Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket.
Identifieur interne : 000785 ( PubMed/Checkpoint ); précédent : 000784; suivant : 000786Molecular 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
Burkholderia ambifaria is an opportunistic respiratory pathogen belonging to the Burkholderia cepacia complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the B. ambifaria 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(x) 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(a), Le(b), and Le(y)) 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.
DOI: 10.3389/fphar.2017.00393
PubMed: 28680402
Affiliations:
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Ramsland</name><affiliation wicri:level="1"><nlm:affiliation>School of Science, RMIT UniversityMelbourne, VIC, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Science, RMIT UniversityMelbourne, VIC</wicri:regionArea><wicri:noRegion>VIC</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in pharmacology</title><idno type="ISSN">1663-9812</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Burkholderia ambifaria is an opportunistic respiratory pathogen belonging to the Burkholderia cepacia complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the B. ambifaria 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(x) 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(a), Le(b), and Le(y)) 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.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">28680402</PMID><DateCreated><Year>2017</Year><Month>07</Month><Day>06</Day></DateCreated><DateRevised><Year>2017</Year><Month>08</Month><Day>16</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1663-9812</ISSN><JournalIssue CitedMedium="Print"><Volume>8</Volume><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>Frontiers in pharmacology</Title><ISOAbbreviation>Front Pharmacol</ISOAbbreviation></Journal><ArticleTitle>Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket.</ArticleTitle><Pagination><MedlinePgn>393</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fphar.2017.00393</ELocationID><Abstract><AbstractText>Burkholderia ambifaria is an opportunistic respiratory pathogen belonging to the Burkholderia cepacia complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the B. ambifaria 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(x) 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(a), Le(b), and Le(y)) 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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dingjan</LastName><ForeName>Tamir</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourne, VIC, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Imberty</LastName><ForeName>Anne</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Centre de Recherches sur les Macromolécules Végétales, Centre National de la Recherche Scientifique UPR5301, Université Grenoble AlpesGrenoble, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pérez</LastName><ForeName>Serge</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Département de Pharmacochimie Moléculaire, Centre National de la Recherche Scientifique, UMR5063, Université Grenoble AlpesGrenoble, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yuriev</LastName><ForeName>Elizabeth</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourne, VIC, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ramsland</LastName><ForeName>Paul A</ForeName><Initials>PA</Initials><AffiliationInfo><Affiliation>School of Science, RMIT UniversityMelbourne, VIC, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Surgery Austin Health, University of MelbourneMelbourne, VIC, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Immunology, Central Clinical School, Monash UniversityMelbourne, VIC, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Burnet InstituteMelbourne, VIC, Australia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>06</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Pharmacol</MedlineTA><NlmUniqueID>101548923</NlmUniqueID><ISSNLinking>1663-9812</ISSNLinking></MedlineJournalInfo><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>J Chem Inf Model. 2014 Oct 27;54(10):2744-50</RefSource><PMID Version="1">25289680</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Cyst Fibros. 2004 Jun;3(2):133-4</RefSource><PMID Version="1">15463897</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Med Chem. 2006 Oct 19;49(21):6177-96</RefSource><PMID Version="1">17034125</PMID></CommentsCorrections><CommentsCorrections 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Version="1">26620784</PMID></CommentsCorrections></CommentsCorrectionsList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Burkholderia ambifaria</Keyword><Keyword MajorTopicYN="N">blood group determinants</Keyword><Keyword MajorTopicYN="N">docking</Keyword><Keyword MajorTopicYN="N">fucose</Keyword><Keyword MajorTopicYN="N">molecular dynamics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>03</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>06</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>7</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>7</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>7</Month><Day>7</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28680402</ArticleId><ArticleId IdType="doi">10.3389/fphar.2017.00393</ArticleId><ArticleId IdType="pmc">PMC5478714</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Australie</li><li>France</li></country></list><tree><country name="Australie"><noRegion><name sortKey="Dingjan, Tamir" sort="Dingjan, Tamir" uniqKey="Dingjan T" first="Tamir" last="Dingjan">Tamir Dingjan</name></noRegion><name sortKey="Ramsland, Paul A" sort="Ramsland, Paul A" uniqKey="Ramsland P" first="Paul A" last="Ramsland">Paul A. Ramsland</name><name sortKey="Yuriev, Elizabeth" sort="Yuriev, Elizabeth" uniqKey="Yuriev E" first="Elizabeth" last="Yuriev">Elizabeth Yuriev</name></country><country name="France"><noRegion><name sortKey="Imberty, Anne" sort="Imberty, Anne" uniqKey="Imberty A" first="Anne" last="Imberty">Anne Imberty</name></noRegion><name sortKey="Perez, Serge" sort="Perez, Serge" uniqKey="Perez S" first="Serge" last="Pérez">Serge Pérez</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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