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Molecular simulations of RNA 2'-O-transesterification reaction models in solution
Brian K Radak1, Michael E Harris, Darrin M York
1BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, United States.
The Journal of Physical Chemistry. B
|December 11, 2012
Summary
This study models RNA 2'-O-transesterification using quantum/molecular mechanical simulations. Results reveal how structural changes and solvation impact RNA backbone cleavage, matching experimental data.
Area of Science:
- Biochemistry
- Computational Chemistry
- Molecular Biology
Background:
- RNA is crucial in biology, and its backbone cleavage is fundamental.
- Understanding uncatalyzed RNA transesterification aids in studying catalytic cleavage.
- Alkaline conditions are relevant for RNA degradation and processing.
Purpose of the Study:
- To investigate the free energy surfaces of RNA 2 -O-transesterification reactions.
- To understand the influence of structural environment and solvation on the reaction.
- To compare simulation results with experimental data for RNA backbone cleavage.
Main Methods:
- Quantum mechanical/molecular mechanical (QM/MM) umbrella sampling simulations.
- AM1/d-PhoT quantum model for reactive atoms and molecular mechanics force field for solvation.
- Comparison of different simulation protocols, ionic conditions, and force field models.
Main Results:
- Free energy profiles for RNA 2 -O-transesterification were determined for various models.
- Structural variations significantly affect the reaction's free energy profile.
- Calculated free energies of activation closely matched experimental results for UpG dinucleotide cleavage (19.9-20.8 vs 19.9 kcal/mol).
Conclusions:
- Solvation plays a critical role in stabilizing the transition state through hydrogen bonding.
- The study provides valuable insights into the mechanisms of RNA backbone cleavage.
- Computational models accurately predict experimental outcomes for RNA transesterification reactions.
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