Figure 1: The native conformation of HIV-1-PR and
mHIV-1-PR1-95. a) Structure of the HIV-1-PR homodimer
(PDB code 1BVG). The active site is highlighted by yellow spheres. b)
Structure of the 1-95 variant mHIV-1-PR1-95 (PDB code
1Q9P). c) The sequence of mHIV-1-PR; the active site is
highlighted in yellow.
In the present work we have performed titration experiments in different
chemical denaturants using the exact same mHIV-1-PR1-95variant. This allowed us to monitor how the conformational properties of
the denatured state depend on the kind and concentration of the
denaturing agent, eventually extrapolating the properties ofD0 . The main quantity we investigated was the
secondary chemical shifts, measured by heteronuclear NMR experiments. A
non-trivial problem one has to face is then to interpret these data in
terms of conformational properties of the protein. To assist us in this
goal, we performed advanced molecular dynamics simulations of
mHIV-1-PR1-95 in water, building an ensemble of
conformations that describes the denatured stateD0 . The correctness of the simulatedD0 was validated by back-calculating the
secondary chemical shifts from the simulation and comparing them with
those obtained from the extrapolation to zero denaturant of the NMR
results.