The investigation of the disorder content of proteins from four eukaryotic interactomes shows that hub proteins are more disordered than end proteins in all four studied organisms ( and ), even though the predicted disorder content differs among these organisms [11
]. It is established that the proportion of disordered proteins correlates with the complexity of an organism [11
]. The application of two different disorder predictors to proteins from the three kingdoms of life has shown that the disorder content of bacteria and archaea is significantly lower than that of eukaryotes. The amount of predicted disorder also varies among eukaryotes. Comparison of disorder predictions in complete eukaryotic genomes [11
] shows that even though two different predictors were used (PONDR VL-XT [11
] versus DISOPRED2 [12
]), the prediction results agree in terms of the disorder content ranking, i.e., “Fly > Yeast > Worm” [11
] (note that human genome was not available at that time), and “Human > Fly > Yeast > Worm” [12
]. Interestingly, when the prediction of disorder was carried out on all proteins (hubs, ends, and proteins with two to nine partners) from the networks in the present study (unpublished data), the ranking “Human > Fly > Yeast > Worm” agreed with the previous studies that were carried out on complete genomes. At the same time, the relative percentages of predicted disorder in the networks were generally higher than those reported previously for the complete genomes [11
], even though the same predictor PONDR VL-XT was used in both studies. This result may indicate that proteins that interact with other proteins are on average more disordered than proteins that interact with ligands, such as nucleic acids, small molecules, lipids, etc.
Another interesting observation that follows from comparison of the networks to the complete genomes is that the disorder content of the proteomes is closer to the disorder content of ends than to the disorder content of hubs (unpublished data). Although differing views regarding the scale-free nature of the protein interaction networks exist [40
], it is still tempting to speculate that this bias could be explained by a potentially higher fraction of ends as compared with hubs in all genomes.
We previously determined that human cell signaling and cancer-associated proteins are significantly more disordered than proteins from other functional categories [13
]. Interestingly, the disorder content of HUMAN hubs () is very similar to that of human regulatory and cancer-associated proteins, suggesting that many cell signaling and regulatory proteins are network hubs.
The high disorder content of hubs relates directly to their function. Intrinsic disorder provides several important functional benefits for interactions with multiple partners. First, it allows hubs to adapt to the structure of a variety of differently shaped binding partners. Such structural malleability is especially important for hubs that interact with their partners using the same or overlapping binding surfaces. Second, disorder may enable a hub protein to elicit both inhibiting and activating effects on different partners, as was recently noted for moonlighting proteins [42
]. Third, structural plasticity may enable some proteins to serve as hubs in multiple and distinct signaling networks. One example of such a hub is glycogen synthase kinase 3β, which uses two different ID regions to participate in two unrelated signaling pathways, Wnt and insulin signaling [18
While intrinsic disorder is an important feature of hub proteins, many ordered hub proteins also exist [18
]. Interestingly, it has been recently proposed that ordered hubs have higher surface charge than nonhub proteins, and that this increased charge is likely to have an impact on their binding ability [43
]. Furthermore, it has been noted that the binding partners of several ordered hubs are intrinsically disordered [18
]. The examples include the partners of 14-3-3 proteins [44
] the partners of β-catenin [45
], and the partners of several other proteins (such as calmodulin, actin, and Cdk) [18
]. The results of the present study suggest that wholly ordered hubs, as defined by the CDF/CH consensus classification, constitute a substantial fraction of all hub proteins and are especially prevalent in the YEAST dataset ().
Among all the networks examined here, the YEAST interaction network appears to exhibit the smallest difference between hubs and ends in terms of predicted disorder, at least when literature-curated interactions are considered (, and , compare with Figures S1
). Notably, the amino acid composition of proteins from the YEAST network appears to be the least similar to the three other organisms (). In addition, the proportion of wholly ordered proteins within both YEAST hubs and YEAST ends is the highest among the four datasets (, Table S3
). A plausible explanation of the smaller differences in disorder content of YEAST hubs and ends is that the interactomes of the unicellular organisms are inherently simpler than metazoan interactomes due to less sophisticated signaling and regulation pathways. Because of their greater simplicity, these yeast pathways may rely less heavily on disorder than the networks of higher eukaryotes.
In summary, the present study shows that intrinsic structural disorder is a distinctive and common characteristic of eukaryotic hub proteins, and it suggests that disorder may serve as a determinant of protein interactivity. In the future, it would be interesting to compare more specialized signaling and metabolic networks to each other to determine whether the high disorder content of hubs is a common feature of all cellular networks. In addition, it would certainly be interesting to perform the disorder analysis on the complete interactomes (when they are available) to determine whether similar conclusions are reached.