Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

This article is part of the supplement: Selected Articles on Computational Vaccinology

Open Access Research

Bioinformatics analysis of the epitope regions for norovirus capsid protein

Liping Chen1, Di Wu3, Lei Ji1, Xiaofang Wu1, Deshun Xu1, Zhiwei Cao23* and Jiankang Han1*

Author Affiliations

1 Huzhou Center For Disease Control and Prevention, Zhejiang 311000, China

2 School of Life Sciences and Technology, Tongji University, Shanghai 200092, China

3 Shanghai Center for Bioinformation Technology, Shanghai 200235, China

For all author emails, please log on.

BMC Bioinformatics 2013, 14(Suppl 4):S5  doi:10.1186/1471-2105-14-S4-S5

Published: 8 March 2013

Abstract

Background

Norovirus is the major cause of nonbacterial epidemic gastroenteritis, being highly prevalent in both developing and developed countries. Despite of the available monoclonal antibodies (MAbs) for different sub-genogroups, a comprehensive epitope analysis based on various bioinformatics technology is highly desired for future potential antibody development in clinical diagonosis and treatment.

Methods

A total of 18 full-length human norovirus capsid protein sequences were downloaded from GenBank. Protein modeling was performed with program Modeller 9.9. The modeled 3D structures of capsid protein of norovirus were submitted to the protein antigen spatial epitope prediction webserver (SEPPA) for predicting the possible spatial epitopes with the default threshold. The results were processed using the Biosoftware.

Results

Compared with GI, we found that the GII genogroup had four deletions and two special insertions in the VP1 region. The predicted conformational epitope regions mainly concentrated on N-terminal (1~96), Middle Part (298~305, 355~375) and C-terminal (560~570). We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup.

Conclusions

The predicted conformational epitope regions of norovirus VP1 mainly concentrated on N-terminal, Middle Part and C-terminal. We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup. The overlapping with experimental epitopes indicates the important role of latest computational technologies. With the fast development of computational immunology tools, the bioinformatics pipeline will be more and more critical to vaccine design.