1
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Cornet J, Coulonges N, Pezeshkian W, Penissat-Mahaut M, Desgrez-Dautet H, Marrink SJ, Destainville N, Chavent M, Manghi M. There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning. SOFT MATTER 2024; 20:4998-5013. [PMID: 38884641 DOI: 10.1039/d4sm00089g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
We describe a complete methodology to bridge the scales between nanoscale molecular dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species are furthermore embedded. To go from the molecular to the mesoscale, we notably appeal to physical renormalization arguments enabling us to rigorously infer the mesoscale interaction parameters from its molecular counterpart. We also explain how to deal with the physical timescales at stake at the mesoscale. Simulating the as-obtained mesoscale system enables us to equilibrate the long wavelengths of the vesicles of interest, up to the vesicle size. Conversely, we then backmap from the meso- to the nano-scale, which enables us to equilibrate in turn the short wavelengths down to the molecular length-scales. By applying our approach to the specific situation of patterning a vesicle membrane, we show that macroscopic membranes can thus be equilibrated at all length-scales in achievable computational time offering an original strategy to address the fundamental challenge of timescale in simulations of large bio-membrane systems.
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Affiliation(s)
- Julie Cornet
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
| | - Nelly Coulonges
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Maël Penissat-Mahaut
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Hermes Desgrez-Dautet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | | | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
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2
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Schwenzer N, Teiwes NK, Kohl T, Pohl C, Giller MJ, Lehnart SE, Steinem C. Ca V1.3 channel clusters characterized by live-cell and isolated plasma membrane nanoscopy. Commun Biol 2024; 7:620. [PMID: 38783117 PMCID: PMC11116533 DOI: 10.1038/s42003-024-06313-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
A key player of excitable cells in the heart and brain is the L-type calcium channel CaV1.3. In the heart, it is required for voltage-dependent Ca2+-signaling, i.e., for controlling and modulating atrial cardiomyocyte excitation-contraction coupling. The clustering of CaV1.3 in functionally relevant channel multimers has not been addressed due to a lack of stoichiometric labeling combined with high-resolution imaging. Here, we developed a HaloTag-labeling strategy to visualize and quantify CaV1.3 clusters using STED nanoscopy to address the questions of cluster size and intra-cluster channel density. Channel clusters were identified in the plasma membrane of transfected live HEK293 cells as well as in giant plasma membrane vesicles derived from these cells that were spread on modified glass support to obtain supported plasma membrane bilayers (SPMBs). A small fraction of the channel clusters was colocalized with early and recycling endosomes at the membranes. STED nanoscopy in conjunction with live-cell and SPMB imaging enabled us to quantify CaV1.3 cluster sizes and their molecular density revealing significantly lower channel densities than expected for dense channel packing. CaV1.3 channel cluster size and molecular density were increased in SPMBs after treatment of the cells with the sympathomimetic compound isoprenaline, suggesting a regulated channel cluster condensation mechanism.
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Affiliation(s)
- Niko Schwenzer
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert‑Koch‑Str. 42a, 37075, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany
| | - Nikolas K Teiwes
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany
| | - Tobias Kohl
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert‑Koch‑Str. 42a, 37075, Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Celine Pohl
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany
| | - Michelle J Giller
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany
| | - Stephan E Lehnart
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert‑Koch‑Str. 42a, 37075, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
- Collaborative Research Center SFB 1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
| | - Claudia Steinem
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany.
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany.
- Max-Planck-Institut für Dynamik und Selbstorganisation, Am Fassberg 17, 37077, Göttingen, Germany.
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3
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Valdes PA, Yu CC(J, Aronson J, Ghosh D, Zhao Y, An B, Bernstock JD, Bhere D, Felicella MM, Viapiano MS, Shah K, Chiocca EA, Boyden ES. Improved immunostaining of nanostructures and cells in human brain specimens through expansion-mediated protein decrowding. Sci Transl Med 2024; 16:eabo0049. [PMID: 38295184 PMCID: PMC10911838 DOI: 10.1126/scitranslmed.abo0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
Proteins are densely packed in cells and tissues, where they form complex nanostructures. Expansion microscopy (ExM) variants have been used to separate proteins from each other in preserved biospecimens, improving antibody access to epitopes. Here, we present an ExM variant, decrowding expansion pathology (dExPath), that can expand proteins away from each other in human brain pathology specimens, including formalin-fixed paraffin-embedded (FFPE) clinical specimens. Immunostaining of dExPath-expanded specimens reveals, with nanoscale precision, previously unobserved cellular structures, as well as more continuous patterns of staining. This enhanced molecular staining results in observation of previously invisible disease marker-positive cell populations in human glioma specimens, with potential implications for tumor aggressiveness. dExPath results in improved fluorescence signals even as it eliminates lipofuscin-associated autofluorescence. Thus, this form of expansion-mediated protein decrowding may, through improved epitope access for antibodies, render immunohistochemistry more powerful in clinical science and, perhaps, diagnosis.
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Affiliation(s)
- Pablo A. Valdes
- Department of Neurosurgery, University of Texas Medical Branch, Galveston, TX, 77555
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
| | - Chih-Chieh (Jay) Yu
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Engineering, MIT, MA, USA, 02139
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- RIKEN Center for Brain Science, Saitama, Japan, 351-0198
| | - Jenna Aronson
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- RIKEN Center for Brain Science, Saitama, Japan, 351-0198
| | - Debarati Ghosh
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA, 02139
| | - Yongxin Zhao
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA, 15213
| | - Bobae An
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
| | - Joshua D. Bernstock
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Koch Institute, MIT, Cambridge, MA, USA, 02139
| | - Deepak Bhere
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Department of Pathology, Microbiology and Immunology, School of Medicine Columbia, University of South Carolina, Columbia, SC, USA, 29209
- Center for Stem Cell and Translational Immunotherapy, Harvard Medical School/Brigham and Women’s Hospital, Boston, MA, USA, 02115
| | - Michelle M. Felicella
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA, 77555
| | - Mariano S. Viapiano
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA, 13210
| | - Khalid Shah
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Center for Stem Cell and Translational Immunotherapy, Harvard Medical School/Brigham and Women’s Hospital, Boston, MA, USA, 02115
| | - E. Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Edward S. Boyden
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Engineering, MIT, MA, USA, 02139
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA, 02139
- Koch Institute, MIT, Cambridge, MA, USA, 02139
- MIT Center for Neurobiological Engineering and K. Lisa Yang Center for Bionics, MIT, Cambridge, MA, USA, 02139
- Howard Hughes Medical Institute, Cambridge, MA, USA, 02139
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4
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Yang F, Tan Y, Wu C, Xin L, Huang Z, Zhou H, Zhou F. dSTORM-Based Single-Cell Protein Quantitative Analysis Can Effectively Evaluate the Degradation Ability of PROTACs. Chembiochem 2023; 24:e202200680. [PMID: 36564338 DOI: 10.1002/cbic.202200680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022]
Abstract
As an emerging therapeutic strategy, proteolysis-targeting chimeras (PROTACs) have been proven to be superior to traditional drugs in many aspects. However, due to their unique mechanism of action, existing methods for evaluating the degradation still have many limitations, which seriously restricts the development of PROTACs. In this methodological study, using direct stochastic optical reconstruction microscopy (dSTORM)-based single-cell protein quantitative analysis, we systematically investigated the dynamic degradation characteristics of FLT3 protein during PROTACs treatment. We found that the distribution of FLT3 varies between FLT3-ITD mutation and FLT3-WT cells. PROTACs had an obvious time-course effect on protein degradation and present two distinct phases; this provided a basis for deciding when to evaluate protein degradation. High concentrations of PROTACs were more effective than long-time administration because a higher Dmax was achieved. Two-color dSTORM-based colocalization analysis efficiently detected the proportion of ternary complexes, making it very useful in screening PROTACs. Taken together, our findings show that the dSTORM method is an ideal tool for evaluating PROTACs and will accelerate the development of new PROTACs.
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Affiliation(s)
- Fuwei Yang
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Yuxin Tan
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Cheng Wu
- Key Laboratory of Biomedical Engineering of Hainan Province School, of Biomedical Engineering, Hainan University, Haikou, Hainan, 570100, P. R. China
| | - Lilan Xin
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Zhenli Huang
- Key Laboratory of Biomedical Engineering of Hainan Province School, of Biomedical Engineering, Hainan University, Haikou, Hainan, 570100, P. R. China
| | - Haibing Zhou
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430000, P. R. China
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5
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Ejdrup AL, Lycas MD, Lorenzen N, Konomi A, Herborg F, Madsen KL, Gether U. A density-based enrichment measure for assessing colocalization in single-molecule localization microscopy data. Nat Commun 2022; 13:4388. [PMID: 35902578 PMCID: PMC9334352 DOI: 10.1038/s41467-022-32064-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/15/2022] [Indexed: 11/20/2022] Open
Abstract
Dual-color single-molecule localization microscopy (SMLM) provides unprecedented possibilities for detailed studies of colocalization of different molecular species in a cell. However, the informational richness of the data is not fully exploited by current analysis tools that often reduce colocalization to a single value. Here, we describe a tool specifically designed for determination of co-localization in both 2D and 3D from SMLM data. The approach uses a function that describes the relative enrichment of one molecular species on the density distribution of a reference species. The function reframes the question of colocalization by providing a density-context relevant to multiple biological questions. Moreover, the function visualize enrichment (i.e. colocalization) directly in the images for easy interpretation. We demonstrate the approach’s functionality on both simulated data and cultured neurons, and compare it to current alternative measures. The method is available in a Python function for easy and parameter-free implementation. Full information gained from single-molecule localisation microscopy (SMLM) isn't exploited by current analysis tools. Here the authors report relative enrichment which uses a density-based colocalisation measure for both 2D and 3D SMLM data; they apply it to both simulated data and cultured neurons.
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Affiliation(s)
- Aske L Ejdrup
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Matthew D Lycas
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Lorenzen
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ainoa Konomi
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Freja Herborg
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth L Madsen
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulrik Gether
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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6
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Tom AM, Kim WK, Hyeon C. Polymer brush-induced depletion interactions and clustering of membrane proteins. J Chem Phys 2021; 154:214901. [PMID: 34240971 DOI: 10.1063/5.0048554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We investigate the effect of mobile polymer brushes on proteins embedded in biological membranes by employing both Asakura-Oosawa type of theoretical model and coarse-grained molecular dynamics simulations. The brush polymer-induced depletion attraction between proteins changes non-monotonically with the size of brush. The depletion interaction, which is determined by the ratio of the protein size to the grafting distance between brush polymers, increases linearly with the brush size as long as the polymer brush height is shorter than the protein size. When the brush height exceeds the protein size, however, the depletion attraction among proteins is slightly reduced. We also explore the possibility of the brush polymer-induced assembly of a large protein cluster, which can be related to one of many molecular mechanisms underlying recent experimental observations of integrin nanocluster formation and signaling.
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Affiliation(s)
- Anvy Moly Tom
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Won Kyu Kim
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
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7
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Cornet J, Destainville N, Manghi M. Domain formation in bicomponent vesicles induced by composition-curvature coupling. J Chem Phys 2021; 152:244705. [PMID: 32610955 DOI: 10.1063/5.0006756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Lipid vesicles composed of a mixture of two types of lipids are studied by intensive Monte Carlo numerical simulations. The coupling between the local composition and the membrane shape is induced by two different spontaneous curvatures of the components. We explore the various morphologies of these biphasic vesicles coupled to the observed patterns such as nano-domains or labyrinthine mesophases. The effect of the difference in curvatures, the surface tension, and the interaction parameter between components is thoroughly explored. Our numerical results quantitatively agree with the previous analytical results obtained by Gueguen et al. [Eur. Phys. J. E 37, 76 (2014)] in the disordered (high temperature) phase. Numerical simulations allow us to explore the full parameter space, especially close to and below the critical temperature, where analytical results are not accessible. Phase diagrams are constructed and domain morphologies are quantitatively studied by computing the structure factor and the domain size distribution. This mechanism likely explains the existence of nano-domains in cell membranes as observed by super-resolution fluorescence microscopy.
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Affiliation(s)
- Julie Cornet
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, UPS, France
| | - Nicolas Destainville
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, UPS, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, UPS, France
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8
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Quantitative Synaptic Biology: A Perspective on Techniques, Numbers and Expectations. Int J Mol Sci 2020; 21:ijms21197298. [PMID: 33023247 PMCID: PMC7582872 DOI: 10.3390/ijms21197298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/31/2022] Open
Abstract
Synapses play a central role for the processing of information in the brain and have been analyzed in countless biochemical, electrophysiological, imaging, and computational studies. The functionality and plasticity of synapses are nevertheless still difficult to predict, and conflicting hypotheses have been proposed for many synaptic processes. In this review, we argue that the cause of these problems is a lack of understanding of the spatiotemporal dynamics of key synaptic components. Fortunately, a number of emerging imaging approaches, going beyond super-resolution, should be able to provide required protein positions in space at different points in time. Mathematical models can then integrate the resulting information to allow the prediction of the spatiotemporal dynamics. We argue that these models, to deal with the complexity of synaptic processes, need to be designed in a sufficiently abstract way. Taken together, we suggest that a well-designed combination of imaging and modelling approaches will result in a far more complete understanding of synaptic function than currently possible.
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9
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Mayr S, Hauser F, Puthukodan S, Axmann M, Göhring J, Jacak J. Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model. PLoS Comput Biol 2020; 16:e1007902. [PMID: 32603371 PMCID: PMC7384682 DOI: 10.1371/journal.pcbi.1007902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 07/27/2020] [Accepted: 04/22/2020] [Indexed: 11/19/2022] Open
Abstract
We present the software platform 2CALM that allows for a comparative analysis of 3D localisation microscopy data representing protein distributions in two biological samples. The in-depth statistical analysis reveals differences between samples at the nanoscopic level using parameters such as cluster-density and -curvature. An automatic classification system combines multiplex and multi-level statistical approaches into one comprehensive parameter for similarity testing of the compared samples. We demonstrated the biological importance of 2CALM, comparing the protein distributions of CD41 and CD62p on activated platelets in a 3D artificial clot. Additionally, using 2CALM, we quantified the impact of the inflammatory cytokine interleukin-1β on platelet activation in clots. The platform is applicable to any other cell type and biological system and can provide new insights into biological and medical applications.
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Affiliation(s)
- Sandra Mayr
- University of Applied Sciences Upper Austria, Linz, Austria
| | - Fabian Hauser
- University of Applied Sciences Upper Austria, Linz, Austria
| | | | - Markus Axmann
- University of Applied Sciences Upper Austria, Linz, Austria
| | - Janett Göhring
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Jaroslaw Jacak
- University of Applied Sciences Upper Austria, Linz, Austria
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10
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Shashkova S, Andersson M, Hohmann S, Leake MC. Correlating single-molecule characteristics of the yeast aquaglyceroporin Fps1 with environmental perturbations directly in living cells. Methods 2020; 193:46-53. [PMID: 32387484 DOI: 10.1016/j.ymeth.2020.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 01/09/2023] Open
Abstract
Membrane proteins play key roles at the interface between the cell and its environment by mediating selective import and export of molecules via plasma membrane channels. Despite a multitude of studies on transmembrane channels, understanding of their dynamics directly within living systems is limited. To address this, we correlated molecular scale information from living cells with real time changes to their microenvironment. We employed super-resolved millisecond fluorescence microscopy with a single-molecule sensitivity, to track labelled molecules of interest in real time. We use as example the aquaglyceroporin Fps1 in the yeast Saccharomyces cerevisiae to dissect and correlate its stoichiometry and molecular turnover kinetics with various extracellular conditions. We show that Fps1 resides in multi tetrameric clusters while hyperosmotic and oxidative stress conditions cause Fps1 reorganization. Moreover, we demonstrate that rapid exposure to hydrogen peroxide causes Fps1 degradation. In this way we shed new light on aspects of architecture and dynamics of glycerol-permeable plasma membrane channels.
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Affiliation(s)
| | - Mikael Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden.
| | - Stefan Hohmann
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
| | - Mark C Leake
- Department of Physics, University of York, YO10 5DD York, UK.
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11
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Finke J, Mikuličić S, Loster AL, Gawlitza A, Florin L, Lang T. Anatomy of a viral entry platform differentially functionalized by integrins α3 and α6. Sci Rep 2020; 10:5356. [PMID: 32210347 PMCID: PMC7093462 DOI: 10.1038/s41598-020-62202-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
During cell invasion, human papillomaviruses use large CD151 patches on the cell surface. Here, we studied whether these patches are defined architectures with features for virus binding and/or internalization. Super-resolution microscopy reveals that the patches are assemblies of closely associated nanoclusters of CD151, integrin α3 and integrin α6. Integrin α6 is required for virus attachment and integrin α3 for endocytosis. We propose that CD151 organizes viral entry platforms with different types of integrin clusters for different functionalities. Since numerous viruses use tetraspanin patches, we speculate that this building principle is a blueprint for cell-surface architectures utilized by viral particles.
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Affiliation(s)
- Jérôme Finke
- Department of Membrane Biochemistry, Life & Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115, Bonn, Germany
| | - Snježana Mikuličić
- Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Straße 67, 55131, Mainz, Germany
| | - Anna-Lena Loster
- Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Straße 67, 55131, Mainz, Germany
| | - Alexander Gawlitza
- Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Straße 67, 55131, Mainz, Germany
| | - Luise Florin
- Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Straße 67, 55131, Mainz, Germany
| | - Thorsten Lang
- Department of Membrane Biochemistry, Life & Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115, Bonn, Germany.
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12
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Richter KN, Patzelt C, Phan NTN, Rizzoli SO. Antibody-driven capture of synaptic vesicle proteins on the plasma membrane enables the analysis of their interactions with other synaptic proteins. Sci Rep 2019; 9:9231. [PMID: 31239503 PMCID: PMC6592915 DOI: 10.1038/s41598-019-45729-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/13/2019] [Indexed: 01/07/2023] Open
Abstract
Many organelles from the secretory pathway fuse to the plasma membrane, to exocytose different cargoes. Their proteins are then retrieved from the plasma membrane by endocytosis, and the organelles are re-formed. It is generally unclear whether the organelle proteins colocalize when they are on the plasma membrane, or whether they disperse. To address this, we generated here a new approach, which we tested on synaptic vesicles, organelles that are known to exo- and endocytose frequently. We tagged the synaptotagmin molecules of newly exocytosed vesicles using clusters of primary and secondary antibodies targeted against the luminal domains of these molecules. The antibody clusters are too large for endocytosis, and thus sequestered the synaptotagmin molecules on the plasma membrane. Immunostainings for other synaptic molecules then revealed whether they colocalized with the sequestered synaptotagmin molecules. We suggest that such assays may be in the future extended to other cell types and other organelles.
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Affiliation(s)
- Katharina N Richter
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.
| | - Christina Patzelt
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Nhu T N Phan
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.
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13
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Neumann J, Ziegler K, Gelléri M, Fröhlich-Nowoisky J, Liu F, Bellinghausen I, Schuppan D, Birk U, Pöschl U, Cremer C, Lucas K. Nanoscale distribution of TLR4 on primary human macrophages stimulated with LPS and ATI. NANOSCALE 2019; 11:9769-9779. [PMID: 31066732 DOI: 10.1039/c9nr00943d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Toll-like receptor 4 (TLR4) plays a crucial role in the recognition of invading pathogens. Upon activation by lipopolysaccharides (LPS), TLR4 is recruited into specific membrane domains and dimerizes. In addition to LPS, TLR4 can be stimulated by wheat amylase-trypsin inhibitors (ATI). ATI are proteins associated with gluten containing grains, whose ingestion promotes intestinal and extraintestinal inflammation. However, the effect of ATI vs. LPS on the membrane distribution of TLR4 at the nanoscale has not been analyzed. In this study, we investigated the effect of LPS and ATI stimulation on the membrane distribution of TLR4 in primary human macrophages using single molecule localization microscopy (SMLM). We found that in unstimulated macrophages the majority of TLR4 molecules are located in clusters, but with donor-dependent variations from ∼51% to ∼75%. Depending on pre-clustering, we found pronounced variations in the fraction of clustered molecules and density of clusters on the membrane upon LPS and ATI stimulation. Although clustering differed greatly among the human donors, we found an almost constant cluster diameter of ∼44 nm for all donors, independent of treatment. Together, our results show donor-dependent but comparable effects between ATI and LPS stimulation on the membrane distribution of TLR4. This may indicate a general mechanism of TLR4 activation in primary human macrophages. Furthermore, our methodology visualizes TLR4 receptor clustering and underlines its functional role as a signaling platform.
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Affiliation(s)
- Jan Neumann
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128 Mainz, Germany.
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14
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Abstract
Plasma membrane proteins organize into structures named compartments, microdomains, rafts, phases, crowds, or clusters. These structures are often smaller than 100 nm in diameter. Despite their importance in many cellular functions, little is known about their inner organization. For instance, how densely are molecules packed? Being aware of the protein compaction may contribute to our general understanding of why such structures exist and how they execute their functions. In this study, we have investigated plasma membrane crowds formed by the amyloid precursor protein (APP), a protein well known for its involvement in Alzheimer's disease. By combining biochemical experiments with conventional and super-resolution stimulated emission depletion microscopy, we quantitatively determined the protein packing density within APP crowds. We found that crowds occurring with reasonable frequency contain between 20 and 30 molecules occupying a spherical area with a diameter between 65 and 85 nm. Additionally, we found the vast majority of plasmalemmal APP residing in these crowds. The model suggests a high molecular density of protein material within plasmalemmal APP crowds. This should affect the protein's biochemical accessibility and processing by nonpathological α-secretases. As clustering of APP is a prerequisite for endocytic entry into the pathological processing pathway, elucidation of the packing density also provides a deeper understanding of this part of APP's life cycle.
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15
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Maidorn M, Olichon A, Rizzoli SO, Opazo F. Nanobodies reveal an extra-synaptic population of SNAP-25 and Syntaxin 1A in hippocampal neurons. MAbs 2018; 11:305-321. [PMID: 30466346 PMCID: PMC6380399 DOI: 10.1080/19420862.2018.1551675] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Synaptic vesicle fusion (exocytosis) is a precisely regulated process that entails the formation of SNARE complexes between the vesicle protein synaptobrevin 2 (VAMP2) and the plasma membrane proteins Syntaxin 1 and SNAP-25. The sub-cellular localization of the latter two molecules remains unclear, although they have been the subject of many recent investigations. To address this, we generated two novel camelid single domain antibodies (nanobodies) specifically binding to SNAP-25 and Syntaxin 1A. These probes penetrated more easily into samples and detected their targets more efficiently than conventional antibodies in crowded regions. When investigated by super-resolution imaging, the nanobodies revealed substantial extra-synaptic populations for both SNAP-25 and Syntaxin 1A, which were poorly detected by antibodies. Moreover, extra-synaptic Syntaxin 1A molecules were recruited to synapses during stimulation, suggesting that these are physiologically-active molecules. We conclude that nanobodies are able to reveal qualitatively and quantitatively different organization patterns, when compared to conventional antibodies.
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Affiliation(s)
- Manuel Maidorn
- a Institute of Neuro- and Sensory Physiology , University Medical Center Göttingen , Göttingen , Germany.,b Center for Biostructural Imaging of Neurodegeneration (BIN) , University of Göttingen Medical Center , Göttingen , Germany
| | - Aurélien Olichon
- c Inserm, UMR 1037-CRCT , Toulouse , France.,d Université Toulouse III-Paul Sabatier , Toulouse , France
| | - Silvio O Rizzoli
- a Institute of Neuro- and Sensory Physiology , University Medical Center Göttingen , Göttingen , Germany.,b Center for Biostructural Imaging of Neurodegeneration (BIN) , University of Göttingen Medical Center , Göttingen , Germany
| | - Felipe Opazo
- a Institute of Neuro- and Sensory Physiology , University Medical Center Göttingen , Göttingen , Germany.,b Center for Biostructural Imaging of Neurodegeneration (BIN) , University of Göttingen Medical Center , Göttingen , Germany
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16
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A Rationale for Mesoscopic Domain Formation in Biomembranes. Biomolecules 2018; 8:biom8040104. [PMID: 30274275 PMCID: PMC6316292 DOI: 10.3390/biom8040104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/04/2018] [Accepted: 09/06/2018] [Indexed: 12/25/2022] Open
Abstract
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also be observed in vitro on model systems such as supported membranes or lipid vesicles. Lipid mixtures separating in liquid-ordered and liquid-disordered phases below a demixing temperature play a pivotal role in this context. Protein-protein and protein-lipid interactions also contribute to membrane shaping by promoting small domains or clusters. Such phase separations displaying characteristic length-scales falling in-between the nanoscopic, molecular scale on the one hand and the macroscopic scale on the other hand, are named mesophases in soft condensed matter physics. In this review, we propose a classification of the diverse mechanisms leading to mesophase separation in biomembranes. We distinguish between mechanisms relying upon equilibrium thermodynamics and those involving out-of-equilibrium mechanisms, notably active membrane recycling. In equilibrium, we especially focus on the many mechanisms that dwell on an up-down symmetry breaking between the upper and lower bilayer leaflets. Symmetry breaking is an ubiquitous mechanism in condensed matter physics at the heart of several important phenomena. In the present case, it can be either spontaneous (domain buckling) or explicit, i.e., due to an external cause (global or local vesicle bending properties). Whenever possible, theoretical predictions and simulation results are confronted to experiments on model systems or living cells, which enables us to identify the most realistic mechanisms from a biological perspective.
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17
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Richter KN, Revelo NH, Seitz KJ, Helm MS, Sarkar D, Saleeb RS, D'Este E, Eberle J, Wagner E, Vogl C, Lazaro DF, Richter F, Coy-Vergara J, Coceano G, Boyden ES, Duncan RR, Hell SW, Lauterbach MA, Lehnart SE, Moser T, Outeiro TF, Rehling P, Schwappach B, Testa I, Zapiec B, Rizzoli SO. Glyoxal as an alternative fixative to formaldehyde in immunostaining and super-resolution microscopy. EMBO J 2018; 37:139-159. [PMID: 29146773 PMCID: PMC5753035 DOI: 10.15252/embj.201695709] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 09/25/2017] [Accepted: 10/06/2017] [Indexed: 12/02/2022] Open
Abstract
Paraformaldehyde (PFA) is the most commonly used fixative for immunostaining of cells, but has been associated with various problems, ranging from loss of antigenicity to changes in morphology during fixation. We show here that the small dialdehyde glyoxal can successfully replace PFA Despite being less toxic than PFA, and, as most aldehydes, likely usable as a fixative, glyoxal has not yet been systematically tried in modern fluorescence microscopy. Here, we tested and optimized glyoxal fixation and surprisingly found it to be more efficient than PFA-based protocols. Glyoxal acted faster than PFA, cross-linked proteins more effectively, and improved the preservation of cellular morphology. We validated glyoxal fixation in multiple laboratories against different PFA-based protocols and confirmed that it enabled better immunostainings for a majority of the targets. Our data therefore support that glyoxal can be a valuable alternative to PFA for immunostaining.
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Affiliation(s)
- Katharina N Richter
- Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Göttingen, Germany
- Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Natalia H Revelo
- Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Göttingen, Germany
| | - Katharina J Seitz
- Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Göttingen, Germany
- International Max Planck Research School Molecular Biology, Göttingen, Germany
| | - Martin S Helm
- Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Göttingen, Germany
- International Max Planck Research School Molecular Biology, Göttingen, Germany
| | | | - Rebecca S Saleeb
- Edinburgh Super-Resolution Imaging Consortium, Institute of Biological Chemistry, Biophysics, and Bioengineering, Heriot-Watt University, Edinburgh, UK
| | - Elisa D'Este
- Department of NanoBiophotonics, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jessica Eberle
- Department of Neural Systems, Max-Planck-Institute for Brain Research, Frankfurt am Main, Germany
| | - Eva Wagner
- Heart Research Center Göttingen, Department of Cardiology & Pulmonology, University Medical Center Göttingen, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) Site Göttingen
| | - Christian Vogl
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
- Max-Planck-Institute for Experimental Medicine, Auditory Neuroscience Group, Göttingen, Germany
| | - Diana F Lazaro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration University Medical Center Göttingen, Göttingen, Germany
- Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - Frank Richter
- International Max Planck Research School Molecular Biology, Göttingen, Germany
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Javier Coy-Vergara
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Giovanna Coceano
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Edward S Boyden
- Departments of Brain and Cognitive Science and Biological Engineering, MIT Media Lab and McGovern Institute, Cambridge, MA, USA
| | - Rory R Duncan
- Edinburgh Super-Resolution Imaging Consortium, Institute of Biological Chemistry, Biophysics, and Bioengineering, Heriot-Watt University, Edinburgh, UK
| | - Stefan W Hell
- Department of NanoBiophotonics, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marcel A Lauterbach
- Department of Neural Systems, Max-Planck-Institute for Brain Research, Frankfurt am Main, Germany
| | - Stephan E Lehnart
- Heart Research Center Göttingen, Department of Cardiology & Pulmonology, University Medical Center Göttingen, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) Site Göttingen
| | - Tobias Moser
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
- Max-Planck-Institute for Experimental Medicine, Auditory Neuroscience Group, Göttingen, Germany
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration University Medical Center Göttingen, Göttingen, Germany
- Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
- Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Bolek Zapiec
- Max Planck Research Unit for Neurogenetics, Frankfurt am Main, Germany
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Göttingen, Germany
- Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
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18
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Merklinger E, Schloetel JG, Weber P, Batoulis H, Holz S, Karnowski N, Finke J, Lang T. The packing density of a supramolecular membrane protein cluster is controlled by cytoplasmic interactions. eLife 2017; 6. [PMID: 28722652 PMCID: PMC5536946 DOI: 10.7554/elife.20705] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 07/17/2017] [Indexed: 01/24/2023] Open
Abstract
Molecule clustering is an important mechanism underlying cellular self-organization. In the cell membrane, a variety of fundamentally different mechanisms drive membrane protein clustering into nanometre-sized assemblies. To date, it is unknown whether this clustering process can be dissected into steps differentially regulated by independent mechanisms. Using clustered syntaxin molecules as an example, we study the influence of a cytoplasmic protein domain on the clustering behaviour. Analysing protein mobility, cluster size and accessibility to myc-epitopes we show that forces acting on the transmembrane segment produce loose clusters, while cytoplasmic protein interactions mediate a tightly packed state. We conclude that the data identify a hierarchy in membrane protein clustering likely being a paradigm for many cellular self-organization processes. DOI:http://dx.doi.org/10.7554/eLife.20705.001
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Affiliation(s)
- Elisa Merklinger
- Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jan-Gero Schloetel
- Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Pascal Weber
- Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Helena Batoulis
- Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Sarah Holz
- Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nora Karnowski
- Chemical Biology, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jérôme Finke
- Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Thorsten Lang
- Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
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19
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Li Y, Kahraman O, Haselwandter CA. Stochastic lattice model of synaptic membrane protein domains. Phys Rev E 2017; 95:052406. [PMID: 28618626 DOI: 10.1103/physreve.95.052406] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Indexed: 11/07/2022]
Abstract
Neurotransmitter receptor molecules, concentrated in synaptic membrane domains along with scaffolds and other kinds of proteins, are crucial for signal transmission across chemical synapses. In common with other membrane protein domains, synaptic domains are characterized by low protein copy numbers and protein crowding, with rapid stochastic turnover of individual molecules. We study here in detail a stochastic lattice model of the receptor-scaffold reaction-diffusion dynamics at synaptic domains that was found previously to capture, at the mean-field level, the self-assembly, stability, and characteristic size of synaptic domains observed in experiments. We show that our stochastic lattice model yields quantitative agreement with mean-field models of nonlinear diffusion in crowded membranes. Through a combination of analytic and numerical solutions of the master equation governing the reaction dynamics at synaptic domains, together with kinetic Monte Carlo simulations, we find substantial discrepancies between mean-field and stochastic models for the reaction dynamics at synaptic domains. Based on the reaction and diffusion properties of synaptic receptors and scaffolds suggested by previous experiments and mean-field calculations, we show that the stochastic reaction-diffusion dynamics of synaptic receptors and scaffolds provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the observed single-molecule trajectories, and spatial heterogeneity in the effective rates at which receptors and scaffolds are recycled at the cell membrane. Our work sheds light on the physical mechanisms and principles linking the collective properties of membrane protein domains to the stochastic dynamics that rule their molecular components.
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Affiliation(s)
- Yiwei Li
- Department of Physics & Astronomy and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Osman Kahraman
- Department of Physics & Astronomy and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Christoph A Haselwandter
- Department of Physics & Astronomy and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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20
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Tools and limitations to study the molecular composition of synapses by fluorescence microscopy. Biochem J 2017; 473:3385-3399. [PMID: 27729584 DOI: 10.1042/bcj20160366] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/23/2016] [Indexed: 01/21/2023]
Abstract
The synapse is densely packed with proteins involved in various highly regulated processes. Synaptic protein copy numbers and their stoichiometric distribution have a drastic influence on neuronal integrity and function. Therefore, the molecular analysis of synapses is a key element to understand their architecture and function. The overall structure of the synapse has been revealed with an exquisite amount of details by electron microscopy. However, the molecular composition and the localization of proteins are more easily addressed with fluorescence imaging, especially with the improved resolution achieved by super-resolution microscopy techniques. Notably, the fast improvement of imaging instruments has not been reflected in the optimization of biological sample preparation. During recent years, large efforts have been made to generate affinity probes smaller than conventional antibodies adapted for fluorescent super-resolution imaging. In this review, we briefly discuss the current views on synaptic organization and necessary key technologies to progress in the understanding of synaptic physiology. We also highlight the challenges faced by current fluorescent super-resolution methods, and we describe the prerequisites for an ideal study of synaptic organization.
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21
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Wang L, Ta H, Ullal C, Wang F, Wang C, Dong G. Aptamer functionalized silver clusters for STED microscopy. RSC Adv 2017. [DOI: 10.1039/c6ra26991e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Novel STED probe was prepared through aptamer functionalized silver clusters, which preserve specific affinity with smaller size and more photostability.
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Affiliation(s)
- Lan Wang
- Laboratory of Environmental Sciences and Technology
- Key Laboratory of Functional Materials and Devices for Special Environments
- Xinjiang Technical Institute of Physics & Chemistry
- Chinese Academy of Sciences
- Urumqi 830011
| | - Haisen Ta
- Department of NanoBiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen 37077
- Germany
| | - Chaitanya Ullal
- Department of Materials Science and Engineering
- Rensselaer Polytechnic Institute
- Troy
- USA
| | - Fu Wang
- Laboratory of Environmental Sciences and Technology
- Key Laboratory of Functional Materials and Devices for Special Environments
- Xinjiang Technical Institute of Physics & Chemistry
- Chinese Academy of Sciences
- Urumqi 830011
| | - Chuanyi Wang
- Laboratory of Environmental Sciences and Technology
- Key Laboratory of Functional Materials and Devices for Special Environments
- Xinjiang Technical Institute of Physics & Chemistry
- Chinese Academy of Sciences
- Urumqi 830011
| | - Guohui Dong
- Laboratory of Environmental Sciences and Technology
- Key Laboratory of Functional Materials and Devices for Special Environments
- Xinjiang Technical Institute of Physics & Chemistry
- Chinese Academy of Sciences
- Urumqi 830011
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22
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Hirai Y, Hirano Y, Matsuda A, Hiraoka Y, Honda T, Tomonaga K. Borna Disease Virus Assembles Porous Cage-like Viral Factories in the Nucleus. J Biol Chem 2016; 291:25789-25798. [PMID: 27803166 DOI: 10.1074/jbc.m116.746396] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/21/2016] [Indexed: 11/06/2022] Open
Abstract
Animal-derived RNA viruses frequently generate viral factories in infected cells. However, the details of how RNA viruses build such intracellular structures are poorly understood. In this study, we examined the structure and formation of the viral factories, called viral speckle of transcripts (vSPOTs), that are produced in the nuclei of host cells by Borna disease virus (BDV). Super-resolution microscopic analysis showed that BDV assembled vSPOTs as intranuclear cage-like structures with 59-180-nm pores. The viral nucleoprotein formed the exoskeletons of vSPOTs, whereas the other viral proteins appeared to be mainly localized within these structures. In addition, stochastic optical reconstruction microscopy revealed that filamentous structures resembling viral ribonucleoprotein complexes (RNPs) appeared to protrude from the outer surfaces of the vSPOTs. We also found that vSPOTs disintegrated into RNPs concurrently with the breakdown of the nuclear envelope during mitosis. These observations demonstrated that BDV generates viral replication factories whose shape and formation are regulated, suggesting the mechanism of the integrity of RNA virus persistent infection in the nucleus.
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Affiliation(s)
- Yuya Hirai
- From the Department of Biology, Osaka Dental University, Hirakata 573-1121.,the Department of Virus Research, Institute for Frontier Life and Medical Sciences (InFRONT)
| | - Yasuhiro Hirano
- the Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, and
| | - Atsushi Matsuda
- the Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, and.,the Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Yasushi Hiraoka
- the Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, and.,the Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Tomoyuki Honda
- the Department of Virus Research, Institute for Frontier Life and Medical Sciences (InFRONT)
| | - Keizo Tomonaga
- the Department of Virus Research, Institute for Frontier Life and Medical Sciences (InFRONT), .,Departments of Molecular Virology, Graduate School of Medicine, and.,Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507
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23
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Berger M, Manghi M, Destainville N. Nanodomains in Biomembranes with Recycling. J Phys Chem B 2016; 120:10588-10602. [PMID: 27654087 DOI: 10.1021/acs.jpcb.6b07631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cell membranes are out of thermodynamic equilibrium notably because of membrane recycling, i.e., active exchange of material with the cytosol. We propose an analytically tractable model of biomembrane predicting the effects of recycling on the size of protein nanodomains also called protein clusters. The model includes a short-range attraction between proteins and a weaker long-range repulsion which ensures the existence of so-called cluster phases in equilibrium, where monomeric proteins coexist with finite-size domains. Our main finding is that, when taking recycling into account, the typical cluster size at steady state increases logarithmically with the recycling rate at fixed protein concentration. Using physically realistic model parameters, the predicted 2-fold increase due to recycling in living cells is most likely experimentally measurable with the help of super-resolution microscopy.
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Affiliation(s)
- Mareike Berger
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, F-31062 Toulouse, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, F-31062 Toulouse, France
| | - Nicolas Destainville
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, F-31062 Toulouse, France
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24
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Shivanandan A, Unnikrishnan J, Radenovic A. On characterizing protein spatial clusters with correlation approaches. Sci Rep 2016; 6:31164. [PMID: 27507257 PMCID: PMC4979030 DOI: 10.1038/srep31164] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/15/2016] [Indexed: 12/31/2022] Open
Abstract
Spatial aggregation of proteins might have functional importance, e.g., in signaling, and nano-imaging can be used to study them. Such studies require accurate characterization of clusters based on noisy data. A set of spatial correlation approaches free of underlying cluster processes and input parameters have been widely used for this purpose. They include the radius of maximal aggregation ra obtained from Ripley’s L(r) − r function as an estimator of cluster size, and the estimation of various cluster parameters based on an exponential model of the Pair Correlation Function(PCF). While convenient, the accuracy of these methods is not clear: e.g., does it depend on how the molecules are distributed within the clusters, or on cluster parameters? We analyze these methods for a variety of cluster models. We find that ra relates to true cluster size by a factor that is nonlinearly dependent on parameters and that can be arbitrarily large. For the PCF method, for the models analyzed, we obtain linear relationships between the estimators and true parameters, and the estimators were found to be within ±100% of true parameters, depending on the model. Our results, based on an extendable general framework, point to the need for caution in applying these methods.
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Affiliation(s)
- Arun Shivanandan
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Jayakrishnan Unnikrishnan
- Audiovisual Communications Laboratory, School of Computer and Communication Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
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Kahraman O, Koch PD, Klug WS, Haselwandter CA. Bilayer-thickness-mediated interactions between integral membrane proteins. Phys Rev E 2016; 93:042410. [PMID: 27176332 DOI: 10.1103/physreve.93.042410] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Indexed: 12/14/2022]
Abstract
Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations can yield energetically favorable bilayer-mediated interactions between integral membrane proteins, and large-scale organization of integral membrane proteins into protein clusters in cell membranes. Within the continuum elasticity theory of membranes, the energy cost of protein-induced bilayer thickness deformations can be captured by considering compression and expansion of the bilayer hydrophobic core, membrane tension, and bilayer bending, resulting in biharmonic equilibrium equations describing the shape of lipid bilayers for a given set of bilayer-protein boundary conditions. Here we develop a combined analytic and numerical methodology for the solution of the equilibrium elastic equations associated with protein-induced lipid bilayer deformations. Our methodology allows accurate prediction of thickness-mediated protein interactions for arbitrary protein symmetries at arbitrary protein separations and relative orientations. We provide exact analytic solutions for cylindrical integral membrane proteins with constant and varying hydrophobic thickness, and develop perturbative analytic solutions for noncylindrical protein shapes. We complement these analytic solutions, and assess their accuracy, by developing both finite element and finite difference numerical solution schemes. We provide error estimates of our numerical solution schemes and systematically assess their convergence properties. Taken together, the work presented here puts into place an analytic and numerical framework which allows calculation of bilayer-mediated elastic interactions between integral membrane proteins for the complicated protein shapes suggested by structural biology and at the small protein separations most relevant for the crowded membrane environments provided by living cells.
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Affiliation(s)
- Osman Kahraman
- Department of Physics & Astronomy and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Peter D Koch
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - William S Klug
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA
| | - Christoph A Haselwandter
- Department of Physics & Astronomy and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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Analyzing Protein Clusters on the Plasma Membrane: Application of Spatial Statistical Analysis Methods on Super-Resolution Microscopy Images. FOCUS ON BIO-IMAGE INFORMATICS 2016; 219:95-122. [DOI: 10.1007/978-3-319-28549-8_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Destainville N, Schmidt TH, Lang T. Where Biology Meets Physics--A Converging View on Membrane Microdomain Dynamics. CURRENT TOPICS IN MEMBRANES 2015; 77:27-65. [PMID: 26781829 DOI: 10.1016/bs.ctm.2015.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
For several decades, the phenomenon of membrane component segregation into microdomains has been a well-known and highly debated subject, and varying concepts including the raft hypothesis, the fence-and-picket model, hydrophobic-mismatch, and specific protein-protein interactions have been offered as explanations. Here, we review the level of insight into the molecular architecture of membrane domains one is capable of obtaining through biological experimentation. Using SNARE proteins as a paradigm, comprehensive data suggest that several dozens of molecules crowd together into almost circular spots smaller than 100 nm. Such clusters are highly dynamical as they constantly capture and lose molecules. The organization has a strong influence on the functional availability of proteins and likely provides a molecular scaffold for more complex protein networks. Despite this high level of insight, fundamental open questions remain, applying not only to SNARE protein domains but more generally to all types of membrane domains. In this context, we explain the view of physical models and how they are beneficial in advancing our concept of micropatterning. While biological models generally remain qualitative and descriptive, physics aims towards making them quantitative and providing reproducible numbers, in order to discriminate between different mechanisms which have been proposed to account for experimental observations. Despite the fundamental differences in biological and physical approaches as far as cell membrane microdomains are concerned, we are able to show that convergence on common points of views is in reach.
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Affiliation(s)
- Nicolas Destainville
- Laboratoire de Physique Theorique (IRSAMC), Universite Toulouse 3-Paul Sabatier, UPS/CNRS, Toulouse, France
| | - Thomas H Schmidt
- Department of Membrane Biochemistry, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Thorsten Lang
- Department of Membrane Biochemistry, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
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Ullrich A, Böhme MA, Schöneberg J, Depner H, Sigrist SJ, Noé F. Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone. PLoS Comput Biol 2015; 11:e1004407. [PMID: 26367029 PMCID: PMC4569342 DOI: 10.1371/journal.pcbi.1004407] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 06/15/2015] [Indexed: 01/10/2023] Open
Abstract
Synaptic vesicle fusion is mediated by SNARE proteins forming in between synaptic vesicle (v-SNARE) and plasma membrane (t-SNARE), one of which is Syntaxin-1A. Although exocytosis mainly occurs at active zones, Syntaxin-1A appears to cover the entire neuronal membrane. By using STED super-resolution light microscopy and image analysis of Drosophila neuro-muscular junctions, we show that Syntaxin-1A clusters are more abundant and have an increased size at active zones. A computational particle-based model of syntaxin cluster formation and dynamics is developed. The model is parametrized to reproduce Syntaxin cluster-size distributions found by STED analysis, and successfully reproduces existing FRAP results. The model shows that the neuronal membrane is adjusted in a way to strike a balance between having most syntaxins stored in large clusters, while still keeping a mobile fraction of syntaxins free or in small clusters that can efficiently search the membrane or be traded between clusters. This balance is subtle and can be shifted toward almost no clustering and almost complete clustering by modifying the syntaxin interaction energy on the order of only 1 kBT. This capability appears to be exploited at active zones. The larger active-zone syntaxin clusters are more stable and provide regions of high docking and fusion capability, whereas the smaller clusters outside may serve as flexible reserve pool or sites of spontaneous ectopic release.
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Affiliation(s)
- Alexander Ullrich
- Department of Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Mathias A. Böhme
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Berlin, Berlin, Germany
| | | | - Harald Depner
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Stephan J. Sigrist
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Berlin, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Freie Universität Berlin, Berlin, Germany
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29
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Zuidscherwoude M, Göttfert F, Dunlock VME, Figdor CG, van den Bogaart G, van Spriel AB. The tetraspanin web revisited by super-resolution microscopy. Sci Rep 2015; 5:12201. [PMID: 26183063 PMCID: PMC4505338 DOI: 10.1038/srep12201] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 06/17/2015] [Indexed: 12/19/2022] Open
Abstract
The spatial organization of membrane proteins in the plasma membrane is critical for signal transduction, cell communication and membrane trafficking. Tetraspanins organize functional higher-order protein complexes called ‘tetraspanin-enriched microdomains (TEMs)’ via interactions with partner molecules and other tetraspanins. Still, the nanoscale organization of TEMs in native plasma membranes has not been resolved. Here, we elucidated the size, density and distribution of TEMs in the plasma membrane of human B cells and dendritic cells using dual color stimulated emission depletion (STED) microscopy. We demonstrate that tetraspanins form individual nanoclusters smaller than 120 nm and quantified that a single tetraspanin CD53 cluster contains less than ten CD53 molecules. CD53 and CD37 domains were adjacent to and displayed only minor overlap with clusters containing tetraspanins CD81 or CD82. Moreover, CD53 and CD81 were found in closer proximity to their partners MHC class II and CD19 than to other tetraspanins. Although these results indicate that tetraspanin domains are adjacently positioned in the plasma membrane, they challenge the current view of the tetraspanin web of multiple tetraspanin species organized into a single domain. This study increases the molecular understanding of TEMs at the nanoscale level which is essential for comprehending tetraspanin function in cell biology.
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Affiliation(s)
- Malou Zuidscherwoude
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Fabian Göttfert
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vera Marie E Dunlock
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carl G Figdor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Annemiek B van Spriel
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Accounting for limited detection efficiency and localization precision in cluster analysis in single molecule localization microscopy. PLoS One 2015; 10:e0118767. [PMID: 25794150 PMCID: PMC4368834 DOI: 10.1371/journal.pone.0118767] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/14/2015] [Indexed: 11/20/2022] Open
Abstract
Single Molecule Localization Microscopy techniques like PhotoActivated Localization Microscopy, with their sub-diffraction limit spatial resolution, have been popularly used to characterize the spatial organization of membrane proteins, by means of quantitative cluster analysis. However, such quantitative studies remain challenged by the techniques’ inherent sources of errors such as a limited detection efficiency of less than 60%, due to incomplete photo-conversion, and a limited localization precision in the range of 10 – 30nm, varying across the detected molecules, mainly depending on the number of photons collected from each. We provide analytical methods to estimate the effect of these errors in cluster analysis and to correct for them. These methods, based on the Ripley’s L(r) – r or Pair Correlation Function popularly used by the community, can facilitate potentially breakthrough results in quantitative biology by providing a more accurate and precise quantification of protein spatial organization.
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Gao J, Wang Y, Cai M, Pan Y, Xu H, Jiang J, Ji H, Wang H. Mechanistic insights into EGFR membrane clustering revealed by super-resolution imaging. NANOSCALE 2015; 7:2511-9. [PMID: 25569174 DOI: 10.1039/c4nr04962d] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The clustering of membrane receptors such as EGFR is critical for various biological processes, for example cell signaling and tumorigenesis. However, the mechanism involved remains poorly understood. Here, we used a super resolution imaging technique, which has shattered the longstanding resolution barrier of light diffraction, to investigate the distribution of membrane EGFR on apical or basal surfaces of COS-7 cells and on the surface of suspended COS-7 cells. Our data show that more and larger EGFR clusters are detected on the apical surface in comparison with those on the basal surface and this difference is not affected by the EGFR activation state, whereas suspended COS-7 cells exhibit a moderate clustering state and a homogeneous distribution pattern, indicating that the external environment surrounding the cell membrane is the decisive factor in the EGFR clustering pattern. A dual-color dSTORM image reveals the significant colocalization of EGFR and lipid rafts; interestingly MβCD treatment leads to a dramatic decrease of the amount and size of EGFR clusters on both apical and basal surfaces, highlighting a key role of lipid rafts in EGFR cluster formation. Altogether, our results illustrate the distribution pattern of EGFR in polarized cells and uncover the essential role of lipid rafts in EGFR cluster maintenance.
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Affiliation(s)
- Jing Gao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China.
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Almarza NG, Pȩkalski J, Ciach A. Periodic ordering of clusters and stripes in a two-dimensional lattice model. II. Results of Monte Carlo simulation. J Chem Phys 2014; 140:164708. [DOI: 10.1063/1.4871901] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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33
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Deschout H, Shivanandan A, Annibale P, Scarselli M, Radenovic A. Progress in quantitative single-molecule localization microscopy. Histochem Cell Biol 2014; 142:5-17. [PMID: 24748502 PMCID: PMC4072926 DOI: 10.1007/s00418-014-1217-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 01/10/2023]
Abstract
With the advent of single-molecule localization microscopy (SMLM) techniques, intracellular proteins can be imaged at unprecedented resolution with high specificity and contrast. These techniques can lead to a better understanding of cell functioning, as they allow, among other applications, counting the number of molecules of a protein specie in a single cell, studying the heterogeneity in protein spatial organization, and probing the spatial interactions between different protein species. However, the use of these techniques for accurate quantitative measurements requires corrections for multiple inherent sources of error, including: overcounting due to multiple localizations of a single fluorophore (i.e., photoblinking), undercounting caused by incomplete photoconversion, uncertainty in the localization of single molecules, sample drift during the long imaging time, and inaccurate image registration in the case of dual-color imaging. In this paper, we review recent efforts that address some of these sources of error in quantitative SMLM and give examples in the context of photoactivated localization microscopy (PALM).
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Affiliation(s)
- H. Deschout
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - A. Shivanandan
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - P. Annibale
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
- Present Address: Biomedical Engineering Department, University of California, Irvine, CA USA
| | - M. Scarselli
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
- Present Address: Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - A. Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
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Abstract
Synaptic vesicle recycling is one of the best-studied cellular pathways. Many of the proteins involved are known, and their interactions are becoming increasingly clear. However, as for many other pathways, it is still difficult to understand synaptic vesicle recycling as a whole. While it is generally possible to point out how synaptic reactions take place, it is not always easy to understand what triggers or controls them. Also, it is often difficult to understand how the availability of the reaction partners is controlled: how the reaction partners manage to find each other in the right place, at the right time. I present here an overview of synaptic vesicle recycling, discussing the mechanisms that trigger different reactions, and those that ensure the availability of reaction partners. A central argument is that synaptic vesicles bind soluble cofactor proteins, with low affinity, and thus control their availability in the synapse, forming a buffer for cofactor proteins. The availability of cofactor proteins, in turn, regulates the different synaptic reactions. Similar mechanisms, in which one of the reaction partners buffers another, may apply to many other processes, from the biogenesis to the degradation of the synaptic vesicle.
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Affiliation(s)
- Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen European Neuroscience Institute, Göttingen, Germany
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35
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Opazo F. Probing Biological Samples in High-Resolution Microscopy: Making Sense of Spots. NEUROMETHODS 2014. [DOI: 10.1007/978-1-62703-983-3_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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36
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Haselwandter CA, Phillips R. Directional interactions and cooperativity between mechanosensitive membrane proteins. EUROPHYSICS LETTERS 2013; 101:68002p1-68002p6. [PMID: 25309021 PMCID: PMC4193682 DOI: 10.1209/0295-5075/101/68002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
While modern structural biology has provided us with a rich and diverse picture of membrane proteins, the biological function of membrane proteins is often influenced by the mechanical properties of the surrounding lipid bilayer. Here we explore the relation between the shape of membrane proteins and the cooperative function of membrane proteins induced by membrane-mediated elastic interactions. For the experimental model system of mechanosensitive ion channels we find that the sign and strength of elastic interactions depend on the protein shape, yielding distinct cooperative gating curves for distinct protein orientations. Our approach predicts how directional elastic interactions affect the molecular structure, organization, and biological function of proteins in crowded membranes.
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Affiliation(s)
- Christoph A Haselwandter
- Department of Physics and Astronomy, University of Southern California - Los Angeles, CA 90089, USA ; Department of Applied Physics, California Institute of Technology - Pasadena, CA 91125, USA
| | - Rob Phillips
- Department of Applied Physics, California Institute of Technology - Pasadena, CA 91125, USA
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37
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Mohrmann R, Sørensen JB. SNARE requirements en route to exocytosis: from many to few. J Mol Neurosci 2012; 48:387-94. [PMID: 22427188 DOI: 10.1007/s12031-012-9744-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 02/29/2012] [Indexed: 12/30/2022]
Abstract
Although it has been known for almost two decades that the ternary complex of N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) constitutes the functional unit driving membrane fusion, our knowledge about the dynamical arrangement and organization of SNARE proteins and their complexes before and during vesicle exocytosis is still limited. Here, we review recent progress in this expanding field with emphasis on the question of fusion complex stoichiometry, i.e., how many SNARE proteins and complexes are needed for the fusion of a vesicle with the plasma membrane.
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Affiliation(s)
- Ralf Mohrmann
- Department of Physiology, University of Saarland, Homburg, Germany.
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39
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Saka S, Rizzoli SO. Super-resolution imaging prompts re-thinking of cell biology mechanisms: selected cases using stimulated emission depletion microscopy. Bioessays 2012; 34:386-95. [PMID: 22415724 DOI: 10.1002/bies.201100080] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The use of super-resolution imaging techniques in cell biology has yielded a wealth of information regarding cellular elements and processes that were invisible to conventional imaging. Focusing on images obtained by stimulated emission depletion (STED) microscopy, we discuss how the new high-resolution data influence the ways in which we use and interpret images in cell biology. Super-resolution images have lent support to some of our current hypotheses. But, more significantly, they have revealed unexpectedly complex processes that cannot be accounted for by the simpler models based on diffraction-limited imaging. The super-resolution imaging data challenge cell biologists to change their theoretical framework, by including, for instance, interpretations that describe multiple functions, functional errors or lack of function for cellular elements. In this context, we argue that descriptive research using super-resolution microscopy is now as necessary as hypothesis-driven research.
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Affiliation(s)
- Sinem Saka
- European Neuroscience Institute, DFG Center for Molecular Physiology of the Brain/Excellence Cluster, Göttingen, Germany
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40
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Renda A, Nashmi R. Spectral confocal imaging of fluorescently tagged nicotinic receptors in knock-in mice with chronic nicotine administration. J Vis Exp 2012:3516. [PMID: 22349092 DOI: 10.3791/3516] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Ligand-gated ion channels in the central nervous system (CNS) are implicated in numerous conditions with serious medical and social consequences. For instance, addiction to nicotine via tobacco smoking is a leading cause of premature death worldwide (World Health Organization) and is likely caused by an alteration of ion channel distribution in the brain. Chronic nicotine exposure in both rodents and humans results in increased numbers of nicotinic acetylcholine receptors (nAChRs) in brain tissue. Similarly, alterations in the glutamatergic GluN1 or GluA1 channels have been implicated in triggering sensitization to other addictive drugs such as cocaine, amphetamines and opiates. Consequently, the ability to map and quantify distribution and expression patterns of specific ion channels is critically important to understanding the mechanisms of addiction. The study of brain region-specific effects of individual drugs was advanced by the advent of techniques such as radioactive ligands. However, the low spatial resolution of radioactive ligand binding prevents the ability to quantify ligand-gated ion channels in specific subtypes of neurons. Genetically encoded fluorescent reporters, such as green fluorescent protein (GFP) and its many color variants, have revolutionized the field of biology. By genetically tagging a fluorescent reporter to an endogenous protein one can visualize proteins in vivo. One advantage of fluorescently tagging proteins with a probe is the elimination of antibody use, which have issues of nonspecificity and accessibility to the target protein. We have used this strategy to fluorescently label nAChRs, which enabled the study of receptor assembly using Förster Resonance Energy Transfer (FRET) in transfected cultured cells. More recently, we have used the knock-in approach to engineer mice with yellow fluorescent protein tagged α4 nAChR subunits (α4YFP), enabling precise quantification of the receptor ex vivo at submicrometer resolution in CNS neurons via spectral confocal microscopy. The targeted fluorescent knock-in mutation is incorporated in the endogenous locus and under control of its native promoter, producing normal levels of expression and regulation of the receptor when compared to untagged receptors in wildtype mice. This knock-in approach can be extended to fluorescently tag other ion channels and offers a powerful approach of visualizing and quantifying receptors in the CNS. In this paper we describe a methodology to quantify changes in nAChR expression in specific CNS neurons after exposure to chronic nicotine. Our methods include mini-osmotic pump implantation, intracardiac perfusion fixation, imaging and analysis of fluorescently tagged nicotinic receptor subunits from α4YFP knock-in mice (Fig. 1). We have optimized the fixation technique to minimize autofluorescence from fixed brain tissue. We describe in detail our imaging methodology using a spectral confocal microscope in conjunction with a linear spectral unmixing algorithm to subtract autofluoresent signal in order to accurately obtain α4YFP fluorescence signal. Finally, we show results of chronic nicotine-induced upregulation of α4YFP receptors in the medial perforant path of the hippocampus.
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Abstract
Prokaryotes are characterized by an extreme flexibility of their respiratory systems allowing them to cope with various extreme environments. To date, supramolecular organization of respiratory systems appears as a conserved evolutionary feature as supercomplexes have been isolated in bacteria, archaea, and eukaryotes. Most of the yet identified supercomplexes in prokaryotes are involved in aerobic respiration and share similarities with those reported in mitochondria. Supercomplexes likely reflect a snapshot of the cellular respiration in a given cell population. While the exact nature of the determinants for supramolecular organization in prokaryotes is not understood, lipids, proteins, and subcellular localization can be seen as key players. Owing to the well-reported supramolecular organization of the mitochondrial respiratory chain in eukaryotes, several hypotheses have been formulated to explain the consequences of such arrangement and can be tested in the context of prokaryotes. Considering the inherent metabolic flexibility of a number of prokaryotes, cellular distribution and composition of the supramolecular assemblies should be studied in regards to environmental signals. This would pave the way to new concepts in cellular respiration.
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The reserve pool of synaptic vesicles acts as a buffer for proteins involved in synaptic vesicle recycling. Proc Natl Acad Sci U S A 2011; 108:17183-8. [PMID: 21903923 DOI: 10.1073/pnas.1112690108] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Presynaptic nerve terminals contain between several hundred vesicles (for example in small CNS synapses) and several tens of thousands (as in neuromuscular junctions). Although it has long been assumed that such high numbers of vesicles are required to sustain neurotransmission during conditions of high demand, we found that activity in vivo requires the recycling of only a few percent of the vesicles. However, the maintenance of large amounts of reserve vesicles in many evolutionarily distinct species suggests that they are relevant for synaptic function. We suggest here that these vesicles constitute buffers for soluble accessory proteins involved in vesicle recycling, preventing their loss into the axon. Supporting this hypothesis, we found that vesicle clusters contain a large variety of proteins needed for vesicle recycling, but without an obvious function within the clusters. Disrupting the clusters by application of black widow spider venom resulted in the diffusion of numerous soluble proteins into the axons. Prolonged stimulation and ionomycin application had a similar effect, suggesting that calcium influx causes the unbinding of soluble proteins from vesicles. Confirming this hypothesis, we found that isolated synaptic vesicles in vitro sequestered soluble proteins from the cytosol in a process that was inhibited by calcium addition. We conclude that the reserve vesicles support neurotransmission indirectly, ensuring that soluble recycling proteins are delivered upon demand during synaptic activity.
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Grage SL, Keleshian AM, Turdzeladze T, Battle AR, Tay WC, May RP, Holt SA, Contera SA, Haertlein M, Moulin M, Pal P, Rohde PR, Forsyth VT, Watts A, Huang KC, Ulrich AS, Martinac B. Bilayer-mediated clustering and functional interaction of MscL channels. Biophys J 2011; 100:1252-60. [PMID: 21354398 DOI: 10.1016/j.bpj.2011.01.023] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 12/15/2010] [Accepted: 01/04/2011] [Indexed: 01/23/2023] Open
Abstract
Mechanosensitive channels allow bacteria to respond to osmotic stress by opening a nanometer-sized pore in the cellular membrane. Although the underlying mechanism has been thoroughly studied on the basis of individual channels, the behavior of channel ensembles has yet to be elucidated. This work reveals that mechanosensitive channels of large conductance (MscL) exhibit a tendency to spatially cluster, and demonstrates the functional relevance of clustering. We evaluated the spatial distribution of channels in a lipid bilayer using patch-clamp electrophysiology, fluorescence and atomic force microscopy, and neutron scattering and reflection techniques, coupled with mathematical modeling of the mechanics of a membrane crowded with proteins. The results indicate that MscL forms clusters under a wide range of conditions. MscL is closely packed within each cluster but is still active and mechanosensitive. However, the channel activity is modulated by the presence of neighboring proteins, indicating membrane-mediated protein-protein interactions. Collectively, these results suggest that MscL self-assembly into channel clusters plays an osmoregulatory functional role in the membrane.
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Affiliation(s)
- Stephan L Grage
- Karlsruhe Institute of Technology, Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
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44
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Meilhac N, Destainville N. Clusters of proteins in biomembranes: insights into the roles of interaction potential shapes and of protein diversity. J Phys Chem B 2011; 115:7190-9. [PMID: 21528886 DOI: 10.1021/jp1099865] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
It has recently been proposed that proteins embedded in lipidic biomembranes can spontaneously self-organize into stable small clusters, or membrane nanodomains, due to the competition between short-range attractive and longer-range repulsive forces between proteins, specific to these systems. In this paper, we carry on our investigation, by Monte Carlo simulations, of different aspects of cluster phases of proteins in biomembranes. First, we compare different long-range potentials (including notably three-body terms) to demonstrate that the existence of cluster phases should be quite generic. Furthermore, a real membrane contains hundreds of different protein species that are far from being randomly distributed in these nanodomains. We take this protein diversity into account by modulating protein-protein interaction potentials both at short and longer range. We confirm theoretical predictions in terms of biological cluster specialization by deciphering how clusters recruit only a few protein species. In this respect, we highlight that cluster phases can turn out to be an advantage at the biological level, for example by enhancing the cell response to external stimuli.
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Affiliation(s)
- Nicolas Meilhac
- Université de Toulouse, UPS, Laboratoire de Physique Théorique (IRSAMC), Toulouse, France
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The Limitations of Nonlinear Fluorescence Effect in Super Resolution Saturated Structured Illumination Microscopy System. J Fluoresc 2010; 21:1075-82. [DOI: 10.1007/s10895-010-0780-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Accepted: 11/25/2010] [Indexed: 11/26/2022]
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