Identification of a novel family of snake venom proteins Veficolins from Cerberus rynchops using a venom gland transcriptomics and proteomics approach.

Cerberus rynchops (dog-faced water snake) belongs to Homalopsidae of Colubroidea (rear-fanged snakes). So far, venom compositions of snakes of the Homalopsidae family are not known. To determine the venom composition of C. rynchops, we have used both transcriptomics and proteomics approaches. The venom gland transcriptome revealed 104 ESTs and the presence of three known snake protein families, namely, metalloprotease, CRISP, and C-type lectin. In addition, we identified two proteins that showed sequence homology to ficolin, a mammalian protein with collagen-like and fibrinogen-like domains. We named them as ryncolin 1 and ryncolin 2 (rynchops ficolin) and this new family of snake venom proteins as veficolins (venom ficolins). On the basis of its structural similarity to ficolin, we speculate that ryncolins may induce platelet aggregation and/or initiate complement activation. To determine the proteome, the whole C. rynchops venom was trypsinized and fractionated by reverse phase HPLC followed by MALDI-MS/MS analysis of the tryptic peptides. Analysis of the tandem mass spectrometric data indicated the presence of all protein families compared to the translated cDNA library. Overall, our combined approach of transcriptomics and proteomics revealed that C. rynchops venom is among the least complex snake venom characterized to date despite the presence of a new family of snake venom proteins.

Homology model of a novel thermostable xylanase from Bacillus subtilis-AK1.

Xylanases are glycosyl hydrolases that catalyze the hydrolysis of internal beta-1,4 glycosidic bonds of xylan, the major hemi-cellulose component of the plant cell wall. Enzymes such as xylanases are used considerably in industries. Their industrial usage is especially attractive since they can replace some of the environmental pollutants. We have earlier isolated a family 11-xylanase gene from Bacillus subtilis-AK1, which is active at high temperature as well as at alkaline pH. In order to understand the factors liable for the adaptation of this enzyme, three dimensional model of B. subtilis-AK1 xylanase has now been obtained by homology modeling. Modeling was carried out using Molecular Operating Environment (MOE) software developed by Chemical Computing Group Inc., running on Pentium IV workstation. The model showed that B. subtilis-AK1 xylanase having molecular weight around 20 kDa contains in its fold an alpha-helix and two beta-sheets packed against each other forming a beta-sandwich. The conserved active site amino acids E78R, Y80L were mutated in this novel B. subtilis-AK1 strain, but the protein folding and the function was maintained with high thermal stability. Several minor modifications appeared to be responsible for the increased thermo stability of AK1. Docking studies of the substrate xylan with -AK1 shows the possibility of the Arg 78 acting as the nucleophile instead of Glu 78.

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.