Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales

• Published in: Faraday discussions Vol. 144; pp. 347 - 357
• Main Authors: Ayton, Gary S, Lyman, Edward, Voth, Gregory A
• Format: Journal Article
• Language: English
• Published: England 01.01.2010
• Subjects: Computer Simulation; Lipid Bilayers - chemistry; Liposomes - chemistry; Membrane Proteins - chemistry; Models, Molecular
• ISSN: 1359-6640; 1364-5498
• DOI: 10.1039/b901996k

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.