The role of disorder in RNA binding affinity and specificity

Abstract

Most RNA-binding modules are small and bind few nucleotides. RNA-binding proteins typically attain the physiological specificity and affinity for their RNA targets by combining several RNA-binding modules. Here, we review how disordered linkers connecting RNA-binding modules govern the specificity and affinity of RNA-protein interactions by regulating the effective concentration of these modules and their relative orientation. RNA-binding proteins also often contain extended intrinsically disordered regions that mediate protein-protein and RNA-protein interactions with multiple partners. We discuss how these regions can connect proteins and RNA resulting in heterogeneous higher-order assemblies such as membrane-less compartments and amyloid-like structures that have the characteristics of multi-modular entities. The assembled state generates additional RNA-binding specificity and affinity properties that contribute to further the function of RNA-binding proteins within the cellular environment.

Keywords: RNA-binding domains; RNA-binding modules; RNA-binding proteins; amyloids; assemblies; intrinsically disordered regions; linkers.

Figure 1.

Selected examples of RNA-binding modules. (a) RRM1 of the polypyrimidine tract-binding protein (PTB) interacting with CUCUCU RNA (PDB ID 2ad9) [3]. (b) KH domain and QUA2 region of splicing factor 1 (SF1) complexed with UAUACUAACAA RNA (PDB ID 1k1g) [4]. (c) Zinc finger of FUS interacting with UGGUG RNA (PDB ID 6g99) [5]. In all panels, RNA is represented in magenta. Protein α-helices are depicted in orange (with the exception of the QUA2 region, which is depicted in green), β-sheets in teal and loops in black. The zinc atom in (c) is depicted as a yellow sphere. Structures were visualized with PyMOL, version 2.4.

Figure 2.

RNA-binding proteins have a modular structure where intrinsically disordered regions (IDRs) can work as linkers connecting modules within a single protein or as connectors that mediate interactions between several proteins and/or RNA. (a) RNA-binding modules typically recognize short sequences on the RNA. (b) Linkers connecting RNA-binding modules are usually disordered in the free state. Some linkers stay disordered upon RNA binding and enable the RNA-binding modules to contact their RNA targets independently (top). Linkers can mediate molecular recognition by undergoing a disorder-to-order transition in the RNA-bound state and enable cooperative binding (bottom). (c,d) IDRs can interact with RNA (c) and proteins (d), promoting the formation of multimeric complexes. NNN and MM represent two different RNA sequence motifs.

Figure 3.

Intrinsically disordered regions (IDRs) drive the formation of higher-order assemblies, which display different RNA-binding specificity and affinity properties compared to the single components. (a) In membrane-less compartments, IDRs establish homotypic (depicted in black) or heterotypic (in blue) multivalent interactions, enabling the formation of multi-modular complexes of RNA-binding proteins that are able to recruit selected RNA species. (b) Some RNA-binding proteins assemble amyloid-like structures that can constrain the protruding RNA-binding modules to specific topologies, hence selecting specific RNA targets. NNN, MM, XXXX and YY represent four different RNA sequence motifs.