Computational Studies of Substrate Transport and Specificity in a Phospholipid Flippase

Type-IV P-type ATPases are lipid flippases which help maintain asymmetric phospholipid distribution in eukaryotic membranes by using ATP hydrolysis to drive unidirectional translocation of phospholipid substrates. Recent Cryo-EM and crystal structures have provided a detailed view of flippases, and we here use molecular dynamics simulations of the yeast flippase Drs2p:Cdc50p in an outward open conformation to study the first steps of phospholipid transport. Our simulations show phospholipid binding to a groove and subsequent movement towards the centre of the membrane, and reveal a preference for phosphatidylserine lipids. We find that the lipid head group stays solvated in the groove while the lipid tails stay in the membrane during the (half) transport event. The flippase also induces deformation and thinning of the outer leaflet. Together, our simulations provide insight into substrate binding to lipid flippases and suggest that multiple sites and steps in the functional cycle contribute to substrate selectivity.