In Silico Characterization and Motif Election of Neurotoxins from Snake Venom

Abstract

Snake venom is a mixture of many biological components. Snakes usually use their venomic armory to tackle different prey and predators in adverse natural world. Among various components of the snake venom, neurotoxins play an important role in exerting effect by blocking the neuromuscular transmission through selective binding to muscle nicotinic Acetyl-Choline Receptors (nAChR). A set of 30 reference protein sequences representing neurotoxin of snake venom were retrieved from NCBI protein database and characterized for various physic-chemical properties, Multiple Sequence Alignment (MSA), phylogenetic analysis and motifs election. The physic-chemical properties of the selected proteins were analyzed by using ExPASy's Prot Param tool and it was found that the Molecular Weight (M.Wt) of maximum proteins is around 10000 Da. Isoelectric points (pI) of all the organisms were found to be basic in nature. The aliphatic index infers that neurotoxins showed the tendency of having both wide and low range of temperature as 16 proteins showed AI above 70 and others showed AI value below 70. The negative value of GRAVY indicates that there will be better interaction with water. The secondary structure prediction was done by SOPMA which showed that random coils dominated all the other conformations. Multiple sequence analysis and Phylogenetic analysis of neurotoxins were carried out by MEGA 5. Motif election was done by MEME which represents motif 1 (21 sequences), Motif 2 (11 sequences), Motif 3 (3 sequences) and these indicates the region also indicates the DUF3963, Toxin_1 (PF008), CAP (PF0188) protein family respectively which was done by Pfam. Motif 2 gives the insight of functional domain for neurotoxins and also suggests the degenerate primer for neurotoxin protein family.