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

Abstract

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.