Conformation and dynamics of the Gag polyprotein of the human immunodeficiency virus 1 studied by NMR spectroscopy

Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3374-9. doi: 10.1073/pnas.1501985112. Epub 2015 Feb 23.


Assembly and maturation of the human immunodeficiency virus type 1 (HIV-1) are governed by the Gag polyprotein. Here we study the conformation and dynamics of a large HIV-1 Gag fragment comprising the matrix, capsid, spacer peptide 1 and nucleocapsid domains (referred to as ΔGag) by heteronuclear multidimensional NMR spectroscopy. In solution, ΔGag exists in a dynamic equilibrium between monomeric and dimeric states. In the presence of nucleic acids and at low ionic strength ΔGag assembles into immature virus-like particles. The structured domains of ΔGag (matrix, the N- and C-terminal domains of capsid, and the N- and C-terminal zinc knuckles of nucleocapsid) retain their fold and reorient semi-independently of one another; the linkers connecting the structural domains, including spacer peptide 1 that connects capsid to nucleocapsid, are intrinsically disordered. Structural changes in ΔGag upon proteolytic processing by HIV-1 protease, monitored by NMR in real-time, demonstrate that the conformational transition of the N-terminal 13 residues of capsid from an intrinsically disordered coil to a β-hairpin upon cleavage at the matrix|capsid junction occurs five times faster than cleavage at the capsid|spacer peptide 1 junction. Finally, nucleic acids interact with both nucleocapsid and matrix domains, and proteolytic processing at the spacer peptide 1|nucleocapsid junction by HIV-1 protease is accelerated in the presence of single-stranded DNA.

Keywords: HIV-1 Gag; interdomain motion; proteolytic processing; real time NMR; residual dipolar couplings.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Amino Acid Sequence
  • Biophysical Phenomena
  • Capsid / metabolism
  • DNA / metabolism
  • HIV Protease / metabolism
  • HIV-1 / metabolism*
  • Humans
  • Magnetic Resonance Spectroscopy*
  • Molecular Sequence Data
  • Negative Staining
  • Protein Structure, Secondary
  • Proteolysis
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • gag Gene Products, Human Immunodeficiency Virus / chemistry*
  • gag Gene Products, Human Immunodeficiency Virus / metabolism*
  • gag Gene Products, Human Immunodeficiency Virus / ultrastructure


  • Recombinant Proteins
  • gag Gene Products, Human Immunodeficiency Virus
  • DNA
  • HIV Protease
  • p16 protease, Human immunodeficiency virus 1