1
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Das N, Khan T, Halder B, Ghosh S, Sen P. Macromolecular crowding effects on protein dynamics. Int J Biol Macromol 2024:136248. [PMID: 39374718 DOI: 10.1016/j.ijbiomac.2024.136248] [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: 06/29/2024] [Revised: 09/30/2024] [Accepted: 09/30/2024] [Indexed: 10/09/2024]
Abstract
Macromolecular crowding experiments bridge the gap between in-vivo and in-vitro studies by mimicking some of the cellular complexities like high viscosity and limited space, while still manageable for experiments and analysis. Macromolecular crowding impacts all biological processes and is a focus of contemporary research. Recent reviews have highlighted the effect of crowding on various protein properties. One of the essential characteristics of protein is its dynamic nature; however, how protein dynamics get modulated in the crowded milieu has been largely ignored. This article discusses how protein translational, rotational, conformational, and solvation dynamics change under crowded conditions, summarizing key observations in the literature. We emphasize our research on microsecond conformational and water dynamics in crowded milieus and their impact on enzymatic activity and stability. Lastly, we provided our outlook on how this field might move forward in the future.
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Affiliation(s)
- Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Bisal Halder
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Shreya Ghosh
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India.
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2
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Gligonov I, Enderlein J. Variational calculus approach to Zernike polynomials with application to FCS. Biophys J 2024:S0006-3495(24)00557-5. [PMID: 39164968 DOI: 10.1016/j.bpj.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/21/2024] [Accepted: 08/13/2024] [Indexed: 08/22/2024] Open
Abstract
Zernike polynomials are a sequence of orthogonal polynomials that play a crucial role in optics and, in particular, modeling microscopy systems. Introduced by Frits Zernike in 1934, they are particularly useful in expressing wavefront aberrations and, thus, imperfections of imaging systems. However, their origin and properties are rarely discussed and proven. Here, we present a novel approach to Zernike polynomials using variational calculus and apply them to describe aberrations in fluorescence microscopy. In particular, we model the impact of various optical aberrations on the performance of one-photon and two-photon excitation fluorescence microscopy.
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Affiliation(s)
- Ivan Gligonov
- Third Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Jörg Enderlein
- Third Institute of Physics - Biophysics, Georg August University, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Universitätsmedizin Göttingen, Göttingen, Germany.
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3
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Halder B, Ghosh S, Khan T, Pal S, Das N, Sen P. Tracking heterogenous protein aggregation at nanoscale through fluorescence correlation spectroscopy. Photochem Photobiol 2024; 100:989-999. [PMID: 39032082 DOI: 10.1111/php.14004] [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: 02/21/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/22/2024]
Abstract
Various biophysical techniques have been extensively employed to study protein aggregation due to its significance. Traditionally, these methods detect aggregation at micrometer length scales and micromolar concentrations. However, unlike in vitro, protein aggregation typically occurs at nanomolar concentrations in vivo. Here, using fluorescence correlation spectroscopy (FCS), we captured bromelain aggregation at concentrations as low as ~20 nM, surpassing the detection limit of traditional methods like thioflavin T fluorescence, scattering, and fluorescence microscopy by more than one order of magnitude. Moreover, using thioflavin T fluorescence-based FCS, we have detected larger aggregates at higher bromelain concentrations, which is undetectable in FCS otherwise. Importantly, our study reveals inherent heterogeneity in bromelain aggregation, inaccessible to ensemble-averaged techniques. The presented report may provide a platform for the characterization of premature aggregates at very low protein concentrations, which are thought to be functionally significant species in protein aggregation-induced diseases.
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Affiliation(s)
- Bisal Halder
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Shreya Ghosh
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Subhendu Pal
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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4
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Shen YX, Lee PS, Teng MC, Huang JH, Wang CC, Fan HF. Influence of Cigarette Aerosol in Alpha-Synuclein Oligomerization and Cell Viability in SH-SY5Y: Implications for Parkinson's Disease. ACS Chem Neurosci 2024; 15:1484-1500. [PMID: 38483468 PMCID: PMC10995954 DOI: 10.1021/acschemneuro.3c00771] [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: 11/29/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024] Open
Abstract
Although cigarette aerosol exposure is associated with various adverse health issues, its impact on Parkinson's disease (PD) remains elusive. Here, we investigated the effect of cigarette aerosol extract (CAE) on SH-SY5Y cells for the first time, both with and without α-synuclein (α-Syn) overexpression. We found that α-Syn aggravates CAE-induced cell death, oxidative stress, and mitochondrial dysfunction. Fluorescence cross-correlation spectroscopy (FCCS) revealed a dual distribution of α-Syn within the cells, with homogeneous regions indicative of monomeric α-Syn and punctated regions, suggesting the formation of oligomers. Moreover, we observed colocalization of α-Syn oligomers with lysosomes along with a reduction in autophagy activity. These findings suggest that α-Syn overexpression exacerbates CAE-induced intracellular cytotoxicity, mitochondrial dysfunction, and autophagy dysregulation, leading to elevated cell mortality. Our findings provide new insights into the pathogenic mechanisms linking exposure to cigarette aerosols with neurodegenerative diseases.
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Affiliation(s)
- Yu-Xin Shen
- Institute
of Medical Science and Technology, National
Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department
of Chemistry, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Aerosol
Science Research Center, National Sun Yat-sen
University, Kaohsiung 804, Taiwan
| | - Pe-Shuen Lee
- Institute
of Medical Science and Technology, National
Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department
of Chemistry, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Aerosol
Science Research Center, National Sun Yat-sen
University, Kaohsiung 804, Taiwan
| | - Ming-Chu Teng
- Institute
of Medical Science and Technology, National
Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department
of Chemistry, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Aerosol
Science Research Center, National Sun Yat-sen
University, Kaohsiung 804, Taiwan
| | - Jhih-Hong Huang
- Department
of Chemistry, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Aerosol
Science Research Center, National Sun Yat-sen
University, Kaohsiung 804, Taiwan
| | - Chia C. Wang
- Department
of Chemistry, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Aerosol
Science Research Center, National Sun Yat-sen
University, Kaohsiung 804, Taiwan
| | - Hsiu-Fang Fan
- Institute
of Medical Science and Technology, National
Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department
of Chemistry, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Aerosol
Science Research Center, National Sun Yat-sen
University, Kaohsiung 804, Taiwan
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5
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Gresham IJ, Lilley SG, Nelson ARJ, Koynov K, Neto C. Nanostructure Explains the Behavior of Slippery Covalently Attached Liquid Surfaces. Angew Chem Int Ed Engl 2023; 62:e202308008. [PMID: 37550243 DOI: 10.1002/anie.202308008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Slippery covalently-attached liquid surfaces (SCALS) with low contact angle hysteresis (CAH, <5°) and nanoscale thickness display impressive anti-adhesive properties, similar to lubricant-infused surfaces. Their efficacy is generally attributed to the liquid-like mobility of the constituent tethered chains. However, the precise physico-chemical properties that facilitate this mobility are unknown, hindering rational design. This work quantifies the chain length, grafting density, and microviscosity of a range of polydimethylsiloxane (PDMS) SCALS, elucidating the nanostructure responsible for their properties. Three prominent methods are used to produce SCALS, with characterization carried out via single-molecule force measurements, neutron reflectometry, and fluorescence correlation spectroscopy. CO2 snow-jet cleaning was also shown to reduce the CAH of SCALS via a modification of their grafting density. SCALS behavior can be predicted by reduced grafting density, Σ, with the lowest water CAH achieved at Σ≈2. This study provides the first direct examination of SCALS grafting density, chain length, and microviscosity and supports the hypothesis that SCALS properties stem from a balance of layer uniformity and mobility.
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Affiliation(s)
- Isaac J Gresham
- School of Chemistry and the University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
| | - Seamus G Lilley
- School of Chemistry and the University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
| | - Andrew R J Nelson
- Australian Center for Neutron Scattering, ANSTO, Sydney, NSW, Australia
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Chiara Neto
- School of Chemistry and the University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
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6
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Kim HJ. Spectroscopic and Chemical Properties of Ionic Liquids: Computational Study. CHEM REC 2023; 23:e202300075. [PMID: 37166396 DOI: 10.1002/tcr.202300075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/18/2023] [Indexed: 05/12/2023]
Abstract
A brief account is given of highlights of our computational efforts - often in collaboration with experimental groups - to understand spectroscopic and chemical properties of ionic liquids (ILs). Molecular dynamics, including their inhomogeneous character, responsible for key spectral features observed in dielectric absorption, infra-red (IR) and fluorescence correlation spectroscopy (FCS) measurements are elucidated. Mechanisms of chemical processes involving imidazolium-based ILs are illustrated for CO2 capture and related reactions, transesterification of cellulose, and Au nanocluster-catalyzed Suzuki cross-coupling reaction with attention paid to differing roles of IL ions. A comparison with experiments is also made.
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Affiliation(s)
- Hyung J Kim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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7
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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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8
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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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9
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Hirano K, Kinoshita M, Matsumori N. Impact of sphingomyelin acyl chain heterogeneity upon properties of raft-like membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184036. [PMID: 36055359 DOI: 10.1016/j.bbamem.2022.184036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/26/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Sphingomyelin (SM) is a main component of lipid rafts and characteristic of abundance of long and saturated acyl chains. Recently, we reported that fluorescence-labeled lipids including C16:0 and C18:0SMs retained membrane behaviors of inherent lipids. Here, we newly prepared fluorescent SMs with longer acyl chains, C22:0 and C24:1, for observing their partition and diffusion in SM/cholesterol (chol)/dioleoylphosphatidylcholine (DOPC) bilayers. Although fluorescent C24:1SM underwent a uniform distribution between ordered (Lo) and disordered (Ld) phases, other fluorescent SMs with saturated acyl chains were preferentially distributed in the Lo phase. Interestingly, when the acyl chains of fluorescent and membrane SMs are different, distribution of fluorescent SM to the Lo phase was reduced compared to when the acyl chains are the same. This tendency was also observed for C16:0SM/C22:0SM/chol/DOPC quaternary bilayers, where the minor SM was more excluded out of the Lo phase than the major SM. We also found that the coexistence of SMs induces SM efflux out of the Lo phase and simultaneous DOPC influx to the Lo phase, consequently reducing the difference in fluidity between the two phases. These results suggest that physicochemical properties of lipid rafts are regulated by the acyl chain heterogeneity of SMs.
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Affiliation(s)
- Kana Hirano
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masanao Kinoshita
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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10
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Sánchez MF, Dietz MS, Müller U, Weghuber J, Gatterdam K, Wieneke R, Heilemann M, Lanzerstorfer P, Tampé R. Dynamic in Situ Confinement Triggers Ligand-Free Neuropeptide Receptor Signaling. NANO LETTERS 2022; 22:8363-8371. [PMID: 36219818 PMCID: PMC9614963 DOI: 10.1021/acs.nanolett.2c03506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Membrane receptor clustering is fundamental to cell-cell communication; however, the physiological function of receptor clustering in cell signaling remains enigmatic. Here, we developed a dynamic platform to induce cluster formation of neuropeptide Y2 hormone receptors (Y2R) in situ by a chelator nanotool. The multivalent interaction enabled a dynamic exchange of histidine-tagged Y2R within the clusters. Fast Y2R enrichment in clustered areas triggered ligand-independent signaling as determined by an increase in cytosolic calcium and cell migration. Notably, the calcium and motility response to ligand-induced activation was amplified in preclustered cells, suggesting a key role of receptor clustering in sensitizing the dose response to lower ligand concentrations. Ligand-independent versus ligand-induced signaling differed in the binding of arrestin-3 as a downstream effector, which was recruited to the clusters only in the presence of the ligand. This approach allows in situ receptor clustering, raising the possibility to explore different receptor activation modalities.
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Affiliation(s)
- M. Florencia Sánchez
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
| | - Marina S. Dietz
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Ulrike Müller
- School
of Engineering and Environmental Sciences, University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Julian Weghuber
- School
of Engineering and Environmental Sciences, University of Applied Sciences Upper Austria, 4600 Wels, Austria
- FFoQSI
- Austrian Competence Centre for Feed and Food Quality, Safety &
Innovation, FFoQSI GmbH, Technopark 1D, 3430 Tulln, Austria
| | - Karl Gatterdam
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
| | - Ralph Wieneke
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
| | - Mike Heilemann
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Peter Lanzerstorfer
- School
of Engineering and Environmental Sciences, University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Robert Tampé
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
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11
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Galiani S, Reglinski K, Carravilla P, Barbotin A, Urbančič I, Ott J, Sehr J, Sezgin E, Schneider F, Waithe D, Hublitz P, Schliebs W, Erdmann R, Eggeling C. Diffusion and interaction dynamics of the cytosolic peroxisomal import receptor PEX5. BIOPHYSICAL REPORTS 2022; 2:None. [PMID: 36299769 PMCID: PMC9586885 DOI: 10.1016/j.bpr.2022.100055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/24/2022] [Indexed: 11/18/2022]
Abstract
Cellular functions rely on proper actions of organelles such as peroxisomes. These organelles rely on the import of proteins from the cytosol. The peroxisomal import receptor PEX5 takes up target proteins in the cytosol and transports them to the peroxisomal matrix. However, its cytosolic molecular interactions have so far not directly been disclosed. Here, we combined advanced optical microscopy and spectroscopy techniques such as fluorescence correlation spectroscopy and stimulated emission depletion microscopy with biochemical tools to present a detailed characterization of the cytosolic diffusion and interaction dynamics of PEX5. Among other features, we highlight a slow diffusion of PEX5, independent of aggregation or target binding, but associated with cytosolic interaction partners via its N-terminal domain. This sheds new light on the functionality of the receptor in the cytosol as well as highlighting the potential of using complementary microscopy tools to decipher molecular interactions in the cytosol by studying their diffusion dynamics.
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Affiliation(s)
- S. Galiani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - K. Reglinski
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- University Hospital Jena, Jena, Germany
| | - P. Carravilla
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
| | - A. Barbotin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - I. Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Laboratory of Biophysics, Condensed Matter Physics Department, Jožef Stefan Institute, Ljubljana, Slovenia
| | - J. Ott
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - J. Sehr
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - E. Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - F. Schneider
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - D. Waithe
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- WIMM Centre for Computational Biology , MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - P. Hublitz
- WIMM Genome Engineering Services, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - W. Schliebs
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - R. Erdmann
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - C. Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- Jena Center for Soft Matter (JCSM), Jena, Germany
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12
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Stoddart LA, Goulding J, Briddon SJ. Advances in the application of fluorescence correlation spectroscopy to study detergent purified and encapsulated membrane proteins. Int J Biochem Cell Biol 2022; 146:106210. [PMID: 35390493 DOI: 10.1016/j.biocel.2022.106210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/25/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a quantitative spectroscopy technique which could potentially increase throughput and sensitivity of screening for ligand, substrate and inhibitor binding to membrane proteins in solution. However, the purification of membrane proteins in their active forms is complex, as the lipid bilayer provides stability and its removal often causes the protein to become conformationally unstable. This has limited the application of biophysical techniques such as FCS to study the function of membrane proteins. The recent application of native extraction techniques such as styrene maleic acid lipid particles (SMALPs) has resolved this issue and FCS has emerged as a powerful option for studying proteins extracted in this way. This review will discuss the application of FCS to study purified membrane proteins in detergent micelles, nanodiscs and SMALPs and its potential to be used routinely in membrane protein drug discovery.
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Affiliation(s)
- Leigh A Stoddart
- Cell Signalling and Pharmacology Research Group, Division of Physiology Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, The Midlands, UK
| | - Joëlle Goulding
- Cell Signalling and Pharmacology Research Group, Division of Physiology Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, The Midlands, UK
| | - Stephen J Briddon
- Cell Signalling and Pharmacology Research Group, Division of Physiology Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, The Midlands, UK.
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13
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Fan HF, Chen WL, Chen YZ, Huang JW, Shen YX. Change in the Oligomeric State of α-Synuclein Variants in Living Cells. ACS Chem Neurosci 2022; 13:1143-1164. [PMID: 35394271 DOI: 10.1021/acschemneuro.1c00646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The accumulation of β-sheet-rich α-synuclein (α-Syn) protein in human brain cells is a pathological hallmark of Parkinson's disease (PD). Moreover, it has been reported that familial PD mutations (A30P, E46K, H50Q, G51D, and A53T) accumulate at an accelerated rate both in vivo and in vitro. In addition, accumulations of various C-terminal α-Syn truncations, such as C-terminal-truncated N103 α-synuclein (N103), were found in an aggregated form in the brain tissue of PD patients. Fluorescent protein-tagged wild-type α-Syn, A30P, E46K, H50Q, G51D, A53T, and N103 were transfected into HEK293T and SHSY5Y cells, and their diffusion behaviors were investigated with a custom-built fluorescence microscope system. Based on our experimental results, the oligomerization of α-Syn is a time-dependent process in both HEK293T and SHSY5Y cells, and the oligomer state approaches a plateau after 48 h of transfection. The change in the oligomeric state of E46K, H50Q, and G51D exhibited a similar trend to the wild type at a lower concentration but became intense at a higher concentration. A53T and N103 possess smaller diffusion coefficients than wild-type α-synuclein and other family PD mutations, indicating that these two mutants could form higher oligomeric states or stronger interactions in HEK293T and SHSY5Y cells. In contrast, the smallest oligomer and the lowest intracellular interaction among all investigated α-Syn variants were found for A30P. These phenomena indicated the presence of different pathogeneses among familial PD mutants and C-terminal α-Syn truncations.
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Affiliation(s)
- Hsiu-Fang Fan
- Institute of Medical Science and Technology, National Sun Yat-sen University, No. 70 Lien-hai Road, Kaohsiung 80424, Kaohsiung 804, Taiwan
- Department of Chemistry, National Sun Yat-sen University, No. 70 Lien-hai Road, Kaohsiung 80424, Kaohsiung 804, Taiwan
- Aerosol Science Research Center, National Sun Yat-sen University, No. 70 Lien-hai Road, Kaohsiung 80424, Kaohsiung 804, Taiwan
| | - Wen-Ling Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155, Section 2, Linong Street, Taipei 112, Taiwan
| | - Yan-Zhow Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155, Section 2, Linong Street, Taipei 112, Taiwan
| | - Jian-Wei Huang
- Department of Chemistry, National Sun Yat-sen University, No. 70 Lien-hai Road, Kaohsiung 80424, Kaohsiung 804, Taiwan
| | - Yu-Xin Shen
- Department of Chemistry, National Sun Yat-sen University, No. 70 Lien-hai Road, Kaohsiung 80424, Kaohsiung 804, Taiwan
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14
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Carravilla P, Dasgupta A, Zhurgenbayeva G, Danylchuk DI, Klymchenko AS, Sezgin E, Eggeling C. Long-term STED imaging of membrane packing and dynamics by exchangeable polarity-sensitive dyes. BIOPHYSICAL REPORTS 2021; 1:None. [PMID: 34939048 PMCID: PMC8651516 DOI: 10.1016/j.bpr.2021.100023] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/08/2021] [Indexed: 12/28/2022]
Abstract
Understanding the plasma membrane nanoscale organization and dynamics in living cells requires microscopy techniques with high spatial and temporal resolution that permit for long acquisition times and allow for the quantification of membrane biophysical properties, such as lipid ordering. Among the most popular super-resolution techniques, stimulated emission depletion (STED) microscopy offers one of the highest temporal resolutions, ultimately defined by the scanning speed. However, monitoring live processes using STED microscopy is significantly limited by photobleaching, which recently has been circumvented by exchangeable membrane dyes that only temporarily reside in the membrane. Here, we show that NR4A, a polarity-sensitive exchangeable plasma membrane probe based on Nile red, permits the super-resolved quantification of membrane biophysical parameters in real time with high temporal and spatial resolution as well as long acquisition times. The potential of this polarity-sensitive exchangeable dye is showcased by live-cell real-time three-dimensional STED recordings of bleb formation and lipid exchange during membrane fusion as well as by STED-fluorescence correlation spectroscopy experiments for the simultaneous quantification of membrane dynamics and lipid packing that correlate in model and live-cell membranes.
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Affiliation(s)
- Pablo Carravilla
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
| | - Anindita Dasgupta
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
| | - Gaukhar Zhurgenbayeva
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Dmytro I. Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Illkirch, France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Illkirch, France
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Christian Eggeling
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Jena Center for Soft Matter, Jena, Germany
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15
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Leomil FSC, Zoccoler M, Dimova R, Riske KA. PoET: automated approach for measuring pore edge tension in giant unilamellar vesicles. BIOINFORMATICS ADVANCES 2021; 1:vbab037. [PMID: 36700098 PMCID: PMC9710609 DOI: 10.1093/bioadv/vbab037] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/09/2021] [Accepted: 11/17/2021] [Indexed: 01/28/2023]
Abstract
Motivation A reliable characterization of the membrane pore edge tension of single giant unilamellar vesicles (GUVs) requires the measurement of micrometer sized pores in hundreds to thousands of images. When manually performed, this procedure has shown to be extremely time-consuming and to generate inconsistent results among different users and imaging systems. A user-friendly software for such analysis allowing quick processing and generation of reproducible data had not yet been reported. Results We have developed a software (PoET) for automatic pore edge tension measurements on GUVs. The required image processing steps and the characterization of the pore dynamics are performed automatically within the software and its use allowed for a 30-fold reduction in the analysis time. We demonstrate the applicability of the software by comparing the pore edge tension of GUVs of different membrane compositions and surface charges. The approach was applied to electroporated GUVs but is applicable to other means of pore formation. Availability and implementation The complete software is implemented in Python and available for Windows at https://dx.doi.org/10.17617/3.7h. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Fernanda S C Leomil
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 043039-032, Brazil,Department of Theory and Bio Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany
| | - Marcelo Zoccoler
- DFG Cluster of Excellence “Physics of Life”, Technical University of Dresden, Dresden 01307, Germany
| | - Rumiana Dimova
- Department of Theory and Bio Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany,To whom correspondence should be addressed. or
| | - Karin A Riske
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 043039-032, Brazil,To whom correspondence should be addressed. or
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16
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Pir Cakmak F, Marianelli AM, Keating CD. Phospholipid Membrane Formation Templated by Coacervate Droplets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:10366-10375. [PMID: 34398617 DOI: 10.1021/acs.langmuir.1c01562] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We report the formation of coacervate-supported phospholipid membranes by hydrating a dried lipid film in the presence of coacervate droplets. Coacervate-supported membranes were characterized by fluorescence imaging, polarization, fluorescence recovery after photobleaching of labeled lipids, lipid quenching experiments, and solute uptake experiments. Our findings are consistent with the presence of lipid membranes around the coacervates, with many droplets fully coated by what appear to be continuous lipid bilayers. In contrast to traditional giant lipid vesicles formed by gentle hydration in the absence of coacervates, the coacervate-templated membrane vesicles are more uniform in size, shape, and apparent lamellarity. Due to their fully coacervate model cytoplasm, these simple artificial cells are macromolecularly crowded and can be easily pre-loaded with high concentrations of proteins or nucleic acids. Within the same population, in addition to coacervate droplets having intact lipid membrane coatings, other coacervate droplets are coated with membranes having defects or pores that permit solute entry, and some are coated with multilayered membranes. Membranes surrounding protein-based coacervate droplets provided protection from a protease added to the external solution. The simplicity of producing artificial cells having a coacervate model cytoplasm surrounded by a model membrane is at the same time interesting as a potential mechanism for prebiotic protocell formation and appealing for biotechnology. We anticipate that such structures could serve as a new type of model system for understanding interactions between intracellular phases and cell or organelle membranes, which are implicated in a growing number of processes ranging from neurotransmission to signaling.
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Affiliation(s)
- Fatma Pir Cakmak
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Allyson M Marianelli
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Christine D Keating
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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17
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Ti YT, Cheng HC, Li Y, Tu HL. Multiplexed patterning of hybrid lipid membrane and protein arrays for cell signaling study. LAB ON A CHIP 2021; 21:2711-2720. [PMID: 34109339 DOI: 10.1039/d1lc00178g] [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
The supported lipid bilayer (SLB) is a powerful tool for studying dynamic cell-environment interactions and has been widely used for biosensing applications. Using a reusable microfluidic chip, we present here a strategy to fabricate highly multiplexed SLB and protein arrays for cell signaling research. This approach allows for the rapid patterning of hundreds of highly reproducible and size-tunable SLB arrays with distinct lipid composition and mobility. Using fluorescence microscopy and fluorescence correlation spectroscopy, the lipid mobility is found to play a central role for patterning this membrane assay. Adding protein rings as diffusion barriers extends the accessible mobility range and maintains long-term stability of the hybrid array. Subsequent protein functionalizations on the SLB could be conducted using standard conjugation methods. The utility of the hybrid array for cell signaling experiments is demonstrated by studying the immune NF-κB signaling, whose activity is triggered by the binding of the membrane receptor, toll-like-receptor 4 (TLR 4), to its ligand, lipopolysaccharide (LPS), that is functionalized on the SLB. The patterned array allows cells to adhere and spread on areas without LPS before migrating to interact with membrane-bound LPS to initiate NF-κB activation. Overall, the strategy offers an efficient route to rapidly generate easily controllable and multiplexed molecular arrays that can serve as versatile platforms for biosensing and cell signaling research.
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Affiliation(s)
- Yu-Ting Ti
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan. and Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Hsiao-Chi Cheng
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.
| | - Ying Li
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan. and Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taiwan
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18
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Chojnacki J, Eggeling C. Super-Resolution STED Microscopy-Based Mobility Studies of the Viral Env Protein at HIV-1 Assembly Sites of Fully Infected T-Cells. Viruses 2021; 13:608. [PMID: 33918253 PMCID: PMC8067239 DOI: 10.3390/v13040608] [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: 03/05/2021] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 01/08/2023] Open
Abstract
The ongoing threat of human immunodeficiency virus (HIV-1) requires continued, detailed investigations of its replication cycle, especially when combined with the most physiologically relevant, fully infectious model systems. Here, we demonstrate the application of the combination of stimulated emission depletion (STED) super-resolution microscopy with beam-scanning fluorescence correlation spectroscopy (sSTED-FCS) as a powerful tool for the interrogation of the molecular dynamics of HIV-1 virus assembly on the cell plasma membrane in the context of a fully infectious virus. In this process, HIV-1 envelope glycoprotein (Env) becomes incorporated into the assembling virus by interacting with the nascent Gag structural protein lattice. Molecular dynamics measurements at these distinct cell surface sites require a guiding strategy, for which we have used a two-colour implementation of sSTED-FCS to simultaneously target individual HIV-1 assembly sites via the aggregated Gag signal. We then compare the molecular mobility of Env proteins at the inside and outside of the virus assembly area. Env mobility was shown to be highly reduced at the assembly sites, highlighting the distinct trapping of Env as well as the usefulness of our methodological approach to study the molecular mobility of specifically targeted sites at the plasma membrane, even under high-biosafety conditions.
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Affiliation(s)
- Jakub Chojnacki
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK;
- IrsiCaixa AIDS Research Institute, University Hospital Germans Trias i Pujol, Ctra. de Canyet s/n, Badalona, 08916 Barcelona, Spain
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK;
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
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19
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Yoshida S, Schmid W, Vo N, Calabrase W, Kisley L. Computationally-efficient spatiotemporal correlation analysis super-resolves anomalous diffusion. OPTICS EXPRESS 2021; 29:7616-7629. [PMID: 33726259 DOI: 10.1364/oe.416465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Anomalous diffusion dynamics in confined nanoenvironments govern the macroscale properties and interactions of many biophysical and material systems. Currently, it is difficult to quantitatively link the nanoscale structure of porous media to anomalous diffusion within them. Fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) has been shown to extract nanoscale structure and Brownian diffusion dynamics within gels, liquid crystals, and polymers, but has limitations which hinder its wider application to more diverse, biophysically-relevant datasets. Here, we parallelize the least-squares curve fitting step on a GPU improving computation times by up to a factor of 40, implement anomalous diffusion and two-component Brownian diffusion models, and make fcsSOFI more accessible by packaging it in a user-friendly GUI. We apply fcsSOFI to simulations of the protein fibrinogen diffusing in polyacrylamide of varying matrix densities and super-resolve locations where slower, anomalous diffusion occurs within smaller, confined pores. The improvements to fcsSOFI in speed, scope, and usability will allow for the wider adoption of super-resolution correlation analysis to diverse research topics.
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20
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Touizer E, Sieben C, Henriques R, Marsh M, Laine RF. Application of Super-Resolution and Advanced Quantitative Microscopy to the Spatio-Temporal Analysis of Influenza Virus Replication. Viruses 2021; 13:233. [PMID: 33540739 PMCID: PMC7912985 DOI: 10.3390/v13020233] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023] Open
Abstract
With an estimated three to five million human cases annually and the potential to infect domestic and wild animal populations, influenza viruses are one of the greatest health and economic burdens to our society, and pose an ongoing threat of large-scale pandemics. Despite our knowledge of many important aspects of influenza virus biology, there is still much to learn about how influenza viruses replicate in infected cells, for instance, how they use entry receptors or exploit host cell trafficking pathways. These gaps in our knowledge are due, in part, to the difficulty of directly observing viruses in living cells. In recent years, advances in light microscopy, including super-resolution microscopy and single-molecule imaging, have enabled many viral replication steps to be visualised dynamically in living cells. In particular, the ability to track single virions and their components, in real time, now allows specific pathways to be interrogated, providing new insights to various aspects of the virus-host cell interaction. In this review, we discuss how state-of-the-art imaging technologies, notably quantitative live-cell and super-resolution microscopy, are providing new nanoscale and molecular insights into influenza virus replication and revealing new opportunities for developing antiviral strategies.
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Affiliation(s)
- Emma Touizer
- Division of Infection and Immunity, University College London, London WC1E 6AE, UK;
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Christian Sieben
- Department of Cell Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Romain F. Laine
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
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21
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Camarca A, Varriale A, Capo A, Pennacchio A, Calabrese A, Giannattasio C, Murillo Almuzara C, D’Auria S, Staiano M. Emergent Biosensing Technologies Based on Fluorescence Spectroscopy and Surface Plasmon Resonance. SENSORS (BASEL, SWITZERLAND) 2021; 21:906. [PMID: 33572812 PMCID: PMC7866296 DOI: 10.3390/s21030906] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/23/2022]
Abstract
The purpose of this work is to provide an exhaustive overview of the emerging biosensor technologies for the detection of analytes of interest for food, environment, security, and health. Over the years, biosensors have acquired increasing importance in a wide range of applications due to synergistic studies of various scientific disciplines, determining their great commercial potential and revealing how nanotechnology and biotechnology can be strictly connected. In the present scenario, biosensors have increased their detection limit and sensitivity unthinkable until a few years ago. The most widely used biosensors are optical-based devices such as surface plasmon resonance (SPR)-based biosensors and fluorescence-based biosensors. Here, we will review them by highlighting how the progress in their design and development could impact our daily life.
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Affiliation(s)
- Alessandra Camarca
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Antonio Varriale
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
- URT-ISA at Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
| | - Alessandro Capo
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Angela Pennacchio
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Alessia Calabrese
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Cristina Giannattasio
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Carlos Murillo Almuzara
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Sabato D’Auria
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Maria Staiano
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
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22
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Mohammed L, Nourddine H, Saad EF, Abdelali D, Hamid R. Chitosan-covered liposomes as a promising drug transporter: nanoscale investigations. RSC Adv 2021; 11:1503-1516. [PMID: 35424127 PMCID: PMC8693526 DOI: 10.1039/d0ra08305d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/11/2020] [Indexed: 01/11/2023] Open
Abstract
Liposomes are small artificial vesicles spherical shaped of 50-1000 nm in diameter. They are created from natural non-toxic phospholipids membranes. Externally, they are decorated with biocompatible polymers. Chitosan, a natural polymer, demonstrates exceptional advantages in drug delivery, in particular, as liposome cover. In this paper, Molecular Dynamics simulations (MD) are performed in the coupled NPT-NPH and NVT-NVE statistical ensembles to study the static and dynamic properties of DPPC membrane-bilayer with grafted cationic chitosan chains, with added Cl- anions to neutralize the environment, using the Martini coarse-grained force-field. From the NPT-NPH MD simulations we found a chitosan layer L DM ranging from 3.2 to 6.6 nm for graft chains of a degree of polymerization n p = 45 and different grafting molar fractions X p = 0.005, X p = 0.014 and X p = 0.1. Also, the chitosan chains showed three essential grafting regimes: mushroom, critic, and brush depending on X p. The DPPC bilayer thickness D B and the area per lipid A l increased proportionally to X p. From the NVT-NVE MD simulations, the analysis of the radial distribution function showed that the increase of X p gives a more close-packed and rigid liposome. The analysis of the mean square displacement revealed that the diffusion of lipids is anomalous. In contrast, the diffusion of chitosan chains showed a normal diffusion, just after 100 ps. The diffusion regime of ions is found to be normal and independent of time. For the three identified regimes, the chitosan showed a tendency to adhere to the membrane surface and therefore affect the properties of the liposomal membrane.
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Affiliation(s)
- Lemaalem Mohammed
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences, Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
| | - Hadrioui Nourddine
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences, Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
| | - El Fassi Saad
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences, Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
| | - Derouiche Abdelali
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences, Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
| | - Ridouane Hamid
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences, Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
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23
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Fluorescence Correlation Spectroscopy Reveals Interaction of Some Microdomain-Associated Lipids with Cellular Focal Adhesion Sites. Int J Mol Sci 2020; 21:ijms21218149. [PMID: 33142729 PMCID: PMC7662714 DOI: 10.3390/ijms21218149] [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: 08/21/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 11/16/2022] Open
Abstract
Cells adhere to the extracellular matrix at distinct anchoring points, mostly focal adhesions. These are rich in immobile transmembrane- and cytoskeletal-associated proteins, some of which are known to interact with lipids of the plasma membrane. To investigate their effect on lipid mobility and molecular interactions, fluorescently labeled lipids were incorporated into the plasma membranes of primary myofibroblasts using fusogenic liposomes. With fluorescence correlation spectroscopy, we tested mobilities of labeled microdomain-associated lipids such as sphingomyelin (SM), ganglioside (GM1), and cholesterol as well as of a microdomain-excluded phospholipid (PC) and a lipid-like molecule (DiIC18(7)) in focal adhesions (FAs) and in neighboring non-adherent membrane areas. We found significantly slower diffusion of SM and GM1 inside FAs but no effect on cholesterol, PC, and DiIC18(7). These data were compared to the molecular behavior in Lo/Ld-phase separated giant unilamellar vesicles, which served as a model system for microdomain containing lipid membranes. In contrast to the model system, lipid mobility changes in FAs were molecularly selective, and no particle enrichment occurred. Our findings suggest that lipid behavior in FAs cannot be described by Lo/Ld-phase separation. The observed slow-down of some molecules in FAs is potentially due to transient binding between lipids and some molecular constituent(s).
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24
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Gesper A, Wennmalm S, Hagemann P, Eriksson SG, Happel P, Parmryd I. Variations in Plasma Membrane Topography Can Explain Heterogenous Diffusion Coefficients Obtained by Fluorescence Correlation Spectroscopy. Front Cell Dev Biol 2020; 8:767. [PMID: 32903922 PMCID: PMC7443568 DOI: 10.3389/fcell.2020.00767] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/21/2020] [Indexed: 01/18/2023] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is frequently used to study diffusion in cell membranes, primarily the plasma membrane. The diffusion coefficients reported in the plasma membrane of the same cell type and even within single cells typically display a large spread. We have investigated whether this spread can be explained by variations in membrane topography throughout the cell surface, that changes the amount of membrane in the FCS focal volume at different locations. Using FCS, we found that diffusion of the membrane dye DiI in the apical plasma membrane was consistently faster above the nucleus than above the cytoplasm. Using live cell scanning ion conductance microscopy (SICM) to obtain a topography map of the cell surface, we demonstrate that cell surface roughness is unevenly distributed with the plasma membrane above the nucleus being the smoothest, suggesting that the difference in diffusion observed in FCS is related to membrane topography. FCS modeled on simulated diffusion in cell surfaces obtained by SICM was consistent with the FCS data from live cells and demonstrated that topography variations can cause the appearance of anomalous diffusion in FCS measurements. Furthermore, we found that variations in the amount of the membrane marker DiD, a proxy for the membrane, but not the transmembrane protein TCRζ or the lipid-anchored protein Lck, in the FCS focal volume were related to variations in diffusion times at different positions in the plasma membrane. This relationship was seen at different positions both at the apical cell and basal cell sides. We conclude that it is crucial to consider variations in topography in the interpretation of FCS results from membranes.
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Affiliation(s)
| | - Stefan Wennmalm
- SciLifeLab, Royal Institute of Technology, Stockholm, Sweden
| | | | | | | | - Ingela Parmryd
- Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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25
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Subba N, Das N, Sen P. Partial Viscosity Decoupling of Solute Solvation, Rotation, and Translation Dynamics in Lauric Acid/Menthol Deep Eutectic Solvent: Modulation of Dynamic Heterogeneity with Length Scale. J Phys Chem B 2020; 124:6875-6884. [DOI: 10.1021/acs.jpcb.0c04379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Navin Subba
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208 016, India
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208 016, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208 016, India
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26
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Membrane interactions in drug delivery: Model cell membranes and orthogonal techniques. Adv Colloid Interface Sci 2020; 281:102177. [PMID: 32417568 DOI: 10.1016/j.cis.2020.102177] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/05/2020] [Accepted: 05/07/2020] [Indexed: 01/22/2023]
Abstract
To generate the desired effect in the human body, the active pharmaceutical ingredient usually needs to interact with a receptor located on the cell membrane or inside the cell. Thus, understanding membrane interactions is of great importance when it comes to the development and testing of new drug molecules or new drug delivery systems. Nowadays, there is a tremendous selection of both model cell membranes and of techniques that can be used to characterize interactions between selected model cell membranes and a drug molecule, an excipient, or a drug delivery system. Having such a wide selection of model cell membranes and techniques available makes it sometimes challenging to select the optimal combination for a specific study. Furthermore, it is difficult to compare results obtained using different model cell membranes and techniques, and not all in vitro studies translate as well to an estimation of the in vivo biological activity or understanding of mode of action. This review provides an overview of the available lipid bilayer-based model cell membranes and of the most widely employed techniques for studying membrane interactions. Finally, the need for employing complimentary characterization techniques in order to acquire more reliable and in-depth information is highlighted.
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27
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Barbotin A, Urbančič I, Galiani S, Eggeling C, Booth M, Sezgin E. z-STED Imaging and Spectroscopy to Investigate Nanoscale Membrane Structure and Dynamics. Biophys J 2020; 118:2448-2457. [PMID: 32359408 PMCID: PMC7231928 DOI: 10.1016/j.bpj.2020.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/12/2020] [Accepted: 04/06/2020] [Indexed: 12/23/2022] Open
Abstract
Super-resolution stimulated emission depletion (STED) microcopy provides optical resolution beyond the diffraction limit. The resolution can be increased laterally (xy) or axially (z). Two-dimensional STED has been extensively used to elucidate the nanoscale membrane structure and dynamics via imaging or combined with spectroscopy techniques such as fluorescence correlation spectroscopy (FCS) and spectral imaging. On the contrary, z-STED has not been used in this context. Here, we show that a combination of z-STED with FCS or spectral imaging enables us to see previously unobservable aspects of cellular membranes. We show that thanks to an axial resolution of ∼100 nm, z-STED can be used to distinguish axially close-by membranes, early endocytic vesicles, or tubular membrane structures. Combination of z-STED with FCS and spectral imaging showed diffusion dynamics and lipid organization in these structures, respectively.
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Affiliation(s)
- Aurélien Barbotin
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Iztok Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Jožef Stefan Institute, Ljubljana, Slovenia
| | - Silvia Galiani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany; Leibniz Institute of Photonic Technology e.V., Jena, Germany
| | - Martin Booth
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden.
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28
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Hadrioui N, Lemaalem M, Derouiche A, Ridouane H. Physical properties of phospholipids and integral proteins and their biofunctional roles in pulmonary surfactant from molecular dynamics simulation. RSC Adv 2020; 10:8568-8579. [PMID: 35497816 PMCID: PMC9049990 DOI: 10.1039/d0ra00077a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/06/2020] [Indexed: 12/26/2022] Open
Abstract
This work deals with a quantitative investigation of the physical properties of pulmonary surfactant near melting temperature. To this end, we make use of molecular dynamics simulations, using the MARTINI coarse-grained model, for determining the physical properties of the system, such as the potential energy, the specific heat, the microstructure, the diffusion laws, and the elastic properties of the surfactant. The microstructure is studied by computation of the radial-distribution-function upon varying the distance between constituents (lipid molecules or proteins). The diffusion phenomenon is investigated by determination of the mean-squared-displacement and the time dependent velocity-autocorrelation-function for various values of temperature. We show that the dynamics of lipids and proteins exhibit a subdiffusion regime (slow movement) due to the cage effect within pulmonary surfactant. From the obtained mean-squared-displacement, we get the values of the self-diffusion-coefficients and the anomalous exponents at different temperatures close to the melting temperature. For the mathematical description of the cage effect, we make use of the scale relations in terms of the waiting time probability distribution. The last study is concerned with determination of the dependence of the lateral stress upon the strain of pulmonary surfactant, which is found to be linear, and from which we deduce the lateral-elastic-modulus.
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Affiliation(s)
- Nourddine Hadrioui
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
| | - Mohammed Lemaalem
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
| | - Abdelali Derouiche
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
| | - Hamid Ridouane
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
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Basak S, Sengupta S, Chattopadhyay K. Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells. Biophys Rev 2019; 11:851-872. [PMID: 31444739 PMCID: PMC6957588 DOI: 10.1007/s12551-019-00580-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/25/2019] [Indexed: 01/24/2023] Open
Abstract
In order to maintain cellular function, biomolecules like protein, DNA, and RNAs have to diffuse to the target spaces within the cell. Changes in the cytosolic microenvironment or in the nucleus during the fulfillment of these cellular processes affect their mobility, folding, and stability thereby impacting the transient or stable interactions with their adjacent neighbors in the organized and dynamic cellular interior. Using classical Brownian motion to elucidate the diffusion behavior of these biomolecules is hard considering their complex nature. The understanding of biomolecular diffusion inside cells still remains elusive due to the lack of a proper model that can be extrapolated to these cases. In this review, we have comprehensively addressed the progresses in this field, laying emphasis on the different aspects of anomalous diffusion in the different biochemical reactions in cell interior. These experiment-based models help to explain the diffusion behavior of biomolecules in the cytosolic and nuclear microenvironment. Moreover, since understanding of biochemical reactions within living cellular system is our main focus, we coupled the experimental observations with the concept of sub-diffusion from in vitro to in vivo condition. We believe that the pairing between the understanding of complex behavior and structure-function paradigm of biological molecules would take us forward by one step in order to solve the puzzle around diseases caused by cellular dysfunction.
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Affiliation(s)
- Sujit Basak
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA.
| | - Sombuddha Sengupta
- Protein Folding and Dynamics Lab, Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal, 700032, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Lab, Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal, 700032, India
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30
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Subba N, Polok K, Piatkowski P, Ratajska-Gadomska B, Biswas R, Gadomski W, Sen P. Temperature-Dependent Ultrafast Solvation Response and Solute Diffusion in Acetamide–Urea Deep Eutectic Solvent. J Phys Chem B 2019; 123:9212-9221. [DOI: 10.1021/acs.jpcb.9b07794] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Navin Subba
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, UP, India
| | - Kamil Polok
- Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warsaw 02-089, Poland
| | - Piotr Piatkowski
- Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warsaw 02-089, Poland
| | | | - Ranjit Biswas
- Chemical, Biological and Macromolecular Sciences (CBMS), S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700106, WB, India
| | - Wojciech Gadomski
- Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warsaw 02-089, Poland
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, UP, India
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31
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Raghuraman H, Chatterjee S, Das A. Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins. Front Mol Biosci 2019; 6:96. [PMID: 31608290 PMCID: PMC6774292 DOI: 10.3389/fmolb.2019.00096] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.
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Affiliation(s)
- H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata, India
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32
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Kim Y, Puhl HL, Chen E, Taumoefolau GH, Nguyen TA, Kliger DS, Blank PS, Vogel SS. Venus A206 Dimers Behave Coherently at Room Temperature. Biophys J 2019; 116:1918-1930. [PMID: 31060812 DOI: 10.1016/j.bpj.2019.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/28/2019] [Accepted: 04/16/2019] [Indexed: 12/11/2022] Open
Abstract
Fluorescent proteins (FPs) have revolutionized cell biology by allowing genetic tagging of specific proteins inside living cells. In conjunction with Förster's resonance energy transfer (FRET) measurements, FP-tagged proteins can be used to study protein-protein interactions and estimate distances between tagged proteins. FRET is mediated by weak Coulombic dipole-dipole coupling of donor and acceptor fluorophores that behave independently, with energy hopping discretely and incoherently between fluorophores. Stronger dipole-dipole coupling can mediate excitonic coupling in which excitation energy is distributed near instantaneously between coherently interacting excited states that behave as a single quantum entity. The interpretation of FP energy transfer measurements to estimate separation often assumes that donors and acceptors are very weakly coupled and therefore use a FRET mechanism. This assumption is considered reasonable as close fluorophore proximity, typically associated with strong excitonic coupling, is limited by the FP β-barrel structure. Furthermore, physiological temperatures promote rapid vibrational dephasing associated with a rapid decoherence of fluorophore-excited states. Recently, FP dephasing times that are 50 times slower than traditional organic fluorophores have been measured, raising the possibility that evolution has shaped FPs to allow stronger than expected coupling under physiological conditions. In this study, we test if excitonic coupling between FPs is possible at physiological temperatures. FRET and excitonic coupling can be distinguished by monitoring spectral changes associated with fluorophore dimerization. The weak coupling mediating FRET should not cause a change in fluorophore absorption, whereas strong excitonic coupling causes Davydov splitting. Circular dichroism spectroscopy revealed Davydov splitting when the yellow FP VenusA206 dimerizes, and a novel approach combining photon antibunching and fluorescence correlation spectroscopy was used to confirm that the two fluorophores in a VenusA206 homodimer behave as a single-photon emitter. We conclude that excitonic coupling between VenusA206 fluorophores is possible at physiological temperatures.
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Affiliation(s)
- Youngchan Kim
- Section on Cellular Biophotonics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Henry L Puhl
- Section on Cellular Biophotonics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Eefei Chen
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, California
| | - Grace H Taumoefolau
- Section on Cellular Biophotonics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Tuan A Nguyen
- Section on Cellular Biophotonics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - David S Kliger
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, California
| | - Paul S Blank
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Steven S Vogel
- Section on Cellular Biophotonics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland.
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33
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Wrede O, Großkopf S, Seidel T, Hellweg T. Dynamics of proteins confined in non-ionic bicontinuous microemulsions: a FCS study. Phys Chem Chem Phys 2019; 21:6725-6731. [PMID: 30860213 DOI: 10.1039/c8cp06419a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In our present work we present an approach which allows one to confine proteins in structurally nearly identical bicontinuous microemulsions with systematically decreasing water domain size. It is shown that sub-diffusive behaviour occurs already at water domain sizes below 13 nm. However, above 13 nm normal diffusion is seen. Moreover, we compare protein diffusion in microemulsions to the transport of a much smaller fluorescent dye.
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Affiliation(s)
- Oliver Wrede
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany.
| | - Sören Großkopf
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany.
| | - Thorsten Seidel
- Plant Biochemistry and Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Thomas Hellweg
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany.
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34
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Stolle MDN, Fradin C. Anomalous Diffusion in Inverted Variable-Lengthscale Fluorescence Correlation Spectroscopy. Biophys J 2019; 116:791-806. [PMID: 30782396 PMCID: PMC6400862 DOI: 10.1016/j.bpj.2019.01.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/12/2018] [Accepted: 01/14/2019] [Indexed: 11/24/2022] Open
Abstract
Using fluorescence correlation spectroscopy (FCS) to distinguish between different types of diffusion processes is often a perilous undertaking because the analysis of the resulting autocorrelation data is model dependant. Two recently introduced strategies, however, can help move toward a model-independent interpretation of FCS experiments: 1) the obtention of correlation data at different length scales and 2) their inversion to retrieve the mean-squared displacement associated with the process under study. We use computer simulations to examine the signature of several biologically relevant diffusion processes (simple diffusion, continuous-time random walk, caged diffusion, obstructed diffusion, two-state diffusion, and diffusing diffusivity) in variable-length-scale FCS. We show that, when used in concert, length-scale variation and data inversion permit us to identify non-Gaussian processes and, regardless of Gaussianity, to retrieve their mean-squared displacement over several orders of magnitude in time. This makes unbiased discrimination between different classes of diffusion models possible.
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Affiliation(s)
- Michael D N Stolle
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Cécile Fradin
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada.
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35
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Stachura SS, Malajczuk CJ, Kuprusevicius E, Mancera RL. Influence of Bilayer Size and Number in Multi-Bilayer DOPC Simulations at Full and Low Hydration. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:2399-2411. [PMID: 30632763 DOI: 10.1021/acs.langmuir.8b03212] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biophysical studies of model cell membranes at full and low hydration are usually carried out using scattering measurements on multi-bilayer systems. Molecular simulations of lipid bilayers aimed at reproducing those experimental conditions are usually conducted using single bilayers with different amounts of water. These simulation conditions may lead to artifacts arising from size effects and self-interactions because of periodic boundary conditions. We have tested the influence of the size and number of bilayers on membrane properties using the Lipid14 force field for lipids in molecular dynamics simulations of 1,2-dioleoyl- sn-glycero-3-phosphocholine bilayers at full hydration (44 water molecules per lipid), low hydration (18 water molecules per lipid), and dehydration (9 water molecules per lipid). A number of additional simulations were conducted with the Slipids force field for comparison. We have found that the average area per lipid (APL), thickness, mass density profiles, and acyl tail order parameters are insensitive to the size and the number of bilayers for all hydration states. The Lipid14 force field can also successfully reproduce the experimentally observed decrease in APL and corresponding increase in bilayer thickness upon dehydration, reflecting the increase in ordering as the system becomes more gel-like. Additionally, decreasing hydration levels were associated with a trend away from normal lateral diffusion and toward more subdiffusive regimes across both force fields. In summary, at least for the Lipid14 force field, the use of a single bilayer with 128 phospholipid molecules provides an adequate representation of multi-bilayer systems at varying levels of hydration.
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Affiliation(s)
- Sławomir S Stachura
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation , Curtin University , GPO Box U1987, Perth , Western Australia 6845 , Australia
| | - Chris J Malajczuk
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation , Curtin University , GPO Box U1987, Perth , Western Australia 6845 , Australia
| | - Egidijus Kuprusevicius
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation , Curtin University , GPO Box U1987, Perth , Western Australia 6845 , Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation , Curtin University , GPO Box U1987, Perth , Western Australia 6845 , Australia
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36
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Coker HLE, Cheetham MR, Kattnig DR, Wang YJ, Garcia-Manyes S, Wallace MI. Controlling Anomalous Diffusion in Lipid Membranes. Biophys J 2019; 116:1085-1094. [PMID: 30846364 DOI: 10.1016/j.bpj.2018.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/21/2018] [Accepted: 12/14/2018] [Indexed: 12/24/2022] Open
Abstract
Diffusion in cell membranes is not just simple two-dimensional Brownian motion but typically depends on the timescale of the observation. The physical origins of this anomalous subdiffusion are unresolved, and model systems capable of quantitative and reproducible control of membrane diffusion have been recognized as a key experimental bottleneck. Here, we control anomalous diffusion using supported lipid bilayers containing lipids derivatized with polyethylene glycol (PEG) headgroups. Bilayers with specific excluded area fractions are formed by control of PEG lipid mole fraction. These bilayers exhibit a switch in diffusive behavior, becoming anomalous as bilayer continuity is disrupted. Using a combination of single-molecule fluorescence and interferometric imaging, we measure the anomalous behavior in this model over four orders of magnitude in time. Diffusion in these bilayers is well described by a power-law dependence of the mean-square displacement with observation time. Anomaleity in this system can be tailored by simply controlling the mole fraction of PEG lipid, producing bilayers with diffusion parameters similar to those observed for anomalous diffusion in biological membranes.
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Affiliation(s)
- Helena L E Coker
- Department of Chemistry, King's College London, London, United Kingdom; Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Matthew R Cheetham
- Department of Chemistry, King's College London, London, United Kingdom; Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Daniel R Kattnig
- Living Systems Institute & Department of Physics, University of Exeter, Exeter, United Kingdom
| | - Yong J Wang
- Department of Physics, King's College London, London, United Kingdom
| | | | - Mark I Wallace
- Department of Chemistry, King's College London, London, United Kingdom.
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37
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Betaneli V, Mücksch J, Schwille P. Fluorescence Correlation Spectroscopy to Examine Protein-Lipid Interactions in Membranes. Methods Mol Biol 2019; 2003:415-447. [PMID: 31218628 DOI: 10.1007/978-1-4939-9512-7_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a versatile technique to study membrane dynamics and protein-lipid interactions. It can provide information about diffusion coefficients, concentrations, and molecular interactions of proteins and lipids in the membrane. These parameters allow for the determination of protein partitioning into different lipid environments, the identification of lipid domains, and the detection of lipid-protein complexes on the membrane. During the last decades, FCS studies were successfully performed on model membrane systems as also on living cells, to characterize protein-lipid interactions. Recent developments of the method described here improved quantitative measurements on membranes and decreased the number of potential artifacts. The aim of this chapter is to provide the reader with the necessary information and some practical guidelines to perform FCS studies on artificial and cellular membranes.
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Affiliation(s)
- Viktoria Betaneli
- Medical Faculty "Carl Gustav Carus", Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Jonas Mücksch
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany.
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38
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Slenders E, Bové H, Urbain M, Mugnier Y, Sonay AY, Pantazis P, Bonacina L, Vanden Berghe P, vandeVen M, Ameloot M. Image Correlation Spectroscopy with Second Harmonic Generating Nanoparticles in Suspension and in Cells. J Phys Chem Lett 2018; 9:6112-6118. [PMID: 30273489 DOI: 10.1021/acs.jpclett.8b02686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The absence of photobleaching, blinking, and saturation combined with a high contrast provides unique advantages of higher-harmonic generating nanoparticles over fluorescent probes, allowing for prolonged correlation spectroscopy studies. We apply the coherent intensity fluctuation model to study the mobility of second harmonic generating nanoparticles. A concise protocol is presented for quantifying the diffusion coefficient from a single spectroscopy measurement without the need for separate point-spread-function calibrations. The technique's applicability is illustrated on nominally 56 nm LiNbO3 nanoparticles. We perform label-free raster image correlation spectroscopy imaging in aqueous suspension and spatiotemporal image correlation spectroscopy in A549 human lung carcinoma cells. In good agreement with the expected theoretical result, the measured diffusion coefficient in water at room temperature is (7.5 ± 0.3) μm2/s. The diffusion coefficient in the cells is more than 103 times lower and heterogeneous, with an average of (3.7 ± 1.5) × 10-3 μm2/s.
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Affiliation(s)
- Eli Slenders
- Biomedical Research Institute (BIOMED) , Hasselt University , Agoralaan Bldg. C , 3590 Diepenbeek , Belgium
| | - Hannelore Bové
- Biomedical Research Institute (BIOMED) , Hasselt University , Agoralaan Bldg. C , 3590 Diepenbeek , Belgium
| | - Mathias Urbain
- Univ. Savoie Mont Blanc, SYMME , F-74000 Annecy , France
| | | | - Ali Yasin Sonay
- Department of Biosystems Science and Engineering , ETH Zürich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Periklis Pantazis
- Department of Biosystems Science and Engineering , ETH Zürich , Mattenstrasse 26 , 4058 Basel , Switzerland
- Department of Bioengineering , Imperial College London , South Kensington Campus , London SW7 2AZ , U.K
| | - Luigi Bonacina
- Department of Applied Physics , Université de Genève , Chemin de Pinchat 22 , 1211 Geneva , Switzerland
| | - Pieter Vanden Berghe
- Laboratory for Enteric Neuroscience (LENS), TARGID , University of Leuven , Herestraat 49 , 3000 Leuven , Belgium
| | - Martin vandeVen
- Biomedical Research Institute (BIOMED) , Hasselt University , Agoralaan Bldg. C , 3590 Diepenbeek , Belgium
| | - Marcel Ameloot
- Biomedical Research Institute (BIOMED) , Hasselt University , Agoralaan Bldg. C , 3590 Diepenbeek , Belgium
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39
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Schneider F, Waithe D, Lagerholm BC, Shrestha D, Sezgin E, Eggeling C, Fritzsche M. Statistical Analysis of Scanning Fluorescence Correlation Spectroscopy Data Differentiates Free from Hindered Diffusion. ACS NANO 2018; 12:8540-8546. [PMID: 30028588 PMCID: PMC6117752 DOI: 10.1021/acsnano.8b04080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/20/2018] [Indexed: 05/28/2023]
Abstract
Cells rely on versatile diffusion dynamics in their plasma membrane. Quantification of this often heterogeneous diffusion is essential to the understanding of cell regulation and function. Yet such measurements remain a major challenge in cell biology, usually due to low sampling throughput, a necessity for dedicated equipment, sophisticated fluorescent label strategies, and limited sensitivity. Here, we introduce a robust, broadly applicable statistical analysis pipeline for large scanning fluorescence correlation spectroscopy data sets, which uncovers the nanoscale heterogeneity of the plasma membrane in living cells by differentiating free from hindered diffusion modes of fluorescent lipid and protein analogues.
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Affiliation(s)
- Falk Schneider
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Dominic Waithe
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - B. Christoffer Lagerholm
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Dilip Shrestha
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Erdinc Sezgin
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Christian Eggeling
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
- Institute of Applied
Optics, Friedrich-Schiller-University and
Leibniz Institute of Photonic Technology, Helmholtzweg 4, 07743 Jena, Germany
| | - Marco Fritzsche
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
- Kennedy
Institute for Rheumatology, University of
Oxford, Roosevelt Drive, Oxford OX3 7LF, United Kingdom
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40
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Urbančič I, Brun J, Shrestha D, Waithe D, Eggeling C, Chojnacki J. Lipid Composition but Not Curvature Is the Determinant Factor for the Low Molecular Mobility Observed on the Membrane of Virus-Like Vesicles. Viruses 2018; 10:v10080415. [PMID: 30096847 PMCID: PMC6116177 DOI: 10.3390/v10080415] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/03/2018] [Accepted: 08/07/2018] [Indexed: 12/14/2022] Open
Abstract
Human Immunodeficiency Virus type-1 (HIV-1) acquires its lipid membrane from the plasma membrane of the infected cell from which it buds out. Previous studies have shown that the HIV-1 envelope is an environment of very low mobility, with the diffusion of incorporated proteins two orders of magnitude slower than in the plasma membrane. One of the reasons for this difference is thought to be the HIV-1 membrane composition that is characterised by a high degree of rigidity and lipid packing, which has, until now, been difficult to assess experimentally. To further refine the model of the molecular mobility on the HIV-1 surface, we herein investigated the relative importance of membrane composition and curvature in simplified model membrane systems, large unilamellar vesicles (LUVs) of different lipid compositions and sizes (0.1–1 µm), using super-resolution stimulated emission depletion (STED) microscopy-based fluorescence correlation spectroscopy (STED-FCS). Establishing an approach that is also applicable to measurements of molecule dynamics in virus-sized particles, we found, at least for the 0.1–1 µm sized vesicles, that the lipid composition and thus membrane rigidity, but not the curvature, play an important role in the decreased molecular mobility on the vesicles’ surface. This observation suggests that the composition of the envelope rather than the particle geometry contributes to the previously described low mobility of proteins on the HIV-1 surface. Our vesicle-based study thus provides further insight into the dynamic properties of the surface of individual HIV-1 particles, as well as paves the methodological way towards better characterisation of the properties and function of viral lipid envelopes in general.
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Affiliation(s)
- Iztok Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
- "Jožef Stefan" Institute, Jamova c. 39, SI-1000 Ljubljana, Slovenia.
| | - Juliane Brun
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Dilip Shrestha
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Dominic Waithe
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
- Institute of Applied Optics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany.
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany.
| | - Jakub Chojnacki
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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41
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Schneider F, Waithe D, Galiani S, Bernardino de la Serna J, Sezgin E, Eggeling C. Nanoscale Spatiotemporal Diffusion Modes Measured by Simultaneous Confocal and Stimulated Emission Depletion Nanoscopy Imaging. NANO LETTERS 2018; 18:4233-4240. [PMID: 29893574 PMCID: PMC6047073 DOI: 10.1021/acs.nanolett.8b01190] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/05/2018] [Indexed: 05/25/2023]
Abstract
The diffusion dynamics in the cellular plasma membrane provide crucial insights into molecular interactions, organization, and bioactivity. Beam-scanning fluorescence correlation spectroscopy combined with super-resolution stimulated emission depletion nanoscopy (scanning STED-FCS) measures such dynamics with high spatial and temporal resolution. It reveals nanoscale diffusion characteristics by measuring the molecular diffusion in conventional confocal mode and super-resolved STED mode sequentially for each pixel along the scanned line. However, to directly link the spatial and the temporal information, a method that simultaneously measures the diffusion in confocal and STED modes is needed. Here, to overcome this problem, we establish an advanced STED-FCS measurement method, line interleaved excitation scanning STED-FCS (LIESS-FCS), that discloses the molecular diffusion modes at different spatial positions with a single measurement. It relies on fast beam-scanning along a line with alternating laser illumination that yields, for each pixel, the apparent diffusion coefficients for two different observation spot sizes (conventional confocal and super-resolved STED). We demonstrate the potential of the LIESS-FCS approach with simulations and experiments on lipid diffusion in model and live cell plasma membranes. We also apply LIESS-FCS to investigate the spatiotemporal organization of glycosylphosphatidylinositol-anchored proteins in the plasma membrane of live cells, which, interestingly, show multiple diffusion modes at different spatial positions.
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Affiliation(s)
- Falk Schneider
- MRC
Human Immunology Unit and Wolfson Imaging Centre Oxford Weatherall Institute
of Molecular Medicine, University of Oxford, Headley Way Oxford, OX3 9DS United
Kingdom
| | - Dominic Waithe
- MRC
Human Immunology Unit and Wolfson Imaging Centre Oxford Weatherall Institute
of Molecular Medicine, University of Oxford, Headley Way Oxford, OX3 9DS United
Kingdom
| | - Silvia Galiani
- MRC
Human Immunology Unit and Wolfson Imaging Centre Oxford Weatherall Institute
of Molecular Medicine, University of Oxford, Headley Way Oxford, OX3 9DS United
Kingdom
| | - Jorge Bernardino de la Serna
- MRC
Human Immunology Unit and Wolfson Imaging Centre Oxford Weatherall Institute
of Molecular Medicine, University of Oxford, Headley Way Oxford, OX3 9DS United
Kingdom
- Research
Complex at Harwell, Central Laser Facility, Rutherford Appleton Laboratory
Science, Technology Facilities Council, Harwell-Oxford, Didcot OX11 0FA, United Kingdom
| | - Erdinc Sezgin
- MRC
Human Immunology Unit and Wolfson Imaging Centre Oxford Weatherall Institute
of Molecular Medicine, University of Oxford, Headley Way Oxford, OX3 9DS United
Kingdom
| | - Christian Eggeling
- MRC
Human Immunology Unit and Wolfson Imaging Centre Oxford Weatherall Institute
of Molecular Medicine, University of Oxford, Headley Way Oxford, OX3 9DS United
Kingdom
- Institute
of Applied Optics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
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42
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Reina F, Galiani S, Shrestha D, Sezgin E, de Wit G, Cole D, Christoffer Lagerholm B, Kukura P, Eggeling C. Complementary studies of lipid membrane dynamics using iSCAT and super-resolved fluorescence correlation spectroscopy. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:235401. [PMID: 29853718 PMCID: PMC5964363 DOI: 10.1088/1361-6463/aac04f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/12/2018] [Accepted: 04/26/2018] [Indexed: 05/20/2023]
Abstract
Observation techniques with high spatial and temporal resolution, such as single-particle tracking based on interferometric scattering (iSCAT) microscopy, and fluorescence correlation spectroscopy applied on a super-resolution STED microscope (STED-FCS), have revealed new insights of the molecular organization of membranes. While delivering complementary information, there are still distinct differences between these techniques, most prominently the use of fluorescent dye tagged probes for STED-FCS and a need for larger scattering gold nanoparticle tags for iSCAT. In this work, we have used lipid analogues tagged with a hybrid fluorescent tag-gold nanoparticle construct, to directly compare the results from STED-FCS and iSCAT measurements of phospholipid diffusion on a homogeneous supported lipid bilayer (SLB). These comparative measurements showed that while the mode of diffusion remained free, at least at the spatial (>40 nm) and temporal (50 ⩽ t ⩽ 100 ms) scales probed, the diffussion coefficient was reduced by 20- to 60-fold when tagging with 20 and 40 nm large gold particles as compared to when using dye tagged lipid analogues. These FCS measurements of hybrid fluorescent tag-gold nanoparticle labeled lipids also revealed that commercially supplied streptavidin-coated gold nanoparticles contain large quantities of free streptavidin. Finally, the values of apparent diffusion coefficients obtained by STED-FCS and iSCAT differed by a factor of 2-3 across the techniques, while relative differences in mobility between different species of lipid analogues considered were identical in both approaches. In conclusion, our experiments reveal that large and potentially cross-linking scattering tags introduce a significant slow-down in diffusion on SLBs but no additional bias, and our labeling approach creates a new way of exploiting complementary information from STED-FCS and iSCAT measurements.
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Affiliation(s)
- Francesco Reina
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Silvia Galiani
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Dilip Shrestha
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Gabrielle de Wit
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Daniel Cole
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Institute of Applied Optics, Friedrich-Schiller University, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
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43
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Chojnacki J, Eggeling C. Super-resolution fluorescence microscopy studies of human immunodeficiency virus. Retrovirology 2018; 15:41. [PMID: 29884197 PMCID: PMC5994058 DOI: 10.1186/s12977-018-0424-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/28/2018] [Indexed: 11/10/2022] Open
Abstract
Super-resolution fluorescence microscopy combines the ability to observe biological processes beyond the diffraction limit of conventional light microscopy with all advantages of the fluorescence readout such as labelling specificity and non-invasive live-cell imaging. Due to their subdiffraction size (< 200 nm) viruses are ideal candidates for super-resolution microscopy studies, and Human Immunodeficiency Virus type 1 (HIV-1) is to date the most studied virus by this technique. This review outlines principles of different super-resolution techniques as well as their advantages and disadvantages for virological studies, especially in the context of live-cell imaging applications. We highlight the findings of super-resolution based HIV-1 studies performed so far, their contributions to the understanding of HIV-1 replication cycle and how the current advances in super-resolution microscopy may open new avenues for future virology research.
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Affiliation(s)
- Jakub Chojnacki
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Institute of Applied Optics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745, Jena, Germany
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44
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Lahtinen S, Krause S, Arppe R, Soukka T, Vosch T. Upconversion Cross-Correlation Spectroscopy of a Sandwich Immunoassay. Chemistry 2018; 24:9229-9233. [PMID: 29732623 PMCID: PMC6055621 DOI: 10.1002/chem.201801962] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Indexed: 11/10/2022]
Abstract
Fluorescence correlation and cross-correlation spectroscopy (FCS/FCCS) have enabled biologists to study processes of transport, binding, and enzymatic reactions in living cells. However, applying FCS and FCCS to samples such as whole blood and plasma is complicated as the fluorescence bursts of diffusing labels can be swamped by strong autofluorescence. Here we present cross-correlation spectroscopy based on two upconversion nanoparticles emitting at different wavelengths on the anti-Stokes side of a single excitation laser. This upconversion cross-correlation spectroscopy (UCCS) approach allows us to completely remove all Stokes shifted autofluorescence background in biological material such as plasma. As a proof of concept, we evaluate the applicability of UCCS to a homogeneous sandwich immunoassay for thyroid stimulating hormone measured in buffer solution and in plasma.
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Affiliation(s)
- Satu Lahtinen
- Department of Biotechnology, University of Turku, Medisiina D6, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Stefan Krause
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Riikka Arppe
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Tero Soukka
- Department of Biotechnology, University of Turku, Medisiina D6, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Tom Vosch
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
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45
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Fischer J, Kleinau G, Rutz C, Zwanziger D, Khajavi N, Müller A, Rehders M, Brix K, Worth CL, Führer D, Krude H, Wiesner B, Schülein R, Biebermann H. Evidence of G-protein-coupled receptor and substrate transporter heteromerization at a single molecule level. Cell Mol Life Sci 2018; 75:2227-2239. [PMID: 29290039 PMCID: PMC11105501 DOI: 10.1007/s00018-017-2728-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/17/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
Abstract
G-protein-coupled receptors (GPCRs) can constitute complexes with non-GPCR integral membrane proteins, while such interaction has not been demonstrated at a single molecule level so far. We here investigated the potential interaction between the thyrotropin receptor (TSHR) and the monocarboxylate transporter 8 (MCT8), a member of the major facilitator superfamily (MFS), using fluorescence cross-correlation spectroscopy (FCCS). Both the proteins are expressed endogenously on the basolateral plasma membrane of the thyrocytes and are involved in stimulation of thyroid hormone production and release. Indeed, we demonstrate strong interaction between both the proteins which causes a suppressed activation of Gq/11 by TSH-stimulated TSHR. Thus, we provide not only evidence for a novel interaction between the TSHR and MCT8, but could also prove this interaction on a single molecule level. Moreover, this interaction forces biased signaling at the TSHR. These results are of general interest for both the GPCR and the MFS research fields.
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Affiliation(s)
- Jana Fischer
- Institut für Experimentelle Pädiatrische Endokrinologie, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Gunnar Kleinau
- Institut für Experimentelle Pädiatrische Endokrinologie, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Claudia Rutz
- Protein Trafficking Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Denise Zwanziger
- Division of Laboratory Research, Department of Endocrinology, Diabetology and Metabolism, University Hospital Essen, University Duisburg-Essen, 45147, Essen, Germany
| | - Noushafarin Khajavi
- Institut für Experimentelle Pädiatrische Endokrinologie, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Anne Müller
- Institut für Experimentelle Pädiatrische Endokrinologie, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Maren Rehders
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759, Bremen, Germany
| | - Klaudia Brix
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759, Bremen, Germany
| | - Catherine L Worth
- Structural Bioinformatics and Protein Design Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125, Berlin, Germany
| | - Dagmar Führer
- Division of Laboratory Research, Department of Endocrinology, Diabetology and Metabolism, University Hospital Essen, University Duisburg-Essen, 45147, Essen, Germany
| | - Heiko Krude
- Institut für Experimentelle Pädiatrische Endokrinologie, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Burkhard Wiesner
- Protein Trafficking Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Cellular Imaging Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125, Berlin, Germany
| | - Ralf Schülein
- Protein Trafficking Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Heike Biebermann
- Institut für Experimentelle Pädiatrische Endokrinologie, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany.
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46
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Collini M, Bouzin M, Chirico G. Out of the Randomness: Correlating Noise in Biological Systems. Biophys J 2018; 114:2298-2307. [PMID: 29477335 PMCID: PMC6129560 DOI: 10.1016/j.bpj.2018.01.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/23/2018] [Accepted: 01/29/2018] [Indexed: 11/23/2022] Open
Abstract
The study of the dynamics of biological systems requires one to follow relaxation processes in time with micron-size spatial resolution. This need has led to the development of different fluorescence correlation techniques with high spatial resolution and a tremendous (from nanoseconds to seconds) temporal dynamic range. Spatiotemporal information can be obtained even on complex dynamic processes whose time evolution is not forecast by simple Brownian diffusion. Our discussion of the most recent applications of image correlation spectroscopy to the study of anomalous sub- or superdiffusion suggests that this field still requires the development of multidimensional image analyses based on analytical models or numerical simulations. We focus in particular on the framework of spatiotemporal image correlation spectroscopy and examine the critical steps in getting information on anomalous diffusive processes from the correlation maps. We point out how a dual space-time correlative analysis, in both the direct and the Fourier space, can provide quantitative information on superdiffusional processes when these are analyzed through an empirical model based on intermittent active dynamics. We believe that this dual space-time analysis, potentially amenable to mathematical treatment and to the exact fit of experimental data, could be extended to include the rich phenomenology of subdiffusive processes, thereby quantifying relevant parameters for the various motivating biological problems of interest.
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Affiliation(s)
- Maddalena Collini
- Dipartimento di Fisica e Centro di Nanomedicina, Università degli Studi di Milano-Bicocca, Milan, Italy; CNR-ISASI, Center for Complex Systems, Pozzuoli, Italy
| | - Margaux Bouzin
- Dipartimento di Fisica e Centro di Nanomedicina, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Giuseppe Chirico
- Dipartimento di Fisica e Centro di Nanomedicina, Università degli Studi di Milano-Bicocca, Milan, Italy; CNR-ISASI, Center for Complex Systems, Pozzuoli, Italy.
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47
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Nguyen TA, Puhl HL, Pham AK, Vogel SS. Auto-FPFA: An Automated Microscope for Characterizing Genetically Encoded Biosensors. Sci Rep 2018; 8:7374. [PMID: 29743504 PMCID: PMC5943267 DOI: 10.1038/s41598-018-25689-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/26/2018] [Indexed: 12/14/2022] Open
Abstract
Genetically encoded biosensors function by linking structural change in a protein construct, typically tagged with one or more fluorescent proteins, to changes in a biological parameter of interest (such as calcium concentration, pH, phosphorylation-state, etc.). Typically, the structural change triggered by alterations in the bio-parameter is monitored as a change in either fluorescent intensity, or lifetime. Potentially, other photo-physical properties of fluorophores, such as fluorescence anisotropy, molecular brightness, concentration, and lateral and/or rotational diffusion could also be used. Furthermore, while it is likely that multiple photo-physical attributes of a biosensor might be altered as a function of the bio-parameter, standard measurements monitor only a single photo-physical trait. This limits how biosensors are designed, as well as the accuracy and interpretation of biosensor measurements. Here we describe the design and construction of an automated multimodal-microscope. This system can autonomously analyze 96 samples in a micro-titer dish and for each sample simultaneously measure intensity (photon count), fluorescence lifetime, time-resolved anisotropy, molecular brightness, lateral diffusion time, and concentration. We characterize the accuracy and precision of this instrument, and then demonstrate its utility by characterizing three types of genetically encoded calcium sensors as well as a negative control.
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Affiliation(s)
- Tuan A Nguyen
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA
| | - Henry L Puhl
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA
| | - An K Pham
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA
| | - Steven S Vogel
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA.
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48
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Wang R, Brustlein S, Mailfert S, Fabre R, Fallet M, Sivankutty S, Rigneault H, Marguet D. A straightforward STED-background corrected fitting model for unbiased STED-FCS analyses. Methods 2018; 140-141:212-222. [DOI: 10.1016/j.ymeth.2018.02.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/22/2017] [Accepted: 02/09/2018] [Indexed: 11/16/2022] Open
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49
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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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50
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Waithe D, Schneider F, Chojnacki J, Clausen MP, Shrestha D, de la Serna JB, Eggeling C. Optimized processing and analysis of conventional confocal microscopy generated scanning FCS data. Methods 2018; 140-141:62-73. [PMID: 28963070 PMCID: PMC6026296 DOI: 10.1016/j.ymeth.2017.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/09/2017] [Accepted: 09/24/2017] [Indexed: 01/18/2023] Open
Abstract
Scanning Fluorescence Correlation Spectroscopy (scanning FCS) is a variant of conventional point FCS that allows molecular diffusion at multiple locations to be measured simultaneously. It enables disclosure of potential spatial heterogeneity in molecular diffusion dynamics and also the acquisition of a large amount of FCS data at the same time, providing large statistical accuracy. Here, we optimize the processing and analysis of these large-scale acquired sets of FCS data. On one hand we present FoCuS-scan, scanning FCS software that provides an end-to-end solution for processing and analysing scanning data acquired on commercial turnkey confocal systems. On the other hand, we provide a thorough characterisation of large-scale scanning FCS data over its intended time-scales and applications and propose a unique solution for the bias and variance observed when studying slowly diffusing species. Our manuscript enables researchers to straightforwardly utilise scanning FCS as a powerful technique for measuring diffusion across a broad range of physiologically relevant length scales without specialised hardware or expensive software.
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Affiliation(s)
- Dominic Waithe
- Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Falk Schneider
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jakub Chojnacki
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mathias P Clausen
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Dilip Shrestha
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jorge Bernardino de la Serna
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Department of Physics, King's College London, London WC2R 2LS, UK
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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