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Computational identification of epitopes in the glycoproteins of novel bunyavirus (SFTS virus) recognized by a human monoclonal antibody (MAb 4-5)

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Abstract

In this work, we have developed a new approach to predict the epitopes of antigens that are recognized by a specific antibody. Our method is based on the “multiple copy simultaneous search” (MCSS) approach which identifies optimal locations of small chemical functional groups on the surfaces of the antibody, and identifying sequence patterns of peptides that can bind to the surface of the antibody. The identified sequence patterns are then used to search the amino-acid sequence of the antigen protein. The approach was validated by reproducing the binding epitope of HIV gp120 envelop glycoprotein for the human neutralizing antibody as revealed in the available crystal structure. Our method was then applied to predict the epitopes of two glycoproteins of a newly discovered bunyavirus recognized by an antibody named MAb 4-5. These predicted epitopes can be verified by experimental methods. We also discuss the involvement of different amino acids in the antigen–antibody recognition based on the distributions of MCSS minima of different functional groups.

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Acknowledgments

This work was supported by grants from Jiangsu Province community development projects (BE2012768), Jiangsu Province Outstanding Medical Academic Leader Program (RC2011082), National Mega-Projects for Infectious Diseases from Ministry of Science and Technology, China and from the Ministry of Health, China (2013ZX09102029).

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Authors and Affiliations

  1. Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Institute of Pathogenic Microbiology, Ministry Health, Nanjing, 210009, China

    Wenshuai Zhang, Xiaoyan Zeng, Li Zhang, Haiyan Peng & Yongjun Jiao

  2. Monash Institute of Pharmaceutical Sciences (MIPS), Monash University, 399 Royal Parade, Parkville, VIC, 3050, Australia

    Jun Zeng & Herbert R. Treutlein

  3. Computist Bio-Nanotech, 1 Dalmore Drive, Scoresby, VIC, 3179, Australia

    Jun Zeng & Herbert R. Treutlein

Authors
  1. Wenshuai Zhang
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  2. Xiaoyan Zeng
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  3. Li Zhang
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  4. Haiyan Peng
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  5. Yongjun Jiao
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  6. Jun Zeng
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  7. Herbert R. Treutlein
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Corresponding authors

Correspondence to Yongjun Jiao, Jun Zeng or Herbert R. Treutlein.

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Zhang, W., Zeng, X., Zhang, L. et al. Computational identification of epitopes in the glycoproteins of novel bunyavirus (SFTS virus) recognized by a human monoclonal antibody (MAb 4-5). J Comput Aided Mol Des 27, 539–550 (2013). https://doi.org/10.1007/s10822-013-9661-7

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  • DOI: https://doi.org/10.1007/s10822-013-9661-7

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