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Artículo

Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa’s of proteins as a function of pH. Test on a large set of proteins

Vorobjev, Yury N.; Scheraga, Harold A.; Vila, Jorge AlbertoIcon
Fecha de publicación: 24/02/2018
Editorial: Adenine Press
Revista: Journal Of Biomolecular Structure & Dynamics
ISSN: 0739-1102
Idioma: Inglés
Tipo de recurso: Artículo publicado
Clasificación temática:
Física Atómica, Molecular y Química

Resumen

A computational method, to predict the pKa values of the ionizable residues Asp, Glu, His, Tyr, and Lys of proteins, is presented here. Calculation of the electrostatic free-energy of the proteins is based on an efficient version of a continuum dielectric electrostatic model. The conformational flexibility of the protein is taken into account by carrying out molecular dynamics simulations of 10 ns in implicit water. The accuracy of the proposed method of calculation of pKa values is estimated from a test set of experimental pKa data for 297 ionizable residues from 34 proteins. The pKa-prediction test shows that, on average, 57, 86, and 95% of all predictions have an error lower than 0.5, 1.0, and 1.5 pKa units, respectively. This work contributes to our general understanding of the importance of protein flexibility for an accurate computation of pKa, providing critical insight about the significance of the multiple neutral states of acid and histidine residues for pKa-prediction, and may spur significant progress in our effort to develop a fast and accurate electrostatic-based method for pKa-predictions of proteins as a function of pH.
Palabras clave: Continuum Dielectric Model , Molecular Dynamics , Pka-Predictions , Protein Ionization
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info:eu-repo/semantics/openAccess Excepto donde se diga explícitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
Identificadores
URI: http://hdl.handle.net/11336/66696
DOI: https://doi.org/10.1080/07391102.2017.1288169
URL: https://www.tandfonline.com/doi/abs/10.1080/07391102.2017.1288169
Colecciones
Articulos(IMASL)
Articulos de INST. DE MATEMATICA APLICADA DE SAN LUIS
Citación
Vorobjev, Yury N.; Scheraga, Harold A.; Vila, Jorge Alberto; Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa’s of proteins as a function of pH. Test on a large set of proteins; Adenine Press; Journal Of Biomolecular Structure & Dynamics; 36; 3; 24-2-2018; 561-574
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