title: Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull.
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.
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zheng
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, People's Republic of China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China.
authors.forename: Jishou
authors.initials: J
authors.lastname: Ruan
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, People's Republic of China.
authors.forename: Gang
authors.initials: G
authors.lastname: Hu
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, People's Republic of China.
authors.forename: Kui
authors.initials: K
authors.lastname: Wang
authors.affiliation: Department of Physical Sciences, Grant MacEwan University, Alberta, Canada.
authors.forename: Michelle
authors.initials: M
authors.lastname: Hanlon
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, People's Republic of China.
authors.forename: Jianzhao
authors.initials: J
authors.lastname: Gao
mesh_terms: D000596:Amino Acids / Q000737:chemistry / Q000276:immunology; D000818:Animals; D000936:Antigen-Antibody Complex / Q000737:chemistry / Q000276:immunology*; D018985:Epitopes, B-Lymphocyte / Q000737:chemistry* / Q000276:immunology*; D006801:Humans; D008958:Models, Molecular; D008968:Molecular Conformation; D017433:Protein Structure, Secondary
chemical_list: D000596:Amino Acids; D000936:Antigen-Antibody Complex; D018985:Epitopes, B-Lymphocyte