Transient HIV-1 Gag-protease interactions revealed by paramagnetic NMR suggest origins of compensatory drug resistance mutations

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12456-12461. doi: 10.1073/pnas.1615342113. Epub 2016 Oct 17.


Cleavage of the group-specific antigen (Gag) polyprotein by HIV-1 protease represents the critical first step in the conversion of immature noninfectious viral particles to mature infectious virions. Selective pressure exerted by HIV-1 protease inhibitors, a mainstay of current anti-HIV-1 therapies, results in the accumulation of drug resistance mutations in both protease and Gag. Surprisingly, a large number of these mutations (known as secondary or compensatory mutations) occur outside the active site of protease or the cleavage sites of Gag (located within intrinsically disordered linkers connecting the globular domains of Gag to one another), suggesting that transient encounter complexes involving the globular domains of Gag may play a role in guiding and facilitating access of the protease to the Gag cleavage sites. Here, using large fragments of Gag, as well as catalytically inactive and active variants of protease, we probe the nature of such rare encounter complexes using intermolecular paramagnetic relaxation enhancement, a highly sensitive technique for detecting sparsely populated states. We show that Gag-protease encounter complexes are primarily mediated by interactions between protease and the globular domains of Gag and that the sites of transient interactions are correlated with surface exposed regions that exhibit a high propensity to mutate in the presence of HIV-1 protease inhibitors.

Keywords: HIV-1 Gag; HIV-1 protease; drug resistance mutations; invisible states; paramagnetic relaxation enhancement.

Publication types

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

MeSH terms

  • Catalytic Domain
  • Drug Resistance, Viral / genetics
  • HIV Infections / drug therapy
  • HIV Infections / virology
  • HIV Protease / chemistry
  • HIV Protease / genetics
  • HIV Protease / metabolism*
  • HIV Protease Inhibitors / pharmacology
  • HIV-1 / genetics
  • HIV-1 / metabolism*
  • Humans
  • Magnetic Resonance Spectroscopy / methods*
  • Models, Molecular
  • Mutation
  • Protein Binding / drug effects
  • Protein Domains
  • Protein Structure, Secondary
  • gag Gene Products, Human Immunodeficiency Virus / chemistry
  • gag Gene Products, Human Immunodeficiency Virus / genetics
  • gag Gene Products, Human Immunodeficiency Virus / metabolism*


  • HIV Protease Inhibitors
  • gag Gene Products, Human Immunodeficiency Virus
  • HIV Protease
  • p16 protease, Human immunodeficiency virus 1