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The Molecular Mechanisms of Nuclear Transport in Health and Disease

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 32241

Special Issue Editors

Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
Interests: intrinsically disordered proteins; nuclear transport; nuclear pore complex; coarse-grained molecular dynamics
Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
1. Physics Department, University of Toronto, Toronto, ON, Canada
2. Institute for Biomaterials and Bioengineering, University of Toronto, Toronto, ON, Canada
European Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Netherlands Proteomics Centre, Antonius Deusinglaan 1, Groningen, The Netherlands
Interests: Nuclear Pore Complex; nuclear envelope; intrinsically disordered proteins; ageing; aggregation pathology

Special Issue Information

Dear Colleagues,

One of the largest protein complexes of eukaryotic cells is the nuclear pore complex (NPC). The NPC is embedded in the nuclear envelope, is responsible for all molecular trafficking in and out of the nucleus, and as such plays a vital role in molecular cell biology. The constituents of the nuclear pore complex are proteins called nucleoporins (Nups). Two thirds of these proteins are involved in building the scaffold and anchoring the nuclear pore complex inside the nuclear envelope, while one third of the Nups, called FG Nups because they are rich in FG-repeats, are intrinsically disordered and responsible for mediating transport. The collection of FG Nups forms a passage for nuclear transport receptors and their cargo whilst simultaneously acting as a permeability barrier against non-cargo. This selective transport feature is characteristic of the NPC, whose fascinating molecular mechanism has led to intense research activity over the past three decades. Despite the significant progress made through experimental and modeling studies, the fundamental molecular transport mechanisms are still not fully understood. In addition, basic knowledge on the role of nuclear transport in disease is scarce despite its importance in aging, neurodegenerative diseases, and cancer. To be able to develop new therapeutic strategies, an enhanced understanding is required of the fundamental physical and biological mechanisms that drive transport and how these mechanisms are compromised in disease.  The aim of this Special Issue is to present original research articles, commentaries, and review papers that describe new experimental and theoretical/computational research breakthroughs so as to shed further light on the molecular mechanisms of nuclear transport in health and disease.

Prof. Dr. Patrick R. Onck
Prof. Dr. Roderick Lim
Prof. Dr. Anton Zilman
Prof. Dr. Liesbeth Veenhoff
Guest Editors

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Keywords

  • nuclear transport
  • nuclear pore complex
  • intrinsically disordered proteins
  • nuclear transport receptors
  • molecular biology
  • biophysics

Published Papers (11 papers)

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Research

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25 pages, 1531 KiB  
Article
Effects of Sequence Composition, Patterning and Hydrodynamics on the Conformation and Dynamics of Intrinsically Disordered Proteins
by Andrei Vovk and Anton Zilman
Int. J. Mol. Sci. 2023, 24(2), 1444; https://doi.org/10.3390/ijms24021444 - 11 Jan 2023
Cited by 3 | Viewed by 1524
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) perform diverse functions in cellular organization, transport and signaling. Unlike the well-defined structures of the classical natively folded proteins, IDPs and IDRs dynamically span large conformational and structural ensembles. This dynamic disorder impedes the [...] Read more.
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) perform diverse functions in cellular organization, transport and signaling. Unlike the well-defined structures of the classical natively folded proteins, IDPs and IDRs dynamically span large conformational and structural ensembles. This dynamic disorder impedes the study of the relationship between the amino acid sequences of the IDPs and their spatial structures and dynamics, with different experimental techniques often offering seemingly contradictory results. Although experimental and theoretical evidence indicates that some IDP properties can be understood based on their average biophysical properties and amino acid composition, other aspects of IDP function are dictated by the specifics of the amino acid sequence. We investigate the effects of several key variables on the dimensions and the dynamics of IDPs using coarse-grained polymer models. We focus on the sequence “patchiness” informed by the sequence and biophysical properties of different classes of IDPs—and in particular FG nucleoporins of the nuclear pore complex (NPC). We show that the sequence composition and patterning are well reflected in the global conformational variables such as the radius of gyration and hydrodynamic radius, while the end-to-end distance and dynamics are highly sequence-specific. We find that in good solvent conditions highly heterogeneous sequences of IDPs can be well mapped onto averaged minimal polymer models for the purpose of prediction of the IDPs dimensions and dynamic relaxation times. The coarse-grained simulations are in a good agreement with the results of atomistic MD. We discuss the implications of these results for the interpretation of the recent experimental measurements, and for the further applications of mesoscopic models of FG nucleoporins and IDPs more broadly. Full article
(This article belongs to the Special Issue The Molecular Mechanisms of Nuclear Transport in Health and Disease)
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17 pages, 2511 KiB  
Article
p97/UBXD1 Generate Ubiquitylated Proteins That Are Sequestered into Nuclear Envelope Herniations in Torsin-Deficient Cells
by Sarah M. Prophet, Brigitte S. Naughton and Christian Schlieker
Int. J. Mol. Sci. 2022, 23(9), 4627; https://doi.org/10.3390/ijms23094627 - 21 Apr 2022
Cited by 4 | Viewed by 2206
Abstract
DYT1 dystonia is a debilitating neurological movement disorder that arises upon Torsin ATPase deficiency. Nuclear envelope (NE) blebs that contain FG-nucleoporins (FG-Nups) and K48-linked ubiquitin are the hallmark phenotype of Torsin manipulation across disease models of DYT1 dystonia. While the aberrant deposition of [...] Read more.
DYT1 dystonia is a debilitating neurological movement disorder that arises upon Torsin ATPase deficiency. Nuclear envelope (NE) blebs that contain FG-nucleoporins (FG-Nups) and K48-linked ubiquitin are the hallmark phenotype of Torsin manipulation across disease models of DYT1 dystonia. While the aberrant deposition of FG-Nups is caused by defective nuclear pore complex assembly, the source of K48-ubiquitylated proteins inside NE blebs is not known. Here, we demonstrate that the characteristic K48-ubiquitin accumulation inside blebs requires p97 activity. This activity is highly dependent on the p97 adaptor UBXD1. We show that p97 does not significantly depend on the Ufd1/Npl4 heterodimer to generate the K48-ubiquitylated proteins inside blebs, nor does inhibiting translation affect the ubiquitin sequestration in blebs. However, stimulating global ubiquitylation by heat shock greatly increases the amount of K48-ubiquitin sequestered inside blebs. These results suggest that blebs have an extraordinarily high capacity for sequestering ubiquitylated protein generated in a p97-dependent manner. The p97/UBXD1 axis is thus a major factor contributing to cellular DYT1 dystonia pathology and its modulation represents an unexplored potential for therapeutic development. Full article
(This article belongs to the Special Issue The Molecular Mechanisms of Nuclear Transport in Health and Disease)
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16 pages, 5323 KiB  
Article
Phosphorylation but Not Oligomerization Drives the Accumulation of Tau with Nucleoporin Nup98
by Lisa Diez, Larisa E. Kapinos, Janine Hochmair, Sabrina Huebschmann, Alvaro Dominguez-Baquero, Amelie Vogt, Marija Rankovic, Markus Zweckstetter, Roderick Y. H. Lim and Susanne Wegmann
Int. J. Mol. Sci. 2022, 23(7), 3495; https://doi.org/10.3390/ijms23073495 - 23 Mar 2022
Cited by 6 | Viewed by 2595
Abstract
Tau is a neuronal protein that stabilizes axonal microtubules (MTs) in the central nervous system. In Alzheimer’s disease (AD) and other tauopathies, phosphorylated Tau accumulates in intracellular aggregates, a pathological hallmark of these diseases. However, the chronological order of pathological changes in Tau [...] Read more.
Tau is a neuronal protein that stabilizes axonal microtubules (MTs) in the central nervous system. In Alzheimer’s disease (AD) and other tauopathies, phosphorylated Tau accumulates in intracellular aggregates, a pathological hallmark of these diseases. However, the chronological order of pathological changes in Tau prior to its cytosolic aggregation remains unresolved. These include its phosphorylation and detachment from MTs, mislocalization into the somatodendritic compartment, and oligomerization in the cytosol. Recently, we showed that Tau can interact with phenylalanine-glycine (FG)-rich nucleoporins (Nups), including Nup98, that form a diffusion barrier inside nuclear pore complexes (NPCs), leading to defects in nucleocytoplasmic transport. Here, we used surface plasmon resonance (SPR) and bio-layer interferometry (BLI) to investigate the molecular details of Tau:Nup98 interactions and determined how Tau phosphorylation and oligomerization impact the interactions. Importantly, phosphorylation, but not acetylation, strongly facilitates the accumulation of Tau with Nup98. Oligomerization, however, seems to inhibit Tau:Nup98 interactions, suggesting that Tau-FG Nup interactions occur prior to oligomerization. Overall, these results provide fundamental insights into the molecular mechanisms of Tau-FG Nup interactions within NPCs, which might explain how stress-and disease-associated posttranslational modifications (PTMs) may lead to Tau-induced nucleocytoplasmic transport (NCT) failure. Intervention strategies that could rescue Tau-induced NCT failure in AD and tauopathies will be further discussed. Full article
(This article belongs to the Special Issue The Molecular Mechanisms of Nuclear Transport in Health and Disease)
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12 pages, 4407 KiB  
Article
YB-1 Phosphorylation at Serine 209 Inhibits Its Nuclear Translocation
by Ekaterina M. Sogorina, Ekaterina R. Kim, Alexey V. Sorokin, Dmitry N. Lyabin, Lev P. Ovchinnikov, Daria A. Mordovkina and Irina A. Eliseeva
Int. J. Mol. Sci. 2022, 23(1), 428; https://doi.org/10.3390/ijms23010428 - 31 Dec 2021
Cited by 5 | Viewed by 2001
Abstract
YB-1 is a multifunctional DNA- and RNA-binding protein involved in cell proliferation, differentiation, and migration. YB-1 is a predominantly cytoplasmic protein that is transported to the nucleus in certain conditions, including DNA-damaging stress, transcription inhibition, and viral infection. In tumors, YB-1 nuclear localization [...] Read more.
YB-1 is a multifunctional DNA- and RNA-binding protein involved in cell proliferation, differentiation, and migration. YB-1 is a predominantly cytoplasmic protein that is transported to the nucleus in certain conditions, including DNA-damaging stress, transcription inhibition, and viral infection. In tumors, YB-1 nuclear localization correlates with high aggressiveness, multidrug resistance, and a poor prognosis. It is known that posttranslational modifications can regulate the nuclear translocation of YB-1. In particular, well-studied phosphorylation at serine 102 (S102) activates YB-1 nuclear import. Here, we report that Akt kinase phosphorylates YB-1 in vitro at serine 209 (S209), which is located in the vicinity of the YB-1 nuclear localization signal. Using phosphomimetic substitutions, we showed that S209 phosphorylation inhibits YB-1 nuclear translocation and prevents p-S102-mediated YB-1 nuclear import. Full article
(This article belongs to the Special Issue The Molecular Mechanisms of Nuclear Transport in Health and Disease)
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21 pages, 56949 KiB  
Article
Sequestosome 1 Is Part of the Interaction Network of VAPB
by Christina James, Christof Lenz, Henning Urlaub and Ralph H. Kehlenbach
Int. J. Mol. Sci. 2021, 22(24), 13271; https://doi.org/10.3390/ijms222413271 - 09 Dec 2021
Cited by 3 | Viewed by 2118
Abstract
VAPB (Vesicle-Associated-membrane Protein-associated protein B) is a tail-anchored membrane protein of the endoplasmic reticulum that can also be detected at the inner nuclear membrane. As a component of many contact sites between the endoplasmic reticulum and other organelles, VAPB is engaged in multiple [...] Read more.
VAPB (Vesicle-Associated-membrane Protein-associated protein B) is a tail-anchored membrane protein of the endoplasmic reticulum that can also be detected at the inner nuclear membrane. As a component of many contact sites between the endoplasmic reticulum and other organelles, VAPB is engaged in multiple protein interactions with a plethora of binding partners. A mutant version of VAPB, P56S-VAPB, which results from a single point mutation, is involved in a familial form of amyotrophic lateral sclerosis (ALS8). We performed RAPIDS (rapamycin- and APEX-dependent identification of proteins by SILAC) to identify proteins that interact with or are in close proximity to P56S-VAPB. The mutation abrogates the interaction of VAPB with many known binding partners. Here, we identify Sequestosome 1 (SQSTM1), a well-known autophagic adapter protein, as a major interaction/proximity partner of P56S-VAPB. Remarkably, not only the mutant protein, but also wild-type VAPB interacts with SQSTM1, as shown by proximity ligation assays and co-immunoprecipiation experiments. Full article
(This article belongs to the Special Issue The Molecular Mechanisms of Nuclear Transport in Health and Disease)
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15 pages, 1671 KiB  
Article
Characterizing Binding Interactions That Are Essential for Selective Transport through the Nuclear Pore Complex
by Kathleen M. Lennon, Mohammad Soheilypour, Mohaddeseh Peyro, Devin L. Wakefield, Grace E. Choo, Mohammad R. K. Mofrad and Tijana Jovanovic-Talisman
Int. J. Mol. Sci. 2021, 22(19), 10898; https://doi.org/10.3390/ijms221910898 - 08 Oct 2021
Cited by 7 | Viewed by 2102
Abstract
Specific macromolecules are rapidly transported across the nuclear envelope via the nuclear pore complex (NPC). The selective transport process is facilitated when nuclear transport receptors (NTRs) weakly and transiently bind to intrinsically disordered constituents of the NPC, FG Nups. These two types of [...] Read more.
Specific macromolecules are rapidly transported across the nuclear envelope via the nuclear pore complex (NPC). The selective transport process is facilitated when nuclear transport receptors (NTRs) weakly and transiently bind to intrinsically disordered constituents of the NPC, FG Nups. These two types of proteins help maintain the selective NPC barrier. To interrogate their binding interactions in vitro, we deployed an NPC barrier mimic. We created the stationary phase by covalently attaching fragments of a yeast FG Nup called Nsp1 to glass coverslips. We used a tunable mobile phase containing NTR, nuclear transport factor 2 (NTF2). In the stationary phase, three main factors affected binding: the number of FG repeats, the charge of fragments, and the fragment density. We also identified three main factors affecting binding in the mobile phase: the avidity of the NTF2 variant for Nsp1, the presence of nonspecific proteins, and the presence of additional NTRs. We used both experimentally determined binding parameters and molecular dynamics simulations of Nsp1FG fragments to create an agent-based model. The results suggest that NTF2 binding is negatively cooperative and dependent on the density of Nsp1FG molecules. Our results demonstrate the strengths of combining experimental and physical modeling approaches to study NPC-mediated transport. Full article
(This article belongs to the Special Issue The Molecular Mechanisms of Nuclear Transport in Health and Disease)
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Review

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12 pages, 1735 KiB  
Review
Function of the Nuclear Transport Machinery in Maintaining the Distinctive Compositions of the Nucleus and Cytoplasm
by Murray Stewart
Int. J. Mol. Sci. 2022, 23(5), 2578; https://doi.org/10.3390/ijms23052578 - 25 Feb 2022
Cited by 13 | Viewed by 3760
Abstract
Although the separation of transcription and translation, mediated by the nuclear envelope, is the defining characteristic of Eukaryotes, the barrier between the nuclear and cytoplasmic compartments needs to be semipermeable to enable material to be moved between them. Moreover, each compartment needs to [...] Read more.
Although the separation of transcription and translation, mediated by the nuclear envelope, is the defining characteristic of Eukaryotes, the barrier between the nuclear and cytoplasmic compartments needs to be semipermeable to enable material to be moved between them. Moreover, each compartment needs to have a distinctive complement of macromolecules to mediate specific functions and so movement between them needs to be controlled. This is achieved through the selective active transport of macromolecules through the nuclear pores that stud the nuclear envelope, and which serve as a conduit between these compartments. Nuclear pores are huge cylindrical macromolecular assemblies and are constructed from the order of 30 different proteins called nucleoporins. Nuclear pores have a central transport channel that is filled with a dense network of natively unfolded portions of many different nuclear pore proteins (nucleoporins or nups). This network generates a barrier that impedes, but does not entirely prevent, the diffusion of many macromolecules through the pores. The rapid movement of a range of proteins and RNAs through the pores is mediated by a range of transport factors that bind their cargo in one compartment and release it in the other. However, although as their size increases the diffusion of macromolecules through nuclear pores is progressively impaired, additional mechanisms, including the binding of some macromolecules to immobile components of each compartment and also the active removal of macromolecules from the inappropriate compartment, are needed to fully maintain the distinctive compositions of each compartment. Full article
(This article belongs to the Special Issue The Molecular Mechanisms of Nuclear Transport in Health and Disease)
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12 pages, 1271 KiB  
Review
Emerging Connections between Nuclear Pore Complex Homeostasis and ALS
by Sunandini Chandra and C. Patrick Lusk
Int. J. Mol. Sci. 2022, 23(3), 1329; https://doi.org/10.3390/ijms23031329 - 25 Jan 2022
Cited by 10 | Viewed by 3917
Abstract
Developing effective treatments for neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) requires understanding of the underlying pathomechanisms that contribute to the motor neuron loss that defines the disease. As it causes the largest fraction of familial ALS cases, considerable effort has focused [...] Read more.
Developing effective treatments for neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) requires understanding of the underlying pathomechanisms that contribute to the motor neuron loss that defines the disease. As it causes the largest fraction of familial ALS cases, considerable effort has focused on hexanucleotide repeat expansions in the C9ORF72 gene, which encode toxic repeat RNA and dipeptide repeat (DPR) proteins. Both the repeat RNA and DPRs interact with and perturb multiple elements of the nuclear transport machinery, including shuttling nuclear transport receptors, the Ran GTPase and the nucleoporin proteins (nups) that build the nuclear pore complex (NPC). Here, we consider recent work that describes changes to the molecular composition of the NPC in C9ORF72 model and patient neurons in the context of quality control mechanisms that function at the nuclear envelope (NE). For example, changes to NPC structure may be caused by the dysregulation of a conserved NE surveillance pathway mediated by the endosomal sorting complexes required for the transport protein, CHMP7. Thus, these studies are introducing NE and NPC quality control pathways as key elements in a pathological cascade that leads to C9ORF72 ALS, opening entirely new experimental avenues and possibilities for targeted therapeutic intervention. Full article
(This article belongs to the Special Issue The Molecular Mechanisms of Nuclear Transport in Health and Disease)
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25 pages, 1748 KiB  
Review
The Role of Nucleocytoplasmic Transport Defects in Amyotrophic Lateral Sclerosis
by Joni Vanneste and Ludo Van Den Bosch
Int. J. Mol. Sci. 2021, 22(22), 12175; https://doi.org/10.3390/ijms222212175 - 10 Nov 2021
Cited by 11 | Viewed by 2607
Abstract
There is ample evidence that nucleocytoplasmic-transport deficits could play an important role in the pathology of amyotrophic lateral sclerosis (ALS). However, the currently available data are often circumstantial and do not fully clarify the exact causal and temporal role of nucleocytoplasmic transport deficits [...] Read more.
There is ample evidence that nucleocytoplasmic-transport deficits could play an important role in the pathology of amyotrophic lateral sclerosis (ALS). However, the currently available data are often circumstantial and do not fully clarify the exact causal and temporal role of nucleocytoplasmic transport deficits in ALS patients. Gaining this knowledge will be of great significance in order to be able to target therapeutically nucleocytoplasmic transport and/or the proteins involved in this process. The availability of good model systems to study the nucleocytoplasmic transport process in detail will be especially crucial in investigating the effect of different mutations, as well as of other forms of stress. In this review, we discuss the evidence for the involvement of nucleocytoplasmic transport defects in ALS and the methods used to obtain these data. In addition, we provide an overview of the therapeutic strategies which could potentially counteract these defects. Full article
(This article belongs to the Special Issue The Molecular Mechanisms of Nuclear Transport in Health and Disease)
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20 pages, 5491 KiB  
Review
The Great Escape: mRNA Export through the Nuclear Pore Complex
by Paola De Magistris
Int. J. Mol. Sci. 2021, 22(21), 11767; https://doi.org/10.3390/ijms222111767 - 29 Oct 2021
Cited by 15 | Viewed by 3358
Abstract
Nuclear export of messenger RNA (mRNA) through the nuclear pore complex (NPC) is an indispensable step to ensure protein translation in the cytoplasm of eukaryotic cells. mRNA is not translocated on its own, but it forms ribonuclear particles (mRNPs) in association with proteins [...] Read more.
Nuclear export of messenger RNA (mRNA) through the nuclear pore complex (NPC) is an indispensable step to ensure protein translation in the cytoplasm of eukaryotic cells. mRNA is not translocated on its own, but it forms ribonuclear particles (mRNPs) in association with proteins that are crucial for its metabolism, some of which; like Mex67/MTR2-NXF1/NXT1; are key players for its translocation to the cytoplasm. In this review, I will summarize our current body of knowledge on the basic characteristics of mRNA export through the NPC. To be granted passage, the mRNP cargo needs to bind transport receptors, which facilitate the nuclear export. During NPC transport, mRNPs undergo compositional and conformational changes. The interactions between mRNP and the central channel of NPC are described; together with the multiple quality control steps that mRNPs undergo at the different rings of the NPC to ensure only proper export of mature transcripts to the cytoplasm. I conclude by mentioning new opportunities that arise from bottom up approaches for a mechanistic understanding of nuclear export. Full article
(This article belongs to the Special Issue The Molecular Mechanisms of Nuclear Transport in Health and Disease)
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21 pages, 2126 KiB  
Review
Measuring and Interpreting Nuclear Transport in Neurodegenerative Disease—The Example of C9orf72 ALS
by Marije F. W. Semmelink, Anton Steen and Liesbeth M. Veenhoff
Int. J. Mol. Sci. 2021, 22(17), 9217; https://doi.org/10.3390/ijms22179217 - 26 Aug 2021
Cited by 6 | Viewed by 4687
Abstract
Transport from and into the nucleus is essential to all eukaryotic life and occurs through the nuclear pore complex (NPC). There are a multitude of data supporting a role for nuclear transport in neurodegenerative diseases, but actual transport assays in disease models have [...] Read more.
Transport from and into the nucleus is essential to all eukaryotic life and occurs through the nuclear pore complex (NPC). There are a multitude of data supporting a role for nuclear transport in neurodegenerative diseases, but actual transport assays in disease models have provided diverse outcomes. In this review, we summarize how nuclear transport works, which transport assays are available, and what matters complicate the interpretation of their results. Taking a specific type of ALS caused by mutations in C9orf72 as an example, we illustrate these complications, and discuss how the current data do not firmly answer whether the kinetics of nucleocytoplasmic transport are altered. Answering this open question has far-reaching implications, because a positive answer would imply that widespread mislocalization of proteins occurs, far beyond the reported mislocalization of transport reporters, and specific proteins such as FUS, or TDP43, and thus presents a challenge for future research. Full article
(This article belongs to the Special Issue The Molecular Mechanisms of Nuclear Transport in Health and Disease)
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