Molecular dynamics of proteins: Towards function identification via stability

Conformational changes of biomolecules have been proposed as a cause and effect of biological events. Particularly, the content of a specific conformation of a protein in an intracellular localized space has suggested signals addressed to execute specific tasks. Sampling of these structural options, that make of proteins informational molecules, finds in molecular dynamics (MD) a theoretical and computational tool to explain and hypothesize the functionality at atomistic level. Conceptually, if we consider the "final" folded structure as the most functional conformation, possibly we find some obstacle to study the pleiotropicity of proteins and its structural basis. In this order of ideas, the evidence provided by MD in relation to folding and unfolding, where thermodynamic states and kinetic properties characterize conformational changes, sheds light on the pathways towards functionality of a protein. In this chapter, force fields and atomistic interactions considered as relevant parts of a MD simulations are reviewed and a typical protocol of stability is explained. Finally, statistical mechanics as a theoretical frame to explore the conformational space is discussed in the context of available computational methods devoted to discover functional domains in proteins.