Resolving the fine structure in the energy landscapes of repeat proteins

Autores
Sanches, Murilo N.; Parra, R. Gonzalo; Viegas, Rafael G.; Oliveira, Antonio B.; Wolynes, Peter G.; Ferreiro, Diego; Leite, Vitor B. P.
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein-protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions.
Fil: Sanches, Murilo N.. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Fil: Parra, R. Gonzalo. Barcelona Supercomputing Center - Centro Nacional de Supercomputacion; España
Fil: Viegas, Rafael G.. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Fil: Oliveira, Antonio B.. Rice University; Estados Unidos
Fil: Wolynes, Peter G.. Rice University; 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: Leite, Vitor B. P.. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Materia
ENERGY LANDSCAPE VISUALISATION
FOLDING FUNNEL
MOLECULAR DYNAMICS
PROTEIN FOLDING
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:11336/213603
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Resolving the fine structure in the energy landscapes of repeat proteinsSanches, Murilo N.Parra, R. GonzaloViegas, Rafael G.Oliveira, Antonio B.Wolynes, Peter G.Ferreiro, DiegoLeite, Vitor B. P.ENERGY LANDSCAPE VISUALISATIONFOLDING FUNNELMOLECULAR DYNAMICSPROTEIN FOLDINGhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein-protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions.Fil: Sanches, Murilo N.. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Parra, R. Gonzalo. Barcelona Supercomputing Center - Centro Nacional de Supercomputacion; EspañaFil: Viegas, Rafael G.. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Oliveira, Antonio B.. Rice University; Estados UnidosFil: Wolynes, Peter G.. Rice University; 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: Leite, Vitor B. P.. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilCambridge University Press2022-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/213603Sanches, Murilo N.; Parra, R. Gonzalo; Viegas, Rafael G.; Oliveira, Antonio B.; Wolynes, Peter G.; et al.; Resolving the fine structure in the energy landscapes of repeat proteins; Cambridge University Press; QRB Discovery; 3; 6-2022; 1-82633-2892CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1017/qrd.2022.4info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:28:12Zoai:ri.conicet.gov.ar:11336/213603instacron: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 10:28:13.029CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Resolving the fine structure in the energy landscapes of repeat proteins
title Resolving the fine structure in the energy landscapes of repeat proteins
spellingShingle Resolving the fine structure in the energy landscapes of repeat proteins
Sanches, Murilo N.
ENERGY LANDSCAPE VISUALISATION
FOLDING FUNNEL
MOLECULAR DYNAMICS
PROTEIN FOLDING
title_short Resolving the fine structure in the energy landscapes of repeat proteins
title_full Resolving the fine structure in the energy landscapes of repeat proteins
title_fullStr Resolving the fine structure in the energy landscapes of repeat proteins
title_full_unstemmed Resolving the fine structure in the energy landscapes of repeat proteins
title_sort Resolving the fine structure in the energy landscapes of repeat proteins
dc.creator.none.fl_str_mv Sanches, Murilo N.
Parra, R. Gonzalo
Viegas, Rafael G.
Oliveira, Antonio B.
Wolynes, Peter G.
Ferreiro, Diego
Leite, Vitor B. P.
author Sanches, Murilo N.
author_facet Sanches, Murilo N.
Parra, R. Gonzalo
Viegas, Rafael G.
Oliveira, Antonio B.
Wolynes, Peter G.
Ferreiro, Diego
Leite, Vitor B. P.
author_role author
author2 Parra, R. Gonzalo
Viegas, Rafael G.
Oliveira, Antonio B.
Wolynes, Peter G.
Ferreiro, Diego
Leite, Vitor B. P.
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv ENERGY LANDSCAPE VISUALISATION
FOLDING FUNNEL
MOLECULAR DYNAMICS
PROTEIN FOLDING
topic ENERGY LANDSCAPE VISUALISATION
FOLDING FUNNEL
MOLECULAR DYNAMICS
PROTEIN FOLDING
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein-protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions.
Fil: Sanches, Murilo N.. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Fil: Parra, R. Gonzalo. Barcelona Supercomputing Center - Centro Nacional de Supercomputacion; España
Fil: Viegas, Rafael G.. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Fil: Oliveira, Antonio B.. Rice University; Estados Unidos
Fil: Wolynes, Peter G.. Rice University; 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: Leite, Vitor B. P.. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
description Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein-protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions.
publishDate 2022
dc.date.none.fl_str_mv 2022-06
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/11336/213603
Sanches, Murilo N.; Parra, R. Gonzalo; Viegas, Rafael G.; Oliveira, Antonio B.; Wolynes, Peter G.; et al.; Resolving the fine structure in the energy landscapes of repeat proteins; Cambridge University Press; QRB Discovery; 3; 6-2022; 1-8
2633-2892
CONICET Digital
CONICET
url http://hdl.handle.net/11336/213603
identifier_str_mv Sanches, Murilo N.; Parra, R. Gonzalo; Viegas, Rafael G.; Oliveira, Antonio B.; Wolynes, Peter G.; et al.; Resolving the fine structure in the energy landscapes of repeat proteins; Cambridge University Press; QRB Discovery; 3; 6-2022; 1-8
2633-2892
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1017/qrd.2022.4
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
dc.publisher.none.fl_str_mv Cambridge University Press
publisher.none.fl_str_mv Cambridge University Press
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_ 1844614285656850432
score 13.070432

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