Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases
Identifieur interne : 000401 ( Main/Exploration ); précédent : 000400; suivant : 000402Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases
Auteurs : Hao Yu [Japon] ; Patricia Dranchak [États-Unis] ; Zhiru Li [États-Unis] ; Ryan Macarthur [États-Unis] ; Matthew S. Munson [États-Unis] ; Nurjahan Mehzabeen [États-Unis] ; Nathan J. Baird [États-Unis] ; Kevin P. Battalie [États-Unis] ; David Ross [États-Unis] ; Scott Lovell [États-Unis] ; Clotilde K. S. Carlow [États-Unis] ; Hiroaki Suga [Japon] ; James Inglese [États-Unis]Source :
- Nature Communications [ 2041-1723 ] ; 2017.
Abstract
Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >1012 members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanism placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery.
Url:
DOI: 10.1038/ncomms14932
PubMed: 28368002
PubMed Central: 5382265
Affiliations:
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Munson</name><affiliation wicri:level="1"><nlm:aff id="a4"><institution>National Institute of Standards and Technology</institution>, Gaithersburg, Maryland 20899,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Mehzabeen, Nurjahan" sort="Mehzabeen, Nurjahan" uniqKey="Mehzabeen N" first="Nurjahan" last="Mehzabeen">Nurjahan Mehzabeen</name><affiliation wicri:level="1"><nlm:aff id="a5"><institution>Proton Structure Laboratory, Structural Biology Center, University of Kansas</institution>, Lawrence, Kansas 66047,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Baird, Nathan J" sort="Baird, Nathan J" uniqKey="Baird N" first="Nathan J." last="Baird">Nathan J. Baird</name><affiliation wicri:level="1"><nlm:aff id="a6"><institution>National Heart, Lung and Blood Institute, National Institutes of Health</institution>, Bethesda, Maryland 20892,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Battalie, Kevin P" sort="Battalie, Kevin P" uniqKey="Battalie K" first="Kevin P." last="Battalie">Kevin P. Battalie</name><affiliation wicri:level="1"><nlm:aff id="a7"><institution>IMCA-CAT Advanced Photon Source, Argonne National Laboratory</institution>, Argonne, Illinois 60439,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ross, David" sort="Ross, David" uniqKey="Ross D" first="David" last="Ross">David Ross</name><affiliation wicri:level="1"><nlm:aff id="a4"><institution>National Institute of Standards and Technology</institution>, Gaithersburg, Maryland 20899,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Lovell, Scott" sort="Lovell, Scott" uniqKey="Lovell S" first="Scott" last="Lovell">Scott Lovell</name><affiliation wicri:level="1"><nlm:aff id="a5"><institution>Proton Structure Laboratory, Structural Biology Center, University of Kansas</institution>, Lawrence, Kansas 66047,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Carlow, Clotilde K S" sort="Carlow, Clotilde K S" uniqKey="Carlow C" first="Clotilde K. S." last="Carlow">Clotilde K. S. Carlow</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Division of Genome Biology, New England Biolabs</institution>, Ipswich, Massachusetts 01938,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Suga, Hiroaki" sort="Suga, Hiroaki" uniqKey="Suga H" first="Hiroaki" last="Suga">Hiroaki Suga</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Chemistry, Graduate School of Sciences, The University of Tokyo</institution>, Tokyo 113-0033,<country>Japan</country></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Inglese, James" sort="Inglese, James" uniqKey="Inglese J" first="James" last="Inglese">James Inglese</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>National Center for Advancing Translational Sciences, National Institutes of Health</institution>, Rockville, Maryland 20850,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nature Communications</title><idno type="eISSN">2041-1723</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>Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >10<sup>12</sup> members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanism placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Churcher, T S" uniqKey="Churcher T">T. S. Churcher</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Osei Atweneboana, M Y" uniqKey="Osei Atweneboana M">M. Y. Osei-Atweneboana</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kumar, S" uniqKey="Kumar S">S. Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y. Zhang</name></author><author><name sortKey="Foster, J M" uniqKey="Foster J">J. M. 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Winn</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Japon</li><li>États-Unis</li></country></list><tree><country name="Japon"><noRegion><name sortKey="Yu, Hao" sort="Yu, Hao" uniqKey="Yu H" first="Hao" last="Yu">Hao Yu</name></noRegion><name sortKey="Suga, Hiroaki" sort="Suga, Hiroaki" uniqKey="Suga H" first="Hiroaki" last="Suga">Hiroaki Suga</name></country><country name="États-Unis"><noRegion><name sortKey="Dranchak, Patricia" sort="Dranchak, Patricia" uniqKey="Dranchak P" first="Patricia" last="Dranchak">Patricia Dranchak</name></noRegion><name sortKey="Baird, Nathan J" sort="Baird, Nathan J" uniqKey="Baird N" first="Nathan J." last="Baird">Nathan J. Baird</name><name sortKey="Battalie, Kevin P" sort="Battalie, Kevin P" uniqKey="Battalie K" first="Kevin P." last="Battalie">Kevin P. Battalie</name><name sortKey="Carlow, Clotilde K S" sort="Carlow, Clotilde K S" uniqKey="Carlow C" first="Clotilde K. S." last="Carlow">Clotilde K. S. Carlow</name><name sortKey="Inglese, James" sort="Inglese, James" uniqKey="Inglese J" first="James" last="Inglese">James Inglese</name><name sortKey="Li, Zhiru" sort="Li, Zhiru" uniqKey="Li Z" first="Zhiru" last="Li">Zhiru Li</name><name sortKey="Lovell, Scott" sort="Lovell, Scott" uniqKey="Lovell S" first="Scott" last="Lovell">Scott Lovell</name><name sortKey="Macarthur, Ryan" sort="Macarthur, Ryan" uniqKey="Macarthur R" first="Ryan" last="Macarthur">Ryan Macarthur</name><name sortKey="Mehzabeen, Nurjahan" sort="Mehzabeen, Nurjahan" uniqKey="Mehzabeen N" first="Nurjahan" last="Mehzabeen">Nurjahan Mehzabeen</name><name sortKey="Munson, Matthew S" sort="Munson, Matthew S" uniqKey="Munson M" first="Matthew S." last="Munson">Matthew S. Munson</name><name sortKey="Ross, David" sort="Ross, David" uniqKey="Ross D" first="David" last="Ross">David Ross</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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