Function of HIV Matrix

  • HIV Matrix is a structural protein encoded by the gag gene, which provides the basic infrastructure of HIV particles. When cleaved from Gag polyprotein during viral maturation, Matrix proteins organize into ordered hexamers to build a structural layer beneath viral membrane, which protects the integrity of HIV particles [1].

  • The matrix domain in the intact Gag polyprotein is destined to traffic Gag to the plasma membrane for viral budding and to recruit host factors (e.g. TIP47) [2]. Matrix anchors the lipid membrane through the myristoylated N-terminal domain which is critical for plasma membrane targeting and viral assembly [2].

  • To prevent the nonspecific binding, Matrix in the Gag polyprotein binds to nucleic acids through a PIP2-dependent mechanism [1].

Reference

  1. Bell, N. M. & Lever, A. M. HIV Gag polyprotein: processing and early viral particle assembly. Trends in microbiology 21, 136-144, doi:10.1016/j.tim.2012.11.006 (2013). [PubMed Link]
  2. Waheed, A. A. & Freed, E. O. HIV type 1 Gag as a target for antiviral therapy. AIDS research and human retroviruses 28, 54-75, doi:10.1089/AID.2011.0230 (2012). [PubMed Link]

Sequence

(1) Reference sequence for HIV-1 Matrix

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

  • Fasta format: Download

  • Reference sequence: 

  1       10         20         30         40         50
  |        |          |          |          |          | 
  MGARASVLSG GELDRWEKIR LRPGGKKKYK LKHIVWASRE LERFAVNPGL 
  51      60         70         80         90         100
  |        |          |          |          |          | 
  LETSEGCRQI LGQLQPSLQT GSEELRSLYN TVATLYCVHQ RIEIKDTKEA 
  101    110        120        130
  |        |          |          | 
  LDKIEEEQNK SKKKAQQAAA DTGHSNQVSQ NY

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

  • Strain: SIV Mac239 (ID: M33262)

  • Fasta format: Download

  • Reference sequence: 

  1       10         20         30         40         50
  |        |          |          |          |          | 
  MGVRNSVLSG KKADELEKIR LRPNGKKKYM LKHVVWAANE LDRFGLAESL 
  51      60         70         80         90         100
  |        |          |          |          |          | 
  LENKEGCQKI LSVLAPLVPT GSENLKSLYN TVCVIWCIHA EEKVKHTEEA 
  101    110        120        130
  |        |          |          | 
  KQIVQRHLVV ETGTTETMPK TSRPTAPSSG RGGNY

(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 Matrix

Here, we visualize the prevalence of amino acid variations at the HIV-1 Matrix 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 protease inhibitors, RT inhibitors and integrase inhibitors using HIVdb V6.0 .

Visualization

Our sequence dataset of HIV-1 subtype B matrix 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 Matrix

Here, we visualize the secondary structure of HIV-1 Matrix using PDBSum (PDB code: 1HIW)



(2) Tertiary structure of HIV-1 Matrix

Here, we provide a structure movie of Matrix using PyMOL V1.7 (PDB code: 1HIW). Alpha-helix and beta-strand secondary structures are demonstrated by red .

Localization

(1) Coding region of Matrix at the HIV genome


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

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


Anti-HIV inhibitor

(1) Drug binding pocket of HIV-1 Matrix

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



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

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



Protein-protein interactions