Interplay of the folded domain and disordered low-complexity domains along with RNA sequence mediate efficient binding of FUS with RNA

Abstract

Fused in Sarcoma (FUS) is an abundant RNA binding protein, which drives phase separation of cellular condensates and plays multiple roles in RNA regulation. The ordered RNA recognition motif (RRM), Zinc Finger (ZnF) and the disordered (N-terminal low-complexity domain and three RG/RGG-repeats) domains of FUS are responsible for its nucleic acid binding behaviors. These domains of FUS recognize a variety of RNA sequence and structure motifs and can also bring about RNA-dependent phase behavior. Since molecular interactions in FUS-RNA complexes form the basis for RNA recognition and binding behavior, our molecular simulations study explores the structure, stability, and interaction of RRM and RGG domains with RNA and highlights the RNA specificity of FUS. The RRM domain binds to the single-stranded loop of a well-structured RNA through the α1-β2 hairpin loop, while the RGG regions bind the RNA stem. Irrespective of the length of RGG2, the RGG2-RNA interaction is confined to the stem-loop junction and the proximal stem regions. On the other hand, the RGG1-RNA interactions are primarily with the longer RNA stem. We find that the cooperation between folded and disordered regions of FUS efficiently binds RNA structures through different stabilizing mechanisms. Electrostatic interactions with Arginine and Lysine residues in the RRM, hydrophobic interactions with the Glycine residues of RGG2, and electrostatic as well as hydrophobic interactions with the RGG1 region are the major contributing factors. This study provides high-resolution molecular insights into the FUS-RNA interactions and forms the basis for further modeling of a full-length FUS in complex with RNA.