Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations

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
parametrized and tested for a description of canonical structures
and thus may be less accurate for noncanonical RNA elements, including
ribozyme catalytic cores. Here, we show that our recent reparametrization
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–.
On the basis of the new force field, we obtain a reactive conformation
for the hairpin ribozyme active site that is consistent with the most
recent mechanistic and structural data.