Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1

Villar, Sebastián F. - Dalla Rizza Aishemberg, Joaquín - Möller, Matías N. - Ferrer-Sueta, Gerardo - Malacrida, Leonel - Jameson, David M. - Denicola, Ana

Resumen:

Protein self-assembly is a common feature in biology and is often required for a myriad of fundamental processes, such as enzyme activity, signal transduction, and transport of solutes across membranes, among others. There are several techniques to find and assess homo-oligomer formation in proteins. Naturally, all these methods have their limitations, meaning that at least two or more different approaches are needed to characterize a case study. Herein, we present a new method to study protein associations using intrinsic fluorescence lifetime with phasors. In this case, the method is applied to determine the equilibrium dissociation constant (KD) of human peroxiredoxin 1 (hPrx1), an efficient cysteine-dependent peroxidase, that has a quaternary structure comprised of five head-to-tail homodimers non-covalently arranged in a decamer. The hPrx1 oligomeric state not only affects its activity but also its association with other proteins. The excited state lifetime of hPrx1 has distinct values at high and low concentrations, suggesting the presence of two different species. Phasor analysis of hPrx1 emission lifetime allowed for the identification and quantification of hPrx1 decamers, dimers, and their mixture at diverse protein concentrations. Using phasor algebra, we calculated the fraction of hPrx1 decamers at different concentrations and obtained KD (1.1 × 10−24 M4) and C0.5 (1.36 μM) values for the decamer–dimer equilibrium. The results were validated and compared with size exclusion chromatography. In addition, spectral phasors provided similar results despite the small differences in emission spectra as a function of hPrx1 concentration. The phasor approach was shown to be a highly sensitive and quantitative method to assess protein oligomerization and an attractive addition to the biophysicist’s toolkit.


Detalles Bibliográficos
2022
CSIC: I+D 2020
ANII: FCE_1_2017_1_136043
ANII: FCE 2019_155969
Peroxiredoxin 1
Protein oligomerization
Lifetime phasors
Spectral phasors
Tryptophan fluorescence
Dissociation constant
Inglés
Universidad de la República
COLIBRI
https://hdl.handle.net/20.500.12008/41338
Acceso abierto
Licencia Creative Commons Atribución (CC - By 4.0)
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author Villar, Sebastián F.
author2 Dalla Rizza Aishemberg, Joaquín
Möller, Matías N.
Ferrer-Sueta, Gerardo
Malacrida, Leonel
Jameson, David M.
Denicola, Ana
author2_role author
author
author
author
author
author
author_facet Villar, Sebastián F.
Dalla Rizza Aishemberg, Joaquín
Möller, Matías N.
Ferrer-Sueta, Gerardo
Malacrida, Leonel
Jameson, David M.
Denicola, Ana
author_role author
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collection COLIBRI
dc.contributor.filiacion.none.fl_str_mv Villar Sebastián F., Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica.
Dalla Rizza Aishemberg Joaquín, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica.
Möller Matías N., Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica.
Ferrer-Sueta Gerardo, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica.
Malacrida Leonel, Instituto Pasteur (Montevideo).
Jameson David M.
Denicola Ana, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica.
dc.creator.none.fl_str_mv Villar, Sebastián F.
Dalla Rizza Aishemberg, Joaquín
Möller, Matías N.
Ferrer-Sueta, Gerardo
Malacrida, Leonel
Jameson, David M.
Denicola, Ana
dc.date.accessioned.none.fl_str_mv 2023-11-20T17:44:07Z
dc.date.available.none.fl_str_mv 2023-11-20T17:44:07Z
dc.date.issued.none.fl_str_mv 2022
dc.description.abstract.none.fl_txt_mv Protein self-assembly is a common feature in biology and is often required for a myriad of fundamental processes, such as enzyme activity, signal transduction, and transport of solutes across membranes, among others. There are several techniques to find and assess homo-oligomer formation in proteins. Naturally, all these methods have their limitations, meaning that at least two or more different approaches are needed to characterize a case study. Herein, we present a new method to study protein associations using intrinsic fluorescence lifetime with phasors. In this case, the method is applied to determine the equilibrium dissociation constant (KD) of human peroxiredoxin 1 (hPrx1), an efficient cysteine-dependent peroxidase, that has a quaternary structure comprised of five head-to-tail homodimers non-covalently arranged in a decamer. The hPrx1 oligomeric state not only affects its activity but also its association with other proteins. The excited state lifetime of hPrx1 has distinct values at high and low concentrations, suggesting the presence of two different species. Phasor analysis of hPrx1 emission lifetime allowed for the identification and quantification of hPrx1 decamers, dimers, and their mixture at diverse protein concentrations. Using phasor algebra, we calculated the fraction of hPrx1 decamers at different concentrations and obtained KD (1.1 × 10−24 M4) and C0.5 (1.36 μM) values for the decamer–dimer equilibrium. The results were validated and compared with size exclusion chromatography. In addition, spectral phasors provided similar results despite the small differences in emission spectra as a function of hPrx1 concentration. The phasor approach was shown to be a highly sensitive and quantitative method to assess protein oligomerization and an attractive addition to the biophysicist’s toolkit.
dc.description.sponsorship.none.fl_txt_mv CSIC: I+D 2020
ANII: FCE_1_2017_1_136043
ANII: FCE 2019_155969
dc.format.extent.es.fl_str_mv 14 h.
dc.format.mimetype.es.fl_str_mv application/pdf
dc.identifier.citation.es.fl_str_mv Villar, S, Dalla Rizza Aishemberg, J, Möller, M, [y otros autores]. "Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1". International Journal of Molecular Science. [en línea] 2022, 23: 5260. 14 h. DOI: 10.3390/ijms23095260
dc.identifier.doi.none.fl_str_mv 10.3390/ijms23095260
dc.identifier.issn.none.fl_str_mv 1422-0067
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12008/41338
dc.language.iso.none.fl_str_mv en_US
eng
dc.publisher.es.fl_str_mv MDPI
dc.relation.ispartof.es.fl_str_mv International Journal of Molecular Science, 2022, 23(9): 5260.
dc.rights.license.none.fl_str_mv Licencia Creative Commons Atribución (CC - By 4.0)
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
dc.source.none.fl_str_mv reponame:COLIBRI
instname:Universidad de la República
instacron:Universidad de la República
dc.subject.es.fl_str_mv Peroxiredoxin 1
Protein oligomerization
Lifetime phasors
Spectral phasors
Tryptophan fluorescence
Dissociation constant
dc.title.none.fl_str_mv Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1
dc.type.es.fl_str_mv Artículo
dc.type.none.fl_str_mv info:eu-repo/semantics/article
dc.type.version.none.fl_str_mv info:eu-repo/semantics/publishedVersion
description Protein self-assembly is a common feature in biology and is often required for a myriad of fundamental processes, such as enzyme activity, signal transduction, and transport of solutes across membranes, among others. There are several techniques to find and assess homo-oligomer formation in proteins. Naturally, all these methods have their limitations, meaning that at least two or more different approaches are needed to characterize a case study. Herein, we present a new method to study protein associations using intrinsic fluorescence lifetime with phasors. In this case, the method is applied to determine the equilibrium dissociation constant (KD) of human peroxiredoxin 1 (hPrx1), an efficient cysteine-dependent peroxidase, that has a quaternary structure comprised of five head-to-tail homodimers non-covalently arranged in a decamer. The hPrx1 oligomeric state not only affects its activity but also its association with other proteins. The excited state lifetime of hPrx1 has distinct values at high and low concentrations, suggesting the presence of two different species. Phasor analysis of hPrx1 emission lifetime allowed for the identification and quantification of hPrx1 decamers, dimers, and their mixture at diverse protein concentrations. Using phasor algebra, we calculated the fraction of hPrx1 decamers at different concentrations and obtained KD (1.1 × 10−24 M4) and C0.5 (1.36 μM) values for the decamer–dimer equilibrium. The results were validated and compared with size exclusion chromatography. In addition, spectral phasors provided similar results despite the small differences in emission spectra as a function of hPrx1 concentration. The phasor approach was shown to be a highly sensitive and quantitative method to assess protein oligomerization and an attractive addition to the biophysicist’s toolkit.
eu_rights_str_mv openAccess
format article
id COLIBRI_fb4846348c8caaba16d1028c7284c382
identifier_str_mv Villar, S, Dalla Rizza Aishemberg, J, Möller, M, [y otros autores]. "Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1". International Journal of Molecular Science. [en línea] 2022, 23: 5260. 14 h. DOI: 10.3390/ijms23095260
1422-0067
10.3390/ijms23095260
instacron_str Universidad de la República
institution Universidad de la República
instname_str Universidad de la República
language eng
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network_acronym_str COLIBRI
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oai_identifier_str oai:colibri.udelar.edu.uy:20.500.12008/41338
publishDate 2022
reponame_str COLIBRI
repository.mail.fl_str_mv mabel.seroubian@seciu.edu.uy
repository.name.fl_str_mv COLIBRI - Universidad de la República
repository_id_str 4771
rights_invalid_str_mv Licencia Creative Commons Atribución (CC - By 4.0)
spelling Villar Sebastián F., Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica.Dalla Rizza Aishemberg Joaquín, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica.Möller Matías N., Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica.Ferrer-Sueta Gerardo, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica.Malacrida Leonel, Instituto Pasteur (Montevideo).Jameson David M.Denicola Ana, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica.2023-11-20T17:44:07Z2023-11-20T17:44:07Z2022Villar, S, Dalla Rizza Aishemberg, J, Möller, M, [y otros autores]. "Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1". International Journal of Molecular Science. [en línea] 2022, 23: 5260. 14 h. DOI: 10.3390/ijms230952601422-0067https://hdl.handle.net/20.500.12008/4133810.3390/ijms23095260Protein self-assembly is a common feature in biology and is often required for a myriad of fundamental processes, such as enzyme activity, signal transduction, and transport of solutes across membranes, among others. There are several techniques to find and assess homo-oligomer formation in proteins. Naturally, all these methods have their limitations, meaning that at least two or more different approaches are needed to characterize a case study. Herein, we present a new method to study protein associations using intrinsic fluorescence lifetime with phasors. In this case, the method is applied to determine the equilibrium dissociation constant (KD) of human peroxiredoxin 1 (hPrx1), an efficient cysteine-dependent peroxidase, that has a quaternary structure comprised of five head-to-tail homodimers non-covalently arranged in a decamer. The hPrx1 oligomeric state not only affects its activity but also its association with other proteins. The excited state lifetime of hPrx1 has distinct values at high and low concentrations, suggesting the presence of two different species. Phasor analysis of hPrx1 emission lifetime allowed for the identification and quantification of hPrx1 decamers, dimers, and their mixture at diverse protein concentrations. Using phasor algebra, we calculated the fraction of hPrx1 decamers at different concentrations and obtained KD (1.1 × 10−24 M4) and C0.5 (1.36 μM) values for the decamer–dimer equilibrium. The results were validated and compared with size exclusion chromatography. In addition, spectral phasors provided similar results despite the small differences in emission spectra as a function of hPrx1 concentration. The phasor approach was shown to be a highly sensitive and quantitative method to assess protein oligomerization and an attractive addition to the biophysicist’s toolkit.Submitted by Farías Verónica (vfarias@fcien.edu.uy) on 2023-11-20T15:11:13Z No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) 103390ijms23095260.pdf: 2712268 bytes, checksum: 450f0797e01fa7a4bb726e14c02ddf39 (MD5)Approved for entry into archive by Faget Cecilia (lfaget@fcien.edu.uy) on 2023-11-20T17:10:53Z (GMT) No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) 103390ijms23095260.pdf: 2712268 bytes, checksum: 450f0797e01fa7a4bb726e14c02ddf39 (MD5)Made available in DSpace by Luna Fabiana (fabiana.luna@seciu.edu.uy) on 2023-11-20T17:44:07Z (GMT). No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) 103390ijms23095260.pdf: 2712268 bytes, checksum: 450f0797e01fa7a4bb726e14c02ddf39 (MD5) Previous issue date: 2022CSIC: I+D 2020ANII: FCE_1_2017_1_136043ANII: FCE 2019_15596914 h.application/pdfen_USengMDPIInternational Journal of Molecular Science, 2022, 23(9): 5260.Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución (CC - By 4.0)Peroxiredoxin 1Protein oligomerizationLifetime phasorsSpectral phasorsTryptophan fluorescenceDissociation constantFluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1Artículoinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaVillar, Sebastián F.Dalla Rizza Aishemberg, JoaquínMöller, Matías N.Ferrer-Sueta, GerardoMalacrida, LeonelJameson, David M.Denicola, AnaLICENSElicense.txtlicense.txttext/plain; charset=utf-84267http://localhost:8080/xmlui/bitstream/20.500.12008/41338/5/license.txt6429389a7df7277b72b7924fdc7d47a9MD55CC-LICENSElicense_urllicense_urltext/plain; charset=utf-844http://localhost:8080/xmlui/bitstream/20.500.12008/41338/2/license_urla0ebbeafb9d2ec7cbb19d7137ebc392cMD52license_textlicense_texttext/html; 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- Universidad de la Repúblicafalse
spellingShingle Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1
Villar, Sebastián F.
Peroxiredoxin 1
Protein oligomerization
Lifetime phasors
Spectral phasors
Tryptophan fluorescence
Dissociation constant
status_str publishedVersion
title Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1
title_full Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1
title_fullStr Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1
title_full_unstemmed Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1
title_short Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1
title_sort Fluorescence lifetime phasor analysis of the decamer–dimer equilibrium of human peroxiredoxin 1
topic Peroxiredoxin 1
Protein oligomerization
Lifetime phasors
Spectral phasors
Tryptophan fluorescence
Dissociation constant
url https://hdl.handle.net/20.500.12008/41338