International Journal of Computational Bioinformatics and In Silico Modeling
ABSTRACT: Presently, environmental pollution is the most threatening event prevailing across the world. Bioremediation is the only emerging green technology for the catalysis of these pollutants. Microorganisms are largely play pivotal role in bioremediation technology. Rhodococcus pyridinivorans is an important bio warrior against a wide range of polycarbonated pollutants. Catechols 2, 3 dioxygenase, present in the bacteria help greatly to decompose such unhealthy environmental contaminants. The present study deals with physical and chemical characterization of catechols 2, 3 dioxygenase. Conserved domains present within this protein were also investigated. Secondary as well as tertiary structures were deduced and thermodynamic validation of the conjectured model was performed. Finally, ligand binding locations and protein-protein interaction map was generated to find out the interacting partners of the protein.
KeyWords: Bioaugmentation, Catechol 2, 3 dioxygenase, Biodegradation, Homology modeling.
How to cite: Anirban Bhar. Computational Exploration and in silico modeling of Catechol 2, 3 dioxygenase from Rhodococcus pyridinivorans: The Crucial Enzyme for Xenobiotic Clearance and Bioaugmentation. Int J Comput Bioinfo In Silico Model. 5(1) 2016: 761-769
ABSTRACT: The Leishmania donovani is a pathogenic protozoan that is responsible for the visceral leishmaniasis and iron superoxide dismutase (Fe-SOD) helps the pathogen to survive in the host. The properties and three dimensional structure of L. donovani Fe-SODB1 is unknown to the researcher and in these cases we have intended to characterize and predict the comparative model using various bioinformatics tools and servers. The amino acid sequence of Fe-SODB1 protein was retrieved from NCBI database and the model was built through Swiss-Model workspace with the selected template. Different evaluation server ensures the good quality of the protein model and the model submitted to the PMDB database (PM0080412). The Ramachandran plot showed 91.4% residues in the most favored regions. The physico-chemical properties revealed that the protein is stable, weakly acidic and hydrophilic in nature and the STRING server predict 10 interaction with other proteins. The COFACTOR server predicts the active and ligand binding sites and showed Fe bind with His76, Asp161, and His165 residues. The protein showed superoxide dismutase activity and metal ion binding activity as molecular function with significant sore which revealed the actual function of this protein. Finally, it can be anticipated that the structural and functional information of Fe-SODB1 will be helpful for further drug discovery research.
KeyWords: Superoxide dismutase; Comparative modeling; Ligand binding site and Protein-protein interaction.
How to cite: Utpal Kumar Adhikari et al. Characterization and comparative modeling of iron superoxide dismutase B1 (FeSODB1) of Leishmania donovani using an in silico approach. Int J Comput Bioinfo In Silico Model. 5(1) 2016: 770-779