Study of Structural Changes in Bacteriorhodopsin by Microwave Absorption Using Molecular Dynamics Simulation

Bacteriorhodopsin (bR) is a membrane protein that acts as a light-driven proton pump in Halobacterium salinarum. This protein contains seven transmembrane α-helical subunits, helices A–G, one beta-sheet and a retinal chromophore. Studies show that bR have the property of absorbing the microwave. Among several methods molecular dynamics simulation (MD) is the most systemic approach. With this method we can study structural changes and dynamic of macromolecules. In this project, we use modeling and molecular dynamic simulation. To obtain more accurate structures after the equilibration a 15 ns MD simulation was done. After that, in order to find the effective sites of microwave absorption on bR a production run was performed with applying electric field in the time intervals of 786 ps that is equal to one sinusoidal frequency at microwave spectrum. At last, conformational changes under effect of sinusoidal wave has been assigned the effective sites of microwave absorption in the protein. Our study shows that microwave in the frequency of 8 GHZ and the time interval that mentioned above, cannot make significant changes on the protein. In the other hand, we have seen some reversible changes in Beta-sheet and D, C, B helices.