1
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Adler J, Bernhem K, Parmryd I. Membrane topography and the overestimation of protein clustering in single molecule localisation microscopy - identification and correction. Commun Biol 2024; 7:791. [PMID: 38951588 PMCID: PMC11217499 DOI: 10.1038/s42003-024-06472-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
According to single-molecule localisation microscopy almost all plasma membrane proteins are clustered. We demonstrate that clusters can arise from variations in membrane topography where the local density of a randomly distributed membrane molecule to a degree matches the variations in the local amount of membrane. Further, we demonstrate that this false clustering can be differentiated from genuine clustering by using a membrane marker to report on local variations in the amount of membrane. In dual colour live cell single molecule localisation microscopy using the membrane probe DiI alongside either the transferrin receptor or the GPI-anchored protein CD59, we found that pair correlation analysis reported both proteins and DiI as being clustered, as did its derivative pair correlation-photoactivation localisation microscopy and nearest neighbour analyses. After converting the localisations into images and using the DiI image to factor out topography variations, no CD59 clusters were visible, suggesting that the clustering reported by the other methods is an artefact. However, the TfR clusters persisted after topography variations were factored out. We demonstrate that membrane topography variations can make membrane molecules appear clustered and present a straightforward remedy suitable as the first step in the cluster analysis pipeline.
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Affiliation(s)
- Jeremy Adler
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kristoffer Bernhem
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Ingela Parmryd
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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2
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Szomek M, Akkerman V, Lauritsen L, Walther HL, Juhl AD, Thaysen K, Egebjerg JM, Covey DF, Lehmann M, Wessig P, Foster AJ, Poolman B, Werner S, Schneider G, Müller P, Wüstner D. Ergosterol promotes aggregation of natamycin in the yeast plasma membrane. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184350. [PMID: 38806103 DOI: 10.1016/j.bbamem.2024.184350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/11/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024]
Abstract
Polyene macrolides are antifungal substances, which interact with cells in a sterol-dependent manner. While being widely used, their mode of action is poorly understood. Here, we employ ultraviolet-sensitive (UV) microscopy to show that the antifungal polyene natamycin binds to the yeast plasma membrane (PM) and causes permeation of propidium iodide into cells. Right before membrane permeability became compromised, we observed clustering of natamycin in the PM that was independent of PM protein domains. Aggregation of natamycin was paralleled by cell deformation and membrane blebbing as revealed by soft X-ray microscopy. Substituting ergosterol for cholesterol decreased natamycin binding and caused a reduced clustering of natamycin in the PM. Blocking of ergosterol synthesis necessitates sterol import via the ABC transporters Aus1/Pdr11 to ensure natamycin binding. Quantitative imaging of dehydroergosterol (DHE) and cholestatrienol (CTL), two analogues of ergosterol and cholesterol, respectively, revealed a largely homogeneous lateral sterol distribution in the PM, ruling out that natamycin binds to pre-assembled sterol domains. Depletion of sphingolipids using myriocin increased natamycin binding to yeast cells, likely by increasing the ergosterol fraction in the outer PM leaflet. Importantly, binding and membrane aggregation of natamycin was paralleled by a decrease of the dipole potential in the PM, and this effect was enhanced in the presence of myriocin. We conclude that ergosterol promotes binding and aggregation of natamycin in the yeast PM, which can be synergistically enhanced by inhibitors of sphingolipid synthesis.
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Affiliation(s)
- Maria Szomek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Vibeke Akkerman
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Line Lauritsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Hanna-Loisa Walther
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Alice Dupont Juhl
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Katja Thaysen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jacob Marcus Egebjerg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Douglas F Covey
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO 63110, USA; Taylor Family Institute for Innovative Psychiatric Research, USA
| | - Max Lehmann
- Institute for Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany
| | - Pablo Wessig
- Institute for Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany
| | - Alexander J Foster
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 Groningen, the Netherlands
| | - Stephan Werner
- Department of X-Ray Microscopy, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Gerd Schneider
- Department of X-Ray Microscopy, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Peter Müller
- Department of Biology, Humboldt University Berlin, Invalidenstr. 43, D-10115 Berlin, Germany
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
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3
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Fábián B, Javanainen M. Diffusion Analyses along Mean and Gaussian-Curved Membranes with CurD. J Phys Chem Lett 2024; 15:3214-3220. [PMID: 38483514 DOI: 10.1021/acs.jpclett.4c00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Curved cellular membranes are both abundant and functionally relevant. While novel tomography approaches reveal the structural details of curved membranes, their dynamics pose an experimental challenge. Curvature especially affects the diffusion of lipids and macromolecules, yet neither experiments nor continuum models distinguish geometric effects from those caused by curvature-induced changes in membrane properties. Molecular simulations could excel here, yet despite community interest toward curved membranes, tools for their analysis are still lacking. Here, we satisfy this demand by introducing CurD, our novel and openly available implementation of the Vertex-oriented Triangle Propagation algorithm to the study of lipid diffusion along membranes with mean and/or Gaussian curvature. This approach, aided by our highly optimized implementation, computes geodetic distances significantly faster than conventional implementations of path-finding algorithms. Our tool, applied to coarse-grained simulations, allows for the first time the analysis of curvature effects on diffusion at size scales relevant to physiological processes such as endocytosis. Our analyses with different membrane geometries reveal that Gaussian curvature plays a surprisingly small role on lipid motion, whereas mean curvature; i.e., the packing of lipid headgroups largely dictates their mobility.
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Affiliation(s)
- Balázs Fábián
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
- Institute of Biotechnology, University of Helsinki, FI-00790 Helsinki, Finland
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4
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Kockelkoren G, Lauritsen L, Shuttle CG, Kazepidou E, Vonkova I, Zhang Y, Breuer A, Kennard C, Brunetti RM, D'Este E, Weiner OD, Uline M, Stamou D. Molecular mechanism of GPCR spatial organization at the plasma membrane. Nat Chem Biol 2024; 20:142-150. [PMID: 37460675 PMCID: PMC10792125 DOI: 10.1038/s41589-023-01385-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/14/2023] [Indexed: 10/12/2023]
Abstract
G-protein-coupled receptors (GPCRs) mediate many critical physiological processes. Their spatial organization in plasma membrane (PM) domains is believed to encode signaling specificity and efficiency. However, the existence of domains and, crucially, the mechanism of formation of such putative domains remain elusive. Here, live-cell imaging (corrected for topography-induced imaging artifacts) conclusively established the existence of PM domains for GPCRs. Paradoxically, energetic coupling to extremely shallow PM curvature (<1 µm-1) emerged as the dominant, necessary and sufficient molecular mechanism of GPCR spatiotemporal organization. Experiments with different GPCRs, H-Ras, Piezo1 and epidermal growth factor receptor, suggest that the mechanism is general, yet protein specific, and can be regulated by ligands. These findings delineate a new spatiomechanical molecular mechanism that can transduce to domain-based signaling any mechanical or chemical stimulus that affects the morphology of the PM and suggest innovative therapeutic strategies targeting cellular shape.
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Affiliation(s)
- Gabriele Kockelkoren
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Line Lauritsen
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Christopher G Shuttle
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Eleftheria Kazepidou
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Ivana Vonkova
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Yunxiao Zhang
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Artù Breuer
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Celeste Kennard
- Department of Chemical Engineering, Biomedical Engineering Program, University of South Carolina, Columbia, SC, USA
| | - Rachel M Brunetti
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Center for Geometrically Engineered Cellular Membranes, University of California, San Francisco, CA, USA
| | - Elisa D'Este
- Max-Planck-Institute for Medical Research, Optical Microscopy Facility, Heidelberg, Germany
| | - Orion D Weiner
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Center for Geometrically Engineered Cellular Membranes, University of California, San Francisco, CA, USA
| | - Mark Uline
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Department of Chemical Engineering, Biomedical Engineering Program, University of South Carolina, Columbia, SC, USA.
| | - Dimitrios Stamou
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Atomos Biotech, Copenhagen, Denmark.
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5
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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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6
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Huang A, Adler J, Parmryd I. Optimised generalized polarisation analysis of C-laurdan reveals clear order differences between T cell membrane compartments. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184094. [PMID: 36379264 DOI: 10.1016/j.bbamem.2022.184094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022]
Abstract
Heterogenous packing of plasma membrane lipids is important for cellular processes like signalling, adhesion and sorting of membrane components. Solvatochromic membrane fluorophores that respond to changes from liquid-ordered (lo) phase to liquid-disordered (ld) by red shifts in their emission spectra are often used to assess lipid packing. Their response can be quantified using generalized polarisation (GP) using fluorescence microscopy images from two emission ranges, preferably from a region of interest (ROI) limited to a specific membrane compartment. However, image quality is limited by Poisson noise and convolution by the point spread function of the imaging system. Examining GP-analysis of C-laurdan labelled T cells using the image restoration procedure deconvolution, we demonstrate that deconvolution substantially improves the image resolution by making the plasma membrane clearly discernible and facilitating plasma membrane ROI selection. We conclude that automatic ROI selection has advantages over manual ROI selection when it comes to reproducibility and speed, but reliable GP-measurements can also be obtained by manually demarcated ROIs. We find that deconvolution enhances the difference in GP-values between the plasma and intracellular membranes and demonstrate that moving an intensity defined plasma membrane ROI outwards from the cell further improves this differentiation. By systematically changing the key deconvolution regularization parameter signal to noise, we establish a protocol for deconvolution optimisation applicable to any solvatochromic dye and imaging system. The image processing and ROI selection protocol presented improves both the resolution and precision of GP-measurement and will enable detection of smaller changes in membrane order than is currently achievable.
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Affiliation(s)
- Ainsley Huang
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jeremy Adler
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ingela Parmryd
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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7
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Tran PD, Blanpied TA, Atzberger PJ. Protein drift-diffusion dynamics and phase separation in curved cell membranes and dendritic spines: Hybrid discrete-continuum methods. Phys Rev E 2022; 106:044402. [PMID: 36397472 DOI: 10.1103/physreve.106.044402] [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: 10/04/2021] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine discrete particle descriptions with continuum-level models for tracking the individual protein drift-diffusion dynamics when coupled to continuum fields. We show how our approaches can be used to investigate phenomena motivated by protein kinetics within dendritic spines. The spine geometry is hypothesized to play an important biological role regulating synaptic strength, protein kinetics, and self-assembly of clusters. We perform simulation studies for model spine geometries varying the neck size to investigate how phase-separation and protein organization is influenced by different shapes. We also show how our methods can be used to study the roles of geometry in reaction-diffusion systems including Turing instabilities. Our methods provide general approaches for investigating protein kinetics and drift-diffusion dynamics within curved membrane structures.
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Affiliation(s)
- Patrick D Tran
- Physics, College of Creative Studies, University of California, Santa Barbara, Santa Barbara, California 93106-3080, USA
| | - Thomas A Blanpied
- Department of Physiology, University of Maryland, Baltimore, Maryland 21201, USA
| | - Paul J Atzberger
- Department of Mathematics and Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106-3080, USA
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8
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Zapata-Mercado E, Azarova EV, Hristova K. Effect of reversible osmotic stress on live cell plasma membranes, probed via Laurdan general polarization measurements. Biophys J 2022; 121:2411-2418. [PMID: 35596525 DOI: 10.1016/j.bpj.2022.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/10/2021] [Accepted: 05/16/2022] [Indexed: 11/02/2022] Open
Abstract
Here we seek to gain insight into changes in the plasma membrane of live cells upon the application of osmotic stress using Laurdan, a fluorescent probe that reports on membrane organization, hydration, and dynamics. It is known that the application of osmotic stress to lipid vesicles causes a decrease in Laurdan's generalized polarization (GP), which has been interpreted as an indication of membrane stretching. In cells, we see the opposite effects, as GP increases when the osmolarity of the solution is decreased. This increase in GP is associated with the presence of caveolae, which are known to disassemble and flatten in response to osmotic stress.
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Affiliation(s)
- Elmer Zapata-Mercado
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Evgenia V Azarova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218.
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9
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Wirth D, McCall A, Hristova K. Neural network strategies for plasma membrane selection in fluorescence microscopy images. Biophys J 2021; 120:2374-2385. [PMID: 33961865 PMCID: PMC8390876 DOI: 10.1016/j.bpj.2021.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 10/21/2022] Open
Abstract
In recent years, there has been an explosion of fluorescence microscopy studies of live cells in the literature. The analysis of the images obtained in these studies often requires labor-intensive manual annotation to extract meaningful information. In this study, we explore the utility of a neural network approach to recognize, classify, and select plasma membranes in high-resolution images, thus greatly speeding up data analysis and reducing the need for personnel training for highly repetitive tasks. Two different strategies are tested: 1) a semantic segmentation strategy, and 2) a sequential application of an object detector followed by a semantic segmentation network. Multiple network architectures are evaluated for each strategy, and the best performing solutions are combined and implemented in the Recognition Of Cellular Membranes software. We show that images annotated manually and with the Recognition Of Cellular Membranes software yield identical results by comparing Förster resonance energy transfer binding curves for the membrane protein fibroblast growth factor receptor 3. The approach that we describe in this work can be applied to other image selection tasks in cell biology.
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Affiliation(s)
- Daniel Wirth
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - Alec McCall
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.
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10
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P120 catenin potentiates constitutive E-cadherin dimerization at the plasma membrane and regulates trans binding. Curr Biol 2021; 31:3017-3027.e7. [PMID: 34019823 DOI: 10.1016/j.cub.2021.04.061] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/09/2020] [Accepted: 04/26/2021] [Indexed: 11/23/2022]
Abstract
Cadherins are essential adhesion proteins that regulate tissue cohesion and paracellular permeability by assembling dense adhesion plaques at cell-to-cell contacts. Adherens junctions are central to a wide range of tissue functions; identifying protein interactions that potentiate their assembly and regulation has been the focus of research for over 2 decades. Here, we present evidence for a new, unexpected mechanism of cadherin oligomerization on cells. Fully quantified spectral imaging fluorescence resonance energy transfer (FSI-FRET) and fluorescence intensity fluctuation (FIF) measurements directly demonstrate that E-cadherin forms constitutive lateral (cis) dimers at the plasma membrane. Results further show that binding of the cytosolic protein p120ctn binding to the intracellular region is required for constitutive E-cadherin dimerization. This finding differs from a model that attributes lateral (cis) cadherin oligomerization solely to extracellular domain interactions. The present, novel findings are further supported by studies of E-cadherin mutants that uncouple p120ctn binding or with cells in which p120ctn was knocked out using CRISPR-Cas9. Quantitative affinity measurements further demonstrate that uncoupling p120ctn binding reduces the cadherin trans binding affinity and cell adhesion. These findings transform the current model of cadherin assembly at cell surfaces and identify the core building blocks of cadherin-mediated intercellular adhesions. They also identify a new role for p120ctn and reconcile findings that implicate both the extracellular and intracellular cadherin domains in cadherin clustering and intercellular cohesion.
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11
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Paul MD, Rainwater R, Zuo Y, Gu L, Hristova K. Probing Membrane Protein Association Using Concentration‐Dependent Number and Brightness. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael D. Paul
- Program in Molecular Biophysics Johns Hopkins University Baltimore MD 21218 USA
| | - Randall Rainwater
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
| | - Yi Zuo
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
| | - Luo Gu
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
| | - Kalina Hristova
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
- Program in Molecular Biophysics Johns Hopkins University Baltimore MD 21218 USA
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12
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Paul MD, Rainwater R, Zuo Y, Gu L, Hristova K. Probing Membrane Protein Association Using Concentration-Dependent Number and Brightness. Angew Chem Int Ed Engl 2021; 60:6503-6508. [PMID: 33351993 DOI: 10.1002/anie.202010049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/11/2020] [Indexed: 01/13/2023]
Abstract
We introduce concentration-dependent number and brightness (cdN&B), a fluorescence fluctuation technique that can be implemented on a standard confocal microscope and can report on the thermodynamics of membrane protein association in the native plasma membrane. It uses transient transfection to enable measurements of oligomer size as a function of receptor concentration over a broad range, yielding the association constant. We discuss artifacts in cdN&B that are concentration-dependent and can distort the oligomerization curves, and we outline procedures that can correct for them. Using cdN&B, we characterize the association of neuropilin 1 (NRP1), a protein that plays a critical role in the development of the embryonic cardiovascular and nervous systems. We show that NRP1 associates into a tetramer in a concentration-dependent manner, and we quantify the strength of the association. This work demonstrates the utility of cdN&B as a powerful tool in biophysical chemistry.
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Affiliation(s)
- Michael D Paul
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Randall Rainwater
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Yi Zuo
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Luo Gu
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA.,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
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13
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Bernabé-Rubio M, Bosch-Fortea M, García E, Bernardino de la Serna J, Alonso MA. Adaptive Lipid Immiscibility and Membrane Remodeling Are Active Functional Determinants of Primary Ciliogenesis. SMALL METHODS 2021; 5:e2000711. [PMID: 34927881 DOI: 10.1002/smtd.202000711] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/11/2020] [Indexed: 06/14/2023]
Abstract
Lipid liquid-liquid immiscibility and its consequent lateral heterogeneity have been observed under thermodynamic equilibrium in model and native membranes. However, cholesterol-rich membrane domains, sometimes referred to as lipid rafts, are difficult to observe spatiotemporally in live cells. Despite their importance in many biological processes, robust evidence for their existence remains elusive. This is mainly due to the difficulty in simultaneously determining their chemical composition and physicochemical nature, whilst spatiotemporally resolving their nanodomain lifetime and molecular dynamics. In this study, a bespoke method based on super-resolution stimulated emission depletion (STED) microscopy and raster imaging correlation spectroscopy (RICS) is used to overcome this issue. This methodology, laser interleaved confocal RICS and STED-RICS (LICSR), enables simultaneous tracking of lipid lateral packing and dynamics at the nanoscale. Previous work indicated that, in polarized epithelial cells, the midbody remnant licenses primary cilium formation through an unidentified mechanism. LICSR shows that lipid immiscibility and its adaptive collective nanoscale self-assembly are crucial for the midbody remnant to supply condensed membranes to the centrosome for the biogenesis of the ciliary membrane. Hence, this work poses a breakthrough in the field of lipid biology by providing compelling evidence of a functional role for liquid ordered-like membranes in primary ciliogenesis.
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Affiliation(s)
- Miguel Bernabé-Rubio
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, 28049, Spain
- King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London, SE1 9RT, UK
| | - Minerva Bosch-Fortea
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Institute of Bioengineering and School of Engineering and Materials Science, Queen Mary, University of London, Mile End Road, London, E1 4NS, UK
| | - Esther García
- Central Laser Facility, Rutherford Appleton Laboratory, MRC-Research Complex at Harwell, Science and Technology Facilities Council, Harwell, OX11 0QX, UK
- CR-UK Beatson Institute, Switchback Road, Glasgow, G61 1BD, UK
| | - Jorge Bernardino de la Serna
- Central Laser Facility, Rutherford Appleton Laboratory, MRC-Research Complex at Harwell, Science and Technology Facilities Council, Harwell, OX11 0QX, UK
- National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
- NIHR Imperial Biomedical Research Centre, London, SW7 2AZ, UK
| | - Miguel A Alonso
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, 28049, Spain
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14
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Diffusion on Membrane Domes, Tubes, and Pearling Structures. Biophys J 2020; 120:424-431. [PMID: 33359464 DOI: 10.1016/j.bpj.2020.12.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/19/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
Diffusion is a fundamental mechanism for protein distribution in cell membranes. These membranes often exhibit complex shapes, which range from shallow domes to elongated tubular or pearl-like structures. Shape complexity of the membrane influences the diffusive spreading of proteins and molecules. Despite the importance membrane geometry plays in these diffusive processes, it is challenging to establish the dependence between diffusion and membrane morphology. We solve the diffusion equation numerically on various static curved shapes representative for experimentally observed membrane shapes. Our results show that membrane necks become diffusion barriers. We determine the diffusive half-time, i.e., the time that is required to reduce the amount of protein in the budded region by one half, and find a quadratic relation between the diffusive half-time and the averaged mean curvature of the membrane shape, which we rationalize by a scaling law. Our findings thus help estimate the characteristic diffusive timescale based on the simple measure of membrane mean curvature.
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15
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Frias MA, Disalvo EA. Breakdown of classical paradigms in relation to membrane structure and functions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183512. [PMID: 33202248 DOI: 10.1016/j.bbamem.2020.183512] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 01/10/2023]
Abstract
Updates of the mosaic fluid membrane model implicitly sustain the paradigms that bilayers are closed systems conserving a state of fluidity and behaving as a dielectric slab. All of them are a consequence of disregarding water as part of the membrane structure and its essential role in the thermodynamics and kinetics of membrane response to bioeffectors. A correlation of the thermodynamic properties with the structural features of water makes possible to introduce the lipid membrane as a responsive structure due to the relaxation of water rearrangements in the kinetics of bioeffectors' interactions. This analysis concludes that the lipid membranes are open systems and, according to thermodynamic of irreversible formalism, bilayers and monolayers can be reasonable compared under controlled conditions. The inclusion of water in the complex structure makes feasible to reconsider the concept of dielectric slab and fluidity.
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Affiliation(s)
- M A Frias
- Applied Biophysics and Food Research Center, CIBAAL-UNSE-CONICET, Santiago del Estero, Argentina
| | - E A Disalvo
- Applied Biophysics and Food Research Center, CIBAAL-UNSE-CONICET, Santiago del Estero, Argentina.
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16
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Revealing Plasma Membrane Nano-Domains with Diffusion Analysis Methods. MEMBRANES 2020; 10:membranes10110314. [PMID: 33138102 PMCID: PMC7693849 DOI: 10.3390/membranes10110314] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022]
Abstract
Nano-domains are sub-light-diffraction-sized heterogeneous areas in the plasma membrane of cells, which are involved in cell signalling and membrane trafficking. Throughout the last thirty years, these nano-domains have been researched extensively and have been the subject of multiple theories and models: the lipid raft theory, the fence model, and the protein oligomerization theory. Strong evidence exists for all of these, and consequently they were combined into a hierarchal model. Measurements of protein and lipid diffusion coefficients and patterns have been instrumental in plasma membrane research and by extension in nano-domain research. This has led to the development of multiple methodologies that can measure diffusion and confinement parameters including single particle tracking, fluorescence correlation spectroscopy, image correlation spectroscopy and fluorescence recovery after photobleaching. Here we review the performance and strengths of these methods in the context of their use in identification and characterization of plasma membrane nano-domains.
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17
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Gesper A, Wennmalm S, Hagemann P, Eriksson SG, Happel P, Parmryd I. Variations in Plasma Membrane Topography Can Explain Heterogenous Diffusion Coefficients Obtained by Fluorescence Correlation Spectroscopy. Front Cell Dev Biol 2020; 8:767. [PMID: 32903922 PMCID: PMC7443568 DOI: 10.3389/fcell.2020.00767] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/21/2020] [Indexed: 01/18/2023] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is frequently used to study diffusion in cell membranes, primarily the plasma membrane. The diffusion coefficients reported in the plasma membrane of the same cell type and even within single cells typically display a large spread. We have investigated whether this spread can be explained by variations in membrane topography throughout the cell surface, that changes the amount of membrane in the FCS focal volume at different locations. Using FCS, we found that diffusion of the membrane dye DiI in the apical plasma membrane was consistently faster above the nucleus than above the cytoplasm. Using live cell scanning ion conductance microscopy (SICM) to obtain a topography map of the cell surface, we demonstrate that cell surface roughness is unevenly distributed with the plasma membrane above the nucleus being the smoothest, suggesting that the difference in diffusion observed in FCS is related to membrane topography. FCS modeled on simulated diffusion in cell surfaces obtained by SICM was consistent with the FCS data from live cells and demonstrated that topography variations can cause the appearance of anomalous diffusion in FCS measurements. Furthermore, we found that variations in the amount of the membrane marker DiD, a proxy for the membrane, but not the transmembrane protein TCRζ or the lipid-anchored protein Lck, in the FCS focal volume were related to variations in diffusion times at different positions in the plasma membrane. This relationship was seen at different positions both at the apical cell and basal cell sides. We conclude that it is crucial to consider variations in topography in the interpretation of FCS results from membranes.
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Affiliation(s)
| | - Stefan Wennmalm
- SciLifeLab, Royal Institute of Technology, Stockholm, Sweden
| | | | | | | | - Ingela Parmryd
- Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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18
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Llorente García I, Marsh M. A biophysical perspective on receptor-mediated virus entry with a focus on HIV. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2020; 1862:183158. [PMID: 31863725 PMCID: PMC7156917 DOI: 10.1016/j.bbamem.2019.183158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/14/2022]
Abstract
As part of their entry and infection strategy, viruses interact with specific receptor molecules expressed on the surface of target cells. The efficiency and kinetics of the virus-receptor interactions required for a virus to productively infect a cell is determined by the biophysical properties of the receptors, which are in turn influenced by the receptors' plasma membrane (PM) environments. Currently, little is known about the biophysical properties of these receptor molecules or their engagement during virus binding and entry. Here we review virus-receptor interactions focusing on the human immunodeficiency virus type 1 (HIV), the etiological agent of acquired immunodeficiency syndrome (AIDS), as a model system. HIV is one of the best characterised enveloped viruses, with the identity, roles and structure of the key molecules required for infection well established. We review current knowledge of receptor-mediated HIV entry, addressing the properties of the HIV cell-surface receptors, the techniques used to measure these properties, and the macromolecular interactions and events required for virus entry. We discuss some of the key biophysical principles underlying receptor-mediated virus entry and attempt to interpret the available data in the context of biophysical mechanisms. We also highlight crucial outstanding questions and consider how new tools might be applied to advance understanding of the biophysical properties of viral receptors and the dynamic events leading to virus entry.
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Affiliation(s)
| | - Mark Marsh
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
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19
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Arnold AM, Schneider MC, Hüsson C, Sablatnig R, Brameshuber M, Baumgart F, Schütz GJ. Verifying molecular clusters by 2-color localization microscopy and significance testing. Sci Rep 2020; 10:4230. [PMID: 32144344 PMCID: PMC7060173 DOI: 10.1038/s41598-020-60976-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/17/2020] [Indexed: 11/08/2022] Open
Abstract
While single-molecule localization microscopy (SMLM) offers the invaluable prospect to visualize cellular structures below the diffraction limit of light microscopy, its potential has not yet been fully capitalized due to its inherent susceptibility to blinking artifacts. Particularly, overcounting of single molecule localizations has impeded a reliable and sensitive detection of biomolecular nanoclusters. Here we introduce a 2-Color Localization microscopy And Significance Testing Approach (2-CLASTA), providing a parameter-free statistical framework for the qualitative analysis of two-dimensional SMLM data via significance testing methods. 2-CLASTA yields p-values for the null hypothesis of random biomolecular distributions, independent of the blinking behavior of the chosen fluorescent labels. The method is parameter-free and does not require any additional measurements nor grouping of localizations. We validated the method both by computer simulations as well as experimentally, using protein concatemers as a mimicry of biomolecular clustering. As the new approach is not affected by overcounting artifacts, it is able to detect biomolecular clustering of various shapes at high sensitivity down to a level of dimers.
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Affiliation(s)
- Andreas M Arnold
- Institute of Applied Physics, TU Wien, Getreidemarkt 9, A-1060, Vienna, Austria
| | | | - Christoph Hüsson
- Institute of Visual Computing and Human-Centered Technology, TU Wien, Favoritenstrasse 9-11, A-1040, Vienna, Austria
| | - Robert Sablatnig
- Institute of Visual Computing and Human-Centered Technology, TU Wien, Favoritenstrasse 9-11, A-1040, Vienna, Austria
| | - Mario Brameshuber
- Institute of Applied Physics, TU Wien, Getreidemarkt 9, A-1060, Vienna, Austria
| | - Florian Baumgart
- Institute of Applied Physics, TU Wien, Getreidemarkt 9, A-1060, Vienna, Austria.
| | - Gerhard J Schütz
- Institute of Applied Physics, TU Wien, Getreidemarkt 9, A-1060, Vienna, Austria.
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20
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Jacobson K, Liu P, Lagerholm BC. The Lateral Organization and Mobility of Plasma Membrane Components. Cell 2020; 177:806-819. [PMID: 31051105 DOI: 10.1016/j.cell.2019.04.018] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 02/01/2019] [Accepted: 04/09/2019] [Indexed: 01/22/2023]
Abstract
Over the last several decades, an impressive array of advanced microscopic and analytical tools, such as single-particle tracking and nanoscopic fluorescence correlation spectroscopy, has been applied to characterize the lateral organization and mobility of components in the plasma membrane. Such analysis can tell researchers about the local dynamic composition and structure of membranes and is important for predicting the outcome of membrane-based reactions. However, owing to the unresolved complexity of the membrane and the structures peripheral to it, identification of the detailed molecular origin of the interactions that regulate the organization and mobility of the membrane has not proceeded quickly. This Perspective presents an overview of how cell-surface structure may give rise to the types of lateral mobility that are observed and some potentially fruitful future directions to elucidate the architecture of these structures in more molecular detail.
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Affiliation(s)
- Ken Jacobson
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Ping Liu
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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21
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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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22
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Singh DR, King C, Salotto M, Hristova K. Revisiting a controversy: The effect of EGF on EGFR dimer stability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183015. [PMID: 31295474 DOI: 10.1016/j.bbamem.2019.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/23/2019] [Accepted: 07/02/2019] [Indexed: 12/26/2022]
Abstract
EGFR is a receptor tyrosine kinase that plays a critical role in cell proliferation, differentiation, survival and migration. Its activating ligand, EGF, has long been believed to stabilize the EGFR dimer. Two research studies aimed at quantitative measurements of EGFR dimerization, however, have led to contradicting conclusions and have questioned this view. Given the controversy, here we sought to measure the dimerization of EGFR in the absence and in the presence of saturating EGF concentrations, and to tease out the effect of ligand on dimer stability, using a FRET-based quantitative method. Our measurements show that the dissociation constant is decreased ~150 times due to ligand binding, indicative of significant dimer stabilization. In addition, our measurements demonstrate that EGF binding induces a conformational change in the EGFR dimer.
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Affiliation(s)
- Deo R Singh
- Institute of NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America; Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America
| | - Christopher King
- Institute of NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America; Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America
| | - Matt Salotto
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America
| | - Kalina Hristova
- Institute of NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America; Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America; Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America.
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23
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Adler J, Sintorn IM, Strand R, Parmryd I. Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous. Commun Biol 2019; 2:12. [PMID: 30652124 PMCID: PMC6325064 DOI: 10.1038/s42003-018-0240-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 11/26/2018] [Indexed: 01/09/2023] Open
Abstract
Cells are neither flat nor smooth, which has serious implications for prevailing plasma membrane models and cellular processes like cell signalling, adhesion and molecular clustering. Using probability distributions from diffusion simulations, we demonstrate that 2D and 3D Euclidean distance measurements substantially underestimate diffusion on non-flat surfaces. Intuitively, the shortest within surface distance (SWSD), the geodesic distance, should reduce this problem. The SWSD is accurate for foldable surfaces but, although it outperforms 2D and 3D Euclidean measurements, it still underestimates movement on deformed surfaces. We demonstrate that the reason behind the underestimation is that topographical features themselves can produce both super- and subdiffusion, i.e. the appearance of anomalous diffusion. Differentiating between topography-induced and genuine anomalous diffusion requires characterising the surface by simulating Brownian motion on high-resolution cell surface images and a comparison with the experimental data.
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Affiliation(s)
- Jeremy Adler
- Science for Life Laboratory, Medical Cell Biology, Uppsala University, Uppsala University, Box 571, 751 21 Uppsala, Sweden
| | - Ida-Maria Sintorn
- Department of Information Technology, Uppsala University, Box 331, 751 05 Uppsala, Sweden
| | - Robin Strand
- Department of Information Technology, Uppsala University, Box 331, 751 05 Uppsala, Sweden
| | - Ingela Parmryd
- Science for Life Laboratory, Medical Cell Biology, Uppsala University, Uppsala University, Box 571, 751 21 Uppsala, Sweden
- Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
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24
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Dimerization of the Trk receptors in the plasma membrane: effects of their cognate ligands. Biochem J 2018; 475:3669-3685. [PMID: 30366959 DOI: 10.1042/bcj20180637] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 12/18/2022]
Abstract
Receptor tyrosine kinases (RTKs) are cell surface receptors which control cell growth and differentiation, and play important roles in tumorigenesis. Despite decades of RTK research, the mechanism of RTK activation in response to their ligands is still under debate. Here, we investigate the interactions that control the activation of the tropomyosin receptor kinase (Trk) family of RTKs in the plasma membrane, using a FRET-based methodology. The Trk receptors are expressed in neuronal tissues, and guide the development of the central and peripheral nervous systems during development. We quantify the dimerization of human Trk-A, Trk-B, and Trk-C in the absence and presence of their cognate ligands: human β-nerve growth factor, human brain-derived neurotrophic factor, and human neurotrophin-3, respectively. We also assess conformational changes in the Trk dimers upon ligand binding. Our data support a model of Trk activation in which (1) Trks have a propensity to interact laterally and to form dimers even in the absence of ligand, (2) different Trk unliganded dimers have different stabilities, (3) ligand binding leads to Trk dimer stabilization, and (4) ligand binding induces structural changes in the Trk dimers which propagate to their transmembrane and intracellular domains. This model, which we call the 'transition model of RTK activation,' may hold true for many other RTKs.
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25
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Baumgart F, Arnold AM, Rossboth BK, Brameshuber M, Schütz GJ. What we talk about when we talk about nanoclusters. Methods Appl Fluoresc 2018; 7:013001. [PMID: 30412469 DOI: 10.1088/2050-6120/aaed0f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Superresolution microscopy results have sparked the idea that many membrane proteins are not randomly distributed across the plasma membrane but are instead arranged in nanoclusters. Frequently, these new results seemed to confirm older data based on biochemical and electron microscopy experiments. Recently, however, it was recognized that multiple countings of the very same fluorescently labeled protein molecule can be easily confused with true protein clusters. Various strategies have been developed, which are intended to solve the problem of discriminating true protein clusters from imaging artifacts. We believe that there is currently no perfect algorithm for this problem; instead, different approaches have different strengths and weaknesses. In this review, we discuss single molecule localization microscopy in view of its ability to detect nanoclusters of membrane proteins. To capture the different views on nanoclustering, we chose an unconventional style for this article: we placed its scientific content in the setting of a fictive conference, where five researchers from different fields discuss the problem of detecting and quantifying nanoclusters. Using this style, we feel that the different approaches common for different research areas can be well illustrated. Similarities to a short story by Raymond Carver are not unintentional.
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26
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Ponjavic A, McColl J, Carr AR, Santos AM, Kulenkampff K, Lippert A, Davis SJ, Klenerman D, Lee SF. Single-Molecule Light-Sheet Imaging of Suspended T Cells. Biophys J 2018; 114:2200-2211. [PMID: 29742413 PMCID: PMC5961759 DOI: 10.1016/j.bpj.2018.02.044] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 11/26/2022] Open
Abstract
Adaptive immune responses are initiated by triggering of the T cell receptor. Single-molecule imaging based on total internal reflection fluorescence microscopy at coverslip/basal cell interfaces is commonly used to study this process. These experiments have suggested, unexpectedly, that the diffusional behavior and organization of signaling proteins and receptors may be constrained before activation. However, it is unclear to what extent the molecular behavior and cell state is affected by the imaging conditions, i.e., by the presence of a supporting surface. In this study, we implemented single-molecule light-sheet microscopy, which enables single receptors to be directly visualized at any plane in a cell to study protein dynamics and organization in live, resting T cells. The light sheet enabled the acquisition of high-quality single-molecule fluorescence images that were comparable to those of total internal reflection fluorescence microscopy. By comparing the apical and basal surfaces of surface-contacting T cells using single-molecule light-sheet microscopy, we found that most coated-glass surfaces and supported lipid bilayers profoundly affected the diffusion of membrane proteins (T cell receptor and CD45) and that all the surfaces induced calcium influx to various degrees. Our results suggest that, when studying resting T cells, surfaces are best avoided, which we achieve here by suspending cells in agarose.
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Affiliation(s)
- Aleks Ponjavic
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - James McColl
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexander R Carr
- 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
| | - Klara Kulenkampff
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Anna Lippert
- 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.
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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27
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Gesper A, Hagemann P, Happel P. A low-cost, large field-of-view scanning ion conductance microscope for studying nanoparticle-cell membrane interactions. NANOSCALE 2017; 9:14172-14183. [PMID: 28905955 DOI: 10.1039/c7nr04306f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nanoparticles have the potential to become versatile tools in the medical and life sciences. One potential application is delivering drugs or other compounds to the cell cytoplasm, which requires the nanoparticles to bind to or cross the cell membrane. However, there are only a few tools available which allow studying the interaction of nanoparticles and the cell membrane of living cells in a physiological environment. Currently, the tool which least biases living cells is Scanning Ion Conductance Microscopy (SICM). Specialized SICMs allow imaging at high resolution, however, they are cost intensive, particularly when providing a large field-of-view. In contrast, less cost intensive SICMs which provide a large field-of-view do not allow imaging at high resolutions. We have developed a SICM setup consisting of a compact three-axis piezo system and an additional fast shear-force piezo actor. This combination allows imaging fields-of-view of up to 80 μm × 80 μm, recording sections of living cells with a temporal resolution in the range of minutes as well as imaging with a spatial resolution of below 70 nm. Using our SICM we found that the cell membrane of HeLa cells treated with carboxylated latex nanoparticles was significantly more convoluted compared to control cells. The SICM setup we introduce here combines high resolution imaging with a large field-of-view at low costs. Our setup only requires a mounting adapter to extend existing inverted light microscopes, thus it could be a valuable and cost effective tool for researchers in all fields of the medical and life sciences performing investigations at the nanometer scale.
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Affiliation(s)
- Astrid Gesper
- Nanoscopy Group, Central Unit for Ion beams and Radionuclides (RUBION), Ruhr-University Bochum, Universitätsstraβe 150, D-44780 Bochum, Germany.
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Chabanon M, Stachowiak JC, Rangamani P. Systems biology of cellular membranes: a convergence with biophysics. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2017; 9:10.1002/wsbm.1386. [PMID: 28475297 PMCID: PMC5561455 DOI: 10.1002/wsbm.1386] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/02/2017] [Accepted: 02/21/2017] [Indexed: 12/12/2022]
Abstract
Systems biology and systems medicine have played an important role in the last two decades in shaping our understanding of biological processes. While systems biology is synonymous with network maps and '-omics' approaches, it is not often associated with mechanical processes. Here, we make the case for considering the mechanical and geometrical aspects of biological membranes as a key step in pushing the frontiers of systems biology of cellular membranes forward. We begin by introducing the basic components of cellular membranes, and highlight their dynamical aspects. We then survey the functions of the plasma membrane and the endomembrane system in signaling, and discuss the role and origin of membrane curvature in these diverse cellular processes. We further give an overview of the experimental and modeling approaches to study membrane phenomena. We close with a perspective on the converging futures of systems biology and membrane biophysics, invoking the need to include physical variables such as location and geometry in the study of cellular membranes. WIREs Syst Biol Med 2017, 9:e1386. doi: 10.1002/wsbm.1386 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Morgan Chabanon
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jeanne C. Stachowiak
- Department of Biomedical Engineering, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
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29
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King C, Wirth D, Workman S, Hristova K. Cooperative interactions between VEGFR2 extracellular Ig-like subdomains ensure VEGFR2 dimerization. Biochim Biophys Acta Gen Subj 2017; 1861:2559-2567. [PMID: 28847506 DOI: 10.1016/j.bbagen.2017.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/16/2017] [Accepted: 08/24/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUND Prior studies have suggested that the interactions occurring between VEGFR2 extracellular domains in the absence of ligand are complex. Here we seek novel insights into these interactions, and into the role of the different Ig-like domains (D1 through D7) in VEGFR2 dimerization. METHODS We study the dimerization of a single amino acid mutant and of three deletion mutants in the plasma membrane using two photon microscopy and fully quantified spectral imaging. RESULTS We demonstrate that a set of cooperative interactions between the different Ig-like domains ensure that VEGFR2 dimerizes with a specific affinity instead of forming oligomers. CONCLUSIONS The contributions of subunits D7 and D4 seem to be the most critical, as they appear essential for strong lateral interactions and for the formation of dimers, respectively. GENERAL SIGNIFICANCE This study provides new insights into the mechanism of VEGFR2 dimerization and activation.
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Affiliation(s)
- Christopher King
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Daniel Wirth
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Samuel Workman
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States.
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30
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Del Piccolo N, Hristova K. Quantifying the Interaction between EGFR Dimers and Grb2 in Live Cells. Biophys J 2017; 113:1353-1364. [PMID: 28734476 DOI: 10.1016/j.bpj.2017.06.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/19/2017] [Accepted: 06/12/2017] [Indexed: 12/21/2022] Open
Abstract
Adaptor proteins are a class of cytoplasmic proteins that bind to phosphorylated residues in receptor tyrosine kinases and trigger signaling cascades that control critically important cellular processes, such as cell survival, growth, differentiation, and motility. Here, we seek to characterize the interaction between epidermal growth factor receptor (EGFR) and the cytoplasmic adaptor protein growth factor receptor-bound protein 2 (Grb2) in a cellular context. To do so, we explore the utility of a highly biologically relevant model system, mammalian cells under reversible osmotic stress, and a recently introduced Förster resonance energy transfer microscopy method, fully quantified spectral imaging. We present a method that allows us to quantify the stoichiometry and the association constant of the EGFR-Grb2 binding interaction in the plasma membrane, in the presence and absence of activating ligand. The method that we introduce can have broad utility in membrane protein research, as it can be applied to different membrane protein-cytoplasmic protein pairs.
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Affiliation(s)
- Nuala Del Piccolo
- Department of Materials Science and Engineering and Institute for NanoBio Technology, Johns Hopkins University, Baltimore, Maryland
| | - Kalina Hristova
- Department of Materials Science and Engineering and Institute for NanoBio Technology, Johns Hopkins University, Baltimore, Maryland.
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31
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Ng XW, Teh C, Korzh V, Wohland T. The Secreted Signaling Protein Wnt3 Is Associated with Membrane Domains In Vivo: A SPIM-FCS Study. Biophys J 2017; 111:418-429. [PMID: 27463143 DOI: 10.1016/j.bpj.2016.06.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 06/10/2016] [Accepted: 06/16/2016] [Indexed: 10/21/2022] Open
Abstract
Wnt3 is a morphogen that activates the Wnt signaling pathway and regulates a multitude of biological processes ranging from cell proliferation and cell fate specification to differentiation over embryonic induction to neural patterning. Recent studies have shown that the palmitoylation of Wnt3 by Porcupine, a membrane-bound O-acyltransferase, plays a significant role in the intracellular membrane trafficking of Wnt3 and subsequently, its secretion in live zebrafish embryos, where chemical inhibition of Porcupine reduced the membrane-bound and secreted fractions of Wnt3 and eventually led to defective brain development. However, the membrane distribution of Wnt3 in cells remains not fully understood. Here, we determine the membrane organization of functionally active Wnt3-EGFP in cerebellar cells of live transgenic zebrafish embryos and the role of palmitoylation in its organization using single plane illumination microscopy-fluorescence correlation spectroscopy (SPIM-FCS), a multiplexed modality of FCS, which generates maps of molecular dynamics, concentration, and interaction of biomolecules. The FCS diffusion law was applied to SPIM-FCS data to study the subresolution membrane organization of Wnt3. We find that at the plasma membrane in vivo, Wnt3 is associated with cholesterol-dependent domains. This association reduces with increasing concentrations of Porcupine inhibitor (C59), confirming the importance of palmitoylation of Wnt3 for its association with cholesterol-dependent domains. Reduction of membrane cholesterol also results in a decrease of Wnt3 association with cholesterol-dependent domains in live zebrafish. This demonstrates for the first time, to our knowledge, in live vertebrate embryos that Wnt3 is associated with cholesterol-dependent domains.
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Affiliation(s)
- Xue Wen Ng
- Department of Chemistry, National University of Singapore, Singapore, Singapore; Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Cathleen Teh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Vladimir Korzh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Department of Chemistry, National University of Singapore, Singapore, Singapore; Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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32
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Singh DR, Ahmed F, Sarabipour S, Hristova K. Intracellular Domain Contacts Contribute to Ecadherin Constitutive Dimerization in the Plasma Membrane. J Mol Biol 2017; 429:2231-2245. [PMID: 28549925 DOI: 10.1016/j.jmb.2017.05.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/19/2017] [Accepted: 05/19/2017] [Indexed: 01/29/2023]
Abstract
Epithelial cadherin (Ecadherin) is responsible for the intercellular cohesion of epithelial tissues. It forms lateral clusters within adherens cell-cell junctions, but its association state outside these clusters is unknown. Here, we use a quantitative Forster resonance energy transfer (FRET) approach to show that Ecadherin forms constitutive dimers and that these dimers exist independently of the actin cytoskeleton or cytoplasmic proteins. The dimers are stabilized by intermolecular contacts that occur along the entire length of Ecadherin, with the intracellular domains having a surprisingly strong favorable contribution. We further show that Ecadherin mutations and calcium depletion induce structural alterations that propagate from the N terminus all the way to the C terminus, without destabilizing the dimeric state. These findings provide context for the interpretation of Ecadherin adhesion experiments. They also suggest that early events of adherens junction assembly involve interactions between from preformed Ecadherin dimers.
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Affiliation(s)
- Deo R Singh
- Department of Materials Science and Engineering and Institute of NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, USA
| | - Fozia Ahmed
- Department of Materials Science and Engineering and Institute of NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, USA
| | - Sarvenaz Sarabipour
- Department of Materials Science and Engineering and Institute of NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering and Institute of NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, USA.
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33
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Ida H, Takahashi Y, Kumatani A, Shiku H, Matsue T. High Speed Scanning Ion Conductance Microscopy for Quantitative Analysis of Nanoscale Dynamics of Microvilli. Anal Chem 2017; 89:6015-6020. [DOI: 10.1021/acs.analchem.7b00584] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Hiroki Ida
- Graduate
School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8576, Japan
| | - Yasufumi Takahashi
- Division
of Electrical Engineering and Computer Science, Kakuma-machi, Kanazawa University, Kanazawa 920-1192, Japan
- Precursory
Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Akichika Kumatani
- Graduate
School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8576, Japan
- Advanced
Institute for Material Research (AIMR), Tohoku University, Sendai, Miyagi 980-8576, Japan
| | - Hitoshi Shiku
- Department
of Applied Chemistry, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Tomokazu Matsue
- Graduate
School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8576, Japan
- Advanced
Institute for Material Research (AIMR), Tohoku University, Sendai, Miyagi 980-8576, Japan
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34
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Carr AR, Ponjavic A, Basu S, McColl J, Santos AM, Davis S, Laue ED, Klenerman D, Lee SF. Three-Dimensional Super-Resolution in Eukaryotic Cells Using the Double-Helix Point Spread Function. Biophys J 2017; 112:1444-1454. [PMID: 28402886 PMCID: PMC5390298 DOI: 10.1016/j.bpj.2017.02.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/07/2017] [Accepted: 02/21/2017] [Indexed: 02/02/2023] Open
Abstract
Single-molecule localization microscopy, typically based on total internal reflection illumination, has taken our understanding of protein organization and dynamics in cells beyond the diffraction limit. However, biological systems exist in a complicated three-dimensional environment, which has required the development of new techniques, including the double-helix point spread function (DHPSF), to accurately visualize biological processes. The application of the DHPSF approach has so far been limited to the study of relatively small prokaryotic cells. By matching the refractive index of the objective lens immersion liquid to that of the sample media, we demonstrate DHPSF imaging of up to 15-μm-thick whole eukaryotic cell volumes in three to five imaging planes. We illustrate the capabilities of the DHPSF by exploring large-scale membrane reorganization in human T cells after receptor triggering, and by using single-particle tracking to image several mammalian proteins, including membrane, cytoplasmic, and nuclear proteins in T cells and embryonic stem cells.
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Affiliation(s)
- Alexander R. Carr
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Aleks Ponjavic
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Srinjan Basu
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - James McColl
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ana Mafalda Santos
- Radcliffe Department of Clinical Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon Davis
- Radcliffe Department of Clinical Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Steven F. Lee
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom,Corresponding author
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35
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Lagerholm BC, Andrade DM, Clausen MP, Eggeling C. Convergence of lateral dynamic measurements in the plasma membrane of live cells from single particle tracking and STED-FCS. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2017; 50:063001. [PMID: 28458397 PMCID: PMC5390782 DOI: 10.1088/1361-6463/aa519e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/15/2016] [Accepted: 12/05/2016] [Indexed: 05/06/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) in combination with the super-resolution imaging method STED (STED-FCS), and single-particle tracking (SPT) are able to directly probe the lateral dynamics of lipids and proteins in the plasma membrane of live cells at spatial scales much below the diffraction limit of conventional microscopy. However, a major disparity in interpretation of data from SPT and STED-FCS remains, namely the proposed existence of a very fast (unhindered) lateral diffusion coefficient, ⩾5 µm2 s-1, in the plasma membrane of live cells at very short length scales, ≈⩽ 100 nm, and time scales, ≈1-10 ms. This fast diffusion coefficient has been advocated in several high-speed SPT studies, for lipids and membrane proteins alike, but the equivalent has not been detected in STED-FCS measurements. Resolving this ambiguity is important because the assessment of membrane dynamics currently relies heavily on SPT for the determination of heterogeneous diffusion. A possible systematic error in this approach would thus have vast implications in this field. To address this, we have re-visited the analysis procedure for SPT data with an emphasis on the measurement errors and the effect that these errors have on the measurement outputs. We subsequently demonstrate that STED-FCS and SPT data, following careful consideration of the experimental errors of the SPT data, converge to a common interpretation which for the case of a diffusing phospholipid analogue in the plasma membrane of live mouse embryo fibroblasts results in an unhindered, intra-compartment, diffusion coefficient of ≈0.7-1.0 µm2 s-1, and a compartment size of about 100-150 nm.
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Affiliation(s)
- B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Débora M Andrade
- Centre for Neural Circuits and Behaviour, University of Oxford, Mansfield Road, Oxford OX1 3SR, UK
| | - Mathias P Clausen
- MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, Odense M DK-5230, Denmark
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Christian Eggeling
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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36
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Fujimoto T, Parmryd I. Interleaflet Coupling, Pinning, and Leaflet Asymmetry-Major Players in Plasma Membrane Nanodomain Formation. Front Cell Dev Biol 2017; 4:155. [PMID: 28119914 PMCID: PMC5222840 DOI: 10.3389/fcell.2016.00155] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/27/2016] [Indexed: 01/26/2023] Open
Abstract
The plasma membrane has a highly asymmetric distribution of lipids and contains dynamic nanodomains many of which are liquid entities surrounded by a second, slightly different, liquid environment. Contributing to the dynamics is a continuous repartitioning of components between the two types of liquids and transient links between lipids and proteins, both to extracellular matrix and cytoplasmic components, that temporarily pin membrane constituents. This make plasma membrane nanodomains exceptionally challenging to study and much of what is known about membrane domains has been deduced from studies on model membranes at equilibrium. However, living cells are by definition not at equilibrium and lipids are distributed asymmetrically with inositol phospholipids, phosphatidylethanolamines and phosphatidylserines confined mostly to the inner leaflet and glyco- and sphingolipids to the outer leaflet. Moreover, each phospholipid group encompasses a wealth of species with different acyl chain combinations whose lateral distribution is heterogeneous. It is becoming increasingly clear that asymmetry and pinning play important roles in plasma membrane nanodomain formation and coupling between the two lipid monolayers. How asymmetry, pinning, and interdigitation contribute to the plasma membrane organization is only beginning to be unraveled and here we discuss their roles and interdependence.
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Affiliation(s)
- Toyoshi Fujimoto
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine Nagoya, Japan
| | - Ingela Parmryd
- Science for Life Laboratory, Medical Cell Biology, Uppsala University Uppsala, Sweden
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37
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Singh DR, Ahmed F, Paul MD, Gedam M, Pasquale EB, Hristova K. The SAM domain inhibits EphA2 interactions in the plasma membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:31-38. [PMID: 27776928 DOI: 10.1016/j.bbamcr.2016.10.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 10/18/2016] [Indexed: 11/18/2022]
Abstract
All members of the Eph receptor family of tyrosine kinases contain a SAM domain near the C terminus, which has been proposed to play a role in receptor homotypic interactions and/or interactions with binding partners. The SAM domain of EphA2 is known to be important for receptor function, but its contribution to EphA2 lateral interactions in the plasma membrane has not been determined. Here we use a FRET-based approach to directly measure the effect of the SAM domain on the stability of EphA2 dimers on the cell surface in the absence of ligand binding. We also investigate the functional consequences of EphA2 SAM domain deletion. Surprisingly, we find that the EphA2 SAM domain inhibits receptor dimerization and decreases EphA2 tyrosine phosphorylation. This role is dramatically different from the role of the SAM domain of the related EphA3 receptor, which we previously found to stabilize EphA3 dimers and increase EphA3 tyrosine phosphorylation in cells in the absence of ligand. Thus, the EphA2 SAM domain likely contributes to a unique mode of EphA2 interaction that leads to distinct signaling outputs.
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Affiliation(s)
- Deo R Singh
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States
| | - Fozia Ahmed
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States
| | - Michael D Paul
- Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles street, Baltimore, MD 21218, United States
| | - Manasee Gedam
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States
| | - Elena B Pasquale
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Road, La Jolla, San Diego, CA 92037, United States
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States; Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles street, Baltimore, MD 21218, United States.
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38
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Klaus CJS, Raghunathan K, DiBenedetto E, Kenworthy AK. Analysis of diffusion in curved surfaces and its application to tubular membranes. Mol Biol Cell 2016; 27:3937-3946. [PMID: 27733625 PMCID: PMC5170615 DOI: 10.1091/mbc.e16-06-0445] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/08/2016] [Accepted: 10/04/2016] [Indexed: 11/11/2022] Open
Abstract
Diffusion of particles in curved surfaces is inherently complex compared with diffusion in a flat membrane, owing to the nonplanarity of the surface. The consequence of such nonplanar geometry on diffusion is poorly understood but is highly relevant in the case of cell membranes, which often adopt complex geometries. To address this question, we developed a new finite element approach to model diffusion on curved membrane surfaces based on solutions to Fick's law of diffusion and used this to study the effects of geometry on the entry of surface-bound particles into tubules by diffusion. We show that variations in tubule radius and length can distinctly alter diffusion gradients in tubules over biologically relevant timescales. In addition, we show that tubular structures tend to retain concentration gradients for a longer time compared with a comparable flat surface. These findings indicate that sorting of particles along the surfaces of tubules can arise simply as a geometric consequence of the curvature without any specific contribution from the membrane environment. Our studies provide a framework for modeling diffusion in curved surfaces and suggest that biological regulation can emerge purely from membrane geometry.
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Affiliation(s)
| | - Krishnan Raghunathan
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232
| | | | - Anne K Kenworthy
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232 .,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
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39
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Eggeling C, Honigmann A. Closing the gap: The approach of optical and computational microscopy to uncover biomembrane organization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2558-2568. [DOI: 10.1016/j.bbamem.2016.03.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 12/15/2022]
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40
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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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41
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Arnold AM, Sevcsik E, Schütz GJ. Monte Carlo simulations of protein micropatterning in biomembranes: effects of immobile sticky obstacles. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2016; 49:10.1088/0022-3727/49/36/364002. [PMID: 30880837 PMCID: PMC6417683 DOI: 10.1088/0022-3727/49/36/364002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Single molecule trajectories of lipids and proteins can yield valuable information about the nanoscopic organization of the plasma membrane itself. The interpretation of such trajectories, however, is complicated, as the mobility of molecules can be affected by the presence of immobile obstacles, and the transient binding of the tracers to these obstacles. We have previously developed a micropatterning approach that allows for immobilizing a plasma membrane protein and probing the diffusional behavior of a putative interaction partner in living cells. Here, we provide guidelines on how this micropatterning approach can be extended to quantify interaction parameters between plasma membrane constituents in their natural environment. We simulated a patterned membrane system and evaluated the effect of different surface densities of patterned immobile obstacles on the relative mobility as well as the surface density of diffusing tracers. In the case of inert obstacles, the size of the obstacle can be assessed from its surface density at the percolation threshold, which in turn can be extracted from the diffusion behavior of the tracer. For sticky obstacles, two-dimensional dissociation constants can be determined from the tracer diffusion or surface density.
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Affiliation(s)
- Andreas M Arnold
- Institute of Applied Physics, Technische Universität Wien, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - Eva Sevcsik
- Institute of Applied Physics, Technische Universität Wien, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - Gerhard J Schütz
- Institute of Applied Physics, Technische Universität Wien, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
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Sarabipour S, Hristova K. Effect of the achondroplasia mutation on FGFR3 dimerization and FGFR3 structural response to fgf1 and fgf2: A quantitative FRET study in osmotically derived plasma membrane vesicles. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:1436-42. [PMID: 27040652 PMCID: PMC4870120 DOI: 10.1016/j.bbamem.2016.03.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/15/2016] [Accepted: 03/29/2016] [Indexed: 11/20/2022]
Abstract
The G380R mutation in the transmembrane domain of FGFR3 is a germline mutation responsible for most cases of Achondroplasia, a common form of human dwarfism. Here we use quantitative Fӧster Resonance Energy Transfer (FRET) and osmotically derived plasma membrane vesicles to study the effect of the achondroplasia mutation on the early stages of FGFR3 signaling in response to the ligands fgf1 and fgf2. Using a methodology that allows us to capture structural changes on the cytoplasmic side of the membrane in response to ligand binding to the extracellular domain of FGFR3, we observe no measurable effects of the G380R mutation on FGFR3 ligand-bound dimer configurations. Instead, the most notable effect of the achondroplasia mutation is increased propensity for FGFR3 dimerization in the absence of ligand. This work reveals new information about the molecular events that underlie the achondroplasia phenotype, and highlights differences in FGFR3 activation due to different single amino-acid pathogenic mutations.
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Affiliation(s)
- Sarvenaz Sarabipour
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, United States.
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Spatial distribution and activity of Na + /K + -ATPase in lipid bilayer membranes with phase boundaries. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1390-9. [DOI: 10.1016/j.bbamem.2016.03.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 02/20/2016] [Accepted: 03/10/2016] [Indexed: 11/21/2022]
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Sarabipour S, Ballmer-Hofer K, Hristova K. VEGFR-2 conformational switch in response to ligand binding. eLife 2016; 5:e13876. [PMID: 27052508 PMCID: PMC4829425 DOI: 10.7554/elife.13876] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/09/2016] [Indexed: 01/02/2023] Open
Abstract
VEGFR-2 is the primary regulator of angiogenesis, the development of new blood vessels from pre-existing ones. VEGFR-2 has been hypothesized to be monomeric in the absence of bound ligand, and to undergo dimerization and activation only upon ligand binding. Using quantitative FRET and biochemical analysis, we show that VEGFR-2 forms dimers also in the absence of ligand when expressed at physiological levels, and that these dimers are phosphorylated. Ligand binding leads to a change in the TM domain conformation, resulting in increased kinase domain phosphorylation. Inter-receptor contacts within the extracellular and TM domains are critical for the establishment of the unliganded dimer structure, and for the transition to the ligand-bound active conformation. We further show that the pathogenic C482R VEGFR-2 mutant, linked to infantile hemangioma, promotes ligand-independent signaling by mimicking the structure of the ligand-bound wild-type VEGFR-2 dimer.
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Affiliation(s)
- Sarvenaz Sarabipour
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, United States
| | - Kurt Ballmer-Hofer
- Laboratory of Biomolecular Research, Molecular Cell Biology, Paul Scherrer Institute, Villigen, Switzerland
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, United States
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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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King C, Stoneman M, Raicu V, Hristova K. Fully quantified spectral imaging reveals in vivo membrane protein interactions. Integr Biol (Camb) 2016; 8:216-29. [PMID: 26787445 DOI: 10.1039/c5ib00202h] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Here we introduce the fully quantified spectral imaging (FSI) method as a new tool to probe the stoichiometry and stability of protein complexes in biological membranes. The FSI method yields two dimensional membrane concentrations and FRET efficiencies in native plasma membranes. It can be used to characterize the association of membrane proteins: to differentiate between monomers, dimers, or oligomers, to produce binding (association) curves, and to measure the free energies of association in the membrane. We use the FSI method to study the lateral interactions of Vascular Endothelial Growth Factor Receptor 2 (VEGFR2), a member of the receptor tyrosine kinase (RTK) superfamily, in plasma membranes, in vivo. The knowledge gained through the use of the new method challenges the current understanding of VEGFR2 signaling.
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Affiliation(s)
- Christopher King
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
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Fujimoto T, Parmryd I. Interleaflet Coupling, Pinning, and Leaflet Asymmetry-Major Players in Plasma Membrane Nanodomain Formation. Front Cell Dev Biol 2016. [PMID: 28119914 DOI: 10.3389/fcell.2016.0015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
The plasma membrane has a highly asymmetric distribution of lipids and contains dynamic nanodomains many of which are liquid entities surrounded by a second, slightly different, liquid environment. Contributing to the dynamics is a continuous repartitioning of components between the two types of liquids and transient links between lipids and proteins, both to extracellular matrix and cytoplasmic components, that temporarily pin membrane constituents. This make plasma membrane nanodomains exceptionally challenging to study and much of what is known about membrane domains has been deduced from studies on model membranes at equilibrium. However, living cells are by definition not at equilibrium and lipids are distributed asymmetrically with inositol phospholipids, phosphatidylethanolamines and phosphatidylserines confined mostly to the inner leaflet and glyco- and sphingolipids to the outer leaflet. Moreover, each phospholipid group encompasses a wealth of species with different acyl chain combinations whose lateral distribution is heterogeneous. It is becoming increasingly clear that asymmetry and pinning play important roles in plasma membrane nanodomain formation and coupling between the two lipid monolayers. How asymmetry, pinning, and interdigitation contribute to the plasma membrane organization is only beginning to be unraveled and here we discuss their roles and interdependence.
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Affiliation(s)
- Toyoshi Fujimoto
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine Nagoya, Japan
| | - Ingela Parmryd
- Science for Life Laboratory, Medical Cell Biology, Uppsala University Uppsala, Sweden
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Abstract
Membrane nanodomains are dynamic liquid entities surrounded by another type of dynamic liquid. Diffusion can take place inside, around and in and out of the domains, and membrane components therefore continuously shift between domains and their surroundings. In the plasma membrane, there is the further complexity of links between membrane lipids and proteins both to the extracellular matrix and to intracellular proteins such as actin filaments. In addition, new membrane components are continuously delivered and old ones removed. On top of this, cells move. Taking all of this into account imposes great methodological challenges, and in the present chapter we discuss some methods that are currently used for membrane nanodomain studies, what information they can provide and their weaknesses.
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Abstract
Plasma membrane dynamics are an important ruler of cellular activity, particularly through the interaction and diffusion dynamics of membrane-embedded proteins and lipids. FCS (fluorescence correlation spectroscopy) on an optical (confocal) microscope is a popular tool for investigating such dynamics. Unfortunately, its full applicability is constrained by the limited spatial resolution of a conventional optical microscope. The present chapter depicts the combination of optical super-resolution STED (stimulated emission depletion) microscopy with FCS, and why it is an important tool for investigating molecular membrane dynamics in living cells. Compared with conventional FCS, the STED-FCS approach demonstrates an improved possibility to distinguish free from anomalous molecular diffusion, and thus to give new insights into lipid-protein interactions and the traditional lipid 'raft' theory.
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Membrane nanodomains: contribution of curvature and interaction with proteins and cytoskeleton. Essays Biochem 2015; 57:109-19. [PMID: 25658348 DOI: 10.1042/bse0570109] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The understanding of lipid membranes and their organization has undergone significant development with better techniques and therefore more resolved experiments. Many new factors and organizing principles have been discovered, and interplay between these factors is expected to result in rich functional behaviours. The major factors regulating the lateral membrane heterogeneity, apart from the well-studied phase separation, are cytoskeleton pinning, clustering of lipids and curvature. These factors are effective means to create membrane domains that provide rich biological functionality. We review the recent advances and concepts of membrane heterogeneity organization by curvature, cytoskeleton and clustering proteins.
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