Vpu is an 81 amino acid auxiliary protein in HIV-1 which exhibits channel a
ctivity. We used two homo-pentameric bundles with the helical transmembrane
segments derived from FTIR spectroscopy in combination with a global molec
ular dynamics search protocol: (i) tryptophans (W) pointing into the pore,
and (ii) W facing the lipids. Two equivalent bundles have been generated us
ing a simulated annealing via a restrained molecular dynamics simulations (
SA/MD) protocol. A fifth model was generated via SA/MD with all serines fac
ing 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 depend
s on the starting structure. A possible gating mechanism is outlined. (C) 2
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