A Dissection of Specific and Non-specific Protein–Protein Interfaces

Abstract

We compare the geometric and physical–chemical properties of interfaces involved in specific and non-specific protein–protein interactions in crystal structures reported in the Protein Data Bank. Specific interactions are illustrated by 70 protein–protein complexes and by subunit contacts in 122 homodimeric proteins; non-specific interactions are illustrated by 188 pairs of monomeric proteins making crystal-packing contacts selected to bury more than 800 Å 2 of protein surface. A majority of these pairs have 2-fold symmetry and form “crystal dimers” that cannot be distinguished from real dimers on the basis of the interface size or symmetry. The chemical and amino acid compositions of the large crystal-packing interfaces resemble the protein solvent-accessible surface. These interfaces are less hydrophobic than in homodimers and contain much fewer fully buried atoms. We develop a residue propensity score and a hydrophobic interaction score to assess preferences seen in the chemical and amino acid compositions of the different types of interfaces, and we derive indexes to evaluate the atomic packing, which we find to be less compact at non-specific than at specific interfaces. We test the capacity of these parameters to identify homodimeric proteins in crystal structures, and show that a simple combination of the non-polar interface area and the fraction of buried interface atoms assigns the quaternary structure of 88% of the homodimers and 77% of the monomers in our data set correctly. These success rates increase to 93–95% when the residue propensity score of the interfaces is taken into consideration.