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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/98244
Ver los metadatos del registro completo
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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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1844613956681859072 |
score |
13.070432 |