Residue interaction network analysis of Dronpa and a DNA clamp

Abstract

Topology is an essential aspect of protein structure. The network paradigm is increasingly used to describe the topology and dynamics of proteins. In this paper, the effect of topology on residue interaction network was investigated for two different proteins: Dronpa and a DNA clamp, which have cylindrical and toroidal topologies, respectively. Network metrics including characteristic path lengths, clustering coefficients, and diameters were calculated to investigate their global topology parameters such as small-world properties and packing density. Measures of centrality including betweenness, closeness, and residue centrality were computed to predict residues critical to function. Additionally, the detailed topology of the hydrophobic pocket in Dronpa, and communication pathways across the interface in the DNA clamp, were investigated using the network. The results are presented and discussed with regard to existing residue interaction network properties of globular proteins and elastic network models on Dronpa and the DNA clamp. The topological principle underlying residue interaction networks provided insight into the architectural organization of proteins.