FIGURE 2.

Binding of flexible BAR domain loops to lipid headgroups. The binding of Arg and Lys residues to oxygen atoms on lipid headgroups is shown for simulations NBR1 (A) and NBR3 (B). The solid and dashed lines represent the left and right loops, respectively, as depicted in the simulation snapshots (e.g., C). For this study, these loops comprise residues 161–171, inclusive. Residues are considered bound if the nitrogen and oxygen atoms remain within 4.2 Å for at least 1 ns (50-ps sampling interval). The binding of these loops assists in stabilizing the interaction of the BAR domain with the lipid bilayer (compare with Fig. 1, C and E). (C) Close-up snapshot showing the charged binding loops (red arrows) on either end of the BAR domain dissociating from the bilayer surface after 13 ns in simulation NBR3. The DOPC headgroups are purple and the DOPS headgroups are green. The lipid tails are white. Water and NaCl are also present in the simulations, but are left out of the image for clarity. In this and other close-up snapshots, only about half of the 45-nm membrane is shown.