The structure of the HIV-1 Vpu ion channel: modelling and simulation studies.
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,...
| Main Authors: | , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
2001
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| _version_ | 1826283500136824832 |
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| author | Cordes, F Kukol, A Forrest, L Arkin, I Sansom, MS Fischer, W |
| author_facet | Cordes, F Kukol, A Forrest, L Arkin, I Sansom, MS Fischer, W |
| author_sort | Cordes, F |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-07T00:59:48Z |
| format | Journal article |
| id | oxford-uuid:89525138-cb30-4a9c-a37f-01ca02233156 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T00:59:48Z |
| publishDate | 2001 |
| record_format | dspace |
| spelling | oxford-uuid:89525138-cb30-4a9c-a37f-01ca022331562022-03-26T22:23:45ZThe structure of the HIV-1 Vpu ion channel: modelling and simulation studies.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:89525138-cb30-4a9c-a37f-01ca02233156EnglishSymplectic Elements at Oxford2001Cordes, FKukol, AForrest, LArkin, ISansom, MSFischer, WVpu 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. |
| spellingShingle | Cordes, F Kukol, A Forrest, L Arkin, I Sansom, MS Fischer, W The structure of the HIV-1 Vpu ion channel: modelling and simulation studies. |
| title | The structure of the HIV-1 Vpu ion channel: modelling and simulation studies. |
| title_full | The structure of the HIV-1 Vpu ion channel: modelling and simulation studies. |
| title_fullStr | The structure of the HIV-1 Vpu ion channel: modelling and simulation studies. |
| title_full_unstemmed | The structure of the HIV-1 Vpu ion channel: modelling and simulation studies. |
| title_short | The structure of the HIV-1 Vpu ion channel: modelling and simulation studies. |
| title_sort | structure of the hiv 1 vpu ion channel modelling and simulation studies |
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