Relative position and orientation of the peptide in the membrane.

<p>(A) Mean immersion depth () of each residue. The mean (black line) is calculated from the five simulations and its standard deviation is shown as an error bar. For comparison, the immersion depth of the initial structure (grey line) and the experimental results <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047150#pone.0047150-Apostolidou1" target="_blank">[26]</a> (red line/symbol) are also shown. The experimental data are not available for residue 1, 3, 5, 6, and 7. Note that the full length (37 residues) IAPP was used in the experiment. The simulation data may be influenced by the truncation at the C-terminus. (B) Wild-type hIAPP_1–25 (+3) and its nearby molecules (within 4.5 Å) at 100 ns in one of the trajectories. The peptide is represented by the surface model. The solvent exposing residues, Gln10, Arg11, Asn14 and His18, are in green. Other residues are colored according to atom types: sulfur is in yellow and other atoms are colored using the same scheme as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047150#pone-0047150-g001" target="_blank">Fig. 1</a>. The cyan balls represent the oxygen atoms of water molecules. The lipid molecules are rendered by the stick model.