101
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Liu Z, Liu J, Xiao M, Wang R, Chen YL. Conformation-dependent translocation of a star polymer through a nanochannel. BIOMICROFLUIDICS 2014; 8:054107. [PMID: 25332744 PMCID: PMC4189700 DOI: 10.1063/1.4893637] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/11/2014] [Indexed: 06/04/2023]
Abstract
The translocation process of star polymers through a nanochannel is investigated by dissipative particle dynamics simulations. The translocation process is strongly influenced by the star arm arrangement as the polymer enters the channel, and a scaling relation between the translocation time [Formula: see text] and the total number of beads N tot is obtained. Qualitative agreements are found with predictions of the nucleation and growth model for linear block co-polymer translocation. In the intermediate stage where the center of the star polymer is at the channel entrance, the translocation time is found to have power law-dependence on the number of arms outside the channel and very weakly dependent on the number of arms in the channel. Increasing the total number of star arms also increases the star translocation time.
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Affiliation(s)
- Zhu Liu
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Jiannan Liu
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Mengying Xiao
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Rong Wang
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Yeng-Long Chen
- Institute of Physics , Academia Sinica, Taipei 11529, Taiwan
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102
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Osmanović D, Ford IJ, Hoogenboom BW. Model inspired by nuclear pore complex suggests possible roles for nuclear transport receptors in determining its structure. Biophys J 2014; 105:2781-9. [PMID: 24359750 DOI: 10.1016/j.bpj.2013.11.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 10/25/2013] [Accepted: 11/04/2013] [Indexed: 12/20/2022] Open
Abstract
Nuclear transport receptors (NTRs) mediate nucleocytoplasmic transport via their affinity for unstructured proteins (polymers) in the nuclear pore complex (NPC). Here, we have modeled the effect of NTRs on polymeric structure in the nanopore confinement of the NPC central conduit. The model explicitly takes into account inter- and intramolecular interactions, as well as the finite size of the NTRs (∼20% of the NPC channel diameter). It reproduces various proposed scenarios for the channel structure, ranging from a central polymer condensate (selective phase) to brushlike polymer arrangements localized at the channel wall (virtual gate, reduction of dimensionality), with the transport receptors lining the polymer surface. In addition, it predicts a new structure in which NTRs become an integral part of the transport barrier by forming a cross-linked network with the unstructured proteins stretching across the pore. The model provides specific and distinctive predictions for the equilibrium spatial distributions of NTRs for these different scenarios that can be experimentally verified by, e.g., superresolution fluorescence microscopy. Moreover, it suggests mechanisms by which globular macromolecules (colloidal particles) can cause polymer-coated nanopores to switch between open and closed configurations, a possible explanation of the biological function of the NPC, and suggests potential technological applications for filtration and single-molecule sensing.
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Affiliation(s)
- Dino Osmanović
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London, United Kingdom.
| | - Ian J Ford
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Bart W Hoogenboom
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London, United Kingdom
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103
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de Beer S. Switchable friction using contacts of stimulus-responsive and nonresponding swollen polymer brushes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8085-8090. [PMID: 24954240 DOI: 10.1021/la5013473] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Stimulus-responsive (SR), solvated polymers can switch between an expanded state and a collapsed state via external stimuli. Using molecular dynamics simulations, I show that such SR polymers can be employed to control the frictional response between two opposing polymer brushes in relative sliding motion. By using a brush composed of SR polymers in contact with a nonresponding solvated polymer brush, the presence of capillaries and the overlap between molecules of the opposing brushes can be switched. When both brushes are solvated, a capillary is formed and polymers of the opposing brushes interdigitate. Interdigitation dominates friction upon shearing flat brush-bearing surfaces, while the breaking and formation of capillaries dominate friction in the low-velocity limit between rough brush-bearing surfaces. Thus, when either rough or flat polymer-bearing surfaces are sheared, friction between two swollen brushes can be high. In contrast, when the SR brush is collapsed, the solvent absorbs only in the brush that does not respond to the external stimulus. The latter circumvents the presence of capillaries and interdigitation of the brushes, which results in a low friction force upon shearing.
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Affiliation(s)
- Sissi de Beer
- Jülich Supercomputing Centre, Forschungszentrum Jülich , Jülich, Germany
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104
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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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105
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Hou S, Grillo D, Williams CL, Wasserstrom JA, Szleifer I, Zhao M. Membrane phospholipid redistribution in cancer micro-particles and implications in the recruitment of cationic protein factors. J Extracell Vesicles 2014; 3:22653. [PMID: 24959330 PMCID: PMC4056184 DOI: 10.3402/jev.v3.22653] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 04/15/2014] [Accepted: 04/23/2014] [Indexed: 11/14/2022] Open
Abstract
Cancer cell-derived micro-particles (MPs) play important regulatory roles on cellular and system levels. These activities are attributed in part to protein factors carried by MPs. However, recruitment strategies for sequestering certain protein factors in MPs are poorly understood. In the current study, using exogenous and endogenously expressed phospholipid-binding probes, we investigated the distribution of membrane phospholipids in MPs as a potential mechanism for electrostatically enriching cationic protein factors in MPs. We detected a significant level of externalised phosphatidylethanolamine (PE) at the outer surface of MPs. This was accompanied, in the inner leaflet of the MP membrane, by a greater density of negatively charged phospholipids, particularly phosphatidylserine (PS). The local enrichment of PS in the inner surface of MPs was correlated with an elevated presence of small GTPases in a polybasic region (PBR)-dependent fashion. By employing a series of RhoA derivatives, including constitutively active and RhoA derivatives lacking a PBR, we could demonstrate that the congregation of RhoA in MPs was dependent on the presence of the PBR. A chimer with the fusion of PBR sequence alone to GFP significantly enhanced GFP localisation in MPs, indicative of a positive contribution of electrostatic interactions in RhoA recruitment to MPs. Using in silico thermodynamic simulations, we characterised the electrostatic interactions between PBR and anionic lipid membrane surface. In summary, the redistribution of membrane phospholipids in MPs has an impact on the local ionic density, and is likely a contributing factor in the electrostatic recruitment of membrane-associated proteins to MPs in a PBR-dependent fashion.
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Affiliation(s)
- Songwang Hou
- Department of Medicine, Northwestern University, Chicago, IL, USA
| | - Doris Grillo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Carol L Williams
- Department of Pharmacology, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Igal Szleifer
- Department of Medicine, Northwestern University, Chicago, IL, USA ; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA ; Department of Biomedical Engineering and Department of Chemistry, Northwestern University, Evanston, IL, USA ; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Ming Zhao
- Department of Medicine, Northwestern University, Chicago, IL, USA ; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
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106
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Eisele NB, Labokha AA, Frey S, Görlich D, Richter RP. Cohesiveness tunes assembly and morphology of FG nucleoporin domain meshworks - Implications for nuclear pore permeability. Biophys J 2014; 105:1860-70. [PMID: 24138862 DOI: 10.1016/j.bpj.2013.09.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/25/2013] [Accepted: 09/04/2013] [Indexed: 12/20/2022] Open
Abstract
Nuclear pore complexes control the exchange of macromolecules between the cytoplasm and the nucleus. A selective permeability barrier that arises from a supramolecular assembly of intrinsically unfolded nucleoporin domains rich in phenylalanine-glycine dipeptides (FG domains) fills the nuclear pore. There is increasing evidence that selective transport requires cohesive FG domain interactions. To understand the functional roles of cohesive interactions, we studied monolayers of end-grafted FG domains as a bottom-up nanoscale model system of the permeability barrier. Based on detailed physicochemical analysis of the model films and comparison of the data with polymer theory, we propose that cohesiveness is tuned to promote rapid assembly of the permeability barrier and to generate a stable and compact pore-filling meshwork with a small mesh size. Our results highlight the functional importance of weak interactions, typically a few kBT per chain, and contribute important information to understand the mechanism of size-selective transport.
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Affiliation(s)
- Nico B Eisele
- Biosurfaces Unit, CIC biomaGUNE, San Sebastian, Spain; Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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107
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Ando D, Zandi R, Kim YW, Colvin M, Rexach M, Gopinathan A. Nuclear pore complex protein sequences determine overall copolymer brush structure and function. Biophys J 2014; 106:1997-2007. [PMID: 24806932 PMCID: PMC4017316 DOI: 10.1016/j.bpj.2014.03.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 03/07/2014] [Accepted: 03/11/2014] [Indexed: 11/15/2022] Open
Abstract
The transport of cargo across the nuclear membrane is highly selective and accomplished by a poorly understood mechanism involving hundreds of nucleoporins lining the inside of the nuclear pore complex (NPC). Currently, there is no clear picture of the overall structure formed by this collection of proteins within the pore, primarily due to their disordered nature. We perform coarse-grained simulations of both individual nucleoporins and grafted rings of nups mimicking the in vivo geometry of the NPC and supplement this with polymer brush modeling. Our results indicate that different regions or blocks of an individual NPC protein can have distinctly different forms of disorder and that this property appears to be a conserved functional feature. Furthermore, this block structure at the individual protein level is critical to the formation of a unique higher-order polymer brush architecture that can exist in distinct morphologies depending on the effective interaction energy between the phenylalanine glycine (FG) domains of different nups. Because the interactions between FG domains may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability.
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Affiliation(s)
- David Ando
- Department of Physics, University of California at Merced, Merced, California
| | - Roya Zandi
- Department of Physics, University of California at Riverside, Riverside, California
| | - Yong Woon Kim
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Michael Colvin
- Department of Chemistry and Chemical Biology, University of California at Merced, Merced, California
| | - Michael Rexach
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California
| | - Ajay Gopinathan
- Department of Physics, University of California at Merced, Merced, California.
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108
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Kim S, Elbaum M. A simple kinetic model with explicit predictions for nuclear transport. Biophys J 2014; 105:565-9. [PMID: 23931304 DOI: 10.1016/j.bpj.2013.04.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 11/29/2022] Open
Abstract
Molecular exchange between the cell nucleus and cytoplasm is one of the most fundamental features of eukaryotic cell biology. The nuclear pores act as a conduit of this transport, both for cargo that crosses the pore autonomously as well as that whose translocation requires an intermediary receptor. The major class of such receptors is regulated by the small GTPase Ran, via whose interaction the nucleo-cytoplasmic transport system functions as a selective molecular pump. We propose a simple analytical model for transport that includes both translocation and receptor binding kinetics. The model is suitable for steady-state kinetics such as fluorescence recovery after photobleaching. Time constants appear as a combination of parameters whose effects on measured kinetics are not separable. Competitive cargo binding to receptors and large cytoplasmic volume buffer the transport properties of any particular cargo. Specific limits to the solutions provide a qualitative insight and interpretation of nuclear transport in the cellular context. Most significantly, we find that under realistic conditions receptor binding, rather than permeability of the nuclear pores, may be rate-limiting for nucleo-cytoplasmic exchange.
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Affiliation(s)
- Sanghyun Kim
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
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109
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Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating. PLoS Comput Biol 2014; 10:e1003488. [PMID: 24626154 PMCID: PMC3952814 DOI: 10.1371/journal.pcbi.1003488] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 01/12/2014] [Indexed: 01/22/2023] Open
Abstract
Nuclear pore complexes (NPCs) form gateways for material transfer across the nuclear envelope of eukaryotic cells. Disordered proteins, rich in phenylalanine-glycine repeat motifs (FG-nups), form the central transport channel. Understanding how nups are arranged in the interior of the NPC may explain how NPC functions as a selectivity filter for transport of large molecules and a sieve-like filter for diffusion of small molecules (< or ). We employed molecular dynamics to model the structures formed by various assemblies of one kind of nup, namely the 609-aa-long FG domain of Nsp1 (Nsp1-FG). The simulations started from different initial conformations and geometrical arrangements of Nsp1-FGs. In all cases Nsp1-FGs collectively formed brush-like structures with bristles made of bundles of 2–27 nups, however, the bundles being cross-linked through single nups leaving one bundle and joining a nearby one. The degree of cross-linking varies with different initial nup conformations and arrangements. Structural analysis reveals that FG-repeats of the nups not only involve formation of bundle structures, but are abundantly present in cross-linking regions where the epitopes of FG-repeats are highly accessible. Large molecules that are assisted by transport factors (TFs) are selectively transported through NPC apparently by binding to FG-nups through populated FG-binding pockets on the TF surface. Therefore, our finding suggests that TFs bind concertedly to multiple FGs in cross-linking regions and break-up the bundles to create wide pores for themselves and their cargoes to pass. In addition, the cross-linking between Nsp1-FG bundles, arising from simulations, is found to set a molecular size limit of < for passive diffusion of molecules. Our simulations suggest that the NPC central channel, near the periphery where tethering of nups is dominant, features brush-like moderately cross-linked bundles, but in the central region, where tethering loses its effect, features a sieve-like structure of bundles and frequent cross-links. Cells of higher life forms separate their genomes from the rest of the cell in a nucleus that surrounds the genome by a nuclear envelope. Hundreds of pores, each a complex made of many proteins, assure traffic into and out of the nucleus through highly selective transport: small biomolecules can pass unhindered, whereas large biomolecules need to associate with proteins called transport factors, to pass. Little is known about how the nuclear pore complexes function, a key impediment to observation being their huge size and the disordered nature of the pore interior. We investigated computationally what kind of structure the nuclear pore proteins (nups) form. In the computation we place many nups, each a 600 amino acid-long protein, into arrangements considered representative for the nuclear pore, and simulate the subsequent molecular behavior. We find that the nups form bundles of 2–27 proteins, the bundles being cross-linked when a single nup leaves a bundle and joins an adjacent one. The finding suggests an adaptive molecular mesh arrangement of nups in the nuclear pore and explains how selective transport is accomplished, namely that passage of sufficiently small molecules is unhindered by the cross-linking, but that large molecules need the assistance of transport factors to melt the cross-linking.
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110
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Bui KH, von Appen A, DiGuilio AL, Ori A, Sparks L, Mackmull MT, Bock T, Hagen W, Andrés-Pons A, Glavy JS, Beck M. Integrated structural analysis of the human nuclear pore complex scaffold. Cell 2014; 155:1233-43. [PMID: 24315095 DOI: 10.1016/j.cell.2013.10.055] [Citation(s) in RCA: 259] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/22/2013] [Accepted: 10/02/2013] [Indexed: 11/28/2022]
Abstract
The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 nucleoporins. Due to its size and complex composition, determining the structure of the NPC is an enormous challenge, and the overall architecture of the NPC scaffold remains elusive. In this study, we have used an integrated approach based on electron tomography, single-particle electron microscopy, and crosslinking mass spectrometry to determine the structure of a major scaffold motif of the human NPC, the Nup107 subcomplex, in both isolation and integrated into the NPC. We show that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the NPC. This arrangement may explain how changes of the diameter are realized that would accommodate transport of huge cargoes.
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Affiliation(s)
- Khanh Huy Bui
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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111
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Goryaynov A, Yang W. Role of molecular charge in nucleocytoplasmic transport. PLoS One 2014; 9:e88792. [PMID: 24558427 PMCID: PMC3928296 DOI: 10.1371/journal.pone.0088792] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 01/12/2014] [Indexed: 12/17/2022] Open
Abstract
Transport of genetic materials and proteins between the nucleus and cytoplasm of eukaryotic cells is mediated by nuclear pore complexes (NPCs). A selective barrier formed by phenylalanine-glycine (FG) nucleoporins (Nups) with net positive charges in the NPC allows for passive diffusion of signal-independent small molecules and transport-receptor facilitated translocation of signal-dependent cargo molecules. Recently, negative surface charge was postulated to be another essential criterion for selective passage through the NPC. However, the charge-driven mechanism in determining the transport kinetics and spatial transport route for either passive diffusion or facilitated translocation remains obscure. Here we employed high-speed single-molecule fluorescence microscopy with an unprecedented spatiotemporal resolution of 9 nm and 400 µs to uncover these mechanistic fundamentals for nuclear transport of charged substrates through native NPCs. We found that electrostatic interaction between negative surface charges on transiting molecules and the positively charged FG Nups, although enhancing their probability of binding to the NPC, never plays a dominant role in determining their nuclear transport mode or spatial transport route. A 3D reconstruction of transport routes revealed that small signal-dependent endogenous cargo protein constructs with high positive surface charges that are destined to the nucleus, rather than repelled from the NPC as suggested in previous models, passively diffused through an axial central channel of the NPC in the absence of transport receptors. Finally, we postulated a comprehensive map of interactions between transiting molecules and FG Nups during nucleocytoplasmic transport by combining the effects of molecular size, signal and surface charge.
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Affiliation(s)
- Alexander Goryaynov
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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112
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Osmanović D, Fassati A, Ford IJ, Hoogenboom BW. Physical modelling of the nuclear pore complex. SOFT MATTER 2013; 9:10442. [PMCID: PMC4046875 DOI: 10.1039/c3sm50722j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/18/2013] [Indexed: 05/24/2023]
Abstract
An in-depth discussion of nuclear pore complexes illustrates the importance of macromolecular confinement in biological systems.
Physically interesting behaviour can arise when soft matter is confined to nanoscale dimensions. A highly relevant biological example of such a phenomenon is the Nuclear Pore Complex (NPC) found perforating the nuclear envelope of eukaryotic cells. In the central conduit of the NPC, of ∼30–60 nm diameter, a disordered network of proteins regulates all macromolecular transport between the nucleus and the cytoplasm. In spite of a wealth of experimental data, the selectivity barrier of the NPC has yet to be explained fully. Experimental and theoretical approaches are complicated by the disordered and heterogeneous nature of the NPC conduit. Modelling approaches have focused on the behaviour of the partially unfolded protein domains in the confined geometry of the NPC conduit, and have demonstrated that within the range of parameters thought relevant for the NPC, widely varying behaviour can be observed. In this review, we summarise recent efforts to physically model the NPC barrier and function. We illustrate how attempts to understand NPC barrier function have employed many different modelling techniques, each of which have contributed to our understanding of the NPC.
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Affiliation(s)
- Dino Osmanović
- London Centre for Nanotechnology and Department of Physics and Astronomy , University College London , Gower Street , WC1E 6BT , UK .
| | - Ariberto Fassati
- Wohl Virion Centre and MRC Centre for Medical Molecular Virology , University College London , Gower Street , WC1E 6BT , UK
| | - Ian J. Ford
- London Centre for Nanotechnology and Department of Physics and Astronomy , University College London , Gower Street , WC1E 6BT , UK .
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology and Department of Physics and Astronomy , University College London , Gower Street , WC1E 6BT , UK .
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113
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Tu LC, Fu G, Zilman A, Musser SM. Large cargo transport by nuclear pores: implications for the spatial organization of FG-nucleoporins. EMBO J 2013; 32:3220-30. [PMID: 24213245 DOI: 10.1038/emboj.2013.239] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 10/01/2013] [Indexed: 11/09/2022] Open
Abstract
Nuclear pore complexes (NPCs) mediate cargo traffic between the nucleus and the cytoplasm of eukaryotic cells. Nuclear transport receptors (NTRs) carry cargos through NPCs by transiently binding to phenylalanine-glycine (FG) repeats on intrinsically disordered polypeptides decorating the NPCs. Major impediments to understand the transport mechanism are the thousands of FG binding sites on each NPC, whose spatial distribution is unknown, and multiple binding sites per NTR, which leads to multivalent interactions. Using single molecule fluorescence microscopy, we show that multiple NTR molecules are required for efficient transport of a large cargo, while a single NTR promotes binding to the NPC but not transport. Particle trajectories and theoretical modelling reveal a crucial role for multivalent NTR interactions with the FG network and indicate a non-uniform FG repeat distribution. A quantitative model is developed wherein the cytoplasmic side of the pore is characterized by a low effective concentration of free FG repeats and a weak FG-NTR affinity, and the centrally located dense permeability barrier is overcome by multivalent interactions, which provide the affinity necessary to permeate the barrier.
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Affiliation(s)
- Li-Chun Tu
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M University, College Station, TX, USA
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114
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Tagliazucchi M, Rabin Y, Szleifer I. Transport rectification in nanopores with outer membranes modified with surface charges and polyelectrolytes. ACS NANO 2013; 7:9085-9097. [PMID: 24047263 DOI: 10.1021/nn403686s] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This work reports a comprehensive theoretical study of the transport-rectification properties of cylindrical nanopores with neutral inner walls and chemically modified outer membrane. The chemical species on the two outer sides of the membrane have charges of opposite sign and can be either surface-confined species (i.e., surface charges) or polyelectrolyte brushes. The advantage of this design over other types of rectifying nanopores is that it requires controlling the composition of the outer walls of the pore (which are easy to access) rather than the inner walls, thus simplifying the fabrication process. Ion-current rectification in nanopores with charged outer walls is ascribed to applied-potential-induced changes in the ionic concentration within the pore. The rectification efficiency is studied as a function of pore length, radius, surface charge and bulk electrolyte concentration. An analytical model is derived for the case of surface-confined charges that predicts the current-potential curves in very good agreement with the numerical calculations. Neutral nanopores with polyelectrolyte-modified outer walls have two distinct advantages compared to surface-charged systems: (i) they exhibit higher rectification factors due to the large charge density immobilized by the polyelectrolyte brushes, and (ii) the applied potential deforms the polyelectrolyte chains toward the oppositely charged electrode. This deformation brings the polyelectrolyte brushes into the pore in the low conductivity state and expels them from the pore in the high conductivity regime. Calculations of the potentials of mean-force suggest that the applied-field-induced conformational changes can be used to control the translocation of cargoes larger than ions, such as proteins and nanoparticles.
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Affiliation(s)
- Mario Tagliazucchi
- Department of Biomedical Engineering, Department of Chemistry and Chemistry of Life Processes Institute, Northwestern University , Evanston, Illinois 60208, United States
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115
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Ando D, Colvin M, Rexach M, Gopinathan A. Physical motif clustering within intrinsically disordered nucleoporin sequences reveals universal functional features. PLoS One 2013; 8:e73831. [PMID: 24066078 PMCID: PMC3774778 DOI: 10.1371/journal.pone.0073831] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/25/2013] [Indexed: 11/24/2022] Open
Abstract
Bioinformatics of disordered proteins is especially challenging given high mutation rates for homologous proteins and that functionality may not be strongly related to sequence. Here we have performed a novel bioinformatic analysis, based on the spatial clustering of physically relevant features such as binding motifs and charges within disordered proteins, on thousands of Nuclear Pore Complex (NPC) FG motif containing proteins (FG nups). The biophysical mechanism by which FG nups regulate nucleocytoplasmic transport has remained elusive. Our analysis revealed a set of highly conserved spatial features in the sequence structure of individual FG nups, such as the separation, localization, and ordering of FG motifs and charged residues along the protein chain. These functionally conserved features provide insight into the particular biophysical mechanisms responsible for regulation of nucleocytoplasmic traffic in the NPC, strongly constraining current models. Additionally this method allows us to identify potentially functionally analogous disordered proteins across distantly related species.
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Affiliation(s)
- David Ando
- Physics Department, University of California Merced, Merced, California, United States of America
| | - Michael Colvin
- Chemistry and Chemical Biology, University of California Merced, Merced, California, United States of America
| | - Michael Rexach
- Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Ajay Gopinathan
- Physics Department, University of California Merced, Merced, California, United States of America
- * E-mail:
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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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