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Center for Nonlinear Studies |
gProtein-Protein Interaction (PPI) networks in several eucaryotic organisms contain significantly more self-interacting proteins than expected if such homodimers were created randomly. We show that on average homodimers have twice as many interaction partners than non-self-interacting proteins. A duplication of self-interacting proteins creates a pair of paralogous proteins that often interact with each other. We show that such paralogous pairs occur more frequently than could be explained by pure chance. Similar to homodimers, proteins involved in heterodimers with their paralogs, on average have twice as many interacting partners as the rest of the network. The likelihood of a pair of paralogous proteins to interact with each other was also shown to decrease with their sequence similarity. This all points to the conclusion that most of interactions between paralogs are inherited from ancestral homodimeric proteins, rather than established de novo after the duplication. We finally discuss the role of heterodimer links in creating such tightly linked motifs as triangles and higher cliques in PPI networks.