scholarly journals Simple rules for passive diffusion through the nuclear pore complex

2016 ◽  
Vol 215 (1) ◽  
pp. 57-76 ◽  
Author(s):  
Benjamin L. Timney ◽  
Barak Raveh ◽  
Roxana Mironska ◽  
Jill M. Trivedi ◽  
Seung Joong Kim ◽  
...  
Keyword(s):  
Brownian Dynamics ◽  
Passive Diffusion ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Entropic Repulsion ◽  
Time Resolved ◽  
Dynamics Simulations ◽  
Pore Complexes ◽  
Size Threshold

Passive macromolecular diffusion through nuclear pore complexes (NPCs) is thought to decrease dramatically beyond a 30–60-kD size threshold. Using thousands of independent time-resolved fluorescence microscopy measurements in vivo, we show that the NPC lacks such a firm size threshold; instead, it forms a soft barrier to passive diffusion that intensifies gradually with increasing molecular mass in both the wild-type and mutant strains with various subsets of phenylalanine-glycine (FG) domains and different levels of baseline passive permeability. Brownian dynamics simulations replicate these findings and indicate that the soft barrier results from the highly dynamic FG repeat domains and the diffusing macromolecules mutually constraining and competing for available volume in the interior of the NPC, setting up entropic repulsion forces. We found that FG domains with exceptionally high net charge and low hydropathy near the cytoplasmic end of the central channel contribute more strongly to obstruction of passive diffusion than to facilitated transport, revealing a compartmentalized functional arrangement within the NPC.

scholarly journals Size-dependent leak of soluble and membrane proteins through the yeast nuclear pore complex

2015 ◽  
Vol 26 (7) ◽  
pp. 1386-1394 ◽  
Author(s):  
Petra Popken ◽  
Ali Ghavami ◽  
Patrick R. Onck ◽  
Bert Poolman ◽  
Liesbeth M. Veenhoff
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Coarse Grained ◽  
Nuclear Pore ◽  
Permeability Barrier ◽  
Nuclear Pore Complexes ◽  
Structural And Functional Properties ◽  
Dynamics Simulations ◽  
Pore Complexes

Nuclear pore complexes (NPCs) allow selective import and export while forming a barrier for untargeted proteins. Using fluorescence microscopy, we measured in vivo the permeability of the Saccharomyces cerevisiae NPC for multidomain proteins of different sizes and found that soluble proteins of 150 kDa and membrane proteins with an extralumenal domain of 90 kDa were still partly localized in the nucleus on a time scale of hours. The NPCs thus form only a weak barrier for the majority of yeast proteins, given their monomeric size. Using FGΔ-mutant strains, we showed that specific combinations of Nups, especially with Nup100, but not the total mass of FG-nups per pore, were important for forming the barrier. Models of the disordered phase of wild-type and mutant NPCs were generated using a one bead per amino acid molecular dynamics model. The permeability measurements correlated with the density predictions from coarse-grained molecular dynamics simulations in the center of the NPC. The combined in vivo and computational approach provides a framework for elucidating the structural and functional properties of the permeability barrier of nuclear pore complexes.

Recombinant Nup153 Incorporates in Vivo into Xenopus Oocyte Nuclear Pore Complexes

2000 ◽  
Vol 129 (2-3) ◽  
pp. 306-312 ◽  
Author(s):  
Nelly Panté ◽  
Franziska Thomas ◽  
Ueli Aebi ◽  
Brian Burke ◽  
Ricardo Bastos
Keyword(s):  
Xenopus Oocyte ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Pore Complexes

scholarly journals Internuclear exchange of an inner nuclear membrane protein (p55) in heterokaryons: in vivo evidence for the interaction of p55 with the nuclear lamina.

1990 ◽  
Vol 111 (6) ◽  
pp. 2225-2234 ◽  
Author(s):  
L Powell ◽  
B Burke
Keyword(s):  
Nuclear Membrane ◽  
Lateral Diffusion ◽  
Nuclear Lamina ◽  
Membrane System ◽  
Mouse Cell ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Inner Nuclear Membrane ◽  
Pore Complexes

The movement between nuclei of an integral protein of the inner nuclear membrane has been studied in rat/mouse and rat/hamster heterokaryons. This protein, p55, was found to equilibrate between nuclei over a period of approximately 6 h in the absence of new protein synthesis. When rat/mouse heterokaryons were constructed using an undifferentiated murine embryonal carcinoma (P19), which lacks lamins A and C, no accumulation of p55 in the mouse cell nucleus was observed. However, P19 nuclei could be rendered competent to accumulate p55 by transfecting the parent cells with human lamin A before cell fusion, supporting the notion that p55 may interact with the nuclear lamina. Since p55 does not appear to be able to dissociate from the nuclear membrane, it is concluded that this exchange between nuclei does not occur in the aqueous phase and instead is probably membrane mediated. It is proposed that this protein may be free to move between the inner and outer nuclear membranes via the continuities at the nuclear pore complexes and that transfer between nuclei occurs via lateral diffusion through the peripheral ER, which appears to form a single continuous membrane system in these heterokaryons. One implication of these observations is that accumulation of at least some integral proteins in the inner nuclear membrane may be mediated by interactions with other nuclear components and may not require a single defined targeting sequence.

scholarly journals Nuclear protein import is inhibited by an antibody to a lumenal epitope of a nuclear pore complex glycoprotein.

1992 ◽  
Vol 116 (1) ◽  
pp. 15-30 ◽  
Author(s):  
U F Greber ◽  
L Gerace
Keyword(s):  
Nuclear Pore Complex ◽  
Protein Import ◽  
Nuclear Protein ◽  
Complex Structure ◽  
Passive Diffusion ◽  
Nuclear Pore ◽  
Transport Inhibition ◽  
Cell Progression ◽  
Pore Complexes

Gp210 is a major transmembrane glycoprotein associated with the nuclear pore complex that is suggested to be important for organizing pore complex architecture and assembly. A mouse monoclonal IgG directed against an epitope in the lumenal domain of rat gp210 was expressed in cultured rat cells by microinjection of mRNA prepared from a hybridoma cell line. The expressed IgG, which becomes assembled into a functional antibody in the lumen of the endoplasmic reticulum, bound to the nuclear envelope in vivo. Expression of anti-gp210 antibody in interphase cells specifically reduced approximately fourfold the mediated nuclear import of a microinjected nuclear protein (nucleoplasmin) coupled to gold particles. The antibody also significantly decreased nuclear influx of a 10-kD dextran by passive diffusion. This transport inhibition did not result from removal of pore complexes from nuclear membranes or from gross alterations in pore complex structure, as shown by EM and immunocytochemistry. A physiological consequence of this transport inhibition was inhibition of cell progression from G2 into M phase. Hence, binding of this antibody to the lumenal side of gp210 must have a transmembrane effect on the structure and functions of the pore complex. These data argue that gp210 is directly or indirectly connected to pore complex constituents involved in mediated import and passive diffusion.

scholarly journals NDC1 is necessary for stable assembly of the nuclear pore scaffold to establish nuclear transport in early C. elegans embryos

2021 ◽  
Author(s):  
Michael Sean Mauro ◽  
Gunta Celma ◽  
Vitaly Zimyanin ◽  
Kimberley H. Gibson ◽  
Stefanie Redemann ◽  
...  
Keyword(s):  
Outer Ring ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
3D Analysis ◽  
Protein Assemblies ◽  
C Elegans ◽  
Nuclear Assembly ◽  
Stable Association ◽  
Pore Complexes

Nuclear pore complexes (NPCs) are large protein assemblies that facilitate transport of macromolecules across the nuclear envelope (NE) [1, 2]. How thousands of NPCs rapidly assemble to form a functional NE after open mitosis is not known. Recruitment of the outer ring Nup107-160 complex to the NE initiates NPC assembly. The Nup53/93 complex bridges the outer ring to the central channel to form a functional pore [3-6]. Nup53 interacts with the conserved transmembrane nucleoporin Ndc1; however, how Ndc1 contributes to post-mitotic NPC assembly is unclear [7-9]. Here, we use C. elegans embryos to show that the timely formation of a functional NE after mitosis depends on Ndc1. Endogenously tagged Ndc1 is recruited early to the reforming NE and is highly mobile in the nuclear rim. 3D analysis of NE reformation revealed a significant decrease in NPC density in ndc1 deleted embryos: continuous nuclear membranes contained few holes where NPCs are normally located. Nup160 is highly mobile in NEs depleted of Ndc1 and outer ring scaffold components are less enriched at the rim. Nup160 is not recruited to the nuclear rim when both ndc1 and nup53 are absent and nuclear assembly fails. This suggests that Ndc1 and Nup53 function in part in parallel pathways to drive post-mitotic nuclear assembly in vivo. Together, we show that Ndc1 dynamically associates with the NE and promotes stable association of the outer ring scaffold with nascent NEs to facilitate NPC assembly after open mitosis, revealing a previously uncharacterized role for Ndc1 in forming functional NE.

scholarly journals Determination of the intracellular state of soluble macromolecules by gel filtration in vivo in the cytoplasm of amphibian oocytes.

1986 ◽  
Vol 102 (6) ◽  
pp. 2006-2014 ◽  
Author(s):  
M C Dabauvalle ◽  
W W Franke
Keyword(s):  
Light And Electron Microscopy ◽  
Gel Filtration ◽  
Size Exclusion ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Metabolic Labeling ◽  
Two Dimensional Gel Electrophoresis ◽  
Pore Complexes

A method to examine the diffusible state and the sizes of major cytoplasmic proteins in a living cell is described. Small (40-300 microns) commercially available gel filtration beads of a broad range of Mr exclusion limits were microsurgically implanted into the cytoplasm of oocytes of the frog, Xenopus laevis, usually after metabolic labeling of oocyte proteins with [35S]methionine. After equilibration in vivo for several hours, the appearance of the implanted cells, notably the bead-cytoplasm boundary, was examined by light and electron microscopy of sections and found to be unaffected. After incubation the beads were isolated, briefly rinsed, and their protein contents examined by one- or two-dimensional gel electrophoresis. We show that diffusible proteins can be identified by their inclusion in the pores of the gel filtration beads used and that their approximate sizes can be estimated from the size exclusion values of the specific materials used. The application of this method to important cell biological questions is demonstrated by showing that several "karyophobic proteins," i.e., proteins of the cytosolic fraction which accumulate in the cytoplasm in vivo, are indeed diffusible in the living oocyte and appear with sizes similar to those determined in vitro. This indicates that the nucleo-cytoplasmic distribution of certain diffusible proteins is governed, in addition to size exclusion at nuclear pore complexes and karyophilic "signals," by other, as yet unknown forces. Some possible applications of this method of gel filtration in vivo are discussed.

scholarly journals The FG-repeat asymmetry of the nuclear pore complex is dispensable for bulk nucleocytoplasmic transport in vivo

2004 ◽  
Vol 167 (4) ◽  
pp. 583-590 ◽  
Author(s):  
Bryan Zeitler ◽  
Karsten Weis
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Nuclear Pore Complex ◽  
Nucleocytoplasmic Transport ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Nucleocytoplasmic Trafficking ◽  
Transport Pathways ◽  
Pore Complexes ◽  
Biased Distribution

Nucleocytoplasmic transport occurs through gigantic proteinaceous channels called nuclear pore complexes (NPCs). Translocation through the NPC is exquisitely selective and is mediated by interactions between soluble transport carriers and insoluble NPC proteins that contain phenylalanine-glycine (FG) repeats. Although most FG nucleoporins (Nups) are organized symmetrically about the planar axis of the nuclear envelope, very few localize exclusively to one side of the NPC. We constructed Saccharomyces cerevisiae mutants with asymmetric FG repeats either deleted or swapped to generate NPCs with inverted FG asymmetry. The mutant Nups localize properly within the NPC and exhibit exchanged binding specificity for the export factor Xpo1. Surprisingly, we were unable to detect any defects in the Kap95, Kap121, Xpo1, or mRNA transport pathways in cells expressing the mutant FG Nups. These findings suggest that the biased distribution of FG repeats is not required for major nucleocytoplasmic trafficking events across the NPC.

scholarly journals Caenorhabditis elegans Nucleoporins Nup93 and Nup205 Determine the Limit of Nuclear Pore Complex Size Exclusion In Vivo

2003 ◽  
Vol 14 (12) ◽  
pp. 5104-5115 ◽  
Author(s):  
Vincent Galy ◽  
Iain W. Mattaj ◽  
Peter Askjaer
Keyword(s):  
Caenorhabditis Elegans ◽  
Nuclear Envelope ◽  
Protein Import ◽  
Chromatin Condensation ◽  
Size Exclusion ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
C Elegans ◽  
Pore Complexes

Nuclear pore complexes (NPCs) span the nuclear envelope and mediate communication between the nucleus and the cytoplasm. To obtain insight into the structure and function of NPCs of multicellular organisms, we have initiated an extensive analysis of Caenorhabditis elegans nucleoporins. Of 20 assigned C. elegans nucleoporin genes, 17 were found to be essential for embryonic development either alone or in combination. In several cases, depletion of nucleoporins by RNAi caused severe defects in nuclear appearance. More specifically, the C. elegans homologs of vertebrate Nup93 and Nup205 were each found to be required for normal NPC distribution in the nuclear envelope in vivo. Depletion of Nup93 or Nup205 caused a failure in nuclear exclusion of nonnuclear macromolecules of ∼70 kDa without preventing active nuclear protein import or the assembly of the nuclear envelope. The defects in NPC exclusion were accompanied by abnormal chromatin condensation and early embryonic arrest. Thus, the contribution to NPC structure of Nup93 and Nup205 is essential for establishment of normal NPC function and for cell viability.

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