Figure 6.
Coarse-Grained MD Simulation of APH Binding to PA-Enriched Membranes
(A) Snapshots from an individual binding series of PfAPH106-235 (gray) to a 10% PA membrane. The hydrophobic residues I143-F144-H145 that become anchored in the membrane are shown as a green surface. POPA residues within 6 Å of the protein surface are shown as spheres colored individually and the lipid head-groups are shown as a transparent red surface. The recruitment of POPA following the initial association is apparent in the final panel.
(B) Average occupancy of PA (magenta) and PC (yellow) head-groups averaged over five simulations of 50% PA membranes, PfAPH106-235 is shown in light blue. POPA is found to be preferentially in the first shell of lipids around the buried anchor residues I143-F144-H145 (green) whereas PC is found in the second annular layer. Rough lipid shell boundaries are indicated by gray-shaded circles. The protein backbone is shown as a gray trace.
(C) Relationship between average time (μs) bound to membrane and PA membrane enrichment for PfAPH106-235 coarse-grained MD simulation (5 μs total simulation time).
(D) Binding between PfAPH106-235 and a fixed concentration of LUVs (500 μM total available lipid) increasingly enriched with PA (Mol% PA). Hill plot analysis indicates PfAPH106-235 binds to PA in a positively cooperative manner.
(E) Comparison between coarse-grained MD simulation and NMR experiments probing binding between PfAPH106-235 and PA reveal three regions key to interaction with a PA-enriched membrane. Coarse-grained MD simulations indicate residues 99–110 (including β5-β6 loop) are involved in initial contact with a PA-enriched membrane (red). Hydrophobic residues located at the tip of the β1-β2 loop region (green, I143/F144) dip into the membrane. This anchoring is stabilized by electrostatic interaction between conserved charged residues including KxK motifs (blue, K138-K140 and K163-K165), and PA head-groups.