Improving the Hole Picture: Towards a Consensus on the Mechanism of Nuclear Transport

Abstract

Nuclear pore complexes (NPCs) mediate the exchange of materials between the nucleoplasm and cytoplasm, playing a key role in the separation of nucleic acids and proteins into their required compartments. The static structure of the NPC is relatively well defined by recent cryo EM and other studies. The functional roles of dynamic components in the pore of the NPC, phenylalanyl-glycyl (FG) repeat rich nucleoporins, is less clear because of our limited understanding of highly dynamic protein systems. These proteins form a restrained concentrate which interacts with and concentrates nuclear transport factors (NTRs) to provide facilitated nucleocytoplasmic transport of cargoes. Very rapid exchange among FG repeats and NTRs supports extremely fast facilitated transport, close to the rate of macromolecular diffusion in cytoplasm, while complexes without specific interactions are entropically excluded, though details on several aspects of the transport mechanism and FG repeat behaviors remain to be resolved. However, as discussed here, new technical approaches combined with more advanced modeling methods will likely provide an improved dynamic description of NPC transport, potentially at the atomic level in the near future. Such advances are likely to be of major benefit in comprehending the roles the malfunctioning NPC plays in cancer, aging, viral diseases, and neurodegeneration.

Figure 1.

Static representation of an NPC, based on a yeast (S. cerevisiae) structure, with the major features labeled (9).

Figure 2.

Positions of the FG Nups in the yeast NPC. Upper. Representation of observed electron density of the central transporter within the rigid frame of the NPC. Upper Right: detailed observed density local to the central waist illustrating the FG repeat anchor site. Center: distribution of types of FG repeats within the central transporter based on their mapped anchor sites and inferred by assuming random coil behavior of the FG segments and the absence of NTR/cargoes (15). Left: distribution of the anchor sites with color coding of their predominant FG type. Lower: heat map of the contribution of the FG repeat region of each FG Nup to maintaining the passive permeability barrier limiting the passage of nonspecific macromolecules, which appears to be largely maintained by FG Nups enriched in GLFG repeats forming a cap at the cytoplasmic entrance of the NPC (15). Adapted from (18).

Figure 3.

The NPC During Nucleocytoplasmic Transport. Upper: Molecular representation of the nuclear transport mechanism, at the scale of NTRs and non-specific macromolecules in the proximity of FG repeats. Middle Left: Disposition of FG repeats, showing different potential behaviors. Middle Right: Representation of an NPC with transiting macromolecules, to approximate scale and stoichiometry. Lower: Diagram of two adjacent FG repeats (green) interacting in solvent water (red/white) with a cognate interaction site (orange) on an NTR (blue).

Figure 4.

Illustration of the polymorphism associated with FG Nups. Because of their tethering, and lack of tertiary protein structure, the FG Nups are in a polymer brush formation. Controversy centers on whether the brush is entirely intrinsically disordered (61, 65), with the degree and speed of motion varying with distance from the tether, and the grafting density (upper) or whether cohesion of the FG repeats results in varying degrees of condensation leading to gels (68, 69) (middle) or amyloids (70) (71) (lower).