In Silico Homology Modeling and Epitope Prediction of Nucleocapsid Protein region from Japanese Encephalitis Virus

Ingale Ag

doi:10.4172/jcsb.1000056

Abstract

The 3D structure of a protein is a prerequisite for structure based drug design as well as for identifying the conformational epitopes that are essential for the designing vaccines. A 3-dimensional model (3D) was developed for the nucleocapsid protein of Japanese encephalitis virus. A homology modeling method was used for the prediction of the structure. For the modeling, one template proteins were obtained by mGenTHERADER, namely the high-resolution X-ray crystallography structure of NS3 protease helicase of murry vally encephalitis virus(2WV9). By comparing the template protein a rough model was constructed for the target protein using SWISSMODEL, a program for comparative modelling. The model was validated using protein structure checking tools such as Verify3D for reliability. The total of 138 such epitope regions/sites have been identified by kolaskar and tongaokar method. Conformational epitopes are mapped from the 3D structure of nucleocapsid protein of Japanese encephalitis virus modeled using the concept of an antigenic domain. The information thus discussed provides insight to the molecular understanding of nucleocapsid protein of JE virus. The predicted 3-D model may be further used in characterizing the protein in wet laboratory.

Highlights

Japanese encephalitis (JE) is an acute viral infection of the central nervous system
One of the major treatments is gene therapy or recombinant DNA vaccines involve targeting multiple antigenic component of virus to direct and empower the immune system to protect the host from viral infection
The protein sequence of the of nucleocapsid protein of JE virus was obtained from the NCBI sequence database

Summary

Introduction

Japanese encephalitis (JE) is an acute viral infection of the central nervous system. The nucleocapsid protein, is the major protein of the virion This protein is believed to play an important role in a number of processes, including viral attachment, membrane fusion, and entry into the host cell. In response to JEV infection, the host produces virus neutralizing antibodies and cytotoxic T cells (CTLs). The E protein of Japanese encephalitis virus (JEV) is the major antigen used to elicit neutralizing antibody response and protective immunity in hosts (Wu et al, 2003). One of the major treatments is gene therapy or recombinant DNA vaccines involve targeting multiple antigenic component of virus to direct and empower the immune system to protect the host from viral infection. B-cell epitopes on JEV nucleocapsid protein are important determinants of protection against virus infection. It has been showed that, the use of Bioinformatics tools and techniques reduce the time required to identify the candidate peptide as vaccine and provides an insight in structure function relationship of virus protein

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Results

Conclusion