Discrete Kinetic Models from Funneled Energy Landscape Simulations

Autores
Schafer, Nicholas P.; Hoffman, Ryan M. B.; Burger, Anat; Craig, Patricio Oliver; Komives, Elizabeth A.; Wolynes, Peter G.
Año de publicación
2012
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.
Fil: Schafer, Nicholas P.. Rice University; Estados Unidos. University of California at San Diego; Estados Unidos
Fil: Hoffman, Ryan M. B.. University of California at San Diego; Estados Unidos. Rice University; Estados Unidos
Fil: Burger, Anat. University of California at San Diego; Estados Unidos. Rice University; Estados Unidos
Fil: Craig, Patricio Oliver. University of California at San Diego; Estados Unidos. Rice University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Komives, Elizabeth A.. University of California at San Diego; Estados Unidos
Fil: Wolynes, Peter G.. Rice University; Estados Unidos. University of California at San Diego; Estados Unidos
Materia
folding
kinetics
discrete
energy landscape
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/98244

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spelling Discrete Kinetic Models from Funneled Energy Landscape SimulationsSchafer, Nicholas P.Hoffman, Ryan M. B.Burger, AnatCraig, Patricio OliverKomives, Elizabeth A.Wolynes, Peter G.foldingkineticsdiscreteenergy landscapehttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.Fil: Schafer, Nicholas P.. Rice University; Estados Unidos. University of California at San Diego; Estados UnidosFil: Hoffman, Ryan M. B.. University of California at San Diego; Estados Unidos. Rice University; Estados UnidosFil: Burger, Anat. University of California at San Diego; Estados Unidos. Rice University; Estados UnidosFil: Craig, Patricio Oliver. University of California at San Diego; Estados Unidos. Rice University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Komives, Elizabeth A.. University of California at San Diego; Estados UnidosFil: Wolynes, Peter G.. Rice University; Estados Unidos. University of California at San Diego; Estados UnidosPublic Library of Science2012-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/98244Schafer, Nicholas P.; Hoffman, Ryan M. B.; Burger, Anat; Craig, Patricio Oliver; Komives, Elizabeth A.; et al.; Discrete Kinetic Models from Funneled Energy Landscape Simulations; Public Library of Science; Plos One; 7; 12; 12-2012; 1-81932-6203CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050635info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0050635info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:08:39Zoai:ri.conicet.gov.ar:11336/98244instacron: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 10:08:39.43CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Discrete Kinetic Models from Funneled Energy Landscape Simulations
title Discrete Kinetic Models from Funneled Energy Landscape Simulations
spellingShingle Discrete Kinetic Models from Funneled Energy Landscape Simulations
Schafer, Nicholas P.
folding
kinetics
discrete
energy landscape
title_short Discrete Kinetic Models from Funneled Energy Landscape Simulations
title_full Discrete Kinetic Models from Funneled Energy Landscape Simulations
title_fullStr Discrete Kinetic Models from Funneled Energy Landscape Simulations
title_full_unstemmed Discrete Kinetic Models from Funneled Energy Landscape Simulations
title_sort Discrete Kinetic Models from Funneled Energy Landscape Simulations
dc.creator.none.fl_str_mv Schafer, Nicholas P.
Hoffman, Ryan M. B.
Burger, Anat
Craig, Patricio Oliver
Komives, Elizabeth A.
Wolynes, Peter G.
author Schafer, Nicholas P.
author_facet Schafer, Nicholas P.
Hoffman, Ryan M. B.
Burger, Anat
Craig, Patricio Oliver
Komives, Elizabeth A.
Wolynes, Peter G.
author_role author
author2 Hoffman, Ryan M. B.
Burger, Anat
Craig, Patricio Oliver
Komives, Elizabeth A.
Wolynes, Peter G.
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv folding
kinetics
discrete
energy landscape
topic folding
kinetics
discrete
energy landscape
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.
Fil: Schafer, Nicholas P.. Rice University; Estados Unidos. University of California at San Diego; Estados Unidos
Fil: Hoffman, Ryan M. B.. University of California at San Diego; Estados Unidos. Rice University; Estados Unidos
Fil: Burger, Anat. University of California at San Diego; Estados Unidos. Rice University; Estados Unidos
Fil: Craig, Patricio Oliver. University of California at San Diego; Estados Unidos. Rice University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Komives, Elizabeth A.. University of California at San Diego; Estados Unidos
Fil: Wolynes, Peter G.. Rice University; Estados Unidos. University of California at San Diego; Estados Unidos
description A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.
publishDate 2012
dc.date.none.fl_str_mv 2012-12
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/11336/98244
Schafer, Nicholas P.; Hoffman, Ryan M. B.; Burger, Anat; Craig, Patricio Oliver; Komives, Elizabeth A.; et al.; Discrete Kinetic Models from Funneled Energy Landscape Simulations; Public Library of Science; Plos One; 7; 12; 12-2012; 1-8
1932-6203
CONICET Digital
CONICET
url http://hdl.handle.net/11336/98244
identifier_str_mv Schafer, Nicholas P.; Hoffman, Ryan M. B.; Burger, Anat; Craig, Patricio Oliver; Komives, Elizabeth A.; et al.; Discrete Kinetic Models from Funneled Energy Landscape Simulations; Public Library of Science; Plos One; 7; 12; 12-2012; 1-8
1932-6203
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050635
info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0050635
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
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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