Vol. 7, Issue 1 (2018)
A computational characterization and motif election analysis of metalloproteinase proteins from different venomous snake species
Author(s): Mst. Ferdowsi Mahal, Md. Azizul Islam, Md. Kazy Ebnul Hasan, Razia Sultana, Md. Samiul Islam and Md. Amit Hasan
Abstract: Snake venom is a complex mixture of many proteins and polypeptides which have pharmacological activities. These protein components usually comprise a highly evolved and organized armory of biomolecules that attack, often with precision and coordinated synergism, a wide range of molecular targets vital for physiological processes. Snake venom metalloproteinases (SVMPs) are one of the main toxin proteins widely distributed in snake venoms and play significant roles in neurodegenerative disorders, hemostatic disorders and local tissue damage that follows snakebite. The impact of SVMPs on hemostasis has been extensively studied showing diverse effects on soluble factors as well as cellular components. The action of SVMPs involves catalytic and anti-adhesive properties with direct cellular activation or the release of endogenous bioactive components. In this study, a total of 16 metalloproteinases protein sequences were retrieved from NCBI protein database and characterized for different physic-chemical properties, Multiple Sequence Alignment (MSA), phylogenetic analysis and motifs election. ExPASy’s Prot Param tool was used to analyze the physic-chemical properties of the selected proteins. The Molecular Weight (M.Wt) ranges from 27813.6 to 69554.9 Da, Isoelectric points (pI) of ten distinct snake species were found to be acidic in nature and remaining six basic behaviors. The aliphatic index figure outs studied metalloproteinases illustrated the tendency of having both wide and low range of temperature as 9 proteins showed AI above 70 and others showed AI value below 70. The lower GRAVY value signifies that there will be better interaction of protein with water. The secondary structure prediction was carried out by SOPMA which showed that random coils dominated all the other conformations. Multiple sequence analysis and Phylogenetic analysis of metalloproteinases were done by MEGA 5. Motif election was completed by MEME which signifies motif 1 (13 sequences), Motif 2 (15 sequences), Motif 3 (15 sequences) and these shows the region which was done by Pfam also allude the reprolysin protein family.
How to cite this article:
Mst. Ferdowsi Mahal, Md. Azizul Islam, Md. Kazy Ebnul Hasan, Razia Sultana, Md. Samiul Islam and Md. Amit Hasan. A computational characterization and motif election analysis of metalloproteinase proteins from different venomous snake species. Journal of Pharmacognosy and Phytochemistry. 2018; 7(1): 290-295.