Retained Stability of the RNA Structure in DNA Packaging Motor with a Single Mg²⁺ Ion Bound at the Double Mg-Clamp Structure

It has been known that the binding of two Mg2+ ions to the phosphate groups of RNA is essential for enhancing the stability of a three-way junction oligomeric prohead RNA (3WJ-pRNA). Here, we investigate the coupling between binding of two Mg2+ ions and the stability of the complex structure by calculating the rupture force of 3WJ-pRNA using steered molecular dynamics simulations. Our simulations showed that the mechanical stability of the pRNA structure is largely retained with a single Mg2+ ion bound. Because of a strong electrostatic repulsion between the adjacent Mg2+ ions, the rupture force with two Mg2+ ions bound is smaller than the sum of the rupture forces with either one of Mg2+ ions bound. Our results suggest that binding of the second Mg2+ ion could be redundant for maintaining the rigidity of 3WJ-pRNA, which allows 3WJ-pRNA to have a flexible working range of Mg2+ concentration in a cell.