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

© 2014 Springer International Publishing Switzerland. 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-Mg<inf>2</inf>-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.
Original languageEnglish
Pages (from-to)1077-1091
JournalJournal of Computer-Aided Molecular Design
Volume28
Issue number11
DOIs
Publication statusPublished - 1 Jan 2014

Keywords

  • Enzyme catalysis
  • Enzyme models
  • Protein kinase
  • QM/MM calculations
  • Reaction mechanisms

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