A novel bio-orthogonal cross-linker for improved protein/protein interaction analysis.
Identifieur interne : 000420 ( PubMed/Checkpoint ); précédent : 000419; suivant : 000421A novel bio-orthogonal cross-linker for improved protein/protein interaction analysis.
Auteurs : Catherine Nury [France] ; Virginie Redeker ; Sébastien Dautrey ; Anthony Romieu ; Guillaume Van Der Rest ; Pierre-Yves Renard ; Ronald Melki ; Julia Chamot-RookeSource :
- Analytical chemistry [ 1520-6882 ] ; 2015.
English descriptors
- KwdEn :
- Amino Acid Sequence, Azides (chemistry), Carbamates (chemistry), Chromatography, Liquid (methods), Cross-Linking Reagents (chemistry), HSC70 Heat-Shock Proteins (chemistry), HSC70 Heat-Shock Proteins (metabolism), Humans, Mass Spectrometry (methods), Models, Molecular, Molecular Sequence Data, Parkinson Disease (metabolism), Protein Interaction Mapping (methods), Protein Interaction Maps, alpha-Synuclein (chemistry), alpha-Synuclein (metabolism).
- MESH :
- chemical , chemistry : Azides, Carbamates, Cross-Linking Reagents, HSC70 Heat-Shock Proteins, alpha-Synuclein.
- chemical , metabolism : HSC70 Heat-Shock Proteins, alpha-Synuclein.
- metabolism : Parkinson Disease.
- methods : Chromatography, Liquid, Mass Spectrometry, Protein Interaction Mapping.
- Amino Acid Sequence, Humans, Models, Molecular, Molecular Sequence Data, Protein Interaction Maps.
Abstract
The variety of protein cross-linkers developed in recent years illustrates the current requirement for efficient reagents optimized for mass spectrometry (MS) analysis. To date, the most widely used strategy relies on commercial cross-linkers that bear an isotopically labeled tag and N-hydroxysuccinimid-ester (NHS-ester) moieties. Moreover, an enrichment step using liquid chromatography is usually performed after enzymatic digestion of the cross-linked proteins. Unfortunately, this approach suffers from several limitations. First, it requires large amounts of proteins. Second, NHS-ester cross-linkers are poorly efficient because of their fast hydrolysis in water. Finally, data analysis is complicated because of uneven fragmentation of complex isotopic cross-linked peptide mixtures. We therefore synthesized a new type of trifunctional cross-linker to overrule these limitations. This reagent, named NNP9, comprises a rigid core and bears two activated carbamate moieties and an azido group. NNP9 was used to establish intra- and intermolecular cross-links within creatine kinase, then to map the interaction surfaces between α-Synuclein (α-Syn), the aggregation of which leads to Parkinson's disease, and the molecular chaperone Hsc70. We show that NNP9 cross-linking efficiency is significantly higher than that of NHS-ester commercial cross-linkers. The number of cross-linked peptides identified was increased, and a high quality of MS/MS spectra leading to high sequence coverage was observed. Our data demonstrate the potential of NNP9 for an efficient and straightforward characterization of protein-protein interfaces and illustrate the power of using different cross-linkers to map thoroughly the surface interfaces within protein complexes.
DOI: 10.1021/ac503892c
PubMed: 25522193
Affiliations:
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sort="Dautrey, Sebastien" uniqKey="Dautrey S" first="Sébastien" last="Dautrey">Sébastien Dautrey</name></author><author><name sortKey="Romieu, Anthony" sort="Romieu, Anthony" uniqKey="Romieu A" first="Anthony" last="Romieu">Anthony Romieu</name></author><author><name sortKey="Van Der Rest, Guillaume" sort="Van Der Rest, Guillaume" uniqKey="Van Der Rest G" first="Guillaume" last="Van Der Rest">Guillaume Van Der Rest</name></author><author><name sortKey="Renard, Pierre Yves" sort="Renard, Pierre Yves" uniqKey="Renard P" first="Pierre-Yves" last="Renard">Pierre-Yves Renard</name></author><author><name sortKey="Melki, Ronald" sort="Melki, Ronald" uniqKey="Melki R" first="Ronald" last="Melki">Ronald Melki</name></author><author><name sortKey="Chamot Rooke, Julia" sort="Chamot Rooke, Julia" uniqKey="Chamot Rooke J" first="Julia" last="Chamot-Rooke">Julia Chamot-Rooke</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno 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France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, CNRS UMR 3528, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Redeker, Virginie" sort="Redeker, Virginie" uniqKey="Redeker V" first="Virginie" last="Redeker">Virginie Redeker</name></author><author><name sortKey="Dautrey, Sebastien" sort="Dautrey, Sebastien" uniqKey="Dautrey S" first="Sébastien" last="Dautrey">Sébastien Dautrey</name></author><author><name sortKey="Romieu, Anthony" sort="Romieu, Anthony" uniqKey="Romieu A" first="Anthony" last="Romieu">Anthony Romieu</name></author><author><name sortKey="Van Der Rest, Guillaume" sort="Van Der Rest, Guillaume" uniqKey="Van Der Rest G" first="Guillaume" last="Van Der Rest">Guillaume Van Der Rest</name></author><author><name sortKey="Renard, Pierre Yves" sort="Renard, Pierre Yves" uniqKey="Renard P" first="Pierre-Yves" last="Renard">Pierre-Yves Renard</name></author><author><name sortKey="Melki, Ronald" sort="Melki, Ronald" uniqKey="Melki R" first="Ronald" last="Melki">Ronald Melki</name></author><author><name sortKey="Chamot Rooke, Julia" sort="Chamot Rooke, Julia" uniqKey="Chamot Rooke J" first="Julia" last="Chamot-Rooke">Julia Chamot-Rooke</name></author></analytic><series><title level="j">Analytical chemistry</title><idno type="eISSN">1520-6882</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Azides (chemistry)</term><term>Carbamates (chemistry)</term><term>Chromatography, Liquid (methods)</term><term>Cross-Linking Reagents (chemistry)</term><term>HSC70 Heat-Shock Proteins (chemistry)</term><term>HSC70 Heat-Shock Proteins (metabolism)</term><term>Humans</term><term>Mass Spectrometry (methods)</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Parkinson Disease (metabolism)</term><term>Protein Interaction Mapping (methods)</term><term>Protein Interaction Maps</term><term>alpha-Synuclein (chemistry)</term><term>alpha-Synuclein (metabolism)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Azides</term><term>Carbamates</term><term>Cross-Linking Reagents</term><term>HSC70 Heat-Shock Proteins</term><term>alpha-Synuclein</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>HSC70 Heat-Shock Proteins</term><term>alpha-Synuclein</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Parkinson Disease</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Chromatography, Liquid</term><term>Mass Spectrometry</term><term>Protein Interaction Mapping</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Humans</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Protein Interaction Maps</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The variety of protein cross-linkers developed in recent years illustrates the current requirement for efficient reagents optimized for mass spectrometry (MS) analysis. To date, the most widely used strategy relies on commercial cross-linkers that bear an isotopically labeled tag and N-hydroxysuccinimid-ester (NHS-ester) moieties. Moreover, an enrichment step using liquid chromatography is usually performed after enzymatic digestion of the cross-linked proteins. Unfortunately, this approach suffers from several limitations. First, it requires large amounts of proteins. Second, NHS-ester cross-linkers are poorly efficient because of their fast hydrolysis in water. Finally, data analysis is complicated because of uneven fragmentation of complex isotopic cross-linked peptide mixtures. We therefore synthesized a new type of trifunctional cross-linker to overrule these limitations. This reagent, named NNP9, comprises a rigid core and bears two activated carbamate moieties and an azido group. NNP9 was used to establish intra- and intermolecular cross-links within creatine kinase, then to map the interaction surfaces between α-Synuclein (α-Syn), the aggregation of which leads to Parkinson's disease, and the molecular chaperone Hsc70. We show that NNP9 cross-linking efficiency is significantly higher than that of NHS-ester commercial cross-linkers. The number of cross-linked peptides identified was increased, and a high quality of MS/MS spectra leading to high sequence coverage was observed. Our data demonstrate the potential of NNP9 for an efficient and straightforward characterization of protein-protein interfaces and illustrate the power of using different cross-linkers to map thoroughly the surface interfaces within protein complexes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25522193</PMID><DateCreated><Year>2015</Year><Month>02</Month><Day>03</Day></DateCreated><DateCompleted><Year>2015</Year><Month>09</Month><Day>09</Day></DateCompleted><DateRevised><Year>2015</Year><Month>02</Month><Day>03</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1520-6882</ISSN><JournalIssue CitedMedium="Internet"><Volume>87</Volume><Issue>3</Issue><PubDate><Year>2015</Year><Month>Feb</Month><Day>03</Day></PubDate></JournalIssue><Title>Analytical chemistry</Title><ISOAbbreviation>Anal. Chem.</ISOAbbreviation></Journal><ArticleTitle>A novel bio-orthogonal cross-linker for improved protein/protein interaction analysis.</ArticleTitle><Pagination><MedlinePgn>1853-60</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1021/ac503892c</ELocationID><Abstract><AbstractText>The variety of protein cross-linkers developed in recent years illustrates the current requirement for efficient reagents optimized for mass spectrometry (MS) analysis. To date, the most widely used strategy relies on commercial cross-linkers that bear an isotopically labeled tag and N-hydroxysuccinimid-ester (NHS-ester) moieties. Moreover, an enrichment step using liquid chromatography is usually performed after enzymatic digestion of the cross-linked proteins. Unfortunately, this approach suffers from several limitations. First, it requires large amounts of proteins. Second, NHS-ester cross-linkers are poorly efficient because of their fast hydrolysis in water. Finally, data analysis is complicated because of uneven fragmentation of complex isotopic cross-linked peptide mixtures. We therefore synthesized a new type of trifunctional cross-linker to overrule these limitations. This reagent, named NNP9, comprises a rigid core and bears two activated carbamate moieties and an azido group. NNP9 was used to establish intra- and intermolecular cross-links within creatine kinase, then to map the interaction surfaces between α-Synuclein (α-Syn), the aggregation of which leads to Parkinson's disease, and the molecular chaperone Hsc70. We show that NNP9 cross-linking efficiency is significantly higher than that of NHS-ester commercial cross-linkers. The number of cross-linked peptides identified was increased, and a high quality of MS/MS spectra leading to high sequence coverage was observed. Our data demonstrate the potential of NNP9 for an efficient and straightforward characterization of protein-protein interfaces and illustrate the power of using different cross-linkers to map thoroughly the surface interfaces within protein complexes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Nury</LastName><ForeName>Catherine</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Redeker</LastName><ForeName>Virginie</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Dautrey</LastName><ForeName>Sébastien</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Romieu</LastName><ForeName>Anthony</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>van der Rest</LastName><ForeName>Guillaume</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Renard</LastName><ForeName>Pierre-Yves</ForeName><Initials>PY</Initials></Author><Author ValidYN="Y"><LastName>Melki</LastName><ForeName>Ronald</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Chamot-Rooke</LastName><ForeName>Julia</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>01</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Anal Chem</MedlineTA><NlmUniqueID>0370536</NlmUniqueID><ISSNLinking>0003-2700</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D001386">Azides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D002219">Carbamates</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D003432">Cross-Linking Reagents</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D050883">HSC70 Heat-Shock Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D051844">alpha-Synuclein</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001386" MajorTopicYN="N">Azides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002219" MajorTopicYN="N">Carbamates</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002853" MajorTopicYN="N">Chromatography, Liquid</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003432" MajorTopicYN="N">Cross-Linking Reagents</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D050883" MajorTopicYN="N">HSC70 Heat-Shock Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013058" MajorTopicYN="N">Mass Spectrometry</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010300" MajorTopicYN="N">Parkinson Disease</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D025941" MajorTopicYN="N">Protein Interaction Mapping</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D060066" MajorTopicYN="N">Protein Interaction Maps</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D051844" MajorTopicYN="N">alpha-Synuclein</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>12</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>12</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>9</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25522193</ArticleId><ArticleId IdType="doi">10.1021/ac503892c</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Île-de-France</li></region><settlement><li>Paris</li></settlement></list><tree><noCountry><name sortKey="Chamot Rooke, Julia" sort="Chamot Rooke, Julia" uniqKey="Chamot Rooke J" first="Julia" last="Chamot-Rooke">Julia Chamot-Rooke</name><name sortKey="Dautrey, Sebastien" sort="Dautrey, Sebastien" uniqKey="Dautrey S" first="Sébastien" last="Dautrey">Sébastien Dautrey</name><name sortKey="Melki, Ronald" sort="Melki, Ronald" uniqKey="Melki R" first="Ronald" last="Melki">Ronald Melki</name><name sortKey="Redeker, Virginie" sort="Redeker, Virginie" uniqKey="Redeker V" first="Virginie" last="Redeker">Virginie Redeker</name><name sortKey="Renard, Pierre Yves" sort="Renard, Pierre Yves" uniqKey="Renard P" first="Pierre-Yves" last="Renard">Pierre-Yves Renard</name><name sortKey="Romieu, Anthony" sort="Romieu, Anthony" uniqKey="Romieu A" first="Anthony" last="Romieu">Anthony Romieu</name><name sortKey="Van Der Rest, Guillaume" sort="Van Der Rest, Guillaume" uniqKey="Van Der Rest G" first="Guillaume" last="Van Der Rest">Guillaume Van Der Rest</name></noCountry><country name="France"><region name="Île-de-France"><name sortKey="Nury, Catherine" sort="Nury, Catherine" uniqKey="Nury C" first="Catherine" last="Nury">Catherine Nury</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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