Structure and dynamics of adenosine triphosphate at near-molar concentrations

Adenosine-5'-triphosphate (ATP) can accumulate to near-molar concentrations within specific biological compartments, influencing a diverse range of cellular processes. However, its structural organization and molecular dynamics under these crowded conditions remain poorly understood. In this study, ATP gel systems containing ATP at near-molar concentrations were prepared and investigated using solid-state nuclear magnetic resonance (ssNMR) spectroscopy and all-atom molecular dynamics (MD) simulations. The ssNMR results reveal that ATP undergoes spontaneous hydrolysis and yields adenosine diphosphate (ADP) and inorganic phosphate (Pi). Combined ssNMR and MD analyses further suggest local purine-stacked and ion-mediated "tail-to-tail" arrangements of ATP/ADP molecules, in which cationic clusters attract anionic phosphate groups and restrict terminal phosphate mobility. The suppression of ATP β-phosphate signals is attributed to reduced hydration arising from steric hindrance and limited solvent accessibility. A comparison of ATP-HCl and ATP-HAc gels demonstrates that both ATP hydrolysis level and molecular dynamics are strongly modulated by anion identity. MD simulations further reveal a modest increase in Mg²⁺-mediated intermolecular bridging and a slightly higher local mass density in ATP-HCl gels. These results provide molecular-level insight into ATP behavior at high concentrations and highlight the critical role of anion species in regulating ATP stability and organization.