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Sinha, Jayanta
- Studies on Mode of Action of Cnidarian PLA2 Toxin from Adamsia palliata in Triggering Cytotoxicity in Human: an in Silico Approach
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Authors
Affiliations
1 Department of Zoology, B. C. College, Asansol, West Bengal, IN
2 Department of Zoology, Vivekananda College, Kolkata, West Bengal, IN
1 Department of Zoology, B. C. College, Asansol, West Bengal, IN
2 Department of Zoology, Vivekananda College, Kolkata, West Bengal, IN
Source
Journal of Environment and Sociobiology, Vol 13, No 1 (2016), Pagination: 1-14Abstract
Adamsia palliata releases Phospholipase A2 (PLA2) toxins of secretory nature. Phospholipase A2 toxin is predicted to act in two different ways. It either acts on TRPV1 channel in human by blocking them or may disrupt cell membrane and seem to catalyze the hydrolysis of 2-acyl ester bonds of 3-sn-phospholipids producing arachidonic acid and lysophospholipids through protein lipid interaction. This study attempts to in silico portray the bimodal action of PLA2 toxin by docking with Human TRPV1 receptor (Transient receptor potential vanilloid receptor1) and through PLA2 - lipid membrane interaction. Homology modeling of the PLA2 enzyme is performed through Swissmodel. Validation of 3D structure of modeled PLA2 toxin was carried out through servers, such as, ANOLEA, Prosa-II and Verify 3D. Cleft analysis and protein topology of both PLA2 toxin and TRPV1 receptor are carried out by PDBsum. Binding sites of both receptor and ligand were predicted through I-Tasser server. Docking of PLA2 toxin with TRPV1 receptor was analyzed through Cluspro docking server. Ramachandran plot of the docked model was determined through Prochek server. Seqmol server was used to predict the Kd value of the docked protein. Protein-protein interaction and determining H-bonded and non-bonded contacts between amino acids of PLA2 and TRPV1 receptor is performed through Ligplot program. Heliquest sotware was used to characterize lipid binding helices of PLA2 toxin and its physiochemical properties, such as, hydrophobicity, hydrophobic moment and net charge. Monte Carlo simulation of peptide (PLA2) and membrane lipid interaction were carried out through McPep server and diagrammatized using VLC media player. PLA2 toxin and cell membrane interaction and orientation in silico were visualized through ProBLM server. In silico study of this PLA2 toxin predicted that PLA2 may act through two different pathways. One is through interacting with Human TRPV1 receptor and the other by manipulating the helical lipid binding regions of this PLA2 toxin with respect to membrane. Thus this study tried to establish the mode of action of PLA2 toxin of Adamsia palliata on human cell membrane and its subsequent cytotoxicity, thus provides an insight on mechanistic functioning and better understanding of this type of toxin.Keywords
Phospholipase A2, Adamsia palliata, Cytotoxicity, Amphitropic Protein, TRPV1 Channel.
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- Biodiversity Informatics : A Silent Revolution for Management of Biological Diversity Data and Information
Abstract Views :266 |
PDF Views:0
Authors
Affiliations
1 Department of Zoology, B. B. College, Asansol, West Bengal, IN
2 Zoological Garden, Alipore, Kolkata, IN
3 Dept. of Botany, Hooghly Mohosin College, Chinsurah, Hooghly, IN
1 Department of Zoology, B. B. College, Asansol, West Bengal, IN
2 Zoological Garden, Alipore, Kolkata, IN
3 Dept. of Botany, Hooghly Mohosin College, Chinsurah, Hooghly, IN
Source
Journal of Environment and Sociobiology, Vol 8, No 1 (2011), Pagination: 69-78Abstract
Biodiversity is generally categorized into genetic diversity, species diversity and ecosystem diversity. As a part of the global initiative for conservation of biodiversity, floral, faunal and microbial diversity is to be documented providing detailed account of the species of all the countries and regions through an integrated and interactive information system. Such information system or Biodiversity Informatics helps in improved management, presentation, discovery, exploration and analysis of data and information on Biological Diversity.
Biodiversity data are grouped as Global data, Conservation areas data, Species data, Genetic data and Biological Reference Collections. Biodiversity Informatics and its activities may be utilised for different applications that include Forestry, Invasive alien species, Systematics and Evolutionary biology, Taxonomy and Identification systems. Further there must be development of new tools, services and standards for management and access of data.
There are many international efforts of generating and maintaining data on Biological Diversity. These are Bionet, Diversitas, Cenplank, Fishbase, Global Biodiversity Information Facility (GBIF), Forests Resource Assessments (FRA), GOOS, GTOS, IOPI, Ocean Biogeographic Information System (OBIS), MIRCENS and SPECIES 2000, etc.
Many Global Biodiversity Information Centers are developed all around the world. Some of them are Bird Life International, Conservation International, FAO, International Plant Genetic Resources Institute, IUCN, UNEP, Wetland International, WCMC, etc. In India, an attempt to portray vegetation cover, fragmentation, disturbance and biological richness across the landscape is organized in the form of Biodiversity Information System (BIS) under the joint supervision of Department of Space and Department of Biotechnology, Government of India. Further, Geographic Information System (GIS) and Remote Sensing (RS) have paved the way to map and analyze distribution of different biological resources. GIS based procedures can be successfully used for capturing spatial and environmental details on Biodiversity. At present there is a key trend to digitalize biodiversity data by collection, maintenance, and they are then distributed through user friendly Internet.