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Fazel M, Grussmayer KS, Ferdman B, Radenovic A, Shechtman Y, Enderlein J, Pressé S. Fluorescence Microscopy: a statistics-optics perspective. ARXIV 2023:arXiv:2304.01456v3. [PMID: 37064525 PMCID: PMC10104198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fundamental properties of light unavoidably impose features on images collected using fluorescence microscopes. Modeling these features is ever more important in quantitatively interpreting microscopy images collected at scales on par or smaller than light's wavelength. Here we review the optics responsible for generating fluorescent images, fluorophore properties, microscopy modalities leveraging properties of both light and fluorophores, in addition to the necessarily probabilistic modeling tools imposed by the stochastic nature of light and measurement.
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Affiliation(s)
- Mohamadreza Fazel
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Kristin S Grussmayer
- Department of Bionanoscience, Faculty of Applied Science and Kavli Institute for Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Boris Ferdman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Yoav Shechtman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Steve Pressé
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
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2
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Paris JL, Gaspar R, Coelho F, De Beule PAA, Silva BFB. Stability Criterion for the Assembly of Core-Shell Lipid-Polymer-Nucleic Acid Nanoparticles. ACS NANO 2023; 17:17587-17594. [PMID: 37581895 PMCID: PMC10510699 DOI: 10.1021/acsnano.3c07204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 08/16/2023]
Abstract
Hybrid core-shell lipid-polycation-nucleic acid nanoparticles (LPNPs) provide unique delivery strategies for nonviral gene therapeutics. Since LPNPs consist of multiple components, involving different pairwise interactions between them, they are challenging to characterize and understand. Here, we propose a method based on fluorescence cross-correlation spectroscopy to elucidate the association between the three LPNP components. Through this lens, we demonstrate that cationic lipid shells (liposomes) do not displace polycations or DNA from the polycation-DNA cores (polyplexes). Hence, polyplexes and liposomes must be oppositely charged to associate into LPNPs. Furthermore, we identify the liposome:polyplex number ratio (ρN), which was hitherto an intangible quantity, as the primary parameter predicting stable LPNPs. We establish that ρN ≥ 1 ensures that every polyplex is enveloped by a liposome, thus avoiding coexisting oppositely charged species prone to aggregation.
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Affiliation(s)
| | - Ricardo Gaspar
- International Iberian Nanotechnology
Laboratory, Braga, 4715-330, Portugal
| | - Filipe Coelho
- International Iberian Nanotechnology
Laboratory, Braga, 4715-330, Portugal
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3
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Non-Peptide Opioids Differ in Effects on Mu-Opioid (MOP) and Serotonin 1A (5-HT 1A) Receptors Heterodimerization and Cellular Effectors (Ca 2+, ERK1/2 and p38) Activation. Molecules 2022; 27:molecules27072350. [PMID: 35408749 PMCID: PMC9000251 DOI: 10.3390/molecules27072350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/24/2022] [Accepted: 04/02/2022] [Indexed: 11/17/2022] Open
Abstract
The importance of the dynamic interplay between the opioid and the serotonin neuromodulatory systems in chronic pain is well recognized. In this study, we investigated whether these two signalling pathways can be integrated at the single-cell level via direct interactions between the mu-opioid (MOP) and the serotonin 1A (5-HT1A) receptors. Using fluorescence cross-correlation spectroscopy (FCCS), a quantitative method with single-molecule sensitivity, we characterized in live cells MOP and 5-HT1A interactions and the effects of prolonged (18 h) exposure to selected non-peptide opioids: morphine, codeine, oxycodone and fentanyl, on the extent of these interactions. The results indicate that in the plasma membrane, MOP and 5-HT1A receptors form heterodimers that are characterized with an apparent dissociation constant Kdapp = (440 ± 70) nM). Prolonged exposure to all non-peptide opioids tested facilitated MOP and 5-HT1A heterodimerization and stabilized the heterodimer complexes, albeit to a different extent: Kd, Fentanylapp = (80 ± 70) nM), Kd,Morphineapp = (200 ± 70) nM, Kd, Codeineapp = (100 ± 70) nM and Kd, Oxycodoneapp = (200 ± 70) nM. The non-peptide opioids differed also in the extent to which they affected the mitogen-activated protein kinases (MAPKs) p38 and the extracellular signal-regulated kinase (Erk1/2), with morphine, codeine and fentanyl activating both pathways, whereas oxycodone activated p38 but not ERK1/2. Acute stimulation with different non-peptide opioids differently affected the intracellular Ca2+ levels and signalling dynamics. Hypothetically, targeting MOP−5-HT1A heterodimer formation could become a new strategy to counteract opioid induced hyperalgesia and help to preserve the analgesic effects of opioids in chronic pain.
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Dunsing V, Petrich A, Chiantia S. Multicolor fluorescence fluctuation spectroscopy in living cells via spectral detection. eLife 2021; 10:e69687. [PMID: 34494547 PMCID: PMC8545396 DOI: 10.7554/elife.69687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/07/2021] [Indexed: 01/20/2023] Open
Abstract
Signaling pathways in biological systems rely on specific interactions between multiple biomolecules. Fluorescence fluctuation spectroscopy provides a powerful toolbox to quantify such interactions directly in living cells. Cross-correlation analysis of spectrally separated fluctuations provides information about intermolecular interactions but is usually limited to two fluorophore species. Here, we present scanning fluorescence spectral correlation spectroscopy (SFSCS), a versatile approach that can be implemented on commercial confocal microscopes, allowing the investigation of interactions between multiple protein species at the plasma membrane. We demonstrate that SFSCS enables cross-talk-free cross-correlation, diffusion, and oligomerization analysis of up to four protein species labeled with strongly overlapping fluorophores. As an example, we investigate the interactions of influenza A virus (IAV) matrix protein 2 with two cellular host factors simultaneously. We furthermore apply raster spectral image correlation spectroscopy for the simultaneous analysis of up to four species and determine the stoichiometry of ternary IAV polymerase complexes in the cell nucleus.
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Affiliation(s)
- Valentin Dunsing
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
| | - Annett Petrich
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
| | - Salvatore Chiantia
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
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5
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Immuno-profiling and cellular spatial analysis using five immune oncology multiplex immunofluorescence panels for paraffin tumor tissue. Sci Rep 2021; 11:8511. [PMID: 33875760 PMCID: PMC8055659 DOI: 10.1038/s41598-021-88156-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/05/2021] [Indexed: 02/07/2023] Open
Abstract
Multiplex immunofluorescence (mIF) has arisen as an important tool for immuno-profiling tumor tissues. We updated our manual protocol into an automated protocol that allows the use of up to seven markers in five mIF panels to apply to formalin-fixed paraffin-embedded tumor tissues. Using a tyramide signal amplification system, we optimized five mIF panels that included cytokeratin to characterize malignant cells (MCs), immune checkpoint markers (i.e., PD-L1, B7-H3, B7-H4, IDO-1, VISTA, LAG3, ICOS, TIM3, and OX40), tumor-infiltrating lymphocytic markers (i.e., CD3, CD8, CD45RO, granzyme B, PD-1, and FOXP3), and markers to characterize myeloid-derived suppressor cells (i.e., CD68, CD66b, CD14, CD33, Arg-1, and CD11b). To determine analytical reproducibility and the impact of those panels for immuno-profiling tumor tissues, we performed an exploratory analysis in a set of non–small cell lung cancer (NSCLC) samples. The slides were scanned, and the different cell phenotypes were quantified by simultaneous co-localizations with the markers using image analysis software. Comparison between the time points of staining showed high analytical reproducibility. The analysis of NSCLC cases showed an immunosuppressive microenvironment with PD-L1/PD-1 expression as a predominant axis. Interestingly, high density of MCs expressing B7-H4 was correlated with recurrence. Unexpectedly, MCs expressing OX40 were also detected, and those cells were a closer distance to CD3+T-cells than were MCs expressing other immune checkpoints. Two different cellular patterns of spatial distribution were determined according the CD3 distribution, and the predominant pattern was related with active immunosuppressive interaction with MCs. Our study shows that these five mIF panels can identify multiple targets in a single cell with high reproducibility. The study of different cell populations and their spatial relationship can open new ideas for therapeutic approaches.
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Leppert A, Tiiman A, Kronqvist N, Landreh M, Abelein A, Vukojević V, Johansson J. Smallest Secondary Nucleation Competent Aβ Aggregates Probed by an ATP-Independent Molecular Chaperone Domain. Biochemistry 2021; 60:678-688. [PMID: 33621049 PMCID: PMC8028046 DOI: 10.1021/acs.biochem.1c00003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein oligomerization is a commonly encountered strategy by which the functional repertoire of proteins is increased. This, however, is a double-edged sword strategy because protein oligomerization is notoriously difficult to control. Living organisms have therefore developed a number of chaperones that prevent protein aggregation. The small ATP-independent molecular chaperone domain proSP-C BRICHOS, which is mainly trimeric, specifically inhibits fibril surface-catalyzed nucleation reactions that give rise to toxic oligomers during the aggregation of the Alzheimer's disease-related amyloid-β peptide (Aβ42). Here, we have created a stable proSP-C BRICHOS monomer mutant and show that it does not bind to monomeric Aβ42 but has a high affinity for Aβ42 fibrils, using surface plasmon resonance. Kinetic analysis of Aβ42 aggregation profiles, measured by thioflavin T fluorescence, reveals that the proSP-C BRICHOS monomer mutant strongly inhibits secondary nucleation reactions and thereby reduces the level of catalytic formation of toxic Aβ42 oligomers. To study binding between the proSP-C BRICHOS monomer mutant and small soluble Aβ42 aggregates, we analyzed fluorescence cross-correlation spectroscopy measurements with the maximum entropy method for fluorescence correlation spectroscopy. We found that the proSP-C BRICHOS monomer mutant binds to the smallest emerging Aβ42 aggregates that are comprised of eight or fewer Aβ42 molecules, which are already secondary nucleation competent. Our approach can be used to provide molecular-level insights into the mechanisms of action of substances that interfere with protein aggregation.
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Affiliation(s)
- Axel Leppert
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Ann Tiiman
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Nina Kronqvist
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solnavägen 9, 17165 Solna, Sweden
| | - Axel Abelein
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Vladana Vukojević
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Jan Johansson
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 14183 Huddinge, Sweden
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Stoneman MR, Biener G, Raicu V. Proposal for simultaneous analysis of fluorescence intensity fluctuations and resonance energy transfer (IFRET) measurements. Methods Appl Fluoresc 2020; 8:035011. [DOI: 10.1088/2050-6120/ab9b68] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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8
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Menges JA, Grandjean A, Clasen A, Jung G. Kinetics of Palladium(0)‐Allyl Interactions in the Tsuji‐Trost Reaction, derived from Single‐Molecule Fluorescence Microscopy. ChemCatChem 2020. [DOI: 10.1002/cctc.202000032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Johannes A. Menges
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Alexander Grandjean
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Anne Clasen
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Gregor Jung
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
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9
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Bernasek SM, Peláez N, Carthew RW, Bagheri N, Amaral LAN. Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila. PLoS Comput Biol 2020; 16:e1007406. [PMID: 32126077 PMCID: PMC7100978 DOI: 10.1371/journal.pcbi.1007406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 03/27/2020] [Accepted: 01/27/2020] [Indexed: 12/01/2022] Open
Abstract
Mosaic analysis provides a means to probe developmental processes in situ by generating loss-of-function mutants within otherwise wildtype tissues. Combining these techniques with quantitative microscopy enables researchers to rigorously compare RNA or protein expression across the resultant clones. However, visual inspection of mosaic tissues remains common in the literature because quantification demands considerable labor and computational expertise. Practitioners must segment cell membranes or cell nuclei from a tissue and annotate the clones before their data are suitable for analysis. Here, we introduce Fly-QMA, a computational framework that automates each of these tasks for confocal microscopy images of Drosophila imaginal discs. The framework includes an unsupervised annotation algorithm that incorporates spatial context to inform the genetic identity of each cell. We use a combination of real and synthetic validation data to survey the performance of the annotation algorithm across a broad range of conditions. By contributing our framework to the open-source software ecosystem, we aim to contribute to the current move toward automated quantitative analysis among developmental biologists.
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Affiliation(s)
- Sebastian M. Bernasek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Nicolás Peláez
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Richard W. Carthew
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, Illinois, United States of America
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
| | - Luís A. N. Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America
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10
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Rehó B, Lau L, Mocsár G, Müller G, Fadel L, Brázda P, Nagy L, Tóth K, Vámosi G. Simultaneous Mapping of Molecular Proximity and Comobility Reveals Agonist-Enhanced Dimerization and DNA Binding of Nuclear Receptors. Anal Chem 2020; 92:2207-2215. [PMID: 31870146 DOI: 10.1021/acs.analchem.9b04902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Single Plane Illumination Microscopy (SPIM) revolutionized time lapse imaging of live cells and organisms due to its high speed and reduced photodamage. Quantitative mapping of molecular (co)mobility by fluorescence (cross-)correlation spectroscopy (F(C)CS) in a SPIM has been introduced to reveal molecular diffusion and binding. A complementary aspect of interactions is proximity, which can be studied by Förster resonance energy transfer (FRET). Here, we extend SPIM-FCCS by alternating laser excitation, which reduces false positive cross-correlation and facilitates comapping of FRET. Thus, different aspects of interacting systems can be studied simultaneously, and molecular subpopulations can be discriminated by multiparameter analysis. After demonstrating the benefits of the method on the AP-1 transcription factor, the dimerization and DNA binding behavior of retinoic acid receptor (RAR) and retinoid X receptor (RXR) is revealed, and an extension of the molecular switch model of the nuclear receptor action is proposed. Our data imply that RAR agonist enhances RAR-RXR heterodimerization, and chromatin binding/dimerization are positively correlated. We also propose a ligand induced conformational change bringing the N-termini of RAR and RXR closer together. The RXR agonist increased homodimerization of RXR suggesting that RXR may act as an autonomous transcription factor.
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Affiliation(s)
- Bálint Rehó
- Department of Biophysics and Cell Biology, Doctoral School of Molecular Medicine, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary
| | - Lukas Lau
- Division Biophysics of Macromolecules , German Cancer Research Center , Im Neuenheimer Feld 280 , D-69120 Heidelberg , Germany
| | - Gábor Mocsár
- Department of Biophysics and Cell Biology, Doctoral School of Molecular Medicine, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary
| | - Gabriele Müller
- Division Biophysics of Macromolecules , German Cancer Research Center , Im Neuenheimer Feld 280 , D-69120 Heidelberg , Germany
| | - Lina Fadel
- Department of Biophysics and Cell Biology, Doctoral School of Molecular Medicine, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary
| | - Péter Brázda
- Department of Biochemistry and Molecular Biology, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary
| | - László Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary.,Johns Hopkins University School of Medicine , Department of Medicine and Biological Chemistry, Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital , 600 Fifth Street South Saint Petersburg , Florida 33701-4634 , United States
| | - Katalin Tóth
- Division Biophysics of Macromolecules , German Cancer Research Center , Im Neuenheimer Feld 280 , D-69120 Heidelberg , Germany
| | - György Vámosi
- Department of Biophysics and Cell Biology, Doctoral School of Molecular Medicine, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary
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Janovič T, Stojaspal M, Veverka P, Horáková D, Hofr C. Human Telomere Repeat Binding Factor TRF1 Replaces TRF2 Bound to Shelterin Core Hub TIN2 when TPP1 Is Absent. J Mol Biol 2019; 431:3289-3301. [DOI: 10.1016/j.jmb.2019.05.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/17/2022]
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12
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Nguyen TT, Cramb DT. Elucidation of the mechanism and energy barrier for anesthetic triggered membrane fusion in model membranes. CAN J CHEM 2019. [DOI: 10.1139/cjc-2018-0405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Membrane fusion is vital for cellular function and is generally mediated via fusogenic proteins and peptides. The mechanistic details and subsequently the transition state dynamics of membrane fusion will be dependent on the type of the fusogenic agent. We have previously established the potential of general anesthetics as a new class of fusion triggering agents in model membranes. We employed two-photon excitation fluorescence cross-correlation spectroscopy (TPE-FCCS) to report on vesicle association kinetics and steady-state fluorescence dequenching assays to monitor lipid mixing kinetics. Using halothane to trigger fusion in 110 nm diameter dioleoylphosphatidylcholine (DOPC) liposomes, we found that lipid rearrangement towards the formation of the fusion stalk was rate limiting. The activation barrier for halothane induced membrane fusion in 110 nm vesicles was found to be ∼40 kJ mol−1. We calculated the enthalpy and entropy of the transition state to be ∼40 kJ mol−1and ∼180 J mol−1K−1, respectively. We have found that the addition of halothane effectively lowers the energy barrier for membrane fusion in less curved vesicles largely due to entropic advantages.
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Affiliation(s)
- Trinh T. Nguyen
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - David T. Cramb
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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13
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Sgouralis I, Madaan S, Djutanta F, Kha R, Hariadi RF, Pressé S. A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer. J Phys Chem B 2019; 123:675-688. [PMID: 30571128 DOI: 10.1021/acs.jpcb.8b09752] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We develop a Bayesian nonparametric framework to analyze single molecule FRET (smFRET) data. This framework, a variation on infinite hidden Markov models, goes beyond traditional hidden Markov analysis, which already treats photon shot noise, in three critical ways: (1) it learns the number of molecular states present in a smFRET time trace (a hallmark of nonparametric approaches), (2) it accounts, simultaneously and self-consistently, for photophysical features of donor and acceptor fluorophores (blinking kinetics, spectral cross-talk, detector quantum efficiency), and (3) it treats background photons. Point 2 is essential in reducing the tendency of nonparametric approaches to overinterpret noisy single molecule time traces and so to estimate states and transition kinetics robust to photophysical artifacts. As a result, with the proposed framework, we obtain accurate estimates of single molecule properties even when the supplied traces are excessively noisy, subject to photoartifacts, and of short duration. We validate our method using synthetic data sets and demonstrate its applicability to real data sets from single molecule experiments on Holliday junctions labeled with conventional fluorescent dyes.
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Affiliation(s)
- Ioannis Sgouralis
- Center for Biological Physics, Department of Physics , Arizona State University , Tempe , Arizona 85287 , United States
| | - Shreya Madaan
- School of Computing, Informatics, and Decision Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Franky Djutanta
- Biodesign Center for Molecular Design and Biomimetics, Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Rachael Kha
- School for Engineering of Matter, Transport and Energy , Arizona State University , Tempe , Arizona 85287 , United States
| | - Rizal F Hariadi
- Center for Biological Physics, Department of Physics , Arizona State University , Tempe , Arizona 85287 , United States.,Biodesign Center for Molecular Design and Biomimetics, Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Steve Pressé
- Center for Biological Physics, Department of Physics , Arizona State University , Tempe , Arizona 85287 , United States.,School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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14
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Betaneli V, Mücksch J, Schwille P. Fluorescence Correlation Spectroscopy to Examine Protein-Lipid Interactions in Membranes. Methods Mol Biol 2019; 2003:415-447. [PMID: 31218628 DOI: 10.1007/978-1-4939-9512-7_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a versatile technique to study membrane dynamics and protein-lipid interactions. It can provide information about diffusion coefficients, concentrations, and molecular interactions of proteins and lipids in the membrane. These parameters allow for the determination of protein partitioning into different lipid environments, the identification of lipid domains, and the detection of lipid-protein complexes on the membrane. During the last decades, FCS studies were successfully performed on model membrane systems as also on living cells, to characterize protein-lipid interactions. Recent developments of the method described here improved quantitative measurements on membranes and decreased the number of potential artifacts. The aim of this chapter is to provide the reader with the necessary information and some practical guidelines to perform FCS studies on artificial and cellular membranes.
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Affiliation(s)
- Viktoria Betaneli
- Medical Faculty "Carl Gustav Carus", Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Jonas Mücksch
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany.
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15
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Ahmed SM, Nishida-Fukuda H, Li Y, McDonald WH, Gradinaru CC, Macara IG. Exocyst dynamics during vesicle tethering and fusion. Nat Commun 2018; 9:5140. [PMID: 30510181 PMCID: PMC6277416 DOI: 10.1038/s41467-018-07467-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/01/2018] [Indexed: 11/15/2022] Open
Abstract
The exocyst is a conserved octameric complex that tethers exocytic vesicles to the plasma membrane prior to fusion. Exocyst assembly and delivery mechanisms remain unclear, especially in mammalian cells. Here we tagged multiple endogenous exocyst subunits with sfGFP or Halo using Cas9 gene-editing, to create single and double knock-in lines of mammary epithelial cells, and interrogated exocyst dynamics by high-speed imaging and correlation spectroscopy. We discovered that mammalian exocyst is comprised of tetrameric subcomplexes that can associate independently with vesicles and plasma membrane and are in dynamic equilibrium with octamer and monomers. Membrane arrival times are similar for subunits and vesicles, but with a small delay (~80msec) between subcomplexes. Departure of SEC3 occurs prior to fusion, whereas other subunits depart just after fusion. About 9 exocyst complexes are associated per vesicle. These data reveal the mammalian exocyst as a remarkably dynamic two-part complex and provide important insights into assembly/disassembly mechanisms. Exocyst complex tethers vesicles to plasma membranes, but assembly mechanisms remain unclear. Here, the authors use Cas9 gene editing to tag exocyst components in epithelial cells, and find that exocyst subcomplexes are recruited to membranes independently, but are both needed for vesicle fusion.
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Affiliation(s)
- Syed Mukhtar Ahmed
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA.
| | - Hisayo Nishida-Fukuda
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA.,Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Ehime, 7910295, Japan.,Department of Hepato-Biliary-Pancreatic and Breast Surgery, Ehime University Graduate School of Medicine, Toon, Ehime, 7910295, Japan.,Department of Genome Editing, Institute of Biomedical Sciences, Kansai Medical University, Hirakata, 5731010, Japan
| | - Yuchong Li
- Department of Physics, University of Toronto, Toronto, ON, M5S 1A7, Canada.,Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - W Hayes McDonald
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - Claudiu C Gradinaru
- Department of Physics, University of Toronto, Toronto, ON, M5S 1A7, Canada.,Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Ian G Macara
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA.
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16
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Werner S, Ebenhan J, Haupt C, Bacia K. A Quantitative and Reliable Calibration Standard for Dual-Color Fluorescence Cross-Correlation Spectroscopy. Chemphyschem 2018; 19:3436-3444. [PMID: 30489002 DOI: 10.1002/cphc.201800576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/29/2018] [Indexed: 11/06/2022]
Abstract
Dual-color Fluorescence Cross-Correlation Spectroscopy (dcFCCS) allows binding analysis of biomolecules. Combining cross- and autocorrelation amplitudes yields binding degrees and concentrations of bound and unbound species. However, non-ideal detection volume overlap reduces the cross-correlation, causing overestimation of the Kd . The overlap quality factor that relates measured and true cross-correlation amplitudes has been difficult to determine, because neither a perfect 1 : 1 labeled sample nor perfectly overlapping volumes are readily accomplished. Here, we describe how a stochastically labeled sample can be used for quantitative calibration. Lipid vesicles doped with green and red fluorescent dyes yield highly reproducible relative cross-correlations and allow determination of the setup-dependent overlap quality factor. This reliable, affordable and quick-to-prepare calibration standard expedites any quantitative co-localization or binding analysis by dcFCCS.
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Affiliation(s)
- Stefan Werner
- Institute of Chemistry, ZIK HALOmem and Charles-Tanford-Protein Center, University of Halle, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Jan Ebenhan
- Institute of Chemistry, ZIK HALOmem and Charles-Tanford-Protein Center, University of Halle, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Caroline Haupt
- Institute of Chemistry, ZIK HALOmem and Charles-Tanford-Protein Center, University of Halle, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Kirsten Bacia
- Institute of Chemistry, ZIK HALOmem and Charles-Tanford-Protein Center, University of Halle, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
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17
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Hertz E, Terenius L, Vukojević V, Svenningsson P. GPR37 and GPR37L1 differently interact with dopamine 2 receptors in live cells. Neuropharmacology 2018; 152:51-57. [PMID: 30423289 PMCID: PMC6599889 DOI: 10.1016/j.neuropharm.2018.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/26/2018] [Accepted: 11/08/2018] [Indexed: 02/09/2023]
Abstract
Receptor-receptor interactions are essential to fine tune receptor responses and new techniques enable closer characterization of the interactions between involved proteins directly in the plasma membrane. Fluorescence cross-correlation spectroscopy (FCCS), which analyses concurrent movement of bound molecules with single-molecule detection limit, was here used to, in live N2a cells, study interactions between the Parkinson's disease (PD) associated orphan receptor GPR37, its homologue GPR37L1, and the two splice variants of the dopamine 2 receptor (D2R). An interaction between GPR37 and both splice forms of D2R was detected. 4-phenylbutyrate (4-PBA), a neuroprotective chemical chaperone known to increase GPR37 expression at the cell surface, increased the fraction of interacting molecules. The interaction was also increased by pramipexole, a D2R agonist commonly used in the treatment of PD, indicating a possible clinically relevance. Cross-correlation, indicating interaction between GPR37L1 and the short isoform of D2R, was also detected. However, this interaction was not changed with 4-PBA or pramipexole treatment. Overall, these data provide further evidence that heteromeric GPR37-D2R exist and can be pharmacologically modulated, which is relevant for the treatment of PD. This article is part of the Special Issue entitled ‘Receptor heteromers and their allosteric receptor-receptor interactions’. GPCR interaction is studied with fluorescence cross-correlation spectroscopy. Interaction between GPR37 and both isoforms of D2R is detected in live cells. GPR37's homologue GPR37L1 is detected to interact with D2RS in live cells. GPR37-D2R interaction is increased by D2-like agonist and 4-PBA treatment.
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Affiliation(s)
- E Hertz
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden.
| | - L Terenius
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - V Vukojević
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - P Svenningsson
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden.
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18
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Li Y, Shivnaraine RV, Huang F, Wells JW, Gradinaru CC. Ligand-Induced Coupling between Oligomers of the M 2 Receptor and the G i1 Protein in Live Cells. Biophys J 2018; 115:881-895. [PMID: 30131171 DOI: 10.1016/j.bpj.2018.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/23/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023] Open
Abstract
Uncertainty over the mechanism of signaling via G protein-coupled receptors (GPCRs) relates in part to questions regarding their supramolecular structure. GPCRs and heterotrimeric G proteins are known to couple as monomers under various conditions. Many GPCRs form oligomers under many of the same conditions, however, and the biological role of those complexes is unclear. We have used dual-color fluorescence correlation spectroscopy to identify oligomers of the M2 muscarinic receptor and of Gi1 in purified preparations and live Chinese hamster ovary cells. Measurements on differently tagged receptors (i.e., eGFP-M2 and mCherry-M2) and G proteins (i.e., eGFP-Gαi1β1γ2 and mCherry-Gαi1β1γ2) detected significant cross-correlations between the two fluorophores in each case, both in detergent micelles and in live cells, indicating that both the receptor and Gi1 can exist as homo-oligomers. Oligomerization of differently tagged Gi1 decreased upon the activation of co-expressed wild-type M2 receptor by an agonist. Measurements on a tagged M2 receptor (M2-mCherry) and eGFP-Gαi1β1γ2 co-expressed in live cells detected cross-correlations only in the presence of an agonist, which therefore promoted coupling of the receptor and the G protein. The effect of the agonist was retained when a fluorophore-tagged receptor lacking the orthosteric site (i.e., M2(D103A)-mCherry) was co-expressed with the wild-type receptor and eGFP-Gαi1β1γ2, indicating that the ligand acted via an oligomeric receptor. Our results point to a model in which an agonist promotes transient coupling of otherwise independent oligomers of the M2 receptor on the one hand and of Gi1 on the other and that an activated complex leads to a reduction in the oligomeric size of the G protein. They suggest that GPCR-mediated signaling proceeds, at least in part, via oligomers.
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Affiliation(s)
- Yuchong Li
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Rabindra V Shivnaraine
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Fei Huang
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - James W Wells
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Claudiu C Gradinaru
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.
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19
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Schrimpf W, Lemmens V, Smisdom N, Ameloot M, Lamb DC, Hendrix J. Crosstalk-free multicolor RICS using spectral weighting. Methods 2018; 140-141:97-111. [DOI: 10.1016/j.ymeth.2018.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/15/2018] [Accepted: 01/30/2018] [Indexed: 11/16/2022] Open
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20
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Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling. Nat Commun 2017; 8:226. [PMID: 28790300 PMCID: PMC5548745 DOI: 10.1038/s41467-017-00253-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 06/14/2017] [Indexed: 01/28/2023] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of cell surface receptors. They can exist and act as dimers, but the requirement of dimers for agonist-induced signal initiation and structural dynamics remains largely unknown. Frizzled 6 (FZD6) is a member of Class F GPCRs, which bind WNT proteins to initiate signaling. Here, we show that FZD6 dimerizes and that the dimer interface of FZD6 is formed by the transmembrane α-helices four and five. Most importantly, we present the agonist-induced dissociation/re-association of a GPCR dimer through the use of live cell imaging techniques. Further analysis of a dimerization-impaired FZD6 mutant indicates that dimer dissociation is an integral part of FZD6 signaling to extracellular signal-regulated kinases1/2. The discovery of agonist-dependent dynamics of dimers as an intrinsic process of receptor activation extends our understanding of Class F and other dimerizing GPCRs, offering novel targets for dimer-interfering small molecules. Frizzled 6 (FZD6) is a G protein-coupled receptor (GPCR) involved in several cellular processes. Here, the authors use live cell imaging and spectroscopy to show that FZD6 forms dimers, whose association is regulated by WNT proteins and that dimer dissociation is crucial for FZD6 signaling.
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21
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Krüger D, Ebenhan J, Werner S, Bacia K. Measuring Protein Binding to Lipid Vesicles by Fluorescence Cross-Correlation Spectroscopy. Biophys J 2017; 113:1311-1320. [PMID: 28697897 DOI: 10.1016/j.bpj.2017.06.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/21/2017] [Accepted: 06/08/2017] [Indexed: 11/26/2022] Open
Abstract
Fluorescence correlation spectroscopy has been previously used to investigate peptide and protein binding to lipid membranes, as it allows for very low amounts of sample, short measurement times and equilibrium binding conditions. Labeling only one of the binding partners, however, comes with certain drawbacks, as it relies on identifying binding events by a change in diffusion coefficient. Since peptide and protein aggregation can obscure specific binding, and since non-stoichiometric binding necessitates the explicit choice of a statistical distribution for the number of bound ligands, we additionally label the liposomes and perform dual-color fluorescence cross-correlation spectroscopy (dcFCCS). We develop a theoretical framework showing that dcFCCS amplitudes allow calculation of the degree of ligand binding and the concentration of unbound ligand, leading to a model-independent binding curve. As the degree of labeling of the ligands does not factor into the measured quantities, it is permissible to mix labeled and unlabeled ligand, thereby extending the range of usable protein concentrations and accessible dissociation constants, KD. The total protein concentration, but not the fraction of labeled protein, needs to be known. In this work, we apply our dcFCCS analysis scheme to Sar1p, a protein of the COPII complex, which binds "major-minor-mix" liposomes. A Langmuir isotherm model yields KD=(2.1±1.1)μM as the single-site dissociation constant. The dcFCCS framework presented here is highly versatile for biophysical analysis of binding interactions. It may be applied to many types of fluorescently labeled ligands and small diffusing particles, including nanodiscs and liposomes containing membrane protein receptors.
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Affiliation(s)
- Daniela Krüger
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Ebenhan
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Stefan Werner
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Kirsten Bacia
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.
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22
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Shivnaraine RV, Fernandes DD, Ji H, Li Y, Kelly B, Zhang Z, Han YR, Huang F, Sankar KS, Dubins DN, Rocheleau JV, Wells JW, Gradinaru CC. Single-Molecule Analysis of the Supramolecular Organization of the M2 Muscarinic Receptor and the Gαi1 Protein. J Am Chem Soc 2016; 138:11583-98. [DOI: 10.1021/jacs.6b04032] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rabindra V. Shivnaraine
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Dennis D. Fernandes
- Department
of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Huiqiao Ji
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Yuchong Li
- Department
of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Brendan Kelly
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Krembil Research
Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | - Zhenfu Zhang
- Department
of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Yi Rang Han
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Fei Huang
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Krishana S. Sankar
- Department
of Physiology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - David N. Dubins
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Jonathan V. Rocheleau
- Department
of Physiology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Institute
of Biomedical and Biomaterial Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - James W. Wells
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Claudiu C. Gradinaru
- Department
of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
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23
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New Insight into Metal Ion-Driven Catalysis of Nucleic Acids by Influenza PA-Nter. PLoS One 2016; 11:e0156972. [PMID: 27300442 PMCID: PMC4907508 DOI: 10.1371/journal.pone.0156972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/23/2016] [Indexed: 11/24/2022] Open
Abstract
PA subunit of influenza RNA-dependent RNA polymerase deserves constantly increasing attention due to its essential role in influenza life cycle. N-terminal domain of PA (PA-Nter) harbors endonuclease activity, which is indispensable in viral transcription and replication. Interestingly, existing literature reports on in vitro ion preferences of the enzyme are contradictory. Some show PA-Nter activity exclusively with Mn2+, whereas others report Mg2+ as a natural cofactor. To clarify it, we performed a series of experiments with varied ion concentrations and substrate type. We observed cleavage in the presence of both ions, with a slight preference for manganese, however PA-Nter activity highly depended on the amount of residual, co-purified ions. Furthermore, to quantify cleavage reaction rate, we applied fluorescence cross-correlation spectroscopy (FCCS), providing highly sensitive and real-time monitoring of single molecules. Using nanomolar ssDNA in the regime of enzyme excess, we estimated the maximum reaction rate at 0.81± 0.38 and 1.38± 0.34 nM/min for Mg2+ and Mn2+, respectively. However, our calculations of PA-Nter ion occupancy, based on thermodynamic data, suggest Mg2+ to be a canonical metal in PA-Nter processing of RNA in vivo. Presented studies constitute a step toward better understanding of PA-Nter ion-dependent activity, which will possibly contribute to new successful inhibitor design in the future.
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24
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Isokane M, Walter T, Mahen R, Nijmeijer B, Hériché JK, Miura K, Maffini S, Ivanov MP, Kitajima TS, Peters JM, Ellenberg J. ARHGEF17 is an essential spindle assembly checkpoint factor that targets Mps1 to kinetochores. J Cell Biol 2016; 212:647-59. [PMID: 26953350 PMCID: PMC4792069 DOI: 10.1083/jcb.201408089] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 02/11/2016] [Indexed: 12/15/2022] Open
Abstract
The spindle assembly checkpoint (SAC) ensures genome stability during cell division. Here, a new essential SAC factor, ARHGEF17, is characterized by quantitative imaging, biochemical, and biophysical experiments, which show that it targets the checkpoint kinase Mps1 to kinetochores. To prevent genome instability, mitotic exit is delayed until all chromosomes are properly attached to the mitotic spindle by the spindle assembly checkpoint (SAC). In this study, we characterized the function of ARHGEF17, identified in a genome-wide RNA interference screen for human mitosis genes. Through a series of quantitative imaging, biochemical, and biophysical experiments, we showed that ARHGEF17 is essential for SAC activity, because it is the major targeting factor that controls localization of the checkpoint kinase Mps1 to the kinetochore. This mitotic function is mediated by direct interaction of the central domain of ARHGEF17 with Mps1, which is autoregulated by the activity of Mps1 kinase, for which ARHGEF17 is a substrate. This mitosis-specific role is independent of ARHGEF17’s RhoGEF activity in interphase. Our study thus assigns a new mitotic function to ARHGEF17 and reveals the molecular mechanism for a key step in SAC establishment.
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Affiliation(s)
- Mayumi Isokane
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Thomas Walter
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Robert Mahen
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bianca Nijmeijer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jean-Karim Hériché
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kota Miura
- Centre for Molecular and Cellular Imaging, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Miroslav Penchev Ivanov
- Molecular and Cellular Biology, Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Tomoya S Kitajima
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jan-Michael Peters
- Molecular and Cellular Biology, Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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25
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Imaging fluorescence (cross-) correlation spectroscopy in live cells and organisms. Nat Protoc 2015; 10:1948-74. [DOI: 10.1038/nprot.2015.100] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Tittel J, Welz T, Czogalla A, Dietrich S, Samol-Wolf A, Schulte M, Schwille P, Weidemann T, Kerkhoff E. Membrane targeting of the Spir·formin actin nucleator complex requires a sequential handshake of polar interactions. J Biol Chem 2015; 290:6428-44. [PMID: 25564607 DOI: 10.1074/jbc.m114.602672] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Spir and formin (FMN)-type actin nucleators initiate actin polymerization at vesicular membranes necessary for long range vesicular transport processes. Here we studied in detail the membrane binding properties and protein/protein interactions that govern the assembly of the membrane-associated Spir·FMN complex. Using biomimetic membrane models we show that binding of the C-terminal Spir-2 FYVE-type zinc finger involves both the presence of negatively charged lipids and hydrophobic contributions from the turret loop that intrudes the lipid bilayer. In solution, we uncovered a yet unknown intramolecular interaction between the Spir-2 FYVE-type domain and the N-terminal kinase non-catalytic C-lobe domain (KIND) that could not be detected in the membrane-bound state. Interestingly, we found that the intramolecular Spir-2 FYVE/KIND and the trans-regulatory Fmn-2-FSI/Spir-2-KIND interactions are competitive. We therefore characterized co-expressed Spir-2 and Fmn-2 fluorescent protein fusions in living cells by fluorescence cross-correlation spectroscopy. The data corroborate a model according to which Spir-2 exists in two different states, a cytosolic monomeric conformation and a membrane-bound state in which the KIND domain is released and accessible for subsequent Fmn-2 recruitment. This sequence of interactions mechanistically couples membrane binding of Spir to the recruitment of FMN, a pivotal step for initiating actin nucleation at vesicular membranes.
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Affiliation(s)
- Janine Tittel
- From the Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany, Biotechnology Center (BIOTEC), Biophysics Research Group and
| | - Tobias Welz
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany, and
| | - Aleksander Czogalla
- Paul Langerhans Institute, Technische Universität (TU) Dresden, Tatzberg 47-51, D-01307 Dresden, Germany, German Center for Diabetes Research (Deutsches Zentrum für Diabetesforschung), 85764 Neuherberg, Germany
| | - Susanne Dietrich
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany, and
| | - Annette Samol-Wolf
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany, and
| | - Markos Schulte
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany, and
| | - Petra Schwille
- From the Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany, Biotechnology Center (BIOTEC), Biophysics Research Group and
| | - Thomas Weidemann
- From the Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany, Biotechnology Center (BIOTEC), Biophysics Research Group and
| | - Eugen Kerkhoff
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany, and
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27
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Abstract
Fluorescence fluctuation spectroscopy techniques allow the quantification of fluorescent molecules present at the nanomolar concentration level. After a brief introduction to the technique, this chapter presents a protocol including background information in order to measure and quantify the molecular interaction of two signaling proteins inside the living cell using fluorescence cross-correlation spectroscopy.
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Affiliation(s)
- Mark A Hink
- Department Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy (LCAM), University of Amsterdam, Sciencepark 904, 1098 XH, Amsterdam, The Netherlands,
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28
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Gandhi H, Worch R, Kurgonaite K, Hintersteiner M, Schwille P, Bökel C, Weidemann T. Dynamics and interaction of interleukin-4 receptor subunits in living cells. Biophys J 2014; 107:2515-27. [PMID: 25468331 DOI: 10.1016/j.bpj.2014.07.077] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/08/2014] [Accepted: 07/24/2014] [Indexed: 11/19/2022] Open
Abstract
It has long been established that dimerization of Interleukin-4 receptor (IL-4R) subunits is a pivotal step for JAK/STAT signal transduction. However, ligand-induced complex formation at the surface of living cells has been challenging to observe. Here we report an experimental assay employing trisNTA dyes for orthogonal, external labeling of eGFP-tagged receptor constructs that allows the quantification of receptor heterodimerization by dual-color fluorescence cross-correlation spectroscopy. Fluorescence cross-correlation spectroscopy analysis at the plasma membrane shows that IL-4R subunit dimerization is indeed a strictly ligand-induced process. Under conditions of saturating cytokine occupancy, we determined intramembrane dissociation constants (K(d,2D)) of 180 and 480 receptors per μm(2) for the type-2 complexes IL-4:IL-4Rα/IL-13Rα1 and IL-13:IL-13Rα1/IL-4Rα, respectively. For the lower affinity type-1 complex IL-4:IL-4Rα/IL-2Rγ, we estimated a K(d,2D) of ∼1000 receptors per μm(2). The receptor densities required for effective dimerization thus exceed the typical, average expression levels by several orders of magnitude. In addition, we find that all three receptor subunits accumulate rapidly within a subpopulation of early sorting and recycling endosomes stably anchored just beneath the plasma membrane (cortical endosomes, CEs). The receptors, as well as labeled IL-4 and trisNTA ligands are specifically trafficked into CEs by a constitutive internalization mechanism. This may compensate for the inherent weak affinities that govern ligand-induced receptor dimerization at the plasma membrane. Consistently, activated receptors are also concentrated at the CEs. Our observations thus suggest that receptor trafficking may play an important role for the regulation of IL-4R-mediated JAK/STAT signaling.
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Affiliation(s)
- Hetvi Gandhi
- BIOTEC/Biophysics, Technische Universität Dresden, Dresden, Germany
| | - Remigiusz Worch
- BIOTEC/Biophysics, Technische Universität Dresden, Dresden, Germany; Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Kristina Kurgonaite
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | | | - Petra Schwille
- BIOTEC/Biophysics, Technische Universität Dresden, Dresden, Germany; Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christian Bökel
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Thomas Weidemann
- BIOTEC/Biophysics, Technische Universität Dresden, Dresden, Germany; Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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Weidemann T, Mücksch J, Schwille P. Fluorescence fluctuation microscopy: a diversified arsenal of methods to investigate molecular dynamics inside cells. Curr Opin Struct Biol 2014; 28:69-76. [DOI: 10.1016/j.sbi.2014.07.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/11/2014] [Indexed: 11/26/2022]
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Ivell R, Teerds K, Hoffman GE. Proper application of antibodies for immunohistochemical detection: antibody crimes and how to prevent them. Endocrinology 2014; 155:676-87. [PMID: 24428532 PMCID: PMC3929726 DOI: 10.1210/en.2013-1971] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 12/16/2013] [Indexed: 11/19/2022]
Abstract
For several decades antibodies raised against specific proteins, peptides, or peptide epitopes have proven to be versatile and very powerful tools to demonstrate molecular identity in cells and tissues. New techniques of immunohistochemistry and immunofluorescence have improved both the optical resolution of such protein identification as well as its sensitivity, particularly through the use of amplification methodology. However, this improved sensitivity has also increased the risks of false-positive and false-negative staining and thereby raised the necessity for proper and adequate controls. In this review, the authors draw on many years of experience to illuminate many of the more common errors and problematic issues in immunohistochemistry, and how these may be avoided. A key factor in all of this is that techniques need to be properly documented and especially antibodies and procedures must be adequately described. Antibodies are a valuable and shared resource within the scientific community; it is essential therefore that mistakes involving antibodies and their controls are not perpetuated through inadequate reporting in the literature.
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Affiliation(s)
- Richard Ivell
- Leibniz Institute for Farm Animal Biology (R.I.), 18196 Dummerstorf, Germany; School of Molecular and Biomedical Science (R.I.), University of Adelaide, SA5005, Australia; Department of Animal Sciences (K.T.), Wageningen University, 6709 WD Wageningen, The Netherlands; and Department of Biology (G.E.H.), Morgan State University, Baltimore, Maryland 21251
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Benda A, Kapusta P, Hof M, Gaus K. Fluorescence spectral correlation spectroscopy (FSCS) for probes with highly overlapping emission spectra. OPTICS EXPRESS 2014; 22:2973-2988. [PMID: 24663589 DOI: 10.1364/oe.22.002973] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We present a fluorescence correlation spectroscopy (FCS) approach to obtain spectral cross-talk free auto- and cross-correlation functions for probes with highly overlapping emission spectra. Confocal microscopes with either a hyperspectral EM-CCD or six-channel PMT array spectral detection were used, followed by a photon filtering correlation approach that results in spectral unmixing. The method is highly sensitive and can distinguish between Atto488 and Oregon Green 488 signals so that auto-correlation curves can be fitted without the need for cross-talk correction. We also applied the approach to the membrane dye Laurdan whose emission is dependent on the lipid order within the bilayer. With fluorescence spectral correlation spectroscopy (FSCS), we could obtain spectral cross-talk free auto- and cross-correlation functions corresponding to Laurdan located in liquid ordered and liquid disordered phases.
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Hou S, Sun L, Wieczorek SA, Kalwarczyk T, Kaminski TS, Holyst R. Fluorescence correlation spectroscopy analysis for accurate determination of proportion of doubly labeled DNA in fluorescent DNA pool for quantitative biochemical assays. Biosens Bioelectron 2014; 51:8-15. [DOI: 10.1016/j.bios.2013.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 06/29/2013] [Accepted: 07/06/2013] [Indexed: 11/24/2022]
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Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is a single-molecule sensitive technique to quantitatively study interactions among fluorescently tagged biomolecules. Besides the initial implementation as dual-color FCCS (DC-FCCS), FCCS has several powerful derivatives, including single-wavelength FCCS (SW-FCCS), two-photon FCCS (TP-FCCS), and pulsed interleaved excitation FCCS (PIE-FCCS). However, to apply FCCS successfully, one needs to be familiar with procedures ranging from fluorescent labeling, instrumentation setup and alignment, sample preparation, and data analysis. Here, we describe the procedures to apply FCCS in various biological samples ranging from live cells to in vivo measurements, with the focus on DC-FCCS and SW-FCCS.
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Hendrix J, Lamb DC. Implementation and application of pulsed interleaved excitation for dual-color FCS and RICS. Methods Mol Biol 2014; 1076:653-682. [PMID: 24108649 DOI: 10.1007/978-1-62703-649-8_30] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Pulsed interleaved excitation (PIE) employs pulsed laser sources that are interleaved such that differentially colored fluorophores can be measured or imaged quasi-simultaneously in the absence of spectral crosstalk. PIE improves the robustness and reduces data analysis complexity of many fluorescence techniques, such as fluorescence cross-correlation spectroscopy (FCCS) and raster image cross-correlation spectroscopy (ccRICS), two methods used for quantitative investigation of molecular interactions in vitro and in living cells. However, as PIE is most often used for fluorescence fluctuation spectroscopy and burst analysis experiments and utilizes time-correlated single-photon counting detection and advanced optoelectronics, it has remained a technique that is mostly used by specialized single-molecule research groups. This protocols chapter provides an accessible overview of PIE for anyone considering implementing the method on a homebuilt or commercial microscope. We give details on the instrumentation, data collection and analysis software, on how to properly set up and align a PIE microscope, and finally, on how to perform proper dual-color FCS and RICS experiments.
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Affiliation(s)
- Jelle Hendrix
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilian-Universität München, Munich, Germany
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Weidemann T, Schwille P. Dual-color fluorescence cross-correlation spectroscopy with continuous laser excitation in a confocal setup. Methods Enzymol 2013; 518:43-70. [PMID: 23276535 DOI: 10.1016/b978-0-12-388422-0.00003-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Fluorescence correlation spectroscopy evaluates local signal fluctuations arising from stochastic movements of fluorescent particles in solution. The measured fluctuating signal is correlated in time and analyzed with appropriate model functions containing the parameters that describe the underlying molecular behavior. The dual-color extension, fluorescence cross-correlation spectroscopy (FCCS) allows for a comparison between spectrally well-separated channels to extract codiffusion events that reflect interactions between differently labeled molecules. In addition to solution measurements, FCCS can be applied with subcellular resolution and is therefore a very promising approach for a quantitative biochemical assessment of molecular networks in living cells. To derive thermodynamic and kinetic reaction parameters, the influence of a number of other factors like background noise, illumination intensity profiles, photophysical processes, and cross talk between the channels have to be treated. Here, we provide a roadmap to derive binding reaction data with dual-color FCCS using continuous wave laser excitation, as it is now accessible with many state-of-the-art confocal microscopes.
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Affiliation(s)
- Thomas Weidemann
- Biophysics/BIOTEC, Technische Universität Dresden, Dresden, Germany.
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