  The biological function of proteins is encoded in their structure and
expressed through the mediation of their dynamics. Local fluctuations are known
to initiate biologically relevant pathways as they cooperatively enhance the
dynamics in specific regions in the protein. Those biologically active regions
provide energetically-comparable conformational states that can be trapped by a
reacting partner. We analyze this mechanism as we calculate the dynamics of
monomeric and dimerized HIV protease, and free Insulin Growth Factor II
Receptor (IGF2R) domain 11 and its IGF2R:IGF2 complex. We adopt a newly
developed coarse-grained model, the Langevin Equation for Protein Dynamics
(LE4PD), which predicts dynamical relevant mechanisms with high accuracy. Both
simulation-derived and experimental NMR conformers are the input structural
ensembles for the LE4PD. The use of the experimental NMR conformers requires
minimal computational resources.
