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Review
. 2008 Dec;36(Pt 6):1398-403.
doi: 10.1042/BST0361398.

Topological properties of protein interaction networks from a structural perspective

Attila Gursoy  1 , Ozlem Keskin, Ruth Nussinov
Affiliations
Review

Topological properties of protein interaction networks from a structural perspective

Attila Gursoy et al. Biochem Soc Trans. 2008 Dec.

Abstract

Protein-protein interactions are usually shown as interaction networks (graphs), where the proteins are represented as nodes and the connections between the interacting proteins are shown as edges. The graph abstraction of protein interactions is crucial for understanding the global behaviour of the network. In this mini review, we summarize basic graph topological properties, such as node degree and betweenness, and their relation to essentiality and modularity of protein interactions. The classification of hub proteins into date and party hubs with distinct properties has significant implications for relating topological properties to the behaviour of the network. We emphasize that the integration of protein interface structure into interaction graph models provides a better explanation of hub proteins, and strengthens the relationship between the role of the hubs in the cell and their topological properties.

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Figures

Figure 1 |
Figure 1 |. Protein interaction networks
(A) A simple graph model of a protein interaction network. Node A is a hub, node B is a non-hub (a high-betweenness node). (B) A sample protein interaction network derived from yeast protein interactions.
Figure 2 |
Figure 2 |. Use of interfaces to indicate simultaneous and unshared interactions
Circle nodes represent proteins, diamonds indicate their interfaces; S for shared, U for unshared interface. Node A corresponds to a party hub (has many unshared interfaces for simultaneous interactions). Node B is a date hub. The shared interface is used for different interactions at different times.
See this image and copyright information in PMC

References

    1. Watts DJ and Strogatz SH (1998) Collective dynamics of ‘small-world’ networks. Nature 393, 440–442 - PubMed
    1. Strogatz SH (2001) Exploring complex networks. Nature 410, 268–276 - PubMed
    1. Barabasi AL and Albert R (1999) Emergence of scaling in random networks. Science 286, 509–512 - PubMed
    1. Han JD, Dupuy D, Bertin N, Cusick ME and Vidal M (2005) Effect of sampling on topology predictions of protein–protein interaction networks. Nat. Biotechnol. 23, 839–844 - PubMed
    1. Tanaka R, Yi TM and Doyle J (2005) Some protein interaction data do not exhibit power law statistics. FEBS Lett. 579, 5140–5144 - PubMed

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