How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study

Abstract

RNA Recognition Motifs (RRMs) are a key class of proteins that primarily bind single-stranded RNAs. In this study, we use unbiased molecular dynamics simulations to obtain insights into the intricate binding dynamics between uridine-rich RNAs and TbRGG2 RRM. Complementing structural experiments that unveil a primary binding mode with a single uridine bound, our simulations uncover two supplementary binding modes where adjacent nucleotides encroach upon the binding pocket. This leads to a unique molecular mechanism through which TbRGG2 RRM is capable of rapidly transitioning the U-rich sequence. In contrast, presence of non-native cytidines induces stalling and destabilization of the complex. By leveraging extensive equilibrium dynamics and large variety of binding states, TbRGG2 RRM effectively expedites diffusion along the RNA substrate while ensuring robust selectivity for U-rich sequences despite featuring a solitary binding pocket. Using recently developed Stafix potential, we substantiate our description of the complex dynamics by simulating fully spontaneous association process of U-rich sequences to the TbRGG2 RRM. Our study highlights critical role of dynamics and auxiliary binding states in interface dynamics employed by RNA-binding proteins, which is not readily apparent in traditional structural studies, but could represent a general type of binding strategy employed by many RNA-binding proteins.