Artificial Nanopores that Mimic the Transport Selectivity of the Nuclear Pore Complex

Jovanović-Talisman, Tijana; Tetenbaum-Novatt, Jaclyn; McKenney, Anna Sophia; Zilman, Anton; Peters, Reiner; Rout, Michael P.; Chait, Brian T.

doi:10.1016/j.bpj.2008.12.2950

Cited by 53 publications

(82 citation statements)

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“…Therefore, it seems likely that their mechanisms are also similar, although it remains to be seen how changes in the composition of FG Nups affect their biopolymer properties and how these differences are translated to fine-tune the transport system and its interactions with different types of TFs. The effects of confining FG repeats within a constricted channel, and allosteric modulation due to interactions with proteins such as Ran (78,79) also need to be assessed (9).…”

Section: Discussionmentioning

confidence: 99%

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Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

Raveh

Karp

Sparks

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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131

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Nucleocytoplasmic transport is mediated by the interaction of transport factors (TFs) with disordered phenylalanine-glycine (FG) repeats that fill the central channel of the nuclear pore complex (NPC). However, the mechanism by which TFs rapidly diffuse through multiple FG repeats without compromising NPC selectivity is not yet fully understood. In this study, we build on our recent NMR investigations showing that FG repeats are highly dynamic, flexible, and rapidly exchanging among TF interaction sites. We use unbiased long timescale all-atom simulations on the Anton supercomputer, combined with extensive enhanced sampling simulations and NMR experiments, to characterize the thermodynamic and kinetic properties of FG repeats and their interaction with a model transport factor. Both the simulations and experimental data indicate that FG repeats are highly dynamic random coils, lack intrachain interactions, and exhibit significant entropically driven resistance to spatial confinement. We show that the FG motifs reversibly slide in and out of multiple TF interaction sites, transitioning rapidly between a strongly interacting state and a weakly interacting state, rather than undergoing a much slower transition between strongly interacting and completely noninteracting (unbound) states. In the weakly interacting state, FG motifs can be more easily displaced by other competing FG motifs, providing a simple mechanism for rapid exchange of TF/FG motif contacts during transport. This slide-and-exchange mechanism highlights the direct role of the disorder within FG repeats in nucleocytoplasmic transport, and resolves the apparent conflict between the selectivity and speed of transport.nuclear pore | molecular dynamics | nucleoporins | transport factors | NMR T he nuclear pore complex (NPC) regulates macromolecular transport between the nucleus and the cytoplasm in all eukaryotic cells (1, 2). The NPC allows for passive diffusion of small molecules including sugars, ions, and water, while simultaneously imposing size-dependent exclusion of macromolecules without nuclear transport factor (TF) binding sites, generating unique nuclear and cytoplasmic compartments (3, 4). Larger macromolecules can bypass the selectivity barrier of the NPC by interacting with TFs that shuttle cargo through the central channel of the pore. In pathological conditions, including many cancers and viral infections, the NPC is hijacked and used to transport undesired particles, or it is modified to attenuate the cellular responses to disease onset (5, 6).TFs traverse the NPC by selective and reversible association with disordered phenylalanine-glycine (FG) repeat domains of the FG nucleoporin proteins (FG Nups), which line the surface of the NPC (7-14). Each FG repeat domain consists of 5-50 FG repeats. In turn, each FG repeat consists of a single FG motif of various sequence flavors, such as the FSFG and GLFG motifs, and 10-30 spacer residues that separate consecutive FG motifs (15, 16). The spacer residues are strongly hydrophilic (17) and rich ...

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Section: Discussionmentioning

confidence: 99%

“…TFs traverse the NPC by selective and reversible association with disordered phenylalanine-glycine (FG) repeat domains of the FG nucleoporin proteins (FG Nups), which line the surface of the NPC (7)(8)(9)(10)(11)(12)(13)(14). Each FG repeat domain consists of 5-50 FG repeats.…”

mentioning

confidence: 99%

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

Raveh

Karp

Sparks

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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131

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“…21 A third ensued from results showing that the presence of Kaps helped to tighten the barrier against non-specific entities in artificial NPCs 46 and FG Nup gels. 47 Fourth, even non-specific molecules could modulate and weaken Kap-FG Nup binding.…”

Section: Introductionmentioning

confidence: 99%

How to operate a nuclear pore complex by Kap-centric control

Lim

Huang

Kapinos

2015

Nucleus

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“…Whereas in vivo analyses have been confounded by the functional redundancy of FG nups, reductionist approaches carried out in vitro with purified components have provided some insight. Indeed, the selective properties of the NPC toward kaps have been reconstituted in vitro using isolated FG domains on beads (27,28), FG domain hydrogels (29), and FG domains attached to holes in membranes (30), highlighting the inherent capability of these domains to form selective diffusion barriers that can be specifically permeated by kaps. 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).…”

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confidence: 99%

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

Yamada

Phillips

Patel

et al. 2010

Molecular & Cellular Proteomics

317

584

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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

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Artificial Nanopores that Mimic the Transport Selectivity of the Nuclear Pore Complex

Cited by 53 publications

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Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

How to operate a nuclear pore complex by Kap-centric control

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

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