Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions
Identifieur interne : 000B32 ( Pmc/Checkpoint ); précédent : 000B31; suivant : 000B33Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions
Auteurs : Deena Ma Gendoo [Égypte] ; Mahmoud M. El-Hefnawi [Égypte] ; Mark Werner [Égypte] ; Rania Siam [Égypte]Source :
- Virology Journal [ 1743-422X ] ; 2008.
Abstract
Variations in the influenza Hemagglutinin protein contributes to antigenic drift resulting in decreased efficiency of seasonal influenza vaccines and escape from host immune response. We performed an in silico study to determine characteristics of novel variable and conserved motifs in the Hemagglutinin protein from previously reported H3N2 strains isolated from Hong Kong from 1968–1999 to predict viral motifs involved in significant biological functions.
14 MEME blocks were generated and comparative analysis of the MEME blocks identified blocks 1, 2, 3 and 7 to correlate with several biological functions. Analysis of the different Hemagglutinin sequences elucidated that the single block 7 has the highest frequency of amino acid substitution and the highest number of co-mutating pairs. MEME 2 showed intermediate variability and MEME 1 was the most conserved. Interestingly, MEME blocks 2 and 7 had the highest incidence of potential post-translational modifications sites including phosphorylation sites, ASN glycosylation motifs and N-myristylation sites. Similarly, these 2 blocks overlap with previously identified antigenic sites and receptor binding sites.
Our study identifies motifs in the Hemagglutinin protein with different amino acid substitution frequencies over a 31 years period, and derives relevant functional characteristics by correlation of these motifs with potential post-translational modifications sites, antigenic and receptor binding sites.
Url:
DOI: 10.1186/1743-422X-5-91
PubMed: 18681973
PubMed Central: 2553082
Affiliations:
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Variations in the influenza Hemagglutinin protein contributes to antigenic drift resulting in decreased efficiency of seasonal influenza vaccines and escape from host immune response. We performed an in silico study to determine characteristics of novel variable and conserved motifs in the Hemagglutinin protein from previously reported H3N2 strains isolated from Hong Kong from 1968–1999 to predict viral motifs involved in significant biological functions.</p>
</sec>
<sec><title>Results</title>
<p>14 MEME blocks were generated and comparative analysis of the MEME blocks identified blocks 1, 2, 3 and 7 to correlate with several biological functions. Analysis of the different Hemagglutinin sequences elucidated that the single block 7 has the highest frequency of amino acid substitution and the highest number of co-mutating pairs. MEME 2 showed intermediate variability and MEME 1 was the most conserved. Interestingly, MEME blocks 2 and 7 had the highest incidence of potential post-translational modifications sites including phosphorylation sites, ASN glycosylation motifs and N-myristylation sites. Similarly, these 2 blocks overlap with previously identified antigenic sites and receptor binding sites.</p>
</sec>
<sec><title>Conclusion</title>
<p>Our study identifies motifs in the Hemagglutinin protein with different amino acid substitution frequencies over a 31 years period, and derives relevant functional characteristics by correlation of these motifs with potential post-translational modifications sites, antigenic and receptor binding sites.</p>
</sec>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">Virol J</journal-id>
<journal-title>Virology Journal</journal-title>
<issn pub-type="epub">1743-422X</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
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<article-id pub-id-type="publisher-id">1743-422X-5-91</article-id>
<article-id pub-id-type="doi">10.1186/1743-422X-5-91</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research</subject>
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<title-group><article-title>Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions</article-title>
</title-group>
<contrib-group><contrib id="A1" contrib-type="author"><name><surname>Gendoo</surname>
<given-names>Deena MA</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>deena_gendoo@yahoo.com</email>
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<contrib id="A2" contrib-type="author"><name><surname>El-Hefnawi</surname>
<given-names>Mahmoud M</given-names>
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<xref ref-type="aff" rid="I3">3</xref>
<email>mahef@hotmail.com</email>
</contrib>
<contrib id="A3" contrib-type="author"><name><surname>Werner</surname>
<given-names>Mark</given-names>
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<xref ref-type="aff" rid="I4">4</xref>
<email>mwerner@aucegypt.edu</email>
</contrib>
<contrib id="A4" corresp="yes" contrib-type="author"><name><surname>Siam</surname>
<given-names>Rania</given-names>
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<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>rsiam@aucegypt.edu</email>
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<aff id="I1"><label>1</label>
YJ-Science and Technology Research Center (STRC), American University in Cairo, Cairo, Egypt</aff>
<aff id="I2"><label>2</label>
Department of Biology, American University in Cairo, Cairo, Egypt</aff>
<aff id="I3"><label>3</label>
Department of Informatics and Systems, Division of Engineering Sciences Research, National Research Centre (NRC), Cairo, Egypt</aff>
<aff id="I4"><label>4</label>
Department of Mathematics and Actuarial Science, American University in Cairo, Cairo, Egypt</aff>
<pub-date pub-type="collection"><year>2008</year>
</pub-date>
<pub-date pub-type="epub"><day>5</day>
<month>8</month>
<year>2008</year>
</pub-date>
<volume>5</volume>
<fpage>91</fpage>
<lpage>91</lpage>
<ext-link ext-link-type="uri" xlink:href="http://www.virologyj.com/content/5/1/91"></ext-link>
<history><date date-type="received"><day>29</day>
<month>6</month>
<year>2008</year>
</date>
<date date-type="accepted"><day>5</day>
<month>8</month>
<year>2008</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2008 Gendoo et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2008</copyright-year>
<copyright-holder>Gendoo et al; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0"></ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p>
<pmc-comment>
Gendoo
MA
Deena
deena_gendoo@yahoo.com
Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions
2008 Virology Journal 5(1): 91-. (2008) 1743-422X(2008)5:1<91> urn:ISSN:1743-422X </pmc-comment>
</license>
</permissions>
<abstract><sec><title>Background</title>
<p>Variations in the influenza Hemagglutinin protein contributes to antigenic drift resulting in decreased efficiency of seasonal influenza vaccines and escape from host immune response. We performed an in silico study to determine characteristics of novel variable and conserved motifs in the Hemagglutinin protein from previously reported H3N2 strains isolated from Hong Kong from 1968–1999 to predict viral motifs involved in significant biological functions.</p>
</sec>
<sec><title>Results</title>
<p>14 MEME blocks were generated and comparative analysis of the MEME blocks identified blocks 1, 2, 3 and 7 to correlate with several biological functions. Analysis of the different Hemagglutinin sequences elucidated that the single block 7 has the highest frequency of amino acid substitution and the highest number of co-mutating pairs. MEME 2 showed intermediate variability and MEME 1 was the most conserved. Interestingly, MEME blocks 2 and 7 had the highest incidence of potential post-translational modifications sites including phosphorylation sites, ASN glycosylation motifs and N-myristylation sites. Similarly, these 2 blocks overlap with previously identified antigenic sites and receptor binding sites.</p>
</sec>
<sec><title>Conclusion</title>
<p>Our study identifies motifs in the Hemagglutinin protein with different amino acid substitution frequencies over a 31 years period, and derives relevant functional characteristics by correlation of these motifs with potential post-translational modifications sites, antigenic and receptor binding sites.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Égypte</li>
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<tree><country name="Égypte"><noRegion><name sortKey="Gendoo, Deena Ma" sort="Gendoo, Deena Ma" uniqKey="Gendoo D" first="Deena Ma" last="Gendoo">Deena Ma Gendoo</name>
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<name sortKey="Siam, Rania" sort="Siam, Rania" uniqKey="Siam R" first="Rania" last="Siam">Rania Siam</name>
<name sortKey="Siam, Rania" sort="Siam, Rania" uniqKey="Siam R" first="Rania" last="Siam">Rania Siam</name>
<name sortKey="Werner, Mark" sort="Werner, Mark" uniqKey="Werner M" first="Mark" last="Werner">Mark Werner</name>
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