Figure 1.

Features of the biologically realistic implicit membrane model. The implicit membrane is modeled as three phases: two isotropic phases for water and lipid and a transition region that represents the interfacial headgroups. (A) The transition between phases in the z dimension is modeled by a logistic curve that can be parameterized for different lipid compositions. Example curves for DLPC (solid, black) and POPC (dot-dash, black) are shown in comparison to the sigmoid curve used in IMM1 (dashed, gray). (B) Implicit solvent phases are shown for the ammonium transporter Amt-1 (PDB: 2B2F) in the z dimension. The water phase is shown in blue, the interface is in teal, and the lipid is in gray. (C) The transition between phases due to an elliptical pore is modeled by a sigmoid curve. (D) Top view of implicit solvent phases due to a pore in Amt-1 is shown with the same coloring scheme as (B). The three panels of (E) demonstrate the variation in pore shape (purple) for different cross sections in the x, y plane along the z-axis. To see this figure in color, go online.