title: A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant.
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.
authors.affiliation: Departament de Química, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
authors.forename: Ayax
authors.initials: A
authors.lastname: Pérez-Gallegos
authors.forename: Mireia
authors.initials: M
authors.lastname: Garcia-Viloca
authors.forename: Àngels
authors.initials: À
authors.lastname: González-Lafont
authors.forename: José M
authors.initials: JM
authors.lastname: Lluch
mesh_terms: D000818:Animals; D002384:Catalysis; D020134:Catalytic Domain; D017868:Cyclic AMP-Dependent Protein Kinases / Q000737:chemistry* / Q000235:genetics; D004734:Energy Metabolism; D008962:Models, Theoretical; D009154:Mutation; D009842:Oligopeptides / Q000737:chemistry / Q000235:genetics; D010766:Phosphorylation; D011789:Quantum Theory; D013379:Substrate Specificity
chemical_list: D009842:Oligopeptides; C037642:kemptide; D017868:Cyclic AMP-Dependent Protein Kinases