Function of HIV Vif

  • Viral infectivity factor is an accessory protein encoded by all lentiviruses except the equine infectious anemia virus [1].

  • Vif is famous to hijack the human ubiquitin ligase complex CBF-β to counteract the antiviral activity of host proteins, APOBEC-3G and APOBEC-3F, both of which interfere with the correct assembly of HIV-1 viral core [2,3].

  • Vif also interacts with Gag polyprotein to modulate the Protease-mediated proteolytic processing [1].

  • Vif is incorporated in HIV particles [1].

Reference

  1. Henriet S, Mercenne G, Bernacchi S, Paillart JC, Marquet R: Tumultuous relationship between the human immunodeficiency virus type 1 viral infectivity factor (Vif) and the human APOBEC-3G and APOBEC-3F restriction factors. Microbiology and molecular biology reviews : MMBR 2009, 73(2):211-232.(Download Article)

  2. Jager S, Kim DY, Hultquist JF, Shindo K, LaRue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D et al: Vif hijacks CBF-beta to degrade APOBEC3G and promote HIV-1 infection. Nature 2012, 481(7381):371-375.(Download Article)

  3. Harris RS, Liddament MT: Retroviral restriction by APOBEC proteins. Nature reviews Immunology 2004, 4(11):868-877.(Download Article)

Sequence

(1) Reference sequence for HIV-1 Vif

  • Strain: HIV-1 subtype B HXB2 (ID: K03455)

  • Fasta format: Download

  • Reference sequence: 

  1       10         20         30         40         50
  |        |          |          |          |          | 
  MENRWQVMIV WQVDRMRIRT WKSLVKHHMY VSGKARGWFY RHHYESPHPR 
  51      60         70         80         90         100
  |        |          |          |          |          | 
  ISSEVHIPLG DARLVITTYW GLHTGERDWH LGQGVSIEWR KKRYSTQVDP 
  101    110        120        130        140        150
  |        |          |          |          |          | 
  ELADQLIHLY YFDCFSDSAI RKALLGHIVS PRCEYQAGHN KVGSLQYLAL 
  151    160        170        180        190
  |        |          |          |          | 
  AALITPKKIK PPLPSVTKLT EDRWNKPQKT KGHRGSHTMN GH

(2) Reference sequence for HIV-2 and SIV Vif

  • Strain: SIV Mac239 (ID: M33262)

  • Fasta format: Download

  • Reference sequence: 

  1       10         20         30         40         50
  |        |          |          |          |          | 
  MEEEKRWIAV PTWRIPERLE RWHSLIKYLK YKTKDLQKVC YVPHFKVGWA 
  51      60         70         80         90         100
  |        |          |          |          |          | 
  WWTCSRVIFP LQEGSHLEVQ GYWHLTPEKG WLSTYAVRIT WYSKNFWTDV 
  101    110        120        130        140        150
  |        |          |          |          |          | 
  TPNYADILLH STYFPCFTAG EVRRAIRGEQ LLSCCRFPRA HKYQVPSLQY 
  151    160        170        180        190        200
  |        |          |          |          |          | 
  LALKVVSDVR SQGENPTWKQ WRRDNRRGLR MAKQNSRGDK QRGGKPPTKG 
  201    210
  |        | 
  ANFPGLAKVL GILA

(3) Coloring scheme for above amino acids

  1. 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

  2. Amino acids with polar uncharged side chains (may participate in hydrogen bonds):

    • N - Asn - Asparagine

    • Q - Gln - Glutamine

    • S - Ser - Serine

    • T - Thr - Threonine

  3. Amino acids with positive charged side chains:

    • H - His - Histidine

    • K - Lys - Lysine

    • R - Arg - Arginine

  4. Amino acids with negative charged side chains:

    • D - Asp - Aspartic acid

    • E - Glu - Glutamic acid

  5. Amino acids with aromatic side chains:

    • F - Phe - Phenylalanine

    • Y - Tyr - Tyrosine

    • W - Trp - Tryptophan

  6. Cysteine: C - Cys - Cysteine

  7. Glycine: G - Gly - Glycine

  8. Proline: P - Pro - Proline

Amino acid variations at HIV-1 Vif

Here, we visualize the prevalence of amino acid variations at the HIV-1 Vif 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 hypermutations, stop codons, ambiguous nucleotides, which were described in our article [1].

  • We removed sequences conferred partial or full resistance to any of the Vif inhibitors, RT inhibitors and Vif inhibitors using HIVdb V6.0 .

Visualization

Our sequence dataset of HIV-1 subtype B Vif 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.

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Please cite our article:

  1. 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 Vif

Here, we visualize the secondary structure of HIV-1 Vif using PDBSum (PDB code: 4N9F)



(2) Tertiary structure of HIV-1 Vif

Here, we provide a structure movie of Vif using PyMOL V1.7 (PDB code: 4N9F). Alpha-helix and beta-strand secondary structures are demonstrated by red .

Localization

(1) Coding region of Vif at the HIV genome


(2) Localization of Vif during the HIV-1 life cycle

Here, we visualize the localization of Vif during the viral life cycle. Red stars indicate the appearance of HIV-1 Vif.


Anti-HIV inhibitor

(1) Drug binding pocket of HIV-1 Vif

Here, we visualize the drug binding pocket of HIV-1 Vif



(2) List of known inhibitors targeting HIV-1 Vif

Here, we summarize the published anti-HIV inhibitors which bind to HIV-1 Vif.



Protein-protein interactions