Cui Lab Publishes Research article “Force fields matter in DNA pol η mechanistic analysis” in Protein Science
Abstract
DNA polymerase η is of major interest due to debates regarding the role of a
third non-canonical magnesium ion in catalysis. By examining molecular simulations motivated by this mechanistic question and the role of the S113A mutation, we investigate how modern classical force fields compare for treating
protein-DNA complexes and divalent metal ions in enzyme active sites. We
find that while the CHARMM36m protein force field is robust, the nucleic acid
components are unstable and too flexible, leading to the active site conformation in the reactant state not being well maintained. The addition of the third
magnesium ion reduces but does not eliminate these issues, and the observed
trends do not match experimental data and the magnesium ions bind too
strongly. The AMBER19 force field leads to more stable nucleic acid components, but the standard 12-6 magnesium ion parameters do not reproduce
experimental results on magnesium binding either. After comparing these
models with the 12-6-4 ion models from OL15, General Amber force field
GAFF-2, and re-parametrized m12-6-4 set, we find that the m12-6-4 model
best aligns with experimental evidence and semi-empirical QM(DFTB3)/MM
simulations. With these parameters, we conclude that the third magnesium ion
binds transiently to the reactant state and strongly to the product state, stabilizing key active site structural features in both. The S113A mutation predominately disrupts the local water network of the active site.
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