Computational Exploration of the Inhibitory Mechanism of mRNA against the Phase Separation of hnRNPA2 Low Complexity Domains

hnRNPA2, an RNA-binding protein involved in RNA metabolism and regulation, can undergo liquid–liquid phase separation (LLPS) to form dynamic biomolecular condensates. Previous experiments have reported that RNA molecules can inhibit the LLPS of the hnRNPA2 low complexity domain (LCD). However, the atomistic mechanisms underlying this inhibitory effect and RNA–LCD interactions remain largely elusive. Herein, the influence of mRNA A2RE11 on the single-chain conformational ensemble and transient interactions between LCD chains are investigated through all-atom-enhanced sampling molecular dynamics (MD) simulations. Our simulations reveal that aromatic residues are essential to intrachain interactions of single-chain hnRNPA2 LCDs as well as interchain interactions of LCD dimers. Through binding to aromatic and positively charged residues of the hnRNPA2 LCD, A2RE11 undermines the degree of collapse of the single-chain LCD and disrupts the aromatic stacking, hydrogen bonding, and cation−π interchain interactions. Our coarse-grained phase coexistence MD simulations further underscore the preeminence of interchain aromatic and cation−π interactions in regulating the phase behavior of hnRNPA2 LCD and the RNA binding affinity for the RGG and Y/FG(G) motifs. These findings from multiscale simulations lead to a greater appreciation of the complex interaction network underlying the phase separation and RNA–protein interaction of the hnRNPA2 LCD.