Figure 3. Simulations of LiveDrop Suggest Conformational Changes and Energetic Contributions of Specific Sequence Features to LD Targeting.

(A) Equilibrated simulation structures of LiveDrop in a bilayer (left) and monolayer (right) highlighting key residues: R179 and R187 (pink); W166, W172, W197, and P185 (red); and A203 (gray). The phospholipid headgroups and tails are shown in light and medium blue, respectively, the neutral lipid phase in green, and water molecules in dark blue.

(B) P185 depth with respect to the upper phosphate plane of the bilayer (blue) and monolayer (orange). The solid lines show the running averages and the filled areas show the standard deviations from four and two simulations of the bilayer and monolayer, respectively. Extending the simulations in the monolayer to 2 μs (not shown) did not reveal notable changes in the depth or conformation during the last 1 μs.

(C) (upper panel) Free energy of insertion of LiveDrop hydrophobic residues into the bilayer (blue) and monolayer (orange). The defined hairpin regions were residues position (α-helix top (H1 top, H2 top), middle (H1 mid, H2 mid), or hinge) are shown. (lower panel) Free energy differences between the monolayer and bilayer (ΔF_M-B). Bars are colored yellow or violet if the residue is more stable in the monolayer (F_M < F_B) or in the bilayer (F_M > F_B), respectively.

(D) Free energy differences between the monolayer and bilayer (ΔF_M-B) for the phenylalanine (left panel, black) and tryptophan (right panel, black) residues, and for their corresponding valine mutants (blue).