Molecular Modeling and Structural Analysis of Some Snake Venom Specific Toxin Proteins and Cognate Non-Toxin Proteins of Other Chordates.

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.