Peptide Bond Formation Mechanism Catalyzed by Ribosome
Impacte
Scholar |
Altres documents de l'autoria: Świderek, Katarzyna; Martí Forés, Sergio; Tuñón, Iñaki; Moliner, Vicent; Bertran, Joan
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Mostra el registre complet de l'elementcomunitat-uji-handle:10234/9
comunitat-uji-handle2:10234/7013
comunitat-uji-handle3:10234/8638
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http://dx.doi.org/10.1021/jacs.5b05916 |
Metadades
Títol
Peptide Bond Formation Mechanism Catalyzed by RibosomeData de publicació
2015Editor
American Chemical SocietyISSN
0002-7863; 1520-5126Cita bibliogràfica
ŚWIDEREK, Katarzyna, et al. Peptide Bond Formation Mechanism Catalyzed by Ribosome. Journal of the American Chemical Society, 2015, vol. 137, no 37, p. 12024-12034.Tipus de document
info:eu-repo/semantics/articleVersió de l'editorial
http://pubs.acs.org/doi/full/10.1021/jacs.5b05916Versió
info:eu-repo/semantics/publishedVersionParaules clau / Matèries
Resum
In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM ... [+]
In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, where the chemical system has been described by the M06-2X functional and the environment by means of the AMBER force field. According to our results, the most favorable mechanism in the ribosome would proceed through an eight-membered ring transition state, involving a proton shuttle mechanism through the hydroxyl group of the sugar and a water molecule. This transition state is similar to that described for the reaction in solution (J. Am. Chem. Soc. 2013, 135, 8708–8719), but the reaction mechanisms are noticeably different. Our simulations reproduce the experimentally determined catalytic effect of ribosome that can be explained by the different behavior of the two environments. While the solvent reorganizes during the chemical process involving an entropic penalty, the ribosome is preorganized in the formation of the Michaelis complex and does not suffer important changes along the reaction, dampening the charge redistribution of the chemical system. [-]
Publicat a
American Chemical Society, 2015, vol. 137, no 37Drets d'accés
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