title: The structure of the HIV-1 Vpu ion channel: modelling and simulation studies.
abstract: Vpu is an 81 amino acid auxiliary protein in HIV-1 which exhibits channel activity. We used two homo-pentameric bundles with the helical transmembrane segments derived from FTIR spectroscopy in combination with a global molecular dynamics search protocol: (i) tryptophans (W) pointing into the pore, and (ii) W facing the lipids. Two equivalent bundles have been generated using a simulated annealing via a restrained molecular dynamics simulations (SA/MD) protocol. A fifth model was generated via SA/MD with all serines facing the pore. The latter model adopts a very stable structure during the 2 ns of simulation. The stability of the models with W facing the pore depends on the starting structure. A possible gating mechanism is outlined.
authors.affiliation: Laboratory of Molecular Biophysics, Department of Biochemistry, Oxford University, UK.
authors.forename: F S
authors.initials: FS
authors.lastname: Cordes
authors.forename: A
authors.initials: A
authors.lastname: Kukol
authors.forename: L R
authors.initials: LR
authors.lastname: Forrest
authors.forename: I T
authors.initials: IT
authors.lastname: Arkin
authors.forename: M S
authors.initials: MS
authors.lastname: Sansom
authors.forename: W B
authors.initials: WB
authors.lastname: Fischer
mesh_terms: D000595:Amino Acid Sequence; D015497:HIV-1 / Q000502:physiology*; D054298:Human Immunodeficiency Virus Proteins; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D017433:Protein Structure, Secondary; D017550:Spectroscopy, Fourier Transform Infrared; D014364:Tryptophan; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry* / Q000502:physiology; D000086082:Viroporin Proteins
chemical_list: D054298:Human Immunodeficiency Virus Proteins; D010446:Peptide Fragments; D014364:Tryptophan; D054334:Viral Regulatory and Accessory Proteins; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins