Insights into the Phosphoryl-Transfer Mechanism of cAMP-Dependent Protein Kinase from Quantum Chemical Calculations and Molecular Dynamics Simulations

To investigate the molecular details of the phosphoryl-transfer mechanism catalyzed by cAMP-dependent protein kinase, we performed quantum mechanical (QM) calculations on a cluster model of the active site and molecular dynamics (MD) simulations of a ternary complex of the protein with Mg₂ATP and a 20-residue peptide substrate. Overall, our theoretical results confirm the participation of the conserved aspartic acid, Asp₁₆₆, as an acid/base catalyst in the reaction mechanism catalyzed by protein kinases. The MD simulation shows that the contact between the nucleophilic serine side chain and the carboxylate group of Asp₁₆₆ is short and dynamically stable, whereas the QM study indicates that an Asp₁₆₆-assisted pathway is structurally and energetically feasible and is in agreement with previous experimental results.