Detection of active site residues in bovine rhodopsin using network analysis

Abstract

Topological determinants of the protein structures can be obtained by modeling them as undirected network, which may relate to functionally important residues. In this study, we aim to analyze the Bovine rhodopsin structure (PDB ID: 1U19A) a GPCR family protein. We modeled the protein structure as, an undirected network and network parameters were calculated and compared with the control random networks. Our findings show that the protein contact network possesses a small world property. The functionally important residues in the protein contact network were identified using residue centrality. The statistical significance of the central residues was determined using the Z-score values of the residue centrality. Results show that residues with high Z-score values are highly conserved, are in close proximity with the ligand and are also situated closer to the centre of mass of the protein.