Visualizing the disordered nuclear transport machinery in situ

Nature, Journal Year: 2023, Volume and Issue: 617(7959), P. 162 - 169

Published: April 26, 2023

Abstract The approximately 120 MDa mammalian nuclear pore complex (NPC) acts as a gatekeeper for the transport between nucleus and cytosol 1 . central channel of NPC is filled with hundreds intrinsically disordered proteins (IDPs) called FG-nucleoporins (FG-NUPs) 2,3 Although structure scaffold has been resolved in remarkable detail, actual machinery built up by FG-NUPs—about 50 MDa—is depicted an 60-nm hole even highly tomograms and/or structures computed artificial intelligence 4–11 Here we directly probed conformations vital FG-NUP98 inside NPCs live cells permeabilized intact using synthetic biology-enabled site-specific small-molecule labelling approach paired time-resolved fluorescence microscopy. Single cell measurements distance distribution segments combined coarse-grained molecular simulations allowed us to map uncharted environment nanosized channel. We determined that provides—in terminology Flory polymer theory 12 —a ‘good solvent’ environment. This enables FG domain adopt expanded thus control cytoplasm. With more than 30% proteome being formed from IDPs, our study opens window into resolving disorder–function relationships IDPs situ, which are important various processes, such cellular signalling, phase separation, ageing viral entry.

Language: Английский

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The molecular architecture of the nuclear basket

Cell, Journal Year: 2024, Volume and Issue: 187(19), P. 5267 - 5281.e13

Published: Aug. 9, 2024

The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, peripheral regions can exhibit considerable variation within and between species. One such structure cage-like basket. crucial roles mRNA surveillance chromatin organization, an architectural has remained elusive. Using in-cell cryo-electron tomography subtomogram analysis, we explored NPC's structural variations basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), protozoa (T. gondii). integrative modeling, computed a model yeast that revealed how hub nucleoporins (Nups) ring binds to basket-forming Mlp/Tpr proteins: coiled-coil domains form struts basket, while their unstructured termini constitute distal densities, which potentially serve as docking site for preprocessing before

Language: Английский

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The Nuclear Pore Complex: Birth, Life, and Death of a Cellular Behemoth

Cells, Journal Year: 2022, Volume and Issue: 11(9), P. 1456 - 1456

Published: April 25, 2022

Nuclear pore complexes (NPCs) are the only transport channels that cross nuclear envelope. Constructed from ~500–1000 nucleoporin proteins each, they among largest macromolecular assemblies in eukaryotic cells. Thanks to advances structural analysis approaches, construction principles and architecture of NPC have recently been revealed at submolecular resolution. Although overall structure inventory nucleoporins conserved, NPCs exhibit significant compositional functional plasticity even within single cells surprising variability their assembly pathways. Once assembled, remain seemingly unexchangeable post-mitotic There a number as yet unresolved questions about how versatility composition is established, monitor state or could be renewed. Here, we review current progress our understanding key aspects lifecycle.

Language: Английский

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Sculpting nuclear envelope identity from the endoplasmic reticulum during the cell cycle

Nucleus, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 18, 2024

The nuclear envelope (NE) regulates functions, including transcription, nucleocytoplasmic transport, and protein quality control. While the outer membrane of NE is directly continuous with endoplasmic reticulum (ER), has an overall distinct composition from ER, which crucial for its functions. During open mitosis in higher eukaryotes, disassembles during mitotic entry then reforms as a functional territory at end to reestablish compartmentalization. In this review, we examine known mechanisms by reconstitutes ER ER–NE endomembrane system mitosis. Furthermore, based on recent findings indicating that possesses unique lipid metabolism control those explore maintenance identity homeostasis interphase. We also highlight potential significance junctions between NE.

Language: Английский

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Nuclear pore dysfunction and disease: a complex opportunity

Nucleus, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 21, 2024

The separation of genetic material from bulk cytoplasm has enabled the evolution increasingly complex organisms, allowing for development sophisticated forms life. However, this complexity created new categories dysfunction, including those related to movement between cellular compartments. In eukaryotic cells, nucleocytoplasmic trafficking is a fundamental biological process, and cumulative disruptions nuclear integrity transport are detrimental cell survival. This particularly true in post-mitotic neurons, where pore injury errors strongly associated with neurodegenerative disease. review, we summarize current understanding biology physiological pathological contexts discuss potential therapeutic approaches addressing dysfunctional transport.

Language: Английский

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Nuclear pores safeguard the integrity of the nuclear envelope

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 5, 2024

Abstract Nuclear pore complexes (NPCs) constitute giant channels within the nuclear envelope that mediate nucleocytoplasmic exchange. NPC diameter is thought to be regulated by tension, but how such changes are physiologically linked cell differentiation, where mechanical properties of nuclei remodeled and mechanosensing occurs, remains unstudied. Here we used cryo-electron tomography show NPCs dilate during differentiation mouse embryonic stem cells into neural progenitors. In Nup133-deficient cells, which known display impaired however fail dilate. By analyzing architectures individual with template matching, revealed structurally heterogeneous frequently disintegrate, resulting in formation large openings. We propose elasticity scaffold mechanically safeguards envelope. Our studies provide a molecular explanation for genetic perturbation scaffolding components macromolecular causes tissue-specific phenotypes.

Language: Английский

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PDB-IHM: A system for deposition, curation, validation, and dissemination of integrative structures

Journal of Molecular Biology, Journal Year: 2025, Volume and Issue: unknown, P. 168963 - 168963

Published: Jan. 1, 2025

Language: Английский

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Nuclear pore complex proteins are involved in centromere distribution

iScience, Journal Year: 2024, Volume and Issue: 27(2), P. 108855 - 108855

Published: Jan. 11, 2024

The subnuclear distribution of centromeres is cooperatively regulated by condensin II and the linker nucleoskeleton cytoskeleton (LINC) complex. However, other nuclear membrane structures proteins are probably involved in centromere dynamics distribution. Here, we focused on pore complex (NPC), which known to regulate gene expression, transcription memory, chromatin structure addition transport between cytoplasm nucleoplasm. We report here that some nucleoporins (Nups), including Nup85, Nup133, CG1, Nup93b, NUA, scattering

Language: Английский

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Conformational dynamics of the nuclear pore complex central channel

Biochemical Society Transactions, Journal Year: 2025, Volume and Issue: 53(01)

Published: Feb. 7, 2025

The nuclear pore complex (NPC) is a vital regulator of molecular transport between the nucleus and cytoplasm in eukaryotic cells. At heart NPC’s function are intrinsically disordered phenylalanineglycine-rich nucleoporins (FG-Nups), which form dynamic permeability barrier within central channel. This nature facilitates efficient nucleocytoplasmic but also poses significant challenges to its characterization, especially nano-confined environment NPC. Recent advances experimental techniques, such as cryo-electron microscopy, atomic force fluorescence magnetic resonance, along with computational modeling, have illuminated conformational flexibility FG-Nups, underpins their functional versatility. review synthesizes these advancements, emphasizing how disruptions FG-Nup behavior—caused by mutations or pathological interactions—contribute diseases neurodegenerative disorders, aging-related decline, viral infections. Despite progress, persist deciphering dynamics crowded cellular environment, under conditions. Addressing gaps critical for advancing therapeutic strategies targeting NPC dysfunction disease progression.

Language: Английский

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Integrative spatiotemporal modeling of biomolecular processes: Application to the assembly of the nuclear pore complex

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(11)

Published: March 14, 2025

Dynamic processes involving biomolecules are essential for the function of cell. Here, we introduce an integrative method computing models these based on multiple heterogeneous sources information, including time-resolved experimental data and physical dynamic processes. First, each time point, a set coarse compositional structural heterogeneity is computed (heterogeneity models). Second, model, static structure (a snapshot model). Finally, selected connected into series trajectories that optimize likelihood both transitions between them trajectory The demonstrated by application to assembly process human nuclear pore complex in context reforming envelope during mitotic cell division, live-cell correlated electron tomography, bulk fluorescence correlation spectroscopy–calibrated quantitative live imaging, model fully assembled complex. Modeling improves precision over modeling alone. applicable wide range time-dependent systems biology available broader scientific community through implementation open source Integrative Platform (IMP) software.

Language: Английский

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