The Multiple Faces of Disordered Nucleoporins - PubMed (original) (raw)

Review

The Multiple Faces of Disordered Nucleoporins

Edward A Lemke. J Mol Biol. 2016.

Abstract

An evolutionary advantage of intrinsically disordered proteins (IDPs) is their ability to bind a variety of folded proteins-a paradigm that is central to the nucleocytoplasmic transport mechanism, in which nuclear transport receptors mediate the translocation of various cargo through the nuclear pore complex by binding disordered phenylalanine-glycine-rich nucleoporins (FG-Nups). FG-Nups are highly dynamic, which poses a substantial problem when trying to determine precisely their function using common experimental approaches. FG-Nups have been studied under a variety of conditions, ranging from those that constitute single-molecule measurements to physiological concentrations at which they can form supramolecular structures. In this review, I describe the physicochemical properties of FG-Nups and compare them to those of other disordered systems, including well-studied IDPs. From this comparison, it is apparent that FG-Nups not only share some properties with IDPs in general but also possess unique characteristics that might be key to their central role in the nucleocytoplasmic transport machinery.

Keywords: intrinsically disordered proteins; nucleocytoplasmic transport; phase separation; protein folding and dynamics; protein moonlighting.

Copyright © 2016 The Author. Published by Elsevier Ltd.. All rights reserved.

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Figures

Fig. 1

Fig. 1

Top view of an EM tomogram of the human NPC, showing an empty channel, according to Ref. [3]. Disordered proteins that fill the channel are not visible to conventional structural biology approaches, and a hole with an approximate diameter of 41 nm is apparent.

Fig. 2

Fig. 2. Sequences of an assortment of disordered human FG-Nup according to UniProt, with different color-coded FG repeats.

Fig. 3

Fig. 3

The different binding modes observed for IDP interactions (shown in gray, with valencies indicated by gray square markers) with folded proteins (orange). Due to their dynamics, IDPs populate a disordered ensemble in isolation [109]. In the “conformational selection” binding mode, the folded binding partner can bind to a specific conformation of the ensemble, which can also be a folded state. In the “induced-fit” binding mode, the presence of the binding partner induces folding of the IDP. For FG-domain-NTR interactions, it appears as if the native-state ensemble tends to bind to NTRs so that many conformations can readily engage with the NTR without requiring much time or energy. The result appears to be an archetypal, multivalent fuzzy complex that can form remarkably quickly (reprinted from ref. [46]).

Fig. 4

Fig. 4. An experiment to demonstrate how NTRs in solution can rapidly penetrate FG-domain hydrogels.

(a) The interface between an FG-domain hydrogel and a buffer solution. Once a fluorescent NTR (importin-β) was added to the buffer solution outside the gel, the NTR rapidly enriched in the gel boundary. (b) Intensity profiles corresponding to the images in (a), from which it is apparent that a depletion zone exists in at the buffer-gel interface. Adapted from Ref. [71] with permission from Elsevier.

Fig. 5

Fig. 5

An FFGEY peptide gel can be switched from a tough hydrogel-like state (a) to a liquid-like state (b) using a kinase and a phosphatase, as demonstrated by Yang et al. [74]. The right-hand panel shows that the gel has a fibrillar ultrastructure as observed by EM, which gives rise to a mechanically stable gel. If the FFGEY peptide is phosphorylated at the Tyr residue by a kinase, the solution is a liquid. If dephosphorylated by action of a phosphatase, an amyloid fiber network forms to a tough gel (a and c). The process is reversible and can be controlled by the addition of a phosphatase or kinase. Adapted with permission from Ref. [74], Copyright (2006) American Chemical Society.

Fig. 6

Fig. 6

Cartoon of the pathway by which FUS can undergo various phase transitions to form different assemblies. FUS can undergo liquid–liquid phase separation into droplets. Under certain conditions, these droplets can further age and undergo a liquid–solid phase transition into a fibrillar amyloid-like structure. Reprinted from Ref. [78] with permission from Elsevier.

Fig. 7

Fig. 7. Half-bleach experiments of phase-separated FUS and FG-Nup100 assemblages (droplets).

(a) Droplets were formed from GFP-labeled FUS, and then only the right-hand half of a droplet was bleached. The fluorescence recovered rapidly (blue to red indicating increasing fluorescence intensity), which points to the droplet being dynamic (liquid-like), and is the result of a liquid-liquid phase separation. (b) A similar half-bleach experiment from a different study for FG-Nup100 (doped with FG-Nup100 labeled with a synthetic fluorophore, shown in red). The droplets appear rigid, which points to the existence of a liquid-gel phase separation. Reprinted from Refs. [78] with permission from Elsevier and [12], respectively.

Fig. 8

Fig. 8

An experiment in which large beads were coated with NTRs. When these were placed on a layer of densely grafted FG-domains soaked in a solution of NTRs (small spheres in different green and light yellow colors), the beads were able to diffuse on the surface. Adapted with permission from Ref. [91].

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