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Bacteriorhodopsin (BR) is a membrane protein which pumps protons through the plasma membrane. Transmembrane BR helical segments are subjected to simulation studies in order to investigate the effect of bilayer environment in various simulation conditions. A bilayer potential is introduced to the system to mimic the lipid membrane. The structures from the simulations are compared with the experimentally determined structures in terms of geometrical properties. Electrostatic contribution to the helix packing is also investigated. The simulation results show that the packing geometry of the transmembrane helices is highly affected by the bilayer potential. The results obtained from the simulations may be used for further simulation studies and analysis in investigating transmembrane helix packing.

Type

Journal article

Journal

Eur Biophys J

Publication Date

2000

Volume

28

Pages

674 - 682

Keywords

Amino Acid Sequence, Bacteriorhodopsins, Computer Simulation, Dimerization, Kinetics, Lipid Bilayers, Membrane Potentials, Models, Molecular, Molecular Sequence Data, Peptide Fragments, Time Factors