1
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Barrantes FJ. Modulation of a rapid neurotransmitter receptor-ion channel by membrane lipids. Front Cell Dev Biol 2024; 11:1328875. [PMID: 38274273 PMCID: PMC10808158 DOI: 10.3389/fcell.2023.1328875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Membrane lipids modulate the proteins embedded in the bilayer matrix by two non-exclusive mechanisms: direct or indirect. The latter comprise those effects mediated by the physicochemical state of the membrane bilayer, whereas direct modulation entails the more specific regulatory effects transduced via recognition sites on the target membrane protein. The nicotinic acetylcholine receptor (nAChR), the paradigm member of the pentameric ligand-gated ion channel (pLGIC) superfamily of rapid neurotransmitter receptors, is modulated by both mechanisms. Reciprocally, the nAChR protein exerts influence on its surrounding interstitial lipids. Folding, conformational equilibria, ligand binding, ion permeation, topography, and diffusion of the nAChR are modulated by membrane lipids. The knowledge gained from biophysical studies of this prototypic membrane protein can be applied to other neurotransmitter receptors and most other integral membrane proteins.
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Affiliation(s)
- Francisco J. Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA)–National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
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2
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Morales SV, Mahmood A, Pollard J, Mayne J, Figeys D, Wiseman PW. The LDL receptor is regulated by membrane cholesterol as revealed by fluorescence fluctuation analysis. Biophys J 2023; 122:3783-3797. [PMID: 37559362 PMCID: PMC10541495 DOI: 10.1016/j.bpj.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/17/2023] [Accepted: 08/07/2023] [Indexed: 08/11/2023] Open
Abstract
Membrane cholesterol-rich domains have been shown to be important for regulating a range of membrane protein activities. Low-density lipoprotein receptor (LDLR)-mediated internalization of cholesterol-rich LDL particles is tightly regulated by feedback mechanisms involving intracellular sterol sensors. Since LDLR plays a role in maintaining cellular cholesterol homeostasis, we explore the role that membrane domains may have in regulating LDLR activity. We expressed a fluorescent LDLR-mEGFP construct in HEK293T cells and imaged the unligated receptor or bound to an LDL/DiI fluorescent ligand using total internal reflection fluorescence microscopy. We studied the receptor's spatiotemporal dynamics using fluorescence fluctuation analysis methods. Image cross correlation spectroscopy reveals a lower LDL-to-LDLR binding fraction when membrane cholesterol concentrations are augmented using cholesterol esterase, and a higher binding fraction when the cells are treated with methyl-β-cyclodextrin) to lower membrane cholesterol. This suggests that LDLR's ability to metabolize LDL particles is negatively correlated to membrane cholesterol concentrations. We then tested if a change in activity is accompanied by a change in membrane localization. Image mean-square displacement analysis reveals that unligated LDLR-mEGFP and ligated LDLR-mEGFP/LDL-DiI constructs are transiently confined on the cell membrane, and the size of their confinement domains increases with augmented cholesterol concentrations. Receptor diffusion within the domains and their domain-escape probabilities decrease upon treatment with methyl-β-cyclodextrin, consistent with a change in receptor populations to more confined domains, likely clathrin-coated pits. We propose a feedback model to account for regulation of LDLR within the cell membrane: when membrane cholesterol concentrations are high, LDLR is sequestered in cholesterol-rich domains. These LDLR populations are attenuated in their efficacy to bind and internalize LDL. However, when membrane cholesterol levels drop, LDL has a higher binding affinity to its receptor and the LDLR transits to nascent clathrin-coated domains, where it diffuses at a slower rate while awaiting internalization.
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Affiliation(s)
- Sebastian V Morales
- Department of Chemistry, Faculty of Science, McGill University, Montreal, Canada
| | - Ahmad Mahmood
- Department of Physics, Faculty of Science, McGill University, Montreal, Canada
| | - Jacob Pollard
- Department of Chemistry, Faculty of Science, McGill University, Montreal, Canada
| | - Janice Mayne
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Paul W Wiseman
- Department of Chemistry, Faculty of Science, McGill University, Montreal, Canada; Department of Physics, Faculty of Science, McGill University, Montreal, Canada.
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3
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Tantiwong C, Dunster JL, Cavill R, Tomlinson MG, Wierling C, Heemskerk JWM, Gibbins JM. An agent-based approach for modelling and simulation of glycoprotein VI receptor diffusion, localisation and dimerisation in platelet lipid rafts. Sci Rep 2023; 13:3906. [PMID: 36890261 PMCID: PMC9994409 DOI: 10.1038/s41598-023-30884-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/02/2023] [Indexed: 03/10/2023] Open
Abstract
Receptor diffusion plays an essential role in cellular signalling via the plasma membrane microenvironment and receptor interactions, but the regulation is not well understood. To aid in understanding of the key determinants of receptor diffusion and signalling, we developed agent-based models (ABMs) to explore the extent of dimerisation of the platelet- and megakaryocyte-specific receptor for collagen glycoprotein VI (GPVI). This approach assessed the importance of glycolipid enriched raft-like domains within the plasma membrane that lower receptor diffusivity. Our model simulations demonstrated that GPVI dimers preferentially concentrate in confined domains and, if diffusivity within domains is decreased relative to outside of domains, dimerisation rates are increased. While an increased amount of confined domains resulted in further dimerisation, merging of domains, which may occur upon membrane rearrangements, was without effect. Modelling of the proportion of the cell membrane which constitutes lipid rafts indicated that dimerisation levels could not be explained by these alone. Crowding of receptors by other membrane proteins was also an important determinant of GPVI dimerisation. Together, these results demonstrate the value of ABM approaches in exploring the interactions on a cell surface, guiding the experimentation for new therapeutic avenues.
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Affiliation(s)
- Chukiat Tantiwong
- School of Biological Sciences, University of Reading, Reading, UK.,Department of Biochemistry, CARIM, Maastricht University, Maastricht, The Netherlands
| | - Joanne L Dunster
- School of Biological Sciences, University of Reading, Reading, UK
| | - Rachel Cavill
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | | | | | - Johan W M Heemskerk
- Department of Biochemistry, CARIM, Maastricht University, Maastricht, The Netherlands.,Synapse Research Institute, Maastricht, The Netherlands
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4
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Refinement of Singer-Nicolson fluid-mosaic model by microscopy imaging: Lipid rafts and actin-induced membrane compartmentalization. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184093. [PMID: 36423676 DOI: 10.1016/j.bbamem.2022.184093] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
This year celebrates the 50th anniversary of the Singer-Nicolson fluid mosaic model for biological membranes. The next level of sophistication we have achieved for understanding plasma membrane (PM) structures, dynamics, and functions during these 50 years includes the PM interactions with cortical actin filaments and the partial demixing of membrane constituent molecules in the PM, particularly raft domains. Here, first, we summarize our current knowledge of these two structures and emphasize that they are interrelated. Second, we review the structure, molecular dynamics, and function of raft domains, with main focuses on raftophilic glycosylphosphatidylinositol-anchored proteins (GPI-APs) and their signal transduction mechanisms. We pay special attention to the results obtained by single-molecule imaging techniques and other advanced microscopy methods. We also clarify the limitations of present optical microscopy methods for visualizing raft domains, but emphasize that single-molecule imaging techniques can "detect" raft domains associated with molecules of interest in the PM.
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5
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Grusky DS, Moss FR, Boxer SG. Recombination between 13C and 2H to Form Acetylide ( 13C 22H -) Probes Nanoscale Interactions in Lipid Bilayers via Dynamic Secondary Ion Mass Spectrometry: Cholesterol and GM 1 Clustering. Anal Chem 2022; 94:9750-9757. [PMID: 35759338 PMCID: PMC10075087 DOI: 10.1021/acs.analchem.2c01336] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although it is thought that there is lateral heterogeneity of lipid and protein components within biological membranes, probing this heterogeneity has proven challenging. The difficulty in such experiments is due to both the small length scale over which such heterogeneity can occur, and the significant perturbation resulting from fluorescent or spin labeling on the delicate interactions within bilayers. Atomic recombination during dynamic nanoscale secondary ion imaging mass spectrometry (NanoSIMS) is a non-perturbative method for examining nanoscale bilayer interactions. Atomic recombination is a variation on conventional NanoSIMS imaging, whereby an isotope on one molecule combines with a different isotope on another molecule during the ionization process, forming an isotopically enriched polyatomic ion in a distance-dependent manner. We show that the recombinant ion, 13C22H-, is formed in high yield from 13C- and 2H-labeled lipids. The low natural abundance of triply labeled acetylide also makes it an ideal ion to probe GM1 clusters in model membranes and the effects of cholesterol on lipid-lipid interactions. We find evidence supporting the cholesterol condensation effect as well as the presence of nanoscale GM1 clusters in model membranes.
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Affiliation(s)
- Dashiel S Grusky
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Frank R Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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6
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Westra M, MacGillavry HD. Precise Detection and Visualization of Nanoscale Temporal Confinement in Single-Molecule Tracking Analysis. MEMBRANES 2022; 12:membranes12070650. [PMID: 35877853 PMCID: PMC9320997 DOI: 10.3390/membranes12070650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022]
Abstract
The plasma membrane consists of a diverse mixture of molecules that dynamically assemble into a highly non-random organization. The formation of nanoscale domains in the membrane is of particular interest as these domains underlie critical cellular functions. Single-molecule tracking is a powerful method to detect and quantify molecular motion at high temporal and spatial resolution and has therefore been instrumental in understanding mechanisms that underlie membrane organization. In single-molecule trajectories, regions of temporal confinement can be determined that might reveal interesting biophysical interactions important for domain formation. However, analytical methods for the detection of temporal confinement in single-molecule trajectories depend on a variety of parameters that heavily depend on experimental factors and the influence of these factors on the performance of confinement detection are not well understood. Here, we present elaborate confinement analyses on simulated random walks and trajectories that display transient confined behavior to optimize the parameters for different experimental conditions. Furthermore, we demonstrate a heatmap visualization tool that allows spatial mapping of confinement hotspots relative to subcellular markers. Using these optimized tools, we reliably detected subdiffusive behavior of different membrane components and observed differences in the confinement behavior of two types of glutamate receptors in neurons. This study will help in further understanding the dynamic behavior of the complex membrane and its role in cellular functioning.
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8
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Winkler PM, García-Parajo MF. Correlative nanophotonic approaches to enlighten the nanoscale dynamics of living cell membranes. Biochem Soc Trans 2021; 49:2357-2369. [PMID: 34495333 PMCID: PMC8589428 DOI: 10.1042/bst20210457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 01/31/2023]
Abstract
Dynamic compartmentalization is a prevailing principle regulating the spatiotemporal organization of the living cell membrane from the nano- up to the mesoscale. This non-arbitrary organization is intricately linked to cell function. On living cell membranes, dynamic domains or 'membrane rafts' enriched with cholesterol, sphingolipids and other certain proteins exist at the nanoscale serving as signaling and sorting platforms. Moreover, it has been postulated that other local organizers of the cell membrane such as intrinsic protein interactions, the extracellular matrix and/or the actin cytoskeleton synergize with rafts to provide spatiotemporal hierarchy to the membrane. Elucidating the intricate coupling of multiple spatial and temporal scales requires the application of correlative techniques, with a particular need for simultaneous nanometer spatial precision and microsecond temporal resolution. Here, we review novel fluorescence-based techniques that readily allow to decode nanoscale membrane dynamics with unprecedented spatiotemporal resolution and single-molecule sensitivity. We particularly focus on correlative approaches from the field of nanophotonics. Notably, we introduce a versatile planar nanoantenna platform combined with fluorescence correlation spectroscopy to study spatiotemporal heterogeneities on living cell membranes at the nano- up to the mesoscale. Finally, we outline remaining future technological challenges and comment on potential directions to advance our understanding of cell membrane dynamics under the influence of the actin cytoskeleton and extracellular matrix in uttermost detail.
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Affiliation(s)
- Pamina M. Winkler
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - María F. García-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
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9
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Intertwined and Finely Balanced: Endoplasmic Reticulum Morphology, Dynamics, Function, and Diseases. Cells 2021; 10:cells10092341. [PMID: 34571990 PMCID: PMC8472773 DOI: 10.3390/cells10092341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 02/07/2023] Open
Abstract
The endoplasmic reticulum (ER) is an organelle that is responsible for many essential subcellular processes. Interconnected narrow tubules at the periphery and thicker sheet-like regions in the perinuclear region are linked to the nuclear envelope. It is becoming apparent that the complex morphology and dynamics of the ER are linked to its function. Mutations in the proteins involved in regulating ER structure and movement are implicated in many diseases including neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and amyotrophic lateral sclerosis (ALS). The ER is also hijacked by pathogens to promote their replication. Bacteria such as Legionella pneumophila and Chlamydia trachomatis, as well as the Zika virus, bind to ER morphology and dynamics-regulating proteins to exploit the functions of the ER to their advantage. This review covers our understanding of ER morphology, including the functional subdomains and membrane contact sites that the organelle forms. We also focus on ER dynamics and the current efforts to quantify ER motion and discuss the diseases related to ER morphology and dynamics.
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10
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Reina F, Wigg JM, Dmitrieva M, Vogler B, Lefebvre J, Rittscher J, Eggeling C. TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data. F1000Res 2021; 10:838. [PMID: 35186271 PMCID: PMC8829092 DOI: 10.12688/f1000research.54788.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 11/20/2022] Open
Abstract
Single particle tracking (SPT) is one of the most widely used tools in optical microscopy to evaluate particle mobility in a variety of situations, including cellular and model membrane dynamics. Recent technological developments, such as Interferometric Scattering microscopy, have allowed recording of long, uninterrupted single particle trajectories at kilohertz framerates. The resulting data, where particles are continuously detected and do not displace much between observations, thereby do not require complex linking algorithms. Moreover, while these measurements offer more details into the short-term diffusion behaviour of the tracked particles, they are also subject to the influence of localisation uncertainties, which are often underestimated by conventional analysis pipelines. we thus developed a Python library, under the name of TRAIT2D (Tracking Analysis Toolbox - 2D version), in order to track particle diffusion at high sampling rates, and analyse the resulting trajectories with an innovative approach. The data analysis pipeline introduced is more localisation-uncertainty aware, and also selects the most appropriate diffusion model for the data provided on a statistical basis. A trajectory simulation platform also allows the user to handily generate trajectories and even synthetic time-lapses to test alternative tracking algorithms and data analysis approaches. A high degree of customisation for the analysis pipeline, for example with the introduction of different diffusion modes, is possible from the source code. Finally, the presence of graphical user interfaces lowers the access barrier for users with little to no programming experience.
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Affiliation(s)
- Francesco Reina
- Leibniz-Institut für Photonische Technologien e.V, Jena, Germany
| | - John M.A. Wigg
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
| | - Mariia Dmitrieva
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Bela Vogler
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
| | - Joël Lefebvre
- Département d'informatique, University of Quebec at Montreal, Montreal, Canada
| | - Jens Rittscher
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Christian Eggeling
- Leibniz-Institut für Photonische Technologien e.V, Jena, Germany
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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11
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Reina F, Wigg JM, Dmitrieva M, Vogler B, Lefebvre J, Rittscher J, Eggeling C. TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data. F1000Res 2021; 10:838. [PMID: 35186271 PMCID: PMC8829092 DOI: 10.12688/f1000research.54788.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 02/15/2024] Open
Abstract
Single particle tracking (SPT) is one of the most widely used tools in optical microscopy to evaluate particle mobility in a variety of situations, including cellular and model membrane dynamics. Recent technological developments, such as Interferometric Scattering microscopy, have allowed recording of long, uninterrupted single particle trajectories at kilohertz framerates. The resulting data, where particles are continuously detected and do not displace much between observations, thereby do not require complex linking algorithms. Moreover, while these measurements offer more details into the short-term diffusion behaviour of the tracked particles, they are also subject to the influence of localisation uncertainties, which are often underestimated by conventional analysis pipelines. we thus developed a Python library, under the name of TRAIT2D (Tracking Analysis Toolbox - 2D version), in order to track particle diffusion at high sampling rates, and analyse the resulting trajectories with an innovative approach. The data analysis pipeline introduced is more localisation-uncertainty aware, and also selects the most appropriate diffusion model for the data provided on a statistical basis. A trajectory simulation platform also allows the user to handily generate trajectories and even synthetic time-lapses to test alternative tracking algorithms and data analysis approaches. A high degree of customisation for the analysis pipeline, for example with the introduction of different diffusion modes, is possible from the source code. Finally, the presence of graphical user interfaces lowers the access barrier for users with little to no programming experience.
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Affiliation(s)
- Francesco Reina
- Leibniz-Institut für Photonische Technologien e.V, Jena, Germany
| | - John M.A. Wigg
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
| | - Mariia Dmitrieva
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Bela Vogler
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
| | - Joël Lefebvre
- Département d'informatique, University of Quebec at Montreal, Montreal, Canada
| | - Jens Rittscher
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Christian Eggeling
- Leibniz-Institut für Photonische Technologien e.V, Jena, Germany
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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12
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Kim M, Hong S, Yankeelov TE, Yeh HC, Liu YL. Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics. Bioinformatics 2021; 38:243-249. [PMID: 34390568 PMCID: PMC8696113 DOI: 10.1093/bioinformatics/btab581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/09/2021] [Accepted: 08/12/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Motions of transmembrane receptors on cancer cell surfaces can reveal biophysical features of the cancer cells, thus providing a method for characterizing cancer cell phenotypes. While conventional analysis of receptor motions in the cell membrane mostly relies on the mean-squared displacement plots, much information is lost when producing these plots from the trajectories. Here we employ deep learning to classify breast cancer cell types based on the trajectories of epidermal growth factor receptor (EGFR). Our model is an artificial neural network trained on the EGFR motions acquired from six breast cancer cell lines of varying invasiveness and receptor status: MCF7 (hormone receptor positive), BT474 (HER2-positive), SKBR3 (HER2-positive), MDA-MB-468 (triple negative, TN), MDA-MB-231 (TN) and BT549 (TN). RESULTS The model successfully classified the trajectories within individual cell lines with 83% accuracy and predicted receptor status with 85% accuracy. To further validate the method, epithelial-mesenchymal transition (EMT) was induced in benign MCF10A cells, noninvasive MCF7 cancer cells and highly invasive MDA-MB-231 cancer cells, and EGFR trajectories from these cells were tested. As expected, after EMT induction, both MCF10A and MCF7 cells showed higher rates of classification as TN cells, but not the MDA-MB-231 cells. Whereas deep learning-based cancer cell classifications are primarily based on the optical transmission images of cell morphology and the fluorescence images of cell organelles or cytoskeletal structures, here we demonstrated an alternative way to classify cancer cells using a dynamic, biophysical feature that is readily accessible. AVAILABILITY AND IMPLEMENTATION A python implementation of deep learning-based classification can be found at https://github.com/soonwoohong/Deep-learning-for-EGFR-trajectory-classification. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Thomas E Yankeelov
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712, USA,Oden Institute for Computational Engineering and Science, The University of Texas at Austin, TX 78712, USA,Department of Diagnostic Medicine, The University of Texas at Austin, TX 78712, USA,Department of Oncology, The University of Texas at Austin, TX 78712, USA,Livestrong Cancer Institutes, The University of Texas at Austin, TX 78712, USA
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Detecting Transient Trapping from a Single Trajectory: A Structural Approach. ENTROPY 2021; 23:e23081044. [PMID: 34441183 PMCID: PMC8394669 DOI: 10.3390/e23081044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 11/21/2022]
Abstract
In this article, we introduce a new method to detect transient trapping events within a single particle trajectory, thus allowing the explicit accounting of changes in the particle’s dynamics over time. Our method is based on new measures of a smoothed recurrence matrix. The newly introduced set of measures takes into account both the spatial and temporal structure of the trajectory. Therefore, it is adapted to study short-lived trapping domains that are not visited by multiple trajectories. Contrary to most existing methods, it does not rely on using a window, sliding along the trajectory, but rather investigates the trajectory as a whole. This method provides useful information to study intracellular and plasma membrane compartmentalisation. Additionally, this method is applied to single particle trajectory data of β2-adrenergic receptors, revealing that receptor stimulation results in increased trapping of receptors in defined domains, without changing the diffusion of free receptors.
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14
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Hernández-Adame PL, Meza U, Rodríguez-Menchaca AA, Sánchez-Armass S, Ruiz-García J, Gomez E. Determination of the size of lipid rafts studied through single-molecule FRET simulations. Biophys J 2021; 120:2287-2295. [PMID: 33864789 DOI: 10.1016/j.bpj.2021.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/16/2021] [Accepted: 04/08/2021] [Indexed: 11/16/2022] Open
Abstract
Fluorescence resonance energy transfer (FRET) is a high-resolution technique that allows the characterization of spatial and temporal properties of biological structures and mechanisms. In this work, we developed an in silico single-molecule FRET methodology to study the dynamics of fluorophores inside lipid rafts. We monitored the fluorescence of a single acceptor molecule in the presence of several donor molecules. By looking at the average fluorescence, we selected events with single acceptor and donor molecules, and we used them to determine the raft size in the range of 5-16 nm. We conclude that our method is robust and insensitive to variations in the diffusion coefficient, donor density, or selected fluorescence threshold.
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Affiliation(s)
| | - Ulises Meza
- Department of Physiology and Biophysics, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Aldo A Rodríguez-Menchaca
- Department of Physiology and Biophysics, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Sergio Sánchez-Armass
- Department of Physiology and Biophysics, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Jaime Ruiz-García
- Biological Physics Laboratory, Physics Institute, San Luis Potosí, Mexico.
| | - Eduardo Gomez
- Biological Physics Laboratory, Physics Institute, San Luis Potosí, Mexico.
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15
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Mashanov GI, Nenasheva TA, Mashanova T, Maclachlan C, Birdsall NJM, Molloy JE. A method for imaging single molecules at the plasma membrane of live cells within tissue slices. J Gen Physiol 2020; 153:211598. [PMID: 33326014 PMCID: PMC7748802 DOI: 10.1085/jgp.202012657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/21/2020] [Accepted: 11/20/2020] [Indexed: 02/04/2023] Open
Abstract
Recent advances in light microscopy allow individual biological macromolecules to be visualized in the plasma membrane and cytosol of live cells with nanometer precision and ∼10-ms time resolution. This allows new discoveries to be made because the location and kinetics of molecular interactions can be directly observed in situ without the inherent averaging of bulk measurements. To date, the majority of single-molecule imaging studies have been performed in either unicellular organisms or cultured, and often chemically fixed, mammalian cell lines. However, primary cell cultures and cell lines derived from multi-cellular organisms might exhibit different properties from cells in their native tissue environment, in particular regarding the structure and organization of the plasma membrane. Here, we describe a simple approach to image, localize, and track single fluorescently tagged membrane proteins in freshly prepared live tissue slices and demonstrate how this method can give information about the movement and localization of a G protein–coupled receptor in cardiac tissue slices. In principle, this experimental approach can be used to image the dynamics of single molecules at the plasma membrane of many different soft tissue samples and may be combined with other experimental techniques.
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Affiliation(s)
| | - Tatiana A Nenasheva
- Russian Academy of Science, Koltzov Institute of Developmental Biology, Moscow, Russia
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17
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Ren A, Lu D, Wong E, Hauwiller MR, Alivisatos AP, Ren G. Real-time observation of dynamic structure of liquid-vapor interface at nanometer resolution in electron irradiated sodium chloride crystals. Sci Rep 2020; 10:8596. [PMID: 32451405 PMCID: PMC7248077 DOI: 10.1038/s41598-020-65274-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 04/30/2020] [Indexed: 01/29/2023] Open
Abstract
The dynamics and structure of the liquid and vapor interface has remained elusive for decades due to the lack of an effective tool for directly visualization beyond micrometer resolution. Here, we designed a simple liquid-cell for encapsulating the liquid state of sodium for transmission electron microscopic (TEM) observation. The real-time dynamic structure of the liquid-vapor interface was imaged and videoed by TEM on the sample of electron irradiated sodium chloride (NaCl) crystals, a well-studied sample with low melting temperature and quantum super-shells of clusters. The nanometer resolution images exhibit the fine structures of the capillary waves, composed of first-time observed three zones of structures and features, i.e. flexible nanoscale fibers, nanoparticles/clusters, and a low-pressure area that sucks the nanoparticles from the liquid to the interface. Although the phenomenons were observed based on irradiated NaCl crystals, the similarities of the phenomenons to predictions suggest our real-time ovserved dynamic structure might be useful in validating long-debated theoretical models of the liquid-vapor interface, and enhancing our knowledge in understanding the non-equilibrium thermodynamics of the liquid-vapor interface to benefit future engineering designs in microfluidics.
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Affiliation(s)
- Amy Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The Department of Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - David Lu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The Department of Chemistry, Brown University, Providence, RI, 02912, USA
| | - Edward Wong
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Matthew R Hauwiller
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Department of Materials Science, University of California, Berkeley, CA, 94720, USA
- Kavli Energy NanoScience Institute, University of California, Berkeley, CA, 94720, USA
| | - A Paul Alivisatos
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Department of Materials Science, University of California, Berkeley, CA, 94720, USA
- Kavli Energy NanoScience Institute, University of California, Berkeley, CA, 94720, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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18
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Grassi S, Giussani P, Mauri L, Prioni S, Sonnino S, Prinetti A. Lipid rafts and neurodegeneration: structural and functional roles in physiologic aging and neurodegenerative diseases. J Lipid Res 2020; 61:636-654. [PMID: 31871065 PMCID: PMC7193971 DOI: 10.1194/jlr.tr119000427] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/11/2019] [Indexed: 12/14/2022] Open
Abstract
Lipid rafts are small, dynamic membrane areas characterized by the clustering of selected membrane lipids as the result of the spontaneous separation of glycolipids, sphingolipids, and cholesterol in a liquid-ordered phase. The exact dynamics underlying phase separation of membrane lipids in the complex biological membranes are still not fully understood. Nevertheless, alterations in the membrane lipid composition affect the lateral organization of molecules belonging to lipid rafts. Neural lipid rafts are found in brain cells, including neurons, astrocytes, and microglia, and are characterized by a high enrichment of specific lipids depending on the cell type. These lipid rafts seem to organize and determine the function of multiprotein complexes involved in several aspects of signal transduction, thus regulating the homeostasis of the brain. The progressive decline of brain performance along with physiological aging is at least in part associated with alterations in the composition and structure of neural lipid rafts. In addition, neurodegenerative conditions, such as lysosomal storage disorders, multiple sclerosis, and Parkinson's, Huntington's, and Alzheimer's diseases, are frequently characterized by dysregulated lipid metabolism, which in turn affects the structure of lipid rafts. Several events underlying the pathogenesis of these diseases appear to depend on the altered composition of lipid rafts. Thus, the structure and function of lipid rafts play a central role in the pathogenesis of many common neurodegenerative diseases.jlr;61/5/636/F1F1f1.
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Affiliation(s)
- Sara Grassi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Paola Giussani
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Laura Mauri
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Simona Prioni
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Sandro Sonnino
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Alessandro Prinetti
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy. mailto:
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19
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Kulenkampff K, Lippert AH, McColl J, Santos AM, Ponjavic A, Jenkins E, Humphrey J, Winkel A, Franze K, Lee SF, Davis SJ, Klenerman D. The Costs of Close Contacts: Visualizing the Energy Landscape of Cell Contacts at the Nanoscale. Biophys J 2020; 118:1261-1269. [PMID: 32075748 PMCID: PMC7091464 DOI: 10.1016/j.bpj.2020.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/27/2022] Open
Abstract
Cell-cell contacts often underpin signaling between cells. For immunology, the binding of a T cell receptor to an antigen-presenting pMHC initiates downstream signaling and an immune response. Although this contact is mediated by proteins on both cells creating interfaces with gap sizes typically around 14 nm, many, often contradictory observations have been made regarding the influence of the contact on parameters such as the binding kinetics, spatial distribution, and diffusion of signaling proteins within the contact. Understanding the basic physical constraints on probes inside this crowded environment will help inform studies on binding kinetics and dynamics of signaling of relevant proteins in the synapse. By tracking quantum dots of different dimensions for extended periods of time, we have shown that it is possible to obtain the probability of a molecule entering the contact, the change in its diffusion upon entry, and the impact of spatial heterogeneity of adhesion protein density in the contact. By analyzing the contacts formed by a T cell interacting with adhesion proteins anchored to a supported lipid bilayer, we find that probes are excluded from contact entry in a size-dependent manner for gap-to-probe differences of 4.1 nm. We also observed probes being trapped inside the contact and a decrease in diffusion of up to 85% in dense adhesion protein contacts. This approach provides new, to our knowledge, insights into the nature of cell-cell contacts, revealing that cell contacts are highly heterogeneous because of topography- and protein-density-related processes. These effects are likely to profoundly influence signaling between cells.
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Affiliation(s)
- Klara Kulenkampff
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Anna H Lippert
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - James McColl
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ana Mafalda Santos
- Radcliffe Department of Medicine and MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Aleks Ponjavic
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Edward Jenkins
- Radcliffe Department of Medicine and MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Jane Humphrey
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexander Winkel
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Kristian Franze
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Simon J Davis
- Radcliffe Department of Medicine and MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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20
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Abstract
In recent decades, single particle tracking (SPT) has been developed into a sophisticated analytical approach involving complex instruments and data analysis schemes to extract information from time-resolved particle trajectories. Very often, mobility-related properties are extracted from these particle trajectories, as they often contain information about local interactions experienced by the particles while moving through the sample. This tutorial aims to provide a comprehensive overview about the accuracies that can be achieved when extracting mobility-related properties from 2D particle trajectories and how these accuracies depend on experimental parameters. Proper interpretation of SPT data requires an assessment of whether the obtained accuracies are sufficient to resolve the effect under investigation. This is demonstrated by calculating mean square displacement curves that show an apparent super- or subdiffusive behavior due to poor measurement statistics instead of the presence of true anomalous diffusion. Furthermore, the refinement of parameters involved in the design or analysis of SPT experiments is discussed and an approach is proposed in which square displacement distributions are inspected to evaluate the quality of SPT data and to extract information about the maximum distance over which particles should be tracked during the linking process.
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21
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Mancebo A, DeMars L, Ertsgaard CT, Puchner EM. Precisely calibrated and spatially informed illumination for conventional fluorescence and improved PALM imaging applications. Methods Appl Fluoresc 2020; 8:025004. [PMID: 31995796 DOI: 10.1088/2050-6120/ab716a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Spatial light modulation using cost efficient digital micromirror devices (DMD) is finding broad applications in fluorescence microscopy due to the reduction of phototoxicity and bleaching and the ability to manipulate proteins in optogenetic experiments. However, precise illumination by DMDs and their application to single-molecule localization microscopy (SMLM) remained a challenge because of non-linear distortions between the DMD and camera coordinate systems caused by optical components in the excitation and emission path. Here we develop a fast and easy to implement calibration procedure that determines these distortions and matches the DMD and camera coordinate system with a precision below the optical diffraction limit. As a result, a region from a fluorescence image can be selected with a higher precision for illumination compared to a rigid transformation allowed by manual alignment of the DMD. We first demonstrate the application of our precisely calibrated light modulation by performing a proof of concept fluorescence recovery after photobleaching experiment with the endoplasmic reticulum-localized protein IRE1 fused to GFP in budding yeast (S. cerevisiae). Next, we develop a spatially informed photoactivation approach for SMLM in which only regions of the cell that contain photoactivatable fluorescent proteins are selected for photoactivation. The reduced exposure of the cells to 405 nm light increased the possible imaging time by 44% until phototoxic effects cause a dominant fluorescence background and a change in cell morphology. As a result, the mean number of reliable single-molecule localizations was also significantly increased by 28%. Since the localization precision and the ability for single-molecule tracking is not altered compared to traditional photoactivation of the entire field of view, spatially informed photoactivation significantly improves the quality of SMLM images and single-molecule tracking data. Our precise calibration method therefore lays the foundation for improved SMLM with active feedback photoactivation far beyond the applications in this work.
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Affiliation(s)
- Angel Mancebo
- School of Physics and Astronomy, University of Minnesota, Physics and Nanotechnology, 115 Union St. SE, Minneapolis, MN 55455, United States of America
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22
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Falcao RC, Coombs D. Diffusion analysis of single particle trajectories in a Bayesian nonparametrics framework. Phys Biol 2020; 17:025001. [DOI: 10.1088/1478-3975/ab64b3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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23
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Qin X, Liu L, Lee SK, Alsina A, Liu T, Wu C, Park H, Yu C, Kim H, Chu J, Triller A, Tang BZ, Hyeon C, Park CY, Park H. Increased Confinement and Polydispersity of STIM1 and Orai1 after Ca 2+ Store Depletion. Biophys J 2019; 118:70-84. [PMID: 31818466 DOI: 10.1016/j.bpj.2019.11.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 12/18/2022] Open
Abstract
STIM1 (a Ca2+ sensor in the endoplasmic reticulum (ER) membrane) and Orai1 (a pore-forming subunit of the Ca2+-release-activated calcium channel in the plasma membrane) diffuse in the ER membrane and plasma membrane, respectively. Upon depletion of Ca2+ stores in the ER, STIM1 translocates to the ER-plasma membrane junction and binds Orai1 to trigger store-operated Ca2+ entry. However, the motion of STIM1 and Orai1 during this process and its roles to Ca2+ entry is poorly understood. Here, we report real-time tracking of single STIM1 and Orai1 particles in the ER membrane and plasma membrane in living cells before and after Ca2+ store depletion. We found that the motion of single STIM1 and Orai1 particles exhibits anomalous diffusion both before and after store depletion, and their mobility-measured by the radius of gyration of the trajectories, mean-square displacement, and generalized diffusion coefficient-decreases drastically after store depletion. We also found that the measured displacement distribution is non-Gaussian, and the non-Gaussian parameter drastically increases after store depletion. Detailed analyses and simulations revealed that single STIM1 and Orai1 particles are confined in the compartmentalized membrane both before and after store depletion, and the changes in the motion after store depletion are explained by increased confinement and polydispersity of STIM1-Orai1 complexes formed at the ER-plasma membrane junctions. Further simulations showed that this increase in the confinement and polydispersity after store depletion localizes a rapid increase of Ca2+ influx, which can facilitate the rapid activation of local Ca2+ signaling pathways and the efficient replenishing of Ca2+ store in the ER in store-operated Ca2+ entry.
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Affiliation(s)
- Xianan Qin
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Lei Liu
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
| | - Sang Kwon Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Adolfo Alsina
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Teng Liu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | | | - Hojeong Park
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | | | - Hajin Kim
- Department of Biomedical Engineering and Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Jun Chu
- Research Lab for Biomedical Optics and Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Antoine Triller
- Biologie Cellulaire de la Synapse N&P, IBENS, Institut de Biologie de L'ENS, Ecole Normale Supérieure, Paris, France
| | - Ben Zhong Tang
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Department of Chemistry, Kowloon, Hong Kong, China, Kowloon, Hong Kong, China
| | - Changbong Hyeon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.
| | - Chan Young Park
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea.
| | - Hyokeun Park
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Division of Life Science; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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24
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Hirsch M, Wareham R, Yoon JW, Rolfe DJ, Zanetti-Domingues LC, Hobson MP, Parker PJ, Martin-Fernandez ML, Singh SS. A global sampler of single particle tracking solutions for single molecule microscopy. PLoS One 2019; 14:e0221865. [PMID: 31658271 PMCID: PMC6816549 DOI: 10.1371/journal.pone.0221865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 08/16/2019] [Indexed: 12/11/2022] Open
Abstract
The dependence on model-fitting to evaluate particle trajectories makes it difficult for single particle tracking (SPT) to resolve the heterogeneous molecular motions typical of cells. We present here a global spatiotemporal sampler for SPT solutions using a Metropolis-Hastings algorithm. The sampler does not find just the most likely solution but also assesses its likelihood and presents alternative solutions. This enables the estimation of the tracking error. Furthermore the algorithm samples the parameters that govern the tracking process and therefore does not require any tweaking by the user. We demonstrate the algorithm on synthetic and single molecule data sets. Metrics for the comparison of SPT are generalised to be applied to a SPT sampler. We illustrate using the example of the diffusion coefficient how the distribution of the tracking solutions can be propagated into a distribution of derived quantities. We also discuss the major challenges that are posed by the realisation of a SPT sampler.
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Affiliation(s)
- Michael Hirsch
- Central Laser Facility, Science and Technologies Facilities Council, UK Research and Innovation, Didcot, Oxfordshire, United Kingdom
| | - Richard Wareham
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Ji W. Yoon
- Center for Information Security Technology, Korea University, Seoul, South Korea
| | - Daniel J. Rolfe
- Central Laser Facility, Science and Technologies Facilities Council, UK Research and Innovation, Didcot, Oxfordshire, United Kingdom
| | - Laura C. Zanetti-Domingues
- Central Laser Facility, Science and Technologies Facilities Council, UK Research and Innovation, Didcot, Oxfordshire, United Kingdom
| | - Michael P. Hobson
- Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Peter J. Parker
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
- Protein Phosphorylation Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Marisa L. Martin-Fernandez
- Central Laser Facility, Science and Technologies Facilities Council, UK Research and Innovation, Didcot, Oxfordshire, United Kingdom
| | - Sumeetpal S. Singh
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
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25
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Huang T, Phelps C, Wang J, Lin LJ, Bittel A, Scott Z, Jacques S, Gibbs SL, Gray JW, Nan X. Simultaneous Multicolor Single-Molecule Tracking with Single-Laser Excitation via Spectral Imaging. Biophys J 2019; 114:301-310. [PMID: 29401428 DOI: 10.1016/j.bpj.2017.11.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/11/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022] Open
Abstract
Single-molecule tracking (SMT) offers rich information on the dynamics of underlying biological processes, but multicolor SMT has been challenging due to spectral cross talk and a need for multiple laser excitations. Here, we describe a single-molecule spectral imaging approach for live-cell tracking of multiple fluorescent species at once using a single-laser excitation. Fluorescence signals from all the molecules in the field of view are collected using a single objective and split between positional and spectral channels. Images of the same molecule in the two channels are then combined to determine both the location and the identity of the molecule. The single-objective configuration of our approach allows for flexible sample geometry and the use of a live-cell incubation chamber required for live-cell SMT. Despite a lower photon yield, we achieve excellent spatial (20-40 nm) and spectral (10-15 nm) resolutions comparable to those obtained with dual-objective, spectrally resolved Stochastic Optical Reconstruction Microscopy. Furthermore, motions of the fluorescent molecules did not cause loss of spectral resolution owing to the dual-channel spectral calibration. We demonstrate SMT in three (and potentially more) colors using spectrally proximal fluorophores and single-laser excitation, and show that trajectories of each species can be reliably extracted with minimal cross talk.
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Affiliation(s)
- Tao Huang
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Carey Phelps
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Jing Wang
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Li-Jung Lin
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Amy Bittel
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Zubenelgenubi Scott
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Steven Jacques
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Summer L Gibbs
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Joe W Gray
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Xiaolin Nan
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.
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26
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Taylor RD, Heine M, Emptage NJ, Andreae LC. Neuronal Receptors Display Cytoskeleton-Independent Directed Motion on the Plasma Membrane. iScience 2018; 10:234-244. [PMID: 30557785 PMCID: PMC6297241 DOI: 10.1016/j.isci.2018.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/25/2018] [Accepted: 11/30/2018] [Indexed: 11/19/2022] Open
Abstract
Directed transport of transmembrane proteins is generally believed to occur via intracellular transport vesicles. However, using single-particle tracking in rat hippocampal neurons with a pH-sensitive quantum dot probe that specifically reports surface movement of receptors, we have identified a subpopulation of neuronal EphB2 receptors that exhibit directed motion between synapses within the plasma membrane itself. This receptor movement occurs independently of the cytoskeleton but is dependent on cholesterol and is regulated by neuronal activity.
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Affiliation(s)
- Ruth D Taylor
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Martin Heine
- Leibniz Institute of Neurobiology, Research Group Molecular Physiology, Brenneckestrasse 6, Magdeburg 39118, Germany; Otto von Guericke University Magdeburg, Center for Behavioral Brain Sciences (CBBS), Universitätsplatz 2, Magdeburg 39106, Germany; Johannes Gutenberg University Mainz, Institute for Developmental Biology and Neurobiology, AG Funktional Neurobiology, Hanns-Dieter-Hüsch Weg 15, Mainz 55128, Germany
| | - Nigel J Emptage
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK.
| | - Laura C Andreae
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK.
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27
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Zhong Y, Wang G. Three-Dimensional Heterogeneous Structure Formation on a Supported Lipid Bilayer Disclosed by Single-Particle Tracking. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11857-11865. [PMID: 30170491 DOI: 10.1021/acs.langmuir.8b01690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Three-dimensional (3D) single-particle tracking was employed to study the lipid membrane morphology change at different pHs on glass supported lipid bilayers (SLBs) [1,2-dioleoyl- sn-glycero-3-phosphoethanolamine/1,2-dioleoyl- sn-glycero-3-phospho-l-serine (sodium salt)/1,2-dioleoyl- sn-glycero-3-phosphocholine = 5:3:2]. Fluorescently tagged, carboxylated polystyrene nanoparticles (of 100 nm) were used as the probes. At neutral pHs, the particles' diffusion was close to two-dimensional Brownian motion, indicating a mainly planar structure of the SLBs. When the environmental pH was tuned to be basic at 10.0, transiently confined diffusions within small areas were frequently observed. These confinements had a lateral dimension of 100-200 nm. Most interestingly, they showed 3D bulged structures protruding from the planar lipid bilayer. The particles were trapped by these 3D structures for a short period of time (∼0.75 s), with an estimated escape activation energy of ∼4.2 kB T. Nonuniform distribution of pH-sensitive lipids in the membrane was proposed to explain the formation of these 3D heterogeneous structures. This work suggests that the geometry of the 3D lipid structures can play a role in tuning the particle-lipid surface interactions. It sheds new light on the origin of lateral heterogeneity on the lipid membrane.
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Affiliation(s)
- Yaning Zhong
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695-8204 , United States
| | - Gufeng Wang
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695-8204 , United States
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28
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Fathizadeh A, Elber R. A mixed alchemical and equilibrium dynamics to simulate heterogeneous dense fluids: Illustrations for Lennard-Jones mixtures and phospholipid membranes. J Chem Phys 2018; 149:072325. [PMID: 30134684 PMCID: PMC6018062 DOI: 10.1063/1.5027078] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
An algorithm to efficiently simulate multi-component fluids is proposed and illustrated. The focus is on biological membranes that are heterogeneous and challenging to investigate quantitatively. To achieve rapid equilibration of spatially inhomogeneous fluids, we mix conventional molecular dynamics simulations with alchemical trajectories. The alchemical trajectory switches the positions of randomly selected pairs of molecules and plays the role of an efficient Monte Carlo move. It assists in accomplishing rapid spatial de-correlations. Examples of phase separation and mixing are given in two-dimensional binary Lennard-Jones fluid and a DOPC-POPC membrane. The performance of the algorithm is analyzed, and tools to maximize its efficiency are provided. It is concluded that the algorithm is vastly superior to conventional molecular dynamics for the equilibrium study of biological membranes.
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Affiliation(s)
- Arman Fathizadeh
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ron Elber
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
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29
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Fülöp G, Brameshuber M, Arnold AM, Schütz GJ, Sevcsik E. Determination of the Membrane Environment of CD59 in Living Cells. Biomolecules 2018; 8:E28. [PMID: 29772810 PMCID: PMC6023084 DOI: 10.3390/biom8020028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/24/2018] [Accepted: 05/14/2018] [Indexed: 11/24/2022] Open
Abstract
The organization and dynamics of proteins and lipids in the plasma membrane, and their role in membrane functionality, have been subject of a long-lasting debate. Specifically, it is unclear to what extent membrane proteins are affected by their immediate lipid environment and vice versa. Studies on model membranes and plasma membrane vesicles indicated preferences of proteins for lipid phases characterized by different acyl chain order; however, whether such phases do indeed exist in live cells is still not known. Here, we refine a previously developed micropatterning approach combined with single molecule tracking to quantify the influence of the glycosylphosphatidylinositol-anchored (GPI-anchored) protein CD59 on its molecular environment directly in the live cell plasma membrane. We find that locally enriched and immobilized CD59 presents obstacles to the diffusion of fluorescently labeled lipids with a different phase-partitioning behavior independent of cell cholesterol levels and type of lipid. Our results give no evidence for either specific binding of the lipids to CD59 or the existence of nanoscopic ordered membrane regions associated with CD59.
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Affiliation(s)
- Gergő Fülöp
- Institute of Applied Physics, TU Wien, Wiedner Hauptstrasse 8-10, Vienna 1040, Austria.
| | - Mario Brameshuber
- Institute of Applied Physics, TU Wien, Wiedner Hauptstrasse 8-10, Vienna 1040, Austria.
| | - Andreas M Arnold
- Institute of Applied Physics, TU Wien, Wiedner Hauptstrasse 8-10, Vienna 1040, Austria.
| | - Gerhard J Schütz
- Institute of Applied Physics, TU Wien, Wiedner Hauptstrasse 8-10, Vienna 1040, Austria.
| | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Wiedner Hauptstrasse 8-10, Vienna 1040, Austria.
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Yeager AN, Weber PK, Kraft ML. Cholesterol is enriched in the sphingolipid patches on the substrate near nonpolarized MDCK cells, but not in the sphingolipid domains in their plasma membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2004-2011. [PMID: 29684331 DOI: 10.1016/j.bbamem.2018.04.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 03/15/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022]
Abstract
Information about the distributions of cholesterol and sphingolipids within the plasma membranes of mammalian cells provides insight into the roles of these molecules in membrane function. In this report, high-resolution secondary ion mass spectrometry was used to image the distributions of metabolically incorporated rare isotope-labeled sphingolipids and cholesterol on the surfaces of nonpolarized epithelial cells. Sphingolipid domains that were not enriched with cholesterol were detected in the plasma membranes of subconfluent Madin-Darby canine kidney cells. Surprisingly, cholesterol-enriched sphingolipid patches were observed on the substrate adjacent to these cells. Based on the shapes of these cholesterol-enriched sphingolipid patches on the substrate and their proximity to cellular projections, we hypothesize that they are deposits of membranous particles released by the cell.
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Affiliation(s)
- Ashley N Yeager
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL 61801, United States
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, United States
| | - Mary L Kraft
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL 61801, United States.
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31
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Eckstein J, Holzhütter HG, Berndt N. The importance of membrane microdomains for bile salt-dependent biliary lipid secretion. J Cell Sci 2018; 131:jcs211524. [PMID: 29420298 PMCID: PMC5897720 DOI: 10.1242/jcs.211524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022] Open
Abstract
Alternative models explaining the biliary lipid secretion at the canalicular membrane of hepatocytes exist: successive lipid extraction by preformed bile salt micelles, or budding of membrane fragments with formation of mixed micelles. To test the feasibility of the latter mechanism, we developed a mathematical model that describes the formation of lipid microdomains in the canalicular membrane. Bile salt monomers intercalate into the external hemileaflet of the canalicular membrane, to form a rim to liquid disordered domain patches that then pinch off to form nanometer-scale mixed micelles. Model simulations perfectly recapitulate the measured dependence of bile salt-dependent biliary lipid extraction rates upon modulation of the membrane cholesterol (lack or overexpression of the cholesterol transporter Abcg5-Abcg8) and phosphatidylcholine (lack of Mdr2, also known as Abcb4) content. The model reveals a strong dependence of the biliary secretion rate on the protein density of the membrane. Taken together, the proposed model is consistent with crucial experimental findings in the field and provides a consistent explanation of the central molecular processes involved in bile formation.
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Affiliation(s)
- Johannes Eckstein
- Charité - Universitätsmedizin Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
| | - Hermann-Georg Holzhütter
- Charité - Universitätsmedizin Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
| | - Nikolaus Berndt
- Charité - Universitätsmedizin Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
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32
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Gonzalez Porras MA, Durfee P, Giambini S, Sieck GC, Brinker CJ, Mantilla CB. Uptake and intracellular fate of cholera toxin subunit b-modified mesoporous silica nanoparticle-supported lipid bilayers (aka protocells) in motoneurons. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:661-672. [PMID: 29339186 DOI: 10.1016/j.nano.2018.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/30/2017] [Accepted: 01/02/2018] [Indexed: 02/02/2023]
Abstract
Cholera toxin B (CTB) modified mesoporous silica nanoparticle supported lipid bilayers (CTB-protocells) are a promising, customizable approach for targeting therapeutic cargo to motoneurons. In the present study, the endocytic mechanism and intracellular fate of CTB-protocells in motoneurons were examined to provide information for the development of therapeutic application and cargo delivery. Pharmacological inhibitors elucidated CTB-protocells endocytosis to be dependent on the integrity of lipid rafts and macropinocytosis. Using immunofluorescence techniques, live confocal and transmission electron microscopy, CTB-protocells were primarily found in the cytosol, membrane lipid domains and Golgi. There was no difference in the amount of motoneuron activity dependent uptake of CTB-protocells in neuromuscular junctions, consistent with clathrin activation at the axon terminals during low frequency activity. In conclusion, CTB-protocells uptake is mediated principally by lipid rafts and macropinocytosis. Once internalized, CTB-protocells escape lysosomal degradation, and engage biological pathways that are not readily accessible by untargeted delivery methods.
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Affiliation(s)
- Maria A Gonzalez Porras
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, United States
| | - Paul Durfee
- Center for Micro-Engineered Materials, University of New, Mexico
| | - Sebastian Giambini
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, United States
| | - Gary C Sieck
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, United States; Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - C Jeffrey Brinker
- Center for Micro-Engineered Materials, University of New, Mexico; Department of Chemical and Biological Engineering University of New, Mexico; Department of Molecular Genetics and Microbiology University of New, Mexico; Self-Assembled Materials Department, Sandia National Laboratories, Albuquerque, New, Mexico
| | - Carlos B Mantilla
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, United States; Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States.
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33
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Winkler PM, Regmi R, Flauraud V, Brugger J, Rigneault H, Wenger J, García-Parajo MF. Optical Antenna-Based Fluorescence Correlation Spectroscopy to Probe the Nanoscale Dynamics of Biological Membranes. J Phys Chem Lett 2018; 9:110-119. [PMID: 29240442 DOI: 10.1021/acs.jpclett.7b02818] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The plasma membrane of living cells is compartmentalized at multiple spatial scales ranging from the nano- to the mesoscale. This nonrandom organization is crucial for a large number of cellular functions. At the nanoscale, cell membranes organize into dynamic nanoassemblies enriched by cholesterol, sphingolipids, and certain types of proteins. Investigating these nanoassemblies known as lipid rafts is of paramount interest in fundamental cell biology. However, this goal requires simultaneous nanometer spatial precision and microsecond temporal resolution, which is beyond the reach of common microscopes. Optical antennas based on metallic nanostructures efficiently enhance and confine light into nanometer dimensions, breaching the diffraction limit of light. In this Perspective, we discuss recent progress combining optical antennas with fluorescence correlation spectroscopy (FCS) to monitor microsecond dynamics at nanoscale spatial dimensions. These new developments offer numerous opportunities to investigate lipid and protein dynamics in both mimetic and native biological membranes.
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Affiliation(s)
- Pamina M Winkler
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
| | - Raju Regmi
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel , Marseille, France
| | - Valentin Flauraud
- Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Jürgen Brugger
- Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Hervé Rigneault
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel , Marseille, France
| | - Jérôme Wenger
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel , Marseille, France
| | - María F García-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
- ICREA , Pg. Lluís Companys 23, 08010 Barcelona, Spain
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34
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Motegi T, Yamazaki K, Ogino T, Tero R. Substrate-Induced Structure and Molecular Dynamics in a Lipid Bilayer Membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:14748-14755. [PMID: 29236511 DOI: 10.1021/acs.langmuir.7b03212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The solid-substrate-dependent structure and dynamics of molecules in a supported lipid bilayer (SLB) were directly investigated via atomic force microscopy (AFM) and single particle tracking (SPT) measurements. The appearance of either vertical or horizontal heterogeneities in the SLB was found to be strongly dependent on the underlying substrates. SLB has been widely used as a biointerface with incorporated proteins and other biological materials. Both silica and mica are popular substrates for SLB. Using single-molecule dynamics, the fluidity of the upper and lower membrane leaflets was found to depend on the substrate, undergoing coupling and decoupling on the SiO2/Si and mica substrates, respectively. The anisotropic diffusion caused by the locally destabilized structure of the SLB at atomic steps appeared on the Al2O3(0001) substrate because of the strong van der Waals interaction between the SLB and the substrate. Our finding that the well-defined surfaces of mica and sapphire result in asymmetry and anisotropy in the plasma membrane is useful for the design of new plasma-membrane-mimetic systems. The application of well-defined supporting substrates for SLBs should have similar effects as cell membrane scaffolds, which regulate the dynamic structure of the membrane.
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Affiliation(s)
| | - Kenji Yamazaki
- Division of Applied Physics, Graduate School of Engineering, Hokkaido University , Sapporo 060-8628, Japan
| | - Toshio Ogino
- Department of Engineering, Yokohama National University , Yokohama 240-8501, Japan
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35
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Regmi R, Winkler PM, Flauraud V, Borgman KJE, Manzo C, Brugger J, Rigneault H, Wenger J, García-Parajo MF. Planar Optical Nanoantennas Resolve Cholesterol-Dependent Nanoscale Heterogeneities in the Plasma Membrane of Living Cells. NANO LETTERS 2017; 17:6295-6302. [PMID: 28926278 DOI: 10.1021/acs.nanolett.7b02973] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Optical nanoantennas can efficiently confine light into nanoscopic hotspots, enabling single-molecule detection sensitivity at biological relevant conditions. This innovative approach to breach the diffraction limit offers a versatile platform to investigate the dynamics of individual biomolecules in living cell membranes and their partitioning into cholesterol-dependent lipid nanodomains. Here, we present optical nanoantenna arrays with accessible surface hotspots to study the characteristic diffusion dynamics of phosphoethanolamine (PE) and sphingomyelin (SM) in the plasma membrane of living cells at the nanoscale. Fluorescence burst analysis and fluorescence correlation spectroscopy performed on nanoantennas of different gap sizes show that, unlike PE, SM is transiently trapped in cholesterol-enriched nanodomains of 10 nm diameter with short characteristic times around 100 μs. The removal of cholesterol led to the free diffusion of SM, consistent with the dispersion of nanodomains. Our results are consistent with the existence of highly transient and fluctuating nanoscale assemblies enriched by cholesterol and sphingolipids in living cell membranes, also known as lipid rafts. Quantitative data on sphingolipids partitioning into lipid rafts is crucial to understand the spatiotemporal heterogeneous organization of transient molecular complexes on the membrane of living cells at the nanoscale. The proposed technique is fully biocompatible and thus provides various opportunities for biophysics and live cell research to reveal details that remain hidden in confocal diffraction-limited measurements.
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Affiliation(s)
- Raju Regmi
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
- Aix Marseille Univ , CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - Pamina M Winkler
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
| | - Valentin Flauraud
- Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Kyra J E Borgman
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
| | - Jürgen Brugger
- Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Hervé Rigneault
- Aix Marseille Univ , CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - Jérôme Wenger
- Aix Marseille Univ , CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - María F García-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
- ICREA , Pg. Lluı́s Companys 23, 08010 Barcelona, Spain
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36
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Cao F, Gong X, He C, Ngai T. Removing the effect of blooming from potential energy measurement by employing total internal reflection microscopy integrated with video microscopy. J Colloid Interface Sci 2017; 503:142-149. [PMID: 28521216 DOI: 10.1016/j.jcis.2017.05.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/08/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
Abstract
Total internal reflection microscopy (TIRM) measures the interactions between a colloidal particle and a flat surface in aqueous solution. Recently, TIRM has further integrated with video microscopy (VM) and enabled the simultaneous measurements of multi-particle colloid-surface interactions in the same ensemble. However, there still remain challenges about accurate image acquisition due to blooming. Blooming means the number of photons reaching the detector exceeds its maximum capacity, and the excess photons will either spill to adjacent pixels or not be counted, leading to an obstacle from precise determination of intensity. Our result shows that blooming gives rise to a deviation of the measured potential energy from the classical theory of Derjaguin, Landau, Verway, and Overbeek (DLVO). Therefore, a correction method was developed in this work to deduce the real intensity from the experimental measurement. The relationship between scattered light intensity and exposure time deviates from linearity when blooming occurs. A correction equation was developed to recover the real intensity, which was then confirmed by the accordance between the corresponding potential energy profiles and the DLVO theory. This correction method is suitable for VM systems of colloidal probes illuminated by scattered light, broadening the application of VM imaging to investigate colloidal interactions.
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Affiliation(s)
- Feng Cao
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong.
| | - Xiangjun Gong
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, PR China.
| | - Chuanxin He
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518060, PR China.
| | - To Ngai
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong.
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37
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Plewes MR, Burns PD, Hyslop RM, George Barisas B. Influence of omega-3 fatty acids on bovine luteal cell plasma membrane dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2413-2419. [PMID: 28912100 DOI: 10.1016/j.bbamem.2017.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/09/2017] [Accepted: 09/10/2017] [Indexed: 01/07/2023]
Abstract
Fish oil is a rich source of omega-3 fatty acids which disrupt lipid microdomain structure and affect mobility of the prostaglandin F2α (FP) receptor in bovine luteal cells. The objectives of this study were to determine the effects of individual omega-3 fatty acids, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on 1) membrane fatty acid composition, 2) lipid microdomain structure, and 3) lateral mobility of the FP receptor in bovine luteal cells. Ovaries were collected from a local abattoir (n=5/experiment). The corpus luteum was resected and enzymatically digested using collagenase to generate a mixed luteal cell population. In all experiments, luteal cells were treated with 0, 1, 10 or 100μM EPA or DHA for 72h to allow incorporation of fatty acids into membrane lipids. Results from experiment 1 show that culturing luteal cells in the presence of EPA or DHA increased these luteal fatty acids. In experiment 2, both EPA and DHA increased spatial distribution of lipid microdomains in a dose-dependent manner. Single particle tracking results from experiment 3 show that increasing both EPA and DHA concentrations increased micro- and macro-diffusion coefficients, increased domain size, and decreased residence time of FP receptors. Collectively, results from this study demonstrate similar effects of EPA and DHA on lipid microdomain structure and lateral mobility of FP receptors in cultured bovine luteal cells. Moreover, only 10μM of either fatty acid was needed to mimic the effects of fish oil.
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Affiliation(s)
- Michele R Plewes
- School of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, United States
| | - Patrick D Burns
- School of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, United States.
| | - Richard M Hyslop
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO 80639, United States
| | - B George Barisas
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, United States
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38
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Bhatia T, Cornelius F, Ipsen JH. Capturing suboptical dynamic structures in lipid bilayer patches formed from free-standing giant unilamellar vesicles. Nat Protoc 2017; 12:1563-1575. [DOI: 10.1038/nprot.2017.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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39
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Plewes MR, Burns PD, Graham PE, Bruemmer JE, Engle TE, Barisas BG. Effect of fish meal supplementation on spatial distribution of lipid microdomains and on the lateral mobility of membrane-bound prostaglandin F 2α receptors in bovine corpora lutea. Domest Anim Endocrinol 2017; 60:9-18. [PMID: 28273497 PMCID: PMC5515082 DOI: 10.1016/j.domaniend.2017.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 12/25/2022]
Abstract
This study examined the effects of fish meal supplementation on spatial distribution of lipid microdomains and lateral mobility of prostaglandin F2α (FP) receptors on cell plasma membranes of the bovine corpus luteum (CL). Beef cows were stratified by BW and randomly assigned to receive a corn gluten meal supplement (n = 4) or fish meal supplement (n = 4) for 60 d to allow incorporation of fish meal-derived omega-3 fatty acids into luteal tissue. Ovaries bearing the CL were surgically removed between days 10 to 12 after estrus corresponding to approximately day 60 of supplementation. A 200-mg sample of luteal tissue was analyzed for fatty acid content using gas-liquid chromatography (GLC). The remaining tissue was enzymatically digested with collagenase to dissociate individual cells from the tissue. Cells were cultured to determine the effects of dietary supplementation on lipid microdomains and lateral mobility of FP receptors. Luteal tissue collected from fish meal-supplemented cows had increased omega-3 fatty acids content (P < 0.05). Lipid microdomain total fluorescent intensity was decreased in dissociated luteal cells from fish meal-supplemented cows (P < 0.05). Micro and macro diffusion coefficients of FP receptors were greater for cells obtained from fish meal-supplemented cows (P < 0.05). In addition, compartment diameter of domains was larger, whereas resident time was shorter for receptors from cells obtained from fish meal-supplemented cows (P < 0.05). Data indicate that dietary supplementation with fish meal increases omega-3 fatty acid content in luteal tissue causing disruption of lipid microdomains. This disruption leads to increased lateral mobility of the FP receptor, increased compartment sizes, and decreased resident time, which may influence prostaglandin signaling in the bovine CL.
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Affiliation(s)
- M R Plewes
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA
| | - P D Burns
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA.
| | - P E Graham
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA
| | - J E Bruemmer
- Department of Animal Sciences and Equine Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - T E Engle
- Department of Animal Sciences and Equine Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - B G Barisas
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, USA
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40
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Li L, Hu J, Shi X, Shao Y, Song F. Lipid rafts enhance the binding constant of membrane-anchored receptors and ligands. SOFT MATTER 2017; 13:4294-4304. [PMID: 28573272 DOI: 10.1039/c7sm00572e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Gaining insights into the binding of membrane-anchored receptors and ligands that mediate cell adhesion and signal transduction is of great significance for understanding numerous physiological processes driven by intercellular communication. Lipid rafts, microdomains in cell membranes enriched in cholesterol and saturated lipids such as sphingomyelin, are believed to serve as the essential platforms to recruit protein molecules for biological functions. An important question remains how the lipid rafts affect the binding constant of membrane-anchored receptors and ligands. We have investigated the adhesion of multicomponent membranes by using Monte Carlo simulations of a mesoscopic model with biologically relevant parameters. We find that the preferential partitioning of membrane-anchored receptor and ligand proteins in the lipid rafts significantly increases the binding constant of those proteins, in cooperation with the shape fluctuations of the membranes caused by thermal excitations. The binding constant can even be greater than that of the same receptors and ligands anchored to two apposing supported, planar membranes without shape fluctuations. The membrane shape fluctuations facilitate the binding of the anchored receptors and ligands, in contrast to the case of homogeneous membranes. Our results suggest that cells might regulate the binding of membrane-anchored receptor and ligand proteins by modulating the properties of lipid rafts such as area fraction, size and the affinity of rafts to the proteins.
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Affiliation(s)
- Long Li
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China.
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Kinetic disruption of lipid rafts is a mechanosensor for phospholipase D. Nat Commun 2016; 7:13873. [PMID: 27976674 PMCID: PMC5171650 DOI: 10.1038/ncomms13873] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/04/2016] [Indexed: 12/24/2022] Open
Abstract
The sensing of physical force, mechanosensation, underlies two of five human senses—touch and hearing. How transduction of force in a membrane occurs remains unclear. We asked if a biological membrane could employ kinetic energy to transduce a signal absent tension. Here we show that lipid rafts are dynamic compartments that inactivate the signalling enzyme phospholipase D2 (PLD2) by sequestering the enzyme from its substrate. Mechanical disruption of the lipid rafts activates PLD2 by mixing the enzyme with its substrate to produce the signalling lipid phosphatidic acid (PA). We calculate a latency time of <650 μs for PLD activation by mixing. Our results establish a fast, non-tension mechanism for mechanotransduction where disruption of ordered lipids initiates a mechanosensitive signal for cell growth through mechanical mixing.
Mechanosensation by biological membranes can be relayed by mechanical tension to ion channels. Here the authors show that phospholipase D (PLD) is activated by mechanical disruption of lipid rafts which allows PLD to mix with its substrate in the lipid membrane, and propose a kinetic model of force transduction.
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A novel approach for targeted delivery to motoneurons using cholera toxin-B modified protocells. J Neurosci Methods 2016; 273:160-174. [PMID: 27641118 DOI: 10.1016/j.jneumeth.2016.09.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 12/18/2022]
Abstract
BACKGROUND Trophic interactions between muscle fibers and motoneurons at the neuromuscular junction (NMJ) play a critical role in determining motor function throughout development, ageing, injury, or disease. Treatment of neuromuscular disorders is hindered by the inability to selectively target motoneurons with pharmacological and genetic interventions. NEW METHOD We describe a novel delivery system to motoneurons using mesoporous silica nanoparticles encapsulated within a lipid bilayer (protocells) and modified with the atoxic subunit B of the cholera toxin (CTB) that binds to gangliosides present on neuronal membranes. RESULTS CTB modified protocells showed significantly greater motoneuron uptake compared to unmodified protocells after 24h of treatment (60% vs. 15%, respectively). CTB-protocells showed specific uptake by motoneurons compared to muscle cells and demonstrated cargo release of a surrogate drug. Protocells showed a lack of cytotoxicity and unimpaired cellular proliferation. In isolated diaphragm muscle-phrenic nerve preparations, preferential axon terminal uptake of CTB-modified protocells was observed compared to uptake in surrounding muscle tissue. A larger proportion of axon terminals displayed uptake following treatment with CTB-protocells compared to unmodified protocells (40% vs. 6%, respectively). COMPARISON WITH EXISTING METHOD(S) Current motoneuron targeting strategies lack the functionality to load and deliver multiple cargos. CTB-protocells capitalizes on the advantages of liposomes and mesoporous silica nanoparticles allowing a large loading capacity and cargo release. The ability of CTB-protocells to target motoneurons at the NMJ confers a great advantage over existing methods. CONCLUSIONS CTB-protocells constitute a viable targeted motoneuron delivery system for drugs and genes facilitating various therapies for neuromuscular diseases.
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Levental I, Veatch S. The Continuing Mystery of Lipid Rafts. J Mol Biol 2016; 428:4749-4764. [PMID: 27575334 DOI: 10.1016/j.jmb.2016.08.022] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 12/12/2022]
Abstract
Since its initial formalization nearly 20 years ago, the concept of lipid rafts has generated a tremendous amount of attention and interest and nearly as much controversy. The controversy is perhaps surprising because the notion itself is intuitive: compartmentalization in time and space is a ubiquitous theme at all scales of biology, and therefore, the partitioning of cellular membranes into lateral subdivision should be expected. Nevertheless, the physicochemical principles responsible for compartmentalization and the molecular mechanisms by which they are functionalized remain nearly as mysterious today as they were two decades ago. Herein, we review recent literature on this topic with a specific focus on the major open questions in the field including: (1) what are the best tools to assay raft behavior in living membranes? (2) what is the function of the complex lipidome of mammalian cells with respect to membrane organization? (3) what are the mechanisms that drive raft formation and determine their properties? (4) how can rafts be modulated? (5) how is membrane compartmentalization integrated into cellular signaling? Despite decades of intensive research, this compelling field remains full of fundamental questions.
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Affiliation(s)
- Ilya Levental
- McGovern Medical School at the University of Texas Houston, Department of Integrative Biology and Pharmacology
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44
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Yeast ABC transporters in lipid trafficking. Fungal Genet Biol 2016; 93:25-34. [DOI: 10.1016/j.fgb.2016.05.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/28/2016] [Accepted: 05/31/2016] [Indexed: 12/31/2022]
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45
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Liu C, Liu YL, Perillo EP, Dunn AK, Yeh HC. Single-Molecule Tracking and Its Application in Biomolecular Binding Detection. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2016; 22:6804013. [PMID: 27660404 PMCID: PMC5028128 DOI: 10.1109/jstqe.2016.2568160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In the past two decades significant advances have been made in single-molecule detection, which enables the direct observation of single biomolecules at work in real time and under physiological conditions. In particular, the development of single-molecule tracking (SMT) microscopy allows us to monitor the motion paths of individual biomolecules in living systems, unveiling the localization dynamics and transport modalities of the biomolecules that support the development of life. Beyond the capabilities of traditional camera-based tracking techniques, state-of-the-art SMT microscopies developed in recent years can record fluorescence lifetime while tracking a single molecule in the 3D space. This multiparameter detection capability can open the door to a wide range of investigations at the cellular or tissue level, including identification of molecular interaction hotspots and characterization of association/dissociation kinetics between molecules. In this review, we discuss various SMT techniques developed to date, with an emphasis on our recent development of the next generation 3D tracking system that not only achieves ultrahigh spatiotemporal resolution but also provides sufficient working depth suitable for live animal imaging. We also discuss the challenges that current SMT techniques are facing and the potential strategies to tackle those challenges.
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Affiliation(s)
- Cong Liu
- University of Texas at Austin, Austin, TX 78703 USA
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46
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Duncan GA, Fairbrother DH, Bevan MA. Diffusing colloidal probes of cell surfaces. SOFT MATTER 2016; 12:4731-4738. [PMID: 27117575 DOI: 10.1039/c5sm02637g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Measurements and analyses are reported to quantify dynamic and equilibrium interactions between colloidal particles and live cell surfaces using dark field video microscopy. Two-dimensional trajectories of micron-sized polyethylene glycol (PEG)-coated silica colloids relative to adherent epithelial breast cancer cell perimeters are determined allowing measurement of position dependent diffusivities and interaction potentials. PEG was chosen as the material system of interest to assess non-specific interactions with cell surfaces and establishes a basis for investigation of specific interactions in future studies. Analysis of measured potential energies on cell surfaces reveals the spatial dependence in cell topography. With the measured cell topography and models for particle-cell surface hydrodynamic interactions, excellent agreement is obtained between theoretical and measured colloidal transport on cell surfaces. Quantitative analyses of association lifetimes showed that PEG coatings act to stabilize colloids above the cell surface through net repulsive, steric interactions. Our results demonstrate a self-consistent analysis of diffusing colloidal probe interactions due to conservative and non-conservative forces to characterize biophysical cell surface properties.
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47
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Woodsworth DJ, Dunsing V, Coombs D. Design Parameters for Granzyme-Mediated Cytotoxic Lymphocyte Target-Cell Killing and Specificity. Biophys J 2016; 109:477-88. [PMID: 26244730 DOI: 10.1016/j.bpj.2015.06.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 10/23/2022] Open
Abstract
Cytotoxic lymphocytes are key elements of the immune system that are primarily responsible for targeting cells infected with intracellular pathogens, or cells that have become malignantly transformed. Target cells are killed mainly via lymphocyte exocytosis of specialized lysosomes containing perforin, a pore-forming protein, and granzymes, which are proteases that induce apoptosis. Due to its central role in lymphocyte biology, as well as its implication in a host of pathologies from cancer to autoimmunity, the granzyme-perforin pathway has been the subject of extensive investigation. Nevertheless, the details of exactly how granzyme and perforin cooperate to induce target-cell death remain controversial. To further investigate this system, we developed a biophysical model of the immunological synapse between a cytotoxic lymphocyte and a target cell using a spatial stochastic simulation algorithm. We used this model to calculate the spatiotemporal evolution of granzyme B and perforin from the time of their exocytosis to granzyme internalization by the target cell. We used a metric of granzyme internalization to delineate which biological processes were critical for successful target-cell lysis. We found that the high aspect ratio of the immunological synapse was insufficient in this regard, and that molecular crowding within the synapse is critical to preserve sufficient concentrations of perforin and granzyme for consistent pore formation and granzyme transfer to target cells. However, even when pore formation occurs in our model, a large amount of both granzyme and perforin still escape from the synapse. We argue that a tight seal between the cytotoxic lymphocyte and its target cell is not required to avoid bystander killing. Instead, we propose that the requirement for spatiotemporal colocalization of granzyme and perforin acts as an effective bimolecular filter to ensure target specificity.
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Affiliation(s)
- Daniel J Woodsworth
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Valentin Dunsing
- Institut für Physik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Daniel Coombs
- Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, Canada.
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48
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Imaging approaches for analysis of cholesterol distribution and dynamics in the plasma membrane. Chem Phys Lipids 2016; 199:106-135. [PMID: 27016337 DOI: 10.1016/j.chemphyslip.2016.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/04/2016] [Indexed: 11/21/2022]
Abstract
Cholesterol is an important lipid component of the plasma membrane (PM) of mammalian cells, where it is involved in control of many physiological processes, such as endocytosis, cell migration, cell signalling and surface ruffling. In an attempt to explain these functions of cholesterol, several models have been put forward about cholesterol's lateral and transbilayer organization in the PM. In this article, we review imaging techniques developed over the last two decades for assessing the distribution and dynamics of cholesterol in the PM of mammalian cells. Particular focus is on fluorescence techniques to study the lateral and inter-leaflet distribution of suitable cholesterol analogues in the PM of living cells. We describe also several methods for determining lateral cholesterol dynamics in the PM including fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), single particle tracking (SPT) and spot variation FCS coupled to stimulated emission depletion (STED) microscopy. For proper interpretation of such measurements, we provide some background in probe photophysics and diffusion phenomena occurring in cell membranes. In particular, we show the equivalence of the reaction-diffusion approach, as used in FRAP and FCS, and continuous time random walk (CTRW) models, as often invoked in SPT studies. We also discuss mass spectrometry (MS) based imaging of cholesterol in the PM of fixed cells and compare this method with fluorescence imaging of sterols. We conclude that evidence from many experimental techniques converges towards a model of a homogeneous distribution of cholesterol with largely free and unhindered diffusion in both leaflets of the PM.
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49
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Munguira I, Casuso I, Takahashi H, Rico F, Miyagi A, Chami M, Scheuring S. Glasslike Membrane Protein Diffusion in a Crowded Membrane. ACS NANO 2016; 10:2584-90. [PMID: 26859708 DOI: 10.1021/acsnano.5b07595] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Many functions of the plasma membrane depend critically on its structure and dynamics. Observation of anomalous diffusion in vivo and in vitro using fluorescence microscopy and single particle tracking has advanced our concept of the membrane from a homogeneous fluid bilayer with freely diffusing proteins to a highly organized crowded and clustered mosaic of lipids and proteins. Unfortunately, anomalous diffusion could not be related to local molecular details given the lack of direct and unlabeled molecular observation capabilities. Here, we use high-speed atomic force microscopy and a novel analysis methodology to analyze the pore forming protein lysenin in a highly crowded environment and document coexistence of several diffusion regimes within one membrane. We show the formation of local glassy phases, where proteins are trapped in neighbor-formed cages for time scales up to 10 s, which had not been previously experimentally reported for biological membranes. Furthermore, around solid-like patches and immobile molecules a slower glass phase is detected leading to protein trapping and creating a perimeter of decreased membrane diffusion.
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Affiliation(s)
- Ignacio Munguira
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 avenue de Luminy, 13009 Marseille, France
| | - Ignacio Casuso
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 avenue de Luminy, 13009 Marseille, France
| | - Hirohide Takahashi
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 avenue de Luminy, 13009 Marseille, France
| | - Felix Rico
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 avenue de Luminy, 13009 Marseille, France
| | - Atsushi Miyagi
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 avenue de Luminy, 13009 Marseille, France
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel , Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Simon Scheuring
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 avenue de Luminy, 13009 Marseille, France
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50
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Fujiwara TK, Iwasawa K, Kalay Z, Tsunoyama TA, Watanabe Y, Umemura YM, Murakoshi H, Suzuki KGN, Nemoto YL, Morone N, Kusumi A. Confined diffusion of transmembrane proteins and lipids induced by the same actin meshwork lining the plasma membrane. Mol Biol Cell 2016; 27:1101-19. [PMID: 26864625 PMCID: PMC4814218 DOI: 10.1091/mbc.e15-04-0186] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 02/02/2016] [Indexed: 11/11/2022] Open
Abstract
Ultraspeed single-molecule tracking with <25-μs resolution and electron tomography show that transmembrane proteins and phospholipids in the plasma membrane hop among submicrometer compartments of the same size, probably delimited by the anchored-transmembrane-protein pickets lining the actin-based membrane-skeleton fence, once every 1–58 ms. The mechanisms by which the diffusion rate in the plasma membrane (PM) is regulated remain unresolved, despite their importance in spatially regulating the reaction rates in the PM. Proposed models include entrapment in nanoscale noncontiguous domains found in PtK2 cells, slow diffusion due to crowding, and actin-induced compartmentalization. Here, by applying single-particle tracking at high time resolutions, mainly to the PtK2-cell PM, we found confined diffusion plus hop movements (termed “hop diffusion”) for both a nonraft phospholipid and a transmembrane protein, transferrin receptor, and equal compartment sizes for these two molecules in all five of the cell lines used here (actual sizes were cell dependent), even after treatment with actin-modulating drugs. The cross-section size and the cytoplasmic domain size both affected the hop frequency. Electron tomography identified the actin-based membrane skeleton (MSK) located within 8.8 nm from the PM cytoplasmic surface of PtK2 cells and demonstrated that the MSK mesh size was the same as the compartment size for PM molecular diffusion. The extracellular matrix and extracellular domains of membrane proteins were not involved in hop diffusion. These results support a model of anchored TM-protein pickets lining actin-based MSK as a major mechanism for regulating diffusion.
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Affiliation(s)
- Takahiro K Fujiwara
- Center for Meso-Bio Single-Molecule Imaging, Institute for Integrated Cell-Material Sciences, Kyoto 606-8501, Japan
| | - Kokoro Iwasawa
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Ziya Kalay
- Institute for Integrated Cell-Material Sciences, Kyoto 606-8507, Japan
| | - Taka A Tsunoyama
- Institute for Integrated Cell-Material Sciences, Kyoto 606-8507, Japan
| | - Yusuke Watanabe
- Institute for Integrated Cell-Material Sciences, Kyoto 606-8507, Japan
| | - Yasuhiro M Umemura
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hideji Murakoshi
- National Institute for Physiological Sciences, Okazaki 444-8585, Japan
| | - Kenichi G N Suzuki
- Institute for Integrated Cell-Material Sciences, Kyoto 606-8507, Japan Institute for Stem Cell Biology and Regenerative Medicine and National Centre for Biological Sciences, Bangalore 650056, India
| | - Yuri L Nemoto
- Institute for Integrated Cell-Material Sciences, Kyoto 606-8507, Japan
| | - Nobuhiro Morone
- MRC Toxicology Unit, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Akihiro Kusumi
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan Institute for Integrated Cell-Material Sciences, Kyoto 606-8507, Japan Membrane Cooperativity Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa 904-0412, Japan
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