Abstract
Abstract Lipid bilayers affect the structure and dynamics of membrane proteins significantly. In this study, to examine three AMBER-compatible force fields (GAFFlipid, Slipids, and Lipid14), we conducted molecular dynamics (MD) simulations of β2 adrenergic receptor (β2AR) embedded in the palmitoyl-oleoyl-phosphatidyl-choline (POPC) bilayer. We found that the lipid force field affected protein structures (e.g., stability of the ionic lock) largely, even though they were distant from lipids. For example, while the R131-E268 salt bridge (ionic lock), which is involved in protein activation, opened frequently in GAFFlipid and Lipid14 systems, it mostly remained closed in the Slipids system. This difference should be attributed to the difference in the interaction energy between β2AR and POPC bilayer; this energy was much smaller in the Slipids system than in the GAFFlipid and Lipid14 systems.
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