Formation of polymer brushes inside cylindrical pores: a computer simulation study

A designer FG-Nup that reconstitutes the selective transport barrier of the nuclear pore complex

Nuclear Pore Complexes (NPCs) regulate bidirectional transport between the nucleus and the cytoplasm. Intrinsically disordered FG-Nups line the NPC lumen and form a selective barrier, where transport of most proteins is inhibited whereas specific transporter proteins freely pass. The mechanism underlying selective transport through the NPC is still debated. Here, we reconstitute the selective behaviour of the NPC bottom-up by introducing a rationally designed artificial FG-Nup that mimics natural Nups. Using QCM-D, we measure selective binding of the artificial FG-Nup brushes to the transport receptor Kap95 over cytosolic proteins such as BSA. Solid-state nanopores with the artificial FG-Nups lining their inner walls support fast translocation of Kap95 while blocking BSA, thus demonstrating selectivity. Coarse-grained molecular dynamics simulations highlight the formation of a selective meshwork with densities comparable to native NPCs. Our findings show that simple design rules can recapitulate the selective behaviour of native FG-Nups and demonstrate that no specific spacer sequence nor a spatial segregation of different FG-motif types are needed to create selective NPCs.

Physical modelling of the nuclear pore complex

An in-depth discussion of nuclear pore complexes illustrates the importance of macromolecular confinement in biological systems.

Physically interesting behaviour can arise when soft matter is confined to nanoscale dimensions. A highly relevant biological example of such a phenomenon is the Nuclear Pore Complex (NPC) found perforating the nuclear envelope of eukaryotic cells. In the central conduit of the NPC, of ∼30–60 nm diameter, a disordered network of proteins regulates all macromolecular transport between the nucleus and the cytoplasm. In spite of a wealth of experimental data, the selectivity barrier of the NPC has yet to be explained fully. Experimental and theoretical approaches are complicated by the disordered and heterogeneous nature of the NPC conduit. Modelling approaches have focused on the behaviour of the partially unfolded protein domains in the confined geometry of the NPC conduit, and have demonstrated that within the range of parameters thought relevant for the NPC, widely varying behaviour can be observed. In this review, we summarise recent efforts to physically model the NPC barrier and function. We illustrate how attempts to understand NPC barrier function have employed many different modelling techniques, each of which have contributed to our understanding of the NPC.

Bistable collective behavior of polymers tethered in a nanopore

Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective phases of end-grafted polymers in a nanopore and to study their relative stability as a function of intermolecular interactions. Over a range of system parameters that is relevant for nuclear pore complexes, we observe two distinct phases: one with the bulk of the polymers condensed at the wall of the pore, and the other with the polymers condensed along its central axis. The relative stability of these two phases depends on the interpolymer interactions. The existence the two phases suggests a mechanism in which marginal changes in these interactions, possibly induced by nuclear transport receptors, cause the pore to transform between open and closed configurations, which will influence transport through the pore.

Morphology control of hairy nanopores

The properties of polymer layers end-grafted to the inner surface of nanopores connected to solvent reservoirs are studied theoretically as a function of solvent quality and pore geometry. Our systematic study reveals that nanoconfinement is affected by both pore radius and length and that the conformations of the polymer chains strongly depend on their grafting position along the nanopore and on the quality of the solvent. In poor solvent, polymer chains can collapse to the walls, form a compact plug in the pore, or self-assemble into domains of different shape due to microphase separation. The morphology of these domains (aggregates on pore walls or stacked micelles along the pore axis) is mainly determined by the relationship between chain length and pore radius. In other cases the number of aggregates depends on pore length. The presence of reservoirs decreases confinement at pore edges due to the changes in available volume and introduces new organization strategies not available for infinite nanochannels. In good solvent conditions, chains grafted at the pore entrances stretch out of the pore, relieving the internal osmotic pressure and increasing the entropy of the polymers. Our study also addresses the experimentally relevant case of end-grafted chains on the outer walls of the membrane surrounding the nanopore. The effect of these polymer chains on the organization within the nanopore depends on solvent quality. For good solvents the outer chains increase the confinement of the chains at the entrance of the pore; however, the effect does not result in new structures. For poor solvents the presence of the outer polymer layer may lead to changes in the morphology of the microphase-separated domains. Our results show the complex interplay between the different interactions in a confined environment and the need to develop theoretical and experimental tools for their study.