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Simulation of the N ‐terminus of HIV‐1 glycoprotein 41000 fusion peptide in micelles
Author(s) -
Langham Allison,
Kaznessis Yiannis
Publication year - 2005
Publication title -
journal of peptide science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.475
H-Index - 66
eISSN - 1099-1387
pISSN - 1075-2617
DOI - 10.1002/psc.623
Subject(s) - micelle , peptide , chemistry , molecular dynamics , alanine , sodium dodecyl sulfate , protein structure , amphiphile , biophysics , stereochemistry , amino acid , crystallography , biochemistry , organic chemistry , aqueous solution , computational chemistry , biology , copolymer , polymer
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 α‐helical structure from residues 5–16 and a type‐1 β‐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. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd.