Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes

Autores
Craig, Patricio Oliver; Lätzer, Joachim; Weinkam, Patrick; Hoffman, Ryan M. B.; Ferreiro, Diego; Komives, Elizabeth A.; Wolynes, Peter G.
Año de publicación
2011
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Simulations based on perfectly funneled energy landscapes often capture many of the kinetic features of protein folding. We examined whether simulations based on funneled energy functions can also describe fluctuations in native-state protein ensembles. We quantitatively compared the site-specific local stability determined from structure-based folding simulations, with hydrogen exchange protection factors measured experimentally for ubiquitin, chymotrypsin inhibitor 2, and staphylococcal nuclease. Different structural definitions for the open and closed states based on the number of native contacts for each residue, as well as the hydrogen-bonding state, or a combination of both criteria were evaluated. The predicted exchange patterns agree with the experiments under native conditions, indicating that protein topology indeed has a dominant effect on the exchange kinetics. Insights into the simplest mechanistic interpretation of the amide exchange process were thus obtained.
Fil: Craig, Patricio Oliver. Fundación Instituto Leloir; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. University of California San Diego. Department of Chemistry and Biochemistry; Estados Unidos
Fil: Lätzer, Joachim. Rutgers University. BioMaPS Institute; Estados Unidos
Fil: Weinkam, Patrick. University of California at San Francisco. Department of Bioengineering and Therapeutic Sciences; Estados Unidos
Fil: Hoffman, Ryan M. B.. University Of California At San Diego; Estados Unidos
Fil: Ferreiro, Diego. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 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; Argentina
Fil: Komives, Elizabeth A.. University Of California At San Diego; Estados Unidos
Fil: Wolynes, Peter G.. University Of California At San Diego; Estados Unidos
Materia
protein folding
hydrogen exchange
energy landscape
coarse grain models
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:11336/13824
Acceder
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network_name_str CONICET Digital (CONICET)
spelling Prediction of native-state hydrogen exchange from perfectly funneled energy landscapesCraig, Patricio OliverLätzer, JoachimWeinkam, PatrickHoffman, Ryan M. B.Ferreiro, DiegoKomives, Elizabeth A.Wolynes, Peter G.protein foldinghydrogen exchangeenergy landscapecoarse grain modelshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Simulations based on perfectly funneled energy landscapes often capture many of the kinetic features of protein folding. We examined whether simulations based on funneled energy functions can also describe fluctuations in native-state protein ensembles. We quantitatively compared the site-specific local stability determined from structure-based folding simulations, with hydrogen exchange protection factors measured experimentally for ubiquitin, chymotrypsin inhibitor 2, and staphylococcal nuclease. Different structural definitions for the open and closed states based on the number of native contacts for each residue, as well as the hydrogen-bonding state, or a combination of both criteria were evaluated. The predicted exchange patterns agree with the experiments under native conditions, indicating that protein topology indeed has a dominant effect on the exchange kinetics. Insights into the simplest mechanistic interpretation of the amide exchange process were thus obtained.Fil: Craig, Patricio Oliver. Fundación Instituto Leloir; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. University of California San Diego. Department of Chemistry and Biochemistry; Estados UnidosFil: Lätzer, Joachim. Rutgers University. BioMaPS Institute; Estados UnidosFil: Weinkam, Patrick. University of California at San Francisco. Department of Bioengineering and Therapeutic Sciences; Estados UnidosFil: Hoffman, Ryan M. B.. University Of California At San Diego; Estados UnidosFil: Ferreiro, Diego. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 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; ArgentinaFil: Komives, Elizabeth A.. University Of California At San Diego; Estados UnidosFil: Wolynes, Peter G.. University Of California At San Diego; Estados UnidosAmerican Chemical Society2011info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/13824Craig, Patricio Oliver; Lätzer, Joachim; Weinkam, Patrick; Hoffman, Ryan M. B.; Ferreiro, Diego; et al.; Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes; American Chemical Society; Journal Of The American Chemical Society; 133; 43; -1-2011; 17463-174720002-7863enginfo:eu-repo/semantics/altIdentifier/url/http://pubs.acs.org/doi/abs/10.1021/ja207506zinfo:eu-repo/semantics/altIdentifier/doi/10.1021/ja207506zinfo:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203634/info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:43:25Zoai:ri.conicet.gov.ar:11336/13824instacron: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 09:43:25.727CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes
title Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes
spellingShingle Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes
Craig, Patricio Oliver
protein folding
hydrogen exchange
energy landscape
coarse grain models
title_short Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes
title_full Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes
title_fullStr Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes
title_full_unstemmed Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes
title_sort Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes
dc.creator.none.fl_str_mv Craig, Patricio Oliver
Lätzer, Joachim
Weinkam, Patrick
Hoffman, Ryan M. B.
Ferreiro, Diego
Komives, Elizabeth A.
Wolynes, Peter G.
author Craig, Patricio Oliver
author_facet Craig, Patricio Oliver
Lätzer, Joachim
Weinkam, Patrick
Hoffman, Ryan M. B.
Ferreiro, Diego
Komives, Elizabeth A.
Wolynes, Peter G.
author_role author
author2 Lätzer, Joachim
Weinkam, Patrick
Hoffman, Ryan M. B.
Ferreiro, Diego
Komives, Elizabeth A.
Wolynes, Peter G.
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv protein folding
hydrogen exchange
energy landscape
coarse grain models
topic protein folding
hydrogen exchange
energy landscape
coarse grain models
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Simulations based on perfectly funneled energy landscapes often capture many of the kinetic features of protein folding. We examined whether simulations based on funneled energy functions can also describe fluctuations in native-state protein ensembles. We quantitatively compared the site-specific local stability determined from structure-based folding simulations, with hydrogen exchange protection factors measured experimentally for ubiquitin, chymotrypsin inhibitor 2, and staphylococcal nuclease. Different structural definitions for the open and closed states based on the number of native contacts for each residue, as well as the hydrogen-bonding state, or a combination of both criteria were evaluated. The predicted exchange patterns agree with the experiments under native conditions, indicating that protein topology indeed has a dominant effect on the exchange kinetics. Insights into the simplest mechanistic interpretation of the amide exchange process were thus obtained.
Fil: Craig, Patricio Oliver. Fundación Instituto Leloir; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. University of California San Diego. Department of Chemistry and Biochemistry; Estados Unidos
Fil: Lätzer, Joachim. Rutgers University. BioMaPS Institute; Estados Unidos
Fil: Weinkam, Patrick. University of California at San Francisco. Department of Bioengineering and Therapeutic Sciences; Estados Unidos
Fil: Hoffman, Ryan M. B.. University Of California At San Diego; Estados Unidos
Fil: Ferreiro, Diego. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 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; Argentina
Fil: Komives, Elizabeth A.. University Of California At San Diego; Estados Unidos
Fil: Wolynes, Peter G.. University Of California At San Diego; Estados Unidos
description Simulations based on perfectly funneled energy landscapes often capture many of the kinetic features of protein folding. We examined whether simulations based on funneled energy functions can also describe fluctuations in native-state protein ensembles. We quantitatively compared the site-specific local stability determined from structure-based folding simulations, with hydrogen exchange protection factors measured experimentally for ubiquitin, chymotrypsin inhibitor 2, and staphylococcal nuclease. Different structural definitions for the open and closed states based on the number of native contacts for each residue, as well as the hydrogen-bonding state, or a combination of both criteria were evaluated. The predicted exchange patterns agree with the experiments under native conditions, indicating that protein topology indeed has a dominant effect on the exchange kinetics. Insights into the simplest mechanistic interpretation of the amide exchange process were thus obtained.
publishDate 2011
dc.date.none.fl_str_mv 2011
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/11336/13824
Craig, Patricio Oliver; Lätzer, Joachim; Weinkam, Patrick; Hoffman, Ryan M. B.; Ferreiro, Diego; et al.; Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes; American Chemical Society; Journal Of The American Chemical Society; 133; 43; -1-2011; 17463-17472
0002-7863
url http://hdl.handle.net/11336/13824
identifier_str_mv Craig, Patricio Oliver; Lätzer, Joachim; Weinkam, Patrick; Hoffman, Ryan M. B.; Ferreiro, Diego; et al.; Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes; American Chemical Society; Journal Of The American Chemical Society; 133; 43; -1-2011; 17463-17472
0002-7863
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://pubs.acs.org/doi/abs/10.1021/ja207506z
info:eu-repo/semantics/altIdentifier/doi/10.1021/ja207506z
info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203634/
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
application/pdf
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
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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score 13.070432

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