SAD phasing with in-house Cu Kα radiation using barium as anomalous scatterer.

Phasing of lysozyme crystals using co-crystallized barium ions was performed using single-wavelength anomalous diffraction (SAD) method using Cu Kα radiation with in-house source of data collection. As the ion binding sites vary with respect to the pH of the buffer during crystallization, the highly isomorphic forms of lysozyme crystals grown at acidic and alkaline pH were used for the study. Intrinsic sulphur anomalous signal was also utilized with anomalous signal from lower occupancy ions for phasing. The study showed that to solve the structure by SAD technique, 2.8-fold data redundancy was sufficient when barium was used as an anomalous marker in the in-house copper X-ray radiation source for data collection. Therefore, co-crystallization of proteins with barium containing salt can be a powerful tool for structure determination using lab source.

Biosynthesis of gold nanoparticles by actinomycete Streptomyces viridogens strain HM10.

Biosynthesis of gold nanoparticles by Streptomycetes from Himalayan Mountain was undertaken for the first time. Out of 10 actinomycete strains tested, four strains (D10, HM10, ANS2 and MSU) showed evidence for the intracellular biosynthesis of gold nanoparticles, among which the strain HM10 showed high potency. Presence of spherical and rod shaped gold nanoparticles in mycelium of the strain HM10 was determined by transmission electron microscopy (TEM) and X-ray diffraction analysis. The average particle size ranged from 18-20 nm. UV spectral analysis indicated that the reduction of chloroauric acid (HAuCl4) occurred within 24 h of reaction period. Further, the strain HM10 showed enhanced growth at 1 and 10 mM concentration of HAuCl4. The gold nanoparticles synthesized by the strain HM10 showed good antibacterial activity against S. aureus and E. coli in well-diffusion method. The potential actinomycete HM10 strain was phenotypically characterized and identified as Streptomyces viridogens (HM10). Thus, actinomycete strain HM10 reported in this study is a newly added source for the biosynthesis of gold nanoparticles.

Modeling studies on phospholipase A2-inhibitor complexes.

Phospholipase A2 (PLA2) is a ubiquitous enzyme that specifically catalyzes hydrolysis of membrane phospholipids to produce lysophospholipids and free fatty acid, namely arachidonic acid, which provides substrate for eicosanoids biosynthesis. Thus, the compounds inhibiting PLA2 have been implicated as potential therapeutic agents in treatment of inflammation related diseases. Plant and marine organisms serve as sources of compounds that act as potential therapeutic agents for treatment of various diseases. The present study reveals the relationship between the structure and function of the medicinally important herbal compounds (acalyphin, chlorogenic acid, stigmasterol, curcumin and tectoridin) and marine compounds (gracilin A and aplysulphurin A). To understand the binding mechanisms of these compounds, molecular modeling studies has been performed with Russell's viper and bovine pancreatic PLA2 as target molecules using molecular operating environment (MOE) software. These compounds show favorable interactions with the amino acid residues at the active site of Russell's viper and bovine pancreatic PLA2, thereby substantiating their proven efficacy as anti-inflammatory compounds and antidotes.

Quantitative structure-activity relationship of some pesticides.

Herbicides (benzodiazepinediones), insecticides (dioxatricyclododecenes) and larvicides (N-oxalyl derivatives of tebufenozide) have been quantitatively investigated to explore the relationship between the molecular structure and their biological activity using molecular operating environment (MOE) software. The study provides good predictive models, cross-validated by leave-out-one method (Loo). The positive contribution of the descriptor n-O (count of oxygen atom) suggests the additional oxygen atom substitution at R1 position, in addition to benzodiazepine moiety is favorable for herbicidal activity, whereas the negative contribution of y component of dipole moment (Dip(y)) indicates that electronic interactions are also crucial for the activity. The negative correlation of V(SA)2 and globularity (Glo) descriptors clearly indicates that the volume, shape, and rigidity of tebufenozide derivatives determine their larvicidal activity. The biparametric model for insecticides shows that the indicator variable l(CH-CH3) and R(PC) (negative partial charge) are detrimental for its activity. Most of the active compounds in the series have shown less value for these descriptors. The derived QSAR models also provide valuable insights to optimize their toxicity, which remains a major concern for environment safety.

Ion pairs in non-redundant protein structures.

Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent-protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together. This paper deals with the possible ion pair combinations and networks in 25% and 90% non-redundant protein chains. Different types of ion pairs present in various secondary structural elements are analysed. The ion pairs existing between different subunits of multisubunit protein structures are also computed and the results of various analyses are presented in detail. The protein structures used in the analysis are solved using X-ray crystallography, whose resolution is better than or equal to 1.5 A and R-factor better than or equal to 20%. This study can, therefore, be useful for analyses of many protein functions. It also provides insights into the better understanding of the architecture of protein structure.

Iterative ACORN as a high throughput tool in structural genomics.

High throughput macromolecular structure determination is very essential in structural genomics as the available number of sequence information far exceeds the number of available 3D structures. ACORN, a freely available resource in the CCP4 suite of programs is a comprehensive and efficient program for phasing in the determination of protein structures, when atomic resolution data are available. ACORN with the automatic model-building program ARP/wARP and refinement program REFMAC is a suitable combination for the high throughput structural genomics. ACORN can also be run with secondary structural elements like helices and sheets as inputs with high resolution data. In situations, where ACORN phasing is not sufficient for building the protein model, the fragments (incomplete model/dummy atoms) can again be used as a starting input. Iterative ACORN is proved to work efficiently in the subsequent model building stages in congerin (PDB-ID: lis3) and catalase (PDB-ID: 1gwe) for which models are available.

Quantitative structure-activity relationship (QSAR) analysis of a series of indole analogues as inhibitor for human group V secretory phospholipase A2.

Phospholipase A2s (PLA2) are a class of enzymes, which catalyze the hydrolysis of membrane phospholipids at the sn-2 position to release fatty acids and lysophospholipids. When the fatty acid is arachidonic acid (AA), a complementary metabolism leads to pro-inflammatory mediators collectively known as eicosanoids. Thus, inhibiting PLA2 activity remains a prime target for the development of new drugs for the treatment of inflammation-related diseases. More than one type of PLA2s plays a major role in inflammatory disease conditions. In the present study, quantitative structure-activity relationship (QSAR) study was performed for a series of 48 Me-indoxam derivatives as human group V PLA, (hVPLA2) inhibitors, using molecular operating environment (MOE) software. The hVPLA2 is a secretory PLA2 (sPLA2), involved in eicosanoid formation in inflammatory cells such as macrophages and mast cells. These studies have come out with three good predictive models (r = 0.82-0.84), which are cross-validated (rcv = 0.68-0.70) by leave-out-one method (Loo). The positive correlation of spatial descriptor Pmiz with inhibitory activity shows that proper orientation of the substitution at R position towards Z-axis is necessary to facilitate the possible interactions of the indole core with active site residues of the PLA2 enzyme. The negative contribution of b_rotN (atom and bond count-type descriptor) suggests that increasing flexibility conferred by the R substitution is detrimental for the activity. In addition to the hVPLA2 inhibitory activity is found to be highly influenced by molecular size, energy and polarity of the Me-indoxam derivatives.