Development of force-field corrections for the RNA A-bulge motif

Abstract

Many functional RNA motifs adopt structures that deviate from the canonical A-form helix and are emerging targets for RNA-directed therapeutics. The microtubule-associated protein tau (MAPT) A-bulge motif (5'-GCAGU/5'-ACGU) is one such motif. Because its structure is stabilized by a delicate balance of local interactions, its accurate modeling remains a major challenge for molecular dynamics (MD) simulations. The experimentally determined nuclear magnetic resonance (NMR) structure of the MAPT A-bulge motif provides a stringent test of whether RNA force fields can accurately reproduce the experimentally observed conformation. Most current AMBER-family RNA force-field models have incorrectly favored a non-native base-triple state of the MAPT A-bulge motif over the experimentally observed stacked state. Structural comparison of the stacked and base-triple conformations revealed that overly favorable NH-N hydrogen bonds between the bulged adenosine and an adjacent Watson-Crick base pair were the primary source of this imbalance. We developed gHBfix-18Ab, an 18-component hydrogen-bond correction that distinguishes NH and NH2; donors. gHBfix-18Ab was combined with the previously developed OL3CP and NBfix0BPh corrections to generate the composite model gHBfix-18Ab*. This model restored the experimentally observed stacked state as the global minimum in the calculated free-energy profile and improved agreement with NMR-derived distance data for the A-bulge region. Importantly, gHBfix-18Ab* did not produce marked structural destabilization of the cUUCGg tetraloop, a widely used benchmark for RNA force-field validation, suggesting that the refinement preserves the stability of the unrelated RNA motif. These results demonstrate that targeted refinement of hydrogen-bond interactions provides a practical strategy for systematic improvement of RNA force fields toward more accurate modeling of noncanonical RNA motifs.