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.

UN SDGs

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

SDG 3 Good Health and Well-being

Keywords

Gating
HIV-1
Molecular dynamics
Viral ion channel
Vpu

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10.1016/S0005-2736(01)00332-7

Cite this

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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.",

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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. ",

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AU - Arkin, I. T.

AU - Sansom, M. S.P.

AU - Fischer, W. B.

N1 - 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.

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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.

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.

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

Abstract

Bibliographical note

UN SDGs

Keywords

Access to Document

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