1
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Schneider F, Cespedes PF, Karedla N, Dustin ML, Fritzsche M. Quantifying biomolecular organisation in membranes with brightness-transit statistics. Nat Commun 2024; 15:7082. [PMID: 39152104 PMCID: PMC11329664 DOI: 10.1038/s41467-024-51435-1] [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: 03/05/2024] [Accepted: 08/07/2024] [Indexed: 08/19/2024] Open
Abstract
Cells crucially rely on the interactions of biomolecules at their plasma membrane to maintain homeostasis. Yet, a methodology to systematically quantify biomolecular organisation, measuring diffusion dynamics and oligomerisation, represents an unmet need. Here, we introduce the brightness-transit statistics (BTS) method based on fluorescence fluctuation spectroscopy and combine information from brightness and transit times to elucidate biomolecular diffusion and oligomerisation in both cell-free in vitro and in vitro systems incorporating living cells. We validate our approach in silico with computer simulations and experimentally using oligomerisation of EGFP tethered to supported lipid bilayers. We apply our pipeline to study the oligomerisation of CD40 ectodomain in vitro and endogenous CD40 on primary B cells. While we find a potential for CD40 to oligomerize in a concentration or ligand depended manner, we do not observe mobile oligomers on B cells. The BTS method combines sensitive analysis, quantification, and intuitive visualisation of dynamic biomolecular organisation.
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Affiliation(s)
- Falk Schneider
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom.
- Translational Imaging Center, University of Southern California, Los Angeles, California, 90089, United States of America.
| | - Pablo F Cespedes
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
| | - Narain Karedla
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
- Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0FA, United Kingdom
| | - Michael L Dustin
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
| | - Marco Fritzsche
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom.
- Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0FA, United Kingdom.
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2
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Ciuffreda P, Xynomilakis O, Casati S, Ottria R. Fluorescence-Based Enzyme Activity Assay: Ascertaining the Activity and Inhibition of Endocannabinoid Hydrolytic Enzymes. Int J Mol Sci 2024; 25:7693. [PMID: 39062935 PMCID: PMC11276806 DOI: 10.3390/ijms25147693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The endocannabinoid system, known for its regulatory role in various physiological processes, relies on the activities of several hydrolytic enzymes, such as fatty acid amide hydrolase (FAAH), N-acylethanolamine-hydrolyzing acid amidase (NAAA), monoacylglycerol lipase (MAGL), and α/β-hydrolase domains 6 (ABHD6) and 12 (ABHD12), to maintain homeostasis. Accurate measurement of these enzymes' activities is crucial for understanding their function and for the development of potential therapeutic agents. Fluorometric assays, which offer high sensitivity, specificity, and real-time monitoring capabilities, have become essential tools in enzymatic studies. This review provides a comprehensive overview of the principles behind these assays, the various substrates and fluorophores used, and advances in assay techniques used not only for the determination of the kinetic mechanisms of enzyme reactions but also for setting up kinetic assays for the high-throughput screening of each critical enzyme involved in endocannabinoid degradation. Through this comprehensive review, we aim to highlight the strengths and limitations of current fluorometric assays and suggest future directions for improving the measurement of enzyme activity in the endocannabinoid system.
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Affiliation(s)
| | | | | | - Roberta Ottria
- Dipartimento di Scienze Biomediche e Cliniche, Università degli Studi di Milano, 20157 Milan, Italy; (P.C.); (O.X.); (S.C.)
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3
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Ujlaky-Nagy L, Szöllősi J, Vereb G. Disrupting EGFR-HER2 Transactivation by Pertuzumab in HER2-Positive Cancer: Quantitative Analysis Reveals EGFR Signal Input as Potential Predictor of Therapeutic Outcome. Int J Mol Sci 2024; 25:5978. [PMID: 38892166 PMCID: PMC11173106 DOI: 10.3390/ijms25115978] [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: 04/05/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Pertuzumab (Perjeta®), a humanized antibody binding to the dimerization arm of HER2 (Human epidermal growth factor receptor-2), has failed as a monotherapy agent in HER2 overexpressing malignancies. Since the molecular interaction of HER2 with ligand-bound EGFR (epidermal growth factor receptor) has been implied in mitogenic signaling and malignant proliferation, we hypothesized that this interaction, rather than HER2 expression and oligomerization alone, could be a potential molecular target and predictor of the efficacy of pertuzumab treatment. Therefore, we investigated static and dynamic interactions between HER2 and EGFR molecules upon EGF stimulus in the presence and absence of pertuzumab in HER2+ EGFR+ SK-BR-3 breast tumor cells using Förster resonance energy transfer (FRET) microscopy and fluorescence correlation and cross-correlation spectroscopy (FCS/FCCS). The consequential activation of signaling and changes in cell proliferation were measured by Western blotting and MTT assay. The autocorrelation functions of HER2 diffusion were best fitted by a three-component model corrected for triplet formation, and among these components the slowly diffusing membrane component revealed aggregation induced by EGFR ligand binding, as evidenced by photon-counting histograms and co-diffusing fractions. This aggregation has efficiently been prevented by pertuzumab treatment, which also inhibited the post-stimulus interaction of EGFR and HER2, as monitored by changes in FRET efficiency. Overall, the data demonstrated that pertuzumab, by hindering post-stimulus interaction between EGFR and HER2, inhibits EGFR-evoked HER2 aggregation and phosphorylation and leads to a dose-dependent decrease in cell proliferation, particularly when higher amounts of EGF are present. Consequently, we propose that EGFR expression on HER2-positive tumors could be taken into consideration as a potential biomarker when predicting the outcome of pertuzumab treatment.
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Affiliation(s)
- László Ujlaky-Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
- HUN-REN-UD Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
- HUN-REN-UD Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
- HUN-REN-UD Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
- Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
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4
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Kar M, Vogel LT, Chauhan G, Felekyan S, Ausserwöger H, Welsh TJ, Dar F, Kamath AR, Knowles TPJ, Hyman AA, Seidel CAM, Pappu RV. Solutes unmask differences in clustering versus phase separation of FET proteins. Nat Commun 2024; 15:4408. [PMID: 38782886 PMCID: PMC11116469 DOI: 10.1038/s41467-024-48775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Phase separation and percolation contribute to phase transitions of multivalent macromolecules. Contributions of percolation are evident through the viscoelasticity of condensates and through the formation of heterogeneous distributions of nano- and mesoscale pre-percolation clusters in sub-saturated solutions. Here, we show that clusters formed in sub-saturated solutions of FET (FUS-EWSR1-TAF15) proteins are affected differently by glutamate versus chloride. These differences on the nanoscale, gleaned using a suite of methods deployed across a wide range of protein concentrations, are prevalent and can be unmasked even though the driving forces for phase separation remain unchanged in glutamate versus chloride. Strikingly, differences in anion-mediated interactions that drive clustering saturate on the micron-scale. Beyond this length scale the system separates into coexisting phases. Overall, we find that sequence-encoded interactions, mediated by solution components, make synergistic and distinct contributions to the formation of pre-percolation clusters in sub-saturated solutions, and to the driving forces for phase separation.
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Affiliation(s)
- Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Laura T Vogel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Gaurav Chauhan
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Suren Felekyan
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Hannes Ausserwöger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Anjana R Kamath
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Anthony A Hyman
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany.
| | - Claus A M Seidel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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5
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Clayton AHA. Photobleaching FRET-FLIM-ICS for quaternary structure quantification on cells. Theory and simulations. Biochim Biophys Acta Gen Subj 2024; 1868:130618. [PMID: 38621595 DOI: 10.1016/j.bbagen.2024.130618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/04/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The oligomerization of proteins is an important biological control mechanism and has several functions in activity and stability of enzymes, structural proteins, ion channels and transcription factors. The determination of the relevant oligomeric states in terms of geometry (spatial extent), oligomer size (monomer or dimer or oligomer) and affinity (amounts of monomer, dimer and oligomer) is a challenging biophysical problem. Förster resonance energy transfer and fluorescence fluctuation spectroscopy are powerful tools that are sensitive to proximity and oligomerization respectively. Here it is proposed to combine image-based lifetime-detected Forster resonance energy transfer with image correlation spectroscopy and photobleaching to determine distances, oligomer sizes and oligomer distributions. Simulations for simple oligomeric forms illustrate the potential to improve the discrimination between different quaternary states in the cellular milieu.
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Affiliation(s)
- Andrew H A Clayton
- Cell Biophysics Laboratory, Optical Sciences Centre, Department of Physics and Astronomy, School of Science, Computer, and Engineering Sciences, Swinburne University of Technology, Melbourne, Australia.
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6
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Geiser A, Foylan S, Tinning PW, Bryant NJ, Gould GW. GLUT4 dispersal at the plasma membrane of adipocytes: a super-resolved journey. Biosci Rep 2023; 43:BSR20230946. [PMID: 37791639 PMCID: PMC10600063 DOI: 10.1042/bsr20230946] [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: 09/07/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/05/2023] Open
Abstract
In adipose tissue, insulin stimulates glucose uptake by mediating the translocation of GLUT4 from intracellular vesicles to the plasma membrane. In 2010, insulin was revealed to also have a fundamental impact on the spatial distribution of GLUT4 within the plasma membrane, with the existence of two GLUT4 populations at the plasma membrane being defined: (1) as stationary clusters and (2) as diffusible monomers. In this model, in the absence of insulin, plasma membrane-fused GLUT4 are found to behave as clusters. These clusters are thought to arise from exocytic events that retain GLUT4 at their fusion sites; this has been proposed to function as an intermediate hub between GLUT4 exocytosis and re-internalisation. By contrast, insulin stimulation induces the dispersal of GLUT4 clusters into monomers and favours a distinct type of GLUT4-vesicle fusion event, known as fusion-with-release exocytosis. Here, we review how super-resolution microscopy approaches have allowed investigation of the characteristics of plasma membrane-fused GLUT4 and further discuss regulatory step(s) involved in the GLUT4 dispersal machinery, introducing the scaffold protein EFR3 which facilitates localisation of phosphatidylinositol 4-kinase type IIIα (PI4KIIIα) to the cell surface. We consider how dispersal may be linked to the control of transporter activity, consider whether macro-organisation may be a widely used phenomenon to control proteins within the plasma membrane, and speculate on the origin of different forms of GLUT4-vesicle exocytosis.
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Affiliation(s)
- Angéline Geiser
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, U.K
| | - Shannan Foylan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, U.K
| | - Peter W Tinning
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, U.K
| | - Nia J Bryant
- Department of Biology, University of York, Heslington, York, U.K
| | - Gwyn W Gould
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, U.K
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7
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Centofanti E, Wang C, Iyer S, Krichevsky O, Oyler-Yaniv A, Oyler-Yaniv J. The spread of interferon-γ in melanomas is highly spatially confined, driving nongenetic variability in tumor cells. Proc Natl Acad Sci U S A 2023; 120:e2304190120. [PMID: 37603742 PMCID: PMC10468618 DOI: 10.1073/pnas.2304190120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/12/2023] [Indexed: 08/23/2023] Open
Abstract
Interferon-γ (IFNγ) is a critical antitumor cytokine that has varied effects on different cell types. The global effect of IFNγ in the tumor depends on which cells it acts upon and the spatial extent of its spread. Reported measurements of IFNγ spread vary dramatically in different contexts, ranging from nearest-neighbor signaling to perfusion throughout the entire tumor. Here, we apply theoretical considerations to experiments both in vitro and in vivo to study the spread of IFNγ in melanomas. We observe spatially confined niches of IFNγ signaling in 3-D mouse melanoma cultures and human tumors that generate cellular heterogeneity in gene expression and alter the susceptibility of affected cells to T cell killing. Widespread IFNγ signaling only occurs when niches overlap due to high local densities of IFNγ-producing T cells. We measured length scales of ~30 to 40 μm for IFNγ spread in B16 mouse melanoma cultures and human primary cutaneous melanoma. Our results are consistent with IFNγ spread being governed by a simple diffusion-consumption model and offer insight into how the spatial organization of T cells contributes to intratumor heterogeneity in inflammatory signaling, gene expression, and immune-mediated clearance. Solid tumors are often viewed as collections of diverse cellular "neighborhoods": Our work provides a general explanation for such nongenetic cellular variability due to confinement in the spread of immune mediators.
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Affiliation(s)
- Edoardo Centofanti
- The Department of Systems Biology at Harvard Medical School, Boston, MA02115
| | - Chad Wang
- The Systems, Synthetic, and Quantitative Biology Graduate Program at Harvard Medical School, Boston, MA02115
| | - Sandhya Iyer
- The Department of Systems Biology at Harvard Medical School, Boston, MA02115
| | - Oleg Krichevsky
- The Department of Physics at Ben Gurion University of the Negev, Beer-Sheva8410501, Israel
| | - Alon Oyler-Yaniv
- The Department of Systems Biology at Harvard Medical School, Boston, MA02115
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8
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Kar M, Vogel LT, Chauhan G, Ausserwöger H, Welsh TJ, Kamath AR, Knowles TPJ, Hyman AA, Seidel CAM, Pappu RV. Glutamate helps unmask the differences in driving forces for phase separation versus clustering of FET family proteins in sub-saturated solutions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.552963. [PMID: 37609232 PMCID: PMC10441405 DOI: 10.1101/2023.08.11.552963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Multivalent proteins undergo coupled segregative and associative phase transitions. Phase separation, a segregative transition, is driven by macromolecular solubility, and this leads to coexisting phases above system-specific saturation concentrations. Percolation is a continuous transition that is driven by multivalent associations among cohesive motifs. Contributions from percolation are highlighted by the formation of heterogeneous distributions of clusters in sub-saturated solutions, as was recently reported for Fused in sarcoma (FUS) and FET family proteins. Here, we show that clustering and phase separation are defined by a separation of length- and energy-scales. This is unmasked when glutamate is the primary solution anion. Glutamate is preferentially excluded from protein sites, and this enhances molecular associations. Differences between glutamate and chloride are manifest at ultra-low protein concentrations. These differences are amplified as concentrations increase, and they saturate as the micron-scale is approached. Therefore, condensate formation in supersaturated solutions and clustering in sub-saturated are governed by distinct energy and length scales. Glutamate, unlike chloride, is the dominant intracellular anion, and the separation of scales, which is masked in chloride, is unmasked in glutamate. Our work highlights how components of cellular milieus and sequence-encoded interactions contribute to amplifying distinct contributions from associative versus segregative phase transitions.
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9
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Gopich IV, Kim JY, Chung HS. Analysis of photon trajectories from diffusing single molecules. J Chem Phys 2023; 159:024119. [PMID: 37431909 PMCID: PMC10474944 DOI: 10.1063/5.0153114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 07/12/2023] Open
Abstract
In single-molecule free diffusion experiments, molecules spend most of the time outside a laser spot and generate bursts of photons when they diffuse through the focal spot. Only these bursts contain meaningful information and, therefore, are selected using physically reasonable criteria. The analysis of the bursts must take into account the precise way they were chosen. We present new methods that allow one to accurately determine the brightness and diffusivity of individual molecule species from the photon arrival times of selected bursts. We derive analytical expressions for the distribution of inter-photon times (with and without burst selection), the distribution of the number of photons in a burst, and the distribution of photons in a burst with recorded arrival times. The theory accurately treats the bias introduced due to the burst selection criteria. We use a Maximum Likelihood (ML) method to find the molecule's photon count rate and diffusion coefficient from three kinds of data, i.e., the bursts of photons with recorded arrival times (burstML), inter-photon times in bursts (iptML), and the numbers of photon counts in a burst (pcML). The performance of these new methods is tested on simulated photon trajectories and on an experimental system, the fluorophore Atto 488.
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Affiliation(s)
- Irina V. Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jae-Yeol Kim
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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10
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Blum D, Reuter M, Schliebs W, Tomaschewski J, Erdmann R, Wagner R. Membrane binding and pore forming insertion of PEX5 into horizontal lipid bilayer. Biol Chem 2023; 404:157-167. [PMID: 36260915 DOI: 10.1515/hsz-2022-0183] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022]
Abstract
The assembly of the peroxisomal translocon involves the transition of a soluble form of the peroxisomal targeting receptor PEX5 into a membrane-bound form, which becomes an integral membrane component of the import pore for peroxisomal matrix proteins. How this transition occurs is still a mystery. We addressed this question using a artificial horizontal bilayer in combination with fluorescence time-correlated single photon counting (TCSPC) and electrophysiological channel recording. Purified human isoform PEX5L and truncated PEX5L(1-335) lacking the cargo binding domain were selectively labeled with thiol-reactive Atto-dyes. Diffusion coefficients of labeled protein in solution show that PEX5L is monomeric with a rather compact spherical conformation, while the truncated protein appeared in a more extended conformation. Labeled PEX5L and the truncated PEX5L(1-335) bind stably to horizontal bilayer thereby accumulating around 100-fold. The diffusion coefficients of the membrane-bound PEX5L forms are 3-4 times lower than in solution, indicating the formation of larger complexes. Electrophysiological single channel recording shows that membrane-bound labeled and non-labeled PEX5L, but not the truncated PEX5L(1-335), can form ion conducting membrane channels. The data suggest that PEX5L is the pore-forming component of the oligomeric peroxisomal translocon and that spontaneous PEX5L membrane surface binding might be an important step in its assembly.
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Affiliation(s)
- Daniel Blum
- MOLIFE Research Center, Jacobs, University Bremen, D-28759 Bremen, Germany
| | - Maren Reuter
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Wolfgang Schliebs
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Jana Tomaschewski
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Ralf Erdmann
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Richard Wagner
- MOLIFE Research Center, Jacobs, University Bremen, D-28759 Bremen, Germany
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11
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Liu L, Chen Q, Lv J, Li Y, Wang K, Li JR. Stable Metal-Organic Frameworks for Fluorescent Detection of Tetracycline Antibiotics. Inorg Chem 2022; 61:8015-8021. [PMID: 35544341 DOI: 10.1021/acs.inorgchem.2c00754] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rapid detection of antibiotics in agricultural products is of great significance. In this work, two stable fluorescent metal-organic frameworks (MOFs), BUT-178 and BUT-179, are synthesized and used to detect tetracycline antibiotics. Among them, BUT-179 exhibits better performance in the detection of different tetracycline antibiotics in water and eggs. The limits of detection of BUT-179 toward tetracycline, aureomycin, oxytetracycline, and doxycycline all reach the nanomolar level. Furthermore, the cycling tests confirm that BUT-179 can be easily recovered and repeatedly used without an obvious performance loss. This work demonstrates the excellent application potential of MOFs for food safety, especially the fluorescence detection of antibiotics in foods.
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Affiliation(s)
- Lu Liu
- Beijing Key Laboratory for Green Catalysis and Separation and Department of Environmental Chemical Engineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - Qiang Chen
- Beijing Key Laboratory for Green Catalysis and Separation and Department of Environmental Chemical Engineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - Jie Lv
- Beijing Key Laboratory for Green Catalysis and Separation and Department of Environmental Chemical Engineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yaping Li
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Kecheng Wang
- Beijing Key Laboratory for Green Catalysis and Separation and Department of Environmental Chemical Engineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - Jian-Rong Li
- Beijing Key Laboratory for Green Catalysis and Separation and Department of Environmental Chemical Engineering, Beijing University of Technology, Beijing 100124, P. R. China
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12
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Barth A, Opanasyuk O, Peulen TO, Felekyan S, Kalinin S, Sanabria H, Seidel CAM. Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines. J Chem Phys 2022; 156:141501. [PMID: 35428384 PMCID: PMC9014241 DOI: 10.1063/5.0089134] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 01/31/2023] Open
Abstract
Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule studies of Förster Resonance Energy Transfer (smFRET) between a tethered donor and acceptor dye pair are a powerful tool to investigate the structure and dynamics of labeled molecules. However, capturing and quantifying conformational dynamics in intensity-based smFRET experiments remains challenging when the dynamics occur on the sub-millisecond timescale. The method of multiparameter fluorescence detection addresses this challenge by simultaneously registering fluorescence intensities and lifetimes of the donor and acceptor. Together, two FRET observables, the donor fluorescence lifetime τD and the intensity-based FRET efficiency E, inform on the width of the FRET efficiency distribution as a characteristic fingerprint for conformational dynamics. We present a general framework for analyzing dynamics that relates average fluorescence lifetimes and intensities in two-dimensional burst frequency histograms. We present parametric relations of these observables for interpreting the location of FRET populations in E-τD diagrams, called FRET-lines. To facilitate the analysis of complex exchange equilibria, FRET-lines serve as reference curves for a graphical interpretation of experimental data to (i) identify conformational states, (ii) resolve their dynamic connectivity, (iii) compare different kinetic models, and (iv) infer polymer properties of unfolded or intrinsically disordered proteins. For a simplified graphical analysis of complex kinetic networks, we derive a moment-based representation of the experimental data that decouples the motion of the fluorescence labels from the conformational dynamics of the biomolecule. Importantly, FRET-lines facilitate exploring complex dynamic models via easily computed experimental observables. We provide extensive computational tools to facilitate applying FRET-lines.
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Affiliation(s)
- Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Oleg Opanasyuk
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Thomas-Otavio Peulen
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Stanislav Kalinin
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29631, USA
| | - Claus A. M. Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
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13
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Sparrenberg LT, Greiner B, Mathis HP. The Mean Single Molecule Rate (mSMR) in the Analysis of Fluorescence Fluctuations: Measurements on DNA Mixtures of Defined Composition. J Fluoresc 2021; 31:1883-1894. [PMID: 34529200 PMCID: PMC8547212 DOI: 10.1007/s10895-021-02803-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/11/2021] [Indexed: 12/03/2022]
Abstract
We present a method for the evaluation of fluorescence fluctuations on the basis of Mandel’s Q parameter, using sampling time-dependent factorial cumulants. By relating the Q parameter to the sampling time, we obtain the mean single molecule rate (mSMR), an easy to interpret expression that provides both brightness and diffusion information. The model is suitable for the widely used confocal setups with single photon excitation and a single detection channel. We present a way to correct the mSMR for afterpulsing, dead time and background noise. To account for photokinetic effects at short sampling times, we expand the model by a simple on/off isomerization term, which is similar to the well-known triplet model. The functionality of the mSMR is shown using Monte Carlo simulations. The correction mechanisms and the experimental applicability of the model are then demonstrated by DNA measurements of defined composition. By systematically analyzing DNA mixtures, we can show that at large sampling times, the mSMR correctly describes the single molecule brightness rates and the diffusive properties of DNA molecules. At short sampling times, the photokinetic effects of isomerization are accurately described by the mSMR model. Since additionally the mSMR can easily be corrected for measurement artefacts such as detector dead time, afterpulsing and background noise, this is a valuable advantage over the standard method of fluorescence correlation spectroscopy.
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Affiliation(s)
- Lorenz T Sparrenberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany. .,Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany.
| | - Benjamin Greiner
- Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany
| | - Harald P Mathis
- Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany
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14
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Nederveen-Schippers LM, Pathak P, Keizer-Gunnink I, Westphal AH, van Haastert PJM, Borst JW, Kortholt A, Skakun V. Combined FCS and PCH Analysis to Quantify Protein Dimerization in Living Cells. Int J Mol Sci 2021; 22:ijms22147300. [PMID: 34298920 PMCID: PMC8307594 DOI: 10.3390/ijms22147300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 11/29/2022] Open
Abstract
Protein dimerization plays a crucial role in the regulation of numerous biological processes. However, detecting protein dimers in a cellular environment is still a challenge. Here we present a methodology to measure the extent of dimerization of GFP-tagged proteins in living cells, using a combination of fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analysis of single-color fluorescence fluctuation data. We named this analysis method brightness and diffusion global analysis (BDGA) and adapted it for biological purposes. Using cell lysates containing different ratios of GFP and tandem-dimer GFP (diGFP), we show that the average brightness per particle is proportional to the fraction of dimer present. We further adapted this methodology for its application in living cells, and we were able to distinguish GFP, diGFP, as well as ligand-induced dimerization of FKBP12 (FK506 binding protein 12)-GFP. While other analysis methods have only sporadically been used to study dimerization in living cells and may be prone to errors, this paper provides a robust approach for the investigation of any cytosolic protein using single-color fluorescence fluctuation spectroscopy.
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Affiliation(s)
- Laura M. Nederveen-Schippers
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Pragya Pathak
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Ineke Keizer-Gunnink
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Adrie H. Westphal
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (A.H.W.); (J.W.B.)
| | - Peter J. M. van Haastert
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (A.H.W.); (J.W.B.)
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
- Correspondence: (A.K.); (V.S.)
| | - Victor Skakun
- Department of Systems Analysis and Computer Simulation, Belarusian State University, 220030 Minsk, Belarus
- Correspondence: (A.K.); (V.S.)
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15
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Blunck R. Determining stoichiometry of ion channel complexes using single subunit counting. Methods Enzymol 2021; 653:377-404. [PMID: 34099180 DOI: 10.1016/bs.mie.2021.02.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Abstract
Most membrane proteins, and ion channels in particular, assemble to multimeric biological complexes. This starts with the quarternary structure and continues with the recruitment of auxiliary subunits and oligomerization or clustering of the complexes. While the quarternary structure is best determined by atomic-scale structures, stoichiometry of heteromers and dynamic changes in the assembly cannot necessarily be investigated with structural methods. Here, single subunit counting has proven a powerful method to study the composition of these complexes. Single subunit counting uses the irreversible photodestruction of fluorescent tags as means to directly count a labeled subunit and thereby derive the composition of the assemblies. In this chapter, we discuss single subunit counting and its limitations. We present alternative methods and provide a detailed protocol for recording and analysis of single subunit counting data.
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Affiliation(s)
- Rikard Blunck
- Department of Physics, Université de Montréal, Montréal, QC, Canada.
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16
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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17
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Perego E, Köster S. Exploring early time points of vimentin assembly in flow by fluorescence fluctuation spectroscopy. LAB ON A CHIP 2021; 21:735-745. [PMID: 33491697 DOI: 10.1039/d0lc00985g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Despite the importance for cellular processes, the dynamics of molecular assembly, especially on fast time scales, is not yet fully understood. To this end, we present a multi-layer microfluidic device and combine it with fluorescence fluctuation spectroscopy. We apply this innovative combination of methods to investigate the early steps in assembly of vimentin intermediate filaments (IFs). These filaments, together with actin filaments and microtubules, constitute the cytoskeleton of cells of mesenchymal origin and greatly influence their mechanical properties. We are able to directly follow the two-step assembly process of vimentin IFs and quantify the time scale of the first lateral step to tens of ms with a lag time of below 3 ms. Although demonstrated for a specific biomolecular system here, our method may potentially be employed for a wide range of fast molecular reactions in biological or, more generally, soft matter systems, as it allows for a precise quantification of the kinetics underlying the aggregation and assembly.
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Affiliation(s)
- Eleonora Perego
- Institute for X-Ray Physics, University of Göttingen, 37077 Göttingen, Germany.
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, 37077 Göttingen, Germany. and Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
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18
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Application of Advanced Light Microscopy to the Study of HIV and Its Interactions with the Host. Viruses 2021; 13:v13020223. [PMID: 33535486 PMCID: PMC7912744 DOI: 10.3390/v13020223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/24/2022] Open
Abstract
This review highlights the significant observations of human immunodeficiency virus (HIV) assembly, release and maturation made possible with advanced light microscopy techniques. The advances in technology which now enables these light microscopy measurements are discussed with special emphasis on live imaging approaches including Total Internal Reflection Fluorescence (TIRF), high-resolution light microscopy techniques including PALM and STORM and single molecule measurements, including Fluorescence Resonance Energy Transfer (FRET). The review concludes with a discussion on what new insights and understanding can be expected from these measurements.
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19
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Zou C, Zhang Q, Wei X. Compilation of a Coupled Hyper-Chaotic Lorenz System Based on DNA Strand Displacement Reaction Network. IEEE Trans Nanobioscience 2020; 20:92-104. [PMID: 33055027 DOI: 10.1109/tnb.2020.3031360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Ideal formal chemical reaction network is an effective programming language to design complex system dynamical behavior. In this article, a coupled hyper-chaotic Lorenz system can be described by the ordinary differential equations of an ideal formal reaction network, which is constructed by catalysis, annihilation and adjust reaction modules, where the variables of system are represented by the difference in concentration of two chemical species. The ideal formal reaction network can be implemented by DNA strand displacement reaction network. Through Lyapunov exponent, we have analyzed hyper-chaotic dynamical behavior of coupled Lorenz system. In discussion and analysis, we have analyzed effect of noise, reaction rate control error and concentration detection error to DNA strand displacement reaction network.
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20
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Hanami T, Tanabe T, Hanashi T, Yamaguchi M, Nakata H, Mitani Y, Kimura Y, Soma T, Usui K, Isobe M, Ogawa T, Itoh M, Hayashizaki Y, Kondo S. Scanning single-molecule counting system for Eprobe with highly simple and effective approach. PLoS One 2020; 15:e0243319. [PMID: 33320908 PMCID: PMC7737986 DOI: 10.1371/journal.pone.0243319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023] Open
Abstract
Here, we report a rapid and ultra-sensitive detection technique for fluorescent molecules called scanning single molecular counting (SSMC). The method uses a fluorescence-based digital measurement system to count single molecules in a solution. In this technique, noise is reduced by conforming the signal shape to the intensity distribution of the excitation light via a circular scan of the confocal region. This simple technique allows the fluorescent molecules to freely diffuse into the solution through the confocal region and be counted one by one and does not require statistical analysis. Using this technique, 28 to 62 aM fluorescent dye was detected through measurement for 600 s. Furthermore, we achieved a good signal-to-noise ratio (S/N = 2326) under the condition of 100 pM target nucleic acid by only mixing a hybridization-sensitive fluorescent probe, called Eprobe, into the target oligonucleotide solution. Combination of SSMC and Eprobe provides a simple, rapid, amplification-free, and high-sensitive target nucleic acid detection system. This method is promising for future applications to detect particularly difficult to design primers for amplification as miRNAs and other short oligo nucleotide biomarkers by only hybridization with high sensitivity.
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Affiliation(s)
- Takeshi Hanami
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan
| | - Tetsuya Tanabe
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | - Takuya Hanashi
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | - Mitsushiro Yamaguchi
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | - Hidetaka Nakata
- RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | | | | | - Takahiro Soma
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan
| | - Kengo Usui
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan
| | | | | | - Masayoshi Itoh
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | | | - Seiji Kondo
- RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
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21
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Jiang Y, Xu B, Melnykov A, Genin GM, Elson EL. Fluorescence Correlation Spectroscopy and Photon Counting Histograms in Finite, Bounded Domains. Biophys J 2020; 119:265-273. [PMID: 32621863 PMCID: PMC7376089 DOI: 10.1016/j.bpj.2020.05.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/29/2020] [Accepted: 05/18/2020] [Indexed: 01/20/2023] Open
Abstract
Analysis of fluctuations arising as fluorescent particles pass through a focused laser beam has enabled quantitative characterization of a broad range of molecular kinetic processes. Two key mathematical frameworks that have enabled these quantifications are fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analysis. Although these frameworks are effective and accurate when the focused laser beam is well approximated by an infinite Gaussian beam with a waist that is small compared to the size of the region over which the fluorescent particles can diffuse, they cannot be applied to situations in which this region is bounded at the nanoscale. We therefore derived general forms of the FCS and PCH frameworks for bounded systems. The finite-domain form of FCS differs from the classical form in its boundary and initial conditions and requires development of a new Fourier space solution for fitting data. Our finite-domain FCS predicts simulated data accurately and reduces to a previous model for the special case when the system is much larger than the Gaussian beam and can be considered to be infinite. We also derived the PCH form for the bounded systems. Our approach enables estimation of the concentration of diffusing fluorophores within a finite domain for the first time, to our knowledge. The method opens the possibility of quantification of kinetics in several systems for which this has never been possible.
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Affiliation(s)
- Yanfei Jiang
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, Missouri; Division of Biological Sciences, University of California San Diego, La Jolla, California.
| | - Bingxian Xu
- Division of Biological Sciences, University of California San Diego, La Jolla, California
| | - Artem Melnykov
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Guy M Genin
- NSF Science and Technology Center for Engineering Mechanobiology, Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri
| | - Elliot L Elson
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.
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22
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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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23
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Luo F, Qin G, Xia T, Fang X. Single-Molecule Imaging of Protein Interactions and Dynamics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:337-361. [PMID: 32228033 DOI: 10.1146/annurev-anchem-091619-094308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Live-cell single-molecule fluorescence imaging has become a powerful analytical tool to investigate cellular processes that are not accessible to conventional biochemical approaches. This has greatly enriched our understanding of the behaviors of single biomolecules in their native environments and their roles in cellular events. Here, we review recent advances in fluorescence-based single-molecule bioimaging of proteins in living cells. We begin with practical considerations of the design of single-molecule fluorescence imaging experiments such as the choice of imaging modalities, fluorescent probes, and labeling methods. We then describe analytical observables from single-molecule data and the associated molecular parameters along with examples of live-cell single-molecule studies. Lastly, we discuss computational algorithms developed for single-molecule data analysis.
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Affiliation(s)
- Fang Luo
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gege Qin
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tie Xia
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohong Fang
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
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24
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Sankaran J, Wohland T. Fluorescence strategies for mapping cell membrane dynamics and structures. APL Bioeng 2020; 4:020901. [PMID: 32478279 PMCID: PMC7228782 DOI: 10.1063/1.5143945] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/17/2020] [Indexed: 12/20/2022] Open
Abstract
Fluorescence spectroscopy has been a cornerstone of research in membrane dynamics and organization. Technological advances in fluorescence spectroscopy went hand in hand with discovery of various physicochemical properties of membranes at nanometric spatial and microsecond timescales. In this perspective, we discuss the various challenges associated with quantification of physicochemical properties of membranes and how various modes of fluorescence spectroscopy have overcome these challenges to shed light on the structure and organization of membranes. Finally, we discuss newer measurement strategies and data analysis tools to investigate the structure, dynamics, and organization of membranes.
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25
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Resolving dynamics and function of transient states in single enzyme molecules. Nat Commun 2020; 11:1231. [PMID: 32144241 PMCID: PMC7060211 DOI: 10.1038/s41467-020-14886-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/08/2020] [Indexed: 11/23/2022] Open
Abstract
We use a hybrid fluorescence spectroscopic toolkit to monitor T4 Lysozyme (T4L) in action by unraveling the kinetic and dynamic interplay of the conformational states. In particular, by combining single-molecule and ensemble multiparameter fluorescence detection, EPR spectroscopy, mutagenesis, and FRET-positioning and screening, and other biochemical and biophysical tools, we characterize three short-lived conformational states over the ns-ms timescale. The use of 33 FRET-derived distance sets, to screen available T4L structures, reveal that T4L in solution mainly adopts the known open and closed states in exchange at 4 µs. A newly found minor state, undisclosed by, at present, more than 500 crystal structures of T4L and sampled at 230 µs, may be actively involved in the product release step in catalysis. The presented fluorescence spectroscopic toolkit will likely accelerate the development of dynamic structural biology by identifying transient conformational states that are highly abundant in biology and critical in enzymatic reactions. T4 Lysozyme (T4L) is a model protein whose structure is extensively studied. Here the authors combine single-molecule and ensemble FRET measurements, FRET-positioning and screening and EPR spectroscopy to study the structural dynamics of T4L and describe its conformational landscape during the catalytic cycle by an extended Michaelis–Menten mechanism and identify an excited conformational state of the enzyme.
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The centenary of the Stern-Volmer equation of fluorescence quenching: From the single line plot to the SV quenching map. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2020. [DOI: 10.1016/j.jphotochemrev.2019.100338] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Restraining Lysosomal Activity Preserves Hematopoietic Stem Cell Quiescence and Potency. Cell Stem Cell 2020; 26:359-376.e7. [PMID: 32109377 DOI: 10.1016/j.stem.2020.01.013] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/17/2019] [Accepted: 01/17/2020] [Indexed: 12/18/2022]
Abstract
Quiescence is a fundamental property that maintains hematopoietic stem cell (HSC) potency throughout life. Quiescent HSCs are thought to rely on glycolysis for their energy, but the overall metabolic properties of HSCs remain elusive. Using combined approaches, including single-cell RNA sequencing (RNA-seq), we show that mitochondrial membrane potential (MMP) distinguishes quiescent from cycling-primed HSCs. We found that primed, but not quiescent, HSCs relied readily on glycolysis. Notably, in vivo inhibition of glycolysis enhanced the competitive repopulation ability of primed HSCs. We further show that HSC quiescence is maintained by an abundance of large lysosomes. Repression of lysosomal activation in HSCs led to further enlargement of lysosomes while suppressing glucose uptake. This also induced increased lysosomal sequestration of mitochondria and enhanced the competitive repopulation ability of primed HSCs by over 90-fold in vivo. These findings show that restraining lysosomal activity preserves HSC quiescence and potency and may be therapeutically relevant.
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Menezes AGT, Melo DDS, Ramos CL, Moreira SI, Alves E, Schwan RF. Yeasts isolated from Brazilian fermented foods in the protection against infection by pathogenic food bacteria. Microb Pathog 2020; 140:103969. [PMID: 31918000 DOI: 10.1016/j.micpath.2020.103969] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 12/05/2019] [Accepted: 01/05/2020] [Indexed: 12/30/2022]
Abstract
The consumption of probiotics has increased due to the reported health benefits, mainly in preventing or treating gastrointestinal pathology. This study investigated the antimicrobial capacity of yeasts, Saccharomyces cerevisiae and Pichia kluyveri, previously isolated from fermented foods (indigenous beverage, kefir and cocoa) against the adhesion of foodborne pathogens to Caco-2 cells. Co-aggregation of yeasts with pathogens and were evaluated by quantitative analysis and using scanning electron and laser confocal microscopies. All yeasts strains were able to co-aggregate with the tested pathogens, however, this activity was strain-dependent. The inhibition tests showed that the adhesion of Escherichia coli EPEC, Listeria monocytogenes and Salmonella Enteritidis to Caco-2 was reduced by all the yeasts studied. Most of the evaluated yeasts showed inhibition rates equal to or greater than the commercial probiotic Saccharomyces boulardii. The yeasts were able to reduce up to 50% of the bacterial infection, as observed for CCMA0615 towards EPEC in exclusion assay; CCMA0731, CCMA0732 and CCMA0615 towards L. monocytogenes in exclusion and competition assays; and CCMA0731 in exclusion and CCMA0731, CCMA0732, CCMA0615 in competition assay towards S. Enteritidis. No antimicrobial compounds were produced by the yeasts, showing that competition for nutrients and/or receptors in the intestinal mucosa was the mechanism to bacterial inhibition.
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Affiliation(s)
| | - Dirceu de Sousa Melo
- Biology Department, Federal University of Lavras, CEP, 37200-000, Lavras, MG, Brazil.
| | - Cintia Lacerda Ramos
- Basic Sciences Department, Federal University of Vales do Jequitinhonha e Mucuri, CEP, 39.100-000, Diamantina, MG, Brazil.
| | - Silvino Intra Moreira
- Phytopathology Department, Federal University of Lavras, CEP, 37200-000, Lavras, MG, Brazil.
| | - Eduardo Alves
- Phytopathology Department, Federal University of Lavras, CEP, 37200-000, Lavras, MG, Brazil.
| | - Rosane Freitas Schwan
- Biology Department, Federal University of Lavras, CEP, 37200-000, Lavras, MG, Brazil.
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29
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Petazzi RA, Aji AK, Chiantia S. Fluorescence microscopy methods for the study of protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:1-41. [DOI: 10.1016/bs.pmbts.2019.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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30
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Zhang Y, Kong X, Tang Y, Li M, Yin Y, Lin W. The development of a hemicyanine-based ratiometric CO fluorescent probe with a long emission wavelength and its applications for imaging COin vitroandin vivo. NEW J CHEM 2020. [DOI: 10.1039/d0nj00677g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A novel ratiometric fluorescent probe,Hcy-CO, with long-wavelength emission was developed for visualizing CO in living cells and zebrafish.
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Affiliation(s)
- Yunyan Zhang
- Institute of Fluorescent Probes for Biological Imaging
- School of Chemistry and Chemical Engineering
- School of Materials Science and Engineering
- University of Jinan
- Jinan
| | - Xiuqi Kong
- Institute of Fluorescent Probes for Biological Imaging
- School of Chemistry and Chemical Engineering
- School of Materials Science and Engineering
- University of Jinan
- Jinan
| | - Yonghe Tang
- Institute of Optical Materials and Chemical Biology
- School of Chemistry and Chemical Engineering
- Guangxi University
- Nanning
- P. R. China
| | - Min Li
- Institute of Fluorescent Probes for Biological Imaging
- School of Chemistry and Chemical Engineering
- School of Materials Science and Engineering
- University of Jinan
- Jinan
| | - Yaguang Yin
- Institute of Fluorescent Probes for Biological Imaging
- School of Chemistry and Chemical Engineering
- School of Materials Science and Engineering
- University of Jinan
- Jinan
| | - Weiying Lin
- Institute of Fluorescent Probes for Biological Imaging
- School of Chemistry and Chemical Engineering
- School of Materials Science and Engineering
- University of Jinan
- Jinan
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31
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Scales N, Swain PS. Resolving fluorescent species by their brightness and diffusion using correlated photon-counting histograms. PLoS One 2019; 14:e0226063. [PMID: 31887113 PMCID: PMC6936799 DOI: 10.1371/journal.pone.0226063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/19/2019] [Indexed: 12/27/2022] Open
Abstract
Fluorescence fluctuation spectroscopy (FFS) refers to techniques that analyze fluctuations in the fluorescence emitted by fluorophores diffusing in a small volume and can be used to distinguish between populations of molecules that exhibit differences in brightness or diffusion. For example, fluorescence correlation spectroscopy (FCS) resolves species through their diffusion by analyzing correlations in the fluorescence over time; photon counting histograms (PCH) and related methods based on moment analysis resolve species through their brightness by analyzing fluctuations in the photon counts. Here we introduce correlated photon counting histograms (cPCH), which uses both types of information to simultaneously resolve fluorescent species by their brightness and diffusion. We define the cPCH distribution by the probability to detect both a particular number of photons at the current time and another number at a later time. FCS and moment analysis are special cases of the moments of the cPCH distribution, and PCH is obtained by summing over the photon counts in either channel. cPCH is inherently a dual channel technique, and the expressions we develop apply to the dual colour case. Using simulations, we demonstrate that two species differing in both their diffusion and brightness can be better resolved with cPCH than with either FCS or PCH. Further, we show that cPCH can be extended both to longer dwell times to improve the signal-to-noise and to the analysis of images. By better exploiting the information available in fluorescence fluctuation spectroscopy, cPCH will be an enabling methodology for quantitative biology.
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Affiliation(s)
- Nathan Scales
- Department of Physiology, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
| | - Peter S. Swain
- Department of Physiology, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
- School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3BF, United Kingdom
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Yang M, Yuan Q, Gao J, Shu S, Chen F, Sun H, Nishimura K, Wang S, Yi J, Lin CT, Jiang N. A Diamond Temperature Sensor Based on the Energy Level Shift of Nitrogen-Vacancy Color Centers. NANOMATERIALS 2019; 9:nano9111576. [PMID: 31703273 PMCID: PMC6915693 DOI: 10.3390/nano9111576] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 12/01/2022]
Abstract
The nitrogen-vacancy (NV) color center in chemical vapor deposition (CVD) diamond has been widely investigated in quantum information and quantum biosensors due to its excellent photon emission stability and long spin coherence time. However, the temperature dependence of the energy level of NV color centers in diamond is different from other semiconductors with the same diamond cubic structure for the high Debye temperature and very small thermal expansion coefficient of diamond. In this work, a diamond sensor for temperature measurement with high precision was fabricated based on the investigation of the energy level shifts of NV centers by Raman and photoluminescence (PL) spectra. The results show that the intensity and linewidth of the zero-phonon line of NV centers highly depend on the environmental temperature, and the energy level shifts of NV centers in diamond follow the modified Varshni model very well, a model which is better than the traditional version. Accordingly, the NV color center shows the ability in temperature measurement with a high accuracy of up to 98%. The high dependence of NV centers on environmental temperature shows the possibility of temperature monitoring of NV center-based quantum sensors in biosystems.
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Affiliation(s)
- Mingyang Yang
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China; (M.Y.); (J.G.); (S.S.); (F.C.); (H.S.); (S.W.); (J.Y.)
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qilong Yuan
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China; (M.Y.); (J.G.); (S.S.); (F.C.); (H.S.); (S.W.); (J.Y.)
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Q.Y.); (C.-T.L.); (N.J.)
| | - Jingyao Gao
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China; (M.Y.); (J.G.); (S.S.); (F.C.); (H.S.); (S.W.); (J.Y.)
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengcheng Shu
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China; (M.Y.); (J.G.); (S.S.); (F.C.); (H.S.); (S.W.); (J.Y.)
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feiyue Chen
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China; (M.Y.); (J.G.); (S.S.); (F.C.); (H.S.); (S.W.); (J.Y.)
- College of Science, Henan University of Technology, Zhengzhou 10463, China
| | - Huifang Sun
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China; (M.Y.); (J.G.); (S.S.); (F.C.); (H.S.); (S.W.); (J.Y.)
- Faculty of Materials Science and Engineering, Kunming University of Science and Technology, Kunming 650093, China
| | - Kazuhito Nishimura
- Advanced Nano-processing Engineering Lab, Mechanical Engineering, Kogakuin University, Tokyo 192-0015, Japan;
| | - Shaolong Wang
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China; (M.Y.); (J.G.); (S.S.); (F.C.); (H.S.); (S.W.); (J.Y.)
| | - Jian Yi
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China; (M.Y.); (J.G.); (S.S.); (F.C.); (H.S.); (S.W.); (J.Y.)
| | - Cheng-Te Lin
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China; (M.Y.); (J.G.); (S.S.); (F.C.); (H.S.); (S.W.); (J.Y.)
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Q.Y.); (C.-T.L.); (N.J.)
| | - Nan Jiang
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China; (M.Y.); (J.G.); (S.S.); (F.C.); (H.S.); (S.W.); (J.Y.)
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Q.Y.); (C.-T.L.); (N.J.)
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Two-Color Spatial Cumulant Analysis Detects Heteromeric Interactions between Membrane Proteins. Biophys J 2019; 117:1764-1777. [PMID: 31606123 DOI: 10.1016/j.bpj.2019.09.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/19/2019] [Accepted: 09/19/2019] [Indexed: 11/19/2022] Open
Abstract
Fluorescence fluctuation spectroscopy can be used to measure the aggregation of fluorescently labeled molecules and is typically performed using time series data. Spatial intensity distribution analysis and fluorescence moment image analysis are established tools for measuring molecular brightnesses from single-color images collected with laser scanning microscopes. We have extended these tools for analysis of two-color images to resolve heteromeric interactions between molecules labeled with spectrally distinct chromophores. We call these new methods two-color spatial intensity distribution analysis and two-color spatial cumulant analysis (2c-SpCA). To implement these techniques on a hyperspectral imaging system, we developed a spectral shift filtering technique to remove artifacts due to intrinsic cross talk between detector bins. We determined that 2c-SpCA provides better resolution from samples containing multiple fluorescent species; hence, this technique was carried forward to study images of living cells. We used fluorescent heterodimers labeled with enhanced green fluorescent protein and mApple to quantify the effects of resonance energy transfer and incomplete maturation of mApple on brightness measurements. We show that 2c-SpCA can detect the interaction between two components of trimeric G-protein complexes. Thus, 2c-SpCA presents a robust and computationally expedient means of measuring heteromeric interactions in cellular environments.
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Bartels M, Weckbecker D, Kuhn PH, Ryazanov S, Leonov A, Griesinger C, Lichtenthaler SF, Bötzel K, Giese A. Iron-mediated aggregation and toxicity in a novel neuronal cell culture model with inducible alpha-synuclein expression. Sci Rep 2019; 9:9100. [PMID: 31235814 PMCID: PMC6591385 DOI: 10.1038/s41598-019-45298-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 03/11/2019] [Indexed: 01/25/2023] Open
Abstract
Parkinson's disease (PD) represents an increasing problem in society. The oligomerization of alpha-synuclein (αSyn) is a suggested key event in its pathogenesis, yet the pathological modes of action remain to be fully elucidated. To identify potential disease-modifying therapeutics and to study αSyn-mediated toxic mechanisms, we established cell lines with inducible overexpression of different αSyn constructs: αSyn, αSyn coupled to the fluorescence protein Venus (αSyn-Venus), and αSyn coupled to the N-terminal or C-terminal part of Venus (V1S and SV2, respectively) for a bimolecular fluorescence complementation assay (BiFC). Inducibility was achieved by applying modified GAL4-UAS or Cre-loxP systems and addition of tebufenozide or 4-OH-tamoxifen, respectively. Expression constructs were stably integrated into the host genome of H4 neuroglioma cells by lentiviral transduction. We here demonstrate a detailed investigation of the expression characteristics of inducible H4 cells showing low background expression and high inducibility. We observed increased protein load and aggregation of αSyn upon incubation with DMSO and FeCl3 along with an increase in cytotoxicity. In summary, we present a system for the creation of inducibly αSyn-overexpressing cell lines holding high potential for the screening for modulators of αSyn aggregation and αSyn-mediated toxicity.
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Affiliation(s)
- Martin Bartels
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University, Munich, Germany.,Department of Neurology, Klinikum der Universität München, Munich, Germany
| | | | - Peer-Hendrik Kuhn
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Sergey Ryazanov
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Georg-August-University Göttingen, 37073, Göttingen, Germany.,Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Andrei Leonov
- MODAG GmbH, Wendelsheim, Germany.,Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Georg-August-University Göttingen, 37073, Göttingen, Germany.,Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Christian Griesinger
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Georg-August-University Göttingen, 37073, Göttingen, Germany.,Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), and Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, and Institute for Advanced Science, Technical University of Munich, 81675, Munich, Germany
| | - Kai Bötzel
- Department of Neurology, Klinikum der Universität München, Munich, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University, Munich, Germany.
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35
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Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells. Cell 2019; 178:491-506.e28. [PMID: 31155237 DOI: 10.1016/j.cell.2019.05.029] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/23/2018] [Accepted: 05/14/2019] [Indexed: 01/10/2023]
Abstract
Transforming the vast knowledge from genetics, biochemistry, and structural biology into detailed molecular descriptions of biological processes inside cells remains a major challenge-one in sore need of better imaging technologies. For example, transcription involves the complex interplay between RNA polymerase II (Pol II), regulatory factors (RFs), and chromatin, but visualizing these dynamic molecular transactions in their native intracellular milieu remains elusive. Here, we zoom into single tagged genes using nanoscopy techniques, including an active target-locking, ultra-sensitive system that enables single-molecule detection in addressable sub-diffraction volumes, within crowded intracellular environments. We image, track, and quantify Pol II with single-molecule resolution, unveiling its dynamics during the transcription cycle. Further probing multiple functionally linked events-RF-chromatin interactions, Pol II dynamics, and nascent transcription kinetics-reveals detailed operational parameters of gene-regulatory mechanisms hitherto-unseen in vivo. Our approach sets the stage for single-molecule studies of complex molecular processes in live cells.
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Choudhury R, Singh S, Arumugam S, Roguev A, Stewart AF. The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation. Genes Dev 2019; 33:550-564. [PMID: 30842216 PMCID: PMC6499330 DOI: 10.1101/gad.322222.118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/15/2019] [Indexed: 12/19/2022]
Abstract
In this study, Choudhury et al. report that yeast Set1C/COMPASS is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. This presents a new paradigm for the establishment of epigenetic detail, in which dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. Epigenetic modifications can maintain or alter the inherent symmetry of the nucleosome. However, the mechanisms that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.
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Affiliation(s)
- Rupam Choudhury
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Sukhdeep Singh
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Senthil Arumugam
- European Molecular Biology Laboratory Australia Node for Single Molecule Science, ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Assen Roguev
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94518, USA
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
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Khaw I, Croop B, Tang J, Möhl A, Fuchs U, Han KY. Flat-field illumination for quantitative fluorescence imaging. OPTICS EXPRESS 2018; 26:15276-15288. [PMID: 30114777 DOI: 10.1364/oe.26.015276] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/22/2018] [Indexed: 05/26/2023]
Abstract
The uneven illumination of a Gaussian profile makes quantitative analysis highly challenging in laser-based wide-field fluorescence microscopy. Here we present flat-field illumination (FFI) where the Gaussian beam is reshaped into a uniform flat-top profile using a high-precision refractive optical component. The long working distance and high spatial coherence of FFI allows us to accomplish uniform epi and TIRF illumination for multi-color single-molecule imaging. In addition, high-throughput borderless imaging is demonstrated with minimal image overlap.
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38
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Potentials and pitfalls of inverse fluorescence correlation spectroscopy. Methods 2018; 140-141:23-31. [DOI: 10.1016/j.ymeth.2018.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 12/19/2017] [Accepted: 01/12/2018] [Indexed: 11/21/2022] Open
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Papini C, Royer CA. Scanning number and brightness yields absolute protein concentrations in live cells: a crucial parameter controlling functional bio-molecular interaction networks. Biophys Rev 2018; 10:87-96. [PMID: 29383593 DOI: 10.1007/s12551-017-0394-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/29/2017] [Indexed: 12/27/2022] Open
Abstract
Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation. Clearly, a mechanistic understanding of any given high level biological function requires a quantitative characterization of the principal bio-molecular interactions involved and how these may change dynamically. Such information can be obtained using fluctation analysis, in particular scanning number and brightness, and used to build and test mechanistic models of the functional network to define which characteristics are the most important for its regulation.
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Affiliation(s)
- Christina Papini
- Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Catherine A Royer
- Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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40
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Grußmayer KS, Herten DP. Time-resolved molecule counting by photon statistics across the visible spectrum. Phys Chem Chem Phys 2018; 19:8962-8969. [PMID: 28300271 DOI: 10.1039/c7cp00363c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In the past few years quantification of fluorescently labeled (bio-) molecules has become of increasing importance and several approaches have been developed to address this task. Counting by photon statistics measures the distribution of multiple photon detection events that carry information about the number and brightness of independently emitting fluorophores. The method enables absolute and non-destructive quantification, with the quality of estimates critically depending on the ability to accurately measure said photon statistics. Here, we present a combination of simulations and experiments that relate fundamental properties of fluorophores, i.e. their molecular brightness and photostability, to important experimental conditions, i.e. excitation power and acquisition time. Thereby, experimental settings and analysis parameters can be quantitatively evaluated, making counting by photon statistics a robust method for absolute counting of the number of emitters in a diffraction limited observation volume. We show that the time-resolution of counting varies with the fluorophore brightness and can be as fast as 10-100 ms. At the same time, the range of suitable fluorophores can be easily assessed. We evaluated the brightness and photostability of 16 organic dyes across the visible spectrum, providing information crucial for a range of single-molecule spectroscopy applications. This opens up exciting possibilities to analyze absolute stoichiometries in dynamic multi-component complexes.
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Affiliation(s)
- K S Grußmayer
- Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg, Germany.
| | - D-P Herten
- Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg, Germany.
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41
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Shitashima Y, Shimozawa T, Kumagai A, Miyawaki A, Asahi T. Two Distinct Fluorescence States of the Ligand-Induced Green Fluorescent Protein UnaG. Biophys J 2018; 113:2805-2814. [PMID: 29262373 DOI: 10.1016/j.bpj.2017.10.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/27/2017] [Accepted: 10/13/2017] [Indexed: 11/29/2022] Open
Abstract
UnaG is a recently discovered ligand-induced fluorescent protein that utilizes bound bilirubin (BR) as its fluorophore. The fluorescence of the UnaG-BR complex (holoUnaG) compares in quantum efficiency to that of enhanced green fluorescent protein, but it is superior in that the fluorophore formation is instantaneous and not dependent on oxygen; hence, much attention has been paid to UnaG as a new fluorescent probe. However, many important molecular properties of fluorescent probes remain unknown, such as the association/dissociation rates of BR, which determine the stability thereof, and the dispersibility of UnaG in aqueous solutions, which influence the functions of labeled proteins. In this study, we found, in the process of investigating the association rate, that the holoUnaG takes two distinct fluorescence states, which we named holoUnaG1 and holoUnaG2. The holoUnaG1 initially forms after binding BR and then changes to the brighter holoUnaG2 by a reversible intra-molecular reaction, thereby finally reaching an equilibrium between the two states. Spectroscopic analysis indicated that the intra-molecular reaction was associated not with a chemical change of BR but with a change in the environmental conditions surrounding BR. We also revealed that the molecular brightness ratio and equilibrium population ratio of the two states (holoUnaG1/holoUnaG2) were 1:3.9 and 6:4, respectively, using photon number counting analysis. From these results, we have suggested a novel schema, to our knowledge, for the formation of the UnaG and BR complex system and have determined the various rate constants associated therein. Additionally, using analytical ultracentrifugation, we established that UnaG in the apo-state (apoUnaG) and the holoUnaG are monomeric in aqueous solution. These findings provide not only key information for the practical use of UnaG as a fluorescent probe, but also the possibility for development of a brighter UnaG mutant by genetic engineering to constitutive holoUnaG2.
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Affiliation(s)
- Yoh Shitashima
- Department of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan; Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Wako, Saitama, Japan
| | - Togo Shimozawa
- Department of Life Science and Medical Bioscience, Waseda University, Shinjuku-ku, Tokyo, Japan.
| | - Akiko Kumagai
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Wako, Saitama, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Wako, Saitama, Japan
| | - Toru Asahi
- Department of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan; Department of Life Science and Medical Bioscience, Waseda University, Shinjuku-ku, Tokyo, Japan
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42
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Meng L, He S, Zhao XS. Determination of Equilibrium Constant and Relative Brightness in FRET-FCS by Including the Third-Order Correlations. J Phys Chem B 2017; 121:11262-11272. [PMID: 29155588 DOI: 10.1021/acs.jpcb.7b09229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) encodes the information on the equilibrium constant (K), the relative fluorescence brightness of fluorophore (Q), and the forward and backward reaction rate constants (k+ and k-) on a physical or chemical relaxation. However, it has been a long-standing problem to completely resolve the FCS data to get the thermodynamic and kinetic information. Recently, we have solved the problem for fluorescence autocorrelation spectroscopy (FACS). Here, we extend the method to fluorescence cross-correlation spectroscopy (FCCS), which appears when FCS is coupled with fluorescence resonance energy transfer (FRET). Among 12 total second-order and third-order pre-exponential factors in a relaxation process probed by the FRET-FCS technique, 3 are independent. We presented and discussed 3 sets of explicit solutions to use these pre-exponential factors to calculate K and Q. Together with the relaxation time, the acquired K will allow people to obtain k+ and k-, so that the goal of deciphering the FRET-FCS data will be fully reached. The theory is verified by extensive computer simulations and tested experimentally on a system of oligonucleotide hybridization.
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Affiliation(s)
- Lingyi Meng
- Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China.,School of Life Sciences, Peking University , Beijing 100871, China
| | - Shanshan He
- Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Xin Sheng Zhao
- Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
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43
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Elson EL. Introduction to fluorescence correlation Spectroscopy-Brief and simple. Methods 2017; 140-141:3-9. [PMID: 29155128 DOI: 10.1016/j.ymeth.2017.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/13/2017] [Indexed: 02/04/2023] Open
Affiliation(s)
- Elliot L Elson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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44
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Hennen J, Hur KH, Saunders CA, Luxton GWG, Mueller JD. Quantitative Brightness Analysis of Protein Oligomerization in the Nuclear Envelope. Biophys J 2017; 113:138-147. [PMID: 28700912 DOI: 10.1016/j.bpj.2017.05.044] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/20/2017] [Accepted: 05/30/2017] [Indexed: 01/02/2023] Open
Abstract
Brightness analysis of fluorescence fluctuation experiments has been used to successfully measure the oligomeric state of proteins at the plasma membrane, in the nucleoplasm, and in the cytoplasm of living cells. Here we extend brightness analysis to the nuclear envelope (NE), a double membrane barrier separating the cytoplasm from the nucleoplasm. Results obtained by applying conventional brightness analysis to fluorescently tagged proteins within the NE exhibited an unusual concentration dependence. Similarly, the autocorrelation function of the fluorescence fluctuations exhibited unexpected changes with protein concentration. These observations motivated the application of mean-segmented Q analysis, which identified the existence of a fluctuation process distinct from molecular diffusion in the NE. We propose that small changes in the separation of the inner and outer nuclear membrane are responsible for the additional fluctuation process, as suggested by results obtained for luminal and nuclear membrane-associated EGFP-tagged proteins. Finally, we applied these insights to study the oligomerization of the luminal domains of two nuclear membrane proteins, nesprin-2 and SUN2, which interact transluminally to form a nuclear envelope-spanning linker molecular bridge known as the linker of the nucleoskeleton and cytoskeleton complex.
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Affiliation(s)
- Jared Hennen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota
| | - Kwang-Ho Hur
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota
| | - Cosmo A Saunders
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - G W Gant Luxton
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Joachim D Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota; Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota.
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45
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Jiang Y, Pryse KM, Melnykov A, Genin GM, Elson EL. Investigation of Nanoscopic Phase Separations in Lipid Membranes Using Inverse FCS. Biophys J 2017; 112:2367-2376. [PMID: 28591609 PMCID: PMC5475253 DOI: 10.1016/j.bpj.2017.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 11/16/2022] Open
Abstract
Measurement of the sizes of nanoscopic particles is a difficult challenge, especially in two-dimensional systems such as cell membranes. We have extended inverse fluorescence correlation spectroscopy (iFCS) to endow it with unique advantages for measuring particle size from the nano- to the microscale. We have augmented iFCS with an analysis of moments of fluorescence fluctuations and used it to measure stages of phase separation in model lipid bilayer membranes. We observed two different pathways for the growth of phase domains. In one, nanoscopic gel domains appeared first and then gradually grew to micrometer size. In the other, the domains reached micrometer size quickly, and their number gradually increased. These measurements demonstrate the value of iFCS measurements through their ability, to our knowledge, to provide new information about the mechanism of lipid phase separation and potentially about the physical basis of naturally occurring nanodomains such as lipid rafts.
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Affiliation(s)
- Yanfei Jiang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Kenneth M Pryse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Artem Melnykov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Guy M Genin
- Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, Missouri
| | - Elliot L Elson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri.
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46
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Jacobs BKM, Goetghebeur E, Vandesompele J, De Ganck A, Nijs N, Beckers A, Papazova N, Roosens NH, Clement L. Model-Based Classification for Digital PCR: Your Umbrella for Rain. Anal Chem 2017; 89:4461-4467. [PMID: 28350455 DOI: 10.1021/acs.analchem.6b04208] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Standard data analysis pipelines for digital PCR estimate the concentration of a target nucleic acid by digitizing the end-point fluorescence of the parallel micro-PCR reactions, using an automated hard threshold. While it is known that misclassification has a major impact on the concentration estimate and substantially reduces accuracy, the uncertainty of this classification is typically ignored. We introduce a model-based clustering method to estimate the probability that the target is present (absent) in a partition conditional on its observed fluorescence and the distributional shape in no-template control samples. This methodology acknowledges the inherent uncertainty of the classification and provides a natural measure of precision, both at individual partition level and at the level of the global concentration. We illustrate our method on genetically modified organism, inhibition, dynamic range, and mutation detection experiments. We show that our method provides concentration estimates of similar accuracy or better than the current standard, along with a more realistic measure of precision. The individual partition probabilities and diagnostic density plots further allow for some quality control. An R implementation of our method, called Umbrella, is available, providing a more objective and automated data analysis procedure for absolute dPCR quantification.
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Affiliation(s)
- Bart K M Jacobs
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University , Ghent, Belgium
| | - Els Goetghebeur
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University , Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics Ghent (CMGG), Ghent University , Ghent, Belgium.,Biogazelle, Zwijnaarde, Belgium.,Bioinformatics Institute Ghent From Nucleotides to Networks (Big N2N), Ghent University , Ghent, Belgium
| | | | | | | | - Nina Papazova
- Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Nancy H Roosens
- Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Lieven Clement
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University , Ghent, Belgium.,Bioinformatics Institute Ghent From Nucleotides to Networks (Big N2N), Ghent University , Ghent, Belgium
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47
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Benke S, Nettels D, Hofmann H, Schuler B. Quantifying kinetics from time series of single-molecule Förster resonance energy transfer efficiency histograms. NANOTECHNOLOGY 2017; 28:114002. [PMID: 28103588 DOI: 10.1088/1361-6528/aa5abd] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Single-molecule fluorescence spectroscopy is a powerful approach for probing biomolecular structure and dynamics, including protein folding. For the investigation of nonequilibrium kinetics, Förster resonance energy transfer combined with confocal multiparameter detection has proven particularly versatile, owing to the large number of observables and the broad range of accessible timescales, especially in combination with rapid microfluidic mixing. However, a comprehensive kinetic analysis of the resulting time series of transfer efficiency histograms and complementary observables can be challenging owing to the complexity of the data. Here we present and compare three different methods for the analysis of such kinetic data: singular value decomposition, multivariate curve resolution with alternating least square fitting, and model-based peak fitting, where an explicit model of both the transfer efficiency histogram of each species and the kinetic mechanism of the process is employed. While each of these methods has its merits for specific applications, we conclude that model-based peak fitting is most suitable for a quantitative analysis and comparison of kinetic mechanisms.
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Affiliation(s)
- Stephan Benke
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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48
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Abdollah-Nia F, Gelfand MP, Van Orden A. Artifact-Free and Detection-Profile-Independent Higher-Order Fluorescence Correlation Spectroscopy for Microsecond-Resolved Kinetics. 1. Multidetector and Sub-Binning Approach. J Phys Chem B 2017; 121:2373-2387. [DOI: 10.1021/acs.jpcb.7b00407] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Farshad Abdollah-Nia
- Department of Physics and ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Martin P. Gelfand
- Department of Physics and ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Alan Van Orden
- Department of Physics and ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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49
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Abdollah-Nia F, Gelfand MP, Van Orden A. Artifact-Free and Detection-Profile-Independent Higher-Order Fluorescence Correlation Spectroscopy for Microsecond-Resolved Kinetics. 2. Mixtures and Reactions. J Phys Chem B 2017; 121:2388-2399. [DOI: 10.1021/acs.jpcb.7b00408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farshad Abdollah-Nia
- Department
of Physics and ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Martin P. Gelfand
- Department
of Physics and ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Alan Van Orden
- Department
of Physics and ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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50
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Affiliation(s)
- Hans Blom
- Royal Institute of Technology (KTH), Dept Applied Physics, SciLifeLab, 17165 Solna, Sweden
| | - Jerker Widengren
- Royal Institute of Technology (KTH), Dept Applied Physics, Albanova Univ Center, 10691 Stockholm, Sweden
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