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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Distinct Glycan Topology for Avian and Human Sialo-Pentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective</title><author><name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation></author><author><name sortKey="Newhouse, E Irene" sort="Newhouse, E Irene" uniqKey="Newhouse E" first="E. Irene" last="Newhouse">E. Irene Newhouse</name><affiliation><nlm:aff id="A2">Maui High Performance Computing Center, Kihei, Maui, Hawaii 96753</nlm:aff></affiliation></author><author><name sortKey="Amaro, Rommie E" sort="Amaro, Rommie E" uniqKey="Amaro R" first="Rommie E." last="Amaro">Rommie E. Amaro</name><affiliation><nlm:aff id="A3">Department of Chemistry and Biochemistry and NSF Center for Theoretical Biological Physics (CTBP), University of California San Diego, La Jolla, California 92093-0365</nlm:aff></affiliation></author><author><name sortKey="Pao, Hsing C" sort="Pao, Hsing C" uniqKey="Pao H" first="Hsing C." last="Pao">Hsing C. Pao</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation></author><author><name sortKey="Cheng, Lily S" sort="Cheng, Lily S" uniqKey="Cheng L" first="Lily S." last="Cheng">Lily S. Cheng</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation></author><author><name sortKey="Markwick, Phineus R L" sort="Markwick, Phineus R L" uniqKey="Markwick P" first="Phineus R. L." last="Markwick">Phineus R. L. Markwick</name><affiliation><nlm:aff id="A4">Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365</nlm:aff></affiliation></author><author><name sortKey="Mccammon, J Andrew" sort="Mccammon, J Andrew" uniqKey="Mccammon J" first="J. Andrew" last="Mccammon">J. Andrew Mccammon</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation><affiliation><nlm:aff id="A3">Department of Chemistry and Biochemistry and NSF Center for Theoretical Biological Physics (CTBP), University of California San Diego, La Jolla, California 92093-0365</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365</nlm:aff></affiliation><affiliation><nlm:aff id="A5">Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0365</nlm:aff></affiliation></author><author><name sortKey="Li, Wilfred W" sort="Li, Wilfred W" uniqKey="Li W" first="Wilfred W." last="Li">Wilfred W. Li</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation></author><author><name sortKey="Arzberger, Peter W" sort="Arzberger, Peter W" uniqKey="Arzberger P" first="Peter W." last="Arzberger">Peter W. Arzberger</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19356594</idno><idno type="pmc">2892341</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892341</idno><idno type="RBID">PMC:2892341</idno><idno type="doi">10.1016/j.jmb.2009.01.040</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">000547</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000547</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Distinct Glycan Topology for Avian and Human Sialo-Pentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective</title><author><name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation></author><author><name sortKey="Newhouse, E Irene" sort="Newhouse, E Irene" uniqKey="Newhouse E" first="E. Irene" last="Newhouse">E. Irene Newhouse</name><affiliation><nlm:aff id="A2">Maui High Performance Computing Center, Kihei, Maui, Hawaii 96753</nlm:aff></affiliation></author><author><name sortKey="Amaro, Rommie E" sort="Amaro, Rommie E" uniqKey="Amaro R" first="Rommie E." last="Amaro">Rommie E. Amaro</name><affiliation><nlm:aff id="A3">Department of Chemistry and Biochemistry and NSF Center for Theoretical Biological Physics (CTBP), University of California San Diego, La Jolla, California 92093-0365</nlm:aff></affiliation></author><author><name sortKey="Pao, Hsing C" sort="Pao, Hsing C" uniqKey="Pao H" first="Hsing C." last="Pao">Hsing C. Pao</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation></author><author><name sortKey="Cheng, Lily S" sort="Cheng, Lily S" uniqKey="Cheng L" first="Lily S." last="Cheng">Lily S. Cheng</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation></author><author><name sortKey="Markwick, Phineus R L" sort="Markwick, Phineus R L" uniqKey="Markwick P" first="Phineus R. L." last="Markwick">Phineus R. L. Markwick</name><affiliation><nlm:aff id="A4">Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365</nlm:aff></affiliation></author><author><name sortKey="Mccammon, J Andrew" sort="Mccammon, J Andrew" uniqKey="Mccammon J" first="J. Andrew" last="Mccammon">J. Andrew Mccammon</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation><affiliation><nlm:aff id="A3">Department of Chemistry and Biochemistry and NSF Center for Theoretical Biological Physics (CTBP), University of California San Diego, La Jolla, California 92093-0365</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365</nlm:aff></affiliation><affiliation><nlm:aff id="A5">Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0365</nlm:aff></affiliation></author><author><name sortKey="Li, Wilfred W" sort="Li, Wilfred W" uniqKey="Li W" first="Wilfred W." last="Li">Wilfred W. Li</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation></author><author><name sortKey="Arzberger, Peter W" sort="Arzberger, Peter W" uniqKey="Arzberger P" first="Peter W." last="Arzberger">Peter W. Arzberger</name><affiliation><nlm:aff id="A1">National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</nlm:aff></affiliation></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="ISSN">0022-2836</idno><idno type="eISSN">1089-8638</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Hemagglutinin (HA) binds to sialylated glycans exposed on the host cell surface in the initial stage of avian influenza virus infection. It has been previously hypothesized that glycan topology plays a critical role in the human adaptation of avian flu viruses, such as the potentially pandemic H5N1. Comparative molecular dynamics (MD) studies are complementary to experimental techniques including glycan microarray to understand better the mechanism of species specificity switch. The examined systems comprise explicitly solvated trimeric forms of avian H3, H5, and swine H9 in complex with avian and human glycan receptor analogs, α-2,3 linked lactoseries tetrasaccharide a (LSTa) and α-2,6 linked LSTc, respectively. The glycans adopted distinct topological profiles with inducible torsional angles when bound to different HA’s. The corresponding receptor binding domain amino acid contact profiles were also distinct. Avian H5 was able to accommodate LSTc in a tightly “folded-umbrella”-like topology through interactions with all five sugar residues. After considering conformational entropy, the relative binding free energy changes, calculated using the molecular mechanics-generalized Born surface area (MM-GBSA) technique, were in agreement with previous experimental findings, and also provided insights on electrostatic, van der Waals, desolvation and entropic contributions to HA-glycan interactions. The topology profile and the relative abundance of free glycan receptors may influence receptor binding kinetics. Glycan composition and topological changes upon binding different HA may be important determinants in species specificity switch.</p></div></front></TEI><pmc article-type="research-article" xml:lang="EN"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">2985088R</journal-id><journal-id journal-id-type="pubmed-jr-id">4967</journal-id><journal-id journal-id-type="nlm-ta">J Mol Biol</journal-id><journal-title>Journal of molecular biology</journal-title><issn pub-type="ppub">0022-2836</issn><issn pub-type="epub">1089-8638</issn></journal-meta><article-meta><article-id pub-id-type="pmid">19356594</article-id><article-id pub-id-type="pmc">2892341</article-id><article-id pub-id-type="doi">10.1016/j.jmb.2009.01.040</article-id><article-id pub-id-type="manuscript">NIHMS105095</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Distinct Glycan Topology for Avian and Human Sialo-Pentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Dong</given-names></name><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Newhouse</surname><given-names>E. Irene</given-names></name><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Amaro</surname><given-names>Rommie E.</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Pao</surname><given-names>Hsing C.</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Cheng</surname><given-names>Lily S.</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Markwick</surname><given-names>Phineus R. L.</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>McCammon</surname><given-names>J. Andrew</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A3">3</xref><xref ref-type="aff" rid="A4">4</xref><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Wilfred W.</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Arzberger</surname><given-names>Peter W.</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib></contrib-group><aff id="A1"><label>1</label>National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093-0505</aff><aff id="A2"><label>2</label>Maui High Performance Computing Center, Kihei, Maui, Hawaii 96753</aff><aff id="A3"><label>3</label>Department of Chemistry and Biochemistry and NSF Center for Theoretical Biological Physics (CTBP), University of California San Diego, La Jolla, California 92093-0365</aff><aff id="A4"><label>4</label>Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365</aff><aff id="A5"><label>5</label>Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0365</aff><author-notes><corresp id="cor1"><label>*</label>To whom correspondence should be addressed: National Biomedical Computation Resource, University of California, San Diego, 9500 Gilman Drive, Mail Code 0505, La Jolla, CA 92093-0505, 858-534-0587 (Office), 858-534-5034 (Fax), <email>dxu@mccammon.ucsd.edu</email>, 231 MRTC-A, 590 Lipoa Parkway, Kihei HI 96743, <email>einew@hotmail.com</email></corresp></author-notes><pub-date pub-type="nihms-submitted"><day>2</day><month>6</month><year>2010</year></pub-date><pub-date pub-type="epub"><day>5</day><month>2</month><year>2009</year></pub-date><pub-date pub-type="ppub"><day>27</day><month>3</month><year>2009</year></pub-date><pub-date pub-type="pmc-release"><day>25</day><month>6</month><year>2010</year></pub-date><volume>387</volume><issue>2</issue><fpage>465</fpage><lpage>491</lpage><permissions><copyright-statement>© 2008 Elsevier Ltd. All rights reserved</copyright-statement><copyright-year>2008</copyright-year></permissions><abstract><p id="P1">Hemagglutinin (HA) binds to sialylated glycans exposed on the host cell surface in the initial stage of avian influenza virus infection. It has been previously hypothesized that glycan topology plays a critical role in the human adaptation of avian flu viruses, such as the potentially pandemic H5N1. Comparative molecular dynamics (MD) studies are complementary to experimental techniques including glycan microarray to understand better the mechanism of species specificity switch. The examined systems comprise explicitly solvated trimeric forms of avian H3, H5, and swine H9 in complex with avian and human glycan receptor analogs, α-2,3 linked lactoseries tetrasaccharide a (LSTa) and α-2,6 linked LSTc, respectively. The glycans adopted distinct topological profiles with inducible torsional angles when bound to different HA’s. The corresponding receptor binding domain amino acid contact profiles were also distinct. Avian H5 was able to accommodate LSTc in a tightly “folded-umbrella”-like topology through interactions with all five sugar residues. After considering conformational entropy, the relative binding free energy changes, calculated using the molecular mechanics-generalized Born surface area (MM-GBSA) technique, were in agreement with previous experimental findings, and also provided insights on electrostatic, van der Waals, desolvation and entropic contributions to HA-glycan interactions. The topology profile and the relative abundance of free glycan receptors may influence receptor binding kinetics. Glycan composition and topological changes upon binding different HA may be important determinants in species specificity switch.</p></abstract><kwd-group><kwd>Avian influenza</kwd><kwd>Hemagglutinin</kwd><kwd>Glycan topology</kwd><kwd>Binding specificity</kwd><kwd>Molecular dynamics</kwd><kwd>MM-GBSA</kwd><kwd>Binding free energy</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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