Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull

PLoS One. 2015 Aug 5;10(8):e0134835. doi: 10.1371/journal.pone.0134835. eCollection 2015.

Abstract

The prediction of conformational b-cell epitopes plays an important role in immunoinformatics. Several computational methods are proposed on the basis of discrimination determined by the solvent-accessible surface between epitopes and non-epitopes, but the performance of existing methods is far from satisfying. In this paper, depth functions and the k-th surface convex hull are used to analyze epitopes and exposed non-epitopes. On each layer of the protein, we compute relative solvent accessibility and four different types of depth functions, i.e., Chakravarty depth, DPX, half-sphere exposure and half space depth, to analyze the location of epitopes on different layers of the proteins. We found that conformational b-cell epitopes are rich in charged residues Asp, Glu, Lys, Arg, His; aliphatic residues Gly, Pro; non-charged residues Asn, Gln; and aromatic residue Tyr. Conformational b-cell epitopes are rich in coils. Conservation of epitopes is not significantly lower than that of exposed non-epitopes. The average depths (obtained by four methods) for epitopes are significantly lower than that of non-epitopes on the surface using the Wilcoxon rank sum test. Epitopes are more likely to be located in the outer layer of the convex hull of a protein. On the benchmark dataset, the cumulate 10th convex hull covers 84.6% of exposed residues on the protein surface area, and nearly 95% of epitope sites. These findings may be helpful in building a predictor for epitopes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry
  • Amino Acids / immunology
  • Animals
  • Antigen-Antibody Complex / chemistry
  • Antigen-Antibody Complex / immunology*
  • Epitopes, B-Lymphocyte / chemistry*
  • Epitopes, B-Lymphocyte / immunology*
  • Humans
  • Models, Molecular
  • Molecular Conformation
  • Protein Structure, Secondary

Substances

  • Amino Acids
  • Antigen-Antibody Complex
  • Epitopes, B-Lymphocyte

Grants and funding

JG was supported by Specialized Research Fund for the Doctoral Program of Higher Education (SRFDP grant number 20130031120001). WZ was supported by the Ph.D. Candidate Research Innovation Fund of Nankai University (no. 68150003). JR was supported by the International Development Research Center, Ottawa, Canada (no. 104519-010) and the National Natural Science Foundation of China (NSFC, grant numbers 31050110432, 31150110577). GH was supported by NSFC (grant number 11101226). KW was supported by NSFC (grant number 11301286). This work was also supported by the National Natural Science Foundation of China (NSFC, grant number 61170099). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.