The Open Structural Biology Journal

2009, 3 : 75-83
Published online 2009 October 8. DOI: 10.2174/1874199100903010075
Publisher ID: TOSBJ-3-75

Molecular Docking Simulation of Short-Chain Four Disulphide Bridged Scorpion Toxins with Structural Model of Human Voltage-Gated Potassium Ion Channel Kv1.3

C. Sudandiradoss and Rao Sethumadhavan
Bioinformatics Division, School of Biotechnology, Chemical and Biomedical Engineering, Vellore Institute of Technology University, Vellore 632014, Tamil Nadu, India;

ABSTRACT

We report structural model of the human voltage-gated potassium ion channel Kv1.3 obtained based on the crystallographic structure of KcsA by homology modeling. Molecular docking simulations were performed between the model structure of Kv1.3 channel with three short-chain four disulphide bridged scorpion toxins HsTX1 from the venom of Heterometrus spinnifer (Scorpionidae), maurotoxin (MTX) from Scorpiomaurus palmatus and Pandinus toxin 1(Pi1) from Pandinus imperator which belongs to the α-KTx6 subfamily. By integrating the homology modeling and docking simulations we obtained the three dimensional structures of toxin-channel complexes. The final docked complexes were then subject to minimization with CHARMM force field and investigated key interacting residues, electrostatic interaction energies, binding free energies, disulphide bridge pairing determination, folding pattern, hydrogen bond formation, hydrophobic contacts and flexibilities between selected scorpion toxins to the Kv1.3 channel.

Keywords:

K channel, homology modeling, hydrophobic interactions, scorpion toxins.