Evaluation of protein 15N relaxation times by inverse Laplace transformation

Relaxation times (T1, T2, T1rho) are usually evaluated from exponential decay data by least-squares fitting methods. For this procedure, the integrals or amplitudes of signals must be determined, which can be laborious with large data sets. Moreover, the fitting requires a priori knowledge of the number of exponential components responsible for the decay. We have adapted inverse Laplace transformation (ILT) for the analysis of relaxation data. Exponential components are resolved with ILT to reciprocal space on their corresponding relaxation rate values. The ILT approach was applied to 3D linewidth-resolved 15N HSQC experiments to evaluate 15N T1 and T2 relaxation times of ubiquitin. The resulting spectrum is a true 3D spectrum, where the signals are separated by their 1H and 15N chemical shifts (HSQC correlations) and by their relaxation rate values (R1 or R2). From this spectrum, the relaxation times can be obtained directly with a simple peak-picking procedure.     

Development of Luminescent Europium(III) and Terbium(III) chelates of 2,2′:6′,2″- terpyridine derivatives for protein labelling

The synthesis and luminescence properties are reported for 20 different chelates composed of 2,2′:6′,2″-terpyridine as the energy-absorbing and donating group, Eu^IIIand Tb^III as the emitting ions, methylenenitrilo(acetic acids) as the stabel chelate-forming moieties, and isothiocyanato or(4,6-dichloro-1,3,5-triazin-2-yl)amino groups as the activated moieties for coupling to biomolecules.     

Regio-selective synthesis of polyazacyclophanes incorporating a pendant group as potential cleaving agents of mRNA 5′-cap structure

A terpyridine or an imidazole unit has been tethered to an N-protected polyazacyclophane to give the appropriate N-monofunctionalized polyazacyclophane. After mild deprotection, four polyazacyclophanes incorporating a pendant group were obtained in satisfactory yields. Their preliminary cleavage ability of mRNA 5′-cap model was studied at pH 7.2.     

Insertion of noble gas atoms into cyanoacetylene: an ab initio and matrix isolation study

A computational and experimental matrix isolation study of insertion of noble gas atoms into cyanoacetylene (HCCCN) is presented. Twelve novel noble gas insertion compounds are found to be kinetically stable at the MP2 level of theory, including four molecules with argon. The first group of the computationally studied molecules belongs to noble gas hydrides (HNgCCCN and HNgCCNC), and we found their stability for Ng = Ar, Kr, and Xe. The HNgCCCN compounds with Kr and Xe have similar stability to that of previously reported HKrCN and HXeCN. The HArCCCN molecule seems to have a weaker H-Ar bond than in the previously identified HArF molecule. The HNgCCNC molecules are less stable than the HNgCCCN isomers for all noble gas atoms. The second group of the computational insertion compounds, HCCNgCN and HCCNgNC, are of a different type, and they also are kinetically stable for Ng = Ar, Kr, and Xe. Our photolysis and annealing experiments with low-temperature cyanoacetylene/Ng (Ng = Ar, Kr, and Xe) matrixes evidence the formation of two noble gas hydrides for Ng = Kr and Xe, with the strongest IR absorption bands at 1492.1 and 1624.5 cm(-1), and two additional absorption modes for each species are found. The computational spectra of HKrCCCN and HXeCCCN fit most closely the experimental data, which is the basis for our assignment. The obtained species absorb at quite similar frequencies as the known HKrCN and HXeCN molecules, which is in agreement with the theoretical predictions. No strong candidates for an Ar compound are observed in the IR absorption spectra. As an important side product of this work, the data obtained in long-term decay of KrHKr+ cations suggest a tentative assignment for the CCCN radical.     

An adjustment scheme for nonlinear pricing problem with two buyers

We examine a contracting problem with asymmetric information in a monopoly pricing setting. Traditionally, the problem is modeled as a one-period Bayesian game, where the incomplete information about the buyers’ preferences is handled with some subjective probability distribution. Here we suggest an iterative online method to solve the problem. We show that, when the buyers behave myopically, the seller can learn the optimal tariff by selling the product repeatedly. In a practical modification of the method, the seller offers linear tariffs and adjusts them until optimality is reached. The adjustment can be seen as gradient adjustment, and it can be done with limited information and so that it benefits both the seller and the buyers. Our method uses special features of the problem and it is easily implementable.     

The base sequence dependent flexibility of linear single-stranded oligoribonucleotides correlates with the reactivity of the phosphodiester bond

The effect of base sequence on the structure and flexibility of linear single-stranded RNA molecules and the influence of the base sequence on phosphodiester bond reactivity have been studied. Molecular dynamics simulations of 2.1 ns were carried out for nine chimeric oligonucleotides containing only one unsubstituted ribo unit, all the rest of sugars being 2'-O-methylated. The base sequence has recently been reported to make a big contribution to the reactivity of these compounds. A detailed examination of the interaction energies between the base moieties shows that base stacking is strongly context-dependent and cooperative. The strength of stacking at the site susceptible to chain cleavage by intramolecular transesterification was observed to be dependent on both the flanking bases of the cleavage site and those further apart in the molecule. The interaction energies between the bases in the vicinity of the scissile linkage were found to correlate well with the experimental phosphodiester bond cleavage rates: the stronger the bases close to the cleavage site are stacked, the slower the cleavage rate is.     

Preparation of hexaaza and heptaaza macrocycles functionalized with a single aminoalkyl pendant arm

A practical and reproducible route for the preparation of 1,4,7,10,13,16,19-heptaazacyclohenicosane (1), 1,4,7,10,13,16-hexaazacyclooctadecane (2), and 1,4,7,10,13,17-hexaazacycloicosane (3) bearing a single N-(2-aminoethyl) pendant arm has been developed. Richman-Atkins cyclization in the presence of caesium carbonate was applied to construct the macrocycle from 3-benzoyl-N1,N5-ditosyl-3-azapentane-1.5-diamine and the appropriate fully N-tosylated N alpha, N omega-bis(2-mesyloxyethyl) tri- or tetra-amine. The benzoyl group was selectively removed with potassium tert-butoxide, and the exposed nitrogen atom was reacted with N-tosylaziridine. The tosyl protections were removed with hydrogen bromide in acetic acid, and the product was converted to a free base with the aid of a strong anion exchange resin (OH- form).     

New Heteroaromatic Complexing Agents and Luminescence of Their Europium(III) and Terbium(III) Chelates

Twelve heteroaromatic complexing agents 9a–I were synthesized with the purpose to develop suitable labels for time-resolved luminescence-based bioaffinity assays. The relative luminescence yields, excitation maxima, and emission decay constants of their europium(III) and terbium(III) chelates were determined. According to these results, 2,2′,2″,2?-[(2,2′-bipyridine-6,6′-diyl)bis(methylenenitrilo)]tetrakis (acetic acid) ( 9e ) and 2,2′,2″,2?-[(2,2′:6′,2″-terpyridine-6,6″-diyl)bis(methylenenitrilo)] tetrakis(acetic acid) ( 91 ) are the most promising agents.     

Reactions of 9-substituted guanines with bromomalondialdehyde in aqueous solution predominantly yield glyoxal-derived adducts

Reactions of 9-ethylguanine, 2'-deoxyguanosine and guanosine with bromomalondialdehyde in aqueous buffers over a wide pH-range were studied. The main products were isolated and characterized by (1)H and (13)C NMR and mass spectroscopy. The final products formed under acidic and basic conditions were different, but they shared the common feature of being derived from glyoxal. Among the 1 : 1 adducts, 1,N(2)-(trans-1,2-dihydroxyethano)guanine adduct (6) predominated at pH < 6 and N(2)-carboxymethylguanine adduct (10a,b) at pH > 7. In addition to these, an N(2)-(4,5-dihydroxy-1,3-dioxolan-2-yl)methylene adduct (11a,b) and an N(2)-carboxymethyl-1,N(2)-(trans-1,2-dihydroxyethano)guanine adduct (12) were obtained at pH 10. The results of kinetic experiments suggest that bromomalondialdehyde is significantly decomposed to formic acid and glycolaldehyde under the conditions required to obtain guanine adducts. Glycolaldehyde is oxidized to glyoxal, which then modifies the guanine base more readily than bromomalondialdehyde. Besides the glyoxal-derived adducts, 1,N(2)-ethenoguanine (5a-c) and N(2),3-ethenoguanine adducts (4a-c) were formed as minor products, and a transient accumulation of two unstable intermediates, tentatively identified as 1,N(2)-(1,2,2,3-tetrahydroxypropano)(8) and 1,N(2)-(2-formyl-1,2,3-trihydroxypropano)(9) adducts, was observed.     

Effects of short- and long-term ultraviolet B irradiation on the immune system of the common carp (Cyprinus carpio)

Carp (Cyprinus carpio) were repeatedly exposed to 0, 60, 120 and 240 mJ/cm2 ultraviolet B (UVB) radiation three times in 1 week (short-term exposure) or 12 times in 4 weeks (long-term exposure). The effect of UVB on the functioning of the carp immune system was studied on day 2 after the final irradiation. After short-term UVB exposure, the whole-blood respiratory burst and cytotoxic activity were markedly enhanced, with parallel responses in both the number of circulating granulocytes and in the plasma cortisol concentration of the fish. These changes were not detectable after long-term exposure. The respiratory burst by head kidney granulocytes was suppressed dose dependently after both exposures, but cytotoxic activity was not affected. Exposure to UVB also modulated lymphocyte functions: nonstimulated and PHA-stimulated proliferation of head kidney lymphocytes in vitro was enhanced by both short-term and long-term exposure. LPS-stimulated proliferation was not affected by exposure nor was the number of immunoglobulin-secreting cells in the head kidney. In long-term exposure, the highest dose reduced the level of plasma IgM. This study indicates that UVB irradiation induces immunomodulation in the blood and head kidney of the carp and that the effects of short- and long-term exposure differ from each other. The results emphasize the potentially harmful impact of increased solar UVB radiation on fish immune functions.