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.
Original language | English (US) |
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Pages (from-to) | 1077-1091 |
Number of pages | 15 |
Journal | Journal of Computer-Aided Molecular Design |
Volume | 28 |
Issue number | 11 |
DOIs | |
State | Published - Nov 2014 |
Externally published | Yes |
Keywords
- Enzyme catalysis
- Enzyme models
- Protein kinase
- QM/MM calculations
- Reaction mechanisms
ASJC Scopus subject areas
- Drug Discovery
- Computer Science Applications
- Physical and Theoretical Chemistry