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^*

^*Corresponding author for this work

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

49 Scopus citations

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.

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
State	Published - 6 Jun 2001
Externally published	Yes

Bibliographical note

Funding Information:
This work was supported with a grant to M.S.P.S. from the Wellcome Trust. F.S.C. thanks the Deutsche Volk Stiftung for a stipend. This work was supported by the EC with a TMR-Research Fellowship for W.B.F. We acknowledge the Oxford Super Computer facility for providing us with computer time.

Keywords

Gating
HIV-1
Molecular dynamics
Viral ion channel
Vpu

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/S0005-2736(01)00332-7

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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.",

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AU - Sansom, M. S.P.

AU - Fischer, W. B.

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

Abstract

Bibliographical note

Keywords

UN SDGs

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