1
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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.
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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
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2
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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.
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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
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3
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Zheng T, Zilman A. Kinetic cooperativity resolves bidirectional clogging within the nuclear pore complex. Biophys J 2024; 123:1085-1097. [PMID: 38640928 PMCID: PMC11079998 DOI: 10.1016/j.bpj.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/06/2023] [Accepted: 03/22/2024] [Indexed: 04/21/2024] Open
Abstract
As the main gatekeeper of the nucleocytoplasmic transport in eukaryotic cells, the nuclear pore complex (NPC) faces the daunting task of facilitating the bidirectional transport of a high volume of macromolecular cargoes while ensuring the selectivity, speed, and efficiency of this process. The competition between opposing nuclear import and export fluxes passing through the same channel is expected to pose a major challenge to transport efficiency. It has been suggested that phase separation-like radial segregation of import and export fluxes within the assembly of intrinsically disordered proteins that line the NPC pore could be a mechanism for ensuring efficient bidirectional transport. We examine the impact of radial segregation on the efficiency of bidirectional transport through the NPC using a coarse-grained computational model of the NPC. We find little evidence that radial segregation improves transport efficiency. By contrast, surprisingly, we find that NTR crowding may enhance rather than impair the efficiency of bidirectional transport although it decreases the available space in the pore. We identify mechanisms of this novel crowding-induced transport cooperativity through the self-regulation of cargo density and flux in the pore. These findings explain how the functional architecture of the NPC resolves the problem of efficient bidirectional transport, and provide inspiration for the alleviation of clogging in artificial selective nanopores.
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Affiliation(s)
- Tiantian Zheng
- Department of Physics, University of Toronto, Toronto, ON, Canada
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, ON, Canada.
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4
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Tai L, Yin G, Sun F, Zhu Y. Cryo-electron microscopy reveals the structure of the nuclear pore complex. J Mol Biol 2023; 435:168051. [PMID: 36933820 DOI: 10.1016/j.jmb.2023.168051] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
The nuclear pore complex (NPC) is a giant protein assembly that penetrates the double layers of the nuclear membrane. The overall structure of the NPC has approximately eightfold symmetry and is formed by approximately 30 nucleoporins. The great size and complexity of the NPC have hindered the study of its structure for many years until recent breakthroughs were achieved by integrating the latest high-resolution cryo-electron microscopy (cryo-EM), the emerging artificial intelligence-based modeling and all other available structural information from crystallography and mass spectrometry. Here, we review our latest knowledge of the NPC architecture and the history of its structural study from in vitro to in situ with progressively improved resolutions by cryo-EM, with a particular focus on the latest subnanometer-resolution structural studies. The future directions for structural studies of NPCs are also discussed.
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Affiliation(s)
- Linhua Tai
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Yin
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong 510005, China.
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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5
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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.
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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
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6
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A simple thermodynamic description of phase separation of Nup98 FG domains. Nat Commun 2022; 13:6172. [PMID: 36257947 PMCID: PMC9579204 DOI: 10.1038/s41467-022-33697-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
The permeability barrier of nuclear pore complexes (NPCs) controls nucleocytoplasmic transport. It retains inert macromolecules but allows facilitated passage of nuclear transport receptors that shuttle cargoes into or out of nuclei. The barrier can be described as a condensed phase assembled from cohesive FG repeat domains, including foremost the charge-depleted FG domain of Nup98. We found that Nup98 FG domains show an LCST-type phase separation, and we provide comprehensive and orthogonal experimental datasets for a quantitative description of this behaviour. A derived thermodynamic model correlates saturation concentration with repeat number, temperature, and ionic strength. It allows estimating the enthalpy, entropy, and ΔG (0.2 kJ/mol, 0.1 kB·T) contributions per repeat to phase separation and inter-repeat cohesion. While changing the cohesion strength strongly impacts the strictness of barrier, these numbers provide boundary conditions for in-depth modelling not only of barrier assembly but also of NPC passage.
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7
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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.
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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.
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8
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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.
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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
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9
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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.
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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
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10
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Andersson J, Ferrand-Drake del Castillo G, Bilotto P, Höök F, Valtiner M, Dahlin A. Control of Polymer Brush Morphology, Rheology, and Protein Repulsion by Hydrogen Bond Complexation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:4943-4952. [PMID: 33851532 PMCID: PMC8154870 DOI: 10.1021/acs.langmuir.1c00271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Polymer brushes are widely used to alter the properties of interfaces. In particular, poly(ethylene glycol) (PEG) and similar polymers can make surfaces inert toward biomolecular adsorption. Neutral hydrophilic brushes are normally considered to have static properties at a given temperature. As an example, PEG is not responsive to pH or ionic strength. Here we show that, by simply introducing a polymeric acid such as poly(methacrylic acid) (PMAA), the highly hydrated brush barrier can change its properties entirely. This is caused by multivalent hydrogen bonds in an extremely pH-sensitive process. Remarkably, it is sufficient to reduce the pH to 5 for complexation to occur at the interface, which is two units higher than in the corresponding bulk systems. Below this critical pH, PMAA starts to bind to PEG in large amounts (comparable to the PEG amount), causing the brush to gradually compact and dehydrate. The brush also undergoes major rheology changes, from viscoelastic to rigid. Furthermore, the protein repelling ability of PEG is lost after reaching a threshold in the amount of PMAA bound. The changes in brush properties are tunable and become more pronounced when more PMAA is bound. The initial brush state is fully recovered when releasing PMAA by returning to physiological pH. Our findings are relevant for many applications involving functional interfaces, such as capture-release of biomolecules.
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Affiliation(s)
- John Andersson
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 41296 Gothenburg, Sweden
| | | | - Pierluigi Bilotto
- Institute
of Applied Physics, Group of Applied Interface Physics, Vienna University of Technology, 1040 Vienna, Austria
| | - Fredrik Höök
- Department
of Physics, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Markus Valtiner
- Institute
of Applied Physics, Group of Applied Interface Physics, Vienna University of Technology, 1040 Vienna, Austria
| | - Andreas Dahlin
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 41296 Gothenburg, Sweden
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11
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Mohamed MS, Hazawa M, Kobayashi A, Guillaud L, Watanabe-Nakayama T, Nakayama M, Wang H, Kodera N, Oshima M, Ando T, Wong RW. Spatiotemporally tracking of nano-biofilaments inside the nuclear pore complex core. Biomaterials 2020; 256:120198. [DOI: 10.1016/j.biomaterials.2020.120198] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/07/2020] [Accepted: 06/09/2020] [Indexed: 02/07/2023]
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12
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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.
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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
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13
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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.
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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
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14
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Celetti G, Paci G, Caria J, VanDelinder V, Bachand G, Lemke EA. The liquid state of FG-nucleoporins mimics permeability barrier properties of nuclear pore complexes. J Cell Biol 2020; 219:e201907157. [PMID: 31723007 PMCID: PMC7039189 DOI: 10.1083/jcb.201907157] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/21/2019] [Accepted: 10/09/2019] [Indexed: 01/31/2023] Open
Abstract
Nuclear pore complexes (NPCs) regulate all cargo traffic across the nuclear envelope. The transport conduit of NPCs is highly enriched in disordered phenylalanine/glycine-rich nucleoporins (FG-Nups), which form a permeability barrier of still elusive and highly debated molecular structure. Here we present a microfluidic device that triggered liquid-to-liquid phase separation of FG-Nups, which yielded droplets that showed typical properties of a liquid state. On the microfluidic chip, droplets were perfused with different transport-competent or -incompetent cargo complexes, and then the permeability barrier properties of the droplets were optically interrogated. We show that the liquid state mimics permeability barrier properties of the physiological nuclear transport pathway in intact NPCs in cells: that is, inert cargoes ranging from small proteins to large capsids were excluded from liquid FG-Nup droplets, but functional import complexes underwent facilitated import into droplets. Collectively, these data provide an experimental model of how NPCs can facilitate fast passage of cargoes across an order of magnitude in cargo size.
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Affiliation(s)
- Giorgia Celetti
- Biocentre, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Giulia Paci
- Biocentre, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joana Caria
- Biocentre, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Virginia VanDelinder
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM
| | - George Bachand
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM
| | - Edward A. Lemke
- Biocentre, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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15
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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.
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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)
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16
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Chen X, Richter RP. Effect of calcium ions and pH on the morphology and mechanical properties of hyaluronan brushes. Interface Focus 2019; 9:20180061. [PMID: 30842869 PMCID: PMC6388027 DOI: 10.1098/rsfs.2018.0061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2018] [Indexed: 01/13/2023] Open
Abstract
Hyaluronan (HA) is a linear, regular polysaccharide that plays as a chief structural and functional component in peri- and extracellular matrices, thus contributing significantly to many basic cellular processes. To understand more comprehensively the response of the supramolecular organization of HA polymers to changes in their aqueous environment, we study the effects of Ca2+ concentration and pH on the morphology and rigidity of films of end-grafted HA polymers on planar supports (HA brushes), as a well-defined in vitro model system of HA-rich matrices, by reflection interference contrast microscopy and quartz crystal microbalance. The thickness and softness of HA brushes decrease significantly with Ca2+ concentration but do not change with pH, within the physiological ranges of these parameters. The effect of Ca2+ on HA brush thickness is virtually identical to the effect of Na+ at 10-fold higher concentrations. Moreover, the thickness and softness of HA brushes decrease appreciably upon HA protonation at pH less than 6. Effects of pH and calcium ions are fully reversible over large parameter ranges. These findings are relevant for understanding the supramolecular organization and dynamics of HA-rich matrices in biological systems and will also benefit the rational design of synthetic HA-rich materials with tailored properties.
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Affiliation(s)
| | - Ralf P. Richter
- CIC biomaGUNE, San Sebastian, Spain
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- School of Physics and Astronomy, Faculty of Mathematics and Physical Sciences, University of Leeds, Leeds, UK
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds, UK
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17
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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.
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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.
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18
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Ananth A, Genua M, Aissaoui N, Díaz L, Eisele NB, Frey S, Dekker C, Richter RP, Görlich D. Reversible Immobilization of Proteins in Sensors and Solid-State Nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1703357. [PMID: 29611258 DOI: 10.1002/smll.201703357] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/13/2018] [Indexed: 06/08/2023]
Abstract
The controlled functionalization of surfaces with proteins is crucial for many analytical methods in life science research and biomedical applications. Here, a coating for silica-based surfaces is established which enables stable and selective immobilization of proteins with controlled orientation and tunable surface density. The coating is reusable, retains functionality upon long-term storage in air, and is applicable to surfaces of complex geometry. The protein anchoring method is validated on planar surfaces, and then a method is developed to measure the anchoring process in real time using silicon nitride solid-state nanopores. For surface attachment, polyhistidine tags that are site specifically introduced into recombinant proteins are exploited, and the yeast nucleoporin Nsp1 is used as model protein. Contrary to the commonly used covalent thiol chemistry, the anchoring of proteins via polyhistidine tag is reversible, permitting to take proteins off and replace them by other ones. Such switching in real time in experiments on individual nanopores is monitored using ion conductivity. Finally, it is demonstrated that silica and gold surfaces can be orthogonally functionalized to accommodate polyhistidine-tagged proteins on silica but prevent protein binding to gold, which extends the applicability of this surface functionalization method to even more complex sensor devices.
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Affiliation(s)
- Adithya Ananth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - María Genua
- CIC biomaGUNE, Biosurfaces Lab, Paseo Miramon 182, 20014, San Sebastian, Spain
| | - Nesrine Aissaoui
- CIC biomaGUNE, Biosurfaces Lab, Paseo Miramon 182, 20014, San Sebastian, Spain
| | - Leire Díaz
- CIC biomaGUNE, Biosurfaces Lab, Paseo Miramon 182, 20014, San Sebastian, Spain
| | - Nico B Eisele
- CIC biomaGUNE, Biosurfaces Lab, Paseo Miramon 182, 20014, San Sebastian, Spain
| | - Steffen Frey
- Department for Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ralf P Richter
- CIC biomaGUNE, Biosurfaces Lab, Paseo Miramon 182, 20014, San Sebastian, Spain
- Faculty of Biological Sciences, School of Biomedical Sciences, Faculty of Mathematics and Physical Sciences, School of Physics and Astronomy, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Dirk Görlich
- Department for Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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19
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Ketterer P, Ananth AN, Laman Trip DS, Mishra A, Bertosin E, Ganji M, van der Torre J, Onck P, Dietz H, Dekker C. DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex. Nat Commun 2018; 9:902. [PMID: 29500415 PMCID: PMC5834454 DOI: 10.1038/s41467-018-03313-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/02/2018] [Indexed: 11/09/2022] Open
Abstract
The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize artificial NPC mimics that allows controlling the type and copy number of FG-Nups. We constructed 34 nm-wide 3D DNA origami rings and attached different numbers of NSP1, a model yeast FG-Nup, or NSP1-S, a hydrophilic mutant. Using (cryo) electron microscopy, we find that NSP1 forms denser cohesive networks inside the ring compared to NSP1-S. Consistent with this, the measured ionic conductance is lower for NSP1 than for NSP1-S. Molecular dynamics simulations reveal spatially varying protein densities and conductances in good agreement with the experiments. Our technique provides an experimental platform for deciphering the collective behavior of IDPs with full control of their type and position.
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Affiliation(s)
- Philip Ketterer
- Physik Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, D-85748, Germany
| | - Adithya N Ananth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Diederik S Laman Trip
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ankur Mishra
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Eva Bertosin
- Physik Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, D-85748, Germany
| | - Mahipal Ganji
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Patrick Onck
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Hendrik Dietz
- Physik Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, D-85748, Germany.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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20
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Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement. ACS NANO 2018; 12:1508-1518. [PMID: 29350911 PMCID: PMC5834394 DOI: 10.1021/acsnano.7b08044] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.
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Affiliation(s)
- Patrick D. Ellis Fisher
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Bernice Akpinar
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
| | - Luke K. Davis
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Kenny Kwok Hin Chung
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
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21
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Ananth AN, Mishra A, Frey S, Dwarkasing A, Versloot R, van der Giessen E, Görlich D, Onck P, Dekker C. Spatial structure of disordered proteins dictates conductance and selectivity in nuclear pore complex mimics. eLife 2018; 7:31510. [PMID: 29442997 PMCID: PMC5826291 DOI: 10.7554/elife.31510] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 02/05/2018] [Indexed: 12/17/2022] Open
Abstract
Nuclear pore complexes (NPCs) lined with intrinsically disordered FG-domains act as selective gatekeepers for molecular transport between the nucleus and the cytoplasm in eukaryotic cells. The underlying physical mechanism of the intriguing selectivity is still under debate. Here, we probe the transport of ions and transport receptors through biomimetic NPCs consisting of Nsp1 domains attached to the inner surface of solid-state nanopores. We examine both wildtype FG-domains and hydrophilic SG-mutants. FG-nanopores showed a clear selectivity as transport receptors can translocate across the pore whereas other proteins cannot. SG mutant pores lack such selectivity. To unravel this striking difference, we present coarse-grained molecular dynamics simulations that reveal that FG-pores exhibit a high-density, nonuniform protein distribution, in contrast to a uniform and significantly less-dense protein distribution in the SG-mutant. We conclude that the sequence-dependent density distribution of disordered proteins inside the NPC plays a key role for its conductivity and selective permeability.
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Affiliation(s)
- Adithya N Ananth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Ankur Mishra
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Steffen Frey
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Arvind Dwarkasing
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Roderick Versloot
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Erik van der Giessen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Dirk Görlich
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Onck
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
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22
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Chen WG, Witten J, Grindy SC, Holten-Andersen N, Ribbeck K. Charge Influences Substrate Recognition and Self-Assembly of Hydrophobic FG Sequences. Biophys J 2017; 113:2088-2099. [PMID: 29117531 DOI: 10.1016/j.bpj.2017.08.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 08/08/2017] [Accepted: 08/29/2017] [Indexed: 01/19/2023] Open
Abstract
The nuclear pore complex controls the passage of molecules via hydrophobic phenylalanine-glycine (FG) domains on nucleoporins. Such FG domains consist of repeating units of FxFG, FG, or GLFG sequences, many of which are interspersed with highly charged amino acid sequences. Despite the high density of charge in certain FG domains, if and how charge influences FG-domain self-assembly and selective binding of nuclear transport receptors is largely unexplored. Using rationally designed short peptide sequences, we determined that the charge type and identity of amino acids surrounding FG sequences impact the structure and selectivity of FG-based gels. Moreover, we showed that spatial localization of the charged amino acids with respect to the FG sequence determines the degree to which charge influences hydrophobic interactions. Taken together, our study highlights that charge type and placement of amino acids regulate FG-sequence function and are important considerations when studying the mechanism of nuclear pore complex transport in vivo.
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Affiliation(s)
- Wesley G Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jacob Witten
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts; Computational Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Scott C Grindy
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Niels Holten-Andersen
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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23
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Fu G, Tu LC, Zilman A, Musser SM. Investigating molecular crowding within nuclear pores using polarization-PALM. eLife 2017; 6:e28716. [PMID: 28949296 PMCID: PMC5693140 DOI: 10.7554/elife.28716] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022] Open
Abstract
The key component of the nuclear pore complex (NPC) controlling permeability, selectivity, and the speed of nucleocytoplasmic transport is an assembly of natively unfolded polypeptides, which contain phenylalanine-glycine (FG) binding sites for nuclear transport receptors. The architecture and dynamics of the FG-network have been refractory to characterization due to the paucity of experimental methods able to probe the mobility and density of the FG-polypeptides and embedded macromolecules within intact NPCs. Combining fluorescence polarization, super-resolution microscopy, and mathematical analyses, we examined the rotational mobility of fluorescent probes at various locations within the FG-network under different conditions. We demonstrate that polarization PALM (p-PALM) provides a rich source of information about low rotational mobilities that are inaccessible with bulk fluorescence anisotropy approaches, and anticipate that p-PALM is well-suited to explore numerous crowded cellular environments. In total, our findings indicate that the NPC's internal organization consists of multiple dynamic environments with different local properties.
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Affiliation(s)
- Guo Fu
- Department of Molecular and Cellular Medicine, College of MedicineThe Texas A&M University Health Science CenterCollege StationUnited States
| | - Li-Chun Tu
- Department of Molecular and Cellular Medicine, College of MedicineThe Texas A&M University Health Science CenterCollege StationUnited States
| | - Anton Zilman
- Department of PhysicsUniversity of TorontoTorontoCanada
- Institute for Biomaterials and Biomedical EngineeringUniversity of TorontoTorontoCanada
| | - Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of MedicineThe Texas A&M University Health Science CenterCollege StationUnited States
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24
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Stanley GJ, Fassati A, Hoogenboom BW. Biomechanics of the transport barrier in the nuclear pore complex. Semin Cell Dev Biol 2017; 68:42-51. [DOI: 10.1016/j.semcdb.2017.05.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 05/11/2017] [Indexed: 12/14/2022]
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25
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Aramburu IV, Lemke EA. Floppy but not sloppy: Interaction mechanism of FG-nucleoporins and nuclear transport receptors. Semin Cell Dev Biol 2017; 68:34-41. [PMID: 28669824 PMCID: PMC7611744 DOI: 10.1016/j.semcdb.2017.06.026] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 06/29/2017] [Indexed: 12/15/2022]
Abstract
The nuclear pore complex (NPC) forms a permeability barrier between the nucleus and the cytoplasm. Molecules that are able to cross this permeability barrier encounter different disordered phenylalanine glycine rich nucleoporins (FG-Nups) that act as a molecular filter and regulate the selective NPC crossing of biomolecules. In this review, we provide a current overview regarding the interaction mechanism between FG-Nups and the carrier molecules that recognize and enable the transport of cargoes through the NPC aiming to understand the general molecular mechanisms that facilitate the nucleocytoplasmic transport.
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Affiliation(s)
- Iker Valle Aramburu
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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26
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Bano F, Banerji S, Howarth M, Jackson DG, Richter RP. A single molecule assay to probe monovalent and multivalent bonds between hyaluronan and its key leukocyte receptor CD44 under force. Sci Rep 2016; 6:34176. [PMID: 27679982 PMCID: PMC5040960 DOI: 10.1038/srep34176] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/08/2016] [Indexed: 01/31/2023] Open
Abstract
Glycosaminoglycans (GAGs), a category of linear, anionic polysaccharides, are ubiquitous in the extracellular space, and important extrinsic regulators of cell function. Despite the recognized significance of mechanical stimuli in cellular communication, however, only few single molecule methods are currently available to study how monovalent and multivalent GAG·protein bonds respond to directed mechanical forces. Here, we have devised such a method, by combining purpose-designed surfaces that afford immobilization of GAGs and receptors at controlled nanoscale organizations with single molecule force spectroscopy (SMFS). We apply the method to study the interaction of the GAG polymer hyaluronan (HA) with CD44, its receptor in vascular endothelium. Individual bonds between HA and CD44 are remarkably resistant to rupture under force in comparison to their low binding affinity. Multiple bonds along a single HA chain rupture sequentially and independently under load. We also demonstrate how strong non-covalent bonds, which are versatile for controlled protein and GAG immobilization, can be effectively used as molecular anchors in SMFS. We thus establish a versatile method for analyzing the nanomechanics of GAG·protein interactions at the level of single GAG chains, which provides new molecular-level insight into the role of mechanical forces in the assembly and function of GAG-rich extracellular matrices.
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Affiliation(s)
- Fouzia Bano
- CIC biomaGUNE, Paseo Miramon 182, 20009 Donostia-San Sebastian, Spain
| | - Suneale Banerji
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX39DS, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, OX13QU, UK
| | - David G Jackson
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX39DS, UK
| | - Ralf P Richter
- CIC biomaGUNE, Paseo Miramon 182, 20009 Donostia-San Sebastian, Spain.,Université Grenoble Alpes - CNRS, Laboratoire Interdisciplinaire de Physique (LIPhy), BP 87, 38402 Saint Martin d'Hères, France.,University of Leeds, School of Biomedical Sciences and School of Physics and Astronomy, Leeds, LS2 9JT, UK
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27
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Eskandari Nasrabad A, Jasnow D, Zilman A, Coalson RD. Precise control of polymer coated nanopores by nanoparticle additives: Insights from computational modeling. J Chem Phys 2016. [DOI: 10.1063/1.4955191] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
| | - David Jasnow
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Rob D. Coalson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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28
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Lemke EA. The Multiple Faces of Disordered Nucleoporins. J Mol Biol 2016; 428:2011-24. [PMID: 26791761 PMCID: PMC7611686 DOI: 10.1016/j.jmb.2016.01.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 12/30/2015] [Accepted: 01/04/2016] [Indexed: 11/26/2022]
Abstract
An evolutionary advantage of intrinsically disordered proteins (IDPs) is their ability to bind a variety of folded proteins-a paradigm that is central to the nucleocytoplasmic transport mechanism, in which nuclear transport receptors mediate the translocation of various cargo through the nuclear pore complex by binding disordered phenylalanine-glycine-rich nucleoporins (FG-Nups). FG-Nups are highly dynamic, which poses a substantial problem when trying to determine precisely their function using common experimental approaches. FG-Nups have been studied under a variety of conditions, ranging from those that constitute single-molecule measurements to physiological concentrations at which they can form supramolecular structures. In this review, I describe the physicochemical properties of FG-Nups and compare them to those of other disordered systems, including well-studied IDPs. From this comparison, it is apparent that FG-Nups not only share some properties with IDPs in general but also possess unique characteristics that might be key to their central role in the nucleocytoplasmic transport machinery.
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Affiliation(s)
- Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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29
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Vovk A, Gu C, Opferman MG, Kapinos LE, Lim RY, Coalson RD, Jasnow D, Zilman A. Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex. eLife 2016; 5. [PMID: 27198189 PMCID: PMC4874778 DOI: 10.7554/elife.10785] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 03/24/2016] [Indexed: 12/13/2022] Open
Abstract
Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function. DOI:http://dx.doi.org/10.7554/eLife.10785.001 Animal, plant and fungal cells contain a structure called the nucleus, inside which the genetic material of the cell is stored. For the cell to work properly, certain proteins and other molecules need to be able to enter and exit the nucleus. This transport is carried out by pore-like molecular “devices” known as Nuclear Pore Complexes, whose architecture and mode of operation are unique among cellular transporters. Nuclear Pore Complexes are charged with a daunting task of deciding which of the hundreds of molecules it conducts per second should go through and which should not. Small molecules can pass freely through Nuclear Pore Complexes. However, larger molecules can only pass through the pore efficiently if they are bound to specialized transport proteins that interact with the proteins – called FG nucleoporins – that line the pore. A unique feature of the FG nucleoporins is that, unlike typical proteins, they do not have a defined three-dimensional structure. Instead, they form a soft and pliable lining inside the Nuclear Pore Complex passageway. Exactly how interacting with transport proteins affects the structure and spatial arrangements of the FG nucleoporins in a way that allows them to control transport is not well understood. This is in part because existing experimental techniques are unable to study the structures of the FG nucleoporins in enough detail to track how they change during transport. The complexity and the diversity of the FG nucleoporins also make them difficult to model in detail. Vovk, Gu et al. have developed a theoretical model that is based on just three basic physical properties of the FG nucleoporins – their flexibility, their ability to interact with each other, and their binding with the transport proteins. Future work can refine the model by incorporating further molecular details about the interactions between FG nucleoporins and transport proteins. The predictions made by this simple model agree well with experimental results in a wide range of situations – from single molecules to complex spatial assemblies. They also explain why some of the experimental results appear to contradict each other and suggest how several outstanding controversies in the field can be reconciled. Because the model invokes only fundamental physical principles of FG nucleoporin assemblies, it shows that some of their general properties do not depend on the exact conditions. In particular, this might shed light on why Nuclear Pore Complexes in different organisms perform essentially the same function, although the details of their molecular structure may differ. This also suggests how the FG nucleoporins can be manipulated to build artificial devices based on the same principles. DOI:http://dx.doi.org/10.7554/eLife.10785.002
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Affiliation(s)
- Andrei Vovk
- Department of Physics, University of Toronto, Toronto, Canada
| | - Chad Gu
- Department of Physics, University of Toronto, Toronto, Canada
| | - Michael G Opferman
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, United States
| | - Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Roderick Yh Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Rob D Coalson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, United States
| | - David Jasnow
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, United States
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, Canada.,Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
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30
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Zahn R, Osmanović D, Ehret S, Araya Callis C, Frey S, Stewart M, You C, Görlich D, Hoogenboom BW, Richter RP. A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies. eLife 2016; 5. [PMID: 27058170 PMCID: PMC4874776 DOI: 10.7554/elife.14119] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/07/2016] [Indexed: 11/13/2022] Open
Abstract
The permeability barrier of nuclear pore complexes (NPCs) controls bulk nucleocytoplasmic exchange. It consists of nucleoporin domains rich in phenylalanine-glycine motifs (FG domains). As a bottom-up nanoscale model for the permeability barrier, we have used planar films produced with three different end-grafted FG domains, and quantitatively analyzed the binding of two different nuclear transport receptors (NTRs), NTF2 and Importin β, together with the concomitant film thickness changes. NTR binding caused only moderate changes in film thickness; the binding isotherms showed negative cooperativity and could all be mapped onto a single master curve. This universal NTR binding behavior - a key element for the transport selectivity of the NPC - was quantitatively reproduced by a physical model that treats FG domains as regular, flexible polymers, and NTRs as spherical colloids with a homogeneous surface, ignoring the detailed arrangement of interaction sites along FG domains and on the NTR surface.
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Affiliation(s)
- Raphael Zahn
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain
| | - Dino Osmanović
- London Centre for Nanotechnology, University College London, London, United Kingdom.,Department of Physics and Astronomy, University College London, London, United Kingdom.,Department of Physics, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Severin Ehret
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain
| | | | - Steffen Frey
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Murray Stewart
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Changjiang You
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London, United Kingdom.,Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Ralf P Richter
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain.,Laboratory of Interdisciplinary Physics, University Grenoble Alpes - CNRS, Grenoble, France.,Max-Planck-Institute for Intelligent Systems, Stuttgart, Germany
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31
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Musser SM, Grünwald D. Deciphering the Structure and Function of Nuclear Pores Using Single-Molecule Fluorescence Approaches. J Mol Biol 2016; 428:2091-119. [PMID: 26944195 DOI: 10.1016/j.jmb.2016.02.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/05/2016] [Accepted: 02/17/2016] [Indexed: 01/06/2023]
Abstract
Due to its central role in macromolecular trafficking and nucleocytoplasmic information transfer, the nuclear pore complex (NPC) has been studied in great detail using a wide spectrum of methods. Consequently, many aspects of its architecture, general function, and role in the life cycle of a cell are well understood. Over the last decade, fluorescence microscopy methods have enabled the real-time visualization of single molecules interacting with and transiting through the NPC, allowing novel questions to be examined with nanometer precision. While initial single-molecule studies focused primarily on import pathways using permeabilized cells, it has recently proven feasible to investigate the export of mRNAs in living cells. Single-molecule assays can address questions that are difficult or impossible to answer by other means, yet the complexity of nucleocytoplasmic transport requires that interpretation be based on a firm genetic, biochemical, and structural foundation. Moreover, conceptually simple single-molecule experiments remain technically challenging, particularly with regard to signal intensity, signal-to-noise ratio, and the analysis of noise, stochasticity, and precision. We discuss nuclear transport issues recently addressed by single-molecule microscopy, evaluate the limits of existing assays and data, and identify open questions for future studies. We expect that single-molecule fluorescence approaches will continue to be applied to outstanding nucleocytoplasmic transport questions, and that the approaches developed for NPC studies are extendable to additional complex systems and pathways within cells.
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Affiliation(s)
- Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, 1114 TAMU, College Station, TX 77843, USA.
| | - David Grünwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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32
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Transport Selectivity of Nuclear Pores, Phase Separation, and Membraneless Organelles. Trends Biochem Sci 2015; 41:46-61. [PMID: 26705895 DOI: 10.1016/j.tibs.2015.11.001] [Citation(s) in RCA: 292] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 12/21/2022]
Abstract
Nuclear pore complexes (NPCs) provide a selective passageway for receptor-mediated active transport between nucleus and cytoplasm, while maintaining the distinct molecular compositions of both compartments at large. In this review we discuss how NPCs gain a remarkable sorting selectivity from non-globular FG domains and their phase separation into dense polymer meshworks. The resulting sieve-like FG hydrogels are effective barriers to normal macromolecules but are at the same time highly permeable to shuttling nuclear transport receptors, which bind to FG motifs as well as to their designated cargoes. Phase separation driven by disordered protein domains was recently also recognized as being pivotal to the formation of membraneless organelles, making it an important emerging principle in cell biology.
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33
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Plasticity of an ultrafast interaction between nucleoporins and nuclear transport receptors. Cell 2015; 163:734-45. [PMID: 26456112 PMCID: PMC4622936 DOI: 10.1016/j.cell.2015.09.047] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/17/2015] [Accepted: 09/23/2015] [Indexed: 11/23/2022]
Abstract
The mechanisms by which intrinsically disordered proteins engage in rapid and highly selective binding is a subject of considerable interest and represents a central paradigm to nuclear pore complex (NPC) function, where nuclear transport receptors (NTRs) move through the NPC by binding disordered phenylalanine-glycine-rich nucleoporins (FG-Nups). Combining single-molecule fluorescence, molecular simulations, and nuclear magnetic resonance, we show that a rapidly fluctuating FG-Nup populates an ensemble of conformations that are prone to bind NTRs with near diffusion-limited on rates, as shown by stopped-flow kinetic measurements. This is achieved using multiple, minimalistic, low-affinity binding motifs that are in rapid exchange when engaging with the NTR, allowing the FG-Nup to maintain an unexpectedly high plasticity in its bound state. We propose that these exceptional physical characteristics enable a rapid and specific transport mechanism in the physiological context, a notion supported by single molecule in-cell assays on intact NPCs. Integrative structural biology reveals the basis of rapid nuclear transport Transient binding of disordered nucleoporins leaves their plasticity unaffected Multiple minimalistic low-affinity binding motifs create a polyvalent complex A highly reactive and dynamic surface permits an ultrafast binding mechanism
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34
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DeForte S, Reddy KD, Uversky VN. Digested disorder, Quarterly intrinsic disorder digest (October-November-December, 2013). INTRINSICALLY DISORDERED PROTEINS 2015; 3:e984569. [PMID: 28293487 DOI: 10.4161/21690707.2014.984569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 11/19/2022]
Abstract
This is the 4th issue of the Digested Disorder series that represents reader's digest of the scientific literature on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the fourth quarter of 2013; i.e. during the period of October, November, and December of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; These authors contributed equally to this work
| | - Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; These authors contributed equally to this work
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; USF Health Byrd Alzheimer Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Biology Department; Faculty of Science; King Abdulaziz University; Jeddah, Kingdom of Saudi Arabia; Laboratory of Structural Dynamics, Stability, and Folding of Proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia; Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
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35
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Bestembayeva A, Kramer A, Labokha AA, Osmanović D, Liashkovich I, Orlova EV, Ford IJ, Charras G, Fassati A, Hoogenboom BW. Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes. NATURE NANOTECHNOLOGY 2015; 10:60-64. [PMID: 25420031 PMCID: PMC4286247 DOI: 10.1038/nnano.2014.262] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 10/13/2014] [Indexed: 05/17/2023]
Abstract
The nuclear pore complex (NPC) is the gate for transport between the cell nucleus and the cytoplasm. Small molecules cross the NPC by passive diffusion, but molecules larger than ∼5 nm must bind to nuclear transport receptors to overcome a selective barrier within the NPC. Although the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins, and is therefore not well understood. Here, we show that stiffness topography with sharp atomic force microscopy tips can generate nanoscale cross-sections of the NPC. The cross-sections reveal two distinct structures, a cytoplasmic ring and a central plug structure, which are consistent with the three-dimensional NPC structure derived from electron microscopy. The central plug persists after reactivation of the transport cycle and resultant cargo release, indicating that the plug is an intrinsic part of the NPC barrier. Added nuclear transport receptors accumulate on the intact transport barrier and lead to a homogenization of the barrier stiffness. The observed nanomechanical properties in the NPC indicate the presence of a cohesive barrier to transport and are quantitatively consistent with the presence of a central condensate of nuclear pore proteins in the NPC channel.
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Affiliation(s)
- Aizhan Bestembayeva
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Armin Kramer
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Institute of Physiology II, University of Münster, Robert-Koch Strasse 27b, 48149 Münster, Germany
| | - Aksana A. Labokha
- Wohl Virion Centre, Division of Infection & Immunity, MRC Centre for Medical Molecular Virology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Dino Osmanović
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Ivan Liashkovich
- Institute of Physiology II, University of Münster, Robert-Koch Strasse 27b, 48149 Münster, Germany
| | - Elena V. Orlova
- Department of Biological Sciences, Birkbeck College, Institute of Structural and Molecular Biology, Malet Street, London WC1E 7HX, United Kingdom
| | - Ian J. Ford
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Guillaume Charras
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Ariberto Fassati
- Wohl Virion Centre, Division of Infection & Immunity, MRC Centre for Medical Molecular Virology, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Correspondence and requests for materials should be addressed to A.F. () and B.W.H. ()
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Correspondence and requests for materials should be addressed to A.F. () and B.W.H. ()
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36
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Baranova NS, Inforzato A, Briggs DC, Tilakaratna V, Enghild JJ, Thakar D, Milner CM, Day AJ, Richter RP. Incorporation of pentraxin 3 into hyaluronan matrices is tightly regulated and promotes matrix cross-linking. J Biol Chem 2014; 289:30481-30498. [PMID: 25190808 PMCID: PMC4215230 DOI: 10.1074/jbc.m114.568154] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Mammalian oocytes are surrounded by a highly hydrated hyaluronan (HA)-rich extracellular matrix with embedded cumulus cells, forming the cumulus cell·oocyte complex (COC) matrix. The correct assembly, stability, and mechanical properties of this matrix, which are crucial for successful ovulation, transport of the COC to the oviduct, and its fertilization, depend on the interaction between HA and specific HA-organizing proteins. Although the proteins inter-α-inhibitor (IαI), pentraxin 3 (PTX3), and TNF-stimulated gene-6 (TSG-6) have been identified as being critical for COC matrix formation, its supramolecular organization and the molecular mechanism of COC matrix stabilization remain unknown. Here we used films of end-grafted HA as a model system to investigate the molecular interactions involved in the formation and stabilization of HA matrices containing TSG-6, IαI, and PTX3. We found that PTX3 binds neither to HA alone nor to HA films containing TSG-6. This long pentraxin also failed to bind to products of the interaction between IαI, TSG-6, and HA, among which are the covalent heavy chain (HC)·HA and HC·TSG-6 complexes, despite the fact that both IαI and TSG-6 are ligands of PTX3. Interestingly, prior encounter with IαI was required for effective incorporation of PTX3 into TSG-6-loaded HA films. Moreover, we demonstrated that this ternary protein mixture made of IαI, PTX3, and TSG-6 is sufficient to promote formation of a stable (i.e. cross-linked) yet highly hydrated HA matrix. We propose that this mechanism is essential for correct assembly of the COC matrix and may also have general implications in other inflammatory processes that are associated with HA cross-linking.
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Affiliation(s)
| | | | - David C Briggs
- Wellcome Trust Centre for Cell Matrix Research and University of Manchester, Manchester M13 9PT, United Kingdom
| | - Viranga Tilakaratna
- Wellcome Trust Centre for Cell Matrix Research and University of Manchester, Manchester M13 9PT, United Kingdom
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, University of Aarhus, 8000 Aarhus C, Denmark
| | - Dhruv Thakar
- Department of Molecular Chemistry, University Grenoble Alpes and CNRS, 38000 Grenoble, France, and
| | - Caroline M Milner
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Anthony J Day
- Wellcome Trust Centre for Cell Matrix Research and University of Manchester, Manchester M13 9PT, United Kingdom.
| | - Ralf P Richter
- CIC biomaGUNE, 20009 Donostia-San Sebastian, Spain,; Department of Molecular Chemistry, University Grenoble Alpes and CNRS, 38000 Grenoble, France, and; Max-Planck-Institute for Intelligent Systems, 70569 Stuttgart, Germany.
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37
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You C, Piehler J. Multivalent chelators for spatially and temporally controlled protein functionalization. Anal Bioanal Chem 2014; 406:3345-57. [DOI: 10.1007/s00216-014-7803-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 03/26/2014] [Accepted: 03/31/2014] [Indexed: 12/30/2022]
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38
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Kim J, Izadyar A, Shen M, Ishimatsu R, Amemiya S. Ion permeability of the nuclear pore complex and ion-induced macromolecular permeation as studied by scanning electrochemical and fluorescence microscopy. Anal Chem 2014; 86:2090-8. [PMID: 24460147 PMCID: PMC3955255 DOI: 10.1021/ac403607s] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/25/2014] [Indexed: 12/20/2022]
Abstract
Efficient delivery of therapeutic macromolecules and nanomaterials into the nucleus is imperative for gene therapy and nanomedicine. Nucleocytoplasmic molecular transport, however, is tightly regulated by the nuclear pore complex (NPC) with the hydrophobic transport barriers based on phenylalanine and glycine repeats. Herein, we apply scanning electrochemical microscopy (SECM) to quantitatively study the permeability of the NPCs to small probe ions with a wide range of hydrophobicity as a measure of their hydrophobic interactions with the transport barriers. Amperometric detection of the redox-inactive probe ions is enabled by using the ion-selective SECM tips based on the micropipet- or nanopipet-supported interfaces between two immiscible electrolyte solutions. The remarkably high ion permeability of the NPCs is successfully measured by SECM and theoretically analyzed. This analysis demonstrates that the ion permeability of the NPCs is determined by the dimensions and density of the nanopores without a significant effect of the transport barriers on the transported ions. Importantly, the weak ion-barrier interactions become significant at sufficiently high concentrations of extremely hydrophobic ions, i.e., tetraphenylarsonium and perfluorobutylsulfonate, to permeabilize the NPCs to naturally impermeable macromolecules. Dependence of ion-induced permeabilization of the NPC on the pathway and mode of macromolecular transport is studied by using fluorescence microscopy to obtain deeper insights into the gating mechanism of the NPC as the basis of a new transport model.
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Affiliation(s)
| | | | | | | | - Shigeru Amemiya
- Department of Chemistry, University
of Pittsburgh, 219 Parkman
Avenue, Pittsburgh, Pennsylvania 15260, United States
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