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Peptide insertion, positioning, and stabilization in a membrane: Insight from an all-atom molecular dynamics simulation
Arneh Babakhani, Alemayehu A. Gorfe, Justin Gullingsrud, Judy E. Kim, J. Andrew McCammon
Abstract:
Peptide insertion, positioning, and stabilization in a model membrane are probed via an all-atom molecular dynamics simulation. One peptide (WL5) is simulated in each leaflet of a solvated dimyristoylglycero-3-phosphate (DMPC) membrane. Within the first 5 ns, the peptides spontaneously insert into the membrane and then stabilize during the remaining 70 ns of simulation time. In both leaflets, the peptides localize to the membrane interface, and this localization is attributed to the formation of peptide-lipid hydrogen bonds. We show that the single tryptophan residue in each peptide contributes significantly to these hydrogen bonds; specifically, the nitrogen heteroatom of the indole ring plays a critical role. The tilt angles of the indole rings relative to the membrane normal in the upper and lower leaflets are approximately 26° and 54°, respectively. The tilt angles of the entire peptide chain are 62° and 74°. The membrane induces conformations of the peptide that are characteristic of -sheets, and the peptide enhances the lipid ordering in the membrane. Finally, the diffusion rate of the peptides in the membrane plane is calculated (based on experimental peptide concentrations) to be approximately 6 Å2/ns, thus suggesting a 500 ns time scale for intermolecular interactions.