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A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant

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Abstract

Here we analyze in detail the possible catalytic role of the associative mechanism in the γ-phosphoryl transfer reaction in the catalytic subunit of the mammalian cyclic AMP-dependent protein kinase (PKA) enzyme and its D166A mutant. We have used a complete solvated model of the ATP-Mg2-Kemptide/PKA system and good levels of theory (B3LYP/MM and MP2/MM) to determine several potential energy paths from different MD snapshots, and we present a deep analysis of the interaction distances and energies between ligands, metals and enzyme residues. We have also tested the electrostatic stabilization of the transition state structures localized herein with the charge balance hypothesis. Overall, the results obtained in this work reopen the discussion about the plausibility of the associative reaction pathway and highlight the proposed role of the catalytic triad Asp166–Lys168–Thr201.

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Acknowledgments

This work was supported by the “Ministerio de Economía y Competitividad” through Project CTQ2011-24292 and by the “Generalitat de Catalunya” through Project 2009SGR409. Use of computational facilities at the “Centre de Serveis Científics i Acadèmics de Catalunya (CESCA)” is also gratefully acknowledged. Ayax Pérez-Gallegos acknowledges “Consejo Nacional de Ciencia y Tecnología (CONACYT)” Supporting Grant 213582.

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Authors and Affiliations

  1. Departament de Química, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain

    Ayax Pérez-Gallegos, Mireia Garcia-Viloca, Àngels González-Lafont & José M. Lluch

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  1. Ayax Pérez-Gallegos
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  2. Mireia Garcia-Viloca
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Correspondence to Àngels González-Lafont.

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Pérez-Gallegos, A., Garcia-Viloca, M., González-Lafont, À. et al. A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant. J Comput Aided Mol Des 28, 1077–1091 (2014). https://doi.org/10.1007/s10822-014-9786-3

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