Crowding-induced phase separation of nuclear transport receptors in FG nucleoporin assemblies

The rapid (< 1 ms) transport of biological material to and from the cell nucleus is regulated by the nuclear pore complex (NPC). At the core of the NPC is a permeability barrier consisting of intrinsically disordered phenylalanine-glycine nucleoporins (FG Nups). Various types of nuclear transport receptors (NTRs) facilitate transport by partitioning in the FG Nup assembly, overcoming the barrier by their affinity to the FG Nups, and comprise a significant fraction of proteins in the NPC barrier. In previous work (Zahn et al., 2016), we revealed a universal physical behaviour in the experimentally observed binding of two well-characterised NTRs, Nuclear Transport Factor 2 (NTF2) and the larger Importin-beta (Imp-beta), to different planar assemblies of FG Nups, with the binding behaviour defined by negative cooperativity. This was further validated by a minimal physical model that treated the FG Nups as flexible homopolymers and the NTRs as uniformly cohesive spheres. Here, we build upon our original study by first parametrising our model to experimental data, and next predicting the effects of crowding by different types of NTRs. We show how varying the amounts of one type of NTR modulates how the other NTR penetrates the FG Nup assembly. Notably, at similar and physiologically relevant NTR concentrations, our model predicts demixed phases of NTF2 and Imp-beta within the FG Nup assembly. The functional implication of NTR phase separation is that NPCs may sustain separate transport pathways that are determined by inter-NTR competition.

Automated summary

The rapid transport of biological material to and from the cell nucleus is regulated by the nuclear pore complex (NPC), with a core permeability barrier consisting of FG Nups. Nuclear transport receptors (NTRs) facilitate transport by partitioning in the FG Nup assembly and make up a significant portion of proteins in the NPC barrier. Negative cooperativity was observed in the binding behavior of well-characterized NTRs, NTF2 and Imp-beta, to different planar assemblies of FG Nups, suggesting potential demixed phases of NTRs within the FG Nup assembly that could impact inter-NTR competition and separate transport pathways.