Molecular dynamics free energy simulations of ATP:Mg²⁺ and ADP:Mg²⁺ using the polarisable force field AMOEBA

ATPases and GTPases are two important classes of protein that play critical roles in energy transduction, cellular signalling, gene regulation and catalysis. These proteins use cofactors such as nucleoside di and tri-phosphates (NTP, NDP) and can detect the difference between NDP and NTP which then induce different protein conformations. Mechanisms that drive proteins into the NTP or NDP conformation may depend on factors such as ligand structure and how Mg²⁺ coordinates with the ligand, amino acids in the pocket and water molecules. Here, we have used the advanced electrostatic and polarisable force field AMOEBA and molecular dynamics free energy simulations (MDFE) to examine the various binding mechanisms of ATP:Mg²⁺ and ADP:Mg²⁺. We compared the ATP:Mg²⁺ binding with previous studies using non-polarisable force fields and experimental data on the binding affinity. It was found that the total free energy of binding for ATP:Mg²⁺ (−7.00 $\pm$ 2.13 kcal/mol) is in good agreement with experimental values (−8.6 $\pm$ .2 kcal/mol) [1]. In addition, parameters for relevant protonation states of ATP, ADP, GTP and GDP have been derived. These parameters will allow for researchers to investigate biochemical phenomena involving NTP’s and NDP’s with greater accuracy than previous studies involving non-polarisable force fields.