Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket
Identifieur interne : 002361 ( Pmc/Curation ); précédent : 002360; suivant : 002362Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket
Auteurs : Tamir Dingjan [Australie] ; Anne Imberty [France] ; Serge Pérez [France] ; Elizabeth Yuriev [Australie] ; Paul A. Ramsland [Australie]Source :
- Frontiers in Pharmacology [ 1663-9812 ] ; 2017.
Abstract
Url:
DOI: 10.3389/fphar.2017.00393
PubMed: 28680402
PubMed Central: 5478714
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Molecular Simulations of Carbohydrates with a Fucose-Binding <italic>Burkholderia ambifaria</italic> Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket</title><author><name sortKey="Dingjan, Tamir" sort="Dingjan, Tamir" uniqKey="Dingjan T" first="Tamir" last="Dingjan">Tamir Dingjan</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation></author><author><name sortKey="Imberty, Anne" sort="Imberty, Anne" uniqKey="Imberty A" first="Anne" last="Imberty">Anne Imberty</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Centre de Recherches sur les Macromolécules Végétales, Centre National de la Recherche Scientifique UPR5301, Université Grenoble Alpes</institution><country>Grenoble, France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation></author><author><name sortKey="Perez, Serge" sort="Perez, Serge" uniqKey="Perez S" first="Serge" last="Pérez">Serge Pérez</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Département de Pharmacochimie Moléculaire, Centre National de la Recherche Scientifique, UMR5063, Université Grenoble Alpes</institution><country>Grenoble, France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation></author><author><name sortKey="Yuriev, Elizabeth" sort="Yuriev, Elizabeth" uniqKey="Yuriev E" first="Elizabeth" last="Yuriev">Elizabeth Yuriev</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation></author><author><name sortKey="Ramsland, Paul A" sort="Ramsland, Paul A" uniqKey="Ramsland P" first="Paul A." last="Ramsland">Paul A. Ramsland</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>School of Science, RMIT University</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff5"><institution>Department of Surgery Austin Health, University of Melbourne</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff6"><institution>Department of Immunology, Central Clinical School, Monash University</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff7"><institution>Burnet Institute</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">28680402</idno><idno type="pmc">5478714</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478714</idno><idno type="RBID">PMC:5478714</idno><idno type="doi">10.3389/fphar.2017.00393</idno><date when="2017">2017</date><idno type="wicri:Area/Pmc/Corpus">002511</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002511</idno><idno type="wicri:Area/Pmc/Curation">002361</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">002361</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Molecular Simulations of Carbohydrates with a Fucose-Binding <italic>Burkholderia ambifaria</italic> Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket</title><author><name sortKey="Dingjan, Tamir" sort="Dingjan, Tamir" uniqKey="Dingjan T" first="Tamir" last="Dingjan">Tamir Dingjan</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation></author><author><name sortKey="Imberty, Anne" sort="Imberty, Anne" uniqKey="Imberty A" first="Anne" last="Imberty">Anne Imberty</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Centre de Recherches sur les Macromolécules Végétales, Centre National de la Recherche Scientifique UPR5301, Université Grenoble Alpes</institution><country>Grenoble, France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation></author><author><name sortKey="Perez, Serge" sort="Perez, Serge" uniqKey="Perez S" first="Serge" last="Pérez">Serge Pérez</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Département de Pharmacochimie Moléculaire, Centre National de la Recherche Scientifique, UMR5063, Université Grenoble Alpes</institution><country>Grenoble, France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation></author><author><name sortKey="Yuriev, Elizabeth" sort="Yuriev, Elizabeth" uniqKey="Yuriev E" first="Elizabeth" last="Yuriev">Elizabeth Yuriev</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation></author><author><name sortKey="Ramsland, Paul A" sort="Ramsland, Paul A" uniqKey="Ramsland P" first="Paul A." last="Ramsland">Paul A. Ramsland</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>School of Science, RMIT University</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff5"><institution>Department of Surgery Austin Health, University of Melbourne</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff6"><institution>Department of Immunology, Central Clinical School, Monash University</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff7"><institution>Burnet Institute</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Medical Microbiology and Virology, National Health Laboratory Service/University of the Free State, Bloemfontein 9301</wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Pharmacology</title><idno type="eISSN">1663-9812</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Burkholderia ambifaria</italic> is an opportunistic respiratory pathogen belonging to the <italic>Burkholderia cepacia</italic> complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the <italic>B. ambifaria</italic> genome, BambL, is able to adhere to lung tissue, and may play a role in respiratory infection. X-ray crystallography has revealed the bound complex structures for four fucosylated human blood group epitopes (blood group B, H type 1, H type 2, and Le<sup>x</sup> determinants). The present study employed computational approaches, including docking and molecular dynamics (MD), to extend the structural analysis of BambL-oligosaccharide complexes to include four additional blood group saccharides (A, Le<sup>a</sup>, Le<sup>b</sup>, and Le<sup>y</sup>) and a library of blood-group-related carbohydrates. Carbohydrate recognition is dominated by interactions with fucose via a hydrogen-bonding network involving Arg15, Glu26, Ala38, and Trp79 and a stacking interaction with Trp74. Additional hydrogen bonds to non-fucose residues are formed with Asp30, Tyr35, Thr36, and Trp74. BambL recognition is dominated by interactions with fucose, but also features interactions with other parts of the ligands that may modulate specificity or affinity. The detailed computational characterization of the BambL carbohydrate-binding site provides guidelines for the future design of lectin inhibitors.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Agostino, M" uniqKey="Agostino M">M. Agostino</name></author><author><name sortKey="Jene, C" uniqKey="Jene C">C. Jene</name></author><author><name sortKey="Boyle, T" uniqKey="Boyle T">T. Boyle</name></author><author><name sortKey="Ramsland, P A" uniqKey="Ramsland P">P. A. Ramsland</name></author><author><name sortKey="Yuriev, E" uniqKey="Yuriev E">E. Yuriev</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Agostino, M" uniqKey="Agostino M">M. Agostino</name></author><author><name sortKey="Mancera, R L" uniqKey="Mancera R">R. L. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Pharmacol</journal-id><journal-id journal-id-type="iso-abbrev">Front Pharmacol</journal-id><journal-id journal-id-type="publisher-id">Front. Pharmacol.</journal-id><journal-title-group><journal-title>Frontiers in Pharmacology</journal-title></journal-title-group><issn pub-type="epub">1663-9812</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">28680402</article-id><article-id pub-id-type="pmc">5478714</article-id><article-id pub-id-type="doi">10.3389/fphar.2017.00393</article-id><article-categories><subj-group subj-group-type="heading"><subject>Pharmacology</subject><subj-group><subject>Original Research</subject></subj-group></subj-group></article-categories><title-group><article-title>Molecular Simulations of Carbohydrates with a Fucose-Binding <italic>Burkholderia ambifaria</italic> Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Dingjan</surname><given-names>Tamir</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/423084/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Imberty</surname><given-names>Anne</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/157861/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Pérez</surname><given-names>Serge</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/236227/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Yuriev</surname><given-names>Elizabeth</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/31572/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Ramsland</surname><given-names>Paul A.</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><xref ref-type="aff" rid="aff5"><sup>5</sup></xref><xref ref-type="aff" rid="aff6"><sup>6</sup></xref><xref ref-type="aff" rid="aff7"><sup>7</sup></xref><xref ref-type="author-notes" rid="fn002"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/25336/overview"></uri></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University</institution><country>Melbourne, VIC, Australia</country></aff><aff id="aff2"><sup>2</sup><institution>Centre de Recherches sur les Macromolécules Végétales, Centre National de la Recherche Scientifique UPR5301, Université Grenoble Alpes</institution><country>Grenoble, France</country></aff><aff id="aff3"><sup>3</sup><institution>Département de Pharmacochimie Moléculaire, Centre National de la Recherche Scientifique, UMR5063, Université Grenoble Alpes</institution><country>Grenoble, France</country></aff><aff id="aff4"><sup>4</sup><institution>School of Science, RMIT University</institution><country>Melbourne, VIC, Australia</country></aff><aff id="aff5"><sup>5</sup><institution>Department of Surgery Austin Health, University of Melbourne</institution><country>Melbourne, VIC, Australia</country></aff><aff id="aff6"><sup>6</sup><institution>Department of Immunology, Central Clinical School, Monash University</institution><country>Melbourne, VIC, Australia</country></aff><aff id="aff7"><sup>7</sup><institution>Burnet Institute</institution><country>Melbourne, VIC, Australia</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: Leonardo G. Ferreira, University of São Paulo, Brazil</p></fn><fn fn-type="edited-by"><p>Reviewed by: Hugo Verli, Universidade Federal do Rio Grande do Sul, Brazil; David Antony Morton-Blake, Trinity College, Dublin, Ireland</p></fn><corresp id="fn001">*Correspondence: Elizabeth Yuriev <email xlink:type="simple">elizabeth.yuriev@monash.edu</email></corresp><corresp id="fn002">Paul A Ramsland <email xlink:type="simple">paul.ramsland@rmit.edu.au</email></corresp><fn fn-type="other" id="fn003"><p>This article was submitted to Experimental Pharmacology and Drug Discovery, a section of the journal Frontiers in Pharmacology</p></fn></author-notes><pub-date pub-type="epub"><day>21</day><month>6</month><year>2017</year></pub-date><pub-date pub-type="collection"><year>2017</year></pub-date><volume>8</volume><elocation-id>393</elocation-id><history><date date-type="received"><day>12</day><month>3</month><year>2017</year></date><date date-type="accepted"><day>06</day><month>6</month><year>2017</year></date></history><permissions><copyright-statement>Copyright © 2017 Dingjan, Imberty, Pérez, Yuriev and Ramsland.</copyright-statement><copyright-year>2017</copyright-year><copyright-holder>Dingjan, Imberty, Pérez, Yuriev and Ramsland</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><p><italic>Burkholderia ambifaria</italic> is an opportunistic respiratory pathogen belonging to the <italic>Burkholderia cepacia</italic> complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the <italic>B. ambifaria</italic> genome, BambL, is able to adhere to lung tissue, and may play a role in respiratory infection. X-ray crystallography has revealed the bound complex structures for four fucosylated human blood group epitopes (blood group B, H type 1, H type 2, and Le<sup>x</sup> determinants). The present study employed computational approaches, including docking and molecular dynamics (MD), to extend the structural analysis of BambL-oligosaccharide complexes to include four additional blood group saccharides (A, Le<sup>a</sup>, Le<sup>b</sup>, and Le<sup>y</sup>) and a library of blood-group-related carbohydrates. Carbohydrate recognition is dominated by interactions with fucose via a hydrogen-bonding network involving Arg15, Glu26, Ala38, and Trp79 and a stacking interaction with Trp74. Additional hydrogen bonds to non-fucose residues are formed with Asp30, Tyr35, Thr36, and Trp74. BambL recognition is dominated by interactions with fucose, but also features interactions with other parts of the ligands that may modulate specificity or affinity. The detailed computational characterization of the BambL carbohydrate-binding site provides guidelines for the future design of lectin inhibitors.</p></abstract><kwd-group><kwd>blood group determinants</kwd><kwd><italic>Burkholderia ambifaria</italic></kwd><kwd>docking</kwd><kwd>fucose</kwd><kwd>molecular dynamics</kwd></kwd-group><counts><fig-count count="9"></fig-count><table-count count="2"></table-count><equation-count count="0"></equation-count><ref-count count="88"></ref-count><page-count count="16"></page-count><word-count count="9468"></word-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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