Function of HIV Vpu
Viral protein U is a membrane-associated accessory protein with two major functions (CD4 downregulation, Tetherin antagonism) [1].
Vpu hijacks the human ubiquitin machinery to target CD4 and induces the downregulation of CD4 receptors in the endoplasmic reticulum (ER)[1].
Vpu antagonizes Tetherin, an interferon-regulated human restriction factor, to enhance the release of viral particles in a cell-type dependent manner[1].
Vpu is not incorporated in HIV particles [2].
Reference
Dube M, Bego MG, Paquay C, Cohen EA: Modulation of HIV-1-host interaction: role of the Vpu accessory protein. Retrovirology 2010, 7:114.(Download Article)
Giroud C, Chazal N, Briant L: Cellular kinases incorporated into HIV-1 particles: passive or active passengers? Retrovirology 2011, 8:71.(Download Article)
Sequence
(1) Reference sequence for HIV-1 Vpu
1 10 20 30 40 50
| | | | | |
TQPIPIVAIV ALVVAIIIAI VVWSIVIIEY RKILRQRKID RLIDRLIERA
51 60 70 80
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EDSGNESEGE ISALVEMGVE MGHHAPWDVD DL (2) Reference sequence for HIV-2 and SIV Vpu
1 10 20 30 40 50
| | | | | |
MSDPRERIPP GNSGEETIGE AFEWLNRTVE EINREAVNHL PRELIFQVWQ
51 60 70 80 90 100
| | | | | |
RSWEYWHDEQ GMSPSYVKYR YLCLIQKALF MHCKKGCRCL GEGHGAGGWR
101 110
| |
PGPPPPPPPG LA (3) Coloring scheme for above amino acids
Amino acids with hydrophobic side chains (normally buried inside the protein core):
A - Ala - Alanine
I - Ile - Isoleucine
L - Leu - Leucine
M - Met - Methionine
V - Val - Valine
Amino acids with polar uncharged side chains (may participate in hydrogen bonds):
N - Asn - Asparagine
Q - Gln - Glutamine
S - Ser - Serine
T - Thr - Threonine
Amino acids with positive charged side chains:
H - His - Histidine
K - Lys - Lysine
R - Arg - Arginine
Amino acids with negative charged side chains:
D - Asp - Aspartic acid
E - Glu - Glutamic acid
Amino acids with aromatic side chains:
F - Phe - Phenylalanine
Y - Tyr - Tyrosine
W - Trp - Tryptophan
Cysteine: C - Cys - Cysteine
Glycine: G - Gly - Glycine
Proline: P - Pro - Proline
Amino acid variations at HIV-1 Vpu
Here, we visualize the prevalence of amino acid variations at the HIV-1 Vpu from HIV-1 subtype B.
Protocal of our sequence collection
For HIV-1 subtype B, one sequence per patient was extracted from HIV Los Alamos database (www.hiv.lanl.gov/).
We removed misclassified sequences or sequences with hypermuVpuions, stop codons, ambiguous nucleotides, which were described in our article [1].
We removed sequences conferred partial or full resistance to any of the Vpu inhibitors, RT inhibitors and Vpu inhibitors using HIVdb V6.0 .
Visualization
Our sequence dataset of HIV-1 subtype B Vpu included 4725 sequences. In the following picture, HXB2 indices of individual proteins are shown on top of the colored bars. A consensus amino acid at each position is shown beneath the colored bar. Natural variations are shown below the consensus amino acids; proportions (%) are colored red if they were more than 5%; blue otherwise.
HIV-1 protein interaction patterns.
Please cite our article:
Guangdi Li, Supinya Piampongsant, Nuno Rodrigues Faria, Arnout Voet, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Philippe Lemey, Anne-Mieke Vandamme, Kristof Theys. An integrated map of HIV genome-wide variation from a population perspective. Retrovirology 12, 18, doi:10.1186/s12977-015-0148-6 (2015). [PDF] [PubMed Link]
Structure
(1) Secondary structure of HIV-1 Vpu
Here, we visualize the secondary structure of HIV-1 Vpu using PDBSum (PDB code: 1VPU)
(2) Tertiary structure of HIV-1 Vpu
Here, we provide a structure movie of Vpu using PyMOL V1.7 (PDB code: 1VPU). Alpha-helix and beta-strand secondary structures are demonstrated by red .
Localization
(1) Coding region of Vpu at the HIV genome
(2) Localization of Vpu during the HIV-1 life cycle
Here, we visualize the localization of Vpu during the viral life cycle. Red stars indicate the appearance of HIV-1 Vpu.
Anti-HIV inhibitor
(1) Drug binding pocket of HIV-1 Vpu
Here, we visualize the drug binding pocket of HIV-1 Vpu
