Bioinformatics analysis of the epitope regions for norovirus capsid protein

BMC Bioinformatics

Research

Liping Chen¹  Xiaofang Wu¹  Jiankang Han¹  Lei Ji¹  Deshun Xu¹  Zhiwei Cao²  Di Wu³ 

[1] Huzhou Center For Disease Control and Prevention, 311000, Zhejiang, China;School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China;Shanghai Center for Bioinformation Technology, 200235, Shanghai, China;Shanghai Center for Bioinformation Technology, 200235, Shanghai, China;

关键词: Capsid Protein;    Conformational Epitope;    Epitope Prediction;    Epitope Region;    Amino Acid Insertion;   

DOI  :  10.1186/1471-2105-14-S4-S5

来源: Springer

【 摘 要 】

BackgroundNorovirus 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.MethodsA 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.ResultsCompared 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Chen et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.