Network Properties of Protein Structures at Three Different Length Scales

Abstract

From the perspective of topology, the native structure of a protein molecule can be represented as a complex network. In the network, amino acids are vertices and the interactions between them act as edges. The networks of 80 proteins that belong to four structural classes are constructed at three length scales: Protein Contact Networks, Long-range Interaction networks and Short-range Interaction networks, using complex networks analysis. The results show that Protein Contact Networks and Short-range Interaction networks regardless of their structural classes exhibit the ‘small-world’ property and Long-range Interaction networks indicate ‘scale-free’ behavior except all β protein networks. Our results further indicate that all Protein Contact Networks and Short-range Interaction networks are assortative type. While the Long-range Interaction networks of all β, α+β, α/βproteins are also of assortative type, some of them of all α proteins are of disassortative type. This indicates that the differences in structural class may assign specificity to the protein networks of long-range interaction.