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

F. S.  Cordes; A.  Kukol; L. R.  Forrest; I.T. Arkin; M. S. P.  Sansom; W. B.  Fischer

doi:10.1016/S0005-2736(01)00332-7

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

F. S. Cordes, A. Kukol, L. R. Forrest, I.T. Arkin, M. S. P. Sansom, W. B. Fischer

Research output: Contribution to journal › Article › peer-review

47 Citations (Scopus)

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.

Original language	English
Pages (from-to)	291-298
Number of pages	8
Journal	Biochimica et Biophysica Acta - Biomembranes
Volume	1512
Issue number	2
DOIs	https://doi.org/10.1016/S0005-2736(01)00332-7
Publication status	Published - 6 Jun 2001

Keywords

HIV-1
Vpu
viral ion channel
molecular dynamics
gating
INFLUENZA-A VIRUS
SOLID-STATE NMR
MOLECULAR-DYNAMICS SIMULATIONS
TRANSMEMBRANE DOMAIN
M2 CHANNEL
ACETYLCHOLINE-RECEPTOR
CYTOPLASMIC DOMAIN
GRAMICIDIN CHANNEL
INFRARED DICHROISM
MEMBRANE-PROTEIN

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title = "The structure of the HIV-1 Vpu ion channel: modelling and simulation studies",

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.",

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author = "Cordes, {F. S.} and A. Kukol and Forrest, {L. R.} and I.T. Arkin and Sansom, {M. S. P.} and Fischer, {W. B.}",

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AU - Cordes, F. S.

AU - Kukol, A.

AU - Forrest, L. R.

AU - Arkin, I.T.

AU - Sansom, M. S. P.

AU - Fischer, W. B.

PY - 2001/6/6

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N2 - 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.

AB - 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.

KW - HIV-1

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KW - viral ion channel

KW - molecular dynamics

KW - gating

KW - INFLUENZA-A VIRUS

KW - SOLID-STATE NMR

KW - MOLECULAR-DYNAMICS SIMULATIONS

KW - TRANSMEMBRANE DOMAIN

KW - M2 CHANNEL

KW - ACETYLCHOLINE-RECEPTOR

KW - CYTOPLASMIC DOMAIN

KW - GRAMICIDIN CHANNEL

KW - INFRARED DICHROISM

KW - MEMBRANE-PROTEIN

U2 - 10.1016/S0005-2736(01)00332-7

DO - 10.1016/S0005-2736(01)00332-7

M3 - Article

SN - 0005-2736

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JO - Biochimica et Biophysica Acta - Biomembranes

JF - Biochimica et Biophysica Acta - Biomembranes

IS - 2

ER -

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

Abstract

Keywords

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