BPS2026 – Molecular determinants of lipid scrambling from coarse-grained simulations

Lipid bilayers are essential to life. Cells depend on the asymmetric makeup of lipid bilayers, and this asymmetric organization is actively regulated by membrane proteins. Lipid scramblases are key regulators of lipid asymmetry across bilayers that shuffle lipids between the two membrane leaflets. Members of the related TMEM16, OSCA/TMEM63, and TMC families have been implicated in lipid scrambling. Despite significant sequence differences, these proteins share a common structural architecture that features a membrane-exposed groove. Therefore, we hypothesized that lipid scrambling is primarily determined by groove architecture and conformational state. To test this hypothesis, we used coarse-grained molecular dynamics simulations of experimental structures and AlphaFold-generated models of six different scramblases in closed and open states. In these simulations, we observed little scramblase activity by most closed-state configurations and robust scrambling by all open-state models. We then built simplified TMEM16-based scramblases with only three bead types uniformly set for solvent-facing, transmembrane, and groove regions; these models revealed how groove surface hydrophilicity and geometry affect lipid scrambling. To further distill the essential molecular determinants controlling lipid scrambling, we constructed cube-shaped “proteins” with varied groove architecture. Simulations of these simplified systems allowed us to identify a handful of structural prerequisites required for lipid scrambling. Our results suggest that groove architecture, rather than detailed residue identity, is the primary determinant of lipid scrambling. These findings provide a unifying structural framework for understanding how diverse scramblases achieve a shared biological function.