Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints.

ABSTRACT: The routinely employed periodic boundary conditions complicate molecular simulations of physiologically relevant asymmetric lipid membranes together with their distinct solvent environments. Therefore, separating the extracellular fluid from its cytosolic counterpart has often been performed using a costly double-bilayer setup. Here, we demonstrate that the lipid membrane and solvent asymmetry can be efficiently modeled with a single lipid bilayer by applying an inverted flat-bottom potential to ions and other solute molecules, thereby restraining them to only interact with the relevant leaflet. We carefully optimized the parameters of the suggested method so that the results obtained using the flat-bottom and double-bilayer approaches become mutually indistinguishable. Then, we apply the

SUBMITTER: Biriukov D 

PROVIDER: S-EPMC10537000 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature