π–π Interactions in Structural Stability: Role in RNA Binding Proteins

RNA binding proteins play significant roles in many bio-macromolecular systems. Aromatic amino acid residues are vital for several biological functions. In the present work, the influences of π–π interactions in RNA binding proteins are analyzed. There are a total of 3,396 π-residues in RNA binding proteins out of which 1,547, 1,241, and 608 are phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), respectively. Among these 945, 634, and 356 Phe, Tyr, and Trp residues, respectively, are involved in π–π interactions. The observations indicate that majority of the aromatic residues in RNA binding proteins are involved in π–π interactions. Side chain–side chain π–π interactions are the predominant type of interactions in RNA binding proteins. These π–π interactions stabilize the core regions within RNA binding proteins. π–π interacting residues are evolutionary conserved. Residue-wise analysis indicates that π–π interacting residues have higher long-range contacts and hence they are important in the global conformational stability of these proteins.     

A fractal analysis of analyte-estrogen receptor binding and dissociation kinetics using biosensors: environmental and biomedical effects

A fractal analysis is used to model the binding and dissociation kinetics between analytes in solution and estrogen receptors (ERs) immobilized on a sensor chip of a surface plasmon resonance (SPR) biosensor. The influence of different ligands is also analyzed. A better understanding of the kinetics provides physical insights into the interactions, and suggests means by which appropriate interactions (to promote correct signaling) and inappropriate interactions such as with xenoestrogens (to minimize inappropriate and deleterious to health signaling) may be better controlled. The fractal approach is applied to analyte–ER interaction data available in the literature. The units for the different parameters (rate coefficients and affinities) in fractal-type kinetics are different from those obtained in classical kinetics. Numerical values obtained for the binding and the dissociation rate coefficients are linked to the degree of roughness or heterogeneity (fractal dimension, D_f) present on the biosensor chip surface. In general, the binding and the dissociation rate coefficients are very sensitive to the degree of heterogeneity on the surface. A single-fractal analysis is adequate in some cases. In others (that exhibit complexities in the binding or the dissociation curves) a dual-fractal analysis is required to obtain a better fit. This has biomedical and environmental implications in that the dissociation (and the binding) rate coefficient may be used to alleviate (deleterious effects) or enhance (beneficial effects) by selective modulation of the surface. The affinity values obtained in the analysis are consistent with the numbers required to (a) promote signaling between the correct analyte and the estrogen receptor, and (b) minimize the signaling between xenoestrogens and the estrogen receptor.     

Dhanwantaram kashayam,an Ayurvedic polyherbal formulation,reduces oxidative radicals and reverts lipids profile towards normal in diabetic rats

BackgroundHyperglycemia and hyper oxidative stress are indicators of diabetes mellitus which is also accompanied with decreased levels of antioxidant enzymes. While oxidative stress is important in increasing insulin secretion and controlling blood sugar level at the same time excess oxidative stress leads to the destruction of beta cells of pancreas resulting in to low insulin production and hyperglycemia. A balance between the levels of oxidative radicals and insulin production is needed, but is not defined yet. Hyperglycemia also leads to hyperlipidemia which can contribute to various health conditions like cardiovascular diseases.ObjectivesThis study was designed to study the oxidative stress and lipid levels in diabetic rats. This also was designed to elucidate the effect of Dhanwantaram Kashayam, an Ayurvedic polyphenolic derived from plants on lipid metabolism and oxidative radical scavenging in diabetic rats.MethodsRats were made diabetic by injecting streptozotocin. Different enzymes involved in oxidative radical scavenging and lipid profiles including triglycerides, total cholesterol, free fatty acids and phospholipids were estimated using standard methods reported elsewhere.ResultsLevel of antioxidant enzymes were lower in diabetic rats compared to normal controls. Administration of Dhanwantaram Kashayam restored the enzyme activity as well as reduced levels of different lipids in diabetic rats.ConclusionsAdministration of Dhanwantaram Kashayam increased the activity levels of antioxidant enzymes and reduced the levels of total cholesterol, phospholipids and triglycerides. The results of this study point to the possibility of developing Dhanwantaram Kashayam as a dietary supplement which can alleviate the complications associated with diabetes or prevent them altogether.     

Anti-type II collagen immune complex-induced granulocyte reactivity is associated with joint erosions in RA patients with anti-collagen antibodies

IntroductionRheumatoid arthritis (RA) patients with autoantibodies against collagen type II (CII) are characterized by acute RA onset with elevated inflammatory measures and early joint erosions as well as increased production of tumor necrosis factor-α (ΤΝF-α) by peripheral blood mononuclear cells (PBMC) stimulated by anti-CII immune complexes (IC) in vitro. Polymorphonuclear granulocytes (PMN) are abundant in RA synovial fluids, where they might interact directly with anti-CII IC in the articular cartilage, but no studies have investigated PMN responses towards anti-CII IC. The aim was to investigate whether PMN react towards anti-CII IC, and to what extent such reactivity might relate to the clinical acute onset RA phenotype associated with elevated levels of anti-CII.MethodsPMN and PBMC isolated from healthy donors were stimulated with IC made with a set of 72 baseline patient sera (24 anti-CII positive, 48 anti-CII negative) chosen from a clinically well-characterized RA cohort with two-year radiological follow-up with Larsen scoring. PMN expression of cluster of differentiation (CD)11b, CD66b, CD16 and CD32 was measured by flow cytometry, whereas PMN production of myeloperoxidase (MPO) and interleukin (IL)-17, and PBMC production of ΤΝF-α was measured with enzyme linked immunosorbent assay.ResultsPMN expression of CD11b, CD66b and MPO, and PBMC production of ΤΝF-α were upregulated whereas PMN expression of CD16 and CD32 were downregulated by anti-CII IC. CD16, CD66b, and MPO production correlated to serum anti-CII levels (Spearman’s ρ = 0.315, 0.675 and 0.253, respectively). CD16 was associated with early joint erosions (P = 0.024, 0.034, 0.046 at baseline, one and two years) and CD66b was associated with changes in joint erosions (P = 0.017 and 0.016, at one and two years compared to baseline, respectively). CD66b was associated with baseline C-reactive protein and PBMC production of ΤΝF-α was associated with baseline erythrocyte sedimentation rate, in accordance with our earlier findings. No clinical associations were observed for MPO or IL-17.ConclusionPMN responses against anti-CII IC are more closely associated with early joint erosions than are PBMC cytokine responses. PMN reactivity against anti-CII IC may contribute to joint destruction in newly diagnosed RA patients with high levels of anti-CII.     

Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast

Background  

In analyzing the stability of DNA replication origins in Saccharomyces cerevisiae we faced the question whether one set of sequences is significantly enriched in the number and/or the quality of the matches of a particular position weight matrix relative to another set.     

Magnetopriming circumvents the effect of salinity stress on germination in chickpea seeds

Chickpea seeds of Pusa 1053 (Mediterranean) and Pusa 256 (native) were magnetoprimed with 100 mT static magnetic field for 1 h to evaluate the effect of magnetopriming on germination of seeds under saline conditions. Enhanced rate of germination and seedling growth parameters (root and shoot length, and vigour indices) under different salinity levels indicated that magnetopriming was more effective in alleviating salinity stress at early seedling stage in Pusa 1053 as compared to Pusa 256. Dynamics of seed water absorption in magnetoprimed seeds showed increased water uptake in Pusa 1053 under non-saline as compared to saline conditions. This could have resulted in faster hydration of enzymes in primed seeds leading to higher rate of germination. Total amylase, protease and dehydrogenase activities were higher in primed seeds as compared to unprimed seeds under both non-saline and saline conditions. Production of superoxide radicals was enhanced in germinating seeds of both the genotypes under salinity irrespective of priming. Increased levels of hydrogen peroxide in germinating magnetoprimed seeds, under both the growing conditions, suggested its role in promotion of germination. Our results showed that magnetopriming of dry seeds of chickpea can be effectively used as a pre-sowing treatment for mitigating adverse effects of salinity at seed germination and early seedling growth.     

Genetic Analysis of Myoblast Fusion: blown fuse Is Required for Progression Beyond the Prefusion Complex

The events of myoblast fusion in Drosophila are dissected here by combining genetic analysis with light and electron microscopy. We describe a new and essential intermediate step in the process, the formation of a prefusion complex consisting of “paired vesicles.” These pairs of vesicles from different cells align with each other across apposed plasma membranes. This prefusion complex resolves into dense membrane plaques between apposed cells; these cells then establish cytoplasmic continuity by fusion of small areas of plasma membrane followed by vesiculation of apposed membranes. Different steps in this process are specifically blocked by mutations in four genes required for myoblast fusion. One of these genes, blown fuse, encodes a novel cytoplasmic protein expressed in unfused myoblasts that is essential for progression beyond the prefusion complex stage.     

Identification and characterization of the ATP-binding site in human pancreatic glucokinase

The central role of human pancreatic glucokinase in insulin secretion and, consequently, in maintenance of blood glucose levels has prompted investigation into identification of ATP-binding site residues and examination of ATP- and glucose-binding interactions. Because glucokinase has been resistant to crystallization, computer generated homology models were developed based on the X-ray crystal structure of the COOH-terminal domain of human brain hexokinase 1 bound to glucose and ADP or glucose and glucose-6-phosphate. Human pancreatic glucokinase mutants were designed based upon these models and on ATPase domain sequence conservation to identify and characterize potential glucose and ATP-binding sites. Specifically, mutants Asp78Ala, Thr82Ala, Lys90Ala, Lys102Ala, Gly227Ala, Thr228Ala, Ser336Leu, Ser411Ala, and Ser411Leu were constructed, expressed, purified, and kinetically characterized under steady-state conditions. Compared to their respective wild type controls, several mutants demonstrated dramatic changes in V(max), cooperativity of glucose binding and S(0.5) for ATP and glucose. Results suggest a role for Asp78, Thr82, Gly227, Thr228, and Ser336 in ATP binding and indicate these residues are essential for glucose phosphorylation by human pancreatic glucokinase.