Informatics Publishing Limited

R. Barani Kumar ¹, M. Xavier Suresh

Affiliations
1 Department of Bioinformatics, Sathyabama University, Jeppiar Nagar, Rajiv Gandhi Road, Chennai – 600 119, IN

Abstract

A serious of biological studies proves the functions of ion channel proteins and its function. Toxin is one of the best tool reveals the information about ion channels. Slotoxin, from Centruroides noxius plays an important role on blocking of calcium activated potassium channels. In this study we predicted 3D structure slotoxin using comparative modeling method. The predicted model shows 100% residues in allowed conformation. Then protein-protein interaction studies were performed with ion channel protein using ZDOCK and refined with RDOCK and obtained best RDock score of 96.331. Molecular dynamics (MD) simulation studies carried out to know the binding potency and intermolecular interactions. From the overall study we identified the key residues responsible for inhibitions are Thr1, Cys7, Thr8, Lys11, Cys28, Lys31 and Tyr36. The total energy of the protein-protein complex were -7830.152 kcal/mol. The result of these studies will used for identifying a better inhibitor to neutralize the effect of toxin in future.

Keywords

Slotoxin, Comparative Modeling, ZDock, RDock, Molecular Dynamics, Ion Channel, Simulation.

Full Text

     

Balasankar Karavadi ¹, M. Xavier Suresh ¹

Affiliations
1 Department of Bioinformatics, Sathyabama University, Chennai-600119, IN

Abstract

Streptococcus pneumoniae is the major bacterial pathogen causing severe respiratory infections such as pneumonia, meningitis and septicaemia. HUNGARY19A-6 strain of Streptococcus pneumoniae is extremely virulent in pneumococcal pathogenesis which contains rpLD gene which synthesis Ribosomal protein L4. In this article we performed the insilico modeling studies of the virulent protein which is synthesized by the rpLD gene and validated the nature of the receptor based on their atomic interactions for future drug target for HUNGARY19A-6 strain of Streptococcus pneumoniae. We have also analyzed drug targets for the above mentioned protein by using the virtual structure based ligand screening approach. Protein-ligand complexes have been analyzed by docking studies using Discovery Studio and interactions have also been visualized along with the validation of pharmacokinetic descriptors.

Keywords

Pneumonia, Streptococcus pneumoniae, Ribosomal Protein , Hungary19 A-6, Homology, Molecular Docking.

Full Text