crossmark THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 291, NO. 28, pp. 14585–14599, July 8, 2016 © 2016 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A.
Inadequate Reference Datasets Biased toward Short Non-epitopes Confound B-cell Epitope Prediction*□ S
Received for publication, March 23, 2016, and in revised form, May 3, 2016 Published, JBC Papers in Press, May 9, 2016, DOI 10.1074/jbc.M116.729020
Kh. Shamsur Rahman‡, Erfan Ullah Chowdhury‡, Konrad Sachse§, and Bernhard Kaltenboeck‡1 From the ‡Department of Pathobiology, Auburn University, Auburn, Alabama 36849 and the §Federal Institute for Animal Health, D-07743 Jena, Germany X-ray crystallography has shown that an antibody paratope typically binds 15–22 amino acids (aa) of an epitope, of which 2–5 randomly distributed amino acids contribute most of the binding energy. In contrast, researchers typically choose for B-cell epitope mapping short peptide antigens in antibody binding assays. Furthermore, short 6 –11-aa epitopes, and in particular non-epitopes, are over-represented in published B-cell epitope datasets that are commonly used for development of B-cell epitope prediction approaches from protein antigen sequences. We hypothesized that such suboptimal length peptides result in weak antibody binding and cause false-negative results. We tested the influence of peptide antigen length on antibody binding by analyzing data on more than 900 peptides used for B-cell epitope mapping of immunodominant proteins of Chlamydia spp. We demonstrate that short 7–12-aa peptides of B-cell epitopes bind antibodies poorly; thus, epitope mapping with short peptide antigens falsely classifies many B-cell epitopes as non-epitopes. We also show in published datasets of confirmed epitopes and non-epitopes a direct correlation between length of peptide antigens and antibody binding. Elimination of short,
Inadequate Reference Datasets Biased toward Short Non-epitopes Confound B-cell Epitope Prediction*□ S
Received for publication, March 23, 2016, and in revised form, May 3, 2016 Published, JBC Papers in Press, May 9, 2016, DOI 10.1074/jbc.M116.729020
Kh. Shamsur Rahman‡, Erfan Ullah Chowdhury‡, Konrad Sachse§, and Bernhard Kaltenboeck‡1 From the ‡Department of Pathobiology, Auburn University, Auburn, Alabama 36849 and the §Federal Institute for Animal Health, D-07743 Jena, Germany X-ray crystallography has shown that an antibody paratope typically binds 15–22 amino acids (aa) of an epitope, of which 2–5 randomly distributed amino acids contribute most of the binding energy. In contrast, researchers typically choose for B-cell epitope mapping short peptide antigens in antibody binding assays. Furthermore, short 6 –11-aa epitopes, and in particular non-epitopes, are over-represented in published B-cell epitope datasets that are commonly used for development of B-cell epitope prediction approaches from protein antigen sequences. We hypothesized that such suboptimal length peptides result in weak antibody binding and cause false-negative results. We tested the influence of peptide antigen length on antibody binding by analyzing data on more than 900 peptides used for B-cell epitope mapping of immunodominant proteins of Chlamydia spp. We demonstrate that short 7–12-aa peptides of B-cell epitopes bind antibodies poorly; thus, epitope mapping with short peptide antigens falsely classifies many B-cell epitopes as non-epitopes. We also show in published datasets of confirmed epitopes and non-epitopes a direct correlation between length of peptide antigens and antibody binding. Elimination of short,
