The structure of the HIV-1 Vpu ion channel: Modelling and simulation studies

F. S. Cordes, A. Kukol, L. R. Forrest, I. T. Arkin, M. S.P. Sansom, W. B. Fischer*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

49 Scopus citations


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.

Original languageEnglish
Pages (from-to)291-298
Number of pages8
JournalBiochimica et Biophysica Acta - Biomembranes
Issue number2
StatePublished - 6 Jun 2001


  • Gating
  • HIV-1
  • Molecular dynamics
  • Viral ion channel
  • Vpu


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