The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A

Autores
Zhao, Lingci; Suarez, Irina Paula; Gauto, Diego Fernando; Rasia, Rodolfo Maximiliano; Wang, Jin
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The intrinsically disordered protein domain DCL1-A is the first report of a complete double stranded RNA binding domain folding upon binding. DCL1-A recognizes the dsRNA by acquiring a well-folded structure after engagement with its interaction partner. Despite the structural characterization of the interaction complex underlying the recognition of dsRNA has been established, the dynamics of disorder-to-order transitions in the binding process remains elusive. Here we have developed a coarse-grained structure-based model with consideration of electrostatic interactions to explore the mechanism of the coupled folding and binding. Our approach led to remarkable agreements with both experimental and theoretical results. We quantified the global binding-folding landscape, which indicates a synergistic binding induced folding mechanism. We further investigated the effect of electrostatic interactions in this coupled folding and binding process. It reveals that non-native electrostatic interactions dominate the initial stage of the recognition. Our results help improve our understanding of the induced folding of the IDP DCL1-A upon binding to dsRNA. Such methods developed here can be applied for further explorations of the dynamics of coupled folding and binding systems.
Fil: Zhao, Lingci. Jilin University; República de China. Chinese Academy of Sciences; República de China
Fil: Suarez, Irina Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Gauto, Diego Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Rasia, Rodolfo Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Wang, Jin. Jilin University; República de China. Chinese Academy of Sciences; República de China
Materia
INTRINSICALLY DISORDERED PROTEINS
BINDING INDUCED FOLDING
MICRORNA
DCL1
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:11336/88186
Acceder
id CONICETDig_4e8adacae888a66b726f15bb9bd95da6
oai_identifier_str oai:ri.conicet.gov.ar:11336/88186
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-AZhao, LingciSuarez, Irina PaulaGauto, Diego FernandoRasia, Rodolfo MaximilianoWang, JinINTRINSICALLY DISORDERED PROTEINSBINDING INDUCED FOLDINGMICRORNADCL1https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The intrinsically disordered protein domain DCL1-A is the first report of a complete double stranded RNA binding domain folding upon binding. DCL1-A recognizes the dsRNA by acquiring a well-folded structure after engagement with its interaction partner. Despite the structural characterization of the interaction complex underlying the recognition of dsRNA has been established, the dynamics of disorder-to-order transitions in the binding process remains elusive. Here we have developed a coarse-grained structure-based model with consideration of electrostatic interactions to explore the mechanism of the coupled folding and binding. Our approach led to remarkable agreements with both experimental and theoretical results. We quantified the global binding-folding landscape, which indicates a synergistic binding induced folding mechanism. We further investigated the effect of electrostatic interactions in this coupled folding and binding process. It reveals that non-native electrostatic interactions dominate the initial stage of the recognition. Our results help improve our understanding of the induced folding of the IDP DCL1-A upon binding to dsRNA. Such methods developed here can be applied for further explorations of the dynamics of coupled folding and binding systems.Fil: Zhao, Lingci. Jilin University; República de China. Chinese Academy of Sciences; República de ChinaFil: Suarez, Irina Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Gauto, Diego Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Rasia, Rodolfo Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Wang, Jin. Jilin University; República de China. Chinese Academy of Sciences; República de ChinaRoyal Society of Chemistry2018-03info: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/11336/88186Zhao, Lingci; Suarez, Irina Paula; Gauto, Diego Fernando; Rasia, Rodolfo Maximiliano; Wang, Jin; The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A; Royal Society of Chemistry; Physical Chemistry Chemical Physics; 20; 14; 3-2018; 9376-93881463-9076CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1039/c7cp07889ginfo:eu-repo/semantics/altIdentifier/url/https://pubs.rsc.org/en/content/articlelanding/2018/CP/C7CP07889Ginfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:06:47Zoai:ri.conicet.gov.ar:11336/88186instacron: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:34982025-09-03 10:06:47.749CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A
title The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A
spellingShingle The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A
Zhao, Lingci
INTRINSICALLY DISORDERED PROTEINS
BINDING INDUCED FOLDING
MICRORNA
DCL1
title_short The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A
title_full The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A
title_fullStr The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A
title_full_unstemmed The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A
title_sort The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A
dc.creator.none.fl_str_mv Zhao, Lingci
Suarez, Irina Paula
Gauto, Diego Fernando
Rasia, Rodolfo Maximiliano
Wang, Jin
author Zhao, Lingci
author_facet Zhao, Lingci
Suarez, Irina Paula
Gauto, Diego Fernando
Rasia, Rodolfo Maximiliano
Wang, Jin
author_role author
author2 Suarez, Irina Paula
Gauto, Diego Fernando
Rasia, Rodolfo Maximiliano
Wang, Jin
author2_role author
author
author
author
dc.subject.none.fl_str_mv INTRINSICALLY DISORDERED PROTEINS
BINDING INDUCED FOLDING
MICRORNA
DCL1
topic INTRINSICALLY DISORDERED PROTEINS
BINDING INDUCED FOLDING
MICRORNA
DCL1
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 intrinsically disordered protein domain DCL1-A is the first report of a complete double stranded RNA binding domain folding upon binding. DCL1-A recognizes the dsRNA by acquiring a well-folded structure after engagement with its interaction partner. Despite the structural characterization of the interaction complex underlying the recognition of dsRNA has been established, the dynamics of disorder-to-order transitions in the binding process remains elusive. Here we have developed a coarse-grained structure-based model with consideration of electrostatic interactions to explore the mechanism of the coupled folding and binding. Our approach led to remarkable agreements with both experimental and theoretical results. We quantified the global binding-folding landscape, which indicates a synergistic binding induced folding mechanism. We further investigated the effect of electrostatic interactions in this coupled folding and binding process. It reveals that non-native electrostatic interactions dominate the initial stage of the recognition. Our results help improve our understanding of the induced folding of the IDP DCL1-A upon binding to dsRNA. Such methods developed here can be applied for further explorations of the dynamics of coupled folding and binding systems.
Fil: Zhao, Lingci. Jilin University; República de China. Chinese Academy of Sciences; República de China
Fil: Suarez, Irina Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Gauto, Diego Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Rasia, Rodolfo Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Wang, Jin. Jilin University; República de China. Chinese Academy of Sciences; República de China
description The intrinsically disordered protein domain DCL1-A is the first report of a complete double stranded RNA binding domain folding upon binding. DCL1-A recognizes the dsRNA by acquiring a well-folded structure after engagement with its interaction partner. Despite the structural characterization of the interaction complex underlying the recognition of dsRNA has been established, the dynamics of disorder-to-order transitions in the binding process remains elusive. Here we have developed a coarse-grained structure-based model with consideration of electrostatic interactions to explore the mechanism of the coupled folding and binding. Our approach led to remarkable agreements with both experimental and theoretical results. We quantified the global binding-folding landscape, which indicates a synergistic binding induced folding mechanism. We further investigated the effect of electrostatic interactions in this coupled folding and binding process. It reveals that non-native electrostatic interactions dominate the initial stage of the recognition. Our results help improve our understanding of the induced folding of the IDP DCL1-A upon binding to dsRNA. Such methods developed here can be applied for further explorations of the dynamics of coupled folding and binding systems.
publishDate 2018
dc.date.none.fl_str_mv 2018-03
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/11336/88186
Zhao, Lingci; Suarez, Irina Paula; Gauto, Diego Fernando; Rasia, Rodolfo Maximiliano; Wang, Jin; The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A; Royal Society of Chemistry; Physical Chemistry Chemical Physics; 20; 14; 3-2018; 9376-9388
1463-9076
CONICET Digital
CONICET
url http://hdl.handle.net/11336/88186
identifier_str_mv Zhao, Lingci; Suarez, Irina Paula; Gauto, Diego Fernando; Rasia, Rodolfo Maximiliano; Wang, Jin; The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A; Royal Society of Chemistry; Physical Chemistry Chemical Physics; 20; 14; 3-2018; 9376-9388
1463-9076
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1039/c7cp07889g
info:eu-repo/semantics/altIdentifier/url/https://pubs.rsc.org/en/content/articlelanding/2018/CP/C7CP07889G
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 Royal Society of Chemistry
publisher.none.fl_str_mv Royal Society of Chemistry
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
_version_ 1842269974574399488
score 13.13397

Publicaciones similares