Fused in sarcoma (FUS) is an RNA-binding protein implicated in diverse aspects of RNA metabolism and neurodegenerative diseases. Among its domains, the RNA-recognition motif (RRM) and adjacent disordered arginine/glycine-rich (RGG) regions cooperate to engage structured RNAs. Previous studies have shown that the isolated RRM exhibits limited RNA-binding activity, whereas the flanking RGG domains provide essential affinity. Despite this progress, the synergistic contribution of RRM and RGG2 to RNA binding is still not understood well. Here, we address this knowledge gap by performing extensive enhanced sampling atomistic simulations of the RRM-RGG2 region of FUS in complex with a model hairpin RNA. We employed multithermal-multiumbrella on-the-fly probability enhanced sampling (MM-OPES) with 16 walkers, each extended to 3.6 μs for RRM-RGG2 and hairpin RNA together with the control data (RRM-RGG2 only: MM-OPES, 20 walkers, 1.8 μs for each and isolated RRM: MM-OPES, 15 walkers, 1.2 μs for each). Structural analyses of extensively sampled trajectories reveal a broad ensemble of protein-RNA configurations. Notably, our results show that RNA binding freezes the disordered RGG2, and the RGG-RNA contacts remained highly stable, which may explain the essential role of RGG in sustaining these interactions. This stabilization, however, comes at the expense of the RRM secondary structure, as its central β-sheet is destabilized. The fraction of β-sheet formation in the RNA-bound state is reduced, approaching values seen when RGG2 is absent (isolated RRM). This study provides new molecular-level insight into how RGG domains potentiate RRM-RNA interactions. These findings advance understanding of FUS-RNA recognition and offer a framework for future investigations into how misregulation of such interactions contributes to amyotrophic lateral sclerosis and related disorders.
Rahimi et al. (Sun,) studied this question.