Biological functions of proteins are closely connected to their dynamics in the native state. These dynamics are governed by the protein's native energy landscape. Therefore, constructing detailed maps of these landscapes is essential for studying protein function and dynamics, especially, in more interesting cases of allosteric proteins, molecular motors or enzymatic catalysis. However, obtaining free energies of protein conformations from atomistic simulations using explicit solvent is a challenging problem. Recently, we have solved this problem by constructing a special reaction coordinate which smoothly connects two arbitrary protein conformations, where this coordinate obeys important basin compactness requirements near endpoints of the structural transformation. Application of this method to allosteric transitions in adenylate kinase will be discussed. Finally, the energy landscapes analysis of histone tails, which are disordered proteins, will be presented, exploring ideas from polymer physics and spin glasses.
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