Role of protein dynamics in enthalpy-driven recognition of topologically distinct dsRNAs by dsRBDs

Taking leads from the fact that a handful of double-stranded RNA-binding domains (dsRBDs) interact with a massive number of topologically distinct double-stranded RNAs (dsRNAs) in crucial biological pathways, and to understand the adaptability required by dsRBDs to target the pool of dsRNA substrates, we employed two independent model dsRBDs in an ITC and NMR spectroscopy based study. Our previous study revealed the presence of microsecond timescale dynamics in RNA-binding regions in the two dsRBDs studied. In the current study, results from ITC-based titrations showed that the binding of dsRBD with topologically distinct dsRNAs is enthalpy-driven, with each dsRNA-dsRBD pair having distinct combination of enthalpy-entropy yielding a similar change in free energy upon RNA-binding. We also show that the each of the dsRNA, used in this study, binds to the dsRBD in a unique mode. Further, intrinsic conformational exchange present in the RNA-binding regions of the apo-dsRBD was shown to quench upon binding with a dsRNA, while conformational exchange got induced at the residues that are in close proximity to where exchange was present in the apo-protein. This apparent relay of conformational exchange from one site to the other site upon dsRNA-binding thus suggests the importance of intrinsic dynamics to adapt to target a variety of dsRNA-shapes. Statement of SignificanceThis study reports that the interaction between dsRBDs and dsRNAs is enthalpy-driven, is perturbed by subtle changes in dsRNA shapes, and exhibits a classic case of enthalpy-entropy compensation. Further, the intrinsic microsecond timescale conformational exchange present in the apo-dsRBD was observed to get quenched upon RNA-binding. An apparent relay of conformational exchange was also observed from quenched sites to spatially proximal sites upon RNA-binding, suggesting highly adaptive nature of the dsRBD, a critical feature required to target topologically distinct dsRNA.