Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition

Detalhes bibliográficos
Autor(a) principal: Kurt, Louise U.
Data de Publicação: 2021
Outros Autores: Clasen, Milan A., Santos, Marlon D. M., Lyra, Eduardo S. B., Santos, Luana O., Ramos, Carlos H. I., Lima, Diogo B., Gozzo, Fabio C., Carvalho, Paulo Costa
Tipo de documento: Artigo
Idioma: por
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/57182
Resumo: Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.
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spelling Kurt, Louise U.Clasen, Milan A.Santos, Marlon D. M.Lyra, Eduardo S. B.Santos, Luana O.Ramos, Carlos H. I.Lima, Diogo B.Gozzo, Fabio C.Carvalho, Paulo Costa2023-03-02T19:53:54Z2023-03-02T19:53:54Z2021KURT, Louise U. et al. Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition. Bioinformatics, v. 37, n. 18, p. 3035–3037, 2021.2227-9059https://www.arca.fiocruz.br/handle/icict/5718210.1093/bioinformatics/btab149porOxford University PressQUIN-XLCross-Linking ReagentsProtein-Protein InteractionsReactivos de Enlaces CruzadosRéactifs réticulantsReagentes de Ligações CruzadasInteração Proteína-ProteínaCharacterizing protein conformers by cross-linking mass spectrometry and pattern recognitioninfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Universidade Estadual de Campinas. Instituto de Química. Campinas, SP, Brasil.Universidade Estadual de Campinas. Instituto de Química. Campinas, SP, Brasil.Universidade Estadual de Campinas. Instituto de Química. Campinas, SP, Brasil.Department of Chemical Biology, Leibniz. Forschungsinstitut für Molekulare Pharmakologie (FMP). Berlin, Germany.Universidade Estadual de Campinas. Instituto de Química. Campinas, SP, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing with multiple conformers; this scenario can lead to high-quality identifications that are mutually exclusive. This limitation hampers the applicability of XLMS in structural experiments of dynamic protein systems, where less abundant conformers of the target protein are expected in the sample. Results: We present QUIN-XL, a software that uses unsupervised clustering to group cross-link identifications by their quantitative profile across multiple samples. QUIN-XL highlights regions of the protein or system presenting changes in its conformation when comparing different biological conditions. We demonstrate our software’s usefulness by revisiting the HSP90 protein, comparing three of its different conformers. QUIN-XL’s clusters correlate directly to known protein 3D structures of the conformers and therefore validates our software.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/57182/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALbtab149ok.pdfbtab149ok.pdfapplication/pdf140510https://www.arca.fiocruz.br/bitstream/icict/57182/2/btab149ok.pdf11310cd7a7ce15142bf122a556ba5c58MD52icict/571822023-03-02 16:53:55.449oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-03-02T19:53:55Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.en_US.fl_str_mv Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
title Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
spellingShingle Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
Kurt, Louise U.
QUIN-XL
Cross-Linking Reagents
Protein-Protein Interactions
Reactivos de Enlaces Cruzados
Réactifs réticulants
Reagentes de Ligações Cruzadas
Interação Proteína-Proteína
title_short Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
title_full Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
title_fullStr Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
title_full_unstemmed Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
title_sort Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
author Kurt, Louise U.
author_facet Kurt, Louise U.
Clasen, Milan A.
Santos, Marlon D. M.
Lyra, Eduardo S. B.
Santos, Luana O.
Ramos, Carlos H. I.
Lima, Diogo B.
Gozzo, Fabio C.
Carvalho, Paulo Costa
author_role author
author2 Clasen, Milan A.
Santos, Marlon D. M.
Lyra, Eduardo S. B.
Santos, Luana O.
Ramos, Carlos H. I.
Lima, Diogo B.
Gozzo, Fabio C.
Carvalho, Paulo Costa
author2_role author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Kurt, Louise U.
Clasen, Milan A.
Santos, Marlon D. M.
Lyra, Eduardo S. B.
Santos, Luana O.
Ramos, Carlos H. I.
Lima, Diogo B.
Gozzo, Fabio C.
Carvalho, Paulo Costa
dc.subject.other.en_US.fl_str_mv QUIN-XL
topic QUIN-XL
Cross-Linking Reagents
Protein-Protein Interactions
Reactivos de Enlaces Cruzados
Réactifs réticulants
Reagentes de Ligações Cruzadas
Interação Proteína-Proteína
dc.subject.en.en_US.fl_str_mv Cross-Linking Reagents
Protein-Protein Interactions
dc.subject.es.en_US.fl_str_mv Reactivos de Enlaces Cruzados
dc.subject.fr.en_US.fl_str_mv Réactifs réticulants
dc.subject.decs.en_US.fl_str_mv Reagentes de Ligações Cruzadas
Interação Proteína-Proteína
description Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.
publishDate 2021
dc.date.issued.fl_str_mv 2021
dc.date.accessioned.fl_str_mv 2023-03-02T19:53:54Z
dc.date.available.fl_str_mv 2023-03-02T19:53:54Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv KURT, Louise U. et al. Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition. Bioinformatics, v. 37, n. 18, p. 3035–3037, 2021.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/57182
dc.identifier.issn.en_US.fl_str_mv 2227-9059
dc.identifier.doi.none.fl_str_mv 10.1093/bioinformatics/btab149
identifier_str_mv KURT, Louise U. et al. Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition. Bioinformatics, v. 37, n. 18, p. 3035–3037, 2021.
2227-9059
10.1093/bioinformatics/btab149
url https://www.arca.fiocruz.br/handle/icict/57182
dc.language.iso.fl_str_mv por
language por
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/57182/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/57182/2/btab149ok.pdf
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repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
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