Interactions of a transmembrane helix and a membrane: Comparative simulations of bacteriorhodopsin helix A
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 pro...
| Main Authors: | , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
2004
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| Summary: | 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. |
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