1
|
Matsuda A, Mansour A, Mofrad MRK. Deciphering the intrinsically disordered characteristics of the FG-Nups through the lens of polymer physics. Nucleus 2024; 15:2399247. [PMID: 39282864 PMCID: PMC11407397 DOI: 10.1080/19491034.2024.2399247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
The nuclear pore complex (NPC) is a critical gateway regulating molecular transport between the nucleus and cytoplasm. It allows small molecules to pass freely, while larger molecules require nuclear transport receptors to traverse the barrier. This selective permeability is maintained by phenylalanine-glycine-rich nucleoporins (FG-Nups), intrinsically disordered proteins that fill the NPC's central channel. The disordered and flexible nature of FG-Nups complicates their spatial characterization with conventional structural biology techniques. To address this challenge, polymer physics offers a valuable framework for describing FG-Nup behavior, reducing their complex structures to a few key parameters. In this review, we explore how polymer physics models FG-Nups using these parameters and discuss experimental efforts to quantify them in various contexts, providing insights into the conformational properties of FG-Nups.
Collapse
Affiliation(s)
- Atsushi Matsuda
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Abdullah Mansour
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| |
Collapse
|
2
|
Skowicki M, Tarvirdipour S, Kraus M, Schoenenberger CA, Palivan CG. Nanoassemblies designed for efficient nuclear targeting. Adv Drug Deliv Rev 2024; 211:115354. [PMID: 38857762 DOI: 10.1016/j.addr.2024.115354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
One of the key aspects of coping efficiently with complex pathological conditions is delivering the desired therapeutic compounds with precision in both space and time. Therefore, the focus on nuclear-targeted delivery systems has emerged as a promising strategy with high potential, particularly in gene therapy and cancer treatment. Here, we explore the design of supramolecular nanoassemblies as vehicles to deliver specific compounds to the nucleus, with the special focus on polymer and peptide-based carriers that expose nuclear localization signals. Such nanoassemblies aim at maximizing the concentration of genetic and therapeutic agents within the nucleus, thereby optimizing treatment outcomes while minimizing off-target effects. A complex scenario of conditions, including cellular uptake, endosomal escape, and nuclear translocation, requires fine tuning of the nanocarriers' properties. First, we introduce the principles of nuclear import and the role of nuclear pore complexes that reveal strategies for targeting nanosystems to the nucleus. Then, we provide an overview of cargoes that rely on nuclear localization for optimal activity as their integrity and accumulation are crucial parameters to consider when designing a suitable delivery system. Considering that they are in their early stages of research, we present various cargo-loaded peptide- and polymer nanoassemblies that promote nuclear targeting, emphasizing their potential to enhance therapeutic response. Finally, we briefly discuss further advancements for more precise and effective nuclear delivery.
Collapse
Affiliation(s)
- Michal Skowicki
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Shabnam Tarvirdipour
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Manuel Kraus
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
| |
Collapse
|
3
|
Feng Q, Saladin M, Wu C, Cao E, Zheng W, Zhang A, Bhardwaj P, Li X, Shen Q, Kapinos LE, Mariappan M, Lusk CP, Xiong Y, Lim RYH, Lin C. Channel width modulates the permeability of DNA origami based nuclear pore mimics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593438. [PMID: 38766144 PMCID: PMC11100828 DOI: 10.1101/2024.05.09.593438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Nucleoporins (nups) in the central channel of nuclear pore complexes (NPCs) form a selective barrier that suppresses the diffusion of most macromolecules while enabling rapid transport of nuclear transport receptors (NTRs) with bound cargos. The complex molecular interactions between nups and NTRs have been thought to underlie the gatekeeping function of the NPC. Recent studies have shown considerable variation in NPC diameter but how altering NPC diameter might impact the selective barrier properties remains unclear. Here, we build DNA nanopores with programmable diameters and nup arrangement to mimic NPCs of different diameters. We use hepatitis B virus (HBV) capsids as a model for large-size cargos. We find that Nup62 proteins form a dynamic cross-channel meshwork impermeable to HBV capsids when grafted on the interior of 60-nm wide nanopores but not in 79-nm pores, where Nup62 cluster locally. Furthermore, importing substantially changes the dynamics of Nup62 assemblies and facilitates the passage of HBV capsids through NPC mimics containing Nup62 and Nup153. Our study shows the transport channel width is critical to the permeability of nup barriers and underscores the role of NTRs in dynamically remodeling nup assemblies and mediating the nuclear entry of viruses.
Collapse
Affiliation(s)
- Qingzhou Feng
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Chunxiang Wu
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Eason Cao
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | - Wei Zheng
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Amy Zhang
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Xia Li
- Department of Cell Biology, Yale School of Medicine, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
- Department of Biophysics and Biochemistry, Yale University, USA
| | | | - Malaiyalam Mariappan
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Yong Xiong
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Roderick Y. H. Lim
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
- Department of Biomedical Engineering, Yale University, USA
| |
Collapse
|
4
|
Klughammer N, Barth A, Dekker M, Fragasso A, Onck PR, Dekker C. Diameter dependence of transport through nuclear pore complex mimics studied using optical nanopores. eLife 2024; 12:RP87174. [PMID: 38376900 PMCID: PMC10942607 DOI: 10.7554/elife.87174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
The nuclear pore complex (NPC) regulates the selective transport of large biomolecules through the nuclear envelope. As a model system for nuclear transport, we construct NPC mimics by functionalizing the pore walls of freestanding palladium zero-mode waveguides with the FG-nucleoporin Nsp1. This approach enables the measurement of single-molecule translocations through individual pores using optical detection. We probe the selectivity of Nsp1-coated pores by quantitatively comparing the translocation rates of the nuclear transport receptor Kap95 to the inert probe BSA over a wide range of pore sizes from 35 nm to 160 nm. Pores below 55 ± 5 nm show significant selectivity that gradually decreases for larger pores. This finding is corroborated by coarse-grained molecular dynamics simulations of the Nsp1 mesh within the pore, which suggest that leakage of BSA occurs by diffusion through transient openings within the dynamic mesh. Furthermore, we experimentally observe a modulation of the BSA permeation when varying the concentration of Kap95. The results demonstrate the potential of single-molecule fluorescence measurements on biomimetic NPCs to elucidate the principles of nuclear transport.
Collapse
Affiliation(s)
- Nils Klughammer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Maurice Dekker
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| |
Collapse
|
5
|
Kapinos LE, Kalita J, Kassianidou E, Rencurel C, Lim RYH. Mechanism of exportin retention in the cell nucleus. J Cell Biol 2024; 223:e202306094. [PMID: 38241019 PMCID: PMC10798875 DOI: 10.1083/jcb.202306094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/06/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
Exportin receptors are concentrated in the nucleus to transport essential cargoes out of it. A mislocalization of exportins to the cytoplasm is linked to disease. Hence, it is important to understand how their containment within the nucleus is regulated. Here, we have studied the nuclear efflux of exportin2 (cellular apoptosis susceptibility protein or CAS) that delivers karyopherinα (Kapα or importinα), the cargo adaptor for karyopherinβ1 (Kapβ1 or importinβ1), to the cytoplasm in a Ran guanosine triphosphate (RanGTP)-mediated manner. We show that the N-terminus of CAS attenuates the interaction of RanGTPase activating protein 1 (RanGAP1) with RanGTP to slow GTP hydrolysis, which suppresses CAS nuclear exit at nuclear pore complexes (NPCs). Strikingly, a single phosphomimetic mutation (T18D) at the CAS N-terminus is sufficient to abolish its nuclear retention and coincides with metastatic cellular behavior. Furthermore, downregulating Kapβ1 disrupts CAS nuclear retention, which highlights the balance between their respective functions that is essential for maintaining the Kapα transport cycle. Therefore, NPCs play a functional role in selectively partitioning exportins in the cell nucleus.
Collapse
Affiliation(s)
- Larisa E. Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
| | - Joanna Kalita
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
| | - Elena Kassianidou
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
| | - Chantal Rencurel
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
| | - Roderick Y. H. Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
| |
Collapse
|
6
|
Barrientos ECR, Otto TA, Mouton SN, Steen A, Veenhoff LM. A survey of the specificity and mechanism of 1,6 hexanediol-induced disruption of nuclear transport. Nucleus 2023; 14:2240139. [PMID: 37498221 PMCID: PMC10376917 DOI: 10.1080/19491034.2023.2240139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Selective transport through the nuclear pore complex (NPC) depends on the dynamic binding of FG-repeat containing nucleoporins, the FG-nups, with each other and with Karyopherins (Kaps). Here, we assessed the specificity and mechanism by which the aliphatic alcohol 1,6-hexanediol (1,6HD) disrupts the permeability barrier of NPCs in live baker's yeast cells. After a 10-minute exposure to 5% 1,6HD, no notable changes were observed in cell growth, cytosolic pH and ATP levels, or the appearance of organelles. However, effects on the cytoskeleton and Hsp104 were noted. 1,6HD clearly affected the NPC permeability barrier, allowing passive nuclear entry of a 177kDa reporter protein that is normally confined to the cytosol. Moreover, multiple Kaps were displaced from NPCs, and the displacement of Kap122-GFP correlated with the observed passive permeability changes. 1,6HD thus temporarily permeates NPCs, and in line with Kap-centric models, the mechanism includes the release of numerous Kaps from the NPCs.
Collapse
Affiliation(s)
- Elizabeth C Riquelme Barrientos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Tegan A Otto
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Anton Steen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| |
Collapse
|
7
|
Yang Y, Guo L, Chen L, Gong B, Jia D, Sun Q. Nuclear transport proteins: structure, function, and disease relevance. Signal Transduct Target Ther 2023; 8:425. [PMID: 37945593 PMCID: PMC10636164 DOI: 10.1038/s41392-023-01649-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 11/12/2023] Open
Abstract
Proper subcellular localization is crucial for the functioning of biomacromolecules, including proteins and RNAs. Nuclear transport is a fundamental cellular process that regulates the localization of many macromolecules within the nuclear or cytoplasmic compartments. In humans, approximately 60 proteins are involved in nuclear transport, including nucleoporins that form membrane-embedded nuclear pore complexes, karyopherins that transport cargoes through these complexes, and Ran system proteins that ensure directed and rapid transport. Many of these nuclear transport proteins play additional and essential roles in mitosis, biomolecular condensation, and gene transcription. Dysregulation of nuclear transport is linked to major human diseases such as cancer, neurodegenerative diseases, and viral infections. Selinexor (KPT-330), an inhibitor targeting the nuclear export factor XPO1 (also known as CRM1), was approved in 2019 to treat two types of blood cancers, and dozens of clinical trials of are ongoing. This review summarizes approximately three decades of research data in this field but focuses on the structure and function of individual nuclear transport proteins from recent studies, providing a cutting-edge and holistic view on the role of nuclear transport proteins in health and disease. In-depth knowledge of this rapidly evolving field has the potential to bring new insights into fundamental biology, pathogenic mechanisms, and therapeutic approaches.
Collapse
Affiliation(s)
- Yang Yang
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lu Guo
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Chen
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Bo Gong
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.
| | - Qingxiang Sun
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, China.
| |
Collapse
|
8
|
Rush C, Jiang Z, Tingey M, Feng F, Yang W. Unveiling the complexity: assessing models describing the structure and function of the nuclear pore complex. Front Cell Dev Biol 2023; 11:1245939. [PMID: 37876551 PMCID: PMC10591098 DOI: 10.3389/fcell.2023.1245939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/19/2023] [Indexed: 10/26/2023] Open
Abstract
The nuclear pore complex (NPC) serves as a pivotal subcellular structure, acting as a gateway that orchestrates nucleocytoplasmic transport through a selectively permeable barrier. Nucleoporins (Nups), particularly those containing phenylalanine-glycine (FG) motifs, play indispensable roles within this barrier. Recent advancements in technology have significantly deepened our understanding of the NPC's architecture and operational intricacies, owing to comprehensive investigations. Nevertheless, the conspicuous presence of intrinsically disordered regions within FG-Nups continues to present a formidable challenge to conventional static characterization techniques. Historically, a multitude of strategies have been employed to unravel the intricate organization and behavior of FG-Nups within the NPC. These endeavors have given rise to multiple models that strive to elucidate the structural layout and functional significance of FG-Nups. Within this exhaustive review, we present a comprehensive overview of these prominent models, underscoring their proposed dynamic and structural attributes, supported by pertinent research. Through a comparative analysis, we endeavor to shed light on the distinct characteristics and contributions inherent in each model. Simultaneously, it remains crucial to acknowledge the scarcity of unequivocal validation for any of these models, as substantiated by empirical evidence.
Collapse
Affiliation(s)
| | | | | | | | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, United States
| |
Collapse
|
9
|
Kuiper EFE, Prophet SM, Schlieker C. Coordinating nucleoporin condensation and nuclear pore complex assembly. FEBS Lett 2023; 597:2534-2545. [PMID: 37620293 DOI: 10.1002/1873-3468.14725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/24/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
The nuclear pore complex (NPC) is among the most elaborate protein complexes in eukaryotes. While ribosomes and proteasomes are known to require dedicated assembly machinery, our understanding of NPC assembly is at a relatively early stage. Defects in NPC assembly or homeostasis are tied to movement disorders, including dystonia and amyotrophic lateral sclerosis (ALS), as well as aging, requiring a better understanding of these processes to enable therapeutic intervention. Here, we discuss recent progress in the understanding of NPC assembly and highlight how related defects in human disorders can shed light on NPC biogenesis. We propose that the condensation of phenylalanine-glycine repeat nucleoporins needs to be carefully controlled during NPC assembly to prevent aberrant condensation, aggregation, or amyloid formation.
Collapse
Affiliation(s)
- E F Elsiena Kuiper
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Sarah M Prophet
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Christian Schlieker
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
10
|
Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP. Implications of a multiscale structure of the yeast nuclear pore complex. Mol Cell 2023; 83:3283-3302.e5. [PMID: 37738963 PMCID: PMC10630966 DOI: 10.1016/j.molcel.2023.08.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/23/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
Nuclear pore complexes (NPCs) direct the nucleocytoplasmic transport of macromolecules. Here, we provide a composite multiscale structure of the yeast NPC, based on improved 3D density maps from cryogenic electron microscopy and AlphaFold2 models. Key features of the inner and outer rings were integrated into a comprehensive model. We resolved flexible connectors that tie together the core scaffold, along with equatorial transmembrane complexes and a lumenal ring that anchor this channel within the pore membrane. The organization of the nuclear double outer ring reveals an architecture that may be shared with ancestral NPCs. Additional connections between the core scaffold and the central transporter suggest that under certain conditions, a degree of local organization is present at the periphery of the transport machinery. These connectors may couple conformational changes in the scaffold to the central transporter to modulate transport. Collectively, this analysis provides insights into assembly, transport, and NPC evolution.
Collapse
Affiliation(s)
- Christopher W Akey
- Department of Pharmacology, Physiology and Biophysics, Boston University, Chobanian and Avedisian School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christna Ouch
- Department of Pharmacology, Physiology and Biophysics, Boston University, Chobanian and Avedisian School of Medicine, 700 Albany Street, Boston, MA 02118, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605, USA
| | - Ilona Nudelman
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
11
|
Seiler T, Lennartz A, Klein K, Hommel K, Figueroa Bietti A, Hadrovic I, Kollenda S, Sager J, Beuck C, Chlosta E, Bayer P, Juul-Madsen K, Vorup-Jensen T, Schrader T, Epple M, Knauer SK, Hartmann L. Potentiating Tweezer Affinity to a Protein Interface with Sequence-Defined Macromolecules on Nanoparticles. Biomacromolecules 2023; 24:3666-3679. [PMID: 37507377 DOI: 10.1021/acs.biomac.3c00393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Survivin, a well-known member of the inhibitor of apoptosis protein family, is upregulated in many cancer cells, which is associated with resistance to chemotherapy. To circumvent this, inhibitors are currently being developed to interfere with the nuclear export of survivin by targeting its protein-protein interaction (PPI) with the export receptor CRM1. Here, we combine for the first time a supramolecular tweezer motif, sequence-defined macromolecular scaffolds, and ultrasmall Au nanoparticles (us-AuNPs) to tailor a high avidity inhibitor targeting the survivin-CRM1 interaction. A series of biophysical and biochemical experiments, including surface plasmon resonance measurements and their multivalent evaluation by EVILFIT, reveal that for divalent macromolecular constructs with increasing linker distance, the longest linkers show superior affinity, slower dissociation, as well as more efficient PPI inhibition. As a drawback, these macromolecular tweezer conjugates do not enter cells, a critical feature for potential applications. The problem is solved by immobilizing the tweezer conjugates onto us-AuNPs, which enables efficient transport into HeLa cells. On the nanoparticles, the tweezer valency rises from 2 to 16 and produces a 100-fold avidity increase. The hierarchical combination of different scaffolds and controlled multivalent presentation of supramolecular binders was the key to the development of highly efficient survivin-CRM1 competitors. This concept may also be useful for other PPIs.
Collapse
Affiliation(s)
- Theresa Seiler
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Duesseldorf, Universitaetsstraße 1, Duesseldorf 40225, Germany
| | - Annika Lennartz
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Kai Klein
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Katrin Hommel
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Antonio Figueroa Bietti
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Inesa Hadrovic
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Sebastian Kollenda
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Jonas Sager
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Emilia Chlosta
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Kristian Juul-Madsen
- Department of Biomedicine, Aarhus University, Skou Building (1115), Høegh-Guldbergs Gade 10, DK-8000 Aarhus C, Denmark
- Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Thomas Vorup-Jensen
- Department of Biomedicine, Aarhus University, Skou Building (1115), Høegh-Guldbergs Gade 10, DK-8000 Aarhus C, Denmark
| | - Thomas Schrader
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Matthias Epple
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Shirley K Knauer
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Laura Hartmann
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Duesseldorf, Universitaetsstraße 1, Duesseldorf 40225, Germany
| |
Collapse
|
12
|
Montel F. [Structural and mechanical plasticity of the nuclear pore]. Med Sci (Paris) 2023; 39:625-631. [PMID: 37695152 DOI: 10.1051/medsci/2023096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023] Open
Abstract
The nuclear pore, which can be seen as the gateway to the cell nucleus, is central to many processes including gene regulation. It is a complex and dynamic structure composed of more than 30 proteins present in multiple copies that allows the selective and directional transport of RNA and proteins. As shown by recent studies, it is able to adapt its overall structure to the state of the cell. These results suggest that the structural and mechanical plasticity of the nuclear pore is important for its function but also in the development of cancer or viral infections.
Collapse
Affiliation(s)
- Fabien Montel
- Laboratoire de physique, CNRS UMR 5672, école normale supérieure de Lyon, université de Lyon, F-69342 Lyon, France
| |
Collapse
|
13
|
Yu M, Heidari M, Mikhaleva S, Tan PS, Mingu S, Ruan H, Reinkemeier CD, Obarska-Kosinska A, Siggel M, Beck M, Hummer G, Lemke EA. Visualizing the disordered nuclear transport machinery in situ. Nature 2023; 617:162-169. [PMID: 37100914 PMCID: PMC10156602 DOI: 10.1038/s41586-023-05990-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/21/2023] [Indexed: 04/28/2023]
Abstract
The approximately 120 MDa mammalian nuclear pore complex (NPC) acts as a gatekeeper for the transport between the nucleus and cytosol1. The central channel of the NPC is filled with hundreds of intrinsically disordered proteins (IDPs) called FG-nucleoporins (FG-NUPs)2,3. Although the structure of the NPC scaffold has been resolved in remarkable detail, the actual transport machinery built up by FG-NUPs-about 50 MDa-is depicted as an approximately 60-nm hole in even highly resolved tomograms and/or structures computed with artificial intelligence4-11. Here we directly probed conformations of the vital FG-NUP98 inside NPCs in live cells and in permeabilized cells with an intact transport machinery by using a synthetic biology-enabled site-specific small-molecule labelling approach paired with highly time-resolved fluorescence microscopy. Single permeabilized cell measurements of the distance distribution of FG-NUP98 segments combined with coarse-grained molecular simulations of the NPC allowed us to map the uncharted molecular environment inside the nanosized transport channel. We determined that the channel provides-in the terminology of the Flory polymer theory12-a 'good solvent' environment. This enables the FG domain to adopt expanded conformations and thus control transport between the nucleus and cytoplasm. With more than 30% of the proteome being formed from IDPs, our study opens a window into resolving disorder-function relationships of IDPs in situ, which are important in various processes, such as cellular signalling, phase separation, ageing and viral entry.
Collapse
Affiliation(s)
- Miao Yu
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology Mainz, Mainz, Germany
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maziar Heidari
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Sofya Mikhaleva
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology Mainz, Mainz, Germany
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Piau Siong Tan
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sara Mingu
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology Mainz, Mainz, Germany
| | - Hao Ruan
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology Mainz, Mainz, Germany
| | - Christopher D Reinkemeier
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology Mainz, Mainz, Germany
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Marc Siggel
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany.
- Institute of Molecular Biology Mainz, Mainz, Germany.
| |
Collapse
|
14
|
Cowburn D, Rout M. Improving the hole picture: towards a consensus on the mechanism of nuclear transport. Biochem Soc Trans 2023; 51:871-886. [PMID: 37099395 PMCID: PMC10212546 DOI: 10.1042/bst20220494] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/27/2023]
Abstract
Nuclear pore complexes (NPCs) mediate the exchange of materials between the nucleoplasm and cytoplasm, playing a key role in the separation of nucleic acids and proteins into their required compartments. The static structure of the NPC is relatively well defined by recent cryo-EM and other studies. The functional roles of dynamic components in the pore of the NPC, phenylalanyl-glycyl (FG) repeat rich nucleoporins, is less clear because of our limited understanding of highly dynamic protein systems. These proteins form a 'restrained concentrate' which interacts with and concentrates nuclear transport factors (NTRs) to provide facilitated nucleocytoplasmic transport of cargoes. Very rapid on- and off-rates among FG repeats and NTRs supports extremely fast facilitated transport, close to the rate of macromolecular diffusion in cytoplasm, while complexes without specific interactions are entropically excluded, though details on several aspects of the transport mechanism and FG repeat behaviors remain to be resolved. However, as discussed here, new technical approaches combined with more advanced modeling methods will likely provide an improved dynamic description of NPC transport, potentially at the atomic level in the near future. Such advances are likely to be of major benefit in comprehending the roles the malfunctioning NPC plays in cancer, ageing, viral diseases, and neurodegeneration.
Collapse
Affiliation(s)
- David Cowburn
- Departments of Biochemistry and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Michael Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, U.S.A
| |
Collapse
|
15
|
Kozai T, Fernandez-Martinez J, van Eeuwen T, Gallardo P, Kapinos LE, Mazur A, Zhang W, Tempkin J, Panatala R, Delgado-Izquierdo M, Raveh B, Sali A, Chait BT, Veenhoff LM, Rout MP, Lim RYH. Dynamic molecular mechanism of the nuclear pore complex permeability barrier. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535055. [PMID: 37066338 PMCID: PMC10103940 DOI: 10.1101/2023.03.31.535055] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport of specific macromolecules while impeding the exchange of unsolicited material. However, key aspects of this gating mechanism remain controversial. To address this issue, we determined the nanoscopic behavior of the permeability barrier directly within yeast S. cerevisiae NPCs at transport-relevant timescales. We show that the large intrinsically disordered domains of phenylalanine-glycine repeat nucleoporins (FG Nups) exhibit highly dynamic fluctuations to create transient voids in the permeability barrier that continuously shape-shift and reseal, resembling a radial polymer brush. Together with cargo-carrying transport factors the FG domains form a feature called the central plug, which is also highly dynamic. Remarkably, NPC mutants with longer FG domains show interweaving meshwork-like behavior that attenuates nucleocytoplasmic transport in vivo. Importantly, the bona fide nanoscale NPC behaviors and morphologies are not recapitulated by in vitro FG domain hydrogels. NPCs also exclude self-assembling FG domain condensates in vivo, thereby indicating that the permeability barrier is not generated by a self-assembling phase condensate, but rather is largely a polymer brush, organized by the NPC scaffold, whose dynamic gating selectivity is strongly enhanced by the presence of transport factors.
Collapse
Affiliation(s)
- Toshiya Kozai
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940, Leioa, Spain
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
| | - Paola Gallardo
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Netherlands
| | | | - Adam Mazur
- Biozentrum, University of Basel, Switzerland
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, U.S.A
| | - Jeremy Tempkin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, U.S.A. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | | | - Barak Raveh
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, U.S.A. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, U.S.A
| | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Netherlands
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
| | - Roderick Y. H. Lim
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
| |
Collapse
|
16
|
Zheng T, Zilman A. Self-regulation of the nuclear pore complex enables clogging-free crowded transport. Proc Natl Acad Sci U S A 2023; 120:e2212874120. [PMID: 36757893 PMCID: PMC9963888 DOI: 10.1073/pnas.2212874120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/05/2023] [Indexed: 02/10/2023] Open
Abstract
Nuclear pore complexes (NPCs) are the main conduits for macromolecular transport into and out of the nucleus of eukaryotic cells. The central component of the NPC transport mechanism is an assembly of intrinsically disordered proteins (IDPs) that fills the NPC channel. The channel interior is further crowded by large numbers of simultaneously translocating cargo-carrying and free transport proteins. How the NPC can efficiently, rapidly, and selectively transport varied cargoes in such crowded conditions remains ill understood. Past experimental results suggest that the NPC is surprisingly resistant to clogging and that transport may even become faster and more efficient as the concentration of transport protein increases. To understand the mechanisms behind these puzzling observations, we construct a computational model of the NPC comprising only a minimal set of commonly accepted consensus features. This model qualitatively reproduces the previous experimental results and identifies self-regulating mechanisms that relieve crowding. We show that some of the crowding-alleviating mechanisms-such as preventing saturation of the bulk flux-are "robust" and rely on very general properties of crowded dynamics in confined channels, pertaining to a broad class of selective transport nanopores. By contrast, the counterintuitive ability of the NPC to leverage crowding to achieve more efficient single-molecule translocation is "fine-tuned" and relies on the particular spatial architecture of the IDP assembly in the NPC channel.
Collapse
Affiliation(s)
- Tiantian Zheng
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
- Institute for Biomedical Engineering, University of Toronto, Toronto, ONM5S 3G9, Canada
| |
Collapse
|
17
|
Morphology of Polymer Brushes in the Presence of Attractive Nanoparticles: Effects of Temperature. Int J Mol Sci 2023; 24:ijms24010832. [PMID: 36614298 PMCID: PMC9821464 DOI: 10.3390/ijms24010832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023] Open
Abstract
We study the role of temperature on the structure of pure polymer brushes and their mixture with attractive nanoparticles in flat and cylindrical geometries. It has previously been established that the addition of such nanoparticles causes the polymer brush to collapse and the intensity of the collapse depends on the attraction strength, the nanoparticle diameter, and the grafting density. In this work, we carry out molecular dynamics simulation under good solvent conditions to show how the collapse transition is affected by the temperature, for both plane grafted and inside-cylinder grafted brushes. We first examine the pure brush morphology and verify that the brush height is insensitive to temperature changes in both planar and cylindrical geometries, as expected for a polymer brush in a good solvent. On the other hand, for both system geometries, the brush structure in the presence of attractive nanoparticles is quite responsive to temperature changes. Generally speaking, for a given nanoparticle concentration, increasing the temperature causes the brush height to increase. A brush which contracts when nanoparticles are added eventually swells beyond its pure brush height as the system temperature is increased. The combination of two easily controlled external parameters, namely, concentration of nanoparticles in solution and temperature, allows for sensitive and reversible adjustment of the polymer brush height, a feature which could be exploited in designing smart polymer devices.
Collapse
|
18
|
Diez L, Kapinos LE, Lim RYH, Wegmann S. Analysis of Tau/Nucleoporin Interactions by Surface Plasmon Resonance Spectroscopy. Methods Mol Biol 2023; 2551:95-109. [PMID: 36310199 DOI: 10.1007/978-1-0716-2597-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Tau, a soluble and predominantly neuronal protein, is best known for its microtubule (MT)-binding function in the cytosol, where it decisively contributes to stability as well as modulation of MT dynamics. In Alzheimer's disease and other tauopathies, Tau is altered into forming intracellular neurofibrillary tangles; additionally, also a mislocalization from the cytosol to the nucleus has been observed where interactions of Tau with the nucleus become possible. Using surface plasmon resonance (SPR), it was recently shown that Tau can directly interact with certain nucleoporins (e.g., Nup98), components of the nuclear pore complex (NPC). The NPC constitutes large regulated pores in the nuclear envelope that facilitate the bidirectional exchange of proteins, nucleic acids, and other biomolecules between the inner section of the nucleus and the cytosol, the nucleocytoplasmic transport. The mechanism of Tau/Nup interactions is as yet unknown, and a systematic interaction analysis of Tau with different Nups can be of high value to decipher the molecular binding mechanism of Tau to Nups. SPR is a useful tool to analyze binding affinities and kinetic parameters in a label-free environment. While one interaction partner is immobilized on a sensor chip, the second is supplied within a constant flow of buffer. Binding of mobile molecules to immobilized ones changes the refractive index of the medium close to the sensor surface with the signal being proportional to the bound mass. In this chapter, we describe the application of the SPR technique for the investigation of Tau binding to nucleoporins.
Collapse
Affiliation(s)
- Lisa Diez
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | | | | | - Susanne Wegmann
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany.
| |
Collapse
|
19
|
Tingey M, Li Y, Yu W, Young A, Yang W. Spelling out the roles of individual nucleoporins in nuclear export of mRNA. Nucleus 2022; 13:170-193. [PMID: 35593254 PMCID: PMC9132428 DOI: 10.1080/19491034.2022.2076965] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 11/01/2022] Open
Abstract
The Nuclear Pore Complex (NPC) represents a critical passage through the nuclear envelope for nuclear import and export that impacts nearly every cellular process at some level. Recent technological advances in the form of Auxin Inducible Degron (AID) strategies and Single-Point Edge-Excitation sub-Diffraction (SPEED) microscopy have enabled us to provide new insight into the distinct functions and roles of nuclear basket nucleoporins (Nups) upon nuclear docking and export for mRNAs. In this paper, we provide a review of our recent findings as well as an assessment of new techniques, updated models, and future perspectives in the studies of mRNA's nuclear export.
Collapse
Affiliation(s)
- Mark Tingey
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Yichen Li
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Wenlan Yu
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Albert Young
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
20
|
Dubey AK, Kumar P, Mandal D, Ravichandiran V, Singh SK. An introduction to dynamic nucleoporins in Leishmania species: Novel targets for tropical-therapeutics. J Parasit Dis 2022; 46:1176-1191. [PMID: 36457769 PMCID: PMC9606170 DOI: 10.1007/s12639-022-01515-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/20/2022] [Indexed: 11/28/2022] Open
Abstract
As an ailment, leishmaniasis is still an incessant challenge in neglected tropical diseases and neglected infections of poverty worldwide. At present, the diagnosis and treatment to combat Leishmania tropical infections are not substantial remedies and require advanced & specific research. Therefore, there is a need for a potential novel target to overcome established medicament modalities' limitations in pathogenicity. In this review, we proposed a few ab initio findings in nucleoporins of nuclear pore complex in Leishmania sp. concerning other infectious protists. So, through structural analysis and dynamics studies, we hypothesize the nuclear pore molecular machinery & functionality. The gatekeepers Nups, export of mRNA, mitotic spindle formation are salient features in cellular mechanics and this is regulated by dynamic nucleoporins. Here, diverse studies suggest that Nup93/NIC96, Nup155/Nup144, Mlp1/Mlp2/Tpr of Leishmania Species can be a picked out marker for diagnostic, immune-modulation, and novel drug targets. In silico prediction of nucleoporin-functional interactors such as NUP54/57, RNA helicase, Ubiquitin-protein ligase, Exportin 1, putative T-lymphocyte triggering factor, and 9 uncharacterized proteins suggest few more noble targets. The novel drug targeting to importins/exportins of Leishmania sp. and defining mechanism of Leptomycin-B, SINE compounds, Curcumins, Selinexor can be an arc-light in therapeutics. The essence of the review in Leishmania's nucleoporins is to refocus our research on noble molecular targets for tropical therapeutics. Supplementary Information The online version contains supplementary material available at 10.1007/s12639-022-01515-0.
Collapse
Affiliation(s)
- Amit Kumar Dubey
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali, Bihar 844102 India
- Parasite Immunology Lab, Microbiology Department, Indian Council of Medical Research (ICMR)-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna, Bihar 800007 India
| | - Prakash Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali, Bihar 844102 India
| | - Debabrata Mandal
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali, Bihar 844102 India
| | - V. Ravichandiran
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali, Bihar 844102 India
| | - Shubhankar Kumar Singh
- Parasite Immunology Lab, Microbiology Department, Indian Council of Medical Research (ICMR)-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna, Bihar 800007 India
| |
Collapse
|
21
|
Jin L, Zhang G, Yang G, Dong J. Identification of the Karyopherin Superfamily in Maize and Its Functional Cues in Plant Development. Int J Mol Sci 2022; 23:ijms232214103. [PMID: 36430578 PMCID: PMC9699179 DOI: 10.3390/ijms232214103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/06/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
Appropriate nucleo-cytoplasmic partitioning of proteins is a vital regulatory mechanism in phytohormone signaling and plant development. However, how this is achieved remains incompletely understood. The Karyopherin (KAP) superfamily is critical for separating the biological processes in the nucleus from those in the cytoplasm. The KAP superfamily is divided into Importin α (IMPα) and Importin β (IMPβ) families and includes the core components in mediating nucleocytoplasmic transport. Recent reports suggest the KAPs play crucial regulatory roles in Arabidopsis development and stress response by regulating the nucleo-cytoplasmic transport of members in hormone signaling. However, the KAP members and their associated molecular mechanisms are still poorly understood in maize. Therefore, we first identified seven IMPα and twenty-seven IMPβ genes in the maize genome and described their evolution traits and the recognition rules for substrates with nuclear localization signals (NLSs) or nuclear export signals (NESs) in plants. Next, we searched for the protein interaction partners of the ZmKAPs and selected the ones with Arabidopsis orthologs functioning in auxin biosynthesis, transport, and signaling to predict their potential function. Finally, we found that several ZmKAPs share similar expression patterns with their interacting proteins, implying their function in root development. Overall, this article focuses on the Karyopherin superfamily in maize and starts with this entry point by systematically comprehending the KAP-mediated nucleo-cytoplasmic transport process in plants, and then predicts the function of the ZmKAPs during maize development, with a perspective on a closely associated regulatory mechanism between the nucleo-cytoplasmic transport and the phytohormone network.
Collapse
Affiliation(s)
- Lu Jin
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Guobin Zhang
- College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Guixiao Yang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiaqiang Dong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
- Correspondence:
| |
Collapse
|
22
|
Tingey M, Yang W. Unraveling docking and initiation of mRNA export through the nuclear pore complex. Bioessays 2022; 44:e2200027. [PMID: 35754154 PMCID: PMC9308666 DOI: 10.1002/bies.202200027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/18/2022] [Accepted: 06/03/2022] [Indexed: 11/07/2022]
Abstract
The nuclear export of mRNA through the nuclear pore complex (NPC) is a process required for the healthy functioning of human cells, making it a critical area of research. However, the geometries of mRNA and the NPC are well below the diffraction limit of light microscopy, thereby presenting significant challenges in evaluating the discrete interactions and dynamics involved in mRNA nuclear export through the native NPC. Recent advances in biotechnology and single-molecule super-resolution light microscopy have enabled researchers to gain granular insight into the specific contributions made by discrete nucleoporins in the nuclear basket of the NPC to the export of mRNA. Specifically, by expanding upon the docking step facilitated by the protein TPR in the nuclear basket as well as identifying NUP153 as being the primary nuclear basket protein initiating export through the central channel of the NPC.
Collapse
Affiliation(s)
- Mark Tingey
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
23
|
Nag N, Sasidharan S, Uversky VN, Saudagar P, Tripathi T. Phase separation of FG-nucleoporins in nuclear pore complexes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119205. [PMID: 34995711 DOI: 10.1016/j.bbamcr.2021.119205] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
The nuclear envelope (NE) is a bilayer membrane that separates and physically isolates the genetic material from the cytoplasm. Nuclear pore complexes (NPCs) are cylindrical structures embedded in the NE and remain the sole channel of communication between the nucleus and the cytoplasm. The interior of NPCs contains densely packed intrinsically disordered FG-nucleoporins (FG-Nups), consequently forming a permeability barrier. This barrier facilitates the selection and specificity of the cargoes that are imported, exported, or shuttled through the NPCs. Recent studies have revealed that FG-Nups undergo the process of liquid-liquid phase separation into liquid droplets. Moreover, these liquid droplets mimic the permeability barrier observed in the interior of NPCs. This review highlights the phase separation of FG-Nups occurring inside the NPCs rooted in the NE. We discuss the phase separation of FG-Nups and compare the different aspects contributing to their phase separation. Furthermore, several diseases caused by the aberrant phase separation of the proteins are examined with respect to NEs. By understanding the fundamental process of phase separation at the nuclear membrane, the review seeks to explore the parameters influencing this phenomenon as well as its importance, ultimately paving the way for better research on the structure-function relationship of biomolecular condensates.
Collapse
Affiliation(s)
- Niharika Nag
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, United States; Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India.
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
| |
Collapse
|
24
|
Diez L, Kapinos LE, Hochmair J, Huebschmann S, Dominguez-Baquero A, Vogt A, Rankovic M, Zweckstetter M, Lim RYH, Wegmann S. Phosphorylation but Not Oligomerization Drives the Accumulation of Tau with Nucleoporin Nup98. Int J Mol Sci 2022; 23:3495. [PMID: 35408855 PMCID: PMC8998617 DOI: 10.3390/ijms23073495] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
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 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.
Collapse
Affiliation(s)
- Lisa Diez
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
| | - Larisa E. Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland; (L.E.K.); (R.Y.H.L.)
| | - Janine Hochmair
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
| | - Sabrina Huebschmann
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
| | - Alvaro Dominguez-Baquero
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
| | - Amelie Vogt
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
| | - Marija Rankovic
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Goettingen, Germany; (M.R.); (M.Z.)
| | - Markus Zweckstetter
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Goettingen, Germany; (M.R.); (M.Z.)
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Goettingen, Germany
| | - Roderick Y. H. Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland; (L.E.K.); (R.Y.H.L.)
| | - Susanne Wegmann
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117 Berlin, Germany; (L.D.); (J.H.); (S.H.); (A.D.-B.); (A.V.)
| |
Collapse
|
25
|
Kalita J, Kapinos LE, Zheng T, Rencurel C, Zilman A, Lim RY. Karyopherin enrichment and compensation fortifies the nuclear pore complex against nucleocytoplasmic leakage. J Cell Biol 2022; 221:e202108107. [PMID: 35089308 PMCID: PMC8932525 DOI: 10.1083/jcb.202108107] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 12/14/2022] Open
Abstract
Nuclear pore complexes (NPCs) discriminate nonspecific macromolecules from importin and exportin receptors, collectively termed "karyopherins" (Kaps), that mediate nucleocytoplasmic transport. This selective barrier function is attributed to the behavior of intrinsically disordered phenylalanine-glycine nucleoporins (FG Nups) that guard the NPC channel. However, NPCs in vivo are typically enriched with different Kaps, and how they impact the NPC barrier remains unknown. Here, we show that two major Kaps, importinβ1/karyopherinβ1 (Kapβ1) and exportin 1/chromosomal maintenance 1 (CRM1), are required to fortify NPC barrier function in vivo. Their enrichment at the NPC is sustained by promiscuous binding interactions with the FG Nups, which enable CRM1 to compensate for the loss of Kapβ1 as a means to maintain NPC barrier function. However, such a compensatory mechanism is constrained by the cellular abundances and different binding kinetics for each respective Kap, as evidenced for importin-5. Consequently, we find that NPC malfunction and nucleocytoplasmic leakage result from poor Kap enrichment.
Collapse
Affiliation(s)
- Joanna Kalita
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Larisa E. Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Tiantian Zheng
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Chantal Rencurel
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Roderick Y.H. Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| |
Collapse
|
26
|
Stewart M. Function of the Nuclear Transport Machinery in Maintaining the Distinctive Compositions of the Nucleus and Cytoplasm. Int J Mol Sci 2022; 23:2578. [PMID: 35269721 PMCID: PMC8910404 DOI: 10.3390/ijms23052578] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/13/2022] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
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 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.
Collapse
Affiliation(s)
- Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| |
Collapse
|
27
|
Davis LK, Ford IJ, Hoogenboom BW. Crowding-induced phase separation of nuclear transport receptors in FG nucleoporin assemblies. eLife 2022; 11:e72627. [PMID: 35098921 PMCID: PMC8880993 DOI: 10.7554/elife.72627] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid (<1 ms) transport of biological material to and from the cell nucleus is regulated by the nuclear pore complex (NPC). At the core of the NPC is a permeability barrier consisting of intrinsically disordered phenylalanine-glycine nucleoporins (FG Nups). Various types of nuclear transport receptors (NTRs) facilitate transport by partitioning in the FG Nup assembly, overcoming the barrier by their affinity to the FG Nups, and comprise a significant fraction of proteins in the NPC barrier. In previous work (Zahn et al., 2016), we revealed a universal physical behaviour in the experimentally observed binding of two well-characterised NTRs, Nuclear Transport Factor 2 (NTF2) and the larger Importin-β (Imp-β), to different planar assemblies of FG Nups, with the binding behaviour defined by negative cooperativity. This was further validated by a minimal physical model that treated the FG Nups as flexible homopolymers and the NTRs as uniformly cohesive spheres. Here, we build upon our original study by first parametrising our model to experimental data, and next predicting the effects of crowding by different types of NTRs. We show how varying the amounts of one type of NTR modulates how the other NTR penetrates the FG Nup assembly. Notably, at similar and physiologically relevant NTR concentrations, our model predicts demixed phases of NTF2 and Imp-β within the FG Nup assembly. The functional implication of NTR phase separation is that NPCs may sustain separate transport pathways that are determined by inter-NTR competition.
Collapse
Affiliation(s)
- Luke K Davis
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
- Institute for the Physics of Living Systems, University College LondonLondonUnited Kingdom
- London Centre for Nanotechnology, University College LondonLondonUnited Kingdom
| | - Ian J Ford
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
- Institute for the Physics of Living Systems, University College LondonLondonUnited Kingdom
- London Centre for Nanotechnology, University College LondonLondonUnited Kingdom
| | - Bart W Hoogenboom
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
- Institute for the Physics of Living Systems, University College LondonLondonUnited Kingdom
- London Centre for Nanotechnology, University College LondonLondonUnited Kingdom
| |
Collapse
|
28
|
Chowdhury R, Sau A, Musser SM. Super-resolved 3D tracking of cargo transport through nuclear pore complexes. Nat Cell Biol 2022; 24:112-122. [PMID: 35013558 PMCID: PMC8820391 DOI: 10.1038/s41556-021-00815-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/12/2021] [Indexed: 12/14/2022]
Abstract
Nuclear pore complexes (NPCs) embedded within the nuclear envelope (NE) mediate rapid, selective, and bidirectional traffic between the cytoplasm and the nucleoplasm. Deciphering the mechanism and dynamics of this process is challenged by the need for high spatial and temporal precision. We report here a multi-color imaging approach that enables direct 3D visualization of cargo transport trajectories relative to a super-resolved octagonal double-ring structure of the NPC scaffold. The success of this approach is enabled by the high positional stability of NPCs within permeabilized cells, as verified by a combined experimental and simulation analysis. Hourglass-shaped translocation conduits for two cargo complexes representing different nuclear transport receptor (NTR) pathways indicates rapid migration through the permeability barrier on or near the NPC scaffold. Binding sites for cargo complexes extend over 100 nm from the pore openings, consistent with a wide distribution of the FG-polypeptides that bind NTRs.
Collapse
Affiliation(s)
- Rajdeep Chowdhury
- Department of Molecular and Cellular Medicine, Texas A&M University, College of Medicine, The Texas A&M Health Science Center, College Station, TX, USA
| | - Abhishek Sau
- Department of Molecular and Cellular Medicine, Texas A&M University, College of Medicine, The Texas A&M Health Science Center, College Station, TX, USA
| | - Siegfried M Musser
- Department of Molecular and Cellular Medicine, Texas A&M University, College of Medicine, The Texas A&M Health Science Center, College Station, TX, USA.
| |
Collapse
|
29
|
Tarvirdipour S, Skowicki M, Schoenenberger CA, Kapinos LE, Lim R, Benenson Y, Palivan CG. A self-assembling peptidic platform to boost the cellular uptake and nuclear delivery of oligonucleotides. Biomater Sci 2022; 10:4309-4323. [DOI: 10.1039/d2bm00826b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design of non-viral vectors that efficiently deliver genetic materials into cells, in particular to the nucleus, remains a major challenge in gene therapy and vaccine development. To tackle the...
Collapse
|
30
|
Kapinos LE, Lim RYH. Multivalent Interactions with Intrinsically Disordered Proteins Probed by Surface Plasmon Resonance. Methods Mol Biol 2022; 2502:311-328. [PMID: 35412248 DOI: 10.1007/978-1-0716-2337-4_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multivalent interactions underpin associations between intrinsically disordered proteins (IDPs) and their binding partners. This is a subject of considerable interest and governs how nuclear transport receptors (NTRs) orchestrate the nucleocytoplasmic transport (NCT) of signal-specific cargoes through nuclear pore complexes (NPCs) in eukaryotic cells. Specifically, IDPs termed phenylalanine-glycine nucleoporins (FG Nups) exert multivalent interactions with NTRs to facilitate their transport selectivity and speed through the NPC. Here, we document the use of surface plasmon resonance (SPR) to quantify the affinity and kinetics of NTR-FG Nup binding as a function of FG Nup surface density. Moreover, we describe an in situ method that measures conformational height changes that occur in a FG Nup layer following NTR-binding. Protocols by which the as-obtained SPR results are treated with respect to mass transport limitations are further described. Overall, the SPR methodology described here can be applied to studying multivalent interactions and the role of avidity in diverse biological and biointerfacial systems.
Collapse
Affiliation(s)
- Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland.
| |
Collapse
|
31
|
De Magistris P. The Great Escape: mRNA Export through the Nuclear Pore Complex. Int J Mol Sci 2021; 22:ijms222111767. [PMID: 34769195 PMCID: PMC8583845 DOI: 10.3390/ijms222111767] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
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 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.
Collapse
|
32
|
Lennon KM, Soheilypour M, Peyro M, Wakefield DL, Choo GE, Mofrad MRK, Jovanovic-Talisman T. Characterizing Binding Interactions That Are Essential for Selective Transport through the Nuclear Pore Complex. Int J Mol Sci 2021; 22:10898. [PMID: 34639238 PMCID: PMC8509584 DOI: 10.3390/ijms221910898] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
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 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.
Collapse
Affiliation(s)
- Kathleen M. Lennon
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (K.M.L.); (D.L.W.); (G.E.C.)
| | - Mohammad Soheilypour
- Department of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California, Berkeley, CA 94720, USA; (M.S.); (M.P.)
| | - Mohaddeseh Peyro
- Department of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California, Berkeley, CA 94720, USA; (M.S.); (M.P.)
| | - Devin L. Wakefield
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (K.M.L.); (D.L.W.); (G.E.C.)
| | - Grace E. Choo
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (K.M.L.); (D.L.W.); (G.E.C.)
| | - Mohammad R. K. Mofrad
- Department of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California, Berkeley, CA 94720, USA; (M.S.); (M.P.)
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tijana Jovanovic-Talisman
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (K.M.L.); (D.L.W.); (G.E.C.)
| |
Collapse
|
33
|
Cho B, Choi J, Kim R, Yun JN, Choi Y, Lee HH, Koh J. Thermodynamic Models for Assembly of Intrinsically Disordered Protein Hubs with Multiple Interaction Partners. J Am Chem Soc 2021; 143:12509-12523. [PMID: 34362249 DOI: 10.1021/jacs.1c00811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prevalent in diverse protein interactomes, intrinsically disordered proteins or regions (IDPs or IDRs) often drive assembly of higher-order macromolecular complexes, using multiple target-binding motifs. Such IDP hubs are suggested to process various cellular signals and coordinate relevant biological processes. However, the mechanism of assembly and functional regulation of IDP hubs remains elusive due to the challenges in dissecting their intricate protein-protein interaction networks. Here we present basic thermodynamic models for the assembly of simple IDP hubs with multiple target proteins, constructing partition functions from fundamental binding parameters. We combined these basic functions to develop advanced thermodynamic models to analyze the assembly of the Nup153 hubs interacting with multiple karyopherin β1 (Kap) molecules, critical components of nucleocytoplasmic transport. The thermodynamic analysis revealed a complex organization of the Kap binding sites within the C-terminal IDR of Nup153 including a high-affinity 1:1 interaction site and a series of low-affinity sites for binding of multiple Kaps with negative cooperativity. The negative cooperativity arises from the overlapping nature of the low-affinity sites where Kap occupies multiple dipeptide motifs. The quantitative dissection culminated in construction of the Nup153 hub ensemble, elucidating how distribution among various Kap-bound states is modulated by Kap concentration and competing nuclear proteins. In particular, the Kap occupancy of the IDR can be fine-tuned by varying the location of competition within the overlapping sites, suggesting coupling of specific nuclear processes to distinct transport activities. In general, our results demonstrate the feasibility and a potential mechanism for manifold regulation of IDP functions by diverse cellular signals.
Collapse
Affiliation(s)
- ByeongJin Cho
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaejun Choi
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - RyeongHyeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jean Nyoung Yun
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yuri Choi
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Junseock Koh
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| |
Collapse
|
34
|
Shen Q, Tian T, Xiong Q, Ellis Fisher PD, Xiong Y, Melia TJ, Lusk CP, Lin C. DNA-Origami NanoTrap for Studying the Selective Barriers Formed by Phenylalanine-Glycine-Rich Nucleoporins. J Am Chem Soc 2021; 143:12294-12303. [PMID: 34324340 DOI: 10.1021/jacs.1c05550] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA nanotechnology provides a versatile and powerful tool to dissect the structure-function relationship of biomolecular machines like the nuclear pore complex (NPC), an enormous protein assembly that controls molecular traffic between the nucleus and cytoplasm. To understand how the intrinsically disordered, Phe-Gly-rich nucleoporins (FG-nups) within the NPC establish a selective barrier to macromolecules, we built a DNA-origami NanoTrap. The NanoTrap comprises precisely arranged FG-nups in an NPC-like channel, which sits on a baseplate that captures macromolecules that pass through the FG network. Using this biomimetic construct, we determined that the FG-motif type, grafting density, and spatial arrangement are critical determinants of an effective diffusion barrier. Further, we observed that diffusion barriers formed with cohesive FG interactions dominate in mixed-FG-nup scenarios. Finally, we demonstrated that the nuclear transport receptor, Ntf2, can selectively transport model cargo through NanoTraps composed of FxFG but not GLFG Nups. Our NanoTrap thus recapitulates the NPC's fundamental biological activities, providing a valuable tool for studying nuclear transport.
Collapse
Affiliation(s)
- Qi Shen
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States.,Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Taoran Tian
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States.,Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qiancheng Xiong
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States.,Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Patrick D Ellis Fisher
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States.,Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Thomas J Melia
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - C Patrick Lusk
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States.,Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| |
Collapse
|
35
|
Hoogenboom BW, Hough LE, Lemke EA, Lim RYH, Onck PR, Zilman A. Physics of the Nuclear Pore Complex: Theory, Modeling and Experiment. PHYSICS REPORTS 2021; 921:1-53. [PMID: 35892075 PMCID: PMC9306291 DOI: 10.1016/j.physrep.2021.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The hallmark of eukaryotic cells is the nucleus that contains the genome, enclosed by a physical barrier known as the nuclear envelope (NE). On the one hand, this compartmentalization endows the eukaryotic cells with high regulatory complexity and flexibility. On the other hand, it poses a tremendous logistic and energetic problem of transporting millions of molecules per second across the nuclear envelope, to facilitate their biological function in all compartments of the cell. Therefore, eukaryotes have evolved a molecular "nanomachine" known as the Nuclear Pore Complex (NPC). Embedded in the nuclear envelope, NPCs control and regulate all the bi-directional transport between the cell nucleus and the cytoplasm. NPCs combine high molecular specificity of transport with high throughput and speed, and are highly robust with respect to molecular noise and structural perturbations. Remarkably, the functional mechanisms of NPC transport are highly conserved among eukaryotes, from yeast to humans, despite significant differences in the molecular components among various species. The NPC is the largest macromolecular complex in the cell. Yet, despite its significant complexity, it has become clear that its principles of operation can be largely understood based on fundamental physical concepts, as have emerged from a combination of experimental methods of molecular cell biology, biophysics, nanoscience and theoretical and computational modeling. Indeed, many aspects of NPC function can be recapitulated in artificial mimics with a drastically reduced complexity compared to biological pores. We review the current physical understanding of the NPC architecture and function, with the focus on the critical analysis of experimental studies in cells and artificial NPC mimics through the lens of theoretical and computational models. We also discuss the connections between the emerging concepts of NPC operation and other areas of biophysics and bionanotechnology.
Collapse
Affiliation(s)
- Bart W. Hoogenboom
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Loren E. Hough
- Department of Physics and BioFrontiers Institute, University of Colorado, Boulder CO 80309, United States of America
| | - Edward A. Lemke
- Biocenter Mainz, Departments of Biology and Chemistry, Johannes Gutenberg University and Institute of Molecular Biology, 55128 Mainz, Germany
| | - Roderick Y. H. Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Patrick R. Onck
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Anton Zilman
- Department of Physics and Institute for Biomedical Engineering (IBME), University of Toronto, Toronto, ON M5S 1A7, Canada
| |
Collapse
|
36
|
Kalita J, Kapinos LE, Lim RYH. On the asymmetric partitioning of nucleocytoplasmic transport - recent insights and open questions. J Cell Sci 2021; 134:239102. [PMID: 33912945 DOI: 10.1242/jcs.240382] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macromolecular cargoes are asymmetrically partitioned in the nucleus or cytoplasm by nucleocytoplasmic transport (NCT). At the center of this activity lies the nuclear pore complex (NPC), through which soluble factors circulate to orchestrate NCT. These include cargo-carrying importin and exportin receptors from the β-karyopherin (Kapβ) family and the small GTPase Ran, which switches between guanosine triphosphate (GTP)- and guanosine diphosphate (GDP)-bound forms to regulate cargo delivery and compartmentalization. Ongoing efforts have shed considerable light on how these soluble factors traverse the NPC permeability barrier to sustain NCT. However, this does not explain how importins and exportins are partitioned in the cytoplasm and nucleus, respectively, nor how a steep RanGTP-RanGDP gradient is maintained across the nuclear envelope. In this Review, we peel away the multiple layers of control that regulate NCT and juxtapose unresolved features against known aspects of NPC function. Finally, we discuss how NPCs might function synergistically with Kapβs, cargoes and Ran to establish the asymmetry of NCT.
Collapse
Affiliation(s)
- Joanna Kalita
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel CH4056, Switzerland
| | - Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel CH4056, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel CH4056, Switzerland
| |
Collapse
|
37
|
A designer FG-Nup that reconstitutes the selective transport barrier of the nuclear pore complex. Nat Commun 2021; 12:2010. [PMID: 33790297 PMCID: PMC8012357 DOI: 10.1038/s41467-021-22293-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/01/2021] [Indexed: 02/01/2023] Open
Abstract
Nuclear Pore Complexes (NPCs) regulate bidirectional transport between the nucleus and the cytoplasm. Intrinsically disordered FG-Nups line the NPC lumen and form a selective barrier, where transport of most proteins is inhibited whereas specific transporter proteins freely pass. The mechanism underlying selective transport through the NPC is still debated. Here, we reconstitute the selective behaviour of the NPC bottom-up by introducing a rationally designed artificial FG-Nup that mimics natural Nups. Using QCM-D, we measure selective binding of the artificial FG-Nup brushes to the transport receptor Kap95 over cytosolic proteins such as BSA. Solid-state nanopores with the artificial FG-Nups lining their inner walls support fast translocation of Kap95 while blocking BSA, thus demonstrating selectivity. Coarse-grained molecular dynamics simulations highlight the formation of a selective meshwork with densities comparable to native NPCs. Our findings show that simple design rules can recapitulate the selective behaviour of native FG-Nups and demonstrate that no specific spacer sequence nor a spatial segregation of different FG-motif types are needed to create selective NPCs.
Collapse
|
38
|
Perez Sirkin YA, Tagliazucchi M, Szleifer I. Nanopore gates via reversible crosslinking of polymer brushes: a theoretical study. SOFT MATTER 2021; 17:2791-2802. [PMID: 33544104 DOI: 10.1039/d0sm01760d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polymer-brush-modified nanopores are synthetic structures inspired by the gated transport exhibited by their biological counterparts. This work theoretically analyzes how the reversible crosslinking of a polymer network by soluble species can be used to control transport through nanochannels and pores. The study was performed with a molecular theory that allows inhomogeneities in the three spatial dimensions and explicitly takes into account the size, shape and conformations of all molecular species, considers the intermolecular interactions between the polymers and the soluble crosslinkers and includes the presence of a translocating particle inside the pore. It is shown than increasing the concentration of the soluble crosslinkers in bulk solution leads to a gradual increase of its number within the pore until a critical bulk concentration is reached. At the critical concentration, the number of crosslinkers inside the pore increases abruptly. For long chains, this sudden transition triggers the collapse of the polymer brush to the center of the nanopore. The resulting structure increases the free-energy barrier that a translocating particle has to surmount to go across the pore and modifies the route of translocation from the axis of the pore to its walls. On the other hand, for short polymer chains the crosslinkers trigger the collapse of the brush to the pore walls, which reduces the translocation barrier.
Collapse
Affiliation(s)
- Yamila A Perez Sirkin
- INQUIMAE-CONICET and DQIAQF, University of Buenos Aires, School of Sciences, Ciudad Universitaria, Pabellón 2, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina.
| | - Mario Tagliazucchi
- INQUIMAE-CONICET and DQIAQF, University of Buenos Aires, School of Sciences, Ciudad Universitaria, Pabellón 2, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina.
| | - Igal Szleifer
- Department of Biomedical Engineering, Department of Chemistry and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, USA.
| |
Collapse
|
39
|
Frost R, Débarre D, Jana S, Bano F, Schünemann J, Görlich D, Richter RP. A Method to Quantify Molecular Diffusion within Thin Solvated Polymer Films: A Case Study on Films of Natively Unfolded Nucleoporins. ACS NANO 2020; 14:9938-9952. [PMID: 32667780 PMCID: PMC7526988 DOI: 10.1021/acsnano.0c02895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
We present a method to probe molecular and nanoparticle diffusion within thin, solvated polymer coatings. The device exploits the confinement with well-defined geometry that forms at the interface between a planar and a hemispherical surface (of which at least one is coated with polymers) in close contact and uses this confinement to analyze diffusion processes without interference of exchange with and diffusion in the bulk solution. With this method, which we call plane-sphere confinement microscopy (PSCM), information regarding the partitioning of molecules between the polymer coating and the bulk liquid is also obtained. Thanks to the shape of the confined geometry, diffusion and partitioning can be mapped as a function of compression and concentration of the coating in a single experiment. The method is versatile and can be integrated with conventional optical microscopes; thus it should find widespread use in the many application areas exploiting functional polymer coatings. We demonstrate the use of PSCM using brushes of natively unfolded nucleoporin domains rich in phenylalanine-glycine repeats (FG domains). A meshwork of FG domains is known to be responsible for the selective transport of nuclear transport receptors (NTRs) and their macromolecular cargos across the nuclear envelope that separates the cytosol and the nucleus of living cells. We find that the selectivity of NTR uptake by FG domain films depends sensitively on FG domain concentration and that the interaction of NTRs with FG domains obstructs NTR movement only moderately. These observations contribute important information to better understand the mechanisms of selective NTR transport.
Collapse
Affiliation(s)
- Rickard Frost
- School
of Biomedical Sciences, Faculty of Biological Sciences, School of
Physics and Astronomy, Faculty of Engineering and Physical Sciences,
Astbury Centre of Structural Molecular Biology, and Bragg Centre for
Materials Research, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | | | - Saikat Jana
- School
of Biomedical Sciences, Faculty of Biological Sciences, School of
Physics and Astronomy, Faculty of Engineering and Physical Sciences,
Astbury Centre of Structural Molecular Biology, and Bragg Centre for
Materials Research, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Fouzia Bano
- School
of Biomedical Sciences, Faculty of Biological Sciences, School of
Physics and Astronomy, Faculty of Engineering and Physical Sciences,
Astbury Centre of Structural Molecular Biology, and Bragg Centre for
Materials Research, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Jürgen Schünemann
- Department
of Cellular Logistics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Dirk Görlich
- Department
of Cellular Logistics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Ralf P. Richter
- School
of Biomedical Sciences, Faculty of Biological Sciences, School of
Physics and Astronomy, Faculty of Engineering and Physical Sciences,
Astbury Centre of Structural Molecular Biology, and Bragg Centre for
Materials Research, University of Leeds, Leeds, LS2 9JT, United Kingdom
| |
Collapse
|
40
|
Modeling the nucleoporins that form the hairy pores. Biochem Soc Trans 2020; 48:1447-1461. [DOI: 10.1042/bst20190941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/03/2020] [Accepted: 07/16/2020] [Indexed: 11/17/2022]
Abstract
Sitting on the nuclear envelope, nuclear pore complexes (NPCs) control the molecular transport between the nucleus and the cytoplasm. Without definite open or close states, the NPC uses a family of intrinsically disordered nucleoporins called FG-Nups to construct a selective permeability barrier whose functional structure is unclear. Experimental advances have offered high-resolution molecular knowledge of the NPC scaffold and docking of the unfolded FG-Nups, however, the ‘hairy’ barrier structure still appears as blurred lobes even under the state-of-the-art microscopy. Without accurate experimental visualization, the molecular mechanism for the NPC-mediated transport remains a matter of debate. Modeling provides an alternative way to resolve this long-standing mystery. Here, we briefly review different methods employed in modeling the FG-Nups, arranging from all-atom molecular dynamics to mean-field theories. We discuss the advantage and limit of each modeling technique, and summarize the theoretical insights that, despite certain controversy, deepened our understanding of the hairy pore.
Collapse
|
41
|
Paci G, Zheng T, Caria J, Zilman A, Lemke EA. Molecular determinants of large cargo transport into the nucleus. eLife 2020; 9:e55963. [PMID: 32692309 PMCID: PMC7375812 DOI: 10.7554/elife.55963] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/18/2020] [Indexed: 01/03/2023] Open
Abstract
Nucleocytoplasmic transport is tightly regulated by the nuclear pore complex (NPC). Among the thousands of molecules that cross the NPC, even very large (>15 nm) cargoes such as pathogens, mRNAs and pre-ribosomes can pass the NPC intact. For these cargoes, there is little quantitative understanding of the requirements for their nuclear import, especially the role of multivalent binding to transport receptors via nuclear localisation sequences (NLSs) and the effect of size on import efficiency. Here, we assayed nuclear import kinetics of 30 large cargo models based on four capsid-like particles in the size range of 17-36 nm, with tuneable numbers of up to 240 NLSs. We show that the requirements for nuclear transport can be recapitulated by a simple two-parameter biophysical model that correlates the import flux with the energetics of large cargo transport through the NPC. Together, our results reveal key molecular determinants of large cargo import in cells.
Collapse
Affiliation(s)
- Giulia Paci
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Tiantian Zheng
- Department of Physics, University of TorontoTorontoCanada
| | - Joana Caria
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Anton Zilman
- Department of Physics, University of TorontoTorontoCanada
- Institute for Biomaterials and Biomedical Engineering (IBBME), University of TorontoTorontoCanada
| | - Edward A Lemke
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| |
Collapse
|
42
|
Barbato S, Kapinos LE, Rencurel C, Lim RYH. Karyopherin enrichment at the nuclear pore complex attenuates Ran permeability. J Cell Sci 2020; 133:jcs238121. [PMID: 31932502 DOI: 10.1242/jcs.238121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/13/2019] [Indexed: 12/25/2022] Open
Abstract
Ran is a small GTPase whose nucleotide-bound forms cycle through nuclear pore complexes (NPCs) to direct nucleocytoplasmic transport (NCT). Generally, Ran guanosine triphosphate (RanGTP) binds cargo-carrying karyopherin receptors (Kaps) in the nucleus and releases them into the cytoplasm following hydrolysis to Ran guanosine diphosphate (RanGDP). This generates a remarkably steep Ran gradient across the nuclear envelope that sustains compartment-specific cargo delivery and accumulation. However, because NPCs are permeable to small molecules of comparable size, it is unclear how an uncontrolled mixing of RanGTP and RanGDP is prevented. Here, we find that an NPC-enriched pool of karyopherin subunit beta 1 (KPNB1, hereafter referred to as Kapβ1) selectively mediates Ran diffusion across the pore but not passive molecules of similar size (e.g. GFP). This is due to RanGTP having a stronger binding interaction with Kapβ1 than RanGDP. For this reason, the RanGDP importer, nuclear transport factor 2, facilitates the return of RanGDP into the nucleus following GTP hydrolysis. Accordingly, the enrichment of Kapβ1 at NPCs may function as a retention mechanism that preserves the sharp transition of RanGTP and RanGDP in the nucleus and cytoplasm, respectively.
Collapse
Affiliation(s)
- Suncica Barbato
- Biozentrum & The Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Larisa E Kapinos
- Biozentrum & The Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Chantal Rencurel
- Biozentrum & The Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum & The Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| |
Collapse
|
43
|
Zelmer C, Zweifel LP, Kapinos LE, Craciun I, Güven ZP, Palivan CG, Lim RYH. Organelle-specific targeting of polymersomes into the cell nucleus. Proc Natl Acad Sci U S A 2020; 117:2770-2778. [PMID: 31988132 PMCID: PMC7022206 DOI: 10.1073/pnas.1916395117] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Organelle-specific nanocarriers (NCs) are highly sought after for delivering therapeutic agents into the cell nucleus. This necessitates nucleocytoplasmic transport (NCT) to bypass nuclear pore complexes (NPCs). However, little is known as to how comparably large NCs infiltrate this vital intracellular barrier to enter the nuclear interior. Here, we developed nuclear localization signal (NLS)-conjugated polymersome nanocarriers (NLS-NCs) and studied the NCT mechanism underlying their selective nuclear uptake. Detailed chemical, biophysical, and cellular analyses show that karyopherin receptors are required to authenticate, bind, and escort NLS-NCs through NPCs while Ran guanosine triphosphate (RanGTP) promotes their release from NPCs into the nuclear interior. Ultrastructural analysis by regressive staining transmission electron microscopy further resolves the NLS-NCs on transit in NPCs and inside the nucleus. By elucidating their ability to utilize NCT, these findings demonstrate the efficacy of polymersomes to deliver encapsulated payloads directly into cell nuclei.
Collapse
Affiliation(s)
- Christina Zelmer
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, CH-4056 Basel, Switzerland
- Department of Chemistry, University of Basel, CH-4002 Basel, Switzerland
| | - Ludovit P Zweifel
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, CH-4056 Basel, Switzerland
| | - Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, CH-4056 Basel, Switzerland
| | - Ioana Craciun
- Department of Chemistry, University of Basel, CH-4002 Basel, Switzerland
| | - Zekiye P Güven
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, CH-4002 Basel, Switzerland;
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, CH-4056 Basel, Switzerland;
| |
Collapse
|
44
|
Davis LK, Ford IJ, Šarić A, Hoogenboom BW. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Phys Rev E 2020; 101:022420. [PMID: 32168597 DOI: 10.1103/physreve.101.022420] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events.
Collapse
Affiliation(s)
- Luke K Davis
- London Centre for Nanotechnology, University College London, London WC1H OAH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - Ian J Ford
- London Centre for Nanotechnology, University College London, London WC1H OAH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H OAH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| |
Collapse
|
45
|
Abstract
Intrinsically disordered proteins (IDPs) can adopt a range of conformations from globules to swollen coils. This large range of conformational preferences for different IDPs raises the question of how conformational preferences are encoded by sequence. Global compositional features of a sequence such as the fraction of charged residues and the net charge per residue engender certain conformational biases. However, more specific sequence features such as the patterning of oppositely charged residues, expansion driving residues, or residues that can undergo posttranslational modifications can also influence the conformational ensembles of an IDP. Here, we outline how to calculate important global compositional features and patterning metrics that can be used to classify IDPs into different conformational classes and predict relative changes in conformation for sequences with the same amino acid composition. Although increased effort has been devoted to determining conformational properties of IDPs in recent years, quantitative predictions of conformation directly from sequence remain difficult and often inaccurate. Thus, if quantitative predictions of conformational properties are desired, then sequence-specific simulations must be performed.
Collapse
Affiliation(s)
- Kiersten M Ruff
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
| |
Collapse
|
46
|
Maguire L, Betterton MD, Hough LE. Bound-State Diffusion due to Binding to Flexible Polymers in a Selective Biofilter. Biophys J 2019; 118:376-385. [PMID: 31858976 DOI: 10.1016/j.bpj.2019.11.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 01/02/2023] Open
Abstract
Selective biofilters are used by cells to control the transport of proteins, nucleic acids, and other macromolecules. Biological filters demonstrate both high specificity and rapid motion or high flux of proteins. In contrast, high flux comes at the expense of selectivity in many synthetic filters. Binding can lead to selective transport in systems in which the bound particle can diffuse, but the mechanisms that lead to bound diffusion remain unclear. Previous theory has proposed a molecular mechanism of bound-state mobility based only on transient binding to flexible polymers. However, this mechanism has not been directly tested in experiments. We demonstrate that bound mobility via tethered diffusion can be engineered into a synthetic gel using protein fragments derived from the nuclear pore complex. The resulting bound-state diffusion is quantitatively consistent with theory. Our results suggest that synthetic biological filters can be designed to take advantage of tethered diffusion to give rapid, selective transport.
Collapse
Affiliation(s)
- Laura Maguire
- Department of Physics, University of Colorado Boulder, Boulder, Colorado; BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Meredith D Betterton
- Department of Physics, University of Colorado Boulder, Boulder, Colorado; Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado
| | - Loren E Hough
- Department of Physics, University of Colorado Boulder, Boulder, Colorado; BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado.
| |
Collapse
|
47
|
Maguire L, Stefferson M, Betterton MD, Hough LE. Design principles of selective transport through biopolymer barriers. Phys Rev E 2019; 100:042414. [PMID: 31770897 PMCID: PMC7502277 DOI: 10.1103/physreve.100.042414] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Indexed: 12/20/2022]
Abstract
In biological systems, polymeric materials block the movement of some macromolecules while allowing the selective passage of others. In some cases, binding enables selective transport, while in others the most inert particles appear to transit most rapidly. To study the general principles of filtering, we develop a model motivated by features of the nuclear pore complex (NPC) which are highly conserved and could potentially be applied to other biological systems. The NPC allows selective transport of proteins called transport factors, which transiently bind to disordered flexible proteins called phenylalanine-glycine-nucleoporins. While the NPC is tuned for transport factors and their cargo, we show that a single feature is sufficient for selective transport: the bound-state motion resulting from transient binding to flexible filaments. Interchain transfer without unbinding can further improve selectivity, especially for cross-linked chains. We generalize this observation to model nanoparticle transport through mucus and show that bound-state motion accelerates transport of transient nanoparticle application, even with clearance by mucus flow. Our model provides a framework to control binding-induced selective transport in biopolymeric materials.
Collapse
Affiliation(s)
- Laura Maguire
- Department of Physics, University of Colorado Boulder
- BioFrontiers Institute, University of Colorado Boulder
| | - Michael Stefferson
- Department of Physics, University of Colorado Boulder
- Molecular, Cellular and Developmental Biology, University of Colorado Boulder
| | - Meredith D. Betterton
- Department of Physics, University of Colorado Boulder
- Molecular, Cellular and Developmental Biology, University of Colorado Boulder
| | - Loren E. Hough
- Department of Physics, University of Colorado Boulder
- BioFrontiers Institute, University of Colorado Boulder
| |
Collapse
|
48
|
Enhanced Nucleocytoplasmic Transport due to Competition for Elastic Binding Sites. Biophys J 2019; 115:108-116. [PMID: 29972802 DOI: 10.1016/j.bpj.2018.05.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/21/2018] [Accepted: 05/31/2018] [Indexed: 01/08/2023] Open
Abstract
Nuclear pore complexes (NPCs) control all traffic into and out of the cell nucleus. NPCs are molecular machines that simultaneously achieve high selectivity and high transport rates. The biophysical details of how cargoes rapidly traverse the pore remain unclear but are known to be mediated by interactions between cargo-binding chaperone proteins and natively unstructured nucleoporin proteins containing many phenylalanine-glycine repeats (FG nups) that line the pore's central channel. Here, we propose a specific and detailed physical mechanism for the high speed of nuclear import based on the elasticity of FG nups and on competition between individual chaperone proteins for FG nup binding. We develop a mathematical model to support our proposed mechanism. We suggest that the recycling of nuclear import factors back to the cytoplasm is important for driving high-speed import and predict the existence of an optimal cytoplasmic concentration of cargo for enhancing the rate of import over a purely diffusive rate.
Collapse
|
49
|
Hayama R, Sorci M, Keating IV JJ, Hecht LM, Plawsky JL, Belfort G, Chait BT, Rout MP. Interactions of nuclear transport factors and surface-conjugated FG nucleoporins: Insights and limitations. PLoS One 2019; 14:e0217897. [PMID: 31170242 PMCID: PMC6553764 DOI: 10.1371/journal.pone.0217897] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/21/2019] [Indexed: 11/18/2022] Open
Abstract
Protein-protein interactions are central to biological processes. In vitro methods to examine protein-protein interactions are generally categorized into two classes: in-solution and surface-based methods. Here, using the multivalent interactions between nucleocytoplasmic transport factors and intrinsically disordered FG repeat containing nuclear pore complex proteins as a model system, we examined the utility of three surface-based methods: atomic force microscopy, quartz crystal microbalance with dissipation, and surface plasmon resonance. Although results were comparable to those of previous reports, the apparent effect of mass transport limitations was demonstrated. Additional experiments with a loss-of-interaction FG repeat mutant variant demonstrated that the binding events that take place on surfaces can be unexpectedly complex, suggesting particular care must be exercised in interpretation of such data.
Collapse
Affiliation(s)
- Ryo Hayama
- Laboratory of Cellular and Structural Biology, the Rockefeller University, New York, NY, United States of America
| | - Mirco Sorci
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States of America
| | - John J. Keating IV
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States of America
| | - Lee M. Hecht
- Laboratory of Cellular and Structural Biology, the Rockefeller University, New York, NY, United States of America
| | - Joel L. Plawsky
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States of America
| | - Georges Belfort
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States of America
- * E-mail: (GB); (BTC); (MPR)
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Chemistry, the Rockefeller University, New York, NY, United States of America
- * E-mail: (GB); (BTC); (MPR)
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, the Rockefeller University, New York, NY, United States of America
- * E-mail: (GB); (BTC); (MPR)
| |
Collapse
|
50
|
Gu C, Vovk A, Zheng T, Coalson RD, Zilman A. The Role of Cohesiveness in the Permeability of the Spatial Assemblies of FG Nucleoporins. Biophys J 2019; 116:1204-1215. [PMID: 30902367 DOI: 10.1016/j.bpj.2019.02.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/02/2018] [Accepted: 02/26/2019] [Indexed: 12/31/2022] Open
Abstract
Nuclear pore complexes (NPCs) conduct selective, bidirectional transport across the nuclear envelope. The NPC passageway is lined by intrinsically disordered proteins that contain hydrophobic phenylalanine-glycine (FG) motifs, known as FG nucleoporins (FG nups), that play the key role in the NPC transport mechanism. Cohesive interactions among the FG nups, which arise from the combination of hydrophobic, electrostatic, and other forces, have been hypothesized to control the morphology of the assemblies of FG nups in the NPC, as well as their permeability with respect to the transport proteins. However, the role of FG nup cohesiveness is still vigorously debated. Using coarse-grained polymer theory and numerical simulations, we study the effects of cohesiveness on the selective permeability of in vitro FG nup assemblies in different geometries that have served as proxies for the morphological and transport properties of the NPC. We show that in high-density FG nup assemblies, increase in cohesiveness leads to the decrease in their permeability, in accordance with the accepted view. On the other hand, the permeability of low-density assemblies is a nonmonotonic function of the cohesiveness, and a moderate increase in cohesiveness can enhance permeability. The density- and cohesiveness-dependent effects on permeability are explained by considering the free-energy cost associated with penetrating the FG nup assemblies. We discuss the implications of these findings for the organization and function of the NPC.
Collapse
Affiliation(s)
- Chad Gu
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Andrei Vovk
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Tiantian Zheng
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Rob D Coalson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|