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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.


Journal article


Biochim Biophys Acta

Publication Date





291 - 298


Amino Acid Sequence, HIV-1, Human Immunodeficiency Virus Proteins, Humans, Hydrogen Bonding, Models, Molecular, Molecular Sequence Data, Peptide Fragments, Protein Structure, Secondary, Spectroscopy, Fourier Transform Infrared, Tryptophan, Viral Regulatory and Accessory Proteins