Membrane Protein Simulations: Modelling a Complex Environment
Bond PJ., Cuthbertson J., Deol SS., Forrest LR., Johnston J., Patargias G., Sansom MSP.
Molecular dynamics simulations of membrane proteins are reviewed, with especial attention to exploration of the interactions between membrane proteins and their environment. Environments of membrane proteins that have been studied include: (i) solvent mixtures; (ii) detergent micelles; and (iii) lipid bilayers. Mixtures of water and non-aqueous solvents mimic a membrane via local clustering of solvent molecules to provide an anisotropic micro-environment for the protein. Detergent molecules exploit interaction sites on the protein surface that in vivo are occupied by lipid molecules. Simulations present a dynamic picture of lipid/protein interactions, and are starting to reveal specific lipid interaction sites on the surfaces of membrane proteins. More recently it has proved possible to use MD simulations to look at large scale dynamic events, such as self-assembly of protein/detergent micelles. The future will see an expansion of simulation studies to a range of large scale dynamic membrane and membrane protein phenomena.