Network analysis of the protein chain tertiary structures of heterocomplexes.
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.
Li
Jing-Jing
JJ
Intelligent Computing Lab, Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, P. R. China.
Huang
De-Shuang
DS
Lok
Tat-Ming
TM
Lyu
Michael R
MR
Li
Yi-Xue
YX
Zhu
Yun-Ping
YP
D008958:Models, Molecular; D008962:Models, Theoretical; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
D011506:Proteins