Leaflet Asymmetry Modeling in Lipid Composition of Escherichia coli Cytoplasmic Membrane

Lipid composition asymmetry between leaflets is important to cell function and plays a key role in the “positive inside” rule in transmembrane proteins. In this work, E. coli inner plasma membrane models reflecting this asymmetry have been investigated at the early-log and stationary stages during the bacterial lifecycle using all-atom molecular dynamics simulations. The CHARMM36 lipid force field is used, and selected membrane properties are tested for variations between two leaflets and whole membranes. Our models include bacterial lipids containing cyclopropane moiety on the sn-2 acyl chain in the stationary membrane. The PE:PG ratio in two leaflets reflects the “positive inside” rule of membrane proteins, set to 6.8 and 2.8 for the inner and outer leaflets of the two models. We are the first to model leaflet asymmetry in lipid composition on E. Coli cytoplasmic membrane and observe the effect on membrane properties in leaflets and whole membranes. Specifically, our results show that for the stationary phase bilayer, the surface area per lipid (SA/lipid) is larger, the thickness (2DC and DB) is thinner, the tilt angle is larger, the tilt modulus is smaller, and the deuterium order parameter (SCD) of sn-1 and sn-2 tails are lower, compared to the early-log stage. Moreover, the stationary stage bilayer has a negative spontaneous curvature while the early-log stage is near flat spontaneous curvature. For leaflet asymmetry, the inner leaflet has a larger SA/lipid, a smaller thickness, a smaller elastic tilt modulus (a larger tilt angle), and low SCD, compared to the outer leaflet in both stages. Moreover, asymmetric membrane involves a lipid tilt and a lateral extension, varying from a reference state of pre-equilibrium membrane. This work encourages a more profound exploration of leaflet asymmetry in various other membrane models and specifically how this might affect structure and function of membrane-associated peptides and proteins.