RNA Binding Mechanism of the FUS Zinc Finger in Concert with Its Flanking Intrinsically Disordered Region

The zinc finger (ZnF) motif is the most common nucleic acid binding motifs in proteins and comprises approximately 5% of the human genome. Proteins often carry multiple copies of ZnF motifs, enhancing DNA- and RNA-binding affinity and specificity. Fused in Sarcoma (FUS) is an RNA-binding protein that contains one ZnF motif and one RNA recognition motif. We identified the molecular basis for the strong and specific binding of FUS ZnF to RNA at atomic resolution by performing molecular dynamics and dissociation parallel cascade selection molecular dynamics simulations of a single-stranded RNA complexed with FUS ZnF and the flanking intrinsically disordered RGG2 domain, and observed dissociation of the complex. Our results suggest two distinct binding modes of the FUS ZnF-RNA complex. One is that ZnF specifically recognizes the GGU sequence of RNA while the RGG2 domain non-specifically interacts with RNA and distorts the RNA backbone structure. The second is that ZnF similarly recognizes the GGU of RNA specifically, but the RGG2 domain is barely involved in RNA binding, resulting in weaker binding. Further comprehensive analysis of nucleic acid binding site sequences indicates two possible mechanisms for ensuring strong and specific nucleic acid binding in nucleic acid binding proteins: the first is the stabilization of protein-RNA binding using only one or few nucleic acid binding motifs with flanking disordered regions as in the case of FUS ZnF, and the second is the involvement of more nucleic acid binding motifs. Our findings allow us to expand the repertoire of disordered region-assisted nucleic acid binding by ZnF from double-stranded DNAs to single-stranded RNAs.