Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales.
An overall multiscale simulation strategy for large scale coarse-grain simulations of membrane protein systems is presented. The protein is modeled as a heterogeneous elastic network, while the lipids are modeled using the hybrid analytic-systematic (HAS) methodology, where in both cases atomistic level information obtained from molecular dynamics simulation is used to parameterize the model. A feature of this approach is that from the outset liposome length scales are employed in the simulation (i.e., on the order of 1/2 a million lipids plus protein). A route to develop highly coarse-grained models from molecular-scale information is proposed and results for N-BAR domain protein remodeling of a liposome are presented.
Ayton
Gary S
GS
Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 S. 1400 E, Room 2020, Salt Lake City, Utah 84112-0850, USA.
Lyman
Edward
E
Voth
Gregory A
GA
D003198:Computer Simulation; D008051:Lipid Bilayers / Q000737:chemistry; D008081:Liposomes / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular
D008051:Lipid Bilayers; D008081:Liposomes; D008565:Membrane Proteins