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Craig, P.O.; Lätzer, J.; Weinkam, P.; Hoffman, R.M.B.; Ferreiro, D.U.; Komives, E.A.; Wolynes, P.G. "Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes" (2011) Journal of the American Chemical Society. 133(43):17463-17472
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Abstract:

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.

Registro:

Documento: Artículo
Título:Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes
Autor:Craig, P.O.; Lätzer, J.; Weinkam, P.; Hoffman, R.M.B.; Ferreiro, D.U.; Komives, E.A.; Wolynes, P.G.
Filiación:Department of Chemistry and Biochemistry, University of California at San Diego (UCSD), 9500 Gilman Drive, San Diego, CA 92093-0374, United States
Center for Theoretical Biological Physics (CTBP), University of California at San Diego (UCSD), 9500 Gilman Drive, San Diego, CA 92093-0374, United States
BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, United States
Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158-2330, United States
Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA-CONICET), Intendente Guiraldes 2160, Buenos Aires C1428EGA, Argentina
Department of Chemistry, Rice University, 6100 Main St., Houston, TX 77005, United States
Palabras clave: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
Año:2011
Volumen:133
Número:43
Página de inicio:17463
Página de fin:17472
DOI: http://dx.doi.org/10.1021/ja207506z
Título revista:Journal of the American Chemical Society
Título revista abreviado:J. Am. Chem. Soc.
ISSN:00027863
CODEN:JACSA
CAS:hydrogen, 12385-13-6, 1333-74-0; nuclease, 9026-81-7; ubiquitin, 60267-61-0; Micrococcal Nuclease, 3.1.31.1; Peptides; Plant Proteins; Ubiquitin; chymotrypsin inhibitor 2
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00027863_v133_n43_p17463_Craig

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Citas:

---------- APA ----------
Craig, P.O., Lätzer, J., Weinkam, P., Hoffman, R.M.B., Ferreiro, D.U., Komives, E.A. & Wolynes, P.G. (2011) . Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes. Journal of the American Chemical Society, 133(43), 17463-17472.
http://dx.doi.org/10.1021/ja207506z
---------- CHICAGO ----------
Craig, P.O., Lätzer, J., Weinkam, P., Hoffman, R.M.B., Ferreiro, D.U., Komives, E.A., et al. "Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes" . Journal of the American Chemical Society 133, no. 43 (2011) : 17463-17472.
http://dx.doi.org/10.1021/ja207506z
---------- MLA ----------
Craig, P.O., Lätzer, J., Weinkam, P., Hoffman, R.M.B., Ferreiro, D.U., Komives, E.A., et al. "Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes" . Journal of the American Chemical Society, vol. 133, no. 43, 2011, pp. 17463-17472.
http://dx.doi.org/10.1021/ja207506z
---------- VANCOUVER ----------
Craig, P.O., Lätzer, J., Weinkam, P., Hoffman, R.M.B., Ferreiro, D.U., Komives, E.A., et al. Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes. J. Am. Chem. Soc. 2011;133(43):17463-17472.
http://dx.doi.org/10.1021/ja207506z