The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27.
Identifieur interne : 001C86 ( PubMed/Corpus ); précédent : 001C85; suivant : 001C87The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27.
Auteurs : Luke Hecht ; Anton DormerSource :
- Bioinformation [ 0973-2063 ] ; 2013.
Abstract
In silico tools are employed to examine the evolutionary relationship to possible vaccine peptide candidates' development. This perspective sheds light on the proteomic changes affecting the creation of HLA specific T-cell stimulating peptide vaccines for HIV. Full-length sequences of the envelope protein of the HIV subtypes A, B, C and D were obtained through the NCBI Protein database were aligned using CLUSTALW. They were then analyzed using RANKPEP specific to Human Leukocyte Antigen A*02 and B*27. Geneious was used to catalogue the collected gp160 sequences and to construct a phylogenic tree. Mesquite was employed for ancestral state reconstruction to infer the order of amino acid substitutions in the epitopes examined. The results showed that consensus peptide identified SLAEKNITI had changes that indicated predicted escape mutation in strains of HIV responding to pressure exerted by CD8+ cells expressing HLA A*02. The predominating 9-mers IRIGPGQAF of gp120 are significantly less immunogenic toward HLA B*27 than to HLA A*02. The data confirms previous findings on the importance for efficacious binding, of an arginine residue at the 2(nd) position of the gag SL9 epitope, and extends this principle to other epitopes which interacts with HLA B*27. This study shows that the understanding of viral evolution relating T-cell peptide vaccine design is a development that has much relevance for the creation of personalized therapeutics for HIV treatment.
DOI: 10.6026/97320630009315
PubMed: 23745018
Links to Exploration step
pubmed:23745018Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27.</title>
<author><name sortKey="Hecht, Luke" sort="Hecht, Luke" uniqKey="Hecht L" first="Luke" last="Hecht">Luke Hecht</name>
<affiliation><nlm:affiliation>Institute of Evolutionary Biology, The University of Edinburgh, Kings Buildings, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Dormer, Anton" sort="Dormer, Anton" uniqKey="Dormer A" first="Anton" last="Dormer">Anton Dormer</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2013">2013</date>
<idno type="RBID">pubmed:23745018</idno>
<idno type="pmid">23745018</idno>
<idno type="doi">10.6026/97320630009315</idno>
<idno type="wicri:Area/PubMed/Corpus">001C86</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001C86</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27.</title>
<author><name sortKey="Hecht, Luke" sort="Hecht, Luke" uniqKey="Hecht L" first="Luke" last="Hecht">Luke Hecht</name>
<affiliation><nlm:affiliation>Institute of Evolutionary Biology, The University of Edinburgh, Kings Buildings, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Dormer, Anton" sort="Dormer, Anton" uniqKey="Dormer A" first="Anton" last="Dormer">Anton Dormer</name>
</author>
</analytic>
<series><title level="j">Bioinformation</title>
<idno type="ISSN">0973-2063</idno>
<imprint><date when="2013" type="published">2013</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">In silico tools are employed to examine the evolutionary relationship to possible vaccine peptide candidates' development. This perspective sheds light on the proteomic changes affecting the creation of HLA specific T-cell stimulating peptide vaccines for HIV. Full-length sequences of the envelope protein of the HIV subtypes A, B, C and D were obtained through the NCBI Protein database were aligned using CLUSTALW. They were then analyzed using RANKPEP specific to Human Leukocyte Antigen A*02 and B*27. Geneious was used to catalogue the collected gp160 sequences and to construct a phylogenic tree. Mesquite was employed for ancestral state reconstruction to infer the order of amino acid substitutions in the epitopes examined. The results showed that consensus peptide identified SLAEKNITI had changes that indicated predicted escape mutation in strains of HIV responding to pressure exerted by CD8+ cells expressing HLA A*02. The predominating 9-mers IRIGPGQAF of gp120 are significantly less immunogenic toward HLA B*27 than to HLA A*02. The data confirms previous findings on the importance for efficacious binding, of an arginine residue at the 2(nd) position of the gag SL9 epitope, and extends this principle to other epitopes which interacts with HLA B*27. This study shows that the understanding of viral evolution relating T-cell peptide vaccine design is a development that has much relevance for the creation of personalized therapeutics for HIV treatment.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">23745018</PMID>
<DateCompleted><Year>2013</Year>
<Month>06</Month>
<Day>10</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>12</Month>
<Day>25</Day>
</DateRevised>
<Article PubModel="Electronic-Print"><Journal><ISSN IssnType="Print">0973-2063</ISSN>
<JournalIssue CitedMedium="Print"><Volume>9</Volume>
<Issue>6</Issue>
<PubDate><Year>2013</Year>
</PubDate>
</JournalIssue>
<Title>Bioinformation</Title>
<ISOAbbreviation>Bioinformation</ISOAbbreviation>
</Journal>
<ArticleTitle>The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27.</ArticleTitle>
<Pagination><MedlinePgn>315-20</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.6026/97320630009315</ELocationID>
<Abstract><AbstractText>In silico tools are employed to examine the evolutionary relationship to possible vaccine peptide candidates' development. This perspective sheds light on the proteomic changes affecting the creation of HLA specific T-cell stimulating peptide vaccines for HIV. Full-length sequences of the envelope protein of the HIV subtypes A, B, C and D were obtained through the NCBI Protein database were aligned using CLUSTALW. They were then analyzed using RANKPEP specific to Human Leukocyte Antigen A*02 and B*27. Geneious was used to catalogue the collected gp160 sequences and to construct a phylogenic tree. Mesquite was employed for ancestral state reconstruction to infer the order of amino acid substitutions in the epitopes examined. The results showed that consensus peptide identified SLAEKNITI had changes that indicated predicted escape mutation in strains of HIV responding to pressure exerted by CD8+ cells expressing HLA A*02. The predominating 9-mers IRIGPGQAF of gp120 are significantly less immunogenic toward HLA B*27 than to HLA A*02. The data confirms previous findings on the importance for efficacious binding, of an arginine residue at the 2(nd) position of the gag SL9 epitope, and extends this principle to other epitopes which interacts with HLA B*27. This study shows that the understanding of viral evolution relating T-cell peptide vaccine design is a development that has much relevance for the creation of personalized therapeutics for HIV treatment.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hecht</LastName>
<ForeName>Luke</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Institute of Evolutionary Biology, The University of Edinburgh, Kings Buildings, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Dormer</LastName>
<ForeName>Anton</ForeName>
<Initials>A</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2013</Year>
<Month>03</Month>
<Day>19</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>Singapore</Country>
<MedlineTA>Bioinformation</MedlineTA>
<NlmUniqueID>101258255</NlmUniqueID>
<ISSNLinking>0973-2063</ISSNLinking>
</MedlineJournalInfo>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">CLUSTALW</Keyword>
<Keyword MajorTopicYN="N">Geneious</Keyword>
<Keyword MajorTopicYN="N">Human Immunodeficiency Virus type 1</Keyword>
<Keyword MajorTopicYN="N">Human Leukocyte Antigen A*02</Keyword>
<Keyword MajorTopicYN="N">Human Leukocyte Antigen B*27</Keyword>
<Keyword MajorTopicYN="N">Mesquite</Keyword>
<Keyword MajorTopicYN="N">RANKPEP</Keyword>
<Keyword MajorTopicYN="N">‘personalized therapeutics’</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year>
<Month>01</Month>
<Day>01</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2013</Year>
<Month>01</Month>
<Day>29</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2013</Year>
<Month>6</Month>
<Day>8</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2013</Year>
<Month>6</Month>
<Day>8</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2013</Year>
<Month>6</Month>
<Day>8</Day>
<Hour>6</Hour>
<Minute>1</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>epublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">23745018</ArticleId>
<ArticleId IdType="doi">10.6026/97320630009315</ArticleId>
<ArticleId IdType="pii">97320630009315</ArticleId>
<ArticleId IdType="pmc">PMC3607191</ArticleId>
</ArticleIdList>
<ReferenceList><Reference><Citation>Proc Natl Acad Sci U S A. 2006 Dec 19;103(51):19396-401</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17164328</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Vaccine. 2005 Mar 18;23(17-18):2136-48</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15755584</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Retrovirology. 2009;6:15</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19216757</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genetics. 2004 Jul;167(3):1047-58</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15280222</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Clin Invest. 1998 Jun 1;101(11):2559-66</Citation>
<ArticleIdList><ArticleId IdType="pubmed">9616227</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Rev Genet. 2004 Jan;5(1):52-61</Citation>
<ArticleIdList><ArticleId IdType="pubmed">14708016</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2003 Jul 1;31(13):3497-500</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12824352</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Drugs. 2011 Mar 5;71(4):387-414</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21395355</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Tissue Antigens. 2003 May;61(5):403-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12753660</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Infect Dis. 2001 Feb 1;183(3):409-16</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11133372</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Virol. 2002 Aug;76(16):8276-84</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12134033</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Expert Opin Biol Ther. 2010 Dec;10(12):1637-47</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20979567</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Curr Opin HIV AIDS. 2010 Sep;5(5):428-34</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20978385</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Biochemistry. 2009 Aug 25;48(33):7867-77</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19552398</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Vaccine. 2008 Jun 6;26(24):3059-71</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18206276</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Science. 2005 Nov 11;310(5750):1025-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16284180</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Bioinformatics. 2010;11 Suppl 1:S26</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20122198</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Virol. 2007 Nov;81(22):12382-93</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17804494</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Structure. 2000 Dec 15;8(12):1329-39</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11188697</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Science. 1998 Jun 19;280(5371):1884-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">9632381</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Br J Biomed Sci. 2002;59(1):38-41</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12000185</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Immunogenetics. 2004 Sep;56(6):405-19</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15349703</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Mol Recognit. 2011 Sep-Oct;24(5):741-53</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21812050</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Tumour Biol. 2011 Feb;32(1):63-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20711822</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>PLoS Negl Trop Dis. 2011 Sep;5(9):e1295</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21909442</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Virol. 2006 Jan;80(2):835-44</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16378985</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):7131-6</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21467219</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Virol. 1999 Dec;73(12):10191-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">10559335</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>AIDS Res Hum Retroviruses. 2005 May;21(5):395-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15929701</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Hum Immunol. 2010 Mar;71(3):245-54</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20035814</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Sheng Wu Yi Xue Gong Cheng Xue Za Zhi. 2010 Oct;27(5):1146-51</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21089688</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001C86 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 001C86 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= PubMed |étape= Corpus |type= RBID |clé= pubmed:23745018 |texte= The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:23745018" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |