The Sec61/TRAP Translocon Scrambles Lipids

Cell growth relies on the rapid flip-flop of newly synthesized lipids across the ER membrane. This process is facilitated without the need for ATP by specific membrane proteins--scramblases--a few of which have been very recently identified in the ER. We have previously resolved the structure of the translocon-associated protein (TRAP) bound to the Sec61 translocon in the ER membrane, and found this complex to render the membrane locally thinner. Moreover, Sec61 and TRAP each contain a crevice rich in polar residues that can shield a lipid head group as it traverses the hydrophobic membrane environment. We thus hypothesized that both Sec61 and TRAP act as ER scramblases. Here, we characterized the scrambling activity of Sec61 and TRAP using extensive molecular dynamics simulations. We observed that both Sec61 and TRAP efficiently scramble lipids via a credit card mechanism. We analyzed the kinetics and thermodynamics of lipid scrambling and demonstrated that local membrane thinning provides a key contribution to scrambling efficiency. Both proteins appear seemingly selective towards phosphatidylcholine lipids over phosphatidylethanolamine and phosphatidylserine, yet this behavior rather reflects the trends observed for these lipids in a protein-free membrane. The identified scrambling pathway in Sec61 structure is physiologically rarely unoccupied due to its role in protein translocation. Furthermore, we found that the scrambling activity of this pathway might be impeded by the presence of ions at a physiological concentration. However, the trimeric bundle of TRAP{beta}, TRAP{gamma}, and TRAP{delta} might provide scrambling activity insensitive to the functional state of the translocon and the solvent conditions.