A top-down LC-FTICR MS-based strategy for characterizing oxidized calmodulin in activated macrophages

A liquid chromatography-mass spectrometry (LC-MS)-based approach for characterizing the degree of nitration and oxidation of intact calmodulin (CaM) has been used to resolve ～250 CaM oxiforms using only 500 ng of protein. The analysis was based on high-resolution data of the intact CaM isoforms obtained by Fourier-transform ion cyclotron resonance mass spectrometry (FTICR MS) coupled with an on-line reversed-phase LC separation. Tentative identifications of post-translational modifications (PTMs), such as oxidation or nitration, have been assigned by matching observed protein mass to a database containing all theoretically predicted oxidation products of CaM and verified through a combination of tryptic peptide information (generated from bottom-up analyses) and on-line collisionally induced dissociation (CID) tandem mass spectrometry (MS/MS) at the intact protein level. The reduction in abundance and diversity of oxidatively modified CaM (i.e., nitrated tyrosines and oxidized methionines) induced by macrophage activation has been explored and semiquantified for different oxidation degrees (i.e., no oxidation, moderate, and high oxidation). This work demonstrates the power of the top-down approach to identify and quantify hundreds of combinations of PTMs for single protein target such as CaM and implicate competing repair and peptidase activities to modulate cellular metabolism in response to oxidative stress.     

Synthetic UDP-furanoses as potent inhibitors of mycobacterial galactan biogenesis

UDP-galactofuranose (UDP-Galf) is a substrate for two types of enzymes, UDP-galactopyranose mutase and galactofuranosyltransferases, which are present in many pathogenic organisms but absent from mammals. In particular, these enzymes are involved in the biosynthesis of cell wall galactan, a polymer essential for the survival of the causative agent of tuberculosis, Mycobacterium tuberculosis. We describe here the synthesis of derivatives of UDP-Galf modified at C-5 and C-6 using a chemoenzymatic route. In cell-free assays, these compounds prevented the formation of mycobacterial galactan, via the production of short "dead-end" intermediates resulting from their incorporation into the growing oligosaccharide chain. Modified UDP-furanoses thus constitute novel probes for the study of the two classes of enzymes involved in mycobacterial galactan assembly, and studies with these compounds may ultimately facilitate the future development of new therapeutic agents against tuberculosis.     

Engineering enzyme specificity using computational design of a defined-sequence library

Engineered biosynthetic pathways have the potential to produce high-value molecules from inexpensive feedstocks, but a key limitation is engineering enzymes with high activity and specificity for new reactions. Here, we developed a method for combining structure-based computational protein design with library-based enzyme screening, in which inter-residue correlations favored by the design are encoded into a defined-sequence library. We validated this approach by engineering a glucose 6-oxidase enzyme for use in a proposed pathway to convert D-glucose into D-glucaric acid. The most active variant, identified after only one round of diversification and screening of only 10,000 wells, is approximately 400-fold more active on glucose than is the wild-type enzyme. We anticipate that this strategy will be broadly applicable to the discovery of new enzymes for engineered biological pathways.     

Affinity capillary electrophoretic study of K+/Na+ selectivity of hexaarylbenzene-based polyaromatic receptor

Affinity capillary electrophoretic (ACE) study has proved the selectivity of hexaarylbenzene-based polyaromatic receptor (R) for K⁺ ion over Na⁺ ion. The apparent binding constants of the R complexes with K⁺ and Na⁺ ions were determined from the dependence of effective electrophoretic mobility of R on the concentration of the above alkali metal ions in the background electrolyte using a non-linear regression analysis. The apparent binding constants (K_b) of the K-R⁺ and Na–R⁺ complexes in methanolic medium were evaluated as log K_b = 3.20 ± 0.22 for the K–R⁺ complex, and log K_b??0.7 for the Na–R⁺ complex.     

Photo- and radiation-induced preparation of nanocrystalline copper and cuprous oxide catalysts

Spherical copper nanoparticles have been prepared by photo- or radiation-induced reduction of aqueous solutions containing 10⁻³ mol.dm⁻³ copper sulphate or formate, 1.3 mol.dm⁻³ propan-2-ol and polyvinyl alcohol as a stabilizer. Increase of initial copper concentration to 10⁻² mol.dm⁻³ resulted in formation of different reaction product—octahedral cuprous oxide nanoparticles. Solutions were irradiated by means of electron beam, ⁶⁰Co γ rays (dose rate 70 Gy.h⁻¹) or by 400 W medium-pressure mercury lamp and were characterised by UV-Vis spectrophotometry, X-Ray Powder Diffraction, TEM and SEM. Pink to violet colour of colloidal copper solutions corresponded to measured copper surface plasmon band at circa 580 nm and has been found to be very sensitive to oxygen, which causes dissolution of particles. Therefore, the influence of purging by nitrogen gas prior to irradiation was thoroughly examined and has been found to only hinder, not alter irradiation effects. Moreover, the evolution of absorption spectrum of colloidal copper solution in contact with air has been measured, revealing interesting non-monotonous dependence on the air exposure time, probably caused by formation of protective oxide layer. Catalytic activity of prepared cuprous oxide has been measured by catalytic decomposition of hydrogen peroxide and has been found to be higher or comparable to commercial cuprous oxide.     

The effect of meteorological parameters on radon concentration in borehole air and water

Seasonal and short term variations of ²²²Rn activity concentration in borehole air and water of the borehole drilled in cracked quartzite were studied and possible response on meteorological parameters was examined. Seasonal change of radon concentration in borehole air due to atmospheric temperature was confirmed. Short term variation of radon concentration in borehole air coincided with the atmospheric pressure changes. The strong impact of rainfall on radon concentration values was observed both in air and water environments. The decrease of radon content in borehole air and water followed radioactive decay law exclusively in spring and summer month. Contrary to borehole water, rainfall increased radon concentration in borehole air during spring and summer months only. In this paper the results from two and half years of investigation are presented.     

Pulse shape analysis to reduce the background of BEGe detectors

A simple technique for pulse shape discrimination in HPGe-detectors of the so-called BEGe type, based on just one parameter obtained from one signal read out, is presented here. This technique allows discriminating between pulses generated when the deposited energy is located within a small region of about 1 mm³ from the pulses generated when the energy is deposited at different locations several mm or cm apart. Two possible applications using this technique are: (i) experiments that look for neutrinoless double β decay in ⁷⁶Ge, such as GERDA; (ii) γ spectrometry measurements where the Compton continuum can be reduced and the efficiency for cascading γ-rays can remain high. With this active background reduction technique a Compton suppression factor of about 3 was obtained. The detector response may be influenced by the detector size. The detector used for this study had a diameter of 6 cm, a thickness of 2.6 cm and a relative efficiency of 19%. The results obtained with this detector were consistent with the results obtained by Budjá? et al. [J Instrum 4:10, 2009] with a 50% relative efficiency BEGe detector.     

ACE applied to the quantitative characterization of benzo‐18‐crown‐6‐ether binding with alkali metal ions in a methanol–water solvent system

ACE was applied to the quantitative evaluation of noncovalent binding interactions between benzo‐18‐crown‐6‐ether (B18C6) and several alkali metal ions, Li⁺, Na⁺, K⁺, Rb⁺ and Cs⁺, in a mixed binary solvent system, methanol–water (50/50 v/v). The apparent binding (stability) constants (K_b) of B18C6–alkali metal ion complexes in the hydro‐organic medium above were determined from the dependence of the effective electrophoretic mobility of B18C6 on the concentration of alkali metal ions in the BGE using a nonlinear regression analysis. Before regression analysis, the mobilities measured by ACE at ambient temperature and variable ionic strength of the BGE were corrected by a new procedure to the reference temperature, 25°C, and the constant ionic strength, 10 mM . In the 50% v/v methanol–water solvent system, like in pure methanol, B18C6 formed the strongest complex with potassium ion (log K_b=2.89±0.17), the weakest complex with cesium ion (log K_b=2.04±0.20), and no complexation was observed between B18C6 and the lithium ion. In the mixed methanol–water solvent system, the binding constants of the complexes above were found to be about two orders lower than in methanol and about one order higher than in water.     

Analysis of anthocyanin pigments in Lonicera (Caerulea) extracts using chromatographic fractionation followed by microcolumn liquid chromatography-mass spectrometry

Anthocyanins from the fruit Lonicera caerulea L. var. kamtschatica (blueberry honeysuckle, Caprifoliaceae) were studied via (semi)preparative chromatographic fractionation followed by MS and μLC/MS analysis. The extraction procedure was optimized with respect to analytical purposes as well as its potential use for the preparation of nutraceuticals. The highest yield of anthocyanins was obtained using acidified methanol as the extraction medium. A comparable total anthocyanin content was obtained using a mixture of methanol and acetone. However, when Lonicera anthocyanins were in contact with acetone, a condensation reaction occurred to a large extent and related 5-methylpyranoanthocyanins were found. The effect of other extraction media, including ethanol as a "green" solvent, is also discussed. The potential of two fractionation procedures for extract purification differing in their chromatographic selectivity and scale was studied (i.e. using a Sephadex LH-20 gel column and a reversed phase). Fractions obtained by both procedures were used for a detailed analysis. MS and μLC/MS(2) methods were used for monitoring anthocyanin and 5-methylpyranoderivatives content as well as identifying less common and more complex dyes (dimer of cyanidin-3-hexoside, cyanidin-ethyl-catechin-hexosides, etc.). These more complex dyes are most likely formed during fruit treatment.