title: 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 [Formula: see text]. 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.
authors.affiliation: a School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi 110067 , India.
authors.forename: Sudhanshu
authors.initials: S
authors.lastname: Shanker
authors.affiliation: a School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi 110067 , India.
authors.forename: Pradipta
authors.initials: P
authors.lastname: Bandyopadhyay
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D001665:Binding Sites; D002413:Cations, Divalent; D004926:Escherichia coli / Q000737:chemistry; D006860:Hydrogen Bonding; D007700:Kinetics; D008274:Magnesium / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D020871:RNA Stability; D012329:RNA, Bacterial / Q000737:chemistry*; D012341:RNA, Ribosomal, 5S / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D002413:Cations, Divalent; D012329:RNA, Bacterial; D012341:RNA, Ribosomal, 5S; D014867:Water; D008274:Magnesium
keywords: Mg2+ ion; PMF; RISM; RNA with non-WC bases; water network