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Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.

ABSTRACT: Herein we summarize our progress toward the understanding of hammerhead ribozyme (HHR) catalysis through a multiscale simulation strategy. Simulation results collectively paint a picture of HHR catalysis: HHR first folds to form an electronegative active site pocket to recruit a threshold occupation of cationic charges, either a Mg(2+) ion or multiple monovalent cations. Catalytically active conformations that have good in-line fitness are supported by specific metal ion coordination patterns that involve either a bridging Mg(2+) ion or multiple Na(+) ions, one of which is also in a bridging coordination pattern. In the case of a single Mg(2+) ion bound in the active site, the Mg(2+) ion undergoes a migration that is coupled with deprotonation of the nucleophile (C17:O2'). As the reaction proceeds, the Mg(2+) ion stabilizes the accumulating charge of the leaving group and significantly increases the general acid ability of G8:O2'. Further computational mutagenesis simulations suggest that the disruptions due to mutations may severely impact HHR catalysis at different stages of the reaction. Catalytic mechanisms supported by the simulation results are consistent with available structural and biochemical experiments, and together they advance our understanding of HHR catalysis.

SUBMITTER: Lee TS

PROVIDER: S-EPMC4747252 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.

Lee Tai-Sung TS Wong Kin-Yiu KY Giambasu George M GM York Darrin M DM

Progress in molecular biology and translational science 20130101

Herein we summarize our progress toward the understanding of hammerhead ribozyme (HHR) catalysis through a multiscale simulation strategy. Simulation results collectively paint a picture of HHR catalysis: HHR first folds to form an electronegative active site pocket to recruit a threshold occupation of cationic charges, either a Mg(2+) ion or multiple monovalent cations. Catalytically active conformations that have good in-line fitness are supported by specific metal ion coordination patterns th ...[more]

PMID: 24156941

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Project description:Metal nanoparticles, often supported on metal oxide promoters, are a cornerstone of heterogeneous catalysis. Experimentally, size effects are well-established and are manifested through changes to catalyst selectivity, activity and durability. Density Functional Theory (DFT) calculations have provided an attractive way to study these effects and rationalise the change in nanoparticle properties. However such computational studies are typically limited to smaller nanoparticles (approximately up to 50 atoms) due to the large computational cost of DFT. How well can such simulations describe the electronic properties of the much larger nanoparticles that are often used in practice? In this study, we use the ONETEP code, which is able to achieve more favourable computational scaling for metallic nanoparticles, to bridge this size gap. We present DFT calculations on entire Pd and Pd carbide nanoparticles of more than 300 atoms (approximately 2.5 nm diameter), and find major differences in the electronic structure of such large nanoparticles, in comparison to the commonly investigated smaller clusters. These differences are also manifested in the calculated chemical properties such as adsorption energies for C2H2, C2H4 and C2H6 on the pristine Pd and PdC x nanoparticles which are significantly larger (up to twice in value) for the ∼300 atoms structures. Furthermore, the adsorption of C2H2 and C2H4 on PdC x nanoparticles becomes weaker as more C is introduced in the Pd lattice whilst the impact of C concentration is also observed in the calculated reaction energies towards the hydrogenation of C2H2, where the formation of C2H6 is hindered. Our simulations show that PdC x nanoparticles of about 5% C per atom fraction and diameter of 2.5 nm could be potential candidate catalysts of high activity in hydrogenation reactions. The paradigm presented in this study will enable DFT to be applied on similar sized metal catalyst nanoparticles as in experimental investigations, strengthening the synergy between simulation and experiment in catalysis.

Dataset Information

Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.

Publications

Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.

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