Abstract
The structure and function of membrane proteins are intricately coupled to their interaction with the surrounding membrane. However, studying the interaction of proteins with lipid bilayers at the atomistic level remains challenging. Here, we present a general simulation protocol to predicting de novo the solvation, fold, self-assembly, and poration of peptides and proteins in membranes. The method is based on an ensemble of all-atom molecular dynamics simulations. To avoid computational bottlenecks due to the high viscosity of lipid bilayers, we use a membrane mimetic consisting of a biphasic octane-water solvent.
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