Background: Serine proteases are a group of enzymes that hydrolyses the
peptide bonds in proteins. In mammals, these enzymes help in the regulation of
several major physiological functions such as digestion, blood clotting, responses of
immune system, reproductive functions and the complement system.
Objective: Serine proteases obtained from the venom of Octopodidae family is a relatively
unexplored area of research. In the present work, we tried to effectively utilize
comparative composite molecular modeling technique. Our key aim was to propose the
first molecular model structure of unexplored serine protease 5 derived from big blue
octopus. The other objective of this study was to analyze the distribution of negatively and
positively charged amino acid over molecular modeled structure, distribution of secondary
structural elements, hydrophobicity molecular surface analysis and electrostatic potential
analysis with the aid of different bioinformatic tools.
Methods: In the present study, molecular model has been generated with the help of
I-TASSER suite. Afterwards the refined structural model was validated with standard
methods. For functional annotation of protein molecule we used Protein Information
Resource (PIR) database. Serine protease 5 of big blue octopus was analyzed with
different bioinformatical algorithms for the distribution of negatively and positively
charged amino acid over molecular modeled structure, distribution of secondary
structural elements, hydrophobicity molecular surface analysis and electrostatic
potential analysis. The functionally critical amino acids and ligand- binding site
(LBS) of the proteins (modeled) were determined using the COACH program.
Result: The molecular model data in cooperation to other pertinent post model
analysis data put forward molecular insight to proteolytic activity of serine protease
5, which helps in the clear understanding of procoagulant and anticoagulant
characteristics of this natural lead molecule.
Conclusion: Our approach was to investigate the octopus venom protein as a whole
or a part of their structure that may result in the development of new lead molecule.