An insight to conserved water molecular dynamics of catalytic and structural Zn(+2) ions in matrix metalloproteinase 13 of human

Matrix Metalloproteinase (MMP)--13 or Collagenase--3 plays a significant role in the formation and remodeling of bone, tumor invasion and causes osteoarthritis. Water molecular dynamic studies of the five (1XUC, 1XUD, 1XUR, 456C, 830C) PDB and solvated structures of MMP-13 in human have been carried out upto 5 ns on assigning the differential charges (+2, +1, +0.5 e) to both the Zinc ions. The MM and MD-studies have revealed the coordination of three water molecules (W(H), W(I) and W(S)) to Zn(c) and one water to Zn(s). The transition of geometry around the Znc from tetrahedral to octahedral via trigonal bipyramidal, and for Zn(s) from tetrahedral to trigonal bipyramidal are seem interesting. Recognition of two zinc ions through water molecular bridging (Zn(c) - W(H) (W(1))...W(2)....W(3)....H(187) Zn(s)) and the stabilization of variable coordination geometries around metal ions may indicate the possible involvement of Zn(c) ...Zn(s) coupled mechanism in the catalytic process. So the hydrophilic topology and stereochemistry of water mediated coupling between Zn-ions may provide some plausible hope towards the design of some bidentate/polydentate bridging ligands or inhibitors for MMP-13.     

Removal of enzymatic and fermentation inhibitory compounds from biomass slurries for enhanced biorefinery process efficiencies

Within the biorefinery paradigm, many non-monomeric sugar compounds have been shown to be inhibitory to enzymes and microbial organisms that are used for hydrolysis and fermentation. Here, two novel separation technologies, polyelectrolyte polymer adsorption and resin-wafer electrodeionization (RW-EDI), have been evaluated to detoxify a dilute acid pretreated biomass slurry. Results showed that detoxification of a dilute acid pretreated ponderosa pine slurry by sequential polyelectrolyte and RW-EDI treatments was very promising, with significant removal of acetic acid, 5-hydroxymethyl furfural, and furfural (up to 77%, 60%, and 74% removed, respectively) along with >97% removal of sulfuric acid. Removal of these compounds increased the cellulose conversion to 94% and elevated the hydrolysis rate to 0.69 g glucose/L/h. When using Saccharomyces cerevisiae D₅A for fermentation of detoxified slurry, the process achieved 99% of the maximum theoretical ethanol yield and an ethanol production rate nearly five-times faster than untreated slurry.     

Fluorescent water soluble polymers for isozyme-selective interactions with matrix metalloproteinase-9

Matrix metalloproteinases (MMPs) are overexpressed in various pathological conditions, including cancers. Although these isozymes have similar active sites, the patterns of exposed amino acids on their surfaces are different. Herein, we report the synthesis and molecular interactions of two water soluble, fluorescent polymers which demonstrate selective interactions with MMP-9 compared to MMP-7 and -10.     

Odorant binding protein based biomimetic sensors for detection of alcohols associated with Salmonella contamination in packaged beef

Detection of food-borne bacteria present in the food products is critical to prevent the spread of infectious diseases. Intelligent quality sensors are being developed for detecting bacterial pathogens such as Salmonella in beef. One of our research thrusts was to develop novel sensing materials sensitive to specific indicator alcohols at low concentrations. Present work focuses on developing olfactory sensors mimicking insect odorant binding protein to detect alcohols in low concentrations at room temperature. A quartz crystal microbalance (QCM) based sensor in conjunction with synthetic peptide was developed to detect volatile organic compounds indicative to Salmonella contamination in packaged beef. The peptide sequence used as sensing materials was derived from the amino acids sequence of Drosophila odorant binding protein, LUSH. The sensors were used to detect alcohols: 3-methyl-1-butanol and 1-hexanol. The sensors were sensitive to alcohols with estimated lower detection limits of <5 ppm. Thus, the LUSH-derived QCM sensors exhibited potential to detect alcohols at low ppm concentrations.     

Implications for health and disease in the genetic signature of the Ashkenazi Jewish population

Background

Relatively small, reproductively isolated populations with reduced genetic diversity may have advantages for genomewide association mapping in disease genetics. The Ashkenazi Jewish population represents a unique population for study based on its recent (< 1,000 year) history of a limited number of founders, population bottlenecks and tradition of marriage within the community. We genotyped more than 1,300 Ashkenazi Jewish healthy volunteers from the Hebrew University Genetic Resource with the Illumina HumanOmni1-Quad platform. Comparison of the genotyping data with that of neighboring European and Asian populations enabled the Ashkenazi Jewish-specific component of the variance to be characterized with respect to disease-relevant alleles and pathways.

Results

Using clustering, principal components, and pairwise genetic distance as converging approaches, we identified an Ashkenazi Jewish-specific genetic signature that differentiated these subjects from both European and Middle Eastern samples. Most notably, gene ontology analysis of the Ashkenazi Jewish genetic signature revealed an enrichment of genes functioning in transepithelial chloride transport, such as CFTR, and in equilibrioception, potentially shedding light on cystic fibrosis, Usher syndrome and other diseases over-represented in the Ashkenazi Jewish population. Results also impact risk profiles for autoimmune and metabolic disorders in this population. Finally, residual intra-Ashkenazi population structure was minimal, primarily determined by class 1 MHC alleles, and not related to host country of origin.

Conclusions

The Ashkenazi Jewish population is of potential utility in disease-mapping studies due to its relative homogeneity and distinct genomic signature. Results suggest that Ashkenazi-associated disease genes may be components of population-specific genomic differences in key functional pathways.     

In vitro activity of 5-(2,4-dimethylbenzyl) pyrrolidin-2-one extracted from marine Streptomyces VITSVK5 spp. against fungal and bacterial human pathogens

BackgroundPharmacological screening and usage of natural products for the treatment of human diseases has had a long history from traditional medicine to modern drugs. The majority of modern drugs are reported to be mostly from natural products.ObjectiveThe aim of the present study was to evaluate the inhibitory activity of 5-(2,4-dimethylbenzyl) pyrrolidin-2-one (DMBPO) extracted from marine Streptomyces VITSVK5 spp. isolated from sediment samples collected at Marakkanam coast of Bay of Bengal, India.MethodsThe lead compound was isolated by bioactive guided extraction and purified by silica gel column chromatography. Structural elucidation of the lead compound was carried out by using UV, FT-IR, ¹H NMR, ¹³C NMR, DEPT and HR-MS spectral data.ResultsSystematic screening of isolates for antimicrobial activity lead to identification of a potential strain, Streptomyces VITSVK5 spp. (GQ848482). Bioactivity guided extraction yielded a compound DMBPO and its inhibitory activity was tested against selected bacterial and fungal strains. DMBPO showed maximal activity against Escherichia coli with a MIC value of 187 μg/ml, followed by Klebsiella pneumoniae (MIC of 220 μg/ml and 10.3 mm zone of inhibition), Staphylococcus aureus (MIC of >1000 μg/ml and 4.4 mm zone of inhibition) and Bacillus subtilis (MIC of 850 μg/ml and 2.6 mm zone of inhibition). Furthermore, DMBPO was found to be a potent inhibitor of opportunistic fungal pathogens too. It showed a maximum activity against Aspergillus niger with a MIC value of 1 μg/ml and 28 mm zone of inhibition.ConclusionThe result of this study indicates that DMBPO possess antibiotic activity to selected bacterial and fungal pathogens and exhibited better activity against fungi than bacteria.     

Pongaglabol,a new hydroxyfuranoflavone,and aurantiamide acetate,a dipeptide from the flowers of Pongamia glabra

Pongaglabol, a new hydroxyfuranoflavone, and aurantiamide acetate, a rarely occurring modified phenylalanine dipeptide, have been isolated together with 4 furanoflavones, karanjin, lancheolatin B, kanjone and pinnatin, a simple flavone, kanugin, a chromenoflavanone (?)-isolonchocarpin, two furanodiketones pongamol and ovalitenone, and β-sitosterol from the petrol and chloroform extracts of the flowers of Pongamia glabra. The structure of pongaglabol has been established as 5-hydroxyfurano(8,7-4″,5″)flavone on the basis of spectral and chemical evidence.