A Research Of Protein Network Characteristics Based On Complex Network

In the past few years, the science of complex networks have a rapid development, whose main research objective is network. The relationships between structure and properties of networks can be explored by analyzing their topological properties and structural characteristics. Different networks have different characteristics, and complex network theory provides an effective tool to study the characteristics of these different networks. In the post-genomic era, the research of protein-protein interactions is very important to study the relationship between structure and function of proteins.The protein network characteristics is studied based on complex networks. The data sets are selected from the PDB database to construct protein networks, and result indicates that the protein monomer networks have significant small-world property when the cutoff distance R is 7A. The hierarchical organization in the protein networks is analyzed, the hierarchical exponent b decreases while the cutoff distance increasing, when cutoff distance is 24A, the hierarchical exponent b value is positively correlated with network size. Then the relationships between protein network topological parameters and amino acid composition is researched, the results indicate that the residues which have high closeness centrality and high betweenness centrality in protein monomer network and protein complex network are all nonpolar, hydrophobic amino acid. The network parameters, such as clustering coefficient C, characteristic path length L and b of protein complex networks and their compositing monomer networks are compared, we find the difference of C and L are little while the difference of b is bigger relatively. It shows the hierarchical structure of protein networks change greatly after the monomer form complex.Research on motifs and modules in complex networks is important to analyze the relationship between the structure and properties of networks. The motifs and modules in protein interface networks are researched in this paper, it is found that there are differences between the topology properties of protein interface networks and protein peptide networks. The type and number of motifs in protein interface networks are greatly affected by cutoff distance R, when R is different, the type and number of motifs in networks are different. The modules are existed in protein interface networks, the 3-clique-modules are analyzed when R is 5A,7A,12A,24A, it is found that the module partitions are consistent with the fact if R is 7A. At last, the relationship between modules and the topological properties of protein interface networks are researched, result shows that there is a linear relationship between the number of nodes and the number of 3-clique-modules in protein interface networks.