How Does the cAMP-Dependent Protein Kinase Catalyze the Phosphorylation Reaction:  An ab Initio QM/MM Study

• Published in: Journal of the American Chemical Society 2005-02, Vol.127 (5), p.1553-1562
• Main Authors: Cheng, Yuhui, Zhang, Yingkai, McCammon, J. Andrew
• Format: Article
• Language: English
• Subjects: Adenosine Triphosphate - chemistry; Adenosine Triphosphate - metabolism; Amino Acid Sequence; Binding Sites; Biological and medical sciences; Catalysis; Cyclic AMP-Dependent Protein Kinases - chemistry; Cyclic AMP-Dependent Protein Kinases - metabolism; Fundamental and applied biological sciences. Psychology; Kinetics; Magnesium - chemistry; Magnesium - metabolism; Mechanisms. Catalysis. Electron transfer. Models; Models, Molecular; Molecular biophysics; Molecular Sequence Data; Phosphorylation; Physical chemistry in biology; Quantum Theory; Static Electricity
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja0464084

We have carried out density functional theory QM/MM calculations on the catalytic subunit of cAMP-dependent protein kinase (PKA). The QM/MM calculations indicate that the phosphorylation reaction catalyzed by PKA is mainly dissociative, and Asp166 serves as the catalytic base to accept the proton delivered by the substrate peptide. Among the key interactions in the active site, the Mg2+ ions, glycine rich loop, and Lys72 are found to stabilize the transition state through electrostatic interactions. On the other hand, Lys168, Asn171, Asp184, and the conserved waters bound to Mg2+ ions do not directly contribute to lower the energy barrier of the phosphorylation reaction, and possible roles for these residues are proposed. The QM/MM calculations with different QM/MM partition schemes or different initial structures yield consistent results. In addition, we have carried out 12 ns molecular dynamics simulations on both wild type and K168A mutated PKA, respectively, to demonstrate that the catalytic role of Lys168 is to keep ATP and substrate peptide in the near-attack reactive conformation.