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

Citation
Fs. Cordes et al., The structure of the HIV-1 Vpu ion channel: modelling and simulation studies, BBA-BIOMEMB, 1512(2), 2001, pp. 291-298
Citations number
54
Categorie Soggetti
Biochemistry & Biophysics
Journal title
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
ISSN journal
00052736 → ACNP
Volume
1512
Issue
2
Year of publication
2001
Pages
291 - 298
Database
ISI
SICI code
0005-2736(20010606)1512:2<291:TSOTHV>2.0.ZU;2-9
Abstract
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) 2 001 Elsevier Science B.V. All rights reserved.