University of Hertfordshire

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

Research output: Contribution to journalArticle

  • F. S. Cordes
  • A. Kukol
  • L. R. Forrest
  • I.T. Arkin
  • M. S. P. Sansom
  • W. B. Fischer
View graph of relations
Original languageEnglish
Pages (from-to)291-298
Number of pages8
JournalBiochimica et Biophysica Acta - Biomembranes
Volume1512
Issue2
DOIs
Publication statusPublished - 6 Jun 2001

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. (C) 2001 Elsevier Science B.V. All rights reserved.

ID: 420871