Monitoring inhibitor-induced conformational population shifts in HIV-1 protease by pulsed EPR spectroscopy

Biochemistry. 2009 Sep 22;48(37):8765-7. doi: 10.1021/bi901201q.


Double electron-electron resonance (DEER), a pulsed electron paramagnetic resonance (EPR) spectroscopy technique, was utilized to characterize conformational population shifts in HIV-1 protease (HIV-1PR) upon interaction with various inhibitors. Distances between spin-labeled sites in the flap region of HIV-1PR were determined, and detailed analyses provide population percentages for the ensemble flap conformations upon interaction with inhibitor or substrate. Comparisons are made between the percentage of the closed conformer seen with DEER and enzymatic inhibition constants, thermodynamic dissociation constants, and the number of hydrogen bonds identified in crystallographic complexes.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Crystallography, X-Ray
  • HIV Protease / chemistry*
  • HIV Protease / metabolism*
  • HIV Protease Inhibitors / chemistry*
  • HIV Protease Inhibitors / metabolism*
  • HIV-1 / enzymology
  • Hydrogen Bonding
  • Protein Conformation
  • Spectrometry, Mass, Electrospray Ionization / methods*
  • Spin Labels
  • Temperature
  • Thermodynamics


  • HIV Protease Inhibitors
  • Spin Labels
  • HIV Protease
  • p16 protease, Human immunodeficiency virus 1