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. 2015 May 1;26(9):1764–1781. doi: 10.1091/mbc.E14-10-1475

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© 2015 Ghosh, de Campos, et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

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FIGURE 4: — Molecular dynamics simulations of AtSfh1 nodulin peptide on membrane bilayers. (A) Unfolded extended structure of the AtSfh1 nodulin peptide (left) and folded β-hairpin structure after 4 μs of MDS in water (right). (B) Two most-populated clustered structures from REMD simulation at 297 K: 10.85 (A) and 8% (B) probability. Both structures adopt β-hairpins. (C) Chemical structures of lipids used in the simulations. (D) Snapshots of systems simulated with a lipid bilayer. Beginning (A, C, E, G, I) and end of the simulation (B, D, F, H, J) of systems 2 (A, B), 3 (C, D), 4 (E, F), 5 (G, H), and 6 (I, J) in Supplemental Table S1A. PtdIns(4,5)P₂ molecules are in green (H₂O not shown). (E) Time development of peptide::lipid H bonds (DLPC, black; DLPS, red; and PtdIns(4,5)P₂, green). Data averaged over simulations 2–6 in Supplemental Table S1A. Dashed lines show average level of H bonds with each lipid type. (F) Snapshot of the peptide (licorice representation together with “new cartoon”) bound to three PtdIns(4,5)P₂ molecules (yellow licorice) by H bonds (orange dots). Membrane shown as a transparent surface (H₂O not shown). (G) Snapshot of three aggregated nodulin peptides (cyan, violet, and green surface) bound to 3 PtdIns(4,5)P₂ (yellow licorice). Picture generated by VMD (Humphrey et al., 1996). (H) Schematic representation of AtSfh1 nodulin peptide bound to PtdIns(4,5)P₂ (blue) and PtdIns(3,5)P₂ (red). Bottom, H bonds established between nodulin peptide Lys side chain (blue) and PtdIns(4,5)P₂ (red).