Simulation studies on bacteriorhodopsin alpha-helices

Bacteriorhodopsin (BR) is a membrane protein which pumps protons through th e plasma membrane. Transmembrane BR helical segments are subjected to simul ation studies in order to investigate the effect of bilayer environment in various simulation conditions. A bilayer potential is introduced to the sys tem to mimic the lipid membrane. The structures from the simulations are co mpared with the experimentally determined structures in terms of geometrica l properties. Electrostatic contribution to the helix packing is also inves tigated. The simulation results show that the packing geometry of the trans membrane helices is highly affected by the bilayer potential. The results o btained from the simulations may be used for further simulation studies and analysis in investigating transmembrane helix packing.