Biological Units and their Effect upon the Properties and Prediction of Protein–Protein Interactions

Structural data as collated in the Protein Data Bank (PDB) have been widely applied in the study and prediction of protein–protein interactions. However, since the basic PDB Entries contain only the contents of the asymmetric unit rather than the biological unit, some key interactions may be missed by analysing only the PDB Entry. A total of 69,054 SCOP (Structural Classification of Proteins) domains were examined systematically to identify the number of additional novel interacting domain pairs and interfaces found by considering the biological unit as stored in the PQS (Protein Quaternary Structure) database. The PQS data adds 25,965 interacting domain pairs to those seen in the PDB Entries to give a total of 61,783 redundant interacting domain pairs. Redundancy filtering at the level of the SCOP family shows PQS to increase the number of novel interacting domain-family pairs by 302 (13.3%) from 2277, but only 16/302 (1.4%) of the interacting domain pairs have the two domains in different SCOP families. This suggests the biological units add little to the elucidation of novel biological interaction networks. However, when the orientation of the domain pairs is considered, the PQS data increases the number of novel domain–domain interfaces observed by 1455 (34.5%) to give 5677 non-redundant domain–domain interfaces. In all, 162/1455 novel domain–domain interfaces are between domains from different families, an increase of 8.9% over the PDB Entries. Overall, the PQS biological units provide a rich source of novel domain–domain interfaces that are not seen in the studied PDB Entries, and so PQS domain–domain interaction data should be exploited wherever possible in the analysis and prediction of protein–protein interactions.