Classifying Permanent and Transient Protein Interactions

Currently much research is devoted to the characterization and classification of transient and permanent protein-protein interactions. From the literature, we take data sets consisting of 161 permanent (65 homodimers, 96 heterodimers) and 242 transient interactions. We collect over 300 interface attributes relating to size, physiochemical properties, interaction propensities, and secondary structure elements. Our major discovery is a surprisingly simple relationship not yet reported in the literature: interactions with the same molecular weight or very big interfaces are permanent and otherwise transient. We train a support vector machine and achieve the following results: Molecular weight difference alone achieves 80% success rate. Together with the size of the buried surface the success rate improves to 89%. Adding water at the interface and the number of hydrophobic contacts we achieve a success rate of 97%.