IDPs in macromolecular complexes: the roles of multivalent interactions in diverse assemblies

Abstract

Intrinsically disordered proteins (IDPs) have critical roles in a diverse array of cellular functions. Of relevance here is that they are components of macromolecular complexes, where their conformational flexibility helps mediate interactions with binding partners. IDPs often interact with their binding partners through short sequence motifs, commonly repeated within the disordered regions. As such, multivalent interactions are common for IDPs and their binding partners within macromolecular complexes. Here we discuss the importance of IDP multivalency in three very different macromolecular assemblies: biomolecular condensates, the nuclear pore, and the cytoskeleton.

Figure 1. Multivalent IDP interactions diversify the application of disorder in macromolecular complexes

Top right panel: Biomolecular condensates. Weak transient interactions between multivalent proteins harboring IDRs drive liquid-liquid phase separation. a) Patterned electrostatic interactions between oppositely charged tracts of a single molecular species, as in LAF-1 and DDX4. Many RNA-binding proteins have modular architectures in which different sequences of IDRs are appended to various RNA-binding domains, containing RGG repeats (red rectangles). IDRs alone can drive phase separation, but RNA can further promote this process by interacting through RNA-binding domains. b) Phase separation of NICD requires multivalent counterions such as the positively charged partner. NICD contact one another indirectly through positive counterions (blue circles) that likely bind the negatively charged clusters along the contour of NICD and directly through aromatic/hydrophobic interactions. Bottom panel: Nuclear Pore complex (NPC). The central pore scaffold contains IDPs that are used for scaffolding in multiple ways. a) Linker Nups have long IDRs containing SLiMs (orange boxes) that interact with folded domains in other scaffold Nups to form distinct subcomplexes. b) Nup159, located on the cytoplasmic ring of the NPC, contain five tandem repeats of DID which recruit five Dyn2 homodimers to form the scaffold of the Nup82 subcomplex. The permeability barrier of the NPC is made up of intrinsically disordered FG Nups. Nuclear transporters (Kaps; in green) passage through the FG barrier via multivalent interactions with the FG motifs. Top left panel: Cytoskeleton. Actin nucleation/elongation factors are IDPs containing functional repeat motifs. a) Nucleation factor Spire contains four repeats of WH2 motifs (red boxes), each binding to an actin monomer (grey circles) to facilitate actin polymerization. b) Formins contain globular FH2 domains (in turquoise) which bind actin monomers weakly and multiple polyproline repeats within its IDR regions which recognize profilin (orange circles) bound to actin to facilitate actin nucleation and elongation. Microtubule associated proteins (MAPS) are IDPs with repeats of short motifs (green or orange boxes) that bind the microtubule surface and tubulin dimers to stabilize or facilitate elongation of microtubules. Microtubules are made up of α/β tubulin heterodimers (purple and pink ovals) with disordered C-terminal tails that are decorated with PTMs (stars) that are recognized by different MAPs such as +Tip proteins.