Discriminating self from nonself with short peptides from large proteomes.
Identifieur interne : 002371 ( PubMed/Curation ); précédent : 002370; suivant : 002372Discriminating self from nonself with short peptides from large proteomes.
Auteurs : Nigel J. Burroughs [Royaume-Uni] ; Rob J. De Boer ; Can Ke MirSource :
- Immunogenetics [ 0093-7711 ] ; 2004.
Descripteurs français
- KwdFr :
- MESH :
- immunologie : Autoantigènes, Autotolérance, Oligopeptides, Protéome, Présentation d'antigène.
- Humains.
English descriptors
- KwdEn :
- MESH :
- chemical , immunology : Autoantigens, Oligopeptides, Proteome.
- immunology : Antigen Presentation, Self Tolerance.
- Humans.
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.
DOI: 10.1007/s00251-004-0691-0
PubMed: 15322777
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De Boer</name></author><author><name sortKey="Ke Mir, Can" sort="Ke Mir, Can" uniqKey="Ke Mir C" first="Can" last="Ke Mir">Can Ke Mir</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2004">2004</date><idno type="RBID">pubmed:15322777</idno><idno type="pmid">15322777</idno><idno type="doi">10.1007/s00251-004-0691-0</idno><idno type="wicri:Area/PubMed/Corpus">002371</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002371</idno><idno type="wicri:Area/PubMed/Curation">002371</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002371</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Discriminating self from nonself with short peptides from large proteomes.</title><author><name sortKey="Burroughs, Nigel J" sort="Burroughs, Nigel J" uniqKey="Burroughs N" first="Nigel J" last="Burroughs">Nigel J. Burroughs</name><affiliation wicri:level="1"><nlm:affiliation>Mathematics Institute, University of Warwick, Coventry, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Mathematics Institute, University of Warwick, Coventry</wicri:regionArea></affiliation></author><author><name sortKey="De Boer, Rob J" sort="De Boer, Rob J" uniqKey="De Boer R" first="Rob J" last="De Boer">Rob J. De Boer</name></author><author><name sortKey="Ke Mir, Can" sort="Ke Mir, Can" uniqKey="Ke Mir C" first="Can" last="Ke Mir">Can Ke Mir</name></author></analytic><series><title level="j">Immunogenetics</title><idno type="ISSN">0093-7711</idno><imprint><date when="2004" type="published">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Antigen Presentation (immunology)</term><term>Autoantigens (immunology)</term><term>Humans</term><term>Oligopeptides (immunology)</term><term>Proteome (immunology)</term><term>Self Tolerance (immunology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Autoantigènes (immunologie)</term><term>Autotolérance (immunologie)</term><term>Humains</term><term>Oligopeptides (immunologie)</term><term>Protéome (immunologie)</term><term>Présentation d'antigène (immunologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="immunology" xml:lang="en"><term>Autoantigens</term><term>Oligopeptides</term><term>Proteome</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Autoantigènes</term><term>Autotolérance</term><term>Oligopeptides</term><term>Protéome</term><term>Présentation d'antigène</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Antigen Presentation</term><term>Self Tolerance</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Humans</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Humains</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15322777</PMID><DateCompleted><Year>2004</Year><Month>10</Month><Day>19</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0093-7711</ISSN><JournalIssue CitedMedium="Print"><Volume>56</Volume><Issue>5</Issue><PubDate><Year>2004</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Immunogenetics</Title><ISOAbbreviation>Immunogenetics</ISOAbbreviation></Journal><ArticleTitle>Discriminating self from nonself with short peptides from large proteomes.</ArticleTitle><Pagination><MedlinePgn>311-20</MedlinePgn></Pagination><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Burroughs</LastName><ForeName>Nigel J</ForeName><Initials>NJ</Initials><AffiliationInfo><Affiliation>Mathematics Institute, University of Warwick, Coventry, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>de Boer</LastName><ForeName>Rob J</ForeName><Initials>RJ</Initials></Author><Author ValidYN="Y"><LastName>Keşmir</LastName><ForeName>Can</ForeName><Initials>C</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2004</Year><Month>07</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>United 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