Conformational Transitions of Proteins from Atomistic Simulations

The function of many important proteins comes from their dynamic properties, and their ability to undergo conformational transitions. These may be small loop movements that allow access to the protein’s active site, or large movements such as those of motor proteins that are implicated with muscular extension. Yet, in spite of the increasing number of three-dimensional crystal structures of proteins in different conformations, not much is known about the driving forces of these transitions. As an initial step towards exploring the conformational and energetic landscape of protein kinases by computational methods, intramolecular energies and hydration free energies were calculated for different conformations of the catalytic domain of cAMP-dependent protein kinase (cAPK) with a continuum (Poisson) model for the electrostatics. In this paper, we will put the previous results into context and discuss possible extensions into the dynamic regime.