Influence of Magnesium Ion Binding on the Adenosine Diphosphate Structure and Dynamics, Investigated by ³¹P NMR and Molecular Dynamics Simulations

Magnesium (Mg²⁺) is the most abundant divalent cation in the cell and is essential to nearly every biochemical reaction involving adenosine triphosphate (ATP) and its lower energy counterpart, adenosine diphosphate (ADP). In this work, we examine the solution dynamics of ADP at different concentrations and record the changes thereof due to the presence of Mg²⁺ ions. Relaxation and diffusion experiments were performed on a range of ADP solutions with increasing magnesium concentration. The most significant changes of both relaxation and diffusion behaviors are observed when adding Mg²⁺ up to 0.5 ADP equivalent (eq), with most of the changes complete at 1 eq. Molecular dynamics simulations also show a significant structure introduced by Mg²⁺ with very stable pyramidal coordination with the phosphate oxygens. A more extended structure found in the presence of Mg²⁺ is consistent with the experimental slowing of diffusion and an increase in the spin-lattice relaxation rate. We do not observe direct evidence of aggregation in solution, although translational diffusion is slowed down significantly at higher concentrations (while solvent diffusion remains constant).