Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase
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Otros documentos de la autoría: Świderek, Katarzyna; Tuñón, Iñaki; Martí Forés, Sergio; Moliner, Vicent
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http://dx.doi.org/10.1021/cs501704f |
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Título
Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate DehydrogenaseFecha de publicación
2015Editor
ACS PublicationsCita bibliográfica
SWIDEREK, Katarzyna; TUÑÓN, Iñaki; MARTÍ FORÉS, Sergio; MOLINER IBÁÑEZ, Vicente. Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase. ACS Catalysis (2015), v. 2, n. 5, pp. 1172-1185Tipo de documento
info:eu-repo/semantics/articleVersión de la editorial
http://pubs.acs.org/doi/abs/10.1021/cs501704fPalabras clave / Materias
Resumen
In the past decade, L-Lactate Dehydrogenase (LDH) has become an extremely useful marker in both clinical diagnosis and in monitoring the course of many human diseases. It has been assumed since the 1980s that the full ... [+]
In the past decade, L-Lactate Dehydrogenase (LDH) has become an extremely useful marker in both clinical diagnosis and in monitoring the course of many human diseases. It has been assumed since the 1980s that the full catalytic process of LDH starts with the binding of the cofactor and the substrate followed by the enclosure of the active site by a mobile loop of the protein before the reaction takes place. In this paper, we show that the chemical step of the LDH-catalyzed reaction can proceed within the open loop conformation, and the different reactivity of the different protein conformations would be in agreement with the broad range of rate constants measured in single-molecule spectrometry studies. Starting from a recently solved X-ray diffraction structure that presented an open loop conformation in two of the four chains of the tetramer, QM/MM free energy surfaces have been obtained at different levels of theory. Depending on the level of theory used to describe the electronic structure, the free energy barrier for the transformation of pyruvate into lactate with the open conformation of the protein varies between 12.9 and 16.3 kcal/mol, after quantizing the vibrations and adding the contributions of recrossing and tunneling effects. These values are very close to the experimentally deduced one (14.2 kcal·mol–1) and ∼2 kcal·mol–1 smaller than the one obtained with the closed loop conformer. Calculation of primary KIEs and IR spectra in both protein conformations are also consistent with our hypothesis and in agreement with experimental data. Our calculations suggest that the closure of the active site is mainly required for the inverse process—the oxidation of lactate to pyruvate. According to this hypothesis, H4-type LDH enzyme molecules should have a better ability to close the mobile loop than the M4-type LDH molecules. [-]
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ACS Catalysis (2015), v. 2, n. 5Derechos de acceso
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