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Comparative Study
. 2004 Sep 7;101(36):13268-72.
doi: 10.1073/pnas.0404740101. Epub 2004 Aug 23.

Comparative immunopeptidomics of humans and their pathogens

Sorin Istrail  1 , Liliana Florea, Bjarni V Halldórsson, Oliver Kohlbacher, Russell S Schwartz, Von Bing Yap, Jonathan W Yewdell, Stephen L Hoffman
Affiliations
Comparative Study

Comparative immunopeptidomics of humans and their pathogens

Sorin Istrail et al. Proc Natl Acad Sci U S A. .

Abstract

Major histocompatibility complex class I molecules present peptides of 8-10 residues to CD8+ T cells. We used 19 predicted proteomes to determine the influence of CD8+ T cell immune surveillance on protein evolution in humans and microbial pathogens by predicting immunopeptidomes, i.e., sets of class I binding peptides present in proteomes. We find that class I peptide binding specificities (i) have had little, if any, influence on the evolution of immunopeptidomes and (ii) do not take advantage of biases in amino acid distribution in proteins other than the concentration of hydrophobic residues in NH(2)-terminal leader sequences.

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Figures

Fig. 1.
Fig. 1.
Immunopeptidomics of humans and their pathogens. (a) Comparison of the percentage of peptides predicted to bind MHC (percentage of high-binding epitopes, % HBE) in the predicted human proteome and two artificial proteomes generated by randomly permuting the amino acids in each predicted ORF of the human proteome. The figure displays results for the MHC class I alleles A2, A3, A24, and B7. (b) Comparison of the percentage of peptides predicted to bind MHC in the predicted proteomes of H. sapiens, M. musculus, D. melanogaster, and C. elegans. The figure displays results for the MHC class I alleles A2, A3, A24, and B7. Error bars show the deviation between measured results and the results derived from artificial proteomes created by randomly permuting all residues in each ORF. (c) Comparison of the percentage of peptides predicted to bind MHC in the predicted proteomes of H. sapiens, herpesviruses, M. tuberculosis, S. aureus, and M. janaschii. The figure displays results for the MHC class I alleles A2, A3, A24, and B7. Error bars show the deviation between measured results and the results derived from artificial proteomes created by randomly permuting all residues in each ORF. (d) Comparison of the percentage of peptides predicted to bind MHC in the predicted proteomes of H. sapiens, herpesviruses, human papillomaviruses, HIV, vaccinia, and variola. The figure displays results for the MHC class I alleles A2, A3, A24, and B7. Error bars show the deviation between measured results and the results derived from artificial proteomes created by randomly permuting all residues in each ORF.
Fig. 2.
Fig. 2.
Peptides as a function of position in protein. Fraction of predicted high-binding peptides as a function of the position of the first residue of the peptide within its respective protein. Each data point represents the sum of 10 consecutive residue positions to reduce noise in the plots. (a) A2. (b) A3. (c) A24. (d) B7.
Fig. 3.
Fig. 3.
Comparison of predictions derived from different ligand prediction methods. (a) Our voting methods (13). (b) The matrix-based method of Parker et al. (14).
See this image and copyright information in PMC

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