Site-selective labeling strategies for screening by NMR

NMR based screening has become an important tool in the pharmaceutical industry. Methods that provide information on the location of small molecule binding sites on the surface of a drug target (e. g. SAR-by-NMR and related techniques) are of particular interest. In order to extend the applicability of such techniques to drug targets of higher molecular weight, selective labeling strategies may be employed. Dual-amino acid selective labeling and site directed non-native amino acid replacement (SNAAR) allow for the selective detection of NMR resonances of a specific amino acid residue. This results in significantly reduced spectral complexity, which not only enables application to higher molecular weight systems, but also eliminates the need for sequential resonance assignment in order to identify the binding site. Regio-selective (or segmental) labeling of an entire protein domain of a multi domain protein may also be achieved. Labeling only a selected part of a multi domain protein (e. g. a catalytic or ligand binding domain) is an attractive way to simplify the spectral interpretation without disturbing the system under study.     

Solvent-free Mukaiyama aldol reaction of O-silyl dienolates catalyzed by benzoic acid

The vinylogous aldol reaction of O-silyl dienolates deriving from 2,2-dimethyl-[1,3]-dioxin-4-ones proceeds in moderate to excellent yields in the presence of catalytic amounts of PhCOOH under solvent-free conditions. Modest to good yields can be obtained by using silica gel or 3 Å molecular sieves as heterogeneous catalysts.     

Quantitative validation of different protein precipitation methods in proteome analysis of blood platelets

For the preparation of proteins for proteome analysis, precipitation is frequently used to concentrate proteins and to remove interfering compounds. Various methods for protein precipitation are applied, which rely on different chemical principles. This study compares the changes in the protein composition of human blood platelet extracts after precipitation with ethanol (EtOH) or trichloroacetic acid (TCA). Both methods yielded the same amount of proteins from the platelet preparations. However, the EtOH-precipitated samples had to be dialyzed because of the considerable salt content. To characterize single platelet proteins, samples were analyzed by two-dimensional fluorescence differential gel electrophoresis. More than 90% of all the spots were equally present in the EtOH- and TCA-precipitated samples. However, both precipitation methods showed a smaller correlation with nonprecipitated samples (EtOH 74.9%, TCA 79.2%). Several proteins were either reduced or relatively enriched in the precipitated samples. The proteins varied randomly in molecular weight and isoelectric point. This study shows that protein precipitation leads to specific changes in the protein composition of proteomics samples. This depends more on the specific structure of the protein than on the precipitating agent used in the experiment.     

Photometric titration of total iodine at trace levels in concetrated chloride solutions

The method is based on reduction of total iodine (10^?7?10^?5 M), to iodide with sulphite in acidic solution. The excess of sulphur dioxide is removed by bubbling with nitrogen, and the resulting solution is titrated spectrophotometrically with a standard solution of iodate, the absorbance being measured at 230 nm. Some Italian table salts, iodized or common, were analyzed for their iodide and total iodine content.     

Investigation of catalytic activities by differential thermal analysis

A calorimetric method is proposed to evaluate the catalytic activity of a solid catalyst with respect to the exothermic oxidation of Volatile Organic Compounds (VOC).This method employs a differential thermal analyzer in which an inert reference and a catalytically active sample are both fluxed at a constant rate with a reactive gaseous mixture composed of an inert gas (N₂ 90% vol.), oxygen and VOC, the last typically 900 to 5000 ppm. While the temperature is varied according to a predefined cycle, the output signal due to the exothermic reaction on the catalyst is continuously recorded. The design of the test chamber, the amount of catalyst, the shape of the holders and finally the flow rate and composition of the gaseous mixture should be carefully selected in order to achieve reproducible results.     

Role of catechin on collagen type I stability upon oxidation: a NMR approach

Abstract

The study focuses on the understanding, at molecular level, the mechanism of interaction between protein and flavonoids. Collagen and catechin interactions were investigated by NMR in solution and solid state. The effect of catechin on the stability of collagen to oxidation was also explored. Collagen was treated with two concentrations of catechin solutions. Oxidation was carried out by incubation of collagen solution with three oxidation systems: Fe(II)/H₂O₂, Cu(II)/H₂O₂, and NaOCl/H₂O₂. The effects of oxidation systems were evaluated by high resolution 1?D and 2?D proton spectroscopy and solid state NMR (¹³C CP MAS) experiments. Interactions between collagen and catechin preferentially occur between catechin B ring and the amino acids Pro and Hyp of collagen. Results showed that both iron and copper oxidation systems were able to interact with collagen by site specific attack. Moreover, catechin protects collagen proline from oxidation by metal/H₂O₂ systems, preventing copper and iron approach to collagene molecule;this behaviour was more evident for the copper/H₂O₂ system.     

Acceleration of the Passerini reaction in the presence of nucleophilic additives

An accelerating effect of nucleophilic additives was revealed for the Passerini multi-component reaction. The influence of aqueous solutions on the reaction rate was studied in detail and the direct involvement of water in the bond-making step was attributed as the basis of an accelerating effect. Other nucleophiles were tested as alternatives to water; as a result N-hydroxysuccinimide is proposed as an accelerant of the Passerini reaction.     

Production of antitumoral retamycin during fed-batch fermentations of Streptomyces olindensis

Fed-batch runs were performed in order to correlate the production of retamycin, an anthracycline antibiotic produced by Streptomyces olindensis in submerged cultures, with the specific growth rate. Maximum retamycin production was achieved with an exponential feed rate, controlling the specific growth rate at a low value (0.03 h-1, about 10% of the maximum specific growth rate). Control of the specific growth rate at higher values (0.10 and 0.17 h-1) caused a decrease in antibiotic production. Morphology, assessed by image analysis, was shown to be highly relevant in this process. Cell growth mainly in the form of clumps (90% clumps and 10% free filaments) led to better results than growth as clumps (75%) and free filaments (25%).     

Association of model peptides and dehydropeptides: N-acetyl-l-alanine- and dehydroalanine N′,N′-dimethylamides

The comparative studies on the association of Ac-ΔAla-NMe₂ and Ac-l-Ala-NMe₂ in carbon tetrachloride were performed by the analysis of their average molecular weight, dipole moments and FTIR spectra. To aid spectroscopic interpretation and gain some deeper insight into the nature of associates, the geometries of the minimum energy of the dimers of Ac-ΔAla-NMe₂ and Ac-l-Ala-NMe₂ were calculated by the B3LYP/6-31+G** method. The average molecular weight in the studied concentration range, for the ΔAla and l-Ala peptide, as determined by the osmometric method, did not exceed 1.5 and 1.2 of the monomeric mass, respectively. Accordingly, the percentage of the monomeric form (α) decreased as concentration was increased more significantly for the ΔAla analogue than for its saturated counterpart. In the studied concentrations, the dipole moment of the unsaturated compound decreases and that of its counterpart is almost constant. We identified a wider range of dimeric forms of Ac-ΔAla-NMe₂ than those of Ac-l-Ala-NMe₂. While Ac-ΔAla-NMe₂ mainly forms cyclic dimers, built of open conformers H/F, specific for α,β-dehydroamino acids, Ac-l-Ala-NMe₂ forms cyclic and linear dimers, characteristic for the usual amino acids. Ac-ΔAla-NMe₂ has a greater tendency to associate than its saturated variant, which is the result of stronger hydrogen bonds.     

Single electron traps at the surface of polycrystalline MgO: assignment of the main trapping sites

Paramagnetic centers at the surface of ionic oxides in the form of trapped electrons can be generated by exposure of the material to alkali metal or hydrogen atoms or of molecular hydrogen under UV irradiation. For many years, it has been assumed that the resulting paramagnetic centers consist of oxygen vacancies filled by one electron. High-resolution electron spin resonance spectra and ab initio quantum chemical calculations show that the paramagnetic centers consist of (H(+))(e(-)) electron pairs formed at morphological irregularities of the surface. At least three different kinds of (H(+))(e(-)) centers, [A], [B], and [C], have been identified with abundances of 80%, 10%, and 8%, respectively. In this work, we compare a wide set of measured and computed g-factors and hyperfine coupling constants of the unpaired electron with the surrounding (25)Mg, (17)O, and (1)H nuclei and we propose a general assignment of the centers. (H(+))(e(-)) pairs formed at Mg(4c) ions at steps and edges account for species [A], centers formed at Mg(4c) ions at reverse corners correspond to species [B], and species [C] originates from (H(+))(e(-)) pairs formed at Mg(3c) ions at corners and kinks.