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Yu C, Richly M, Hoang TT, El Beheiry M, Türkcan S, Masson JB, Alexandrou A, Bouzigues CI. Confinement energy landscape classification reveals membrane receptor nano-organization mechanisms. Biophys J 2024; 123:1882-1895. [PMID: 38845200 DOI: 10.1016/j.bpj.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/01/2024] [Accepted: 06/03/2024] [Indexed: 06/22/2024] Open
Abstract
The cell membrane organization has an essential functional role through the control of membrane receptor confinement in micro- or nanodomains. Several mechanisms have been proposed to account for these properties, although some features have remained controversial, notably the nature, size, and stability of cholesterol- and sphingolipid-rich domains or lipid rafts. Here, we probed the effective energy landscape acting on single-nanoparticle-labeled membrane receptors confined in raft nanodomains- epidermal growth factor receptor (EGFR), Clostridium perfringens ε-toxin receptor (CPεTR), and Clostridium septicum α-toxin receptor (CSαTR)-and compared it with hop-diffusing transferrin receptors. By establishing a new analysis pipeline combining Bayesian inference, decision trees, and clustering approaches, we systematically classified single-protein trajectories according to the type of effective confining energy landscape. This revealed the existence of only two distinct organization modalities: confinement in a quadratic energy landscape for EGFR, CPεTR, and CSαTR (A), and free diffusion in confinement domains resulting from the steric hindrance due to F-actin barriers for transferrin receptor (B). The further characterization of effective confinement energy landscapes by Bayesian inference revealed the role of interactions with the domain environment in cholesterol- and sphingolipid-rich domains with (EGFR) or without (CPεTR and CSαTR) interactions with F-actin to regulate the confinement energy depth. These two distinct mechanisms result in the same organization type (A). We revealed that the apparent domain sizes for these receptor trajectories resulted from Brownian exploration of the energy landscape in a steady-state-like regime at a common effective temperature, independently of the underlying molecular mechanisms. These results highlight that confinement domains may be adequately described as interaction hotspots rather than rafts with abrupt domain boundaries. Altogether, these results support a new model for functional receptor confinement in membrane nanodomains and pave the way to the constitution of an atlas of membrane protein organization.
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Affiliation(s)
- Chao Yu
- Laboratoire Optique et Biosciences, CNRS UMR74645, Inserm U1182, Ecole Polytechnique, Institut Polytechnique Paris, Palaiseau, France
| | - Maximilian Richly
- Laboratoire Optique et Biosciences, CNRS UMR74645, Inserm U1182, Ecole Polytechnique, Institut Polytechnique Paris, Palaiseau, France
| | - Thi Thuy Hoang
- Laboratoire Optique et Biosciences, CNRS UMR74645, Inserm U1182, Ecole Polytechnique, Institut Polytechnique Paris, Palaiseau, France
| | - Mohammed El Beheiry
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Decision and Bayesian Computation, Paris, France; Épiméthée, INRIA, Paris, France
| | - Silvan Türkcan
- Laboratoire Optique et Biosciences, CNRS UMR74645, Inserm U1182, Ecole Polytechnique, Institut Polytechnique Paris, Palaiseau, France
| | - Jean-Baptiste Masson
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Decision and Bayesian Computation, Paris, France; Épiméthée, INRIA, Paris, France
| | - Antigoni Alexandrou
- Laboratoire Optique et Biosciences, CNRS UMR74645, Inserm U1182, Ecole Polytechnique, Institut Polytechnique Paris, Palaiseau, France
| | - Cedric I Bouzigues
- Laboratoire Optique et Biosciences, CNRS UMR74645, Inserm U1182, Ecole Polytechnique, Institut Polytechnique Paris, Palaiseau, France.
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2
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Zhang Y, Chen X, Yu Y, Huang Y, Qiu M, Liu F, Feng M, Gao C, Deng S, Fu X. A Femtosecond Electron-Based Versatile Microscopy for Visualizing Carrier Dynamics in Semiconductors Across Spatiotemporal and Energetic Domains. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400633. [PMID: 38894590 DOI: 10.1002/advs.202400633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/16/2024] [Indexed: 06/21/2024]
Abstract
Carrier dynamics detection in different dimensions (space, time, and energy) with high resolutions plays a pivotal role in the development of modern semiconductor devices, especially in low-dimensional, high-speed, and ultrasensitive devices. Here, a femtosecond electron-based versatile microscopy is reported that combines scanning ultrafast electron microscopy (SUEM) imaging and time-resolved cathodoluminescence (TRCL) detection, which allows for visualizing and decoupling different dynamic processes of carriers involved in surface and bulk in semiconductors with unprecedented spatiotemporal and energetic resolutions. The achieved spatial resolution is better than 10 nm, and the temporal resolutions for SUEM imaging and TRCL detection are ≈500 fs and ≈4.5 ps, respectively, representing state-of-the-art performance. To demonstrate its unique capability, the surface and bulk carrier dynamics involved in n-type gallium arsenide (GaAs) are directly tracked and distinguished. It is revealed, in real time and space, that hot carrier cooling, defect trapping, and interband-/defect-assisted radiative recombination in the energy domain result in ordinal super-diffusion, localization, and sub-diffusion of carriers at the surface, elucidating the crucial role of surface states on carrier dynamics. The study not only gives a comprehensive physical picture of carrier dynamics in GaAs, but also provides a powerful platform for exploring complex carrier dynamics in semiconductors for promoting their device performance.
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Affiliation(s)
- Yaqing Zhang
- Ultrafast Electron Microscopy Laboratory, MOE Key Laboratory of Weak-Light Nonlinear Photonics, School of Physics, Nankai University, Tianjin, 300071, China
| | - Xiang Chen
- Ultrafast Electron Microscopy Laboratory, MOE Key Laboratory of Weak-Light Nonlinear Photonics, School of Physics, Nankai University, Tianjin, 300071, China
| | - Yaocheng Yu
- Ultrafast Electron Microscopy Laboratory, MOE Key Laboratory of Weak-Light Nonlinear Photonics, School of Physics, Nankai University, Tianjin, 300071, China
| | - Yue Huang
- Ultrafast Electron Microscopy Laboratory, MOE Key Laboratory of Weak-Light Nonlinear Photonics, School of Physics, Nankai University, Tianjin, 300071, China
| | - Moxi Qiu
- Ultrafast Electron Microscopy Laboratory, MOE Key Laboratory of Weak-Light Nonlinear Photonics, School of Physics, Nankai University, Tianjin, 300071, China
| | - Fang Liu
- Ultrafast Electron Microscopy Laboratory, MOE Key Laboratory of Weak-Light Nonlinear Photonics, School of Physics, Nankai University, Tianjin, 300071, China
| | - Min Feng
- Ultrafast Electron Microscopy Laboratory, MOE Key Laboratory of Weak-Light Nonlinear Photonics, School of Physics, Nankai University, Tianjin, 300071, China
| | - Cuntao Gao
- Ultrafast Electron Microscopy Laboratory, MOE Key Laboratory of Weak-Light Nonlinear Photonics, School of Physics, Nankai University, Tianjin, 300071, China
| | - Shibing Deng
- Ultrafast Electron Microscopy Laboratory, MOE Key Laboratory of Weak-Light Nonlinear Photonics, School of Physics, Nankai University, Tianjin, 300071, China
| | - Xuewen Fu
- Ultrafast Electron Microscopy Laboratory, MOE Key Laboratory of Weak-Light Nonlinear Photonics, School of Physics, Nankai University, Tianjin, 300071, China
- School of Materials Science and Engineering, Smart Sensing Interdisciplinary Science Center, Nankai University, Tianjin, 300350, China
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3
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Singh A, Thutupalli S, Kumar M, Ameta S. Constrained dynamics of DNA oligonucleotides in phase-separated droplets. Biophys J 2024; 123:1458-1466. [PMID: 38169216 PMCID: PMC11163293 DOI: 10.1016/j.bpj.2023.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Understanding the dynamics of biomolecules in complex environments is crucial for elucidating the effect of condensed and heterogeneous environments on their functional properties. A relevant environment-and one that can also be mimicked easily in vitro-is that of phase-separated droplets. While phase-separated droplet systems have been shown to compartmentalize a wide range of functional biomolecules, the effects of internal structuration of droplets on the dynamics and mobility of internalized molecules remain poorly understood. Here, we use fluorescence correlation spectroscopy to measure the dynamics of short oligonucleotides encapsulated within two representative kinds of uncharged and charged phase-separated droplets. We find that the internal structuration controls the oligonucleotide dynamics in these droplets, revealed by measuring physical parameters at high spatiotemporal resolution. By varying oligonucleotide length and salt concentrations (and thereby charge screening), we found that the dynamics are significantly affected in the noncharged droplets compared to the charged system. Our work lays the foundation for unraveling and quantifying the physical parameters governing biomolecular transport in the condensed environment.
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Affiliation(s)
- Anupam Singh
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Shashi Thutupalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India; International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Manoj Kumar
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.
| | - Sandeep Ameta
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India; Trivedi School of Biosciences, Ashoka University, Sonepat, India.
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Tripathy A, Priyadarsinee S, Bag N. Evaluation of functional transbilayer coupling in live cells by controlled lipid exchange and imaging fluorescence correlation spectroscopy. Methods Enzymol 2024; 700:1-32. [PMID: 38971596 DOI: 10.1016/bs.mie.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
Biophysical coupling between the inner and outer leaflets, known as inter-leaflet or transbilayer coupling, is a fundamental organizational principle in the plasma membranes of live mammalian cells. Lipid-based interactions between the two leaflets are proposed to be a primary mechanism underlying transbilayer coupling. However, there are only a few experimental evidence supporting the existence of such interactions in live cells. This is seemingly due to the lack of experimental strategies to perturb the lipid composition in one leaflet and quantitative techniques to evaluate the biophysical properties of the opposite leaflet. The existing strategies often dependent on immobilization and clustering a component in one of the leaflets and technically demanding biophysical tools to evaluate the effects on the opposing leaflet. In the recent years, the London group developed a simple but elegant method, namely methyl-alpha-cyclodextrin catalyzed lipid exchange (LEX), to efficiently exchange outer leaflet lipids with an exogenous lipid of choice. Here, we adopted this method to perturb outer leaflet lipid composition. The corresponding changes in the inner leaflet is evaluated by comparing the diffusion of lipid probes localized in this leaflet in unperturbed and perturbed conditions. We employed highly multiplexed imaging fluorescence correlation spectroscopy (ImFCS), realized in a commercially available or home-built total internal reflection fluorescence microsocope equipped with a fast and sensitive camera, to determine diffusion coefficient of the lipid probes. Using the combination of LEX and ImFCS, we directly demonstrate lipid-based transbilayer coupling that does not require immobilization of membrane components in live mast cells in resting conditions. Overall, we present a relatively straightforward experimental strategy to evaluate transbilayer coupling quantitively in live cells.
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Affiliation(s)
- Arpita Tripathy
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Sudipti Priyadarsinee
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Nirmalya Bag
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India.
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5
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Zulueta Díaz YDLM, Kure JL, Grosso RA, Andersen C, Pandzic E, Sengupta P, Wiseman PW, Arnspang EC. Quantitative image mean squared displacement (iMSD) analysis of the dynamics of Aquaporin 2 within the membrane of live cells. Biochim Biophys Acta Gen Subj 2023; 1867:130449. [PMID: 37748662 DOI: 10.1016/j.bbagen.2023.130449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
Nanodomains are a biological membrane phenomenon which have a large impact on various cellular processes. They are often analysed by looking at the lateral dynamics of membrane lipids or proteins. The localization of the plasma membrane protein aquaporin-2 in nanodomains has so far been unknown. In this study, we use total internal reflection fluorescence microscopy to image Madin-Darby Canine Kidney (MDCK) cells expressing aquaporin-2 tagged with mEos 3.2. Then, image mean squared displacement (iMSD) approach was used to analyse the diffusion of aquaporin-2, revealing that aquaporin-2 is confined within membrane nanodomains. Using iMSD analysis, we found that the addition of the drug forskolin increases the diffusion of aquaporin-2 within the confined domains, which is in line with previous studies. Finally, we observed an increase in the size of the membrane domains and the extent of trapping of aquaporin-2 after stimulation with forskolin.
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Affiliation(s)
| | - Jakob Lavrsen Kure
- Department of Green Technology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Rubén Adrián Grosso
- Department of Green Technology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Camilla Andersen
- Department of Green Technology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Elvis Pandzic
- Mark Wainwright Analytical Centre, Lowy Cancer Research Centre C25, University of New South Wales, NSW, 2052, Australia
| | - Prabuddha Sengupta
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Paul W Wiseman
- Department of Chemistry, McGill University, Montreal, Québec, Canada; Department of Physics, McGill University, Montreal, Québec, Canada
| | - Eva C Arnspang
- Department of Green Technology, University of Southern Denmark, 5230 Odense M, Denmark; The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
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Kettmayer C, Gratton E, Estrada LC. Comparison of MSD analysis from single particle tracking with MSD from images. Getting the best of both worlds. Methods Appl Fluoresc 2023; 12:015001. [PMID: 37751748 DOI: 10.1088/2050-6120/acfd7e] [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: 05/18/2023] [Accepted: 09/26/2023] [Indexed: 09/28/2023]
Abstract
Fluorescence microscopy can provide valuable information about cell interior dynamics. Particularly, mean squared displacement (MSD) analysis is widely used to characterize proteins and sub-cellular structures' mobility providing the laws of molecular diffusion. The MSD curve is traditionally extracted from individual trajectories recorded by single-particle tracking-based techniques. More recently, image correlation methods like iMSD have been shown capable of providing averaged dynamic information directly from images, without the need for isolation and localization of individual particles. iMSD is a powerful technique that has been successfully applied to many different biological problems, over a wide spatial and temporal scales. The aim of this work is to review and compare these two well-established methodologies and their performance in different situations, to give an insight on how to make the most out of their unique characteristics. We show the analysis of the same datasets by the two methods. Regardless of the experimental differences in the input data for MSD or iMSD analysis, our results show that the two approaches can address equivalent questions for free diffusing systems. We focused on studying a range of diffusion coefficients between D = 0.001μm2s-1and D = 0.1μm2s-1, where we verified that the equivalence is maintained even for the case of isolated particles. This opens new opportunities for studying intracellular dynamics using equipment commonly available in any biophysical laboratory.
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Affiliation(s)
- Constanza Kettmayer
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física. Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA). Buenos Aires, Argentina
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, United States of America
| | - Laura C Estrada
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física. Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA). Buenos Aires, Argentina
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7
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Morales SV, Mahmood A, Pollard J, Mayne J, Figeys D, Wiseman PW. The LDL receptor is regulated by membrane cholesterol as revealed by fluorescence fluctuation analysis. Biophys J 2023; 122:3783-3797. [PMID: 37559362 PMCID: PMC10541495 DOI: 10.1016/j.bpj.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/17/2023] [Accepted: 08/07/2023] [Indexed: 08/11/2023] Open
Abstract
Membrane cholesterol-rich domains have been shown to be important for regulating a range of membrane protein activities. Low-density lipoprotein receptor (LDLR)-mediated internalization of cholesterol-rich LDL particles is tightly regulated by feedback mechanisms involving intracellular sterol sensors. Since LDLR plays a role in maintaining cellular cholesterol homeostasis, we explore the role that membrane domains may have in regulating LDLR activity. We expressed a fluorescent LDLR-mEGFP construct in HEK293T cells and imaged the unligated receptor or bound to an LDL/DiI fluorescent ligand using total internal reflection fluorescence microscopy. We studied the receptor's spatiotemporal dynamics using fluorescence fluctuation analysis methods. Image cross correlation spectroscopy reveals a lower LDL-to-LDLR binding fraction when membrane cholesterol concentrations are augmented using cholesterol esterase, and a higher binding fraction when the cells are treated with methyl-β-cyclodextrin) to lower membrane cholesterol. This suggests that LDLR's ability to metabolize LDL particles is negatively correlated to membrane cholesterol concentrations. We then tested if a change in activity is accompanied by a change in membrane localization. Image mean-square displacement analysis reveals that unligated LDLR-mEGFP and ligated LDLR-mEGFP/LDL-DiI constructs are transiently confined on the cell membrane, and the size of their confinement domains increases with augmented cholesterol concentrations. Receptor diffusion within the domains and their domain-escape probabilities decrease upon treatment with methyl-β-cyclodextrin, consistent with a change in receptor populations to more confined domains, likely clathrin-coated pits. We propose a feedback model to account for regulation of LDLR within the cell membrane: when membrane cholesterol concentrations are high, LDLR is sequestered in cholesterol-rich domains. These LDLR populations are attenuated in their efficacy to bind and internalize LDL. However, when membrane cholesterol levels drop, LDL has a higher binding affinity to its receptor and the LDLR transits to nascent clathrin-coated domains, where it diffuses at a slower rate while awaiting internalization.
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Affiliation(s)
- Sebastian V Morales
- Department of Chemistry, Faculty of Science, McGill University, Montreal, Canada
| | - Ahmad Mahmood
- Department of Physics, Faculty of Science, McGill University, Montreal, Canada
| | - Jacob Pollard
- Department of Chemistry, Faculty of Science, McGill University, Montreal, Canada
| | - Janice Mayne
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Paul W Wiseman
- Department of Chemistry, Faculty of Science, McGill University, Montreal, Canada; Department of Physics, Faculty of Science, McGill University, Montreal, Canada.
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8
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Philipp N, Gratton E, Estrada LC. Measuring protein-membrane interaction through radial fluorescence correlation in 2 dimensions. Methods Appl Fluoresc 2023; 11:045009. [PMID: 37586380 DOI: 10.1088/2050-6120/acf118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]
Abstract
The cell membrane has a fundamental role in the cell life cycle but there's still much to be learned about its heterogeneous structure, regulation, and protein interaction. Additionally, the protein-membrane interaction is often overlooked when studying specific protein dynamics. In this work, we present a new tool for a better understanding of protein dynamics and membrane function using live cells and fast non-invasive techniques without the need for individual particle tracking. To this end, we used the 2D-pair correlation function (2D-pCF) to study protein interactions across cellular membranes. We performed numerical simulations and confocal experiments using a GAP-mEGFP fusion construct known to interact with the plasmatic membrane. Our results demonstrate that based on a quantitative correlation analysis as the 2D pair correlation of the signal intensities, is possible to characterize protein-membrane interactions in live systems and real-time. Combining experimental and numerical results this work presents a new powerful approach to the study of the dynamic protein-membrane interaction.
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Affiliation(s)
- N Philipp
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física. Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA). Buenos Aires, Argentina
| | - E Gratton
- Department of Biomedical Engineering, University of California, Irvine, CA, United States of America
| | - L C Estrada
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física. Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA). Buenos Aires, Argentina
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9
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Digiacomo L, Renzi S, Quagliarini E, Pozzi D, Amenitsch H, Ferri G, Pesce L, De Lorenzi V, Matteoli G, Cardarelli F, Caracciolo G. Investigating the mechanism of action of DNA-loaded PEGylated lipid nanoparticles. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2023; 53:102697. [PMID: 37507061 DOI: 10.1016/j.nano.2023.102697] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/26/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023]
Abstract
PEGylated lipid nanoparticles (LNPs) are commonly used to deliver bioactive molecules, but the role of PEGylation in DNA-loaded LNP interactions at the cellular and subcellular levels remains poorly understood. In this study, we investigated the mechanism of action of DNA-loaded PEGylated LNPs using gene reporter technologies, dynamic light scattering (DLS), synchrotron small angle X-ray scattering (SAXS), and fluorescence confocal microscopy (FCS). We found that PEG has no significant impact on the size or nanostructure of DNA LNPs but reduces their zeta potential and interaction with anionic cell membranes. PEGylation increases the structural stability of LNPs and results in lower DNA unloading. FCS experiments revealed that PEGylated LNPs are internalized intact inside cells and largely shuttled to lysosomes, while unPEGylated LNPs undergo massive destabilization on the plasma membrane. These findings can inform the design, optimization, and validation of DNA-loaded LNPs for gene delivery and vaccine development.
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Affiliation(s)
- Luca Digiacomo
- NanoDelivery Lab, Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Serena Renzi
- NanoDelivery Lab, Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Erica Quagliarini
- NanoDelivery Lab, Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Daniela Pozzi
- NanoDelivery Lab, Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Gianmarco Ferri
- Laboratorio NEST, Scuola Normale Superiore, 56127 Pisa, Italy
| | - Luca Pesce
- Laboratorio NEST, Scuola Normale Superiore, 56127 Pisa, Italy
| | | | - Giulia Matteoli
- Laboratorio NEST, Scuola Normale Superiore, 56127 Pisa, Italy
| | | | - Giulio Caracciolo
- NanoDelivery Lab, Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy.
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10
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Pugliese LA, De Lorenzi V, Bernardi M, Ghignoli S, Tesi M, Marchetti P, Pesce L, Cardarelli F. Unveiling nanoscale optical signatures of cytokine-induced β-cell dysfunction. Sci Rep 2023; 13:13342. [PMID: 37587148 PMCID: PMC10432522 DOI: 10.1038/s41598-023-40272-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023] Open
Abstract
Pro-inflammatory cytokines contribute to β-cell failure in both Type-1 and Type-2 Diabetes. Data collected so far allowed to dissect the genomic, transcriptomic, proteomic and biochemical landscape underlying cytokine-induced β-cell progression through dysfunction. Yet, no report thus far complemented such molecular information with the direct optical nanoscopy of the β-cell subcellular environment. Here we tackle this issue in Insulinoma 1E (INS-1E) β-cells by label-free fluorescence lifetime imaging microscopy (FLIM) and fluorescence-based super resolution imaging by expansion microscopy (ExM). It is found that 24-h exposure to IL-1β and IFN-γ is associated with a neat modification of the FLIM signature of cell autofluorescence due to the increase of either enzyme-bound NAD(P)H molecules and of oxidized lipid species. At the same time, ExM-based direct imaging unveils neat alteration of mitochondrial morphology (i.e. ~ 80% increase of mitochondrial circularity), marked degranulation (i.e. ~ 40% loss of insulin granules, with mis-localization of the surviving pool), appearance of F-actin-positive membrane blebs and an hitherto unknown extensive fragmentation of the microtubules network (e.g. ~ 37% reduction in the number of branches). Reported observations provide an optical-microscopy framework to interpret the amount of molecular information collected so far on β-cell dysfunction and pave the way to future ex-vivo and in-vivo investigations.
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Affiliation(s)
- Licia Anna Pugliese
- NEST Laboratory - Scuola Normale Superiore, Piazza San Silvestro 12, Pisa, Italy.
| | - Valentina De Lorenzi
- NEST Laboratory - Scuola Normale Superiore, Piazza San Silvestro 12, Pisa, Italy
| | - Mario Bernardi
- NEST Laboratory - Scuola Normale Superiore, Piazza San Silvestro 12, Pisa, Italy
| | - Samuele Ghignoli
- NEST Laboratory - Scuola Normale Superiore, Piazza San Silvestro 12, Pisa, Italy
| | - Marta Tesi
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - Luca Pesce
- NEST Laboratory - Scuola Normale Superiore, Piazza San Silvestro 12, Pisa, Italy.
| | - Francesco Cardarelli
- NEST Laboratory - Scuola Normale Superiore, Piazza San Silvestro 12, Pisa, Italy.
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11
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He H, Qin G, Bi S, Feng Z, Mao J, Guan X, Xue M, Wang Z, Wang X, Yu D, Huang F. Deep-Learning-Enhanced Diffusion Imaging Assay for Resolving Local-Density Effects on Membrane Receptors. Anal Chem 2023; 95:3300-3308. [PMID: 36716433 DOI: 10.1021/acs.analchem.2c04326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
G-protein-coupled receptor (GPCR) density at the cell surface is thought to regulate receptor function. Spatially resolved measurements of local-density effects on GPCRs are needed but technically limited by density heterogeneity and mobility of membrane receptors. We now develop a deep-learning (DL)-enhanced diffusion imaging assay that can measure local-density effects on ligand-receptor interactions in the plasma membrane of live cells. In this method, the DL algorithm allows the transformation of 100 ms exposure images to density maps that report receptor numbers over any specified region with ∼95% accuracy by 1 s exposure images as ground truth. With the density maps, a diffusion assay is further established for spatially resolved measurements of receptor diffusion coefficient as well as to express relationships between receptor diffusivity and local density. By this assay, we scrutinize local-density effects on chemokine receptor CXCR4 interactions with various ligands, which reveals that an agonist prefers to act with CXCR4 at low density while an inverse agonist dominates at high density. This work suggests a new insight into density-dependent receptor regulation as well as provides an unprecedented assay that can be applicable to a wide variety of receptors in live cells.
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Affiliation(s)
- Hua He
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Guangyong Qin
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Simin Bi
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Zhenzhen Feng
- Technical Center of Qingdao Customs District, Qingdao266500, China
| | - Jian Mao
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Xin Guan
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Minmin Xue
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Zhirui Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Daoyong Yu
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao266580, China
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12
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Andersen C, Zulueta Díaz YDLM, Kure JL, Hessellund Eriksen M, Lovatt AL, Lagerholm C, Morales S, Sehayek S, Sheard TMD, Wiseman PW, Arnspang EC. Angiotensin II Treatment Induces Reorganization and Changes in the Lateral Dynamics of Angiotensin II Type 1 Receptor in the Plasma Membrane Elucidated by Photoactivated Localization Microscopy Combined with Image Spatial Correlation Analysis. Anal Chem 2023; 95:730-738. [PMID: 36574961 DOI: 10.1021/acs.analchem.2c02720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The mechanisms by which angiotensin II type 1 receptor is distributed and the diffusional pattern in the plasma membrane (PM) remain unclear, despite their crucial role in cardiovascular homeostasis. In this work, we obtained quantitative information of angiotensin II type 1 receptor (AT1R) lateral dynamics as well as changes in the diffusion properties after stimulation with ligands in living cells using photoactivated localization microscopy (PALM) combined with image spatial-temporal correlation analysis. To study the organization of the receptor at the nanoscale, expansion microscopy (ExM) combined with PALM was performed. This study revealed that AT1R lateral diffusion increased after binding to angiotensin II (Ang II) and the receptor diffusion was transiently confined in the PM. In addition, ExM revealed that AT1R formed nanoclusters at the PM and the cluster size significantly decreased after Ang II treatment. Taking these results together suggest that Ang II binding and activation cause reorganization and changes in the dynamics of AT1R at the PM.
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Affiliation(s)
- Camilla Andersen
- SDU Biotechnology, Department of Green Technology, University of Southern Denmark, Odense M5230, Denmark
| | | | - Jakob L Kure
- SDU Biotechnology, Department of Green Technology, University of Southern Denmark, Odense M5230, Denmark
| | - Mathias Hessellund Eriksen
- SDU Biotechnology, Department of Green Technology, University of Southern Denmark, Odense M5230, Denmark
| | - Adam Leslie Lovatt
- SDU Biotechnology, Department of Green Technology, University of Southern Denmark, Odense M5230, Denmark
| | | | - Sebastian Morales
- Department of Physics and Department of Chemistry, McGill University, MontrealH3A 0B8, Canada
| | - Simon Sehayek
- Department of Physics and Department of Chemistry, McGill University, MontrealH3A 0B8, Canada
| | - Thomas M D Sheard
- School of Biosciences, University of Sheffield, SheffieldS10 2TN, U.K
| | - Paul W Wiseman
- Department of Physics and Department of Chemistry, McGill University, MontrealH3A 0B8, Canada
| | - Eva C Arnspang
- SDU Biotechnology, Department of Green Technology, University of Southern Denmark, Odense M5230, Denmark
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13
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Breaking the Concentration Limit in Fluorescence Fluctuation Spectroscopy with Camera-Based Detection. Int J Mol Sci 2022; 23:ijms23179840. [PMID: 36077237 PMCID: PMC9456017 DOI: 10.3390/ijms23179840] [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: 08/08/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 12/02/2022] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is an extremely versatile tool that has been widely used to measure chemical reaction rates, protein binding, nanoparticle-protein interactions, and biomolecular dynamics in vitro and in vivo. As an inherently micro-sized approach, FCS is compatible with high-throughput screening applications, as demanded for drug design, but typically limited to nanomolar concentrations, which restricts possible applications. Here, we show how massively parallel camera-based detection with side illumination can extend the usable concentration range of FCS more than 100-fold to measure low affinity processes. Our line illumination (LIM) approach is robust, fast (1 s acquisition times), and does not require any reference measurements to characterize the observation volume size.
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14
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Measuring Molecular Diffusion in Dynamic Subcellular Nanostructures by Fast Raster Image Correlation Spectroscopy and 3D Orbital Tracking. Int J Mol Sci 2022; 23:ijms23147623. [PMID: 35886970 PMCID: PMC9323805 DOI: 10.3390/ijms23147623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 06/21/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
Here we provide demonstration that fast fluorescence fluctuation spectroscopy is a fast and robust approach to extract information on the dynamics of molecules enclosed within subcellular nanostructures (e.g., organelles or vesicles) which are also moving in the complex cellular environment. In more detail, Raster Image Correlation Spectroscopy (RICS) performed at fast timescales (i.e., microseconds) reveals the fast motion of fluorescently labeled molecules within two exemplary dynamic subcellular nanostructures of biomedical interest, the lysosome and the insulin secretory granule (ISG). The measurement of molecular diffusion is then used to extract information on the average properties of subcellular nanostructures, such as macromolecular crowding or molecular aggregation. Concerning the lysosome, fast RICS on a fluorescent tracer allowed us to quantitatively assess the increase in organelle viscosity in the pathological condition of Krabbe disease. In the case of ISGs, fast RICS on two ISG-specific secreting peptides unveiled their differential aggregation propensity depending on intragranular concentration. Finally, a combination of fast RICS and feedback-based 3D orbital tracking was used to subtract the slow movement of subcellular nanostructures from the fast diffusion of molecules contained within them and independently validate the results. Results presented here not only demonstrate the acquired ability to address the dynamic behavior of molecules in moving, nanoscopic reference systems, but prove the relevance of this approach to advance our knowledge on cell function at the subcellular scale.
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15
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The Impact of Membrane Protein Diffusion on GPCR Signaling. Cells 2022; 11:cells11101660. [PMID: 35626696 PMCID: PMC9139411 DOI: 10.3390/cells11101660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 12/10/2022] Open
Abstract
Spatiotemporal signal shaping in G protein-coupled receptor (GPCR) signaling is now a well-established and accepted notion to explain how signaling specificity can be achieved by a superfamily sharing only a handful of downstream second messengers. Dozens of Gs-coupled GPCR signals ultimately converge on the production of cAMP, a ubiquitous second messenger. This idea is almost always framed in terms of local concentrations, the differences in which are maintained by means of spatial separation. However, given the dynamic nature of the reaction-diffusion processes at hand, the dynamics, in particular the local diffusional properties of the receptors and their cognate G proteins, are also important. By combining some first principle considerations, simulated data, and experimental data of the receptors diffusing on the membranes of living cells, we offer a short perspective on the modulatory role of local membrane diffusion in regulating GPCR-mediated cell signaling. Our analysis points to a diffusion-limited regime where the effective production rate of activated G protein scales linearly with the receptor–G protein complex’s relative diffusion rate and to an interesting role played by the membrane geometry in modulating the efficiency of coupling.
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16
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Bag N, London E, Holowka DA, Baird BA. Transbilayer Coupling of Lipids in Cells Investigated by Imaging Fluorescence Correlation Spectroscopy. J Phys Chem B 2022; 126:2325-2336. [PMID: 35294838 DOI: 10.1021/acs.jpcb.2c00117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plasma membranes host numerous receptors, sensors, and ion channels involved in cellular signaling. Phase separation within the plasma membrane has emerged as a key biophysical regulator of signaling reactions in multiple physiological and pathological contexts. There is much evidence that plasma membrane composition supports the coexistence of liquid-ordered (Lo) and liquid-disordered (Ld) phases or domains at physiological conditions. However, this phase/domain separation is nanoscopic and transient in live cells. It has been recently proposed that transbilayer coupling between the inner and outer leaflets of the plasma membrane is driven by their asymmetric lipid distribution and by dynamic cytoskeleton-lipid composites that contribute to the formation and transience of Lo/Ld phase separation in live cells. In this Perspective, we highlight new approaches to investigate how transbilayer coupling may influence phase separation. For quantitative evaluation of the impact of these interactions, we introduce an experimental strategy centered around Imaging Fluorescence Correlation Spectroscopy (ImFCS), which measures membrane diffusion with very high precision. To demonstrate this strategy, we choose two well-established model systems for transbilayer interactions: cross-linking by multivalent antigen of immunoglobulin E bound to receptor FcεRI and cross-linking by cholera toxin B of GM1 gangliosides. We discuss emerging methods to systematically perturb membrane lipid composition, particularly exchange of outer leaflet lipids with exogenous lipids using methyl alpha cyclodextrin. These selective perturbations may be quantitatively evaluated with ImFCS and other high-resolution biophysical tools to discover novel principles of lipid-mediated phase separation in live cells in the context of their pathophysiological relevance.
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Affiliation(s)
- Nirmalya Bag
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - David A Holowka
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Barbara A Baird
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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17
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Intertwined and Finely Balanced: Endoplasmic Reticulum Morphology, Dynamics, Function, and Diseases. Cells 2021; 10:cells10092341. [PMID: 34571990 PMCID: PMC8472773 DOI: 10.3390/cells10092341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 02/07/2023] Open
Abstract
The endoplasmic reticulum (ER) is an organelle that is responsible for many essential subcellular processes. Interconnected narrow tubules at the periphery and thicker sheet-like regions in the perinuclear region are linked to the nuclear envelope. It is becoming apparent that the complex morphology and dynamics of the ER are linked to its function. Mutations in the proteins involved in regulating ER structure and movement are implicated in many diseases including neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and amyotrophic lateral sclerosis (ALS). The ER is also hijacked by pathogens to promote their replication. Bacteria such as Legionella pneumophila and Chlamydia trachomatis, as well as the Zika virus, bind to ER morphology and dynamics-regulating proteins to exploit the functions of the ER to their advantage. This review covers our understanding of ER morphology, including the functional subdomains and membrane contact sites that the organelle forms. We also focus on ER dynamics and the current efforts to quantify ER motion and discuss the diseases related to ER morphology and dynamics.
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18
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Ferri G, Tesi M, Pesce L, Bugliani M, Grano F, Occhipinti M, Suleiman M, De Luca C, Marselli L, Marchetti P, Cardarelli F. Spatiotemporal Correlation Spectroscopy Reveals a Protective Effect of Peptide-Based GLP-1 Receptor Agonism against Lipotoxicity on Insulin Granule Dynamics in Primary Human β-Cells. Pharmaceutics 2021; 13:pharmaceutics13091403. [PMID: 34575477 PMCID: PMC8464798 DOI: 10.3390/pharmaceutics13091403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/18/2021] [Accepted: 09/02/2021] [Indexed: 12/25/2022] Open
Abstract
Glucagon-like peptide-1 receptor (GLP-1R) agonists are being used for the treatment of type 2 diabetes (T2D) and may have beneficial effects on the pancreatic β-cells. Here, we evaluated the effects of GLP-1R agonism on insulin secretory granule (ISG) dynamics in primary β-cells isolated from human islets exposed to palmitate-induced lipotoxic stress. Islets cells were exposed for 48 h to 0.5 mM palmitate (hereafter, ‘Palm’) with or without the addition of a GLP-1 agonist, namely 10 nM exendin-4 (hereafter, ‘Ex-4’). Dissociated cells were first transfected with syncollin-EGFP in order to fluorescently mark the ISGs. Then, by applying a recently established spatiotemporal correlation spectroscopy technique, the average structural (i.e., size) and dynamic (i.e., the local diffusivity and mode of motion) properties of ISGs are extracted from a calculated imaging-derived Mean Square Displacement (iMSD) trace. Besides defining the structural/dynamic fingerprint of ISGs in human cells for the first time, iMSD analysis allowed to probe fingerprint variations under selected conditions: namely, it was shown that Palm affects ISGs dynamics in response to acute glucose stimulation by abolishing the ISGs mobilization typically imparted by glucose and, concomitantly, by reducing the extent of ISGs active/directed intracellular movement. By contrast, co-treatment with Ex-4 normalizes ISG dynamics, i.e., re-establish ISG mobilization and ability to perform active transport in response to glucose stimulation. These observations were correlated with standard glucose-stimulated insulin secretion (GSIS), which resulted in being reduced in cells exposed to Palm but preserved in cells concomitantly exposed to 10 nM Ex-4. Our data support the idea that GLP-1R agonism may exert its beneficial effect on human β-cells under metabolic stress by maintaining ISGs’ proper intracellular dynamics.
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Affiliation(s)
- Gianmarco Ferri
- Laboratorio NEST-Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy; (G.F.); (L.P.)
| | - Marta Tesi
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56127 Pisa, Italy; (M.T.); (M.B.); (F.G.); (M.O.); (M.S.); (C.D.L.); (L.M.); (P.M.)
| | - Luca Pesce
- Laboratorio NEST-Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy; (G.F.); (L.P.)
| | - Marco Bugliani
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56127 Pisa, Italy; (M.T.); (M.B.); (F.G.); (M.O.); (M.S.); (C.D.L.); (L.M.); (P.M.)
| | - Francesca Grano
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56127 Pisa, Italy; (M.T.); (M.B.); (F.G.); (M.O.); (M.S.); (C.D.L.); (L.M.); (P.M.)
| | - Margherita Occhipinti
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56127 Pisa, Italy; (M.T.); (M.B.); (F.G.); (M.O.); (M.S.); (C.D.L.); (L.M.); (P.M.)
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56127 Pisa, Italy; (M.T.); (M.B.); (F.G.); (M.O.); (M.S.); (C.D.L.); (L.M.); (P.M.)
| | - Carmela De Luca
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56127 Pisa, Italy; (M.T.); (M.B.); (F.G.); (M.O.); (M.S.); (C.D.L.); (L.M.); (P.M.)
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56127 Pisa, Italy; (M.T.); (M.B.); (F.G.); (M.O.); (M.S.); (C.D.L.); (L.M.); (P.M.)
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56127 Pisa, Italy; (M.T.); (M.B.); (F.G.); (M.O.); (M.S.); (C.D.L.); (L.M.); (P.M.)
| | - Francesco Cardarelli
- Laboratorio NEST-Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy; (G.F.); (L.P.)
- Correspondence:
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19
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Abstract
The miniSPIM is a miniaturized light-sheet microscope that enables imaging with optical sectioning on mobile camera devices such as smartphones and single-board computers. Applications of the miniSPIM include biosensing, field research, and education where maximum portability and robustness, low power consumption, and low cost are key. Here, it is shown how all of the components of a simple light-sheet microscope can be integrated within a footprint smaller than the average smartphone. Example applications include the quantification of the motion of microparticles and bacteria in fluids, the characterization of solvent polarity based on spectral shifts of the lipid probe Nile Red, and three-dimensional (3D) and time-lapse autofluorescence imaging of a live zebrafish embryo.
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Affiliation(s)
- Per Niklas Hedde
- Beckman Laser Institute, University of California Irvine, Irvine, California 92612, United States
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697, United States
- Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, California 92697, United States
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20
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Bermudez JG, Deiters A, Good MC. Patterning Microtubule Network Organization Reshapes Cell-Like Compartments. ACS Synth Biol 2021; 10:1338-1350. [PMID: 33988978 DOI: 10.1021/acssynbio.0c00575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eukaryotic cells contain a cytoskeletal network comprised of dynamic microtubule filaments whose spatial organization is highly plastic. Specialized microtubule architectures are optimized for different cell types and remodel with the oscillatory cell cycle. These spatially distinct microtubule networks are thought to arise from the activity and localization of microtubule regulators and motors and are further shaped by physical forces from the cell boundary. Given complexities and redundancies of a living cell, it is challenging to disentangle the separate biochemical and physical contributions to microtubule network organization. Therefore, we sought to develop a minimal cell-like system to manipulate and spatially pattern the organization of cytoskeletal components in real-time, providing an opportunity to build distinct spatial structures and to determine how they are shaped by or reshape cell boundaries. We constructed a system for induced spatial patterning of protein components within cell-sized emulsion compartments and used it to drive microtubule network organization in real-time. We controlled dynamic protein relocalization using small molecules and light and slowed lateral diffusion within the lipid monolayer to create stable micropatterns with focused illumination. By fusing microtubule interacting proteins to optochemical dimerization domains, we directed the spatial organization of microtubule networks. Cortical patterning of polymerizing microtubules leads to symmetry breaking and forces that dramatically reshape the compartment. Our system has applications in cell biology to characterize the contributions of biochemical components and physical boundary conditions to microtubule network organization. Additionally, active shape control has uses in protocell engineering and for augmenting the functionalities of synthetic cells.
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Affiliation(s)
- Jessica G. Bermudez
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alexander Deiters
- Chemistry Department, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Matthew C. Good
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Cell and Developmental Biology Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Bioengineering Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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21
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Bernabé-Rubio M, Bosch-Fortea M, Alonso MA, Bernardino de la Serna J. Multi-dimensional and spatiotemporal correlative imaging at the plasma membrane of live cells to determine the continuum nano-to-micro scale lipid adaptation and collective motion. Methods 2021; 193:136-147. [PMID: 34126167 DOI: 10.1016/j.ymeth.2021.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/25/2022] Open
Abstract
The primary cilium is a specialized plasma membrane protrusion with important receptors for signalling pathways. In polarized epithelial cells, the primary cilium assembles after the midbody remnant (MBR) encounters the centrosome at the apical surface. The membrane surrounding the MBR, namely remnant-associated membrane patch (RAMP), once situated next to the centrosome, releases some of its lipid components to form a centrosome-associated membrane patch (CAMP) from which the ciliary membrane stems. The RAMP undergoes a spatiotemporal membrane refinement during the formation of the CAMP, which becomes highly enriched in condensed membranes with low lateral mobility. To better understand this process, we have developed a correlative imaging approach that yields quantitative information about the lipid lateral packing, its mobility and collective assembly at the plasma membrane at different spatial scales over time. Our work paves the way towards a quantitative understanding of the spatiotemporal lipid collective assembly at the plasma membrane as a functional determinant in cell biology and its direct correlation with the membrane physicochemical state. These findings allowed us to gain a deeper insight into the mechanisms behind the biogenesis of the ciliary membrane of polarized epithelial cells.
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Affiliation(s)
- Miguel Bernabé-Rubio
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain; King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK
| | - Minerva Bosch-Fortea
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain; Institute of Bioengineering and School of Engineering and Materials Science, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Miguel A Alonso
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jorge Bernardino de la Serna
- Central Laser Facility, Rutherford Appleton Laboratory, MRC-Research Complex at Harwell, Science and Technology Facilities Council, Harwell OX11 0QX, UK; National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK; NIHR Imperial Biomedical Research Centre, London SW7 2AZ, UK.
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22
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Bathe-Peters M, Gmach P, Boltz HH, Einsiedel J, Gotthardt M, Hübner H, Gmeiner P, Lohse MJ, Annibale P. Visualization of β-adrenergic receptor dynamics and differential localization in cardiomyocytes. Proc Natl Acad Sci U S A 2021; 118:e2101119118. [PMID: 34088840 PMCID: PMC8201832 DOI: 10.1073/pnas.2101119118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A key question in receptor signaling is how specificity is realized, particularly when different receptors trigger the same biochemical pathway(s). A notable case is the two β-adrenergic receptor (β-AR) subtypes, β1 and β2, in cardiomyocytes. They are both coupled to stimulatory Gs proteins, mediate an increase in cyclic adenosine monophosphate (cAMP), and stimulate cardiac contractility; however, other effects, such as changes in gene transcription leading to cardiac hypertrophy, are prominent only for β1-AR but not for β2-AR. Here, we employ highly sensitive fluorescence spectroscopy approaches, in combination with a fluorescent β-AR antagonist, to determine the presence and dynamics of the endogenous receptors on the outer plasma membrane as well as on the T-tubular network of intact adult cardiomyocytes. These techniques allow us to visualize that the β2-AR is confined to and diffuses within the T-tubular network, as opposed to the β1-AR, which is found to diffuse both on the outer plasma membrane as well as on the T-tubules. Upon overexpression of the β2-AR, this compartmentalization is lost, and the receptors are also seen on the cell surface. Such receptor segregation depends on the development of the T-tubular network in adult cardiomyocytes since both the cardiomyoblast cell line H9c2 and the cardiomyocyte-differentiated human-induced pluripotent stem cells express the β2-AR on the outer plasma membrane. These data support the notion that specific cell surface targeting of receptor subtypes can be the basis for distinct signaling and functional effects.
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MESH Headings
- Animals
- Cell Line
- Cell Membrane/genetics
- Cell Membrane/metabolism
- Humans
- Induced Pluripotent Stem Cells/metabolism
- Mice
- Mice, Transgenic
- Molecular Imaging
- Myocytes, Cardiac/metabolism
- Receptors, Adrenergic, beta-1/genetics
- Receptors, Adrenergic, beta-1/metabolism
- Receptors, Adrenergic, beta-2/genetics
- Receptors, Adrenergic, beta-2/metabolism
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Affiliation(s)
- Marc Bathe-Peters
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Institute of Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany
| | - Philipp Gmach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Institute of Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany
| | - Horst-Holger Boltz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Department for Modelling and Simulation of Complex Processes, Zuse Institute Berlin, 14195 Berlin, Germany
| | - Jürgen Einsiedel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Michael Gotthardt
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Martin J Lohse
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany;
- Institute of Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany
- Department of Chemistry and Biochemistry, Free University of Berlin, 14195 Berlin, Germany
- ISAR Bioscience Institute, 82152 Munich-Planegg, Germany
| | - Paolo Annibale
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany;
- Institute of Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany
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23
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Fluorescence Fluctuation Spectroscopy enables quantification of potassium channel subunit dynamics and stoichiometry. Sci Rep 2021; 11:10719. [PMID: 34021177 PMCID: PMC8140153 DOI: 10.1038/s41598-021-90002-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/15/2021] [Indexed: 11/08/2022] Open
Abstract
Voltage-gated potassium (Kv) channels are a family of membrane proteins that facilitate K+ ion diffusion across the plasma membrane, regulating both resting and action potentials. Kv channels comprise four pore-forming α subunits, each with a voltage sensing domain, and they are regulated by interaction with β subunits such as those belonging to the KCNE family. Here we conducted a comprehensive biophysical characterization of stoichiometry and protein diffusion across the plasma membrane of the epithelial KCNQ1-KCNE2 complex, combining total internal reflection fluorescence (TIRF) microscopy and a series of complementary Fluorescence Fluctuation Spectroscopy (FFS) techniques. Using this approach, we found that KCNQ1-KCNE2 has a predominant 4:4 stoichiometry, while non-bound KCNE2 subunits are mostly present as dimers in the plasma membrane. At the same time, we identified unique spatio-temporal diffusion modalities and nano-environment organization for each channel subunit. These findings improve our understanding of KCNQ1-KCNE2 channel function and suggest strategies for elucidating the subunit stoichiometry and forces directing localization and diffusion of ion channel complexes in general.
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Li F, Yu S, Huang X, Dong C, Ren J. Studying Homo-oligomerization and Hetero-oligomerization of MDMX and MDM2 Proteins in Single Living Cells by Using In Situ Fluorescence Correlation Spectroscopy. Biochemistry 2021; 60:1498-1505. [PMID: 33870698 DOI: 10.1021/acs.biochem.1c00153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein oligomerization plays a very important role in many physiological processes. p53 acts as a key tumor suppressor by regulating cell cycle arrest, DNA repair, and apoptosis, and its antitumor activity is regulated by the hetero- and homo-oligomerization of MDMX and MDM2 proteins. So far, some traditional methods have been utilized to study the oligomerization of MDMX and MDM2 in vitro, but they have not clarified some controversial issues or whether the extracellular results can represent the intracellular results. Here, we put forward an in situ method for studying protein homo- and hetero-oligomerization in single living cells by using fluorescence correlation spectroscopy. In this study, MDMX and MDM2 were labeled with fluorescent proteins using lentiviral transfection. Autocorrelation spectroscopy and cross-correlation spectroscopy methods were used to study the oligomerization of MDMX and MDM2 in situ and the effect of regulation of MDMX oligomerization on p53-MDMX interactions in single living cells. We observed the homo- and hetero-oligomerization of MDMX and MDM2 in living cells. Meanwhile, the levels of the homo-oligomers of MDMX and MDM2 were increased due to the lack of hetero-oligomerization. Finally, the binding affinity of MDMX for p53 was improved with an increase in the level of MDMX hetero-oligomerization.
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Affiliation(s)
- Fucai Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Shengrong Yu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Xiangyi Huang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Chaoqing Dong
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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25
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Sankaran J, Balasubramanian H, Tang WH, Ng XW, Röllin A, Wohland T. Simultaneous spatiotemporal super-resolution and multi-parametric fluorescence microscopy. Nat Commun 2021; 12:1748. [PMID: 33741958 PMCID: PMC7979808 DOI: 10.1038/s41467-021-22002-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 02/15/2021] [Indexed: 11/29/2022] Open
Abstract
Super-resolution microscopy and single molecule fluorescence spectroscopy require mutually exclusive experimental strategies optimizing either temporal or spatial resolution. To achieve both, we implement a GPU-supported, camera-based measurement strategy that highly resolves spatial structures (~100 nm), temporal dynamics (~2 ms), and molecular brightness from the exact same data set. Simultaneous super-resolution of spatial and temporal details leads to an improved precision in estimating the diffusion coefficient of the actin binding polypeptide Lifeact and corrects structural artefacts. Multi-parametric analysis of epidermal growth factor receptor (EGFR) and Lifeact suggests that the domain partitioning of EGFR is primarily determined by EGFR-membrane interactions, possibly sub-resolution clustering and inter-EGFR interactions but is largely independent of EGFR-actin interactions. These results demonstrate that pixel-wise cross-correlation of parameters obtained from different techniques on the same data set enables robust physicochemical parameter estimation and provides biological knowledge that cannot be obtained from sequential measurements.
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Affiliation(s)
- Jagadish Sankaran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Harikrushnan Balasubramanian
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Wai Hoh Tang
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Xue Wen Ng
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Adrian Röllin
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore.
- Department of Chemistry, National University of Singapore, Singapore, Singapore.
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26
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Slenders E, Castello M, Buttafava M, Villa F, Tosi A, Lanzanò L, Koho SV, Vicidomini G. Confocal-based fluorescence fluctuation spectroscopy with a SPAD array detector. LIGHT, SCIENCE & APPLICATIONS 2021; 10:31. [PMID: 33542179 PMCID: PMC7862647 DOI: 10.1038/s41377-021-00475-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/17/2020] [Accepted: 01/14/2021] [Indexed: 05/13/2023]
Abstract
The combination of confocal laser-scanning microscopy (CLSM) and fluorescence fluctuation spectroscopy (FFS) is a powerful tool in studying fast, sub-resolution biomolecular processes in living cells. A detector array can further enhance CLSM-based FFS techniques, as it allows the simultaneous acquisition of several samples-essentially images-of the CLSM detection volume. However, the detector arrays that have previously been proposed for this purpose require tedious data corrections and preclude the combination of FFS with single-photon techniques, such as fluorescence lifetime imaging. Here, we solve these limitations by integrating a novel single-photon-avalanche-diode (SPAD) array detector in a CLSM system. We validate this new implementation on a series of FFS analyses: spot-variation fluorescence correlation spectroscopy, pair-correlation function analysis, and image-derived mean squared displacement analysis. We predict that the unique combination of spatial and temporal information provided by our detector will make the proposed architecture the method of choice for CLSM-based FFS.
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Affiliation(s)
- Eli Slenders
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Marco Castello
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Mauro Buttafava
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Federica Villa
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Alberto Tosi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Fisica e Astronomia, Università di Catania, Catania, Italy
| | - Sami Valtteri Koho
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy.
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27
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Egloff S, Runser A, Klymchenko A, Reisch A. Size-Dependent Electroporation of Dye-Loaded Polymer Nanoparticles for Efficient and Safe Intracellular Delivery. SMALL METHODS 2021; 5:e2000947. [PMID: 34927896 DOI: 10.1002/smtd.202000947] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/13/2020] [Indexed: 06/14/2023]
Abstract
Efficient and safe delivery of nanoparticles (NPs) into the cytosol of living cells constitutes a major methodological challenge in bio-nanotechnology. Electroporation allows direct transfer of NPs into the cytosol by forming transient pores in the cell membrane, but it is criticized for invasiveness, and the applicable particle sizes are not well defined. Here, in order to establish principles for efficient delivery of NPs into the cytosol with minimal cytotoxicity, the influence of the size of NPs on their electroporation and intracellular behavior is investigated. For this study, fluorescent dye-loaded polymer NPs with core sizes between 10 and 40 nm are prepared. Optimizing the electroporation protocol allows minimizing contributions of endocytosis and to study directly the effect of NP size on electroporation. NPs of <20 nm hydrodynamic size are efficiently delivered into the cytosol, whereas this is not the case for NPs of >30 nm. Moreover, only particles of core size <15 nm diffuse freely throughout the cytosol. While electroporation at excessive electric fields induces cytotoxicity, the use of small NPs <20 nm allows efficient delivery at mild electroporation conditions. These results give clear methodological and design guidelines for the safe delivery of NPs for intracellular applications.
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Affiliation(s)
- Sylvie Egloff
- Université de Strasbourg, CNRS, Laboratoire de Bioimagerie et Pathologies UMR 7021, Strasbourg, F-67000, France
| | - Anne Runser
- Université de Strasbourg, CNRS, Laboratoire de Bioimagerie et Pathologies UMR 7021, Strasbourg, F-67000, France
| | - Andrey Klymchenko
- Université de Strasbourg, CNRS, Laboratoire de Bioimagerie et Pathologies UMR 7021, Strasbourg, F-67000, France
| | - Andreas Reisch
- Université de Strasbourg, CNRS, Laboratoire de Bioimagerie et Pathologies UMR 7021, Strasbourg, F-67000, France
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28
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Urbina FL, Menon S, Goldfarb D, Edwards R, Ben Major M, Brennwald P, Gupton SL. TRIM67 regulates exocytic mode and neuronal morphogenesis via SNAP47. Cell Rep 2021; 34:108743. [PMID: 33567284 PMCID: PMC7941186 DOI: 10.1016/j.celrep.2021.108743] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
Neuronal morphogenesis involves dramatic plasma membrane expansion, fueled by soluble N-ethylmaleimide-sensitive factor attachment protein eceptors (SNARE)-mediated exocytosis. Distinct fusion modes described at synapses include full-vesicle fusion (FVF) and kiss-and-run fusion (KNR). During FVF, lumenal cargo is secreted and vesicle membrane incorporates into the plasma membrane. During KNR, a transient fusion pore secretes cargo but closes without membrane addition. In contrast, fusion modes are not described in developing neurons. Here, we resolve individual exocytic events in developing murine cortical neurons and use classification tools to identify four distinguishable fusion modes: two FVF-like modes that insert membrane material and two KNR-like modes that do not. Discrete fluorescence profiles suggest distinct behavior of the fusion pore. Simulations and experiments agree that FVF-like exocytosis provides sufficient membrane material for morphogenesis. We find the E3 ubiquitin ligase TRIM67 promotes FVF-like exocytosis in part by limiting incorporation of the Qb/Qc SNARE SNAP47 into SNARE complexes and, thus, SNAP47 involvement in exocytosis. Urbina et al. identify four exocytic modes in developing neurons: KNRd, KNRi, FVFd, FVFi. Simulations and experiments suggest that FVFi and FVFd provide material for plasma membrane expansion. Deletion of Trim67 decreases FVFi and FVFd while reducing surface area. SNAP47 incorporation into SNARE complexes alters fusion pore behavior, increasing KNRd.
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Affiliation(s)
- Fabio L Urbina
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shalini Menon
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dennis Goldfarb
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Institute for Informatics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Reginald Edwards
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - M Ben Major
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Patrick Brennwald
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie L Gupton
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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29
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Schneider F, Colin-York H, Fritzsche M. Quantitative Bio-Imaging Tools to Dissect the Interplay of Membrane and Cytoskeletal Actin Dynamics in Immune Cells. Front Immunol 2021; 11:612542. [PMID: 33505401 PMCID: PMC7829180 DOI: 10.3389/fimmu.2020.612542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Cellular function is reliant on the dynamic interplay between the plasma membrane and the actin cytoskeleton. This critical relationship is of particular importance in immune cells, where both the cytoskeleton and the plasma membrane work in concert to organize and potentiate immune signaling events. Despite their importance, there remains a critical gap in understanding how these respective dynamics are coupled, and how this coupling in turn may influence immune cell function from the bottom up. In this review, we highlight recent optical technologies that could provide strategies to investigate the simultaneous dynamics of both the cytoskeleton and membrane as well as their interplay, focusing on current and future applications in immune cells. We provide a guide of the spatio-temporal scale of each technique as well as highlighting novel probes and labels that have the potential to provide insights into membrane and cytoskeletal dynamics. The quantitative biophysical tools presented here provide a new and exciting route to uncover the relationship between plasma membrane and cytoskeletal dynamics that underlies immune cell function.
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Affiliation(s)
- Falk Schneider
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Huw Colin-York
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Marco Fritzsche
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
- Rosalind Franklin Institute, Harwell Campus, Didcot, United Kingdom
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30
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Bock A, Annibale P, Konrad C, Hannawacker A, Anton SE, Maiellaro I, Zabel U, Sivaramakrishnan S, Falcke M, Lohse MJ. Optical Mapping of cAMP Signaling at the Nanometer Scale. Cell 2020; 182:1519-1530.e17. [PMID: 32846156 DOI: 10.1016/j.cell.2020.07.035] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/30/2020] [Accepted: 07/23/2020] [Indexed: 10/23/2022]
Abstract
Cells relay a plethora of extracellular signals to specific cellular responses by using only a few second messengers, such as cAMP. To explain signaling specificity, cAMP-degrading phosphodiesterases (PDEs) have been suggested to confine cAMP to distinct cellular compartments. However, measured rates of fast cAMP diffusion and slow PDE activity render cAMP compartmentalization essentially impossible. Using fluorescence spectroscopy, we show that, contrary to earlier data, cAMP at physiological concentrations is predominantly bound to cAMP binding sites and, thus, immobile. Binding and unbinding results in largely reduced cAMP dynamics, which we term "buffered diffusion." With a large fraction of cAMP being buffered, PDEs can create nanometer-size domains of low cAMP concentrations. Using FRET-cAMP nanorulers, we directly map cAMP gradients at the nanoscale around PDE molecules and the areas of resulting downstream activation of cAMP-dependent protein kinase (PKA). Our study reveals that spatiotemporal cAMP signaling is under precise control of nanometer-size domains shaped by PDEs that gate activation of downstream effectors.
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Affiliation(s)
- Andreas Bock
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany.
| | - Paolo Annibale
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Charlotte Konrad
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Annette Hannawacker
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Selma E Anton
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Isabella Maiellaro
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Ulrike Zabel
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Martin Falcke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Department of Physics, Humboldt University, Newtonstr. 15, 12489 Berlin, Germany
| | - Martin J Lohse
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany; Institute for Chemistry and Biochemistry, Free University, Takustr. 3, 14195 Berlin, Germany; ISAR Bioscience Institute, 82152 Munich/Planegg, Germany.
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31
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Li W, Hu J, Shi B, Palomba F, Digman MA, Gratton E, Jiang H. Biophysical properties of AKAP95 protein condensates regulate splicing and tumorigenesis. Nat Cell Biol 2020; 22:960-972. [PMID: 32719551 PMCID: PMC7425812 DOI: 10.1038/s41556-020-0550-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 06/24/2020] [Indexed: 12/14/2022]
Abstract
It remains unknown if biophysical or material properties of biomolecular condensates regulate cancer. Here we show that AKAP95, a nuclear protein that regulates transcription and RNA splicing, plays an important role in tumorigenesis by supporting cancer cell growth and suppressing oncogene-induced senescence. AKAP95 forms phase-separated and liquid-like condensates in vitro and in nucleus. Mutations of key residues to different amino acids perturb AKAP95 condensation in opposite directions. Importantly, the activity of AKAP95 in splice regulation is abolished by disruption of condensation, significantly impaired by hardening of condensates, and regained by substituting its condensation-mediating region with other condensation-mediating regions from irrelevant proteins. Moreover, the abilities of AKAP95 in regulating gene expression and supporting tumorigenesis require AKAP95 to form condensates with proper liquidity and dynamicity. These results link phase separation to tumorigenesis and uncover an important role of appropriate biophysical properties of protein condensates in gene regulation and cancer.
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Affiliation(s)
- Wei Li
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Jing Hu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Bi Shi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Francesco Palomba
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Michelle A Digman
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Enrico Gratton
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA.
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32
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Back to the Future: Genetically Encoded Fluorescent Proteins as Inert Tracers of the Intracellular Environment. Int J Mol Sci 2020; 21:ijms21114164. [PMID: 32545175 PMCID: PMC7312867 DOI: 10.3390/ijms21114164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 01/08/2023] Open
Abstract
Over the past decades, the discovery and development of genetically encoded fluorescent proteins (FPs) has brought a revolution into our ability to study biologic phenomena directly within living matter. First, FPs enabled fluorescence-labeling of a variety of molecules of interest to study their localization, interactions and dynamic behavior at various scales-from cells to whole organisms/animals. Then, rationally engineered FP-based sensors facilitated the measurement of physicochemical parameters of living matter-especially at the intracellular level, such as ion concentration, temperature, viscosity, pressure, etc. In addition, FPs were exploited as inert tracers of the intracellular environment in which they are expressed. This oft-neglected role is made possible by two distinctive features of FPs: (i) the quite null, unspecific interactions of their characteristic β-barrel structure with the molecular components of the cellular environment; and (ii) their compatibility with the use of time-resolved fluorescence-based optical microscopy techniques. This review seeks to highlight the potential of such unique combinations of properties and report on the most significative and original applications (and related advancements of knowledge) produced to date. It is envisioned that the use of FPs as inert tracers of living matter structural organization holds a potential for several lines of further development in the next future, discussed in the last section of the review, which in turn can lead to new breakthroughs in bioimaging.
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33
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Llorente García I, Marsh M. A biophysical perspective on receptor-mediated virus entry with a focus on HIV. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2020; 1862:183158. [PMID: 31863725 PMCID: PMC7156917 DOI: 10.1016/j.bbamem.2019.183158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/14/2022]
Abstract
As part of their entry and infection strategy, viruses interact with specific receptor molecules expressed on the surface of target cells. The efficiency and kinetics of the virus-receptor interactions required for a virus to productively infect a cell is determined by the biophysical properties of the receptors, which are in turn influenced by the receptors' plasma membrane (PM) environments. Currently, little is known about the biophysical properties of these receptor molecules or their engagement during virus binding and entry. Here we review virus-receptor interactions focusing on the human immunodeficiency virus type 1 (HIV), the etiological agent of acquired immunodeficiency syndrome (AIDS), as a model system. HIV is one of the best characterised enveloped viruses, with the identity, roles and structure of the key molecules required for infection well established. We review current knowledge of receptor-mediated HIV entry, addressing the properties of the HIV cell-surface receptors, the techniques used to measure these properties, and the macromolecular interactions and events required for virus entry. We discuss some of the key biophysical principles underlying receptor-mediated virus entry and attempt to interpret the available data in the context of biophysical mechanisms. We also highlight crucial outstanding questions and consider how new tools might be applied to advance understanding of the biophysical properties of viral receptors and the dynamic events leading to virus entry.
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Affiliation(s)
| | - Mark Marsh
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
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34
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Shaban HA, Seeber A. Monitoring global chromatin dynamics in response to DNA damage. Mutat Res 2020; 821:111707. [PMID: 32505939 DOI: 10.1016/j.mrfmmm.2020.111707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 05/08/2020] [Accepted: 05/16/2020] [Indexed: 02/08/2023]
Abstract
DNA damage induced global chromatin motion has been observed in yeast and mammalian cells. Currently, it is unclear what mechanisms may be driving these changes in whole genome dynamics. Recent advances in live-cell microscopy now enable chromatin motion to be quantified throughout the whole nucleus. In addition, much work has improved quantification of single particle trajectories. This topic is particularly important to the field of DNA repair as there are a large number of unanswered questions that can be tackled by monitoring global chromatin movement. Foremost, is how local DNA repair mechanisms interact and change global chromatin structure and whether this impacts repair pathway choice or efficiency. In this review, we describe methodologies to monitor global chromatin movement putting them into context with the DNA repair field highlighting how these techniques can drive new discoveries.
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Affiliation(s)
- Haitham A Shaban
- Center for Advanced Imaging, Harvard University, Cambridge, MA, 02138, USA; Spectroscopy Department, Physics Division, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Andrew Seeber
- Center for Advanced Imaging, Harvard University, Cambridge, MA, 02138, USA.
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35
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Sankaran J, Wohland T. Fluorescence strategies for mapping cell membrane dynamics and structures. APL Bioeng 2020; 4:020901. [PMID: 32478279 PMCID: PMC7228782 DOI: 10.1063/1.5143945] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/17/2020] [Indexed: 12/20/2022] Open
Abstract
Fluorescence spectroscopy has been a cornerstone of research in membrane dynamics and organization. Technological advances in fluorescence spectroscopy went hand in hand with discovery of various physicochemical properties of membranes at nanometric spatial and microsecond timescales. In this perspective, we discuss the various challenges associated with quantification of physicochemical properties of membranes and how various modes of fluorescence spectroscopy have overcome these challenges to shed light on the structure and organization of membranes. Finally, we discuss newer measurement strategies and data analysis tools to investigate the structure, dynamics, and organization of membranes.
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36
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Durso W, Martins M, Marchetti L, Cremisi F, Luin S, Cardarelli F. Lysosome Dynamic Properties during Neuronal Stem Cell Differentiation Studied by Spatiotemporal Fluctuation Spectroscopy and Organelle Tracking. Int J Mol Sci 2020; 21:ijms21093397. [PMID: 32403391 PMCID: PMC7247004 DOI: 10.3390/ijms21093397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 01/20/2023] Open
Abstract
We investigated lysosome dynamics during neuronal stem cell (NSC) differentiation by two quantitative and complementary biophysical methods based on fluorescence: imaging-derived mean square displacement (iMSD) and single-particle tracking (SPT). The former extracts the average dynamics and size of the whole population of moving lysosomes directly from imaging, with no need to calculate single trajectories; the latter resolves the finest heterogeneities and dynamic features at the single-lysosome level, which are lost in the iMSD analysis. In brief, iMSD analysis reveals that, from a structural point of view, lysosomes decrement in size during NSC differentiation, from 1 μm average diameter in the embryonic cells to approximately 500 nm diameter in the fully differentiated cells. Concomitantly, iMSD analysis highlights modification of key dynamic parameters, such as the average local organelle diffusivity and anomalous coefficient, which may parallel cytoskeleton remodeling during the differentiation process. From average to local, SPT allows mapping heterogeneous dynamic responses of single lysosomes in different districts of the cells. For instance, a dramatic decrease of lysosomal transport in the soma is followed by a rapid increase of transport in the projections at specific time points during neuronal differentiation, an observation compatible with the hypothesis that lysosomal active mobilization shifts from the soma to the newborn projections. Our combined results provide new insight into the lysosome size and dynamics regulation throughout NSC differentiation, supporting new functions proposed for this organelle.
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Affiliation(s)
- William Durso
- NEST Laboratory—Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy;
| | - Manuella Martins
- Bio@SNS Laboratory—Scuola Normale Superiore, via G. Moruzzi, 1, 56126 Pisa, Italy; (M.M.); (F.C.)
| | - Laura Marchetti
- Center for Nanotechnology Innovation@NEST (CNI@NEST), Piazza San Silvestro 12, 56126 Pisa, Italy;
| | - Federico Cremisi
- Bio@SNS Laboratory—Scuola Normale Superiore, via G. Moruzzi, 1, 56126 Pisa, Italy; (M.M.); (F.C.)
| | - Stefano Luin
- NEST Laboratory—Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy;
- NEST, Istituto Nanoscienze, CNR, Piazza San Silvestro 12, 56127 Pisa, Italy
- Correspondence: (S.L.); (F.C.)
| | - Francesco Cardarelli
- NEST Laboratory—Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy;
- Correspondence: (S.L.); (F.C.)
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Rodríguez-Suárez JM, Butler CS, Gershenson A, Lau BLT. Heterogeneous Diffusion of Polystyrene Nanoparticles through an Alginate Matrix: The Role of Cross-linking and Particle Size. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:5159-5166. [PMID: 32182039 DOI: 10.1021/acs.est.9b06113] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Most bacteria in natural and engineered environments grow and exist in biofilms. Recent investigations have shown that nanoparticles (NPs) interact with environmental biofilms, but these interactions are still not well characterized. Extracellular polymeric substances (EPS) are polymers secreted by bacteria to establish the functional and structural integrity of biofilms, and EPS porosity is a major contributor to NP access to and diffusion in biofilms. We used a synergistic combination of total internal reflection fluorescence microscopy and image correlation spectroscopy to monitor and map diffusion of fluorescent NPs in alginate yielding a detailed picture of the heterogeneous structure and connectivity of pores within a model EPS polymer. Using different sizes (20, 100, and 200 nm) of carboxylated polystyrene NPs, we examined how NP diffusive behaviors change as a result of calcium-induced cross-linking of the alginate matrix. This study reveals that cross-linking decreases NP diffusion coefficients and pore accessibility in an NP size-dependent manner and that NP movement through alginate matrices is anisotropic and heterogeneous. These results on heterogeneous and size-dependent movement within biofilms have important implications for future studies and simulations of NP-biofilm interactions.
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Affiliation(s)
- Joann M Rodríguez-Suárez
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst Massachusetts 01003, United States
| | - Caitlyn S Butler
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst Massachusetts 01003, United States
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst Massachusetts 01003, United States
| | - Boris L T Lau
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst Massachusetts 01003, United States
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38
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Shaban HA, Barth R, Recoules L, Bystricky K. Hi-D: nanoscale mapping of nuclear dynamics in single living cells. Genome Biol 2020; 21:95. [PMID: 32312289 PMCID: PMC7168861 DOI: 10.1186/s13059-020-02002-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 03/20/2020] [Indexed: 02/06/2023] Open
Abstract
Bulk chromatin motion has not been analyzed at high resolution. We present Hi-D, a method to quantitatively map dynamics of chromatin and abundant nuclear proteins for every pixel simultaneously over the entire nucleus from fluorescence image series. Hi-D combines reconstruction of chromatin motion and classification of local diffusion processes by Bayesian inference. We show that DNA dynamics in the nuclear interior are spatially partitioned into 0.3-3-μm domains in a mosaic-like pattern, uncoupled from chromatin compaction. This pattern was remodeled in response to transcriptional activity. Hi-D can be applied to any dense and bulk structures opening new perspectives towards understanding motion of nuclear molecules.
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Affiliation(s)
- Haitham A Shaban
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, University of Toulouse, UPS, 31062, Toulouse, France.
- Spectroscopy Department, Physics Division, National Research Centre, 33 El Bohouth Str., P.O. 12622, Cairo, Egypt.
| | - Roman Barth
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, University of Toulouse, UPS, 31062, Toulouse, France
- Present Address: Bionanoscience Department, Faculty of Applied Sciences, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Ludmila Recoules
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, University of Toulouse, UPS, 31062, Toulouse, France
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, University of Toulouse, UPS, 31062, Toulouse, France.
- Institut Universitaire de France (IUF), Paris, France.
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39
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Shaban HA, Seeber A. Monitoring the spatio-temporal organization and dynamics of the genome. Nucleic Acids Res 2020; 48:3423-3434. [PMID: 32123910 PMCID: PMC7144944 DOI: 10.1093/nar/gkaa135] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/17/2020] [Accepted: 02/23/2020] [Indexed: 12/22/2022] Open
Abstract
The spatio-temporal organization of chromatin in the eukaryotic cell nucleus is of vital importance for transcription, DNA replication and genome maintenance. Each of these activities is tightly regulated in both time and space. While we have a good understanding of chromatin organization in space, for example in fixed snapshots as a result of techniques like FISH and Hi-C, little is known about chromatin dynamics in living cells. The rapid development of flexible genomic loci imaging approaches can address fundamental questions on chromatin dynamics in a range of model organisms. Moreover, it is now possible to visualize not only single genomic loci but the whole genome simultaneously. These advances have opened many doors leading to insight into several nuclear processes including transcription and DNA repair. In this review, we discuss new chromatin imaging methods and how they have been applied to study transcription.
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Affiliation(s)
- Haitham A Shaban
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA
- Spectroscopy Department, Physics Division, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Andrew Seeber
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA
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40
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Yu S, Li F, Huang X, Dong C, Ren J. In Situ Study of Interactions between Endogenous c-myc mRNA with CRDBP in a Single Living Cell by Combining Fluorescence Cross-Correlation Spectroscopy with Molecular Beacons. Anal Chem 2020; 92:2988-2996. [DOI: 10.1021/acs.analchem.9b03934] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Shengrong Yu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Fucai Li
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Xiangyi Huang
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
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Runser A, Dujardin D, Ernst P, Klymchenko AS, Reisch A. Zwitterionic Stealth Dye-Loaded Polymer Nanoparticles for Intracellular Imaging. ACS APPLIED MATERIALS & INTERFACES 2020; 12:117-125. [PMID: 31872751 DOI: 10.1021/acsami.9b15396] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Intracellular applications of fluorescent nanoparticles (NPs) as probes and labels are currently limited by significant molecular crowding and the high level of complexity encountered inside living cells. The solution is to develop very small, bright, and noninteracting (stealth) NPs. Combining these properties requires implementing the stealth behavior through the thinnest possible hydrophilic shell. Here, we propose a one-step process for preparing ultrasmall and bright stealth NPs based on a zwitterionic (ZI) methacrylate-based copolymer. Dye-loaded polymer NPs are assembled through nanoprecipitation of the copolymer together with the salt of a rhodamine B derivative and a bulky hydrophobic counterion to achieve high particle brightness. We found that 10 mol % ZI groups in the polymer yield NPs of less than 15 nm that are stable in physiological salt conditions and practically resistant to protein adsorption, as suggested by fluorescence correlation spectroscopy. The combination of the very small size with the nonfouling nature of these particles enables spreading of ZI polymer NPs in the whole cytosol after their microinjection into living cells. In addition, single-particle tracking showed up to four times faster diffusion of ZI NPs in the cytosol compared to PEGylated NPs. The obtained dye-loaded ZI polymer NPs open the route to intracellular single-particle tracking and biosensing applications.
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Affiliation(s)
- Anne Runser
- Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie , CNRS UMR 7021, Université de Strasbourg , 67401 Illkirch Cedex , France
| | - Denis Dujardin
- Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie , CNRS UMR 7021, Université de Strasbourg , 67401 Illkirch Cedex , France
| | - Pauline Ernst
- Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie , CNRS UMR 7021, Université de Strasbourg , 67401 Illkirch Cedex , France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie , CNRS UMR 7021, Université de Strasbourg , 67401 Illkirch Cedex , France
| | - Andreas Reisch
- Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie , CNRS UMR 7021, Université de Strasbourg , 67401 Illkirch Cedex , France
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42
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Hedde PN, Staaf E, Singh SB, Johansson S, Gratton E. Pair Correlation Analysis Maps the Dynamic Two-Dimensional Organization of Natural Killer Cell Receptors at the Synapse. ACS NANO 2019; 13:14274-14282. [PMID: 31747251 PMCID: PMC8427743 DOI: 10.1021/acsnano.9b07486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In living systems, the contact between cells is the basis of recognition, differentiation, and orchestration of an immune response. Obstacles and barriers to biomolecular motion, especially for receptors at cellular synapses, critically control these functions by creating an anisotropic environment. Whereas conventional fluorescence fluctuation methods, such as fluorescence correlation spectroscopy or fluorescence recovery after photobleaching, can only measure the isotropic diffusion of molecules, the two-dimensional pair correlation function (2D-pCF) approach probes the anisotropic paths at different spatial locations within an image, allowing the creation of high-resolution maps that can visualize and quantify how molecules move in a living cell. In this work, we show how the 2D-pCF method maps the environment in cellular synapses as perceived by natural killer (NK) cell receptors. In cultured human HLA null 721.221 cells, 2D-pCF reveals the motion of inhibitory receptor HLA-Cw4-YFP coexpressed with KIR3DL1 to be highly directional around specific loci, while these restrictions were absent in the case of HLA-B51-YFP coexpressed with KIR2DL1. Further, in freshly isolated educated (H-2Dd) and uneducated (MHC-/-) primary murine NK cells, the 2D-pCF method shows significant differences in the paths taken by activating receptor NKp46 and inhibitory receptor Ly49A in educated compared to uneducated cells. Altogether, we demonstrate that the 2D-pCF method is very powerful in informing about the spatial organization of motion in cells. Our data support the hypothesis that flexibility in the spatial arrangement of membrane receptors, that is, the absence of barriers, is crucial for NK cell function.
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Affiliation(s)
- Per Niklas Hedde
- Laboratory
for Fluorescence Dynamics, University of
California Irvine, Irvine, California 92697, United States
- Department
of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii 96813, United States
- E-mail:
| | - Elina Staaf
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Sunitha Bagawath Singh
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Sofia Johansson
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Enrico Gratton
- Laboratory
for Fluorescence Dynamics, University of
California Irvine, Irvine, California 92697, United States
- E-mail: (lead contact)
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43
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Interferometric fluorescence cross correlation spectroscopy. PLoS One 2019; 14:e0225797. [PMID: 31851670 PMCID: PMC6919592 DOI: 10.1371/journal.pone.0225797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/12/2019] [Indexed: 11/20/2022] Open
Abstract
Measuring transport properties like diffusion and directional flow is essential for understanding dynamics within heterogeneous systems including living cells and novel materials. Fluorescent molecules traveling within these inhomogeneous environments under the forces of Brownian motion and flow exhibit fluctuations in their concentration, which are directly linked to the transport properties. We present a method utilizing single photon interference and fluorescence correlation spectroscopy (FCS) to simultaneously measure transport of fluorescent molecules within aqueous samples. Our method, within seconds, measures transport in thousands of homogenous voxels (100 nm)3 and under certain conditions, eliminates photo-physical artifacts associated with blinking of fluorescent molecules. A comprehensive theoretical framework is presented and validated by measuring transport of quantum dots, associated with VSV-G receptor along cellular membranes as well as within viscous gels.
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44
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Planes N, Vanderheyden PPML, Gratton E, Caballero-George C. Image mean square displacement to study the lateral mobility of Angiotensin II type 1 and Endothelin 1 type A receptors on living cells. Microsc Res Tech 2019; 83:381-392. [PMID: 31837080 DOI: 10.1002/jemt.23425] [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: 11/13/2019] [Accepted: 12/02/2019] [Indexed: 11/10/2022]
Abstract
The lateral mobility of membrane receptors provides insights into the molecular interactions of protein binding and the complex dynamic plasma membrane. The image mean square displacement (iMSD) analysis is a method used to extract qualitative and quantitative information of the protein diffusion law and infers how diffusion dynamic processes may change when the cellular environment is modified. The aim of the study was to describe the membrane diffusing properties of two G-protein-coupled receptors namely Angiotensin II type 1 (AT1 ) and Endothelin 1 type A (ETA ) receptors and their corresponding receptor-ligand complexes in living cells using total internal reflection fluorescent microscopy and iMSD analysis. This study showed that both AT1 and ETA receptors displayed a mix of three modes of diffusion: free, confined, and partially confined. The confined mode was the predominant at the plasma membrane of living cells and was not affected by ligand binding. However, the local diffusivity and the confinement zone of AT1 receptors were reduced by the binding of its antagonist losartan, and the long-range diffusion with the local diffusivity coefficient of ETA receptors was reduced upon exposure to its antagonist BQ123. To the best of our knowledge, this is the first study addressing the protein diffusion laws of these two receptors on living cells using total internal reflection fluorescence microscopy and iMSD.
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Affiliation(s)
- Nadir Planes
- Center of Innovation and Technology Transfer, Institute of Scientific Research and High Technology Services (INDICASAT AIP), Panama City, Panama.,Department of Biotechnology, Acharya Nagarjuna University, Guntur, Andhra Pradesh, India
| | | | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Catherina Caballero-George
- Center of Innovation and Technology Transfer, Institute of Scientific Research and High Technology Services (INDICASAT AIP), Panama City, Panama
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45
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Bohr SSR, Lund PM, Kallenbach AS, Pinholt H, Thomsen J, Iversen L, Svendsen A, Christensen SM, Hatzakis NS. Direct observation of Thermomyces lanuginosus lipase diffusional states by Single Particle Tracking and their remodeling by mutations and inhibition. Sci Rep 2019; 9:16169. [PMID: 31700110 PMCID: PMC6838188 DOI: 10.1038/s41598-019-52539-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/08/2019] [Indexed: 12/11/2022] Open
Abstract
Lipases are interfacially activated enzymes that catalyze the hydrolysis of ester bonds and constitute prime candidates for industrial and biotechnological applications ranging from detergent industry, to chiral organic synthesis. As a result, there is an incentive to understand the mechanisms underlying lipase activity at the molecular level, so as to be able to design new lipase variants with tailor-made functionalities. Our understanding of lipase function primarily relies on bulk assay averaging the behavior of a high number of enzymes masking structural dynamics and functional heterogeneities. Recent advances in single molecule techniques based on fluorogenic substrate analogues revealed the existence of lipase functional states, and furthermore so how they are remodeled by regulatory cues. Single particle studies of lipases on the other hand directly observed diffusional heterogeneities and suggested lipases to operate in two different modes. Here to decipher how mutations in the lid region controls Thermomyces lanuginosus lipase (TLL) diffusion and function we employed a Single Particle Tracking (SPT) assay to directly observe the spatiotemporal localization of TLL and rationally designed mutants on native substrate surfaces. Parallel imaging of thousands of individual TLL enzymes and HMM analysis allowed us to observe and quantify the diffusion, abundance and microscopic transition rates between three linearly interconverting diffusional states for each lipase. We proposed a model that correlate diffusion with function that allowed us to predict that lipase regulation, via mutations in lid region or product inhibition, primarily operates via biasing transitions to the active states.
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Affiliation(s)
- Søren S-R Bohr
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Philip M Lund
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Amalie S Kallenbach
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Henrik Pinholt
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Lars Iversen
- Novozymes A/S, Krogshøjsvej 36, DK 2880, Bagværd, Denmark
| | - Allan Svendsen
- Novozymes A/S, Krogshøjsvej 36, DK 2880, Bagværd, Denmark
| | | | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark.
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
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46
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An alternative framework for fluorescence correlation spectroscopy. Nat Commun 2019; 10:3662. [PMID: 31413259 PMCID: PMC6694112 DOI: 10.1038/s41467-019-11574-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
Fluorescence correlation spectroscopy (FCS), is a widely used tool routinely exploited for in vivo and in vitro applications. While FCS provides estimates of dynamical quantities, such as diffusion coefficients, it demands high signal to noise ratios and long time traces, typically in the minute range. In principle, the same information can be extracted from microseconds to seconds long time traces; however, an appropriate analysis method is missing. To overcome these limitations, we adapt novel tools inspired by Bayesian non-parametrics, which starts from the direct analysis of the observed photon counts. With this approach, we are able to analyze time traces, which are too short to be analyzed by existing methods, including FCS. Our new analysis extends the capability of single molecule fluorescence confocal microscopy approaches to probe processes several orders of magnitude faster and permits a reduction of photo-toxic effects on living samples induced by long periods of light exposure. Fluorescence correlation spectroscopy is widely used for in vivo and in vitro applications, yet extracting information from experiments still requires long acquisition times. Here, the authors exploit Bayesian non-parametrics to directly analyze the output of confocal fluorescence experiments thereby probing physical processes on much faster timescales.
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47
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Temperature Dependence of the Structure and Dynamics of a Dye-Labeled Lipid in a Planar Phospholipid Bilayer: A Computational Study. J Membr Biol 2019; 252:227-240. [PMID: 31332471 DOI: 10.1007/s00232-019-00081-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Abstract
Fluorescent probes are widely employed to label lipids for the investigation of structural and dynamic properties of model and cell membranes through optical microscopy techniques. Although the effect of tagging a lipid with an organic dye is generally assumed to be negligible, optically modified lipids can nonetheless affect the local lipid structure and, in turn, the lipid lateral mobility. To better assess this potential issue, all-atom (MD) molecular dynamics simulations have been performed to study structural and dynamic effects in a model DOPC membrane in the presence of a standard Rhodamine B-labeled DOPE lipid (RHB) as a function of temperature, i.e., 293 K, 303 K, and 320 K. As the temperature is increased, we observe similar changes in the structural properties of both pure DOPC and RHB-DOPC lipid bilayers: an increase of the area per lipid, a reduction of the membrane thickness and a decrease of lipid order parameters. The partial density profile of the RHB headgroups and their orientation within the lipid bilayer confirm the amphiphilic nature of the RHB fluorescent moiety, which mainly partitions in the DOPC glycerol backbone region at each temperature. Moreover, at all temperatures, our results on lipid lateral diffusion support a non-neutral role of the dye with respect to the unlabeled lipid mobility, thus suggesting important implications for optical microscopy studies of lipid membranes.
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48
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Fluorescence fluctuation spectroscopy: an invaluable microscopy tool for uncovering the biophysical rules for navigating the nuclear landscape. Biochem Soc Trans 2019; 47:1117-1129. [DOI: 10.1042/bst20180604] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Nuclear architecture is fundamental to the manner by which molecules traverse the nucleus. The nucleoplasm is a crowded environment where dynamic rearrangements in local chromatin compaction locally redefine the space accessible toward nuclear protein diffusion. Here, we review a suite of methods based on fluorescence fluctuation spectroscopy (FFS) and how they have been employed to interrogate chromatin organization, as well as the impact this structural framework has on nuclear protein target search. From first focusing on a set of studies that apply FFS to an inert fluorescent tracer diffusing inside the nucleus of a living cell, we demonstrate the capacity of this technology to measure the accessibility of the nucleoplasm. Then with a baseline understanding of the exploration volume available to nuclear proteins during target search, we review direct applications of FFS to fluorescently labeled transcription factors (TFs). FFS can detect changes in TF mobility due to DNA binding, as well as the formation of TF complexes via changes in brightness due to oligomerization. Collectively, we find that FFS-based methods can uncover how nuclear proteins in general navigate the nuclear landscape.
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Serfling R, Seidel L, Bock A, Lohse MJ, Annibale P, Coin I. Quantitative Single-Residue Bioorthogonal Labeling of G Protein-Coupled Receptors in Live Cells. ACS Chem Biol 2019; 14:1141-1149. [PMID: 31074969 DOI: 10.1021/acschembio.8b01115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
High-end microscopy studies of G protein-coupled receptors (GPCRs) require installing onto the receptors bright and photostable dyes. Labeling must occur in quantitative yields, to allow stoichiometric data analysis, and in a minimally invasive fashion, to avoid perturbing GPCR function. We demonstrate here that the genetic incorporation of trans-cyclooct-2-ene lysine (TCO*) allows achieving quantitative single-residue labeling of the extracellular loops of the β2-adrenergic and the muscarinic M2 class A GPCRs, as well as of the corticotropin releasing factor class B GPCR. Labeling occurs within a few minutes by reaction with dye-tetrazine conjugates on the surface of live cells and preserves the functionality of the receptors. To precisely quantify the labeling yields, we devise a method based on fluorescence fluctuation microscopy that extracts the number of labeling sites at the single-cell level. Further, we show that single-residue labeling is better suited for studies of GPCR diffusion than fluorescent-protein tags, since the latter can affect the mobility of the receptor. Finally, by performing dual-color competitive labeling on a single TCO* site, we devise a method to estimate the oligomerization state of a GPCR without the need for a biological monomeric reference, which facilitates the application of fluorescence methods to oligomerization studies. As TCO* and the dye-tetrazines used in this study are commercially available and the described microscopy techniques can be performed on a commercial microscope, we expect our approach to be widely applicable to fluorescence microscopy studies of membrane proteins in general.
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Affiliation(s)
- Robert Serfling
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
| | - Lisa Seidel
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
| | - Andreas Bock
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Martin J. Lohse
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Paolo Annibale
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Irene Coin
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
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Visualizing Biological Membrane Organization and Dynamics. J Mol Biol 2019; 431:1889-1919. [DOI: 10.1016/j.jmb.2019.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 11/22/2022]
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