1
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Winkelmann H, Richter CP, Eising J, Piehler J, Kurre R. Correlative single-molecule and structured illumination microscopy of fast dynamics at the plasma membrane. Nat Commun 2024; 15:5813. [PMID: 38987559 PMCID: PMC11236984 DOI: 10.1038/s41467-024-49876-9] [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: 09/25/2023] [Accepted: 06/21/2024] [Indexed: 07/12/2024] Open
Abstract
Total internal reflection fluorescence (TIRF) microscopy offers powerful means to uncover the functional organization of proteins in the plasma membrane with very high spatial and temporal resolution. Traditional TIRF illumination, however, shows a Gaussian intensity profile, which is typically deteriorated by overlaying interference fringes hampering precise quantification of intensities-an important requisite for quantitative analyses in single-molecule localization microscopy (SMLM). Here, we combine flat-field illumination by using a standard πShaper with multi-angular TIR illumination by incorporating a spatial light modulator compatible with fast super-resolution structured illumination microscopy (SIM). This distinct combination enables quantitative multi-color SMLM with a highly homogenous illumination. By using a dual camera setup with optimized image splitting optics, we achieve a versatile combination of SMLM and SIM with up to three channels. We deploy this setup for establishing robust detection of receptor stoichiometries based on single-molecule intensity analysis and single-molecule Förster resonance energy transfer (smFRET). Homogeneous illumination furthermore enables long-term tracking and localization microscopy (TALM) of cell surface receptors identifying spatial heterogeneity of mobility and accessibility in the plasma membrane. By combination of TALM and SIM, spatially and molecularly heterogenous diffusion properties can be correlated with nanoscale cytoskeletal organization and dynamics.
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Affiliation(s)
- Hauke Winkelmann
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Christian P Richter
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Jasper Eising
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Jacob Piehler
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Center for Cellular Nanoanalytics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
| | - Rainer Kurre
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Center for Cellular Nanoanalytics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Integrated Bioimaging Facility iBiOs, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
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2
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Puff N. Critical Role of Molecular Packing in Lo Phase Membrane Solubilization. MEMBRANES 2023; 13:652. [PMID: 37505018 PMCID: PMC10385406 DOI: 10.3390/membranes13070652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
Membrane solubilization induced by Triton X-100 (TX-100) was investigated. Different membrane compositions and phase states were studied along the detergent titration. Expected solubilization profiles were obtained but new information is provided. The fluorescence of nitrobenzoxadiazole (NBD)-labeled lipids indicates that the liquid-ordered (Lo)/liquid-disordered (Ld) phase coexistence is barely unaffected at sub-solubilizing detergent concentrations and highlights the vesicle-to-micelle transition. Moreover, the location of the NBD group in the bilayer emphasizes a detergent-membrane interaction in the case of the insoluble Lo phase membrane. It has also been shown that the molecular packing of the membrane loosens in the presence of TX-100, regardless of the solubilization profile. Motivated by studies on GPMVs, the solubilization of less ordered Lo phase membranes was considered in order to improve the effect of molecular packing on the extent of solubilization. Membranes composed of SM and Chol in an equimolar ratio doped with different amounts of PC were studied. The more ordered the Lo phase membrane is in the absence of detergent, the less likely it is to be solubilized. Furthermore, and in contrast to what is observed for membranes exhibiting an Lo/Ld phase coexistence, a very small decrease in the molecular packing of the Lo phase membrane radically modifies the extent of solubilization. These results have implications for the reliability of TX-100 insolubility as a method to detect ordered domains.
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Affiliation(s)
- Nicolas Puff
- Faculté des Sciences et Ingénierie, Sorbonne Université, UFR 925 Physics, F-75005 Paris, France
- Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, Université Paris Cité, F-75013 Paris, France
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3
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Sotolongo Bellón J, Birkholz O, Richter CP, Eull F, Kenneweg H, Wilmes S, Rothbauer U, You C, Walter MR, Kurre R, Piehler J. Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane. CELL REPORTS METHODS 2022; 2:100165. [PMID: 35474965 PMCID: PMC9017138 DOI: 10.1016/j.crmeth.2022.100165] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/19/2021] [Accepted: 01/13/2022] [Indexed: 12/22/2022]
Abstract
Localization and tracking of individual receptors by single-molecule imaging opens unique possibilities to unravel the assembly and dynamics of signaling complexes in the plasma membrane. We present a comprehensive workflow for imaging and analyzing receptor diffusion and interaction in live cells at single molecule level with up to four colors. Two engineered, monomeric GFP variants, which are orthogonally recognized by anti-GFP nanobodies, are employed for efficient and selective labeling of target proteins in the plasma membrane with photostable fluorescence dyes. This labeling technique enables us to quantitatively resolve the stoichiometry and dynamics of the interferon-γ (IFNγ) receptor signaling complex in the plasma membrane of living cells by multicolor single-molecule imaging. Based on versatile spatial and spatiotemporal correlation analyses, we identify ligand-induced receptor homo- and heterodimerization. Multicolor single-molecule co-tracking and quantitative single-molecule Förster resonance energy transfer moreover reveals transient assembly of IFNγ receptor heterotetramers and confirms its structural architecture.
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Affiliation(s)
- Junel Sotolongo Bellón
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Oliver Birkholz
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Christian P. Richter
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Florian Eull
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Hella Kenneweg
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Stephan Wilmes
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
- Division of Cell Signalling and Immunology, University of Dundee, School of Life Sciences, Dundee, UK
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard-Karls-University, Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Changjiang You
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Mark R. Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rainer Kurre
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
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4
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Binotti B, Jahn R, Pérez-Lara Á. An overview of the synaptic vesicle lipid composition. Arch Biochem Biophys 2021; 709:108966. [PMID: 34139199 DOI: 10.1016/j.abb.2021.108966] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 11/29/2022]
Abstract
Chemical neurotransmission is the major mechanism of neuronal communication. Neurotransmitters are released from secretory organelles, the synaptic vesicles (SVs) via exocytosis into the synaptic cleft. Fusion of SVs with the presynaptic plasma membrane is balanced by endocytosis, thus maintaining the presynaptic membrane at steady-state levels. The protein machineries responsible for exo- and endocytosis have been extensively investigated. In contrast, less is known about the role of lipids in synaptic transmission and how the lipid composition of SVs is affected by dynamic exo-endocytotic cycling. Here we summarize the current knowledge about the composition, organization, and function of SV membrane lipids. We also cover lipid biogenesis and maintenance during the synaptic vesicle cycle.
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Affiliation(s)
- Beyenech Binotti
- Department of Biochemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Reinhard Jahn
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
| | - Ángel Pérez-Lara
- Department of Physical Chemistry, University of Granada, Campus Universitario de Cartuja, 18071, Granada, Spain.
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5
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Janáček J, Brejchová J, Svoboda P. Determination of δ-opioid receptor molecules mobility in living cells plasma membrane by novel method of FRAP analysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1346-1354. [PMID: 31071299 DOI: 10.1016/j.bbamem.2019.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 04/09/2019] [Accepted: 04/29/2019] [Indexed: 11/18/2022]
Abstract
Fluorescence recovery after photobleaching (FRAP) is the preferred method for analyzing the lateral mobility of fluorescently-tagged proteins in the plasma membranes (PMs) of live cells. FRAP experiments are described as being easy to perform; however, the analysis of the acquired data can be difficult. The evaluation procedure must be properly combined with the imaging setup of the confocal microscope to provide unbiased results. With the aim of increasing the accuracy of determining the diffusion coefficient (D) and mobile fraction (Mf) of PM proteins, we developed a novel method for FRAP analysis in the equatorial plane of the cell. This method is based on the calculation of photobleaching characteristics, derived from the light intensity profile and optical parameters of the confocal microscope, and on the model of fluorescent molecule diffusion in PM regions outside of the focal plane. Furthermore, cell movement artifacts in the FRAP data are ameliorated by using a region of interest, which is not fixed but instead moves adaptively in coordination with the movement of cells. When this method was used to determine the mobility of the δ-opioid receptor-eYFP in HEK293 cells, a highly significant decrease in receptor mobility was detected in cholesterol-depleted cells. This decrease was fully reversible by the replenishment of cholesterol levels. Our results demonstrate the crucial role played by cholesterol in the dynamic organization of δ-opioid receptors in the PM under in vivo conditions. Our method may be applied for the determination of the D and Mf values of other PM proteins.
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Affiliation(s)
- Jiří Janáček
- Department of Biomathematics, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic.
| | - Jana Brejchová
- Department of Biomathematics, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Petr Svoboda
- Department of Biomathematics, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic
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6
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Horrevorts SK, Duinkerken S, Bloem K, Secades P, Kalay H, Musters RJ, van Vliet SJ, García-Vallejo JJ, van Kooyk Y. Toll-Like Receptor 4 Triggering Promotes Cytosolic Routing of DC-SIGN-Targeted Antigens for Presentation on MHC Class I. Front Immunol 2018; 9:1231. [PMID: 29963041 PMCID: PMC6010527 DOI: 10.3389/fimmu.2018.01231] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 05/16/2018] [Indexed: 11/20/2022] Open
Abstract
DC-SIGN is an antigen uptake receptor expressed on dendritic cells (DCs) with specificity for glycans present on a broad variety of pathogens and is capable of directing its cargo to MHC-I and MHC-II pathways for the induction of CD8+ and CD4+ T cell responses, respectively. Therefore, DC-SIGN is a very promising target for the delivery of antigen for anti-cancer vaccination. Although the endocytic route leading to MHC-II presentation is characterized to a large extent, the mechanisms controlling DC-SIGN targeted cross-presentation of exogenous peptides on MHC-I, are not completely resolved yet. In this paper, we used imaging flow cytometry and antigen-specific CD8+ T cells to investigate the intracellular fate of DC-SIGN and its cargo in human DCs. Our data demonstrates that immature DCs and toll-like receptor 4 (TLR4) stimulated DCs had similar internalization capacity and were both able to cross-present antigen targeted via DC-SIGN. Interestingly, simultaneous triggering of TLR4 and DC-SIGN on DCs resulted in the translocation of cargo to the cytosol, leading to proteasome-dependent processing and increased CD8+ T cell activation. Understanding the dynamics of DC-SIGN-mediated uptake and processing is essential for the design of optimal DC-SIGN-targeting vaccination strategies aimed at enhancing CD8+ T cell responses.
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Affiliation(s)
- Sophie K Horrevorts
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, Netherlands
| | - Sanne Duinkerken
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, Netherlands
| | - Karien Bloem
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, Netherlands.,Centre for Specialized Nutrition, Danone Research, Wageningen, Netherlands
| | - Pablo Secades
- Division of Cell Biology, Dutch Cancer Institute, Amsterdam, Netherlands
| | - Hakan Kalay
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, Netherlands
| | - René J Musters
- Department of Physiology, VU University Medical Center, Amsterdam, Netherlands
| | - Sandra J van Vliet
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, Netherlands
| | - Juan J García-Vallejo
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, Netherlands
| | - Yvette van Kooyk
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, Netherlands
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7
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Ligand-induced type II interleukin-4 receptor dimers are sustained by rapid re-association within plasma membrane microcompartments. Nat Commun 2017; 8:15976. [PMID: 28706306 PMCID: PMC5519985 DOI: 10.1038/ncomms15976] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 05/16/2017] [Indexed: 12/14/2022] Open
Abstract
The spatiotemporal organization of cytokine receptors in the plasma membrane is still debated with models ranging from ligand-independent receptor pre-dimerization to ligand-induced receptor dimerization occurring only after receptor uptake into endosomes. Here, we explore the molecular and cellular determinants governing the assembly of the type II interleukin-4 receptor, taking advantage of various agonists binding the receptor subunits with different affinities and rate constants. Quantitative kinetic studies using artificial membranes confirm that receptor dimerization is governed by the two-dimensional ligand–receptor interactions and identify a critical role of the transmembrane domain in receptor dimerization. Single molecule localization microscopy at physiological cell surface expression levels, however, reveals efficient ligand-induced receptor dimerization by all ligands, largely independent of receptor binding affinities, in line with the similar STAT6 activation potencies observed for all IL-4 variants. Detailed spatiotemporal analyses suggest that kinetic trapping of receptor dimers in actin-dependent microcompartments sustains robust receptor dimerization and signalling. The contribution of ligands for cytokine receptor dimerization is still not fully understood. Here, the authors show the efficient ligand-induced dimerization of type II interleukin-4 receptor at the plasma membrane and the kinetic trapping of signalling complexes by actin-dependent membrane microdomains.
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8
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DE JONGE N. Membrane protein stoichiometry studied in intact mammalian cells using liquid-phase electron microscopy. J Microsc 2017; 269:134-142. [DOI: 10.1111/jmi.12570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/15/2017] [Accepted: 03/25/2017] [Indexed: 02/02/2023]
Affiliation(s)
- N. DE JONGE
- Leibniz Institute for New Materials; Saarbrücken Germany
- Department of Physics; University of Saarland; Saarbrücken Germany
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9
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Mo GCH, Ross B, Hertel F, Manna P, Yang X, Greenwald E, Booth C, Plummer AM, Tenner B, Chen Z, Wang Y, Kennedy EJ, Cole PA, Fleming KG, Palmer A, Jimenez R, Xiao J, Dedecker P, Zhang J. Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution. Nat Methods 2017; 14:427-434. [PMID: 28288122 PMCID: PMC5388356 DOI: 10.1038/nmeth.4221] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/06/2017] [Indexed: 12/17/2022]
Abstract
Compartmentalized biochemical activities are essential to all cellular processes, but there is no generalizable method to visualize dynamic protein activities in living cells at a resolution commensurate with their compartmentalization. Here we introduce a new class of fluorescent biosensors that detect biochemical activities in living cells at a resolution up to three-fold better than the diffraction limit. Utilizing specific, binding-induced changes in protein fluorescence dynamics, these biosensors translate kinase activities or protein-protein interactions into changes in fluorescence fluctuations, which are quantifiable through stochastic optical fluctuation imaging. A Protein Kinase A (PKA) biosensor allowed us to resolve minute PKA activity microdomains on the plasma membrane of living cells and uncover the role of clustered anchoring proteins in organizing these activity microdomains. Together, these findings suggest that biochemical activities of the cell are spatially organized into an activity architecture, whose structural and functional characteristics can be revealed by these new biosensors.
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Affiliation(s)
- Gary C H Mo
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Brian Ross
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Fabian Hertel
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Premashis Manna
- JILA, University of Colorado and NIST, Boulder, Colorado, USA.,Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, Colorado, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eric Greenwald
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Chris Booth
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Ashlee M Plummer
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Brian Tenner
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zan Chen
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yuxiao Wang
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, USA
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, USA
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Karen G Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Amy Palmer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, Colorado, USA.,BioFrontiers Institute, University of Colorado, Boulder, Boulder, Colorado, USA
| | - Ralph Jimenez
- JILA, University of Colorado and NIST, Boulder, Colorado, USA.,Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, Colorado, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA.,Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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10
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Tenner B, Mehta S, Zhang J. Optical sensors to gain mechanistic insights into signaling assemblies. Curr Opin Struct Biol 2016; 41:203-210. [PMID: 27611602 PMCID: PMC5423777 DOI: 10.1016/j.sbi.2016.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/29/2016] [Indexed: 11/17/2022]
Abstract
Protein complexes play a major role in transducing information from outside the cell into instructions for growth and survival, and understanding how these complexes relay and shape intracellular signals has been a central question in signaling biology. Fluorescent proteins have proven paramount in opening windows for researchers to peer into the architecture and inner workings of signaling assemblies within the living cell and in real-time. In this review, we will provide readers with a current perspective on the development and use of genetically encoded optical probes to dissect the function of signaling complexes.
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Affiliation(s)
- Brian Tenner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States; Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States; Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States.
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11
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You C, Marquez-Lago TT, Richter CP, Wilmes S, Moraga I, Garcia KC, Leier A, Piehler J. Receptor dimer stabilization by hierarchical plasma membrane microcompartments regulates cytokine signaling. SCIENCE ADVANCES 2016; 2:e1600452. [PMID: 27957535 PMCID: PMC5135388 DOI: 10.1126/sciadv.1600452] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 10/26/2016] [Indexed: 06/06/2023]
Abstract
The interaction dynamics of signaling complexes is emerging as a key determinant that regulates the specificity of cellular responses. We present a combined experimental and computational study that quantifies the consequences of plasma membrane microcompartmentalization for the dynamics of type I interferon receptor complexes. By using long-term dual-color quantum dot (QD) tracking, we found that the lifetime of individual ligand-induced receptor heterodimers depends on the integrity of the membrane skeleton (MSK), which also proved important for efficient downstream signaling. By pair correlation tracking and localization microscopy as well as by fast QD tracking, we identified a secondary confinement within ~300-nm-sized zones. A quantitative spatial stochastic diffusion-reaction model, entirely parameterized on the basis of experimental data, predicts that transient receptor confinement by the MSK meshwork allows for rapid reassociation of dissociated receptor dimers. Moreover, the experimentally observed apparent stabilization of receptor dimers in the plasma membrane was reproduced by simulations of a refined, hierarchical compartment model. Our simulations further revealed that the two-dimensional association rate constant is a key parameter for controlling the extent of MSK-mediated stabilization of protein complexes, thus ensuring the specificity of this effect. Together, experimental evidence and simulations support the hypothesis that passive receptor confinement by MSK-based microcompartmentalization promotes maintenance of signaling complexes in the plasma membrane.
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Affiliation(s)
- Changjiang You
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | | | | | - Stephan Wilmes
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - K. Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - André Leier
- Isaac Newton Institute for Mathematical Sciences, University of Cambridge, Cambridge, U.K
- Okinawa Institute of Science and Technology, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
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12
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Rodriguez EA, Campbell RE, Lin JY, Lin MZ, Miyawaki A, Palmer AE, Shu X, Zhang J, Tsien RY. The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins. Trends Biochem Sci 2016; 42:111-129. [PMID: 27814948 DOI: 10.1016/j.tibs.2016.09.010] [Citation(s) in RCA: 393] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/21/2016] [Accepted: 09/26/2016] [Indexed: 02/08/2023]
Abstract
Over the past 20 years, protein engineering has been extensively used to improve and modify the fundamental properties of fluorescent proteins (FPs) with the goal of adapting them for a fantastic range of applications. FPs have been modified by a combination of rational design, structure-based mutagenesis, and countless cycles of directed evolution (gene diversification followed by selection of clones with desired properties) that have collectively pushed the properties to photophysical and biochemical extremes. In this review, we provide both a summary of the progress that has been made during the past two decades, and a broad overview of the current state of FP development and applications in mammalian systems.
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Affiliation(s)
- Erik A Rodriguez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
| | - John Y Lin
- School of Medicine, University of Tasmania, Hobart, TAS 7000, Australia.
| | - Michael Z Lin
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA.
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Amy E Palmer
- Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA.
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Roger Y Tsien
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, 92093, USA.
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13
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Peckys DB, Alansary D, Niemeyer BA, de Jonge N. Visualizing Quantum Dot Labeled ORAI1 Proteins in Intact Cells Via Correlative Light and Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:902-912. [PMID: 27515473 DOI: 10.1017/s1431927616011491] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
ORAI1 proteins are ion channel subunits and the essential pore-forming units of the calcium release-activated calcium channel complex essential for T-cell activation and many other cellular processes. In this study, we used environmental scanning electron microscopy (ESEM) with scanning transmission electron microscopy (STEM) detection to image plasma membrane expressed ORAI1 proteins in whole Jurkat T cells in the liquid state. Utilizing a stably transfected Jurkat T cell clone expressing human ORAI1 with an extracellular human influenza hemagglutinin (HA) tag we investigated if liquid-phase STEM can be applied to detect recombinant surface expressed protein. Streptavidin coated quantum dots were coupled in a one-to-one stoichiometry to ORAI1 proteins detected by biotinylated anti-HA fragmented antibody fragments. High-resolution electron microscopic images revealed the individual label locations from which protein pair distances were determined. These data were analyzed using the pair correlation function and, in addition, an analysis of cluster size and frequency was performed. ORAI1 was found to be present in hexamers in a small fraction only, and ORAI1 resided mostly in monomers and dimers.
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Affiliation(s)
- Diana B Peckys
- 1Department of Molecular Biophysics,Saarland University,CIPMM,66421 Homburg,Germany
| | - Dalia Alansary
- 1Department of Molecular Biophysics,Saarland University,CIPMM,66421 Homburg,Germany
| | - Barbara A Niemeyer
- 1Department of Molecular Biophysics,Saarland University,CIPMM,66421 Homburg,Germany
| | - Niels de Jonge
- 2INM - Leibniz Institute for New Materials,66123 Saarbrücken,Germany
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14
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Eich C, Manzo C, de Keijzer S, Bakker GJ, Reinieren-Beeren I, García-Parajo MF, Cambi A. Changes in membrane sphingolipid composition modulate dynamics and adhesion of integrin nanoclusters. Sci Rep 2016; 6:20693. [PMID: 26869100 PMCID: PMC4751618 DOI: 10.1038/srep20693] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/11/2016] [Indexed: 12/14/2022] Open
Abstract
Sphingolipids are essential constituents of the plasma membrane (PM) and play an important role in signal transduction by modulating clustering and dynamics of membrane receptors. Changes in lipid composition are therefore likely to influence receptor organisation and function, but how this precisely occurs is difficult to address given the intricacy of the PM lipid-network. Here, we combined biochemical assays and single molecule dynamic approaches to demonstrate that the local lipid environment regulates adhesion of integrin receptors by impacting on their lateral mobility. Induction of sphingomyelinase (SMase) activity reduced sphingomyelin (SM) levels by conversion to ceramide (Cer), resulting in impaired integrin adhesion and reduced integrin mobility. Dual-colour imaging of cortical actin in combination with single molecule tracking of integrins showed that this reduced mobility results from increased coupling to the actin cytoskeleton brought about by Cer formation. As such, our data emphasizes a critical role for the PM local lipid composition in regulating the lateral mobility of integrins and their ability to dynamically increase receptor density for efficient ligand binding in the process of cell adhesion.
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Affiliation(s)
- Christina Eich
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
| | - Sandra de Keijzer
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands
| | - Gert-Jan Bakker
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands
| | - Inge Reinieren-Beeren
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands
| | - Maria F García-Parajo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain.,ICREA-Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Alessandra Cambi
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands
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15
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Bosch PJ, Kanger JS, Subramaniam V. Classification of dynamical diffusion states in single molecule tracking microscopy. Biophys J 2015; 107:588-598. [PMID: 25099798 DOI: 10.1016/j.bpj.2014.05.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/04/2014] [Accepted: 05/29/2014] [Indexed: 12/21/2022] Open
Abstract
Single molecule tracking of membrane proteins by fluorescence microscopy is a promising method to investigate dynamic processes in live cells. Translating the trajectories of proteins to biological implications, such as protein interactions, requires the classification of protein motion within the trajectories. Spatial information of protein motion may reveal where the protein interacts with cellular structures, because binding of proteins to such structures often alters their diffusion speed. For dynamic diffusion systems, we provide an analytical framework to determine in which diffusion state a molecule is residing during the course of its trajectory. We compare different methods for the quantification of motion to utilize this framework for the classification of two diffusion states (two populations with different diffusion speed). We found that a gyration quantification method and a Bayesian statistics-based method are the most accurate in diffusion-state classification for realistic experimentally obtained datasets, of which the gyration method is much less computationally demanding. After classification of the diffusion, the lifetime of the states can be determined, and images of the diffusion states can be reconstructed at high resolution. Simulations validate these applications. We apply the classification and its applications to experimental data to demonstrate the potential of this approach to obtain further insights into the dynamics of cell membrane proteins.
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Affiliation(s)
- Peter J Bosch
- Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, The Netherlands
| | - Johannes S Kanger
- MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, The Netherlands
| | - Vinod Subramaniam
- Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, The Netherlands; MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, The Netherlands.
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16
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Peckys DB, Korf U, de Jonge N. Local variations of HER2 dimerization in breast cancer cells discovered by correlative fluorescence and liquid electron microscopy. SCIENCE ADVANCES 2015; 1:e1500165. [PMID: 26601217 PMCID: PMC4646781 DOI: 10.1126/sciadv.1500165] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/03/2015] [Indexed: 05/17/2023]
Abstract
The formation of HER2 homodimers plays an important role in breast cancer aggressiveness and progression; however, little is known about its localization. We have studied the intra- and intercellular variation of HER2 at the single-molecule level in intact SKBR3 breast cancer cells. Whole cells were visualized in hydrated state with correlative fluorescence microscopy and environmental scanning electron microscopy (ESEM). The locations of individual HER2 receptors were detected using an anti-HER2 affibody in combination with a quantum dot (QD), a fluorescent nanoparticle. Fluorescence microscopy revealed considerable differences of HER2 membrane expression between individual cells and between different membrane regions of the same cell (that is, membrane ruffles and flat areas). Subsequent ESEM of the corresponding cellular regions provided images of individually labeled HER2 receptors. The high spatial resolution of 3 nm and the close proximity between the QD and the receptor allowed quantifying the stoichiometry of HER2 complexes, distinguishing between monomers, dimers, and higher-order clusters. Downstream data analysis based on calculating the pair correlation function from receptor positions showed that cellular regions exhibiting membrane ruffles contained a substantial fraction of HER2 in homodimeric state. Larger-order clusters were also present. Membrane areas with homogeneous membrane topography, on the contrary, displayed HER2 in random distribution. Second, HER2 homodimers appeared to be absent from a small subpopulation of cells exhibiting a flat membrane topography, possibly resting cells. Local differences in homodimer presence may point toward functional differences with possible relevance for studying metastasis and drug response.
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Affiliation(s)
- Diana B. Peckys
- INM—Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Ulrike Korf
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Niels de Jonge
- INM—Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
- Department of Physics, University of Saarland, Campus A5 1, 66123 Saarbrücken, Germany
- Corresponding author. E-mail:
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17
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van Spriel AB, van den Bogaart G, Cambi A. Editorial: Membrane domains as new drug targets. Front Physiol 2015; 6:172. [PMID: 26082723 PMCID: PMC4451355 DOI: 10.3389/fphys.2015.00172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/20/2015] [Indexed: 01/19/2023] Open
Affiliation(s)
- Annemiek B van Spriel
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Netherlands
| | - Alessandra Cambi
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Netherlands
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18
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Bosch PJ, Corrêa IR, Sonntag MH, Ibach J, Brunsveld L, Kanger JS, Subramaniam V. Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single-molecule tracking microscopy in live cells. Biophys J 2015; 107:803-14. [PMID: 25140415 DOI: 10.1016/j.bpj.2014.06.040] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 05/22/2014] [Accepted: 06/10/2014] [Indexed: 11/19/2022] Open
Abstract
Single-molecule tracking has become a widely used technique for studying protein dynamics and their organization in the complex environment of the cell. In particular, the spatiotemporal distribution of membrane receptors is an active field of study due to its putative role in the regulation of signal transduction. The SNAP-tag is an intrinsically monovalent and highly specific genetic tag for attaching a fluorescent label to a protein of interest. Little information is currently available on the choice of optimal fluorescent dyes for single-molecule microscopy utilizing the SNAP-tag labeling system. We surveyed 6 green and 16 red excitable dyes for their suitability in single-molecule microscopy of SNAP-tag fusion proteins in live cells. We determined the nonspecific binding levels and photostability of these dye conjugates when bound to a SNAP-tag fused membrane protein in live cells. We found that only a limited subset of the dyes tested is suitable for single-molecule tracking microscopy. The results show that a careful choice of the dye to conjugate to the SNAP-substrate to label SNAP-tag fusion proteins is very important, as many dyes suffer from either rapid photobleaching or high nonspecific staining. These characteristics appear to be unpredictable, which motivated the need to perform the systematic survey presented here. We have developed a protocol for evaluating the best dyes, and for the conditions that we evaluated, we find that Dy 549 and CF 640 are the best choices tested for single-molecule tracking. Using an optimal dye pair, we also demonstrate the possibility of dual-color single-molecule imaging of SNAP-tag fusion proteins. This survey provides an overview of the photophysical and imaging properties of a range of SNAP-tag fluorescent substrates, enabling the selection of optimal dyes and conditions for single-molecule imaging of SNAP-tagged fusion proteins in eukaryotic cell lines.
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Affiliation(s)
- Peter J Bosch
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | | | - Michael H Sonntag
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Jenny Ibach
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Johannes S Kanger
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Vinod Subramaniam
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands.
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19
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Pawar AB, Deshpande SA, Gopal SM, Wassenaar TA, Athale CA, Sengupta D. Thermodynamic and kinetic characterization of transmembrane helix association. Phys Chem Chem Phys 2015; 17:1390-8. [DOI: 10.1039/c4cp03732d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The transient dimerization of transmembrane proteins is an important event in several cellular processes and here we use coarse-grain and meso-scale modeling methods to quantify their underlying dynamics.
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Affiliation(s)
| | | | | | - Tsjerk A. Wassenaar
- Department of Biology
- Computational Biology
- University of Erlangen-Nürnberg
- 91058 Erlangen
- Germany
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20
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Roder F, Wilmes S, Richter CP, Piehler J. Rapid transfer of transmembrane proteins for single molecule dimerization assays in polymer-supported membranes. ACS Chem Biol 2014; 9:2479-84. [PMID: 25203456 DOI: 10.1021/cb5005806] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Dimerization of transmembrane receptors is a key regulatory factor in cellular communication, which has remained challenging to study under well-defined conditions in vitro. We developed a novel strategy to explore membrane protein interactions in a controlled lipid environment requiring minute sample quantities. By rapid transfer of transmembrane proteins from mammalian cells into polymer-supported membranes, membrane proteins could be efficiently fluorescence labeled and reconstituted with very low background. Thus, differential ligand-induced dimerization of the type I interferon (IFN) receptor subunits IFNAR1 and IFNAR2 could be probed quantitatively at physiologically relevant concentrations by single molecule imaging. These measurements clearly support a regulatory role of the affinity of IFNs toward IFNAR1 for controlling the level of receptor dimerization.
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Affiliation(s)
- Friedrich Roder
- Division
of Biophysics, Department
of Biology, University of Osnabrück, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Stephan Wilmes
- Division
of Biophysics, Department
of Biology, University of Osnabrück, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Christian P. Richter
- Division
of Biophysics, Department
of Biology, University of Osnabrück, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Division
of Biophysics, Department
of Biology, University of Osnabrück, Barbarastr. 11, 49076 Osnabrück, Germany
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21
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Berry H, Soula HA. Spatial distributions at equilibrium under heterogeneous transient subdiffusion. Front Physiol 2014; 5:437. [PMID: 25429273 PMCID: PMC4228838 DOI: 10.3389/fphys.2014.00437] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 10/27/2014] [Indexed: 11/18/2022] Open
Abstract
Experimental measurements of the mobility of macromolecules, especially proteins, in cells and their membranes consistently report transient subdiffusion with possibly position-dependent—non-homogeneous—properties. However, the spatiotemporal dynamics of protein mobility when transient subdiffusion is restricted to a subregion of space is still unclear. Here, we investigated the spatial distribution at equilibrium of proteins undergoing transient subdiffusion due to continuous-time random walks (CTRW) in a restricted subregion of a two-dimensional space. Our Monte-Carlo simulations suggest that this process leads to a non-homogeneous spatial distribution of the proteins at equilibrium, where proteins increasingly accumulate in the CTRW subregion as its anomalous properties are increasingly marked. In the case of transient CTRW, we show that this accumulation is dictated by the asymptotic Brownian regime and not by the initial anomalous transient dynamics. Moreover, our results also show that this dominance of the asymptotic Brownian regime cannot be simply generalized to other scenarios of transient subdiffusion. In particular, non-homogeneous transient subdiffusion due to hindrance by randomly-located immobile obstacles does not lead to such a strong local accumulation. These results suggest that, even though they exhibit the same time-dependence of the mean-squared displacement, the different scenarios proposed to account for subdiffusion in the cell lead to different protein distribution in space, even at equilibrium and without coupling with reaction.
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Affiliation(s)
- Hugues Berry
- Beagle, Institut National de Recherche en Informatique et en Automatique Villeurbanne, France ; Laboratoire d'InfoRmatique en Image et Systèmes d'information, UMR 5205 CNRS-INSA, Université de Lyon Villeurbanne, France
| | - Hédi A Soula
- Beagle, Institut National de Recherche en Informatique et en Automatique Villeurbanne, France ; Institut Multidisciplinaire de Biochimie des Lipides, Inserm UMR1060, Université de Lyon Villeurbanne, France
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22
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García-Vallejo JJ, Unger WWJ, Kalay H, van Kooyk Y. Glycan-based DC-SIGN targeting to enhance antigen cross-presentation in anticancer vaccines. Oncoimmunology 2014; 2:e23040. [PMID: 23525136 PMCID: PMC3601176 DOI: 10.4161/onci.23040] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In vivo dendritic-cell targeting constitutes a promising strategy for anticancer vaccination. Here, we discuss the usage of multivalent DC-SIGN-targeting glycan platforms that allow for the efficient routing of antigens to the endo-lysosomal pathway as well as to a yet uncharacterized cross-presentation mechanism inducing CD4+ and CD8+ T-cell responses.
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Affiliation(s)
- Juan J García-Vallejo
- Department of Molecular Cell Biology and Immunology; VU University Medical Center; Amsterdam, The Netherlands
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23
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You C, Richter CP, Löchte S, Wilmes S, Piehler J. Dynamic Submicroscopic Signaling Zones Revealed by Pair Correlation Tracking and Localization Microscopy. Anal Chem 2014; 86:8593-602. [DOI: 10.1021/ac501127r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Changjiang You
- Department
of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Christian P. Richter
- Department
of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Sara Löchte
- Department
of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Stephan Wilmes
- Department
of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Department
of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
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24
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Puff N, Watanabe C, Seigneuret M, Angelova MI, Staneva G. Lo/Ld phase coexistence modulation induced by GM1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2105-14. [DOI: 10.1016/j.bbamem.2014.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 04/30/2014] [Accepted: 05/03/2014] [Indexed: 01/31/2023]
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25
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Saka SK, Honigmann A, Eggeling C, Hell SW, Lang T, Rizzoli SO. Multi-protein assemblies underlie the mesoscale organization of the plasma membrane. Nat Commun 2014; 5:4509. [PMID: 25060237 PMCID: PMC4124874 DOI: 10.1038/ncomms5509] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 06/25/2014] [Indexed: 02/07/2023] Open
Abstract
Most proteins have uneven distributions in the plasma membrane. Broadly speaking, this may be caused by mechanisms specific to each protein, or may be a consequence of a general pattern that affects the distribution of all membrane proteins. The latter hypothesis has been difficult to test in the past. Here, we introduce several approaches based on click chemistry, through which we study the distribution of membrane proteins in living cells, as well as in membrane sheets. We found that the plasma membrane proteins form multi-protein assemblies that are long lived (minutes), and in which protein diffusion is restricted. The formation of the assemblies is dependent on cholesterol. They are separated and anchored by the actin cytoskeleton. Specific proteins are preferentially located in different regions of the assemblies, from their cores to their edges. We conclude that the assemblies constitute a basic mesoscale feature of the membrane, which affects the patterning of most membrane proteins, and possibly also their activity. Although many proteins adopt uneven distributions in the plasma membrane, it is not clear how these nanoscale heterogeneities relate to the general protein patterning of the membrane. Saka et al. use click chemistry to reveal the mesoscale organization of membrane proteins into multi-protein assemblies.
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Affiliation(s)
- Sinem K Saka
- 1] Department of Neuro- and Sensory Physiology, University of Göttingen Medical Centre, and Centre for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37075 Göttingen, Germany [2] International Max Planck Research School Molecular Biology, 37077 Göttingen, Germany
| | - Alf Honigmann
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Stefan W Hell
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Thorsten Lang
- Department of Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University of Göttingen Medical Centre, and Centre for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37075 Göttingen, Germany
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26
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Epidermal growth factor receptor subunit locations determined in hydrated cells with environmental scanning electron microscopy. Sci Rep 2014; 3:2626. [PMID: 24022088 PMCID: PMC3769654 DOI: 10.1038/srep02626] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/21/2013] [Indexed: 11/15/2022] Open
Abstract
Imaging single epidermal growth factor receptors (EGFR) in intact cells is presently limited by the available microscopy methods. Environmental scanning electron microscopy (ESEM) of whole cells in hydrated state in combination with specific labeling with gold nanoparticles was used to localize activated EGFRs in the plasma membranes of COS7 and A549 cells. The use of a scanning transmission electron microscopy (STEM) detector yielded a spatial resolution of 3 nm, sufficient to identify the locations of individual EGFR dimer subunits. The sizes and distribution of dimers and higher order clusters of EGFRs were determined. The distance between labels bound to dimers amounted to 19 nm, consistent with a molecular model. A fraction of the EGFRs was found in higher order clusters with sizes ranging from 32–56 nm. ESEM can be used for quantitative whole cell screening studies of membrane receptors, and for the study of nanoparticle-cell interactions in general.
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27
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Zuidscherwoude M, de Winde CM, Cambi A, van Spriel AB. Microdomains in the membrane landscape shape antigen-presenting cell function. J Leukoc Biol 2013; 95:251-63. [PMID: 24168856 DOI: 10.1189/jlb.0813440] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The plasma membrane of immune cells is a highly organized cell structure that is key to the initiation and regulation of innate and adaptive immune responses. It is well-established that immunoreceptors embedded in the plasma membrane have a nonrandom spatial distribution that is important for coupling to components of intracellular signaling cascades. In the last two decades, specialized membrane microdomains, including lipid rafts and TEMs, have been identified. These domains are preformed structures ("physical entities") that compartmentalize proteins, lipids, and signaling molecules into multimolecular assemblies. In APCs, different microdomains containing immunoreceptors (MHC proteins, PRRs, integrins, among others) have been reported that are imperative for efficient pathogen recognition, the formation of the immunological synapse, and subsequent T cell activation. In addition, recent work has demonstrated that tetraspanin microdomains and lipid rafts are involved in BCR signaling and B cell activation. Research into the molecular mechanisms underlying membrane domain formation is fundamental to a comprehensive understanding of membrane-proximal signaling and APC function. This review will also discuss the advances in the microscopy field for the visualization of the plasma membrane, as well as the recent progress in targeting microdomains as novel, therapeutic approach for infectious and malignant diseases.
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Affiliation(s)
- Malou Zuidscherwoude
- 1.Nijmegen Centre for Molecular Life Sciences/278 TIL, Radboud University Medical Centre, Geert Grooteplein 28, 6525GA, Nijmegen, The Netherlands.
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28
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Bloem K, Vuist IM, van der Plas AJ, Knippels LMJ, Garssen J, García-Vallejo JJ, van Vliet SJ, van Kooyk Y. Ligand binding and signaling of dendritic cell immunoreceptor (DCIR) is modulated by the glycosylation of the carbohydrate recognition domain. PLoS One 2013; 8:e66266. [PMID: 23776650 PMCID: PMC3679074 DOI: 10.1371/journal.pone.0066266] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 05/03/2013] [Indexed: 11/18/2022] Open
Abstract
C-type lectins are innate receptors expressed on antigen-presenting cells that are involved in the recognition of glycosylated pathogens and self-glycoproteins. Upon ligand binding, internalization and/or signaling often occur. Little is known on the glycan specificity and ligands of the Dendritic Cell Immunoreceptor (DCIR), the only classical C-type lectin that contains an intracellular immunoreceptor tyrosine-based inhibitory motif (ITIM). Here we show that purified DCIR binds the glycan structures Lewisb and Man3. Interestingly, binding could not be detected when DCIR was expressed on cells. Since DCIR has an N-glycosylation site inside its carbohydrate recognition domain (CRD), we investigated the effect of this glycan in ligand recognition. Removing or truncating the glycans present on purified DCIR increased the affinity for DCIR-binding glycans. Nevertheless, altering the glycosylation status of the DCIR expressing cell or mutating the N-glycosylation site of DCIR itself did not increase glycan binding. In contrast, cis and trans interactions with glycans induced DCIR mediated signaling, resulting in a decreased phosphorylation of the ITIM sequence. These results show that glycan binding to DCIR is influenced by the glycosylation of the CRD region in DCIR and that interaction with its ligands result in signaling via its ITIM motif.
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Affiliation(s)
- Karien Bloem
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
- Danone Research, Centre for Specialized Nutrition, Wageningen, The Netherlands
| | - Ilona M. Vuist
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
| | - Arend-Jan van der Plas
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
| | - Léon M. J. Knippels
- Danone Research, Centre for Specialized Nutrition, Wageningen, The Netherlands
- Department of Pharmacology and Pathophysiology, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, The Netherlands
| | - Johan Garssen
- Danone Research, Centre for Specialized Nutrition, Wageningen, The Netherlands
- Department of Pharmacology and Pathophysiology, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, The Netherlands
| | - Juan J. García-Vallejo
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sandra J. van Vliet
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
| | - Yvette van Kooyk
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
- * E-mail:
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29
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Hovanyecz P, Guibert E, Pellegrino J, Rodriguez J, Sigot V. Extended cold storage of cultured hepatocytes impairs endocytic uptake during normothermic rewarming. Cryobiology 2013; 66:112-20. [DOI: 10.1016/j.cryobiol.2012.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/23/2012] [Accepted: 12/15/2012] [Indexed: 12/27/2022]
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30
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You C, Wilmes S, Richter CP, Beutel O, Liße D, Piehler J. Electrostatically controlled quantum dot monofunctionalization for interrogating the dynamics of protein complexes in living cells. ACS Chem Biol 2013. [PMID: 23186299 DOI: 10.1021/cb300543t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Quantum dots (QD) are powerful labels for probing diffusion and interaction dynamics of proteins on the single molecule level in living cells. Protein cross-linking due to multifunctional QD strongly affects these properties. This becomes particularly critical when labeling interaction partners with QDs for interrogating the dynamics of complexes. We have here implemented a generic method for QD monofunctionalization based on electrostatic repulsion of a highly negatively charged peptide carrier. On the basis of this method, monobiotinylated QDs were prepared with high yield as confirmed by single molecule assays. These QDs were successfully employed for probing the assembly and diffusion dynamics of binary and ternary cytokine-receptor complexes on the surface of living cells by dual color single QD tracking. Thus, sequential and dynamic recruitment of the type I interferon receptor subunits by the ligand could be observed.
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Affiliation(s)
- Changjiang You
- Division
of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück,
Germany
| | - Stephan Wilmes
- Division
of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück,
Germany
| | - Christian P. Richter
- Division
of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück,
Germany
| | - Oliver Beutel
- Division
of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück,
Germany
| | - Domenik Liße
- Division
of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück,
Germany
| | - Jacob Piehler
- Division
of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück,
Germany
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31
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Yu X, Wang J, Feizpour A, Reinhard BM. Illuminating the lateral organization of cell-surface CD24 and CD44 through plasmon coupling between Au nanoparticle immunolabels. Anal Chem 2013; 85:1290-4. [PMID: 23320416 PMCID: PMC3669593 DOI: 10.1021/ac303310j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CD44 and CD24 are important cell surface glycoproteins whose relative expression levels are used to identify so-called cancer stem cells (CSCs). While current diagnostic applications of CD44 and CD24 focus primarily on their expression levels, we demonstrate here that noble metal nanoparticle (NP) immunolabeling in combination with plasmon coupling microscopy (PCM) can reveal more subtle differences, such as the spatial organization of these surface species on subdiffraction limit length scales. We quantified both expression and spatial clustering of CD44 and CD24 on MCF7 and SKBR3 breast cancer cells through analysis of the labeling intensity and the electromagnetic coupling of the NP labels, respectively. The labeling intensity was well correlated with the receptor expression, but the inspection of the labeled cell surface in the optical microscope revealed that the NP immunolabels were not homogeneously distributed. Consistent with a heterogeneous spatial distribution of the targeted CD24 and CD44 in the plasma membrane, a significant fraction of the NPs were organized into clusters, which were easily detectable in the optical microscope as discrete spots with colors ranging from green to orange. To further quantify the spatial organization of the targeted proteins, we characterized individual NP clusters through spatially resolved elastic scattering spectroscopy. The statistical analysis of the single cluster spectra revealed a higher clustering affinity for CD24 than for CD44 in the investigated cancer models. This preferential clustering was removed upon lipid raft disruption through cholesterol sequestration. Overall, these observations confirm a preferential enrichment of CD24 in lipid rafts and a more random distribution of CD44 in the plasma membrane as cause for the observed differences in protein clustering.
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Affiliation(s)
- Xinwei Yu
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02215, United States
| | - Jing Wang
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02215, United States
| | - Amin Feizpour
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02215, United States
| | - Björn M. Reinhard
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02215, United States
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32
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Unsay JD, García-Sáez AJ. Scanning fluorescence correlation spectroscopy in model membrane systems. Methods Mol Biol 2013; 1033:185-205. [PMID: 23996179 DOI: 10.1007/978-1-62703-487-6_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is an emerging technique employed in biophysical studies that exploits the temporal autocorrelation of fluorescence intensity fluctuations measured in a tiny volume (in the order of fL). The autocorrelation curve derived from the fluctuations can then be fitted with diffusion models to obtain parameters such as diffusion time and number of particles in the diffusion volume/area. Application of FCS to membranes allows studying membrane component dynamics, which includes mobility and interactions between the components. However, FCS encounters several difficulties like accurate positioning and stability of the setup when applied to membranes. Here, we describe the theoretical basis of point FCS as well as the scanning FCS (SFCS) approach, which is a practical way to address the challenges of FCS with membranes. We also list materials necessary for FCS experiments on two model membrane systems: (1) supported lipid bilayers and (2) giant unilamellar vesicles. Finally, we present simple protocols for the preparation of these model membrane systems, calibration of the microscope setup for FCS, and acquisition and analysis of point FCS and SFCS data so that diffusion coefficients and concentrations of fluorescent probes within lipid membranes can be calculated.
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