What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?

The many interactions of hub proteins can only partly be explained by bindings to similar proteins or domains. It is evident that domain repeats, which are associated with binding, are enriched in hubs. Moreover, there is an over representation of multi-domain proteins and long proteins among the hubs. In addition, there are clear differences between party hubs and date hubs. Fewer of the party hubs contain long disordered regions compared to date hubs, indicating that these regions are important for flexible binding but less so for static interactions. Furthermore, party hubs interact to a large extent with each other, supporting the idea of party hubs as the cores of highly clustered functional modules. In addition, hub proteins, and in particular party hubs, are more often ancient. Finally, the more recent paralogs of party hubs are underrepresented.Our results indicate that multiple and repeated domains are enriched in hub proteins and, further, that long disordered regions, which are common in date hubs, are particularly important for flexible binding.Physical interactions between proteins are fundamental to most biological processes, since proteins need to interact with other proteins to accomplish their functions. Hence, knowledge about the interactions between proteins is crucial for understanding biological functions. Furthermore, the functions of many proteins are unknown and identification of the physical interactions in which these proteins participate is likely to give an indication of their function. In the past few years new technologies have facilitated high-throughput determination of protein-protein interactions. In large-scale experiments, tandem-affinity purification (TAP) followed by mass spectrometry is a common technique for identifying protein complexes [1], while the yeast two hybrid method is used for identifying individual protein-protein interactions [2-4]. Once a large subset of the interactions between proteins has been characterized, t