Characterization of conformational dynamics at microsecond timescale in the RNA-binding regions of dsRNA-binding domains

Abstract

Double-stranded RNA-binding domains (dsRBDs) are involved in a variety of biological functions via recognition and processing of dsRNAs. Though the primary substrate of the dsRBDs are dsRNAs with A-form helical geometry; they are known to interact with structurally diverse dsRNAs. Here, we have employed two model dsRBDs - TAR-RNA binding protein and Adenosine deaminase that acts on RNA - to understand the role of intrinsic protein dynamics in RNA binding. We have performed a detailed characterization of the residue-level dynamics by NMR spectroscopy for the two dsRBDs. While the dynamics profiles at the ps-ns timescale of the two dsRBDs were found to be different, a striking similarity was observed in the s-ms timescale dynamics for both the dsRBDs. Motions at fast s timescale (kex > 50000 s-1) were found to be present not only in the RNA-binding residues but also in some allosteric residues of the dsRBDs. We propose that this intrinsic s timescale dynamics observed independently in two distinct dsRBDs allows them to undergo conformational rearrangement that may aid dsRBDs to target substrate dsRNA from the pool of structurally different RNAs in cellular environment. Statement of SignificanceThis study reports for the first time the detailed characterization of microsecond timescale dynamics observed in RNA-binding regions of two distinct double-stranded RNA-binding domains (dsRBDs) using NMR relaxation dispersion experiments. dsRBDs have been known to target topologically distinct dsRNAs. However, the mechanistic details of the structural adaptation of proteins is not fully understood. We propose that the presence of such dynamics may have large-scale implications in understanding the RNA recognition mechanisms by the dsRBDs.