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

Abstract

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 propose that hexahydrated Mg²⁺ is an integral part of this RNA and geometry of base pairs surrounding it adjust to accommodate the $\text{Mg}{({\text{H}}_2\text{O})}_6^{2+}$. Overall the findings from this work can help in understanding the basis of the complex structure and stability of RNA with non-WC base pairs.

Keywords:

• RNA with non-WC bases
• Mg²⁺ ion
• PMF
• water network
• RISM

Acknowledgements

The authors would like to thank Dr Dhananjay Bhattacharyya for introducing them to the area of RNA with non-WC base pairs. Sudhanshu Shanker acknowledges DBT-BINC for the financial support.