energy variation of the dissociation of the complex. The
obtained profile in our case is shown on Fig.6.The estimated energetic barrier needed to leave the active site is
estimated to be 27.5 kcal/mol, obtained for a distance value of
about 30 A ̊between THR104 and the ligand. The global minimum
of the profile, corresponding to the crystallographic position of the
ligand in the cavity, is characterized at a distance of 6.5 A ̊. At the
end of the simulation, the PMF profile has reached a plateau
meaning that the ligand does not interact anymore with the recep-
tor, and progress in the bulk solvent. This profile could be used to
extract thermodynamic and kinetic properties of the molecule of
interest, but some replicas of US simulation are required in order to
make definitive conclusions on the pathway and on the energetic
values.
Umbrella Sampling is one of the state-of-the-art methods to
predict free energy variation associated to a rare event, as unbinding
and binding process of compounds or catalytic reactions of
enzymes (in combination with QM/MM hybrid method). How-
ever, it requires a correct representation of the reaction coordinate
related to the considered event, and it is less suitable to very
complex biological events such as protein folding and protein–pro-
tein interaction disruption.
From these two examples, we aimed at illustrating a RC non-
dependent method (aMD) and RC dependent method (US). The
aMD simulation has been used here to generate an ensemble of
protein conformations to enrich the limited conformational space
determined by experimental structures and explored by classical
3030 40150Energy (kcal.mol-1
)051010202025ς(Å)Fig. 6Potential of mean force obtained for the unbinding process of the inhibitor
with p38αMAP kinase
Enhanced Molecular Dynamics 421