Prediction of residues in discontinuous B-cell epitopes using protein 3D structures

Abstract

Discovery of discontinuous B-cell epitopes is a major challenge in vaccine design. Previous epitope prediction methods have mostly been based on protein sequences and are not very effective. Here, we present DiscoTope, a novel method for discontinuous epitope prediction that uses protein three-dimensional structural data. The method is based on amino acid statistics, spatial information, and surface accessibility in a compiled data set of discontinuous epitopes determined by X-ray crystallography of antibody/antigen protein complexes. DiscoTope is the first method to focus explicitly on discontinuous epitopes. We show that the new structure-based method has a better performance for predicting residues of discontinuous epitopes than methods based solely on sequence information, and that it can successfully predict epitope residues that have been identified by different techniques. DiscoTope detects 15.5% of residues located in discontinuous epitopes with a specificity of 95%. At this level of specificity, the conventional Parker hydrophilicity scale for predicting linear B-cell epitopes identifies only 11.0% of residues located in discontinuous epitopes. Predictions by the DiscoTope method can guide experimental epitope mapping in both rational vaccine design and development of diagnostic tools, and may lead to more efficient epitope identification.

Figure 1.

Analysis of the complete data set of discontinuous B-cell epitopes. (A) Distribution of the number of residues per epitope. (B) Distribution of the number of residues per sequential stretch of epitopes. (C) Distribution of the maximum length of a sequential stretch per epitope.

Figure 2.

Contact numbers of epitope residues in the data set compared to nonepitope residues. The curves show the distribution of contact numbers for epitope residues (red curve) compared to nonepitope residues (black curve). The vertical lines represent the mean value of contact numbers for the epitope residues (red line) and for the nonepitope residues (black line).

Figure 3.

Evaluation of B-cell epitope prediction methods. The average AUC of various methods on the five evaluation sets. “Log e-ne” denotes raw log-odds ratios; “Parker” denotes the Parker hydrophilicity scale; “Win9 log e-ne” denotes the log-odds ratios used with a smoothing window of nine residues; “Contact” denotes contact numbers; and “Naccess” denotes NACCESS RSA values. (A) The performance of single methods. (B) The performance of simple combination methods using contact numbers. (C) The performance of simple combination methods using NACCESS RSA values. (D) The performance of the structural proximity sum methods.

Figure 4.

Dot plots showing comparisons of performances of the Parker method, the NACCESS RSA method, and the DiscoTope method. Circles indicate average AUC per group showed for the 25 groups of different antigens. The dotted lines indicate points where the methods perform equally.

Figure 5.

Structure of the 1AR1 antigen. The antigen is a subunit of the cytochrome c oxidase (Ostermeier et al. 1997). (A) The 30% of residues with lowest contact numbers are shown in green. In red is shown a residue that is part of the 30% with lowest contact numbers and of the epitope from the data set. The rest of the epitope is shown in blue. (B) The structure mentioned above and rotated 90 degrees. (C) The complex of the cytochrome c oxidase with antibody fragments. The 1AR1 antigen is color coded as in A and B. Antibody fragments are shown in light blue. The other subunit of the cytochrome c oxidase is shown in yellow. Membrane spanning helices of the 1AR1 antigen are part of the lower half of the structure.

Figure 6.

Predicted epitope residues of the AMA1 ectodomain. Backbone atoms of residues predicted by DiscoTope as parts of epitopes are highlighted in green. Side chains of the residues mapped to the monoclonal antibodies 1F9 and 4G2 are shown in black.