Structure, Composition, and Modeling of Protein Complexes

Proteins exert their biological function via interactions with other molecules, in particular by participating in large multimeric complexes. These complexes play key roles in most biological processes within living cells. Experimental data on these interactions are hard to obtain and often controversial. Hence, computational tools for predicting the three-dimensional (3D) structure of multi-protein assemblies are of pivotal importance. One needs to differentiate between (i) methods aimed at identification of the correct biologically relevant assembly from experimental (i.e. crystallographic) data, and (ii) predicting the structure of complexes, for which only experimentally resolved structures of individual components exist. In this chapter, we first introduce the background on the biological relevance of multi-protein complexes and the relevant experimental techniques and then consider these two classes of computational tools. In the latter section, we also review additional tools that can leverage limited amounts of experimental data, such as electron-microscopy maps or crosslinking studies.