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

ABSTRACT: ATPases and GTPases are two important classes of protein that play critical roles in energy transduction, cellular signaling, 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 polarizable 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:Mg

SUBMITTER: Walker B 

PROVIDER: S-EPMC8375395 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature