Differential conformational dynamics in two type-A RNA-binding domains drive the double-stranded RNA recognition and binding

Abstract

TAR RNA binding protein (TRBP) has emerged as a key player in the RNA interference (RNAi) pathway, wherein it binds to different pre-miRNAs and siRNAs, each varying in sequence and/or structure. We hypothesize that TRBP displays dynamic adaptability to accommodate heterogeneity in target RNA structures. Thus, it is crucial to ascertain the role of intrinsic and RNA-induced protein dynamics in RNA recognition and binding. We have previously elucidated the role of intrinsic and RNA-induced conformational exchange in the double-stranded RNA-binding domain 1 (dsRBD1) of TRBP in shape-dependent RNA recognition. The current study delves into the intrinsic and RNA-induced conformational dynamics of the TRBP-dsRBD2 and then compares it with the dsRBD1 study carried out previously. Remarkably, the two domains exhibit differential binding affinity to a 12 bp dsRNA owing to the presence of critical residues and structural plasticity. Further, we report that dsRBD2 depicts constrained conformational plasticity when compared to dsRBD1. Although, in the presence of RNA, dsRBD2 undergoes induced conformational exchange within the designated RNA-binding regions and other residues, the amplitude of the motions remains modest when compared to those observed in dsRBD1. We propose a dynamics-driven model of the two tandem domains of TRBP, substantiating their contributions to the versatility of dsRNA recognition and binding.Exploring the intricacies of RNA-protein interactions by delving into dynamics-based measurements not only adds valuable insights into the mechanics of RNA-protein interactions but also underscores the significance of conformational dynamics in dictating the functional outcome in such tightly regulated biological processes. In this study, we measure intrinsic and RNA-induced conformational dynamics in the second dsRBD, i.e., TRBP-dsRBD2, and compare the same with that carried out in the first dsRBD (TRBP-dsRBD1) of TRBP protein, a key player of the RNAi pathway. The study unveils the differential conformational space accessible to the two domains of TRBP, even though they both adopt a canonical dsRBD fold, thereby affecting how they interact with target RNAs.