title: Simulation of the N-terminus of HIV-1 glycoprotein 41000 fusion peptide in micelles.
abstract: In this paper, the N-terminus of glycoprotein-41, the HIV-1 fusion peptide, was studied by molecular dynamics simulations in an explicit sodium dodecyl sulfate micelle. The simulation provides a detailed picture of the equilibrium structure and peptide stability as it interacts with the micelle. The equilibrium location of the peptide shows the peptide at the surface of the micelle with hydrophobic residues interacting with the micelle's core. At equilibrium, the peptide adopts an alpha-helical structure from residues 5-16 and a type-1 beta-turn from 17-20 with the other residues exhibiting more flexible conformations. The primary hydrophobic interactions with the micelle are from the leucine and phenylalanine residues (Leu-7, Phe-8, Leu-9, Phe-11, Leu-12) while the alanine and glycine residues (Ala-1, Gly-3, Gly-5, Ala-6, Gly-10, Gly-13, Ala-14, Ala-15, Gly-16, Gly-10, Ala-21) interact favorably with water molecules. The results suggest that Phe-8, part of the highly conserved FLG motif of the fusion peptide, plays a key role in the interaction of the peptide with membranes. Our simulations corroborate experimental investigations of the fusion peptide in SDS micelles, providing a high-resolution picture that explains the experimental findings.
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota, MN 55455, USA.
authors.forename: Allison
authors.initials: A
authors.lastname: Langham
authors.forename: Yiannis
authors.initials: Y
authors.lastname: Kaznessis
mesh_terms: D003198:Computer Simulation; D015700:HIV Envelope Protein gp41 / Q000737:chemistry*; D008823:Micelles; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D012967:Sodium Dodecyl Sulfate / Q000737:chemistry
chemical_list: D015700:HIV Envelope Protein gp41; D008823:Micelles; D012967:Sodium Dodecyl Sulfate