ArticleImmunogenetics2004
Discriminating self from nonself with short peptides from large proteomes.
Article in Immunogenetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 73 citations in OpenAlex.
- Central T cell tolerance from sparse peptide sampling.Science advances · 2026Article
- Is the exquisite specificity of lymphocytes generated by thymic selection or due to evolution?Frontiers in immunology · 2024Article
- HLA variants have different preferences to present proteins with specific molecular functions which are complemented in frequent haplotypes.Frontiers in immunology · 2022Article
- Unique Pathogen Peptidomes Facilitate Pathogen-Specific Selection and Specialization of MHC Alleles.Molecular biology and evolution · 2021Article
- Self-mediated positive selection of T cells sets an obstacle to the recognition of nonself.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Modeling the Dynamics of T-Cell Development in the Thymus.Entropy (Basel, Switzerland) · 2021Review
- Significant non-existence of sequences in genomes and proteomes.Nucleic acids research · 2021Article
- HLA binding of self-peptides is biased towards proteins with specific molecular functions.bioRxiv : the preprint server for biology · 2021Article
- Article
- Can the Immune System Perform a t-Test?PloS one · 2017Article
- How many TCR clonotypes does a body maintain?Journal of theoretical biology · 2016Article
- TCR contact residue hydrophobicity is a hallmark of immunogenic CD8+ T cell epitopes.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Theories and quantification of thymic selection.Frontiers in immunology · 2014Review
- Social discrimination by quantitative assessment of immunogenetic similarity.Proceedings. Biological sciences · 2012Article
- Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire.PLoS computational biology · 2012Article
- Specific T-cell activation in an unspecific T-cell repertoire.Science progress · 2011Review
- The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes.BMC evolutionary biology · 2009Article
- The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.PloS one · 2008Article
- Polyspecificity of T cell and B cell receptor recognition.Seminars in immunology · 2007Review
- Modelling the human immune system by combining bioinformatics and systems biology approaches.Journal of biological physics · 2006Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We studied whether the peptides of nine amino acids (9-mers) that are typically used in MHC class I presentation are sufficiently unique for self:nonself discrimination. The human proteome contains 28,783 proteins, comprising 10(7) distinct 9-mers. Enumerating distinct 9-mers for a variety of microorganisms we found that the average overlap, i.e., the probability that a foreign peptide also occurs in the human self, is about 0.2%. This self:nonself overlap increased when shorter peptides were used, e.g., was 30% for 6-mers and 3% for 7-mers. Predicting all 9-mers that are expected to be cleaved by the immunoproteasome and to be translocated by TAP, we find that about 25% of the self and the nonself 9-mers are processed successfully. For the HLA-A*0201 and HLA-A*0204 alleles, we predicted which of the processed 9-mers from each proteome are expected to be presented on the MHC. Both alleles prefer to present processed 9-mers to nonprocessed 9-mers, and both have small preference to present foreign peptides. Because a number of amino acids from each 9-mer bind the MHC, and are therefore not exposed to the TCR, antigen presentation seems to involve a significant loss of information. Our results show that this is not the case because the HLA molecules are fairly specific. Removing the two anchor residues from each presented peptide, we find that the self:nonself overlap of these exposed 7-mers resembles that of 9-mers. Summarizing, the 9-mers used in MHC class I presentation tend to carry sufficient information to detect nonself peptides amongst self peptides.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.