Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes
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 l...
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2011
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00027863_v133_n43_p17463_Craig http://hdl.handle.net/20.500.12110/paper_00027863_v133_n43_p17463_Craig |
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paper:paper_00027863_v133_n43_p17463_Craig2023-06-08T14:22:50Z Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes Ferreiro, Diego U. Chymotrypsin inhibitor 2 Energy functions Energy landscape Exchange kinetics Exchange process Hydrogen bondings Hydrogen exchange Kinetic features Local stability Mechanistic interpretations Native-state protein Protein topology Site-specific Staphylococcal nuclease Structure-based Ubiquitin Amides Protein folding Proteins Hydrogen chymotrypsin inhibitor hydrogen nuclease ubiquitin article chemical reaction chemical reaction kinetics chemical structure energy yield hydrogen bond landscape predictive value protein conformation protein localization Deuterium Exchange Measurement Humans Micrococcal Nuclease Models, Molecular Peptides Plant Proteins Protein Conformation Protein Folding Thermodynamics Ubiquitin 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. © 2011 American Chemical Society. Fil:Ferreiro, D.U. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2011 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00027863_v133_n43_p17463_Craig http://hdl.handle.net/20.500.12110/paper_00027863_v133_n43_p17463_Craig |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Chymotrypsin inhibitor 2 Energy functions Energy landscape Exchange kinetics Exchange process Hydrogen bondings Hydrogen exchange Kinetic features Local stability Mechanistic interpretations Native-state protein Protein topology Site-specific Staphylococcal nuclease Structure-based Ubiquitin Amides Protein folding Proteins Hydrogen chymotrypsin inhibitor hydrogen nuclease ubiquitin article chemical reaction chemical reaction kinetics chemical structure energy yield hydrogen bond landscape predictive value protein conformation protein localization Deuterium Exchange Measurement Humans Micrococcal Nuclease Models, Molecular Peptides Plant Proteins Protein Conformation Protein Folding Thermodynamics Ubiquitin |
| spellingShingle |
Chymotrypsin inhibitor 2 Energy functions Energy landscape Exchange kinetics Exchange process Hydrogen bondings Hydrogen exchange Kinetic features Local stability Mechanistic interpretations Native-state protein Protein topology Site-specific Staphylococcal nuclease Structure-based Ubiquitin Amides Protein folding Proteins Hydrogen chymotrypsin inhibitor hydrogen nuclease ubiquitin article chemical reaction chemical reaction kinetics chemical structure energy yield hydrogen bond landscape predictive value protein conformation protein localization Deuterium Exchange Measurement Humans Micrococcal Nuclease Models, Molecular Peptides Plant Proteins Protein Conformation Protein Folding Thermodynamics Ubiquitin Ferreiro, Diego U. Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes |
| topic_facet |
Chymotrypsin inhibitor 2 Energy functions Energy landscape Exchange kinetics Exchange process Hydrogen bondings Hydrogen exchange Kinetic features Local stability Mechanistic interpretations Native-state protein Protein topology Site-specific Staphylococcal nuclease Structure-based Ubiquitin Amides Protein folding Proteins Hydrogen chymotrypsin inhibitor hydrogen nuclease ubiquitin article chemical reaction chemical reaction kinetics chemical structure energy yield hydrogen bond landscape predictive value protein conformation protein localization Deuterium Exchange Measurement Humans Micrococcal Nuclease Models, Molecular Peptides Plant Proteins Protein Conformation Protein Folding Thermodynamics Ubiquitin |
| 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. © 2011 American Chemical Society. |
| author |
Ferreiro, Diego U. |
| author_facet |
Ferreiro, Diego U. |
| author_sort |
Ferreiro, Diego U. |
| title |
Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes |
| 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 |
| publishDate |
2011 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00027863_v133_n43_p17463_Craig http://hdl.handle.net/20.500.12110/paper_00027863_v133_n43_p17463_Craig |
| work_keys_str_mv |
AT ferreirodiegou predictionofnativestatehydrogenexchangefromperfectlyfunneledenergylandscapes |
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1768541728322617344 |