Environment influences on the aromatic character of nucleobases and amino acids

Geometric (HOMA) and magnetic (NICS) indices of aromaticity were estimated for aromatic rings of amino acids and nucleobases. Cartesian coordinates were taken directly either from PDB files deposited in public databases at the finest resolution available (≤1.5?Å), or from structures resulting from full gradient geometry optimization in a hybrid QM/MM approach. Significant environmental effects imposing alterations of HOMA values were noted for all aromatic rings analysed. Furthermore, even extra fine resolution (≤1.0?Å) is not sufficient for direct estimation of HOMA values based on Cartesian coordinates provided by PDB files. The values of mean bond errors seem to be much higher than the 0.05?Å often reported for PDB files. The use of quantum chemistry geometry optimization is strongly advised; even a simple QM/MM model comprising only the aromatic substructure within the QM region and the rest of biomolecule treated classically within the MM framework proved to be a promising means of describing aromaticity inside native environments. According to the results presented, three consequences of the interaction with the environment can be observed that induce changes in structural and magnetic indices of aromaticity. First, broad ranges of HOMA or NICS values are usually obtained for different conformations of nearest neighborhood. Next, these values and their means can differ significantly from those characterising isolated monomers. The most significant increase in aromaticities is expected for the six-membered rings of guanine, thymine and cytosine. The same trend was also noticed for all amino acids inside proteins but this effect was much smaller, reaching the highest value for the five-membered ring of tryptophan. Explicit water solutions impose similar changes on HOMA and NICS distributions. Thus, environment effects of protein, DNA and even explicit water molecules are non-negligible sources of aromaticity changes appearing in the rings of nucleobases and aromatic amino acids residues.     

The in vivo and in vitro influence of methyl jasmonate on oxidative processes in Arabidopsis thaliana leaves

In Arabidopsis thaliana leaves a strong increase of H₂O₂ content was induced by application of methyl jasmonate (JAMe) through the root system, but the induction only slightly depended on JAMe concentration. The activity of superoxide dismutase and ascorbic acid peroxidase increased at lower JAMe concentrations and decreased at higher ones. Catalase activity decreased proportionally to JAMe concentration (in comparison with control plants). The sum of ascorbic acid and dehydroascorbate content at 10⁻⁶ M JAMe was similar to the control, but at higher concentrations it increased, especially due to a higher ascorbate accumulation. Methyl jasmonate applied directly to the extract of leaves (in vitro experiment) also induced a strong increase in H₂O₂ level, even at a low concentration (10⁻⁸ M). Since lower JAMe concentrations induced weak superoxide dismutase and did not change catalase and peroxidase activity, it is suggested that in this case a high level of hydrogen peroxide was not the result of the activity of the mentioned enzymes. JAMe-induction of H₂O₂ increase at the highest JAMe concentration resulted from SOD activity. Our in vivo and in vitro experiments suggest that jasmonate can influence oxidative stress not only through gene expression but also by its direct effect on enzyme activity.     

Effect of leucine and metabolites of branched chain amino acids on protein turnover in heart.

Leucine, but not isoleucine or valine, inhibited protein degradation and accelerated protein synthesis in hearts perfused with buffer that contained glucose (15 mM) and normal plasma levels of other amino acids, except for the branched chain compounds. Products of leucine, isoleucine, and valine metabolism also inhibited protein degradation and stimulated protein synthesis. These compounds included the transamination and decarboxylation products, as well as acetate, acetoacetate, and propionate. In some, but not all instances, inhibition of degradation and acceleration of synthesis were accompanied by an increase in intracellular leucine. When insulin was added to the perfusate, the rate of degradation was reduced by 40%, but addition of leucine was ineffective in the presence of the hormone. Insulin, leucine (2 mM) and a mixture of branched chain amino acids at normal plasma levels increased latency of cathepsin D in hearts that were perfused with buffer containing glucose. A combination of leucine and insulin increased latency more than either substance alone. These studies indicate that leucine as well as a variety of substrates that are oxidized in the citric acid cycle are involved in regulation of protein turnover in heart muscle.     

Effect of amino acids on rooting of apple dwarf rootstocksin vitro

The effect of twelve amino acids and lactalbumin hydrolysate in concentration of 200 mg 1^?1 on rooting of the dwarf apple rootstocks P 2 and P 60 was testedin vitro. Arginine, omithine, glutamic acid and glycine enhanced root number of the P 60 rootstock; proline and lactalbumin hydrolysate were neutral; and asparagine, tyrosine, methionine, cysteine and glutamine lowered the root number. Tyrosine, methionine, cysteine and glutamine reduced almost completely rooting of P 60. In the recalcitrant P 2 rootstock aspartic acid, glutamic acid and omithine significantly enhanced the number of roots and rooted shoots, arginine and tryptophan increased the root number only slightly, asparagine was neutral, and proline reduced the root number.     

Effect of carbostimulin on the concentration of tricarboxylic cycle metabolites, oxidative processes and antibody biosynthesis in the rat

Carbostimulin is studied for the effect it exerts on indices of the acid-base equilibrium of blood, content of certain tricarboxylic-cycle metabolites and free amino acids and formation of antibodies in rats. It is established that carbostimulin feeding increases the total carbon dioxide, pyruvate and lactate concentration in blood, the content of ammonium, glutamine and certain free amino acids being decreased. Oxidation processes in the liver mitochondria and biosynthesis of antibodies in experimental animals are shown to be more intensive than in the control ones.     

Cerebral amino acids and lipids in drug-induced status epilepticus

—Dogs were given repeated doses of pentylenetetrazol to maintain a condition of status epilepticus for periods of 30–40 min. Analyses of cerebral tissue frozen in situ showed significant increases in alanine, arginine, γ-aminobutyric acid, glycine, histidine, leucine, lysine, phenylalanine, serine, tyrosine, and valine. Decreases occurred in the glutamic and aspartic acid levels. Other measured amino compounds were unchanged. Ammonia was increased, but not more than occurs in seizures of brief duration. A large decrease was noted in the ganglioside fraction, and a decrease also in a fraction containing the lecithins and sphingomyelins. The cephalin, cerebroside–sulphatide, and cholesterol fractions were not affected. Similar repetitive seizures induced by bemegride and continuing for shorter periods (5–9 min) brought about less extensive changes. Glutamic acid was increased, in contrast to the pentylenetetrazol effect, and the apparent decrease in aspartic acid was not statistically significant. Increases were noted in alanine, γ-aminobutyric acid, lysine, and ammonia. The ganglioside and lecithin-sphingomyelin fractions were decreased.     

Distinct mechanisms of oxidative DNA damage by two metabolites of carcinogenic o-toluidine

Mechanisms of DNA damage by metabolites of carcinogenic o-toluidine in the presence of metals were investigated by the DNA sequencing technique using (32)P-labeled human DNA fragments. 4-Amino-3-methylphenol, a major metabolite, caused DNA damage in the presence of Cu(II). Predominant cleavage sites were thymine and cytosine residues. o-Nitrosotoluene, a minor metabolite, did not induce DNA damage even in the presence of Cu(II), but addition of NADH induced DNA damage very efficiently. The DNA cleavage pattern was similar to that in the case of 4-amino-3-methylphenol. Bathocuproine and catalase inhibited DNA damage by these o-toluidine metabolites, indicating the participation of Cu(I) and H(2)O(2) in the DNA damage. Typical free hydroxyl radical scavengers showed no inhibitory effects on the DNA damage. o-Toluidine metabolites increased the formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine in calf thymus DNA in the presence of Cu(II). UV-visible and ESR spectroscopic studies have demonstrated that 4-amino-3-methylphenol is autoxidized to form the aminomethylphenoxyl radical and o-nitrosotoluene is reduced by NADH to the o-toluolhydronitroxide radical in the presence and absence of Cu(II). Consequently, it is considered that these radicals react with O(2) to form O(-)(2) and subsequently H(2)O(2), and that the reactive species generated by the reaction of H(2)O(2) with Cu(I) participate in the DNA damage. Metal-mediated DNA damage by o-toluidine metabolites through H(2)O(2) seems to be relevant for the expression of the carcinogenicity of o-toluidine.