Groove architecture controls lipid scrambling in simulations of protein and model systems

Abstract

Lipid bilayers are essential to life as they surround most cells and membrane-bound organelles. The integrity and fate of cells depend on the asymmetric makeup of lipid bilayers with various membrane proteins regulating the lipid composition of a bilayers two leaflets. Lipids scramblases are one of the primary regulators of lipid asymmetry in bilayers, spontaneously transferring lipids between membrane leaflets. Members of the TMEM16, OSCA/TMEM63, and TMC families have been suggested to be lipid scramblases. Despite significant differences, these proteins share a common structural architecture that features a membrane-exposed groove. The "credit card" mechanism proposes that lipids switch leaflets by moving their polar head groups either inside (partially dry) or on the surface of (wet) membrane-exposed, open hydrophilic grooves. However, emerging evidence of closed-groove scrambling challenges this model. Given the sequence diversity of groove-lining amino acids in TMEM16, OSCA/TMEM63, and TMC proteins, we hypothesized that lipid scrambling is primarily determined by groove architecture. To test this hypothesis and the credit card mechanism, 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 in most closed-state configurations but 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. We used this and further simplified models to vary groove surface hydrophilicity, groove surface geometry, and groove architecture. Our models support the partially dry and wet credit card mechanisms and suggest that groove architecture plays a more important role in facilitating lipid scrambling than the detailed sequence of groove-lining amino acids. STATEMENT OF SIGNIFICANCEMany biological processes, including blood clotting and apoptosis, are triggered by exposure of specific lipids on the outer leaflet of a lipid bilayer. Spontaneous diffusion of lipids between leaflets is slow, but scramblases can speed up transbilayer lipid exchange, a key step in signaling cascades. Here we used coarse-grained simulations to isolate and quantify the key biophysical properties of scramblases that modulate lipid movement across the bilayer. We found that the architecture of scramblases membrane-exposed groove is key to their function. This can be used to generate hypotheses about disease-causing mutations in known scramblases, guide drug design, and suggest favorable properties for de novo designed scramblases.