Structural features of protein-protein recognition

The interfaces formed by protein-protein interactions can be of three types: a) contacts between components of protein-protein complexes; b) contacts between protein subunits in oligomeric proteins and c) contacts between symmetry-related molecules in the crystal lattice. Individual components in complexes can exist as independent molecules under physiological conditions, and their affinities could be as low as millimolar to as high as femtomolar. The oligomers are usually permanent (obligatory) and individual subunits do not have independent existence; in the present work only the homodimers are considered. The crystal contacts, on the other hand, are ‘nonphysiological' and occur when a supersaturated solution of a protein crystallizes. The first two categories are called specific interfaces due to their nature of specific interactions within the cells and the last category is called non-specific interfaces, as they do not have any biological selection and are formed due to the crystal artifacts. The non-covalent interactions that hold crystals together are the same as in protein-protein complexes and oligomeric proteins,
yet they are not subject to natural selection, and thus, they lack biological specificity. To understand the origin of affinity and specificity of these interfaces, it will be of interest to compare the physico-chemical and geometric properties of these interfaces and to use them to identify the biologically relevant dimeric interface.

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