Molecular dynamics simulation study of nerve ion channel

Ion channels are naturally occurring proteins that form hole in membrane. They play multiple roles in many important biological processes. Deletion or alteration of these channels often leads to serious problems in the physiological processes as it controls the flow of ions through it. The proper maintenance of the flow of ions, in turn, is required for normal health. The role of ions channels are now a proved factor behind nerve impulse. Here we have analyzed the nerve ion channel protein, with PDB entry 1BL8, which is basically an ion channel protein in Streptomyces Lividans. The equilibrium energy as well as molecular dynamics simulation is performed first. The possibility of ligand binding is investigated. The change of channel structure is found to be dependent on ligand binding. Implicit water model of the protein is subjected to molecular dynamics simulation to find their energy minimized value. Simulation of the protein in the environment of water and ions has given us important results too.