Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus.
Identifieur interne : 002111 ( PubMed/Checkpoint ); précédent : 002110; suivant : 002112Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus.
Auteurs : Asif M. Khan [Singapour] ; A T Heiny ; Kenneth X. Lee ; K N Srinivasan ; Tin Wee Tan ; J Thomas August ; Vladimir BrusicSource :
- BMC bioinformatics [ 1471-2105 ] ; 2006.
Descripteurs français
- KwdFr :
- Bases de données de protéines, Biologie informatique (), Données de séquences moléculaires, Déterminants antigéniques des lymphocytes T (analyse), Fragments peptidiques (immunologie), Protéines virales (immunologie), Similitude de séquences d'acides aminés, Séquence d'acides aminés, Sérotypage, Variation des antigènes, Virus de la dengue (immunologie).
- MESH :
- analyse : Déterminants antigéniques des lymphocytes T.
- immunologie : Fragments peptidiques, Protéines virales, Virus de la dengue.
- Bases de données de protéines, Biologie informatique, Données de séquences moléculaires, Similitude de séquences d'acides aminés, Séquence d'acides aminés, Sérotypage, Variation des antigènes.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Epitopes, T-Lymphocyte.
- immunology : Dengue Virus, Peptide Fragments, Viral Proteins.
- methods : Computational Biology.
- Amino Acid Sequence, Antigenic Variation, Databases, Protein, Molecular Sequence Data, Sequence Homology, Amino Acid, Serotyping.
Abstract
Antigenic diversity in dengue virus strains has been studied, but large-scale and detailed systematic analyses have not been reported. In this study, we report a bioinformatics method for analyzing viral antigenic diversity in the context of T-cell mediated immune responses. We applied this method to study the relationship between short-peptide antigenic diversity and protein sequence diversity of dengue virus. We also studied the effects of sequence determinants on viral antigenic diversity. Short peptides, principally 9-mers were studied because they represent the predominant length of binding cores of T-cell epitopes, which are important for formulation of vaccines.
DOI: 10.1186/1471-2105-7-S5-S4
PubMed: 17254309
Affiliations:
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Lee</name></author><author><name sortKey="Srinivasan, K N" sort="Srinivasan, K N" uniqKey="Srinivasan K" first="K N" last="Srinivasan">K N Srinivasan</name></author><author><name sortKey="Tan, Tin Wee" sort="Tan, Tin Wee" uniqKey="Tan T" first="Tin Wee" last="Tan">Tin Wee Tan</name></author><author><name sortKey="August, J Thomas" sort="August, J Thomas" uniqKey="August J" first="J Thomas" last="August">J Thomas August</name></author><author><name sortKey="Brusic, Vladimir" sort="Brusic, Vladimir" uniqKey="Brusic V" first="Vladimir" last="Brusic">Vladimir Brusic</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:17254309</idno><idno type="pmid">17254309</idno><idno type="doi">10.1186/1471-2105-7-S5-S4</idno><idno type="wicri:Area/PubMed/Corpus">002201</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002201</idno><idno type="wicri:Area/PubMed/Curation">002201</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002201</idno><idno type="wicri:Area/PubMed/Checkpoint">002111</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002111</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus.</title><author><name sortKey="Khan, Asif M" sort="Khan, Asif M" uniqKey="Khan A" first="Asif M" last="Khan">Asif M. Khan</name><affiliation wicri:level="1"><nlm:affiliation>The Division of Biomedical Sciences, Johns Hopkins Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore. g0501159@nus.edu.sg</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>The Division of Biomedical Sciences, Johns Hopkins Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669</wicri:regionArea><wicri:noRegion>Singapore 138669</wicri:noRegion></affiliation></author><author><name sortKey="Heiny, A T" sort="Heiny, A T" uniqKey="Heiny A" first="A T" last="Heiny">A T Heiny</name></author><author><name sortKey="Lee, Kenneth X" sort="Lee, Kenneth X" uniqKey="Lee K" first="Kenneth X" last="Lee">Kenneth X. Lee</name></author><author><name sortKey="Srinivasan, K N" sort="Srinivasan, K N" uniqKey="Srinivasan K" first="K N" last="Srinivasan">K N Srinivasan</name></author><author><name sortKey="Tan, Tin Wee" sort="Tan, Tin Wee" uniqKey="Tan T" first="Tin Wee" last="Tan">Tin Wee Tan</name></author><author><name sortKey="August, J Thomas" sort="August, J Thomas" uniqKey="August J" first="J Thomas" last="August">J Thomas August</name></author><author><name sortKey="Brusic, Vladimir" sort="Brusic, Vladimir" uniqKey="Brusic V" first="Vladimir" last="Brusic">Vladimir Brusic</name></author></analytic><series><title level="j">BMC bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Antigenic Variation</term><term>Computational Biology (methods)</term><term>Databases, Protein</term><term>Dengue Virus (immunology)</term><term>Epitopes, T-Lymphocyte (analysis)</term><term>Molecular Sequence Data</term><term>Peptide Fragments (immunology)</term><term>Sequence Homology, Amino Acid</term><term>Serotyping</term><term>Viral Proteins (immunology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données de protéines</term><term>Biologie informatique ()</term><term>Données de séquences moléculaires</term><term>Déterminants antigéniques des lymphocytes T (analyse)</term><term>Fragments peptidiques (immunologie)</term><term>Protéines virales (immunologie)</term><term>Similitude de séquences d'acides aminés</term><term>Séquence d'acides aminés</term><term>Sérotypage</term><term>Variation des antigènes</term><term>Virus de la dengue (immunologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Epitopes, T-Lymphocyte</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Déterminants antigéniques des lymphocytes T</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Fragments peptidiques</term><term>Protéines virales</term><term>Virus de la dengue</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Dengue Virus</term><term>Peptide Fragments</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Antigenic Variation</term><term>Databases, Protein</term><term>Molecular Sequence Data</term><term>Sequence Homology, Amino Acid</term><term>Serotyping</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données de protéines</term><term>Biologie informatique</term><term>Données de séquences moléculaires</term><term>Similitude de séquences d'acides aminés</term><term>Séquence d'acides aminés</term><term>Sérotypage</term><term>Variation des antigènes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Antigenic diversity in dengue virus strains has been studied, but large-scale and detailed systematic analyses have not been reported. In this study, we report a bioinformatics method for analyzing viral antigenic diversity in the context of T-cell mediated immune responses. We applied this method to study the relationship between short-peptide antigenic diversity and protein sequence diversity of dengue virus. We also studied the effects of sequence determinants on viral antigenic diversity. Short peptides, principally 9-mers were studied because they represent the predominant length of binding cores of T-cell epitopes, which are important for formulation of vaccines.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17254309</PMID><DateCompleted><Year>2007</Year><Month>04</Month><Day>26</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN><JournalIssue CitedMedium="Internet"><Volume>7 Suppl 5</Volume><PubDate><Year>2006</Year><Month>Dec</Month><Day>18</Day></PubDate></JournalIssue><Title>BMC bioinformatics</Title><ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus.</ArticleTitle><Pagination><MedlinePgn>S4</MedlinePgn></Pagination><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Antigenic diversity in dengue virus strains has been studied, but large-scale and detailed systematic analyses have not been reported. In this study, we report a bioinformatics method for analyzing viral antigenic diversity in the context of T-cell mediated immune responses. We applied this method to study the relationship between short-peptide antigenic diversity and protein sequence diversity of dengue virus. We also studied the effects of sequence determinants on viral antigenic diversity. Short peptides, principally 9-mers were studied because they represent the predominant length of binding cores of T-cell epitopes, which are important for formulation of vaccines.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Our analysis showed that the number of unique protein sequences required to represent complete antigenic diversity of short peptides in dengue virus is significantly smaller than that required to represent complete protein sequence diversity. Short-peptide antigenic diversity shows an asymptotic relationship to the number of unique protein sequences, indicating that for large sequence sets (approximately 200) the addition of new protein sequences has marginal effect to increasing antigenic diversity. A near-linear relationship was observed between the extent of antigenic diversity and the length of protein sequences, suggesting that, for the practical purpose of vaccine development, antigenic diversity of short peptides from dengue virus can be represented by short regions of sequences (approximately <100 aa) within viral antigens that are specific targets of immune responses (such as T-cell epitopes specific to particular human leukocyte antigen alleles).</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">This study provides evidence that there are limited numbers of antigenic combinations in protein sequence variants of a viral species and that short regions of the viral protein are sufficient to capture antigenic diversity of T-cell epitopes. The approach described herein has direct application to the analysis of other viruses, in particular those that show high diversity and/or rapid evolution, such as influenza A virus and human immunodeficiency virus (HIV).</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Khan</LastName><ForeName>Asif M</ForeName><Initials>AM</Initials><AffiliationInfo><Affiliation>The Division of Biomedical Sciences, Johns Hopkins Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore. g0501159@nus.edu.sg</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Heiny</LastName><ForeName>A T</ForeName><Initials>AT</Initials></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Kenneth X</ForeName><Initials>KX</Initials></Author><Author ValidYN="Y"><LastName>Srinivasan</LastName><ForeName>K N</ForeName><Initials>KN</Initials></Author><Author ValidYN="Y"><LastName>Tan</LastName><ForeName>Tin Wee</ForeName><Initials>TW</Initials></Author><Author ValidYN="Y"><LastName>August</LastName><ForeName>J Thomas</ForeName><Initials>JT</Initials></Author><Author ValidYN="Y"><LastName>Brusic</LastName><ForeName>Vladimir</ForeName><Initials>V</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>U19 AI056541</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>5 U19 AI56541</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>HHSN2662-00400085C</GrantID><Agency>PHS HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType></PublicationTypeList><ArticleDate 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Kenneth X" sort="Lee, Kenneth X" uniqKey="Lee K" first="Kenneth X" last="Lee">Kenneth X. Lee</name><name sortKey="Srinivasan, K N" sort="Srinivasan, K N" uniqKey="Srinivasan K" first="K N" last="Srinivasan">K N Srinivasan</name><name sortKey="Tan, Tin Wee" sort="Tan, Tin Wee" uniqKey="Tan T" first="Tin Wee" last="Tan">Tin Wee Tan</name></noCountry><country name="Singapour"><noRegion><name sortKey="Khan, Asif M" sort="Khan, Asif M" uniqKey="Khan A" first="Asif M" last="Khan">Asif M. Khan</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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