Enhanced-Sampling Molecular Dynamics Recovers Rare Functional RNA Conformations Across Diverse Structural Contexts

Abstract

Accurate determination of RNA conformational ensembles is essential for understanding RNA function and advancing RNA-targeted drug discovery, yet lowly-populated alternative states remain difficult to resolve with atomistic detail. A central constraint is that experimental refinement can only select conformations already present in the starting library, making library generation the limiting step. Using the HIV-1 trans-activation response element (TAR) as a model system, we benchmarked conventional MD (cMD) against the enhanced sampling methods Gaussian-accelerated MD (GaMD), replica-exchange Gaussian-accelerated MD (Rex-GaMD), replica-exchange with solute tempering (REST2), and temperature replica-exchange MD (T-REMD), as well as the structure-prediction based methods FARFAR2 and AlphaFold 3. Each library was refined against experimental residual dipolar couplings (RDC) and validated independently using ensemble-averaged QM/MM chemical shifts. We showed that T-REMD produced the most accurate ensemble by both measures, and its advantage tracked with broader, more continuous coverage of the interhelical conformational landscape. Broad temperature-range T-REMD also sampled conformations resembling excited state 1 (ES1) and the U23-A27-U38 base-triple, without requiring these states to be specified during library generation. More accurate ensembles further improved coverage of experimentally observed ligand-bound TAR conformations and enhanced ensemble-based virtual screening, linking structural accuracy to functional utility. The same workflow applied to the preQ1 class I riboswitch and the UUCG tetraloop improved agreement with experimental data in both cases. Together, these results establish replica-exchange enhanced sampling, particularly T-REMD, as an effective strategy for constructing experimentally validated RNA ensembles and accessing conformations corresponding to rare functional substates.