Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain

Autores
Devries, Ingrid; Ferreiro, Diego; Sánchez Miguel, Ignacio Enrique; Komives, Elizabeth A.
Año de publicación
2011
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The ankyrin repeat (AR) domain of IκBα consists of a cooperative folding unit of roughly four ARs (AR1-AR4) and of two weakly folded repeats (AR5 and AR6). The kinetic folding mechanism of the cooperative subdomain, IκBα 67-206, was analyzed using rapid mixing techniques. Despite its apparent architectural simplicity, IκBα 67-206 displays complex folding kinetics, with two sequential on-pathway high-energy intermediates. The effect of mutations to or away from the consensus sequences of ARs on folding behavior was analyzed, particularly the GXTPLHLA motif, which have not been examined in detail previously. Mutations toward the consensus generally resulted in an increase in folding stability, whereas mutations away from the consensus resulted in decreased overall stability. We determined the free energy change upon mutation for three sequential transition state ensembles along the folding route for 16 mutants. We show that folding initiates with the formation of the interface of the outer helices of AR3 and AR4, and then proceeds to consolidate structure in these repeats. Subsequently, AR1 and AR2 fold in a concerted way in a single kinetic step. We show that this mechanism is robust to the presence of AR5 and AR6 as they do not strongly affect the folding kinetics. Overall, the protein appears to fold on a rather smooth energy landscape, where the folding mechanism conforms a one-dimensional approximation. However, we note that the AR does not necessarily act as a single folding element. © 2011 Elsevier Ltd.
Fil: Devries, Ingrid. University of California at San Diego; Estados Unidos
Fil: Ferreiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Sánchez Miguel, Ignacio Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Komives, Elizabeth A.. University of California at San Diego; Estados Unidos
Materia
Α Value; Folding LandscapenfΚB
Protein Folding
Repeat Protein
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/66443

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spelling Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domainDevries, IngridFerreiro, DiegoSánchez Miguel, Ignacio EnriqueKomives, Elizabeth A.Α Value; Folding LandscapenfΚBProtein FoldingRepeat Proteinhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The ankyrin repeat (AR) domain of IκBα consists of a cooperative folding unit of roughly four ARs (AR1-AR4) and of two weakly folded repeats (AR5 and AR6). The kinetic folding mechanism of the cooperative subdomain, IκBα 67-206, was analyzed using rapid mixing techniques. Despite its apparent architectural simplicity, IκBα 67-206 displays complex folding kinetics, with two sequential on-pathway high-energy intermediates. The effect of mutations to or away from the consensus sequences of ARs on folding behavior was analyzed, particularly the GXTPLHLA motif, which have not been examined in detail previously. Mutations toward the consensus generally resulted in an increase in folding stability, whereas mutations away from the consensus resulted in decreased overall stability. We determined the free energy change upon mutation for three sequential transition state ensembles along the folding route for 16 mutants. We show that folding initiates with the formation of the interface of the outer helices of AR3 and AR4, and then proceeds to consolidate structure in these repeats. Subsequently, AR1 and AR2 fold in a concerted way in a single kinetic step. We show that this mechanism is robust to the presence of AR5 and AR6 as they do not strongly affect the folding kinetics. Overall, the protein appears to fold on a rather smooth energy landscape, where the folding mechanism conforms a one-dimensional approximation. However, we note that the AR does not necessarily act as a single folding element. © 2011 Elsevier Ltd.Fil: Devries, Ingrid. University of California at San Diego; Estados UnidosFil: Ferreiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Sánchez Miguel, Ignacio Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Komives, Elizabeth A.. University of California at San Diego; Estados UnidosAcademic Press Ltd - Elsevier Science Ltd2011-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/66443Devries, Ingrid; Ferreiro, Diego; Sánchez Miguel, Ignacio Enrique; Komives, Elizabeth A.; Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain; Academic Press Ltd - Elsevier Science Ltd; Journal Of Molecular Biology; 408; 1; 4-2011; 163-1760022-2836CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1016/j.jmb.2011.02.021info:eu-repo/semantics/altIdentifier/url/https://linkinghub.elsevier.com/retrieve/pii/S0022283611001653info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:38:42Zoai:ri.conicet.gov.ar:11336/66443instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:38:42.293CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain
title Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain
spellingShingle Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain
Devries, Ingrid
Α Value; Folding LandscapenfΚB
Protein Folding
Repeat Protein
title_short Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain
title_full Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain
title_fullStr Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain
title_full_unstemmed Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain
title_sort Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain
dc.creator.none.fl_str_mv Devries, Ingrid
Ferreiro, Diego
Sánchez Miguel, Ignacio Enrique
Komives, Elizabeth A.
author Devries, Ingrid
author_facet Devries, Ingrid
Ferreiro, Diego
Sánchez Miguel, Ignacio Enrique
Komives, Elizabeth A.
author_role author
author2 Ferreiro, Diego
Sánchez Miguel, Ignacio Enrique
Komives, Elizabeth A.
author2_role author
author
author
dc.subject.none.fl_str_mv Α Value; Folding LandscapenfΚB
Protein Folding
Repeat Protein
topic Α Value; Folding LandscapenfΚB
Protein Folding
Repeat Protein
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The ankyrin repeat (AR) domain of IκBα consists of a cooperative folding unit of roughly four ARs (AR1-AR4) and of two weakly folded repeats (AR5 and AR6). The kinetic folding mechanism of the cooperative subdomain, IκBα 67-206, was analyzed using rapid mixing techniques. Despite its apparent architectural simplicity, IκBα 67-206 displays complex folding kinetics, with two sequential on-pathway high-energy intermediates. The effect of mutations to or away from the consensus sequences of ARs on folding behavior was analyzed, particularly the GXTPLHLA motif, which have not been examined in detail previously. Mutations toward the consensus generally resulted in an increase in folding stability, whereas mutations away from the consensus resulted in decreased overall stability. We determined the free energy change upon mutation for three sequential transition state ensembles along the folding route for 16 mutants. We show that folding initiates with the formation of the interface of the outer helices of AR3 and AR4, and then proceeds to consolidate structure in these repeats. Subsequently, AR1 and AR2 fold in a concerted way in a single kinetic step. We show that this mechanism is robust to the presence of AR5 and AR6 as they do not strongly affect the folding kinetics. Overall, the protein appears to fold on a rather smooth energy landscape, where the folding mechanism conforms a one-dimensional approximation. However, we note that the AR does not necessarily act as a single folding element. © 2011 Elsevier Ltd.
Fil: Devries, Ingrid. University of California at San Diego; Estados Unidos
Fil: Ferreiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Sánchez Miguel, Ignacio Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Komives, Elizabeth A.. University of California at San Diego; Estados Unidos
description The ankyrin repeat (AR) domain of IκBα consists of a cooperative folding unit of roughly four ARs (AR1-AR4) and of two weakly folded repeats (AR5 and AR6). The kinetic folding mechanism of the cooperative subdomain, IκBα 67-206, was analyzed using rapid mixing techniques. Despite its apparent architectural simplicity, IκBα 67-206 displays complex folding kinetics, with two sequential on-pathway high-energy intermediates. The effect of mutations to or away from the consensus sequences of ARs on folding behavior was analyzed, particularly the GXTPLHLA motif, which have not been examined in detail previously. Mutations toward the consensus generally resulted in an increase in folding stability, whereas mutations away from the consensus resulted in decreased overall stability. We determined the free energy change upon mutation for three sequential transition state ensembles along the folding route for 16 mutants. We show that folding initiates with the formation of the interface of the outer helices of AR3 and AR4, and then proceeds to consolidate structure in these repeats. Subsequently, AR1 and AR2 fold in a concerted way in a single kinetic step. We show that this mechanism is robust to the presence of AR5 and AR6 as they do not strongly affect the folding kinetics. Overall, the protein appears to fold on a rather smooth energy landscape, where the folding mechanism conforms a one-dimensional approximation. However, we note that the AR does not necessarily act as a single folding element. © 2011 Elsevier Ltd.
publishDate 2011
dc.date.none.fl_str_mv 2011-04
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/66443
Devries, Ingrid; Ferreiro, Diego; Sánchez Miguel, Ignacio Enrique; Komives, Elizabeth A.; Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain; Academic Press Ltd - Elsevier Science Ltd; Journal Of Molecular Biology; 408; 1; 4-2011; 163-176
0022-2836
CONICET Digital
CONICET
url http://hdl.handle.net/11336/66443
identifier_str_mv Devries, Ingrid; Ferreiro, Diego; Sánchez Miguel, Ignacio Enrique; Komives, Elizabeth A.; Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain; Academic Press Ltd - Elsevier Science Ltd; Journal Of Molecular Biology; 408; 1; 4-2011; 163-176
0022-2836
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1016/j.jmb.2011.02.021
info:eu-repo/semantics/altIdentifier/url/https://linkinghub.elsevier.com/retrieve/pii/S0022283611001653
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Academic Press Ltd - Elsevier Science Ltd
publisher.none.fl_str_mv Academic Press Ltd - Elsevier Science Ltd
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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