Title:Molecular Modeling and Structural Analysis of Some Snake Venom Specific Toxin Proteins and Cognate Non-Toxin Proteins of Other Chordates
VOLUME: 14 ISSUE: 1
Author(s):Subhamay Panda and Goutam Chandra
Affiliation:Mosquito, Microbiology and Nanotechnology Research Units, Parasitology Laboratory, Department of Zoology, The University of Burdwan, Burdwan -713104, West Bengal
Keywords:Snake venom, cytotoxin, short neurotoxin, molecular modeling, structural analysis, drug designing.
Abstract:Background: Protein three-dimensional structures are very much important
in terms of functional and evolutionary context. In the present work we evaluated the
snake venom constituent cytotoxin, short neurotoxin and related non-toxin proteins of
other chordates with reference to structure prediction, validation of the models,
distribution of secondary structural elements, hydrophobicity molecular surface
analysis, functional annotation and functionally critical binding site identification with
the assistance of different bioinformatical tools.
Methods: Homology models have been generated with the help of Swiss-model and ITASSER
suite during the present study. Afterwards the refined structural models were
validated with standard methods. For functional annotation of protein molecules we
used Protein Information Resource (PIR) database. The functionally critical amino acids
and ligand- binding site (LBS) of the proteins (modeled) was determined using the
COACH program.
Results: Structural analysis of snake venom toxin proteins and related non-toxin
proteins of other chordates elucidated their structural level conservation of molecular
structural surfaces and biophysical characteristics to different extents. Different
structural level improvement strategies were observed which are necessary for better
system dependent adaptation to diverse biological environment and functional
necessities of these protein molecules.
Conclusion: Molecular models and their structural characterization of these proteins as
documented in this study may provide a valuable aid for drug designing in future.
