Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems

Molecular dynamics
(MD) simulations are an important
and well-established
tool for investigating RNA structural dynamics, but their accuracy
relies heavily on the quality of the employed force field (ff). In this work, we present a comprehensive evaluation
of widely used pair-additive and polarizable RNA ffs using the challenging UUCG tetraloop (TL) benchmark system. Extensive
standard MD simulations, initiated from the NMR structure of the 14-mer
UUCG TL, revealed that most ffs did not maintain
the native state, instead favoring alternative loop conformations.
Notably, three very recent variants of pair-additive ffs, OL3CP–gHBfix21, DES-Amber, and OL3R2.7, successfully preserved the native structure over a 10 × 20
μs time scale. To further assess these ffs,
we performed enhanced sampling folding simulations of the shorter
8-mer UUCG TL, starting from the single-stranded conformation. Estimated
folding free energies (ΔG°fold) varied significantly among these three ffs, with
values of 0.0 ± 0.6, 2.4 ± 0.8, and 7.4 ± 0.2 kcal/mol
for OL3CP–gHBfix21, DES-Amber, and OL3R2.7, respectively. The ΔG°fold value predicted by the OL3CP–gHBfix21 ff was closest to experimental estimates, ranging from −1.6
to −0.7 kcal/mol. In contrast, the higher ΔG°fold values obtained using DES-Amber and OL3R2.7 were unexpected, suggesting that key interactions are
inaccurately described in the folded, unfolded, or misfolded ensembles.
These discrepancies led us to further test DES-Amber and OL3R2.7 ffs on additional RNA and DNA systems, where further
performance issues were observed. Our results emphasize the complexity
of accurately modeling RNA dynamics and suggest that creating an RNA ff capable of reliably performing across a wide range of
RNA systems remains extremely challenging. In conclusion, our study
provides valuable insights into the capabilities of current RNA ffs and highlights key areas for future ff development.