Computational Prediction of the Epitopes of HA1 Protein of Influenza Viruses to its Neutralizing Antibodies
Identifieur interne : 000900 ( Pmc/Curation ); précédent : 000899; suivant : 000901Computational Prediction of the Epitopes of HA1 Protein of Influenza Viruses to its Neutralizing Antibodies
Auteurs : Xiaoyan Zeng ; Fiona S. Legge ; Chao Huang ; Xiao Zhang ; Yongjun Jiao ; Herbert R. Treutlein ; Jun ZengSource :
- Antibodies [ 2073-4468 ] ; 2018.
Abstract
In this work, we have used a new method to predict the epitopes of HA1 protein of influenza virus to several antibodies HC19, CR9114, BH151 and 4F5. While our results reproduced the binding epitopes of H3N2 or H5N1 for the neutralizing antibodies HC19, CR9114, and BH151 as revealed from the available crystal structures, additional epitopes for these antibodies were also suggested. Moreover, the predicted epitopes of H5N1 HA1 for the newly developed antibody 4F5 are located at the receptor binding domain, while previous study identified a region 76-WLLGNP-81 as the epitope. The possibility of antibody recognition of influenza virus via different mechanism by binding to different epitopes of an antigen is also discussed.
Url:
DOI: 10.3390/antib8010002
PubMed: 31544808
PubMed Central: 6640696
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Computational Prediction of the Epitopes of HA1 Protein of Influenza Viruses to its Neutralizing Antibodies</title><author><name sortKey="Zeng, Xiaoyan" sort="Zeng, Xiaoyan" uniqKey="Zeng X" first="Xiaoyan" last="Zeng">Xiaoyan Zeng</name><affiliation><nlm:aff id="af1-antibodies-08-00002">Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing 210009, China;<email>zengxiaoyan6164@sina.com</email> (X.Z.);<email>nestar1987@126.com</email> (C.H.);<email>yongjunjiao@jscdc.cn</email> (Y.J.)</nlm:aff></affiliation></author><author><name sortKey="Legge, Fiona S" sort="Legge, Fiona S" uniqKey="Legge F" first="Fiona S." last="Legge">Fiona S. Legge</name><affiliation><nlm:aff id="af2-antibodies-08-00002">MedChemSoft Solutions, Level 3, 2 Brandon Park Drive, Wheelers Hill, VIC 3150, Australia;<email>suelegge@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Huang, Chao" sort="Huang, Chao" uniqKey="Huang C" first="Chao" last="Huang">Chao Huang</name><affiliation><nlm:aff id="af1-antibodies-08-00002">Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing 210009, China;<email>zengxiaoyan6164@sina.com</email> (X.Z.);<email>nestar1987@126.com</email> (C.H.);<email>yongjunjiao@jscdc.cn</email> (Y.J.)</nlm:aff></affiliation></author><author><name sortKey="Zhang, Xiao" sort="Zhang, Xiao" uniqKey="Zhang X" first="Xiao" last="Zhang">Xiao Zhang</name><affiliation><nlm:aff id="af3-antibodies-08-00002">Key Laboratory of Antibody Technique, Ministry Health, Nanjing 210029, China;<email>zhangxiao@njmu.edu.cn</email></nlm:aff></affiliation></author><author><name sortKey="Jiao, Yongjun" sort="Jiao, Yongjun" uniqKey="Jiao Y" first="Yongjun" last="Jiao">Yongjun Jiao</name><affiliation><nlm:aff id="af1-antibodies-08-00002">Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing 210009, China;<email>zengxiaoyan6164@sina.com</email> (X.Z.);<email>nestar1987@126.com</email> (C.H.);<email>yongjunjiao@jscdc.cn</email> (Y.J.)</nlm:aff></affiliation></author><author><name sortKey="Treutlein, Herbert R" sort="Treutlein, Herbert R" uniqKey="Treutlein H" first="Herbert R." last="Treutlein">Herbert R. Treutlein</name><affiliation><nlm:aff id="af4-antibodies-08-00002">Sanoosa Pty Ltd., Level 30, 35 Collins Street, Melbourne, VIC 3000, Australia;<email>herbertin@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Zeng, Jun" sort="Zeng, Jun" uniqKey="Zeng J" first="Jun" last="Zeng">Jun Zeng</name><affiliation><nlm:aff id="af2-antibodies-08-00002">MedChemSoft Solutions, Level 3, 2 Brandon Park Drive, Wheelers Hill, VIC 3150, Australia;<email>suelegge@gmail.com</email></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">31544808</idno><idno type="pmc">6640696</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6640696</idno><idno type="RBID">PMC:6640696</idno><idno type="doi">10.3390/antib8010002</idno><date when="2018">2018</date><idno type="wicri:Area/Pmc/Corpus">000900</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000900</idno><idno type="wicri:Area/Pmc/Curation">000900</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000900</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Computational Prediction of the Epitopes of HA1 Protein of Influenza Viruses to its Neutralizing Antibodies</title><author><name sortKey="Zeng, Xiaoyan" sort="Zeng, Xiaoyan" uniqKey="Zeng X" first="Xiaoyan" last="Zeng">Xiaoyan Zeng</name><affiliation><nlm:aff id="af1-antibodies-08-00002">Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing 210009, China;<email>zengxiaoyan6164@sina.com</email> (X.Z.);<email>nestar1987@126.com</email> (C.H.);<email>yongjunjiao@jscdc.cn</email> (Y.J.)</nlm:aff></affiliation></author><author><name sortKey="Legge, Fiona S" sort="Legge, Fiona S" uniqKey="Legge F" first="Fiona S." last="Legge">Fiona S. Legge</name><affiliation><nlm:aff id="af2-antibodies-08-00002">MedChemSoft Solutions, Level 3, 2 Brandon Park Drive, Wheelers Hill, VIC 3150, Australia;<email>suelegge@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Huang, Chao" sort="Huang, Chao" uniqKey="Huang C" first="Chao" last="Huang">Chao Huang</name><affiliation><nlm:aff id="af1-antibodies-08-00002">Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing 210009, China;<email>zengxiaoyan6164@sina.com</email> (X.Z.);<email>nestar1987@126.com</email> (C.H.);<email>yongjunjiao@jscdc.cn</email> (Y.J.)</nlm:aff></affiliation></author><author><name sortKey="Zhang, Xiao" sort="Zhang, Xiao" uniqKey="Zhang X" first="Xiao" last="Zhang">Xiao Zhang</name><affiliation><nlm:aff id="af3-antibodies-08-00002">Key Laboratory of Antibody Technique, Ministry Health, Nanjing 210029, China;<email>zhangxiao@njmu.edu.cn</email></nlm:aff></affiliation></author><author><name sortKey="Jiao, Yongjun" sort="Jiao, Yongjun" uniqKey="Jiao Y" first="Yongjun" last="Jiao">Yongjun Jiao</name><affiliation><nlm:aff id="af1-antibodies-08-00002">Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing 210009, China;<email>zengxiaoyan6164@sina.com</email> (X.Z.);<email>nestar1987@126.com</email> (C.H.);<email>yongjunjiao@jscdc.cn</email> (Y.J.)</nlm:aff></affiliation></author><author><name sortKey="Treutlein, Herbert R" sort="Treutlein, Herbert R" uniqKey="Treutlein H" first="Herbert R." last="Treutlein">Herbert R. Treutlein</name><affiliation><nlm:aff id="af4-antibodies-08-00002">Sanoosa Pty Ltd., Level 30, 35 Collins Street, Melbourne, VIC 3000, Australia;<email>herbertin@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Zeng, Jun" sort="Zeng, Jun" uniqKey="Zeng J" first="Jun" last="Zeng">Jun Zeng</name><affiliation><nlm:aff id="af2-antibodies-08-00002">MedChemSoft Solutions, Level 3, 2 Brandon Park Drive, Wheelers Hill, VIC 3150, Australia;<email>suelegge@gmail.com</email></nlm:aff></affiliation></author></analytic><series><title level="j">Antibodies</title><idno type="eISSN">2073-4468</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In this work, we have used a new method to predict the epitopes of HA1 protein of influenza virus to several antibodies HC19, CR9114, BH151 and 4F5. While our results reproduced the binding epitopes of H3N2 or H5N1 for the neutralizing antibodies HC19, CR9114, and BH151 as revealed from the available crystal structures, additional epitopes for these antibodies were also suggested. Moreover, the predicted epitopes of H5N1 HA1 for the newly developed antibody 4F5 are located at the receptor binding domain, while previous study identified a region 76-WLLGNP-81 as the epitope. The possibility of antibody recognition of influenza virus via different mechanism by binding to different epitopes of an antigen is also discussed.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Schafer, J R" uniqKey="Schafer J">J.R. Schafer</name></author><author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y. Kawaoka</name></author><author><name sortKey="Bean, W J" uniqKey="Bean W">W.J. Bean</name></author><author><name sortKey="Suss, J" uniqKey="Suss J">J. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Antibodies (Basel)</journal-id><journal-id journal-id-type="iso-abbrev">Antibodies (Basel)</journal-id><journal-id journal-id-type="publisher-id">antibodies</journal-id><journal-title-group><journal-title>Antibodies</journal-title></journal-title-group><issn pub-type="epub">2073-4468</issn><publisher><publisher-name>MDPI</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">31544808</article-id><article-id pub-id-type="pmc">6640696</article-id><article-id pub-id-type="doi">10.3390/antib8010002</article-id><article-id pub-id-type="publisher-id">antibodies-08-00002</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Computational Prediction of the Epitopes of HA1 Protein of Influenza Viruses to its Neutralizing Antibodies</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zeng</surname><given-names>Xiaoyan</given-names></name><xref ref-type="aff" rid="af1-antibodies-08-00002">1</xref></contrib><contrib contrib-type="author"><name><surname>Legge</surname><given-names>Fiona S.</given-names></name><xref ref-type="aff" rid="af2-antibodies-08-00002">2</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0002-4061-1573</contrib-id><name><surname>Huang</surname><given-names>Chao</given-names></name><xref ref-type="aff" rid="af1-antibodies-08-00002">1</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Xiao</given-names></name><xref ref-type="aff" rid="af3-antibodies-08-00002">3</xref></contrib><contrib contrib-type="author"><name><surname>Jiao</surname><given-names>Yongjun</given-names></name><xref ref-type="aff" rid="af1-antibodies-08-00002">1</xref></contrib><contrib contrib-type="author"><name><surname>Treutlein</surname><given-names>Herbert R.</given-names></name><xref ref-type="aff" rid="af4-antibodies-08-00002">4</xref></contrib><contrib contrib-type="author"><name><surname>Zeng</surname><given-names>Jun</given-names></name><xref ref-type="aff" rid="af2-antibodies-08-00002">2</xref><xref rid="c1-antibodies-08-00002" ref-type="corresp">*</xref></contrib></contrib-group><aff id="af1-antibodies-08-00002"><label>1</label>Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing 210009, China;<email>zengxiaoyan6164@sina.com</email> (X.Z.);<email>nestar1987@126.com</email> (C.H.);<email>yongjunjiao@jscdc.cn</email> (Y.J.)</aff><aff id="af2-antibodies-08-00002"><label>2</label>MedChemSoft Solutions, Level 3, 2 Brandon Park Drive, Wheelers Hill, VIC 3150, Australia;<email>suelegge@gmail.com</email></aff><aff id="af3-antibodies-08-00002"><label>3</label>Key Laboratory of Antibody Technique, Ministry Health, Nanjing 210029, China;<email>zhangxiao@njmu.edu.cn</email></aff><aff id="af4-antibodies-08-00002"><label>4</label>Sanoosa Pty Ltd., Level 30, 35 Collins Street, Melbourne, VIC 3000, Australia;<email>herbertin@gmail.com</email></aff><author-notes><corresp id="c1-antibodies-08-00002"><label>*</label>Correspondence: <email>Jun.Zeng@medchemsoft.com</email>; Tel.: +61-413323321</corresp></author-notes><pub-date pub-type="epub"><day>20</day><month>12</month><year>2018</year></pub-date><pub-date pub-type="collection"><month>3</month><year>2019</year></pub-date><volume>8</volume><issue>1</issue><elocation-id>2</elocation-id><history><date date-type="received"><day>05</day><month>10</month><year>2018</year></date><date date-type="accepted"><day>19</day><month>12</month><year>2018</year></date></history><permissions><copyright-statement>© 2018 by the authors.</copyright-statement><copyright-year>2018</copyright-year><license license-type="open-access"><license-p>Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>).</license-p></license></permissions><abstract><p>In this work, we have used a new method to predict the epitopes of HA1 protein of influenza virus to several antibodies HC19, CR9114, BH151 and 4F5. While our results reproduced the binding epitopes of H3N2 or H5N1 for the neutralizing antibodies HC19, CR9114, and BH151 as revealed from the available crystal structures, additional epitopes for these antibodies were also suggested. Moreover, the predicted epitopes of H5N1 HA1 for the newly developed antibody 4F5 are located at the receptor binding domain, while previous study identified a region 76-WLLGNP-81 as the epitope. The possibility of antibody recognition of influenza virus via different mechanism by binding to different epitopes of an antigen is also discussed.</p></abstract><kwd-group><kwd>multiple copy simultaneous search</kwd><kwd>computational chemistry</kwd><kwd>antibodies</kwd><kwd>epitope mapping</kwd></kwd-group></article-meta></front><floats-group><fig id="antibodies-08-00002-f001" orientation="portrait" position="float"><label>Figure 1</label><caption><p>Model structure (<bold>A</bold>) and surface representation (<bold>B</bold>) of antibody HC19. Residues important for the antibody interactions are shown in stick form in (<bold>A</bold>). (L) and (H) denote the L and H chain of the antibody respectively. The figure was prepared using PyMOL [<xref rid="B44-antibodies-08-00002" ref-type="bibr">44</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g001"></graphic></fig><fig id="antibodies-08-00002-f002" orientation="portrait" position="float"><label>Figure 2</label><caption><p>Selected MCSS minima of functional groups on the surface of antibody HC19. (<bold>A</bold>) BENZ; (<bold>B</bold>) IMIA; (<bold>C</bold>) PHEN; (<bold>D</bold>) INDO; (<bold>E</bold>) MAMM; (<bold>F</bold>) MGUA; (<bold>G</bold>) ACET. Figures were prepared using PyMOL [<xref rid="B44-antibodies-08-00002" ref-type="bibr">44</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g002"></graphic></fig><fig id="antibodies-08-00002-f003" orientation="portrait" position="float"><label>Figure 3</label><caption><p>(<bold>A</bold>) the predicted epitopes of H3N2 HA1 that binds to antibody HC19. The epitopes are highlighted in lower case and colored orange in the protein sequence. (<bold>B</bold>) Backbone representation of the antigen H3N2 HA1 showing the predicted epitopes in orange and the antibody in surface. (<bold>C</bold>) Sequence alignment of HA1 protein of influenza viruses H3N2 and H5N1. The boxes highlight the epitopes predicted for H3N2 (<bold>orange</bold>) and H5N1 (<bold>green</bold>). The overlay regions between two subtypes are underlined in purple. Figures were prepared using PyMOL [<xref rid="B44-antibodies-08-00002" ref-type="bibr">44</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g003"></graphic></fig><fig id="antibodies-08-00002-f004" orientation="portrait" position="float"><label>Figure 4</label><caption><p>Model structure (<bold>A</bold>) and surface representation (<bold>B</bold>) of antibody CR9114. The important residues for the antibody interaction are shown in stick form in (<bold>A</bold>). (L) and (H) denote the VL and VH domain of the antibody respectively. The figure was prepared using PyMOL [<xref rid="B44-antibodies-08-00002" ref-type="bibr">44</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g004"></graphic></fig><fig id="antibodies-08-00002-f005" orientation="portrait" position="float"><label>Figure 5</label><caption><p>Selected MCSS minima of functional groups on the surface of antibody CR9114. (<bold>A</bold>) BENZ; (<bold>B</bold>) PHEN; (<bold>C</bold>) INDO; (<bold>D</bold>) MGUA; (<bold>E</bold>) ACET. Figures were prepared using PyMOL [<xref rid="B44-antibodies-08-00002" ref-type="bibr">44</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g005"></graphic></fig><fig id="antibodies-08-00002-f006" orientation="portrait" position="float"><label>Figure 6</label><caption><p>(<bold>A</bold>) the predicted epitopes of H5N1 HA1 (<bold>A</bold>) binding to antibody CR9114. The epitopes are highlighted in lower case and colored orange in the protein sequence. (<bold>B</bold>) Backbone representation of the antigen H3N2 HA1 showing the predicted epitopes in orange and the antibody in surface. (<bold>C</bold>) Sequence alignment of HA1 protein of influenza viruses H3N2 and H5N1. The boxes highlight the epitopes predicted for H3N2 (<bold>green</bold>) and H5N1 (<bold>orange</bold>). The overlay regions between two subtypes are underlined in purple. Figures were prepared using PyMOL [<xref rid="B44-antibodies-08-00002" ref-type="bibr">44</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g006"></graphic></fig><fig id="antibodies-08-00002-f007" orientation="portrait" position="float"><label>Figure 7</label><caption><p>Model structure (<bold>A</bold>) and surface representation (<bold>B</bold>) of antibody BH151. Residues for the antibody interactions are shown in stick representation in (<bold>A</bold>). (L) and (H) denote the VL and VH domain of the antibody respectively. The figure was prepared using PyMOL [<xref rid="B24-antibodies-08-00002" ref-type="bibr">24</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g007"></graphic></fig><fig id="antibodies-08-00002-f008" orientation="portrait" position="float"><label>Figure 8</label><caption><p>Selected MCSS minima of functional groups on the surface of antibody BH151. (<bold>A</bold>) BENZ; (<bold>B</bold>) PHEN; (<bold>C</bold>) ACET. Figures were prepared using PyMOL [<xref rid="B24-antibodies-08-00002" ref-type="bibr">24</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g008"></graphic></fig><fig id="antibodies-08-00002-f009" orientation="portrait" position="float"><label>Figure 9</label><caption><p>(<bold>A</bold>) the predicted epitopes of H3N2 HA1 (<bold>A</bold>) binding to antibody BH151. The epitopes are highlighted in lower case and colored orange in the protein sequence. (<bold>B</bold>) Backbone representation of the antigen H3N2 HA1 showing the predicted epitopes in orange and the antibody in surface. (<bold>C</bold>) Sequence alignment of HA1 protein of influenza viruses H3N2 and H5N1. The boxes highlight the epitopes predicted for H3N2 (<bold>orange</bold>) and H5N1 (<bold>green</bold>). The overlay regions between two subtypes are underlined in purple. Figures were prepared using PyMOL [<xref rid="B44-antibodies-08-00002" ref-type="bibr">44</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g009"></graphic></fig><fig id="antibodies-08-00002-f010" orientation="portrait" position="float"><label>Figure 10</label><caption><p>(<bold>A</bold>) Sequence alignment of VL domain of 4F5 to its templates 2XZA [<xref rid="B34-antibodies-08-00002" ref-type="bibr">34</xref>], 4EVN [<xref rid="B35-antibodies-08-00002" ref-type="bibr">35</xref>], and 4XVJ [<xref rid="B36-antibodies-08-00002" ref-type="bibr">36</xref>] for VL domain, and VH domain of 4F5 to its templates 1W72 [<xref rid="B37-antibodies-08-00002" ref-type="bibr">37</xref>], 3EYQ [<xref rid="B38-antibodies-08-00002" ref-type="bibr">38</xref>], and 3QOS [<xref rid="B39-antibodies-08-00002" ref-type="bibr">39</xref>]. (<bold>B</bold>) The model structure of antibody 4F5. The important residues for the antibody interaction are shown in stick representation in (<bold>A</bold>). (L) and (H) denote the VL and VH domain of the antibody respectively. (C) surface representation of antibody 4F5. The figure was prepared using PyMOL [<xref rid="B44-antibodies-08-00002" ref-type="bibr">44</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g010"></graphic></fig><fig id="antibodies-08-00002-f011" orientation="portrait" position="float"><label>Figure 11</label><caption><p>Selected MCSS minima of functional groups on the surface of antibody 4F5. (<bold>A</bold>) BENZ; (<bold>B</bold>) IMIAl (<bold>C</bold>) PHEN; (<bold>D</bold>) INDO; (<bold>E</bold>) ACEM; (<bold>F</bold>) MAMM; (<bold>G</bold>) MGUA. Figures were prepared using PyMOL [<xref rid="B44-antibodies-08-00002" ref-type="bibr">44</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g011"></graphic></fig><fig id="antibodies-08-00002-f012" orientation="portrait" position="float"><label>Figure 12</label><caption><p>(<bold>A</bold>) the predicted epitopes of H5N1 HA1 (<bold>A</bold>) to antibody 4F5. The epitopes are highlighted in lower case and colored orange in the protein sequence. (<bold>B</bold>) Backbone representation of the antigen H5N1 HA1 showing the predicted epitopes in orange and the antibody in surface. (<bold>C</bold>) Sequence alignment of HA1 protein of influenza viruses H3N2 and H5N1. The boxes highlight the epitopes predicted for H3N2 (green) and H5N1 (orange). The overlay regions between two subtypes are underlined in purple. Figures were prepared using PyMOL [<xref rid="B44-antibodies-08-00002" ref-type="bibr">44</xref>].</p></caption><graphic xlink:href="antibodies-08-00002-g012"></graphic></fig><table-wrap id="antibodies-08-00002-t001" orientation="portrait" position="float"><object-id pub-id-type="pii">antibodies-08-00002-t001_Table 1</object-id><label>Table 1</label><caption><p>Relationship between the functional groups used and amino acids.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1"></th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Functional group</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Abbreviation</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Amino Acids</th></tr></thead><tbody><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Charged (-)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Acetate ion</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ACET</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ASP, GLU</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Charged (+)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Methylguanidinium</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">MGUA</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ARG</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Charged (+)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Methylammonium</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">MAMM</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">LYS</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Polar</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Acetamide</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ACEM</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ASN,GLN</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Polar</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Methanol</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">MEOH</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">SER,THR</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Hydrophobic</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Methanethiol</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">MESH</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">CYS,MET</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Aromatic Polar</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Phenol</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">PHEN</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">TYR</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Aromatic Polar</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Indole</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">INDO</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">TRP</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Aromatic Polar</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Imidazole</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">IMIA</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">HIS</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Aromatic Hydrophobic </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Benzene</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">BENZ</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">PHE</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Hydrophobic</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Ibutane</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">IBUT</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">VAL, ILE, LEU, ALA</td></tr></tbody></table></table-wrap><table-wrap id="antibodies-08-00002-t002" orientation="portrait" position="float"><object-id pub-id-type="pii">antibodies-08-00002-t002_Table 2</object-id><label>Table 2</label><caption><p>Definition of binding sites for each antibody, based on our MFMD calculations.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Antibodies</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">L Chain</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">H Chain</th></tr></thead><tbody><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">AbHC19</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Asn33, Tyr34, Asn36, Asn55,Pro58, Trp93</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Asn32, Trp52,Ala53, Arg97, Asp98, Trp100, Tyr107</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">AbCR9114</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Arg31,Tyr36,Tyr49,Pro55,Trp91</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Asn25,Phe48,Ser50,Arg91, Asn94,Tyr96,Ser97</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">AbBH151</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Ser30,Tyr49,Ala55,Arg91,Ser92,Tyr94</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Tyr32,Phe33,Asn57,Arg98, Gly101,Arg102</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">4F5</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Tyr32,Phe59,Gly101,His102,Tyr104,Phe105,Tyr106,ser108,Tyr112</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Tyr33,Asp51,Pro56</td></tr></tbody></table></table-wrap><table-wrap id="antibodies-08-00002-t003" orientation="portrait" position="float"><object-id pub-id-type="pii">antibodies-08-00002-t003_Table 3</object-id><label>Table 3</label><caption><p>Distribution of key minima and the derived sequence pattern for the binding epitope peptides to antibody HC19. A sequence pattern of “X-J” [X = R/K,F,W,Y and J = (Y,D/E) ] was obtained.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Binding Surface</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">S2</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">9.00 Å </th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">S1</th></tr></thead><tbody><tr><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"><bold>MCSS Minima Pattern</bold></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">BENZ</td><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">PHEN</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">PHEN</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ACET</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">INDO</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">MAMM</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">MGUA</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"><bold>Sequence Pattern</bold></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">F</td><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1">Gap of one amino acid </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Y</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Y</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">D/E</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">W</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">W</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">R/K</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr></tbody></table></table-wrap><table-wrap id="antibodies-08-00002-t004" orientation="portrait" position="float"><object-id pub-id-type="pii">antibodies-08-00002-t004_Table 4</object-id><label>Table 4</label><caption><p>Distribution of key minima and the derived sequence pattern for the binding epitope peptides to the antibody CR9114. A sequence pattern of “X-J” (X = R,FW,Y,D/E, and J = F, W,Y,D/E) was obtained.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Binding Surface</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">B1</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">11.50 Å </th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">B2</th></tr></thead><tbody><tr><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"><bold>MCSS Minima Pattern</bold></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">BENZ</td><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">BENZ</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">PHEN</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">PHEN</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">INDO</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">INDO</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">MGUA</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ACET</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ACET</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"><bold>Sequence Pattern</bold></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">F</td><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1">Gap of 2 amino acid </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">F</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Y</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Y</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">W</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">W</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">R</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> D/E</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">D/E</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr></tbody></table></table-wrap><table-wrap id="antibodies-08-00002-t005" orientation="portrait" position="float"><object-id pub-id-type="pii">antibodies-08-00002-t005_Table 5</object-id><label>Table 5</label><caption><p>Distribution of key minima and the derived sequence pattern for the binding epitope peptides to the antibody BH151. A sequence pattern of “X-J”(X = D/E, and J = F, Y,D/E) was obtained.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Binding Surface</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">B1</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">9.50 Å </th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">B2</th></tr></thead><tbody><tr><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"><bold>MCSS Minima Pattern</bold></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ACET</td><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">BENZ</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">PHEN</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> ACET</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"><bold>Sequence Pattern</bold></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">D/E</td><td rowspan="5" align="center" valign="middle" style="border-bottom:solid thin" colspan="1">Gap of one amino acid </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">F</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Y</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">D/E</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr></tbody></table></table-wrap><table-wrap id="antibodies-08-00002-t006" orientation="portrait" position="float"><object-id pub-id-type="pii">antibodies-08-00002-t006_Table 6</object-id><label>Table 6</label><caption><p>Distribution of key minima and the derived sequence pattern for the binding epitope peptides to the antibody 4F5. A sequence pattern of “X-J”(X = R/K,Q/N,W,F/Y/H, and J = F/Y/H, W) was obtained.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Binding Surface</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">B1</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">13.00 Å </th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">B2</th></tr></thead><tbody><tr><td rowspan="7" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"><bold>MCSS Minima Pattern</bold></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> BENZ</td><td rowspan="7" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"> </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">BENZ</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> IMIA</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">IMIA</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> PHEN</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> PHEN</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> INDO</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> INDO</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ACEM</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">MAMM</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">MGUA</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td rowspan="6" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"><bold>Sequence Pattern</bold></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">F</td><td rowspan="6" align="center" valign="middle" style="border-bottom:solid thin" colspan="1">Gap of two amino acid </td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">F</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">H</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">H</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Y</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> Y</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">W</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> W</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Q/N</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">R/K</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"> </td></tr></tbody></table></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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