Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel.
The recently developed multiscale coarse-graining (MS-CG) method (Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469; J. Chem. Phys. 2005, 123, 134105) is used to build a mixed all-atom and coarse-grained (AA-CG) model of the gramicidin A (gA) ion channel embedded in a dimyristoylphosphatidylcholine (DMPC) lipid bilayer and water environment. In this model, the gA peptide was described in full atomistic detail, while the lipid and water molecules were described using coarse-grained representations. The atom-CG and CG-CG interactions in the mixed AA-CG model were determined using the MS-CG method. Molecular dynamics (MD) simulations were performed using the resulting AA-CG model. The results from simulations of the AA-CG model compare very favorably to those from all-atom MD simulations of the entire system. Since the MS-CG method employs a general and systematic approach to obtain effective interactions from the underlying all-atom models, the present approach to rigorously develop mixed AA-CG models has the potential to be extended to many other systems.
Shi
Qiang
Q
Izvekov
Sergei
S
Voth
Gregory A
GA
D003198:Computer Simulation; D004134:Dimyristoylphosphatidylcholine / Q000737:chemistry; D006096:Gramicidin / Q000737:chemistry*; D007473:Ion Channels / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory; D014867:Water / Q000737:chemistry
D007473:Ion Channels; D008051:Lipid Bilayers; D010455:Peptides; D014867:Water; D006096:Gramicidin; D004134:Dimyristoylphosphatidylcholine