planes by 10.5 and 14.8°, respectively.