101
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Corsetti S, Gunn-Moore F, Dholakia K. Light sheet fluorescence microscopy for neuroscience. J Neurosci Methods 2019; 319:16-27. [DOI: 10.1016/j.jneumeth.2018.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/03/2018] [Accepted: 07/16/2018] [Indexed: 12/29/2022]
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102
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Abstract
Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60-80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis.
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103
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Zhao Y, Chen S, Swensen AC, Qian WJ, Gouaux E. Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM. Science 2019; 364:355-362. [PMID: 30975770 DOI: 10.1126/science.aaw8250] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/26/2019] [Indexed: 12/11/2022]
Abstract
Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric assemblies composed of four subunits, GluA1-GluA4. Despite decades of study, the subunit composition, subunit arrangement, and molecular structure of native AMPA receptors remain unknown. Here we elucidate the structures of 10 distinct native AMPA receptor complexes by single-particle cryo-electron microscopy (cryo-EM). We find that receptor subunits are arranged nonstochastically, with the GluA2 subunit preferentially occupying the B and D positions of the tetramer and with triheteromeric assemblies comprising a major population of native AMPA receptors. Cryo-EM maps define the structure for S2-M4 linkers between the ligand-binding and transmembrane domains, suggesting how neurotransmitter binding is coupled to ion channel gating.
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Affiliation(s)
- Yan Zhao
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Shanshuang Chen
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Adam C Swensen
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. .,Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
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104
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Pereira PM, Albrecht D, Culley S, Jacobs C, Marsh M, Mercer J, Henriques R. Fix Your Membrane Receptor Imaging: Actin Cytoskeleton and CD4 Membrane Organization Disruption by Chemical Fixation. Front Immunol 2019; 10:675. [PMID: 31024536 PMCID: PMC6460894 DOI: 10.3389/fimmu.2019.00675] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/12/2019] [Indexed: 12/25/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) techniques allow near molecular scale resolution (~ 20 nm) as well as precise and robust analysis of protein organization at different scales. SMLM hardware, analytics and probes have been the focus of a variety of studies and are now commonly used in laboratories across the world. Protocol reliability and artifact identification are increasingly seen as important aspects of super-resolution microscopy. The reliability of these approaches thus requires in-depth evaluation so that biological findings are based on solid foundations. Here we explore how different fixation approaches that disrupt or preserve the actin cytoskeleton affect membrane protein organization. Using CD4 as a model, we show that fixation-mediated disruption of the actin cytoskeleton correlates with changes in CD4 membrane organization. We highlight how these artifacts are easy to overlook and how careful sample preparation is essential for extracting meaningful results from super-resolution microscopy.
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Affiliation(s)
- Pedro M. Pereira
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - David Albrecht
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Siân Culley
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Caron Jacobs
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Mark Marsh
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Jason Mercer
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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105
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Wieneke R, Tampé R. Multivalent Chelators for In Vivo Protein Labeling. Angew Chem Int Ed Engl 2019; 58:8278-8290. [PMID: 30919542 DOI: 10.1002/anie.201811293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Indexed: 01/09/2023]
Abstract
With the advent of single-molecule methods, chemoselective and site-specific labeling of proteins evolved to become a central aspect in chemical biology as well as cell biology. Protein labeling demands high specificity, rapid as well as efficient conjugation, while maintaining low concentration and biocompatibility under physiological conditions. Generic methods that do not interfere with the function, dynamics, subcellular localization of proteins, and crosstalk with other factors are crucial to probe and image proteins in vitro and in living cells. Alternatives to enzyme-based tags or autofluorescent proteins are short peptide-based recognition tags. These tags provide high specificity, enhanced binding rates, bioorthogonality, and versatility. Here, we report on recent applications of multivalent chelator heads, recognizing oligohistidine-tagged proteins. The striking features of this system has facilitated the analysis of protein complexes by single-molecule approaches.
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Affiliation(s)
- Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M., Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M., Germany
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106
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Wieneke R, Tampé R. Multivalent Chelators for In Vivo Protein Labeling. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ralph Wieneke
- Institute of BiochemistryBiocenterGoethe University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt/M. Germany
| | - Robert Tampé
- Institute of BiochemistryBiocenterGoethe University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt/M. Germany
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107
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Padmanabhan P, Bademosi AT, Kasula R, Lauwers E, Verstreken P, Meunier FA. Need for speed: Super-resolving the dynamic nanoclustering of syntaxin-1 at exocytic fusion sites. Neuropharmacology 2019; 169:107554. [PMID: 30826343 DOI: 10.1016/j.neuropharm.2019.02.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 01/08/2023]
Abstract
Communication between cells relies on regulated exocytosis, a multi-step process that involves the docking, priming and fusion of vesicles with the plasma membrane, culminating in the release of neurotransmitters and hormones. Key proteins and lipids involved in exocytosis are subjected to Brownian movement and constantly switch between distinct motion states which are governed by short-lived molecular interactions. Critical biochemical reactions between exocytic proteins that occur in the confinement of nanodomains underpin the precise sequence of priming steps which leads to the fusion of vesicles. The advent of super-resolution microscopy techniques has provided the means to visualize individual molecules on the plasma membrane with high spatiotemporal resolution in live cells. These techniques are revealing a highly dynamic nature of the nanoscale organization of the exocytic machinery. In this review, we focus on soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) syntaxin-1, which mediates vesicular fusion. Syntaxin-1 is highly mobile at the plasma membrane, and its inherent speed allows fast assembly and disassembly of syntaxin-1 nanoclusters which are associated with exocytosis. We reflect on recent studies which have revealed the mechanisms regulating syntaxin-1 nanoclustering on the plasma membrane and draw inferences on the effect of synaptic activity, phosphoinositides, N-ethylmaleimide-sensitive factor (NSF), α-soluble NSF attachment protein (α-SNAP) and SNARE complex assembly on the dynamic nanoscale organization of syntaxin-1. This article is part of the special issue entitled 'Mobility and trafficking of neuronal membrane proteins'.
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Affiliation(s)
- Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Adekunle T Bademosi
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Ravikiran Kasula
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Elsa Lauwers
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia.
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108
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DNA-Based Super-Resolution Microscopy: DNA-PAINT. Genes (Basel) 2018; 9:genes9120621. [PMID: 30544986 PMCID: PMC6315775 DOI: 10.3390/genes9120621] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/02/2018] [Accepted: 12/03/2018] [Indexed: 12/19/2022] Open
Abstract
Super-resolution microscopies, such as single molecule localization microscopy (SMLM), allow the visualization of biomolecules at the nanoscale. The requirement to observe molecules multiple times during an acquisition has pushed the field to explore methods that allow the binding of a fluorophore to a target. This binding is then used to build an image via points accumulation for imaging nanoscale topography (PAINT), which relies on the stochastic binding of a fluorescent ligand instead of the stochastic photo-activation of a permanently bound fluorophore. Recently, systems that use DNA to achieve repeated, transient binding for PAINT imaging have become the cutting edge in SMLM. Here, we review the history of PAINT imaging, with a particular focus on the development of DNA-PAINT. We outline the different variations of DNA-PAINT and their applications for imaging of both DNA origamis and cellular proteins via SMLM. Finally, we reflect on the current challenges for DNA-PAINT imaging going forward.
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109
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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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110
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Hrabetova S, Cognet L, Rusakov DA, Nägerl UV. Unveiling the Extracellular Space of the Brain: From Super-resolved Microstructure to In Vivo Function. J Neurosci 2018; 38:9355-9363. [PMID: 30381427 PMCID: PMC6706003 DOI: 10.1523/jneurosci.1664-18.2018] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 11/21/2022] Open
Abstract
The extracellular space occupies approximately one-fifth of brain volume, molding a spider web of gaps filled with interstitial fluid and extracellular matrix where neurons and glial cells perform in concert. Yet, very little is known about the spatial organization and dynamics of the extracellular space, let alone its influence on brain function, owing to a lack of appropriate techniques (and a traditional bias toward the inside of cells, not the spaces in between). At the same time, it is clear that understanding fundamental brain functions, such as synaptic transmission, memory, sleep, and recovery from disease, calls for more focused research on the extracellular space of the brain. This review article highlights several key research areas, covering recent methodological and conceptual progress that illuminates this understudied, yet critically important, brain compartment, providing insights into the opportunities and challenges of this nascent field.
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Affiliation(s)
- Sabina Hrabetova
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Laurent Cognet
- Université de Bordeaux, Laboratoire Photonique Numérique et Nanosciences, F-33400 Talence, France
- Institut d'Optique and Centre National de la Recherche Scientifique, F-33400 Talence, France
| | - Dmitri A Rusakov
- Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
| | - U Valentin Nägerl
- Institut Interdisciplinaire des Neurosciences, Université de Bordeaux, 33077 Bordeaux, France, and
- Institut Interdisciplinaire des Neurosciences, Centre National de la Recherche, 33077 Bordeaux, France
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111
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De Keersmaecker H, Camacho R, Rantasa DM, Fron E, Uji-I H, Mizuno H, Rocha S. Mapping Transient Protein Interactions at the Nanoscale in Living Mammalian Cells. ACS NANO 2018; 12:9842-9854. [PMID: 30192513 DOI: 10.1021/acsnano.8b01227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protein-protein interactions (PPIs) form the basis of cellular processes, regulating cell behavior and fate. PPIs can be extremely transient in nature, which hinders their detection. In addition, traditional biochemical methods provided limited information on the spatial distribution and temporal dynamics of PPIs that is crucial for their regulation in the crowded cellular environment. Given the pivotal role of membrane micro- and nanodomains in the regulation of PPIs at the plasma membrane, the development of methods to visualize PPIs with a high spatial resolution is imperative. Here, we present a super-resolution fluorescence microscopy technique that can detect and map short-lived transient protein-protein interactions on a nanometer scale in the cellular environment. This imaging method is based on single-molecule fluorescence microscopy and exploits the effect of the difference in the mobility between cytosolic and membrane-bound proteins in the recorded fluorescence signals. After the development of the proof of concept using a model system based on membrane-bound modular protein domains and fluorescently labeled peptides, we applied this imaging approach to investigate the interactions of cytosolic proteins involved in the epidermal growth factor signaling pathway (namely, Grb2, c-Raf, and PLCγ1). The detected clusters of Grb2 and c-Raf were correlated with the distribution of the receptor at the plasma membrane. Additionally, the interactions of wild type PLCγ1 were compared with those detected with truncated mutants, which provided important information regarding the role played by specific domains in the interaction with the membrane. The results presented here demonstrate the potential of this technique to unravel the role of membrane heterogeneity in the spatiotemporal regulation of cell signaling.
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Affiliation(s)
| | | | | | | | - Hiroshi Uji-I
- Research Institute for Electronic Science , Hokkaido University , N20W10 Kita Ward, Sapporo 001-0020 , Japan
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112
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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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113
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Spahn CK, Glaesmann M, Grimm JB, Ayala AX, Lavis LD, Heilemann M. A toolbox for multiplexed super-resolution imaging of the E. coli nucleoid and membrane using novel PAINT labels. Sci Rep 2018; 8:14768. [PMID: 30282984 PMCID: PMC6170473 DOI: 10.1038/s41598-018-33052-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/21/2018] [Indexed: 11/09/2022] Open
Abstract
Maintenance of the bacterial homeostasis initially emanates from interactions between proteins and the bacterial nucleoid. Investigating their spatial correlation requires high spatial resolution, especially in tiny, highly confined and crowded bacterial cells. Here, we present super-resolution microscopy using a palette of fluorescent labels that bind transiently to either the membrane or the nucleoid of fixed E. coli cells. The presented labels are easily applicable, versatile and allow long-term single-molecule super-resolution imaging independent of photobleaching. The different spectral properties allow for multiplexed imaging in combination with other localisation-based super-resolution imaging techniques. As examples for applications, we demonstrate correlated super-resolution imaging of the bacterial nucleoid with the position of genetic loci, of nascent DNA in correlation to the entire nucleoid, and of the nucleoid of metabolically arrested cells. We furthermore show that DNA- and membrane-targeting labels can be combined with photoactivatable fluorescent proteins and visualise the nano-scale distribution of RNA polymerase relative to the nucleoid in drug-treated E. coli cells.
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Affiliation(s)
- Christoph K Spahn
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mathilda Glaesmann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA
| | - Anthony X Ayala
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA.
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
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114
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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115
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Dynamics, nanoscale organization, and function of synaptic adhesion molecules. Mol Cell Neurosci 2018; 91:95-107. [DOI: 10.1016/j.mcn.2018.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 12/13/2022] Open
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116
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Sigal YM, Zhou R, Zhuang X. Visualizing and discovering cellular structures with super-resolution microscopy. Science 2018; 361:880-887. [PMID: 30166485 DOI: 10.1126/science.aau1044] [Citation(s) in RCA: 340] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Super-resolution microscopy has overcome a long-held resolution barrier-the diffraction limit-in light microscopy and enabled visualization of previously invisible molecular details in biological systems. Since their conception, super-resolution imaging methods have continually evolved and can now be used to image cellular structures in three dimensions, multiple colors, and living systems with nanometer-scale resolution. These methods have been applied to answer questions involving the organization, interaction, stoichiometry, and dynamics of individual molecular building blocks and their integration into functional machineries in cells and tissues. In this Review, we provide an overview of super-resolution methods, their state-of-the-art capabilities, and their constantly expanding applications to biology, with a focus on the latter. We will also describe the current technical challenges and future advances anticipated in super-resolution imaging.
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Affiliation(s)
- Yaron M Sigal
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Ruobo Zhou
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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117
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Zhao M, Nicovich PR, Janco M, Deng Q, Yang Z, Ma Y, Böcking T, Gaus K, Gooding JJ. Ultralow- and Low-Background Surfaces for Single-Molecule Localization Microscopy of Multistep Biointerfaces for Single-Molecule Sensing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:10012-10018. [PMID: 30067032 DOI: 10.1021/acs.langmuir.8b01487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Single-molecule localization microscopy (SMLM) has created the opportunity of pushing fluorescence microscopy from being a biological imaging tool to a surface characterization and possibly even a quantitative analytical tool. The latter could be achieved by molecular counting using pointillist SMLM data sets. However, SMLM is especially sensitive to background fluorescent signals, which influences any subsequent analysis. Therefore, fabricating sensing surfaces that resist nonspecific adsorption of proteins, even after multiple modification steps, has become paramount. Herein is reported two different ways to modify surfaces: dichlorodimethylsilane-biotinylated bovine serum albumin-Tween-20 (DbT20) and poly-l-lysine grafted polyethylene glycol (PLL-PEG) mixed with biotinylated PLL-PEG (PLL-PEG/PEGbiotin). The results show that the ability to resist nonspecific adsorption of DbT20 surfaces deteriorates with an increase in the number of modification steps required after the addition of the DbT20, which limits the applicability of this surface for SMLM. As such, a new surface for SMLM that employs PLL-PEG/PEGbiotin was developed that exhibits ultralow amounts of nonspecific protein adsorption even after many modification steps. The utility of the surface was demonstrated for human influenza hemagglutinin-tagged mEos2, which was directly pulled down from cell lysates onto the PLL-PEG/PEGbiotin surface. The results strongly indicated that the PLL-PEG/PEGbiotin surface satisfies the criteria of SMLM imaging of a negligible background signal and negligible nonspecific adsorption.
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118
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Haas KT, Compans B, Letellier M, Bartol TM, Grillo-Bosch D, Sejnowski TJ, Sainlos M, Choquet D, Thoumine O, Hosy E. Pre-post synaptic alignment through neuroligin-1 tunes synaptic transmission efficiency. eLife 2018; 7:e31755. [PMID: 30044218 PMCID: PMC6070337 DOI: 10.7554/elife.31755] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 07/24/2018] [Indexed: 12/25/2022] Open
Abstract
The nanoscale organization of neurotransmitter receptors regarding pre-synaptic release sites is a fundamental determinant of the synaptic transmission amplitude and reliability. How modifications in the pre- and post-synaptic machinery alignments affects synaptic currents, has only been addressed with computer modelling. Using single molecule super-resolution microscopy, we found a strong spatial correlation between AMPA receptor (AMPAR) nanodomains and the post-synaptic adhesion protein neuroligin-1 (NLG1). Expression of a truncated form of NLG1 disrupted this correlation without affecting the intrinsic AMPAR organization, shifting the pre-synaptic release machinery away from AMPAR nanodomains. Electrophysiology in dissociated and organotypic hippocampal rodent cultures shows these treatments significantly decrease AMPAR-mediated miniature and EPSC amplitudes. Computer modelling predicts that ~100 nm lateral shift between AMPAR nanoclusters and glutamate release sites induces a significant reduction in AMPAR-mediated currents. Thus, our results suggest the synapses necessity to release glutamate precisely in front of AMPAR nanodomains, to maintain a high synaptic responses efficiency.
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Affiliation(s)
- Kalina T Haas
- Interdisciplinary Institute for NeuroscienceUniversity of Bordeaux, UMR 5297, F-33000BordeauxFrance
- Interdisciplinary Institute for NeuroscienceCNRS, UMR 5297, F-33000BordeauxFrance
| | - Benjamin Compans
- Interdisciplinary Institute for NeuroscienceUniversity of Bordeaux, UMR 5297, F-33000BordeauxFrance
- Interdisciplinary Institute for NeuroscienceCNRS, UMR 5297, F-33000BordeauxFrance
| | - Mathieu Letellier
- Interdisciplinary Institute for NeuroscienceUniversity of Bordeaux, UMR 5297, F-33000BordeauxFrance
- Interdisciplinary Institute for NeuroscienceCNRS, UMR 5297, F-33000BordeauxFrance
| | - Thomas M Bartol
- Howard Hughes Medical InstituteSalk Institute for Biological StudiesLa JollaUnited States
| | - Dolors Grillo-Bosch
- Interdisciplinary Institute for NeuroscienceUniversity of Bordeaux, UMR 5297, F-33000BordeauxFrance
- Interdisciplinary Institute for NeuroscienceCNRS, UMR 5297, F-33000BordeauxFrance
| | - Terrence J Sejnowski
- Howard Hughes Medical InstituteSalk Institute for Biological StudiesLa JollaUnited States
| | - Matthieu Sainlos
- Interdisciplinary Institute for NeuroscienceUniversity of Bordeaux, UMR 5297, F-33000BordeauxFrance
- Interdisciplinary Institute for NeuroscienceCNRS, UMR 5297, F-33000BordeauxFrance
| | - Daniel Choquet
- Interdisciplinary Institute for NeuroscienceUniversity of Bordeaux, UMR 5297, F-33000BordeauxFrance
- Interdisciplinary Institute for NeuroscienceCNRS, UMR 5297, F-33000BordeauxFrance
- Bordeaux Imaging CenterUMS 3420 CNRS, Université de Bordeaux, US4 INSERM, F-33000BordeauxFrance
| | - Olivier Thoumine
- Interdisciplinary Institute for NeuroscienceUniversity of Bordeaux, UMR 5297, F-33000BordeauxFrance
- Interdisciplinary Institute for NeuroscienceCNRS, UMR 5297, F-33000BordeauxFrance
| | - Eric Hosy
- Interdisciplinary Institute for NeuroscienceUniversity of Bordeaux, UMR 5297, F-33000BordeauxFrance
- Interdisciplinary Institute for NeuroscienceCNRS, UMR 5297, F-33000BordeauxFrance
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119
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Gatterdam K, Joest EF, Gatterdam V, Tampé R. The Scaffold Design of Trivalent Chelator Heads Dictates Affinity and Stability for Labeling His-tagged Proteins in vitro and in Cells. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Karl Gatterdam
- Institute of Biochemistry; Biocenter; Goethe University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Eike F. Joest
- Institute of Biochemistry; Biocenter; Goethe University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Volker Gatterdam
- Institute of Biochemistry; Biocenter; Goethe University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Robert Tampé
- Institute of Biochemistry; Biocenter; Goethe University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
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120
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Gatterdam K, Joest EF, Gatterdam V, Tampé R. The Scaffold Design of Trivalent Chelator Heads Dictates Affinity and Stability for Labeling His-tagged Proteins in vitro and in Cells. Angew Chem Int Ed Engl 2018; 57:12395-12399. [PMID: 29845721 DOI: 10.1002/anie.201802746] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/01/2018] [Indexed: 11/08/2022]
Abstract
Small chemical/biological interaction pairs are at the forefront in tracing protein function and interaction at high signal-to-background ratios in cellular pathways. However, the optimal design of scaffold, linker, and chelator head still deserve systematic investigation to achieve the highest affinity and kinetic stability for in vitro and especially cellular applications. We report on a library of N-nitrilotriacetic acid (NTA)-based multivalent chelator heads (MCHs) built on linear, cyclic, and dendritic scaffolds and compare these with regard to their binding affinity and stability for the labeling of cellular His-tagged proteins. Furthermore, we describe a new approach for tracing cellular target proteins at picomolar probe concentrations in cells. Finally, we outline fundamental differences between the MCH scaffolds and define a cyclic trisNTA chelator that displays the highest affinity and kinetic stability of all reported reversible, low-molecular-weight interaction pairs.
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Affiliation(s)
- Karl Gatterdam
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Eike F Joest
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Volker Gatterdam
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
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121
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Baddeley D, Bewersdorf J. Biological Insight from Super-Resolution Microscopy: What We Can Learn from Localization-Based Images. Annu Rev Biochem 2018; 87:965-989. [PMID: 29272143 DOI: 10.1146/annurev-biochem-060815-014801] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Super-resolution optical imaging based on the switching and localization of individual fluorescent molecules [photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), etc.] has evolved remarkably over the last decade. Originally driven by pushing technological limits, it has become a tool of biological discovery. The initial demand for impressive pictures showing well-studied biological structures has been replaced by a need for quantitative, reliable data providing dependable evidence for specific unresolved biological hypotheses. In this review, we highlight applications that showcase this development, identify the features that led to their success, and discuss remaining challenges and difficulties. In this context, we consider the complex topic of defining resolution for this imaging modality and address some of the more common analytical methods used with this data.
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Affiliation(s)
- David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Auckland Bioengineering Institute, University of Auckland, Auckland 1010, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA
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122
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Modi S, Higgs NF, Sheehan D, Griffin LD, Kittler JT. Quantum dot conjugated nanobodies for multiplex imaging of protein dynamics at synapses. NANOSCALE 2018; 10:10241-10249. [PMID: 29790493 PMCID: PMC5977936 DOI: 10.1039/c7nr09130c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/12/2018] [Indexed: 06/08/2023]
Abstract
Neurons communicate with each other through synapses, which show enrichment for specialized receptors. Although many studies have explored spatial enrichment and diffusion of these receptors in dissociated neurons using single particle tracking, much less is known about their dynamic properties at synapses in complex tissue like brain slices. Here we report the use of smaller and highly specific quantum dots conjugated with a recombinant single domain antibody fragment (VHH fragment) against green fluorescent protein to provide information on diffusion of adhesion molecules at the growth cone and neurotransmitter receptors at synapses. Our data reveals that QD-nanobodies can measure neurotransmitter receptor dynamics at both excitatory and inhibitory synapses in primary neuronal cultures as well as in ex vivo rat brain slices. We also demonstrate that this approach can be applied to tagging multiple proteins to simultaneously monitor their behavior. Thus, we provide a strategy for multiplex imaging of tagged membrane proteins to study their clustering, diffusion and transport both in vitro as well as in native tissue environments such as brain slices.
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Affiliation(s)
- Souvik Modi
- Neuroscience
, Physiology and Pharmacology
, University College London. Gower Street
,
London
, WC1E 6BT
, UK
.
- Tata Institute of Fundamental Research
,
Homi Bhabha Road
, Mumbai
, 400005
, India
| | - Nathalie F. Higgs
- Neuroscience
, Physiology and Pharmacology
, University College London. Gower Street
,
London
, WC1E 6BT
, UK
.
| | - David Sheehan
- Neuroscience
, Physiology and Pharmacology
, University College London. Gower Street
,
London
, WC1E 6BT
, UK
.
| | | | - Josef T. Kittler
- Neuroscience
, Physiology and Pharmacology
, University College London. Gower Street
,
London
, WC1E 6BT
, UK
.
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123
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Adelizzi B, Aloi A, Van Zee NJ, Palmans ARA, Meijer EW, Voets IK. Painting Supramolecular Polymers in Organic Solvents by Super-resolution Microscopy. ACS NANO 2018; 12:4431-4439. [PMID: 29697958 PMCID: PMC5968428 DOI: 10.1021/acsnano.8b00396] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/26/2018] [Indexed: 05/29/2023]
Abstract
Despite the rapid development of complex functional supramolecular systems, visualization of these architectures under native conditions at high resolution has remained a challenging endeavor. Super-resolution microscopy was recently proposed as an effective tool to unveil one-dimensional nanoscale structures in aqueous media upon chemical functionalization with suitable fluorescent probes. Building upon our previous work, which enabled photoactivation localization microscopy in organic solvents, herein, we present the imaging of one-dimensional supramolecular polymers in their native environment by interface point accumulation for imaging in nanoscale topography (iPAINT). The noncovalent staining, typical of iPAINT, allows the investigation of supramolecular polymers' structure in situ without any chemical modification. The quasi-permanent adsorption of the dye to the polymer is exploited to identify block-like arrangements within supramolecular fibers, which were obtained upon mixing homopolymers that were prestained with different colors. The staining of the blocks, maintained by the lack of exchange of the dyes, permits the imaging of complex structures for multiple days. This study showcases the potential of PAINT-like strategies such as iPAINT to visualize multicomponent dynamic systems in their native environment with an easy, synthesis-free approach and high spatial resolution.
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Affiliation(s)
- Beatrice Adelizzi
- Institute
for Complex Molecular Systems, Laboratory of Macromolecular and
Organic Chemistry, Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing
Soft Matter, Department of Chemical Engineering and Chemistry, and Laboratory of
Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Antonio Aloi
- Institute
for Complex Molecular Systems, Laboratory of Macromolecular and
Organic Chemistry, Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing
Soft Matter, Department of Chemical Engineering and Chemistry, and Laboratory of
Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Nathan J. Van Zee
- Institute
for Complex Molecular Systems, Laboratory of Macromolecular and
Organic Chemistry, Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing
Soft Matter, Department of Chemical Engineering and Chemistry, and Laboratory of
Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Anja R. A. Palmans
- Institute
for Complex Molecular Systems, Laboratory of Macromolecular and
Organic Chemistry, Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing
Soft Matter, Department of Chemical Engineering and Chemistry, and Laboratory of
Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - E. W. Meijer
- Institute
for Complex Molecular Systems, Laboratory of Macromolecular and
Organic Chemistry, Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing
Soft Matter, Department of Chemical Engineering and Chemistry, and Laboratory of
Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Ilja K. Voets
- Institute
for Complex Molecular Systems, Laboratory of Macromolecular and
Organic Chemistry, Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing
Soft Matter, Department of Chemical Engineering and Chemistry, and Laboratory of
Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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124
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Harwardt MLIE, Dietz MS, Heilemann M, Wohland T. SPT and Imaging FCS Provide Complementary Information on the Dynamics of Plasma Membrane Molecules. Biophys J 2018; 114:2432-2443. [PMID: 29650369 PMCID: PMC6129459 DOI: 10.1016/j.bpj.2018.03.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/10/2018] [Accepted: 03/12/2018] [Indexed: 12/27/2022] Open
Abstract
The dynamics of biomolecules in the plasma membrane is of fundamental importance to understanding cellular processes. Cellular signaling often starts with extracellular ligand binding to a membrane receptor, which then transduces an intracellular signal. Ligand binding and receptor-complex activation often involve a complex rearrangement of proteins in the membrane, which results in changes in diffusion properties. Two widely used methods to characterize biomolecular diffusion are single-particle tracking (SPT) and imaging total internal reflection fluorescence correlation spectroscopy (ITIR-FCS). Here, we compare the results of recovered diffusion coefficients and mean-square displacements of the two methods by simulations of free, domain-confined, or meshwork diffusion. We introduce, to our knowledge, a new method for the determination of confinement radii from ITIR-FCS data. We further establish and demonstrate simultaneous SPT/ITIR-FCS for direct comparison within living cells. Finally, we compare the results obtained by SPT and ITIR-FCS for the receptor tyrosine kinase MET. Our results show that SPT and ITIR-FCS yield complementary information on diffusion properties of biomolecules in cell membranes.
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Affiliation(s)
- Marie-Lena I E Harwardt
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Marina S Dietz
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt, Germany.
| | - Thorsten Wohland
- Departments of Biological Sciences and Chemistry, Center for Bioimaging Sciences, National University of Singapore, Singapore, Singapore.
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125
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Gatterdam K, Joest EF, Dietz MS, Heilemann M, Tampé R. Super-Chelators for Advanced Protein Labeling in Living Cells. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Karl Gatterdam
- Institute of Biochemistry; Biocenter; Goethe-University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Eike F. Joest
- Institute of Biochemistry; Biocenter; Goethe-University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Marina S. Dietz
- Institute of Physical and Theoretical Chemistry; Goethe-University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry; Goethe-University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Robert Tampé
- Institute of Biochemistry; Biocenter; Goethe-University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
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126
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Gatterdam K, Joest EF, Dietz MS, Heilemann M, Tampé R. Super-Chelators for Advanced Protein Labeling in Living Cells. Angew Chem Int Ed Engl 2018; 57:5620-5625. [PMID: 29464841 DOI: 10.1002/anie.201800827] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/17/2018] [Indexed: 12/17/2022]
Abstract
Live-cell labeling, super-resolution microscopy, single-molecule applications, protein localization, or chemically induced assembly are emerging approaches, which require specific and very small interaction pairs. The minimal disturbance of protein function is essential to derive unbiased insights into cellular processes. Herein, we define a new class of hexavalent N-nitrilotriacetic acid (hexaNTA) chelators, displaying the highest affinity and stability of all NTA-based small interaction pairs described so far. Coupled to bright organic fluorophores with fine-tuned photophysical properties, the super-chelator probes were delivered into human cells by chemically gated nanopores. These super-chelators permit kinetic profiling, multiplexed labeling of His6 - and His12 -tagged proteins as well as single-molecule-based super-resolution imaging.
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Affiliation(s)
- Karl Gatterdam
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Eike F Joest
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Marina S Dietz
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
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127
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Compartmentalization of the plasma membrane. Curr Opin Cell Biol 2018; 53:15-21. [PMID: 29656224 DOI: 10.1016/j.ceb.2018.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 11/23/2022]
Abstract
The compartmentalization of the plasma membrane is essential for cells to perform specialized biochemical functions, in particular those responsible for intracellular and intercellular signaling pathways. Study of membrane compartmentalization requires state-of-the-art imaging tools that can reveal dynamics of individual molecules with high spatial and temporal resolution. In addition, quantitative analyses are employed to identify transient changes in molecule dynamics. In this review, membrane compartments are classified as stable domains, transient compartments, or nanodomains where proteins aggregate. Interestingly, in most cases, the cortical cytoskeleton plays important roles. Recent studies of the membrane-cytoskeleton interface are providing new insights about membrane organization involving a scale-free self-similar fractal structure and cytoskeleton active processes coupled to membrane dynamics.
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128
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Venkataramani V, Kardorff M, Herrmannsdörfer F, Wieneke R, Klein A, Tampé R, Heilemann M, Kuner T. Enhanced labeling density and whole-cell 3D dSTORM imaging by repetitive labeling of target proteins. Sci Rep 2018; 8:5507. [PMID: 29615726 PMCID: PMC5882651 DOI: 10.1038/s41598-018-23818-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/21/2018] [Indexed: 12/21/2022] Open
Abstract
With continuing advances in the resolving power of super-resolution microscopy, the inefficient labeling of proteins with suitable fluorophores becomes a limiting factor. For example, the low labeling density achieved with antibodies or small molecule tags limits attempts to reveal local protein nano-architecture of cellular compartments. On the other hand, high laser intensities cause photobleaching within and nearby an imaged region, thereby further reducing labeling density and impairing multi-plane whole-cell 3D super-resolution imaging. Here, we show that both labeling density and photobleaching can be addressed by repetitive application of trisNTA-fluorophore conjugates reversibly binding to a histidine-tagged protein by a novel approach called single-epitope repetitive imaging (SERI). For single-plane super-resolution microscopy, we demonstrate that, after multiple rounds of labeling and imaging, the signal density is increased. Using the same approach of repetitive imaging, washing and re-labeling, we demonstrate whole-cell 3D super-resolution imaging compensated for photobleaching above or below the imaging plane. This proof-of-principle study demonstrates that repetitive labeling of histidine-tagged proteins provides a versatile solution to break the ‘labeling barrier’ and to bypass photobleaching in multi-plane, whole-cell 3D experiments.
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Affiliation(s)
- Varun Venkataramani
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Markus Kardorff
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Frank Herrmannsdörfer
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Alina Klein
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Mike Heilemann
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany. .,Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany.
| | - Thomas Kuner
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany.
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129
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Bartoschik T, Galinec S, Kleusch C, Walkiewicz K, Breitsprecher D, Weigert S, Muller YA, You C, Piehler J, Vercruysse T, Daelemans D, Tschammer N. Near-native, site-specific and purification-free protein labeling for quantitative protein interaction analysis by MicroScale Thermophoresis. Sci Rep 2018; 8:4977. [PMID: 29563556 PMCID: PMC5862892 DOI: 10.1038/s41598-018-23154-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/05/2018] [Indexed: 12/21/2022] Open
Abstract
MicroScale Thermophoresis (MST) is a frequently used method for the quantitative characterization of intermolecular interactions with several advantages over other technologies. One of these is its capability to determine equilibrium constants in solution including complex biological matrices such as cell lysates. MST requires one binding partner to be fluorescent, which is typically achieved by labeling target proteins with a suitable fluorophore. Here, we present a near-native, site-specific in situ labeling strategy for MST experiments that enables reliable measurements in cell lysates and that has distinct advantages over routine covalent labeling techniques. To this end, we exploited the high-affinity interaction of tris-NTA with oligohistidine-tags, which are popular for purification, immobilization or detection of recombinant proteins. We used various DYE-tris-NTA conjugates to successfully label His-tagged proteins that were either purified or a component of cell lysate. The RED-tris-NTA was identified as the optimal dye conjugate with a high affinity towards oligohistidine-tags, a high fluorescence signal and an optimal signal-to-noise ratio in MST binding experiments. Owing to its emission in the red region of the spectrum, it also enables reliable measurements in complex biological matrices such as cell lysates allowing a more physiologically realistic assessment and eliminating the need for protein purification.
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Affiliation(s)
- Tanja Bartoschik
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany
| | - Stefanie Galinec
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany
| | - Christian Kleusch
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany
| | | | | | - Sebastian Weigert
- Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen, Nuremberg Henkestr 91, 91052, Erlangen, Germany
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen, Nuremberg Henkestr 91, 91052, Erlangen, Germany
| | - Changjiang You
- Division of Biophysics, Department of Biology, University Osnabrück, Barbarastr 11, 49076, Osnabrück, Germany
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University Osnabrück, Barbarastr 11, 49076, Osnabrück, Germany
| | - Thomas Vercruysse
- KU Leuven Department of Immunology and Microbiology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000, Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Immunology and Microbiology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000, Leuven, Belgium
| | - Nuska Tschammer
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany.
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130
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Vangindertael J, Camacho R, Sempels W, Mizuno H, Dedecker P, Janssen KPF. An introduction to optical super-resolution microscopy for the adventurous biologist. Methods Appl Fluoresc 2018; 6:022003. [DOI: 10.1088/2050-6120/aaae0c] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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131
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Kundel F, Tosatto L, Whiten DR, Wirthensohn DC, Horrocks MH, Klenerman D. Shedding light on aberrant interactions - a review of modern tools for studying protein aggregates. FEBS J 2018; 285:3604-3630. [PMID: 29453901 DOI: 10.1111/febs.14409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/27/2018] [Accepted: 02/12/2018] [Indexed: 12/15/2022]
Abstract
The link between protein aggregation and neurodegenerative disease is well established. However, given the heterogeneity of species formed during the aggregation process, it is difficult to delineate details of the molecular events involved in generating pathological aggregates from those producing soluble monomers. As aberrant aggregates are possible pharmacological targets for the treatment of neurodegenerative diseases, the need to observe and characterise soluble oligomers has pushed traditional biophysical techniques to their limits, leading to the development of a plethora of new tools capable of detecting soluble oligomers with high precision and specificity. In this review, we discuss a range of modern biophysical techniques that have been developed to study protein aggregation, and give an overview of how they have been used to understand, in detail, the aberrant aggregation of amyloidogenic proteins associated with the two most common neurodegenerative disorders, Alzheimer's disease and Parkinson's disease.
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Affiliation(s)
| | - Laura Tosatto
- Centre for Integrative Biology, Università degli Studi di Trento, Italy
| | | | | | | | - David Klenerman
- Department of Chemistry, University of Cambridge, UK.,UK Dementia Research Institute, University of Cambridge, UK
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132
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133
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Abstract
Far-field super-resolution fluorescence microscopy has allowed observation of biomolecular and synthetic nanoscale systems with features on the nanometre scale, with chemical specificity and multiplexing capability. DNA-PAINT (DNA-based point accumulation for imaging in nanoscale topography) is a super-resolution method that exploits programmable transient hybridization between short oligonucleotide strands, and allows multiplexed, single-molecule, single-label visualization with down to ~5-10 nm resolution. DNA-PAINT provides a method for structural characterisation of nucleic acid nanostructures with high spatial resolution and single-strand visibility.
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Affiliation(s)
- Mingjie Dai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, CLSB 5th Floor, Blackfan Circle, Boston, MA, 02115, USA. .,Program in Biophysics, Harvard University, Boston, MA, 02115, USA.
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134
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Renner M, Wang L, Levi S, Hennekinne L, Triller A. A Simple and Powerful Analysis of Lateral Subdiffusion Using Single Particle Tracking. Biophys J 2018; 113:2452-2463. [PMID: 29211999 DOI: 10.1016/j.bpj.2017.09.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 09/01/2017] [Accepted: 09/11/2017] [Indexed: 11/29/2022] Open
Abstract
In biological membranes, many factors such as cytoskeleton, lipid composition, crowding, and molecular interactions deviate lateral diffusion from the expected random walks. These factors have different effects on diffusion but act simultaneously, so the observed diffusion is a complex mixture of diffusive behaviors (directed, Brownian, anomalous, or confined). Therefore, commonly used approaches to quantify diffusion based on averaging of the displacements such as the mean square displacement, are not adapted to the analysis of this heterogeneity. We introduce a parameter-the packing coefficient Pc, which gives an estimate of the degree of free movement that a molecule displays in a period of time independently of its global diffusivity. Applying this approach to two different situations (diffusion of a lipid probe and trapping of receptors at synapses), we show that Pc detected and localized temporary changes of diffusive behavior both in time and in space. More importantly, it allowed the detection of periods with very high confinement as well as their frequency and duration, and thus it can be used to calculate the effective kon and koff of scaffolding interactions such as those that immobilize receptors at synapses.
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Affiliation(s)
- Marianne Renner
- École Normale Supérieure, PSL Research University, CNRS, INSERM, Institute of Biology (IBENS), Paris, France; INSERM UMR-S 839, Université Pierre et Marie Curie, Institut du Fer à Moulin, Paris, France.
| | - Lili Wang
- École Normale Supérieure, PSL Research University, CNRS, INSERM, Institute of Biology (IBENS), Paris, France
| | - Sabine Levi
- INSERM UMR-S 839, Université Pierre et Marie Curie, Institut du Fer à Moulin, Paris, France
| | - Laetitia Hennekinne
- École Normale Supérieure, PSL Research University, CNRS, INSERM, Institute of Biology (IBENS), Paris, France
| | - Antoine Triller
- École Normale Supérieure, PSL Research University, CNRS, INSERM, Institute of Biology (IBENS), Paris, France.
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135
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Abstract
To get a complete understanding of cell migration, it is critical to study its orchestration at the molecular level. Since the recent developments in single-molecule imaging, it is now possible to study molecular phenomena at the single-molecule level inside living cells. In this chapter, we describe how such approaches have been and can be used to decipher molecular mechanisms involved in cell migration.
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136
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Rey I, Garcia DA, Wheatley BA, Song W, Upadhyaya A. Biophysical Techniques to Study B Cell Activation: Single-Molecule Imaging and Force Measurements. Methods Mol Biol 2018; 1707:51-68. [PMID: 29388099 DOI: 10.1007/978-1-4939-7474-0_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells of the adaptive immune system recognize pathogenic peptides through specialized receptors on their membranes. The engagement of these receptors with antigen leads to cell activation, which induces profound changes in the cell including cytoskeleton remodeling and membrane deformation. During this process, receptors and signaling molecules undergo spatiotemporal reorganization to form signaling microclusters and the immunological synapse. The cytoskeletal and membrane dynamics also leads to exertion of forces on the cell-substrate interface. In this chapter we describe two techniques-one for single-molecule imaging of B cell receptors to measure their diffusive properties as cells get activated on supported lipid bilayers; and the second for visualizing and quantifying cellular forces using elastic surfaces to stimulate T and B cells.
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Affiliation(s)
- Ivan Rey
- Biophysics Program, University of Maryland, College Park, MD, 20742, USA
| | - David A Garcia
- Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | | | - Wenxia Song
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Arpita Upadhyaya
- Biophysics Program, University of Maryland, College Park, MD, 20742, USA. .,Department of Physics, University of Maryland, College Park, MD, 20742, USA. .,Institute for Physical Science and Technology, University of Maryland, 1151, PSC Bldg., College Park, MD, 20742, USA.
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137
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Sikora G, Wyłomańska A, Gajda J, Solé L, Akin EJ, Tamkun MM, Krapf D. Elucidating distinct ion channel populations on the surface of hippocampal neurons via single-particle tracking recurrence analysis. Phys Rev E 2017; 96:062404. [PMID: 29347346 DOI: 10.1103/physreve.96.062404] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Indexed: 01/08/2023]
Abstract
Protein and lipid nanodomains are prevalent on the surface of mammalian cells. In particular, it has been recently recognized that ion channels assemble into surface nanoclusters in the soma of cultured neurons. However, the interactions of these molecules with surface nanodomains display a considerable degree of heterogeneity. Here, we investigate this heterogeneity and develop statistical tools based on the recurrence of individual trajectories to identify subpopulations within ion channels in the neuronal surface. We specifically study the dynamics of the K^{+} channel Kv1.4 and the Na^{+} channel Nav1.6 on the surface of cultured hippocampal neurons at the single-molecule level. We find that both these molecules are expressed in two different forms with distinct kinetics with regards to surface interactions, emphasizing the complex proteomic landscape of the neuronal surface. Further, the tools presented in this work provide new methods for the analysis of membrane nanodomains, transient confinement, and identification of populations within single-particle trajectories.
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Affiliation(s)
- Grzegorz Sikora
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology, 50-370 Wrocław, Poland.,Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Agnieszka Wyłomańska
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology, 50-370 Wrocław, Poland
| | - Janusz Gajda
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology, 50-370 Wrocław, Poland
| | - Laura Solé
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Elizabeth J Akin
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Michael M Tamkun
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, USA.,Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Diego Krapf
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523, USA.,School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
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138
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Joensuu M, Martínez-Mármol R, Padmanabhan P, Glass NR, Durisic N, Pelekanos M, Mollazade M, Balistreri G, Amor R, Cooper-White JJ, Goodhill GJ, Meunier FA. Visualizing endocytic recycling and trafficking in live neurons by subdiffractional tracking of internalized molecules. Nat Protoc 2017; 12:2590-2622. [PMID: 29189775 DOI: 10.1038/nprot.2017.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Our understanding of endocytic pathway dynamics is restricted by the diffraction limit of light microscopy. Although super-resolution techniques can overcome this issue, highly crowded cellular environments, such as nerve terminals, can also dramatically limit the tracking of multiple endocytic vesicles such as synaptic vesicles (SVs), which in turn restricts the analytical dissection of their discrete diffusional and transport states. We recently introduced a pulse-chase technique for subdiffractional tracking of internalized molecules (sdTIM) that allows the visualization of fluorescently tagged molecules trapped in individual signaling endosomes and SVs in presynapses or axons with 30- to 50-nm localization precision. We originally developed this approach for tracking single molecules of botulinum neurotoxin type A, which undergoes activity-dependent internalization and retrograde transport in autophagosomes. This method was then adapted to localize the signaling endosomes containing cholera toxin subunit-B that undergo retrograde transport in axons and to track SVs in the crowded environment of hippocampal presynapses. We describe (i) the construction of a custom-made microfluidic device that enables control over neuronal orientation; (ii) the 3D printing of a perfusion system for sdTIM experiments performed on glass-bottom dishes; (iii) the dissection, culturing and transfection of hippocampal neurons in microfluidic devices; and (iv) guidance on how to perform the pulse-chase experiments and data analysis. In addition, we describe the use of single-molecule-tracking analytical tools to reveal the average and the heterogeneous single-molecule mobility behaviors. We also discuss alternative reagents and equipment that can, in principle, be used for sdTIM experiments and describe how to adapt sdTIM to image nanocluster formation and/or tubulation in early endosomes during sorting events. The procedures described in this protocol take ∼1 week.
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Affiliation(s)
- Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Ramon Martínez-Mármol
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Pranesh Padmanabhan
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Nick R Glass
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Nela Durisic
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthew Pelekanos
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Mahdie Mollazade
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giuseppe Balistreri
- Division of General Microbiology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Rumelo Amor
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Justin J Cooper-White
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.,Division of General Microbiology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,School of Chemical Engineering, The University of Queensland, Brisbane, Queensland, Australia.,Materials Science and Engineering Division, CSIRO, Clayton, Victoria, Australia.,UQ Centre for Stem Cell Ageing and Regenerative Engineering, The University of Queensland, Brisbane, Queensland, Australia
| | - Geoffrey J Goodhill
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland, Australia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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139
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Tas RP, Chazeau A, Cloin BMC, Lambers MLA, Hoogenraad CC, Kapitein LC. Differentiation between Oppositely Oriented Microtubules Controls Polarized Neuronal Transport. Neuron 2017; 96:1264-1271.e5. [PMID: 29198755 PMCID: PMC5746200 DOI: 10.1016/j.neuron.2017.11.018] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/11/2017] [Accepted: 11/08/2017] [Indexed: 12/21/2022]
Abstract
Microtubules are essential for polarized transport in neurons, but how their organization guides motor proteins to axons or dendrites is unclear. Because different motors recognize distinct microtubule properties, we used optical nanoscopy to examine the relationship between microtubule orientations, stability, and modifications. Nanometric tracking of motors to super-resolve microtubules and determine their polarity revealed that in dendrites, stable and acetylated microtubules are mostly oriented minus-end out, while dynamic and tyrosinated microtubules are oriented oppositely. In addition, microtubules with similar orientations and modifications form bundles that bias transport. Importantly, because the plus-end-directed Kinesin-1 selectively interacts with acetylated microtubules, this organization guides this motor out of dendrites and into axons. In contrast, Kinesin-3 prefers tyrosinated microtubules and can enter both axons and dendrites. This separation of distinct microtubule subsets into oppositely oriented bundles constitutes a key architectural principle of the neuronal microtubule cytoskeleton that enables polarized sorting by different motor proteins. Motor-based nanoscopy enables direct observation of microtubule (MT) polarity In neurons, MTs organize into polarized bundles that locally bias transport In dendrites, bundles of opposite orientation differ in stability and composition Dendritic MTs bias Kinesin-1 transport toward the soma, ensuring axon selectivity
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Affiliation(s)
- Roderick P Tas
- Division of Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Anaël Chazeau
- Division of Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Bas M C Cloin
- Division of Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Maaike L A Lambers
- Division of Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Casper C Hoogenraad
- Division of Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Lukas C Kapitein
- Division of Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands.
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140
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Heller JP, Rusakov DA. The Nanoworld of the Tripartite Synapse: Insights from Super-Resolution Microscopy. Front Cell Neurosci 2017; 11:374. [PMID: 29225567 PMCID: PMC5705901 DOI: 10.3389/fncel.2017.00374] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/10/2017] [Indexed: 12/17/2022] Open
Abstract
Synaptic connections between individual nerve cells are fundamental to the process of information transfer and storage in the brain. Over the past decades a third key partner of the synaptic machinery has been unveiled: ultrathin processes of electrically passive astroglia which often surround pre- and postsynaptic structures. The recent advent of super-resolution (SR) microscopy has begun to uncover the dynamic nanoworld of synapses and their astroglial environment. Here we overview and discuss the current progress in our understanding of the synaptic nanoenvironment, as gleaned from the imaging methods that go beyond the diffraction limit of conventional light microscopy. We argue that such methods are essential to achieve a new level of comprehension pertinent to the principles of signal integration in the brain.
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Affiliation(s)
- Janosch P Heller
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Dmitri A Rusakov
- UCL Institute of Neurology, University College London, London, United Kingdom.,Institute of Neuroscience, University of Nizhny Novgorod, Nizhny Novgorod, Russia
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141
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Localization-based super-resolution imaging meets high-content screening. Nat Methods 2017; 14:1184-1190. [PMID: 29083400 DOI: 10.1038/nmeth.4486] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/26/2017] [Indexed: 11/08/2022]
Abstract
Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.
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142
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Auer A, Strauss MT, Schlichthaerle T, Jungmann R. Fast, Background-Free DNA-PAINT Imaging Using FRET-Based Probes. NANO LETTERS 2017; 17:6428-6434. [PMID: 28871786 DOI: 10.1021/acs.nanolett.7b03425] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
DNA point accumulation in nanoscale topography (DNA-PAINT) enables super-resolution microscopy by harnessing the predictable, transient hybridization between short dye-labeled "imager" and complementary target-bound "docking" strands. DNA-PAINT microscopy allows sub-5 nm spatial resolution, spectrally unlimited multiplexing, and quantitative image analysis. However, these abilities come at the cost of nonfluorogenic imager strands, also emitting fluorescence when not bound to their docking strands. This has thus far prevented rapid image acquisition with DNA-PAINT, as the blinking rate of probes is limited by an upper-bound of imager strand concentrations, which in turn is dictated by the necessity to facilitate the detection of single-molecule binding events over the background of unbound, freely diffusing probes. To overcome this limitation and enable fast, background-free DNA-PAINT microscopy, we here introduce FRET-based imaging probes, alleviating the concentration-limit of imager strands and speeding up image acquisition by several orders of magnitude. We assay two approaches for FRET-based DNA-PAINT (or FRET-PAINT) using either fixed or transient acceptor dyes in combination with transiently binding donor-labeled DNA strands and achieve high-quality super-resolution imaging on DNA origami structures in a few tens of seconds. Finally, we also demonstrate the applicability of FRET-PAINT in a cellular environment by performing super-resolution imaging of microtubules in under 30 s. FRET-PAINT combines the advantages of conventional DNA-PAINT with fast image acquisition times, facilitating the potential study of dynamic processes.
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Affiliation(s)
- Alexander Auer
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University , Munich, Germany
- Max Planck Institute of Biochemistry , Martinsried, Germany
| | - Maximilian T Strauss
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University , Munich, Germany
- Max Planck Institute of Biochemistry , Martinsried, Germany
| | - Thomas Schlichthaerle
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University , Munich, Germany
- Max Planck Institute of Biochemistry , Martinsried, Germany
| | - Ralf Jungmann
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University , Munich, Germany
- Max Planck Institute of Biochemistry , Martinsried, Germany
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143
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Thompson AD, Bewersdorf J, Toomre D, Schepartz A. HIDE Probes: A New Toolkit for Visualizing Organelle Dynamics, Longer and at Super-Resolution. Biochemistry 2017; 56:5194-5201. [PMID: 28792749 PMCID: PMC5854879 DOI: 10.1021/acs.biochem.7b00545] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Living cells are complex and dynamic assemblies that carefully sequester and orchestrate multiple diverse processes that enable growth, division, regulation, movement, and communication. Membrane-bound organelles such as the endoplasmic reticulum, mitochondria, plasma membrane, and others are integral to these processes, and their functions demand dynamic reorganization in both space and time. Visualizing these dynamics in live cells over long time periods demands probes that label discrete organelles specifically, at high density, and withstand long-term irradiation. Here we describe the evolution of our work on the development of a set of high-density environmentally sensitive (HIDE) membrane probes that enable long-term, live-cell nanoscopy of the dynamics of multiple organelles in live cells using single-molecule switching and stimulated emission depletion imaging modalities.
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Affiliation(s)
- Alexander D Thompson
- Department of Chemistry, ‡Department of Molecular, Cellular and Developmental Biology, §Department of Cell Biology, and ∥Department of Biomedical Engineering, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Joerg Bewersdorf
- Department of Chemistry, ‡Department of Molecular, Cellular and Developmental Biology, §Department of Cell Biology, and ∥Department of Biomedical Engineering, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Derek Toomre
- Department of Chemistry, ‡Department of Molecular, Cellular and Developmental Biology, §Department of Cell Biology, and ∥Department of Biomedical Engineering, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Alanna Schepartz
- Department of Chemistry, ‡Department of Molecular, Cellular and Developmental Biology, §Department of Cell Biology, and ∥Department of Biomedical Engineering, Yale University , New Haven, Connecticut 06520-8107, United States
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144
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Super resolution imaging of chromatin in pluripotency, differentiation, and reprogramming. Curr Opin Genet Dev 2017; 46:186-193. [DOI: 10.1016/j.gde.2017.07.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/10/2017] [Accepted: 07/24/2017] [Indexed: 12/23/2022]
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145
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Hippocampal LTP and contextual learning require surface diffusion of AMPA receptors. Nature 2017; 549:384-388. [PMID: 28902836 PMCID: PMC5683353 DOI: 10.1038/nature23658] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 07/21/2017] [Indexed: 12/21/2022]
Abstract
Long-term potentiation (LTP) of excitatory synaptic transmission has long been considered a cellular correlate for learning and memory1,2. Early LTP (eLTP, <1 hour) had initially been explained either by presynaptic increases in glutamate release3–5 or by direct modification of post-synaptic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) function6,7. Compelling models have more recently proposed that synaptic potentiation can occur by the recruitment of additional post-synaptic AMPARs8, sourced either from an intracellular reserve pool by exocytosis or from nearby extra synaptic receptors pre-existing on the neuronal surface9–12. However, the exact mechanism through which synapses can rapidly recruit new AMPARs during eLTP is still unknown. In particular, direct evidence for a pivotal role of AMPAR surface diffusion as a trafficking mechanism in synaptic plasticity is still lacking. Using AMPAR immobilization approaches, we show that interfering with AMPAR surface diffusion dramatically impaired synaptic potentiation of Schaffer collateral/commissural inputs to cornu ammonis area 1 (CA1) in cultured slices, acute slices and in vivo. Our data also identifies distinct contributions of various AMPAR trafficking routes to the temporal profile of synaptic potentiation. In addition, AMPAR immobilization in vivo in the dorsal hippocampus (DH) before fear conditioning, indicated that AMPAR diffusion is important for the early phase of contextual learning. Therefore, our results provide a direct demonstration that the recruitment of new receptors to synapses by surface diffusion is a critical mechanism for the expression of LTP and hippocampal learning. Since AMPAR surface diffusion is dictated by weak Brownian forces that are readily perturbed by protein-protein interactions, we anticipate that this fundamental trafficking mechanism will be a key target for modulating synaptic potentiation and learning.
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146
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Harwardt MLIE, Young P, Bleymüller WM, Meyer T, Karathanasis C, Niemann HH, Heilemann M, Dietz MS. Membrane dynamics of resting and internalin B-bound MET receptor tyrosine kinase studied by single-molecule tracking. FEBS Open Bio 2017; 7:1422-1440. [PMID: 28904870 PMCID: PMC5586345 DOI: 10.1002/2211-5463.12285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 11/09/2022] Open
Abstract
The human MET receptor tyrosine kinase contributes to vertebrate development and cell proliferation. As a proto-oncogene, it is a target in cancer therapies. MET is also relevant for bacterial infection by Listeria monocytogenes and is activated by the bacterial protein internalin B. The processes of ligand binding, receptor activation, and the diffusion behavior of MET within the plasma membrane as well as its interconnections with various cell components are not fully understood. We investigated the receptor diffusion dynamics using single-particle tracking and imaging fluorescence correlation spectroscopy and elucidated mobility states of resting and internalin B-bound MET. We show that internalin B-bound MET exhibits lower diffusion coefficients and diffuses in a more confined area in the membrane. We report that the fraction of immobile receptors is larger for internalin B-bound receptors than for resting MET. Results of single-particle tracking in cells treated with various cytotoxins depleting cholesterol from the membrane and disrupting the actin cytoskeleton and microtubules suggest that cholesterol and actin influence MET diffusion dynamics, while microtubules do not have any effect.
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Affiliation(s)
- Marie-Lena I E Harwardt
- Institute of Physical and Theoretical Chemistry Johann Wolfgang Goethe-University Frankfurt Germany
| | - Phoebe Young
- Institute of Physical and Theoretical Chemistry Johann Wolfgang Goethe-University Frankfurt Germany
| | - Willem M Bleymüller
- Structural Biochemistry Department of Chemistry Bielefeld University Germany
| | - Timo Meyer
- Structural Biochemistry Department of Chemistry Bielefeld University Germany
| | - Christos Karathanasis
- Institute of Physical and Theoretical Chemistry Johann Wolfgang Goethe-University Frankfurt Germany
| | - Hartmut H Niemann
- Structural Biochemistry Department of Chemistry Bielefeld University Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry Johann Wolfgang Goethe-University Frankfurt Germany
| | - Marina S Dietz
- Institute of Physical and Theoretical Chemistry Johann Wolfgang Goethe-University Frankfurt Germany
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147
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Bannai H. Molecular membrane dynamics: Insights into synaptic function and neuropathological disease. Neurosci Res 2017; 129:47-56. [PMID: 28826905 DOI: 10.1016/j.neures.2017.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/14/2017] [Accepted: 07/26/2017] [Indexed: 11/19/2022]
Abstract
The fluid mosaic model states that molecules in the plasma membrane can freely undergo lateral diffusion; however, in neurons and glia, specific membrane molecules are concentrated in cellular microdomains to overcome the randomizing effects of free diffusion. This specialized distribution of membrane molecules is crucial for various cell functions; one example is the accumulation of neurotransmitter receptors at the postsynaptic neuronal membrane, which enables efficient synaptic transmission. Quantum dot-single particle tracking (QD-SPT) is a super-resolution imaging technique that uses semiconductor nanocrystal quantum dots as fluorescent probes, and is a powerful tool for analyzing protein and lipid behavior in the plasma membrane. In this article, we review studies implementing QD-SPT in neuroscience research and important data gleaned using this technology. Recent QD-SPT experiments have provided critical insights into the mechanism and physiological relevance of membrane self-organization in neurons and astrocytes in the brain. The mobility of some membrane molecules may become abnormal in cellular models of epilepsy and Alzheimer's disease. Based on these findings, we propose that the behavior of membrane molecules reflects the condition of neurons in pathological disease states.
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Affiliation(s)
- Hiroko Bannai
- Laboratory for Developmental Neurobiology, RIKEN Brain Science Institute (BSI), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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148
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Multi-color single-molecule tracking and subtrajectory analysis for quantification of spatiotemporal dynamics and kinetics upon T cell activation. Sci Rep 2017; 7:6994. [PMID: 28765585 PMCID: PMC5539329 DOI: 10.1038/s41598-017-06960-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/20/2017] [Indexed: 11/08/2022] Open
Abstract
The dynamic properties of molecules in living cells are attracting increasing interest. We propose a new method, moving subtrajectory analysis using single-molecule tracking, and demonstrate its utility in the spatiotemporal quantification of not only dynamics but also the kinetics of interactions using single-color images. Combining this technique with three-color simultaneous single-molecule imaging, we quantified the dynamics and kinetics of molecules in spatial relation to T cell receptor (TCR) microclusters, which trigger TCR signaling. CD3ε, a component of the TCR/CD3 complex, and CD45, a phosphatase positively and negatively regulating signaling, were each found in two mobility states: faster (associated) and slower (dissociated) states. Dynamics analysis suggests that the microclusters are loosely composed of heterogeneous nanoregions, possibly surrounded by a weak barrier. Kinetics analysis quantified the association and dissociation rates of interactions with the microclusters. The associations of both CD3ε and CD45 were single-step processes. In contrast, their dissociations were each composed of two components, indicating transient and stable associated states. Inside the microclusters, the association was accelerated, and the stable association was increased. Only CD45 showed acceleration of association at the microcluster boundary, suggesting specific affinity on the boundary. Thus, this method is an innovative and versatile tool for spatiotemporal quantification.
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149
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Lee SH, Jin C, Cai E, Ge P, Ishitsuka Y, Teng KW, de Thomaz AA, Nall D, Baday M, Jeyifous O, Demonte D, Dundas CM, Park S, Delgado JY, Green WN, Selvin PR. Super-resolution imaging of synaptic and Extra-synaptic AMPA receptors with different-sized fluorescent probes. eLife 2017; 6:27744. [PMID: 28749340 PMCID: PMC5779237 DOI: 10.7554/elife.27744] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022] Open
Abstract
Previous studies tracking AMPA receptor (AMPAR) diffusion at synapses observed a large mobile extrasynaptic AMPAR pool. Using super-resolution microscopy, we examined how fluorophore size and photostability affected AMPAR trafficking outside of, and within, post-synaptic densities (PSDs) from rats. Organic fluorescent dyes (≈4 nm), quantum dots, either small (≈10 nm diameter; sQDs) or big (>20 nm; bQDs), were coupled to AMPARs via different-sized linkers. We find that >90% of AMPARs labeled with fluorescent dyes or sQDs were diffusing in confined nanodomains in PSDs, which were stable for 15 min or longer. Less than 10% of sQD-AMPARs were extrasynaptic and highly mobile. In contrast, 5-10% of bQD-AMPARs were in PSDs and 90-95% were extrasynaptic as previously observed. Contrary to the hypothesis that AMPAR entry is limited by the occupancy of open PSD 'slots', our findings suggest that AMPARs rapidly enter stable 'nanodomains' in PSDs with lifetime >15 min, and do not accumulate in extrasynaptic membranes.
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Affiliation(s)
- Sang Hak Lee
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Chaoyi Jin
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - En Cai
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Pinghua Ge
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Yuji Ishitsuka
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Kai Wen Teng
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Andre A de Thomaz
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Duncan Nall
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Murat Baday
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Okunola Jeyifous
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - Daniel Demonte
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Christopher M Dundas
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Sheldon Park
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Jary Y Delgado
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - William N Green
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - Paul R Selvin
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
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150
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Mollazade M, Tabarin T, Nicovich PR, Soeriyadi A, Nieves DJ, Gooding JJ, Gaus K. Can single molecule localization microscopy be used to map closely spaced RGD nanodomains? PLoS One 2017; 12:e0180871. [PMID: 28723958 PMCID: PMC5516992 DOI: 10.1371/journal.pone.0180871] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 06/22/2017] [Indexed: 11/22/2022] Open
Abstract
Cells sense and respond to nanoscale variations in the distribution of ligands to adhesion receptors. This makes single molecule localization microscopy (SMLM) an attractive tool to map the distribution of ligands on nanopatterned surfaces. We explore the use of SMLM spatial cluster analysis to detect nanodomains of the cell adhesion-stimulating tripeptide arginine-glycine-aspartic acid (RGD). These domains were formed by the phase separation of block copolymers with controllable spacing on the scale of tens of nanometers. We first determined the topology of the block copolymer with atomic force microscopy (AFM) and then imaged the localization of individual RGD peptides with direct stochastic optical reconstruction microscopy (dSTORM). To compare the data, we analyzed the dSTORM data with DBSCAN (density-based spatial clustering application with noise). The ligand distribution and polymer topology are not necessary identical since peptides may attach to the polymer outside the nanodomains and/or coupling and detection of peptides within the nanodomains is incomplete. We therefore performed simulations to explore the extent to which nanodomains could be mapped with dSTORM. We found that successful detection of nanodomains by dSTORM was influenced by the inter-domain spacing and the localization precision of individual fluorophores, and less by non-specific absorption of ligands to the substratum. For example, under our imaging conditions, DBSCAN identification of nanodomains spaced further than 50 nm apart was largely independent of background localisations, while nanodomains spaced closer than 50 nm required a localization precision of ~11 nm to correctly estimate the modal nearest neighbor distance (NDD) between nanodomains. We therefore conclude that SMLM is a promising technique to directly map the distribution and nanoscale organization of ligands and would benefit from an improved localization precision.
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Affiliation(s)
- Mahdie Mollazade
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Thibault Tabarin
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Philip R Nicovich
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Alexander Soeriyadi
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Daniel J Nieves
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
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