1
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Vorsmann CF, Del Galdo S, Capone B, Locatelli E. Colloidal adsorption in planar polymeric brushes. NANOSCALE ADVANCES 2024; 6:816-825. [PMID: 38298587 PMCID: PMC10825936 DOI: 10.1039/d3na00598d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/20/2023] [Indexed: 02/02/2024]
Abstract
The design of nano-functionalised membranes or channels, able to effectively adsorb pollutants in aqueous solutions, is a topic that is gaining a great deal of attention in the materials science community. With this work we explore, through a combination of scaling theories and molecular dynamics simulations, the adsorption of spherical non-deformable colloidal nanoparticles within planar polymeric brushes. Our strategy is twofold: first, we generalise the Alexander-de Gennes theory for planar homopolymeric brushes to the case of diblock copolymer brushes, then we map the adsorbing homopolymeric brushes onto a diblock copolymer system, where the adsorbed colloids and all interacting monomers are considered monomers in bad solvent and we apply the generalised scaling theory to this effective diblock copolymer. This allows the prediction of the average conformation of the grafted substrate, i.e. its average height, as a function of the amount of loaded particles, as well as the introduction of a continuous mapping between a homopolymeric brush, the fraction of loaded particles and the average height of the adsorbing substrate.
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Affiliation(s)
- Clemens Franz Vorsmann
- Dipartimento di Fisica e Astronomia, Università di Padova Sezione di Padova, via Marzolo 8 I-35131 Padova 2INFN Italy
- INFN Sezione di Padova, via Marzolo 8 I-35131 Padova Italy
| | - Sara Del Galdo
- Science Department, University of Roma Tre Via della Vasca Navale 84 00146 Rome Italy
| | - Barbara Capone
- Science Department, University of Roma Tre Via della Vasca Navale 84 00146 Rome Italy
| | - Emanuele Locatelli
- Dipartimento di Fisica e Astronomia, Università di Padova Sezione di Padova, via Marzolo 8 I-35131 Padova 2INFN Italy
- INFN Sezione di Padova, via Marzolo 8 I-35131 Padova Italy
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2
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Effects of Sequence Composition, Patterning and Hydrodynamics on the Conformation and Dynamics of Intrinsically Disordered Proteins. Int J Mol Sci 2023; 24:ijms24021444. [PMID: 36674958 PMCID: PMC9867189 DOI: 10.3390/ijms24021444] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/24/2022] [Accepted: 12/25/2022] [Indexed: 01/13/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) perform diverse functions in cellular organization, transport and signaling. Unlike the well-defined structures of the classical natively folded proteins, IDPs and IDRs dynamically span large conformational and structural ensembles. This dynamic disorder impedes the study of the relationship between the amino acid sequences of the IDPs and their spatial structures and dynamics, with different experimental techniques often offering seemingly contradictory results. Although experimental and theoretical evidence indicates that some IDP properties can be understood based on their average biophysical properties and amino acid composition, other aspects of IDP function are dictated by the specifics of the amino acid sequence. We investigate the effects of several key variables on the dimensions and the dynamics of IDPs using coarse-grained polymer models. We focus on the sequence "patchiness" informed by the sequence and biophysical properties of different classes of IDPs-and in particular FG nucleoporins of the nuclear pore complex (NPC). We show that the sequence composition and patterning are well reflected in the global conformational variables such as the radius of gyration and hydrodynamic radius, while the end-to-end distance and dynamics are highly sequence-specific. We find that in good solvent conditions highly heterogeneous sequences of IDPs can be well mapped onto averaged minimal polymer models for the purpose of prediction of the IDPs dimensions and dynamic relaxation times. The coarse-grained simulations are in a good agreement with the results of atomistic MD. We discuss the implications of these results for the interpretation of the recent experimental measurements, and for the further applications of mesoscopic models of FG nucleoporins and IDPs more broadly.
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3
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Morphology of Polymer Brushes in the Presence of Attractive Nanoparticles: Effects of Temperature. Int J Mol Sci 2023; 24:ijms24010832. [PMID: 36614298 PMCID: PMC9821464 DOI: 10.3390/ijms24010832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023] Open
Abstract
We study the role of temperature on the structure of pure polymer brushes and their mixture with attractive nanoparticles in flat and cylindrical geometries. It has previously been established that the addition of such nanoparticles causes the polymer brush to collapse and the intensity of the collapse depends on the attraction strength, the nanoparticle diameter, and the grafting density. In this work, we carry out molecular dynamics simulation under good solvent conditions to show how the collapse transition is affected by the temperature, for both plane grafted and inside-cylinder grafted brushes. We first examine the pure brush morphology and verify that the brush height is insensitive to temperature changes in both planar and cylindrical geometries, as expected for a polymer brush in a good solvent. On the other hand, for both system geometries, the brush structure in the presence of attractive nanoparticles is quite responsive to temperature changes. Generally speaking, for a given nanoparticle concentration, increasing the temperature causes the brush height to increase. A brush which contracts when nanoparticles are added eventually swells beyond its pure brush height as the system temperature is increased. The combination of two easily controlled external parameters, namely, concentration of nanoparticles in solution and temperature, allows for sensitive and reversible adjustment of the polymer brush height, a feature which could be exploited in designing smart polymer devices.
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4
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Mohammadyarloo Z, Sommer JU. Co-nonsolvency Transition in Polymer Solutions: A Simulation Study. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zahra Mohammadyarloo
- Leibniz-Institute fur Polymerforschung Dresden, Institute Theory of Polymers, Hohe Strasse 6, 01069Dresden, Germany
- Institute for Theoretical Physics, TU Dresden, Zellescher Weg 17, 01069Dresden, Germany
| | - Jens-Uwe Sommer
- Leibniz-Institute fur Polymerforschung Dresden, Institute Theory of Polymers, Hohe Strasse 6, 01069Dresden, Germany
- Institute for Theoretical Physics, TU Dresden, Zellescher Weg 17, 01069Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, 01307Dresden, Germany
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5
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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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6
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Zhu PW. Effects of cosolvent partitioning on conformational transitions and tethered chain flexibility in spherical polymer brushes. SOFT MATTER 2021; 17:6817-6832. [PMID: 34223603 DOI: 10.1039/d1sm00523e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this work, based on the framework of preferential adsorption concept and analytical self-consistent field (SCF) theory, a model is proposed to investigate the reentrant transition experimentally observed from the thermoresponsive spherical brush in a series of aqueous alcohol solutions. The interaction between monomers is incorporated into the model. Conformational transitions of the spherical brush are quantitatively correlated to the physical parameters, including the number of adsorbed cosolvents which facilitates the solvent quality, the number of cosolvent bridges which drives the brush collapse, as well as their partition coefficients between the brush and the bulk solution. An analytical formula for the number of Kuhn segments per tethered chain is obtained based on the analytical SCF theory, which elucidates the flexibility of tethered chains in the intricate system of multicomponents involving the conformational transitions. Under the experimental conditions associated with the cosolvent-brush interaction, the variation of the monomer chemical potential with the monomer concentration indicates that the monomer distribution of the spherical brush remains continuous. The analysis based on the SFC theory also reveals that the distribution of adsorbed cosolvents is a positive parabola while the distribution of cosolvent bridges appears to be an exponential decay function, implying that the intervening space between tethered chains, rather than the number of adsorbed cosolvents, plays a crucial role in forming the cosolvent bridge. We demonstrate that the model formulated for the reentrant transition under weaker cosolvent-brush interactions provides guidelines for the one under stronger nanoparticle-brush interactions.
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Affiliation(s)
- Peng Wei Zhu
- Department of Materials Science and Engineering, Monash University, Clayton, VIC 3800, Australia.
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7
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Amemiya S. Nanoelectrochemical Study of Molecular Transport through the Nuclear Pore Complex. CHEM REC 2021; 21:1430-1441. [PMID: 33502100 PMCID: PMC8217113 DOI: 10.1002/tcr.202000175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 11/10/2022]
Abstract
The nuclear pore complex (NPC) is the proteinaceous nanopore that solely mediates the transport of both small molecules and macromolecules between the nucleus and cytoplasm of a eukaryotic cell to regulate gene expression. In this personal account, we introduce recent progress in our nanoelectrochemical study of molecular transport through the NPC. Our work represents the importance of chemistry in understanding and controlling of NPC-mediated molecular transport to enable the efficient and safe delivery of genetic therapeutics into the nucleus, thereby fundamentally contributing to human health. Specifically, we employ nanoscale scanning electrochemical microscopy to test our hypothesis that the nanopore of the NPC is divided by transport barriers concentrically into peripheral and central routes to efficiently mediate the bimodal traffic of protein transport and RNA export, respectively, through cooperative hydrophobic and electrostatic interactions.
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Affiliation(s)
- Shigeru Amemiya
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, 15260, PA
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8
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Ritsema van Eck GC, Veldscholte LB, Nijkamp JHWH, de Beer S. Sorption Characteristics of Polymer Brushes in Equilibrium with Solvent Vapors. Macromolecules 2020; 53:8428-8437. [PMID: 33071358 PMCID: PMC7558291 DOI: 10.1021/acs.macromol.0c01637] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/11/2020] [Indexed: 12/13/2022]
Abstract
![]()
While
polymer brushes in contact with liquids have been researched
intensively, the characteristics of brushes in equilibrium with vapors
have been largely unexplored, despite their relevance for many applications,
including sensors and smart adhesives. Here, we use molecular dynamics
simulations to show that solvent and polymer density distributions
for brushes exposed to vapors are qualitatively different from those
of brushes exposed to liquids. Polymer density profiles for vapor-solvated
brushes decay more sharply than for liquid-solvated brushes. Moreover,
adsorption layers of enhanced solvent density are formed at the brush–vapor
interface. Interestingly and despite all of these effects, we find
that solvent sorption in the brush is described rather well with a
simple mean-field Flory–Huggins model that incorporates an
entropic penalty for stretching of the brush polymers, provided that
parameters such as the polymer–solvent interaction parameter,
grafting density, and relative vapor pressure are varied individually.
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Affiliation(s)
- Guido C Ritsema van Eck
- Materials Science and Technology of Polymers, University of Twente, Enschede 7522 NB, The Netherlands
| | - Lars B Veldscholte
- Materials Science and Technology of Polymers, University of Twente, Enschede 7522 NB, The Netherlands
| | - Jan H W H Nijkamp
- Materials Science and Technology of Polymers, University of Twente, Enschede 7522 NB, The Netherlands
| | - Sissi de Beer
- Materials Science and Technology of Polymers, University of Twente, Enschede 7522 NB, The Netherlands
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9
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Zhang X, Zong J, Meng D. A unified understanding of the cononsolvency of polymers in binary solvent mixtures. SOFT MATTER 2020; 16:7789-7796. [PMID: 32744548 DOI: 10.1039/d0sm00811g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The standard random phase approximation (RPA) model is applied to investigate the cononsolvency of polymers in mixtures of two good solvents. It is shown that in the RPA framework, the two types of cononsolvency behaviors reported in previous theoretical studies can be unified under the same concept of mean-field density correlations. The two types of cononsolvency are distinguished by the solvent composition at which maximum immiscibility is predicted to occur. The maximum immiscibility occurs with the cosolvent being the minor solvent if the driving mechanism is the preferential solvation of polymers. For the cononsolvency driven by the preferential mixing of solvents, the maximum immiscibility is predicted at a symmetric solvent composition. An interplay of the two driving forces gives rise to a reentrant behavior in which the cononsolvency of the two types switches from one to the other, through a "conventional" region where the overall solvent quality varies monotonically with the solvent composition. The RPA model developed in this work provides a unified analytical framework for understanding the conformational and solubility transition of polymers in multi-solvent mixtures. Such findings highlight the complex role played by the solvents in polymer solutions, a problem of fundamental and practical interest in diverse applications of materials science.
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Affiliation(s)
- Xiangyu Zhang
- The Swalm School of Chemical Engineering, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Jing Zong
- The Swalm School of Chemical Engineering, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Dong Meng
- The Swalm School of Chemical Engineering, Mississippi State University, Mississippi State, MS 39762, USA.
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10
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Li CW, Merlitz H, Sommer JU. Mean-Field Model of the Collapse Transition of Brushes inside Cylindrical Nanopores. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00618] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Cheng-Wu Li
- Leibniz-Institut of Polymer Research Dresden, 01069 Dresden, Germany
| | - Holger Merlitz
- Leibniz-Institut of Polymer Research Dresden, 01069 Dresden, Germany
| | - Jens-Uwe Sommer
- Leibniz-Institut of Polymer Research Dresden, 01069 Dresden, Germany
- Institute for Theoretical Physics, TU Dresden, Zellescher Weg 13, 01069 Dresden, Germany
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11
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Yong H, Merlitz H, Fery A, Sommer JU. Polymer Brushes and Gels in Competing Solvents: The Role of Different Interactions and Quantitative Predictions for Poly(N-isopropylacrylamide) in Alcohol–Water Mixtures. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00033] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Huaisong Yong
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany
| | - Holger Merlitz
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
| | - Andreas Fery
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany
| | - Jens-Uwe Sommer
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
- Institute for Theoretical Physics, Technische Universität Dresden, 01062 Dresden, Germany
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12
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Yong H, Bittrich E, Uhlmann P, Fery A, Sommer JU. Co-Nonsolvency Transition of Poly(N-isopropylacrylamide) Brushes in a Series of Binary Mixtures. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01286] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Huaisong Yong
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
| | - Eva Bittrich
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
| | - Petra Uhlmann
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
- Department of Chemistry, University of Nebraska-Lincoln, Hamilton Hall, Lincoln, Nebraska 68588, United States
| | - Andreas Fery
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
| | - Jens-Uwe Sommer
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
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13
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Galuschko A, Sommer JU. Co-Nonsolvency Response of a Polymer Brush: A Molecular Dynamics Study. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00569] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Andre Galuschko
- Leibniz-Institut für Polymerforschung Dresden, Institute Theory of Polymers, Hohe Strasse 6, 01069 Dresden, Germany
| | - Jens-Uwe Sommer
- Institute for Theoretical Physics, TU Dresden, Zellescher Weg 17, 01069 Dresden, Germany
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14
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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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15
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Ozmaian M, Freitas BA, Coalson RD. Controlling the Surface Properties of Binary Polymer Brush-Coated Colloids via Targeted Nanoparticles. J Phys Chem B 2019; 123:258-265. [PMID: 30495948 DOI: 10.1021/acs.jpcb.8b05520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper explores a novel mechanism for controlling the surface properties of polymer-coated colloids using targeted ("sticky") nanoparticles which attract monomers of certain polymer species. In our study, colloids are coated by two types of tethered polymer chains having different chemical properties. Attraction of nanoparticles to the monomers of one polymer type causes these polymer chains to contract toward the grafting surface, rendering the other type more exposed to the environment. Thus, the effective surface properties of the colloid are dominated by the intended polymer type. We use coarse-grained molecular dynamics (CGMD) simulation to demonstrate that introducing nanoparticles which interact preferentially with certain types of polymers makes it possible to switch between different surface properties of the colloid. This mechanism can in principle be exploited in drug delivery systems and self-assembly applications.
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Affiliation(s)
- Masoumeh Ozmaian
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Brayden A Freitas
- Department of Physics and Astronomy , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Rob D Coalson
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
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16
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Li CW, Merlitz H, Wu CX, Sommer JU. Nanopores as Switchable Gates for Nanoparticles: A Molecular Dynamics Study. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01149] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Cheng-Wu Li
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Holger Merlitz
- Leibniz-Institut für Polymerforschung Dresden, 01069 Dresden, Germany
| | - Chen-Xu Wu
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Jens-Uwe Sommer
- Leibniz-Institut für Polymerforschung Dresden, 01069 Dresden, Germany
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17
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Sommer JU. Gluonic and Regulatory Solvents: A Paradigm for Tunable Phase Segregation in Polymers. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00370] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jens-Uwe Sommer
- Leibniz-Institut für Polymerforschung Dresden, Institute Theory of Polymers, Hohe Strasse 6, 01069 Dresden, Germany
- Institute for Theoretical Physics, TU Dresden, Zellescher Weg 17, 01069 Dresden, Germany
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18
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Ozmaian M, Jasnow D, Eskandari Nasrabad A, Zilman A, Coalson RD. Effects of cross-linking on partitioning of nanoparticles into a polymer brush: Coarse-grained simulations test simple approximate theories. J Chem Phys 2018; 148:024902. [DOI: 10.1063/1.4990796] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Masoumeh Ozmaian
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - David Jasnow
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Anton Zilman
- Department of Physics and Institute for Biomaterials and Biomedical Engineering, 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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19
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Cheng S, Stevens MJ, Grest GS. Ordering nanoparticles with polymer brushes. J Chem Phys 2017; 147:224901. [DOI: 10.1063/1.5006048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Shengfeng Cheng
- Department of Physics, Center for Soft Matter and Biological Physics, and Macromolecules Innovation Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Mark J. Stevens
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Gary S. Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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20
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Budkov YA, Kolesnikov AL. Statistical description of co-nonsolvency suppression at high pressures. SOFT MATTER 2017; 13:8362-8367. [PMID: 29116278 DOI: 10.1039/c7sm01637a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present an application of Flory-type theory of a flexible polymer chain dissolved in a binary mixture of solvents to theoretical description of co-nonsolvency. We show that our theoretical predictions are in good quantitative agreement with the recently published MD simulation results for the conformational behavior of a Lennard-Jones flexible chain in a binary mixture of the Lennard-Jones fluids. We show that our theory is able to describe co-nonsolvency suppression through pressure enhancement to extremely high values recently discovered in experiments and reproduced by full atomistic MD simulations. By analysing the co-solvent concentration in the internal polymer volume at different pressure values, we speculate that this phenomenon is caused by the suppression of the co-solvent preferential solvation of the polymer backbone at the rather high pressure imposed. We show that when the co-solvent-induced coil-globule transition takes place, the entropy and enthalpy contributions to the solvation free energy abruptly decrease, while the solvation free energy remains continuous.
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Affiliation(s)
- Yu A Budkov
- Tikhonov Moscow Institute of Electronics and Mathematics, School of Applied Mathematics, National Research University Higher School of Economics, Tallinskaya St. 34, 123458 Moscow, Russia.
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21
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Im H, Oh Y, Cho HW, Kim J, Paeng K, Sung BJ. The spatial arrangement of a single nanoparticle in a thin polymer film and its effect on the nanoparticle diffusion. SOFT MATTER 2017; 13:5897-5904. [PMID: 28766660 DOI: 10.1039/c7sm01115f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The spatial arrangement of nanoparticles (NPs) within thin polymer films may influence their properties such as the glass transition temperature. Questions regarding what may affect the spatial arrangement of NPs, however, still remain unanswered at a molecular level. In this work, we perform molecular dynamics simulations for a free-standing thin polymer film with a single NP. We find from simulations that depending on the NP size and the inter-particle interaction between the NP and polymers, one may control the spatial arrangement of the NP. When the interaction between the NP and polymers is sufficiently attractive (repulsive), the NP is likely to be placed at the center (at the surface) of the thin film in equilibrium. Interestingly, for a moderate interaction between the NP and polymers, the first-order transition occurs in the spatial arrangement of the NP as one increases the NP size: a small NP prefers the surface of the polymer film whereas a large NP prefers the center. Such a first-order transition is corroborated by calculating the free energy of the NP as a function of the position and can be understood in terms of a sixth-order Landau free energy. More interestingly, the diffusion of the NP also changes drastically due to the first-order transition in the spatial arrangement. The NP diffusion is enhanced drastically (more than expected in bulk polymer melts) as the NP is shifted to the polymer film surface.
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Affiliation(s)
- Hesang Im
- Department of Chemistry and Research Institute for Basic Science, Sogang University, Seoul 04107, Republic of Korea.
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22
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Gu C, Coalson RD, Jasnow D, Zilman A. Free Energy of Nanoparticle Binding to Multivalent Polymeric Substrates. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b00868] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chad Gu
- Department
of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Rob D. Coalson
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - David Jasnow
- Department
of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anton Zilman
- Department
of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
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23
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Affiliation(s)
- Jens-Uwe Sommer
- Institute Theory of Polymers, Leibniz-Insitut für Polymerforschung Dresden, Hohe Strasse 6, 01069 Dresden, Germany
- Institute for Theoretical
Physics, TU Dresden, Zellescher Weg 17, 01069 Dresden, Germany
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24
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Zhu PW, Chen L. Conformational collapse of spherical poly(N-isopropylacrylamide) brushes under the constraint of bound micelles. Phys Chem Chem Phys 2017; 19:31362-31376. [DOI: 10.1039/c7cp06406c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we investigate the micelle (charge)-constrained collapse of a spherical poly(N-isopropylacrylamide) (PNIPAM) brush.
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Affiliation(s)
- Peng-Wei Zhu
- Department of Materials Science and Engineering
- Monash University
- Clayton
- Australia
| | - Luguang Chen
- Department of Chemical Engineering
- Monash University
- Clayton
- Australia
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25
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Abstract
Nuclear pore complexes (NPCs) mediate molecular transport between the nucleus and cytoplasm in eukaryotic cells. Tethered within each NPC lie numerous intrinsically disordered proteins known as FG nucleoporins (FG Nups) that are central to this process. Over two decades of investigation has converged on a view that a barrier mechanism consisting of FG Nups rejects non-specific macromolecules while promoting the speed and selectivity of karyopherin (Kaps) receptors (and their cargoes). Yet, the number of NPCs in the cell is exceedingly small compared to the number of Kaps, so that in fact there is a high likelihood the pores are always populated by Kaps. Here, we contemplate a view where Kaps actively participate in regulating the selectivity and speed of transport through NPCs. This so-called "Kap-centric" control of the NPC accounts for Kaps as essential barrier reinforcements that play a prerequisite role in facilitating fast transport kinetics. Importantly, Kap-centric control reconciles both mechanistic and kinetic requirements of the NPC, and in so doing potentially resolves incoherent aspects of FG-centric models. On this basis, we surmise that Kaps prime the NPC for nucleocytoplasmic transport by fine-tuning the NPC microenvironment according to the functional needs of the cell.
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Affiliation(s)
- Roderick Y H Lim
- a Biozentrum and the Swiss Nanoscience Institute; University of Basel ; Basel, Switzerland
| | - Binlu Huang
- a Biozentrum and the Swiss Nanoscience Institute; University of Basel ; Basel, Switzerland
| | - Larisa E Kapinos
- a Biozentrum and the Swiss Nanoscience Institute; University of Basel ; Basel, Switzerland
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26
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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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27
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Léonforte F, Müller M. Functional Poly(N-isopropylacrylamide)/Poly(acrylic acid) Mixed Brushes for Controlled Manipulation of Nanoparticles. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00535] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fabien Léonforte
- Institut
für Theoretische Physik, Georg-August-Universität, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Marcus Müller
- Institut
für Theoretische Physik, Georg-August-Universität, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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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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Kreer T. Polymer-brush lubrication: a review of recent theoretical advances. SOFT MATTER 2016; 12:3479-3501. [PMID: 27029521 DOI: 10.1039/c5sm02919h] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This review compiles recent theoretical advances to describe compressive and shear forces of polymer-brush bilayers, which consist of two opposing brushes in contact. Such model systems for polymer-brush lubrication are frequently used as a benchmark to gain insight into biological problems, e.g., synovial joint lubrication. Based on scaling theory, I derive conformational and collective properties of polymer-brush bilayers in equilibrium and out-of-equilibrium situations, such as shear forces in the linear and nonlinear response regimes of stationary shear and under non-stationary shear. Furthermore, I discuss the influence of macromolecular inclusions and electrostatic interactions on polymer-brush lubrication. Comparisons to alternative analytical approaches, experiments and numerical results are performed. Special emphasis is given to methods for simulating polymer-brush bilayers using molecular dynamics simulations.
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Affiliation(s)
- T Kreer
- Leibniz-Institut für Polymerforschung Dresden, Hohe Straße 6, 01069 Dresden, Germany.
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31
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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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32
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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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33
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Promiscuous binding of Karyopherinβ1 modulates FG nucleoporin barrier function and expedites NTF2 transport kinetics. Biophys J 2015; 108:918-927. [PMID: 25692596 PMCID: PMC4336380 DOI: 10.1016/j.bpj.2014.12.041] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/05/2014] [Accepted: 12/19/2014] [Indexed: 12/22/2022] Open
Abstract
The transport channel of nuclear pore complexes (NPCs) contains a high density of intrinsically disordered proteins that are rich in phenylalanine-glycine (FG)-repeat motifs (FG Nups). The FG Nups interact promiscuously with various nuclear transport receptors (NTRs), such as karyopherins (Kaps), that mediate the trafficking of nucleocytoplasmic cargoes while also generating a selectively permeable barrier against other macromolecules. Although the binding of NTRs to FG Nups increases molecular crowding in the NPC transport channel, it is unclear how this impacts FG Nup barrier function or the movement of other molecules, such as the Ran importer NTF2. Here, we use surface plasmon resonance to evaluate FG Nup conformation, binding equilibria, and interaction kinetics associated with the multivalent binding of NTF2 and karyopherinβ1 (Kapβ1) to Nsp1p molecular brushes. NTF2 and Kapβ1 show different long- and short-lived binding characteristics that emerge from varying degrees of molecular retention and FG repeat binding avidity within the Nsp1p brush. Physiological concentrations of NTF2 produce a collapse of Nsp1p brushes, whereas Kapβ1 binding generates brush extension. However, the presence of prebound Kapβ1 inhibits Nsp1p brush collapse during NTF2 binding, which is dominated by weak, short-lived interactions that derive from steric hindrance and diminished avidity with Nsp1p. This suggests that binding promiscuity confers kinetic advantages to NTF2 by expediting its facilitated diffusion and reinforces the proposal that Kapβ1 contributes to the integral barrier function of the NPC.
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34
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Coalson RD, Eskandari Nasrabad A, Jasnow D, Zilman A. A Polymer-Brush-Based Nanovalve Controlled by Nanoparticle Additives: Design Principles. J Phys Chem B 2015. [PMID: 26222480 DOI: 10.1021/acs.jpcb.5b02623] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Polymer-grafted surfaces and channels are increasingly used for the design of responsive materials and sensors due to robust performance and ease of use. Various strategies for the control of the nanoscale morphologies of such materials and devices are being tested. Entropic repulsion between the polymer chains in a grafted brush of sufficient density causes the chains to extend in the direction perpendicular to the grafting surface in comparison to the position of unattached polymers. When nanoparticles having attractive interactions with the polymers are introduced into the solvent, these nanoparticles tend to infiltrate into the brush and reduce its extension. Under certain conditions, a sharp reduction in brush height extension can occur over a narrow range of nanoparticle concentrations in solution. We describe a way of controlling transport through polymer-functionalized nanochannels with nanoparticle additives, relying on the physics of nanoparticles and polymer brushes under confinement, and we suggest a blueprint for the creation of a tunable nanovalve. The nanovalve is modeled as a cylinder with a polymer brush grafted on its inside surface. Brush properties such as the chain length and the grafting density are chosen so that the brush chains extend into the center of the cylinder in the absence of nanoparticles, occluding the flux of analyte molecules through the pore. When nanoparticles that are attracted to the polymers are introduced into solution, they infiltrate into the brush and partially collapse it against the cylindrical grafting surface, opening space in the center of the cylinder through which analyte molecules can flow. The operation of such a nanovalve is analyzed via self-consistent field theory calculations in the strong-stretching approximation. Self-consistent field analysis is supported by Langevin dynamics simulations of the underlying coarse-grained model of the polymer-nanoparticle system.
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Affiliation(s)
| | | | | | - Anton Zilman
- Department of Physics and Institute for Biomaterials and Biomedical Engineering, University of Toronto , Toronto, Ontario M5S 1A7, Canada
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35
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Miura T, Seki K. Effects of surface affinity on the ordering dynamics of self-assembled monolayers of chain molecules: Transition from a parallel to a perpendicular structure. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:052604. [PMID: 26066191 DOI: 10.1103/physreve.91.052604] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 06/04/2023]
Abstract
The effects of surface interactions on the ordering dynamics of self-assembled monolayers (SAM) of chain molecules were studied using molecular dynamics simulations. When the strength of surface-chain interactions was equal to or less than that of chain-chain interactions, domains of chain molecules adsorbed perpendicular to the surface ("upright" chains) formed on the surface. Although chain molecules adsorbed parallel to the surface ("lying" chains) were initially observed on the surface, they did not develop into two-dimensionally aligned structures. In contrast, when the strength of surface-chain interactions was at least twice that of chain-chain interactions, the proportion of upright chain molecules was initially small, and the reorientation of lying chains was observed shortly afterwards. In this case, the reorientation from lying to upright configuration developed slowly from the domain boundaries of two-dimensionally aligned structures late in the calculation period. Although the orientation processes of chain molecules on surfaces were strongly influenced by the strength of surface-chain interactions, the total adsorption rate on the surface was not. We also analyzed the maximum area of domains formed by lying chains. The development of two-dimensionally aligned domains required strong surface-chain interactions to prevent the spontaneous formation of nuclei of upright domains.
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Affiliation(s)
- Toshiaki Miura
- National Institute of Advanced Industrial Science and Technology (AIST), AIST Central2, 1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kazuhiko Seki
- National Institute of Advanced Industrial Science and Technology (AIST), AIST Central2, 1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
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36
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Fuxreiter M, Tóth-Petróczy Á, Kraut DA, Matouschek AT, Lim RYH, Xue B, Kurgan L, Uversky VN. Disordered proteinaceous machines. Chem Rev 2014; 114:6806-43. [PMID: 24702702 PMCID: PMC4350607 DOI: 10.1021/cr4007329] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Monika Fuxreiter
- MTA-DE
Momentum Laboratory of Protein Dynamics, Department of Biochemistry
and Molecular Biology, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
| | - Ágnes Tóth-Petróczy
- Department
of Biological Chemistry, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Daniel A. Kraut
- Department
of Chemistry, Villanova University, 800 East Lancaster Avenue, Villanova, Pennsylvania 19085, United States
| | - Andreas T. Matouschek
- Section
of Molecular Genetics and Microbiology, Institute for Cellular &
Molecular Biology, The University of Texas
at Austin, 2506 Speedway, Austin, Texas 78712, United States
| | - Roderick Y. H. Lim
- Biozentrum
and the Swiss Nanoscience Institute, University
of Basel, Klingelbergstrasse
70, CH-4056 Basel, Switzerland
| | - Bin Xue
- Department of Cell Biology,
Microbiology and Molecular Biology, College
of Fine Arts and Sciences, and Department of Molecular Medicine and USF Health
Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Lukasz Kurgan
- Department
of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Vladimir N. Uversky
- Department of Cell Biology,
Microbiology and Molecular Biology, College
of Fine Arts and Sciences, and Department of Molecular Medicine and USF Health
Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute
for Biological Instrumentation, Russian
Academy of Sciences, 142290 Pushchino, Moscow Region 119991, Russia
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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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Opferman MG, Coalson RD, Jasnow D, Zilman A. Morphology of polymer brushes infiltrated by attractive nanoinclusions of various sizes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8584-8591. [PMID: 23758614 DOI: 10.1021/la4013922] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Addition of nanoparticles can control the morphologies of grafted polymer layers that are important in a variety of natural and artificial systems. We study the morphologies of grafted polymer layers interacting attractively with nanoparticle inclusions, as a function of particle size and the interaction strength, using self-consistent field theory and Langevin dynamics simulations. We find that the addition of nanoparticles causes distinctive changes in the layer morphology. For sufficiently strong interaction/binding, increasing the concentration of nanoparticles causes a compression of the polymer layer into a compact, low height state, followed by a subsequent rebound and swelling at sufficiently high concentrations. For nanoparticles of small size, the compression of the layer is sharp and occurs over a narrow range of nanoparticle concentrations. The transition region widens as the nanoparticle size increases. The transition is initiated via a dense layer of tightly bound monomers and nanoparticles near the grafting surface, with a low density region above it. For nanoparticles much larger than the characteristic graft spacing in the brush, the behavior is reversed: the nanoparticles penetrate only the dilute region near the top of the polymer layer without causing the layer to collapse.
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Affiliation(s)
- Michael G Opferman
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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