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ABSTRACT: The hepatitis delta virus ribozyme catalyzes an RNA cleavage reaction using a catalytic nucleobase and a divalent metal ion. The catalytic base, C75, serves as a general acid and has a pK(a) shifted toward neutrality. Less is known about the role of metal ions in the mechanism. A recent crystal structure of the precleavage ribozyme identified a Mg(2+) ion that interacts through its partial hydration sphere with the G25·U20 reverse wobble. In addition, this Mg(2+) ion is in position to directly coordinate the nucleophile, the 2'-hydroxyl of U(-1), suggesting it can serve as a Lewis acid to facilitate deprotonation of the 2'-hydroxyl. To test the role of the active site Mg(2+) ion, we replaced the G25·U20 reverse wobble with an isosteric A25·C20 reverse wobble. This change was found to significantly reduce the negative potential at the active site, as supported by electrostatics calculations, suggesting that active site Mg(2+) binding could be adversely affected by the mutation. The kinetic analysis and molecular dynamics of the A25·C20 double mutant suggest that this variant stably folds into an active structure. However, pH-rate profiles of the double mutant in the presence of Mg(2+) are inverted relative to the profiles for the wild-type ribozyme, suggesting that the A25·C20 double mutant has lost the active site metal ion. Overall, these studies support a model in which the partially hydrated Mg(2+) positioned at the G25·U20 reverse wobble is catalytic and could serve as a Lewis acid, a Brønsted base, or both to facilitate deprotonation of the nucleophile.
Biochemistry 01/2013; · 3.42 Impact Factor
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ABSTRACT: A recent crystal structure of the precleaved HDV ribozyme along with biochemical data support a mechanism for phosphodiester bond self-cleavage in which C75 acts as a general acid and bound Mg(2+) ion acts as a Lewis acid. Herein this precleaved crystal structure is used as the basis for quantum mechanical/molecular mechanical calculations. These calculations indicate that the self-cleavage reaction is concerted with a phosphorane-like transition state when a divalent ion, Mg(2+) or Ca(2+), is bound at the catalytic site but is sequential with a phosphorane intermediate when a monovalent ion, such as Na(+), is at this site. Electrostatic potential calculations suggest that the divalent metal ion at the catalytic site lowers the pK(a) of C75, leading to the concerted mechanism in which the proton is partially transferred to the leaving group in the phosphorane-like transition state. These observations are consistent with experimental data, including pK(a) measurements, reaction kinetics, and proton inventories with divalent and monovalent ions.
Journal of Physical Chemistry Letters 11/2011; 2(22):2906-2911. · 6.21 Impact Factor
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ABSTRACT: The crystal structure of the precleaved form of the hepatitis delta virus (HDV) ribozyme reveals two G•U wobbles near the active site: a rare reverse G•U wobble involving a syn G base, and a standard G•U wobble at the cleavage site. The catalytic mechanism for this ribozyme has been proposed to involve a Mg(2+) ion bound to the reverse G•U wobble, as well as a protonated C75 base. We carried out molecular dynamics simulations to analyze metal ion interaction with the reverse and standard G•U wobbles and to investigate the impact of C75 protonation on the structure and motions of the ribozyme. We identified two types of Mg(2+) ions associated with the ribozyme, chelated and diffuse, at the reverse and standard G•U wobbles, respectively, which appear to contribute to catalysis and stability, respectively. These two metal ion sites exhibit relatively independent behavior. Protonation of C75 was observed to locally organize the active site in a manner that facilitates the catalytic mechanism, in which C75(+) acts as a general acid and Mg(2+) as a Lewis acid. The simulations also indicated that the overall structure and thermal motions of the ribozyme are not significantly influenced by the catalytic Mg(2+) interaction or C75 protonation. This analysis suggests that the reaction pathway of the ribozyme is dominated by small local motions at the active site rather than large-scale global conformational changes. These results are consistent with a wealth of experimental data.
The Journal of Physical Chemistry B 06/2011; 115(25):8346-57. · 3.70 Impact Factor
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ABSTRACT: The hepatitis delta virus (HDV) ribozyme uses both metal ion and nucleobase catalysis in its cleavage mechanism. A reverse G·U wobble was observed in a recent crystal structure of the precleaved state. This unusual base pair positions a Mg(2+) ion to participate in catalysis. Herein, we used molecular dynamics (MD) and X-ray crystallography to characterize the conformation and metal binding characteristics of this base pair in product and precleaved forms. Beginning with a crystal structure of the product form, we observed formation of the reverse G·U wobble during MD trajectories. We also demonstrated that this base pair is compatible with the diffraction data for the product-bound state. During MD trajectories of the product form, Na(+) ions interacted with the reverse G·U wobble in the RNA active site, and a Mg(2+) ion, introduced in certain trajectories, remained bound at this site. Beginning with a crystal structure of the precleaved form, the reverse G·U wobble with bound Mg(2+) remained intact during MD simulations. When we removed Mg(2+) from the starting precleaved structure, Na(+) ions interacted with the reverse G·U wobble. In support of the computational results, we observed competition between Na(+) and Mg(2+) in the precleaved ribozyme crystallographically. Nonlinear Poisson-Boltzmann calculations revealed a negatively charged patch near the reverse G·U wobble. This anionic pocket likely serves to bind metal ions and to help shift the pK(a) of the catalytic nucleobase, C75. Thus, the reverse G·U wobble motif serves to organize two catalytic elements, a metal ion and catalytic nucleobase, within the active site of the HDV ribozyme.
Biochemistry 02/2011; 50(13):2672-82. · 3.42 Impact Factor
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ABSTRACT: Metropolis Monte Carlo simulations on the square-shoulder fluid of Malescio and Pellicane are used to trace the temperature dependent excess entropy, the heat capacity, and configurational energy along several isochores, including those for which mechanically stable zero-temperature structures have been predicted. Thermodynamic signatures of structural phase transitions are identified along several isochores, in addition to the low-density triangular solid and stripe phase transitions identified earlier. The finite temperature phases illustrate the competition between cluster formation and stripe formation as competing mechanisms for generating minimum free energy configurations as a function of density, consistent with earlier results at zero temperature. We also critically examine the usefulness of a phase-ordering rule based on the residual multiparticle entropy (RMPE) in predicting the formation of this diverse set of ordered structures from a disordered fluid phase. For the majority of the isochores studied, the RMPE prediction and the thermodynamic evidence for a phase transition were consistent. However, this criterion fails along isochores that are in regions of coexistence. Thus, the zero-RMPE rule is only likely to be approximately predictive in systems with small phase coexistence regimes, e.g., in the case of liquid crystal forming systems.
The Journal of chemical physics 02/2010; 132(7):074503. · 3.09 Impact Factor
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ABSTRACT: Molecular dynamics simulations of liquid silica and beryllium fluoride are performed using the van Beest-Kramer-van Santen and transferable rigid ion model potentials, respectively, in order to compare transport properties. The ionic conductivity (sigma), shear viscosity (eta) and ionic self-diffusivities (D(+/-)) are computed over a fairly wide range of temperatures and densities and deviations from Arrhenius behavior along different isochores is studied. The Stokes-Einstein relation is shown to hold over the entire range of state points, though the effective hydrodynamic radius shows small variations due to thermal fluctuations, compression, and local tetrahedral order. Several alternative tests of the Nernst-Einstein relation are implemented which show that significant network-formation in the anomalous regime leads to a breakdown of this relationship. The relaxation times, tau(sigma) and tau(M), associated with the decay of the charge-flux and pressure ACFs respectively, are computed. In the anomalous regime, as the tetrahedral network formation progresses, tau(M) increases rapidly while tau(sigma) shows very little variation, indicating a decoupling of charge and momentum transport processes.
The Journal of Physical Chemistry B 11/2009; 113(46):15284-92. · 3.70 Impact Factor
