Prediction of three-dimensional structure and mapping of conformational epitopes of envelope glycoprotein of Japanese encephalitis virus

Abstract

Japanese encephalitis virus (JEV), a mosquito-borne flavivirus, is an important human pathogen. The envelope glycoprotein (Egp), a major structural antigen, is responsible for viral haemagglutination and eliciting neutralising antibodies. The three-dimensional structure of the Egp of JEV was predicted using the knowledge-based homology modeling approach and X-ray structure data of the Egp of tick-home encephalitis virus as a template (Rey et al., 1995). In the initial stages of optimisation, a distance-dependent dielectric constant of 4r(ij) was used to simulate the solvent effect. The predicted structure was refined by solvating the protein in a 10-Å layer of water by explicitly considering 4867 water molecules. Four independent structure evaluation methods report this structure to be acceptable stereochemically and geometrically. The Egp of JEV has an extended structure with seven β-sheets, two α-helices, and three domains. The water-solvated structure was used to delineate conformational and sequential epitopes. These results document the importance of tertiary structure in understanding the antigenic properties of flaviviruses in general and JEV in particular. The conformational epitope prediction method could be used to identify conformational epitopes on any protein antigen with known three-dimensional structure. This is one of the largest proteins whose three-dimensional structure has been predicted using an homology modeling approach and water as a solvent.