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Helix A of bacteriorhodopsin was simulated by using molecular dynamics both in isolation and as part of the complete protein. A POPC lipid bilayer and an octane monolayer were used as model membranes. Comparison of various systems showed octane to be a good alternative to lipid bilayer membranes providing fast equilibration, increased sampling, and decreased computational cost. Similarly single-helix simulations were found to capture some of the details of the full-protein simulations. In particular, aromatic side chains were found to anchor in identical conformations in all simulations, regardless of the absence of a lipid-water interface or the remainder of the protein. Simulations displayed a remarkable robustness with respect to simulation parameters and system set up.

Type

Journal article

Journal

Journal of Physical Chemistry B

Publication Date

15/07/2004

Volume

108

Pages

10149 - 10159