Free Energy Landscape of Magnesium Chelation Reveals Dynamic Pre-Chelate Complexes Stabilized by Meta-Sphere RNA-Ion Coordination

Abstract

Magnesium ions (Mg{superscript 2}) play a critical role in RNA structure stabilization by forming various coordinated complexes, preferentially interacting with the backbone phosphate groups. Using extensive atomistic and free energy simulations across simple models and RNA structures of varying complexity, we characterized critical components of the RNA-ion-atmosphere. Radial distribution function analysis reveals distinct peak positions for direct (inner) and solvent-separated (outer-sphere) Mg2+-phosphate coordination layers, aligning with solution X-ray diffraction data. Addressing forcefield limitations, the free energy calculations quantify the kinetic barriers for Mg{superscript 2}-phosphate binding, benchmarking parameters against {superscript 2}Mg NMR measurement. Free energy calculations further explore Mg{superscript 2} chelation with bi-phosphate coordinated Mg2+ systems, identifying a dynamic ensemble of pre-chelate complexes, in addition to a chelated and outer-sphere hexa-hydrated state of Mg2+. In the pre-chelated states, Mg{superscript 2} maintains one inner-sphere interaction while simultaneously coordinating with multiple other phosphates in a solvent-separated manner, referred to as meta-sphere coordination. The pre-chelated complexes from different solvents-separated layers undergo a frequent transition and mediate a unique oxygen exchange mechanism between phosphate and water ligands. Insights into the free energy landscape of SAM-I RNA aptamer further emphasize the significance of pre-chelate complexes for complex RNA structure stabilization, where a number of such solvent-separated dynamic phosphate groups are found to influence Mg2+-RNA coordination. The comprehensive thermodynamic analysis of Mg{superscript 2} chelation and quantitative characterizations of various RNA-ion coordination modes, including this new meta-sphere coordination, provides vital insights for advancing RNA modelling and experimental exploration of complex phosphate networks in the RNA structures.