Mg²⁺ Sensing by an RNA Fragment: Role of Mg²⁺-Coordinated Water Molecules

Abstract

RNA molecules selectively bind to specific metal ions to populate their functional active states making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied the role of different metal ions (Mg 2+ , Ca 2+ and K + ) in the folding of a small RNA hairpin motif (5 -ucCAAAga-3 ) using unbiased all-atom molecular dynamics simulations. The advantage in studying this small system is that it requires specific binding of a single metal ion to fold to its native state. We find that even for this small RNA, the folding free energy surface (FES) is multidimensional as different metal ions present in the solution can simultaneously facilitate folding. The FES shows that specific binding of a metal ion is indispensable for its folding. We further show that in addition to the negatively charged phosphate groups, spatial organization of electronegative nucleobase atoms drive the site specific binding of the metal ion. Even though the binding site cannot discriminate between different metal ions, RNA folds efficiently only in Mg 2+ solution. We show that the rigid network of Mg 2+ coordinated water molecules facilitate the formation of important interactions in the transition state. The other metal ions such as K + and Ca 2+ cannot facilitate the formation of such interactions. These results allow us to hypothesize possible metal sensing mechanisms in large metallo-riboswitches and they also provide useful insights for the design of appropriate collective variables for studying large RNA molecules using enhanced sampling methods.

Local RNA Structure, Ion Hydration Shell and the Energy Barrier for Water Exchange from the Ion Hydration Shell Determine the Mechanism of Ion Condensation on Specific RNA Sites

“…(3) The ion solvation shell's rigidity determines the ion's interaction with the RNA atoms in the binding pocket. 12 These principles can be utilized in the rational design of RNA sequences, which selectively bind to toxic metal ions present in low concentrations, 47 that can be used in developing sensors of toxic ions.…”

“…10 The cations do not condense homogeneously over the polyanionic RNA backbone. [11][12][13][14] Non-coding RNAs selectively recognize metal ions for binding in specific sites, especially in metalloriboswitches. 15,16 Metalloriboswitches are located at the 5 ′ -UTR of mRNAs encoding ion uptake or efflux channels in bacteria.…”

“…[21][22][23][24][25][26][27][28] Computational studies complement such experiments as they can overcome the limitations imposed by the fluctuating nature of the ionic environment around RNA. 11,12,[29][30][31][32][33] The consensus is that hydrated metal ions can interact with the electronegative RNA atoms in two modes, viz. inner shell and outer shell (Figure 1E).…”

“…Other than a few exceptions, 30,31 ion-RNA interactions are usually studied with isolated RNA structural motifs, such as dinucleotide, 32 helix 29 or hairpin loop. 12 In a large RNA structure, such isolated motifs interact with each other but under some structural constraints. Hence, the structural flexibility of the isolated motifs gets restricted.…”

Riboswitch Folds to Holo-Form Like Structure Even in the Absence of Cognate Ligand at High Mg2+ Concentration

“…Whereas in site-specific binding, Mg 2+ bind in the pockets created by the specific arrangement of nucleotides and aid in the stabilization of secondary and tertiary structures. 6,7 However, for the functioning of riboswitches, in addition to the Mg 2+ , cognate ligand binding is equally essential. The cognate ligand binding to the AD leads to structural changes in both the AD and EP domains, which signal the attenuation or initiation of the transcription or translation process.…”