Gyration Radius and Energy Study at Different Temperatures for Acetylcholine Receptor Protein in Gas Phase by Monte Carlo, Molecular and Langevin Dynamics Simulations

Subject Areas : Journal of Physical & Theoretical Chemistry

M. Monajjemi ¹ , A. R. Oliaey ²

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Received: 2015-05-09 Accepted : 2015-05-09 Published : 2009-02-01

Keywords: Protein folding, Monte Carlo simulation, Molecular dynamics simulation, langevin dynamics&#x0D, &#x0D, simulation, Gyration Radius,

Abstract :

The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with native structure, - helix and - sheet conformation by Monte Carlo, Molecular andlangevin dynamics simulations. It was found when the temperature is increased the kinetic energyis increased too, and its diagram is linear. Monte Carlo simulation is a stochastic method andtherefore, is the best method to evaluate gyration radius. Considering the gained values fromMonte Carlo, Molecular and langeving dynamics simulations for - helix conformation and littledeviations from the experimental value, it can be understood that the second structure of thisprotein is the kind in which - helix is more. All the calculations were carried out usingHyperchem 8.0 program package. Gyration radius is calculated using VMD 1.8.6 Software.