scholarly journals Is the intrinsic disorder of proteins the cause of the scale-free architecture of protein–protein interaction networks?

PROTEOMICS ◽  
2007 ◽  
Vol 7 (6) ◽  
pp. 961-964 ◽  
Author(s):  
Santiago Schnell ◽  
Santo Fortunato ◽  
Sourav Roy
Keyword(s):  
Protein Interaction ◽  
Intrinsic Disorder ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Scale Free ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks

HIERARCHICAL AND TOPOLOGICAL STUDY OF THE PROTEIN–PROTEIN INTERACTION NETWORKS

2005 ◽  
Vol 08 (04) ◽  
pp. 383-397 ◽  
Author(s):  
PO-HAN LEE ◽  
CHIEN-HUNG HUANG ◽  
JYWE-FEI FANG ◽  
HSIANG-CHUAN LIU ◽  
KA-LOK NG
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Clustering Coefficient ◽  
Interaction Networks ◽  
Node Degree ◽  
Hierarchical Network ◽  
Scale Free ◽  
E Coli ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks

We employ the random graph theory approach to analyze the protein–protein interaction database DIP. Several global topological parameters are used to characterize the protein–protein interaction networks (PINs) for seven organisms. We find that the seven PINs are well approximated by the scale-free networks, that is, the node degree cumulative distribution P cum (k) scales with the node degree k (P cum (k) ~ k-α). We also find that the logarithm of the average clustering coefficient C ave (k) scales with k (C ave (k) ~ k-β), for E. coli and S. cerevisiae. In particular, we determine that the E. coli and the S. cerevisiae PINs are better represented by the stochastic and deterministic hierarchical network models, respectively. The current fruit fly protein–protein interaction dataset does not have convincing evidence in favor of the hierarchical network model. These findings lead us to conclude that, in contrast to scale-free structure, hierarchical structure model applies for certain species' PINs only. We also demonstrate that PINs are robust when subject to random perturbation where up to 50% of the nodes are rewired. Average node degree correlation study supports the fact that nodes of low connectivity are correlated, whereas nodes of high connectivity are not directly linked.

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