1
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Ashby G, Keng KE, Hayden CC, Gollapudi S, Houser JR, Jamal S, Stachowiak JC. Selective Endocytic Uptake of Targeted Liposomes Occurs within a Narrow Range of Liposome Diameters. ACS Appl Mater Interfaces 2023; 15:49988-50001. [PMID: 37862704 DOI: 10.1021/acsami.3c09399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Cell surface receptors facilitate signaling and nutrient uptake. These processes are dynamic, requiring receptors to be actively recycled by endocytosis. Due to their differential expression in disease states, receptors are often the target of drug-carrier particles, which are adorned with ligands that bind specifically to receptors. These targeted particles are taken into the cell by multiple routes of internalization, where the best-characterized pathway is clathrin-mediated endocytosis. Most studies of particle uptake have utilized bulk assays rather than observing individual endocytic events. As a result, the detailed mechanisms of particle uptake remain obscure. To address this gap, we employed a live-cell imaging approach to study the uptake of individual liposomes as they interact with clathrin-coated structures. By tracking individual internalization events, we find that the size of liposomes rather than the density of the ligands on their surfaces primarily determines their probability of uptake. Interestingly, targeting has the greatest impact on endocytosis of liposomes of intermediate diameters, with the smallest and largest liposomes being internalized or excluded, respectively, regardless of whether they are targeted. These findings, which highlight a previously unexplored limitation of targeted delivery, can be used to design more effective drug carriers.
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Affiliation(s)
- Grant Ashby
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kayla E Keng
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Carl C Hayden
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sadhana Gollapudi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Justin R Houser
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sabah Jamal
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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2
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Vargas KJ, Colosi PL, Girardi E, Park JM, Harmon LE, Chandra SS. α-Synuclein colocalizes with AP180 and affects the size of clathrin lattices. J Biol Chem 2023; 299:105091. [PMID: 37516240 PMCID: PMC10470054 DOI: 10.1016/j.jbc.2023.105091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/31/2023] Open
Abstract
α-Synuclein and family members β- and γ-synuclein are presynaptic proteins that sense and generate membrane curvature, properties important for synaptic vesicle (SV) cycling. αβγ-synuclein triple knockout neurons exhibit SV endocytosis deficits. Here, we investigated if α-synuclein affects clathrin assembly in vitro. Visualizing clathrin assembly on membranes using a lipid monolayer system revealed that α-synuclein increases clathrin lattices size and curvature. On cell membranes, we observe that α-synuclein is colocalized with clathrin and its adapter AP180 in a concentric ring pattern. Clathrin puncta that contain both α-synuclein and AP180 were significantly larger than clathrin puncta containing either protein alone. We determined that this effect occurs in part through colocalization of α-synuclein with the phospholipid PI(4,5)P2 in the membrane. Immuno-electron microscopy (EM) of synaptosomes uncovered that α-synuclein relocalizes from SVs to the presynaptic membrane upon stimulation, positioning α-synuclein to function on presynaptic membranes during or after stimulation. Additionally, we show that deletion of synucleins impacts brain-derived clathrin-coated vesicle size. Thus, α-synuclein affects the size and curvature of clathrin structures on membranes and functions as an endocytic accessory protein.
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Affiliation(s)
- Karina J Vargas
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, USA; Marine Biological Laboratory, Woods Hole, Massachusetts, USA; Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - P L Colosi
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, USA; PREP Program, Yale University, New Haven, Connecticut, USA
| | - Eric Girardi
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, USA
| | - Jae-Min Park
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, USA
| | - Leah E Harmon
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, USA
| | - Sreeganga S Chandra
- Departments of Neurology and Neuroscience, Yale University, New Haven, Connecticut, USA.
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3
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Kesharwani K, Singh R, Kumar N, Singh N, Gupta P, Joshi KB. Mercury-instructed assembly (MiA): architecting clathrin triskelion-inspired highly functional C3-symmetric triskelion nanotorus functional structures into microtorus structures. Nanoscale 2022; 14:10200-10210. [PMID: 35796347 DOI: 10.1039/d2nr01524b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To detect heavy metal toxicity using self-assembled nanostructures, a clathrin triskelion-inspired highly functional C3-symmetric trimerized biotinylated di-tryptophan peptide was used. This triskelion peptide is known to self-assemble into nanotorus-like structures and can therefore act as a nanocage for various analytes. In this work, in addition to spectroscopy, force and electron microscopy were successfully used to detect the effect of toxic metal ions such as zinc, cadmium, and mercury by exploiting the change in the nanotorus morphology. Different concentrations of mercury led to the expansion of nanotorus structures into microtori. Therefore, we provide a unique application of heavy metal toxicity by utilizing "material nanoarchitectonics" to architect nanotorus structures into higher-order microtorus structures, as instructed by mercury. Such a strategy can make heavy metal sensing easier for materials scientists and open new avenues for biomedical/environmental science applications.
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Affiliation(s)
- Khushboo Kesharwani
- Department of Chemistry, School of Chemical Science and Technology, Dr.HarisinghGourVishwavidyalaya (A Central University), Sagar, M.P., 470003, India.
| | - Ramesh Singh
- Department of Chemistry, School of Chemical Science and Technology, Dr.HarisinghGourVishwavidyalaya (A Central University), Sagar, M.P., 470003, India.
| | - Nikunj Kumar
- Computational Chemistry Center, Department of Chemistry, Indian Institute of Technology, Roorkee-247667.
| | - Narendra Singh
- Department of Chemistry, Indian Institute of Technology of Kanpur, U.P. 208016, India
| | - Puneet Gupta
- Computational Chemistry Center, Department of Chemistry, Indian Institute of Technology, Roorkee-247667.
| | - Khashti Ballabh Joshi
- Department of Chemistry, School of Chemical Science and Technology, Dr.HarisinghGourVishwavidyalaya (A Central University), Sagar, M.P., 470003, India.
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4
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Guo SK, Sodt AJ, Johnson ME. Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins. PLoS Comput Biol 2022; 18:e1009969. [PMID: 35312692 PMCID: PMC8979592 DOI: 10.1371/journal.pcbi.1009969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 03/31/2022] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
Clathrin-coated structures must assemble on cell membranes to internalize receptors, with the clathrin protein only linked to the membrane via adaptor proteins. These structures can grow surprisingly large, containing over 20 clathrin, yet they often fail to form productive vesicles, instead aborting and disassembling. We show that clathrin structures of this size can both form and disassemble spontaneously when adaptor protein availability is low, despite high abundance of clathrin. Here, we combine recent in vitro kinetic measurements with microscopic reaction-diffusion simulations and theory to differentiate mechanisms of stable vs unstable clathrin assembly on membranes. While in vitro conditions drive assembly of robust, stable lattices, we show that concentrations, geometry, and dimensional reduction in physiologic-like conditions do not support nucleation if only the key adaptor AP-2 is included, due to its insufficient abundance. Nucleation requires a stoichiometry of adaptor to clathrin that exceeds 1:1, meaning additional adaptor types are necessary to form lattices successfully and efficiently. We show that the critical nucleus contains ~25 clathrin, remarkably similar to sizes of the transient and abortive structures observed in vivo. Lastly, we quantify the cost of bending the membrane under our curved clathrin lattices using a continuum membrane model. We find that the cost of bending the membrane could be largely offset by the energetic benefit of forming curved rather than flat structures, with numbers comparable to experiments. Our model predicts how adaptor density can tune clathrin-coated structures from the transient to the stable, showing that active energy consumption is therefore not required for lattice disassembly or remodeling during growth, which is a critical advance towards predicting productive vesicle formation.
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Affiliation(s)
- Si-Kao Guo
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Alexander J. Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Margaret E. Johnson
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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5
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Hoshino F, Sakane F. Docosahexaenoic acid-containing phosphatidic acid interacts with clathrin coat assembly protein AP180 and regulates its interaction with clathrin. Biochem Biophys Res Commun 2022; 587:69-77. [PMID: 34864549 PMCID: PMC8628603 DOI: 10.1016/j.bbrc.2021.11.097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/12/2021] [Accepted: 11/27/2021] [Indexed: 11/18/2022]
Abstract
The clathrin coat assembly protein AP180 drives endocytosis, which is crucial for numerous physiological events, such as the internalization and recycling of receptors, uptake of neurotransmitters and entry of viruses, including SARS-CoV-2, by interacting with clathrin. Moreover, dysfunction of AP180 underlies the pathogenesis of Alzheimer's disease. Therefore, it is important to understand the mechanisms of assembly and, especially, disassembly of AP180/clathrin-containing cages. Here, we identified AP180 as a novel phosphatidic acid (PA)-binding protein from the mouse brain. Intriguingly, liposome binding assays using various phospholipids and PA species revealed that AP180 most strongly bound to 1-stearoyl-2-docosahexaenoyl-PA (18:0/22:6-PA) to a comparable extent as phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), which is known to associate with AP180. An AP180 N-terminal homology domain (1–289 aa) interacted with 18:0/22:6-PA, and a lysine-rich motif (K38–K39–K40) was essential for binding. The 18:0/22:6-PA in liposomes in 100 nm diameter showed strong AP180-binding activity at neutral pH. Notably, 18:0/22:6-PA significantly attenuated the interaction of AP180 with clathrin. However, PI(4,5)P2 did not show such an effect. Taken together, these results indicate the novel mechanism by which 18:0/22:6-PA selectively regulates the disassembly of AP180/clathrin-containing cages.
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Affiliation(s)
- Fumi Hoshino
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
| | - Fumio Sakane
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan.
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6
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Jagannathan NS, Hogue CWV, Tucker-Kellogg L. Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2. PLoS Comput Biol 2021; 17:e1008474. [PMID: 33406091 PMCID: PMC7787433 DOI: 10.1371/journal.pcbi.1008474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/27/2020] [Indexed: 11/22/2022] Open
Abstract
Intrinsically disordered regions (IDRs) are prevalent in the eukaryotic proteome. Common functional roles of IDRs include forming flexible linkers or undergoing allosteric folding-upon-binding. Recent studies have suggested an additional functional role for IDRs: generating steric pressure on the plasma membrane during endocytosis, via molecular crowding. However, in order to accomplish useful functions, such crowding needs to be regulated in space (e.g., endocytic hotspots) and time (e.g., during vesicle formation). In this work, we explore binding-induced regulation of IDR steric volume. We simulate the IDRs of two proteins from Clathrin-mediated endocytosis (CME) to see if their conformational spaces are regulated via binding-induced expansion. Using Monte-Carlo computational modeling of excluded volumes, we generate large conformational ensembles (3 million) for the IDRs of Epsin and Eps15 and dock the conformers to the alpha subunit of Adaptor Protein 2 (AP2α), their CME binding partner. Our results show that as more molecules of AP2α are bound, the Epsin-derived ensemble shows a significant increase in global dimensions, measured as the radius of Gyration (RG) and the end-to-end distance (EED). Unlike Epsin, Eps15-derived conformers that permit AP2α binding at one motif were found to be more likely to accommodate binding of AP2α at other motifs, suggesting a tendency toward co-accessibility of binding motifs. Co-accessibility was not observed for any pair of binding motifs in Epsin. Thus, we speculate that the disordered regions of Epsin and Eps15 perform different roles during CME, with accessibility in Eps15 allowing it to act as a recruiter of AP2α molecules, while binding-induced expansion of the Epsin disordered region could impose steric pressure and remodel the plasma membrane during vesicle formation. Protein functions were originally believed to arise from ordered protein structures. This dogma was later challenged by the identification of intrinsically disordered proteins that lack specific structure. The functional roles of such proteins usually fell in two categories–exploiting the disorder for flexibility (like floppy connector), or imposing order upon binding to an external partner. In this study we explore the possibility of an alternative mechanism that harnesses disorder for function through regulated molecular crowding. Specifically, we use modeling to study two proteins involved in reshaping the cell membrane, Epsin and Eps15. We ask if they undergo binding-induced expansion, where binding of an external partner AP2 causes not a transition toward order, but rather an energetically favorable increase in propensity to occupy larger volumes. Our results show that Epsin tends to occupy a larger volume when bound to AP2, consistent with increased molecular crowding, which could help reshape the cell membrane. Such regulation of disorder via binding (without folding) opens hitherto unexplored avenues that cells might employ to harness disorder.
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Affiliation(s)
- N. Suhas Jagannathan
- Cancer & Stem Cell Biology, and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore
- Singapore-MIT Alliance, Computation and Systems Biology Program, National University of Singapore, Singapore
| | - Christopher W. V. Hogue
- Singapore-MIT Alliance, Computation and Systems Biology Program, National University of Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Lisa Tucker-Kellogg
- Cancer & Stem Cell Biology, and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore
- Singapore-MIT Alliance, Computation and Systems Biology Program, National University of Singapore, Singapore
- * E-mail:
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7
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Spark A, Kitching A, Esteban-Ferrer D, Handa A, Carr AR, Needham LM, Ponjavic A, Santos AM, McColl J, Leterrier C, Davis SJ, Henriques R, Lee SF. vLUME: 3D virtual reality for single-molecule localization microscopy. Nat Methods 2020; 17:1097-1099. [PMID: 33046895 PMCID: PMC7612967 DOI: 10.1038/s41592-020-0962-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 08/24/2020] [Indexed: 12/17/2022]
Abstract
vLUME is a virtual reality software package designed to render large three-dimensional single-molecule localization microscopy datasets. vLUME features include visualization, segmentation, bespoke analysis of complex local geometries and exporting features. vLUME can perform complex analysis on real three-dimensional biological samples that would otherwise be impossible by using regular flat-screen visualization programs.
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Affiliation(s)
| | | | | | - Anoushka Handa
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | | | - Aleks Ponjavic
- School of Physics and Astronomy, University of Leeds, Leeds, UK
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Ana Mafalda Santos
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James McColl
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Simon J Davis
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Cambridge, UK.
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8
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Skruzny M, Pohl E, Gnoth S, Malengo G, Sourjik V. The protein architecture of the endocytic coat analyzed by FRET microscopy. Mol Syst Biol 2020; 16:e9009. [PMID: 32400111 PMCID: PMC7218409 DOI: 10.15252/msb.20199009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 12/16/2022] Open
Abstract
Endocytosis is a fundamental cellular trafficking pathway, which requires an organized assembly of the multiprotein endocytic coat to pull the plasma membrane into the cell. Although the protein composition of the endocytic coat is known, its functional architecture is not well understood. Here, we determine the nanoscale organization of the endocytic coat by FRET microscopy in yeast Saccharomyces cerevisiae. We assessed pairwise proximities of 18 conserved coat-associated proteins and used clathrin subunits and protein truncations as molecular rulers to obtain a high-resolution protein map of the coat. Furthermore, we followed rearrangements of coat proteins during membrane invagination and their binding dynamics at the endocytic site. We show that the endocytic coat proteins are not confined inside the clathrin lattice, but form distinct functional layers above and below the lattice. Importantly, key endocytic proteins transverse the clathrin lattice deeply into the cytoplasm connecting thus the membrane and cytoplasmic parts of the coat. We propose that this design enables an efficient and regulated function of the endocytic coat during endocytic vesicle formation.
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Affiliation(s)
- Michal Skruzny
- Department of Systems and Synthetic MicrobiologyMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Emma Pohl
- Department of Systems and Synthetic MicrobiologyMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Sandina Gnoth
- Department of Systems and Synthetic MicrobiologyMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Gabriele Malengo
- Department of Systems and Synthetic MicrobiologyMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Victor Sourjik
- Department of Systems and Synthetic MicrobiologyMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
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9
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Zhang X, Xu Y, Zhang W, Fu X, Hao Z, He M, Trefilov D, Ning X, Ge H, Chen Y. Controllable Subtractive Nanoimprint Lithography for Precisely Fabricating Paclitaxel-Loaded PLGA Nanocylinders to Enhance Anticancer Efficacy. ACS Appl Mater Interfaces 2020; 12:14797-14805. [PMID: 32160750 DOI: 10.1021/acsami.9b21346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nanoimprint lithography presents a new strategy for preparing uniform nanostructures with predefined sizes and shapes and has the potential for developing nanosized drug delivery systems. However, the current nanoimprint lithography is a type of an additive nanofabrication method that has limited potential due to its restricted template-dependent innate character. Herein, we have developed a novel subtractive UV-nanoimprint lithography (sUNL) for the scalable fabrication of PLGA nanostructures with variable sizes for the first time. sUNL can not only fabricate a variety of predefined nanostructures by simply utilizing different nanoimprint molds but also precisely prepare scalable nanocylinders with different length to diameter ratios. Particularly, sUNL can fabricate paclitaxel-loaded PLGA nanocylinders (PTX-PLGA NCs) with high drug-loading rate of 40% and long storage stability over a year. We demonstrate that PTX-PLGA NCs target clathrin- and caveolae-mediated cell transport pathways and display increased cellular uptake, in comparison to traditional PTX-loaded PLGA nanoparticles (PTX-PLGA NPs), leading to enhanced anticancer effects. Therefore, sUNL represents a promising nanofabrication method for efficiently developing predefined drug delivery systems.
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Affiliation(s)
- Xiang Zhang
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Yurui Xu
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Weiwei Zhang
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Xinxin Fu
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Zongbin Hao
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Mengjia He
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Denis Trefilov
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Xinghai Ning
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210093, China
| | - Haixiong Ge
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Yanfeng Chen
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
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10
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Baumann K, Piantanida L, García-Nafría J, Sobota D, Voïtchovsky K, Knowles TPJ, Hernández-Ainsa S. Coating and Stabilization of Liposomes by Clathrin-Inspired DNA Self-Assembly. ACS Nano 2020; 14:2316-2323. [PMID: 31976654 PMCID: PMC7302506 DOI: 10.1021/acsnano.9b09453] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 01/24/2020] [Indexed: 05/17/2023]
Abstract
The self-assembly of the protein clathrin on biological membranes facilitates essential processes of endocytosis and has provided a source of inspiration for materials design by the highly ordered structural appearance. By mimicking the architecture of the protein building blocks and clathrin self-assemblies to coat liposomes with biomaterials, advanced hybrid carriers can be derived. Here, we present a method for fabricating DNA-coated liposomes by hydrophobically anchoring and subsequently connecting DNA-based triskelion structures on the liposome surface inspired by the assembly of the protein clathrin. Dynamic light scattering, ζ-potential, confocal microscopy, and cryo-electron microscopy measurements independently demonstrate successful DNA coating. Nanomechanical measurements conducted with atomic force microscopy show that the DNA coating enhances the mechanical stability of the liposomes relative to uncoated ones. Furthermore, we provide the possibility to reverse the coating process by triggering the disassembly of the DNA coats through a toehold-mediated displacement reaction. Our results describe a straightforward, versatile, and reversible approach for coating and stabilizing lipid vesicles through the assembly of rationally designed DNA structures. This method has potential for further development toward the ordered arrangement of tailored functionalities on the surface of liposomes and for applications as hybrid nanocarriers.
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Affiliation(s)
- Kevin
N. Baumann
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Luca Piantanida
- Department
of Physics, University of Durham, Durham DH1 3LE, United Kingdom
| | | | - Diana Sobota
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Kislon Voïtchovsky
- Department
of Physics, University of Durham, Durham DH1 3LE, United Kingdom
| | - Tuomas P. J. Knowles
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Silvia Hernández-Ainsa
- Instituto
de Nanociencia de Aragón, University
of Zaragoza, Zaragoza 50018, Spain
- Instituto
de Ciencia de Materiales de Aragón, University of Zaragoza-CSIC, Zaragoza 50009, Spain
- ARAID
Foundation, Government of Aragon, Zaragoza 50018, Spain
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11
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Journot CA, Ramakrishna V, Wallace MI, Turberfield AJ. Modifying Membrane Morphology and Interactions with DNA Origami Clathrin-Mimic Networks. ACS Nano 2019; 13:9973-9979. [PMID: 31418553 PMCID: PMC6764109 DOI: 10.1021/acsnano.8b07734] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 08/16/2019] [Indexed: 05/21/2023]
Abstract
We describe the triggered assembly of a bioinspired DNA origami meshwork on a lipid membrane. DNA triskelia, three-armed DNA origami nanostructures inspired by the membrane-modifying protein clathrin, are bound to lipid mono- and bilayers using cholesterol anchors. Polymerization of triskelia, triggered by the addition of DNA staples, links triskelion arms to form a mesh. Using transmission electron microscopy, we observe nanoscale local deformation of a lipid monolayer induced by triskelion polymerization that is reminiscent of the formation of clathrin-coated pits. We also show that the polymerization of triskelia bound to lipid bilayers modifies interactions between them, inhibiting the formation of a synapse between giant unilamellar vesicles and a supported lipid bilayer.
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Affiliation(s)
- Céline
M. A. Journot
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Vivek Ramakrishna
- Department
of Chemistry, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
- London
Centre for Nanotechnology, Strand, London WC2R 2LS, United
Kingdom
| | - Mark I. Wallace
- Department
of Chemistry, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
- London
Centre for Nanotechnology, Strand, London WC2R 2LS, United
Kingdom
| | - Andrew J. Turberfield
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
- E-mail:
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12
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Le NQK, Huynh TT, Yapp EKY, Yeh HY. Identification of clathrin proteins by incorporating hyperparameter optimization in deep learning and PSSM profiles. Comput Methods Programs Biomed 2019; 177:81-88. [PMID: 31319963 DOI: 10.1016/j.cmpb.2019.05.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/06/2019] [Accepted: 05/16/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND OBJECTIVES Clathrin is an adaptor protein that serves as the principal element of the vesicle-coating complex and is important for the membrane cleavage to dispense the invaginated vesicle from the plasma membrane. The functional loss of clathrins has been tied to a lot of human diseases, i.e., neurodegenerative disorders, cancer, Alzheimer's diseases, and so on. Therefore, creating a precise model to identify its functions is a crucial step towards understanding human diseases and designing drug targets. METHODS We present a deep learning model using a two-dimensional convolutional neural network (CNN) and position-specific scoring matrix (PSSM) profiles to identify clathrin proteins from high throughput sequences. Traditionally, the 2D CNNs take images as an input so we treated the PSSM profile with a 20 × 20 matrix as an image of 20 × 20 pixels. The input PSSM profile was then connected to our 2D CNN in which we set a variety of parameters to improve the performance of the model. Based on the 10-fold cross-validation results, hyper-parameter optimization process was employed to find the best model for our dataset. Finally, an independent dataset was used to assess the predictive ability of the current model. RESULTS Our model could identify clathrin proteins with sensitivity of 92.2%, specificity of 91.2%, accuracy of 91.8%, and MCC of 0.83 in the independent dataset. Compared to state-of-the-art traditional neural networks, our method achieved a significant improvement in all typical measurement metrics. CONCLUSIONS Throughout the proposed study, we provide an effective tool for investigating clathrin proteins and our achievement could promote the use of deep learning in biomedical research. We also provide source codes and dataset freely at https://www.github.com/khanhlee/deep-clathrin/.
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Affiliation(s)
- Nguyen Quoc Khanh Le
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639798 Singapore.
| | - Tuan-Tu Huynh
- Department of Electrical Electronic and Mechanical Engineering, Lac Hong University, No. 10 Huynh Van Nghe Road, Bien Hoa, Dong Nai, Vietnam
| | - Edward Kien Yee Yapp
- Singapore Institute of Manufacturing Technology, 2 Fusionopolis Way, #08-04, Innovis, 138634 Singapore
| | - Hui-Yuan Yeh
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639798 Singapore.
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13
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Abstract
The unusual structure of clathrin, combined with its ability to assemble and disassemble rapidly in cells provides a model system for us to learn about the ways in which proteins can contribute mechanically to a functioning cell. In this article, we discuss the structural properties of clathrin cages and the triskelions which assemble to form them. The function of clathrin depends on the structure of these triskelions and the interactions they make both with each other during assembly and with the adaptor protein network that drives coated vesicle formation. The atomic resolution structure of clathrin domains has been revealed by X-ray crystallography while scattering studies have enabled the shape of a triskelion in solution to be deduced. Cryo-electron microscopy maps have shown the secondary structure of entire cages, how individual triskelion legs are arranged to form a cage and enabled some bound adaptor proteins to be located. Cage formation itself is energetically finely balanced and requires specific interactions between triskelion legs to be productive, as biochemical studies and in silico modeling have shown. Theoretical, structural and cell biological investigations over many years have contributed to our knowledge of clathrin structure and assembly. It now remains to determine the precise nature of the interactions which occur between clathrin triskelions, light chain and heavy chain and the adaptor protein network.
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Affiliation(s)
- Mary Halebian
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Kyle Morris
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Corinne Smith
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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14
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Giani M, den Otter WK, Briels WJ. Clathrin Assembly Regulated by Adaptor Proteins in Coarse-Grained Models. Biophys J 2017; 111:222-35. [PMID: 27410749 DOI: 10.1016/j.bpj.2016.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/29/2016] [Accepted: 06/01/2016] [Indexed: 11/18/2022] Open
Abstract
The assembly of clathrin triskelia into polyhedral cages during endocytosis is regulated by adaptor proteins (APs). We explore how APs achieve this by developing coarse-grained models for clathrin and AP2, employing a Monte Carlo click interaction, to simulate their collective aggregation behavior. The phase diagrams indicate that a crucial role is played by the mechanical properties of the disordered linker segment of AP. We also present a statistical-mechanical theory for the assembly behavior of clathrin, yielding good agreement with our simulations and experimental data from the literature. Adaptor proteins are found to regulate the formation of clathrin coats under certain conditions, but can also suppress the formation of cages.
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Affiliation(s)
- Matteo Giani
- Multi Scale Mechanics, Faculty of Engineering Technology, University of Twente, Enschede, The Netherlands; Computational BioPhysics, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands; MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands
| | - Wouter K den Otter
- Multi Scale Mechanics, Faculty of Engineering Technology, University of Twente, Enschede, The Netherlands; Computational BioPhysics, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands; MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands.
| | - Wim J Briels
- Computational BioPhysics, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands; MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands; Forschungszentrum Jülich, Jülich, Germany
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15
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Chen Z, Zhu C, Kuo CJ, Robustelli J, Baumgart T. The N-Terminal Amphipathic Helix of Endophilin Does Not Contribute to Its Molecular Curvature Generation Capacity. J Am Chem Soc 2016; 138:14616-14622. [PMID: 27755867 PMCID: PMC5562367 DOI: 10.1021/jacs.6b06820] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-BAR proteins such as endophilin are thought to bend lipid membranes via scaffolding (the molding of membranes through the crescent protein shape) and membrane insertion (also called wedging) of amphipathic helices. However, the contributions from these distinct mechanisms to membrane curvature generation and sensing have remained controversial. Here we quantitatively demonstrate that the amphipathic N-terminal H0 helix of endophilin is important for recruiting this protein to the membrane, but does not contribute significantly to its intrinsic membrane curvature generation capacity. These observations elevate the importance of the scaffolding mechanism, rather than H0 insertion, for the membrane curvature generation by N-BAR domains. Furthermore, consistent with the thermodynamically required coupling between curvature generation and sensing, we observed that the H0-truncated N-BAR domain is capable of sensing membrane curvature. Overall, our contribution clarifies an important mechanistic controversy in the function of N-BAR domain proteins.
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Affiliation(s)
- Zhiming Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Chen Zhu
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Curtis J. Kuo
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Jaclyn Robustelli
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
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16
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Marinval N, Saboural P, Haddad O, Maire M, Bassand K, Geinguenaud F, Djaker N, Ben Akrout K, Lamy de la Chapelle M, Robert R, Oudar O, Guyot E, Laguillier-Morizot C, Sutton A, Chauvierre C, Chaubet F, Charnaux N, Hlawaty H. Identification of a Pro-Angiogenic Potential and Cellular Uptake Mechanism of a LMW Highly Sulfated Fraction of Fucoidan from Ascophyllum nodosum. Mar Drugs 2016; 14:E185. [PMID: 27763505 PMCID: PMC5082333 DOI: 10.3390/md14100185] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 09/28/2016] [Accepted: 10/10/2016] [Indexed: 02/04/2023] Open
Abstract
Herein we investigate the structure/function relationships of fucoidans from Ascophyllum nodosum to analyze their pro-angiogenic effect and cellular uptake in native and glycosaminoglycan-free (GAG-free) human endothelial cells (HUVECs). Fucoidans are marine sulfated polysaccharides, which act as glycosaminoglycans mimetics. We hypothesized that the size and sulfation rate of fucoidans influence their ability to induce pro-angiogenic processes independently of GAGs. We collected two fractions of fucoidans, Low and Medium Molecular Weight Fucoidan (LMWF and MMWF, respectively) by size exclusion chromatography and characterized their composition (sulfate, fucose and uronic acid) by colorimetric measurement and Raman and FT-IR spectroscopy. The high affinities of fractionated fucoidans to heparin binding proteins were confirmed by Surface Plasmon Resonance. We evidenced that LMWF has a higher pro-angiogenic (2D-angiogenesis on Matrigel) and pro-migratory (Boyden chamber) potential on HUVECs, compared to MMWF. Interestingly, in a GAG-free HUVECs model, LMWF kept a pro-angiogenic potential. Finally, to evaluate the association of LMWF-induced biological effects and its cellular uptake, we analyzed by confocal microscopy the GAGs involvement in the internalization of a fluorescent LMWF. The fluorescent LMWF was mainly internalized through HUVEC clathrin-dependent endocytosis in which GAGs were partially involved. In conclusion, a better characterization of the relationships between the fucoidan structure and its pro-angiogenic potential in GAG-free endothelial cells was required to identify an adapted fucoidan to enhance vascular repair in ischemia.
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Affiliation(s)
- Nicolas Marinval
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
| | - Pierre Saboural
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
| | - Oualid Haddad
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
| | - Murielle Maire
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
| | - Kevin Bassand
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
| | - Frederic Geinguenaud
- Laboratoire CSPBAT, CNRS UMR 7244, UFR SMBH, Université Paris 13, Sorbonne Paris Cité, Bobigny F-93017, France.
| | - Nadia Djaker
- Laboratoire CSPBAT, CNRS UMR 7244, UFR SMBH, Université Paris 13, Sorbonne Paris Cité, Bobigny F-93017, France.
| | - Khadija Ben Akrout
- Laboratoire CSPBAT, CNRS UMR 7244, UFR SMBH, Université Paris 13, Sorbonne Paris Cité, Bobigny F-93017, France.
| | - Marc Lamy de la Chapelle
- Laboratoire CSPBAT, CNRS UMR 7244, UFR SMBH, Université Paris 13, Sorbonne Paris Cité, Bobigny F-93017, France.
| | - Romain Robert
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
| | - Olivier Oudar
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
| | - Erwan Guyot
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
- Laboratoire de Biochimie, Hôpital Jean Verdier, Assistance Publique-Hôpitaux de Paris, Bondy 93140, France.
| | - Christelle Laguillier-Morizot
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
- Laboratoire de Biochimie, Hôpital Jean Verdier, Assistance Publique-Hôpitaux de Paris, Bondy 93140, France.
| | - Angela Sutton
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
- Laboratoire de Biochimie, Hôpital Jean Verdier, Assistance Publique-Hôpitaux de Paris, Bondy 93140, France.
| | - Cedric Chauvierre
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
| | - Frederic Chaubet
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
| | - Nathalie Charnaux
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
- Laboratoire de Biochimie, Hôpital Jean Verdier, Assistance Publique-Hôpitaux de Paris, Bondy 93140, France.
| | - Hanna Hlawaty
- Inserm U1148, LVTS, Université Paris 13, Sorbonne Paris Cité, Paris 75018, France.
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17
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Mercado SA, Orellana-Tavra C, Chen A, Slater NKH. The intracellular fate of an amphipathic pH-responsive polymer: Key characteristics towards drug delivery. Mater Sci Eng C Mater Biol Appl 2016; 69:1051-7. [PMID: 27612802 DOI: 10.1016/j.msec.2016.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/30/2016] [Accepted: 08/02/2016] [Indexed: 12/18/2022]
Abstract
Biopolymers have become important drug delivery systems for therapeutic molecules by enhancing their accessibility and efficacy intracellularly. However, the transport of these drugs across the cell membrane and their release into the cytosol remain a challenge. The trafficking of poly (l-lysine iso-phthalamide) grafted with phenylalanine (PP-50) was investigated using an osteosarcoma cell line (SAOS-2). Colocalisation of this amphipathic biopolymer with endocytosis tracers, such as transferrin and lactosylceramide, suggested that PP-50 is partially internalised by both clathrin and caveolin-mediated endocytosis. Macropinocytosis was also investigated, but a smaller correlation was found between this mechanism and PP-50 transport. A significant decrease in polymer-mediated calcein uptake was found when cells were pre-incubated with endocytosis inhibitors, suggesting also the use of a combination of mechanisms for cell internalisation. In addition, PP-50 colocalisation with endosome and lysosome pathway markers showed that the polymer was able to escape the endolysosomal compartment before maturation. This is a critical characteristic of a biopolymer towards use as drug delivery systems and biomedical applications.
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Affiliation(s)
- S A Mercado
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, United Kingdom
| | - C Orellana-Tavra
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, United Kingdom
| | - A Chen
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, United Kingdom
| | - N K H Slater
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, United Kingdom.
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18
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Wang XF, Liu QH, Wu Y, Huang J. Litopenaeus vannamei clathrin coat AP17 involved in white spot syndrome virus infection. Fish Shellfish Immunol 2016; 52:309-316. [PMID: 26988289 DOI: 10.1016/j.fsi.2016.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/04/2016] [Accepted: 03/06/2016] [Indexed: 06/05/2023]
Abstract
White spot syndrome virus (WSSV) is the main pathogen of shrimp culture, and has brought great losses of the shrimp aquaculture industry every year since it has been found. However, the specific mechanism of the virus into the cell is not very clear. Recent research suggests that clathrin-mediated endocytosis is involved in WSSV infection. By sequence analysis, clathrin coat AP17 is an σ subunit of AP-2 complex which is involved in clathrin-mediated endocytosis. To obtain the full-length sequence of Clathrin coat AP17 of Litopenaeus vannamei (LvCCAP17), the rapid amplification of cDNA ends (RACE) was performed to get the sequence of 3'and 5' end and splicing by DNAMAN. The full-length sequence of LvCCAP17 is 842 bp and expected to encoding 142 amino acids, and the amino acid sequence was analyzed by online software. The mRNA expression of LvCCAP17 in different tissues was carried out with quantitative real-time PCR and the LvCCAP17 was detected in all tested tissues of Litopenaeus vannamei. The transcriptional expression level of LvCCAP17 in epithelium and hepatopancreas was significantly up-regulated after WSSV infection. Far-Western blotting and ELISA assay showed that LvCCAP17 interacted with rVP26 and rVP37. Silencing of LvCCAP17 gene by double-strand RNA (dsRNA) interference significantly delay of cumulative mortality rate in WSSV infected shrimp and reduced the expression level of immediate early gene 1(ie1) and vp28. These results indicated that clathrin-meated endocytosis is responsible for WSSV infection.
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Affiliation(s)
- Xiu-Fang Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Dalian Ocean University, Dalian, China
| | - Qing-Hui Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Yin Wu
- Dalian Ocean University, Dalian, China
| | - Jie Huang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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19
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He B, Yuan L, Dai W, Gao W, Zhang H, Wang X, Fang W, Zhang Q. Dynamic bio-adhesion of polymer nanoparticles on MDCK epithelial cells and its impact on bio-membranes, endocytosis and paracytosis. Nanoscale 2016; 8:6129-45. [PMID: 26932537 DOI: 10.1039/c5nr08858e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nowadays, concern about the use of nanotechnology for biomedical application is unprecedentedly increasing. In fact, nanosystems applied for various potential clinical uses always have to cross the primary biological barrier consisting of epithelial cells. However, little is really known currently in terms of the influence of the dynamic bio-adhesion of nanosystems on bio-membranes as well as on endocytosis and transcytosis. This was investigated here using polymer nanoparticles (PNs) and MDCK epithelial cells as the models. Firstly, the adhesion of PNs on cell membranes was found to be time-dependent with a shift of both location and dispersion pattern, from the lateral adhesion of mainly mono-dispersed PNs initially to the apical coverage of the PN aggregate later. Then, it was interesting to observe in this study that the dynamic bio-adhesion of PNs only affected their endocytosis but not their transcytosis. It was important to find that the endocytosis of PNs was not a constant process. A GM1 dependent CDE (caveolae dependent endocytosis) pathway was dominant in the preliminary stage, followed by the co-existence of a CME (clathrin-mediated endocytosis) pathway for the PN aggregate at a later stage, in accordance with the adhesion features of PNs, suggesting the modification of PN adhesion patterns on the endocytosis pathways. Next, the PN adhesion was noticed to affect the structure of cell junctions, via altering the extra- and intra-cellular calcium levels, leading to the enhanced paracellular transport of small molecules, but not favorably enough for the obviously increased passing of PNs themselves. Finally, FRAP and other techniques all demonstrated the obvious impact of PN adhesion on the membrane confirmation, independent of the adhesion location and time, which might lower the threshold for the internalization of PNs, even their aggregates. Generally, these findings confirm that the transport pathway mechanism of PNs through epithelial cells is rather dynamic, and is remarkably affected by the adhesion patterns of PNs on the cell membrane.
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Affiliation(s)
- Bing He
- Department of Pathology, School of Basic Medical Sciences, Peking University, Beijing 100191, China. and Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Lan Yuan
- Medical and Healthy Analytical Center, Peking University, Beijing 100191, China
| | - Wenbing Dai
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Wei Gao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Hua Zhang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Xueqing Wang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Weigang Fang
- Department of Pathology, School of Basic Medical Sciences, Peking University, Beijing 100191, China.
| | - Qiang Zhang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
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20
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Dannhauser PN, Platen M, Böning H, Schaap IAT. Durable protein lattices of clathrin that can be functionalized with nanoparticles and active biomolecules. Nat Nanotechnol 2015; 10:954-957. [PMID: 26367107 DOI: 10.1038/nnano.2015.206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 08/11/2015] [Indexed: 06/05/2023]
Abstract
Biological molecules that self-assemble and interact with other molecules are attractive building blocks for engineering biological devices. DNA has been widely used for the creation of nanomaterials, but the use of proteins remains largely unexplored. Here, we show that clathrin can form homogeneous and extended two-dimensional lattices on a variety of substrates, including glass, metal, carbon and plastic. Clathrin is a three-legged protein complex with unique self-assembling properties and is relevant in the formation of membrane transport vesicles in eukaryotic cells. We used a fragment of the adaptor protein epsin to immobilize clathrin lattices on the substrates. The lattices span multiple square millimetres with a regular periodicity of 30 nm and can be functionalized via modified subunits of clathrin with either inorganic nanoparticles or active enzymes. The lattices can be stored for months after crosslinking and stabilization with uranyl acetate. They could be dehydrated and rehydrated without loss of function, offering potential applications in sensing and as biosynthetic reactors.
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Affiliation(s)
- P N Dannhauser
- Institute of Cell Biology, Centre of Anatomy, Hannover Medical School, 30625 Hannover, Germany
- Structural &Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - M Platen
- IIIrd Institute of Physics, Georg August University, 37073 Göttingen, Germany
| | - H Böning
- Institute of Cell Biology, Centre of Anatomy, Hannover Medical School, 30625 Hannover, Germany
| | - I A T Schaap
- IIIrd Institute of Physics, Georg August University, 37073 Göttingen, Germany
- Centre for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37077 Göttingen, Germany
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21
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Abstract
Clathrin self-assembles into a coat around vesicles filled with cargo such as nutrients, hormones, and proteins destined for degradation. Recent developments indicate clathrin is not a specialist, but is involved in different processes relevant to health and disease. Clathrin is used to strengthen centrosomes and mitotic spindles essential for chromosome segregation in cell division. In Wnt signaling, clathrin is a component of signalosomes on the plasma membrane needed to produce functional Wnt receptors. In glucose metabolism, a muscle-specific isoform, CHC22 clathrin, is key to the formation of storage compartments for GLUT4 receptor, and CHC22 dysfunction has been tied to type 2 diabetes. The activity of clathrin to self-assemble and to work with huntingtin-interacting proteins to organize actin is exploited by Listeria and enteropathic Escherichia coli in their infection pathways. Finally, there is an important connection between clathrin and human malignancies. Clathrin is argued to help transactivate tumor suppressor p53 that controls specific genes in DNA repair and apoptosis. However, this is debatable because trimeric clathrin must be made monomeric. To get insight on how the clathrin structure could be converted, the crystal structure of the trimerization domain is used in the development of the detrimerization switch hypothesis. This novel hypothesis will be relevant if connections continue to be found between CHC17 and p53 anti-cancer activity in the nucleus.
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22
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Abstract
Nanoparticle interacts with live cells depending on their surface chemistry, enters into cell via endocytosis, and is commonly trafficked to an endosome/lysozome that restricts subcellular targeting options. Here we show that nanoparticle surface chemistry can be tuned to alter their cell uptake mechanism and subcellular trafficking. Quantum dot based nanoprobes of 20-30 nm hydrodynamic diameters have been synthesized with tunable surface charge (between +15 mV to -25 mV) and lipophilicity to influence their cellular uptake processes and subcellular trafficking. It is observed that cationic nanoprobe electrostatically interacts with cell membrane and enters into cell via clathrin-mediated endocytosis. At lower surface charge (between +10 mV to -10 mV), the electrostatic interaction with cell membrane becomes weaker, and additional lipid raft endocytosis is initiated. If a lipophilic functional group is introduced on a weakly anionic nanoparticle surface, the uptake mechanism shifts to predominant lipid raft-mediated endocytosis. In particular, the zwitterionic-lipophilic nanoprobe has the unique advantage as it weakly interacts with anionic cell membrane, migrates toward lipid rafts for interaction through lipophilic functional group, and induces lipid raft-mediated endocytosis. While predominate or partial clathrin-mediated entry traffics most of the nanoprobes to lysozome, predominate lipid raft-mediated entry traffics them to perinuclear region, particularly to the Golgi apparatus. This finding would guide in designing appropriate nanoprobe for subcellular targeting and delivery.
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Affiliation(s)
- Atanu Chakraborty
- Centre for Advanced Materials, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Nikhil R Jana
- Centre for Advanced Materials, Indian Association for the Cultivation of Science, Kolkata 700032, India
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23
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Abstract
Clathrin-mediated endocytosis involves the coordinated assembly of clathrin cages around membrane indentations, necessitating fluid-like reorganization followed by solid-like stabilization. This apparent duality in clathrin's in vivo behavior provides some indication that the physical interactions between clathrin triskelia and the membrane effect a local response that triggers fluid-solid transformations within the clathrin lattice. We develop a computational model to study the response of clathrin protein lattices to spherical deformations of the underlying flexible membrane. These deformations are similar to the shapes assumed during intracellular trafficking of nanoparticles. Through Monte Carlo simulations of clathrin-on-membrane systems, we observe that these membrane indentations give rise to a greater than normal defect density within the overlaid clathrin lattice. In many cases, the bulk surrounding lattice remains in a crystalline phase, and the extra defects are localized to the regions of large curvature. This can be explained by the fact that the in-plane elastic stress in the clathrin lattice are reduced by coupling defects to highly curved regions. The presence of defects brought about by indentation can result in the fluidization of a lattice that would otherwise be crystalline, resulting in an indentation-driven, defect-mediated phase transition. Altering subunit elasticity or membrane properties is shown to drive a similar transition, and we present phase diagrams that map out the combined effects of these parameters on clathrin lattice properties.
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Affiliation(s)
- Nicholas Cordella
- Department of Chemical Engineering, Stanford University, Stanford CA 94305, USA.
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VanDersarl JJ, Mehraeen S, Schoen AP, Heilshorn SC, Spakowitz AJ, Melosh NA. Rheology and simulation of 2-dimensional clathrin protein network assembly. Soft Matter 2014; 10:6219-6227. [PMID: 25012232 DOI: 10.1039/c4sm00025k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Clathrin is a three-legged protein complex that assembles into lattice structures on the cell membrane and transforms into fullerene-like cages during endocytosis. This dynamic structural flexibility makes clathrin an attractive building block for guided assembly. The assembly dynamics and the mechanical properties of clathrin protein lattices are studied using rheological measurements and theoretical modelling in an effort to better understand two dynamic processes: protein adsorption to the interface and assembly into a network. We find that percolation models for protein network formation are insufficient to describe clathrin network formation, but with Monte Carlo simulations we can describe the dynamics of network formation very well. Insights from this work can be used to design new bio-inspired nano-assembly systems.
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Affiliation(s)
- Jules J VanDersarl
- Materials Science & Engineering, Stanford University, Stanford, CA 94305, USA.
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25
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Abdel-Hamid MK, McCluskey A. In silico docking, molecular dynamics and binding energy insights into the bolinaquinone-clathrin terminal domain binding site. Molecules 2014; 19:6609-22. [PMID: 24858095 PMCID: PMC6270888 DOI: 10.3390/molecules19056609] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/06/2014] [Accepted: 05/14/2014] [Indexed: 11/29/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) is a process that regulates selective internalization of important cellular cargo using clathrin-coated vesicles. Perturbation of this process has been linked to many diseases including cancer and neurodegenerative conditions. Chemical proteomics identified the marine metabolite, 2-hydroxy-5-methoxy-3-(((1S,4aS,8aS)-1,4a,5-trimethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-2-yl)methyl)cyclohexa-2,5-diene-1,4-dione (bolinaquinone) as a clathrin inhibitor. While being an attractive medicinal chemistry target, the lack of data about bolinaquinone’s mode of binding to the clathrin enzyme represents a major limitation for its structural optimization. We have used a molecular modeling approach to rationalize the observed activity of bolinaquinone and to predict its mode of binding with the clathrin terminal domain (CTD). The applied protocol started by global rigid-protein docking followed by flexible docking, molecular dynamics and linear interaction energy calculations. The results revealed the potential of bolinaquinone to interact with various pockets within the CTD, including the clathrin-box binding site. The results also highlight the importance of electrostatic contacts over van der Waals interactions for proper binding between bolinaquinone and its possible binding sites. This study provides a novel model that has the potential to allow rapid elaboration of bolinaquinone analogues as a new class of clathrin inhibitors.
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Affiliation(s)
- Mohammed K Abdel-Hamid
- Chemistry, Centre for Chemical Biology, The University of Newcastle, University Drive Callaghan, NSW 2308, Australia
| | - Adam McCluskey
- Chemistry, Centre for Chemical Biology, The University of Newcastle, University Drive Callaghan, NSW 2308, Australia.
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26
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Brandt KJ, Fickentscher C, Boehlen F, Kruithof EKO, de Moerloose P. NF-κB is activated from endosomal compartments in antiphospholipid antibodies-treated human monocytes. J Thromb Haemost 2014; 12:779-91. [PMID: 24612386 DOI: 10.1111/jth.12536] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/12/2014] [Indexed: 01/07/2023]
Abstract
BACKGROUND The antiphospholipid antibody syndrome (APS) is an autoimmune disease associated with arterial or venous thrombosis and/or recurrent fetal loss and is caused by pathogenic antiphospholipid antibodies (aPLA). We recently demonstrated that Toll-like receptor 2 (TLR2) and CD14 contribute to monocyte activation of aPLA. OBJECTIVE To study the mechanisms of cell activation by aPLA, leading to pro-coagulant and pro-inflammatory responses. METHODS AND RESULTS For this study, we used purified antibodies from the plasmas of 10 different patients with APS and healthy donors. We demonstrate that aPLA, but not control IgG, co-localizes with TLR2 and TLR1 or TLR6 on human monocytes. Blocking antibodies to TLR2, TLR1 or TLR6, but not to TLR4, decreased TNF and tissue factor (TF) responses to aPLA. Pharmacological and siRNA approaches revealed the importance of the clathrin/dynamin-dependent endocytic pathway in cell activation by aPLA. In addition, soluble aPLA induced NF-κB activation, while bead-immobilized aPLA beads, which cannot be internalized, were unable to activate NF-κB. Internalization of aPLA in monocytes and NF-κB activation were dependent on the presence of CD14. CONCLUSION We show that TLR2 and its co-receptors, TLR1 and TLR6, contribute to the pathogenicity of aPLA, that aPLA are internalized via clathrin- and CD14-dependent endocytosis and that endocytosis is required for NF-κB activation. Our results contribute to a better understanding of the APS and provide a possible therapeutic approach.
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Affiliation(s)
- K J Brandt
- Division of Angiology and Hemostasis, University Hospital of Geneva and Faculty of Medicine, Geneva, Switzerland
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27
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Liang L, Shen H, De Camilli P, Duncan JS. A novel multiple hypothesis based particle tracking method for clathrin mediated endocytosis analysis using fluorescence microscopy. IEEE Trans Image Process 2014; 23:1844-57. [PMID: 24808351 PMCID: PMC4373089 DOI: 10.1109/tip.2014.2303633] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In order to quantitatively analyze biological images and study underlying mechanisms of the cellular and subcellular processes, it is often required to track a large number of particles involved in these processes. Manual tracking can be performed by the biologists, but the workload is very heavy. In this paper, we present an automatic particle tracking method for analyzing an essential subcellular process, namely clathrin mediated endocytosis. The framework of the tracking method is an extension of the classical multiple hypothesis tracking (MHT), and it is designed to manage trajectories, solve data association problems, and handle pseudo-splitting/merging events. In the extended MHT framework, particle tracking becomes evaluating two types of hypotheses. The first one is the trajectory-related hypothesis, to test whether a recovered trajectory is correct, and the second one is the observation-related hypothesis, to test whether an observation from an image belongs to a real particle. Here, an observation refers to a detected particle and its feature vector. To detect the particles in 2D fluorescence images taken using total internal reflection microscopy, the images are segmented into regions, and the features of the particles are obtained by fitting Gaussian mixture models into each of the image regions. Specific models are developed according to the properties of the particles. The proposed tracking method is demonstrated on synthetic data under different scenarios and applied to real data.
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Affiliation(s)
- Liang Liang
- Department of Electrical Engineering, Yale University, New Haven, CT 06511 USA
| | - Hongying Shen
- Department of Cell Biology, Yale University, New Haven, CT 06511 USA
| | - Pietro De Camilli
- Department of Cell Biology, Yale University, New Haven, CT 06511 USA
| | - James S. Duncan
- Department of Electrical Engineering, Biomedical Engineering and Diagnostic Radiology, Yale University, New Haven, CT 06511 USA
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28
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Cordella N, Lampo TJ, Mehraeen S, Spakowitz AJ. Membrane fluctuations destabilize clathrin protein lattice order. Biophys J 2014; 106:1476-88. [PMID: 24703309 PMCID: PMC3976529 DOI: 10.1016/j.bpj.2013.11.4505] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 11/15/2013] [Accepted: 11/19/2013] [Indexed: 10/25/2022] Open
Abstract
We develop a theoretical model of a clathrin protein lattice on a flexible cell membrane. The clathrin subunit is modeled as a three-legged pinwheel with elastic deformation modes and intersubunit binding interactions. The pinwheels are constrained to lie on the surface of an elastic sheet that opposes bending deformation and is subjected to tension. Through Monte Carlo simulations, we predict the equilibrium phase behavior of clathrin lattices at various levels of tension. High membrane tensions, which correspond to suppressed membrane fluctuations, tend to stabilize large, flat crystalline structures similar to plaques that have been observed in vivo on cell membranes that are adhered to rigid surfaces. Low tensions, on the other hand, give rise to disordered, defect-ridden lattices that behave in a fluidlike manner. The principles of two-dimensional melting theory are applied to our model system to further clarify how high tensions can stabilize crystalline order on flexible membranes. These results demonstrate the importance of environmental physical cues in dictating the collective behavior of self-assembled protein structures.
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Affiliation(s)
- Nicholas Cordella
- Chemical Engineering, Stanford University, Stanford, California; Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Thomas J Lampo
- Chemical Engineering, Stanford University, Stanford, California
| | | | - Andrew J Spakowitz
- Chemical Engineering, Stanford University, Stanford, California; Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California; Biophysics Program, Stanford University, Stanford, California.
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29
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Ansar M, Serrano D, Papademetriou I, Bhowmick TK, Muro S. Biological functionalization of drug delivery carriers to bypass size restrictions of receptor-mediated endocytosis independently from receptor targeting. ACS Nano 2013; 7:10597-10611. [PMID: 24237309 PMCID: PMC3901850 DOI: 10.1021/nn404719c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Targeting of drug carriers to cell-surface receptors involved in endocytosis is commonly used for intracellular drug delivery. However, most endocytic receptors mediate uptake via clathrin or caveolar pathways associated with ≤200-nm vesicles, restricting carrier design. We recently showed that endocytosis mediated by intercellular adhesion molecule 1 (ICAM-1), which differs from clathrin- and caveolae-mediated pathways, allows uptake of nano- and microcarriers in cell culture and in vivo due to recruitment of cellular sphingomyelinases to the plasmalemma. This leads to ceramide generation at carrier binding sites and formation of actin stress-fibers, enabling engulfment and uptake of a wide size-range of carriers. Here we adapted this paradigm to enhance uptake of drug carriers targeted to receptors associated with size-restricted pathways. We coated sphingomyelinase onto model (polystyrene) submicro- and microcarriers targeted to clathrin-associated mannose-6-phosphate receptor. In endothelial cells, this provided ceramide enrichment at the cell surface and actin stress-fiber formation, modifying the uptake pathway and enhancing carrier endocytosis without affecting targeting, endosomal transport, cell-associated degradation, or cell viability. This improvement depended on the carrier size and enzyme dose, and similar results were observed for other receptors (transferrin receptor) and cell types (epithelial cells). This phenomenon also enhanced tissue accumulation of carriers after intravenous injection in mice. Hence, it is possible to maintain targeting toward a selected receptor while bypassing natural size restrictions of its associated endocytic route by functionalization of drug carriers with biological elements mimicking the ICAM-1 pathway. This strategy holds considerable promise to enhance flexibility of design of targeted drug delivery systems.
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Affiliation(s)
- Maria Ansar
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD
| | - Daniel Serrano
- Department of Cell Biology & Molecular Genetics and Biological Sciences Graduate Program, University of Maryland, College Park, MD
| | - Iason Papademetriou
- Fischell Department of Bioengineering, University of Maryland, College Park, MD
| | - Tridib Kumar Bhowmick
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD
| | - Silvia Muro
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD
- Fischell Department of Bioengineering, University of Maryland, College Park, MD
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30
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Lagache T, Lang G, Sauvonnet N, Olivo-Marin JC. Analysis of the spatial organization of molecules with robust statistics. PLoS One 2013; 8:e80914. [PMID: 24349021 PMCID: PMC3857798 DOI: 10.1371/journal.pone.0080914] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 10/15/2013] [Indexed: 02/07/2023] Open
Abstract
One major question in molecular biology is whether the spatial distribution of observed molecules is random or organized in clusters. Indeed, this analysis gives information about molecules’ interactions and physical interplay with their environment. The standard tool for analyzing molecules’ distribution statistically is the Ripley’s K function, which tests spatial randomness through the computation of its critical quantiles. However, quantiles’ computation is very cumbersome, hindering its use. Here, we present an analytical expression of these quantiles, leading to a fast and robust statistical test, and we derive the characteristic clusters’ size from the maxima of the Ripley’s K function. Subsequently, we analyze the spatial organization of endocytic spots at the cell membrane and we report that clathrin spots are randomly distributed while clathrin-independent spots are organized in clusters with a radius of , which suggests distinct physical mechanisms and cellular functions for each pathway.
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Affiliation(s)
- Thibault Lagache
- Unité d’Analyse d’Images Quantitative, Institut Pasteur, Paris, France
- Unité de Recherche Associée 2582, Centre National de la Recherche Scientifique, Paris, France
- * E-mail: (TL); (JCOM)
| | - Gabriel Lang
- Unité Mixte de Recherche 518 Mathématiques et Informatique Appliquées, AgroParisTech and INRA, Paris, France
| | - Nathalie Sauvonnet
- Unité de Recherche Associée 2582, Centre National de la Recherche Scientifique, Paris, France
- Unité de Biologie des Interactions Cellulaires, Institut Pasteur, Paris, France
| | - Jean-Christophe Olivo-Marin
- Unité d’Analyse d’Images Quantitative, Institut Pasteur, Paris, France
- Unité de Recherche Associée 2582, Centre National de la Recherche Scientifique, Paris, France
- * E-mail: (TL); (JCOM)
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31
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Abstract
A thermodynamic model is used to investigate the conditions under which clathrin triskelions form polyhedral baskets. The analysis, which is similar to classical methods used to study micelle formation, relates clathrin basket energetics to system parameters linked to triskelial rigidity, the natural curvature of an isolated triskelion, and interactions between triskelial legs in the assembled polyhedra. Mathematical theory predicts that a minimal ("critical") clathrin concentration, C(C), needs to be surpassed in order for basket polymerization to occur, and indicates how C(C), and the amount of polymerized material, depend on the chosen parameters. Analytical expressions are obtained to indicate how changes in the parameters affect the sizes of the polyhedra which arise when the total clathrin concentration exceeds C(C). A continuum analytic approximation then is used to produce numerical results that illustrate the derived dependences.
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Affiliation(s)
- M Muthukumar
- Polymer Science and Engineering Department, Physics Department, University of Massachusetts, Amherst, Massachusetts 01003, USA
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32
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Kastl L, Sasse D, Wulf V, Hartmann R, Mircheski J, Ranke C, Carregal-Romero S, Martínez-López JA, Fernández-Chacón R, Parak WJ, Elsasser HP, Rivera Gil P. Multiple internalization pathways of polyelectrolyte multilayer capsules into mammalian cells. ACS Nano 2013; 7:6605-6618. [PMID: 23826767 DOI: 10.1021/nn306032k] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Polyelectrolyte multilayer (PEM) capsules are carrier vehicles with great potential for biomedical applications. With the future aim of designing biocompatible, effective therapeutic delivery systems (e.g., for cancer), the pathway of internalization (uptake and fate) of PEM capsules was investigated. In particular the following experiments were performed: (i) the study of capsule co-localization with established endocytic markers, (ii) switching-off endocytotic pathways with pharmaceutical/chemical inhibitors, and (iii) characterization and quantification of capsule uptake with confocal and electron microscopy. As result, capsules co-localized with lipid rafts and with phagolysosomes, but not with other endocytic vesicles. Chemical interference of endocytosis with chemical blockers indicated that PEM capsules enter the investigated cell lines through a mechanism slightly sensitive to electrostatic interactions, independent of clathrin and caveolae, and strongly dependent on cholesterol-rich domains and organelle acidification. Microscopic characterization of cells during capsule uptake showed the formation of phagocytic cups (vesicles) to engulf the capsules, an increased number of mitochondria, and a final localization in the perinuclear cytoplasma. Combining all these indicators we conclude that PEM capsule internalization in general occurs as a combination of different sequential mechanisms. Initially, an adsorptive mechanism due to strong electrostatic interactions governs the stabilization of the capsules at the cell surface. Membrane ruffling and filopodia extensions are responsible for capsule engulfing through the formation of a phagocytic cup. Co-localization with lipid raft domains activates the cell to initiate a lipid-raft-mediated macropinocytosis. Internalization vesicles are very acidic and co-localize only with phagolysosome markers, excluding caveolin-mediated pathways and indicating that upon phagocytosis the capsules are sorted to heterophagolysosomes.
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Affiliation(s)
- Lena Kastl
- Fachbereich Physik, Philipps-Universität Marburg, Renthof 7, 35037 Marburg, Germany
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Jin AJ, Lafer EM, Peng JQ, Smith PD, Nossal R. Unraveling protein-protein interactions in clathrin assemblies via atomic force spectroscopy. Methods 2013; 59:316-27. [PMID: 23270814 PMCID: PMC3608793 DOI: 10.1016/j.ymeth.2012.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 12/08/2012] [Accepted: 12/14/2012] [Indexed: 01/14/2023] Open
Abstract
Atomic force microscopy (AFM), single molecule force spectroscopy (SMFS), and single particle force spectroscopy (SPFS) are used to characterize intermolecular interactions and domain structures of clathrin triskelia and clathrin-coated vesicles (CCVs). The latter are involved in receptor-mediated endocytosis (RME) and other trafficking pathways. Here, we subject individual triskelia, bovine-brain CCVs, and reconstituted clathrin-AP180 coats to AFM-SMFS and AFM-SPFS pulling experiments and apply novel analytics to extract force-extension relations from very large data sets. The spectroscopic fingerprints of these samples differ markedly, providing important new information about the mechanism of CCV uncoating. For individual triskelia, SMFS reveals a series of events associated with heavy chain alpha-helix hairpin unfolding, as well as cooperative unraveling of several hairpin domains. SPFS of clathrin assemblies exposes weaker clathrin-clathrin interactions that are indicative of inter-leg association essential for RME and intracellular trafficking. Clathrin-AP180 coats are energetically easier to unravel than the coats of CCVs, with a non-trivial dependence on force-loading rate.
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Affiliation(s)
- Albert J Jin
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, DHHS, Bethesda, MD 20892, United States.
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Abstract
A coarse-grained computational model is used to investigate the effect of a fluid membrane on patchy-particle assembly into biologically relevant structures motivated by viral cores and clathrin. For cores, we demonstrate a nonmonotonic dependence of the promotion of assembly on membrane stiffness. If the membrane is significantly deformable, cores are enveloped in buds, although this effect is suppressed for very flexible membranes. In the less deformable regime, we observe no marked enhancement for cores, even for strong adhesion to the surface. For clathrinlike particles, we again observe the formation of buds, whose morphology depends on membrane flexibility.
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Affiliation(s)
- Richard Matthews
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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35
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Vitaliano GD, Vitaliano F, Rios JD, Renshaw PF, Teicher MH. New clathrin-based nanoplatforms for magnetic resonance imaging. PLoS One 2012; 7:e35821. [PMID: 22563470 PMCID: PMC3341379 DOI: 10.1371/journal.pone.0035821] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 03/26/2012] [Indexed: 12/31/2022] Open
Abstract
Background Magnetic Resonance Imaging (MRI) has high spatial resolution, but low sensitivity for visualization of molecular targets in the central nervous system (CNS). Our goal was to develop a new MRI method with the potential for non-invasive molecular brain imaging. We herein introduce new bio-nanotechnology approaches for designing CNS contrast media based on the ubiquitous clathrin cell protein. Methodology/Principal Findings The first approach utilizes three-legged clathrin triskelia modified to carry 81 gadolinium chelates. The second approach uses clathrin cages self-assembled from triskelia and designed to carry 432 gadolinium chelates. Clathrin triskelia and cages were characterized by size, structure, protein concentration, and chelate and gadolinium contents. Relaxivity was evaluated at 0.47 T. A series of studies were conducted to ascertain whether fluorescent-tagged clathrin nanoplatforms could cross the blood brain barriers (BBB) unaided following intranasal, intravenous, and intraperitoneal routes of administration. Clathrin nanoparticles can be constituted as triskelia (18.5 nm in size), and as cages assembled from them (55 nm). The mean chelate: clathrin heavy chain molar ratio was 27.04±4.8: 1 for triskelia, and 4.2±1.04: 1 for cages. Triskelia had ionic relaxivity of 16 mM−1s−1, and molecular relaxivity of 1,166 mM−1s−1, while cages had ionic relaxivity of 81 mM−1s−1 and molecular relaxivity of 31,512 mM−1s−1. Thus, cages exhibited 20 times higher ionic relaxivity and 8,000-fold greater molecular relaxivity than gadopentetate dimeglumine. Clathrin nanoplatforms modified with fluorescent tags were able to cross or bypass the BBB without enhancements following intravenous, intraperitoneal and intranasal administration in rats. Conclusions/Significance Use of clathrin triskelia and cages as carriers of CNS contrast media represents a new approach. This new biocompatible protein-based nanotechnology demonstrated suitable physicochemical properties to warrant further in vivo imaging and drug delivery studies. Significantly, both nanotransporters crossed and/or bypassed the BBB without enhancers. Thus, clathrin nanoplatforms could be an appealing alternative to existing CNS bio-nanotechnologies.
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Affiliation(s)
- Gordana D Vitaliano
- Laboratory of Developmental Psychopharmacology, Brain Imaging Center, Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, Massachusetts, United States of America.
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36
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Carvajal-Gonzalez JM, Gravotta D, Mattera R, Diaz F, Perez Bay A, Roman AC, Schreiner RP, Thuenauer R, Bonifacino JS, Rodriguez-Boulan E. Basolateral sorting of the coxsackie and adenovirus receptor through interaction of a canonical YXXPhi motif with the clathrin adaptors AP-1A and AP-1B. Proc Natl Acad Sci U S A 2012; 109:3820-5. [PMID: 22343291 PMCID: PMC3309744 DOI: 10.1073/pnas.1117949109] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The coxsackie and adenovirus receptor (CAR) plays key roles in epithelial barrier function at the tight junction, a localization guided in part by a tyrosine-based basolateral sorting signal, (318)YNQV(321). Sorting motifs of this type are known to route surface receptors into clathrin-mediated endocytosis through interaction with the medium subunit (μ2) of the clathrin adaptor AP-2, but how they guide new and recycling membrane proteins basolaterally is unknown. Here, we show that YNQV functions as a canonical YxxΦ motif, with both Y318 and V321 required for the correct basolateral localization and biosynthetic sorting of CAR, and for interaction with a highly conserved pocket in the medium subunits (μ1A and μ1B) of the clathrin adaptors AP-1A and AP-1B. Knock-down experiments demonstrate that AP-1A plays a role in the biosynthetic sorting of CAR, complementary to the role of AP-1B in basolateral recycling of this receptor. Our study illustrates how two clathrin adaptors direct basolateral trafficking of a plasma membrane protein through interaction with a canonical YxxΦ motif.
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Affiliation(s)
- Jose Maria Carvajal-Gonzalez
- Department of Ophthalmology, Department of Cell and Developmental Biology, Department of Physiology and Biophysics, Margaret Dyson Vision Research Institute, Weill Cornell Medical College, New York, NY 10065
| | - Diego Gravotta
- Department of Ophthalmology, Department of Cell and Developmental Biology, Department of Physiology and Biophysics, Margaret Dyson Vision Research Institute, Weill Cornell Medical College, New York, NY 10065
| | - Rafael Mattera
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Fernando Diaz
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Andres Perez Bay
- Department of Ophthalmology, Department of Cell and Developmental Biology, Department of Physiology and Biophysics, Margaret Dyson Vision Research Institute, Weill Cornell Medical College, New York, NY 10065
| | - Angel C. Roman
- Instituto Cajal–Consejo Superior de Investigaciones Cientificas, 28002 Madrid, Spain; and
| | - Ryan P. Schreiner
- Department of Ophthalmology, Department of Cell and Developmental Biology, Department of Physiology and Biophysics, Margaret Dyson Vision Research Institute, Weill Cornell Medical College, New York, NY 10065
| | | | - Juan S. Bonifacino
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Enrique Rodriguez-Boulan
- Department of Ophthalmology, Department of Cell and Developmental Biology, Department of Physiology and Biophysics, Margaret Dyson Vision Research Institute, Weill Cornell Medical College, New York, NY 10065
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Abstract
RNA interference (RNAi) has a range of physiological functions including as a defence mechanism against viruses. To protect uninfected cells in a multicellular organism, not only a cell-autonomous RNAi response is required but also a systemic one. However, the route of RNA spread in systemic RNAi remains unclear. Here we show that phagocytosis can be a route for double-stranded RNA uptake. Double-stranded RNA expressed in Escherichia coli induces robust RNAi in Drosophila S2 cells, with effectiveness comparable to that of naked dsRNA. We could separate this phagocytic uptake route from that for RNAi induced by naked dsRNA. Therefore, phagocytic uptake of dsRNA offers a potential route for systemic spread of RNAi.
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Affiliation(s)
- João J. E. Rocha
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (JJER); (CJO'K)
| | | | - Iain M. Robinson
- Peninsula College of Medicine and Dentistry, University of Exeter, Plymouth, United Kingdom
| | - Cahir J. O'Kane
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (JJER); (CJO'K)
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Parhamifar L, Sime W, Yudina Y, Vilhardt F, Mörgelin M, Sjölander A. Ligand-induced tyrosine phosphorylation of cysteinyl leukotriene receptor 1 triggers internalization and signaling in intestinal epithelial cells. PLoS One 2010; 5:e14439. [PMID: 21203429 PMCID: PMC3010979 DOI: 10.1371/journal.pone.0014439] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 11/30/2010] [Indexed: 12/17/2022] Open
Abstract
Background Leukotriene D4 (LTD4) belongs to the bioactive lipid group known as eicosanoids and has implications in pathological processes such as inflammation and cancer. Leukotriene D4 exerts its effects mainly through two different G-protein-coupled receptors, CysLT1 and CysLT2. The high affinity LTD4 receptor CysLT1R exhibits tumor-promoting properties by triggering cell proliferation, survival, and migration in intestinal epithelial cells. In addition, increased expression and nuclear localization of CysLT1R correlates with a poorer prognosis for patients with colon cancer. Methodology/Principal Findings Using a proximity ligation assay and immunoprecipitation, this study showed that endogenous CysLT1R formed heterodimers with its counter-receptor CysLT2R under basal conditions and that LTD4 triggers reduced dimerization of CysLTRs in intestinal epithelial cells. This effect was dependent upon a parallel LTD4-induced increase in CysLT1R tyrosine phosphorylation. Leukotriene D4 also led to elevated internalization of CysLT1Rs from the plasma membrane and a simultaneous increase at the nucleus. Using sucrose, a clathrin endocytic inhibitor, dominant-negative constructs, and siRNA against arrestin-3, we suggest that a clathrin-, arrestin-3, and Rab-5-dependent process mediated the internalization of CysLT1R. Altering the CysLT1R internalization process at either the clathrin or the arrestin-3 stage led to disruption of LTD4-induced Erk1/2 activation and up-regulation of COX-2 mRNA levels. Conclusions/Significance Our data suggests that upon ligand activation, CysLT1R is tyrosine-phosphorylated and released from heterodimers with CysLT2R and, subsequently, internalizes from the plasma membrane to the nuclear membrane in a clathrin-, arrestin-3-, and Rab-5-dependent manner, thus, enabling Erk1/2 signaling and downstream transcription of the COX-2 gene.
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Affiliation(s)
- Ladan Parhamifar
- Cell and Experimental Pathology, Department of Laboratory Medicine, Clinical Research Center, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Wondossen Sime
- Cell and Experimental Pathology, Department of Laboratory Medicine, Clinical Research Center, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Yuliana Yudina
- Cell and Experimental Pathology, Department of Laboratory Medicine, Clinical Research Center, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Frederik Vilhardt
- Institute of Cellular and Molecular Medicine, Panum Institute, Copenhagen University, Copenhagen, Denmark
| | - Matthias Mörgelin
- Infectious Medicine, Department of Clinical Science, Lund University, Lund, Sweden
| | - Anita Sjölander
- Cell and Experimental Pathology, Department of Laboratory Medicine, Clinical Research Center, Lund University, Skåne University Hospital, Malmö, Sweden
- * E-mail:
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39
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Abstract
In eukaryotic cells, the internalization of extracellular cargo via the endocytic machinery is an important regulatory process required for many essential cellular functions. The role of cooperative protein-protein and protein-membrane interactions in the ubiquitous endocytic pathway in mammalian cells, namely the clathrin-dependent endocytosis, remains unresolved. We employ the Helfrich membrane Hamiltonian together with surface evolution methodology to address how the shapes and energetics of vesicular-bud formation in a planar membrane are stabilized by presence of the clathrin-coat assembly. Our results identify a unique dual role for the tubulating protein epsin: multiple epsins localized spatially and orientationally collectively play the role of a curvature inducing capsid; in addition, epsin serves the role of an adapter in binding the clathrin coat to the membrane. Our results also suggest an important role for the clathrin lattice, namely in the spatial- and orientational-templating of epsins. We suggest that there exists a critical size of the coat above which a vesicular bud with a constricted neck resembling a mature vesicle is stabilized. Based on the observed strong dependence of the vesicle diameter on the bending rigidity, we suggest that the variability in bending stiffness due to variations in membrane composition with cell type can explain the experimentally observed variability on the size of clathrin-coated vesicles, which typically range 50-100 nm. Our model also provides estimates for the number of epsins involved in stabilizing a coated vesicle, and without any direct fitting reproduces the experimentally observed shapes of vesicular intermediates as well as their probability distributions quantitatively, in wildtype as well as CLAP IgG injected neuronal cell experiments. We have presented a minimal mesoscale model which quantitatively explains several experimental observations on the process of vesicle nucleation induced by the clathrin-coated assembly prior to vesicle scission in clathrin dependent endocytosis.
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Affiliation(s)
- Neeraj J Agrawal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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40
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Agrawal NJ, Nukpezah J, Radhakrishnan R. Minimal mesoscale model for protein-mediated vesiculation in clathrin-dependent endocytosis. PLoS Comput Biol 2010; 6:e1000926. [PMID: 20838575 PMCID: PMC2936510 DOI: 10.1371/journal.pcbi.1000926] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 08/09/2010] [Indexed: 11/21/2022] Open
Abstract
In eukaryotic cells, the internalization of extracellular cargo via the endocytic machinery is an important regulatory process required for many essential cellular functions. The role of cooperative protein-protein and protein-membrane interactions in the ubiquitous endocytic pathway in mammalian cells, namely the clathrin-dependent endocytosis, remains unresolved. We employ the Helfrich membrane Hamiltonian together with surface evolution methodology to address how the shapes and energetics of vesicular-bud formation in a planar membrane are stabilized by presence of the clathrin-coat assembly. Our results identify a unique dual role for the tubulating protein epsin: multiple epsins localized spatially and orientationally collectively play the role of a curvature inducing capsid; in addition, epsin serves the role of an adapter in binding the clathrin coat to the membrane. Our results also suggest an important role for the clathrin lattice, namely in the spatial- and orientational-templating of epsins. We suggest that there exists a critical size of the coat above which a vesicular bud with a constricted neck resembling a mature vesicle is stabilized. Based on the observed strong dependence of the vesicle diameter on the bending rigidity, we suggest that the variability in bending stiffness due to variations in membrane composition with cell type can explain the experimentally observed variability on the size of clathrin-coated vesicles, which typically range 50-100 nm. Our model also provides estimates for the number of epsins involved in stabilizing a coated vesicle, and without any direct fitting reproduces the experimentally observed shapes of vesicular intermediates as well as their probability distributions quantitatively, in wildtype as well as CLAP IgG injected neuronal cell experiments. We have presented a minimal mesoscale model which quantitatively explains several experimental observations on the process of vesicle nucleation induced by the clathrin-coated assembly prior to vesicle scission in clathrin dependent endocytosis.
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Affiliation(s)
- Neeraj J. Agrawal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jonathan Nukpezah
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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41
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Wilbur JD, Hwang PK, Ybe JA, Lane M, Sellers BD, Jacobson MP, Fletterick RJ, Brodsky FM. Conformation switching of clathrin light chain regulates clathrin lattice assembly. Dev Cell 2010; 18:841-8. [PMID: 20493816 DOI: 10.1016/j.devcel.2010.04.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 01/25/2010] [Accepted: 03/05/2010] [Indexed: 11/19/2022]
Abstract
Clathrin-coated vesicle formation is responsible for membrane traffic to and from the endocytic pathway during receptor-mediated endocytosis and organelle biogenesis, influencing how cells relate to their environment. Generating these vesicles involves self-assembly of clathrin molecules into a latticed coat on membranes that recruits receptors and organizes protein machinery necessary for budding. Here we define a molecular mechanism regulating clathrin lattice formation by obtaining structural information from co-crystals of clathrin subunits. Low resolution X-ray diffraction data (7.9-9.0 A) was analyzed using a combination of molecular replacement with an energy-minimized model and noncrystallographic symmetry averaging. Resulting topological information revealed two conformations of the regulatory clathrin light chain bound to clathrin heavy chain. Based on protein domain positions, mutagenesis, and biochemical assays, we identify an electrostatic interaction between the clathrin subunits that allows the observed conformational variation in clathrin light chains to alter the conformation of the clathrin heavy chain and thereby regulates assembly.
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Affiliation(s)
- Jeremy D Wilbur
- Graduate Program in Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
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42
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Moorman NJ, Sharon-Friling R, Shenk T, Cristea IM. A targeted spatial-temporal proteomics approach implicates multiple cellular trafficking pathways in human cytomegalovirus virion maturation. Mol Cell Proteomics 2010; 9:851-60. [PMID: 20023299 PMCID: PMC2871419 DOI: 10.1074/mcp.m900485-mcp200] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 12/16/2009] [Indexed: 11/06/2022] Open
Abstract
The assembly of infectious virus particles is a complex event. For human cytomegalovirus (HCMV) this process requires the coordinated expression and localization of at least 60 viral proteins that comprise the infectious virion. To gain insight into the mechanisms controlling this process, we identified protein binding partners for two viral proteins, pUL99 (also termed pp28) and pUL32 (pp150), which are essential for HCMV virion assembly. We utilized HCMV strains expressing pUL99 or pUL32 carboxyl-terminal green fluorescent protein fusion proteins from their native location in the HCMV genome. Based on the presence of ubiquitin in the pUL99 immunoisolation, we discovered that this viral protein colocalizes with components of the cellular endosomal sorting complex required for transport (ESCRT) pathway during the initial stages of virion assembly. We identified the nucleocapsid and a large number of tegument proteins as pUL32 binding partners, suggesting that events controlling trafficking of this viral protein in the cytoplasm regulate nucleocapsid/tegument maturation. The finding that pUL32, but not pUL99, associates with clathrin led to the discovery that the two viral proteins traffic via distinct pathways during the early stages of virion assembly. Additional investigation revealed that the majority of the major viral glycoprotein gB initially resides in a third compartment. Analysis of the trafficking of these three viral proteins throughout a time course of virion assembly allowed us to visualize their merger into a single large cytoplasmic structure during the late stages of viral assembly. We propose a model of HCMV virion maturation in which multiple components of the virion traffic independently of one another before merging.
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Affiliation(s)
- Nathaniel J. Moorman
- From the Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Ronit Sharon-Friling
- From the Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Thomas Shenk
- From the Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Ileana M. Cristea
- From the Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
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43
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Abstract
The self-assembly of rigid three-legged building blocks into polyhedral cages is investigated by patchy particle simulations. A four-site anisotropic interaction potential is introduced to make pairs of overlapping legs bind in an anti-parallel fashion, thereby forming the edges of a polyhedron of pentagons and hexagons. A torsional potential, reflecting an asymmetry or polarity in the legs' binding potential, proves crucial for the successful formation of closed fullerene-like cages. Self-assembly proceeds by a nucleation-and-growth mechanism, with a high success rate of cage closure. The size distribution of the self-assembled buckyballs is largely determined by the pucker angle of the particle. Nature explores a similar building block, the clathrin triskelion, to regulate vesicle formation at the cell membrane during endocytosis.
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Affiliation(s)
- Wouter K den Otter
- Computational Biophysics Group, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands.
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44
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Abstract
Liposomes have been utilized for variety of membrane transport studies including clathrin-mediated endocytosis. Here we introduce clathrin-coated structures that are generated on large unilamellar liposomes by incubating with clathrin coat proteins. Large unilamellar liposomes are also used to reconstitute vesicle formation in a cell-free system, and the vesicle formation can be quantified by using dynamic light scattering (DLS). Furthermore, phagocytosis assay using liposome-conjugated styrene beads is demonstrated.
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Affiliation(s)
- Kohji Takei
- Department of Neuroscience, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan
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45
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Abstract
Background Sorting nexins (SNXs) constitute a family of proteins classified by their phosphatidylinositol (PI) binding Phox homology (PX) domain. Some members regulate intracellular trafficking. We have here investigated mechanisms underlying SNX4 mediated endosome to Golgi transport. Methodology/Principal Findings We show that SNX4 forms complexes with clathrin and dynein. The interactions were inhibited by wortmannin, a PI3-kinase inhibitor, suggesting that they form when SNX4 is associated with PI(3)P on endosomes. We further localized the clathrin interacting site on SNX4 to a clathrin box variant. A short peptide containing this motif was sufficient to pull down both clathrin and dynein. Knockdown studies demonstrated that clathrin is not required for the SNX4/dynein interaction. Moreover, clathrin knockdown led to increased Golgi transport of the toxin ricin, as well as redistribution of endosomes. Conclusions/Significance We discuss the possibility of clathrin serving as a regulator of SNX4-dependent transport. Upon clathrin release, dynein may bind SNX4 and mediate retrograde movement.
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Affiliation(s)
- Sigrid S. Skånland
- Centre for Cancer Biomedicine, Faculty Division Norwegian Radium Hospital, University of Oslo, Oslo, Norway
- Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Montebello, Oslo, Norway
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Sébastien Wälchli
- Department of Immunology, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Montebello, Oslo, Norway
| | - Andreas Brech
- Centre for Cancer Biomedicine, Faculty Division Norwegian Radium Hospital, University of Oslo, Oslo, Norway
- Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Montebello, Oslo, Norway
| | - Kirsten Sandvig
- Centre for Cancer Biomedicine, Faculty Division Norwegian Radium Hospital, University of Oslo, Oslo, Norway
- Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Montebello, Oslo, Norway
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- * E-mail:
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46
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Abstract
Endocytosis is a protein and lipid-trafficking pathway that occurs in all eukaryotic cells. It involves the internalization of plasma membrane proteins and lipids into the cell and the subsequent degradation of proteins in the lysosome or the recycling of proteins and lipids back to the plasma membrane. Over the past decade, studies in yeast and mammalian cells have revealed endocytosis to be a very complex molecular process that depends on regulated interactions between a variety of proteins and lipids. The Eps15 homology (EH) domain is a conserved, modular protein-interaction domain found in several endocytosis proteins. EH proteins can function as key regulators of endocytosis through their ability to interact with many of the other proteins involved in this process.
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Affiliation(s)
- Nicholas B Miliaras
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
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47
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Saffarian S, Kirchhausen T. Differential evanescence nanometry: live-cell fluorescence measurements with 10-nm axial resolution on the plasma membrane. Biophys J 2008; 94:2333-42. [PMID: 17993495 PMCID: PMC2257884 DOI: 10.1529/biophysj.107.117234] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 10/24/2007] [Indexed: 11/18/2022] Open
Abstract
We present a method to resolve components within a diffraction-limited object by tracking simultaneously the average axial positions of two different sets of fluorescent molecules within it. The axial positions are then subtracted from each other to determine the separation of the two sets of fluorophores. This method follows the dynamic changes in the separation of the two sets of fluorophores with freely rotating dipoles using sequential acquisitions with total internal reflection and wide-field illumination, and it can be used to measure the formation of small structures on living cells. We have verified that we can achieve a resolution of 10 nm, and we have used the method to follow the location of clathrin and its adaptor AP-2 as they are recruited to a diffraction-limited coated pit during its assembly at the plasma membrane. We find a gradually increasing axial separation between the centroids of clathrin and AP-2 distribution, up to a final value of 30 nm just before coated-pit pinching and formation of the coated vesicle.
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Affiliation(s)
- Saveez Saffarian
- Department of Cell Biology and Immune Disease Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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48
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Goodman OB, Barwe SP, Ritter B, McPherson PS, Vasko AJ, Keen JH, Nanus DM, Bander NH, Rajasekaran AK. Interaction of prostate specific membrane antigen with clathrin and the adaptor protein complex-2. Int J Oncol 2007; 31:1199-203. [PMID: 17912448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Prostate-specific membrane antigen (PSMA) is an integral membrane glycoprotein expressed in prostatic epithelia and is being evaluated as a therapeutic target in prostate cancer. It undergoes constitutive receptor-mediated endocytosis via clathrin-coated pits, which is enhanced in the presence of monoclonal antibodies directed against it. We describe distinct interactions of PSMA with clathrin and the clathrin adaptor protein-2 (AP-2) complex, two components of clathrin-coated pits. The intracellular N-terminal domain of PSMA interacts with the N-terminal globular domain of clathrin heavy chain. Deletion analysis revealed an important determinant of this interaction residing within the proximal portion of the clathrin heavy chain N-terminal domain (amino acids 1-85) distinct from the clathrin binding sites of other known clathrin-binding proteins. Furthermore, PSMA interacts with the ear domain of alpha-adaptin (an AP-2 subunit), and a glutamic acid residue at position 7 in the cytoplasmic tail of PSMA is essential for this interaction. These data indicate that PSMA exhibits a high affinity, specific association with the clathrin-based endocytic machinery by distinct interactions with both clathrin and AP-2. Thus, although PSMA is a new member of the dual AP and clathrin binding proteins, its alpha-adaptin and clathrin heavy chain binding determinants are distinct from those of other members.
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Affiliation(s)
- Oscar B Goodman
- Urologic Oncology Research Laboratory, Department of Urology, Weill Medical College of Cornell University-New York Presbyterian Hospital, New York, NY, USA
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49
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Ritter B, Denisov AY, Philie J, Allaire PD, Legendre-Guillemin V, Zylbergold P, Gehring K, McPherson PS. The NECAP PHear domain increases clathrin accessory protein binding potential. EMBO J 2007; 26:4066-77. [PMID: 17762867 PMCID: PMC2230672 DOI: 10.1038/sj.emboj.7601836] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Accepted: 07/30/2007] [Indexed: 11/08/2022] Open
Abstract
AP-2 is a key regulator of the endocytic protein machinery driving clathrin-coated vesicle (CCV) formation. One critical function, mediated primarily by the AP-2 alpha-ear, is the recruitment of accessory proteins. NECAPs are alpha-ear-binding proteins that enrich on CCVs. Here, we have solved the structure of the conserved N-terminal region of NECAP 1, revealing a unique module in the pleckstrin homology (PH) domain superfamily, which we named the PHear domain. The PHear domain binds accessory proteins bearing FxDxF motifs, which were previously thought to bind exclusively to the AP-2 alpha-ear. Structural analysis of the PHear domain reveals the molecular surface for FxDxF motif binding, which was confirmed by site-directed mutagenesis. The reciprocal analysis of the FxDxF motif in amphiphysin I identified distinct binding requirements for binding to the alpha-ear and PHear domain. We show that NECAP knockdown compromises transferrin uptake and establish a functional role for NECAPs in clathrin-mediated endocytosis. Our data uncover a striking convergence of two evolutionarily and structurally distinct modules to recognize a common peptide motif and promote efficient endocytosis.
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Affiliation(s)
- Brigitte Ritter
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Alexei Yu Denisov
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jacynthe Philie
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Patrick D Allaire
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Valerie Legendre-Guillemin
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Peter Zylbergold
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Canada H3G 1Y6. Tel.: +514 398 7287; Fax: +514 847 0220; E-mail:
| | - Peter S McPherson
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, 3801 University Street, Montreal, Canada H3A 2B4. Tel.: +514 398 7355; Fax: +514 398 8106; E-mail:
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50
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Deinhardt K, Reversi A, Berninghausen O, Hopkins CR, Schiavo G. Neurotrophins Redirect p75NTRfrom a Clathrin‐Independent to a Clathrin‐Dependent Endocytic Pathway Coupled to Axonal Transport. Traffic 2007; 8:1736-1749. [PMID: 17897318 DOI: 10.1111/j.1600-0854.2007.00645.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The p75 neurotrophin receptor (p75(NTR)) plays multiple roles in neuronal physiology through interactions with many ligands and coreceptors. However, its intracellular neuronal trafficking prior to and after neurotrophin activation is still poorly characterized. We have previously shown that in response to nerve growth factor (NGF), p75(NTR) is retrogradely transported along the axons of motor neurons (MNs) in carriers shared with NGF, brain-derived neurotrophic factor and the tyrosine kinase receptor TrkB. Here, we report that NGF does not enhance the internalization or degradation of p75(NTR), which undergoes a rapid dynamin-dependent and clathrin-independent recycling process in MNs. Instead, incubation of cells with NGF leads to the redirection of a pool of plasma membrane p75(NTR) into clathrin-coated pits. The subsequent internalization of p75(NTR) via clathrin-mediated endocytosis, as well as the activity of Rab5, are essential for the sorting of the p75(NTR)-containing endosomes to the axonal retrograde transport pathway and for the delivery of p75(NTR) to the soma. Our findings suggest that the spatial regulation of p75(NTR) signalling is controlled by these ligand-driven routes of endocytosis.
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Affiliation(s)
- Katrin Deinhardt
- Molecular Neuropathobiology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, WC2A 3PX, London, UK
- Current address: Molecular Neurobiology Program, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Alessandra Reversi
- Molecular Neuropathobiology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, WC2A 3PX, London, UK
| | - Otto Berninghausen
- Department of Biological Sciences, Imperial College London, SW7 2AZ, London, UK
- Current address: LMU Gene Center, University of Munich, Feodor-Lynen-Str 25, 81377 Muenchen, Germany
| | - Colin R Hopkins
- Department of Biological Sciences, Imperial College London, SW7 2AZ, London, UK
| | - Giampietro Schiavo
- Molecular Neuropathobiology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, WC2A 3PX, London, UK
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