Extraordinary rates of transition metal ion-mediated ribozyme catalysis

Roychowdhury-Saha, Manami; Burke, Donald H.

doi:10.1261/rna.128906

Cited by 83 publications

(120 citation statements)

References 35 publications

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“…Moreover, the mechanistic model for metal ion binding proposed here that involves interaction with 2′OH of G8, is consistent with kinetic analysis indicating that the pK a of the general acid is down-shifted by around 4-7 pK a units in a metal-dependent manner, correlated with the metal pK a . 59 The simulation results suggest that the Mg 2+ interacts strongly with the 2′OH of G8 in the early TS mimic and could contribute to a significant lowering of the pK a value, and in the late TS mimic the G8 2′OH is hydrogen bonded to the leaving group and poised to act as a general acid catalyst. The Mg 2+ ion may additionally play a direct role in stabilizing the negative charge accumulated in the leaving group in the late TS, and when the proton from the G8 2′OH is ultimately transferred, the coordination of Mg 2+ is positioned to revert back to stabilize the resulting G8 2′-alkoxide.…”

Section: Mechanistic Interpretationmentioning

confidence: 88%

Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from Molecular Simulation

et al. 2008

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Molecular dynamics simulations have been performed to investigate the role of Mg 2+ in the fulllength hammerhead ribozyme cleavage reaction. In particular, the aim of this work is to characterize the binding mode and conformational events that give rise to catalytically active conformations and stabilization of the transition state. Toward this end, a series of eight 12 ns molecular dynamics simulations have been performed with different divalent metal binding occupations for the reactant, early and late transition state using recently developed force field parameters for metal ions and reactive intermediates in RNA catalysis. In addition, hybrid QM/ MM calculations of the early and late transition state were performed to study the proton-transfer step in general acid catalysis that is facilitated by the catalytic Mg 2+ ion. The simulations suggest that Mg 2+ is profoundly involved in the hammerhead ribozyme mechanism both at structural and catalytic levels. Binding of Mg 2+ in the active site plays a key structural role in the stabilization of stem I and II and to facilitate formation of near attack conformations and interactions between the nucleophile and G12, the implicated general base catalyst. In the transition state, Mg 2+ binds in a bridging position where it stabilizes the accumulated charge of the leaving group while interacting with the 2′OH of G8, the implicated general acid catalyst. The QM/MM simulations provide support that, in the late transition state, the 2′OH of G8 can transfer a proton to the leaving group while directly coordinating the bridging Mg 2+ ion. The present study provides evidence for the role of Mg 2+ in hammerhead ribozyme catalysis. The proposed simulation model reconciles the interpretation of available experimental structural and biochemical data, and provides a starting point for more detailed investigation of the chemical reaction path with combined QM/MM methods.

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Section: Mechanistic Interpretationmentioning

confidence: 88%

Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from Molecular Simulation

et al. 2008

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“…Indeed, an in vitro selection experiment identified numerous additional tertiary interactions not found in biology which also enhanced the cleavage rate (14). Analysis of one of these indicated that it promoted cleavage hundreds of times faster than minimal hammerheads (15).…”

mentioning

confidence: 99%

Catalytic Diversity of Extended Hammerhead Ribozymes

Shepotinovskaya

Uhlenbeck

2008

Biochemistry

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Chimeras of the well characterized minimal hammerhead 16 and nine extended hammerheads derived from natural viroids and satellite RNAs were constructed with the goal of assessing whether their very different peripheral tertiary interactions modulate their catalytic properties. For each chimera, three different assays were used to determine the rate of cleavage and the fraction of full length hammerhead at equilibrium and thereby deduce the elemental cleavage (k 2 ) and ligation (k -2 ) rate constants. The nine chimeras were all more active than minimal hammerheads and showed a very broad range of catalytic properties, with values of k 2 varying by 750-fold and k -2 by 100-fold. At least two of the hammerheads showed an altered dependence of k obs on magnesium concentration. Since much less catalytic diversity is observed among minimal hammerheads that lack the tertiary interactions, a possible role for the different tertiary interaction is to modulate the hammerhead cleavage properties in viroids. For example, differing hammerhead cleavage and ligation rates could affect the steady state concentrations of linear, circular, and polymeric genomes in infected cells.

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“…This leads to reduced solvent exchange rates and increased solvation enthalpy, but at the same time also makes it a most suitable interaction partner for the non-bridging phosphoryl oxygens of the nucleic acid backbone, allowing them to pack particularly closely [51], which is a prerequisite for the physiological folding of large RNAs. In accordance, a nearly perfect correlation between the cleavage rate of the hammerhead ribozyme [52,53] and the metal ion affinity towards phosphate monoesters can be established [34]. Nevertheless, such a correlation cannot be established, for example, for the glmS ribozyme [54], indicating a crucial influence of further ligand sites.…”

Section: Dominance Of Mg 2+mentioning

confidence: 83%

“…Zn 2+ is also very thiophilic and more similar in size to Mg 2+ , but engages in variable coordination geometries [87]. Tl + has been employed as a substitute for K + , making use either of its thiophilicity or of the abundant spin 1/2 nucleus of 205 [52,53] or Ca 2+ in the case of the antigenomic form of the hepatitis delta virus (HDV) ribozyme [88]. While in the case of the two Hammerhead ribozymes, the observed cleavage rates correlate with the respective phosphate affinity of the metal ion applied [34], in the case of the glmS ribozyme, no such correlation is observed [54].…”

Section: Influences Of Metal Ions Other Than Mgmentioning

confidence: 99%

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

Pechlaner

Sigel

2011

Metal Ions in Life Sciences

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Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.

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Extraordinary rates of transition metal ion-mediated ribozyme catalysis

Cited by 83 publications

References 35 publications

Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from Molecular Simulation

Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from Molecular Simulation

Catalytic Diversity of Extended Hammerhead Ribozymes

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

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Extraordinary rates of transition metal ion-mediated ribozyme catalysis

Cited by 83 publications

References 35 publications

Role of Mg2+ in Hammerhead Ribozyme Catalysis from Molecular Simulation

Role of Mg2+ in Hammerhead Ribozyme Catalysis from Molecular Simulation

Catalytic Diversity of Extended Hammerhead Ribozymes

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

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Product

Resources

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Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from Molecular Simulation

Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from Molecular Simulation