Thomas D. Newport, Mark S.P. Sansom, Phillip J. Stansfeld
Many biophysical studies indicate interactions with lipid/detergent molecules are critical to the folding/stability of membrane proteins, but only limited structural data are available on these interactions. In principle, atomistic molecular dynamics (MD) simulations may be used to follow the self-assembly of proteins with lipid/detergent. However, MD studies are limited to system sizes of up to ~100,000 atoms and time lengths of up to ~100 ns. Coarse grained (CG) models, in which small groups of atoms are treated collectively as large particles, provide a method for increasing timescales and system dimensions.
Membrane protein structures are automatically identified in the PDB and converted to Coarse Grained (CG) representation. Membrane lipids and solvent are then added and a 100 ns Coarse-Grained Molecular Dynamics simulation is performed to allow a lipid bilayer to self-assemble. A further 900 ns simulation is performed to study the dynamics of the assembled membrane. Simulations are then converted to atomistic resolution and analysed. Lipids in the assembled membrane are then exchanged with other species to give a more physiologically realistic membrane composition and further simulations are run.
1. Download structure from PDB
2. Convert to Coarse Grained (CG)
3. Add membrane lipids and solvent
4. CG self-assembly and further simulation
5. Convert from CG to atomistic (CG2AT)
6. Analyse lipid-protein dynamics
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