A Bimodal Distribution of Two Distinct Categories of Intrinsically Disordered Structures with Separate Functions in FG Nucleoporins

Justin Yamada,Joshua L Phillips,Samir Patel,Gabriel Goldfien,Alison Calestagne-Morelli,Hans Huang,Ryan Reza,Justin Acheson,Viswanathan V Krishnan,Shawn Newsam,Ajay Gopinathan,Edmond Y Lau,Michael E Colvin,Vladimir N Uversky,Michael F Rexach

doi:10.1074/mcp.m000035-mcp201

Abstract

Nuclear pore complexes (NPCs) gate the only conduits for nucleocytoplasmic transport in eukaryotes. Their gate is formed by nucleoporins containing large intrinsically disordered domains with multiple phenylalanine-glycine repeats (FG domains). In combination, these are hypothesized to form a structurally and chemically homogeneous network of random coils at the NPC center, which sorts macromolecules by size and hydrophobicity. Instead, we found that FG domains are structurally and chemically heterogeneous. They adopt distinct categories of intrinsically disordered structures in non-random distributions. Some adopt globular, collapsed coil configurations and are characterized by a low charge content. Others are highly charged and adopt more dynamic, extended coil conformations. Interestingly, several FG nucleoporins feature both types of structures in a bimodal distribution along their polypeptide chain. This distribution functionally correlates with the attractive or repulsive character of their interactions with collapsed coil FG domains displaying cohesion toward one another and extended coil FG domains displaying repulsion. Topologically, these bipartite FG domains may resemble sticky molten globules connected to the tip of relaxed or extended coils. Within the NPC, the crowding of FG nucleoporins and the segregation of their disordered structures based on their topology, dimensions, and cohesive character could force the FG domains to form a tubular gate structure or transporter at the NPC center featuring two separate zones of traffic with distinct physicochemical properties.

Highlights

Nuclear pore complexes (NPCs) gate the only conduits for nucleocytoplasmic transport in eukaryotes
Distinct Categories of Intrinsically Disordered Structures in FG Nups: from Collapsed Coils to Extended Coils—We recently characterized the dynamic structure of a portion of the intrinsically disordered FG domain of Nup116 and found that it adopts an ensemble of collapsed coil conformations [36]
The FG domain of Nup159 best matched a protein in the relaxed coil configuration, and the FXFG-rich regions of Nup1 (Nup1m), Nup2, and Nsp1 (Nsp1m) had dimensions that best matched the dimensions predicted for proteins in extended coil configurations

Summary

Introduction

Nuclear pore complexes (NPCs) gate the only conduits for nucleocytoplasmic transport in eukaryotes Their gate is formed by nucleoporins containing large intrinsically disordered domains with multiple phenylalanine-glycine repeats (FG domains). The molecular architecture of the NPC is similar in all eukaryotes examined It features a ring-shaped scaffold that forms a central ϳ50 nm transport conduit, eight short fibers extending from the scaffold into the cytoplasm, and a fibrous basket structure extending from the scaffold into the nucleoplasm [5, 6]. The rest of the nups contain multiple copies of phenylalanine-glycine (FG) motifs dispersed over 150 –700-amino acid (AA) domains that are intrinsically disordered (i.e. natively unfolded FG domains) (see Fig. 1) [21] These disordered FG domains populate the transport conduit, but are anchored to the NPC ring scaffold by structured domains [22] (see Fig. 1). The exact configuration of FG domains within the NPC and the mechanism of kap movement across the NPC are the subject of much speculation [31], but it seems clear that kaps and passing macromolecules must overcome a hydrophobic barrier imposed by FG domains [24, 32, 33]

Results

Discussion

Conclusion