STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

Background  

The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user.     

Molecular cloning of the human insulin gene

Isolation of genomic clones containing the human insulin gene by screening the human genomic library for this gene using the cDNA rat insulin probe is reported. The analysis of promoter-enhancer region and exons sequences has revealed their identity to analogous sequences determined earlier.     

Oxidative processes at initial stages of interaction of nodule bacteria (<Emphasis Type="Italic">Rhizobium leguminosarum</Emphasis>) and pea (<Emphasis Type="Italic">Pisum sativum</Emphasis> L.): A review

A possible physiological mechanism of legume-Rhizobium symbiosis, consisting in regulation of the intensity of oxidative processes by the macrosymbiont in response to infection with Rhizobium, was analyzed using our own and published data. The results used in the analysis included data on the content of reactive oxygen species (O ₂ ^·? and H₂O₂), activity of antioxidant enzymes (superoxide dismutase, catalase, and peroxidase), and intensity of lipid peroxidation proceeding with the involvement of lipophilic phenolic compounds of the microsymbiont.     

Postnatal development of corticosteroid function of the adrenals in C57BL/6J-Ay mice

We studied postnatal development of corticosteroid function of the adrenals in mice during the period of elevated activity of the hypothalamic-pituitary-adrenal system and the influence of mutant gene Ay on this process. Normally, a corticosterone peak in blood and increased basal and stimulated steroidogenesis in vitro are observed in 3-week old mice. In 3-week old Ay/a mice (hyperexpression of protein agouti) a corticosterone peak in blood is lowered and genotypic differences in steroidogenesis in vitro are absent, as compared to a/A mice (absence of agouti), while at the ages of 10 and 15 weeks, there were no genotypic differences in the blood level of corticosterone and steroidogenesis in vitro was elevated. Thus, a high level of corticosterone during the period of elevated activity of the hypothalamic-pituitary-adrenal system in 3-week old mice is determined by enhanced steroidogenic function of the adrenals. Mutant gene Ay in male mice affected the postnatal development of the adrenal function: the peak of corticosterone in blood was lowered during the period of elevated activity of the system.     

The effect of the phenolic compounds exuded by pea roots in darkness on the reproduction of Rhizobium

The exudation, composition, and biological activity of the phenolic compounds (PC) of pea (Pisum sativum L.) roots in the light and darkness were studied. The roots of leguminous plants grown for 5 days in darkness exuded a smaller amount of PC that displayed a weaker stimulation of Rhizobium reproduction. Moreover, the root exudates contained antimicrobial compounds, stilbenes. It is assumed that a lower PC exudation by roots and the specific features of PC composition influencing the biological activity are among the reasons causing a delayed nodulation of legumes grown in darkness.     

Increase in the sensitivity and a simplification of the method for the separate determination of antibiotic activities in combined preparations (oletetrin) by using media with a varying pH value

An agar-diffusion method for determination of oleandomycin and tetracycline low levels in solutions of the drug combination was developed. The medhod may be used for investigation of oletetrin absorption and distribution in humans and animals. It provides high accuracy in separate determination of oleandomycin and tetracycline activity in solutions of the drugs at a ratio of 1 : 2. The same test-culture, Bac. subtilis, variant L2 is used for the assay of tetracycline and oleandomycin activity. The only differences are in the values of pH and the buffer solution and the standards.     

Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions

Structure-guided analysis of the new dimeric dUTPase family revealed its sequence relationship to the phage T4 dCTPase, phosphoribosyl-ATP pyrophosphatase HisE, NTP pyrophosphatase MazG, and several uncharacterized protein families, including the human protein XTP3TPA (RS21-C6), which is overexpressed in embryonic and cancer cells. Comparison with the recently determined structure of a MazG-like protein from Sulfolobus solfataricus supported the unification of these enzymes in one superfamily of all-alpha NTP pyrophosphatases, suggesting that dimeric dUTPases evolved from a tetrameric MazG-like ancestor by gene duplication. Analysis of the structure of the Sulfolobus MazG points to 2-hydroxyadenosine (isoguanosine) triphosphate, a product of oxidative damage of ATP, as the most likely substrate. We predict that uncharacterized members of this superfamily perform "house-cleaning" functions by hydrolyzing abnormal NTPs and are functionally analogous to the structurally unrelated hydrolases of the Nudix superfamily. We outline probable tertiary and quaternary structures of the all-alpha NTP pyrophosphatase superfamily members.     

Temperature impact on localization of "free" phenolic compounds in the root tissues and deformation of root hairs in pea seedlings inoculated by Rhizobium

The study was focused on localization of "free" phenolic compounds in pea Pisum sativum L. seedling roots grown at 22 and 8 degrees C 24 h after their inoculation with Rhizobium leguminosarum bv. viceae bacteria. A comparison of phenolic compound distribution along the root in root tissues, and results of observation of root hair development on the root surface, response of root hairs to inoculation, manifesting itself in various deformation degree (bends, twists, ect.) enabled us to reveal differences between roots grown at different temperatures. These differences are basically referred to a sector localized 0-5 mm away from the root tip containing meristematic and extending cells. A distribution of phenolic compounds in sectors with root hairs responding to inoculation by various degrees of contortion practically did not depend on the temperature of plant growth. The evidence provided in the course of this work enabled us to suggest that inhibition of pea root infection at low temperature is caused by decelerated growth processes characteristic of both the root itself and root hairs, as well by a slow increase in the root hair zone.     

Changes of lipid-carbohydrate metabolism during development of melanocortin obesity in the mice with the Agouti yellow mutation

Melanocortin obesity develops after puberty in mice with Agouti yellow mutation. The aim of the work was to study dynamics of the main characteristics oflipidcarbohydrate metabolism during the obesity development. We used female mice of C57BI/6J strain homozygous for recessive mutation nonagouti (a/a-mice) who were predisposed to the obesity, and heterozygous for dominant mutation Agouti yellow (Ay-mice) who were not predisposed to the obesity. Food consumption and body weights were measured from week 4 to week 22. Some animals were decapitated on 8, 11, 13, 15, 22 weeks. Hyperphagia (6 week) proceeds to body weight increasing (7 week) in the Ay-mice. In the Ay-mice compared to a/a-mice, adiposyte size and blood level of leptin were increased on the 11th week, blood levels of fatty acids and glucose--on the 13th week, blood level of insulin--on the 15th week. The hyperphagia seems to promote development ofmelanocortin obesity, stable disturbances of lipid metabolism appearing before those in glucose metabolism. Complete metabolic obesity syndrome was formed after the 15th week of life.