Kolaskar AS: Prediction of 3D structure of envelope glycoprotein of Sri Lanka strain of Japanese encephalitis virus. the proceedings of first APBC conference: 4–7 February 2003; Conferences in research and practice in information technology 19

Abstract

Abstract This paper describes knowledge-based homology modeling studies of envelope glycoprotein (Egp) of Sri Lanka strain of Japanese encephalitis virus (JEVS). JEVS is a mosquito-borne Flavivirus, which is an important human pathogen. The Egp is a major structural antigen and is responsible for viral hemagglutination and neutralisation. The 3D structure of 399 amino acids from the extra cellular domain of Egp of JEVS has been predicted using the x-ray crystal structure of Egp of Tickborne encephalitis virus as a template and the knowledge-based homology modeling approach. Even though the homology modeling is the best method for prediction of 3D structure, prediction of structures of loop regions is still a challenge. A novel approach of molecular dynamics simulations and geometry optimisation has been used to sample the conformations of loop regions. The Egp of JEVS has an extended structure with nine β-sheets, two α-helices and three domains. The predicted structure was compared with the model of Egp of Nakayama strain of Japanese encephalitis virus (JEVN), which was developed earlier (Kolaskar & KulkarniKale, 1999). Similarities and differences between the structures of Egps of two strains of JEV are discussed. These models illustrate effect of mutations on the local and global conformation of Egp and help to explain strain specific properties. The sequential and conformational epitopes of Egp of JEV were predicted using an algorithm developed in hous