Ribozyme Mechanisms

Takagi, Yoko; Ikeda, Yutaka; Taira, Kazunari

doi:10.1007/b13783

Cited by 37 publications

(46 citation statements)

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“…In this way, the Mg 2+ provides electrostatic stabilization of the accumulating charge of the leaving group (i.e., a Lewis acid catalyst). [7] At the same time, the 2′OH of G8 forms a hydrogen bond with the leaving group O 5′ and is positioned to act as a general acid catalyst (Figure 2, right).…”

Section: In the Late Ts The Mg 2+ Ion Can Act As A Lewis Acid Catalymentioning

confidence: 99%

Insight into the Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from X-ray Crystallography and Molecular Dynamics Simulation

López

Martick

et al. 2007

J. Chem. Theory Comput.

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Results of a series of 12 ns molecular dynamics (MD) simulations of the reactant state (with and without a Mg 2+ ion), early and late transition state mimics are presented based on a recently reported crystal structure of a full-length hammerhead RNA. The simulation results support a catalytically active conformation with a Mg 2+ ion bridging the A9 and scissile phosphates. In the reactant state, the Mg 2+ spends significant time closely associated with the 2′OH of G8, but remains fairly distant from the leaving group O 5′ position. In the early TS mimic simulation, where the nucleophilic O 2′ and leaving group O 5′ are equidistant from the phosphorus, the Mg 2+ ion remains tightly coordinated to the 2′OH of G8, but is positioned closer to the O 5′ leaving group, stabilizing the accumulating charge. In the late TS mimic simulation, the coordination around the bridging Mg 2+ ion undergoes a transition whereby the coordination with the 2′OH of G8 is replace by the leaving group O 5′ that has developed significant charge. At the same time, the 2′OH of G8 forms a hydrogen bond with the leaving group O 5′ and is positioned to act as a general acid catalyst. This work represents the first reported simulations of the full-length hammerhead structure and TS mimics, and provides direct evidence for the possible role of a bridging Mg 2+ ion in catalysis that is consistent with both crystallographic and biochemical data.The hammerhead ribozyme [1] is an archetype system to study RNA catalysis. [2,3] A detailed understanding of the hammerhead mechanism provides insight into the inner workings of more complex cellular catalytic RNA machinery such as the ribosome, and ultimately may aid the rational design of new medical therapies [4] and biotechnology. [5,6] Despite a tremendous amount of experimental and theoretical effort, [1,2,7,8] the details of the hammerhead ribozyme mechanism have been elusive. In particular, one of the main puzzles involves the apparent inconsistency between the interpretation of thio effect experiments [9,10] and mutational data [8] with available crystallographic structural information of the minimal hammerhead sequence. [11,12,13] Results from the biochemical experiments suggest that a pH-dependent conformational change, inconsistent with crystallographic data, [11,12,13] must precede or be concomitant with the catalytic chemical step. This includes a possible metal ion bridge between the A9 and scissile phosphates that in previous crystal structures were ~20 Å apart. Moreover, the function of the 2′OH group of G8 remains unclear. A stable Mg 2+ ion bridge between the A9 and scissile phosphates is formed in the catalytically active conformationThe simulation results support a catalytic role for a Mg 2+ ion bridging the A9 and scissile phosphates. In the simulations with a bridging Mg 2+ ion, the average distance between the A9 and scissile phosphates remain within the crystallographic value of 4.3 Å, whereas in the absence of Mg 2+ this key contact between stems I and II drifts to over 7 ...

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Section: In the Late Ts The Mg 2+ Ion Can Act As A Lewis Acid Catalymentioning

confidence: 99%

Insight into the Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from X-ray Crystallography and Molecular Dynamics Simulation

López

Martick

et al. 2007

J. Chem. Theory Comput.

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“…Metal ions can have both structural and chemical roles in catalysis. Possible (chemical) catalytic roles for metal ions include acting as: 11,17 • General acid-base catalyst by accepting/donating protons from coordinated water molecules to the nucleophilic (2′) and leaving group (5′) positions…”

Section: Magnesium Complexesmentioning

confidence: 99%

“…A common biological reaction catalyzed by several prototype ribozyme systems, such as the hammerhead, 10,11 hairpin, 12,13 and hepatitis delta virus 14,15 ribozymes, involves cleavage of a phosphate group through a transesterification reaction 16,17 (Figure 1). In this reaction, the 2′ OH of the ribose sugar ring becomes activated via deprotonation and makes an in-line attack to the adjacent 3′-phosphate along the phosphodiester backbone.…”

Section: Introductionmentioning

confidence: 99%

CHARMM force field parameters for simulation of reactive intermediates in native and thio‐substituted ribozymes

et al. 2006

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Force field parameters specifically optimized for residues important in the study of RNA catalysis are derived from density-functional calculations in a fashion consistent with the CHARMM27 allatom empirical force field. Parameters are presented for residues that model reactive RNA intermediates and transition state analogs, thio-substituted phosphates and phosphoranes, and bound Mg 2+ and di-metal bridge complexes. Target data was generated via density-functional calculations at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) level. Partial atomic charges were initially derived from the CHelpG electrostatic potential fitting and subsequently adjusted to be consistent with the CHARMM27 charges and Lennard-Jones parameters were determined to reproduce interaction energies with water molecules. Bond, angle and torsion parameters were derived from the density-functional calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters for standard residues. The extension of the CHARMM27 force field parameters for the non-standard biological residues presented here will have considerable use in simulations of ribozymes, including the study of freeze-trapped catalytic intermediates, metal ion binding and occupation, and thio effects.

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“…Of particular interest is the study of RNA enzymes or ribozymes. 5 The understanding of the molecular mechanisms of ribozyme catalysis has been greatly facilitated by the study of small prototype self-cleaving RNA 6 such as the hammerhead, 7,8 hairpin, 9,10 and hepatitis delta virus [11][12][13] ribozymes.…”

Section: Introductionmentioning

confidence: 99%

Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms

Nam

Cui

Gao

et al. 2007

J. Chem. Theory Comput.

196

355

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Abstract:A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined quantum mechanical/molecular mechanical simulations. The model, designated AM1/d-PhoT, is parametrized for H, O, and P atoms to reproduce high-level density-functional results from a recently constructed database of quantum calculations for RNA catalysis (http://theory.chem.umn.edu/Database/QCRNA), including geometries and relative energies of minima, transition states and reactive intermediates, dipole moments, proton affinities, and other relevant properties. The model is tested in the gas phase and in solution using a QM/MM potential. The results indicate that the method provides significantly higher accuracy than MNDO/ d, AM1, and PM3 methods and, for the transphosphorylation reactions, is in close agreement with the density-functional calculations at the B3LYP/6-311++G(3df,2p) level with a reduction in computational cost of 3-4 orders of magnitude. The model is expected to have considerable impact on the application of semiempirical QM/MM methods to transphosphorylation reactions in solution, enzymes, and ribozymes and to ultimately facilitate the design of improved nextgeneration multiscale quantum models.

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Ribozyme Mechanisms

Cited by 37 publications

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Insight into the Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from X-ray Crystallography and Molecular Dynamics Simulation

Insight into the Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from X-ray Crystallography and Molecular Dynamics Simulation

CHARMM force field parameters for simulation of reactive intermediates in native and thio‐substituted ribozymes

Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms

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Ribozyme Mechanisms

Cited by 37 publications

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Insight into the Role of Mg2+ in Hammerhead Ribozyme Catalysis from X-ray Crystallography and Molecular Dynamics Simulation

Insight into the Role of Mg2+ in Hammerhead Ribozyme Catalysis from X-ray Crystallography and Molecular Dynamics Simulation

CHARMM force field parameters for simulation of reactive intermediates in native and thio‐substituted ribozymes

Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms

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Insight into the Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from X-ray Crystallography and Molecular Dynamics Simulation

Insight into the Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from X-ray Crystallography and Molecular Dynamics Simulation