| Literature DB >> 11406106 |
F S Cordes1, A Kukol, L R Forrest, I T Arkin, M S Sansom, W B Fischer.
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.Entities:
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Year: 2001 PMID： 11406106 DOI： 10.1016/s0005-2736(01)00332-7
Source DB: PubMed Journal: Biochim Biophys Acta ISSN： 0006-3002