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Townsend JA, Marty MT. What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry. Methods 2023; 218:1-13. [PMID: 37482149 PMCID: PMC10529358 DOI: 10.1016/j.ymeth.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.
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Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA.
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2
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Kenworthy AK. What's past is prologue: FRAP keeps delivering 50 years later. Biophys J 2023; 122:3577-3586. [PMID: 37218127 PMCID: PMC10541474 DOI: 10.1016/j.bpj.2023.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023] Open
Abstract
Fluorescence recovery after photobleaching (FRAP) has emerged as one of the most widely utilized techniques to quantify binding and diffusion kinetics of biomolecules in biophysics. Since its inception in the mid-1970s, FRAP has been used to address an enormous array of questions including the characteristic features of lipid rafts, how cells regulate the viscosity of their cytoplasm, and the dynamics of biomolecules inside condensates formed by liquid-liquid phase separation. In this perspective, I briefly summarize the history of the field and discuss why FRAP has proven to be so incredibly versatile and popular. Next, I provide an overview of the extensive body of knowledge that has emerged on best practices for quantitative FRAP data analysis, followed by some recent examples of biological lessons learned using this powerful approach. Finally, I touch on new directions and opportunities for biophysicists to contribute to the continued development of this still-relevant research tool.
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Affiliation(s)
- Anne K Kenworthy
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.
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3
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Srikantha N, Teijeiro-Gonzalez Y, Simpson A, Elsaid N, Somavarapu S, Suhling K, Jackson TL. Determining vitreous viscosity using fluorescence recovery after photobleaching. PLoS One 2022; 17:e0261925. [PMID: 35143514 PMCID: PMC8830689 DOI: 10.1371/journal.pone.0261925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 12/14/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Vitreous humor is a complex biofluid whose composition determines its structure and function. Vitreous viscosity will affect the delivery, distribution, and half-life of intraocular drugs, and key physiological molecules. The central pig vitreous is thought to closely match human vitreous viscosity. Diffusion is inversely related to viscosity, and diffusion is of fundamental importance for all biochemical reactions. Fluorescence Recovery After Photobleaching (FRAP) may provide a novel means of measuring intravitreal diffusion that could be applied to drugs and physiological macromolecules. It would also provide information about vitreous viscosity, which is relevant to drug elimination, and delivery. METHODS Vitreous viscosity and intravitreal macromolecular diffusion of fluorescently labelled macromolecules were investigated in porcine eyes using fluorescence recovery after photobleaching (FRAP). Fluorescein isothiocyanate conjugated (FITC) dextrans and ficolls of varying molecular weights (MWs), and FITC-bovine serum albumin (BSA) were employed using FRAP bleach areas of different diameters. RESULTS The mean (±standard deviation) viscosity of porcine vitreous using dextran, ficoll and BSA were 3.54 ± 1.40, 2.86 ± 1.13 and 4.54 ± 0.13 cP respectively, with an average of 3.65 ± 0.60 cP. CONCLUSIONS FRAP is a feasible and practical optical method to quantify the diffusion of macromolecules through vitreous.
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Affiliation(s)
- Nishanthan Srikantha
- School of Medicine, King’s College London, London, United Kingdom
- Department of Ophthalmology, King’s College Hospital, London, United Kingdom
- * E-mail:
| | | | - Andrew Simpson
- School of Medicine, King’s College London, London, United Kingdom
- Department of Ophthalmology, King’s College Hospital, London, United Kingdom
| | - Naba Elsaid
- Anglia Ruskin University, Bishop Hall Lane, Chelmsford, United Kingdom
| | - Satyanarayana Somavarapu
- Department of Pharmaceutics, University College London School of Pharmacy, London, United Kingdom
| | - Klaus Suhling
- Department of Physics, King’s College London, Strand, London, United Kingdom
| | - Timothy L. Jackson
- School of Medicine, King’s College London, London, United Kingdom
- Department of Ophthalmology, King’s College Hospital, London, United Kingdom
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4
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Line-FRAP, A Versatile Method to Measure Diffusion Rates In Vitro and In Vivo. J Mol Biol 2021; 433:166898. [PMID: 33647289 DOI: 10.1016/j.jmb.2021.166898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022]
Abstract
The crowded cellular milieu affect molecular diffusion through hard (occluded space) and soft (weak, non-specific) interactions. Multiple methods have been developed to measure diffusion coefficients at physiological protein concentrations within cells, each with its limitations. Here, we show that Line-FRAP, combined with rigours data analysis, is able to determine diffusion coefficients in a variety of environments, from in vitro to in vivo. The use of Line mode greatly improves time resolution of FRAP data acquisition, from 20-100 Hz in the classical mode to 800 Hz in the line mode. This improves data analysis, as intensity and radius of the bleach at the first post-bleach frame is critical. We evaluated the method on different proteins labelled chemically or fused to YFP in a wide range of environments. The diffusion coefficients measured in HeLa and in E. coli were ~2.5-fold and 15-fold slower than in buffer, and were comparable to previously published data. Increasing the osmotic pressure on E. coli further decreases diffusion, to the point at which proteins virtually stop moving. The method presented here, which requires a confocal microscope equipped with dual scanners, can be applied to study a large range of molecules with different sizes, and provides robust results in a wide range of environments and protein concentrations for fast diffusing molecules.
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Greig J, Bulgakova NA. Fluorescence Recovery After Photobleaching to Study the Dynamics of Membrane-Bound Proteins In Vivo Using the Drosophila Embryo. Methods Mol Biol 2021; 2179:145-159. [PMID: 32939719 DOI: 10.1007/978-1-0716-0779-4_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The epithelial-to-mesenchymal transition is a highly dynamic cell process and tools such as fluorescence recovery after photobleaching (FRAP), which allow the study of rapid protein dynamics, enable the following of this process in vivo. This technique uses a short intense pulse of photons to disrupt the fluorescence of a tagged protein in a region of a sample. The fluorescent signal intensity after this bleaching is then recorded and the signal recovery used to provide an indicator of the dynamics of the protein of interest. This technique can be applied to any fluorescently tagged protein, but membrane-bound proteins present an interesting challenge as they are spatially confined and subject to specialized cellular trafficking. Several methods of analysis can be applied which can disentangle these various processes and enable the extraction of information from the recovery curves. Here we describe this technique when applied to the quantification of the plasma membrane-bound E-cadherin protein in vivo using the epidermis of the late embryo of Drosophila melanogaster (Drosophila) as an example of this technique.
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Affiliation(s)
- Joshua Greig
- Department of Biomedical Science and Bateson Centre, The University of Sheffield, Sheffield, UK
| | - Natalia A Bulgakova
- Department of Biomedical Science and Bateson Centre, The University of Sheffield, Sheffield, UK.
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6
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Femia MR, Evans RM, Zhang J, Sun X, Lebegue CJ, Roggero VR, Allison LA. Mediator subunit MED1 modulates intranuclear dynamics of the thyroid hormone receptor. J Cell Biochem 2019; 121:2909-2926. [PMID: 31692077 DOI: 10.1002/jcb.29532] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022]
Abstract
The thyroid hormone receptors (TRs) mediate thyroid hormone (T3 )-dependent gene expression. The nuclear import and export signals that direct TR shuttling are well characterized, but little is known about factors modulating nuclear retention. We used fluorescence-based nucleocytoplasmic scoring and fluorescence recovery after photobleaching in transfected cells to investigate whether Mediator subunits MED1 and MED13 play a role in nuclear retention of TR. When MED1 was overexpressed, there was a striking shift towards a greater nuclear localization of TRβ1 and the oncoprotein v-ErbA, subtypes with cytosolic populations at steady-state, and TRβ1 intranuclear mobility was reduced. For TRα1, there was no observable change in its predominantly nuclear distribution pattern or mobility. Consistent with a role for MED1 in nuclear retention, the cytosolic TRα1 and TRβ1 population were significantly greater in MED1-/- cells, compared with MED1+/+ cells. Exposure to T3 and epidermal growth factor, which induces MED1 phosphorylation, also altered TR intranuclear dynamics. Overexpression of miR-208a, which downregulates MED13, led to a more cytosolic distribution of nuclear-localized TRα1; however, overexpression of MED13 had no effect on TRβ1 localization. The known binding site of MED1 overlaps with a transactivation domain and nuclear export signal in helix 12 of TR's ligand-binding domain (LBD). Coimmunoprecipitation assays demonstrated that TR's LBD interacts directly with exportins 5 and 7, suggesting that binding of exportins and MED1 to TR may be mutually exclusive. Collectively, our data provide evidence that MED1 promotes nuclear retention of TR, and highlight the dual functionality of helix 12 in TR transactivation and nuclear export.
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Affiliation(s)
- Matthew R Femia
- Department of Biology, William and Mary, Williamsburg, Viginia
| | | | - Jibo Zhang
- Department of Biology, William and Mary, Williamsburg, Viginia
| | - Xiaopeng Sun
- Department of Biology, William and Mary, Williamsburg, Viginia
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7
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Anyetei-Anum CS, Evans RM, Back AM, Roggero VR, Allison LA. Acetylation modulates thyroid hormone receptor intracellular localization and intranuclear mobility. Mol Cell Endocrinol 2019; 495:110509. [PMID: 31319097 PMCID: PMC6708479 DOI: 10.1016/j.mce.2019.110509] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/05/2019] [Accepted: 07/14/2019] [Indexed: 01/07/2023]
Abstract
The thyroid hormone receptor (TR) undergoes nucleocytoplasmic shuttling, but is primarily nuclear-localized and mediates expression of genes involved in development and homeostasis. Given the proximity of TR acetylation and sumoylation sites to nuclear localization (NLS) and nuclear export signals, we investigated their role in regulating intracellular localization. The nuclear/cytosolic fluorescence ratio (N/C) of fluorescent protein-tagged acetylation mimic, nonacetylation mimic, and sumoylation-deficient TR was quantified in transfected mammalian cells. While nonacetylation mimic and sumoylation-deficient TRs displayed wild-type N/C, the acetylation mimic's N/C was significantly lower. Importins that interact with wild-type TR also interact with acetylation and nonacetylation mimics, suggesting factors other than reduced importin binding alter nuclear localization. FRAP analysis showed wild-type intranuclear dynamics of acetylation mimic and sumoylation-deficient TRs, whereas the nonacetylation mimic had significantly reduced mobility and transcriptional activity. Acetyltransferase CBP/p300 inhibition enhanced TR's nuclear localization, further suggesting that nonacetylation correlates with nuclear retention, while acetylation promotes cytosolic localization.
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Affiliation(s)
- Cyril S Anyetei-Anum
- Department of Biology, College of William and Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23187, USA
| | - Rochelle M Evans
- Department of Biology, College of William and Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23187, USA
| | - Amanda M Back
- Department of Biology, College of William and Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23187, USA
| | - Vincent R Roggero
- Department of Biology, College of William and Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23187, USA
| | - Lizabeth A Allison
- Department of Biology, College of William and Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23187, USA.
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8
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Lippincott-Schwartz J, Snapp EL, Phair RD. The Development and Enhancement of FRAP as a Key Tool for Investigating Protein Dynamics. Biophys J 2018; 115:1146-1155. [PMID: 30219286 DOI: 10.1016/j.bpj.2018.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/27/2018] [Accepted: 08/06/2018] [Indexed: 01/18/2023] Open
Abstract
The saga of fluorescence recovery after photobleaching (FRAP) illustrates how disparate technical developments impact science. Starting with the classic 1976 Axelrod et al. work in Biophysical Journal, FRAP (originally fluorescence photobleaching recovery) opened the door to extraction of quantitative information from photobleaching experiments, laying the experimental and theoretical groundwork for quantifying both the mobility and the mobile fraction of a labeled population of proteins. Over the ensuing years, FRAP's reach dramatically expanded, with new developments in GFP technology and turn-key confocal microscopy, which enabled measurement of protein diffusion and binding/dissociation rates in virtually every compartment within the cell. The FRAP technique and data catalyzed an exchange of ideas between biophysicists studying membrane dynamics, cell biologists focused on intracellular dynamics, and systems biologists modeling the dynamics of cell activity. The outcome transformed the field of cellular biology, leading to a fundamental rethinking of long-held theories of cellular dynamism. Here, we review the pivotal FRAP studies that made these developments and conceptual changes possible, which gave rise to current models of complex cell dynamics.
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Affiliation(s)
| | - Erik Lee Snapp
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia.
| | - Robert D Phair
- Integrative Bioinformatics, Inc., Mountain View, California
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9
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Abstract
Cardiac transverse (t-) tubules carry both electrical excitation and solutes toward the cell center but their ability to transport small molecules is unclear. While fluorescence recovery after photobleaching (FRAP) can provide an approach to measure local solute movement, extraction of diffusion coefficients is confounded by cell and illumination beam geometries. In this study, we use measured cellular geometry and detailed computer modeling to derive the apparent diffusion coefficient of a 1-kDa solute inside the t-tubular system of rabbit and mouse ventricular cardiomyocytes. This approach shows that diffusion within individual t-tubules is more rapid than previously reported. T-tubule tortuosity, varicosities, and the presence of longitudinal elements combine to substantially reduce the apparent rate of solute movement. In steady state, large (>4 kDa) solutes did not freely fill the t-tubule lumen of both species and <50% of the t-tubule volume was available to solutes >70 kDa. Detailed model fitting of FRAP data suggests that solute diffusion is additionally restricted at the t-tubular entrance and this effect was larger in mouse than in rabbit. The possible structural basis of this effect was investigated using electron microscopy and tomography. Near the cell surface, mouse t-tubules are more tortuous and filled with an electron-dense ground substance, previously identified as glycocalyx and a polyanionic mesh. Solute movement in the t-tubule network of rabbit and mouse appears to be explained by their different geometric properties, which impacts the use of these species for understanding t-tubule function and the consequences of changes associated with t-tubule disease.
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10
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Bläßle A, Soh G, Braun T, Mörsdorf D, Preiß H, Jordan BM, Müller P. Quantitative diffusion measurements using the open-source software PyFRAP. Nat Commun 2018; 9:1582. [PMID: 29679054 PMCID: PMC5910415 DOI: 10.1038/s41467-018-03975-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 03/26/2018] [Indexed: 11/18/2022] Open
Abstract
Fluorescence Recovery After Photobleaching (FRAP) and inverse FRAP (iFRAP) assays can be used to assess the mobility of fluorescent molecules. These assays measure diffusion by monitoring the return of fluorescence in bleached regions (FRAP), or the dissipation of fluorescence from photoconverted regions (iFRAP). However, current FRAP/iFRAP analysis methods suffer from simplified assumptions about sample geometry, bleaching/photoconversion inhomogeneities, and the underlying reaction-diffusion kinetics. To address these shortcomings, we developed the software PyFRAP, which fits numerical simulations of three-dimensional models to FRAP/iFRAP data and accounts for bleaching/photoconversion inhomogeneities. Using PyFRAP we determined the diffusivities of fluorescent molecules spanning two orders of magnitude in molecular weight. We measured the tortuous effects that cell-like obstacles exert on effective diffusivity and show that reaction kinetics can be accounted for by model selection. These applications demonstrate the utility of PyFRAP, which can be widely adapted as a new extensible standard for FRAP analysis. FRAP analysis often relies on simplified assumptions that can affect measurement accuracy. Here the authors present a Python-based FRAP analysis software using simulations instead of simplified theoretical models to fit the data, which accounts for complex sample geometries and bleach conditions.
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Affiliation(s)
- Alexander Bläßle
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Gary Soh
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Theresa Braun
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany.,University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - David Mörsdorf
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Hannes Preiß
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Ben M Jordan
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany.
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11
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Prakash P, Pahal S, Varma M. Fluorescence Recovery after Photobleaching in Ultrathin Polymer Films. MACROMOL CHEM PHYS 2018. [DOI: 10.1002/macp.201700543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Praneet Prakash
- Center for Nano Science and Engineering; Indian Institute of Science; Bangalore 560012 India
| | - Suman Pahal
- Center for Nano Science and Engineering; Indian Institute of Science; Bangalore 560012 India
| | - Manoj Varma
- Center for Nano Science and Engineering; Indian Institute of Science; Bangalore 560012 India
- Robert Bosch Centre for Cyber Physical Systems; Indian Institute of Science; Bangalore 560012 India
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12
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Kitamura A, Kinjo M. Determination of diffusion coefficients in live cells using fluorescence recovery after photobleaching with wide-field fluorescence microscopy. Biophys Physicobiol 2018; 15:1-7. [PMID: 29450109 PMCID: PMC5812315 DOI: 10.2142/biophysico.15.0_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/25/2017] [Indexed: 12/23/2022] Open
Abstract
Fluorescence recovery after photobleaching (FRAP) enables characterization of quantitative dynamic properties such as diffusion coefficients of fluorescent molecules in living cells by analyzing the recovery of fluorescence intensity after photobleaching in a specific cellular compartment or area. To quantitatively determine high intracellular diffusion coefficients, a suitable optical system as well as an appropriate model for fast diffusion analysis is necessary. Here, we propose a procedure to quantify the diffusion coefficient of rapidly-diffusing fluorescent molecules that makes use of an epi-fluorescence microscope with a photobleaching laser in combination with established models for diffusion analysis. Analysis for the diffusion coefficients of tandemly oligomerized green flurescent proteins (GFPs) in living cells when changing the photobleaching times showed that photobleaching with shorter times than the diffusion speed indicated not the only way to obtain appropriate diffusion coefficients of fast-moving molecules. Our results also showed that the apparent spreading of the effective radius of the photobleached area works as a correction factor for determining appropriate diffusion coefficients of fast-moving molecules like monomeric GFPs. Our procedure provides a useful approach for quantitative measurement of diffusion coefficients in living cells. This procedure is relevant for characterizing dynamic molecular interactions, especially of fast-moving molecules, and is relevant for studies in many biological fields.
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Affiliation(s)
- Akira Kitamura
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
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13
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Sustr D, Hlaváček A, Duschl C, Volodkin D. Multi-Fractional Analysis of Molecular Diffusion in Polymer Multilayers by FRAP: A New Simulation-Based Approach. J Phys Chem B 2018; 122:1323-1333. [PMID: 29257689 DOI: 10.1021/acs.jpcb.7b11051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Comprehensive analysis of the multifractional molecular diffusion provides a deeper understanding of the diffusion phenomenon in the fields of material science, molecular and cell biology, advanced biomaterials, etc. Fluorescence recovery after photobleaching (FRAP) is commonly employed to probe the molecular diffusion. Despite FRAP being a very popular method, it is not easy to assess multifractional molecular diffusion due to limited possibilities of approaches for analysis. Here we present a novel simulation-optimization-based approach (S-approach) that significantly broadens possibilities of the analysis. In the S-approach, possible fluorescence recovery scenarios are primarily simulated and afterward compared with a real measurement while optimizing parameters of a model until a sufficient match is achieved. This makes it possible to reveal multifractional molecular diffusion. Fluorescent latex particles of different size and fluorescein isothiocyanate in an aqueous medium were utilized as test systems. Finally, the S-approach has been used to evaluate diffusion of cytochrome c loaded into multilayers made of hyaluronan and polylysine. Software for evaluation of multifractional molecular diffusion by S-approach has been developed aiming to offer maximal versatility and user-friendly way for analysis.
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Affiliation(s)
- David Sustr
- Faculty of Science, University of Potsdam, Institute of Biochemistry and Biology , Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.,Department of Molecular and Cellular Bioanalytics, Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI) , Am Mühlenberg 13, 14476 Potsdam-Golm, Germany
| | - Antonín Hlaváček
- Institute of Analytical Chemistry of the Czech Academy of Sciences , v. v. i., Veveří 97, Brno 602 00, Czech Republic
| | - Claus Duschl
- Department of Molecular and Cellular Bioanalytics, Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI) , Am Mühlenberg 13, 14476 Potsdam-Golm, Germany
| | - Dmitry Volodkin
- Department of Molecular and Cellular Bioanalytics, Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI) , Am Mühlenberg 13, 14476 Potsdam-Golm, Germany.,School of Science and Technology, Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS, United Kingdom
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14
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Fradin C. On the importance of protein diffusion in biological systems: The example of the Bicoid morphogen gradient. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1676-1686. [PMID: 28919007 DOI: 10.1016/j.bbapap.2017.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 08/16/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
Morphogens are proteins that form concentration gradients in embryos and developing tissues, where they act as postal codes, providing cells with positional information and allowing them to behave accordingly. Bicoid was the first discovered morphogen, and remains one of the most studied. It regulates segmentation in flies, forming a striking exponential gradient along the anterior-posterior axis of early Drosophila embryos, and activating the transcription of multiple target genes in a concentration-dependent manner. In this review, the work done by us and by others to characterize the mobility of Bicoid in D. melanogaster embryos is presented. The central role played by the diffusion of Bicoid in both the establishment of the gradient and the activation of target genes is discussed, and placed in the context of the need for these processes to be all at once rapid, precise and robust. The Bicoid system, and morphogen gradients in general, remain amongst the most amazing examples of the coexistence, often observed in living systems, of small-scale disorder and large-scale spatial order. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Cécile Fradin
- Dept. of Physics and Astronomy, McMaster University, 1280 Main St W., Hamilton, ON L8S 4M1, Canada
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15
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Basset A, Bouthemy P, Boulanger J, Waharte F, Salamero J, Kervrann C. An extended model of vesicle fusion at the plasma membrane to estimate protein lateral diffusion from TIRF microscopy images. BMC Bioinformatics 2017; 18:352. [PMID: 28738814 PMCID: PMC5525284 DOI: 10.1186/s12859-017-1765-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Characterizing membrane dynamics is a key issue to understand cell exchanges with the extra-cellular medium. Total internal reflection fluorescence microscopy (TIRFM) is well suited to focus on the late steps of exocytosis at the plasma membrane. However, it is still a challenging task to quantify (lateral) diffusion and estimate local dynamics of proteins. RESULTS A new model was introduced to represent the behavior of cargo transmembrane proteins during the vesicle fusion to the plasma membrane at the end of the exocytosis process. Two biophysical parameters, the diffusion coefficient and the release rate parameter, are automatically estimated from TIRFM image sequences, to account for both the lateral diffusion of molecules at the membrane and the continuous release of the proteins from the vesicle to the plasma membrane. Quantitative evaluation on 300 realistic computer-generated image sequences demonstrated the efficiency and accuracy of the method. The application of our method on 16 real TIRFM image sequences additionally revealed differences in the dynamic behavior of Transferrin Receptor (TfR) and Langerin proteins. CONCLUSION An automated method has been designed to simultaneously estimate the diffusion coefficient and the release rate for each individual vesicle fusion event at the plasma membrane in TIRFM image sequences. It can be exploited for further deciphering cell membrane dynamics.
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Affiliation(s)
- Antoine Basset
- Inria, Campus de Beaulieu, Rennes, 35042 France
- CNES, 18 avenue Edouard Belin, Toulouse, 31401 France
| | | | - Jérôme Boulanger
- Institut Curie, PSL Research University, CNRS UMR 144 and PICT-Cell and Tissue Imaging Facility, 12 rue Lhomond, Paris, 75005 France
- MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, CBC Cambridge Biomedical Campus, Cambridge, CB2 0QH UK
| | - François Waharte
- Institut Curie, PSL Research University, CNRS UMR 144 and PICT-Cell and Tissue Imaging Facility, 12 rue Lhomond, Paris, 75005 France
| | - Jean Salamero
- Institut Curie, PSL Research University, CNRS UMR 144 and PICT-Cell and Tissue Imaging Facility, 12 rue Lhomond, Paris, 75005 France
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16
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Ciocanel MV, Kreiling JA, Gagnon JA, Mowry KL, Sandstede B. Analysis of Active Transport by Fluorescence Recovery after Photobleaching. Biophys J 2017; 112:1714-1725. [PMID: 28445762 PMCID: PMC5406284 DOI: 10.1016/j.bpj.2017.02.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 02/17/2017] [Accepted: 02/27/2017] [Indexed: 12/11/2022] Open
Abstract
Fluorescence recovery after photobleaching (FRAP) is a well-established experimental technique to study binding and diffusion of molecules in cells. Although a large number of analytical and numerical models have been developed to extract binding and diffusion rates from FRAP recovery curves, active transport of molecules is typically not included in the existing models that are used to estimate these rates. Here we present a validated numerical method for estimating diffusion, binding/unbinding rates, and active transport velocities using FRAP data that captures intracellular dynamics through partial differential equation models. We apply these methods to transport and localization of mRNA molecules in Xenopus laevis oocytes, where active transport processes are essential to generate developmental polarity. By providing estimates of the effective velocities and diffusion, as well as expected run times and lengths, this approach can help quantify dynamical properties of localizing and nonlocalizing RNA. Our results confirm the distinct transport dynamics in different regions of the cytoplasm, and suggest that RNA movement in both the animal and vegetal directions may influence the timescale of RNA localization in Xenopus oocytes. We also show that model initial conditions extracted from FRAP postbleach intensities prevent underestimation of diffusion, which can arise from the instantaneous bleaching assumption. The numerical and modeling approach presented here to estimate parameters using FRAP recovery data is a broadly applicable tool for systems where intracellular transport is a key molecular mechanism.
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Affiliation(s)
| | - Jill A Kreiling
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - James A Gagnon
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | - Kimberly L Mowry
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Björn Sandstede
- Division of Applied Mathematics, Brown University, Providence, Rhode Island.
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17
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G-protein coupling and nuclear translocation of the human abscisic acid receptor LANCL2. Sci Rep 2016; 6:26658. [PMID: 27222287 PMCID: PMC4879523 DOI: 10.1038/srep26658] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/27/2016] [Indexed: 02/03/2023] Open
Abstract
Abscisic acid (ABA), a long known phytohormone, has been recently demonstrated to be present also in humans, where it targets cells of the innate immune response, mesenchymal and hemopoietic stem cells and cells involved in the regulation of systemic glucose homeostasis. LANCL2, a peripheral membrane protein, is the mammalian ABA receptor. We show that N-terminal glycine myristoylation causes LANCL2 localization to the plasmamembrane and to cytoplasmic membrane vesicles, where it interacts with the α subunit of a Gi protein and starts the ABA signaling pathway via activation of adenylate cyclase. Demyristoylation of LANCL2 by chemical or genetic means triggers its nuclear translocation. Nuclear enrichment of native LANCL2 is also induced by ABA treatment. Therefore human LANCL2 is a non-transmembrane G protein-coupled receptor susceptible to hormone-induced nuclear translocation.
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18
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Amor R, McDonald A, Trägårdh J, Robb G, Wilson L, Abdul Rahman NZ, Dempster J, Amos WB, Bushell TJ, McConnell G. Widefield Two-Photon Excitation without Scanning: Live Cell Microscopy with High Time Resolution and Low Photo-Bleaching. PLoS One 2016; 11:e0147115. [PMID: 26824845 PMCID: PMC4732674 DOI: 10.1371/journal.pone.0147115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 11/16/2015] [Indexed: 12/16/2022] Open
Abstract
We demonstrate fluorescence imaging by two-photon excitation without scanning in biological specimens as previously described by Hwang and co-workers, but with an increased field size and with framing rates of up to 100 Hz. During recordings of synaptically-driven Ca(2+) events in primary rat hippocampal neurone cultures loaded with the fluorescent Ca(2+) indicator Fluo-4 AM, we have observed greatly reduced photo-bleaching in comparison with single-photon excitation. This method, which requires no costly additions to the microscope, promises to be useful for work where high time-resolution is required.
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Affiliation(s)
- Rumelo Amor
- Centre for Biophotonics, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- * E-mail:
| | - Alison McDonald
- Centre for Biophotonics, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Johanna Trägårdh
- Centre for Biophotonics, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Gillian Robb
- Centre for Biophotonics, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Louise Wilson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Nor Zaihana Abdul Rahman
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - John Dempster
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - William Bradshaw Amos
- Centre for Biophotonics, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Trevor J. Bushell
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Gail McConnell
- Centre for Biophotonics, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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19
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Guigas G, Weiss M. Effects of protein crowding on membrane systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:2441-2450. [PMID: 26724385 DOI: 10.1016/j.bbamem.2015.12.021] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/19/2015] [Accepted: 12/21/2015] [Indexed: 10/22/2022]
Abstract
Cellular membranes are typically decorated with a plethora of embedded and adsorbed macromolecules, e.g. proteins, that participate in numerous vital processes. With typical surface densities of 30,000 proteins per μm(2) cellular membranes are indeed crowded places that leave only few nanometers of private space for individual proteins. Here, we review recent advances in our understanding of protein crowding in membrane systems. We first give a brief overview on state-of-the-art approaches in experiment and simulation that are frequently used to study crowded membranes. After that, we review how crowding can affect diffusive transport of proteins and lipids in membrane systems. Next, we discuss lipid and protein sorting in crowded membrane systems, including effects like protein cluster formation, phase segregation, and lipid droplet formation. Subsequently, we highlight recent progress in uncovering crowding-induced conformational changes of membranes, e.g. membrane budding and vesicle formation. Finally, we give a short outlook on potential future developments in the field of crowded membrane systems. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Gernot Guigas
- Experimental Physics I, Universitaetsstr. 30, Bayreuth University, D-95440 Bayreuth, Germany
| | - Matthias Weiss
- Experimental Physics I, Universitaetsstr. 30, Bayreuth University, D-95440 Bayreuth, Germany.
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20
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Bajanca F, Gonzalez-Perez V, Gillespie SJ, Beley C, Garcia L, Theveneau E, Sear RP, Hughes SM. In vivo dynamics of skeletal muscle Dystrophin in zebrafish embryos revealed by improved FRAP analysis. eLife 2015; 4. [PMID: 26459831 PMCID: PMC4601390 DOI: 10.7554/elife.06541] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 09/10/2015] [Indexed: 12/30/2022] Open
Abstract
Dystrophin forms an essential link between sarcolemma and cytoskeleton, perturbation of which causes muscular dystrophy. We analysed Dystrophin binding dynamics in vivo for the first time. Within maturing fibres of host zebrafish embryos, our analysis reveals a pool of diffusible Dystrophin and complexes bound at the fibre membrane. Combining modelling, an improved FRAP methodology and direct semi-quantitative analysis of bleaching suggests the existence of two membrane-bound Dystrophin populations with widely differing bound lifetimes: a stable, tightly bound pool, and a dynamic bound pool with high turnover rate that exchanges with the cytoplasmic pool. The three populations were found consistently in human and zebrafish Dystrophins overexpressed in wild-type or dmd(ta222a/ta222a) zebrafish embryos, which lack Dystrophin, and in Gt(dmd-Citrine)(ct90a) that express endogenously-driven tagged zebrafish Dystrophin. These results lead to a new model for Dystrophin membrane association in developing muscle, and highlight our methodology as a valuable strategy for in vivo analysis of complex protein dynamics.
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Affiliation(s)
- Fernanda Bajanca
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.,CNRS and Université Paul Sabatier, Toulouse, France
| | | | - Sean J Gillespie
- Department of Physics, University of Surrey, Guildford, United Kingdom
| | - Cyriaque Beley
- Université Versailles Saint-Quentin, Montigny-le-Bretonneux, France.,Laboratoire International Associé-Biologie appliquée aux handicaps neuromusculaires, Centre Scientifique de Monaco, Monaco, Monaco
| | - Luis Garcia
- Université Versailles Saint-Quentin, Montigny-le-Bretonneux, France.,Laboratoire International Associé-Biologie appliquée aux handicaps neuromusculaires, Centre Scientifique de Monaco, Monaco, Monaco
| | | | - Richard P Sear
- Department of Physics, University of Surrey, Guildford, United Kingdom
| | - Simon M Hughes
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
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21
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Verissimo F, Halavatyi A, Pepperkok R, Weiss M. A microtubule-independent role of p150glued in secretory cargo concentration at endoplasmic reticulum exit sites. J Cell Sci 2015; 128:4160-70. [PMID: 26459637 DOI: 10.1242/jcs.172395] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/05/2015] [Indexed: 01/08/2023] Open
Abstract
Newly synthesized proteins are sorted into COPII-coated transport carriers at the endoplasmic reticulum (ER). Assembly of the COPII coat complex, which occurs at ER exit sites (ERES), is initiated by membrane association and GTP loading of SAR1, followed by the recruitment of the SEC23-SEC24 and SEC13-SEC31 subcomplexes. Both of these two subcomplexes stimulate GTP hydrolysis and coat disassembly. This inherent disassembly capacity of COPII complexes needs to be regulated to allow sufficient time for cargo sorting and transport carrier formation. By performing fluorescence recovery after photobleaching (FRAP) and mathematical modeling, we show that p150(glued) (also known as DCTN1), a component of the dynactin complex, stabilizes the COPII pre-budding complex on ER membranes in a microtubule-independent manner. Concentration of the secretory marker ts-O45-G at ERES is reduced in the presence of a C-terminal p150(glued) fragment that prevents binding of endogenous p150(glued) to SEC23. A similar cargo reduction is observed upon p150(glued) knockdown. Taken together, our data suggest that cargo concentration at ERES is regulated by p150(glued) to coordinate protein sorting and transport carrier formation with the subsequent long-range transport towards the Golgi complex along microtubules.
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Affiliation(s)
- Fatima Verissimo
- Cell Biology and Biophysics Unit, EMBL, Meyerhofstraße 1, Heidelberg D-69117, Germany
| | - Aliaksandr Halavatyi
- Cell Biology and Biophysics Unit, EMBL, Meyerhofstraße 1, Heidelberg D-69117, Germany
| | - Rainer Pepperkok
- Cell Biology and Biophysics Unit, EMBL, Meyerhofstraße 1, Heidelberg D-69117, Germany
| | - Matthias Weiss
- Experimental Physics I, Universitaetsstr. 30, University of Bayreuth, Bayreuth D-95440, Germany
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22
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Fluorescence recovery after photobleaching in material and life sciences: putting theory into practice. Q Rev Biophys 2015; 48:323-87. [PMID: 26314367 DOI: 10.1017/s0033583515000013] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
AbstractFluorescence recovery after photobleaching (FRAP) is a versatile tool for determining diffusion and interaction/binding properties in biological and material sciences. An understanding of the mechanisms controlling the diffusion requires a deep understanding of structure–interaction–diffusion relationships. In cell biology, for instance, this applies to the movement of proteins and lipids in the plasma membrane, cytoplasm and nucleus. In industrial applications related to pharmaceutics, foods, textiles, hygiene products and cosmetics, the diffusion of solutes and solvent molecules contributes strongly to the properties and functionality of the final product. All these systems are heterogeneous, and accurate quantification of the mass transport processes at the local level is therefore essential to the understanding of the properties of soft (bio)materials. FRAP is a commonly used fluorescence microscopy-based technique to determine local molecular transport at the micrometer scale. A brief high-intensity laser pulse is locally applied to the sample, causing substantial photobleaching of the fluorescent molecules within the illuminated area. This causes a local concentration gradient of fluorescent molecules, leading to diffusional influx of intact fluorophores from the local surroundings into the bleached area. Quantitative information on the molecular transport can be extracted from the time evolution of the fluorescence recovery in the bleached area using a suitable model. A multitude of FRAP models has been developed over the years, each based on specific assumptions. This makes it challenging for the non-specialist to decide which model is best suited for a particular application. Furthermore, there are many subtleties in performing accurate FRAP experiments. For these reasons, this review aims to provide an extensive tutorial covering the essential theoretical and practical aspects so as to enable accurate quantitative FRAP experiments for molecular transport measurements in soft (bio)materials.
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23
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Kang M, Andreani M, Kenworthy AK. Validation of Normalizations, Scaling, and Photofading Corrections for FRAP Data Analysis. PLoS One 2015; 10:e0127966. [PMID: 26017223 PMCID: PMC4446327 DOI: 10.1371/journal.pone.0127966] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 04/22/2015] [Indexed: 01/14/2023] Open
Abstract
Fluorescence Recovery After Photobleaching (FRAP) has been a versatile tool to study transport and reaction kinetics in live cells. Since the fluorescence data generated by fluorescence microscopy are in a relative scale, a wide variety of scalings and normalizations are used in quantitative FRAP analysis. Scaling and normalization are often required to account for inherent properties of diffusing biomolecules of interest or photochemical properties of the fluorescent tag such as mobile fraction or photofading during image acquisition. In some cases, scaling and normalization are also used for computational simplicity. However, to our best knowledge, the validity of those various forms of scaling and normalization has not been studied in a rigorous manner. In this study, we investigate the validity of various scalings and normalizations that have appeared in the literature to calculate mobile fractions and correct for photofading and assess their consistency with FRAP equations. As a test case, we consider linear or affine scaling of normal or anomalous diffusion FRAP equations in combination with scaling for immobile fractions. We also consider exponential scaling of either FRAP equations or FRAP data to correct for photofading. Using a combination of theoretical and experimental approaches, we show that compatible scaling schemes should be applied in the correct sequential order; otherwise, erroneous results may be obtained. We propose a hierarchical workflow to carry out FRAP data analysis and discuss the broader implications of our findings for FRAP data analysis using a variety of kinetic models.
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Affiliation(s)
- Minchul Kang
- School of Science, Technology & Engineering Management, St. Thomas University, Miami Gardens, Florida, USA
- * E-mail:
| | - Manuel Andreani
- School of Science, Technology & Engineering Management, St. Thomas University, Miami Gardens, Florida, USA
| | - Anne K. Kenworthy
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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24
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Dissecting protein reaction dynamics in living cells by fluorescence recovery after photobleaching. Nat Protoc 2015; 10:660-80. [DOI: 10.1038/nprot.2015.042] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Kiskin NI, Babich V, Knipe L, Hannah MJ, Carter T. Differential cargo mobilisation within Weibel-Palade bodies after transient fusion with the plasma membrane. PLoS One 2014; 9:e108093. [PMID: 25233365 PMCID: PMC4169479 DOI: 10.1371/journal.pone.0108093] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 08/19/2014] [Indexed: 01/13/2023] Open
Abstract
Inflammatory chemokines can be selectively released from Weibel-Palade bodies (WPBs) during kiss-and-run exocytosis. Such selectivity may arise from molecular size filtering by the fusion pore, however differential intra-WPB cargo re-mobilisation following fusion-induced structural changes within the WPB may also contribute to this process. To determine whether WPB cargo molecules are differentially re-mobilised, we applied FRAP to residual post-fusion WPB structures formed after transient exocytosis in which some or all of the fluorescent cargo was retained. Transient fusion resulted in WPB collapse from a rod to a spheroid shape accompanied by substantial swelling (>2 times by surface area) and membrane mixing between the WPB and plasma membranes. Post-fusion WPBs supported cumulative WPB exocytosis. To quantify diffusion inside rounded organelles we developed a method of FRAP analysis based on image moments. FRAP analysis showed that von Willebrand factor-EGFP (VWF-EGFP) and the VWF-propolypeptide-EGFP (Pro-EGFP) were immobile in post-fusion WPBs. Because Eotaxin-3-EGFP and ssEGFP (small soluble cargo proteins) were largely depleted from post-fusion WPBs, we studied these molecules in cells preincubated in the weak base NH4Cl which caused WPB alkalinisation and rounding similar to that produced by plasma membrane fusion. In these cells we found a dramatic increase in mobilities of Eotaxin-3-EGFP and ssEGFP that exceeded the resolution of our method (∼ 2.4 µm2/s mean). In contrast, the membrane mobilities of EGFP-CD63 and EGFP-Rab27A in post-fusion WPBs were unchanged, while P-selectin-EGFP acquired mobility. Our data suggest that selective re-mobilisation of chemokines during transient fusion contributes to selective chemokine secretion during transient WPB exocytosis. Selective secretion provides a mechanism to regulate intravascular inflammatory processes with reduced risk of thrombosis.
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Affiliation(s)
- Nikolai I. Kiskin
- Division of Physical Biochemistry, Medical Research Council National Institute for Medical Research, London, United Kingdom
- Division of Neurophysiology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Victor Babich
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Laura Knipe
- Division of Physical Biochemistry, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Matthew J. Hannah
- Microbiology Services Colindale, Public Health England, London, United Kingdom
| | - Tom Carter
- Division of Physical Biochemistry, Medical Research Council National Institute for Medical Research, London, United Kingdom
- Cardiovascular and Cell Sciences Research Institute, St George’s University, London, United Kingdom
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26
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Solanko LM, Honigmann A, Midtiby HS, Lund FW, Brewer JR, Dekaris V, Bittman R, Eggeling C, Wüstner D. Membrane orientation and lateral diffusion of BODIPY-cholesterol as a function of probe structure. Biophys J 2014; 105:2082-92. [PMID: 24209853 DOI: 10.1016/j.bpj.2013.09.031] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/26/2013] [Accepted: 09/16/2013] [Indexed: 11/29/2022] Open
Abstract
Cholesterol tagged with the BODIPY fluorophore via the central difluoroboron moiety of the dye (B-Chol) is a promising probe for studying intracellular cholesterol dynamics. We synthesized a new BODIPY-cholesterol probe (B-P-Chol) with the fluorophore attached via one of its pyrrole rings to carbon-24 of cholesterol (B-P-Chol). Using two-photon fluorescence polarimetry in giant unilamellar vesicles and in the plasma membrane (PM) of living intact and actin-disrupted cells, we show that the BODIPY-groups in B-Chol and B-P-Chol are oriented perpendicular and almost parallel to the bilayer normal, respectively. B-Chol is in all three membrane systems much stronger oriented than B-P-Chol. Interestingly, we found that the lateral diffusion in the PM was two times slower for B-Chol than for B-P-Chol, although we found no difference in lateral diffusion in model membranes. Stimulated emission depletion microscopy, performed for the first time, to our knowledge, with fluorescent sterols, revealed that the difference in lateral diffusion of the BODIPY-cholesterol probes was not caused by anomalous subdiffusion, because diffusion of both analogs in the PM was free but not hindered. Our combined measurements show that the position and orientation of the BODIPY moiety in cholesterol analogs have a severe influence on lateral diffusion specifically in the PM of living cells.
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Affiliation(s)
- Lukasz M Solanko
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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27
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Wachsmuth M. Molecular diffusion and binding analyzed with FRAP. PROTOPLASMA 2014; 251:373-382. [PMID: 24390250 DOI: 10.1007/s00709-013-0604-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 12/16/2013] [Indexed: 06/03/2023]
Abstract
Intracellular molecular transport and localization are crucial for cells (plant cells as much as mammalian cells) to proliferate and to adapt to diverse environmental conditions. Here, some aspects of the microscopy-based method of fluorescence recovery after photobleaching (FRAP) are introduced. In the course of the last years, this has become a very powerful tool to study dynamic processes in living cells and tissue, and it is expected to experience further increasing demand because quantitative information on biological systems becomes more and more important. This review introduces the FRAP methodology, including some theoretical background, describes challenges and pitfalls, and presents some recent advanced applications.
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Affiliation(s)
- Malte Wachsmuth
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany,
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28
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Weiss M. Crowding, Diffusion, and Biochemical Reactions. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:383-417. [DOI: 10.1016/b978-0-12-800046-5.00011-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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29
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Abstract
Microscopic imaging techniques play a pivotal role in the life sciences. Here we describe labeling and imaging methods for live yeast cell imaging. Yeast is an excellent reference organism for biomedical research to investigate fundamental cellular processes, and has gained great popularity also for large-scale imaging-based screens. Methods are described to label live yeast cells with organelle-specific fluorescent dyes or GFP-tagged proteins, and how cells are maintained viable over extended periods of time during microscopy. We point out common pitfalls and potential microscopy artifacts arising from inhomogeneous labeling and depending on cellular physiology. Application and limitation of bleaching techniques to address dynamic processes in the yeast cell are described.
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Affiliation(s)
- Heimo Wolinski
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
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30
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Mai J, Trump S, Lehmann I, Attinger S. Parameter importance in FRAP acquisition and analysis: a simulation approach. Biophys J 2013; 104:2089-97. [PMID: 23663852 DOI: 10.1016/j.bpj.2013.03.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 11/24/2022] Open
Abstract
Fluorescence recovery after photobleaching (FRAP) is a widespread technique used to determine intracellular reaction and diffusion parameters. In recent years, due to technical advances and an increasing number of mathematical models for analysis, there was a resurging interest in FRAP applications. However, care has to be taken when inverting parameters from such data. We study potential influences on FRAP acquisition and analysis like initial fluorescence distribution, membrane passage, and geometrical aspects. Monte Carlo simulations are employed for the investigation of reaction-diffusion processes to additionally include cases in which no analytical description is available. To assess the importance of influencing factors we apply a sensitivity method based on elementary effects providing an estimate for the global parameter space. The combination of simulations and sensitivity measure helps us to predict ranges of parameters used in acquisition and analysis for which a reliably inversion of reaction-diffusion parameters is possible. Using this approach, we show that FRAP data are highly susceptible to misinterpretation. However, by identifying the parameters of susceptibility, our analysis provides the means for taking measures to significantly improve FRAP data interpretation and analysis.
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Affiliation(s)
- Juliane Mai
- Department of Computational Hydrosystems, Helmholtz Centre for Environmental Research, Leipzig, Germany.
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31
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Diffusion and binding analyzed with combined point FRAP and FCS. Cytometry A 2013; 83:876-89. [DOI: 10.1002/cyto.a.22316] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 03/13/2013] [Accepted: 05/12/2013] [Indexed: 01/13/2023]
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32
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Quantitative image analysis approaches for probing Rab GTPase localization and function in mammalian cells. Biochem Soc Trans 2013; 40:1389-93. [PMID: 23176486 DOI: 10.1042/bst20120145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Membrane traffic pathways play an essential role in cells, providing a mechanism for organelles of the endomembrane system to communicate and exchange material between each other. A significant number of infections and diseases are associated with trafficking pathways, and as such gaining a greater understanding of their regulation is essential. Fluorescence-based imaging techniques are widely used to probe the trafficking machinery within cells, and many of these methods have the potential to be applied in a quantitative manner. In the present mini-review, we highlight several recent examples of how image intensity, kinetic measurements, co-localization and texture feature analysis have been used to study the function of one key family of membrane traffic regulators, the Rab GTPases. We give specific emphasis to the importance of the quantitative nature of these recent studies and comment on their potential applicability to a high-throughput format.
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33
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Staras K, Mikulincer D, Gitler D. Monitoring and quantifying dynamic physiological processes in live neurons using fluorescence recovery after photobleaching. J Neurochem 2013; 126:213-22. [PMID: 23496032 DOI: 10.1111/jnc.12240] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 12/27/2022]
Abstract
The direct visualization of subcellular dynamic processes is often hampered by limitations in the resolving power achievable with conventional microscopy techniques. Fluorescence recovery after photobleaching has emerged as a highly informative approach to address this challenge, permitting the quantitative measurement of the movement of small organelles and proteins in living functioning cells, and offering detailed insights into fundamental cellular phenomena of physiological importance. In recent years, its implementation has benefited from the increasing availability of confocal microscopy systems and of powerful labeling techniques based on genetically encoded fluorescent proteins or other chemical markers. In this review, we present fluorescence recovery after photobleaching and related techniques in the context of contemporary neurobiological research and discuss quantitative and semi-quantitative approaches to their interpretation.
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Affiliation(s)
- Kevin Staras
- School of Life Sciences, University of Sussex, Brighton, UK
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Priya R, Gomez G. Measurement of Junctional Protein Dynamics Using Fluorescence Recovery After Photobleaching (FRAP). Bio Protoc 2013. [DOI: 10.21769/bioprotoc.937] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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35
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Kang M, Day CA, Kenworthy AK, DiBenedetto E. Simplified equation to extract diffusion coefficients from confocal FRAP data. Traffic 2012; 13:1589-600. [PMID: 22984916 DOI: 10.1111/tra.12008] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/09/2012] [Accepted: 09/17/2012] [Indexed: 12/13/2022]
Abstract
Quantitative measurements of diffusion can provide important information about how proteins and lipids interact with their environment within the cell and the effective size of the diffusing species. Confocal fluorescence recovery after photobleaching (FRAP) is one of the most widely accessible approaches to measure protein and lipid diffusion in living cells. However, straightforward approaches to quantify confocal FRAP measurements in terms of absolute diffusion coefficients are currently lacking. Here, we report a simplified equation that can be used to extract diffusion coefficients from confocal FRAP data using the half time of recovery and effective bleach radius for a circular bleach region, and validate this equation for a series of fluorescently labeled soluble and membrane-bound proteins and lipids. We show that using this approach, diffusion coefficients ranging over three orders of magnitude can be obtained from confocal FRAP measurements performed under standard imaging conditions, highlighting its broad applicability.
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Affiliation(s)
- Minchul Kang
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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36
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Srikantha N, Mourad F, Suhling K, Elsaid N, Levitt J, Chung PH, Somavarapu S, Jackson TL. Influence of molecular shape, conformability, net surface charge, and tissue interaction on transscleral macromolecular diffusion. Exp Eye Res 2012; 102:85-92. [DOI: 10.1016/j.exer.2012.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/06/2012] [Accepted: 07/13/2012] [Indexed: 11/24/2022]
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37
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Multiscale diffusion in the mitotic Drosophila melanogaster syncytial blastoderm. Proc Natl Acad Sci U S A 2012; 109:8588-93. [PMID: 22592793 DOI: 10.1073/pnas.1204270109] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the fundamental importance of diffusion for embryonic morphogen gradient formation in the early Drosophila melanogaster embryo, there remains controversy regarding both the extent and the rate of diffusion of well-characterized morphogens. Furthermore, the recent observation of diffusional "compartmentalization" has suggested that diffusion may in fact be nonideal and mediated by an as-yet-unidentified mechanism. Here, we characterize the effects of the geometry of the early syncytial Drosophila embryo on the effective diffusivity of cytoplasmic proteins. Our results demonstrate that the presence of transient mitotic membrane furrows results in a multiscale diffusion effect that has a significant impact on effective diffusion rates across the embryo. Using a combination of live-cell experiments and computational modeling, we characterize these effects and relate effective bulk diffusion rates to instantaneous diffusion coefficients throughout the syncytial blastoderm nuclear cycle phase of the early embryo. This multiscale effect may be related to the effect of interphase nuclei on effective diffusion, and thus we propose that an as-yet-unidentified role of syncytial membrane furrows is to temporally regulate bulk embryonic diffusion rates to balance the multiscale effect of interphase nuclei, which ultimately stabilizes the shapes of various morphogen gradients.
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38
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Sanderson JM. Resolving the kinetics of lipid, protein and peptide diffusion in membranes. Mol Membr Biol 2012; 29:118-43. [DOI: 10.3109/09687688.2012.678018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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39
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Vogt C, Ball V, Mutterer J, Schaaf P, Voegel JC, Senger B, Lavalle P. Mobility of Proteins in Highly Hydrated Polyelectrolyte Multilayer Films. J Phys Chem B 2012; 116:5269-78. [DOI: 10.1021/jp300028v] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Cédric Vogt
- Institut National de la Santé et de la Recherche Médicale, Unité 977, 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie
Dentaire, Université de Strasbourg, 1 place de l’Hôpital, 67000 Strasbourg, France
| | - Vincent Ball
- Institut National de la Santé et de la Recherche Médicale, Unité 977, 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie
Dentaire, Université de Strasbourg, 1 place de l’Hôpital, 67000 Strasbourg, France
| | - Jérôme Mutterer
- Centre National de la Recherche
Scientifique, UPR 2357, Institut de Biologie Moléculaire des Plantes, 12 rue du Général Zimmer,
67084 Strasbourg Cedex, France
| | - Pierre Schaaf
- Centre National de la Recherche
Scientifique, UPR 22, Institut Charles Sadron, 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2, France
| | - Jean-Claude Voegel
- Institut National de la Santé et de la Recherche Médicale, Unité 977, 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie
Dentaire, Université de Strasbourg, 1 place de l’Hôpital, 67000 Strasbourg, France
| | - Bernard Senger
- Institut National de la Santé et de la Recherche Médicale, Unité 977, 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie
Dentaire, Université de Strasbourg, 1 place de l’Hôpital, 67000 Strasbourg, France
| | - Philippe Lavalle
- Institut National de la Santé et de la Recherche Médicale, Unité 977, 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie
Dentaire, Université de Strasbourg, 1 place de l’Hôpital, 67000 Strasbourg, France
- Hôpitaux Universitaires de Strasbourg, 1 place de l’Hôpital,
67000 Strasbourg, France
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40
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González-González IM, Jaskolski F, Goldberg Y, Ashby MC, Henley JM. Measuring membrane protein dynamics in neurons using fluorescence recovery after photobleach. Methods Enzymol 2012; 504:127-46. [PMID: 22264532 PMCID: PMC3314508 DOI: 10.1016/b978-0-12-391857-4.00006-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The use of genetically encoded fluorescent tags such as green fluorescent protein (GFP) as reporters to monitor processes in living cells has transformed cell biology. One major application for these tools has been to analyze protein dynamics in neurons. In particular, fluorescence recovery after photobleach (FRAP) of surface expressed fluorophore-tagged proteins has been instrumental to addressing outstanding questions about how neurons orchestrate the synaptic delivery of proteins. Here, we provide an overview of the methodology, equipment, and analysis required to perform, analyze, and interpret these experiments.
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Affiliation(s)
- Inmaculada M González-González
- MRC Centre for Synaptic Plasticity, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, United Kingdom
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41
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Mueller F, Karpova TS, Mazza D, McNally JG. Monitoring dynamic binding of chromatin proteins in vivo by fluorescence recovery after photobleaching. Methods Mol Biol 2012; 833:153-76. [PMID: 22183594 DOI: 10.1007/978-1-61779-477-3_11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Fluorescence recovery after photobleaching (FRAP) has now become widely used to investigate nuclear protein binding to chromatin in live cells. FRAP can be applied qualitatively to assess if chromatin binding interactions are altered by various biological perturbations. It can also be applied semi-quantitatively to allow numerical comparisons between FRAP curves, and even fully quantitatively to yield estimates of in vivo diffusion constants and nuclear protein binding rates to chromatin. Here we describe how FRAP data should be collected and processed for these qualitative, semi-quantitative, and quantitative analyses.
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Affiliation(s)
- Florian Mueller
- Groupe Imagerie et Modélisation, Institut Pasteur, CNRS, URA 2582, Paris, France
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42
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Liesche J, Schulz A. Quantification of plant cell coupling with three-dimensional photoactivation microscopy. J Microsc 2011; 247:2-9. [PMID: 22171617 DOI: 10.1111/j.1365-2818.2011.03584.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plant cells are directly connected by plasmodesmata that form channels through the cell wall and enable the intercellular movement of cytosolic solutes, membrane lipids and signalling molecules. Transport through plasmodesmata is regulated not only by a fixed size-exclusion limit, but also by physiological and pathological adaptation. To understand plant cell communication, carbon allocation and pathogen attack, the capacities for a specific molecule to pass a specific cell-wall interface is an essential parameter. So far, the degree of cell coupling was derived from frequency and diameter of plasmodesmata in relevant tissues as assessed by electron microscopy of fixed material. However, plasmodesmata functionality and capacity can only be determined in live material, not from electron microscopy, which is static and prone to fixation artefacts. Plasmodesmata functionality was a few times assessed using fluorescent tracers with diffusion properties similar to cytosolic solutes. Here, we used three-dimensional photoactivation microscopy to quantify plasmodesmata-mediated cell-wall permeability between living Cucurbita maxima leaf mesophyll cells with caged fluorescein as tracer. For the first time, all necessary functional and anatomical data were gathered for each individual cell from three-dimensional time series. This approach utilized a confocal microscope equipped with resonant scanner, which provides the high acquisition speed necessary to record optical sections of whole cells and offers time resolution high enough to follow the kinetics of photoactivation. The results were compared to two-dimensional measurements, which are shown to give a good estimate of cell coupling adequate for homogenous tissues. The two-dimensional approach is limited whenever tissues interfaces are studied that couple different cell types with diverse cell geometries.
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Affiliation(s)
- J Liesche
- Department of Plant Biology and Biotechnology, University of Copenhagen, Copenhagen, Denmark
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43
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Abstract
Biological research has always tremendously benefited from the development of key methodology. In fact, it was the advent of microscopy that shaped our understanding of cells as the fundamental units of life. Microscopic techniques are still central to the elucidation of biological units and processes, but equally important are methods that allow access to the dimension of time, to investigate the dynamics of molecular functions and interactions. Here, fluorescence spectroscopy with its sensitivity to access the single-molecule level, and its large temporal resolution, has been opening up fully new perspectives for cell biology. Here we summarize the key fluorescent techniques used to study cellular dynamics, with the focus on lipid and membrane systems.
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Berkovich R, Wolfenson H, Eisenberg S, Ehrlich M, Weiss M, Klafter J, Henis YI, Urbakh M. Accurate quantification of diffusion and binding kinetics of non-integral membrane proteins by FRAP. Traffic 2011; 12:1648-57. [PMID: 21810156 DOI: 10.1111/j.1600-0854.2011.01264.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Non-integral membrane proteins frequently act as transduction hubs in vital signaling pathways initiated at the plasma membrane (PM). Their biological activity depends on dynamic interactions with the PM, which are governed by their lateral and cytoplasmic diffusion and membrane binding/unbinding kinetics. Accurate quantification of the multiple kinetic parameters characterizing their membrane interaction dynamics has been challenging. Despite a fair number of approximate fitting functions for analyzing fluorescence recovery after photobleaching (FRAP) data, no approach was able to cope with the full diffusion-exchange problem. Here, we present an exact solution and matlab fitting programs for FRAP with a stationary Gaussian laser beam, allowing simultaneous determination of the membrane (un)binding rates and the diffusion coefficients. To reduce the number of fitting parameters, the cytoplasmic diffusion coefficient is determined separately. Notably, our equations include the dependence of the exchange kinetics on the distribution of the measured protein between the PM and the cytoplasm, enabling the derivation of both k(on) and k(off) without prior assumptions. After validating the fitting function by computer simulations, we confirm the applicability of our approach to live-cell data by monitoring the dynamics of GFP-N-Ras mutants under conditions with different contributions of lateral diffusion and exchange to the FRAP kinetics.
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Affiliation(s)
- Ronen Berkovich
- School of Chemistry, Raymond and Beverley Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
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45
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Sequestration of CaMKII in dendritic spines in silico. J Comput Neurosci 2011; 31:581-94. [PMID: 21491127 DOI: 10.1007/s10827-011-0323-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 02/05/2011] [Accepted: 03/08/2011] [Indexed: 12/26/2022]
Abstract
Calcium calmodulin dependent kinase II (CaMKII) is sequestered in dendritic spines within seconds upon synaptic stimulation. The program Smoldyn was used to develop scenarios of single molecule CaMKII diffusion and binding in virtual dendritic spines. We first validated simulation of diffusion as a function of spine morphology. Additional cellular structures were then incorporated to simulate binding of CaMKII to the post-synaptic density (PSD); binding to cytoskeleton; or their self-aggregation. The distributions of GFP tagged native and mutant constructs in dissociated hippocampal neurons were measured to guide quantitative analysis. Intra-spine viscosity was estimated from fluorescence recovery after photo-bleach (FRAP) of red fluorescent protein. Intra-spine mobility of the GFP-CaMKIIα constructs was measured, with hundred-millisecond or better time resolution, from FRAP of distal spine tips in conjunction with fluorescence loss (FLIP) from proximal regions. Different FRAP \ FLIP profiles were predicted from our Scenarios and provided a means to differentiate binding to the PSDs from self-aggregation. The predictions were validated by experiments. Simulated fits of the Scenarios provided estimates of binding and rate constants. We utilized these values to assess the role of self-aggregation during the initial response of native CaMKII holoenzymes to stimulation. The computations revealed that self-aggregation could provide a concentration-dependent switch to amplify CaMKII sequestration and regulate its activity depending on its occupancy of the actin cytoskeleton.
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46
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Kiskin NI, Hellen N, Babich V, Hewlett L, Knipe L, Hannah MJ, Carter T. Protein mobilities and P-selectin storage in Weibel-Palade bodies. J Cell Sci 2011; 123:2964-75. [PMID: 20720153 DOI: 10.1242/jcs.073593] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Using fluorescence recovery after photobleaching (FRAP) we measured the mobilities of EGFP-tagged soluble secretory proteins in the endoplasmic reticulum (ER) and in individual Weibel-Palade bodies (WPBs) at early (immature) and late (mature) stages in their biogenesis. Membrane proteins (P-selectin, CD63, Rab27a) were also studied in individual WPBs. In the ER, soluble secretory proteins were mobile; however, following insertion into immature WPBs larger molecules (VWF, Proregion, tPA) and P-selectin became immobilised, whereas small proteins (ssEGFP, eotaxin-3) became less mobile. WPB maturation led to further decreases in mobility of small proteins and CD63. Acute alkalinisation of mature WPBs selectively increased the mobilities of small soluble proteins without affecting larger molecules and the membrane proteins. Disruption of the Proregion-VWF paracrystalline core by prolonged incubation with NH(4)Cl rendered P-selectin mobile while VWF remained immobile. FRAP of P-selectin mutants revealed that immobilisation most probably involves steric entrapment of the P-selectin extracellular domain by the Proregion-VWF paracrystal. Significantly, immobilisation contributed to the enrichment of P-selectin in WPBs; a mutation of P-selectin preventing immobilisation led to a failure of enrichment. Together these data shed new light on the transitions that occur for soluble and membrane proteins following their entry and storage into post-Golgi-regulated secretory organelles.
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Affiliation(s)
- Nikolai I Kiskin
- Division of Molecular Neuroendocrinology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.
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47
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Kang M, Day CA, DiBenedetto E, Kenworthy AK. A quantitative approach to analyze binding diffusion kinetics by confocal FRAP. Biophys J 2011; 99:2737-47. [PMID: 21044570 DOI: 10.1016/j.bpj.2010.09.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Revised: 09/09/2010] [Accepted: 09/13/2010] [Indexed: 11/15/2022] Open
Abstract
Most of the important types of interactions that occur in cells can be characterized as binding-diffusion type processes, and can be quantified by kinetic rate constants such as diffusion coefficients (D) and binding rate constants (k(on) and k(off)). Confocal FRAP is a potentially important tool for the quantitative analysis of intracellular binding-diffusion kinetics, but how to dependably extract accurate kinetic constants from such analyses is still an open question. To this end, in this study, we developed what we believe is a new analytical model for confocal FRAP-based measurements of intracellular binding-diffusion processes, based on a closed-form equation of the FRAP formula for a spot photobleach geometry. This approach incorporates a binding diffusion model that allows for diffusion of both the unbound and bound species, and also compensates for binding diffusion that occurs during photobleaching, a critical consideration in confocal FRAP analysis. In addition, to address the problem of parametric multiplicity, we propose a scheme to reduce the number of fitting parameters in the effective diffusion subregime when D's for the bound and unbound species are known. We validate this method by measuring kinetic rate constants for the CAAX-mediated binding of Ras to membranes of the endoplasmic reticulum, obtaining binding constants of k(on) ∼ 255/s and k(off) ∼ 31/s.
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Affiliation(s)
- Minchul Kang
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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48
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Zhang HY, Hill RJ. Concentration dependence of lipopolymer self-diffusion in supported bilayer membranes. J R Soc Interface 2011; 8:127-43. [PMID: 20504804 PMCID: PMC3024821 DOI: 10.1098/rsif.2010.0200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 05/05/2010] [Indexed: 12/23/2022] Open
Abstract
Self-diffusion coefficients of poly(ethylene glycol)2k-derivatized lipids (DSPE-PEG2k-CF) in glass-supported DOPC phospholipid bilayers are ascertained from quantitative fluorescence recovery after photobleaching (FRAP). We developed a first-order reaction-diffusion model to ascertain the bleaching constant, mobile fraction and lipopolymer self-diffusion coefficient D(s) at concentrations in the range c ≈ 0.5-5 mol%. In contrast to control experiments with 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl) (ammonium salt) (DOPE-NBD) in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), the lipopolymer self-diffusion coefficient decreases monotonically with increasing concentration, without a distinguishing mushroom-to-brush transition. Our data yield a correlation D(s) = D(0)/(1 + αc), where D(0) ≈ 3.36 µm(2) s(-1) and α ≈ 0.56 (with c expressed as a mole percent). Interpreting the dilute limit with the Scalettar-Abney-Owicki statistical mechanical theory for transmembrane proteins yields an effective disc radius a(e) ≈ 2.41 nm. On the other hand, the Bussell-Koch-Hammer theory, which includes hydrodynamic interactions, yields a(e) ≈ 2.92 nm. As expected, both measures are smaller than the Flory radius of the 2 kDa poly(ethylene glycol) (PEG) chains, R(F) ≈ 3.83 nm, and significantly larger than the nominal radius of the phospholipid heads, a(l) ≈ 0.46 nm. The diffusion coefficient at infinite dilution D(0) was interpreted using the Evans-Sackmann theory, furnishing an inter-leaflet frictional drag coefficient b(s) ≈ 1.33 × 10(8) N s m(-3). Our results suggest that lipopolymer interactions are dominated by the excluded volume of the PEG-chain segments, with frictional drag dominated by the two-dimensional bilayer hydrodynamics.
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Affiliation(s)
| | - Reghan J. Hill
- Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada H3A 2B2
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49
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Goehring NW, Chowdhury D, Hyman AA, Grill SW. FRAP analysis of membrane-associated proteins: lateral diffusion and membrane-cytoplasmic exchange. Biophys J 2010; 99:2443-52. [PMID: 20959084 PMCID: PMC2956213 DOI: 10.1016/j.bpj.2010.08.033] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 08/13/2010] [Accepted: 08/13/2010] [Indexed: 10/18/2022] Open
Abstract
Obtaining quantitative kinetic parameters from fluorescence recovery after photobleaching (FRAP) experiments generally requires a theoretical analysis of protein mobility and appropriate solutions for FRAP recovery derived for a given geometry. Here we provide a treatment of FRAP recovery for a molecule undergoing a combined process of reversible membrane association and lateral diffusion on the plasma membrane for two commonly used bleach geometries: stripes, and boxes. Such analysis is complicated by the fact that diffusion of a molecule during photobleaching can lead to broadening of the bleach area, resulting in significant deviations of the actual bleach shape from the desired bleach geometry, which creates difficulty in accurately measuring kinetic parameters. Here we overcome the problem of deviations between actual and idealized bleach geometries by parameterizing, more accurately, the initial postbleach state. This allows for reconstruction of an accurate and analytically tractable approximation of the actual fluorescence distribution. Through simulated FRAP experiments, we demonstrate that this method can be used to accurately measure a broad range of combinations of diffusion constants and exchange rates. Use of this method to analyze the plextrin homology domain of PLC-δ1 in Caenorhabditis elegans results in quantitative agreement with prior analysis of this domain in other cells using other methods. Because of the flexibility, relative ease of implementation, and its use of standard, easily obtainable bleach geometries, this method should be broadly applicable to investigation of protein dynamics at the plasma membrane.
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Affiliation(s)
- Nathan W. Goehring
- Max Planck Institute of Molecular Cell Biology & Genetics, Dresden, Germany
| | - Debanjan Chowdhury
- Max Planck Institute for Physics of Complex Systems, Dresden, Germany
- Department of Physics, Indian Institute of Technology, Kanpur, India
| | - Anthony A. Hyman
- Max Planck Institute of Molecular Cell Biology & Genetics, Dresden, Germany
| | - Stephan W. Grill
- Max Planck Institute of Molecular Cell Biology & Genetics, Dresden, Germany
- Max Planck Institute for Physics of Complex Systems, Dresden, Germany
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50
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Yang J, Köhler K, Davis DM, Burroughs NJ. An improved strip FRAP method for estimating diffusion coefficients: correcting for the degree of photobleaching. J Microsc 2010; 238:240-53. [PMID: 20579262 DOI: 10.1111/j.1365-2818.2009.03347.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence recovery after photobleaching is a widely established method for the estimation of diffusion coefficients, strip bleaching with an associated recovery curve analysis being one of the simplest techniques. However, its implementation requires near 100% bleaching in the region of interest with negligible fluorescence loss outside, both constraints being hard to achieve concomitantly for fast diffusing molecules. We demonstrate that when these requirements are not met there is an error in the estimation of the diffusion coefficient D, either an under- or overestimation depending on which assumption is violated the most. We propose a simple modification to the recovery curve analysis incorporating the concept of the relative bleached mass m giving a revised recovery time parametrization tau=m(2)w(2)/4piD for a strip of width w. This modified model removes the requirement of 100% bleaching in the region of interest and allows for limited diffusion of the fluorophore during bleaching. We validate our method by estimating the (volume) diffusion coefficient of FITC-labelled IgG in 60% glycerol solution, D= 4.09 +/- 0.21 microm(2) s(-1), and the (surface) diffusion coefficient of a green-fluorescent protein-tagged class I MHC protein expressed at the surface of a human B cell line, D= 0.32 +/- 0.03 microm(2) s(-1) for a population of cells.
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Affiliation(s)
- J Yang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
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