Assessing the effect of calcium and magnesium ions in the structural stability of the protein kinase A through molecular dynamics simulations

Abstract

Protein kinase A (PKA) is part of the big family of protein kinases, whose role consists in catalyzing the transfer of a phosphate group from an ATP molecule to a peptide substrate. While Mg2+ is the preferred cofactor in kinases, it has been proven experimentally than other divalent metals such as Ca2+ can also promote the phosphoryl transfer but not with the same efficiency achieved with Mg2+. Recent crystallographic and kinetic data for PKA have shown that the presence of Ca2+ would allow the transfer of a phosphate group from ATP to the substrate SP20 but the products would be trapped at the active site of the enzyme. Based on these experimental results, the main goal of this research was to determine how the retention of the products occurs and to identify which interactions in the presence of Ca2+ overstabilize the final state of the catalysis in PKA. In order to get a better understanding of these events, PKA in its product state was evaluated through molecular dynamics simulations using two previously crystallized systems, one using the ion Mg2+ as a cofactor, and other using the Ca2+ ion. The results obtained suggest that the stable coordination of seven ligands around Ca2+ not only allows to the phosphorylated substrate to coordinate Ca1, but also Ca2, interaction not present in the crystal structure. By means of structural analysis, it was corroborated that in PKA with Ca2+ there is a reduced mobility of the glycine-rich loop, moiety whose function is to cover the active site by hydrogen bonds that interact with the phosphorylated substrate. In this way, it was identified that the residues Thr51 and Ser53 located in this loop form hydrogen bonds with the substrate pSP20 which are more stable in the system with Ca2+ compared to Mg2+. These results were supported by binding energy calculations, using the MMPBSA method. Overall, this information provides a better understanding of the structural mechanism by which Ca2+ inhibits the activity of protein kinase A and gives new insights into the possible regulatory mechanism of Ca2+ on protein kinases.