1
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Chen T, Karedla N, Enderlein J. Measuring sub-nanometer undulations at microsecond temporal resolution with metal- and graphene-induced energy transfer spectroscopy. Nat Commun 2024; 15:1789. [PMID: 38413608 PMCID: PMC10899616 DOI: 10.1038/s41467-024-45822-x] [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: 06/01/2023] [Accepted: 02/01/2024] [Indexed: 02/29/2024] Open
Abstract
Out-of-plane fluctuations, also known as stochastic displacements, of biological membranes play a crucial role in regulating many essential life processes within cells and organelles. Despite the availability of various methods for quantifying membrane dynamics, accurately quantifying complex membrane systems with rapid and tiny fluctuations, such as mitochondria, remains a challenge. In this work, we present a methodology that combines metal/graphene-induced energy transfer (MIET/GIET) with fluorescence correlation spectroscopy (FCS) to quantify out-of-plane fluctuations of membranes with simultaneous spatiotemporal resolution of approximately one nanometer and one microsecond. To validate the technique and spatiotemporal resolution, we measure bending undulations of model membranes. Furthermore, we demonstrate the versatility and applicability of MIET/GIET-FCS for studying diverse membrane systems, including the widely studied fluctuating membrane system of human red blood cells, as well as two unexplored membrane systems with tiny fluctuations, a pore-spanning membrane, and mitochondrial inner/outer membranes.
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Affiliation(s)
- Tao Chen
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, Göttingen, 37077, Germany
| | - Narain Karedla
- The Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 OFA, UK
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7LF, UK
| | - Jörg Enderlein
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, Göttingen, 37077, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Universitätsmedizin Göttingen, Robert-Koch-Str. 40, Göttingen, 37075, Germany.
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2
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Gandhi SA, Sanders MA, Granneman JG, Kelly CV. Four-color fluorescence cross-correlation spectroscopy with one laser and one camera. BIOMEDICAL OPTICS EXPRESS 2023; 14:3812-3827. [PMID: 37497523 PMCID: PMC10368031 DOI: 10.1364/boe.486937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 07/28/2023]
Abstract
The diffusion and reorganization of phospholipids and membrane-associated proteins are fundamental for cellular function. Fluorescence cross-correlation spectroscopy (FCCS) measures diffusion and molecular interactions at nanomolar concentration in biological systems. We have developed an economical method to simultaneously monitor diffusion and complexation with the use of super-continuum laser and spectral deconvolution from a single detector. Customizable excitation wavelengths were chosen from the wide-band source and spectral fitting of the emitted light revealed the interactions for up to four chromatically overlapping fluorophores simultaneously. This method was applied to perform four-color FCCS that we demonstrated with polystyrene nanoparticles, lipid vesicles, and membrane-bound molecules. Up to four individually customizable excitation channels were selected from the broad-spectrum fiber laser to excite the diffusers within a diffraction-limited spot. The fluorescence emission passed through a cleanup filter and a dispersive prism prior to being collected by a sCMOS or EMCCD camera with up to 1.8 kHz frame rates. The emission intensity versus time of each fluorophore was extracted through a linear least-square fitting of each camera frame and temporally correlated via custom software. Auto- and cross-correlation functions enabled the measurement of the diffusion rates and binding partners. We have measured the induced aggregation of nanobeads and lipid vesicles in solution upon increasing the buffer salinity. Because of the adaptability of investigating four fluorophores simultaneously with a cost-effective method, this technique will have wide application for examining macromolecular complex formation in model and living systems.
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Affiliation(s)
- Sonali A. Gandhi
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
| | - Matthew A. Sanders
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 40201, USA
| | - James G. Granneman
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 40201, USA
- Center for Integrative Metabolic and Endocrine Research, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Christopher V. Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
- Center for Integrative Metabolic and Endocrine Research, School of Medicine, Wayne State University, Detroit, MI 48201, USA
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3
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Gandhi SA, Sanders MA, Granneman JG, Kelly CV. Four-color fluorescence cross-correlation spectroscopy with one laser and one camera. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526256. [PMID: 36778294 PMCID: PMC9915509 DOI: 10.1101/2023.01.30.526256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The diffusion and reorganization of phospholipids and membrane-associated proteins are fundamental for cellular function. Fluorescence cross-correlation spectroscopy (FCCS) measures the diffusion and molecular interactions at nanomolar concentration in biological systems. We have developed a novel, economical method to simultaneously monitor diffusion and oligomerization with the use of super-continuum laser and spectral deconvolution from a single detector. Customizable excitation wavelengths were chosen from the wide-band source and spectral fitting of the emitted light revealed the interactions for up to four spectrally overlapping fluorophores simultaneously. This method was applied to perform four-color FCCS, as demonstrated with polystyrene nanoparticles, lipid vesicles, and membrane-bound molecules. Up to four individually customizable excitation channels were selected from the broad-spectrum fiber laser to excite the diffusers within a diffraction-limited spot. The fluorescence emission passed through a cleanup filter and a dispersive prism prior to being collected by a sCMOS or EMCCD camera with up to 10 kHz frame rates. The emission intensity versus time of each fluorophore was extracted through a linear least-square fitting of each camera frame and temporally correlated via custom software. Auto- and cross-correlation functions enabled the measurement of the diffusion rates and binding partners. We have measured the induced aggregation of nanobeads and lipid vesicles in solution upon increasing the buffer salinity. Because of the adaptability of investigating four fluorophores simultaneously with a cost-effective method, this technique will have wide application for examining complex homo- and heterooligomerization in model and living systems.
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Affiliation(s)
- Sonali A. Gandhi
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, USA, 48201
| | - Matthew A. Sanders
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA, 40201
| | - James G. Granneman
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA, 40201,Center for Integrative Metabolic and Endocrine Research, School of Medicine, Wayne State University, Detroit, MI, USA. 48201
| | - Christopher V. Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, USA, 48201,Center for Integrative Metabolic and Endocrine Research, School of Medicine, Wayne State University, Detroit, MI, USA. 48201,Corresponding author:
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4
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Biophysical quantification of unitary solute and solvent permeabilities to enable translation to membrane science. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.121308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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5
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Sakhapov D, Gregor I, Karedla N, Enderlein J. Measuring Photophysical Transition Rates with Fluorescence Correlation Spectroscopy and Antibunching. J Phys Chem Lett 2022; 13:4823-4830. [PMID: 35616286 DOI: 10.1021/acs.jpclett.2c00896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We present a new method that combines fluorescence correlation spectroscopy (FCS) on the microsecond time scale with fluorescence antibunching measurements on the nanosecond time scale for measuring photophysical rate constants of fluorescent molecules. The antibunching measurements allow us to quantify the average excitation rate of fluorescent molecules within the confocal detection volume of the FCS measurement setup. Knowledge of this value allows us then to quantify, in an absolute manner, the intersystem crossing rate and triplet state lifetime from the microsecond temporal decay of the FCS curves. We present a theoretical analysis of the method and estimate the maximum bias caused by the averaging of all quantities (excitation rate and photophysical rates) over the confocal detection volume, and we show that this bias is smaller than 5% in most cases. We apply the method for measuring the photophysical rate constants of the widely used dyes Rhodamine 110 and ATTO 655.
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Affiliation(s)
- Damir Sakhapov
- III. Institute of Physics - Biophysics, Georg-August-University, 37077 Göttingen, Germany
| | - Ingo Gregor
- III. Institute of Physics - Biophysics, Georg-August-University, 37077 Göttingen, Germany
| | - Narain Karedla
- The Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0FA, U.K
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg-August-University, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg August University, 37077 Göttingen, Germany
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6
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Iriarte-Alonso MA, Bittner AM, Chiantia S. Influenza A virus hemagglutinin prevents extensive membrane damage upon dehydration. BBA ADVANCES 2022; 2:100048. [PMID: 37082591 PMCID: PMC10074934 DOI: 10.1016/j.bbadva.2022.100048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
While the molecular mechanisms of virus infectivity are rather well known, the detailed consequences of environmental factors on virus biophysical properties are poorly understood. Seasonal influenza outbreaks are usually connected to the low winter temperature, but also to the low relative air humidity. Indeed, transmission rates increase in cold regions during winter. While low temperature must slow degradation processes, the role of low humidity is not clear. We studied the effect of relative humidity on a model of Influenza A H1N1 virus envelope, a supported lipid bilayer containing the surface glycoprotein hemagglutinin (HA), which is present in the viral envelope in very high density. For complete cycles of hydration, dehydration and rehydration, we evaluate the membrane properties in terms of structure and dynamics, which we assess by combining confocal fluorescence microscopy, raster image correlation spectroscopy, line-scan fluorescence correlation spectroscopy and atomic force microscopy. Our findings indicate that the presence of HA prevents macroscopic membrane damage after dehydration. Without HA, fast membrane disruption is followed by irreversible loss of lipid and protein mobility. Although our model is principally limited by the membrane composition, the macroscopic effects of HA under dehydration stress reveal new insights on the stability of the virus at low relative humidity.
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7
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Rose M, Kurylowicz M, Mahmood M, Winkel S, Moran-Mirabal JM, Fradin C. Direct Measurement of the Affinity between tBid and Bax in a Mitochondria-Like Membrane. Int J Mol Sci 2021; 22:8240. [PMID: 34361006 PMCID: PMC8348223 DOI: 10.3390/ijms22158240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 01/05/2023] Open
Abstract
The execution step in apoptosis is the permeabilization of the outer mitochondrial membrane, controlled by Bcl-2 family proteins. The physical interactions between the different proteins in this family and their relative abundance literally determine the fate of the cells. These interactions, however, are difficult to quantify, as they occur in a lipid membrane and involve proteins with multiple conformations and stoichiometries which can exist both in soluble and membrane. Here we focus on the interaction between two core Bcl-2 family members, the executor pore-forming protein Bax and the truncated form of the activator protein Bid (tBid), which we imaged at the single particle level in a mitochondria-like planar supported lipid bilayer. We inferred the conformation of the proteins from their mobility, and detected their transient interactions using a novel single particle cross-correlation analysis. We show that both tBid and Bax have at least two different conformations at the membrane, and that their affinity for one another increases by one order of magnitude (with a 2D-KD decreasing from ≃1.6μm-2 to ≃0.1μm-2) when they pass from their loosely membrane-associated to their transmembrane form. We conclude by proposing an updated molecular model for the activation of Bax by tBid.
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Affiliation(s)
- Markus Rose
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada; (M.R.); (M.K.); (M.M.); (S.W.)
| | - Martin Kurylowicz
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada; (M.R.); (M.K.); (M.M.); (S.W.)
| | - Mohammad Mahmood
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada; (M.R.); (M.K.); (M.M.); (S.W.)
| | - Sheldon Winkel
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada; (M.R.); (M.K.); (M.M.); (S.W.)
| | - Jose M. Moran-Mirabal
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada;
| | - Cécile Fradin
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada; (M.R.); (M.K.); (M.M.); (S.W.)
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
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8
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Zec N, Mangiapia G, Hendry AC, Barker R, Koutsioubas A, Frielinghaus H, Campana M, Ortega-Roldan JL, Busch S, Moulin JF. Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments. MEMBRANES 2021; 11:507. [PMID: 34357157 PMCID: PMC8304056 DOI: 10.3390/membranes11070507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022]
Abstract
We showcase the combination of experimental neutron scattering data and molecular dynamics (MD) simulations for exemplary phospholipid membrane systems. Neutron and X-ray reflectometry and small-angle scattering measurements are determined by the scattering length density profile in real space, but it is not usually possible to retrieve this profile unambiguously from the data alone. MD simulations predict these density profiles, but they require experimental control. Both issues can be addressed simultaneously by cross-validating scattering data and MD results. The strengths and weaknesses of each technique are discussed in detail with the aim of optimizing the opportunities provided by this combination.
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Affiliation(s)
- Nebojša Zec
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Hereon, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (N.Z.); (G.M.)
| | - Gaetano Mangiapia
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Hereon, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (N.Z.); (G.M.)
| | - Alex C. Hendry
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (A.C.H.); (J.L.O.-R.)
| | - Robert Barker
- School of Physical Sciences, University of Kent, Canterbury CT2 7NH, UK;
| | - Alexandros Koutsioubas
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (A.K.); (H.F.)
| | - Henrich Frielinghaus
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (A.K.); (H.F.)
| | - Mario Campana
- ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, UK;
| | | | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Hereon, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (N.Z.); (G.M.)
| | - Jean-François Moulin
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Hereon, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (N.Z.); (G.M.)
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9
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Intracellular Ionic Strength Sensing Using NanoLuc. Int J Mol Sci 2021; 22:ijms22020677. [PMID: 33445497 PMCID: PMC7826950 DOI: 10.3390/ijms22020677] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/20/2022] Open
Abstract
Intracellular ionic strength regulates myriad cellular processes that are fundamental to cellular survival and proliferation, including protein activity, aggregation, phase separation, and cell volume. It could be altered by changes in the activity of cellular signaling pathways, such as those that impact the activity of membrane-localized ion channels or by alterations in the microenvironmental osmolarity. Therefore, there is a demand for the development of sensitive tools for real-time monitoring of intracellular ionic strength. Here, we developed a bioluminescence-based intracellular ionic strength sensing strategy using the Nano Luciferase (NanoLuc) protein that has gained tremendous utility due to its high, long-lived bioluminescence output and thermal stability. Biochemical experiments using a recombinantly purified protein showed that NanoLuc bioluminescence is dependent on the ionic strength of the reaction buffer for a wide range of ionic strength conditions. Importantly, the decrease in the NanoLuc activity observed at higher ionic strengths could be reversed by decreasing the ionic strength of the reaction, thus making it suitable for sensing intracellular ionic strength alterations. Finally, we used an mNeonGreen–NanoLuc fusion protein to successfully monitor ionic strength alterations in a ratiometric manner through independent fluorescence and bioluminescence measurements in cell lysates and live cells. We envisage that the biosensing strategy developed here for detecting alterations in intracellular ionic strength will be applicable in a wide range of experiments, including high throughput cellular signaling, ion channel functional genomics, and drug discovery.
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10
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A Bayesian framework for the detection of diffusive heterogeneity. PLoS One 2020; 15:e0221841. [PMID: 32379846 PMCID: PMC7205219 DOI: 10.1371/journal.pone.0221841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 04/16/2020] [Indexed: 11/19/2022] Open
Abstract
Cells are crowded and spatially heterogeneous, complicating the transport of organelles, proteins and other substrates. One aspect of this complex physical environment, the mobility of passively transported substrates, can be quantitatively characterized by the diffusion coefficient: a descriptor of how rapidly substrates will diffuse in the cell, dependent on their size and effective local viscosity. The spatial dependence of diffusivity is challenging to quantitatively characterize, because temporally and spatially finite observations offer limited information about a spatially varying stochastic process. We present a Bayesian framework that estimates diffusion coefficients from single particle trajectories, and predicts our ability to distinguish differences in diffusion coefficient estimates, conditional on how much they differ and the amount of data collected. This framework is packaged into a public software repository, including a tutorial Jupyter notebook demonstrating implementation of our method for diffusivity estimation, analysis of sources of uncertainty estimation, and visualization of all results. This estimation and uncertainty analysis allows our framework to be used as a guide in experimental design of diffusivity assays.
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11
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Li Z, Yang J, Hollingsworth JV, Zhao J. Lateral diffusion of single polymer molecules at interfaces between water and oil. RSC Adv 2020; 10:16565-16569. [PMID: 35498844 PMCID: PMC9052869 DOI: 10.1039/d0ra02630a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/14/2020] [Indexed: 11/21/2022] Open
Abstract
Lateral diffusion of polymer molecules at the interfaces between immiscible oil and water is investigated at the single molecular level. The interfaces between water and alkanes are chosen as the model systems and polyethylene oxide (PEO) is the model polymer. Fluorescence correlation spectroscopy is used to measure the interfacial diffusion of fluorescence-labeled PEO with its molecular weight ranging over more than an order of magnitude. It is discovered that the interfacial diffusion coefficient scales with the molecular weight by the exponent of -0.5. Detailed analysis shows that the PEO chain takes an ideal two-dimensional random coil conformation at these fluidic interfaces and the bigger contribution from water's hydrodynamic friction is discovered.
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Affiliation(s)
- Zhuo Li
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | - Jingfa Yang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | | | - Jiang Zhao
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
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12
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Cebecauer M, Amaro M, Jurkiewicz P, Sarmento MJ, Šachl R, Cwiklik L, Hof M. Membrane Lipid Nanodomains. Chem Rev 2018; 118:11259-11297. [PMID: 30362705 DOI: 10.1021/acs.chemrev.8b00322] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lipid membranes can spontaneously organize their components into domains of different sizes and properties. The organization of membrane lipids into nanodomains might potentially play a role in vital functions of cells and organisms. Model membranes represent attractive systems to study lipid nanodomains, which cannot be directly addressed in living cells with the currently available methods. This review summarizes the knowledge on lipid nanodomains in model membranes and exposes how their specific character contrasts with large-scale phase separation. The overview on lipid nanodomains in membranes composed of diverse lipids (e.g., zwitterionic and anionic glycerophospholipids, ceramides, glycosphingolipids) and cholesterol aims to evidence the impact of chemical, electrostatic, and geometric properties of lipids on nanodomain formation. Furthermore, the effects of curvature, asymmetry, and ions on membrane nanodomains are shown to be highly relevant aspects that may also modulate lipid nanodomains in cellular membranes. Potential mechanisms responsible for the formation and dynamics of nanodomains are discussed with support from available theories and computational studies. A brief description of current fluorescence techniques and analytical tools that enabled progress in lipid nanodomain studies is also included. Further directions are proposed to successfully extend this research to cells.
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Affiliation(s)
- Marek Cebecauer
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Mariana Amaro
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Maria João Sarmento
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Radek Šachl
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Lukasz Cwiklik
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
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13
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Veerapathiran S, Wohland T. Fluorescence techniques in developmental biology. J Biosci 2018; 43:541-553. [PMID: 30002271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Advanced fluorescence techniques, commonly known as the F-techniques, measure the kinetics and the interactions of biomolecules with high sensitivity and spatiotemporal resolution. Applications of the F-techniques, which were initially limited to cells, were further extended to study in vivo protein organization and dynamics in whole organisms. The integration of F-techniques with multi-photon microscopy and light-sheet microscopy widened their applications in the field of developmental biology. It became possible to penetrate the thick tissues of living organisms and obtain good signal-to-noise ratio with reduced photo-induced toxicity. In this review, we discuss the principle and the applications of the three most commonly used F-techniques in developmental biology: Fluorescence Recovery After Photo-bleaching (FRAP), Fo¨ rster Resonance Energy Transfer (FRET), and Fluorescence Correlation and Cross-Correlation Spectroscopy (FCS and FCCS).
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Affiliation(s)
- Sapthaswaran Veerapathiran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
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14
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15
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Sarangi NK, Roobala C, Basu JK. Unraveling complex nanoscale lipid dynamics in simple model biomembranes: Insights from fluorescence correlation spectroscopy in super-resolution stimulated emission depletion mode. Methods 2018; 140-141:198-211. [DOI: 10.1016/j.ymeth.2017.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/18/2017] [Accepted: 11/19/2017] [Indexed: 12/24/2022] Open
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16
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Li L, Dwivedi M, Erwin N, Möbitz S, Nussbaumer P, Winter R. Interaction of KRas4B protein with C6-ceramide containing lipid model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1008-1014. [PMID: 29357287 DOI: 10.1016/j.bbamem.2018.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/14/2018] [Accepted: 01/15/2018] [Indexed: 01/02/2023]
Abstract
Ras proteins are oncoproteins which play a pivotal role in cellular signaling pathways. All Ras proteins' signaling strongly depends on their correct localization in the cell membrane. Over 30% of cancers are driven by mutant Ras proteins, and KRas4B is the Ras isoform most frequently mutated. C6-ceramide has been shown to inhibit the growth activity of KRas4B mutated cells. However, the mechanism underlying this inhibition remains elusive. Here, we established a heterogeneous model biomembrane containing C6-ceramide. C6-ceramide incorporation does not disrupt the lipid membrane. Addition of KRas4B leads to drastic changes in the lateral membrane organization of the membrane, however. In contrast to the partitioning behavior in other membranes, KRas4B forms small, monodisperse nanoclusters dispersed in a fluid-like environment, in all likelihood induced by some kind of lipid sorting mechanism. Fluorescence cross-correlation data indicate no direct interaction between C6-ceramide and KRas4B, suggesting that KRas4B essentially recruits other lipids. A FRET-based binding assay reveals that the stability of KRas4B proteins inserted into the membrane containing C6-ceramide is reduced. Based on the combined results obtained, we postulate a molecular mechanism for the inhibition of KRas4B mutated cells' activity through C6-ceramide.
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Affiliation(s)
- Lei Li
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44221 Dortmund, Germany; International Max Planck Research School (IMPRS) in Chemical and Molecular Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Mridula Dwivedi
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44221 Dortmund, Germany
| | - Nelli Erwin
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44221 Dortmund, Germany; International Max Planck Research School (IMPRS) in Chemical and Molecular Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Simone Möbitz
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44221 Dortmund, Germany
| | - Peter Nussbaumer
- Lead Discovery Center GmbH, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44221 Dortmund, Germany.
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17
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Veerapathiran S, Wohland T. The imaging FCS diffusion law in the presence of multiple diffusive modes. Methods 2017; 140-141:140-150. [PMID: 29203404 DOI: 10.1016/j.ymeth.2017.11.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 01/21/2023] Open
Abstract
The cellular plasma membrane is the barrier over which cells exchange materials and communicate with their surroundings, and thus plays the central role in cellular sensing and metabolism. Therefore, the investigation of plasma membrane organization and dynamics is required for understanding of cellular functions. The plasma membrane is a heterogeneous matrix. The presence of structures such as lipid and protein domains and the cytoskeleton meshwork poses a hindrance to the free diffusion of membrane associated biomolecules. However, these domains and the cytoskeleton meshwork barriers are below the optical diffraction limit with potentially short lifetimes and are not easily detected even in super-resolution microscopy. Therefore, dynamic measurements are often used to indirectly prove the existence of domains and barriers by analyzing the mode of diffusion of probe molecules. One of these tools is the Fluorescence Correlation Spectroscopy (FCS) diffusion law. The FCS diffusion law is a plot of diffusion time (τd) versus observation area. For at least three different diffusive modes - free, domain confined, and meshwork hindered hop diffusion - the expected plots have been characterized, typically by its y-intercept (τ0) when fit with a linear model, and have been verified in many cases. However, a description of τ0 has only been given for pure diffusive modes. But in many experimental cases it is not evident that a protein will undergo only one kind of diffusion, and thus the interpretation of the τ0 value is problematic. Here, we therefore address the question about the absolute value of τ0 in the case of complex diffusive modes, i.e. when either one molecule is domain confined and cytoskeleton hindered or when two molecules exhibit different diffusive behavior at the same position in a sample. In addition, we investigate how τ0 changes when the diffusive mode of a probe alters upon disruption of domains or the cytoskeleton by drug treatments. By a combination of experimental studies and simulations, we show that τ0 is not influenced equally by the different diffusive modes as typically found in cellular environments, and that it is the relative change of τ0 rather than its absolute value that provides information on the mode of diffusion.
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Affiliation(s)
- Sapthaswaran Veerapathiran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore, Singapore; Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore, Singapore.
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18
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Doktorova M, Heberle FA, Kingston RL, Khelashvili G, Cuendet MA, Wen Y, Katsaras J, Feigenson GW, Vogt VM, Dick RA. Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties. Biophys J 2017; 113:2004-2015. [PMID: 29117524 DOI: 10.1016/j.bpj.2017.08.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/07/2017] [Accepted: 08/09/2017] [Indexed: 01/28/2023] Open
Abstract
Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here, using a broad set of in vitro and in silico techniques we addressed molecular mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.
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Affiliation(s)
- Milka Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Frederick A Heberle
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Michel A Cuendet
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Yi Wen
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - John Katsaras
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Gerald W Feigenson
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Volker M Vogt
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Robert A Dick
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York.
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19
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Doktorova M, Heberle FA, Kingston RL, Khelashvili G, Cuendet MA, Wen Y, Katsaras J, Feigenson GW, Vogt VM, Dick RA. Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties. Biophys J 2017. [PMID: 29117524 DOI: 10.1016/j.bpj.2017.08.055.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here, using a broad set of in vitro and in silico techniques we addressed molecular mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.
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Affiliation(s)
- Milka Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Frederick A Heberle
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Michel A Cuendet
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Yi Wen
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - John Katsaras
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Gerald W Feigenson
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Volker M Vogt
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Robert A Dick
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York.
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20
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Khadem SMJ, Hille C, Löhmannsröben HG, Sokolov IM. Spot variation fluorescence correlation spectroscopy by data post-processing. Sci Rep 2017; 7:5614. [PMID: 28717215 PMCID: PMC5514068 DOI: 10.1038/s41598-017-05672-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/26/2017] [Indexed: 11/09/2022] Open
Abstract
Spot variation fluorescence correlation spectroscopy (SV-FCS) is a variant of the FCS techniques which may give useful information about the structural organisation of the medium in which the diffusion takes place. We show that the same results can be obtained by post-processing the photon count data from ordinary FCS measurements. By using this method, one obtains the fluorescence autocorrelation functions for sizes of confocal volume, which are effectively smaller than that of the initial FCS measurement. The photon counts of the initial experiment are first transformed into smooth intensity trace using kernel smoothing method or to a piecewise-continuous intensity trace using binning and then a non-linear transformation is applied to this trace. The result of this transformation mimics the photon count rate in an experiment performed with a smaller confocal volume. The applicability of the method is established in extensive numerical simulations and directly supported in in-vitro experiments. The procedure is then applied to the diffusion of AlexaFluor647-labeled streptavidin in living cells.
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Affiliation(s)
- S M J Khadem
- Humboldt University Berlin, Institute of Physics, Berlin, D-12489, Germany. .,Humboldt University Berlin, School of Analytical Sciences Adlershof (SALSA), Berlin, D-12489, Germany.
| | - C Hille
- University of Potsdam, Institute of Chemistry, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - H-G Löhmannsröben
- Humboldt University Berlin, School of Analytical Sciences Adlershof (SALSA), Berlin, D-12489, Germany.,University of Potsdam, Institute of Chemistry, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - I M Sokolov
- Humboldt University Berlin, Institute of Physics, Berlin, D-12489, Germany.,Humboldt University Berlin, School of Analytical Sciences Adlershof (SALSA), Berlin, D-12489, Germany
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21
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Lipid Driven Nanodomains in Giant Lipid Vesicles are Fluid and Disordered. Sci Rep 2017; 7:5460. [PMID: 28710349 PMCID: PMC5511215 DOI: 10.1038/s41598-017-05539-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/30/2017] [Indexed: 11/30/2022] Open
Abstract
It is a fundamental question in cell biology and biophysics whether sphingomyelin (SM)- and cholesterol (Chol)- driven nanodomains exist in living cells and in model membranes. Biophysical studies on model membranes revealed SM and Chol driven micrometer-sized liquid-ordered domains. Although the existence of such microdomains has not been proven for the plasma membrane, such lipid mixtures have been often used as a model system for ‘rafts’. On the other hand, recent super resolution and single molecule results indicate that the plasma membrane might organize into nanocompartments. However, due to the limited resolution of those techniques their unambiguous characterization is still missing. In this work, a novel combination of Förster resonance energy transfer and Monte Carlo simulations (MC-FRET) identifies directly 10 nm large nanodomains in liquid-disordered model membranes composed of lipid mixtures containing SM and Chol. Combining MC-FRET with solid-state wide-line and high resolution magic angle spinning NMR as well as with fluorescence correlation spectroscopy we demonstrate that these nanodomains containing hundreds of lipid molecules are fluid and disordered. In terms of their size, fluidity, order and lifetime these nanodomains may represent a relevant model system for cellular membranes and are closely related to nanocompartments suggested to exist in cellular membranes.
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22
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Drabik D, Przybyło M, Sikorski A, Langner M. The Effect of a Fluorophore Photo-Physics on the Lipid Vesicle Diffusion Coefficient Studied by Fluorescence Correlation Spectroscopy. J Fluoresc 2016; 26:661-9. [PMID: 26695945 PMCID: PMC4773467 DOI: 10.1007/s10895-015-1752-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/14/2015] [Indexed: 11/28/2022]
Abstract
Fluorescence Correlation Spectroscopy (FCS) is a technique, which allows determination of the diffusion coefficient and concentration of fluorescent objects suspended in the solution. The measured parameter is the fluctuation of the fluorescence signal emitted by diffusing molecules. When 100 nm DOPC vesicles labeled with various fluorescent dyes (Fluorescein-PE, NBD-PE, Atto488 DOPE or βBodipy FL) were measured, different values of diffusion coefficients have been obtained. These diffusion coefficients were different from the expected values measured using the dynamic light scattering method (DLS). The FCS was initially developed for solutions containing small fluorescent molecules therefore the observed inconsistency may result from the nature of vesicle suspension itself. The duration of the fluorescence signal may depend on the following factors: the exposure time of the labeled object to the excitation beam, the photo-physical properties (e.g., stability) of a fluorophore, the theoretical model used for the calculations of the diffusion coefficient and optical properties of the vesicle suspension. The diffusion coefficients determined for differently labeled liposomes show that its dependence on vesicle size and quantity of fluorescent probed used for labeling was significant demonstrating that the fluorescence properties of the fluorophore itself (bleaching and/or blinking) were critical factors for a correct outcome of FCS experiment. The new, based on combined FCS and DLS measurements, method for the determination of the focal volume prove itself to be useful for the evaluation of a fluorescence dye with respect to its applicability for FCS experiment.
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Affiliation(s)
- Dominik Drabik
- Laboratory for Biophysics of Macromolecular Aggregates, Department of Biomedical Engineering, Wroclaw University of Technology, Pl. Grunwaldzki 13, 50-377, Wroclaw, Poland.
| | - Magda Przybyło
- Laboratory for Biophysics of Macromolecular Aggregates, Department of Biomedical Engineering, Wroclaw University of Technology, Pl. Grunwaldzki 13, 50-377, Wroclaw, Poland
- Lipid Systems sp. z. o. o. [Ltd], ul. Duńska 9, 54-066, Wrocław, Poland
| | - Aleksander Sikorski
- Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, Wrocław, Poland
| | - Marek Langner
- Laboratory for Biophysics of Macromolecular Aggregates, Department of Biomedical Engineering, Wroclaw University of Technology, Pl. Grunwaldzki 13, 50-377, Wroclaw, Poland
- Lipid Systems sp. z. o. o. [Ltd], ul. Duńska 9, 54-066, Wrocław, Poland
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23
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Rose M, Hirmiz N, Moran-Mirabal JM, Fradin C. Lipid Diffusion in Supported Lipid Bilayers: A Comparison between Line-Scanning Fluorescence Correlation Spectroscopy and Single-Particle Tracking. MEMBRANES 2015; 5:702-21. [PMID: 26610279 PMCID: PMC4704007 DOI: 10.3390/membranes5040702] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 11/06/2015] [Indexed: 11/16/2022]
Abstract
Diffusion in lipid membranes is an essential component of many cellular process and fluorescence a method of choice to study membrane dynamics. The goal of this work was to directly compare two common fluorescence methods, line-scanning fluorescence correlation spectroscopy and single-particle tracking, to observe the diffusion of a fluorescent lipophilic dye, DiD, in a complex five-component mitochondria-like solid-supported lipid bilayer. We measured diffusion coefficients of DFCS ~ 3 um2 * s-1 and DSPT ~ 2 um2 * s-1, respectively. These comparable, yet statistically different values are used to highlight the main message of the paper, namely that the two considered methods give access to distinctly different dynamic ranges: D sup or approximatively 1um2 * s-1 for FCS and D inf or approximatively 5 um2 s-1 for SPT (with standard imaging conditions). In the context of membrane diffusion, this means that FCS allows studying lipid diffusion in fluid membranes, as well as the diffusion of loosely-bound proteins hovering above the membrane. SPT, on the other hand, is ideal to study the motions of membrane-inserted proteins, especially those presenting different conformations, but only allows studying lipid diffusion in relatively viscous membranes, such as supported lipid bilayers and cell membranes.
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Affiliation(s)
- Markus Rose
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada.
| | - Nehad Hirmiz
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada.
| | - Jose M Moran-Mirabal
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4L8, Canada.
| | - Cécile Fradin
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada.
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24
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Basit H, Lopez SG, Keyes TE. Fluorescence correlation and lifetime correlation spectroscopy applied to the study of supported lipid bilayer models of the cell membrane. Methods 2014; 68:286-99. [DOI: 10.1016/j.ymeth.2014.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/21/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022] Open
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25
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Bag N, Yap DHX, Wohland T. Temperature dependence of diffusion in model and live cell membranes characterized by imaging fluorescence correlation spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014. [DOI: 10.1016/j.bbamem.2013.10.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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26
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Montis C, Baglioni P, Berti D. Monitoring the interaction of nucleolipoplexes with model membranes. SOFT MATTER 2014; 10:39-43. [PMID: 24651954 DOI: 10.1039/c3sm52254g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report on the interaction of nucleolipid/DNA assemblies with model membranes, studied with small angle X-ray scattering, fluorescence microscopy and correlation spectroscopy. The fusion with the membrane can be monitored by following the diffusion properties of a lipid probe, shedding light on the parameters that regulate the internalization of the complexes.
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Affiliation(s)
- Costanza Montis
- CSGI and Department of Chemistry, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy.
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27
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Steinberger T, Macháň R, Hof M. Z-scan fluorescence correlation spectroscopy as a tool for diffusion measurements in planar lipid membranes. Methods Mol Biol 2014; 1076:617-634. [PMID: 24108647 DOI: 10.1007/978-1-62703-649-8_28] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Studies of lateral diffusion are used for the characterization of the dynamics of biological membranes. One of the techniques that can be used for this purpose is fluorescence correlation spectroscopy (FCS), which belongs to the single-molecule techniques. Unfortunately, FCS measurements, when performed in planar lipid systems, are associated with a few sources of inaccuracy in the determination of the lateral diffusion coefficient. The main problems are related to the imperfect positioning of the laser focus relative to the plane of the sample. Another source of inaccuracy is the requirement for external calibration of the detection volume size. This protocol introduces a calibration-free method called Z-scan fluorescence correlation spectroscopy (Z-scan FCS), which is based on the determination of the diffusion time and particle number in steps along the optical (z-) axis by sequential FCS measurements. Z-scan FCS could be employed for diffusion measurements in planar membrane model systems-supported phospholipid bilayers (SPBs) and giant unilamellar vesicles (GUVs) and also in biological membranes. A result from measurements in SPBs is also presented in the protocol as a principle example of the Z-scan technique.
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Affiliation(s)
- Tomáš Steinberger
- Faculty of Biomedical Engineering, Czech Technical University in Prague, Kladno, Czech Republic
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28
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NMR methods for measuring lateral diffusion in membranes. Chem Phys Lipids 2013; 166:31-44. [DOI: 10.1016/j.chemphyslip.2012.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/11/2012] [Accepted: 12/12/2012] [Indexed: 02/07/2023]
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29
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Substrate Effects on the Formation Process, Structure and Physicochemical Properties of Supported Lipid Bilayers. MATERIALS 2012. [PMCID: PMC5449048 DOI: 10.3390/ma5122658] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Supported lipid bilayers are artificial lipid bilayer membranes existing at the interface between solid substrates and aqueous solution. Surface structures and properties of the solid substrates affect the formation process, fluidity, two-dimensional structure and chemical activity of supported lipid bilayers, through the 1–2 nm thick water layer between the substrate and bilayer membrane. Even on SiO2/Si and mica surfaces, which are flat and biologically inert, and most widely used as the substrates for the supported lipid bilayers, cause differences in the structure and properties of the supported membranes. In this review, I summarize several examples of the effects of substrate structures and properties on an atomic and nanometer scales on the solid-supported lipid bilayers, including our recent reports.
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30
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Kapusta P, Macháň R, Benda A, Hof M. Fluorescence Lifetime Correlation Spectroscopy (FLCS): concepts, applications and outlook. Int J Mol Sci 2012; 13:12890-910. [PMID: 23202928 PMCID: PMC3497302 DOI: 10.3390/ijms131012890] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/14/2012] [Accepted: 09/19/2012] [Indexed: 11/16/2022] Open
Abstract
Fluorescence Lifetime Correlation Spectroscopy (FLCS) is a variant of fluorescence correlation spectroscopy (FCS), which uses differences in fluorescence intensity decays to separate contributions of different fluorophore populations to FCS signal. Besides which, FLCS is a powerful tool to improve quality of FCS data by removing noise and distortion caused by scattered excitation light, detector thermal noise and detector afterpulsing. We are providing an overview of, to our knowledge, all published applications of FLCS. Although these are not numerous so far, they illustrate possibilities for the technique and the research topics in which FLCS has the potential to become widespread. Furthermore, we are addressing some questions which may be asked by a beginner user of FLCS. The last part of the text reviews other techniques closely related to FLCS. The generalization of the idea of FLCS paves the way for further promising application of the principle of statistical filtering of signals. Specifically, the idea of fluorescence spectral correlation spectroscopy is here outlined.
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Affiliation(s)
- Peter Kapusta
- J. Heyrovský Institute of Physical Chemistry of ASCR, v.v.i, Dolejškova 3, 18223 Prague 8, Czech Republic; E-Mails: (P.K.); (R.M.)
| | - Radek Macháň
- J. Heyrovský Institute of Physical Chemistry of ASCR, v.v.i, Dolejškova 3, 18223 Prague 8, Czech Republic; E-Mails: (P.K.); (R.M.)
- Czech Technical University in Prague, Faculty of Biomedical Engineering, Sítná 3105, 272 01 Kladno, Czech Republic
| | - Aleš Benda
- Centre for Vascular Research and Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia; E-Mail:
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of ASCR, v.v.i, Dolejškova 3, 18223 Prague 8, Czech Republic; E-Mails: (P.K.); (R.M.)
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31
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Lateral diffusion of bilayer lipids measured via 31P CODEX NMR. Chem Phys Lipids 2012; 165:721-30. [DOI: 10.1016/j.chemphyslip.2012.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/17/2012] [Accepted: 08/18/2012] [Indexed: 11/18/2022]
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32
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Bag N, Sankaran J, Paul A, Kraut RS, Wohland T. Calibration and Limits of Camera-Based Fluorescence Correlation Spectroscopy: A Supported Lipid Bilayer Study. Chemphyschem 2012; 13:2784-94. [DOI: 10.1002/cphc.201200032] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 04/19/2012] [Indexed: 12/22/2022]
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33
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Kraut R, Bag N, Wohland T. Fluorescence Correlation Methods for Imaging Cellular Behavior of Sphingolipid-Interacting Probes. Methods Cell Biol 2012; 108:395-427. [DOI: 10.1016/b978-0-12-386487-1.00018-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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34
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Ghosh S, Mandal AK, Das AK, Mondal T, Bhattacharyya K. Diffusion of organic dyes in a niosome immobilized on a glass surface using fluorescence correlation spectroscopy. Phys Chem Chem Phys 2012; 14:9749-57. [DOI: 10.1039/c2cp41212h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Perevoshchikova IV, Kotova EA, Antonenko YN. Fluorescence correlation spectroscopy in biology, chemistry, and medicine. BIOCHEMISTRY (MOSCOW) 2011; 76:497-516. [PMID: 21639831 DOI: 10.1134/s0006297911050014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This review describes the method of fluorescence correlation spectroscopy (FCS) and its applications. FCS is used for investigating processes associated with changes in the mobility of molecules and complexes and allows researchers to study aggregation of particles, binding of fluorescent molecules with supramolecular complexes, lipid vesicles, etc. The size of objects under study varies from a few angstroms for dye molecules to hundreds of nanometers for nanoparticles. The described applications of FCS comprise various fields from simple chemical systems of solution/micelle to sophisticated regulations on the level of living cells. Both the methodical bases and the theoretical principles of FCS are simple and available. The present review is concentrated preferentially on FCS applications for studies on artificial and natural membranes. At present, in contrast to the related approach of dynamic light scattering, FCS is poorly known in Russia, although it is widely employed in laboratories of other countries. The goal of this review is to promote the development of FCS in Russia so that this technique could occupy the position it deserves in modern Russian science.
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Affiliation(s)
- I V Perevoshchikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
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Abstract
This minireview focuses on diffusion NMR studies in bicelles. Following a discourse on diffusion fundamentals, and a comparative overview of fluorescence and NMR-based techniques for measuring diffusion, the pulsed field gradient (PFG) NMR diffusion method is introduced, emphasizing its specific advantages and limitations when applied to diffusion measurements in macroscopically oriented lamellar systems such as magnetically aligned bicelles. The utility of PFG NMR diffusion measurements in bicellar model membrane systems for examining lateral diffusion of membrane-bound molecular species is demonstrated, along with certain features of lateral diffusion that such studies illuminate. Further, those aspects of bicelle morphology that have been resolved using PFG NMR diffusion studies of various molecular weight soluble polymeric species are reviewed. The discussion concludes with an outline of future prospects for diffusion NMR studies in bicelles.
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Affiliation(s)
- Peter M. Macdonald
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - Ronald Soong
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
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Mears M, Tarmey DS, Geoghegan M. Single macromolecule diffusion in confined environments. Macromol Rapid Commun 2011; 32:1411-8. [PMID: 21751276 DOI: 10.1002/marc.201100076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Indexed: 11/08/2022]
Abstract
We consider the behaviour of single molecules on surfaces and, more generally, in confined environments. These are loosely split into three sections: single molecules in biology, the physics of single molecules on surfaces and controlled (directed) diffusion. With recent advances in single molecule detection techniques, the importance and mechanisms of single molecule processes such as localised enzyme production and intracellular diffusion across membranes has been highlighted, emphasising the extra information that cannot be obtained with techniques that present average behaviour. Progress has also been made in producing artificial systems that can control the rate and direction of diffusion, and because these are still in their infancy (especially in comparison to complex biological systems), we discuss the new physics revealed by these phenomena.
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Macháň R, Hof M, Chernovets T, Zhmak MN, Ovchinnikova TV, Sýkora J. Formation of arenicin-1 microdomains in bilayers and their specific lipid interaction revealed by Z-scan FCS. Anal Bioanal Chem 2011; 399:3547-54. [PMID: 21293959 DOI: 10.1007/s00216-011-4694-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/10/2011] [Accepted: 01/17/2011] [Indexed: 11/30/2022]
Abstract
Z-scan fluorescence correlation spectroscopy (FCS) is employed to characterize the interaction between arenicin-1 and supported lipid bilayers (SLBs) of different compositions. Lipid analogue C8-BODIPY 500/510C5-HPC and ATTO 465 labelled arenicin-1 are used to detect changes in lipid and peptide diffusion upon addition of unlabelled arenicin-1 to SLBs. Arenicin-1 decreases lipid mobility in negatively charged SLBs. According to diffusion law analysis, microdomains of significantly lower lipid mobility are formed. The analysis of peptide FCS data confirms the presence of microdomains for anionic SLBs. No indications of microdomain formation are detected in SLBs composed purely of zwitterionic lipids. Additionally, our FCS results imply that arenicin-1 exists in the form of oligomers and/or aggregates when interacting with membranes of both compositions.
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Affiliation(s)
- Radek Macháň
- J. Heyrovský Institute of Physical Chemistry v.v.i, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
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Guo J, Baker GA, Hillesheim PC, Dai S, Shaw RW, Mahurin SM. Fluorescence correlation spectroscopy evidence for structural heterogeneity in ionic liquids. Phys Chem Chem Phys 2011; 13:12395-8. [DOI: 10.1039/c1cp20929a] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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40
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Owen DM, Gaus K, Magee AI, Cebecauer M. Dynamic organization of lymphocyte plasma membrane: lessons from advanced imaging methods. Immunology 2010; 131:1-8. [PMID: 20646076 DOI: 10.1111/j.1365-2567.2010.03319.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Lipids and lipid domains are suggested to play an essential role in the heterogeneous organization of the plasma membrane in eukaryotic cells, including cells of the immune system. We summarize the results of advanced imaging and physical studies of membrane organization with special focus on the plasma membrane of lymphocytes. We provide a comprehensive up-to-date view on the existence of membrane lipid and protein clusters such as lipid rafts and suggest research directions to better understand these highly dynamic entities on the surface of immune cells.
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Affiliation(s)
- Dylan M Owen
- Centre for Vascular Research, University of New South Wales, Sydney, NSW, Australia
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