Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme

Abstract

The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of approximately 200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations find that an Mg2+ cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or artificial placement of this Mg2+ into the product structure result in its swift expulsion from the active site. These findings are consistent with a concerted reaction mechanism in which C75 and hydrated Mg2+ act as general base and acid, respectively. Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized.

RNA dynamics: it is about time

“…Molecular dynamics (MD) simulations in combination with fluorescence studies have highlighted the role of cross-linking structural water molecules in the catalytic core dynamics of the hairpin ribozyme [32•] and have described conformational dynamics in the hepatitis delta virus (HDV) ribozyme core, suggesting plausible reaction trajectories for catalysis [33,34] that now can be tested by emerging quantum mechanical tools [35,36]. Only recently have advanced NMR techniques been employed to elucidate the conformational dynamics of a core element of a ribozyme, specifically the catalytic domain 5 of a group II intron [37].…”

“…While evidence is emerging that structural water molecules can mediate coupled molecular motions throughout a folded RNA core [32•] and that bound metal ions heavily modulate the electrostatic surface potential of RNA [33] and its conformational dynamics [48], the extent to which solvent dynamics couples with RNA dynamics at all timescales is still ill-understood. These open questions promise to yield many more surprising discoveries on RNA dynamics over years to come.…”

Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

“…[58][59][60][61] Accurate local positioning of bases is also important elsewhere, for example in the catalytic centers of ribozymes. 62,63 Local conformational variations are assumed to be primarily caused by base stacking forces and are of primary importance for indirect readout of proteins, sequence-dependent DNA elasticity, etc. Studies, experiments as well as theory, of local conformational variations turned out to be very difficult, as local conformational variations are associated with very subtle energy changes.…”

Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

“…[3][4][5][6][7][8][9][10][22][23][24][25][26][27][28][29][30][31][32] The AMBER force fields have also been successful in studies of RNA molecules, including those that exhibit a wide range of non-Watson-Crick base pairings, tertiary interactions, and complex backbone topologies. [33][34][35][36][37][38][39][40][41][42][43] These studies have also emphasized the importance of NAs' sugar-phosphate backbone flexibility, which is delimited by six main-chain torsion angles (designated as R through ), in addition to the five internal sugar torsions (denoted as τ 0 through τ 4 , which can be succinctly described by the puckering and the phase angle 44 ), and the glycosidic angle 45 (see Figure 1). Free duplex B-DNA frequently populates two distinct backbone conformational substates, referred to as B I and B II .…”