Protein dynamics and function: Making new strides with an old warhorse, the alkaline conformational transition of cytochrome c

Protein dynamics is intimately linked to function. In metalloproteins, dynamics are often coupled to redox activity, ligand binding and enzyme function. We provide a concise overview of the field and then focus on the use of the alkaline conformer of cytochrome c as a model system to probe the factors that control the conformational dynamics of proteins in general and metalloproteins in particular. We consider the effects of ligands on metal-mediated dynamics, the interplay between intrinsic metal-ligand dynamics and barriers imposed by the protein scaffold itself, and the effects of local and overall protein stability on dynamics. Discussed within are the collected results from equilibrium thermodynamic methods, pH jump kinetics and conformationally gated redox reactions between small inorganic reagents and metalloproteins used as a means to probe conformational switching. 1Mutations used as variant names are abbreviated using the one letter code for the wild type amino acid followed by the position number and the one letter code for the new amino acid. in metalloproteins.