1
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Fessl T, Majellaro M, Bondar A. Microscopy and spectroscopy approaches to study GPCR structure and function. Br J Pharmacol 2023. [PMID: 38087925 DOI: 10.1111/bph.16297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/03/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
The GPCR signalling cascade is a key pathway responsible for the signal transduction of a multitude of physical and chemical stimuli, including light, odorants, neurotransmitters and hormones. Understanding the structural and functional properties of the GPCR cascade requires direct observation of signalling processes in high spatial and temporal resolution, with minimal perturbation to endogenous systems. Optical microscopy and spectroscopy techniques are uniquely suited to this purpose because they excel at multiple spatial and temporal scales and can be used in living objects. Here, we review recent developments in microscopy and spectroscopy technologies which enable new insights into GPCR signalling. We focus on advanced techniques with high spatial and temporal resolution, single-molecule methods, labelling strategies and approaches suitable for endogenous systems and large living objects. This review aims to assist researchers in choosing appropriate microscopy and spectroscopy approaches for a variety of applications in the study of cellular signalling.
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Affiliation(s)
- Tomáš Fessl
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Alexey Bondar
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Laboratory of Microscopy and Histology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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2
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Nieves DJ, Pike JA, Levet F, Williamson DJ, Baragilly M, Oloketuyi S, de Marco A, Griffié J, Sage D, Cohen EAK, Sibarita JB, Heilemann M, Owen DM. A framework for evaluating the performance of SMLM cluster analysis algorithms. Nat Methods 2023; 20:259-267. [PMID: 36765136 DOI: 10.1038/s41592-022-01750-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/06/2022] [Indexed: 02/12/2023]
Abstract
Single-molecule localization microscopy (SMLM) generates data in the form of coordinates of localized fluorophores. Cluster analysis is an attractive route for extracting biologically meaningful information from such data and has been widely applied. Despite a range of cluster analysis algorithms, there exists no consensus framework for the evaluation of their performance. Here, we use a systematic approach based on two metrics to score the success of clustering algorithms in simulated conditions mimicking experimental data. We demonstrate the framework using seven diverse analysis algorithms: DBSCAN, ToMATo, KDE, FOCAL, CAML, ClusterViSu and SR-Tesseler. Given that the best performer depended on the underlying distribution of localizations, we demonstrate an analysis pipeline based on statistical similarity measures that enables the selection of the most appropriate algorithm, and the optimized analysis parameters for real SMLM data. We propose that these standard simulated conditions, metrics and analysis pipeline become the basis for future analysis algorithm development and evaluation.
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Affiliation(s)
- Daniel J Nieves
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
| | - Jeremy A Pike
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Florian Levet
- Interdisciplinary Institute for Neuroscience, CNRS, IINS, UMR 5297, Université de Bordeaux, Bordeaux, France.,Bordeaux Imaging Center, CNRS, INSERM, BIC, UMS 3420, US 4, Université de Bordeaux, Bordeaux, France
| | - David J Williamson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Mohammed Baragilly
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Department of Mathematics, Insurance and Applied Statistics, Helwan University, Helwan, Egypt
| | - Sandra Oloketuyi
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Rožna Dolina, Slovenia
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Rožna Dolina, Slovenia
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Daniel Sage
- Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Jean-Baptiste Sibarita
- Interdisciplinary Institute for Neuroscience, CNRS, IINS, UMR 5297, Université de Bordeaux, Bordeaux, France
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK. .,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK. .,School of Mathematics, University of Birmingham, Birmingham, UK.
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3
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Wang Q, Zhang Q, He H, Feng Z, Mao J, Hu X, Wei X, Bi S, Qin G, Wang X, Ge B, Yu D, Ren H, Huang F. Carbon Dot Blinking Fingerprint Uncovers Native Membrane Receptor Organizations via Deep Learning. Anal Chem 2022; 94:3914-3921. [PMID: 35188385 DOI: 10.1021/acs.analchem.1c04947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Oligomeric organization of G protein-coupled receptors is proposed to regulate receptor signaling and function, yet rapid and precise identification of the oligomeric status especially for native receptors on a cell membrane remains an outstanding challenge. By using blinking carbon dots (CDs), we now develop a deep learning (DL)-based blinking fingerprint recognition method, named deep-blinking fingerprint recognition (BFR), which allows automatic classification of CD-labeled receptor organizations on a cell membrane. This DL model integrates convolutional layers, long-short-term memory, and fully connected layers to extract time-dependent blinking features of CDs and is trained to a high accuracy (∼95%) for identifying receptor organizations. Using deep blinking fingerprint recognition, we found that CXCR4 mainly exists as 87.3% monomers, 12.4% dimers, and <1% higher-order oligomers on a HeLa cell membrane. We further demonstrate that the heterogeneous organizations can be regulated by various stimuli at different degrees. The receptor-binding ligands, agonist SDF-1α and antagonist AMD3100, can induce the dimerization of CXCR4 to 33.1 and 20.3%, respectively. In addition, cytochalasin D, which inhibits actin polymerization, similarly prompts significant dimerization of CXCR4 to 30.9%. The multi-pathway organization regulation will provide an insight for understanding the oligomerization mechanism of CXCR4 as well as for elucidating their physiological functions.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Qian Zhang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Hua He
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Zhenzhen Feng
- Technical Center of Qingdao Customs District, Qingdao 266500, China
| | - Jian Mao
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiang Hu
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaoyun Wei
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Simin Bi
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Guangyong Qin
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Daoyong Yu
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
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4
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Visualizing G protein-coupled receptor homomers using photoactivatable dye localization microscopy. Methods Cell Biol 2022; 169:27-41. [DOI: 10.1016/bs.mcb.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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5
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Integration and Spatial Organization of Signaling by G Protein-Coupled Receptor Homo- and Heterodimers. Biomolecules 2021; 11:biom11121828. [PMID: 34944469 PMCID: PMC8698773 DOI: 10.3390/biom11121828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 01/14/2023] Open
Abstract
Information flow from a source to a receiver becomes informative when the recipient can process the signal into a meaningful form. Information exchange and interpretation is essential in biology and understanding how cells integrate signals from a variety of information-coding molecules into complex orchestrated responses is a major challenge for modern cell biology. In complex organisms, cell to cell communication occurs mostly through neurotransmitters and hormones, and receptors are responsible for signal recognition at the membrane level and information transduction inside the cell. The G protein-coupled receptors (GPCRs) are the largest family of membrane receptors, with nearly 800 genes coding for these proteins. The recognition that GPCRs may physically interact with each other has led to the hypothesis that their dimeric state can provide the framework for temporal coincidence in signaling pathways. Furthermore, the formation of GPCRs higher order oligomers provides the structural basis for organizing distinct cell compartments along the plasma membrane where confined increases in second messengers may be perceived and discriminated. Here, we summarize evidence that supports these conjectures, fostering new ideas about the physiological role played by receptor homo- and hetero-oligomerization in cell biology.
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6
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Wolf P, Mohr A, Gavins G, Behr V, Mörl K, Seitz O, Beck-Sickinger AG. Orthogonal Peptide-Templated Labeling Elucidates Lateral ET A R/ET B R Proximity and Reveals Altered Downstream Signaling. Chembiochem 2021; 23:e202100340. [PMID: 34699123 PMCID: PMC9298254 DOI: 10.1002/cbic.202100340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/03/2021] [Indexed: 12/21/2022]
Abstract
Fine‐tuning of G protein‐coupled receptor (GPCR) signaling is important to maintain cellular homeostasis. Recent studies demonstrated that lateral GPCR interactions in the cell membrane can impact signaling profiles. Here, we report on a one‐step labeling method of multiple membrane‐embedded GPCRs. Based on short peptide tags, complementary probes transfer the cargo (e. g. a fluorescent dye) by an acyl transfer reaction with high spatial and temporal resolution within 5 min. We applied this approach to four receptors of the cardiovascular system: the endothelin receptor A and B (ETAR and ETBR), angiotensin II receptor type 1, and apelin. Wild type‐like G protein activation after N‐terminal modification was demonstrated for all receptor species. Using FRET‐competent dyes, a constitutive proximity between hetero‐receptors was limited to ETAR/ETBR. Further, we demonstrate, that ETAR expression regulates the signaling of co‐expressed ETBR. Our orthogonal peptide‐templated labeling of different GPCRs provides novel insight into the regulation of GPCR signaling.
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Affiliation(s)
- Philipp Wolf
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Alexander Mohr
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Georgina Gavins
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Victoria Behr
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Karin Mörl
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Oliver Seitz
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Annette G Beck-Sickinger
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
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7
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Goulding J, Kondrashov A, Mistry SJ, Melarangi T, Vo NTN, Hoang DM, White CW, Denning C, Briddon SJ, Hill SJ. The use of fluorescence correlation spectroscopy to monitor cell surface β2-adrenoceptors at low expression levels in human embryonic stem cell-derived cardiomyocytes and fibroblasts. FASEB J 2021; 35:e21398. [PMID: 33710675 DOI: 10.1096/fj.202002268r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/05/2021] [Accepted: 01/12/2021] [Indexed: 12/31/2022]
Abstract
The importance of cell phenotype in determining the molecular mechanisms underlying β2 -adrenoceptor (β2AR) function has been noted previously when comparing responses in primary cells and recombinant model cell lines. Here, we have generated haplotype-specific SNAP-tagged β2AR human embryonic stem (ES) cell lines and applied fluorescence correlation spectroscopy (FCS) to study cell surface receptors in progenitor cells and in differentiated fibroblasts and cardiomyocytes. FCS was able to quantify SNAP-tagged β2AR number and diffusion in both ES-derived cardiomyocytes and CRISPR/Cas9 genome-edited HEK293T cells, where the expression level was too low to detect using standard confocal microscopy. These studies demonstrate the power of FCS in investigating cell surface β2ARs at the very low expression levels often seen in endogenously expressing cells. Furthermore, the use of ES cell technology in combination with FCS allowed us to demonstrate that cell surface β2ARs internalize in response to formoterol-stimulation in ES progenitor cells but not following their differentiation into ES-derived fibroblasts. This indicates that the process of agonist-induced receptor internalization is strongly influenced by cell phenotype and this may have important implications for drug treatment with long-acting β2AR agonists.
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Affiliation(s)
- Joëlle Goulding
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Alexander Kondrashov
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Cancer & Stem Cells, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Sarah J Mistry
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Tony Melarangi
- Division of Cancer & Stem Cells, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Nguyen T N Vo
- Division of Cancer & Stem Cells, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Duc M Hoang
- Division of Cancer & Stem Cells, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK.,Department of Cellular Manufacturing, Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam
| | - Carl W White
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK.,Harry Perkins Institute of Medical Research and Centre for Medical Research, QEII Medical Centre, The University of Western Australia, Nedlands, WA, Australia.,Australian Research Council Centre for Personalised Therapeutics Technologies, Melbourne, VIC, Australia
| | - Chris Denning
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Cancer & Stem Cells, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Stephen J Briddon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Stephen J Hill
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
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8
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Valli J, Garcia-Burgos A, Rooney LM, Vale de Melo E Oliveira B, Duncan RR, Rickman C. Seeing beyond the limit: A guide to choosing the right super-resolution microscopy technique. J Biol Chem 2021; 297:100791. [PMID: 34015334 PMCID: PMC8246591 DOI: 10.1016/j.jbc.2021.100791] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023] Open
Abstract
Super-resolution microscopy has become an increasingly popular and robust tool across the life sciences to study minute cellular structures and processes. However, with the increasing number of available super-resolution techniques has come an increased complexity and burden of choice in planning imaging experiments. Choosing the right super-resolution technique to answer a given biological question is vital for understanding and interpreting biological relevance. This is an often-neglected and complex task that should take into account well-defined criteria (e.g., sample type, structure size, imaging requirements). Trade-offs in different imaging capabilities are inevitable; thus, many researchers still find it challenging to select the most suitable technique that will best answer their biological question. This review aims to provide an overview and clarify the concepts underlying the most commonly available super-resolution techniques as well as guide researchers through all aspects that should be considered before opting for a given technique.
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Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom.
| | - Adrian Garcia-Burgos
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Liam M Rooney
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Beatriz Vale de Melo E Oliveira
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Rory R Duncan
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Colin Rickman
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom.
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9
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Bondar A, Lazar J. Optical sensors of heterotrimeric G protein signaling. FEBS J 2020; 288:2570-2584. [DOI: 10.1111/febs.15655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Alexey Bondar
- Center for Nanobiology and Structural Biology Institute of Microbiology of the Czech Academy of Sciences Nove Hrady Czech Republic
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic
- Faculty of Science University of South Bohemia Ceske Budejovice Czech Republic
| | - Josef Lazar
- Center for Nanobiology and Structural Biology Institute of Microbiology of the Czech Academy of Sciences Nove Hrady Czech Republic
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic
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10
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Calebiro D, Koszegi Z, Lanoiselée Y, Miljus T, O'Brien S. G protein-coupled receptor-G protein interactions: a single-molecule perspective. Physiol Rev 2020; 101:857-906. [PMID: 33331229 DOI: 10.1152/physrev.00021.2020] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) regulate many cellular and physiological processes, responding to a diverse range of extracellular stimuli including hormones, neurotransmitters, odorants, and light. Decades of biochemical and pharmacological studies have provided fundamental insights into the mechanisms of GPCR signaling. Thanks to recent advances in structural biology, we now possess an atomistic understanding of receptor activation and G protein coupling. However, how GPCRs and G proteins interact in living cells to confer signaling efficiency and specificity remains insufficiently understood. The development of advanced optical methods, including single-molecule microscopy, has provided the means to study receptors and G proteins in living cells with unprecedented spatio-temporal resolution. The results of these studies reveal an unexpected level of complexity, whereby GPCRs undergo transient interactions among themselves as well as with G proteins and structural elements of the plasma membrane to form short-lived signaling nanodomains that likely confer both rapidity and specificity to GPCR signaling. These findings may provide new strategies to pharmaceutically modulate GPCR function, which might eventually pave the way to innovative drugs for common diseases such as diabetes or heart failure.
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Affiliation(s)
- Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Zsombor Koszegi
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Yann Lanoiselée
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Tamara Miljus
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Shannon O'Brien
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
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11
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Modular transient nanoclustering of activated β2-adrenergic receptors revealed by single-molecule tracking of conformation-specific nanobodies. Proc Natl Acad Sci U S A 2020; 117:30476-30487. [PMID: 33214152 DOI: 10.1073/pnas.2007443117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
None of the current superresolution microscopy techniques can reliably image the changes in endogenous protein nanoclustering dynamics associated with specific conformations in live cells. Single-domain nanobodies have been invaluable tools to isolate defined conformational states of proteins, and we reasoned that expressing these nanobodies coupled to single-molecule imaging-amenable tags could allow superresolution analysis of endogenous proteins in discrete conformational states. Here, we used anti-GFP nanobodies tagged with photoconvertible mEos expressed as intrabodies, as a proof-of-concept to perform single-particle tracking on a range of GFP proteins expressed in live cells, neurons, and small organisms. We next expressed highly specialized nanobodies that target conformation-specific endogenous β2-adrenoreceptor (β2-AR) in neurosecretory cells, unveiling real-time mobility behaviors of activated and inactivated endogenous conformers during agonist treatment in living cells. We showed that activated β2-AR (Nb80) is highly immobile and organized in nanoclusters. The Gαs-GPCR complex detected with Nb37 displayed higher mobility with surprisingly similar nanoclustering dynamics to that of Nb80. Activated conformers are highly sensitive to dynamin inhibition, suggesting selective targeting for endocytosis. Inactivated β2-AR (Nb60) molecules are also largely immobile but relatively less sensitive to endocytic blockade. Expression of single-domain nanobodies therefore provides a unique opportunity to capture highly transient changes in the dynamic nanoscale organization of endogenous proteins.
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12
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Michel MC, Michel-Reher MB, Hein P. A Systematic Review of Inverse Agonism at Adrenoceptor Subtypes. Cells 2020; 9:E1923. [PMID: 32825009 PMCID: PMC7564766 DOI: 10.3390/cells9091923] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/16/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022] Open
Abstract
As many, if not most, ligands at G protein-coupled receptor antagonists are inverse agonists, we systematically reviewed inverse agonism at the nine adrenoceptor subtypes. Except for β3-adrenoceptors, inverse agonism has been reported for each of the adrenoceptor subtypes, most often for β2-adrenoceptors, including endogenously expressed receptors in human tissues. As with other receptors, the detection and degree of inverse agonism depend on the cells and tissues under investigation, i.e., they are greatest when the model has a high intrinsic tone/constitutive activity for the response being studied. Accordingly, they may differ between parts of a tissue, for instance, atria vs. ventricles of the heart, and within a cell type, between cellular responses. The basal tone of endogenously expressed receptors is often low, leading to less consistent detection and a lesser extent of observed inverse agonism. Extent inverse agonism depends on specific molecular properties of a compound, but inverse agonism appears to be more common in certain chemical classes. While inverse agonism is a fascinating facet in attempts to mechanistically understand observed drug effects, we are skeptical whether an a priori definition of the extent of inverse agonism in the target product profile of a developmental candidate is a meaningful option in drug discovery and development.
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Affiliation(s)
- Martin C. Michel
- Department of Pharmacology, Johannes Gutenberg University, 55131 Mainz, Germany;
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13
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Nanometric targeting of type 9 adenylyl cyclase in heart. Biochem Soc Trans 2020; 47:1749-1756. [PMID: 31769471 DOI: 10.1042/bst20190227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 12/15/2022]
Abstract
Adenylyl cyclases (ACs) convert ATP into the classical second messenger cyclic adenosine monophosphate (cAMP). Cardiac ACs, specifically AC5, AC6, and AC9, regulate cAMP signaling controlling functional outcomes such as heart rate, contractility and relaxation, gene regulation, stress responses, and glucose and lipid metabolism. With so many distinct functional outcomes for a single second messenger, the cell creates local domains of cAMP signaling to correctly relay signals. Targeting of ACs to A-kinase anchoring proteins (AKAPs) not only localizes ACs, but also places them within signaling nanodomains, where cAMP levels and effects can be highly regulated. Here we will discuss the recent work on the structure, regulation and physiological functions of AC9 in the heart, where it accounts for <3% of total AC activity. Despite the small contribution of AC9 to total cardiac cAMP production, AC9 binds and regulates local PKA phosphorylation of Yotiao-IKs and Hsp20, demonstrating a role for nanometric targeting of AC9.
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14
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Erlendsson S, Thorsen TS, Madsen KL. Supported Cell Membrane Sheets to Monitor Protein Assembly. Bio Protoc 2019; 9:e3368. [PMID: 33654865 DOI: 10.21769/bioprotoc.3368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 08/11/2019] [Accepted: 08/19/2019] [Indexed: 11/02/2022] Open
Abstract
Studying protein-protein and protein-lipid interactions in their native environment is highly desirable, yet, the heterogeneity and complexity of cellular systems limits the repertoire of experimental methods available. In cells, interactions are often taking place in confined microenvironments where factors such as avidity, hindered diffusion, reduced dimensionality, crowding etc. strongly influence the binding kinetics and therefore it can be problematic to equate binding affinities obtained by bulk in-solution methods (e.g., Fluorescence Polarization, Isothermal titration calorimetry, Microscale thermophoresis) with those occurring in real cellular environments. The Supported Cell Membrane Sheet method presented here, addresses these issues by allowing access to the inner leaflet of the apical plasma membrane. The method is a highly versatile, near-native platform for both qualitative and quantitative studies of protein-protein and protein-lipid interactions occurring directly in or on the plasma membrane.
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Affiliation(s)
- Simon Erlendsson
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, The Panum Institute-Maersk Tower 7.5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Thor Seneca Thorsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, The Panum Institute-Maersk Tower 7.5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Kenneth Lindegaard Madsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, The Panum Institute-Maersk Tower 7.5, University of Copenhagen, 2200 Copenhagen N, Denmark
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15
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Single Proteoliposome High-Content Analysis Reveals Differences in the Homo-Oligomerization of GPCRs. Biophys J 2019; 115:300-312. [PMID: 30021106 DOI: 10.1016/j.bpj.2018.05.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 11/23/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) control vital cellular signaling pathways. GPCR oligomerization is proposed to increase signaling diversity. However, many reports have arrived at disparate conclusions regarding the existence, stability, and stoichiometry of GPCR oligomers, partly because of cellular complexity and ensemble averaging of intrareconstitution heterogeneities that complicate the interpretation of oligomerization data. To overcome these limitations, we exploited fluorescence-microscopy-based high-content analysis of single proteoliposomes. This allowed multidimensional quantification of intrinsic monomer-monomer interactions of three class A GPCRs (β2-adrenergic receptor, cannabinoid receptor type 1, and opsin). Using a billion-fold less protein than conventional assays, we quantified oligomer stoichiometries, association constants, and the influence of two ligands and membrane curvature on oligomerization, revealing key similarities and differences for three GPCRs with decidedly different physiological functions. The assays introduced here will assist with the quantitative experimental observation of oligomerization for transmembrane proteins in general.
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16
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Martínez-Muñoz L, Rodríguez-Frade JM, Barroso R, Sorzano CÓS, Torreño-Pina JA, Santiago CA, Manzo C, Lucas P, García-Cuesta EM, Gutierrez E, Barrio L, Vargas J, Cascio G, Carrasco YR, Sánchez-Madrid F, García-Parajo MF, Mellado M. Separating Actin-Dependent Chemokine Receptor Nanoclustering from Dimerization Indicates a Role for Clustering in CXCR4 Signaling and Function. Mol Cell 2019; 70:106-119.e10. [PMID: 29625032 DOI: 10.1016/j.molcel.2018.02.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 01/08/2018] [Accepted: 02/27/2018] [Indexed: 01/03/2023]
Abstract
A current challenge in cell motility studies is to understand the molecular and physical mechanisms that govern chemokine receptor nanoscale organization at the cell membrane, and their influence on cell response. Using single-particle tracking and super-resolution microscopy, we found that the chemokine receptor CXCR4 forms basal nanoclusters in resting T cells, whose extent, dynamics, and signaling strength are modulated by the orchestrated action of the actin cytoskeleton, the co-receptor CD4, and its ligand CXCL12. We identified three CXCR4 structural residues that are crucial for nanoclustering and generated an oligomerization-defective mutant that dimerized but did not form nanoclusters in response to CXCL12, which severely impaired signaling. Overall, our data provide new insights to the field of chemokine biology by showing that receptor dimerization in the absence of nanoclustering is unable to fully support CXCL12-mediated responses, including signaling and cell function in vivo.
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Affiliation(s)
- Laura Martínez-Muñoz
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CSIC), 41092 Sevilla, Spain.
| | - José Miguel Rodríguez-Frade
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Rubén Barroso
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Carlos Óscar S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Juan A Torreño-Pina
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - César A Santiago
- X-ray Crystallography Unit, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain; Universitat de Vic, Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Spain
| | - Pilar Lucas
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Eva M García-Cuesta
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Enric Gutierrez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - Laura Barrio
- B Cell Dynamics Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Javier Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Graciela Cascio
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Yolanda R Carrasco
- B Cell Dynamics Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | | | - María F García-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Mario Mellado
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
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17
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Felce JH, MacRae A, Davis SJ. Constraints on GPCR Heterodimerization Revealed by the Type-4 Induced-Association BRET Assay. Biophys J 2019; 116:31-41. [PMID: 30558888 PMCID: PMC6341220 DOI: 10.1016/j.bpj.2018.09.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/14/2018] [Accepted: 09/21/2018] [Indexed: 01/24/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) comprise the largest and most pharmacologically important family of cell-surface receptors encoded by the human genome. In many instances, the distinct signaling behavior of certain GPCRs has been explained in terms of the formation of heteromers with, for example, distinct signaling properties and allosteric cross-regulation. Confirmation of this has, however, been limited by the paucity of reliable methods for probing heteromeric GPCR interactions in situ. The most widely used assays for GPCR stoichiometry, based on resonance energy transfer, are unsuited to reporting heteromeric interactions. Here, we describe a targeted bioluminescence resonance energy transfer (BRET) assay, called type-4 BRET, which detects both homo- and heteromeric interactions using induced multimerization of protomers within such complexes, at constant expression. Using type-4 BRET assays, we investigate heterodimerization among known GPCR homodimers: the CXC chemokine receptor 4 and sphingosine-1-phosphate receptors. We observe that CXC chemokine receptor 4 and sphingosine-1-phosphate receptors can form heterodimers with GPCRs from their immediate subfamilies but not with more distantly related receptors. We also show that heterodimerization appears to disrupt homodimeric interactions, suggesting the sharing of interfaces. Broadly, these observations indicate that heterodimerization results from the divergence of homodimeric receptors and will therefore likely be restricted to closely related homodimeric GPCRs.
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Affiliation(s)
- James H Felce
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom; Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, United Kingdom.
| | - Alasdair MacRae
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom; Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Simon J Davis
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom; Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, United Kingdom
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18
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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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19
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Bieberich E. Sphingolipids and lipid rafts: Novel concepts and methods of analysis. Chem Phys Lipids 2018; 216:114-131. [PMID: 30194926 PMCID: PMC6196108 DOI: 10.1016/j.chemphyslip.2018.08.003] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/20/2018] [Accepted: 08/25/2018] [Indexed: 12/12/2022]
Abstract
About twenty years ago, the functional lipid raft model of the plasma membrane was published. It took into account decades of research showing that cellular membranes are not just homogenous mixtures of lipids and proteins. Lateral anisotropy leads to assembly of membrane domains with specific lipid and protein composition regulating vesicular traffic, cell polarity, and cell signaling pathways in a plethora of biological processes. However, what appeared to be a clearly defined entity of clustered raft lipids and proteins became increasingly fluid over the years, and many of the fundamental questions about biogenesis and structure of lipid rafts remained unanswered. Experimental obstacles in visualizing lipids and their interactions hampered progress in understanding just how big rafts are, where and when they are formed, and with which proteins raft lipids interact. In recent years, we have begun to answer some of these questions and sphingolipids may take center stage in re-defining the meaning and functional significance of lipid rafts. In addition to the archetypical cholesterol-sphingomyelin raft with liquid ordered (Lo) phase and the liquid-disordered (Ld) non-raft regions of cellular membranes, a third type of microdomains termed ceramide-rich platforms (CRPs) with gel-like structure has been identified. CRPs are "ceramide rafts" that may offer some fresh view on the membrane mesostructure and answer several critical questions for our understanding of lipid rafts.
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Affiliation(s)
- Erhard Bieberich
- Department of Physiology at the University of Kentucky, Lexington, KY, United States.
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20
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Wijesooriya CS, Nyamekye CKA, Smith EA. Optical Imaging of the Nanoscale Structure and Dynamics of Biological Membranes. Anal Chem 2018; 91:425-440. [DOI: 10.1021/acs.analchem.8b04755] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Charles K. A. Nyamekye
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- The Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
| | - Emily A. Smith
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- The Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
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21
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Felce JH, Davis SJ, Klenerman D. Single-Molecule Analysis of G Protein-Coupled Receptor Stoichiometry: Approaches and Limitations. Trends Pharmacol Sci 2018; 39:96-108. [PMID: 29122289 DOI: 10.1016/j.tips.2017.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 10/06/2017] [Accepted: 10/10/2017] [Indexed: 01/17/2023]
Abstract
How G protein-coupled receptors (GPCRs) are organized at the cell surface remains highly contentious. Single-molecule (SM) imaging is starting to inform this debate as receptor behavior can now be visualized directly, without the need for interpreting ensemble data. The limited number of SM studies of GPCRs undertaken to date have strongly suggested that dimerization is at most transient, and that most receptors are monomeric at any given time. However, even SM data has its caveats and needs to be interpreted carefully. Here, we discuss the types of SM imaging strategies used to examine GPCR stoichiometry and consider some of these caveats. We also emphasize that attempts to resolve the debate ought to rely on orthogonal approaches to measuring receptor stoichiometry.
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Affiliation(s)
- James H Felce
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK.
| | - Simon J Davis
- Radcliffe Department of Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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22
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Sezgin E. Super-resolution optical microscopy for studying membrane structure and dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:273001. [PMID: 28481213 PMCID: PMC5952331 DOI: 10.1088/1361-648x/aa7185] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Investigation of cell membrane structure and dynamics requires high spatial and temporal resolution. The spatial resolution of conventional light microscopy is limited due to the diffraction of light. However, recent developments in microscopy enabled us to access the nano-scale regime spatially, thus to elucidate the nanoscopic structures in the cellular membranes. In this review, we will explain the resolution limit, address the working principles of the most commonly used super-resolution microscopy techniques and summarise their recent applications in the biomembrane field.
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Affiliation(s)
- Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX39DS, United Kingdom
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23
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Jonas KC, Hanyaloglu AC. Impact of G protein-coupled receptor heteromers in endocrine systems. Mol Cell Endocrinol 2017; 449:21-27. [PMID: 28115188 DOI: 10.1016/j.mce.2017.01.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/05/2017] [Accepted: 01/19/2017] [Indexed: 12/26/2022]
Abstract
The fine-tuning of endocrine homeostasis is regulated by dynamic receptor mediated processes. The superfamily of G protein-coupled receptors (GPCRs) have diverse roles in the modulation of all endocrine axes, thus understanding the mechanisms underpinning their functionality is paramount for treatment of endocrinopathies. Evidence over the last 20 years has highlighted homo and heteromerization as a key mode of mediating GPCR functional diversity. This review will discuss the concept of GPCR heteromerization and its relevance to endocrine function, detailing in vitro and in vivo evidence, and exploring current and potential pharmacological strategies for specific targeting of GPCR heteromers in endocrine heath and disease.
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Affiliation(s)
- K C Jonas
- Cell Biology and Genetics Research Centre, Centre for Medical and Biomedical Education, St George's, University of London, UK.
| | - A C Hanyaloglu
- Institute of Reproductive and Developmental Biology, Dept. Surgery and Cancer, Imperial College London, UK
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24
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Jiang S, Park S, Challapalli SD, Fei J, Wang Y. Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy. PLoS One 2017; 12:e0179975. [PMID: 28636661 PMCID: PMC5479598 DOI: 10.1371/journal.pone.0179975] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 06/07/2017] [Indexed: 01/26/2023] Open
Abstract
We report a robust nonparametric descriptor, J'(r), for quantifying the density of clustering molecules in single-molecule localization microscopy. J'(r), based on nearest neighbor distribution functions, does not require any parameter as an input for analyzing point patterns. We show that J'(r) displays a valley shape in the presence of clusters of molecules, and the characteristics of the valley reliably report the clustering features in the data. Most importantly, the position of the J'(r) valley ([Formula: see text]) depends exclusively on the density of clustering molecules (ρc). Therefore, it is ideal for direct estimation of the clustering density of molecules in single-molecule localization microscopy. As an example, this descriptor was applied to estimate the clustering density of ptsG mRNA in E. coli bacteria.
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Affiliation(s)
- Shenghang Jiang
- Department of Physics, University of Arkansas, Fayetteville, Arkansas, 72701, United States of America
| | - Seongjin Park
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Sai Divya Challapalli
- Microelectronics and Photonics Graduate Program, University of Arkansas, Fayetteville, Arkansas, 72701, United States of America
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637, United States of America
- Institute of Biophysical Dynamics, The University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Yong Wang
- Department of Physics, University of Arkansas, Fayetteville, Arkansas, 72701, United States of America
- Microelectronics and Photonics Graduate Program, University of Arkansas, Fayetteville, Arkansas, 72701, United States of America
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, 72701, United States of America
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25
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Stone MB, Shelby SA, Veatch SL. Super-Resolution Microscopy: Shedding Light on the Cellular Plasma Membrane. Chem Rev 2017; 117:7457-7477. [PMID: 28211677 PMCID: PMC5471115 DOI: 10.1021/acs.chemrev.6b00716] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Lipids and the membranes they form are fundamental building blocks of cellular life, and their geometry and chemical properties distinguish membranes from other cellular environments. Collective processes occurring within membranes strongly impact cellular behavior and biochemistry, and understanding these processes presents unique challenges due to the often complex and myriad interactions between membrane components. Super-resolution microscopy offers a significant gain in resolution over traditional optical microscopy, enabling the localization of individual molecules even in densely labeled samples and in cellular and tissue environments. These microscopy techniques have been used to examine the organization and dynamics of plasma membrane components, providing insight into the fundamental interactions that determine membrane functions. Here, we broadly introduce the structure and organization of the mammalian plasma membrane and review recent applications of super-resolution microscopy to the study of membranes. We then highlight some inherent challenges faced when using super-resolution microscopy to study membranes, and we discuss recent technical advancements that promise further improvements to super-resolution microscopy and its application to the plasma membrane.
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Affiliation(s)
- Matthew B Stone
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
| | - Sarah A Shelby
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
| | - Sarah L Veatch
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
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26
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Deshpande SA, Pawar AB, Dighe A, Athale CA, Sengupta D. Role of spatial inhomogenity in GPCR dimerisation predicted by receptor association–diffusion models. Phys Biol 2017; 14:036002. [DOI: 10.1088/1478-3975/aa6b68] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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27
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Zhang Z, Nishimura Y, Kanchanawong P. Extracting microtubule networks from superresolution single-molecule localization microscopy data. Mol Biol Cell 2016; 28:333-345. [PMID: 27852898 PMCID: PMC5231901 DOI: 10.1091/mbc.e16-06-0421] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 12/05/2022] Open
Abstract
Microtubule filaments form ubiquitous networks. However, quantitative analysis of this structure is difficult due to its complex architecture. A tool is given for the automated retrieval of microtubule filaments from superresolution microscopy images and used for a quantitative analysis of microtubule network architecture phenotypes in fibroblasts. Microtubule filaments form ubiquitous networks that specify spatial organization in cells. However, quantitative analysis of microtubule networks is hampered by their complex architecture, limiting insights into the interplay between their organization and cellular functions. Although superresolution microscopy has greatly facilitated high-resolution imaging of microtubule filaments, extraction of complete filament networks from such data sets is challenging. Here we describe a computational tool for automated retrieval of microtubule filaments from single-molecule-localization–based superresolution microscopy images. We present a user-friendly, graphically interfaced implementation and a quantitative analysis of microtubule network architecture phenotypes in fibroblasts.
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Affiliation(s)
- Zhen Zhang
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Yukako Nishimura
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, 117411 Singapore .,Department of Biomedical Engineering, National University of Singapore, 117411 Singapore
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28
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Di Rienzo C, Annibale P. Visualizing the molecular mode of motion from a correlative analysis of localization microscopy datasets. OPTICS LETTERS 2016; 41:4503-4506. [PMID: 27749866 DOI: 10.1364/ol.41.004503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The determination of the mode and rapidity of motion of individual molecules within a biological sample is becoming a more and more common analysis in biophysical investigations. Single molecule tracking (SMT) techniques allow reconstructing the trajectories of individual molecules within a movie, provided that the position from one frame to the other can be correctly linked. The outcomes, however, appear to depend on the specific method used, and most techniques display a limitation to capture fast modes of motion in a crowded environment. We demonstrate here that the limitations encountered by conventional SMT can be significantly overcome by employing alternative approaches based on image spatial-temporal correlations, enabling to visually extract quantitative insights on the ensemble mode of motion of fluorescently labeled biomolecules that would otherwise be inaccessible.
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29
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Jorand R, Biswas S, Wakefield DL, Tobin SJ, Golfetto O, Hilton K, Ko M, Ramos JW, Small AR, Chu P, Singh G, Jovanovic-Talisman T. Molecular signatures of mu opioid receptor and somatostatin receptor 2 in pancreatic cancer. Mol Biol Cell 2016; 27:3659-3672. [PMID: 27682590 PMCID: PMC5221597 DOI: 10.1091/mbc.e16-06-0427] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/20/2016] [Indexed: 12/21/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), a particularly aggressive malignancy, has been linked to atypical levels, certain mutations, and aberrant signaling of G-protein-coupled receptors (GPCRs). GPCRs have been challenging to target in cancer because they organize into complex networks in tumor cells. To dissect such networks with nanometer-scale precision, here we combine traditional biochemical approaches with superresolution microscopy methods. A novel interaction specific to PDAC is identified between mu opioid receptor (MOR) and somatostatin receptor 2 (SSTR2). Although MOR and SSTR2 did not colocalize in healthy pancreatic cells or matching healthy patient tissues, the pair did significantly colocalize in pancreatic cancer cells, multicellular tumor spheroids, and cancerous patient tissues. Moreover, this association in pancreatic cancer cells correlated with functional cross-talk and increased metastatic potential of cells. Coactivation of MOR and SSTR2 in PDAC cells led to increased expression of mesenchymal markers and decreased expression of an epithelial marker. Together these results suggest that the MOR-SSTR2 heteromer may constitute a novel therapeutic target for PDAC.
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Affiliation(s)
- Raphael Jorand
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010
| | - Sunetra Biswas
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010
| | - Devin L Wakefield
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010
| | - Steven J Tobin
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010
| | - Ottavia Golfetto
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010
| | - Kelsey Hilton
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010
| | - Michelle Ko
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010
| | - Joe W Ramos
- Cancer Biology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813
| | - Alexander R Small
- Department of Physics and Astronomy, California State Polytechnic University, Pomona, CA 91768
| | - Peiguo Chu
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010
| | - Gagandeep Singh
- Division of Surgical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010
| | - Tijana Jovanovic-Talisman
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010
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Finkenstaedt-Quinn SA, Qiu TA, Shin K, Haynes CL. Super-resolution imaging for monitoring cytoskeleton dynamics. Analyst 2016; 141:5674-5688. [PMID: 27549146 DOI: 10.1039/c6an00731g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The cytoskeleton is a key cellular structure that is important in the control of cellular movement, structure, and sensing. To successfully image the individual cytoskeleton components, high resolution and super-resolution fluorescence imaging methods are needed. This review covers the three basic cytoskeletal elements and the relative benefits and drawbacks of fixed versus live cell imaging before moving on to recent studies using high resolution and super-resolution techniques. The techniques covered include the near-diffraction limited imaging methods of confocal microscopy and TIRF microscopy and the super-resolution fluorescence imaging methods of STORM, PALM, and STED.
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31
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Latty SL, Felce JH, Weimann L, Lee SF, Davis SJ, Klenerman D. Referenced Single-Molecule Measurements Differentiate between GPCR Oligomerization States. Biophys J 2016; 109:1798-806. [PMID: 26536257 PMCID: PMC4643199 DOI: 10.1016/j.bpj.2015.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 08/25/2015] [Accepted: 09/08/2015] [Indexed: 11/24/2022] Open
Abstract
The extent to which Rhodopsin family G-protein-coupled receptors (GPCRs) form invariant oligomers is contentious. Recent single-molecule fluorescence imaging studies mostly argue against the existence of constitutive receptor dimers and instead suggest that GPCRs only dimerize transiently, if at all. However, whether or not even transient dimers exist is not always clear due to difficulties in unambiguously distinguishing genuine interactions from chance colocalizations, particularly with respect to short-lived events. Previous single-molecule studies have depended critically on calculations of chance colocalization rates and/or comparison with unfixed control proteins whose diffusional behavior may or may not differ from that of the test receptor. Here, we describe a single-molecule imaging assay that 1) utilizes comparisons with well-characterized control proteins, i.e., the monomer CD86 and the homodimer CD28, and 2) relies on cell fixation to limit artifacts arising from differences in the distribution and diffusion of test proteins versus these controls. The improved assay reliably reports the stoichiometry of the Glutamate-family GPCR dimer, γ-amino butyric acid receptor b2, whereas two Rhodopsin-family GPCRs, β2-adrenergic receptor and mCannR2, exhibit colocalization levels comparable to those of CD86 monomers, strengthening the case against invariant GPCR oligomerization.
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Affiliation(s)
- Sarah L Latty
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - James H Felce
- Radcliffe Department of Clinical Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Laura Weimann
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Simon J Davis
- Radcliffe Department of Clinical Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
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Georgieva M, Cattoni DI, Fiche JB, Mutin T, Chamousset D, Nollmann M. Nanometer resolved single-molecule colocalization of nuclear factors by two-color super resolution microscopy imaging. Methods 2016; 105:44-55. [PMID: 27045944 DOI: 10.1016/j.ymeth.2016.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/30/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022] Open
Abstract
In order to study the detailed assembly and regulation mechanisms of complex structures and machineries in the cell, simultaneous in situ observation of all the individual interacting components should be achieved. Multi-color Single-Molecule Localization Microscopy (SMLM) is ideally suited for these quantifications. Here, we build on previous developments and thoroughly discuss a protocol for two-color SMLM combining PALM and STORM, including sample preparation details, image acquisition and data postprocessing analysis. We implement and evaluate a recently proposed colocalization analysis method (aCBC) that allows single-molecule colocalization quantification with the potential of revealing fine, nanometer-scaled, structural details of multicomponent complexes. Finally, using a doubly-labeled nuclear factor (Beaf-32) in Drosophila S2 cells we experimentally validate the colocalization quantification algorithm, highlight its advantages and discuss how using high molecular weight fluorescently labeled tags compromises colocalization precision in two-color SMLM experiments.
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Affiliation(s)
- Mariya Georgieva
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Diego I Cattoni
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Thibaut Mutin
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Delphine Chamousset
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France.
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34
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Lange Y, Steck TL. Active membrane cholesterol as a physiological effector. Chem Phys Lipids 2016; 199:74-93. [PMID: 26874289 DOI: 10.1016/j.chemphyslip.2016.02.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/04/2016] [Accepted: 02/08/2016] [Indexed: 02/05/2023]
Abstract
Sterols associate preferentially with plasma membrane sphingolipids and saturated phospholipids to form stoichiometric complexes. Cholesterol in molar excess of the capacity of these polar bilayer lipids has a high accessibility and fugacity; we call this fraction active cholesterol. This review first considers how active cholesterol serves as an upstream regulator of cellular sterol homeostasis. The mechanism appears to utilize the redistribution of active cholesterol down its diffusional gradient to the endoplasmic reticulum and mitochondria, where it binds multiple effectors and directs their feedback activity. We have also reviewed a broad literature in search of a role for active cholesterol (as opposed to bulk cholesterol or lipid domains such as rafts) in the activity of diverse membrane proteins. Several systems provide such evidence, implicating, in particular, caveolin-1, various kinds of ABC-type cholesterol transporters, solute transporters, receptors and ion channels. We suggest that this larger role for active cholesterol warrants close attention and can be tested easily.
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Affiliation(s)
- Yvonne Lange
- Department of Pathology, Rush University Medical Center, 1653 W. Congress Parkway, Chicago, IL 60612, USA.
| | - Theodore L Steck
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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Analyzing Protein Clusters on the Plasma Membrane: Application of Spatial Statistical Analysis Methods on Super-Resolution Microscopy Images. FOCUS ON BIO-IMAGE INFORMATICS 2016; 219:95-122. [DOI: 10.1007/978-3-319-28549-8_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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37
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Sydor AM, Czymmek KJ, Puchner EM, Mennella V. Super-Resolution Microscopy: From Single Molecules to Supramolecular Assemblies. Trends Cell Biol 2015; 25:730-748. [DOI: 10.1016/j.tcb.2015.10.004] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/03/2015] [Accepted: 10/05/2015] [Indexed: 11/25/2022]
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38
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Scarselli M, Annibale P, McCormick PJ, Kolachalam S, Aringhieri S, Radenovic A, Corsini GU, Maggio R. Revealing G-protein-coupled receptor oligomerization at the single-molecule level through a nanoscopic lens: methods, dynamics and biological function. FEBS J 2015; 283:1197-217. [PMID: 26509747 DOI: 10.1111/febs.13577] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/29/2015] [Accepted: 10/23/2015] [Indexed: 11/30/2022]
Abstract
The introduction of super-resolution fluorescence microscopy has allowed the visualization of single proteins in their biological environment. Recently, these techniques have been applied to determine the organization of class A G-protein-coupled receptors (GPCRs), and to determine whether they exist as monomers, dimers and/or higher-order oligomers. On this subject, this review highlights recent evidence from photoactivated localization microscopy (PALM), which allows the visualization of single molecules in dense samples, and single-molecule tracking (SMT), which determines how GPCRs move and interact in living cells in the presence of different ligands. PALM has demonstrated that GPCR oligomerization depends on the receptor subtype, the cell type, the actin cytoskeleton, and other proteins. Conversely, SMT has revealed the transient dynamics of dimer formation, whereby receptors show a monomer-dimer equilibrium characterized by rapid association and dissociation. At steady state, depending on the subtype, approximately 30-50% of receptors are part of dimeric complexes. Notably, the existence of many GPCR dimers/oligomers is also supported by well-known techniques, such as resonance energy transfer methodologies, and by approaches that exploit fluorescence fluctuations, such as fluorescence correlation spectroscopy (FCS). Future research using single-molecule methods will deepen our knowledge related to the function and druggability of homo-oligomers and hetero-oligomers.
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Affiliation(s)
- Marco Scarselli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
| | - Paolo Annibale
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | | | - Shivakumar Kolachalam
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
| | - Stefano Aringhieri
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - Giovanni U Corsini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
| | - Roberto Maggio
- Biotechnological and Applied Clinical Sciences Department, University of L'Aquila, Italy
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Courtney J, Woods E, Scholz D, Hall WW, Gautier VW. MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells. PLoS One 2015; 10:e0140209. [PMID: 26485569 PMCID: PMC4616565 DOI: 10.1371/journal.pone.0140209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 09/23/2015] [Indexed: 11/18/2022] Open
Abstract
We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip.
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Affiliation(s)
- Jane Courtney
- Dublin Institute of Technology, Kevin St, Dublin, Ireland
- * E-mail:
| | - Elena Woods
- UCD Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin (UCD), Dublin, Ireland
| | - Dimitri Scholz
- UCD Conway Institute of Biomolecular & Biomedical Research, School of Medicine and Biomedical Science University College Dublin (UCD), Dublin, Ireland
| | - William W. Hall
- UCD Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin (UCD), Dublin, Ireland
| | - Virginie W. Gautier
- UCD Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin (UCD), Dublin, Ireland
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40
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Levet F, Hosy E, Kechkar A, Butler C, Beghin A, Choquet D, Sibarita JB. SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data. Nat Methods 2015; 12:1065-71. [DOI: 10.1038/nmeth.3579] [Citation(s) in RCA: 290] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 07/03/2015] [Indexed: 12/18/2022]
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41
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Gater DL, Saurel O, Iordanov I, Liu W, Cherezov V, Milon A. Two classes of cholesterol binding sites for the β2AR revealed by thermostability and NMR. Biophys J 2015; 107:2305-12. [PMID: 25418299 DOI: 10.1016/j.bpj.2014.10.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/19/2014] [Accepted: 10/09/2014] [Indexed: 11/24/2022] Open
Abstract
Cholesterol binding to G protein-coupled receptors (GPCRs) and modulation of their activities in membranes is a fundamental issue for understanding their function. Despite the identification of cholesterol binding sites in high-resolution x-ray structures of the ?2 adrenergic receptor (β2AR) and other GPCRs, the binding affinity of cholesterol for this receptor and exchange rates between the free and bound cholesterol remain unknown. In this study we report the existence of two classes of cholesterol binding sites in β2AR. By analyzing the β2AR unfolding temperature in lipidic cubic phase (LCP) as a function of cholesterol concentration we observed high-affinity cooperative binding of cholesterol with sub-nM affinity constant. In contrast, saturation transfer difference (STD) NMR experiments revealed the existence of a second class of cholesterol binding sites, in fast exchange on the STD NMR timescale. Titration of the STD signal as a function of cholesterol concentration provided a lower limit of 100 mM for their dissociation constant. However, these binding sites are specific for both cholesterol and β2AR, as shown with control experiments using ergosterol and a control membrane protein (KpOmpA). We postulate that this specificity is mediated by the high-affinity bound cholesterol molecules and propose the formation of transient cholesterol clusters around the high-affinity binding sites.
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Affiliation(s)
- Deborah L Gater
- Institute of Pharmacology and Structural Biology - UMR 5089, CNRS and Université de Toulouse - UPS, 205 Route de Narbonne, 31077 Toulouse, France; Khalifa University of Science, Technology and Research, P.O. Box 127788, Abu Dhabi, UAE
| | - Olivier Saurel
- Institute of Pharmacology and Structural Biology - UMR 5089, CNRS and Université de Toulouse - UPS, 205 Route de Narbonne, 31077 Toulouse, France
| | - Iordan Iordanov
- Institute of Pharmacology and Structural Biology - UMR 5089, CNRS and Université de Toulouse - UPS, 205 Route de Narbonne, 31077 Toulouse, France
| | - Wei Liu
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California
| | - Vadim Cherezov
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California.
| | - Alain Milon
- Institute of Pharmacology and Structural Biology - UMR 5089, CNRS and Université de Toulouse - UPS, 205 Route de Narbonne, 31077 Toulouse, France.
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42
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Maiti P, Manna J, McDonald MP. Merging advanced technologies with classical methods to uncover dendritic spine dynamics: A hot spot of synaptic plasticity. Neurosci Res 2015; 96:1-13. [DOI: 10.1016/j.neures.2015.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 01/08/2023]
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43
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Ziomkiewicz I, Sporring J, Pomorski TG, Schulz A. Novel approach to measure the size of plasma-membrane nanodomains in single molecule localization microscopy. Cytometry A 2015; 87:868-77. [PMID: 26109552 DOI: 10.1002/cyto.a.22708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 05/14/2015] [Accepted: 05/26/2015] [Indexed: 01/20/2023]
Abstract
Many membrane proteins are not evenly distributed over the plasma membrane, but gathered in domains assumed to have a particular lipid composition. Using single molecule localization microscopy (SMLM) we have immunolocalized a glycosylphosphatidylinositol (GPI)-anchor protein that labels nanodomains in a specialized plant cell type, and compared the suitability of three methods to estimate their size. As conventional methods full width at half maximum (FWHM) and the full diameter (FWMin) of domains were used. A boundary detection method of the domain area (DA) was performed in order to take irregular shapes into account. In order to compare the influence of the chosen measurement methods, we have developed a MatLab program that allows for automated analysis of domain sizes from multiple SMLM images and provides the statistics of three key features of domains: FWHM and FWMin along their long and short axes as well as the DA, derived from the molecular density. Domains formed by the GPI-anchor protein are approximating elliptical shapes. Direct and indirect immunolabeling resulted in a statistically significant difference in apparent domain size, reflecting the fact that the secondary antibody molecules extend the uncertainty along the nanodomain border. FWMin values along the long and short axis give good estimates of regular, geometrically centred domain shapes, while the DA value matches regular as well as irregular shapes best, as derived from computer-generated, irregular point clusters.
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Affiliation(s)
- Iwona Ziomkiewicz
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Jon Sporring
- Department of Computer Science, University of Copenhagen, Denmark
| | | | - Alexander Schulz
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
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Accounting for limited detection efficiency and localization precision in cluster analysis in single molecule localization microscopy. PLoS One 2015; 10:e0118767. [PMID: 25794150 PMCID: PMC4368834 DOI: 10.1371/journal.pone.0118767] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/14/2015] [Indexed: 11/20/2022] Open
Abstract
Single Molecule Localization Microscopy techniques like PhotoActivated Localization Microscopy, with their sub-diffraction limit spatial resolution, have been popularly used to characterize the spatial organization of membrane proteins, by means of quantitative cluster analysis. However, such quantitative studies remain challenged by the techniques’ inherent sources of errors such as a limited detection efficiency of less than 60%, due to incomplete photo-conversion, and a limited localization precision in the range of 10 – 30nm, varying across the detected molecules, mainly depending on the number of photons collected from each. We provide analytical methods to estimate the effect of these errors in cluster analysis and to correct for them. These methods, based on the Ripley’s L(r) – r or Pair Correlation Function popularly used by the community, can facilitate potentially breakthrough results in quantitative biology by providing a more accurate and precise quantification of protein spatial organization.
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45
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Diffraction-unlimited imaging: from pretty pictures to hard numbers. Cell Tissue Res 2015; 360:151-78. [DOI: 10.1007/s00441-014-2109-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/22/2014] [Indexed: 10/23/2022]
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46
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Jonas KC, Fanelli F, Huhtaniemi IT, Hanyaloglu AC. Single molecule analysis of functionally asymmetric G protein-coupled receptor (GPCR) oligomers reveals diverse spatial and structural assemblies. J Biol Chem 2014; 290:3875-92. [PMID: 25516594 PMCID: PMC4326798 DOI: 10.1074/jbc.m114.622498] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Formation of G protein-coupled receptors (GPCRs) into dimers and higher order oligomers represents a key mechanism in pleiotropic signaling, yet how individual protomers function within oligomers remains poorly understood. We present a super-resolution imaging approach, resolving single GPCR molecules to ∼8 nm resolution in functional asymmetric dimers and oligomers using dual-color photoactivatable dyes and localization microscopy (PD-PALM). PD-PALM of two functionally defined mutant luteinizing hormone receptors (LHRs), a ligand-binding deficient receptor (LHRB−) and a signaling-deficient (LHRS−) receptor, which only function via intermolecular cooperation, favored oligomeric over dimeric formation. PD-PALM imaging of trimers and tetramers revealed specific spatial organizations of individual protomers in complexes where the ratiometric composition of LHRB− to LHRS− modulated ligand-induced signal sensitivity. Structural modeling of asymmetric LHR oligomers strongly aligned with PD-PALM-imaged spatial arrangements, identifying multiple possible helix interfaces mediating inter-protomer associations. Our findings reveal that diverse spatial and structural assemblies mediating GPCR oligomerization may acutely fine-tune the cellular signaling profile.
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Affiliation(s)
- Kim C Jonas
- From the Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 0NN, United Kingdom
| | - Francesca Fanelli
- the Computational Structural Biology Lab, Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 183-41100 Modena, Italy, and
| | - Ilpo T Huhtaniemi
- From the Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 0NN, United Kingdom, the Institute for Biomedicine, Department of Physiology, University of Turku, 20520 Turku, Finland
| | - Aylin C Hanyaloglu
- From the Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 0NN, United Kingdom,
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47
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Falke JJ, Piasta KN. Architecture and signal transduction mechanism of the bacterial chemosensory array: progress, controversies, and challenges. Curr Opin Struct Biol 2014; 29:85-94. [PMID: 25460272 DOI: 10.1016/j.sbi.2014.10.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/27/2014] [Accepted: 10/02/2014] [Indexed: 12/15/2022]
Abstract
Recent research has deepened our understanding of the ancient, conserved chemosensory array that detects small molecule attractants and repellents, and directs the chemotaxis of bacterial and archaeal cells towards an optimal chemical environment. Here we review advances towards a molecular description of the ultrastable lattice architecture and ultrasensitive signal transduction mechanism of the chemosensory array, as well as controversies and challenges requiring further research. Ultimately, a full molecular understanding of array structure and on-off switching will foster (i) the design of novel therapies that block pathogenic wound seeking and infection, (ii) the development of highly specific, sensitive, stable biosensors, and (iii) the elucidation of general functional principles shared by receptor patches in all branches of life.
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Affiliation(s)
- Joseph J Falke
- Department of Chemistry and Biochemistry and the Molecular Biophysics Program, University of Colorado, Boulder, CO 80309-0215, USA.
| | - Kene N Piasta
- Department of Chemistry and Biochemistry and the Molecular Biophysics Program, University of Colorado, Boulder, CO 80309-0215, USA
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48
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Coltharp C, Yang X, Xiao J. Quantitative analysis of single-molecule superresolution images. Curr Opin Struct Biol 2014; 28:112-21. [PMID: 25179006 DOI: 10.1016/j.sbi.2014.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/14/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022]
Abstract
This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10-50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images.
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Affiliation(s)
- Carla Coltharp
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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49
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Habuchi S. Super-resolution molecular and functional imaging of nanoscale architectures in life and materials science. Front Bioeng Biotechnol 2014; 2:20. [PMID: 25152893 PMCID: PMC4126472 DOI: 10.3389/fbioe.2014.00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/30/2014] [Indexed: 11/13/2022] Open
Abstract
Super-resolution (SR) fluorescence microscopy has been revolutionizing the way in which we investigate the structures, dynamics, and functions of a wide range of nanoscale systems. In this review, I describe the current state of various SR fluorescence microscopy techniques along with the latest developments of fluorophores and labeling for the SR microscopy. I discuss the applications of SR microscopy in the fields of life science and materials science with a special emphasis on quantitative molecular imaging and nanoscale functional imaging. These studies open new opportunities for unraveling the physical, chemical, and optical properties of a wide range of nanoscale architectures together with their nanostructures and will enable the development of new (bio-)nanotechnology.
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Affiliation(s)
- Satoshi Habuchi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology , Jeddah , Saudi Arabia
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Shivanandan A, Deschout H, Scarselli M, Radenovic A. Challenges in quantitative single molecule localization microscopy. FEBS Lett 2014; 588:3595-602. [PMID: 24928440 DOI: 10.1016/j.febslet.2014.06.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/01/2014] [Accepted: 06/02/2014] [Indexed: 11/18/2022]
Abstract
Single molecule localization microscopy (SMLM), which can provide up to an order of magnitude improvement in spatial resolution over conventional fluorescence microscopy, has the potential to be a highly useful tool for quantitative biological experiments. It has already been used for this purpose in varied fields in biology, ranging from molecular biology to neuroscience. In this review article, we briefly review the applications of SMLM in quantitative biology, and also the challenges involved and some of the solutions that have been proposed. Due to its advantages in labeling specificity and the relatively low overcounting caused by photoblinking when photo-activable fluorescent proteins (PA-FPs) are used as labels, we focus specifically on Photo-Activated Localization Microscopy (PALM), even though the ideas presented might be applicable to SMLM in general. Also, we focus on the following three quantitative measurements: single molecule counting, analysis of protein spatial distribution heterogeneity and co-localization analysis.
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Affiliation(s)
- A Shivanandan
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - H Deschout
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - M Scarselli
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - A Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland.
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