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

Document Type : Research Paper




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.