How Mg2+ ion and water network affect the stability and structure of non-Watson–Crick base pairs in E. coli loop E of 5S rRNA: a molecular dynamics and reference interaction site model (RISM) study

The non-Watson–Crick (non-WC) base pairs of Escherichia coli loop E of 5S rRNA are stabilized by Mg2+ ions through water-mediated interaction. It is important to know the synergic role of Mg2+ and the water network surrounding Mg2+ in stabilizing the non-WC base pairs of RNA. For this purpose, free energy change of the system is calculated using molecular dynamics (MD) simulation as Mg2+ is pulled from RNA, which causes disturbance of the water network. It was found that Mg2+ remains hexahydrated unless it is close to or far from RNA. In the pentahydrated form, Mg2+ interacts directly with RNA. Water network has been identified by two complimentary methods; MD followed by a density-based clustering algorithm and three-dimensional-reference interaction site model. These two methods gave similar results. Identification of water network around Mg2+ and non-WC base pairs gives a clue to the strong effect of water network on the stability of this RNA. Based on sequence analysis of all Eubacteria 5s rRNA, we pr...