Evolution of protein structures and interactions from the perspective of residue contact networks

Abstract

Here we review mechanisms of protein evolution leading to structural changes in protein complexes. These mechanisms include mutations directly within protein interfaces, as well as the effects of mutations that propagate from distant regions of the protein. We also discuss the constraints protein complex structures impose on sequence evolution. We interpret, wherever possible, these mechanisms using amino acid residue contact networks. Many insights into protein evolution come from studies of monomers, and these results facilitate our understanding of evolution of protein complexes. Finally, we highlight the potential of formalizing a phylogenetic framework to integrate residue evolution, structure evolution, and to quantify changes in residue contact networks in protein families.