Computer Simulation of Protein−Protein Interactions

The use of computer simulations in investigations of protein−protein interactions is discussed. First, crystallographic analyses of known protein−protein complexes are summarized with particular emphasis being placed on the atomic nature of the interactions. Models available for describing macromolecular association energetics are then discussed, with special reference to the treatment of electrostatic and nonpolar interactions. The use of these models in combination with efficient search methods is discussed in the context of the so-called protein docking problem and in the description of weaker (i.e., noncrystallizable) protein−protein interactions. Finally, simulations of the dynamics of protein−protein association events are outlined. In all cases, differences are stressed between the atomically detailed view of protein−protein interactions and the view implicit in the use of simpler colloidal models.