Profiling DUBs and Ubl-specific proteases with activity-based probes.
Identifieur interne : 000616 ( PubMed/Curation ); précédent : 000615; suivant : 000617Profiling DUBs and Ubl-specific proteases with activity-based probes.
Auteurs : Paul P. Geurink [Pays-Bas] ; Gerbrand J. Van Der Heden Van Noort [Pays-Bas] ; Monique P C. Mulder [Pays-Bas] ; Robert C M. Knaap [Pays-Bas] ; Marjolein Kikkert [Pays-Bas] ; Huib Ovaa [Pays-Bas]Source :
- Methods in enzymology [ 1557-7988 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- enzymologie : Virus.
- métabolisme : Enzymes de désubiquitinylation, Peptide hydrolases, Sondes moléculaires, Ubiquitine, Ubiquitines.
- Animaux, Dosages enzymatiques, Humains, Intéines, Sondes moléculaires, Spécificité du substrat.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Molecular Probes.
- chemical , metabolism : Deubiquitinating Enzymes, Molecular Probes, Peptide Hydrolases, Ubiquitin, Ubiquitins.
- enzymology : Viruses.
- methods : Enzyme Assays.
- Animals, Humans, Inteins, Substrate Specificity.
Abstract
Protein (poly-)ubiquitination is a posttranslational modification that plays a key role in almost all cellular processes. It involves the installment of either single ubiquitin (Ub) moieties or one of eight different polyUb linkage types, each giving a distinct cellular outcome. Deubiquitinating enzymes (DUBs) reverse Ub signaling by disassembly of one or multiple poly-Ub chain types and their malfunction is often associated with human disease. The Ub system displays significant crosstalk with structurally homologous ubiquitin-like proteins (Ubls), including SUMO, Nedd8, and ISG15. This can be seen with the existence of heterogeneous chains made from Ub-Ubl mixtures as well as the proteolytic cross reactivity displayed by several DUBs toward other Ubl systems. In addition, numerous pathogens have been found to encode Ub(l)-ligases and deconjugating enzymes in order to facilitate infection and fight the host immune response. Studying the activity of DUBs and Ubl-specific proteases, both human as well as pathogen-derived, gives fundamental insights into their physiological roles. Activity-based probes (ABPs) have proven to be valuable tools to achieve this, as they report on enzyme activities by making a (often irreversible) covalent complex, rather than on their relative abundance. In this chapter, we explain the potential of ABPs to assess substrate preferences, structural features, and activity of Ub and Ubl deconjugating enzymes. We further demonstrate the practical use of ABPs to (1) characterize the activity of viral proteases toward Ub and Ubls and (2) to gain more insight in the structural determinants of substrate preference of DUBs.
DOI: 10.1016/bs.mie.2018.12.037
PubMed: 30850060
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Geurink</name><affiliation wicri:level="1"><nlm:affiliation>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden</wicri:regionArea></affiliation></author><author><name sortKey="Van Der Heden Van Noort, Gerbrand J" sort="Van Der Heden Van Noort, Gerbrand J" uniqKey="Van Der Heden Van Noort G" first="Gerbrand J" last="Van Der Heden Van Noort">Gerbrand J. Van Der Heden Van Noort</name><affiliation wicri:level="1"><nlm:affiliation>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden</wicri:regionArea></affiliation></author><author><name sortKey="Mulder, Monique P C" sort="Mulder, Monique P C" uniqKey="Mulder M" first="Monique P C" last="Mulder">Monique P C. Mulder</name><affiliation wicri:level="1"><nlm:affiliation>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden</wicri:regionArea></affiliation></author><author><name sortKey="Knaap, Robert C M" sort="Knaap, Robert C M" uniqKey="Knaap R" first="Robert C M" last="Knaap">Robert C M. Knaap</name><affiliation wicri:level="1"><nlm:affiliation>Department of Medical Microbiology, Section Molecular Virology, Leiden University Medical Centre, Leiden, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Medical Microbiology, Section Molecular Virology, Leiden University Medical Centre, Leiden</wicri:regionArea></affiliation></author><author><name sortKey="Kikkert, Marjolein" sort="Kikkert, Marjolein" uniqKey="Kikkert M" first="Marjolein" last="Kikkert">Marjolein Kikkert</name><affiliation wicri:level="1"><nlm:affiliation>Department of Medical Microbiology, Section Molecular Virology, Leiden University Medical Centre, Leiden, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Medical Microbiology, Section Molecular Virology, Leiden University Medical Centre, Leiden</wicri:regionArea></affiliation></author><author><name sortKey="Ovaa, Huib" sort="Ovaa, Huib" uniqKey="Ovaa H" first="Huib" last="Ovaa">Huib Ovaa</name><affiliation wicri:level="1"><nlm:affiliation>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands. Electronic address: h.ovaa@lumc.nl.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden</wicri:regionArea></affiliation></author></analytic><series><title level="j">Methods in enzymology</title><idno type="eISSN">1557-7988</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Deubiquitinating Enzymes (metabolism)</term><term>Enzyme Assays (methods)</term><term>Humans</term><term>Inteins</term><term>Molecular Probes (chemistry)</term><term>Molecular Probes (metabolism)</term><term>Peptide Hydrolases (metabolism)</term><term>Substrate Specificity</term><term>Ubiquitin (metabolism)</term><term>Ubiquitins (metabolism)</term><term>Viruses (enzymology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Dosages enzymatiques ()</term><term>Enzymes de désubiquitinylation (métabolisme)</term><term>Humains</term><term>Intéines</term><term>Peptide hydrolases (métabolisme)</term><term>Sondes moléculaires ()</term><term>Sondes moléculaires (métabolisme)</term><term>Spécificité du substrat</term><term>Ubiquitine (métabolisme)</term><term>Ubiquitines (métabolisme)</term><term>Virus (enzymologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Molecular Probes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Deubiquitinating Enzymes</term><term>Molecular Probes</term><term>Peptide Hydrolases</term><term>Ubiquitin</term><term>Ubiquitins</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Virus</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Enzyme Assays</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Enzymes de désubiquitinylation</term><term>Peptide hydrolases</term><term>Sondes moléculaires</term><term>Ubiquitine</term><term>Ubiquitines</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Humans</term><term>Inteins</term><term>Substrate Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Dosages enzymatiques</term><term>Humains</term><term>Intéines</term><term>Sondes moléculaires</term><term>Spécificité du substrat</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Protein (poly-)ubiquitination is a posttranslational modification that plays a key role in almost all cellular processes. It involves the installment of either single ubiquitin (Ub) moieties or one of eight different polyUb linkage types, each giving a distinct cellular outcome. Deubiquitinating enzymes (DUBs) reverse Ub signaling by disassembly of one or multiple poly-Ub chain types and their malfunction is often associated with human disease. The Ub system displays significant crosstalk with structurally homologous ubiquitin-like proteins (Ubls), including SUMO, Nedd8, and ISG15. This can be seen with the existence of heterogeneous chains made from Ub-Ubl mixtures as well as the proteolytic cross reactivity displayed by several DUBs toward other Ubl systems. In addition, numerous pathogens have been found to encode Ub(l)-ligases and deconjugating enzymes in order to facilitate infection and fight the host immune response. Studying the activity of DUBs and Ubl-specific proteases, both human as well as pathogen-derived, gives fundamental insights into their physiological roles. Activity-based probes (ABPs) have proven to be valuable tools to achieve this, as they report on enzyme activities by making a (often irreversible) covalent complex, rather than on their relative abundance. In this chapter, we explain the potential of ABPs to assess substrate preferences, structural features, and activity of Ub and Ubl deconjugating enzymes. We further demonstrate the practical use of ABPs to (1) characterize the activity of viral proteases toward Ub and Ubls and (2) to gain more insight in the structural determinants of substrate preference of DUBs.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30850060</PMID><DateCompleted><Year>2019</Year><Month>11</Month><Day>11</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>07</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1557-7988</ISSN><JournalIssue CitedMedium="Internet"><Volume>618</Volume><PubDate><Year>2019</Year></PubDate></JournalIssue><Title>Methods in enzymology</Title><ISOAbbreviation>Meth. Enzymol.</ISOAbbreviation></Journal><ArticleTitle>Profiling DUBs and Ubl-specific proteases with activity-based probes.</ArticleTitle><Pagination><MedlinePgn>357-387</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0076-6879(18)30534-2</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/bs.mie.2018.12.037</ELocationID><Abstract><AbstractText>Protein (poly-)ubiquitination is a posttranslational modification that plays a key role in almost all cellular processes. It involves the installment of either single ubiquitin (Ub) moieties or one of eight different polyUb linkage types, each giving a distinct cellular outcome. Deubiquitinating enzymes (DUBs) reverse Ub signaling by disassembly of one or multiple poly-Ub chain types and their malfunction is often associated with human disease. The Ub system displays significant crosstalk with structurally homologous ubiquitin-like proteins (Ubls), including SUMO, Nedd8, and ISG15. This can be seen with the existence of heterogeneous chains made from Ub-Ubl mixtures as well as the proteolytic cross reactivity displayed by several DUBs toward other Ubl systems. In addition, numerous pathogens have been found to encode Ub(l)-ligases and deconjugating enzymes in order to facilitate infection and fight the host immune response. Studying the activity of DUBs and Ubl-specific proteases, both human as well as pathogen-derived, gives fundamental insights into their physiological roles. Activity-based probes (ABPs) have proven to be valuable tools to achieve this, as they report on enzyme activities by making a (often irreversible) covalent complex, rather than on their relative abundance. In this chapter, we explain the potential of ABPs to assess substrate preferences, structural features, and activity of Ub and Ubl deconjugating enzymes. We further demonstrate the practical use of ABPs to (1) characterize the activity of viral proteases toward Ub and Ubls and (2) to gain more insight in the structural determinants of substrate preference of DUBs.</AbstractText><CopyrightInformation>© 2019 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Geurink</LastName><ForeName>Paul P</ForeName><Initials>PP</Initials><AffiliationInfo><Affiliation>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van der Heden van Noort</LastName><ForeName>Gerbrand J</ForeName><Initials>GJ</Initials><AffiliationInfo><Affiliation>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mulder</LastName><ForeName>Monique P C</ForeName><Initials>MPC</Initials><AffiliationInfo><Affiliation>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Knaap</LastName><ForeName>Robert C M</ForeName><Initials>RCM</Initials><AffiliationInfo><Affiliation>Department of Medical Microbiology, Section Molecular Virology, Leiden University Medical Centre, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kikkert</LastName><ForeName>Marjolein</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Medical Microbiology, Section Molecular Virology, Leiden University Medical Centre, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ovaa</LastName><ForeName>Huib</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Cell and Chemical Biology, Chemical Immunology, Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands. Electronic address: h.ovaa@lumc.nl.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>02</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Methods Enzymol</MedlineTA><NlmUniqueID>0212271</NlmUniqueID><ISSNLinking>0076-6879</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015335">Molecular Probes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D025801">Ubiquitin</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014452">Ubiquitins</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.-</RegistryNumber><NameOfSubstance UI="D010447">Peptide Hydrolases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.19.12</RegistryNumber><NameOfSubstance UI="D000072017">Deubiquitinating Enzymes</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000072017" MajorTopicYN="N">Deubiquitinating Enzymes</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D057075" MajorTopicYN="N">Enzyme Assays</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D047668" MajorTopicYN="N">Inteins</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015335" MajorTopicYN="N">Molecular Probes</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010447" MajorTopicYN="N">Peptide Hydrolases</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013379" MajorTopicYN="N">Substrate Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D025801" MajorTopicYN="N">Ubiquitin</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014452" MajorTopicYN="N">Ubiquitins</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014780" MajorTopicYN="N">Viruses</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="N">enzymology</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">(di)ubiquitin-based probes</Keyword><Keyword MajorTopicYN="Y">Activity-based probes</Keyword><Keyword MajorTopicYN="Y">Deubiquitinating enzymes</Keyword><Keyword MajorTopicYN="Y">MERS-CoV PLpro</Keyword><Keyword MajorTopicYN="Y">SARS-CoV PLpro</Keyword><Keyword MajorTopicYN="Y">Ub linkage specificity</Keyword><Keyword MajorTopicYN="Y">Ubl-specific proteases</Keyword><Keyword MajorTopicYN="Y">Ub–Ubl crosstalk</Keyword><Keyword MajorTopicYN="Y">Viral DUBs</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>3</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>3</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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