Network Analysis of the Protein Chain Tertiary Structures of Heterocomplexes+

Jing-Jing      Li; De-Shuang      Huang; Tat-Ming      Lok; Michael   R.   Lyu; Yi-Xue      Li; Yun-Ping      Zhu

Abstract

In this paper, the tertiary structures of protein chains of heterocomplexes were mapped to 2D networks; based on the mapping approach, statistical properties of these networks were systematically studied. Firstly, our experimental results confirmed that the networks derived from protein structures possess small-world properties. Secondly, an interesting relationship between network average degree and the network size was discovered, which was quantified as an empirical function enabling us to estimate the number of residue contacts of the protein chains accurately. Thirdly, by analyzing the average clustering coefficient for nodes having the same degree in the network, it was found that the architectures of the networks and protein structures analyzed are hierarchically organized. Finally, network motifs were detected in the networks which are believed to determine the family or superfamily the networks belong to. The study of protein structures with the new perspective might shed some light on understanding the underlying laws of evolution, function and structures of proteins, and therefore would be complementary to other currently existing methods.

Keywords: two-dimensional array, small-world networks, clustering coefficient, hierarchical architectures, over-represented graphlets

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