ISSN 2736-1756
Advanced Journal of Microbiology Research ISSN 2241-9837 Vol. 12 (11), pp. 001-009, November, 2018. © International Scholars Journals
Full Length Research Paper
Nanomolecular simulation of the voltage–gated potassium channel protein by gyration radius study
F. Mollaamin1*, I. Layali2, A. R. Ilkhani3 and M. Monajjemi1
1Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran, Iran.
2Science and Research Branch, Islamic Azad University, Tehran, Iran.
3Department of Chemistry, Yazd Branch, Islamic Azad University, Yazd, Iran.
Accepted 23 July, 2018
Abstract
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 have already been studied. The molecular potassium channel function is universally conserved. 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. In this work, to characterize protein behavior, we observed quantities such as gyration radius and energy average. We studied the changes of these factors for voltage – gated potassium channel protein in gas phase with native conformation by Monte Carlo, Molecular and Langevin Dynamics simulations. Monte Carlo simulation is a stochastic method and therefore, is the best method to evaluate the radius of gyration. 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 determination of gyration radius is spectacular for configuration of a macromolecule. It also reflects molecular compactness shape. The radius of gyration is calculated by VMD 1.8.7 software.
Key words: Monte Carlo simulation, molecular dynamics simulation, Langevin dynamics simulation, protein folding, gyration radius.