American Chemical Society, Journal of Physical Chemistry B (Soft Condensed Matter and Biophysical Chemistry), 11(119), p. 4220-4229, 2015
DOI: 10.1021/jp512069n
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X-ray crystallography can provide important insights into the structure of RNA enzymes (ribozymes). However, the details of a ribozyme's active site architecture are often altered by the inactivating chemical modifications necessary to inhibit self-cleavage. Molecular dynamics (MD) simulations are able to complement crystallographic data and model the conformation of the ribozyme's active site in its native form. However, the performance of MD simulations is driven by the quality of the force field used. Force fields are primarily parameterized and tested for a description of canonical structures, and thus may be less accurate for non-canonical RNA elements, including ribozyme catalytic cores. Here, we show that our recent reparameterization of ε/ζ torsions significantly improves the description of the hairpin ribozyme's scissile phosphate conformational behavior. In addition, we find that an imbalance in the force field description of the nonbonded interactions of the ribose 2'-OH contributes to the conformational behavior observed for the scissile phosphate in the presence of a deprotonated G8(‒). Based on the new force fields, we obtain a reactive conformation for the hairpin ribozyme active site that is consistent with the most recent mechanistic and structural data.