Protein complexes subunits interaction topology and sequence identity

Many protein complexes prediction approaches are based on the assumptions that (i) protein complexes have dense protein-protein interactions (PPI) among their subunits, and (ii) high functional similarity for the subunits. We suggest to investigate those assumptions by studying the subunits´ interaction topology and sequences identity. Such consideration can possibly provide better insights for our understanding of protein complexes architecture. Two topological parameters, density of protein-protein interaction (PPI) and connectedness, are defined to test whether protein complex are found in PPI dense region or not. The present data indicated that interaction dense regions represent protein complexes up to 20% cases. A rather large proportion of protein complexes have a lower density of PPI, and connectedness. It is conjectured that prediction approaches based on the assumption that complexes are composed of highly PPI dense regions, connectedness can predict a rather limited numbers of the complexes. On the other hand, our result indicates that protein complexes do composing of subunits with higher sequence identity or similarity.