A novel and efficient tool for locating and characterizing protein cavities and binding sites

Systematic investigation of a protein and its binding site characteristics are crucial for designing small molecules that modulate protein functions. However, fundamental uncertainties in binding site interactions and insufficient knowledge of the properties of even well‐defined binding pockets can make it difficult to design optimal drugs. Herein, we report the development and implementation of a cavity detection algorithm built with HINT toolkit functions that we are naming Vectorial Identification of Cavity Extents (VICE). This very efficient algorithm is based on geometric criteria applied to simple integer grid maps. In testing, we carried out a systematic investigation on a very diverse data set of proteins and protein–protein/protein–polynucleotide complexes for locating and characterizing the indentations, cavities, pockets, grooves, channels, and surface regions. Additionally, we evaluated a curated data set of unbound proteins for which a ligand‐bound protein structures are also known; here the VICE algorithm located the actual ligand in the largest cavity in 83% of the cases and in one of the three largest in 90% of the cases. An interactive front‐end provides a quick and simple procedure for locating, displaying and manipulating cavities in these structures. Information describing the cavity, including its volume and surface area metrics, and lists of atoms, residues, and/or chains lining the binding pocket, can be easily obtained and analyzed. For example, the relative cross‐sectional surface area (to total surface area) of cavity openings in well‐enclosed cavities is 0.06 ± 0.04 and in surface clefts or crevices is 0.25 ± 0.09. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Fortification of sorghum (Sorghum vulgare) and pearl millet (Pennisetum glaucum) flour with zinc

Deficiency of zinc is believed to be as widespread as that of iron, with equally serious consequences. Fortification of staple foods with this mineral is a cost-effective method that can be used to combat this deficiency. In the present study, flours of pearl millet and sorghum were evaluated as vehicles for fortification with zinc. Zinc stearate was used as the fortificant, and added at a level that provided 5 mg Zn/100 g flour. The metal chelator EDTA was used as a co-fortificant, the molar ratio of exogenous Zn:EDTA being 1:1. Bioaccessibility of zinc from the fortified flours, both raw and cooked, was determined by an in vitro simulated gastrointestinal digestion procedure. The results of the study revealed that there were differences among these two flours with respect to the feasibility of fortification with zinc. Although fortified pearl millet flour provided a higher amount of bioaccessible zinc, this was attributable to the presence of EDTA, rather than to the fortified zinc. The benefit of fortification with zinc was more evident in sorghum flour, compared to that in pearl millet flour, the increase in bioaccessible zinc content being more than 1.5 times higher as a result of fortification. Fortified sorghum and pearl millet flours were stable during storage for a period of up to 60 days. Thus, millet flours seem to be satisfactory candidates for fortification with zinc, and can be exploited to address zinc deficiency.     

Micropropagation of a tropical fruit tree Spondias mangifera Willd. through direct organogenesis

An efficient in vitro propagation is described for Spondias mangifera Willd., a medicinally important tree, using nodal explants obtained from 4-week-old seedlings. The frequency of shoot regeneration from seedling node was affected by various concentrations of BAP and successive transfer of mother explant. MS (Murashige and Skoog, Physiol Plant 15:473–497, 1962) medium supplemented with 1.0 mg l⁻¹ of 6-benzylaminopurine (BAP) was optimal for shoot multiplication. Upon this medium, highest number of shoots (about 10.6) per explants was obtained after fourth subculture of mother explants. Half-strength MS medium containing IAA (1.0 mg l⁻¹) was most effective for rooting of shoots. Regenerated plantlets were successfully acclimatized and transferred into soil with 80–90% survival rate. The regenerated plants were morphologically uniform and exhibited similar growth characteristics and vegetative morphology to the mother plants. This is the first report on micropropagation of S. mangifera, which can be applied for further genetic transformation assays and pharmaceutical purposes.     

Network based analysis of hepatitis C virus core and NS4B protein interactions

Hepatitis C virus (HCV) is a major cause of chronic liver disease worldwide. Here we attempt to further our understanding of the biological context of protein interactions in HCV pathogenesis, by investigating interactions between HCV proteins Core and NS4B and human host proteins. Using the yeast two-hybrid (Y2H) membrane protein system, eleven human host proteins interacting with Core and 45 interacting with NS4B were identified, most of which are novel. These interactions were used to infer overall protein interaction maps linking the viral proteins with components of the host cellular networks. Core and NS4B proteins contribute to highly compact interaction networks that may enable the virus to respond rapidly to host physiological responses to HCV infection. Analysis of the interaction networks highlighted enriched biological pathways likely influenced in HCV infection. Inspection of individual interactions offered further insights into the possible mechanisms that permit HCV to evade the host immune response and appropriate host metabolic machinery. Follow-up cellular assays with cell lines infected with HCV genotype 1b and 2a strains validated Core interacting proteins ENO1 and SLC25A5 and host protein PXN as novel regulators of HCV replication and viral production. ENO1 siRNA knockdown was found to inhibit HCV replication in both the HCV genotypes and viral RNA release in genotype 2a. PXN siRNA inhibition was observed to inhibit replication specifically in genotype 1b but not in genotype 2a, while SLC25A5 siRNA facilitated a minor increase in the viral RNA release in genotype 2a. Thus, our analysis can provide potential targets for more effective anti-HCV therapeutic intervention.     

Methanogenic diversity studies within the rumen of Surti buffaloes based on methyl coenzyme M reductase A (mcrA) genes point to Methanobacteriales

Methane emissions from ruminant livestock are considered to be one of the more potent forms of greenhouse gases contributing to global warming. Many strategies to reduce emissions are targeting the methanogens that inhabit the rumen, but such an approach can only be successful if it targets all the major groups of ruminant methanogens. Therefore, basic knowledge of the diversity of these microbes in breeds of buffalo is required. Therefore, the methanogenic community in the rumen of Surti buffaloes was analyzed by PCR amplification, cloning, and sequencing of methyl coenzyme M reductase (mcrA) gene. A total of 76 clones were identified, revealing 14 different sequences (phylotypes). All 14 sequences were similar to methanogens belonging to the order Methanobacteriales. Within Methanobacteriales, 12 clones (6 OTUs) were similar to Methanosphaera stadtmanae and the remaining 8 phylotypes (64 clones) were similar to unclassified Methanobacteriales. Overall, members of the Methanobacteriales dominated the mcrA clone library in the rumen of Surti buffalo. Further studies and effective strategies can be made to inhibit the growth of Methanobacteriales to reduce methane emission from the rumen which would help in preventing global warming.     

Difuranonaphthoquinones from Plumbago zeylanica roots

The naphthoquinones, lapachol (1), plumbagin (2), 2-isopropenyl-9-methoxy-1,8-di-oxa-dicyclopenta[b,g]naphthalene-4,10-dione (3), 9-hydroxy-2-isopropenyl-1,8-dioxa-dicyclopenta[b,g]naphthalene-4,10-dione (4), 2-(1-hydroxy-1-methyl-ethyl)-9-methoxy-1,8-dioxa-dicyclopenta[b,g]naphthalene-4,10-dione (5) and 5,7-dihydroxy-8-methoxy-2-methyl-1,4-naphthoquinone (6) were isolated isolated from roots of Plumbago zeylanica. The new constituents (3–5) in addition to known compounds (1, 2 and 6) were characterized by spectral analysis (UV, IR, 1D & 2D NMR and MS).     

Synthesis and antitubercular activities of bis-glycosylated diamino alcohols

Conjugate addition of diamines to glycosyl olefinic esters 1a and 1b followed by reduction of resulting bis-glycosyl beta-amino esters (2-7 and 14-19) with lithium aluminium hydride led to the respective glycosyl amino alcohols (8-13 and 20-25) in moderate to good yields. All the compounds were evaluated for antitubercular activity against Mycobacterium tuberculosis H(37)Ra and H(37)Rv. Few of the compounds exhibited antitubercular activity with MIC as low as 6.25-3.12microg/mL in virulent and avirulent strains. Compound 13 was found to be active against MDR strain and showed mild protection in mice.     

Influence of extrinsic factors on granulation in UASB reactor

The aim of this mini-review is to synthesize and analyze information on how the process of granulation is affected by environmental and operational conditions in the reactor. The factors reviewed are temperature, pH, alkalinity, organic loading rate, upflow velocity, nature and strength of substrate, nutrients, multivalent cations and heavy metals, microbial ecology of seed sludge, exo-cellular polymer, and addition of natural and synthetic polymers. Careful temperature control and adequate alkalinity is required for generation and maintenance of granules. Nature and strength of substrate in conjunction with intra-granular diffusion to a large extent determines the microstructure of the granules. The divalent cations such as calcium and iron may enhance granulation by ionic bridging and linking exo-cellular polymers. However, their presence in excess may lead to cementation due to precipitation leading to increased ash content and mass transfer limitation. The addition of external additives such as ionic polymers may enhance granulation in the upflow anaerobic sludge blanket reactors.