FIGURE 3.

Starting peptide structures (left) and intermediate structures (right) of the two pilot simulations described in the text, without lipid environment (top), and with simplified lipid environment (bottom). In the top right figure, the spheres show the residue pair forming a hydrophobic contact, which stabilized the final structure of the peptide, i.e., the linker residue Ala-261 (orange) and the TM residue Ile-270 (yellow). In the bottom panel, the position-restrained water oxygen atoms that mimic the sterical effect of a bilayer are shown as red spheres. In the bottom right figure, the black circle marks the two linker residues that spontaneously folded from loop into α-helical conformation.