Energy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations

Potassium Channels allow potassium flux and are essential for the generation of electric current across excitable membranes. Potassium Channels are also the targets of various intracellular control mechanisms; such that the suboptimal regulation of channel function might be related to pathological conditions. Realistic studies of ion current in biologic channels present a major challenge for computer simulation approaches. Molecular dynamics simulations may be used to probe the interactions of membrane proteins with lipids and with detergents at atomic resolution .Examples of such simulations for ion channels and for bacterial outer membrane has already been studied. In this work, to characterize protein behavior, we observed quantities such as gyration radius and energy average. It was studied the changes of these factors for potassium channel Protein in gas, water, Methanol and Ethanol phases with native conformation by Monte Carlo, Molecular and Langevin Dynamics simulations. Monte Carlo simulation is stochastic method and therefore, is the best method to evaluate the radius of gyration in gas phase. when the temperature is increased the kinetic energy is increased too, and its correlation is linear. All the calculations were carried out By Hyperchem 8.0 program. The radius of gyration for different solvent is calculated by VMD 1.8.7 Software. The determination of gyration radius is a spectacular for configuration of a Macromolecule. It also reflects molecular compactness shape. Monte Carlo simulation is the best method to evaluate gyration radius.