Transient interdomain interactions shape the conformational ensemble governing RNA recognition by the tandem RRMs of Sex-lethal

Transient interactions between domains in RNA recognition proteins can significantly influence their conformational flexibility, according to a study on the Drosophila melanogaster splicing regulator Sex-lethal (Sxl). The researchers utilized solution NMR spectroscopy alongside rational protein engineering, restrained docking, and RNA-binding studies to explore the structural organization of Sxl's tandem RRMs.

Extending the native interdomain linker led to a reduction in rotational coupling between the two RRMs, suggesting that Sxl operates as a dynamic conformational ensemble rather than two separate, independent domains.

NMR-guided docking revealed a compact arrangement aligned with experimental data, pointing to a transient interface that partially overlaps RNA-binding surfaces. Interestingly, a mutant designed to weaken this interface unexpectedly resulted in enhanced rotational coupling and a more stable native fold, indicating a redistribution of the conformational ensemble instead of disorganization of the domain architecture.

This mutant also exhibited reduced RNA-binding affinity and diminished sequence discrimination, suggesting that alterations affecting the conformational equilibrium in either direction impair high-affinity and sequence-selective RNA binding.

These findings demonstrate that RNA recognition by Sxl is not governed by a single apo structure but by a finely balanced conformational ensemble. The study underscores the importance of understanding transient interdomain interactions in elucidating the complex mechanisms that underlie RNA recognition by RRMs.